gebhart/patrepeval huggingface dataset:
Review of Tripleplay Plus! English (1998)

TriplePlay Plus! English is a CD-ROM-based multimedia package designed for beginning to intermediate ESL learners, ages 8 to adult.The program comes with a user's guide, plug-and-play microphone, and technical manual.TriplePlay Plus! is claimed to assist learners in developing three skills: listening, speaking, and reading.Vocabulary development, and a few other areas such as verb tenses and prepositions, are also targeted through a variety of games.This multimedia language learning program can be used by learners for self-study, by teachers in classroom settings (in computer labs), and also by second language acquisition (SLA) researchers.The software, which includes automatic speech recognition and 32 separate games, covers six main topics or themes.These include food, numbers, home and office, people, activities, and places and transportation.The current version under review here expands the activities and material from previous versions.The software is also available for Spanish, French, German, English, Hebrew, Japanese, and Italian.
Metal nanogap devices fabricated by conventional photolithography and their application to deoxyribose nucleic acid analysis (2003)

A low-cost and simple fabrication technique is proposed to prepare the metal nanogap devices (MNGDs) of sub-50 nm size. Only currently available mass-production technologies such as photolithography and anodic oxidation of patterned metal films are utilized in the technique. The gap width of MNGD can be easily and accurately controlled by the applied voltage of the anodic oxidation process. For example, the gap width formed between titanium electrodes by anodic voltage 15 V is about 10 nm, and the standard deviation (σ) of the width fluctuation is about only 2 nm (20% of the fabrication size). Thus, the accuracy of the fabrication technique is on the almost same level with the electron beam (EB) lithography. Multigap MNGD containing several different gap widths were fabricated for the use of deoxyribose nucleic acid (DNA) analysis. As an application of MNGD, pure water containing DNA was dropped on MNGD, dried in air and the current–voltage characteristics of DNA were measured. From these results, it is expected that low-cost DNA analyzer can be provided by the present technique to fabricate MNGD.
Non-invasive physical treatments for chronic/recurrent headache (2004)

A few non-invasive physical treatments may be effective as prophylactic treatments for chronic/recurrent headaches. Based on trial results, these treatments appear to be associated with little risk of serious adverse effects. The clinical effectiveness and cost-effectiveness of non-invasive physical treatments require further research using scientifically rigorous methods. The heterogeneity of the studies included in this review means that the results of a few additional high-quality trials in the future could easily change the conclusions of our review.
Induction of cell surface expression of HLA antigens by human IFN-gamma encoded by recombinant vaccinia virus. (1989)

A recombinant vaccinia virus (VV) encoding human IFN-gamma (VV-huIFN-gamma) was constructed and its effects on MHC Ag expression in human and murine cells in vitro analyzed by flow cytometry. At high multiplicities of infection (5 pfu/cell) the IFN-gamma expressed by vaccinia was not able to overcome the profound decrease of MHC concentration, normally associated with VV infection, in any of the cells tested. However, at successively decreasing multiplicities of infection, a gradual increase in MHC class I concentration above control levels was observed in human 143B cells but not in murine L929 cells, thus indicating that the species specificity of IFN-gamma is preserved in VV-huIFN-gamma-infected cells. We infer from these data that the IFN-gamma secreted by infected 143B cells is able to exert an MHC upregulating effect on uninfected cells in the vicinity. Antiviral activity of the IFN-gamma expressed by the virus was also assessed. Pretreatment for 24 to 48 h of human 143B cells with IFN-gamma containing supernatants had a significant antiviral effect comparable to rhuIFN-gamma. However, when added 1 h after virus infection, antiviral activity was much less evident. Also, the IFN-gamma secreted by infected 143B cells in monolayers infected at low multiplicity did not efficiently inhibit spread of infection to other cells in the vicinity.
SGS3 and RDR6 interact and colocalize in cytoplasmic SGS3/RDR6‐bodies (2009)

