The SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain is an evolutionarily conserved sequence of approximately 130-150 amino acids, and constitutes the catalytic site of lysine methyltransferases (KMTs). KMTs perform many crucial biological functions via histone methylation of chromatin. Histone methylation marks are interpreted differently depending on the histone type (i.e. H3 or H4), the lysine position (e.g. H3K4, H3K9, H3K27, H3K36 or H4K20) and the number of added methyl groups (i.e. me1, me2 or me3). For example, H3K4me3 and H3K36me3 are associated with transcriptional activation, but H3K9me2 and H3K27me3 are associated with gene silencing. The substrate specificity and activity of KMTs are determined by sequences within the SET domain and other regions of the protein.
Here we identified 49 SET-domain proteins from the recently sequenced Brassica rapa genome. We performed sequence similarity and protein domain organization analysis of these proteins, along with the SET-domain proteins from the dicot Arabidopsis thaliana, the monocots Oryza sativa and Brachypodium distachyon, and the green alga Ostreococcus tauri. We showed that plant SET-domain proteins can be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET. Apart from the S-ET class, which has an interrupted SET domain and may be involved in methylation of nonhistone proteins, the other classes have characteristics of histone methyltransferases exhibiting different substrate specificities: KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27 and KMT7 also for H3K4. We also propose a coherent and rational nomenclature for plant SET-domain proteins. Comparisons of sequence similarity and synteny of B. rapa and A. thaliana SET-domain proteins revealed recent gene duplication events for some KMTs.
This study provides the first characterization of the SET-domain KMT proteins of B. rapa. Phylogenetic analysis data allowed the development of a coherent and rational nomenclature of this important family of proteins in plants, as in animals. The results obtained in this study will provide a base for nomenclature of KMTs in other plant species and facilitate the functional characterization of these important epigenetic regulatory genes in Brassica crops.
Epigenetic regulation acts through heritable changes in genome function that occur without a change in DNA sequence. One well-known epigenetic mechanism is through posttranslational covalent modifications of histones; these modifications include acetylation, methylation, ubiquitylation and others, and form the basis of the 'histone code' for gene regulation . Histone lysine methylation plays a pivotal role in a wide range of cellular processes including heterochromatin formation, transcriptional regulation, parental imprinting, and cell fate determination . At least six lysine residues, five on histone H3 (K4, K9, K27, K36, K79) and one on H4 (K20), are subject to methylation. Each lysine can carry one, two or three methyl residue(s), known as mono-, di- and tri-methylation, respectively. In general, di-/tri- methylation of H3K4 and H3K36 correlates with transcriptional activation, whereas di-methylation of H3K9 and trimethylation of H3K27 correlates with gene silencing in plants and animals [2, 3].
All known lysine methylation modifications, with the exception of H3K79 methylation, are carried out by methyltransferases that contain an evolutionarily conserved SET domain, named after three Drosophila genes (Su(var), E(z), and Trithorax) . The SET domain encompasses approximately 130-150 amino acids that form a knot-like structure and constitute the enzyme catalytic site for lysine methylation . In addition to the SET domain, flanking sequences, more distant protein domains, and possibly some cofactors are also important for enzyme activity and specificity. The genes encoding SET-domain proteins are ancient, existing in prokaryotes and eukaryotes, but have proliferated and evolved novel functions connected with the appearance of eukaryotes .
The first plant genes encoding SET-domain proteins to be genetically characterized were CURLY LEAF (CLF) and MEDEA (MEA) in Arabidopsis thaliana [7, 8]. Chromatin-binding properties and histone methylation activity of plant SET-domain proteins were first reported for tobacco NtSET1 and Arabidopsis KRYPTONITE (KYP) [9, 10]. Phylogenetic analysis of plant SET domain proteins has proven helpful as a guide for genetic and molecular studies of this large family of proteins [11, 12]. To date, some of the Arabidopsis SET-domain family members have been characterized and shown to play crucial functions in diverse processes including flowering time control, cell fate determination, leaf morphogenesis, floral organogenesis, parental imprinting and seed development [3, 13–15].
Genome sequences of an increasing number of plant species, in addition to the model plants (Arabidopsis thaliana, Oryza sativa, and Brachypodium distachyon), have also been completed. Other Brassica species are of particular interest because of their agro-economical importance and their close relationship with Arabidopsis, thus providing insights into recent SET-domain gene amplification during evolution of Brassica species. Here, we identified and analyzed 49 SET-domain proteins from the recently completed Brassica rapa whole genome sequence . Our data provide a platform for future functional characterization of these important epigenetic regulatory genes in Brassica species.
Using BLASTp and tBLASTn with the full complement of known Arabidopsis and rice SET-domain proteins as queries, we identified 49 genes encoding different SET-domain proteins from the B. rapa genome (http://brassicadb.org/brad). We used the nomenclature recently proposed for lysine methyltransferases (KMTs, ) and named the newly identified B. rapa genes based on our phylogenetic analysis of their corresponding protein sequences (see below). Apart from BrKMT1B;1a and BrKMT1B;2b genes, whose chromosomal locations are yet unknown, the other 47 genes are distributed on the ten B. rapa chromosomes, with 1-7 KMT genes per chromosome (Table 1).
To analyze the B. rapa SET-domain protein sequences, we extracted SET-domain proteins from several other green lineage species, including 37 proteins from A. thaliana, 36 proteins from O. sativa, 41 proteins from B. distachyon, and 10 proteins from Ostreococcus tauri (Table 1). We also included the Saccharomyces cerevisiae ScKMT2/Set1 and ScKMT3/Set2 proteins, which are H3K4- and H3K36-specific KMTs, respectively [18, 19], and can be used to represent ancient eukaryotic SET-domain proteins from an evolutionary point of view. Phylogenetic analysis of the aforementioned 175 SET-domain proteins revealed that they could be grouped into 6 distinct classes, namely KMT1, KMT2, KMT3, KMT6, KMT7 and S-ET class (Figure 1). The first four class numbers used here are consistent with the nomenclature previously proposed for yeast and animal KMTs . Furthermore, two plant-specific subclasses (namely A and B) were identified for KMT1 and KMT6. Representative members of each class/subclass are found in A. thaliana, B. rapa, O. sativa and B. distachyon. The S-ET class members contain an interrupted SET domain and are likely involved in methylation of nonhistone proteins, e.g. RUBISCO subunits; however, their biological functions remain largely unknown. Hereafter, we focused on the KMT classes/subclasses that are involved in histone methylation.
Phylogenetic tree of SET-domain proteins. The SET domain sequences of the 175 different proteins were aligned using ClustalW, and the phylogenetic tree analysis was performed using MEGA4. Closed circles and triangles indicate Arabidopsis thaliana (At) and Brassica rapa (Br) proteins, respectively; open circles and triangles indicate Brachypodium distachyon (Bd) and Oryza sativa (Os) proteins, respectively; open and closed squares indicate Ostreococcus tauri (Ot) and Saccharomyces cerevisiae (Sc) proteins, respectively.
The KMT1A subclass is the largest class and can be further divided into 4distinct groups (Figure 2). In each group, proteins from dicots (B. rapa and A. thaliana) and monocots (O. sativa and B. distachyon) clearly fall into separate branches, indicating that they are derived from a common ancestral gene but diverged before the monocot/dicot separation. The first three groups have a relatively simple relationship and small number of genes, but Group-4 is more complex: each plant species has 4-8 members that diverged at various times during evolution. In the case of B. rapa, among the 8 members belonging to Group-4, BrKMT1A;4a, BrKMT1A;4c, BrKMT1A;4d, and BrKMT1A;4f are clustered with the Arabidopsis AtKMT1A;4a/SDG32/SUVH1; BrKMT1A;4b with AtKMT1A;4b/SDG19/SUVH3; and BrKMT1A;4e, BrKMT1A;4 g and BrKMT1A;4 h with AtKMT1A;4e/SDG11/SUVH10 (Figure 2). Examination of synteny between B. rapa and A. thaliana (http://brassicadb.org/brad/searchSynteny.php) revealed that BrKMT1A;4a, BrKMT1A;4c and BrKMT1A;4d but not BrKMT1A;4f are syntenic with AtKMT1A;4a/SDG32/SUVH1, and BrKMT1A;4 h but not BrKMT1A;4e nor BrKMT1A;4 g is syntenic with AtKMT1A;4e/SDG11/SUVH10. It thus appears that multiple duplication events occurred, in either a chromosome segment or single gene scale, resulting in more recent amplification of Group-4 genes in B. rapa after separation from A. thaliana during evolution. In agreement with previous studies in Arabidopsis, rice and maize [11, 12], few introns are present in BrKMT1A genes (Additional File 1: Figure S1). Most BrKMT1A genes are represented by ESTs, but some do not have any ESTs in current databases (Additional File 2: Table S1). Our RT-PCR analysis revealed that indeed two genes that lack ESTs, BrKMT1A;2a and BrKMT1A;2c, are very weakly expressed. Strong expression was detected for BrKMT1A;4a, but relatively weak expression was detected for BrKMY1A;4d and expression was undetectable for BrKMT1A;4c (Additional File 3: Figure S2). Together, these data indicate that expression levels of different BrKMT1A genes varied considerably and thus these genes may regulate genome function to different degrees.
Domain organization of the KMT1A subclass proteins. Schematic diagrams show the domain organization of KMT1A proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. Different conserved protein domains (SRA, Pre-SET, SET, and Post-SET) are colored as indicated. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
The plant KMT1A subclass proteins show high sequence similarity to the animal KMT1 proteins both within the SET domain and in the surrounding regions known as the Pre-SET and post-SET domains. Additionally, most of the plant proteins contain a specific domain named SRA (SET and RING associated). Similar to previously studied Arabidopsis proteins [12, 20], most of the BrKMT1A proteins also contain SRA, Pre-SET, SET and post-SET domains (Figure 2). These domains are missing in some of the Group-4 proteins; for example, BrKMT1A.4e, BrKMT1A;4f and BrKMT1A;4 g lack a Post-SET domain, and BrKMT1A.4 h lacks SRA, Pre-SET and post-SET domains (Figure 2). Several functions have been reported for SRA domains, including binding with the N-terminal tail of histone H3 and with DNA cytosine methylation . The crystal structure of AtKMT1A;3a/SDG9/SUVH5 revealed that SRA recognizes the methylation status of CG and CHH sequences . The Pre-SET domain contains 9 conserved cysteines. The Post-SET domain is a small cysteine-rich region often found at the C-terminal side of SET domains. Both Pre-SET and Post-SET domains have been shown to affect histone methyltransferase activity of the SET domain [23, 24].
Members of the plant KMT1A subclass, like animal KMT1 proteins, are likely to be responsible for H3K9 methylation, an epigenetic mark involved in heterochromatin formation and gene silencing. Consistent with this, analysis of AtKMT1A;1/SDG33/SUVH4/KYP, AtKMT1A;2a/SDG3/SUVH2, AtKMT1A;3a/SDG9/SUVH5 and AtKMT1A;3b/SDG23/SUVH6 has revealed their important roles in H3K9 methylation, in heterochromatic gene silencing and in cross-talk between H3K9 and DNA methylation [9, 21, 22, 25–28]. Work in rice also confirmed that several members of this subclass are involved in H3K9 methylation and in transposon silencing [29–31]. Some of the BrKMT1A genes might also have similar functions.
Six B. rapa proteins belong to the KMT1B subclass, which can be further divided into 4 groups (Figure 3). Group-1 contains two B. rapa proteins (BrKMT1B;1a and BrKMT1B;1b) whose genes show synteny with AtKMT1B;1/SDG31/SUVR4. Moreover, sequence analysis showed that BrKMT1B;1b and AtKMT1B;1/SDG31/SUVR4 have highly similar protein domain organization, indicating that BrKMT1B;1b is more conserved and BrKMT1B;1a diverged relatively late during evolution after the B. rapa/A. thaliana separation. Group-2 has two B. rapa, two A. thaliana proteins, one O. sativa protein, and three B. distachyon proteins. Both BrKMT1B;2a and BrKMT1B;2b show synteny with AtKMT1B;2b/SDG18/SUVR2. Group-3 and 4 each have one representative member in each of the four examined higher plant species.
