gebhart/patrepeval huggingface dataset:
Localization of E-cadherin in Peripheral Glia after Nerve Injury and Repair (1996)

Peripheral nerve injury results in histological and histochemical changes in neurons and glia. We have recently found that Ca(2+)-dependent cell adhesion molecule E-cadherin plays an important role in the selective fasciculation of a particular subset of unmyelinated sensory fibers. In the present immunohistochemical and immunoblot analyses, the temporal profile of the subcellular expression of this molecule in spinal nerves was examined after crushing, transecting, or ligaturing the sciatic nerve in mice with special attention paid to E-cadherin expression in glial cells. After axotomy of the sciatic nerve, distal axons of the proximal stump and the fibers of the distal stump degenerated, but E-cadherin was still detectable at the outer mesaxons of the myelinated axons as long as they remained morphologically intact. Subsequently, Schwann cells proliferated and migrated to form Schwann cell columns (Büngner's bands) as initial responses to denervation, and expressed E-cadherin at their site of contact with each other and later with sprouting axons. At the initial stage of myelin formation, slender processes of a single Schwann cell interdigitated with an enveloped axons, and expressed E-cadherin at the contact site elaborated by a single Schwann cell. Immunoblot analysis on day 7 revealed that E-cadherin was detected in both the proximal nerve segments and the regenerative distal segments, but was negative in the degenerative distal segments. On the basis of present data, it is suggested that E-cadherin might be involved in the stabilization of the peripheral glial network which provides the guidance of sprouting axons and myelination.
Hypermethylated-capped selenoprotein mRNAs in mammals (2014)

Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m(7)G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5'-end maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo.
Synthesis and Antiviral Activity of 5-Substituted Cytidine Analogues:  Identification of a Potent Inhibitor of Viral RNA-Dependent RNA Polymerases (2006)

As part of our studies of lethal viral mutagens, a series of 5-substituted cytidine analogues were synthesized and evaluated for antiviral activity. Among the compounds examined, 5-nitrocytidine was effective against poliovirus (PV) and coxsackievirus B3 (CVB3) and exhibited greater activity than the clinically employed drug ribavirin. Instead of promoting viral mutagenesis, 5-nitrocytidine triphosphate inhibited PV RNA-dependent RNA polymerase (K(d) = 1.1 +/- 0.1 microM), and this inhibition is sufficient to explain the observed antiviral activity.
Encore: Lightweight Measurement of Web Censorship with Cross-Origin Requests (2014)

Despite the pervasiveness of Internet censorship, we have scant data on its extent, mechanisms, and evolution. Measuring censorship is challenging: it requires continual measurement of reachability to many target sites from diverse vantage points. Amassing suitable vantage points for longitudinal measurement is difficult; existing systems have achieved only small, short-lived deployments. We observe, however, that most Internet users access content via Web browsers, and the very nature of Web site design allows browsers to make requests to domains with different origins than the main Web page. We present Encore, a system that harnesses cross-origin requests to measure Web filtering from a diverse set of vantage points without requiring users to install custom software, enabling longitudinal measurements from many vantage points. We explain how Encore induces Web clients to perform cross-origin requests that measure Web filtering, design a distributed platform for scheduling and collecting these measurements, show the feasibility of a global-scale deployment with a pilot study and an analysis of potentially censored Web content, identify several cases of filtering in six months of measurements, and discuss ethical concerns that would arise with widespread deployment.
The Plasma Protamine Paracoagulation Test: Clinical and Laboratory Evaluation (1972)