Suppressor of gene silencing 3 (SGS3) is involved in RNA-dependent RNA polymerase 6 (RDR6)-dependent small-interfering RNA (siRNA) pathways in Arabidopsis. However, the roles of SGS3 in those pathways are unclear. Here, we show that SGS3 interacts and colocalizes with RDR6 in cytoplasmic granules. Interestingly, the granules containing SGS3 and RDR6 (named SGS3/RDR6-bodies) were distinct from the processing bodies where mRNAs are decayed and/or stored. Microscopic analyses and complementation experiments using SGS3-deletion mutants suggested that proper localization of SGS3 is important for its function. These results provide novel insights into RDR6-dependent siRNA formation in plants.
Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin (2013)

Lysine specific demethylase-1 (LSD1/KDM1A) in complex with its corepressor protein CoREST is a promising target for epigenetic drugs. No therapeutic that targets LSD1/CoREST, however, has been reported to date. Recently, extended molecular dynamics (MD) simulations indicated that LSD1/CoREST nanoscale clamp dynamics is regulated by substrate binding and highlighted key hinge points of this large-scale motion as well as the relevance of local residue dynamics. Prompted by the urgent need for new molecular probes and inhibitors to understand LSD1/CoREST interactions with small-molecules, peptides, protein partners, and chromatin, we undertake here a configurational ensemble approach to expand LSD1/CoREST druggability. The independent algorithms FTMap and SiteMap and our newly developed Druggable Site Visualizer (DSV) software tool were used to predict and inspect favorable binding sites. We find that the hinge points revealed by MD simulations at the SANT2/Tower interface, at the SWIRM/AOD interface, and at the AOD/Tower interface are new targets for the discovery of molecular probes to block association of LSD1/CoREST with chromatin or protein partners. A fourth region was also predicted from simulated configurational ensembles and was experimentally validated to have strong binding propensity. The observation that this prediction would be prevented when using only the X-ray structures available (including the X-ray structure bound to the same peptide) underscores the relevance of protein dynamics in protein interactions. A fifth region was highlighted corresponding to a small pocket on the AOD domain. This study sets the basis for future virtual screening campaigns targeting the five novel regions reported herein and for the design of LSD1/CoREST mutants to probe LSD1/CoREST binding with chromatin and various protein partners.
Relationship between alpha-smooth muscle actin expression and fibrotic changes in human kidney. (1997)

The alpha-smooth muscle (alpha-SM) actin isoform is expressed normally by vascular SM cells and by stromal fibroblastic cells in pathological conditions leading to fibrosis. In order to investigate the relation between kidney fibrosis and alpha-SM actin expression, we studied 51 renal biopsies from 45 patients: 30 with various forms of glomerulonephritis; 1 with acute tubular necrosis; 1 with acute interstitial nephritis, and 13 renal transplant recipients. The presence of alpha-SM actin was examined by using anti-alpha SM-1, a mouse monoclonal antibody (IgG2 alpha) specific for alpha-SM actin. alpha-SM actin scores were estimated semiquantitatively, as were glomerulosclerosis and interstitial fibrosis. In acute tubular necrosis and in well-functioning grafts, alpha-SM actin expression was limited to vascular SM cells. In glomerular diseases, alpha-SM actin expression was upregulated in mesangial area in 25 of 36 biopsies, and even more frequently in the periglomerular and peritubular interstitium (34 of 36 cases, chi 2 = 7.6, P < 0.01). Whereas glomerular alpha-SM actin expression seemed to decrease as glomerulosclerosis progressed, there was a positive correlation between interstitial alpha-SM actin scores and the degree of interstitial fibrosis. Similarly, interstitial alpha-SM actin expression was found in acutely or chronically rejected kidneys, but not in well-functioning grafts. We conclude that upregulation of alpha-SM actin in the glomerulus indicates mesangial cell activation and is not always correlated with the degree of glomerulosclerosis. In contrast, interstitial upregulation of alpha-SM actin which indicates myofibroblast activation is correlated with the degree of interstitial fibrosis.
Antibodies That Selectively Inhibit Leukocyte Function-associated Antigen 1 Binding to Intercellular Adhesion Molecule-3 Recognize a Unique Epitope within the CD11a I Domain (1996)