Domain organization of the KMT1B subclass proteins. Schematic diagrams show the domain organization of KMT1B proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. Different conserved protein domains (WIYL, Pre-SET, SET, Post-SET, and Ribosomal) are colored as indicated. The KMT1B;3-group proteins are large in size; therefore the corresponding schematic diagram is drawn with a remove of ~800 aa from the N-terminus, a region without any detectable known protein domains. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
The KMT1B subclass differs from the KMT1A subclass in protein domain organization; specifically, these proteins lack the SRA domain (Figure 3). A recent study demonstrated that AtKMT1B;1/SDG31/SUVR4 possesses H3K9-methyltransferase activities and its binding with ubiquitin converts H3K9me1 to H3K9me3 deposition on transposon chromatin . Notably, the WIYLD domain, which binds ubiquitin, is conserved in BrKMT1B;1a, BrKMT1B;1b, BrKMT1B;2a and BrKMT1B;2b (Figure 3). It was reported that AtKMT1B;3/SDG6/SUVR5/AtCZS is involved in regulation of flowering time, possibly through deposition of H3K9 methylation at the flowering time repressor FLC . The functions of other members of the KMT1B subclass remain uncharacterized so far.
The KMT2 class includes six B. rapa and six A. thaliana proteins in 3 groups (Figure 4). This class features highly conserved SET and Post-SET domains with the yeast H3K4-methyltransferase ScKMT2/Set1. Nevertheless, some plant proteins have acquired specific domains during evolution, namely PWWP, PHD, FYR and/or GYF. The PWWP domain is also found in eukaryotic proteins involved in DNA methylation, DNA repair, and regulation of transcription , and regulates cell growth and differentiation by mediating protein-protein interactions . The PHD domain is found in a number of chromatin-associated proteins and is thought to be involved in protein-protein interactions important for the assembly of multiprotein complexes . The PWWP domain of the animal BRPF1 protein binds H3K36me3 , and the PHD domain is also an important module in proteins that read histone modifications . The FYR domain is composed of FYR-C and FYR-N terminal portions, which are often located close to each other but can also be separated . The GYF domain is proposed to be involved in recognition of proline-rich sequences in protein-protein interactions .
Domain organization of the KMT2 class proteins. Schematic diagrams show the domain organization of KMT2 proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. Different conserved protein domains (PWWP, FYR, GYF, PHD, SET, and Post-SET) are colored as indicated. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
KMT2 Group-1 members contain one PWWP, one FYR and two PHD domains. Only one member belonging to Group-1 is found in O. sativa or B. distachyon, but two members are found in B. rapa and A. thaliana. Our examination revealed that BrKMT2;1a has synteny with AtKMT2;1a/SDG27/ATX1, and BrKMT2;1b with AtKMT2;1b/SDG30/ATX2, suggesting that they are derived from two different ancestral copies before the B. rapa/A. thaliana separation. Consistent with this, the atx1 mutant plants exhibit strong and pleiotropic defects , but the atx2 mutant plants have a normal phenotype . The atx2 mutation can enhance atx1 in reduction of expression of the flowering repressor gene FLC through reduced levels of H3K4me3 at the FLC locus .
The PWWP and FYR domains are absent from the Group-2 members and the PHD domain is found only in some monocot proteins (Figure 4). Only one Group-2 representative member is found in the dicot species B. rapa or A. thaliana, but the monocot O. sativa has two members and B. distachyon has three members. The B. rapa and A. thaliana proteins, as well as one member each from O. sativa and B. distachyon, contain a GYF domain in the N-terminal part of the protein (Figure 4). The fact that this domain is conserved in KMT2;2 proteins from all four higher plant species suggests that the acquisition of the GYF domain occurred before the monocot/dicot separation and may have a conserved function in higher plants. Genetic analysis demonstrated that AtKMT2;2/SDG25/ATXR7 is necessary in preventing early flowering [43, 44]. The recombinant AtKMT2;2/SDG25/ATXR7 protein was shown to methylate histone H3 in vitro and the depletion of AtKMT2;2/SDG25/ATXR7 in planta slightly reduced H3K4 and H3K36 methylation at FLC chromatin [43, 44]. OsKMT2;2b/SDG732 and BdKMT2;2c contain two PHD domains, but BdKMT2;2b, like the yeast protein ScKMT2/Set1, does not contain a recognizable PHD domain. Future study of these monocot proteins will likely provide a deeper understanding of the domain evolution of KMT2 proteins.
The Group-3 KMT2 proteins have a domain organization more similar to Group-1 except that they lack the FYR domain (Figure 4). B. rapa and A. thaliana both have three Group-3 members, but each of the other two higher plant species has only two Group-3 members. Synteny was observed for BrKMT2;3c with AtKMT2;3c/SDG29/ATX5 but not with AtKMT2;3b/SDG16/ATX4, suggesting that AtKMT2;3b/SDG16/ATX4 was derived from a relatively recent duplication event. This is in agreement with a previous study revealing that AtKMT2;3b/SDG16/ATX4 and AtKMT2;3c/SDG29/ATX5 are collinearly duplicated with AtKMT2;1a/SDG27/ATX1 and AtKMT2;1b/SDG30/ATX2 . To date, none of the Group-3 proteins has been functionally characterized.
The KMT3 class contains 5 members in A. thaliana but 7 members in B. rapa, and these can be further divided into four groups (Figure 5). The other groups contain a single member per plant species, but Group-4 contains 2 members in A. thaliana and 4 members in B. rapa. Our examination indicates that BrKMT3;4a and BrKMT3;4c are syntenic with AtKMT3;4a/SDG7/ASHH3, and BrKMT3;4b and BrKMT3;4d with AtKMT3;4b/SDG24/ASHH4. The ESTs found in the current databases match all four BrKMT3;4 genes (Additional File 2: Table S1), and thus do not allow us to distinguish expression of each gene. Our RT-PCR analysis indicated that BrKMT3;4a and BrKMT3;4c are expressed at higher levels and more broadly in different examined organs/tissues, whereas only weak expression was detected for BrKMT3;4b and BrKMT3;4d in some organs/tissues (Additional File 3: Figure S2).
Domain organization of the KMT3 class proteins. Schematic diagrams show the domain organization of KMT3 proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. Different conserved protein domains (AWS, PHD, CW, SET, and Post-SET) are colored as indicated. The KMT3;1-group proteins are large in size; therefore the corresponding schematic diagram is drawn with a remove of ~500 aa from the C-terminus, a region without any detectable known protein domains. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
The KMT3 class plant proteins share high sequence similarity and share the AWS (a subdomain of Pre-SET, ), SET and Post-SET domain organization with the yeast H3K36-methyltransferase ScKMT3/Set2 (Figure 5). The Group-1 proteins have a long sequence and contain an additional CW domain specific to this group. The CW domain of AtKMT3;1/SDG8/ASHH2/EFS/CCR1 was recently shown to bind H3K4me1/me2 , suggesting a novel link between H3K4 and H3K36 methylation in plants. AtKMT3;1/SDG8/ASHH2/EFS/CCR1 is the major H3K36-methyltransferase specifically required for H3K36me2 and H3K36me3 deposition, and activates expression of hundreds of genes including FLC and MAFs . Depletion of AtKMT3;1/SDG8/ASHH2/EFS/CCR1 causes pleiotropic phenotypes, including early flowering, reduced organ size, increased shoot branching, perturbed fertility and carotenoid composition, and impaired plant defenses against pathogens [47–54]. The other group of KMT3 plant proteins have a shorter sequence and do not contain the CW domain; interestingly the depletion of AtKMT3;2/SDG26/ASHH1 resulted in a late-flowering phenotype associated with elevated levels of FLC expression . The Group-3 KMT3 proteins, with the exception of BdKMT3;3b and OsKMT3;3b/SDG707, contain a PHD domain; and AtKMT3;3/SDG4/ASHR3 was reported to be involved in pollen and stamen development possibly through mediating H3K4me2 and H3K36me3 deposition [55, 56]. The functions of the Group-4 proteins remain unexamined so far. Examination of this group in B. rapa could be a challenge because of gene multiplication and more diverged sequences (Figure 5).
The KMT6A subclass includes 4 members in B. rapa and 3 well-characterized members in A. thaliana, AtKMT6A;1/SDG1/CLF, AtKMT6A;2/SDG10/EZA1/SWN and AtKMT6A;3/SDG5/MEA, which represent three distinct groups (Figure 6a). AtKMT6A;1/SDG1/CLF and AtKMT6A;2/SDG10/EZA1/SWN are broadly expressed and partially redundant in regulation of vegetative and reproductive development, whereas AtKMT6A;3/SDG5/MEA appears to function specifically in gametophyte and seed development [7, 8, 57]. The three Arabidopsis proteins can act as a key component of the evolutionarily conserved Polycomb Repressive Complex 2 (PRC2), which trimethylates H3K27 involved in transcriptional repression . AtKMT6A;1/SDG1/CLF and AtKMT6A;2/SDG10/EZA1/SWN represent Group-1 and Group-2, respectively, and each has an orthologue in different higher plant species. AtKMT6A;3/SDG5/MEA, which belongs to Group-3, has no orthologue in monocots but has two orthologues in B. rapa. Both BrKMT6A;3a and BrKMT6A;3b are syntenic with AtKMT6A;3/SDG5/MEA, and BrKMT6A;3a has a more similar protein domain organization to AtKMT6A;3/SDG5/MEA than does BrKMT6A;3b, suggesting that BrKMT6A;3b may have diverged after the A. thaliana/B. rapa separation during evolution.
Domain organization of the KMT6 class proteins. The KMT6 class can be divided into 2 subclasses (a and b). Schematic diagrams show the domain organization of KMT6 proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. Different conserved protein domains (SANT, PHD, and SET) are colored as indicated. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
The SANT (SWI3, ADA2, N-CoR, and TFIIIB DNA-binding) domain is found in most of the plant KMT6A subclass proteins. This domain is also found in a number of other chromatin remodeling proteins with multiple activities such as DNA-binding, histone tail binding, and protein-protein interactions . Nevertheless, the precise role of the SANT domain in KMT6A proteins is currently unknown. Notably, BrKMT6A;3b does not contain a SANT domain. As expected from restricted AtKMT6A;3/SDG5/MEA expression in only a small number of cells during reproduction, expression of both BrKMT6A;3a and BrKMT6A;3b is barely detectable in the examined tissues (Additional File 3: Figure S2). It will be interesting to investigate BrKMT6A;3a and BrKMT6A;3b expression during reproduction and to examine whether both genes are functionally important.
The KMT6B subclass includes two members each in A. thaliana, B. distachyon and O. sativa, and four members in B. rapa, which together can be divided into two distinct groups (Figure 6b). The two members from A. thaliana, AtKMT6B;1/SDG15/ATXR5 and AtKMT6B;2/SDG34/ATXR6, were classified as trithorax-related in the first genome analysis of Arabidopsis SET-domain proteins . However, our study as well as two previous studies that included a more complete set of plant SET-domain proteins clearly show that AtKMT6B;1/SDG15/ATXR5 and AtKMT6B;2/SDG34/ATXR6 belong to the KMT6B subclass (Figure 1) [12, 20]. Consistent with this, functional analysis revealed that AtKMT6B;1/SDG15/ATXR5 and AtKMT6B;2/SDG34/ATXR6 are involved in monomethylation of H3K27 . They appear to act redundantly, because depletion of H3K27 monomethylation is only detectable in the atxr5 atxr6 double mutant . KMT6A-mediated H3K27me3 is mainly present in euchromatic regions and is important for gene silencing , but KMT6B-mediated H3K27me1 is found in heterochromatic chromocenters and is important for heterochromatin condensation and replication in Arabidopsis .
Distinct from KMT6A proteins containing a SANT domain, many plant KMT6B subclass proteins contain a PHD domain (Figure 6). The PHD domain of both AtKMT6B;1/SDG15/ATXR5 and AtKMT6B;2/SDG34/ATXR6 strongly bind unmethylated H3 tail peptides (amino acids 1-21), and this binding is negatively affected by methylation on H3K4 . This binding preference may help to assure that these KMT6B proteins are not targeted to euchromatin and active genes enriched in H3K4 methylation. Remarkably, both Group-1 and Group-2 members are duplicated in B. rapa. Both BrKMT6B;1a and BrKMT6B;1b are syntenic with AtKMT6B;1/SDG15/ATXR5, and both BrKMT6B;2a and BrKMT6B;2b with AtKMT6B;2/SDG34/ATXR6. Expression of BrKMT6B;1a, BrKMT6B;2a and BrKMT6B;2b was detected in different tissues, but we failed to detect BrKMT6B;1b expression (Additional File 3: Figure S2). It is reasonable to speculate that BrKMT6B;1a, BrKMT6B;2a and BrKMT6B;2b might have redundant functions.
