gebhart/patrepeval huggingface dataset:
Trihexyphenidyl (Artane) abuse in schizophrenic patients (1996)

Trihexyphenidyl (THP) and other anticholinergics are liable to abuse by schizophrenic patients. Data concerning the incidence and characteristics of the abusers are scarce. In the present study an evaluation of 214 consecutive admissions of schizophrenic patients revealed 14 THP abusers, an incidence of 6.5%. The demographic and clinical variables of the THP abusers were compared with a randomized control group of 28 schizophrenic patients using the four-dimensional factors of the BPRS (Brief Psychiatric Rating Scale). No significant differences were found in demographic variables and comorbidity for antisocial personality disorder and other substances abuse. On admission, a trend towards more negative symptoms was detected among abusers. At discharge abusers had significantly higher mean BPRS scores and higher scores on the dimensional factor of hostile-suspiciousness. The results suggest that THP abuse is not rare among schizophrenic patients who may abuse anticholinergic agents to relieve negative symptoms and/or drug-induced Parkinsonism, or alternatively for its non-specific stimulant effects, on account of worsening of positive symptoms.
Long-Form Information Retrieval for Enterprise Matchmaking (2023)

Understanding customer requirements is a key success factor for both business-to-consumer (B2C) and business-to-business (B2B) enterprises. In a B2C context, most requirements are directly related to products and therefore expressed in keyword-based queries. In comparison, B2B requirements contain more information about customer needs and as such the queries are often in a longer form. Such long-form queries pose significant challenges to the information retrieval task in B2B context. In this work, we address the long-form information retrieval challenges by proposing a combination of (i) traditional retrieval methods, to leverage the lexical match from the query, and (ii) state-of-the-art sentence transformers, to capture the rich context in the long queries. We compare our method against traditional TF-IDF and BM25 models on an internal dataset of 12,368 pairs of long-form requirements and products sold. The evaluation shows promising results and provides directions for future work.
Quantitative genetic screening reveals a Ragulator-FLCN feedback loop that regulates the mTORC1 pathway (2020)

Forward genetic screens in mammalian cell lines, such as RNAi and CRISPR-Cas9 screens, have made major contributions to the elucidation of diverse signaling pathways. Here, we exploited human haploid cells as a robust comparative screening platform and report a set of quantitative forward genetic screens for identifying regulatory mechanisms of mTORC1 signaling, a key growth control pathway that senses diverse metabolic states. Selected chemical and genetic perturbations in this screening platform, including rapamycin treatment and genetic ablation of the Ragulator subunit LAMTOR4, revealed the known core mTORC1 regulatory signaling complexes and the intimate interplay of the mTORC1 pathway with lysosomal function, validating the approach. In addition, we identified a differential requirement for LAMTOR4 and LAMTOR5 in regulating the mTORC1 pathway under fed and starved conditions. Furthermore, we uncovered a previously unknown "synthetic-sick" interaction between the tumor suppressor folliculin and LAMTOR4, which may have therapeutic implications in cancer treatment. Together, our study demonstrates the use of iterative "perturb and observe" genetic screens to uncover regulatory mechanisms driving complex mammalian signaling networks.
Evaluación del desprendimiento de oocistos de Eimeria maxima y Eimeria acervulina en pollos de engorde (2020)

The purpose of the present study was to evaluate the day and the time of sample collection of an experimental challenge with Eimeria maxima (EM) and Eimeria acervulina (EA) in broiler chickens. One-day old male Cobb-Vantress broiler chickens were randomly allocated to one of three groups with ten replicates (n=8 chickens/replicate). Chickens were placed in battery cages with a controlled age-appropriate environment: Group 1) Negative control (no challenge or treatment); 2) Challenge control (Eimeria challenge only); 3) Challenge + Salinomycin. Challenged chickens were orally gavaged with the mixed culture of EM/EA (10,000 sporulated EM containing 4% wild-type EA) at 14 days of age. Performance parameters were recorded at days 7, 14, 20, and 23. Lesions scores were recorded post-mortem on days 20 and 23. Oocyst per gram (OPG) was performed on days six, seven, and eight post-challenge, and samples were collected at 9:00 AM and 6:00 PM on each day, respectively. Oocyst counts were significantly different (P < 0.05) between morning and afternoon on day six post coccidia challenge. The results of this study show that the day and the time at which samples are collected can have a significant effect on the reliability and validity of data.
Self-Assembly of Hydrogen-Bonded Polymeric Rods Based on the Cyanuric Acid·Melamine Lattice (1999)

