gebhart/patrepeval huggingface dataset:
O-Glycan Sialylation and the Structure of the Stalk-like Region of the T Cell Co-receptor CD8 (2003)

Studies of mucins suggest that the structural effects of O-glycans are restricted to steric interactions between peptide-linked GalNAc residues and adjacent polypeptide residues. It has been proposed, however, that differential O-glycan sialylation alters the structure of the stalk-like region of the T cell co-receptor, CD8, and that this, in turn, modulates ligand binding (Daniels, M. A., Devine, L., Miller, J. D., Moser, J. M., Lukacher, A. E., Altman, J. D., Kavathas, P., Hogquist, K. A., and Jameson, S. C. (2001) Immunity 15, 1051-1061; Moody, A. M., Chui, D., Reche, P. A., Priatel, J. J., Marth, J. D., and Reinherz, E. L. (2001) Cell 107, 501-512). We characterize the glycosylation of soluble, chimeric forms of the alphaalpha- and alphabeta-isoforms of murine CD8 containing the O-glycosylated stalk of rat CD8alphaalpha, and we show that the stalk O-glycans are differentially sialylated in CHO K1 versus Lec3.2.8.1 cells (82 versus approximately 6%, respectively). Sedimentation analysis indicates that the Perrin functions, Pexp, which reflect overall molecular shape, are very similar (1.61 versus 1.54), whereas the sedimentation coefficients (s) of the CHO K1- and Lec3.2.8.1-derived proteins differ considerably (3.73 versus 3.13 S). The hydrodynamic properties of molecular models also strongly imply that the sialylated and non-sialylated forms of the chimera have parallel, equally highly extended stalks ( approximately 2.6 A/residue). Our analysis indicates that, as in the case of mucins, the overall structure of O-glycosylated stalk-like peptides is sialylation-independent and that the functional effects of differential CD8 O-glycan sialylation need careful interpretation.
Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates (1997)

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five polymorphisms differed by the presence of two to six copies of the 12-bp tandem repeat 5'-CAATATCAACAA-3'. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations.
A submicrometer NMOS multiplexer-demultiplexer chip set for 622.08-Mb/s SONET applications (1992)

The development of a low-power 12-channel multiplexer-demultiplexer pair that is clocked at the standard synchronous optical network (SONET) rate of 622.08 MHz is discussed. Each device has been integrated in silicon using a 0.75- mu m NMOS VLSI technology that provides high fabrication yield at relatively low cost. Highlighted are the analog interface circuits of the two chips. These include a phase splitter and amplifier for the maser clock input, a precision 50- Omega output driver for high-speed synchronous-transport-signal-12 (STS-12) data, as well as input amplifier and an output stage for low-speed differential STS-1 data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Systemic anti-hepatocyte growth factor monoclonal antibody therapy induces the regression of intracranial glioma xenografts. (2006)

These findings show that blocking the HGF-Met interaction with systemically given anti-HGF mAb can have profound antitumor effects even within the central nervous system, a site previously believed to be resistant to systemic antibody-based therapeutics.
Amino acid sequence of PR‐39 (1991)

We recently isolated from pig intestine and characterized a 31-residue antibacterial peptide named cecropin-P1 with activity against Escherichia coli and several other Gram-negative bacteria. The isolation involved a number of batch-wise steps followed by several chromatography steps. The continued investigation of these antibacterial peptides has now yielded another antibacterial peptide with high activity against both E. coli and Bacillus megaterium. Amino acid analysis showed a very high content of proline (49 mol%) and arginine (26 mol%), an intermediate level of phenylalanine and low levels of leucine, tyrosine, isoleucine, and glycine. The primary structure was determined by a combination of Edman degradation, plasma desorption mass spectrometry and C-terminal sequence analysis by carboxypeptidase Y degradation using capillary zone electrophoresis for detection of liberated residues. The calculated molecular mass was 4719.7 Da, which is in excellent agreement with 4719 Da obtained by plasma desorption mass spectrometry. The peptide was named PR-39 (proline-arginine-rich with a size of 39 residues). The lethal concentration of the peptide was determined against six Gram-negative and four Gram-positive strains of bacteria.
Intent detection and semantic parsing for navigation dialogue language processing (2017)

