gebhart/patrepeval huggingface dataset:
The genomic evaluation system in the United States: Past, present, future (2011)

Implementation of genomic evaluation has caused profound changes in dairy cattle breeding. All young bulls bought by major artificial insemination organizations now are selected based on such evaluation. Evaluation reliability can reach approximately 75% for yield traits, which is adequate for marketing semen of 2-yr-old bulls. Shortened generation interval from using genomic evaluations is the most important factor in increasing the rate of genetic improvement. Genomic evaluations are based on 42,503 single nucleotide polymorphisms (SNP) genotyped with technology that became available in 2007. The first unofficial USDA genomic evaluations were released in 2008 and became official for Holsteins, Jerseys, and Brown Swiss in 2009. Evaluation accuracy has increased steadily from including additional bulls with genotypes and traditional evaluations (predictor animals). Some of that increase occurs automatically as young genotyped bulls receive a progeny test evaluation at 5 yr of age. Cow contribution to evaluation accuracy is increased by decreasing mean and variance of their evaluations so that they are similar to bull evaluations. Integration of US and Canadian genotype databases was critical to achieving acceptable initial accuracy and continues to benefit both countries. Genotype exchange with other countries added predictor bulls for Brown Swiss. In 2010, a low-density chip with 2,900 SNP and a high-density chip with 777,962 SNP were released. The low-density chip has increased greatly the number of animals genotyped and is expected to replace microsatellites in parentage verification. The high-density chip can increase evaluation accuracy by better tracking of loci responsible for genetic differences. To integrate information from chips of various densities, a method to impute missing genotypes was developed based on splitting each genotype into its maternal and paternal haplotypes and tracing their inheritance through the pedigree. The same method is used to impute genotypes of nongenotyped dams based on genotyped progeny and mates. Reliability of resulting evaluations is discounted to reflect errors inherent in the process. Further increases in evaluation accuracy are expected because of added predictor animals and more SNP. The large population of existing genotypes can be used to evaluate new traits; however, phenotypic observations must be obtained for enough animals to allow estimation of SNP effects with sufficient accuracy for application to the general population.
Monoclonal antibody against human interleukin 2 (IL 2). I. Purification of IL 2 for the production of monoclonal antibodies. (1982)

Human interleukin 2 (IL 2) was produced under serum-free conditions by stimulating mononuclear cells with concanavalin A (Con A) in the presence of phorbol myristate acetate (PMA) and hydroxyurea. The IL 2 was partially purified by sequential chromatography by using phenyl-Sepharose, DEAE Sephacel, and AcA 54 gel filtration. This partially purified material was used to immunize BALB/c mice. After immunization with a total of 48,000 U (spec. act. approximately 10(5) units/mg protein), the spleen cells were adoptively transferred into x-irradiated syngeneic mice and the animals were boosted with another 12,000 U of IL 2. Four days later their spleen cells were hybridized with plasmacytoma cells. Supernatants of the hybridoma cultures were screened for their capacity to inhibit the IL 2-induced proliferation of the CT6 cell line. After expansion and cloning eight different lines were selected for ascitic antibody production. The monoclonal antibodies inhibited the proliferation of the IL 2-dependent cell line in response to either human crude or purified IL 2, as well as rat and mouse IL 2. However, these anti-IL 2 antibodies did not inhibit the proliferation of human T cell lines capable of producing IL 2. Monoclonal antibodies coupled to Sepharose 4B absorbed IL 2 crude culture supernatant, confirming that they react directly with IL 2. The absorbed IL 2 could, for the most part, be eluted by using sodium dodecyl sulfate, thus providing a means for further immunoaffinity purification of IL 2.
Configurationally Stable Longitudinally Twisted Polycyclic Aromatic Compounds (2008)