Journal Article The Plasma Protamine Paracoagulation Test: Clinical and Laboratory Evaluation Get access Wayne R. Kidder, M.D., Wayne R. Kidder, M.D. Department of Medicine, University of Southern California School of Medicine, and Departments of Medicine and Laboratories, Los Angeles County–University of Southern California Medical Center, Los Angeles, California 90033 Search for other works by this author on: Oxford Academic Google Scholar Laurence J. Logan, M.D., Laurence J. Logan, M.D. Department of Medicine, University of Southern California School of Medicine, and Departments of Medicine and Laboratories, Los Angeles County–University of Southern California Medical Center, Los Angeles, California 90033 Search for other works by this author on: Oxford Academic Google Scholar Samuel I. Rapaport, M.D., Samuel I. Rapaport, M.D. Department of Medicine, University of Southern California School of Medicine, and Departments of Medicine and Laboratories, Los Angeles County–University of Southern California Medical Center, Los Angeles, California 90033 Search for other works by this author on: Oxford Academic Google Scholar Mary Jane Patch, B.A. Mary Jane Patch, B.A. Department of Medicine, University of Southern California School of Medicine, and Departments of Medicine and Laboratories, Los Angeles County–University of Southern California Medical Center, Los Angeles, California 90033 Search for other works by this author on: Oxford Academic Google Scholar American Journal of Clinical Pathology, Volume 58, Issue 6, 1 December 1972, Pages 675–686, https://doi.org/10.1093/ajcp/58.6.675 Published: 01 December 1972 Article history Received: 22 November 1971 Accepted: 27 January 1972 Published: 01 December 1972
Time-frequency distribution technique in biological signal processing. (1995)

Time-frequency distribution (TFD) has gained wide acceptance for deterministic non-stationary signal processing, particularly for biological signals, in both basic research and commercial production. This paper presents the results of a comparison of the TFD technique with other methods for determining physiologic parameters, particularly the ventricular ejection time (VET) and (dZ/dtmax), the differentiation of the thoracic-fluid signal Z0 from non-stationary impedence cardiography dZ/dt. The TFD technique was found to be more accurate--in terms of both time and signal magnitude--than traditional methods such as the baseline and ensemble-averaging techniques when compared with phonocardiograms and hand calculations by experts in the field. It is shown that TFD can also reduce ventilatory/respiratory noise, electrical and muscle noise, and patient-motion artifacts. Correlation analysis and regression analysis as well as Bland-Altman studies showed stronger correlational methods tested.
Modeling complex astrophysics data (2002)

Scientific data are often characterized by large volumes of data, complex data relationships, and complex algorithms that operate on those data. Databases at the Space Telescope Science Institute are used to illustrate some of the differences between traditional data management schemes and the requirements of scientific data. Data from radio astronomy are modeled using conceptual enhancements to flexible image transport system (FITS) binary tables, which are compared to relational database tables. These enhancements are used to capture features of a more general notion of an observation. Finally, it is argued that accessing and manipulating each data, in order to support the entire process of data analysis, requires the construction of an abstract data model that intuitively models how a domain specialist views the data.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale (2014)

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate 'true' microbial taxa. Here, we explore the ecological consistency of OTUs--based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale.
Increased tissue levels of omega-3 polyunsaturated fatty acids prevents pathological preterm birth (2013)

Omega-3 polyunsaturated fatty acids such as eicosapentaenoic acid (EPA) have anti-inflammatory effects. Preterm birth is an important problem in modern obstetrics and one of the main causes is an inflammation. We here showed that abundance of omega-3 fatty acids reduced the incidence of preterm birth induced by LPS with fat-1 mice, capable of converting omega-6 to omega-3 fatty acids. We also indicated that the gene expression of IL-6 and IL-1β in uteruses and the number of cervical infiltrating macrophages were reduced in fat-1 mice. The analyses of lipid metabolomics showed the high level of 18-hydroxyeicosapentaenoate in fat-1 mice, which was derived from EPA and was metabolized to anti-inflammatory product named resolvin E3 (RvE3). We finally showed that the administration of RvE3 to LPS-exposed pregnant wild type mice lowered the incidence of preterm birth. Our data suggest that RvE3 could be a potential new therapeutic for the prevention of preterm birth.
Activity-based ubiquitin-specific protease (USP) profiling of virus-infected and malignant human cells (2004)

