gebhart/patrepeval huggingface dataset:
The Antidepressant Duloxetine Inhibits Platelet Function and Protects against Thrombosis (2021)

Cardiovascular disease (CVD) is the leading cause of death. Patients with major depressive disorder (MDD) are at higher risk of developing CVD. It has been shown that serotonin plays a key role in the biochemical mechanisms of MDD as well in primary hemostasis mediated by potentiation platelet activity. Consequently, drugs targeting serotonin reuptake such as the FDA‐approved duloxetine are commonly prescribed for MDD. Since platelets also express the serotonin transporter (SERT) and serotonin is known to enhance platelet aggregation, this drug can potentially be repurposed as an antiplatelet medication and could be useful in MDD patients who have a higher risk of developing CVD. Based on these considerations, we investigated the antiplatelet activity of duloxetine by employing a host of in vitro and in vivo platelet assays using human blood and mouse model. Our results show that duloxetine has the capacity to dose‐dependently inhibit agonist‐induced platelet aggregation in vitro . Furthermore, agonist induced dense and α‐ granule secretion, αIIbβ3 integrin activation, phosphatidylserine expression, and clot retraction were inhibited in duloxetine treated platelets compared to those treated with vehicle control. Moreover, in the carotid artery injury thrombosis model, duloxetine‐treated mice had a significantly prolonged occlusion time in comparison with those treated with vehicle control. Collectively, our data indicate that the duloxetine exerts antiplatelet effects and protects against thrombosis. Consequently, duloxetine can serve as a potential antiplatelet drug in MDD patients who have a higher risk of developing CVD.
Scalable and Rechargeable Antimicrobial Coating for Food Safety Applications (2018)

Environmental surfaces are common avenues for microbial contamination and transmission in food-processing establishments. We recently synthesized a polymer that combines both N-halamine and dopamine functional groups to form a novel antimicrobial coating material. A series of chemical (titration) and biological (“sandwich” and anti-inhabitation) tests were designed to prove the stability and functionality of as-developed coating material. Halamine–dopamine polymer-coated stainless-steel surface inactivated 6 log10 CFU of both Staphylococcus aureus and Escherichia coli O157:H7 under experimental detection limit within 10 min of contact time. After three “discharge–recharge” cycles, the surface maintained the same antimicrobial effectiveness; 60% of the surface chlorine remained after 10 “discharge–recharge” cycles. In addition, the coating thickness and chlorine content could be further tuned through adjusting the formulation of the coating. We also demonstrated that this coating material could be easily scaled up to apply on real food equipment parts through a spray-coating method. Thus our polymer material has great potential to produce a high-performance, low-cost, and easy-to-apply coating on food-associated environmental surfaces for food safety preventive-control applications.
A Novel Long-Term Graves’ Disease Animal Model Confirmed by Functional Thyrotropin Receptor Antibodies (2020)

TBAb/TSAb were highly prevalent in Ad-TSHR-immunized mice, thus confirming the successful establishment of a novel, long-term murine model for GD. All TBAb- and TSAb-positive Ad-TSHR-immunized mice were TBII-positive. Thus, the binding immunoassay did not differentiate between TSHR-Ab functionality.
Use of the Syrian hamster embryo cell transformation assay for carcinogenicity prediction of chemicals currently being tested by the National Toxicology Program in rodent bioassays. (1996)

The Syrian hamster embryo (SHE) cell transformation assay was used to predict the carcinogenicity of 26 chemicals currently being tested in the rodent bioassay by the National Toxicology Program as part of its program titled "Strategies for Predicting Chemical Carcinogenesis in Rodents." Of these 26 chemicals, 17 were found to be positive in the SHE cell transformation assay while 9 were negative. Carcinogenicity predictions were made for these chemicals, based upon the SHE cell transformation assay results. Our predictions will be compared with the rodent bioassay results as they become available.
Photon pharmacology of an iron‐sulphur cluster nitrosyl compound acting on smooth muscle (1994)