Voice-based human-machine interface has become a prevalent feature for modern intelligent vehicles, especially in navigation and infotainment applications. Automatic Speech Recognition (ASR) converts spoken audio streams to plain texts, but a follow-up Natural Language Processing (NLP) sub-system is needed to understand the contextual meaning from the text and act. For the specific human-vehicle navigation dialogue application, the two major tasks include (1) intent detection - decide whether a sentence is navigation-related, and (2) semantic parsing - retrieve important information (e.g., point-of-interest destinations) from the words. To address these two tasks, this study proposes a Recurrent Neural Network (RNN) architecture, with the consideration of (1) one joint model vs. two separate models, (2) a context window approach vs. sequence-to-sequence translation approach, as well as (3) alternate model hyper-parameter selections. The experiment is conducted with both the benchmark ATIS dataset and the CU-Move in-vehicle dialogue corpus, and the result is compared against related state-of-the-art methods. Overall, the proposed solution on the CU-Move data achieves accuracies of 98.24% for intent detection and 99.60% for semantic parsing, outperforming other related methods.
Visualization of Myelin Basic Protein (Mbp) T Cell Epitopes in Multiple Sclerosis Lesions Using a Monoclonal Antibody Specific for the Human Histocompatibility Leukocyte Antigen (Hla)-Dr2–Mbp 85–99 Complex (2000)

Susceptibility to multiple sclerosis (MS) is associated with the human histocompatibility leukocyte antigen (HLA)-DR2 haplotype, suggesting that major histocompatibility complex class II-restricted presentation of central nervous system-derived antigens is important in the disease process. Antibodies specific for defined HLA-DR2-peptide complexes may therefore be valuable tools for studying antigen presentation in MS. We have used phage display technology to select HLA-DR2-peptide-specific antibodies from HLA-DR2-transgenic mice immunized with HLA-DR2 molecules complexed with an immunodominant myelin basic protein (MBP) peptide (residues 85-99). Detailed characterization of one clone (MK16) demonstrated that both DR2 and the MBP peptide were required for recognition. Furthermore, MK16 labeled intra- and extracellular HLA-DR2-MBP peptide complexes when antigen-presenting cells (APCs) were pulsed with recombinant MBP. In addition, MK16 inhibited interleukin 2 secretion by two transfectants that expressed human MBP-specific T cell receptors. Analysis of the structural requirement for MK16 binding demonstrated that the two major HLA-DR2 anchor residues of MBP 85-99 and the COOH-terminal part of the peptide, in particular residues Val-96, Pro-98, and Arg-99, were important for binding. Based on these results, the antibody was used to determine if the HLA-DR2-MBP peptide complex is presented in MS lesions. The antibody stained APCs in MS lesions, in particular microglia/macrophages but also in some cases hypertrophic astrocytes. Staining of APCs was only observed in MS cases with the HLA-DR2 haplotype but not in cases that carried other haplotypes. These results demonstrate that HLA-DR2 molecules in MS lesions present a myelin-derived self-peptide and suggest that microglia/macrophages rather than astrocytes are the predominant APCs in these lesions.
Targeting the Heat Shock Protein 90 Dimer with Dimeric Inhibitors (2011)

The design, synthesis, and biological evaluation of conformationally constrained coumermycin A1 analogues are reported. Compounds were evaluated against both breast cancer (SKBr3 and MCF7) and prostate cancer (PC3 mm2, A549, and HT29) cell lines. Non-noviosylated coumermycin A1 analogues that manifest potent antiproliferative activity resulting from Hsp90 inhibition are provided, wherein replacement of the stereochemically complex noviose sugar with readily available piperidine rings resulted in ∼100 fold increase in antiproliferative activities as compared to coumermycin A1, producing small molecule Hsp90 inhibitors that exhibit nanomolar activities.
Inhibition of human endothelial cell proliferation by heparin and steroids (1988)