The family of ubiquitin (Ub)-specific proteases (USP) removes Ub from Ub conjugates and regulates a variety of cellular processes. The human genome contains many putative USP-encoding genes, but little is known about USP tissue distribution, pattern of expression, activity, and substrate specificity. We have used a chemistry-based functional proteomics approach to identify active USPs in normal, virus-infected, and tumor-derived human cells. Depending on tissue origin and stage of activation/differentiation, different USP activity profiles were revealed. The activity of specific USPs, including USP5, -7, -9, -13, -15, and -22, was up-regulated by mitogen activation or virus infection in normal T and B lymphocytes. UCH-L1 was highly expressed in tumor cell lines of epithelial and hematopoietic cell origin but was not detected in freshly isolated and mitogen-activated cells. Up-regulation of this USP was a late event in the establishment of Epstein-Barr virus-immortalized lymphoblastoid cell lines and correlated with enhanced proliferation, suggesting a possible role in growth transformation.
Relation between Preoperative Inspiratory Lung Resistance and the Outcome of Lung-Volume–Reduction Surgery for Emphysema (1998)

Preoperative lung resistance during inspiration appears to be a useful measure for selecting patients with emphysema for lung-volume-reduction surgery.
Subunit composition of the glycyl radical enzyme p ‐hydroxyphenylacetate decarboxylase (2004)

p-Hydroxyphenylacetate decarboxylase from Clostridium difficile catalyses the decarboxylation of p-hydroxyphenylacetate to yield the cytotoxic compound p-cresol. The three genes encoding two subunits of the glycyl-radical enzyme and the activating enzyme have been cloned and expressed in Escherichia coli. The recombinant enzymes were used to reconstitute a catalytically functional system in vitro. In contrast with the decarboxylase purified from C. difficile, which was an almost inactive homo-dimeric protein (beta(2)), the recombinant enzyme was a hetero-octameric (beta(4)gamma(4)), catalytically competent complex, which was activated using endogenous activating enzyme from C. difficile or recombinant activating enzyme to a specific activity of 7 U.mg(-1). Preliminary results suggest that phosphorylation of the small subunit is responsible for the change of the oligomeric state. These data point to an essential function of the small subunit of the decarboxylase and may indicate unique regulatory properties of the system.
Modeling, Synthesis, and Biological Evaluation of Potential Retinoid X Receptor (RXR)-Selective Agonists: Analogues of 4-[1-(3,5,5,8,8-Pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic Acid (Bexarotene) and 6-(Ethyl(5,5,8,8-tetrahydronaphthalen-2-yl)amino)nicotinic Acid (NEt-TMN) (2016)

Sulfonic acid analogues of 4-[1-(3,5,5,8,8-pentamethyl-5,6,7,8-tetrahydro-2-naphthyl)ethynyl]benzoic acid (bexarotene, 1) as well as seven novel and two reported analogues of 6-(ethyl(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)amino)nicotinic acid (NEt-TMN) were synthesized and assessed for selective retinoid X receptor (RXR) agonism. Compound 1 is FDA-approved for treatment of cutaneous T-cell lymphoma (CTCL); however, 1 can provoke side effects by impacting RXR-dependent receptor pathways. All of the analogues in this study were evaluated for their potential to bind RXR through modeling and then assayed in an RXR-RXR mammalian-2-hybrid (M2H) system and in RXR-responsive element (RXRE)-mediated transcriptional experiments. The EC<sub>50</sub> profiles for these unique analogues and their analogous effectiveness to inhibit proliferation in CTCL cells relative to 1 suggest that these compounds possess similar or even enhanced therapeutic potential. Several compounds also displayed more selective RXR activation with minimal cross-signaling of the retinoic acid receptor. These results suggest that modifications of potent RXR agonists such as NEt-TMN can lead to improved biological selectivity and potency compared with the known therapeutic.
UKPDS 28: A Randomized Trial of Efficacy of Early Addition of Metformin in Sulfonylurea-Treated Type 2 Diabetes (1998)