This paper describes the self-assembly of hydrogen-bonded polymeric rods based on the lattice of cyanuric acid and melamine (CA·M). Data from 1H NMR spectroscopy, IR spectroscopy, gel permeation chromatography (GPC), and transmission electron microscopy (TEM) are interpreted as indicating that the self-assembly of a bisisocyanuric acid (bisCA) and a bismelamine (bisM) formed polymeric nanorods [(bisCA)n(bisM)n] composed of parallel CA·M rosettes. The TEM results suggest that these rods aggregate as bundles. The length of the bundles ranged from 100 to 1500 nm, and their diameter was in the range from 15 to 500 nm.
Helminth-induced arginase-1 exacerbates lung inflammation and disease severity in tuberculosis (2015)

Parasitic helminth worms, such as Schistosoma mansoni, are endemic in regions with a high prevalence of tuberculosis (TB) among the population. Human studies suggest that helminth coinfections contribute to increased TB susceptibility and increased rates of TB reactivation. Prevailing models suggest that T helper type 2 (Th2) responses induced by helminth infection impair Th1 immune responses and thereby limit Mycobacterium tuberculosis (Mtb) control. Using a pulmonary mouse model of Mtb infection, we demonstrated that S. mansoni coinfection or immunization with S. mansoni egg antigens can reversibly impair Mtb-specific T cell responses without affecting macrophage-mediated Mtb control. Instead, S. mansoni infection resulted in accumulation of high arginase-1-expressing macrophages in the lung, which formed type 2 granulomas and exacerbated inflammation in Mtb-infected mice. Treatment of coinfected animals with an antihelminthic improved Mtb-specific Th1 responses and reduced disease severity. In a genetically diverse mouse population infected with Mtb, enhanced arginase-1 activity was associated with increased lung inflammation. Moreover, in patients with pulmonary TB, lung damage correlated with increased serum activity of arginase-1, which was elevated in TB patients coinfected with helminths. Together, our data indicate that helminth coinfection induces arginase-1-expressing type 2 granulomas, thereby increasing inflammation and TB disease severity. These results also provide insight into the mechanisms by which helminth coinfections drive increased susceptibility, disease progression, and severity in TB.
Abstract 1387: Application of target enrichment combined with unique molecular identifiers to determine allelic frequencies of human cancers (2016)

Abstract Existing target enrichment and library preparation for next-generation sequencing typically utilize PCR amplification steps that introduce substantial bias and sequencing of duplicate reads, which in turn affect the quantification accuracy of somatic allele frequencies. Unique molecular identifiers (UMIs) are random molecular tags that uniquely label each molecule prior to library amplification and aid in the identification of true PCR duplicates and thereby improve the accuracy in estimating the relative molecular copy number of the original sample. Here, we applied a target enrichment method for hybridization-based capture of regions of interest, combined with unique molecule labeling and next-generation sequencing to determine allelic frequencies of select cancer targets. Target enrichment and library preparation can be performed in just under seven hours, and our UMI method is compatible with sample indexing using separate barcodes. To demonstrate the robustness and accuracy of our method, we present the detection and assessment of allelic frequencies of multiple cancer genes across multiple reference standards. The result is a fast and cost-efficient method that enables the determination of even low allelic frequencies with high confidence. Citation Format: Daniel C. Kraushaar, Sarah K. Bowman, Theodore B. Davis, Amy B. Emerman, Noa Henig, Kruti M. Patel, Salvatore Russello, Cynthia L. Hendrickson. Application of target enrichment combined with unique molecular identifiers to determine allelic frequencies of human cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1387.
Line Impedance Estimation Using Active and Reactive Power Variations (2007)

This paper proposes an estimation method of power system impedance based on power variations caused by a distributed power generation system (DPGS) at the point of common coupling (PCC). The proposed algorithm is computationally simple and uses the voltage variations at the point of common coupling (PCC) caused by the variations of the power delivered to utility network to derive the value of grid impedance. Accurate estimation of both resistive and inductive part of the impedance is obtained, as the results presented show.
Hydrolytically stable cellulose‐derivative coatings for capillary electrophoresis of peptides, proteins and glycoconjugates (1995)