The KMT7 class contains a single member each in A. thaliana, O. sativa and B. distachyon, but three members in B. rapa (Figure 7). Although the Arabidopsis protein AtKMT7;1/SDG2/ATXR3 was considered to be related to members of the KMT2 class in some previous studies [11, 20], it was located outside of any classes in the phylogenetic tree analysis by Springer and colleagues , and our analysis here revealed that it is grouped together with some other green lineage proteins, forming the plant KMT7 class (Figure 1). Unlike the classes described above, the plant and animal KMT7 classes do not cluster although they are predicted to have similar functions in H3K4 methylation. Representatives of the animal KMT7 class are only found in mammals and include the human SET7/9, which monomethylates H3K4 and also methylates a number of nonhistone proteins . The plant KMT7 proteins did not show the highest sequence similarities with the human SET7/9, and depletion of AtKMT7;1/SDG2/ATXR3 resulted in a global reduction of H3K4me3 and caused pleiotropic defects in both sporophyte and gametophyte development [61, 62]. Both BrKMT7;1a and BrKMT7;1b but not BrKMT7;1c have synteny with AtKMT7;1/SDG2/ATXR3, and phylogenetic analysis showed that BrKMT7;1a is more closely related to AtKMT7;1/SDG2/ATXR3. RT-PCR analysis revealed that BrKMT7;1b is expressed at a higher level than BrKMT7;1a (Additional File 3: Figure S2). In view of the important function of AtKMT7;1a/SDG2/ATXR3, it will be interesting to investigate roles of BrKMT7;1a and BrKMT7;1b in histone methylation and plant development in B. rapa.
Domain organization of the KMT7 class proteins. Schematic diagrams show the domain organization of KMT7 proteins and are placed on the right side of the phylogenetic tree. The scale bar indicates the evolutionary distance, the number along the tree branch indicates bootstrap value, and the other information about tree construction and symbol indication can be found in legend of Figure 1. The conserved SET-domain is indicated. The protein is indicated on top of the schematic diagram and other similar domain organization proteins are indicated in parentheses.
Over last 10 years, a number of SET-domain genes in Arabidopsis and in rice have been characterized and shown to exert crucial chromatin-based functions via histone methylation during plant growth and development [3, 15]. However, the nomenclature of plant SET-domain proteins remains complex, and multiple synonyms exist for many Arabidopsis proteins (Table 1), which could cause considerable confusion in this important field. Nomenclature based on sequence similarity has several advantages, informing the prediction of KMT enzyme substrate specificity for its histone lysine residue and providing a global view of KMT types in an organism once its whole genome sequence becomes available. However, the SDG nomenclature failed to provide information concerning enzyme substrate specificity and the number following "SDG" could be long and difficult to remember [12, 63], e.g., the first SDG from B. rapa (ID = 197) would have been named SDG19701. While the nomenclature by Baumbusch and colleagues provided information about homology to animal proteins, an incomplete list of Arabidopsis SET-domain proteins and the limitation (at that time) of having only one plant species with a genome-wide analysis restricted the precision and correctness of phylogenetic grouping in this study . In addition, animal KMT nomenclature had also been noncoherent; a rational nomenclature was proposed only recently . Therefore, the nomenclature we propose here is in line with the latest advances in the field.
In accordance with the guidelines of the Commission on Plant Gene Nomenclature , the nomenclature of plant KMTs is defined by species initials (e.g. Br for Brasica rapa) before KMT, which is followed by the class number (Figure 8). The class number is based on the yeast and animal systems indicating the enzyme substrate specificity, i.e. KMT1 for H3K9, KMT2 for H3K4, KMT3 for H3K36, KMT6 for H3K27, and KMT7 also for H3K4 . Multiple subclasses are indicated by upper-case letters (e.g. KMT1A and KMT1B), and distinct groups within the class/subclass are indicated by an arabic numeral suffix (e.g. KMT1A;1). Members within the group are indicated by lower-case letters (e.g. KMT1A;1a and KMT1A;1b). Subgroups are not currently defined but may be designated in the future as functional analysis and an increasing number of sequenced genomes demonstrate sequence conservation between species or distinct functions for several members of a defined KMT group. The use of a given subgroup suffix should indicate highly similar sequences or equivalent functional roles between several species. The new nomenclature may be difficult to adopt in Arabidopsis because the original names for a number of SET-domain proteins are familiar to researchers, but a coherent and rational nomenclature for different species is important and useful because of the enormous interest in KMTs. The guidelines proposed here will be particularly useful for nomenclature of newly identified SET-domain proteins, which are being discovered at an exponentially increasing rate as genome sequences become available for additional plant species.
Nomenclature for plant KMTs. The BrKMT1A;2a protein serves as an example to show assignment of various layers of information within the nomenclature of a plant KMT. Refer to text for class, subclass, group and member definition.
We identified 49 SET-domain proteins from the recently completed whole genome sequence of B. rapa. Among them, 5 proteins belong to the S-ET class likely involved in nonhistone protein methylation, 20 proteins belong to the KMT1 class potentially involved in H3K9 methylation, 6 proteins belong to the KMT2 class potentially involved in H3K4 methylation, 7 proteins belong to the KMT3 class potentially involved in H3K36 methylation, 8 proteins belong to the KMT6 class potentially involved in H3K27 methylation, and 3 belong to the KMT7 class also potentially involved in H3K4 methylation. This in silico survey is useful for future functional analysis of this important family of epigenetic regulators in Brassica. H4K20 methylation was detected in Arabidopsis using antibodies [28, 65], but the catalyzing enzyme(s) involved is(are) not yet known and the current phylogenetic analysis did not allow prediction of a specific KMT class involved in H4K20 methylation. It is possible that some members of the aforementioned KMT classes catalyze H4K20 methylation. The total number of KMTs in B. rapa (49) is slightly higher than that identified in A. thaliana (37), O. sativa (36) and B. distachyon (41). Nevertheless, we could not exclude the possibility that a few more KMTs may be missing from the currently available genome sequence of B. rapa.
Gene duplication is one of the primary driving forces in the evolution of genomes and genetic systems, and is considered to be a major mechanism for the establishment of new gene functions and the generation of evolutionary novelty [66, 67]. Contrary to what would be expected from the chromosome number duplication in B. rapa compared to A. thaliana, the number of KMT genes in B. rapa (49) is much less than double the number of A. thaliana KMTs (74). Many duplicated genes show synteny with their A. thaliana homologues, suggesting that they are derived from chromosome/genome segment duplications. Three alternative outcomes can occur in the evolution of duplicated genes: (i) one copy may simply become silenced by degenerative mutations (nonfunctionalization); (ii) one copy may acquire a novel, beneficial function and become preserved by natural selection (neofunctionalization); (iii) both copies may become partially compromised by mutation so that their total capacity adds up to the capacity of the single-copy ancestral gene (subfunctionalization) . These different outcomes likely apply to different duplicated KMT genes, judging from their expression patterns (Additional File 3: Figure S2). Expression of BrKMT1A;4c and BrKMT6B;1b was undetectable, suggesting that they might have been nonfunctionalized. The duplicated pairs BrKMT1B;2a and BrKMT1B;2b, BrKMT3;4b and BrKMT3;4d, or BrKMT7;1a and BrKMT7;1b are differentially expressed in plant organs, suggesting that they might have acquired distinct tissue-specific functions. Finally, expression of some duplicated genes, e.g. BrKMT1A;2a and BrKMT1A;2c, BrKMT1B;1a and BrKMT1B;1b, or BrKMT6A;3a and BrKMT6A;3b showed similar patterns, suggesting that they might be subfunctionalized and/or have redundant functions.
Among the groups showing gene duplications in B. rapa, it is worth to note that in Arabidopsis, AtKMT6A;3/SDG5/MEA is critical for parental gene imprinting and seed development [8, 68], AtKMT6B;1/SDG15/ATX5 and AtKMT6B;2/SDG34/ATX6 are important for heterochromatin condensation and replication in Arabidopsis [59, 60], and AtKMT7;1/SDG2/ATXR3 is essential for both sporophyte and gametophyte development [61, 62]. It will be of great interest to investigate these groups of genes for their regulation and function in chromatin organization, plant growth and development in B. rapa.
Our study shows that the plant SET-domain KMT proteins can be phylogenetically grouped into distinct classes and that the classes involved in histone methylation can be named in accordance with the nomenclature proposed for animal and yeast SET-domain KMTs. Such a coherent and rational nomenclature in different organisms will help avoid confusion caused by the existence of multiple names for the same protein or gene. The information provided on the B. rapa KMTs will also be beneficial for future research to unravel the mechanisms of epigenetic regulation in Brassica crops.
Sequences of SET-domain proteins from A. thaliana, O. sativa, O. tauri and S. cerevisiae were retrieved from the Chromatin Database with the key word SDG in species database respectively (ChromDB, http://www.chromdb.org). These sequences, primarily those from A. thaliana and O. sativa, were used as queries to search the B. distachyon genome (http://www.brachypodium.org) and the B. rapa genome (http://brassicadb.org/brad/index.php) by using the BLASTp and tBLASTn tools (http://blast.ncbi.nlm.nih.gov). The Expect threshold was set at 1.0 and other parameters were set at default values. We did not use a strict E-value threshold; rather we examined each of the resulting hits for the presence of the SET or S-ET domain to collect previously unidentified sequences. The synteny analysis was performed using the online viewer tool (http://brassicadb.org/brad/index.php). ESTs of the B. rapa SET-domain protein genes were retrieved from the Brassica Database (http://brassicadb.org/brad/index.php) and from NCBI (http://blast.ncbi.nlm.nih.gov), using an Expect threshold of 1, and a minimum sequence length of 50 bp.
The protein sequences were analyzed for domain organization using NCBI-CD searches (http://ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi). The low-complexity filter was turned off, and the Expect value was set at 1.0 to detect short domains or regions of less conservation in this analysis. Domains were also verified and named according to the SMART database (http://smart.embl-heidelberg.de/).
Multiple sequence alignments of SET-domain sequences were performed using the ClustalW program . The resulting file was subjected to phylogenic analysis using the MEGA4.0 program . The trees were constructed with the following settings: Tree Inference as Neighbor-Joining; Include Sites as pairwise deletion option for total sequences analysis and complete deletion option for each class analysis; Substitution Model: Poisson correction; and Bootstrap test of 1,000 replicates for internal branch reliability.
B. rapa plants were grown at 18-22°C under a 12 h light (10,000 Lx)/12 h dark photoperiod. Leaves were collected from 2-, 4-, 6-, 8- or 10-week-old plants; roots and stems were collected from 6-week-old plants; flower buds were collected from 10-week-old plants. Total RNA was extracted using Trizol reagent (Invitrogen, USA) from about 100 mg of collected plant tissue. The RNA preparation was then treated with DNaseI (Promega, USA) for 30 min at 37°C, followed by enzyme inactivation by incubation at 65°C for 5 min. First strand cDNA was made using an RT-PCR Kit (RevertAid™ First Strand cDNA Synthesis Kit, Fermentas, CA). The RT-solution with first strand cDNA was stored at -80°C. Primers used for the RT-PCR reactions are listed in Additional File 4: Table S2. Conditions for the PCR reactions were as follows: 94°C for 3 min; then 30 cycles of 94°C for 30 s, 50-63°C for 30 s, and 72°C for 1 min; and finally 72°C for 8 min. PCR products were separated in a 1.5% (w/v) agarose Tris-borate/EDTA buffer gel and visualized by ethidium bromide staining.
We thank Dr Xiaowu Wang, Jian Wu and Fen Chen, from the Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences, for providing sequences and helping in synteny analysis. This work was supported in part by National Basic Research Program of China (973 Program, 2012CB910500) and National Natural Science Foundation of China (NSFC31071129 and NSFC31071455).
YH conducted most of the experiments and drafted the manuscript; CL contributed to the RT-PCR experiment and participated in the drafting of the manuscript; WHS and YR conceived and directed the study, and wrote the final version of the manuscript. All authors read and approved the final manuscript.


