gebhart/patrepeval huggingface dataset:
APELIN promotes hematopoiesis from human embryonic stem cells (2012)

Transcriptional profiling of differentiating human embryonic stem cells (hESCs) revealed that MIXL1-positive mesodermal precursors were enriched for transcripts encoding the G-protein-coupled APELIN receptor (APLNR). APLNR-positive cells, identified by binding of the fluoresceinated peptide ligand, APELIN (APLN), or an anti-APLNR mAb, were found in both posterior mesoderm and anterior mesendoderm populations and were enriched in hemangioblast colony-forming cells (Bl-CFC). The addition of APLN peptide to the media enhanced the growth of embryoid bodies (EBs), increased the expression of hematoendothelial genes in differentiating hESCs, and increased the frequency of Bl-CFCs by up to 10-fold. Furthermore, APLN peptide also synergized with VEGF to promote the growth of hESC-derived endothelial cells. These studies identified APLN as a novel growth factor for hESC-derived hematopoietic and endothelial cells.
Designing access methods for bitemporal databases (1998)

By supporting the valid and transaction time dimensions, bitemporal databases represent reality more accurately than conventional databases. The authors examine the issues involved in designing efficient access methods for bitemporal databases, and propose the partial-persistence and the double-tree methodologies. The partial-persistence methodology reduces bitemporal queries to partial persistence problems for which an efficient access method is then designed. The double-tree methodology "sees" each bitemporal data object as consisting of two intervals (a valid-time and a transaction-time interval) and divides objects into two categories according to whether the right endpoint of the transaction time interval is already known. A common characteristic of both methodologies is that they take into account the properties of each time dimension. Their performance is compared with a straightforward approach that "sees" the intervals associated with a bitemporal object as composing one rectangle, which is stored in a single multidimensional access method. Given that some limited additional space is available, the experimental results show that the partial-persistence methodology provides the best overall performance, especially for transaction timeslice queries. For those applications that require ready, off-the-shelf, access methods, the double-tree methodology is a good alternative.
Role of Different T Cell Receptors in the Development of Pre–T Cells (1997)

The development of pre-T cells with productive TCR-beta rearrangements can be mediated by each the pre-T cell receptor (pre-TCR), the TCR-alphabeta as well as the TCR-gammadelta, albeit by distinct mechanisms. Although the TCR-gammadelta affects CD4-8- precursor cells irrespective of their rearrangement status by TCR-beta mechanisms not involving TCR-beta selection, both the pre-TCR and the TCR-alphabeta select only cells with productive TCR-beta genes for expansion and maturation. The TCR-alphabeta appears to be much less effective than the pre-TCR because of the paucity of TCR-alpha proteins in TCR-beta-positive precursors since an early expressed transgenic TCR-alphabeta can largely substitute for the pre-TCR. Thus, the TCR-alphabeta can assume a role not only in the rescue from programmed cell death of CD4+8+ but also of CD4-8- thymocytes. In evolution this double function of the TCR-alphabeta may have been responsible for the maturation of alphabeta T cells before the advent of the pre-TCR-alpha chain.
Design of the CMU sphinx-4 decoder (2003)

Sphinx-4 is an open source HMM-based speech recognition system written in the Java™ programming language.The design of the Sphinx-4 decoder incorporates several new features in response to current demands on HMM-based large vocabulary systems.Some new design aspects include graph construction for multilevel parallel decoding with multiple feature streams without the use of compound HMMs, the incorporation of a generalized search algorithm that subsumes Viterbi decoding as a special case, token stack decoding for efficient maintenance of multiple paths during search, design of a generalized language HMM graph from grammars and language models of multiple standard formats, that can potentially toggle between flat search structure, tree search structure, etc.This paper describes a few of these design aspects, and reports some preliminary performance measures for speed and accuracy.
Limbic seizures induce P-glycoprotein in rodent brain: functional implications for pharmacoresistance. (2002)

