gebhart/patrepeval huggingface dataset:
Stability of baclofen, captopril, diltiazem hydrochloride, dipyridamole, and flecainide acetate in extemporaneously compounded oral liquids (1996)

The stability of drugs commonly prescribed for use in oral liquid dosage forms but not commercially available as such was studied. Baclofen 10 mg/mL, captopril 0.75 mg/mL, diltiazem hydrochloride 12 mg/mL, dipyridamole 10 mg/mL, and flecainide acetate 20 mg/mL were prepared in a 1:1 mixture of Ora-Sweet and Ora-Plus (Paddock Laboratories), a 1:1 mixture of Ora-Sweet SF and Ora-Plus (Paddock Laboratories), and cherry syrup and placed in 120-mL amber, clear polyethylene terephthalate bottles. The source of all the drugs was tablets. Six bottles were prepared per liquid; three were stored at 5 degrees C and three at 25 degrees C, all in the dark. A sample was removed from each bottle immediately after preparation and at various intervals up to 60 days and analyzed for drug concentration by stability-indicating high-performance liquid chromatography. A mean of at least 92% of the initial drug concentration was retained for up to 60 days in the baclofen, diltiazem hydrochloride, dipyridamole, and flecainide acetate liquids at both 5 and 25 degrees C. There were no substantial changes in the appearance or odor of any of the liquids or in the pH. Baclofen 10 mg/mL, diltiazem hydrochloride 12 mg/mL, dipyridamole 10 mg/mL, and flecainide acetate 20 mg/mL were stable for up to 60 days at 5 and 25 degrees C in three extemporaneously compounded oral liquids.
Defective Control of Latent Epstein-Barr Virus Infection in Systemic Lupus Erythematosus (2004)

EBV infection is more common in patients with systemic lupus erythematosus (SLE) than in control subjects, suggesting that this virus plays an etiologic role in disease and/or that patients with lupus have impaired EBV-specific immune responses. In the current report we assessed immune responsiveness to EBV in patients with SLE and healthy controls, determining virus-specific T cell responses and EBV viral loads using whole blood recall assays, HLA-A2 tetramers, and real-time quantitative PCR. Patients with SLE had an approximately 40-fold increase in EBV viral loads compared with controls, a finding not explained by disease activity or immunosuppressive medications. The frequency of EBV-specific CD69+ CD4+ T cells producing IFN-gamma was higher in patients with SLE than in controls. By contrast, the frequency of EBV-specific CD69+ CD8+ T cells producing IFN-gamma in patients with SLE appeared lower than that in healthy controls, although this difference was not statistically significant. These findings suggest a role for CD4+ T cells in controlling, and a possible defect in CD8+ T cells in regulating, increased viral loads in lupus. These ideas were supported by correlations between viral loads and EBV-specific T cell responses in lupus patients. EBV viral loads were inversely correlated with the frequency of EBV-specific CD69+ CD4+ T cells producing IFN-gamma and were positively correlated with the frequencies of CD69+ CD8+ T cells producing IFN-gamma and with EBV-specific, HLA-A2 tetramer-positive CD8+ T cells. These results demonstrate that patients with SLE have defective control of latent EBV infection that probably stems from altered T cell responses against EBV.
Intrapatient Variations in Type 1 Diabetes-specific iPS Cell Differentiation Into Insulin-producing Cells (2012)

Nuclear reprogramming of adult somatic tissue enables embryo-independent generation of autologous, patient-specific induced pluripotent stem (iPS) cells. Exploiting this emergent regenerative platform for individualized medicine applications requires the establishment of bioequivalence criteria across derived pluripotent lines and lineage-specified derivatives. Here, from individual patients with type 1 diabetes (T1D) multiple human iPS clones were produced and prospectively screened using a battery of developmental markers to assess respective differentiation propensity and proficiency in yielding functional insulin (INS)-producing progeny. Global gene expression profiles, pluripotency expression patterns, and the capacity to differentiate into SOX17- and FOXA2-positive definitive endoderm (DE)-like cells were comparable among individual iPS clones. However, notable intrapatient variation was evident upon further guided differentiation into HNF4α- and HNF1β-expressing primitive gut tube, and INS- and glucagon (GCG)-expressing islet-like cells. Differential dynamics of pluripotency-associated genes and pancreatic lineage-specifying genes underlined clonal variance. Successful generation of glucose-responsive INS-producing cells required silencing of stemness programs as well as the induction of stage-specific pancreatic transcription factors. Thus, comprehensive fingerprinting of individual clones is mandatory to secure homogenous pools amenable for diagnostic and therapeutic applications of iPS cells from patients with T1D.
Animal spongiform encephalopathies ‐ an update part 1. Scrapie and lesser known animal spongiform encephalopathies (1994)