1. The mechanisms of action on smooth muscle of the iron-sulphur cluster nitrosyl compound, heptanitrosyl-tri-mu 3-thioxotetraferrate (1-), (RBS), a photosensitive nitric oxide donor, have been investigated in the guinea-pig taenia caeci (coli) in vitro. 2. After exposure to RBS (50 microM) for 30 min, and subsequent washout, a sustained contraction was recorded in the absence of light to either the agonist carbachol (50 microM) or a depolarizing concentration of KCl (23.5 mM). Photon irradiation (> 400 nm) caused a prompt relaxation of precontracted RBS-treated muscle, the magnitude of which depended upon the intensity (1.1 x 10(3) to 1.1 x 10(5) lux), duration (30 s to 20 min) and wavelength (400 to 800 nm), of the incident illumination. 3. Repeated periods of illumination at 1.1 x 10(4) lux produced a reversible relaxation of both carbachol and KCl-evoked tone in muscle pretreated with RBS (50 microM). These photorelaxations were reproducible at 10 min intervals for several hours with a maximal relaxation amounting to 80 to 90% that of the tone produced by carbachol (50 microM). 4. The nitric oxide synthase inhibitor, NG-nitro-L-arginine (60 microM), caused no inhibition of the photon-induced relaxation of RBS-treated muscle. In contrast, N-methylhydroxylamine (2 mM), L-cysteine (10 mM), DL-dithiothreitol (2 mM), methylene blue (30 microM), and haemoglobin (20 microM), all reversibly but significantly inhibited (P < 0.001) the photorelaxation response. However, neither the aminothiol N-acetyl-L-cysteine (10 mM) nor the tripeptide glutathione (10 mM) blocked the RBS-induced photorelaxation. 5 The photolytic cleavage of RBS depended on the intensity and duration of illumination; it was accompanied by a corresponding decrease in absorbance and by the liberation of NO as measured by the Griess diazo reaction with sulphanilic acid. L-Cysteine (10 mM) prevented the decrease in absorbance and the photolytic liberation of NO.6 It is concluded that (i) sequestered or bound RBS, when photon-activated, liberates NO by a process which can be controlled by the wavelength, intensity and duration of the incident light, (ii) the photon-released NO rapidly relaxes the smooth muscle cells of the taenia coli primarily via cyclic GMP-dependent pathways which can be blocked by use of appropriate inhibitors, and (iii) the RBS-induced photorelaxation effect does not involve the activation of NO synthase. RBS is therefore a valuable photosensitive NO donor for establishing the functional and pharmacological significance of NO.
The GOMS SIG (1999)

GOMS is many things to many people. It is the only validated analytic usability evaluation method (UEM) in the field of human-computer interaction. It is being used by practitioners at some of the world's largest and some of the smallest software companies. It is a research agenda that is being pursued at universities the world over. It is a task analysis technique with roots in both cognitive psychology and artificial intelligence. It is a flexible tool that can be used with protocol analysis. It is a technique that makes detailed profiling possible. It is an important adjunct to usability testing. It is something that can be done at the early stages of the design process. It is a way of intelligently playing what if games with interface possibilities. It is all of these things and more.
Local B1+ shimming for prostate imaging with transceiver arrays at 7T based on subject‐dependent transmit phase measurements (2008)

High-quality prostate images were obtained with transceiver arrays at 7T after performing subject-dependent local transmit B(1) (B(1) (+)) shimming to minimize B(1) (+) losses resulting from destructive interferences. B(1) (+) shimming was performed by altering the input phase of individual RF channels based on relative B(1) (+) phase maps rapidly obtained in vivo for each channel of an eight-element stripline coil. The relative transmit phases needed to maximize B(1) (+) coherence within a limited region around the prostate greatly differed from those dictated by coil geometry and were highly subject-dependent. A set of transmit phases determined by B(1) (+) shimming provided a gain in transmit efficiency of 4.2 +/- 2.7 in the prostate when compared to the standard transmit phases determined by coil geometry. This increased efficiency resulted in large reductions in required RF power for a given flip angle in the prostate which, when accounted for in modeling studies, resulted in significant reductions of local specific absorption rates. Additionally, B(1) (+) shimming decreased B(1) (+) nonuniformity within the prostate from (24 +/- 9%) to (5 +/- 4%). This study demonstrates the tremendous impact of fast local B(1) (+) phase shimming on ultrahigh magnetic field body imaging.
Comparison of the role of alcohol consumption and qualitative abdominal fat on NAFLD and MAFLD in males and females (2022)

