gebhart/patrepeval huggingface dataset:
Unfolding free energy changes determined by the linear extrapolation method. 1. Unfolding of phenylmethanesulfonyl .alpha.-chymotrypsin using different denaturants (1988)

Characteristics and properties of the unfolding free energy change, delta G degrees N-U, as determined by the linear extrapolation method are assessed for the unfolding of phenylmethanesulfonyl chymotrypsin (PMS-Ct). Difference spectral measurements at 293 nm were used to define PMS-Ct unfolding brought about with guanidinium chloride, urea, and 1,3-dimethylurea. All three denaturants were shown to give identical extinction coefficient differences (delta epsilon N-U) between native and unfolded forms of the protein in the limit of zero concentration of denaturant. The independence of delta epsilon N-U on denaturant supports the linear extension of pre- and postdenaturational base lines into the transition zone, allowing evaluation of unfolding equilibrium constants based on the two-state assumption. An expression, based on the linear extrapolation method, was used to provide estimates of delta G degrees N-U for the three denaturants using nonlinear least-squares fitting of the primary data, delta epsilon versus [denaturant]. The three delta G degrees N-U values were identical, within error, suggesting that the free energy change is a property of the protein system and independent of denaturant. It is suggested that the error in delta G degrees N-U determined from use of the linear extrapolation method is significantly larger than commonly reported in the literature.
Development of standard tests to examine viscoelastic properties of blood of experimental animals for pediatric mechanical support device evaluation. (2006)

We investigated the applicability of measuring the viscoelasticity of bovine, ovine, and porcine whole blood for the evaluation of sublethal damage to red blood cells (RBCs). An increase in blood viscosity and elasticity without changes in hematocrit and plasma viscosity would signify a decrease in RBC deformability. Blood viscoelasticity was assessed using a Vilastic Scientific viscoelastometer. Due to the natural absence of RBC aggregation and small RBC size in normal bovine and ovine blood, viscoelastic properties are less readily detected. However, we found that adjustment of blood hematocrit to a standard level of 40-50% allows for sensitive assessment of viscoelasticity in these blood types demonstrating a marked non-Newtonian behavior mostly related to RBC deformability. Porcine blood showed a pronounced non-Newtonian behavior at all tested hematocrit values, which makes it rheologically comparable to human blood. Both viscosity and elasticity were elevated after blood exposure to a uniform mechanical stress. RBCs rigidified by heat exposure demonstrated a loss of viscoelasticity dependence on shear rate. Measurements of blood viscoelasticity can be meaningful in bovine, ovine, and, especially, porcine blood, and can be used for evaluation of sublethal blood damage during in vitro and animal trials of heart-assist devices.
Cortico-cortical Communication and Superior Performance in Skilled Marksmen: An EEG Coherence Analysis (2003)

Electroencephalographic (EEG) coherence was assessed during a 4-s aiming period prior to trigger pull in expert marksmen ( n = 10) and skilled shooters ( n = 9) over the course of a regulation round of small-bore rifle shooting. Although both groups were highly experienced, the skilled group had lower ability. Given that specialization of cortical function occurs as domain-specific expertise increases, experts were predicted to exhibit less cortico-cortical communication, especially between cognitive and motor areas, compared to the skilled group. Coherence was assessed for three frequency bands (low alpha, 8–10 Hz; high alpha, 10–13 Hz; and low beta, 13–22 Hz) using sites F3, Fz, F4, C3, Cz, C4, T3, T4, P3, Pz, P4, O1, and O2. Compared to the skilled group, experts exhibited lower coherence between left temporal (T3) and mid-line frontal (Fz) regions for low-alpha and low-beta frequencies, lower coherence for high-alpha between all left hemisphere sites and (Fz), and lower coherence between T3 and all midline sites for the low-beta band. The results reveal that, compared to lesser skilled shooters, experts engage in less cortico-cortical communication, particularly between left temporal association and motor control regions, which implies decreased involvement of cognition with motor processes.
Patterns for normal colon mucosa and colon adenocarcinoma compared by two-dimensional gel electrophoresis. (1982)