Previous works have reported the controversial effects of heparin and steroids on angiogenesis. In this study, we investigated the effect of these compounds on human endothelial cell (EC) growth in vitro. An antiproliferative heparin activity was found in low human serum concentrations (2%). When EC were exposed to heparin (10(-6) M), their proliferation index was reduced in the presence of endothelial cell growth factor added 6 hours or more later. These results suggest that there is an intracellular effect of heparin which reduces 3H-methylthymidine uptake. Hydrocortisone acetate and tetrahydroS induced inhibition of EC growth in a dose-dependent manner. Steroids inhibited proliferation of EC in culture medium in the presence or the absence of growth factor and in different human serum concentrations. These results suggest a possible synergistic antiangiogenic action of heparin plus steroids.
O-Acetylation status of the capsular polysaccharides of serogroup Y and W135 meningococci isolated in the UK (2002)

At a time when tetravalent conjugate vaccines for meningococcal serogroups A/C/Y/W135 are being formulated the O-acetylation status of their respective capsular polysaccharides has not previously been studied in the UK for all components. Although this has been elucidated for serogroup C, little is known about the O-acetylation status of serogroups W135 and Y. Meningococcal serogroup W135 (n=181) and Y (n=90) isolates submitted to the PHLS Meningococcal Reference Unit in 1996, 2000 and 2001 were investigated for O-acetylation capsular status by dot blot assay. Eight per cent of W135 and 79% of Y isolates respectively were found to be O-acetylated with a similar distribution found in both carrier and case isolates. An increase in O-acetylated W135 isolates was noted between 2000 (0%) and 2001 (21%) which was not due to the introduction of the Hajj associated W135 (ET 37 complex; serosubtype P1.5,2) isolates, all of which were de-O-acetylated. Although the biological relevance of O-acetylation status is unknown for these serogroups, an understanding of O-acetylation status of the respective polysaccharides may provide useful insights into the optimal vaccine formulation.
An ant colony optimisation-based approach for clustering in a data matrix (2014)

Clustering is a process of classifying similar objects into different groups, such that the data within the same groups share the common features. As a common technique in statistical data analysis, it has been addressed in different contexts and by researchers in different disciplines. In this paper, we study the problem of clustering data into a diagonal block structure in a data matrix. This kind of clustering is very useful for analysing the interaction between the objects and their associated attributes in a dataset. In this work, we explore the use of ant colony optimisation-based approach to perform data clustering. Our approach offers several advantages. First, the objects and their attributes are re-arranged in the matrix such that a diagonal block structure is formed. This is useful for visual analysis. Second, our approach can deal with the case when the objects and attributes have weighting associated with them. Third, our approach is a non-parametric clustering method, (i.e., no explicit clustering criterion is required). Our computational study demonstrates the performance of our approach in data clustering.
Effects of Na2HPO4 and NaH2PO4 on hydroxyapatite formation (1993)

Particulate solids CaHPO4 (DCP) and Ca4(PO4)2O (TetCP) can react to form hydroxyapatite (HAp) under conditions which may be compatible with those in vivo. Effects of sodium phosphate solutions on the formation of calcium deficient HAp at 25 degrees C by this reaction in dilute suspensions (liquid-to-solids ratio of 100) and at 1/s = 1 were studied. An 1/s ratio of one is not greatly different from that at which monolithic HAp forms. Solution chemistry results showed that the sodium phosphate used and its concentration strongly influenced the kinetics of HAp formation and the HAp composition. HAp formation occurred by the same mechanism in water and in the Na2HPO4 solutions investigated; however, HAp formation occurred more rapidly in Na2HPO4 solutions. DCP dissolution was congruent in these solutions and this delayed the overgrowth of DCP by HAp. Reaction in NaH2PO4 solutions resulted in the formation of CaHPO4.2H2O as an intermediate product. The final product formed in the NaH2PO4 solutions was affected by the l/s ratio used. CaHPO4.2H2O, not HAp, was the product formed from dilute suspension but it was not observed during reaction at l/s = 1. Variations in solution were correlated with the formation of HAp and intermediate products, with the consumption of reactants, and with the heat evolution characteristics. The latter were determined by isothermal calorimetry. Calorimetric analysis of the reactions indicated increased heat evolution in sodium phosphate solutions and acceleration in HAp formation. This appears to be related to accelerated dissolution of CaHPO4, which was rate limiting.
Advances in the management of leg ulcers – the potential role of growth factors (2006)