The present article (part I) reviews recent developments in animal spongiform encephalopathies (SEs), with the exception of bovine spongiform encephalopathy (BSE), which is dealt with in part II. The article focuses on scrapie and describes epidemiological aspects and the prospects for a preclinical diagnosis. Up to now, confirmatory diagnosis of scrapie depended on histological examination of the brain, collected during post-mortem examination from sheep with clinical signs of the disease. An altered protein, PrPSc, can be detected in the brain of diseased animals. The demonstration of the same protein in the spleen and in peripheral lymph nodes of infected animals seems to offer interesting possibilities of arriving at a method for a preclinical diagnosis, and thus a diagnosis in the live animal. Progress has also been made in our understanding of the relationship between the genetic constitution and susceptibility of the host. Susceptibility is expressed as the survival time of sheep inoculated with scrapie. This was thought to be determined by a single genetic locus designated the Sip gene (scrapie incubation period gene). Putative markers for the two alleles of the Sip gene, sA and pA, have been discovered, consisting of restriction fragment length polymorphisms (RFLPs). In field tests, however, the link between these markers and the length of incubation time was far from consistent. These RFLPs were found to be situated outside the prion-protein-coding region of the ovine gene. In later studies, RFLPs were detected inside this region. These markers appear to be more informative, i.e. they correspond with a difference in the length of the scrapie incubation period.(ABSTRACT TRUNCATED AT 250 WORDS)
The human blastocyst: cell number, death and allocation during late preimplantation development in vitro (1989)

The development of 181 surplus human embryos, including both normally and abnormally fertilized, was observed from day 2 to day 5, 6 or 7 in vitro. 63/149 (42%) normally fertilized embryos reached the blastocyst stage on day 5 or 6. Total, trophectoderm (TE) and inner cell mass (ICM) cell numbers were analyzed by differential labelling of the nuclei with polynucleotide-specific fluorochromes. The TE nuclei were labelled with one fluorochrome during immunosurgical lysis, before fixing the embryo and labelling both sets of nuclei with a second fluorochrome (Handyside and Hunter, 1984, 1986). Newly expanded normally fertilized blastocysts on day 5 had a total of 58.3 +/- 8.1 cells, which increased to 84.4 +/- 5.7 and 125.5 +/- 19 on days 6 and 7, respectively. The numbers of TE cells were similar on days 5 and 6 (37.9 +/- 6.0 and 40.3 +/- 5.0, respectively) and then doubled on day 7 (80.6 +/- 15.2). In contrast, ICM cell numbers doubled between days 5 and 6 (20.4 +/- 4.0 and 41.9 +/- 5.0, respectively) and remained virtually unchanged on day 7 (45.6 +/- 10.2). There was widespread cell death in both the TE and ICM as evidenced by fragmenting nuclei, which increased substantially by day 7. These results are compared with the numbers of cells in morphologically abnormal blastocysts and blastocysts derived from abnormally fertilized embryos. The nuclei of arrested embryos were also examined. The number of TE and ICM cells allocated in normally fertilized blastocysts appears to be similar to the numbers allocated in the mouse. Unlike the mouse, however, the proportion of ICM cells remains higher, despite cell death in both lineages.
IRT-1, a Novel Interferon-γ-responsive Transcript Encoding a Growth-suppressing Basic Leucine Zipper Protein (1998)

