gebhart/patrepeval huggingface dataset:
Symptom Duration and Risk Factors for Delayed Return to Usual Health Among Outpatients with COVID-19 in a Multistate Health Care Systems Network — United States, March–June 2020 (2020)

Prolonged symptom duration and disability are common in adults hospitalized with severe coronavirus disease 2019 (COVID-19). Characterizing return to baseline health among outpatients with milder COVID-19 illness is important for understanding the full spectrum of COVID-19-associated illness and tailoring public health messaging, interventions, and policy. During April 15-June 25, 2020, telephone interviews were conducted with a random sample of adults aged ≥18 years who had a first positive reverse transcription-polymerase chain reaction (RT-PCR) test for SARS-CoV-2, the virus that causes COVID-19, at an outpatient visit at one of 14 U.S. academic health care systems in 13 states. Interviews were conducted 14-21 days after the test date. Respondents were asked about demographic characteristics, baseline chronic medical conditions, symptoms present at the time of testing, whether those symptoms had resolved by the interview date, and whether they had returned to their usual state of health at the time of interview. Among 292 respondents, 94% (274) reported experiencing one or more symptoms at the time of testing; 35% of these symptomatic respondents reported not having returned to their usual state of health by the date of the interview (median = 16 days from testing date), including 26% among those aged 18-34 years, 32% among those aged 35-49 years, and 47% among those aged ≥50 years. Among respondents reporting cough, fatigue, or shortness of breath at the time of testing, 43%, 35%, and 29%, respectively, continued to experience these symptoms at the time of the interview. These findings indicate that COVID-19 can result in prolonged illness even among persons with milder outpatient illness, including young adults. Effective public health messaging targeting these groups is warranted. Preventative measures, including social distancing, frequent handwashing, and the consistent and correct use of face coverings in public, should be strongly encouraged to slow the spread of SARS-CoV-2.
Development- and differentiation-dependent reorganization of intermediate filaments in fiber cells. (2001)

Beaded filament protein accumulation lags significantly behind both primary and secondary fiber cell elongation, suggesting a functional role subsequent to elongation. The subcellular distribution of vimentin and the beaded filament proteins showed marked differences within the cell, with differentiation, and with development. The differences in time of initial synthesis and in distribution of these IF proteins may bear on hypotheses about the role of IFs in fiber cell elongation and in structural-functional polarity of the fiber cell.
Model-Based Event Detection in Wireless Sensor Networks (2009)

In this paper we present an application of techniques from statistical signal processing to the problem of event detection in wireless sensor networks used for environmental monitoring. The proposed approach uses the well-established Principal Component Analysis (PCA) technique to build a compact model of the observed phenomena that is able to capture daily and seasonal trends in the collected measurements. We then use the divergence between actual measurements and model predictions to detect the existence of discrete events within the collected data streams. Our preliminary results show that this event detection mechanism is sensitive enough to detect the onset of rain events using the temperature modality of a wireless sensor network.
Mycotoxins in food. (1991)

The presence of mycotoxins in a wide range of foodstuffs can lead to many different toxic conditions in both man and domestic animals. The major fungi responsible for producing these toxins are species of Aspergillus, Penicillium, Fusarium and Alternaria, although other genera are involved as well, for example Claviceps, Diplodia and Arthrinium. An overview is given of the major mycotoxins responsible for illnesses following ingestion of contaminated foods, with particular emphasis on the effects produced in humans. Compounds discussed include the aflatoxins, cyclopiazonic acid, tenuazonic acid, the trichothecenes, zearalenone, wortmannin, fumonisins B1 and B2, patulin, ochratoxin A, diplodiatoxin and diplosporin.
Toll-like Receptor 4 (TLR4) Antagonist Eritoran Tetrasodium Attenuates Liver Ischemia and Reperfusion Injury through Inhibition of High-Mobility Group Box Protein B1 (HMGB1) Signaling (2014)

Toll-like receptor 4 (TLR4) is ubiquitously expressed on parenchymal and immune cells of the liver and is the most studied TLR responsible for the activation of proinflammatory signaling cascades in liver ischemia and reperfusion (I/R). Since pharmacological inhibition of TLR4 during the sterile inflammatory response of I/R has not been studied, we sought to determine whether eritoran, a TLR4 antagonist trialed in sepsis, could block hepatic TLR4-mediated inflammation and end organ damage. When C57BL/6 mice were pretreated with eritoran and subjected to warm liver I/R, there was significantly less hepatocellular injury compared to control counterparts. Additionally, we found that eritoran is protective in liver I/R through inhibition of high-mobility group box protein B1 (HMGB1)-mediated inflammatory signaling. When eritoran was administered in conjunction with recombinant HMGB1 during liver I/R, there was significantly less injury, suggesting that eritoran blocks the HMGB1-TLR4 interaction. Not only does eritoran attenuate TLR4-dependent HMGB1 release in vivo, but this TLR4 antagonist also dampened HMGB1's release from hypoxic hepatocytes in vitro and thereby weakened HMGB1's activation of innate immune cells. HMGB1 signaling through TLR4 makes an important contribution to the inflammatory response seen after liver I/R. This study demonstrates that novel blockade of HMGB1 by the TLR4 antagonist eritoran leads to the amelioration of liver injury.
Reproducibility of Maximal Versus Submaximal Efforts in an Isometric Lumbar Extension Task (1991)