Venous ulcers are a major health problem because of the increased costs of the treatment and the refractory nature of the ulcers. The treatment cost is estimated to be around 1 billion dollars per year in the United States (US), and the average cost for one patient over a lifetime exceeds dollars 400,000. There has been an increasing trend in the use of growth factors in their management. Genetic engineering has revolutionised the research of wound healing, as the majority of recombinant growth factors are now available for in vitro and in vivo studies. Online searches of Medline, Pub Medical and Embase were carried out using the terms venous ulcers, leg ulcers, growth factors and growth hormone. The literature regarding the potential role of growth factors in the management of leg ulcers is reviewed. The important clinical studies are critically analysed with a view to appreciate the emerging therapies and the further research possibilities in the management of venous leg ulcers. Clinical results with the use of growth factors in non-healing wounds are encouraging. However, small sample sizes and inconsistent end points in different clinical studies have been the main hurdle in reaching a definite conclusion. Further research is needed to provide the definite evidence. Future developments may include different delivery methods for the growth factors, use of different combinations of growth factors administered simultaneously or, sequentially, bioengineered skin grafts and chemical induction of angiogenesis with the use of gene transfer techniques.
Transforming Growth Factor-β Can Suppress Tumorigenesis through Effects on the Putative Cancer Stem or Early Progenitor Cell and Committed Progeny in a Breast Cancer Xenograft Model (2007)

The transforming growth factor-beta (TGF-beta) pathway has tumor-suppressor activity in many epithelial tissues. Because TGF-beta is a potent inhibitor of epithelial cell proliferation, it has been widely assumed that this property underlies the tumor-suppressor effect. Here, we have used a xenograft model of breast cancer to show that endogenous TGF-beta has the potential to suppress tumorigenesis through a novel mechanism, involving effects at two distinct levels in the hierarchy of cellular progeny that make up the epithelial component of the tumor. First, TGF-beta reduces the size of the putative cancer stem or early progenitor cell population, and second it promotes differentiation of a more committed, but highly proliferative, progenitor cell population to an intrinsically less proliferative state. We further show that reduced expression of the type II TGF-beta receptor correlates with loss of luminal differentiation in a clinical breast cancer cohort, suggesting that this mechanism may be clinically relevant. At a molecular level, the induction of differentiation by TGF-beta involves down-regulation of Id1, and forced overexpression of Id1 can promote tumorigenesis despite persistence of the antiproliferative effect of TGF-beta. These data suggest new roles for the TGF-beta pathway in regulating tumor cell dynamics that are independent of direct effects on proliferation.
Protective Role of R-spondin1, an Intestinal Stem Cell Growth Factor, against Radiation-Induced Gastrointestinal Syndrome in Mice (2009)

Rspo1 promoted radioprotection against RIGS and improved survival of mice exposed to WBI. The mechanism was likely related to induction of the Wnt-beta-catenin pathway and promotion of intestinal stem cell regeneration. Rspo1 has protective effect only on normal intestinal tissue but not in tumors after AIR and thereby may increase the therapeutic ratio of chemoradiation therapy in patients undergoing abdominal irradiation for GI malignancies.
Treatment of Inflammatory Diseases with Mesenchymal Stem Cells (2009)