text:
Un Institut d'éducation secondaire ( IES) est en Espagne une école publique d'enseignement secondaire.

Fonctionnement

Il fonctionne tant pour la partie obligatoire (, généralement entre 12 et ) que pour la partie non obligatoire (), ainsi qu'un enseignement de formation professionnelle (cycles de formation de niveau moyen et supérieur), ainsi que d'autres programmes de « garantie sociale » ou d'« éducation compensatoire ». De nombreux IES n'assurent que l'ESO.

Notes et références

Voir aussi

Articles connexes
 Éducation en Espagne
 Enseignement secondaire
 Collège en France - Lycée en France

Enseignement en Espagne

redpajama_set_name: RedPajamaWikipedia


On January 18, 2018, the American Civil Rights Union (ACRU) helped successfully urge the U.S. Supreme Court to issue a stay in Rucho v. Common Cause. ACRU's amicus brief argued that the district court's demand for a redrawn legislative map was unreasonable, because it created a new set of incredibly complex tests and then gave the North Carolina legislature just 14 days to create a new map. Illogically, the court said some types of partisan map-making were acceptable, while other types were illegal—which made it even more difficult for anyone to apply these new standards. This last-minute redistricting hurt candidates and voters, and it disrupted the election process.
In addition, the ACRU argued that the court's ruling created a system that required federal courts to oversee nearly all redistricting efforts by state legislatures, redistricting commissions, and even other courts. According to Article I, Section IV of the Constitution, redistricting should be a state matter, not something run by federal courts.
READ THE AMICUS BRIEF HERE.


View US 45, Eagle River - Vilas County project in a larger map.
The purpose of the project is to preserve the pavement.
Reconfiguring the roadway, between WIS 70 east and US 45 north, from four lanes to three lanes. This will reduce crashes and improve safety for vehicles and pedestrians.
US 45 will remain open to traffic. Motorists can expect to encounter periodic, daytime single lane closures in each direction.
Construction will be scheduled to minimize impacts during the tourist season.
Lane widths on US 45 may be temporarily reduced for certain types of work.
Some temporary interruptions in access will occur at driveways when work is occurring directly in front of residences or businesses. The contractor will be required to contact homeowners and businesses in advance of the work.
Real estate acquisition is under way.
Final design plans scheduled for completion in February 2019.