A two-dimensional gel "map" of the proteins in normal cells and transformed cells may well help establish the presence of putative tumor-specific protein antigens, which can be isolated and used as antigens. We so examined normal colon mucosa and colon adenocarcinoma, using a sensitive silver stain. Samples were promptly prepared after excision by rapidly trimming the tissue to a small, grossly homogeneous piece, which was frozen on solid CO2. Frozen histological sections and permanent mounts were also prepared for several areas, to document the cellular constitution and to grade the carcinoma. Sample preparation for electrophoresis is described. The DNA was pelleted by centrifugation (108 000 x g x 1.5 h). Little or no pellet was observed, indicating complete solubilization. Many of the tumors contained proteases, liberated during sample preparation, so protease inhibitors were included. A highly reproducible pattern was observed for normal mucosa. Comparison of the gels from paired samples with histological data allows many of the spots to be tentatively assigned to the different cell types present in the mucosa (epithelium, connective tissue, or muscularis mucosa) and, in most tumors analyzed, detection of a series of spots that are not detectable in the pattern for normal tissue. These apparently tumor-associated proteins may be of epithelial cell or stromal origin.
CD1c restricts responses of mycobacteria-specific T cells. Evidence for antigen presentation by a second member of the human CD1 family (1996)

Previous studies suggest that CD1 is a family of Ag-presenting molecules distantly related to those encoded by the MHC. However, of the four known human CD1 proteins, only CD1b has been shown to restrict Ag-specific T cell responses. In this study, we have shown that a second member of the human CD1 family, CD1c, could also mediate Ag presentation to T cells. Three T cell lines recognizing mycobacterial Ags in a CD1c-restricted manner were isolated from normal donor blood. These T cells were MHC unrestricted, and their recognition of Ag was independent of the products of the transporter associated with Ag presentation-1/2 and DMA/B genes that are generally required for Ag presentation by MHC-encoded Ag-presenting molecules. Furthermore, unlike MHC-restricted responses to peptides, the CD1c-restricted T cell lines recognized protease-resistant mycobacterial lipid Ags. These T cell lines also showed significant cytotoxicity toward CD1c-expressing target cells even in the absence of mycobacterial Ags, which was shown by clonal analysis to be mediated by a subpopulation of T cells directly reactive to CD1c molecules. Our findings establish the ability of a second member of the CD1 family to restrict responses of Ag-specific T cells, and thus support the general hypothesis that the CD1 family comprises a third lineage of Ag-presenting molecules that presents a novel class of foreign and self Ags to MHC-unrestricted T cells.
Confirmation of the Department of Transportation Criteria for a Substituted Urine Specimen (2002)

The purpose of this study was to determine whether people could naturally produce urine sufficiently dilute to meet the federal criteria for a "substituted" specimen. The United States Department of Transportation Regulations (49 Code of Federal Regulations Part 40) defines a urine specimen as substituted if it has a creatinine concentration of < or = 5 mg/dL and a specific gravity of < or = 1.001 or > or = 1.020. These criteria have been criticized based on the contention that an insufficient number of specimens had been tested from the same urine sample for both creatinine and specific gravity measurements. We reviewed the results of 803,130 random urine specimens measured for creatinine and/or specific gravity in a hospital-based laboratory. In this database, 13,467 urine specimens had both creatinine and specific gravity measurements. None of these 13,467 paired urine specimens met the lower limit of specific gravity (< or = 1.001) and creatinine (< or = 5 mg/dL) criteria for a Department of Transportation substituted specimen. We also examined the medical records of those patients meeting even one of the two criteria; creatinine concentration < or = 5 mg/dL or specific gravity < or = 1.001. These patients were neonatal, moribund, or so severely ill that essentially none could have been among the working population. These data in patients with various pathologic states support our belief that normal individuals do not produce urine dilute enough to meet the lower limit of the specific gravity (< or = 1.001) and creatinine (< or = 5 mg/dL) required for meeting substituted specimen criteria. Eleven patients met the criteria for a substituted specimen, with elevated specific gravity of > or = 1.020 and creatinine concentration of < or = 5 mg/dL; however, these patients were seriously ill or terminally ill.
The Tetrodotoxin‐Resistant Na+ Channel Nav1.8 is Essential for the Expression of Spontaneous Activity in Damaged Sensory Axons of Mice (2003)

