gebhart/patrepeval huggingface dataset:
DNA Adenine Methylase Is Essential for Viability and Plays a Role in the Pathogenesis of Yersinia pseudotuberculosis and Vibrio cholerae (2001)

Salmonella strains that lack or overproduce DNA adenine methylase (Dam) elicit a protective immune response to different Salmonella species. To generate vaccines against other bacterial pathogens, the dam genes of Yersinia pseudotuberculosis and Vibrio cholerae were disrupted but found to be essential for viability. Overproduction of Dam significantly attenuated the virulence of these two pathogens, leading to, in Yersinia, the ectopic secretion of virulence proteins (Yersinia outer proteins) and a fully protective immune response in vaccinated hosts. Dysregulation of Dam activity may provide a means for the development of vaccines against varied bacterial pathogens.
HTLV x Gene Mutants Exhibit Novel Transcriptional Regulatory Phenotypes (1987)

The human T-cell leukemia viruses, HTLV-I and HTLV-II, contain a gene, termed x, with transcriptional regulatory function. The properties of the x proteins were analyzed by constructing mutant genes containing site-directed deletions and point mutations. The results demonstrate that the amino terminal 17 amino acids of the x protein constitute part of a functional domain that is critical for the transcriptional activating properties of the protein. Within this region, substitution of a leucine residue for a proline residue results in major changes in the trans-activation phenotype of the protein. The mutant HTLV-II x protein, though incapable of activating the HTLV-II long terminal repeat, will block trans-activation of the HTLV-II long terminal repeat by the wild-type protein. The altered phenotype of this mutant suggests a potential negative regulatory function of the x protein.
Quadrupole Magnetic Sorting of Porcine Islets of Langerhans (2009)

Islet transplantation is emerging as a treatment option for selected patients with type 1 diabetes. Inconsistent isolation, purification, and recovery of large numbers of high-quality islets remain substantial impediments to progress in the field. Removing islets as soon as they are liberated from the pancreas during digestion and circumventing the need for density gradient purification is likely to result in substantially increased viable islet yields by minimizing exposure to proteolytic enzymes, reactive oxygen intermediates, and mechanical stress associated with centrifugation. This study capitalized on the hypervascularity of islets compared with acinar tissue to explore their preferential enrichment with magnetic beads to enable immediate separation in a magnetic field utilizing a quadrupole magnetic sorting. The results demonstrate that (1) preferential enrichment of porcine islets is achievable, but homogeneous bead distribution within the pancreas is difficult to achieve with current protocols; (2) greater than 70% of islets in the dissociated pancreatic tissue were recovered by quadrupole magnetic sorting, but their purity was low; and (3) infused islets purified by density gradients and subsequently passed through quadrupole magnetic sorting had similar potency as uninfused islets. These results demonstrate proof of concept and define the steps for implementation of this technology in pig and human islet isolation.
Angiotensinergic Signaling in the Brain Mediates Metabolic Effects of Deoxycorticosterone (DOCA)-Salt in C57 Mice (2011)

Low-renin hypertension accounts for ≈ 25% of essential hypertensive patients. It is modeled in animals by chronic delivery of deoxycorticosterone acetate and excess dietary sodium (the DOCA-salt model). Previous studies have demonstrated that DOCA-salt hypertension is mediated through activation of the brain renin-angiotensin system. Here, we demonstrate robust metabolic phenotypes of DOCA-salt treatment. Male C57BL/6J mice (6 to 8 weeks old) received a subcutaneous pellet of DOCA (50 mg for 21 days) and were offered a 0.15 mol/L NaCl drink solution in addition to regular chow and tap water. Treatment resulted in mild hypertension, a blunting of weight gain, gross polydipsia, polyuria, and sodium intake, alterations in urinary sodium and potassium turnover, and serum sodium retention. Most strikingly, DOCA-salt mice exhibited no difference in food intake but did exhibited a large elevation in basal metabolic rate. Normalization of blood pressure by hydralazine (500 mg/L in drink solutions) attenuated the hydromineral phenotypes and renal renin suppression effects of DOCA-salt but had no effect on the elevated metabolic rate. In contrast, intracerebroventricular infusion of the angiotensin II type 1 receptor antagonist losartan (5 μg/h) attenuated the elevation in metabolic rate with DOCA-salt treatment. Together, these data illustrate the necessity of angiotensinergic signaling within the brain, independent of blood pressure alterations, in the metabolic consequences of DOCA-salt treatment.
Lifetime Risk and Age at Diagnosis of Symptomatic Knee Osteoarthritis in the US (2012)