A method for the preparation of versatile, hydrolytically stable coatings of fused silica capillaries is described. First, the HNO3-pretreated silica surface is reacted with 7-oct-1-enyltrimethoxysilane to form a stable self-assembled alkylsilane monolayer. Secondly, the copolymer of hydroxypropylcellulose and 2-hydroxyethyl methacrylate is statically coated onto a hydrophobized wall. This allows the formation of a highly crosslinked copolymer layer which is tightly bound to the wall surface. Hydrolytical stability in the pH range of 2-10 for several weeks has been demonstrated. The coating generates a low electroosmotic flow at alkaline pH, which can be easily masked by using special buffers. The versatility of this column technology is documented by separations of peptides, glycoproteins and derivatized oligosaccharides.
Porcine-specific expression of the three functional CYP19 paralogs in early conceptus, placenta, and gonads (2023)

Although three porcine aromatase isoforms have been identified, their gene expression profiles in reproduction are still poorly understood. Here, we identified by Sanger sequencing unique nucleotide signatures for the three paralogous copies of Cyp19 and analyzed by RT-PCR the occurrence of the Cyp19 and Cyp17a1 transcripts at different tissues and stages of conceptus and fetal-placental development. Cyp19a1 and Cyp19a3 expressions were detected in conceptuses and gonads, respectively. Cyp19a2 transcripts were identified on both the conceptuses and the placenta samples. Transcripts for Cyp17a1 were detected predominantly in conceptus and gonads. In the endometrium of day 21 pregnant females, as well as days 12 and 17 pseudopregnant females, we did not detect the expression of Cyp19a1, Cyp19a2, or Cyp19a3. In our study, we have demonstrated distinct transcriptional regulation for the three functional Cyp19 paralogs and a potential role for Cyp17a1 in controlling the secretion of estrogen from the conceptus and the placenta.
A modified lightly doped drain structure for VLSI MOSFET's (1986)

A new n-MOS LDD-like device structure (the J-MOS transistor) is proposed. It’s design, simulation, and fabrication are studied in this paper. n-channel MOSFET’s with Le, below 2µm suffer from high-field effects that must be overcome to secure reliable 5-V operation. LDD structures alleviate these effects, but their reliability is better than that of conventional MOSFET’s only if the n¯ regions have a peak doping density above 1 X 10 18 cm¯3. To overcome this limitation and to allow constant voltage scaling for devices into the submicrometer regime, the J-MOS structure uses a series drain JFET to drop part of the supply voltage. Both 2-D device simulations and experimental results are presented to demonstrate the operation of this device and its potential for applications requiring reliable submicrometer device operation under maximum supply voltage.(Continue0 The major experimental findings are that the J-MOS structure can sustain 5-V operation even for submicrometer effective channel lengths. As has been the case with all LDD-like structures, improved device reliability has been achieved at the expense of some performance. However, the advantages of keeping 5-V operation in micrometer-sized devices may outweigh this performance loss.
The landscape of antigen-specific T cells in human cancers (2018)

Abstract Antigen-specific T cells can be orchestrated to kill cancer cells in immunotherapies but the utilities of the TCR information have not been fully explored. Here, we leveraged previous efforts on tumor TCR repertoire, and developed a novel algorithm to characterize antigen-specific TCR clusters. Joint analysis with gene expression revealed novel regulators for T cell activation. Investigation of single-cell sequencing data revealed a novel subset of tissue-resident memory T cell population with elevated metabolic status. Integrative analysis of TCR clusters with HLA alleles and cancer genomics data identified candidate antigens derived from missense mutations, frameshift indels, and tumor-associated gene overexpression. Predicted antigen HSFX1 was further validated using vaccinated humanized HLA-A*02:01 mice. Finally, high abundant cancer-associated TCRs were observed in the blood repertoire of early breast cancer patients, suggesting new avenues for noninvasive early detection. Thus, our analysis identified cancer-associated T cells with broad utilities in immune monitoring and cancer immunotherapies.
Regio‐ and Stereoselective Carbon‐Boron Bond Formation via Heterogeneous Palladium‐Catalyzed Hydroboration of Enallenes (2023)