The clinical difference between nonalcoholic fatty liver disease (NAFLD) and metabolic-associated fatty liver disease (MAFLD) between the two sexes is unclear. This study aimed to determine the influences of alcohol consumption and qualitative abdominal fat between male and female patients with NAFLD and MAFLD. This cross-sectional study examined 11,766 participants who underwent health check-ups comparing lifestyle habits, biochemical features, and noninvasive liver fibrosis scores, between non-MAFLD and MAFLD groups. Furthermore, differences in alcohol consumption and qualitative abdominal fat were examined between male and female patients with NAFLD and MAFLD. The prevalence of metabolic dysregulation, ratio of visceral fat area to subcutaneous fat area, and noninvasive liver fibrosis scores were significantly higher in male patients with MAFLD than in those with NAFLD (p < 0.05), but these were not significantly different in female patients. Among male patients with an alcohol consumption of > 70 g/week, several noninvasive liver fibrosis scores were significantly higher in the MAFLD group than in the NAFLD group (all p < 0.05). The influences of alcohol consumption and qualitative abdominal fat on NAFLD and MAFLD were different between sexes. The development of liver fibrosis should be considered in male patients with MAFLD who exceed mild drinking.
A New Induction Motor Drive Based on the Flux Vector Acceleration Method (2005)

A novel control strategy for the induction motor drive, based on the field acceleration method, is presented. The torque is controlled through variations of the stator flux angular velocity. The stator flux is controlled by using a feedforward control scheme, with the stator flux reference vector adjusted so as to obtain the fixed rotor flux amplitude. The applied controller assures a fast torque response, low torque ripple in the steady state, and drive operation with a constant switching frequency. The algorithm includes the improved stator and rotor flux estimation that guarantees the stable drive operation in all operating conditions, even at low speeds. The experimental tests verify the performance of the proposed algorithm, proving that good behavior of the drive is achieved in the transient and steady-state operating conditions.
Glycemic index profiling of germinated quinoa (Chenopodium quinoa wild) (2017)

Quinoa has potential health benefits and exceptional nutritional value like high concentration of protein, unsaturated fatty acids and low glycemic index (35- 53). Studies on glycemic index (GI) profile of germinated quinoa are lacking, so the present study was carried out to assess the glycemic index of germinated quinoa. Quinoa was germinated, cooked and was given to the subjects, blood glucose levels were examined for every 15mins upto 120mins. The mean fasting blood glucose level was 84.2 mg/dl and blood glucose levels after consumption of germinated quinoa was ranged from 114 to 68.4 mg/dl. The glycemic index of 75gm of germinated quinoa (having 50g of carbohydrates) ranged from 51.2 â€“ 64.7 with an average of 59. The glycemic load of germinated quinoa was ranged from 25.6 to 29.7 with an average of 29.54. Hence, concluded that germinated quinoa can be categorized into medium GI and high Glycemic Load (GL) food.
Ad4BP regulating steroidogenic P-450 gene is a member of steroid hormone receptor superfamily. (1993)

Bovine cytochrome P-450(11 beta) gene (CYP11B) has six different cis-acting elements, Ad1, Ad2, Ad3, Ad4, Ad5, and Ad6, in the promoter region. The Ad4 site also exists in the promoter regions of other steroidogenic P-450 genes as well as in CYP11B1. An Ad4-binding protein (Ad4BP) which specifically binds to the Ad4 site was purified from bovine adrenal cortex nuclear extract, and its molecular mass was 53 kDa. A complementary DNA encoding Ad4BP was isolated from a bovine adrenal cortex cDNA library. The cDNA clone contained an open reading frame of 1383 base pairs encoding 461 amino acids, whose calculated molecular weight was 51,020. The predicted amino acid sequence of Ad4BP revealed that the protein has a zinc finger domain and a ligand binding/dimerization domain. Ad4BP is a novel member of the steroid hormone receptor superfamily. Comparison of the primary structures of the hormone receptor superfamily showed that Ad4BP was highly homologous to FTZ-F1, which regulates the fushi tarazu gene, and ELP, which is expressed in the murine embryonal carcinoma cells. Transfection of a Ad4BP expression plasmid into CV-1 cells activated the transcription of the CAT reporter gene carrying the Ad4 sequence in the promoter region.
Rapid, inexpensive methods for exploring SARS CoV-2 D614G mutation (2021)