I have to say, that I have always been appalled at people who dress their dogs (and cats) in humiliating costumes. So it really pains me to admit that I have become such a person. I can't help myself. The minute the air starts to get a little cooler, my thoughts turn to Halloween and what I can do to my wonderfully-passive, 4-legged mannequin, Ray.
He is such a good dog. He will stand stock still while I fit and pin and mark whatever fabric I'm using to make him into whatever alter ego I have chosen for the year, and will goodnaturedly wear it to the neighbors to show off.
You said that this year Ray wasn't going to have to wear a hat for Halloween, and I guess that technically, lamb ears aren't a hat. Very creative, but the look on Ray's face clearly says, "My mother is so baaaaaaaaaaad!"
Really? Because I think I see a sly smile on his face. I think he's imagining himself a wolf in sheep's clothing.
Yeah, probably. He is a good boy to his mom.


text:
package org.tensorflow.framework.op;

import org.tensorflow.Operand;
import org.tensorflow.framework.op.nn.GELU;
import org.tensorflow.framework.op.nn.SigmoidCrossEntropyWithLogits;
import org.tensorflow.framework.op.nn.SoftmaxCrossEntropyWithLogits;
import org.tensorflow.framework.op.nn.SparseSoftmaxCrossEntropyWithLogits;
import org.tensorflow.op.Scope;
import org.tensorflow.types.family.TNumber;

/**
 * Creates Framework nerual network Operations
 *
 *
These are higher level ops that may invoke core ops. Higher level Ops may perform the
 * operation solely in the TensorFlow framework or do preprocessing of the Operands before invoking
 * a core level Op.
 *
 *
{@link FrameworkOps}
 */
public class NnOps {
  private final Scope scope;

  private final FrameworkOps frameworkOps;

  /**
   * Creates Framework {@code nn} Operations
   *
   * @param frameworkOps the TensorFLow framework Ops
   */
  NnOps(FrameworkOps frameworkOps) {
    this.scope = frameworkOps.scope();
    this.frameworkOps = frameworkOps;
  }

  /**
   * Computes sigmoid cross entropy given {@code logits}.
   *
   *
Measures the probability error in discrete classification tasks in which each class is
   * independent and not mutually exclusive. For instance, one could perform multilabel
   * classification where a picture can contain both an elephant and a dog at the same time.
   *
   *
For brevity, let {@code x = logits}, {@code z = labels}. The logistic loss in pseudo-code is
   *
   *

   *  z * -log(sigmoid(x)) + (1 - z) * -log(1 - sigmoid(x))
   *   = z * -log(1 / (1 + exp(-x))) + (1 - z) * -log(exp(-x) / (1 + exp(-x)))
   *   = z * log(1 + exp(-x)) + (1 - z) * (-log(exp(-x)) + log(1 + exp(-x)))
   *   = z * log(1 + exp(-x)) + (1 - z) * (x + log(1 + exp(-x))
   *   = (1 - z) * x + log(1 + exp(-x))
   *   = x - x * z + log(1 + exp(-x))
   *

   *
   *
For {@code x < 0}, to avoid overflow in {@code exp(-x)}, we reformulate the above
   *
   *

   *  x - x * z + log(1 + exp(-x))
   *   = log(exp(x)) - x * z + log(1 + exp(-x))
   *   = - x * z + log(1 + exp(x))
   *

   *
   *
Hence, to ensure stability and avoid overflow, the implementation uses this equivalent
   * formulation
   *
   *

   *    max(x, 0) - x * z + log(1 + exp(-abs(x)))
   *

   *
   *
{@code logits} and {@code labels} must have the same type and shape.
   *
   *

   *
   * @param labels the labels
   * @param logits the logits of type float32 or float64
   * @param <T> the type of labels and logits
   * @return the component-wise logistic losses.
   * @throws IllegalArgumentException if logits and labels do not have the same shape
   */
  public <T extends TNumber> Operand<T> sigmoidCrossEntropyWithLogits(
      Operand<T> labels, Operand<T> logits) {
    return SigmoidCrossEntropyWithLogits.sigmoidCrossEntropyWithLogits(scope, labels, logits);
  }

  /**
   * Computes softmax cross entropy between {@code logits} and {@code labels}.
   *
   *
Measures the probability error in discrete classification tasks in which the classes are
   * mutually exclusive (each entry is in exactly one class). For example, each CIFAR-10 image is
   * labeled with one and only one label: an image can be a dog or a truck, but not both.
   *
   *
NOTE:
   *
   *
While the classes are mutually exclusive, their probabilities need not be. All that is
   * required is that each row of {@code labels} is a valid probability distribution. If they are
   * not, the computation of the gradient will be incorrect.
   *
   *
If using exclusive {@code labels} (wherein one and only one class is true at a time), see
   * {@link org.tensorflow.op.NnOps#sparseSoftmaxCrossEntropyWithLogits}
   *
   *
Usage:
   *
   *

   *    Operand<TFloat32> logits =
   *        tf.constant(new float[][] {{4.0F, 2.0F, 1.0F}, {0.0F, 5.0F, 1.0F}} );
   *    Operand<TFloat32> labels =
   *        tf.constant(new float[][] {{1.0F, 0.0F, 0.0F}, {0.0F, 0.8F, 0.2F}} );
   *    Operand<TFloat32> output =
   *        tf.nn.softmaxCrossEntropyWithLogits(labels, logits, -1);
   *    // output Shape = [2]
   *    // dataType = FLOAT (1)
   *    // values { 0.169846, 0.824745 }
   *

   *
   *
Backpropagation will happen into both {@code logits} and {@code labels}. To disallow
   * backpropagation into {@code labels}, pass label tensors through {@code tf.stopGradient} before
   * feeding it to this function.
   *
   * @param labels Each vector along the class dimension should hold a valid probability
   *     distribution e.g. for the case in which labels are of shape {@code [batch_size,
   *     num_classes] }, each row of {@code labels[i]} must be a valid probability distribution.
   * @param logits Per-label activations, typically a linear output. These activation energies are
   *     interpreted as unnormalized log probabilities.
   * @param axis The class dimension. -1 is the last dimension.
   * @param <T> the number type of the operands
   * @param  the data type for the labels.
   * @return the softmax cross entropy loss. Its type is the same as {@code logits} and its shape is
   *     the same as {@code labels} except that it does not have the last dimension of {@code
   *     labels}.
   */
  public <T extends TNumber, U extends TNumber> Operand<T> softmaxCrossEntropyWithLogits(
      Operand labels, Operand<T> logits, int axis) {
    return SoftmaxCrossEntropyWithLogits.softmaxCrossEntropyWithLogits(scope, labels, logits, axis);
  }

  /**
   * Computes sparse softmax cross entropy between {@code logits} and {@code labels}.
   *
   *
Measures the probability error in discrete classification tasks in which the classes are
   * mutually exclusive (each entry is in exactly one class). For example, each CIFAR-10 image is
   * labeled with one and only one label: an image can be a dog or a truck, but not both.
   *
   *
NOTE:
   *
   *
For this operation, the probability of a given label is considered exclusive. That is, soft
   * classes are not allowed, and the {@code labels} vector must provide a single specific index for
   * the true class for each row of {@code logits} (each minibatch entry). For soft softmax
   * classification with a probability distribution for each entry, {@link
   * org.tensorflow.op.NnOps#softmaxCrossEntropyWithLogits}.
   *
   *
WARNING:
   *
   *
This op expects unscaled logits, since it performs a {@code softmax} on {@code logits }
   * internally for efficiency. Do not call this op with the output of {@code softmax}, as it will
   * produce incorrect results.
   *
   *
A common use case is to have logits of shape {@code [batchSize, numClasses]} and have labels
   * of shape {@code [batchSize]}, but higher dimensions are supported, in which case the {@code
   * dim}-th dimension is assumed to be of size {@code numClasses}. {@code logits} must have the
   * {@code dataType} of {@code TFloat16}, {@code TFloat32} , or {@code TFloat64}, and {@code
   * labels} must have the dtype of {@code TInt32} or {@code TInt64}.
   *
   * @param labels {@code Tensor} of shape {@code [d_0, d_1, ..., d_{r-1}]} (where {@code r } is
   *     rank of {@code labels} and result) and the dataType is {@code TInt32} or {@code TInt64}.
   *     Each entry in {@code labels} must be an index in {@code [0, numClasses)}. Other values will
   *     raise an exception when this op is run on CPU, and return {@code NaN} for corresponding
   *     loss and gradient rows on GPU.
   * @param logits Per-label activations (typically a linear output) of shape {@code [d_0, d_1, ...,
   *     d_{r-1}, numClasses]} and dataType of {@code TFloat16}, {@code TFloat32}, or {@code
   *     TFloat64}. These activation energies are interpreted as unnormalized log probabilities.
   * @param  the data type for the labels
   * @param <T> the data tyoe for the loss and logits.
   * @return the loss
   * @throws IllegalArgumentException If logits are scalars (need to have {@code rank >= 1}) or if
   *     the rank of the labels is not equal to the rank of the logits minus one.
   */
  public <T extends TNumber, U extends TNumber> Operand<T> sparseSoftmaxCrossEntropyWithLogits(
      Operand labels, Operand<T> logits) {
    return SparseSoftmaxCrossEntropyWithLogits.sparseSoftmaxCrossEntropyWithLogits(
        scope, labels, logits);
  }

  /**
   * Compute the Gaussian Error Linear Unit (GELU) activation function without approximation.
   *
   *
Gaussian error linear unit (GELU) computes {@code x * P(X <= x)}, where {@code P(X) ~ N(0,
   * 1)}. The (GELU) nonlinearity weights inputs by their value, rather than gates inputs by their
   * sign as in ReLU.
   *
   * @param input the input
   * @param <T> the data type for the input and result
   * @return The Gaussian Error Linear Unit computation
   */
  public <T extends TNumber> Operand<T> gelu(Operand<T> input) {
    return GELU.gelu(scope, input);
  }