Several studies indicate that the I domain located in the alpha chain (CD11a) of leukocyte function-associated antigen-1 (LFA-1; CD11a/CD18) plays an essential role in ligand recognition. We recently identified three distinct epitopes (IdeA, IdeB, and IdeC) within the CD11a I domain, recognized by antibodies that block binding of LFA-1 to intercellular adhesion molecules (ICAM) 1, 2, and 3. In the present study, we used a series of human/murine CD11a I domain chimeras, to localize a fourth I domain epitope (IdeD), recognized by three independently derived anti-CD11a antibodies that selectively block the binding of LFA-1 to ICAM-3, but not to ICAM-1. The IdeD epitope depended on human CD11a residues Asp182 and Ser184 and was not present in CD11b or CD11c. Although mutation of Asp182 and Ser184 failed to abolish ICAM-3 adhesion of LFA-1 transfectants, alignment of these residues with the crystal structure of the CD11a I domain suggested that the IdeD epitope is located in close proximity to residues (Ile126 and Asn129) recently implicated in the ICAM-3 binding site. Interestingly, the IdeB and IdeC epitopes appeared to be in close proximity of a divalent cation binding pocket within the CD11a I domain that regulates both ICAM-1 and ICAM-3 adhesion. Taken together, these data indicate that distinct regions of the CD11a I domain contain epitopes for antibodies that either selectively inhibit binding of LFA-1 to ICAM-3, or interfere with both ICAM-1 and ICAM-3 binding of LFA-1.
Unbiased MMSE-Based Noise Power Estimation With Low Complexity and Low Tracking Delay (2011)

Recently, it has been proposed to estimate the noise power spectral density by means of minimum mean-square error (MMSE) optimal estimation. We show that the resulting estimator can be interpreted as a voice activity detector (VAD)-based noise power estimator, where the noise power is updated only when speech absence is signaled, compensated with a required bias compensation. We show that the bias compensation is unnecessary when we replace the VAD by a soft speech presence probability (SPP) with fixed priors. Choosing fixed priors also has the benefit of decoupling the noise power estimator from subsequent steps in a speech enhancement framework, such as the estimation of the speech power and the estimation of the clean speech. We show that the proposed speech presence probability (SPP) approach maintains the quick noise tracking performance of the bias compensated minimum mean-square error (MMSE)-based approach while exhibiting less overestimation of the spectral noise power and an even lower computational complexity.
Spin pumping and spin transfer (2017)

This chapter discusses the interaction between currents and magnetization, which can cause undesirable effects such as enhanced magnetic noise in read heads made from magnetic multilayers. While most research has been carried out on metallic structures, current-induced magnetization dynamics in semiconductors or even insulators has been pursued as well. These issues have attracted many physicists because, on top of the practical aspects, the underlying phenomena are fascinating. Berger and Slonczewski are acknowledged to have started the field in general through their introduction of the concept of current-induced magnetization dynamics by the transfer of spin. The reciprocal effect, i.e., spin pumping, was expected long ago, but it took some time before Tserkovnyak <italic>et al</italic>. developed a rigorous theory of spin pumping for magnetic multilayers, including the associated increased magnetization damping.
Kinetic modelling of lactate utilization and butyrate production by key human colonic bacterial species (2011)

Butyrate is the preferred energy source for colonocytes and has an important role in gut health; in contrast, accumulation of high concentrations of lactate is detrimental to gut health. The major butyrate-producing bacterial species in the human colon belong to the Firmicutes. Eubacterium hallii and a new species, Anaerostipes coli SS2/1, members of clostridial cluster XIVa, are able to utilize lactate and acetate via the butyryl CoA : acetate CoA transferase route, the main metabolic pathway for butyrate synthesis in the human colon. Here we provide a mathematical model to analyse the production of butyrate by lactate-utilizing bacteria from the human colon. The model is an aggregated representation of the fermentation pathway. The parameters of the model were estimated using total least squares and maximum likelihood, based on in vitro experimental data with E. hallii L2-7 and A. coli SS2/1. The findings of the mathematical model adequately match those from the bacterial batch culture experiments. Such an in silico approach should provide insight into carbohydrate fermentation and short-chain fatty acid cross-feeding by dominant species of the human colonic microbiota.
Cloning of 16S rRNA genes amplified from normal and disturbed vaginal microflora suggests a strong association between Atopobium vaginae, Gardnerella vaginalis and bacterial vaginosis (2004)