The tetrodotoxin-resistant sodium channel alpha subunit, Nav1.8, is exclusively expressed in primary sensory neurons and is suggested to play a role in the generation of ectopic action potentials after axonal injury and thereby contribute to neuropathic pain. Here we investigated the involvement of Nav1.8 in ectopic impulse generation in damaged axons by examining spontaneous activity and mechanosensitivity in neuromas formed by section of the saphenous nerve in Nav1.8 null mice and in their wild-type littermates. We recorded 522 identified units from 24 neuromas in vitro at two time points, 8-11 days (median 10 days) and 19-29 days (median 22 days) post-operatively. At approximately 10 days, neither genotype showed spontaneous activity, but a significantly higher proportion of fibres were mechanosensitive in wild-type (54%) compared to Nav1.8 null neuromas (18%). At approximately 22 days, 19% of fibres recorded in wild-type neuromas showed spontaneous activity, whereas only one fibre of the 238 (0. %) recorded in neuromas taken from null mice showed ongoing activity. In recordings at approximately 22 days, a similar proportion of fibres were mechanosensitive in wild-type and Nav1.8 null neuromas (51 and 46%, respectively). We conclude that Nav1.8 is essential for the expression of spontaneous activity in damaged sensory axons, and may also contribute to the development of ectopic mechanosensitivity.
The genomics of preterm birth: from animal models to human studies (2013)

Preterm birth (delivery at less than 37 weeks of gestation) is the leading cause of infant mortality worldwide. So far, the application of animal models to understand human birth timing has not substantially revealed mechanisms that could be used to prevent prematurity. However, with amassing data implicating an important role for genetics in the timing of the onset of human labor, the use of modern genomic approaches, such as genome-wide association studies, rare variant analyses using whole-exome or genome sequencing, and family-based designs, holds enormous potential. Although some progress has been made in the search for causative genes and variants associated with preterm birth, the major genetic determinants remain to be identified. Here, we review insights from and limitations of animal models for understanding the physiology of parturition, recent human genetic and genomic studies to identify genes involved in preterm birth, and emerging areas that are likely to be informative in future investigations. Further advances in understanding fundamental mechanisms, and the development of preventative measures, will depend upon the acquisition of greater numbers of carefully phenotyped pregnancies, large-scale informatics approaches combining genomic information with information on environmental exposures, and new conceptual models for studying the interaction between the maternal and fetal genomes to personalize therapies for mothers and infants. Information emerging from these advances will help us to identify new biomarkers for earlier detection of preterm labor, develop more effective therapeutic agents, and/or promote prophylactic measures even before conception.
Difference in volume of X- and Y-chromosome-bearing bovine sperm heads matches difference in DNA content (1999)

Our findings indicate that volume can be used as a criterion to distinguish X- and Y-chromosome-bearing sperm, making development of a technique to sort X- and Y-chromosome-bearing sperm based on head volume theoretically possible. A strong advantage of such a technique over the existing technique based on DNA content would be that X- and Y-chromosome-bearing sperm cells could thus be sorted without subjecting them to any staining.
Computational molecular biology: sources and methods for sequence analysis (1989)

Part 1 Introduction: an overview of computing with DNA and protein sequences. Part 2 Sources of information: databanks of protein sequences - the National Biomedical Research Foundation (NBRF) protein sequence database, peptide and protein databanks in Japan, additional protein sequence databanks databanks of nucleic acid sequences - GenBank, the EMBL data library databanks of three-dimensional structures - the protein databank. Part 3 Program systems: computer access to sequence databanks the Protein Identification Resource (PIR) software program systems for minicomputers. Part 4 The technical background: gels to sequences computers in modern science an introduction to computer networks. Part 5 Scientific applications: sequence comparison and alignment - the measurement and interpretation of sequence similarity analysis of DNA sequence data prediction of secondary structure of proteins hydrophobicity profiles molecular evolution conclusion - what shall one do with a newly-determined sequence. Part 6 Prospects: the future of computational molecular biology.
Pneumococcal Pneumonia: Potential for Diagnosis through a Urinary Metabolic Profile (2009)

