gebhart/patrepeval huggingface dataset:
HLA DR4w4-binding motifs illustrate the biochemical basis of degeneracy and specificity in peptide-DR interactions. (1993)

In the present study, we describe the definition of a DRB1*0401 (DR4w4)-specific motif. The strategy used entailed a three-step process: 1) screening a large set of unrelated peptide ligands to identify good MHC binders; 2) truncation analysis of several DR4w4 binding peptides of high affinity to identify the crucial core-binding regions; 3) the use of single amino acid substitutions of the DR4w4-binding peptide hemagglutinin (HA) 307-319 to elucidate the specific residues crucial for binding. The DR4w4 motif is characterized by the presence of a hydrophobic or aromatic (F, W, Y, L, I, V, M) anchor residue in position 1, and a second hydroxyl (S, T) or aliphatic (L, I, V, or M) anchor residue in position 6. Furthermore, positive charges (R, K) are not allowed in positions 4, 7, and 9, and negative charges (D, E) are not allowed in position 9. This motif was present in 92% of good (IC50 < or = 100 nM) DR4w4-binding peptides, but less than 25% of the negative (IC50 > 45 microM) binders, indicating that the presence of the motif is necessary, but not sufficient for good DR4w4 binding capacity. The results of the present study are discussed in relation to previous work defining binding motifs and rules for other DR alleles, illustrating how different DR alleles bind variations on a similar structural theme. Finally, using two different peptide ligands [tetanus toxoid 830-843 and HA 307-319] as model systems, it is demonstrated how the fine allelic specificity of the DR binders can be predictably modulated by introducing subtle changes in the primary amino acid sequence.
In vitro and in vivo characteristics of frozen/thawed neonatal pig split-skin strips: A novel biologically active dressing for areas of severe, acute or chronic skin loss (2007)

The recurrent shortage of human skin autografts or allografts used to close extensive wounds has rekindled the search for feasible alternatives. In the past, adult pig skin was a popular biological dressing, yet doubts regarding its benefits have induced most people to abandon its use. Here we investigated the aptness of neonatal pig split-skin (NPSS) strips to be used as a novel kind of temporary dressing for areas of skin loss. NPSS strips are able to be prepared in bulk amounts, stored at -80 degrees C for up to six months, and recovered by swift thawing at 45 degrees C with no change in histological structure. When set into organ cultures in vitro for up to three weeks, these frozen/thawed NPSS strips exhibited both a skin-typical energy-linked metabolism (i.e., a predominant consumption of L-glutamine instead of glucose), and an enduring ability to secrete cytokines/chemokines such as IL-1alpha, IL-6, GM-CSF, and TNF-alpha; all features alike in quantitative terms to those exhibited by freshly prepared NPSS strips directly set into culture. Moreover, once applied as temporary dressings onto deep burn wounds in vivo, frozen/thawed NPSS strips produced, for at least seven days, porcine IL-1alpha, IL-6, GM-CSF, TNF-alpha, and TGF-beta; the cytokines/chemokines importantly involved in wound healing. Hence, frozen/thawed NPSS strips not only are capable of closing extensive areas of skin loss, but even release several cytokines/chemokines beneficial to tissue regeneration and repair.
WOUND HEALING AND COLLAGEN FORMATION (1962)

The sequence encountered in healing skin wounds in scorbutic guinea pigs has been examined by methods of light and electron microscopy. Linear incisions in the skin of female guinea pigs fed a scorbutigenic diet were allowed to heal. The wounds were removed for examination at 1, 3, 5, 9, and 14 days after wounding. The fibroblasts of the scorbutic wounds differ from those of the controls in three major aspects. First, little collagen is present within the intercellular spaces, although small groups of individual collagen fibrils can be found adjacent to some of the fibroblasts; in addition, large amounts of somewhat fibrillar, poorly structured, dense matter are present throughout the extracellular regions. The second alteration consists of large aggregates of intracytoplasmic lipid deposits present within the majority of the fibroblasts. Third, the endoplasmic reticulum of the fibroblasts is altered in form from that of the controls. The profiles of the cisternae are round, non-continuous within the plane of section, and are less extensively developed than in the controls. An increased macrophagic activity of the histiocytes is also described. These changes are discussed in light of the available biochemical data associated with this abnormality of protein synthesis.
Storage of whole blood overnight in different blood bags preceding preparation of blood components: in vitro effects on red blood cells. (2009)