  /**
   * Compute the Gaussian Error Linear Unit (GELU) activation function.
   *
   *
Gaussian error linear unit (GELU) computes {@code x * P(X <= x)}, where {@code P(X) ~ N(0,
   * 1)}. The (GELU) nonlinearity weights inputs by their value, rather than gates inputs by their
   * sign as in ReLU.
   *
   * @param input the input
   * @param approximate Whether to enable approximation.
   * @param <T> the data type for the input and result
   * @return The Gaussian Error Linear Unit computation
   */
  public <T extends TNumber> Operand<T> gelu(Operand<T> input, boolean approximate) {
    return GELU.gelu(scope, input, approximate);
  }
}

redpajama_set_name: RedPajamaGithub


Joseph Mullin (August 6, 1811 – May 17, 1882) was an American lawyer and politician from New York.
Mullin was born near Dromore, County Down in Ireland on August 6, 1811. He came to the United States in 1820 with his parents, and they settled in Watertown, New York. He attended Union Academy at Belleville, and graduated from Union College in 1833.
Following his graduation from Union College, he taught school and was Principal of Union Academy, and subsequently taught at Watertown Academy. Then he studied law, and was admitted to the bar in 1837.
Mullin was District Attorney of Jefferson County from 1843 to 1845. He was elected as a Whig to the 30th United States Congress, holding office from March 4, 1847, to March 3, 1849. He was President of the Village of Watertown in 1853 and 1854.
In 1855, he ran on the Republican ticket for the New York Court of Appeals, but was defeated by the American Party candidate George F. Comstock.
He was a justice of the New York Supreme Court (5th District) from 1858 to 1881, and was ex officio a judge of the Court of Appeals in 1864. He retired from the bench in January 1881.
In January 29, 1837, he married Lydia Maria Ten Eyck (1815–1884), a daughter of fellow U.S. Representative Egbert Ten Eyck. Together, they were the parents of five children: Anthony Ten Eyck Mullin, Catherine Mullin, Lydia Mullin, Rebecca Ten Eyck Mullin, and Joseph Mullin (1848–1897), who served in the New York State Senate.
Mullin died on May 17, 1882 in Saratoga Springs, New York. He was buried at the Brookside Cemetery, in Watertown.
^ a b c "OBITUARY NOTES" (PDF). The New York Times. May 18, 1882. Retrieved 26 June 2018.
^ a b c "MULLIN, Joseph - Biographical Information". bioguide.congress.gov. Biographical Directory of the United States Congress. Retrieved 26 June 2018.
^ a b c New York State Unified Court System. "Hon. Joseph Mullin | New York Legal History / Antebellum, Civil War, & Reconstruction: 1847-1869". www.nycourts.gov. The Historical Society of the New York Courts. Retrieved 26 June 2018.
^ Hough, Franklin Benjamin (1858). The New York Civil List: Containing the names and origin of the civil divisions, and the names and dates of election or appointment of the principal state and county officers from the Revolution to the present time. Weed, Parsons and Co. p. 351. Retrieved 26 June 2018.
^ Foley, Janet Wethy (July 1937). Early Settlers of New York State: Their Ancestors and Descendants, Volu: Their Ancestors and Descendants, Volumes I-VI (PART II - iv-vi). Heritage Books. p. 7. ISBN 9780788437120. Retrieved 26 June 2018.
^ a b Genealogical Notes of New York and New England Families. Heritage Books. 2000. p. 251. ISBN 9780788419560. Retrieved 26 June 2018.
^ "SENATOR MULLIN IS DEAD. Stricken by Heart Disease in His Room in the University Clubhouse. BODY FOUND BY A SERVANT He Was Lying, Almost Fully Dressed, Across the Bed, with His Spectacles On--Watertown's Representative in the Senate Since 1891" (PDF). The New York Times. September 3, 1897. Retrieved 26 June 2018.
United States Congress. "Joseph Mullin (id: M001072)". Biographical Directory of the United States Congress.