Pneumonia, an infection of the lower respiratory tract, is caused by any of a number of different microbial organisms including bacteria, viruses, fungi, and parasites. Community-acquired pneumonia (CAP) causes a significant number of deaths worldwide, and is the sixth leading cause of death in the United States. However, the pathogen(s) responsible for CAP can be difficult to identify, often leading to delays in appropriate antimicrobial therapies. In the present study, we use nuclear magnetic resonance spectroscopy to quantitatively measure the profile of metabolites excreted in the urine of patients with pneumonia caused by Streptococcus pneumoniae and other microbes. We found that the urinary metabolomic profile for pneumococcal pneumonia was significantly different from the profiles for viral and other bacterial forms of pneumonia. These data demonstrate that urinary metabolomic profiles may be useful for the effective diagnosis of CAP.
Effect of p38 Mitogen-Activated Protein Kinase on the Replication of Encephalomyocarditis Virus (2003)

Cellular phosphorylation events during viral infection are necessary for effective viral replication. Encephalomyocarditis (EMC) virus has been used for studies on the molecular mechanisms of viral replication, but little is known about the cellular signaling pathways involved. This investigation was initiated to determine whether mitogen-activated protein kinases (MAPKs), which are central components of signal transduction pathways in the regulation of cell proliferation, play a role in the replication of EMC virus. We examined the phosphorylation of MAPKs, including extracellular signal-regulated kinase (ERK1/2), p38 MAPK, and stress-activated protein kinase 1/c-Jun NH(2)-terminal kinase (SAPK/JNK) in EMC virus-infected L929 cells and found that p38 MAPK and SAPK-JNK, but not ERK1/2, were activated during viral infection. We then examined the effect of these kinases on the replication of EMC virus in L929 cells by using specific inhibitors, including genistein or herbimycin A for tyrosine kinase, SB203580 or SB202190 for p38 MAPK, and PD98059 for ERK1/2. We found that the tyrosine kinase and p38 MAPK inhibitors, but not the ERK1/2 inhibitor, suppressed viral replication and that the inhibitory effect was primarily on viral protein synthesis. Finally, we examined whether p38 MAPK is involved in the translation of EMC viral transcripts by using L929 cells transfected with a gene construct containing the internal ribosomal entry site (IRES) of EMC virus and a luciferase reporter gene. We found that the p38 MAPK inhibitor suppressed the translation of EMC viral RNA. On the basis of these observations, we conclude that p38 MAPK plays a critical role in the replication of EMC virus, probably in the translation of viral RNA.
Evaluation of a new p16INK4A ELISA test and a high‐risk HPV DNA test for cervical cancer screening: Results from proof‐of‐concept study (2007)

p16(INK4a), a cell cycle regulation protein, accumulates in abnormal epithelial cells infected with high-risk human papilloma virus (HPV). In immunostaining studies, p16(INK4a) has shown potential as a marker of high grade cervical intraepithelial neoplasia (CIN) and invasive cervical cancer. To evaluate its potential use in cervical cancer screening, we conducted a feasibility study to compare the performance of a new enzyme linked immunosorbant assay (ELISA) for p16(INK4a) (mtm laboratories, Heidelberg, Germany) to that of the Hybrid Capture 2 (hc2) test for high-risk HPV DNA for the detection of CIN3. Three hundred and nineteen women were referred from Western Washington Planned Parenthood clinics for colposcopy examination and cervical biopsy because of abnormal Pap test results. Cervical samples were obtained from study participants for p16(INK4a) ELISA, liquid-based cytology and hc2. The order (first and second) for obtaining samples for cervical cytology and p16(INK4a) ELISA changed with every other subject. Concentrations of p16(INK4a) protein were higher when the sample was taken before the cytology. The sensitivity of p16(INK4a) ELISA (concentration > or = 8 units/ml) taken as first sample was 90.0% for CIN3, and the sensitivity of HC2 taken as a second sample was 85%. In the same group, the specificity of p16(INK4a) ELISA (46.9%) was slightly better than hc2 (35.4%) Results from this proof-of-concept study suggest that p16(INK4a) ELISA has a similar sensitivity and slightly better specificity for CIN3 compared to hc2. These findings support proceeding with a larger study with samples from a population of women presenting for routine cytology screening.
Evidence for an alternative glycolytic pathway in rapidly proliferating cells (2010)