The diagnosis of symptomatic knee OA occurs relatively early in life, suggesting that prevention programs should be offered relatively early in the life course. Further research is needed to understand the future burden of health care utilization resulting from earlier diagnosis of knee OA.
Measurement of T1 of the Ultrashort T2* Components in White Matter of the Brain at 3T (2014)

Recent research demonstrates that white matter of the brain contains not only long T2 components, but a minority of ultrashort T2* components. Adiabatic inversion recovery prepared dual echo ultrashort echo time (IR-dUTE) sequences can be used to selectively image the ultrashort T2* components in white matter of the brain using a clinical whole body scanner. The T2*s of the ultrashort T2* components can be quantified using mono-exponential decay fitting of the IR-dUTE signal at a series of different TEs. However, accurate T1 measurement of the ultrashort T2* components is technically challenging. Efficient suppression of the signal from the majority of long T2 components is essential for robust T1 measurement. In this paper we describe a novel approach to this problem based on the use of IR-dUTE data acquisitions with different TR and TI combinations to selectively detect the signal recovery of the ultrashort T2* components. Exponential recovery curve fitting provides efficient T1 estimation, with minimized contamination from the majority of long T2 components. A rubber phantom and a piece of bovine cortical bone were used for validation of this approach. Six healthy volunteers were studied. An averaged T2* of 0.32 ± 0.09 ms, and a short mean T1 of 226 ± 46 ms were demonstrated for the healthy volunteers at 3T.
Renal folate absorption and the kidney folate binding protein. I. Urinary clearance studies (1987)

The kidney possesses a high concentration of a folate binding protein (FBP) that resides primarily in the brush-border membrane (BBM) of the proximal tubular cells. To assess the possible involvement of this protein in renal conservation of folate we determined the urinary clearance, in rats, of three forms of folates with sharply different affinities for FBP. After single intravenous injections of 0.1 to 1.0-nmol doses of radioactive folates the urinary clearance based on radioisotope determination was in the sequence: folic acid less than 5-methyltetrahydrofolate (5-CH3 THF) much less than methotrexate. At higher doses the urinary folate clearance was increased and the differences between the three injected forms were narrowed and were no longer noticeable at 100-nmol doses. Under conditions of continuous infusion to attain plasma folate levels of 2.3-5.7 pmol/ml, the urinary clearance based on chromatographic analyses of plasma and urine after correction for plasma folate binding was 0.20 ml/min for folic acid, 0.37 ml/min for 5-CH3 THF, and 1.76 ml/min for methotrexate. These chromatographic analyses have also shown the presence in both plasma and urine of metabolites formed from infused folates. Metabolites found after infusion of folic acid include 5-CH3 THF with a urinary clearance of 0.3 ml/min and an unknown with a urinary clearance of 0.8 ml/min. The latter metabolite appears also to occur in plasma and urine after infusion of 5-CH3 THF. Infusion of methotrexate was associated with the appearance of a metabolite with a urinary clearance of 2.5 ml/min. This sequence of urinary clearance is in inverse order to the affinities of these three forms of folate for the kidney BBM FBP.(ABSTRACT TRUNCATED AT 250 WORDS)
Oligosaccharides in infant formula (2002)