Significant differences in in vitro parameters were observed between RBC prepared within 8 hours and 18-24 hours after blood collection. The results were consistent irrespective of the blood container used. New alkaline solutions may decrease the differences.
Mouse sciatic nerve regeneration through semipermeable tubes: A quantitative model (1983)

The regeneration of transected mouse sciatic nerves using semipermeable acrylic copolymer tubes to enclose both stumps has been qualitatively assessed from 1 to 30 weeks post-operative. Quantitative morphometric analysis of electron micrograph montages of complete transverse sections of the segment regenerated between stumps has permitted determinations of the percents of total area occupied by the various tissue constituents--blood vessels, epineurium, perineurium, endoneurium, myelinated axon/Schwann cell units, and unmyelinated axon/Schwann cell units. Significant differences were found in the total cross-sectional area of segments regenerated through tubes of 1.0 mm versus 0.5 mm internal diameters. Segments regenerated with the distal stump inserted in the tube contained significantly greater percentages of neural units and were significantly larger at 8 weeks post-operative compared to segments regenerated for 9-10 weeks with the distal stump avulsed. The morphometric method permits rapid quantitation of sizeable electron micrograph montages which at 1300 X permit all types of tissue components, including the unmyelinated axons, to be visualized.
Nuclear localization of ?-catenin is an important prognostic factor in hepatoblastoma (2001)

In this study, mutational and immunohistochemical analyses of beta-catenin were performed in 30 hepatoblastomas, to assess the prevalence of alterations of the Wnt pathway with respect to clinicopathological parameters and survival. Four missense mutations of beta-catenin (13.3%) were detected and there was strong immunoreactivity for beta-catenin in the cytoplasm and/or the nucleus in 97% of hepatoblastomas. Nuclear and cytoplasmic staining was demonstrated in 19 of 30 tumours (63%), while ten revealed only cytoplasmic staining. Statistically, this nuclear beta-catenin staining was significantly higher in the embryonal (Fisher exact test; p=0.00393) or undifferentiated type (p=0.00156) of hepatoblastoma than in the fetal type, but there was no difference between clinical stages I and II and clinical stages III and IV (p=0.175). Cumulative survival curves showed that nuclear beta-catenin staining (generalized Wilcoxon test; p=0.0088), undifferentiated histological type (p=0.0305), and clinical stages III and IV (p=0.0107) were significantly correlated with shorter survival time in these patients. Moreover, Cox multivariate analysis provides evidence that nuclear beta-catenin staining is the most important prognostic factor for survival (p=0.0090). It is therefore concluded that immunohistochemical analysis of beta-catenin might be a useful clinical tool for estimating the prognosis for patients with hepatoblastoma.
Cartilage matrix glycoprotein is present in serum in experimental canine osteoarthritis. (1989)

We have described previously a disulfide-bonded 550,000-D cartilage matrix glycoprotein (CMGP), which is found in normal hyaline cartilage, fibrocartilage, and the vitreous of the eye, and consists of subunits with apparent molecular weights of 130,000 in 4% gels (116,000 in 9% gels). In osteoarthritic cartilage from dogs subjected to transection of the anterior cruciate ligament (ACL), CMGP is cleaved to major immunoreactive fragments with apparent molecular weights of 65,000 and 75,000 after reduction with 2-mercaptoethanol. In the present study, using immunolocation analysis, a monoclonal antibody to CMGP did not react with serum from 8 of 12 dogs before ACL transection but did react with serum from seven of these animals 4 wk after surgery and with serum from 10 dogs at sacrifice, 8-14 wk after ACL transection. Serum from four dogs reacted with the monoclonal antibody before ACL transection. Serum from two dogs was negative at all time points. Immunolocation studies using a polyclonal antiserum to CMGP were performed in seven of these dogs and produced results identical with the monoclonal antibody in four dogs. In contrast, analysis of serial serum samples from three dogs with cartilage atrophy revealed no evidence of CMGP at any time point. These data suggest that CMGP may be a serum marker for osteoarthritis in this canine model.
Drugging RAS: Know the enemy (2017)