The purpose of this study was to investigate the differences in test-retest reliability between maximal and submaximal efforts in an isometric lumbar extension task and to test the hypothesis that submaximal efforts would be less consistent than maximal efforts. Twenty subjects were asked to produce maximum voluntary contractions at seven different positions in a lumbar extension machine. Each subject was tested twice in a maximal-effort condition and twice in a 50% effort condition. The order of the effort conditions was counterbalanced across subjects so that half of the subjects performed the maximal-effort tests first and half performed the submaximal effort first. Results indicated high test-retest correlations at all angles in both conditions. There were no differences in test-retest reliability between effort conditions. Therapist ratings of consistency did not differ between conditions, and therapists could not discriminate between conditions on the basis of effort consistency. Because subjects could reliably reproduce a submaximal effort, it was concluded that consistency interpretations of isometric strength testing may be misleading.
DNA Strand Invasion Promoted by Escherichia coli RecT Protein (1998)

The RecT protein of Escherichia coli is a DNA-pairing protein required for the RecA-independent recombination events promoted by the RecE pathway. The RecT protein was found to bind to both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) in the absence of Mg2+. In the presence of Mg2+, RecT binding to dsDNA was inhibited drastically, whereas binding to ssDNA was inhibited only to a small extent. RecT promoted the transfer of a single-stranded oligonucleotide into a supercoiled homologous duplex to form a D (displacement)-loop. D-loop formation occurred in the absence of Mg2+ and at 1 mM Mg2+ but was inhibited by increasing concentrations of Mg2+ and did not require a high energy cofactor. Strand transfer was mediated by a RecT-ssDNA nucleoprotein complex reacting with a naked duplex DNA and was prevented by the formation of RecT-dsDNA nucleoprotein complexes. Finally, RecT mediated the formation of joint molecules between a supercoiled DNA and a linear dsDNA substrate with homologous 3'-single-stranded tails. Together these results indicate that RecT is not a helix-destabilizing protein promoting a reannealing reaction but rather is a novel type of pairing protein capable of promoting recombination by a DNA strand invasion mechanism. These results are consistent with the observation that RecE (exonuclease VIII) and RecT can promote RecA-independent double-strand break repair in E. coli.
Selected eicosanoids increase the proliferation rate of human colon carcinoma cell lines and mouse colonocytes in vivo (1995)

Eicosanoids have been implicated in colon carcinogenesis, but their role remains unclear. The levels of PGE2 are elevated in colon cancer tissues and in blood draining colon tumors. The effect of eicosanoids on the proliferation of colonic cells is unknown. We studied the effect of several prostaglandins (PGs) and leukotriene (LT)B4 on the proliferation rate of the human colon adenocarcinoma cell lines SW1116 and HT-29 and of 16,16-dimethyl PGE2 (dmPGE2) on the colon of BALB/c mice. PGs E2, F2 alpha, I2, the methyl ester of PGE2, dmPGE2, and LTB4 (10(-10), 10(-8), 10(-6) M), administered for up to 72 h, stimulated cell proliferation in SW1116 cells and all but PGF2 alpha and PGI2 stimulated proliferation in HT-29 cells. The proliferative effect was time- and concentration-dependent. However, in SW1116 cells the response to PGs was 'bell-shaped', being maximal at 10(-8) M, with the 10(-10) and 10(-6) M concentrations being less effective. In HT-29 cells, the addition of methyl groups to the PGE2 molecule increased the proliferative effect. None of these eicosanoids affected the distribution of these cells in the cell cycle or their rate of programmed cell death (apoptosis). dmPGE2 stimulated 3.6-fold the proliferation of colonocytes in normal BALB/c mice. This was determined by bivariate flow cytometric analysis of the expression of proliferating cell nuclear antigen (PCNA) in virtually pure populations of mouse colonocytes. dmPGE2 did not alter the cell cycle distribution of these cells. We conclude that several PGs as well as LTB4 stimulate the proliferation of human colon carcinoma cells in vitro, while dmPGE2 has a similar effect on mouse colonocytes in vivo. These findings raise the possibility that eicosanoids may contribute to colonic carcinogenesis by stimulating the proliferation rate of tumor cells in the colon.
Lamprey lymphocyte-like cells express homologs of genes involved in immunologically relevant activities of mammalian lymphocytes (2002)