Interferon-gamma (IFN-gamma) inhibits proliferation of vascular smooth muscle cells (VSMCs) in culture and reduces arterial restenosis post-balloon angioplasty. The identification and characterization of IFN-gamma-specific transcripts in VSMCs are an important approach to discern the molecular mechanisms underlying vascular proliferative disease. In this report, we describe IRT-1, a novel mRNA transcript constitutively expressed in a number of human tissues, but expressed in human VSMCs only when they are stimulated with IFN-gamma. This mRNA expression is induced >200-fold 72 h after IFN-gamma treatment. IRT-1 mRNA is also acutely expressed in rat carotid arteries that are injured by balloon angioplasty. The IRT-1 cDNA transcript encodes a basic protein that contains a leucine zipper motif, a core nuclear localization sequence, and a single strongly hydrophobic region. Constitutive IRT-1 mRNA expression in human peripheral blood lymphocytes is reduced when these cells are stimulated to proliferate. Overexpression of IRT-1 protein in VSMCs alters their morphology and dramatically reduces their proliferative capacity. This study suggests that IRT-1 is an IFN-gamma-inducible factor that may regulate the progression of vascular proliferative diseases.
Inaudible Voice Commands (2017)

Voice assistants like Siri enable us to control IoT devices conveniently with voice commands, however, they also provide new attack opportunities for adversaries. Previous papers attack voice assistants with obfuscated voice commands by leveraging the gap between speech recognition system and human voice perception. The limitation is that these obfuscated commands are audible and thus conspicuous to device owners. In this paper, we propose a novel mechanism to directly attack the microphone used for sensing voice data with inaudible voice commands. We show that the adversary can exploit the microphone's non-linearity and play well-designed inaudible ultrasounds to cause the microphone to record normal voice commands, and thus control the victim device inconspicuously. We demonstrate via end-to-end real-world experiments that our inaudible voice commands can attack an Android phone and an Amazon Echo device with high success rates at a range of 2-3 meters.
Midline signaling in the primordium of the zebrafish anterior central nervous system. (1994)

In all vertebrates the brain develops from the enlarged anterior part of the neural plate. However, in the zebrafish mutant cyclops, the girth of the central nervous system (CNS) is nearly uniform along its length. Changes in expression patterns of homeobox genes and neuronal markers reveal a massive deletion of the ventral forebrain, particularly the diencephalon, as well as its precursor region in the neural plate. The deletion is due to a nonautonomous action of the mutation: very few wild-type cells transplanted to the midline of a mutant embryo can rescue the forebrain phenotype, including cyclopia. Establishment of forebrain ventral positional coordinates may thus require inductive signaling by forebrain midline cells whose specification depends upon the cyclops gene product.
Groundwater Level Monitoring for Hydraulic Characterization of an Unconfined Aquifer by Common Mid-point Measurements using GPR (2014)

Abstract Because of its limited bandwidth, ground penetrating radar (GPR) signal has an oscillating character that degrades the ability to distinguish reflection events and introduces an error in the velocity analysis. In this paper, we use the analytic signal to calculate the envelope velocity spectrum, which is void of the oscillating nature of a GPR wavelet. A comparison study on a synthetic common mid-point (CMP) gather demonstrates that the envelope velocity spectrum gives a more robust velocity estimation. We applied this technique to explore the potential of GPR for monitoring the pumping-induced groundwater level change, then estimating the hydraulic properties of an aquifer in Ulaanbaatar, the capital of Mongolia. A field survey was conducted along three different directions when a production well was under pumping and static conditions. In addition, a simple velocity picking scheme was suggested based on the maximum coherency curve. From the velocity picks, the vertical profiles of interval electromagnetic velocity and water content were estimated. The groundwater table was easily identified in these profiles. The groundwater level changes under the CMP sounding locations along the northeast and north survey lines were estimated to be 27 and 23 cm, respectively, whereas it failed to detect the groundwater level change on the northwest survey line because of the effect of strong scatterers near the groundwater table. The estimated groundwater level change was input into the unconfined aquifer model for estimating the hydraulic conductivity, which yields comparable results with a previous study. We conclude that the hydraulic parameter estimation using GPR is much easier and effective than the conventional hydraulic test methods.
Effect of Nitrogen Application Timing on Corn Production Using Subsurface Drip Irrigation (2009)