A highly efficient regio- and stereoselective heterogeneous palladium-catalyzed hydroboration reaction of enallenes was developed. Nanopalladium immobilized on microcrystalline cellulose (MCC) was successfully employed as an efficient catalyst for the enallene hydroboration reaction. The nanopalladium particles were shown by HAADF-STEM to have an average size of 2.4 nm. The cellulose-supported palladium catalyst exhibits high stability and provides vinyl boron products in good to high isolated yields (up to 90 %). The nanopalladium catalyst can be efficiently recycled and it was demonstrated that the catalyst can be used in 7 runs with a maintained high yield (>80 %). The vinylboron compounds prepared from enallenes are important synthetic intermediates that can be used in various organic synthetic transformations.
Neural Stem Cells as a Novel Platform for Tumor-Specific Delivery of Therapeutic Antibodies (2009)

Taken together, these results suggest that NSCs modified to secrete HER2-targeting antibodies constitute a promising novel platform for targeted cancer immunotherapy. Specifically, this NSC-mediated antibody delivery system has the potential to significantly improve clinical outcome for patients with HER2-overexpressing breast cancer.
Unravelling the Molecular Determinants of Bee Sensitivity to Neonicotinoid Insecticides (2018)

The impact of neonicotinoid insecticides on the health of bee pollinators is a topic of intensive research and considerable current debate [1]. As insecticides, certain neonicotinoids, i.e., N-nitroguanidine compounds such as imidacloprid and thiamethoxam, are as intrinsically toxic to bees as to the insect pests they target. However, this is not the case for all neonicotinoids, with honeybees orders of magnitude less sensitive to N-cyanoamidine compounds such as thiacloprid [2]. Although previous work has suggested that this is due to rapid metabolism of these compounds [2-5], the specific gene(s) or enzyme(s) involved remain unknown. Here, we show that the sensitivity of the two most economically important bee species to neonicotinoids is determined by cytochrome P450s of the CYP9Q subfamily. Radioligand binding and inhibitor assays showed that variation in honeybee sensitivity to N-nitroguanidine and N-cyanoamidine neonicotinoids does not reside in differences in their affinity for the receptor but rather in divergent metabolism by P450s. Functional expression of the entire CYP3 clade of P450s from honeybees identified a single P450, CYP9Q3, that metabolizes thiacloprid with high efficiency but has little activity against imidacloprid. We demonstrate that bumble bees also exhibit profound differences in their sensitivity to different neonicotinoids, and we identify CYP9Q4 as a functional ortholog of honeybee CYP9Q3 and a key metabolic determinant of neonicotinoid sensitivity in this species. Our results demonstrate that bee pollinators are equipped with biochemical defense systems that define their sensitivity to insecticides and this knowledge can be leveraged to safeguard bee health.
Cavity Characteristics of Selectively Oxidized Vertical-Cavity Lasers (1995)

Vertical-cavity surface emitting lasers (VCSELs) are of interest from both scientific and technological points of view. For example, distributed Bragg reflector (DBR) mirrors used to produce microcavities with a single longitudinal mode have been employed to study novel optical phenomena and are critical to VCSEL performance. Optical and electrical confinement in the transverse direction has been commonly achieved using etched post index-guided structures, or ion implanted "gain-guided" devices. We report the optical and electrical properties of VCSEL diodes fabricated using a buried oxide layer with a current aperture within an all semiconductor DBR mirror. We show this oxide layer has profound implications, leading to new transverse optical effects in the cavity as well as significant advances in VCSEL performance.
Entropy as a measure of uncertainty in queueing system (2011)

In the present paper we discussed the operating performance uncertainty in queues using principle of maximum entropy. Entropy was discussed by Shannon (1948) in information theory to measure message uncertainty and communication channel uncertainty. Since the concept of steady-state of a queue concern a probability function, it seems logical to consider a connection between entropy and uncertainty in queueing system. This paper presents an entropy based uncertainty metric for measuring the operating performance in queueing system, when the prior information available is in the form of mean arrival rate, mean service rate distribution.
PanIN Neuroendocrine Cells Promote Tumorigenesis via Neuronal Cross-talk (2017)