Although historically the literature regarding bacterial vaginosis has largely focused on G. vaginalis in particular, several findings of this study--like the abundance of A. vaginae in disturbed vaginal microflora and the presence of several novel species--indicate that much is to be learned about the composition of the vaginal microflora and its relation to the etiology of BV.
Comparative Genomics of Cultured and Uncultured Strains Suggests Genes Essential for Free-Living Growth of Liberibacter (2014)

The full genomes of two uncultured plant pathogenic Liberibacter, Ca. Liberibacter asiaticus and Ca. Liberibacter solanacearum, are publicly available. Recently, the larger genome of a closely related cultured strain, Liberibacter crescens BT-1, was described. To gain insights into our current inability to culture most Liberibacter, a comparative genomics analysis was done based on the RAST, KEGG, and manual annotations of these three organisms. In addition, pathogenicity genes were examined in all three bacteria. Key deficiencies were identified in Ca. L. asiaticus and Ca. L. solanacearum that might suggest why these organisms have not yet been cultured. Over 100 genes involved in amino acid and vitamin synthesis were annotated exclusively in L. crescens BT-1. However, none of these deficiencies are limiting in the rich media used to date. Other genes exclusive to L. crescens BT-1 include those involved in cell division, the stringent response regulatory pathway, and multiple two component regulatory systems. These results indicate that L. crescens is capable of growth under a much wider range of conditions than the uncultured Liberibacter strains. No outstanding differences were noted in pathogenicity-associated systems, suggesting that L. crescens BT-1 may be a plant pathogen on an as yet unidentified host.
Identification of two HSP70-related Xenopus oocyte proteins that are capable of recycling across the nuclear envelope. (1990)

Two 70-kD polypeptides, B3 and B4, are present in equivalent concentrations in the nucleus and cytoplasm of Xenopus oocytes. The objectives of this study were to determine if they (a) are members of the 70-kD family of heat shock proteins, and (b) recycle between the nuclear and cytoplasmic compartments. Evidence based on high-affinity binding to ATP, cross-reactivity of B3/B4-specific antibodies with rat hsc70, and a comparison of cyanogen bromide cleavage peptide maps with hsc70, verified that B3 and B4 are members of the 70-kD family of heat-shock proteins. Nuclear uptake studies were performed by microinjecting 125I-labeled B3/B4, rat hsc70, and BSA into the cytoplasm of oocytes, and examining their subsequent intracellular distributions. By 6 h postinjection, the nuclear concentration of B3/B4 and hsc70 were approximately 24-fold greater than BSA controls. It was also found that B3/B4-coated gold particles as large as 120A in diameter were able to enter the nucleus by passing through the pores. Nuclear efflux was analyzed by microinjecting the iodinated proteins directly into the oocyte nuclei. 2 h after nuclear injection, at least 46% of the B3/B4 and 60% of the hsc70 were found in the cytoplasmic fractions, compared with less than 10% for the BSA controls. Cell fusion experiments, in which labeled, anucleate oocyte vegetal hemispheres were fused, under oil, with nucleate unlabeled animal hemispheres, demonstrated that cytoplasmic B3 and B4 could enter the nucleus after equilibration was reached, arguing against the existence of separate nuclear and cytoplasmic populations. Collectively, these results show that B3, B4, and rat hsc70 are transported across the nuclear envelope and recycle between the nucleus and cytoplasm.
Gel Lubrication of the Tracheal Tube Cuff Reduces Pulmonary Aspiration (2001)

Cuff lubrication with a water-soluble gel reduces pulmonary aspiration in anesthetized patients. In the critically ill patient with a tracheostomy the protective effect is lost after 24-120 h.
Post-transplant obstructive lung disease ("bronchiolitis obliterans"): a clinical comparative study of bone marrow and lung transplant patients (1995)