Two strategies for the synthesis of configurationally stable twisted polycyclic aromatic compounds (PACs) were pursued. The first approach employed dissymmetrically positioned 1-naphthyl substituents to bias the direction of twist in highly substituted PACs. 2,3-Bis(1-naphthyl)-1,4-diphenyltriphenylene (7) was prepared, and its meso cis-dinaphthyl and enantiomeric trans-dinaphthyl isomers were resolved by preparative supercritical fluid chromatography (SFC) on chiral supports. Similarly, several naphthyl-substituted derivatives of the more highly twisted 9,10,11,12,13,14-hexaphenylbenzo[b]triphenylene (2) were prepared. Of these, 10-(1-naphthyl)-9,11,12,14-tetraphenylbenzo[b]triphenylene (13) was resolved by SFC on a chiral support. The pure enantiomers of trans-7 showed moderately large specific rotations ([alpha]D(25) = -330 and +320 degrees), but the specific rotations for the enantiomers of 13 were unexpectedly small ([alpha]D(25) = -23 and +23 degrees). Computational studies suggest that the latter result is due to presence of a minor conformation of 13 possessing a larger rotation of opposite sign than the major conformation. Both 7 and 13 showed strong circular dichroism and moderately strong circularly polarized luminescence. A byproduct of these syntheses was 9,10,19,21-tetraphenyldiphenanthro[9,10-b:9,10-h]carbazole (15), a very crowded carbazole that exhibits an 81 degree end-to-end twist but is not resolvable. In the second approach, the large, twisted, polycyclic aromatic ligand 9,10,11,12,13,14-hexaphenylbenzo[h]naphtho[2,3-f]quinoline (21, an aza-2) was used to prepare the chiral, cyclometallated iridium(III) complex 4. The ligand 21 was prepared via an unusually stable benzannulated norbornadienone, for which the free energy of activation for decarbonylation was a remarkable 33.5 kcal/mol. The iridium complex 4 proved to be configurationally stable and resolvable by analytical HPLC on chiral supports, but the low solubility of 4 prevented its resolution on a preparative scale. A much more soluble dibutyl analogue of 4 (complex 28) was then prepared, but it was not resolvable on any of the available media.
Increased expression of type 2 3α-hydroxysteroid dehydrogenase/type 5 17β-hydroxysteroid dehydrogenase (AKR1C3) and its relationship with androgen receptor in prostate carcinoma (2006)

Type 2 3alpha-hydroxysteroid dehydrogenase (3alpha-HSD) is a multi-functional enzyme that possesses 3alpha-, 17beta- and 20alpha-HSD, as well as prostaglandin (PG) F synthase activities and catalyzes androgen, estrogen, progestin and PG metabolism. Type 2 3alpha-HSD was cloned from human prostate, is a member of the aldo-keto reductase (AKR) superfamily and was named AKR1C3. In androgen target tissues such as the prostate, AKR1C3 catalyzes the conversion of Delta(4)-androstene-3,17-dione to testosterone, 5alpha-dihydrotestosterone to 5alpha-androstane-3alpha,17beta-diol (3alpha-diol), and 3alpha-diol to androsterone. Thus AKR1C3 may regulate the balance of androgens and hence trans-activation of the androgen receptor in these tissues. Tissue distribution studies indicate that AKR1C3 transcripts are highly expressed in human prostate. To measure AKR1C3 protein expression and its distribution in the prostate, we raised a monoclonal antibody specifically recognizing AKR1C3. This antibody allowed us to distinguish AKR1C3 from other AKR1C family members in human tissues. Immunoblot analysis showed that this monoclonal antibody binds to one species of protein in primary cultures of prostate epithelial cells and in LNCaP prostate cancer cells. Immunohistochemistry with this antibody on human prostate detected strong nuclear immunoreactivity in normal stromal and smooth muscle cells, perineurial cells, urothelial (transitional) cells, and endothelial cells. Normal prostate epithelial cells were only faintly immunoreactive or negative. Positive immunoreactivity was demonstrated in primary prostatic adenocarcinoma in 9 of 11 cases. Variable increases in immunoreactivity for AKR1C3 was also demonstrated in non-neoplastic changes in the prostate including chronic inflammation, atrophy and urothelial (transitional) cell metaplasia. We conclude that elevated expression of AKR1C3 is highly associated with prostate carcinoma. Although the biological significance of elevated AKR1C3 in prostatic carcinoma is uncertain, AKR1C3 may be responsible for the trophic effects of androgens and/or PGs on prostatic epithelial cells.
Nutraceuticals: (6) Proanthocyanidins and grape seed extract (2001)

Proanthocyanidins, particularly grape seed extract, are attracting increasing attention as potential preventives of heart disease and cancer and as antiviral compounds. This article looks at the evidence.
Expression and phosphorylation of TOPK during spermatogenesis (2005)