Breast-feeding is the golden standard for infant feeding. However, the majority of a few week old infants are fed with a second choice infant feeding, cow's milk based formula. Amongst the multiple differences between human and cow's milk regards the development of the gastro-intestinal flora: the flora of the breast-fed infant being richer in bifidobacteria and lactobacilli. Both species are known to be potentially beneficial for the health of the host. The absence of oligosaccharides, the third largest component in human milk, in cow's milk is likely to account for the differences in colonic flora. The oligosaccharide content and concentration in breast milk is — just as for the other macronutrients — a dynamic process, making it impossible for industry to mimic nature. However, if the composition cannot be mimicked, the effect and function can be imitated. The addition of two oligosaccharides, galacto-oligosaccharides and inulin, to cow's milk based infant formula has been shown to have a bifidogenic effect, and to stimulate the growth of bifidi and lactobacilli. In conclusion, the addition of oligosaccharides to cow's milk based infant formula brings this alternative, second choice infant feeding one step closer to the golden standard of human milk. But, prolonged breast-feeding should still be promoted with maximum effort.
IL-6 activates serum and glucocorticoid kinase via p38α mitogen-activated protein kinase pathway (2005)

Interleukin-6 (IL-6) has been implicated as an autocrine factor involved in growth of several human cancers, such as tumors arising from the biliary tract or cholangiocarcinoma. In malignant biliary tract epithelia, IL-6 activates the p38 MAPK pathway, which mediates a dominant survival signaling pathway. Serum and glucocorticoid-stimulated kinase (SGK) has been implicated as a survival kinase, but its role in survival signaling by IL-6 is unknown. After IL-6 stimulation, p38 MAPK activation preceded phosphorylation of SGK at Ser78. Pretreatment with the pharmacological inhibitors of p38 MAPK SB-203580 or SB-202190 blocked IL-6-induced SGK phosphorylation at Ser78 and SGK activation. Overexpression of p38alpha increased constitutive SGK phosphorylation at Ser78, whereas dominant negative p38alpha MAPK blocked IL-6-induced SGK phosphorylation and nuclear translocation. Interestingly, in addition to stimulating SGK phosphorylation, both IL-6 stimulation and p38alpha MAPK overexpression increased SGK mRNA and protein expression. An increase in p38 MAPK and SGK occurred following enforced expression of IL-6 in vivo. Furthermore, inhibition of SGK expression by siRNA increased toxicity due to chemotherapeutic drugs. Taken together, these data identify SGK as both a downstream kinase substrate as well as a transcriptionally regulated gene target of p38 MAPK in response to IL-6 and support a role of SGK during survival signaling by IL-6 in human cancers, such as cholangiocarcinoma.
Influence of Different Intravenous Lipid Emulsions on Hepatobiliary Dysfunction in a Rabbit Model (2007)

In our animal model, the use of a lipid emulsion with a reduced amount of polyunsaturated fatty acids was not superior to a lipid emulsion based on soybean oil. Long-term application of n-3 fatty acids was associated with more extensive fibrosis. Therefore, intravenous n-3 fatty acids containing lipid preparations (fish oil) should not be used in patients for long-term TPN.
<i>Ureaplasma urealyticum</i> Induces Apoptosis in Human Lung Epithelial Cells and Macrophages (2002)

Chronic lung disease (CLD) of prematurity remains a significant cause of morbidity among premature infants. It is a multifactorial disorder and characterized by an early increased number of neutrophils and alveolar macrophages, with later architectural epithelial and endothelial cell damage. Recently, apoptosis of type 2 pneumocytes in the lung of preterm neonates with acute and chronic lung disease has been examined and apoptosis of mesenchymal cells was detected in the chronic stage of bronchopulmonary dysplasia. Infection and inflammatory responses in the lungs play important roles. However, the contribution of Ureaplasma urealyticum to the development of CLD is debated. We found that U. urealyticum induced apoptosis in human type II lung epithelial cells (A549 cell line) and macrophages (derived from human monocytic cell line THP-1) by measuring the outer leaflets translocation of phosphatidylserine (flow cytometry analysis and fluorescence microscopy assessment), DNA fragmentation analysis, cell morphology changes such as diminution in cell volume, increased cytoplasmic staining, and nuclear pyknosis (hematoxylin and eosin staining) and viable counting (trypan blue exclusion). Anti-TNF-alpha monoclonal antibody partially protected the macrophages from undergoing apoptosis after infection with U. urealyticum. Our findings imply that U. urealyticum might be involved in impairing lung structure and host immune response during the development of CLD.
Targeting Amyloid-β Peptide (Aβ) Oligomers by Passive Immunization with a Conformation-selective Monoclonal Antibody Improves Learning and Memory in Aβ Precursor Protein (APP) Transgenic Mice (2005)