text:
Home GENERAL NEWS Morgan Tsvangirai suspended, amid crisis in Zimbabwe's Main opposition party
Morgan Tsvangirai suspended, amid crisis in Zimbabwe's Main opposition party
Morgan Tsvangirai suspended,
A faction in Zimbabwe's main opposition movement has said it is no longer recognising Morgan Tsvangirai as the party leader, blaming "fascist" tendencies and his failure to oust President Robert Mugabe.
The group led by Tendai Biti, secretary general of the Movement for Democratic Change (MDC), said it had suspended Tsvangirai but their authority to do so was immediately disputed by rivals within the MDC.
Biti's group accused Tsvangirai his lieutenants of resisting a leadership change after losing a third general election to Mugabe last July, and of using violence against internal challengers.
The 90-year-old Mugabe, Africa's oldest leader, has ruled Zimbabwe since independence in 1980 despite frequent western criticism over human rights and accusations of economic mismanagement.
In a statement after a day-long meeting, Biti's faction said Tsvangirai and his deputy Thokozani Khupe had been suspended for deviating from democracy and failing to effectively tackle Mugabe.
"The MDC as we know it has abandoned its original founding values and principles," it said. "The party has been hijacked by a dangerous fascist clique bent on destroying the same and totally working against the working people of Zimbabwe."
Tsvangirai's faction dismissed the removal as unconstitutional and meaningless. "The MDC leadership cannot be changed by a bunch of desperate power-hungry officials, a minority that cannot win a leadership contest at party congress," national party spokesman Douglas Mwonzora told reporters.
Tsvangirai has resisted pressure to quit after losing the 2013 election, which he says was rigged by Mugabe's supporters. Analysts predict the MDC will break apart.
The 62-year-old Tsvangirai has led the MDC since its formation in 1999, when the former trade unionist emerged as the biggest threat to Mugabe. But he has failed to dislodge his rival in three presidential polls that his MDC and many western observers say were neither free or fair.
While accusing Mugabe's Zanu-PF party of using violence and vote-rigging to retain power, some senior MDC officials also say Tsvangirai has become bogged down by sex scandals and failed to adopt the right tactics to win power.
An ally of Biti, Elton Mangoma, ignited debate over Tsvangirai with an open letter early this year calling on him to step down as party president.
He said Tsvangirai could no longer drive a reform agenda for Zimbabwe, having failed to do so in the four years he served as prime minister and shared executive powers with Mugabe. Their unity government ended last year and Zanu-PF has ruled alone since then.
Analysts say Tsvangirai's MDC critics have so far failed convince the party's national executive to hold an early congress before one scheduled for 2016. They have also struggled to persuade ordinary members that Tsvangirai is to blame for the MDC's poll losses.
Reuters contributed to this report
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Key Tips to Quickly Recover and Build Language Fluency
Tips To Quickly Recover Your Fluency In A Language You Previously Studied
By Eva Drago
If there's one unavoidable fact when it comes to learning languages, it's that it takes a time commitment. It doesn't necessarily have to be a huge amount of time each day, a lot of us are busy, and only in a position to study between other responsibilities. The key is consistency, putting in at least a little time as frequently as possible.
Unfortunately it's not uncommon for 'real life' to get in the way, and it's very easy to break your routine. Before you know it, quite a while may have passed since the last time you practiced your chosen language. The most common symptom of time away from study is a loss of fluency and a lack of confidence. The need to then think carefully about what you want to say leads to a slowdown in your spoken production.
If this describes you, then don't worry! You're certainly not alone; a lot of language learners take breaks in their studies and then manage to get back to their previous level - and then surpass it. Here are a few tips for those of us who are coming back to a language we've studied before.
Immerse Yourself In The Target Language
When you're learning a language, there's no such thing as too much input. This is equally true when you're returning to a language that you've studied before, with the added advantage that your level will be higher than when you started, so things should come back to you quickly. You should read as much as possible, from language apps or the internet.
If you're a beginner, then you may want to put Post-It notes in your home to label objects in the target language. If you're at a higher level, then try reading stories and news articles with your native language side-by-side, or even listening to TV shows on Netflix that are in your target language. Feel free to use subtitles to help you out; the goal is not to understand every single word but just to restore your familiarity with the language.
It can be harder to find opportunities to produce the target language, especially spoken production. Again, using the internet is your best option here. Try looking for websites that allow you to chat with other people in your target language, either native speakers or even other language students. Writing should be easier, as you can always find social media channels or blogs in your target language that you can contribute to. Remember, it's not about being perfect, it's about exposing yourself to as much of the language as possible.
Schedule Your Study
If you only study when you feel like it, or when it's convenient, you'll probably find that you study less than you really want to. Pick your preferred language app and set yourself a time each day when you plan to use it. For example, with Beelinguapp you can plan to read a story, or a part of a story, every day just after you eat your lunch. The most important thing when it comes to scheduling is not to give up if you need to break your routine.
Once again, 'real life' may not allow you to study at the same time every day. If this happens and you miss your scheduled study, don't give up! Just try again the next day and, if possible, do a little extra work to make up for your missing day. If you find that you frequently break your schedule then try shifting it to a different time, until you find something that usually works for you.
Record Yourself
When you're 'in the moment', it can be difficult to accurately gauge how well you're coming along with your language learning. But as well all now carry a video camera in our pockets, it's easier than ever to record ourselves speaking our target language on our cell phones and then watching it back. This can be a little uncomfortable at first; a lot of us can be uncomfortable seeing and hearing ourselves speak, especially in another language. However, this is a really great tool when it comes to language learning.
Watching a recording of yourself is an important way of practicing self-correction. You may notice errors when you watch a recording that you weren't aware of when you were concentrating on speaking. And in terms of pronunciation and fluency, it's a way of taking an external view of yourself and comparing it to the native examples of the target language you've been studying. Once you get over the initial nervousness of hearing your own voice speaking a foriegn language, it's an ideal way of improving pronunciation and fluency.
No Fear! Accuracy vs Fluency
It's normal to want it all when we're studying a language. We want to speak, read, write and listen, and we want to do it quickly, accurately and sound good when we're doing it. That's a great goal, but it's important to understand that sometimes we have to study skills separately from one another. A good example of this is fluency and accuracy, which are often at odds with one another.
When we consider fluency, we're usually talking about fast, smooth and confident production. However, speed usually comes at the cost of accuracy. The more we try to be fluent, the more likely we are to make small errors in our production. The key here is to strike a balance between the two. There are times when we will want to improve our accuracy, which usually means being as slow, methodical and careful as possible. But the other side of the coin is that, if we want to push our fluency, we have to accept that small errors are going to creep in. When you're aiming for fluency, don't be afraid of making small mistakes, especially ones that don't cause problems with communication. As long as you're getting your message across, it's fine to sometimes sacrifice a few errors.
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text:
Sowmya Guru
The Unconventional Woman
A story of a girl, woman, other and a mother
Sometimes being a woman can make you wince and cringe about your very existence. I can easily say every woman would have asked "the" question- "Why was I born a woman?" at least once in her lifetime. Besides enduring the biological fluctuations of various degrees in physical and mental health at different points in time, she has to remain strong, empowered, and independent regardless of situations that might bring her to her knees. This is my humble attempt to share a story very close to my heart and has been long due.
When I was a little girl in the 90s, it was customary to spend our summer vacation at my grandparent's farmhouse. It was a joint family where my third and fourth maternal uncles and their families lived under the same roof with my great-grandma and grandpa managing the estate. My second uncle's family lived in a nearby village close to my grandparent's home and his daughter, who was around two years older than me (38 in 2023) also came to spend her summer with us.
Summer vacations transformed the farmhouse into a madhouse full of rampant kids, in the absence of parents, who seemed like unleashed prisoners from a year-long grinding of school and enslavement, awaiting an ultimate passage to freedom. We knew we'd be coaxed, fed, spoiled, and undoubtedly brushing our teeth twice a day or going to bed on time weren't obligatory anymore as they'd go unnoticed in the grand scheme of things. Talk about the perks of being one of the many kids in the household. My granny singlehandedly tried her best to keep the menace under control while we went around infuriating the house guests, molesting the pets, wrecking the farm, climbing coconut trees to harvest honey, plucking mangoes, etc. Granny used to scream — 'Hushaaruuuu' (Careful).. To add to that havoc, my brother wouldn't leave the neighbor kids alone and was frequently summoned for lectures by my youngest aunt, other times also got a spanking or two. I must say, I was not only happy to be part of the beautiful chaos but also looked forward to finishing my exams and meeting my very special cousin Rathna (meaning "gem" in Kannada) who was a soul sister to me.
Rathna was quieter than the rest of us, she was bright, street-smart, and wasn't much into studies. Nonetheless, she was confident and had a warm persona. At nightfall, she'd narrate horror stories about paranormal activities in her village that spooked the pants outta us. She took care of me and protected me from my other cousins who were plain evil and picked fights often! I knew we had a bizarre attachment to one another like we were sisters from other mothers. Whenever it was time to leave and get back to our lives we cried truck loadsa tears and refused to go home as we knew this was an annual thing.
The madness ensued until we almost reached high school, after which most of us stopped visiting our farmhouse because like regular teenagers we had much cooler things to do like attending a summer camp or going swimming. Also, for me it wasn't the same anymore after we lost our ajji when I was in 9th grade, going back just made me sad. Naturally, at the time, since we didn't have mobile phones or even telephones widely available, and as Rathna's family lived in a village 80 km from Bengaluru our meetups became rare.
I hit puberty like a farm bred chicken -as my aunt called it, the day I got my first period at the age of 12. I could sense my family was worried, they said but she's just a child. As a result, they started imposing restrictions on what I could do and what wasn't allowed like before. It was time to say Goodbye to childhood. On the other hand, girls in my school were growing annoyingly curious about menstruation and had all these questions I was too awkward to answer. They looked up to me like I was some female Jesus born to tell them the truth about turning into a woman. The boys and men in the family started to protect me like I was some kinda treasure a stranger would wanna steal. I felt like everyone around me was onto me for having my period. All in all, I hated every bit of it.
I remember when I was around 16, our family gathered to celebrate Ugadi [Kannada New Year] festival like every year. Sitting under the shade of the big blooming Raspuri tree next to our family house, one of my aunts as she oiled my hair turned to my other aunt and said Rathna turned 18 and still hasn't got her period yet. By then it was an open secret in the family. She had been visiting different doctors for a while but the diagnosis didn't differ much. She suffered from a reproductive disorder, which when googled, figured was called "Mayer-Rokitansky-Küster-Hauser" syndrome where women usually do not have menstrual periods due to the underdeveloped or absent uterus. After taking a second, third, and "n" number of opinions from doctors all over India, her parents gave up and just hoped that she would somehow learn to live with it someday. As I sat there hearing them talk, I wished I had it too so I could go back to being a child again.
In the coming years, I noticed a complete transformation in her behaviour as she absolutely refrained from attending any gatherings or public events as people talked about her disability to her face. They looked at her with their snobby pitiful faces as though they'd just discovered she was an alien from another planet. She house-arrested herself and strictly disagreed to go out which eventually disconnected us for quite a few years. I and another cousin who is two years younger than me Rashmi had completely stopped discussing boys or crushes when she was around. We told her we all hated to undergo puberty and she was if anything but the luckiest. I realise, we were only naive and failed to acknowledge the gravity of her pain. Now that I'm way older, I might have the slightest idea of what she might have craved and missed as a young woman.
I pondered how society was responsible for a wonderful girl with tremendous potential for being wasted due to her fertility issues. She was to society like those discarded bones on the plate after they'd juiced out every last bit of meat on it. No man wanted to even meet her, leave alone date her after hearing her story. Because at the end of the day, women are just baby-making machines serving a purpose. At least that's what society wants you to believe. She was another victim of society's ways. Breaking free is like trying to tuck in octopus' arms in bed.
The more you realise your limitations eventually you'd find yourself suffused by the obsession to pursue what you can't have. That's just human nature isn't it? In India, there is no concept of being a single mother like in the west. You either have children with the man you marry or you don't. If you can't have a child then you adopt one — As a couple. But there is no way a woman is going to adopt one by herself. Something never heard of!
My ajji was a single mother majority of her life, she died at the age of 96. When our taata(great-grandpa) died she was just 19 years old but she already had a daughter. She never remarried or dated anyone as we don't have the concept of dating in Indian culture. Even now it's a taboo in rural areas and among the conservatives. My ajji was a one-man woman. You marry once and that's it! If your man is dead you are a widow for life. That's just destiny set in stone. 'You accept it and move the heck on' — she once said.
We grew up watching our ajji who was a strong role model for us girls. We admired how she commanded respect from everyone. Rathna could've been a single mother if she wanted. Her family was well off or rather some might say even rich. But adoption didn't even occur as an option to her as it was a notion uncommon in the culture. No seeds of such empowering ideas should be sown into women. You can't let women think and want things for themselves. It'd merely break the foundation of the society and disrupt its crooked plans to keep women oppressed isn't it? On the other hand, she herself felt like a liability to her parents because of giving up on her career and education, how'd she ever provide for a child? Who was she kidding?
When we were kids, she always talked about — how she felt like an ugly duckling, and now she felt worthless too. In my eyes, she will always be the prettiest and the strongest girl I know.
Unfortunately, after all that Indian culture boasts of, it boils down to the fact that infertility is yet one of the major issues our society finds socially unacceptable. The mentality of self-righteous people who think adoption is taboo and every woman is meant to bear children or fails to fulfill the primary credential of womanhood is an abomination. The very idea makes me rethink and question if I want to be a part of it. It smothers you and leaves you feeling helpless, hopeless, and unworthy of existence when every human has the right to be respected and treated equally regardless of what society finds acceptable or unacceptable, theoretically.
In the summer of 2013, when mangoes were ripe and trees were bursting with jackfruits outside, sweltering in the peak summer sun's heat, my uncle paid us a visit. His visits were intentional and occasional. Other times he'd always come up with excuses like how the cattle needed to be fed, or he had to help the neighbors with milking their cows and yada yada. He was a silent observer one could find in the pictures only during historical events of our family. Sadly, he passed away due to cancer a few months ago. When he visited us back then, he said- a family approached them with a marriage proposal (because arranged marriages are still very much common in India), the man had a two-year-old daughter and a bedridden wife with an incurable neurological illness. It was her wish to entrust the future of her child in the safe hands of a woman. Someone who could promise her love like herself. She didn't want to depart the child motherless. My sister was moved by their situation and agreed to the marriage. Her happiness was boundless. She thought she had been bestowed with the opportunity to foster a child and help someone in need. 'Probably this is God's will' — she exclaimed priggishly. Some women have always amused me by demonstrating extraordinary levels of kindness and compassion stepping up like no other human I've ever known. I sometimes wonder if men would do the same for women.
To summarise, she had agreed to an arrangement where the wife was still alive, who she had to take care of her, while she was not even legally this wedded man's wife. Because in India, like most countries, you can be married to just one person at a time. Now, don't ask me about legal rights when it comes to consensual polyamory, I can't be sure the lawmakers have heard about certain "western ideas" yet! Though polygamy has been a common practice for thousands of years in India among certain groups and majorly Muslims. It became an abolished practice when the constitution was copied verbatim from the Brits in 1950. One could if they wished to marry anyone consensually, it's a free country, but wouldn't fly in a court of law. So, the second wife though wedded in front of hundreds of people had absolutely no legal rights but still very much had social rights and a sense of authority. Surprisingly fascinating isn't it? But somehow being the other woman didn't seem to bother her. She was okay to be the other, as long as she was a mother! Tears rolled down when I heard the news. She had spoken like a real Rathna — an unconventionally phenomenal gem of a person.
Rathna's wedding was a small, intimate ceremony in a temple with just family (of course of almost more than 100 people, that's India). I was her trusted wedding photographer, which explains the kind of satisfier she is. I was also the only one with a DSLR, so technically she didn't have much of a choice. She seemed happy.
I felt like maybe this was the magical ending to her suffering. She was just a woman who wanted a family. Something she had only dreamed of! After facing a million rejections you'd think it can get to your head but she had a stoic perspective which is more or less the Hindu way of life. You accept things as they come. You don't judge and try to suffer less.
Countless women in India undergo such mental trauma and hundreds of children are devoid of parental love. Not all women have the courage to stand up for their rights and not all children have the privilege of leading a regular life. They silently wait to be embraced and accepted with their disabilities and shortcomings. I'm quite certain my sister feels alive and empowered all over again but the scars left behind by society will remain forever.
First appeared in my blog, with some modifications, editing, and changed life facts ever since. Based on true story.
Hope you enjoy this as much as I enjoyed writing it!
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text:
Home | Society
Social anxiety rising among young people
By ZOU SHUO | China Daily | Updated: 2022-12-02 07:35
Many say they lack the requisite skills to cope with work and community life
A new college graduate's decision to become a cemetery custodian has ignited a heated discussion on social media about how young people nowadays can deal with social anxiety and benefit from genuine interpersonal relationships.
The Generation Z student from Chongqing said she is very pleased with her job because she only has four colleagues and does not need to worry about any complicated relationships.
Moreover, her office, dormitory and canteen are in the same building, the pace of work is slow and she almost feels as if she has retired early.
Her decision became a trending topic on Sina Weibo, with many netizens saying they envied her position.
"Young people would rather work in a cemetery than network," said one comment, which received more than 10,000 likes.
Meanwhile, a 29-year-old man in Shenzhen, Guangdong province, made headlines after he called for emergency assistance twice in a month because he was experiencing social anxiety.
The man, surnamed Zhong, has a doctorate. He was diagnosed with a panic disorder when he began work and had difficulty adjusting to the pressure of his job and his new social circle. He also experienced two relationship breakups.
Previously, he had lived an isolated life and had not participated in social gatherings.
According to a survey conducted last year by China Youth Daily, more than 80 percent of the nearly 5,000 college students questioned said they had mild social anxiety disorder, with only 12 percent saying they did not have any problems.
The survey found that the disorder surfaces most frequently when speaking in front of large groups, communicating with strangers and asking for favors. One-third of the students said they would pretend not to notice acquaintances when passing them on the street.
Cheng Qiang, 29, who works for a media group in Beijing said he has experienced social anxiety disorder since middle school.
He said he always wears a face mask in the office to try to avoid contact with coworkers. He also chooses the long route whenever he goes to the toilet or kitchen so he will encounter fewer people.
"The disorder becomes more severe when I am around people who know me but are not close," he said. "Their attention makes me nervous, and I don't know how to respond."
Chen Mo, 29, a doctoral candidate at a university in Beijing, said she avoids talking to other people over the phone or in person because her voice is soft and she feels it does not sound professional enough.
"I would much rather text as I can use a meme to end a conversation or avoid awkwardness," she said. "I am more comfortable and seem more positive when texting, and it takes much more energy and mental strength to be as positive when talking in person."
Wang Wenda, a psychology lecturer at Ningxia University's Xinhua College in Yinchuan, capital of the Ningxia Hui autonomous region, said people tend to have social anxiety disorder if they are introverted or lack confidence or social skills such as those required to communicate with others, deal with conflict or find the strength to say no.
Others experience the disorder because they have suffered traumatic interpersonal relationships, he said.
The disorder is not trivial. Severe social anxiety can lead to panic attacks and trigger other psychological problems as a result of a lack of contact with other people, Wang said.
Some people are very socially active online but timid in real life because face-to-face communication requires more social skills than texting, he added.
"Instant messaging apps are not really 'instant' because people can choose not to respond to messages or can take time to come up with the best response, while in real life, they must react right away and understand different facial expressions and gestures," he noted.
He suggested that people with social anxiety disorder should go out and expose themselves to more social gatherings and practice their social skills, adding that through greater social experience and small successes in social encounters, they will reap the benefits of a real social life and come to enjoy positive interpersonal relations.
zoushuo@chinadaily.com.cn