Among normal organs and tissues, the MAPKK-like mitotic protein kinase TOPK is expressed exclusively in the testis. We analyzed the expression and phosphorylation of TOPK to address the functional role of this kinase during spermatogenesis. TOPK protein is expressed mainly in the cytosol of spermatocytes and spermatids, but not in spermatids and spermatogonia in situ. TOPK-Thr-9, a cdk1/cyclin B target residue, was specifically phosphorylated during mitotic and meiotic phases, while TOPK-Thr-198, a key amino acid for the ATP pocket, was constantly phosphorylated irrespective of the cell cycle. These data indicate that spermatogenic germ cells with vital proliferation activity express TOPK. As TOPK-Thr-9 was phosphorylated during both mitosis and meiosis, TOPK was indicted to play a role in cytokinesis and/or chromosomal segregation but not in DNA replication.
Crucial Role of the Interleukin 1 Receptor Family Member T1/St2 in T Helper Cell Type 2–Mediated Lung Mucosal Immune Responses (1999)

T1/ST2 is an orphan receptor of unknown function that is expressed on the surface of murine T helper cell type 2 (Th2), but not Th1 effector cells. In vitro blockade of T1/ST2 signaling with an immunoglobulin (Ig) fusion protein suppresses both differentiation to and activation of Th2, but not Th1 effector populations. In a nascent Th2-dominated response, anti-T1/ST2 monoclonal antibody (mAb) inhibited eosinophil infiltration, interleukin 5 secretion, and IgE production. To determine if these effects were mediated by a direct effect on Th2 cells, we next used a murine adoptive transfer model of Th1- and Th2-mediated lung mucosal immune responses. Administration of either T1/ST2 mAb or T1/ST2-Ig abrogated Th2 cytokine production in vivo and the induction of an eosinophilic inflammatory response, but failed to modify Th1-mediated inflammation. Taken together, our data demonstrate an important role of T1/ST2 in Th2-mediated inflammatory responses and suggest that T1/ST2 may prove to be a novel target for the selective suppression of Th2 immune responses.
American Peptide Symposium (9th) held at Toronto, Ontario, Canada on June 23-28, 1985. (1986)

The Ninth American Peptide Symposium was held on the campus of the Univ. of Toronto June 23-28, 1985. There were 685 registrants at the meeting, which dealt with the Chemistry and Biology of Peptides. This report consists of the program of this meeting.
Critical Dependence of cAMP Response Element-Binding Protein Phosphorylation on L-Type Calcium Channels Supports a Selective Response to EPSPs in Preference to Action Potentials (2000)

Activity-dependent gene expression in neurons shows a remarkable ability to differentiate between different types of stimulation: orthodromic inputs that engage synaptic transmission are much more effective than antidromic stimuli that do not. We have studied the basis of such selectivity in cultured hippocampal neurons in which nuclear cAMP response element-binding protein (CREB) phosphorylation is induced by synaptic activity but not by action potential (AP) stimulation in the absence of EPSPs, although spikes by themselves generate large elevations in intracellular Ca(2+). Previous work has shown that Ca(2+) entry through L-type Ca(2+) channels plays a dominant role in triggering calmodulin mobilization and activation of calmodulin-dependent kinases that phosphorylate CREB, raising the possibility that L-type channels contribute to the selective response to EPSPs rather than APs. Accordingly, we performed voltage-clamp experiments to compare the currents carried by L-type channels during depolarizing waveforms that approximated APs or dendritic EPSPs. The integrated current generated by L-type channels was significantly less after mock APs than with EPSP-like depolarizations. The difference was traced to two distinct factors. Compared with other channels, L-type channels activated at relatively negative potentials, favoring their opening with EPSP stimulation; they also exhibited relatively slow activation kinetics, weighing against their contribution during an AP. The relative ineffectiveness of APs as a stimulus for CREB phosphorylation could be overcome by exposure to the agonist Bay K8644, which potentiated the AP-induced influx through L-type channels by approximately 10-fold. Under normal conditions, the unique biophysical properties of L-type channels allow them to act as a kinetic filter to support spike-EPSP discrimination.
Fate mapping the mouse embryo (1999)

The use of clonal analysis to obtain a fate map of the epiblast of the mouse embryo and to investigate cell distribution during gastrulation and early neurulation is described in a personal reminiscence. A revised fate map of the epiblast at 6.5 days gestation is provided, and the development of 3-dimensional, quantitative image analysis techniques outlined.
1-D dictionary mode for screen content coding (2014)