Passive immunization of murine models of Alzheimer disease amyloidosis reduces amyloid-beta peptide (Abeta) levels and improves cognitive function. To specifically address the role of Abeta oligomers in learning and memory, we generated a novel monoclonal antibody, NAB61, that preferentially recognizes a conformational epitope present in dimeric, small oligomeric, and higher order Abeta structures but not full-length amyloid-beta precursor protein or C-terminal amyloid-beta precursor protein fragments. NAB61 also recognized a subset of brain Abeta deposits, preferentially mature senile plaques, and amyloid angiopathy. Using NAB61 as immunotherapy, we showed that aged Tg2576 transgenic mice treated with NAB61 displayed significant improvements in spatial learning and memory relative to control mice. These data implicated Abeta oligomers as a pathologic substrate for cognitive decline in Alzheimer disease.
The blind‐spot of regulatory T cells (2006)

CD4+ CD25+ Foxp3+ regulatory T cells (Treg) are natural suppressors of autoimmunity but they can also dampen the effective clearance of infectious organisms. These cells have the potential to be exploited to prevent transplant rejection and to treat autoimmune disease. A paper in this issue of the European Journal of Immunology details a method to selectively expand antigen-specific Treg from a polyclonal Treg population, by using a specific dendritic cell (DC) subset. Furthermore, the authors show that such Treg can be used to prevent experimental type I diabetes; however, as Treg are positively selected by thymic epithelial cells (TEC) on the basis of self-reactivity, they would systematically suppress protective immune responses unless their repertoire is devoid of recognition towards peripheral antigen-presenting cells. This may be achieved by negative selection of developing Treg on thymic DC, thus creating a 'blind-spot' corresponding to DC-self-antigens in the mature Treg repertoire. Therefore, therapeutic use of DC subsets for the expansion of rare Treg populations should take into account this blind-spot, as peptides that are not accessible to thymic DC may be significantly more effective for the expansion of Treg.
Dynamic maximum power point tracking of photovoltaic arrays using ripple correlation control (2006)

A dynamically rapid method used for tracking the maximum power point of photovoltaic arrays, known as ripple correlation control, is presented and verified against experiment. The technique takes advantage of the signal ripple, which is automatically present in power converters. The ripple is interpreted as a perturbation from which a gradient ascent optimization can be realized. The technique converges asymptotically at maximum speed to the maximum power point without the benefit of any array parameters or measurements. The technique has simple circuit implementations
Fame-a flexible appearance modeling environment (2003)

Combined modeling of pixel intensities and shape has proven to be a very robust and widely applicable approach to interpret images. As such the active appearance model (AAM) framework has been applied to a wide variety of problems within medical image analysis. This paper summarizes AAM applications within medicine and describes a public domain implementation, namely the flexible appearance modeling environment (FAME). We give guidelines for the use of this research platform, and show that the optimization techniques used renders it applicable to interactive medical applications. To increase performance and make models generalize better, we apply parallel analysis to obtain automatic and objective model truncation. Further, two different AAM training methods are compared along with a reference case study carried out on cross-sectional short-axis cardiac magnetic resonance images and face images. Source code and annotated data sets needed to reproduce the results are put in the public domain for further investigation.
Design, Synthesis, and Crystal Structure of Selective 2-Pyridone Tissue Factor VIIa Inhibitors (2003)

Targeted 2-pyridones were selected as tissue Factor VIIa inhibitors and prepared from 2,6-dibromopyridine via a multistep synthesis. A variety of chemical transformations, including regioselective nucleophilic addition, selective nitrogen alkylation, and a Suzuki coupling, afforded the targeted tissue Factor VIIa inhibitors. The pyridone core was selected as a replacement for the pyrazinone core of noncovalent tissue Factor VIIa inhibitors and designed such that their substitution pattern would occupy and interact with the S(1), S(2), and S(3) pockets of the tissue Factor VIIa enzyme. These compounds were tested in several serine protease enzyme assays involved in the coagulation cascade exhibiting modest activity on tissue Factor VIIa with excellent selectivity over thrombin and Factor Xa. Finally, an X-ray crystal structure of inhibitor 14a bound to tissue Factor VIIa was obtained and will be described.
Supercapacitors Based on Flexible Graphene/Polyaniline Nanofiber Composite Films (2010)