Abstract Nerves are a notable feature of the tumor microenvironment in some epithelial tumors, but their role in the malignant progression of pancreatic ductal adenocarcinoma (PDAC) is uncertain. Here, we identify dense innervation in the microenvironment of precancerous pancreatic lesions, known as pancreatic intraepithelial neoplasms (PanIN), and describe a unique subpopulation of neuroendocrine PanIN cells that express the neuropeptide substance P (SP) receptor neurokinin 1-R (NK1-R). Using organoid culture, we demonstrated that sensory neurons promoted the proliferation of PanIN organoids via SP-NK1-R signaling and STAT3 activation. Nerve-responsive neuroendocrine cells exerted trophic influences and potentiated global PanIN organoid growth. Sensory denervation of a genetically engineered mouse model of PDAC led to loss of STAT3 activation, a decrease in the neoplastic neuroendocrine cell population, and impaired PanIN progression to tumor. Overall, our data provide evidence that nerves of the PanIN microenvironment promote oncogenesis, likely via direct signaling to neoplastic neuroendocrine cells capable of trophic influences. These findings identify neuroepithelial cross-talk as a potential novel target in PDAC treatment. Cancer Res; 77(8); 1868–79. ©2017 AACR.
Supplementary Table 1 from EGF816 Exerts Anticancer Effects in Non–Small Cell Lung Cancer by Irreversibly and Selectively Targeting Primary and Acquired Activating Mutations in the EGF Receptor (2023)

&lt;p&gt;This file contains the supplementary Table S1 that describes the characteristics and anti-proliferative activities of EGF816 on a number of patient-derived cell lines&lt;/p&gt;
SubstrateAware MixedSignal Macrocell Placement in WRIGHT (2009)

We describe a set of placement algorithms for handling substrate-coupled switching noise. A typical mixed-signal IC has both sensitive analog and noisy digital circuits, and the common substrate parasitically couples digital switching transients into the sensitive analog regions of the chip. To preserve the integrity of sensitive analog signals, it is thus necessary to electrically isolate the analog and digital. We argue that optimal area utilization requires such isolation be designed into the system during first-cut chip-level placement. We present algorithms that incorporate commonly used isolation techniques within an automatic placement framework. Our substrate-noise evaluation mechanism uses a simplified substrate model and simple electrical representations for the noisy digital macrocells. The digital/analog interactions determined through these models are incorporated into a simulated annealing macrocell placement framework. Automatic placement results indicate these substrateaware algorithms allow efficient mixed-signal placement optimization.
Human Induced Pluripotent Stem Cell–Derived Cardiomyocytes as Models for Cardiac Channelopathies (2018)

Life threatening ventricular arrhythmias leading to sudden cardiac death are a major cause of morbidity and mortality. In the absence of structural heart disease, these arrhythmias, especially in the younger population, are often an outcome of genetic defects in specialized membrane proteins called ion channels. In the heart, exceptionally well-orchestrated activity of a diversity of ion channels mediates the cardiac action potential. Alterations in either the function or expression of these channels can disrupt the configuration of the action potential, leading to abnormal electrical activity of the heart that can sometimes initiate an arrhythmia. Understanding the pathophysiology of inherited arrhythmias can be challenging because of the complexity of the disorder and lack of appropriate cellular and in vivo models. Recent advances in human induced pluripotent stem cell technology have provided remarkable progress in comprehending the underlying mechanisms of ion channel disorders or channelopathies by modeling these complex arrhythmia syndromes in vitro in a dish. To fully realize the potential of induced pluripotent stem cells in elucidating the mechanistic basis and complex pathophysiology of channelopathies, it is crucial to have a basic knowledge of cardiac myocyte electrophysiology. In this review, we will discuss the role of the various ion channels in cardiac electrophysiology and the molecular and cellular mechanisms of arrhythmias, highlighting the promise of human induced pluripotent stem cell-cardiomyocytes as a model for investigating inherited arrhythmia syndromes and testing antiarrhythmic strategies. Overall, this review aims to provide a basic understanding of the electrical activity of the heart and related channelopathies, especially to clinicians or research scientists in the cardiovascular field with limited electrophysiology background.