This paper introduces 1-D dictionary mode designed for screen content coding. Two 1-D dictionary modes are designed to improve the coding efficiency for screen content. The first one is called normal dictionary mode, in which a virtual dictionary should be maintained and all the prediction comes from the virtual dictionary. The other one is called reconstruction based dictionary mode, where no virtual dictionary is to be maintained and all the previously reconstructed pixels in the same picture can be used for prediction. Hash based search is designed to find matching for both dictionary modes efficiently. 1-D dictionary mode with variable block sizes are also supported in the proposed scheme. The experimental results show the proposed algorithm achieves about 10% ~ 18.4% bit saving for different coding structures. The bit saving is up to 60% for the proposed method.
Analysis of radiation‐induced apoptosis in human lymphocytes: Flow cytometry using Annexin V and propidium iodide versus the neutral comet assay (2002)

The comet assay is a useful tool for measuring the late stages of apoptosis whereas the Annexin V assay measures higher amounts of apoptosis because it can detect cells in an earlier stage of the apoptotic pathway.
Sparks begin to fly in nonconventional friction welding and surfacing (1993)

A technology with enormous potential for welding and surfacing is the linear or consumable-rod friction welding process. The jet engine manufacturers are interested in the process both for welding and surfacing of alloys and materials that would be difficult to handle by any other means. In most present engines, slots are provided in the disks in order to accept the turbine blades. So, when a blade becomes worn or damaged, it is removed and a replacement blade is inserted in its place. In the new BLISK or bladed disk design of engines, the blades will be integral parts of the engine. Linear friction welding could play a major role in the manufacture and repair of engines of BLISK design. The new design is expected to improve engine performance significantly. According to TWI, potential applications for linear friction welding include gears, turbine wheels, chain links, electrical bus bar components, such plastic automotive parts as bumpers, boot lids and floor pans, bimetallic chisel blades, and multiple joints in metals or plastics. This paper discusses some of the research done by various companies into the newer variations of friction welding.
Genetic Variation in the Plasmodium falciparum Circumsporozoite Protein in India and Its Relevance to RTS,S Malaria Vaccine (2012)

RTS,S is the most advanced malaria vaccine candidate, currently under phase-III clinical trials in Africa. This Plasmodium falciparum vaccine contains part of the central repeat region and the complete C-terminal T cell epitope region (Th2R and Th3R) of the circumsporozoite protein (CSP). Since naturally occurring polymorphisms at the vaccine candidate loci are critical determinants of the protective efficacy of the vaccines, it is imperative to investigate these polymorphisms in field isolates. In this study we have investigated the genetic diversity at the central repeat, C-terminal T cell epitope (Th2R and Th3R) and N-terminal T cell epitope regions of the CSP, in P. falciparum isolates from Madhya Pradesh state of India. These isolates were collected through a 5-year prospective study aimed to develop a well-characterized field-site for the future evaluation of malaria vaccine in India. Our results revealed that the central repeat (63 haplotypes, n = 161) and C-terminal Th2R/Th3R epitope (24 haplotypes, n = 179) regions were highly polymorphic, whereas N-terminal non-repeat region was less polymorphic (5 haplotypes, n = 161) in this population. We did not find any evidence of the role of positive natural selection in maintaining the genetic diversity at the Th2R/Th3R regions of CSP. Comparative analysis of the Th2R/Th3R sequences from this study to the global isolates (n = 1160) retrieved from the GenBank database revealed two important points. First, the majority of the sequences (~61%, n = 179) from this study were identical to the Dd2/Indochina type, which is also the predominant Th2R/Th3R haplotype in Asia (~59%, n = 974). Second, the Th2R/Th3R sequences in Asia, South America and Africa are geographically distinct with little allele sharing between continents. In conclusion, this study provides an insight on the existing polymorphisms in the CSP in a parasite population from India that could potentially influence the efficacy of RTS,S vaccine in this region.
Molecular and functional analysis of the LYS1 gene of Candida albicans (1994)