The use of subsurface drip irrigation (SDI) in row-crop agriculture is increasing because of potential increases in water and nutrient use efficiency. Research-based information is needed to manage N applications through SDI systems in field corn (Zea mays L.) production. This study was conducted to assess the effect of different in-season SDI system N application timings on corn production and residual soil NO3-N at the University of Nebraska-Lincoln West Central Research and Extension Center in North Platte, Neb, on a Cozad silt loam (fine-silty, mixed, mesic Fluventic Haplustoll). We evaluated the effect of three N application timing methods (varying percentages of the total N rate [48% of total N] applied at the V10, VT, and R3 growth stages, in addition to uniform N applications [52% of total N] over all treatments at preplant, planting, and V14 growth stage) at two N application rates (University of Nebraska-Lincoln [UNL] recommended rate and the UNL rate minus 20%) on corn grain and biomass yield and end-of-study distribution of residual soil NO3-N. In 2006, there were no significant differences in corn grain yields between the two N application rates. In 2007, the grain yield under the UNL recommended N rate was significantly higher (190 kg ha−1) than the UNL-minus-20% N rate. The average grain yield for this study was close to the predicted yields (based on average 5-year historic yields + a 5% yield increase), indicating that corn production under SDI is satisfactory. In 2006 and 2007, grain yield and biomass production for the N application timing treatments were not significantly different (P > 0.05). The application of 13% of the total N at as late as R3 did not result in decreased yields. The lack of response to different N application timing treatments indicates that there is flexibility in N application timing for corn production under SDI. The distribution of NO3-N in the 0- to 0.9-m and 0.9- to 1.8-m soil profiles was not significantly different among all the treatments.
The effect of the source pressure on the abundance of ions of noncovalent protein assemblies in an electrospray ionization orthogonal time‐of‐flight instrument (2001)

The effect of elevating the pressure in the interface region of an electrospray ionization orthogonal time-of-flight mass spectrometer on the ion intensity of different noncovalent protein assemblies has been investigated. Elevating the pressure in the interface region generally led to an enhanced detection of high m/z ions. The optimum pressure was found to be dependent on the m/z value of the ions. This pressure effect should be carefully addressed when relating ion abundance in the mass spectra to solution phase abundance of noncovalent protein assemblies.
Stable glow plasma at atmospheric pressure (1988)

A stable glow plasma at atmospheric pressure has been achieved for plasma treatment under selected conditions, for example the structure of electrodes, the kind of dilute gas, and the frequency of power. The surface fluorination of PET film and carbon thin-film deposition by such a plasma is described here. The surface energy can be controlled by plasma treatment of various concentrations (O2/CF4/He) in the same way as the lower pressure method that has been reported by Kogoma and co-workers (1987). Active species in plasma are identified by emission spectroscopy.
Chronic Lymphocytic Leukemia: Treating an Incurable Disease (2013)

Thomas J Kipps speaks to Sophie Breeze, Assistant Commissioning Editor: Thomas Kipps, MD, PhD, is Professor of Medicine, Evelyn and Edwin Tasch Chair in Cancer Research, and Deputy Director of Research Operations at the UC San Diego Moores Cancer Center. Dr Kipps has a national and international reputation for his work in cancer research, immunology and gene therapy. As Deputy Director of Research Operations, Dr Kipps is working to further integrate basic and translational research investigators at the Moores Cancer Center with clinical investigators, epidemiologists and physicians offering state-of-the art therapies for patients with various forms of cancer. A major focus of his laboratory group is the immunobiology and genetics of human B-cell, with emphasis on chronic lymphocytic leukemia (CLL). Discovery of features that distinguish CLL from their normal cell counterparts has helped identify new targets for therapy and/or define surrogate markers associated with more rapid rates of cancer progression or resistance to standard therapy. These studies are integrated with a clinical investigative program that attracts patients seeking improved modalities of treatment for CLL. To further these efforts on a national scale, Dr Kipps has organized and leads the CLL Research Consortium that is comprised of leading CLL investigators at major cancer centers across the country and abroad.
An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function (2017)