25 linear feet of shelf space.
The papers of Sam Hamill consist of documents related to Hamill's own poetry, his role as the editor of other poets' works at Copper Canyon Press, and records of some of his other activities. The collection includes correspondence, manuscripts, printed material, Hamill's appointment calendars, and ephemeral items.
[Item Description]. Cage 700, Sam Hamill Papers. Manuscripts, Archives, and Special Collections, Washington State University Libraries, Pullman, WA.
Sam Hamill is the author of over 30 books, including original poetry, essays, and translations from Chinese, Japanese, Estonian, Latin, and Greek. Included among his works are Nootka Rose (1987), A Poet's Work: The Other Side of Poetry (1990), Only Companion: Japanese Poems of Love and Longing (1992), Destination Zero: Poems, 1970-1995 (1995), Gratitude (1998), and Dumb Luck (2002).
Hamill received a National Endowment for the Arts fellowship, a Guggenheim Memorial fellowship, a Pushcart Prize, two Washington Governor's Arts Awards, and many other honors.
Details of Hamill's earliest years are vague. He was born in 1943 to unknown parents. He was adopted from foster care at the age of three by Sam and Freeda Hamill, who raised him near Holladay, UT. He attended Los Angeles Valley College and the University of California, Santa Barbara. He has one daughter, Eron, from his first marriage.
Along with being a poet and editor, Hamill is also a teacher: he taught inmates in prisons for fourteen years, and participated in artist-in-residence programs for twenty years.
Sam Hamill, a few fellow poets, and Tree Swenson (who later became Hamill's wife) established Copper Canyon Press in Denver, CO. The initial capital for the press was a five hundred dollar check Hamill had received for "producing the best college or university literary journal in the country" as the editor of Spectrum, a University of California, Santa Barbara, journal. Copper Canyon's first title, Badlands by Gerald Costanzo, was published in 1973.
In 1974 the press was moved to Port Townsend, WA, to Centrum, a non-profit arts center located at Fort Worden State Park, becoming Centrum's press-in-residence. The press became a not-for-profit operation in 1990.
The Sam Hamill Papers consist of documents related to Hamill's own poetry, his work as the editor of other poets' works, and records of some of his other activities.
Series 1: Correspondence, 1972-2001. Hamill's correspondence is arranged alphabetically by name of author, and includes correspondence with many poets, along with some poems and other related material.
Series 2: Manuscripts, 1972-1998. This series is arranged alphabetically by name of author, and includes material from various stages of the publication process.
Series 3: Miscellaneous, 1976-1997. This series includes a wide variety of documents, including correspondence, Hamill's calendars, printed items such as publisher catalogs, articles, and publicity materials, and other items. These are organized in a single alphabetical sequence, generally by name of author, but occasionally by document title, type, or topic.
The papers of Sam Hamill were purchased from Copper Canyon Press by the Washington State University Libraries in 2002.


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text:
Cod stocks in the Baltic Sea. Jarosław Wałęsa MEP
"This is already the fifth year that the plan for cod stocks in the Baltic Sea has been in force and according to scientific data, a significant increase in cod stocks has been observed. However, in light of the Lisbon Treaty in force there was a need to amend and align the multi-annual plan. The most important changes which were voted today are updating the value of fishing mortality and allowing small-scale fishermen to fish cod during the closed season, particularly during summer months, with no negative effect on pre-spawning and spawning concentrations. This may prove economically important for this fleet segment as prices during the relevant period are high", said Jarosław Wałęsa MEP, Rapporteur on changes to the plan for cod stocks in the Baltic Sea.
"The European Parliament recognises that the said plan leads to the renewal of the stock. However, certain shortcomings had to be addressed, such as a lack of flexibility. It is the key to adjusting fishing opportunities with changing conditions of the cod stocks. Today's vote meets the needs of the sector representatives, as well as recognising that the future plans and reforms must take into account the specificity of the area, fostering the regionalisation", said Jarosław Wałęsa.
The next step, before the Regulation comes into force, is trialogues with the European Commission and the Council. Unfortunately, due to the dispute over powers between the Parliament and the Council, the entry-into-force of these provisions may be significantly delayed. The dispute concerns the allocation of fishing opportunities. The Council, which for years has stated that it has exclusive competence in this area, is blocking the work on the multi-annual management plans.
"The situation has a negative impact on the developing legislation in fisheries, aggravates relations between the Institutions and deserves to be condemned", concluded Jarosław Wałęsa.
Jarosław Leszek WAŁĘSA MEP, Tel: +33-3-88-175304
Katarzyna Klaus, EPP Group Press and Communications Service, Tel: +32-484-138359
The EPP Group is by far the largest political group in the European Parliament with 270 Members and 3 Croatian Observer Members.
« 17.1. Violence against women in India - debate
Jaroslaw Walesa MEP on the occasion of Turkey's Journalists Day »
First ever fisheries management plan for the Western Mediterranean agreed
EPP Political Assembly discusses rule of law in Poland and elects new EPP Vice President
The members of the European People's Party (EPP) Political Assembly discussed the rule of law in Poland and the political situation of the country at its meeting in Warsaw. In the margins of the meeting, EPP President Joseph Daul made the following statement:
Statement for: Engaging Legislators in Building the Framework for a Nuclear Weapons Free World
PNND event during the 2013 Conference of States Parties to the nuclear Non-Proliferation Treaty (NPT Prep Com) at the United Nations in Geneva
Newsletter - 22-23 June 2016 - Plenary session - Brussels


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