Early addition of metformin improved glycemic control in patients with suboptimal glycemic control while taking maximum sulfonylurea therapy, irrespective of obesity or baseline FPG concentrations.
Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli. (1975)

A low-molecular-weight (7000), heat-stable protein--HU--that stimulates transcription of bacteriophage lambda DNA by E. coli RNA polymerase was purified from E. coli extracts using affinity chromatography on DNA-cellulose. HU binds to native DNA, resulting in an apparent thickening of the DNA chains as revealed by electron microscopy. Contrary to DNA unwinding proteins, it causes no destabilization of the double helix. HU differs from previously described transcription factors (H1, D, etc.) and from the low-molecular-weight omega subunit of the RNA polymerase. By its amino-acid composition and characteristics, HU displays an interesting resemblance to some eukaryotic histones, such as H2B and H1.
[Role of the time of administration of calcium carbonate (before or during mealtime) in the control of hyperphosphatemia in patients on maintenance hemodialysis]. (1999)

a) administration of CaCO3 before the meal decreases its efficiency in controlling hyperphosphatemia since plasma PO4 was actually slightly higher with this timing of administration; b) administration of CaCO3 before the meal is associated with significantly lower plasma corrected calcium suggesting a smaller absorption of calcium which may be an advantage but only in hypercalcemic patients; c) there is no reason other than the prevention of its hypercalcemic effect to recommend the administration of CaCO3 just before the meals than during the meals.
DEVELOPMENT OF HYPOTHALAMIC–PITUITARY–ADRENAL RESPONSE TO STRESS IN RATS MADE HYPOTHYROID BY EXPOSURE TO THIOURACIL FROM CONCEPTION (1981)

The functional maturation of the hypothalamic-pituitary-adrenal (HPA) axis has been studied in rats of 20-35 days of age made hypothyroid by the administration of thiouracil from conception. Basal concentrations of corticosterone in serum were normal in hypothyroid animals. Ether stress led to an increase corticosterone content of the adrenal glands of hypothyroid and normal rats but not to a rise in serum corticosterone of hypothyroid rats until 30 days of age. Corticosterone secretion in response to ACTH administration was subnormal in hypothyroid rats. The hypothyroid state delays the development of the hypothalamic-pituitary-portion of the HPA axis until 30 days of age and causes a diminution in adrenal response to ACTH beyond this time.
Granzyme B-H22(scFv), a human immunotoxin targeting CD64 in acute myeloid leukemia of monocytic subtypes (2008)

Acute myeloid leukemia (AML) cells of subtypes M4 and M5 show enhanced expression of CD64 (FcgammaRI), the high-affinity receptor for IgG, which is normally expressed at high levels only on activated cells of the myeloid lineage. CD64 is therefore a prime target for the specific delivery of cytotoxic agents. A promising toxin candidate is granzyme B, a human serine protease originating from cytotoxic granules of CD8+ T lymphocytes and natural killer cells. After evaluating the sensitivity of the AML-related cell line U937 toward cytosolic granzyme B, we genetically fused granzyme B to H22, a humanized single-chain antibody fragment (scFv) specific for CD64, to obtain Gb-H22(scFv), a fusion protein lacking the immunogenic properties of nonhuman immunofusions. Gb-H22(scFv) was successfully expressed in human 293T cells, secreted, and purified from cell culture supernatants. The purified protein bound specifically to CD64+ U937 cells. Despite linkage to the binding domain, the proteolytic activity of functional Gb-H22(scFv) was identical to that of free granzyme B. Target cell-specific cytotoxicity was observed with a half-maximal inhibitory concentration (IC50) between 1.7 and 17 nmol/L. In addition, the induction of apoptosis in U937 cells was confirmed by Annexin A5 staining and the detection of activated caspase-3 in the cytosol. Finally, apoptosis was observed in primary CD64+ AML cells, whereas CD64(-) AML cells were unaffected. This is the first report of a completely human granzyme B-based immunotoxin directed against CD64, with activity against an AML-related cell line and primary AML cells.
The risk of myocardial infarction is enhanced by a synergistic interaction between serum insulin and smoking : European Journal of Endocrinology (2002)