Patients at a single pulmonary centre who developed obstructive lung disease after bone marrow transplantation (BMT) and lung transplantation (LT) were studied, in order to compare the clinical expression of post-transplant obstructive lung disease (PTOLD) (bronchiolitis obliterans) in these two conditions, which have so far been studied separately. Nine out of 179 patients surviving more than 100 days after BMT (5%) and 9 out of 44 patients surviving more than 100 days after LT (20%) developed post-transplant obstructive lung disease. This was defined by an irreversible airflow obstruction, as characterized by a forced expiratory volume in one second divided by forced vital capacity (FEV1/FVC) of less than 70%, and a FEV1 of less than 70% of predicted value. The mean interval between transplantation and the diagnosis of post-transplant obstructive lung disease was 262 days and 217 days for BMT and LT patients, respectively. In all cases, pulmonary symptoms consisted of dyspnoea and progressively productive cough. Bronchial dilatation on high-resolution computed tomography scans was the main imaging feature present in both groups of patients at the onset of post-transplant obstructive lung disease. The mean FEV1/FVC ratio was 51 and 54% for BMT and LT patients, respectively. All BMT and LT patients had normal transfer coefficient. Clinical chronic graft-versus-host disease was present in all BMT patients before or concurrent with the onset of post-transplant obstructive lung disease, and all LT patients had presented at least one episode of acute lung rejection.(ABSTRACT TRUNCATED AT 250 WORDS)
Incidence and clinical consequences of surface and polymerase gene mutations in liver transplant recipients on hepatitis B immunoglobulin (1998)

Mutations in the "a" determinant of the surface gene have been associated with failure of hepatitis B immunoglobulin (HBIg) prophylaxis. We compared sequences from the surface and polymerase regions of hepatitis B virus (HBV) from 4 patients who failed high-dose HBIg therapy with two control groups: HBIg-treated patients who remained hepatitis B surface antigen (HBsAg)-negative (n = 4) and HBV-infected transplant recipients who never received HBIg (n = 4). Mutations within the surface and overlapping polymerase region were more common in patients failing HBIg than controls (P = .03), and mutations in the region of the "a" determinant were present only in patients failing HBIg. To examine the relationship between HBIg failure and duration of therapy, five additional treatment failures from a second transplantation center were sequenced (total with HBIg failure = 9). Mutations in the "a" determinant developed in 1 of 3 patients receiving HBIg for less than 6 months compared with 5 of 6 patients failing HBIg after 6 months of therapy (P = .23). The most frequently identified amino acid substitution was glycine to arginine at position 145 (present in 4 of 6 patients who failed HBIg after at least 6 months of treatment). A unique mutation within the YMDD motif (methionine to leucine) was present in 1 patient who failed HBIg treatment and who received a short course of ganciclovir. We conclude that the emergence of mutations in the "a" determinant accounts for some, but not all, treatment failures in patients receiving HBIg prophylaxis. Mutations in other regions of the S gene were more common in patients failing HBIg than controls, suggesting that domains other than the "a" determinant may be important.
Nanoenabled microelectromechanical sensor for volatile organic chemical detection (2009)

A nanoenabled gravimetric chemical sensor prototype based on the large scale integration of single-stranded DNA (ss-DNA) decorated single-walled carbon nanotubes (SWNTs) as nanofunctionalization layer for aluminum nitride contour-mode resonant microelectromechanical (MEM) gravimetric sensors has been demonstrated. The capability of two distinct single strands of DNA bound to SWNTs to enhance differently the adsorption of volatile organic compounds such as dinitroluene (simulant for explosive vapor) and dymethyl-methylphosphonate (simulant for nerve agent sarin) has been verified experimentally. Different levels of sensitivity (17.3 and 28 KHz μm2/fg) due to separate frequencies of operation (287 and 450 MHz) on the same die have also been shown to prove the large dynamic range of sensitivity attainable with the sensor. The adsorption process in the ss-DNA decorated SWNTs does not occur in the bulk of the material, but solely involves the surface, which permits to achieve 50% recovery in less than 29 s.