Stress granules (SG) are membrane-less compartments involved in regulating mRNAs during stress. Aberrant forms of SGs have been implicated in age-related diseases, such as amyotrophic lateral sclerosis (ALS), but the molecular events triggering their formation are still unknown. Here, we find that misfolded proteins, such as ALS-linked variants of SOD1, specifically accumulate and aggregate within SGs in human cells. This decreases the dynamics of SGs, changes SG composition, and triggers an aberrant liquid-to-solid transition of <i>in vitro</i> reconstituted compartments. We show that chaperone recruitment prevents the formation of aberrant SGs and promotes SG disassembly when the stress subsides. Moreover, we identify a backup system for SG clearance, which involves transport of aberrant SGs to the aggresome and their degradation by autophagy. Thus, cells employ a system of SG quality control to prevent accumulation of misfolded proteins and maintain the dynamic state of SGs, which may have relevance for ALS and related diseases.
Nucleotide sequence and protein overproduction of bacteriophage T4 thioredoxin (1986)

The bacteriophage T4 thioredoxin gene was cloned and physically mapped to 47.6 kilobases from the reference BamHI site. The DNA sequence is consistent with that reported from earlier protein sequence studies. The gene was subcloned into a lambda pL overexpression vector which allowed for the isolation of approximately 5 mg/liter.
BRAF Inhibition Is Associated with Enhanced Melanoma Antigen Expression and a More Favorable Tumor Microenvironment in Patients with Metastatic Melanoma (2013)

Together, these data suggest that treatment with BRAF inhibition enhances melanoma antigen expression and facilitates T-cell cytotoxicity and a more favorable tumor microenvironment, providing support for potential synergy of BRAF-targeted therapy and immunotherapy. Interestingly, markers of T-cell exhaustion and the immunosuppressive ligand PDL1 are also increased with BRAF inhibition, further implying that immune checkpoint blockade may be critical in augmenting responses to BRAF-targeted therapy in patients with melanoma.
A stable, radioactive substrate emulsion for assay of lipoprotein lipase (1976)

A method is described for the assay of lipoprotein lipase, using a stable, radioactive substrate emulsion. Fatty acid-labeled trioleoylglycerol was emulsified by homogenization in glycerol with lecithin as detergent. This anhydrous emulsion was stable for at least six weeks. Substrate solutions for enzyme assay were prepared by diluting the emulsion with buffer containing serum and albumin. The fatty acid produced on hydrolysis was isolated in a one-step liquid-liquid partition system. Incubations with extracts of acetone powders from adipose tissue displayed characteristics of lipoprotein lipase activity, i.e., serum dependence and inhibition by NaCl and protamine. The method is rapid (less than 1 hour), sensitive and reproducible, and suitable for routine use.
Human Biliverdin Reductase Suppresses Goodpasture Antigen-binding Protein (GPBP) Kinase Activity (2010)

The Ser/Thr/Tyr kinase activity of human biliverdin reductase (hBVR) and the expression of Goodpasture antigen-binding protein (GPBP), a nonconventional Ser/Thr kinase for the type IV collagen of basement membrane, are regulated by tumor necrosis factor (TNF-alpha). The pro-inflammatory cytokine stimulates kinase activity of hBVR and activates NF-kappaB, a transcriptional regulator of GPBP mRNA. Increased GPBP activity is associated with several autoimmune conditions, including Goodpasture syndrome. Here we show that in HEK293A cells hBVR binds to GPBP and down-regulates its TNF-alpha-stimulated kinase activity; this was not due to a decrease in GPBP expression. Findings with small interfering RNA to hBVR and to the p65 regulatory subunit of NF-kappaB show the hBVR role in the initial stimulation of GPBP expression by TNF-alpha-activated NF-kappaB; hBVR was not a factor in mediating GPBP mRNA stability. The interacting domain was mapped to the (281)CX(10)C motif in the C-terminal 24 residues of hBVR. A 7-residue peptide, KKRILHC(281), corresponding to the core of the consensus D(delta)-Box motif in the interacting domain, was as effective as the intact 296-residue hBVR polypeptide in inhibiting GPBP kinase activity. GPBP neither regulated hBVR expression nor TNF-alpha dependent NF-kappaB expression. Collectively, our data reveal that hBVR is a regulator of the TNF-alpha-GPBP-collagen type IV signaling cascade and uncover a novel biological interaction that may be of relevance in autoimmune pathogenesis.