The risk of myocardial infarction is enhanced by a synergistic interaction between serum insulin and smoking : European Journal of Endocrinology
Inflammatory processes in muscle injury and repair (2005)

Modified muscle use or injury can produce a stereotypic inflammatory response in which neutrophils rapidly invade, followed by macrophages. This inflammatory response coincides with muscle repair, regeneration, and growth, which involve activation and proliferation of satellite cells, followed by their terminal differentiation. Recent investigations have begun to explore the relationship between inflammatory cell functions and skeletal muscle injury and repair by using genetically modified animal models, antibody depletions of specific inflammatory cell populations, or expression profiling of inflamed muscle after injury. These studies have contributed to a complex picture in which inflammatory cells promote both injury and repair, through the combined actions of free radicals, growth factors, and chemokines. In this review, recent discoveries concerning the interactions between skeletal muscle and inflammatory cells are presented. New findings clearly show a role for neutrophils in promoting muscle damage soon after muscle injury or modified use. No direct evidence is yet available to show that neutrophils play a beneficial role in muscle repair or regeneration. Macrophages have also been shown capable of promoting muscle damage in vivo and in vitro through the release of free radicals, although other findings indicate that they may also play a role in muscle repair and regeneration through growth factors and cytokine-mediated signaling. However, this role for macrophages in muscle regeneration is still not definitive; other cells present in muscle can also produce the potentially regenerative factors, and it remains to be proven whether macrophage-derived factors are essential for muscle repair or regeneration in vivo. New evidence also shows that muscle cells can release positive and negative regulators of inflammatory cell invasion, and thereby play an active role in modulating the inflammatory process. In particular, muscle-derived nitric oxide can inhibit inflammatory cell invasion of healthy muscle and protect muscle from lysis by inflammatory cells in vivo and in vitro. On the other hand, muscle-derived cytokines can signal for inflammatory cell invasion, at least in vitro. The immediate challenge for advancing our current understanding of the relationships between muscle and inflammatory cells during muscle injury and repair is to place what has been learned in vitro into the complex and dynamic in vivo environment.
Insulin-like growth factor I preserves renal function postoperatively (1997)

Deterioration of renal function, which can lead to postoperative renal failure, is a complication of surgery involving the suprarenal aorta and surgery involving the renal arteries. Fifty-four patients who were at risk for developing this complication were enrolled in a double-blind, randomized, placebo-controlled trial of insulin-like growth factor (IGF-I) as a therapeutic agent to prevent the decline in renal function. The primary end point was the incidence of renal dysfunction, defined as a reduction of the glomerular filtration rate (creatinine clearance) at each of three measurements over 72 h. IGF-I (100 microg/kg subcutaneously every 12 h for 6 doses) or placebo was administered on admission to the intensive care unit immediately postoperatively. IGF-I- and placebo-treated groups were well matched for sex, age, type of surgery, renal ischemic time during surgery (ischemic index), baseline creatinine clearance, and baseline serum creatinine. No patient in the study developed acute renal failure postoperatively. IGF-I was well tolerated. A smaller proportion of patients in the IGF-I group had a postoperative decline in renal function (22%) than in the placebo-treated group (33%). There were no significant differences in levels of serum creatinine at time of discharge, length of hospital stay, length of intensive care unit stay, length of intubation, or incidence of dialysis or death. Our findings establish the feasibility and potential utility for the use of IGF-I to reduce the incidence of postoperative renal dysfunction in high-risk patients.