To shed light on the origin of adaptive immunity, a cDNA library was prepared from purified lymphocyte-like cells of a jawless vertebrate, the sea lamprey ( Petromyzon marinus ). Randomly selected cDNA clones were sequenced, and their homologies to proteins in the databases were determined. Of the sequences homologous to proteins involved in immune responses, five were selected for further characterization. Their encoding genes corresponded to loci that in jawed vertebrates are essential for activities of lymphocytes. These activities include regulation of T and B cell stimulation and proliferation ( CD45 ); stabilization of molecular complexes involved in lymphocyte activation, adhesion, migration, and differentiation ( CD9 / CD81 ); adaptor functions in signaling leading to the activation of B lymphocytes ( BCAP ) and T lymphocytes (CAST); and amino acid transport associated with cell activation ( CD98 ). The presence of these genes in the lamprey genome and their expression in lymphocyte-like cells support the notion that these cells perform many of the functions of gnathostome lymphocytes. It reopens the question of the stage jawless fishes reached in the evolution of their immune system.
Crystallization and preliminary X-ray crystallographic analysis of MbtI, a protein essential for siderophore biosynthesis inMycobacterium tuberculosis (2004)

Mycobacterium tuberculosis, the causative agent of tuberculosis, depends on the secretion of salicylate-based siderophores called mycobactins for the acquisition of extracellular iron, which is essential for the growth and virulence of the bacterium. The protein MbtI is thought to be the isochorismate synthase enzyme responsible for the conversion of chorismate to isochorismate, the first step in the salicylate production required for mycobactin biosynthesis. MbtI has been overexpressed in Escherichia coli, purified and crystallized. The crystals diffract to a maximum resolution of 1.8 A. They belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.8, b = 163.4, c = 194.9 A, consistent with the presence of either two, three or four molecules in the asymmetric unit.
Tagging speech repairs (1994)

This paper describes a method of detecting speech repairs that uses a part-of-speech tagger. The tagger is given knowledge about category transitions for speech repairs, and so is able to mark a transition either as a likely repair or as fluent speech. Other contextual clues, such as editing terms, word fragments, and word matchings, are also factored in by modifying the transition probabilities.
Effect of pressure and stress on water transport in intact and fractured gabbro and granite (1980)

New laboratory data are reported on the effect of confining pressure (to 60 MPa), pore‐water pressure (to 30 MPa), and stress difference (to 0.88 of the fracture stress) on permeability of intact and fractured White Lake gneissic granite, Westerly granite, and Creighton gabbro. Permeabilities as low as 10 −24 m 2 (10 −12 darcy) have been measured using a transient technique. Fracture displacement, electrical conductance, compressional velocity, and pulse amplitude are determined simultaneously. The loads applied to the 0.15‐m‐diameter by 0.28‐m‐length test sample are controlled automatically, and most data are taken by microprocessor. Tests on the intact gneissic granite indicated permeabilities of 10 −22 to 10 −24 m 2 that appeared to be unaffected either by effective pressure or by stress. The granite yielded permeabilities of 4×10 −20 m 2 that decreased by a factor of 2 as effective pressure increased to 25 MPa and varied by a factor of 2 as stress was increased to 0.5 of the fracture stress. Permeability of the gabbro linearly decreased from 2×10 −22 to 8×10 −24 m 2 with effective pressures to 25 MPa. Loading of the gabbro up to 0.88 of the fracture stress increased permeability by a factor of 7. The introduction of a throughgoing fracture increased the apparent permeability by 10 6 to 10 9 over the intact values in both granite and gabbro. When compared to the initial value, compressional velocities increased by 5% with pressure to 30 MPa in the gneissic granite. For granite, pressurization from 2 to 25 MPa increased the velocity and pulse amplitude by 5 and 30%, respectively, and decreased the conductance by 50%. Velocity, amplitude, and conductance were weakly dependent on pressure in gabbro. The addition of stress decreased velocity and amplitude while increasing conductance markedly in both granite and gabbro. All data on both intact and fractured rock are consistent with crack closure and dilatancy with pressure and stress. Conductance and amplitude exhibit the best potential for monitoring changes in permeability and joint behavior in situ.
Spoken Language Understanding for a Nutrition Dialogue System (2017)