Abstract A common mutation has occurred in the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), known as D614G (A23403G). There are discrepancies in impacting of this mutation on the virus’s infectivity, and the whole genome sequencings are expensive and time-consuming. This study aims to develop three fast economical assays for prompt identifications of the D614G mutation including Taqman probe-based real-time reverse transcriptase polymerase chain reaction (rRT PCR), an amplification refractory mutation system (ARMS) RT and restriction fragment length polymorphism (RFLP), in nasopharyngeal swab samples. Both rRT and ARMS data showed G614 mutant indicated by presence of HEX probe and 176bp, respectively. Additionally, the results of the RFLP data and DNA sequencings confirmed the prevalence of G614 mutant. These methods will be important, in epidemiological, reinfections and zoonotic aspects, through detecting the G614 mutant in retro-perspective samples to track its origins and future re-emergence of D614 wild type.
Strengthening tuberculosis diagnosis in a low-resource setting: experience learned in Dodoma, Tanzania (2013)

Implementing tuberculosis diagnosis in resource-constrained settings is feasible and represents a basis for further strengthening.
Beta 1 integrin activation mediates adhesive differences between trisomy 21 and non‐trisomic fibroblasts on type VI collagen (2002)

Trisomy 21 (Down syndrome) is a common genetic condition with a high incidence of congenital heart defects (CHD), particularly those involving abnormal development of the embryonic atrioventricular (AV) canal. Type VI collagen (Col VI) is expressed in the developing AV canal extracellular matrix, and has been associated with trisomy 21 AV canal defects in human genetic studies. Although the molecular mechanisms linking Col VI and trisomy 21 AV canal defects are not well understood, a computer model predicts increased cell adhesiveness is responsible for these CHD. We compared integrin-mediated cell adhesive properties for skin fibroblasts isolated from trisomy 21 and non-trisomic individuals on Col VI, fibronectin (FN) and type I collagen (Col I). Cell lines demonstrate similar adhesion profiles to FN and Col I, but all trisomy 21 cells display increased adhesive capacity for Col VI compared to non-trisomic fibroblasts. Cell adhesion to type VI collagen was shown to be GRGDS independent, but beta(1) integrin family dependent. Function-blocking antibodies identified alpha(3)beta(1) as the predominant integrin mediating trisomy 21 and non-trisomic skin fibroblast adhesion on Col VI. Trisomy 21 and non-trisomic fibroblasts display similar expression levels for each of the integrin receptors examined. A beta(1) integrin-activating antibody augments non-trisomic cell adhesion on Col VI, but has no effect upon trisomy 21 fibroblasts. These results demonstrate that beta(1) integrin family members mediate trisomy 21 and non-trisomic skin fibroblast adhesion for Col VI. Altered activation state of the beta(1) integrin is a mechanism responsible for increased trisomy 21 cell adhesion on Col VI.
Carbon Dioxide Laser Endoscopic Diverticulotomy for Zenker’s Diverticulum: Results and Complications in a Consecutive Series of 40 Patients (2008)

To avoid severe complications we recommend postoperative antibiotic treatment and parenteral feeding. In comparison to the stapler-assisted technique the use of the CO2 laser allows a good view at the diverticular wall throughout the procedure. The transcervical technique should be reserved for cases of anatomic abnormalities or for complicated revision surgeries.
In Vivo Imaging of Brain Aromatase in Female Baboons: [11C]Vorozole Kinetics and Effect of the Menstrual Cycle (2013)

The aim of this work was to quantify the brain distribution of the enzyme aromatase in the female baboon with positron emission tomography and the tracer [11C]vorozole using three different quantification methods for estimating the total distribution volume (V(T)): a graphical method, compartment modeling, and a tissue to plasma ratio. The graphical model and the compartment modeling gave similar estimates to the data and similar values (correlation R = .988; p = .0001). [11C]Vorozole shows a rapid uptake by the brain followed by a relatively constant accumulation, suggesting the possibility of using the tissue to plasma ratio as an estimate of V(T). The highest uptake of [11C]vorozole in the baboon brain was measured in the amygdala, followed by the preoptic area and hypothalamus, basal ganglia, and cortical areas. Pretreatment studies with vorozole or letrozole showed a generalized decrease in brain accumulation and V(T). The results suggested that the physiologic changes in gonadal hormone levels accompanying the menstrual cycle had a significant effect on brain aromatase V(T).
Study of clarinet reeds using digital holography (2014)