Proliferating cells, including cancer cells, require altered metabolism to efficiently incorporate nutrients such as glucose into biomass. The M2 isoform of pyruvate kinase (PKM2) promotes the metabolism of glucose by aerobic glycolysis and contributes to anabolic metabolism. Paradoxically, decreased pyruvate kinase enzyme activity accompanies the expression of PKM2 in rapidly dividing cancer cells and tissues. We demonstrate that phosphoenolpyruvate (PEP), the substrate for pyruvate kinase in cells, can act as a phosphate donor in mammalian cells as PEP participates in the phosphorylation of the glycolytic enzyme phosphoglycerate mutase (PGAM1) in PKM2 expressing cells. We used mass spectrometry to show that the phosphate from PEP is transferred to the catalytic histidine (His-11) on human PGAM1. This reaction occurred at physiological concentrations of PEP and produced pyruvate in the absence of PKM2 activity. The presence of histidine-phosphorylated PGAM1 correlated with the expression PKM2 in cancer cell lines and tumor tissues. Thus, decreased pyruvate kinase activity in PKM2-expressing cells allows PEP-dependent histidine phosphorylation of PGAM1, and may provide an alternate glycolytic pathway that decouples ATP production from PEP-mediated phosphotransfer, allowing for the high rate of glycolysis to support anabolic metabolism observed in many proliferating cells.
From Pattern Recognition Receptor to Regulator of Homeostasis: The Double-Faced Macrophage Mannose Receptor (2004)

The mannose receptor (MR) is an endocytic and phagocytic receptor belonging to the C-type lectin superfamily. A number of functions have been ascribed to this receptor, which is involved in innate and adaptive immune responses. The MR binds carbohydrate moieties on several pathogens, such as bacteria, fungi, parasites, and viruses, and, therefore, is considered a pattern recognition receptor (PRR). In addition, MR binds endogenous molecules and was originally described as a membrane-associated component binding lysosomal glycosidases in alveolar macrophages. Since its identification more than 25 years ago, many other endogenous ligands were described, including hormones, enzymes, cell membranes, extracellular matrix components, and normal as well as tumoral mucins. The MR is preferentially expressed on immune cells of myeloid lineage, especially subsets of dendritic cells (DC) and tissue macrophages. In addition to immune cells, specialized endothelial cells are also MR-positive. Increasing evidence shows that the MR is involved in the silent clearance of inflammatory molecules. In this review, we discuss current knowledge about the receptor and show that endogenous ligands activate an anti-inflammatory and tolerogenic program in DC and macrophages, thus reinforcing the hypothesis that the MR has an important role in the maintenance of homeostasis.
Public Health 2020 (2020)

Journal of Public Health and Nutrition is an international peer-reviewed, open access journal that prioritizes publication of articles in the field of Public Health Research and Nutritional Science. The journal has special focus upon various research outputs and social determinant factors and encourages publishing multidisciplinary articles. The journal publishes current developments and scientific information as Research articles, Review articles, Case reports, Short communications, Mini Reviews, Commentaries, Image articles, Special issues, Thesis, etc. and provide online access without any restrictions or subscriptions to the researchers worldwide.
Solid‐State Hydrogen Sensors Using Palladium‐Nickel Alloys: Effect of Alloy Composition on Sensor Response (1995)

Thin film alloys of Pd and Ni make good sensors for hydrogen partial pressures over a very wide range: from . For from 1 to 700 Torr the atomic percent of Ni in the alloy has a strong effect on the change in film resistance which is used as the sensing property. The phase transition from the α‐ to the hydride β‐phase must be avoided to maintain a reversible sensor. The characteristics of alloys with Ni of 3, 5.3, 8, and 15% are reported. The phase transition was found in the 5.3% alloy at about 250 Torr, but alloys of showed no phase change behavior up to 630 Torr (pure) at ambient temperatures. Other characteristics of the Pd/Ni alloy sensors are also reported, including the effect of temperature, oxygen, and relative humidity, and the speed of response to step changes in .