Food logging is recommended by dieticians for prevention and treatment of obesity, but currently available mobile applications for diet tracking are often too difficult and time-consuming for patients to use regularly. For this reason, we propose a novel approach to food journaling that uses speech and language understanding technology in order to enable efficient self-assessment of energy and nutrient consumption. This paper presents ongoing language understanding experiments conducted as part of a larger effort to create a nutrition dialogue system that automatically extracts food concepts from a user's spoken meal description. We first summarize the data collection and annotation of food descriptions performed via Amazon Mechanical Turk (AMT), for both a written corpus and spoken data from an in-domain speech recognizer. We show that the addition of word vector features improves conditional random field (CRF) performance for semantic tagging of food concepts, achieving an average F1 test score of 92.4 on written data; we also demonstrate that a convolutional neural network (CNN) with no hand-crafted features outperforms the best CRF on spoken data, achieving an F1 test score of 91.3. We illustrate two methods for associating foods with properties: segmenting meal descriptions with a CRF, and a complementary method that directly predicts associations with a feed-forward neural network. Finally, we conduct an end-to-end system evaluation through an AMT user study with worker ratings of 83% semantic tagging accuracy.
Parathyroid hormone accelerates decompensation following left ventricular hypertrophy (2010)

Parathyroid hormone (PTH) treatment was previously shown to improve cardiac function after myocardial infarction by enhancing neovascularization and cell survival. In this study, pressure overload-induced left ventricular hypertrophy (LVH) was induced in mice by transverse aortic banding (TAB) for 2 weeks. We subsequently evaluated the effects of a 2-week treatment with PTH or saline on compensated LVH. After another 4 weeks, the hearts of the mice were analyzed by echocardiography, histology, and molecular biology. Echocardiography showed that hearts of the PTH-treated mice have more severe failing phenotypes than the saline-treated mice following TAB with a greater reduction in fractional shortening and left ventricular posterior wall thickness and with a greater increase in left ventricular internal dimension. Increases in the heart weight to body weight ratio and lung weight to body weight ratio following TAB were significantly exacerbated in PTH-treated mice compared to saline-treated mice. Molecular markers for heart failure, fibrosis, and angiogenesis were also altered in accordance with more severe heart failure in the PTH-treated mice compared to the saline-treated mice following TAB. In addition, the PTH-treated hearts were manifested with increased fibrosis accompanied by an enhanced SMAD2 phosphorylation. These data suggest that the PTH treatment may accelerate the process of decompensation of LV, leading to heart failure.
Glypicans in growth control and cancer (2001)

The name glypican has been assigned to a family of heparan sulfate (HS) proteoglycans that are linked to the cell membrane by a glycosyl-phosphatidylinositol anchor. To date, six family members of this family have been identified in mammals (GPC1 to GPC6) and two in Drosophila. Glypicans are expressed predominantly during development, and they are thought to play a role in morphogenesis. As HS-carrying molecules, glypicans were initially considered potential regulators of heparin-binding growth factors. This has been recently confirmed by genetic interaction experiments showing that glypicans regulate wingless signaling in Drosophila. The involvement of glypicans in the in vivo regulation of other heparin-binding growth factors, such as fibroblast growth factors, remains to be determined. Interestingly and unexpectedly, a role for GPC3 in the regulation of insulin-like growth factors has been proposed. This hypothesis is based on the phenotype of patients with Simpson-Golabi-Behmel syndrome (SGBS), an overgrowth and dysmorphic syndrome in which the GPC3 gene is mutated. Thus, it is possible that glypicans regulate different kinds of growth factors in a tissue-specific manner. In addition to its involvement in SGBS, down-regulation of GPC3 has been recently associated with the progression of several types of malignant tumors, including mesotheliomas and ovarian cancer. A role for GPC1 in pancreatic cancer progression has also been proposed.
Validation of biomarkers to predict response to immunotherapy in cancer: Volume I — pre-analytical and analytical validation (2016)

Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers for cancer immunotherapy. To illustrate the requirements for validation, we discuss examples of biomarker assays that have shown preliminary evidence of an association with clinical benefit from immunotherapeutic interventions. The scope includes only those assays and technologies that have established a certain level of validation for clinical use (fit-for-purpose). Recommendations to meet challenges and strategies to guide the choice of analytical and clinical validation design for specific assays are also provided.
The effect of quantization in a digital signal component separator for LINC transmitters (1996)

Spectrally efficient modulation schemes have been chosen for the second generation of cellular systems in the United States and Japan, as well as for private mobile radio (PMR) systems. This paper analyzes the effect of quantization in a digital signal component separator (SCS) for linear amplification with nonlinear components (LINC) transmitters. The analysis relies on the fact that the two signal components can be obtained as the source signal plus/minus a signal in quadrature to the source signal. The equations derived are vital because they allow the designer to optimize digital signal processor (DSP) power consumption and bandwidth. The word lengths that are required for the source signal and the quadrature signal can be calculated from the amplifier gain characteristic, the probability density function for the modulation scheme, and the specified adjacent channel interference (ACI). The validity of the analysis has been verified by means of simulations.