The LYS1 gene of Candida albicans has been localized to a 1.8-kb DNA fragment present on the plasmid YpBRG2. YpBRG2 has been shown to complement the saccharopine dehydrogenase mutant Stx4-4A of Saccharomyces cerevisiae. Transformants of S. cerevisiae Stx4-4A exhibited significant saccharopine dehydrogenase activity, and cells that had lost YpBRG2 after nonselective growth had no enzyme activity. The DNA sequence of the LYS1 gene has been determined. The LYS1 DNA contains typical yeast upstream regulatory sequences, including the GCN4 motif and candidate sequences responsible for transcription termination within the 3' noncoding region. The fragment contained an open reading frame of 1,146 nucleotides coding for a putative protein of 382 amino acids. The open reading frame has 60% identity at the nucleotide level and 71% similarity at the amino acid level to the LYS5 gene of Yarrowia lipolytica, which is believed to code for saccharopine dehydrogenase. A peptide of 11 amino acids has been found, which is present in S. cerevisiae, Y. lipolytica, and C. albicans. This peptide can be expanded to 16 amino acids when the sequences from Y. lipolytica and C. albicans are compared. A motif responsible for the binding of the adenosine residue of NADH has been described previously and is very similar to this peptide, which may be the site of NADH binding in the saccharopine dehydrogenase of C. albicans.
Using Internet services to generate a research sampling frame (2001)

The purpose of this paper is to describe how the authors used Internet services to generate a sampling frame for their on-going pilot study, which evaluates the psychometric properties of Chen's Nursing Home Tool, a community needs assessment instrument for nursing homes. The proposed sampling frame may be used to survey nursing home residents and family members, nursing home providers and community leaders for any selected community in the USA. The availability of a user-friendly sampling frame can assist health-care professionals to determine required and desired services and further contribute to the development of a more comprehensive health-service system.
Treatment of alkali-injured rabbit corneas with a synthetic inhibitor of matrix metalloproteinases. (1992)

Healing of corneal alkali injuries remains a severe clinical challenge. The authors evaluated the effect of a new synthetic inhibitor of matrix metalloproteinases (GM6001 or N-[2(R)-2-(hydroxamido carbonylmethyl)-4-methylpentanoyl]-L-tryptophane methylamide) on preventing ulceration of rabbit corneas after alkali injury. Topical treatment of corneas with severe alkali injuries with 400 micrograms/ml or 40 micrograms/ml GM6001 alone prevented ulceration for 28 days, although 8 of 10 corneas treated with vehicle perforated. Corneas treated with 4 micrograms/ml GM6001 had midstromal depth ulcers. Corneas treated with 400 micrograms/ml of GM6001 contained very few inflammatory cells and had significantly reduced vessel ingrowth compared with vehicle-treated corneas. Epithelial regeneration after moderate alkali injuries also was investigated. Persistent epithelial defects developed 4 days after moderate alkali injury in rabbit corneas treated with vehicle and progressively increased to an average of 20% of the original 6 mm diameter wound by 27 days after moderate alkali injury. By contrast, epithelial regeneration was complete and persisted for 21 days for corneas treated with a formulation containing GM6001 (400 micrograms/ml), epidermal growth factor (10 micrograms/ml), fibronectin (500 micrograms/ml), and aprotinin (400 micrograms/ml). Sporadic punctate staining developed in 20% of the corneas treated with the combination of agents between days 21-28 after moderate alkali injury. These results demonstrate that topical application of GM6001 prevented corneal ulceration after severe alkali injury and that a combination containing GM6001, epidermal growth factor, fibronectin, and aprotinin promoted stable regeneration of corneal epithelium after moderate alkali injury.
12R-lipoxygenase deficiency disrupts epidermal barrier function (2007)

12R-lipoxygenase (12R-LOX) and the epidermal LOX-3 (eLOX-3) constitute a novel LOX pathway involved in terminal differentiation in skin. This view is supported by recent studies showing that inactivating mutations in 12R-LOX and eLOX-3 are linked to the development of autosomal recessive congenital ichthyosis. We show that 12R-LOX deficiency in mice results in a severe impairment of skin barrier function. Loss of barrier function occurs without alterations in proliferation and stratified organization of the keratinocytes, but is associated with ultrastructural anomalies in the upper granular layer, suggesting perturbance of the assembly/extrusion of lamellar bodies. Cornified envelopes from skin of 12R-LOX-deficient mice show increased fragility. Lipid analysis demonstrates a disordered composition of ceramides, in particular a decrease of ester-bound ceramide species. Moreover, processing of profilaggrin to monomeric filaggrin is impaired. This study indicates that the 12R-LOX-eLOX-3 pathway plays a key role in the process of epidermal barrier acquisition by affecting lipid metabolism, as well as protein processing.