The three RAS oncogenes make up the most frequently mutated gene family in human cancer. The well-validated role of mutationally activated RAS genes in driving cancer development and growth has stimulated comprehensive efforts to develop therapeutic strategies to block mutant RAS function for cancer treatment. Disappointingly, despite more than three decades of research effort, clinically effective anti-RAS therapies have remained elusive, prompting a perception that RAS may be undruggable. However, with a greater appreciation of the complexities of RAS that thwarted past efforts, and armed with new technologies and directions, the field is experiencing renewed excitement that mutant RAS may finally be conquered. Here we summarize where these efforts stand.
WT1, the Wilms' tumor suppressor gene product, represses transcription through an interactive nuclear protein. (1995)

The Wilms' tumor suppressor gene, wt1, encodes a transcription factor of the zinc finger family. Mutations in WT1 have been detected in subsets of Wilms' tumor and in patients with the Denys-Drash Syndrome. In order to determine how WT1 regulates transcription and perhaps the consequences that mutations in WT1 may have, we established that residues 85-124 and 181-250 of WT1 constitute domains that function independently with a DNA binding domain to repress or activate transcription, respectively, and function equally effectively with heterologous promoters, suggesting the activator and repressor domains interact with nuclear components of general importance. To seek evidence for such components, increasing concentrations of WT1 repressor domain without a zinc finger DNA binding domain were co-transfected with fixed concentrations of wild-type (wt) WT1 and PDGF A-chain promoter/reporter gene constructs. As levels of the repressor domain were increased, a progressive loss of wt WT1 repressor activity and a progressive increase in its activation were observed, suggesting that the repressor domain of WT1 competes with wt WT1 for an interactive protein that is an essential component of the repressor activity of wt WT1. Because the most common mutation associated with Denys-Drash Syndrome disrupts the zinc finger domains of WT1, the results also suggest that the mutant WT1 may have aberrant DNA binding activity and perhaps function as a dominant negative effector of wt WT1.
Sperm competition and sperm cooperation: the potential role of diploid and haploid expression (2008)

Sperm competition is a powerful selective force driving the evolution of sperm shape and function. Recent findings suggest that sperm cooperation is a potential evolutionary response to sperm competition. Sperm cooperation may enhance the performance of the ejaculate increasing a male's chance to outcompete rival males in competition for fertilisation. Whether and how sperm cooperation may evolve is the focal point of this review. The relative importance of haploid and diploid gene expression for the evolution of sperm cooperation and the potential conflict of interest between (i) haploid sperm and diploid male and (ii) among sibling sperm, since sibling sperm only share an average of 50% of their genes in a diploid organism, are discussed. Furthermore, sperm cooperation is defined and the literature for empirical evidence of sperm cooperation is reviewed in light of the author's definitions.
Development of Lentiviral Vectors Expressing siRNA (2007)

The MLPA method was accurate, precise and at the same time effective in screening a large number of FH patients for large deletions in the LDL receptor gene.
Gibberellin mutants (1997)