A study of clarinet reeds demonstrates the capabilities of digital holography for identification and measurement of vibration modes, measurement of static displacement and creep, and measurement of shape profile. Three types of synthetic reeds were examined together with a number of cane reeds both wet and dry. It is shown that the synthetic reeds have fundamental vibration mode frequencies that are lower than those of natural cane reeds. The fundamental modes of cane reeds all lie above the range of notes played by the instrument whereas those of synthetic reeds do not. Examination of static displacements due to steady air flow showed creep effects due to inelasticity. Finally, projected fringes were used to measure the reed profile.
Parallel Pair-HMM SNP Detection (2012)

I. MOTIVATION: Due to the massive amounts of data generated from each instrument run, next generation sequencing technologies have presented researchers with unique analytical challenges which require innovative, computationally efficient statistical solutions. Here we present a parallel implementation of a probabilistic Pair-Hidden Markov Model for base calling and SNP detection in next generation sequencing data. Our approach incorporates multiple sources of error into the base calling procedure which leads to more accurate results. In addition, our approach applies a likelihood ratio test that provides researchers with straight-forward SNP calling cutoffs based on a p-value cutoff or a false discovery control. II. RESULTS: We have developed GNUMAP-SNP, which is a highly accurate approach for the identification of SNPs in next generation sequencing data. By utilizing a novel probabilistic Pair-Hidden Markov Model, GNUMAP-SNP effectively accounts for uncertainty in the read calls as well as read mapping in an unbiased fashion. Our results show that GNUMAP-SNP has both high sensitivity and high specificity throughout the genome, which is especially true in repeat regions or in areas with low read coverage. In addition, we propose a statistical framework that accounts for the background noise using straightforward statistical cutoffs which filters out false-positive results. The parallel implementation of SNP calling achieves near linear speedup on distributed memory or shared memory platforms. III. AVAILABILITY: GNUMAP-SNP is available as a module in the GNUMAP probabilistic read mapping software. GNUMAP is freely available for download at: http://dna.cs.byu.edu/gnumap/.
Effects of peripheral administration of PYY3–36 on feed intake and plasma acyl-ghrelin levels in pigs (2006)

These studies were designed to investigate the effects of i.v. administration of peptide YY(3-36) (PYY(3-36)) on feed intake, acylghrelin, and GH levels in castrated male pigs. Feed intake levels were evaluated during both ad libitum and fast-refed conditions, and plasma hormone responses were evaluated during fasting. During ad libitum feeding, i.v. injection of PYY(3-36) (30 microg/kg body weight, BW) significantly reduced feed intake levels within 3 h post-treatment. In the fast-refed condition, both single bolus injection (30 microg/kg BW) and i.v. infusion (0.25 microg/kg BW per min) of PYY(3-36) suppressed feed intake levels 1 h post-treatment. Duration of the elevation of plasma PYY levels induced by i.v. injection of porcine PYY(3-36) in ad libitum-fed pigs was longer compared with the values of fasted or fast-refed pigs. In the infusion study, the elevation of plasma PYY levels was maintained throughout the infusion period and values were reduced less than half at 15 min after termination of infusion. These results showed that the anorexigenic short-term effect of PYY(3-36) treatment corresponds to its half-life. However, i.v. PYY(3-36) injection did not influence plasma acyl-ghrelin levels. On the other hand, single bolus injection of PYY(3-36) increased plasma GH levels 30 min after treatment. Similar to previous findings in other mammalian species, the results of these studies show that PYY(3-36) can reduce feed intake levels; in particular, the effect is potent and acute in pigs. Furthermore, basal plasma PYY levels were higher in ad libitum-fed pigs than in fasted pigs suggesting that circulating PYY(3-36) levels influence satiety and contribute to the termination of feed intake in pigs.
Considerations on a multi-user MIMO system using channel prediction based on an AR model (2013)

We consider a multi-user multiple-input multiple-output (MIMO) system using block diagonalization and eigenbeam-space division multiplexing to suppress inter-user interference and inter-stream interference. In time-varying environments, the performance seriously degrades due to mistracking of beamforming. A channel prediction scheme can eliminate the effect of the time-varying environments. In this paper, using indoor measurement data, we evaluate the bit error rate (BER) performance of a multi-user MIMO system with channel prediction based on an autoregressive model. It is shown that the proposed channel prediction technique can improve the BER performance significantly.