Human mesenchymal stem cells (hMSCs) are rare progenitor cells present in adult bone marrow that have the capacity to differentiate into a variety of tissue types, including bone, cartilage, tendon, fat, and muscle. In addition to multilineage differentiation capacity, MSCs regulate immune and inflammatory responses, providing therapeutic potential for treating diseases characterized by the presence of an inflammatory component. The availability of bone marrow and the ability to isolate and expand hMSCs ex vivo make these cells an attractive candidate for drug development. The low immunogenicity of these cells suggests that hMSCs can be transplanted universally without matching between donors and recipients. MSCs universality, along with the ability to manufacture and store these cells long-term, present a unique opportunity to produce an "off-the-shelf" cellular drug ready for treatment of diseases in acute settings. Accumulated animal and human data support MSC therapeutic potential for inflammatory diseases. Several phase III clinical trials for treatment of acute Graft Versus Host Disease (GVHD) and Crohn's disease are currently in progress. The current understanding of cellular and molecular targets underlying the mechanisms of MSCs action in inflammatory settings as well as clinical experience with hMSCs is summarized in this review.
Ajuga Turkestanica as a Countermeasure Against Sarcopenia and Dynapenia (2014)

The effects of phytoecdysteroid supplementation on 20-month old male mouse skeletal muscle was tested. Three treatment groups were employed for the 28-day supplementation protocol: control (CT; vehicle only of 100% non-denatured ethanol), Ajuga turkestanica extract (ATE), and 20-hydroxecdysone (20E). Following 28 days of consecutive supplementation with ATE, 20E, or vehicle only (CT) each animal was tested for in vivo contractile function of the gastrocnemius-plantaris-soleus complex. Skeletal muscles and organs were then dissected and utilized for Western blot analysis, muscle and organ wet weights, or histological and cross-sectional area (CSA) analysis. Results demonstrated no significant differences (NSD) in body, muscle, or organ masses between treatments. NSD were found in protein synthesis signaling and non-contracted mitochondrial biogenesis signaling. Significantly larger fiber CSA was found in 20E-treated mice, compared to CT. Additionally, 20E-treated mice had significantly greater activation contraction-induced AMPK pathway signaling, compared to CT and ATE. In conclusion, these data suggest that 20E rescues the loss of muscle fiber size and increases the activation of contraction-induced AMPK pathway signaling in sedentary aged skeletal muscle.
Adverse Effects of Antidepressants for Chronic Pain: A Systematic Review and Meta-analysis (2017)

Our synthesized data analysis confirmed overall tolerability of low-dose antidepressants for the treatment of chronic pain and revealed drug specific risk profiles. This encompassing characterization of adverse effect profiles might be useful in defining multimodal treatment regimens for chronic pain which also consider patients' comorbidities and co-medication.
Automated structure solution, density modification and model building (2002)

The approaches that form the basis of automated structure solution in SOLVE and RESOLVE are described. The use of a scoring scheme to convert decision making in macromolecular structure solution to an optimization problem has proven very useful and in many cases a single clear heavy-atom solution can be obtained and used for phasing. Statistical density modification is well suited to an automated approach to structure solution because the method is relatively insensitive to choices of numbers of cycles and solvent content. The detection of non-crystallographic symmetry (NCS) in heavy-atom sites and checking of potential NCS operations against the electron-density map has proven to be a reliable method for identification of NCS in most cases. Automated model building beginning with an FFT-based search for helices and sheets has been successful in automated model building for maps with resolutions as low as 3 A. The entire process can be carried out in a fully automatic fashion in many cases.
A comparison of DFT, PLP and cochleagram for alphabet recognition (2002)

The authors used speaker-independent classification of isolated English letters to evaluate the relative performance of the discrete Fourier transform, perceptual linear predictive (PLP) analysis, and the cochleagram auditory model. Feedforward neural network classifiers were trained using all three representations on 60 speakers and tested on 60 new speakers. Training and testing data were independently modified by adding two levels of Gaussian noise and babble (20 random letter utterances, attenuated and given random offsets). PLP gave the best results, especially when trained or tested on Gaussian noise.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>