Research on gibberellin (GA) mutants is reviewed, focusing on reports, published since 1993. The mutants have usually been identified via a shoot elongation screen. This screen exposes mutations influencing GA synthesis, deactivation and reception, and also those acting further down the elongation pathway. Mutations blocking synthesis lead to a dwarf. GA‐responsive phenotype. Numerous such mutations are now known. For some steps homologous mutations are known across 4 to 6 model species. Examples include the early step, geranylgeranyl diphosphate to copalyl diphosphate, and the activation step, GA 26 to GA 1 . Several GA‐synthesis mutations have now been characterised at the molecular level and all are in structural genes. It is now clear some steps are controlled by gene families with distinct tissue specificity. Further, some enzymes control more than one step in the biosynthetic pathway. The only mutation known to block deactivation. sin in pea, leads to an elongated phenotype. The GA response mutants are less well understood and are a more diverse group. They include elongated mutants with a constitutive GA response ( spy in arabidopsis. la cry‐s in pea and sln in barley) or an enhanced GA response ( phyB in arabidopsis. lv in pea and Ih in cucumber). Short response mutants include at least three types. One group accumulates GAs and are mostly unresponsive to applied GA ( gai in arabidopsis. D8 in maize. Rht3 in wheat). A recently identified group, exemplified by Igr in pea and gas in barley, have a short stature and reduced response but attain full responses with very high doses of exogenous GA. How close these mutations act to GA reception remains to be determined. Lastly, a number of mutants with short stature and reduced GA response differ in overall phenotype from GA‐deficient plants and cannot be made to mimic wild type even at high GA application rates. These mutations act beyond GA reception and some have already proved useful in elucidating other pathways that affect shoot elongation. For example, the lk and lkb mutations in pea appear to block brassinolide synthesis and this in turn prevents normal GA‐mediated elongation responses.
A systematic review of the skeletal effects of estrogen therapy in postmenopausal women. I. An assessment of the quality of randomized trials published between 1977 and 1995 (1998)

This body of literature fails to address whether estrogen therapy reduces fracture rates, and does not allow for comparison of the effects of different active therapies on change in bone density. Although there were improvements in the techniques for estimating bone mass and delivering estrogen treatment, the studies published in the 1990s were no more informative for making clinical or policy decisions than those published in the 1970s.
A multimedia medical communications system (1990)

The problem of communicating the radiologist's findings to the attending physician is introduced, and it is shown why it is essentially a multimedia communication problem. A multimedia communications system that was designed with a focus on database and medical reports organization and architecture is described. A report is presented of some of the key results of an in-house trial linking the Department of Radiological Sciences and the Emergency Department at the Ottawa Civic Hospital, Canada, a 950-bed tertiary-care teaching hospital.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
NFAT5/TonEBP mutant mice define osmotic stress as a critical feature of the lymphoid microenvironment (2004)

Osmotic stress responses are critical not only to the survival of unicellular organisms but also to the normal function of the mammalian kidney. However, the extent to which cells outside the kidney rely on osmotic stress responses in vivo remains unknown. Nuclear factor of activated T cells 5 (NFAT5)/tonicity enhancer binding protein (TonEBP), the only known osmosensitive mammalian transcription factor, is expressed most abundantly in the thymus and is induced upon lymphocyte activation. Here we report that NFAT5/TonEBP is not only essential for normal cell proliferation under hyperosmotic conditions but also necessary for optimal adaptive immunity. Targeted deletion of exons 6 and 7 of the Nfat5 gene, which encode a critical region of the DNA-binding domain, gave rise to a complete loss of function in the homozygous state and a partial loss of function in the heterozygous state. Complete loss of function resulted in late gestational lethality. Furthermore, hypertonicity-induced NFAT5/TonEBP transcriptional activity and hsp70.1 promoter function were completely eliminated, and cell proliferation under hyperosmotic culture conditions was markedly impaired. Partial loss of NFAT5/TonEBP function resulted in lymphoid hypocellularity and impaired antigen-specific antibody responses in viable heterozygous animals. In addition, lymphocyte proliferation ex vivo was reduced under hypertonic, but not isotonic, culture conditions. Direct measurement of tissue osmolality further revealed lymphoid tissues to be hyperosmolar. These results indicate that lymphocyte-mediated immunity is contingent on adaptation to physiologic osmotic stress, thus providing insight into the lymphoid microenvironment and the importance of the NFAT5/TonEBP osmotic stress response pathway in vivo.
Virtual Machine Introspection: Observation or Interference? (2008)

As virtualization becomes increasingly mainstream, virtual machine introspection techniques and tools are evolving to monitor VM behavior. A survey of existing approaches highlights key requirements, which are addressed by a new tool suite for the Xen VM monitoring system.
A novel probe for the cannabinoid receptor (1992)