Composite films of chemically converted graphene (CCG) and polyaniline nanofibers (PANI-NFs) were prepared by vacuum filtration the mixed dispersions of both components. The composite film has a layered structure, and PANI-NFs are sandwiched between CCG layers. Furthermore, it is mechanically stable and has a high flexibility; thus, it can be bent into large angles or be shaped into various desired structures. The conductivity of the composite film containing 44% CCG (5.5 x 10(2) S m(-1)) is about 10 times that of a PANI-NF film. Supercapacitor devices based on this conductive flexible composite film showed large electrochemical capacitance (210 F g(-1)) at a discharge rate of 0.3 A g(-1). They also exhibited greatly improved electrochemical stability and rate performances.
Estimating human shape and pose from a single image (2009)

We describe a solution to the challenging problem of estimating human body shape from a single photograph or painting. Our approach computes shape and pose parameters of a 3D human body model directly from monocular image cues and advances the state of the art in several directions. First, given a user-supplied estimate of the subject's height and a few clicked points on the body we estimate an initial 3D articulated body pose and shape. Second, using this initial guess we generate a tri-map of regions inside, outside and on the boundary of the human, which is used to segment the image using graph cuts. Third, we learn a low-dimensional linear model of human shape in which variations due to height are concentrated along a single dimension, enabling height-constrained estimation of body shape. Fourth, we formulate the problem of parametric human shape from shading. We estimate the body pose, shape and reflectance as well as the scene lighting that produces a synthesized body that robustly matches the image evidence. Quantitative experiments demonstrate how smooth shading provides powerful constraints on human shape. We further demonstrate a novel application in which we extract 3D human models from archival photographs and paintings.
Splash-3: A properly synchronized benchmark suite for contemporary research (2016)

Benchmarks are indispensable in evaluating the performance implications of new research ideas. However, their usefulness is compromised if they do not work correctly on a system under evaluation or, in general, if they cannot be used consistently to compare different systems. A well-known benchmark suite of parallel applications is the Splash-2 suite. Since its creation in the context of the DASH project, Splash-2 benchmarks have been widely used in research. However, Splash-2 was released over two decades ago and does not adhere to the recent C memory consistency model. This leads to unexpected and often incorrect behavior when some Splash-2 benchmarks are used in conjunction with contemporary compilers and hardware (simulated or real). Most importantly, we discovered critical performance bugs that may question some of the reported benchmark results. In this work, we analyze the Splash-2 benchmarks and expose data races and related performance bugs. We rectify the problematic benchmarks and evaluate the resulting performance. Our work contributes to the community a new sanitized version of the Splash-2 benchmarks, called the Splash-3 benchmark suite.
TRAF5, an Activator of NF-κB and Putative Signal Transducer for the Lymphotoxin-β Receptor (1996)

Tumor necrosis factor (TNF) receptor-associated factors (TRAFs) are signal transducers for several members of the TNF receptor superfamily. We have identified a novel member of the TRAF family by degenerate oligonucleotide polymerase chain reaction amplification that contains a zinc RING finger and zinc finger motifs, a coiled-coil region, and a C-terminal "TRAF" homology domain. In vitro translated TRAF5 binds to the cytoplasmic region of the lymphotoxin-beta receptor (LT-betaR) but not to several other related receptors including CD40, both TNF receptors, Fas, and nerve growth factor receptor. TRAF5 and LT-betaR coimmunoprecipitate when overexpressed in COS7 cells. TRAF5 mRNA expression is found in all visceral organs and overlaps with LT-betaR. These features distinguish TRAF5 from the other members of the TRAF family. The transcription factor NF-kappaB is activated in HEK293 cells by overexpression of full-length TRAF5 but not a truncated form lacking the zinc binding region. Furthermore, overexpression of LT-betaR in HEK293 cells also results in activation of NF-kappaB, which is partially inhibited by the truncated TRAF5 mutant. These results show TRAF5 is functionally similar to TRAF2 in that both mediate activation NF-kappaB and implicate TRAF5 as a signal transducer for LT-betaR.