The 1,1-dimethylheptyl (DMH) homologue of 7-hydroxy-delta 6-tetrahydrocannabinol (3) is the most potent cannabimimetic substance reported so far. Hydrogenation of 3 leads to a mixture of the epimers of 5'-(1,1-dimethylheptyl)-7-hydroxyhexahydrocannabinol or to either the equatorial (7) or to the axial epimer (8), depending on the catalysts and conditions used. Compound 7 discriminates for delta 1-THC (2) in pigeons (ED50 = 0.002 mg/kg, after 4.5 h), at the potency level of 3, and binds to the cannabinoid receptor with a KD of 45 pM, considerably lower than the Ki of 180 pM measured for compound 3 and the Ki of 2.0 nM measured for CP-55940 (1), a widely employed ligand. Tritiated 7 was used as a novel probe for the cannabinoid receptor.
Instability growth seeded by oxygen in CH shells on the National Ignition Facility (2015)

Fusion targets imploded on the National Ignition Facility are subject to hydrodynamic instabilities. These have generally been assumed to be seeded primarily by surface roughness, as existing work had suggested that internal inhomogeneity was small enough not to contribute significantly. New simulations presented here examine this in more detail, and consider modulations in internal oxygen content in CH plastic ablators. The oxygen is configured in a way motivated by measurement of oxygen in the shells. We find that plausible oxygen nonuniformity, motivated by target characterization experiments, seeds instability growth that is 3–5× bigger than expected from surface roughness. Pertinent existing capsule characterization is discussed, which suggests the presence of internal modulations that could be oxygen at levels large enough to be the dominant seed for hydrodynamic instability growth. Oxygen-seeded growth is smaller for implosions driven by high-foot pulse shapes, consistent with the performance improvement seen with these pulse shapes. Growth is somewhat smaller for planned future pulse shapes that were optimized to minimize growth of surface ripples. A possible modified specification for oxygen modulations is discussed, which is about 1/5 of the current requirement.
Catalytic mechanism of a family 3 β-glucosidase and mutagenesis study on residue Asp-247 (2001)

A family 3 beta-glucosidase (EC 3.2.1.21) from Flavobacterium meningosepticum has been cloned and overexpressed. The mechanistic action of the enzyme was probed by NMR spectroscopy and kinetic investigations, including substrate reactivity, secondary kinetic isotope effects and inhibition studies. The stereochemistry of enzymic hydrolysis was identified as occurring with the retention of an anomeric configuration, indicating a double-displacement reaction. Based on the k(cat) values with a series of aryl glucosides, a Bronsted plot with a concave-downward shape was constructed. This biphasic behaviour is consistent with a two-step mechanism involving the formation and breakdown of a glucosyl-enzyme intermediate. The large Bronsted constant (beta=-0.85) for the leaving-group-dependent portion (pK(a) of leaving phenols >7) indicates substantial bond cleavage at the transition state. Secondary deuterium kinetic isotope effects with 2,4-dinitrophenyl beta-D-glucopyanoside, o-nitrophenyl beta-D-glucopyanoside and p-cyanophenyl beta-D-glucopyanoside as substrates were 1.17+/-0.02, 1.19+/-0.02 and 1.04+/-0.02 respectively. These results support an S(N)1-like mechanism for the deglucosylation step and an S(N)2-like mechanism for the glucosylation step. Site-directed mutagenesis was also performed to study essential amino acid residues. The activities (k(cat)/K(m)) of the D247G and D247N mutants were 30000- and 200000-fold lower respectively than that of the wild-type enzyme, whereas the D247E mutant retained 20% of wild-type activity. These results indicate that Asp-247 is an essential amino acid. It is likely that this residue functions as a nucleophile in the reaction. This conclusion is supported by the kinetics of the irreversible inactivation of the wild-type enzyme by conduritol-B-epoxide, compared with the much slower inhibition of the D247E mutant and the lack of irreversible inhibition of the D247G mutant.
Refracturing: Observations and Theories (1993)

ABSTRACT Treating pressures from refracturing treatments and simulations of horizontal stress changes due to production suggest that the initiation of the refracture plane will be normal to that of the initial treatment. This possibility makes more wells candidates for refracturing.