The causes and mechanisms underlying multidrug resistance (MDR) in epilepsy are still elusive and may depend on inadequate drug concentration in crucial brain areas. We studied whether limbic seizures or anticonvulsant drug treatments in rodents enhance the brain expression of the MDR gene (mdr) encoding a permeability glycoprotein (P-gp) involved in MDR to various cancer chemotherapeutic agents. We also investigated whether changes in P-gp levels affect anticonvulsant drug concentrations in the brain. Mdr mRNA measured by RT-PCR increased by 85% on average in the mouse hippocampus 3-24 hr after kainic acid-induced limbic seizures, returning to control levels by 72 hr. Treatment with therapeutic doses of phenytoin or carbamazepine for 7 d did not change mdr mRNA expression in the mouse hippocampus 1-72 hr after the last drug administration. Six hours after seizures, the brain/plasma ratio of phenytoin was reduced by 30% and its extracellular concentration estimated by microdialysis was increased by twofold compared with control mice. Knock-out mice (mdr1a/b -/-) lacking P-gp protein showed a 46% increase in phenytoin concentrations in the hippocampus 1 and 4 hr after injection compared with wild-type mice. A significant 23% increase was found in the cerebellum at 1 hr and in the cortex at 4 hr. Carbamazepine concentrations were measurable in the hippocampus at 3 hr in mdr1a/b -/- mice, whereas they were undetectable at the same time interval in wild-type mice. In rats having spontaneous seizures 3 months after electrically induced status epilepticus, mdr1 mRNA levels were enhanced by 1.8-fold and fivefold on average in the hippocampus and entorhinal cortex, respectively. Thus, changes in P-gp mRNA levels occur in limbic areas after both acute and chronic epileptic activity. P-gp alterations significantly affect antiepileptic drugs concentrations in the brain, suggesting that seizure-induced mdr mRNA expression contributes to MDR in epilepsy.
Delineation of distinct subgroups of multiple myeloma and a model for clonal evolution based on interphase cytogenetics (2005)

To delineate multiple myeloma (MM) subgroups and their clonal evolution, we analyzed 81 newly diagnosed patients by interphase fluorescence in situ hybridization using a comprehensive probe set for 10 chromosomes and two IGH rearrangements. A median of 5 probes per patient displayed aberrant signal numbers (range, 1-10). Additional copies most frequently found were for 15q22, 19q13, 9q34, 11q23, and 1q21. Losses commonly observed were of 13q14.3, 17p13, and 22q11. Predominance of gain or loss was quantified by a copy number score (CS) for each patient. Two peaks (CS = +3 and CS = 0) were found by plotting patient copy number scores over CS values corresponding to hyperdiploid and nonhyperdiploid MM. Cluster analysis revealed four major branches: (i) gain of 9q, 15q, 19q, and/or 11q; (ii) deletion of 13q and t(4;14); (iii) t(11;14); and (iv) gain of 1q. Statistical modeling of an oncogenetic tree indicated that early independent events were gain of 15q/9q and/or 11q, t(11;14); deletion of 13q followed by t(4;14); and gain of 1q. Aberrations of 17p13, 22q11, 8p12, and 6q21 were found as subsequent events. MM with gain of 1q was delineated as a subentity with significantly higher beta-2-microglobulin and lower hemoglobin levels, indicating a poor prognosis. From our results, we propose a model of MM for clonal evolution.
Inhibition of NFκB Activity through Maintenance of IκBα Levels Contributes to Dihydrotestosterone-mediated Repression of the Interleukin-6 Promoter (1996)

Androgens repress expression of many genes, yet the mechanism of this activity has remained elusive. The cytokine, interleukin-6, is active in a variety of biological systems, and its expression is repressed by androgens. Accordingly we dissected the mechanism of androgen's ability to inhibit interleukin-6 expression at the molecular level. In a series of co-transfection assays, we found that 5alpha-dihydrotestosterone, through the androgen receptor, repressed activation of the interleukin-6 promoter, in part, by inhibiting NFkappaB activity. It did not appear that 5alpha-dihydrotestosterone inhibited NFkappaB by activating the androgen receptor to compete for the NFkappaB response element as we could not detect androgen receptor binding to the IL-6 promoter by DNase I footprinting assay. However, by electrophoretic mobility shift assay we found that 5alpha-dihydrotestosterone repressed formation of NFkappaB middle dotNFkappaB response element complex formation. In LNCaP prostate carcinoma cells, 5alpha-dihydrotestosterone achieved this effect through maintenance of IkappaBalpha protein levels in the face of phorbol ester, a stimulus that results in IkappaBalpha degradation. Finally, we confirmed that IkappaBalpha inhibits NFkappaB-mediated activation of the interleukin-6 promoter. These data suggest that maintenance of IkappaBalpha levels may represent the first identified mechanism for androgen-mediated repression of a natural androgen-regulated gene.
GENERATION OF GERMLINECOMPETENT INDUCED PLURIPOTENT STEM CELLS (2007)

Abstract We have previously shown that pluripotent stem cells can be induced from mouse fibroblasts by retroviral introduction of Oct3/4 (also called Pou5f1), Sox2, c-Myc and Klf4, and subsequent selection for Fbx15 (also called Fbxo15) expression. These induced pluripotent stem (iPS) cells (hereafter called Fbx15 iPS cells) are similar to embryonic stem (ES) cells in morphology, proliferation and teratoma formation; however, they are different with regards to gene expression and DNA methylation patterns, and fail to produce adult chimaeras. Here we show that selection for Nanog expression results in germline-competent iPS cells with increased ES-cell-like gene expression and DNA methylation patterns compared with Fbx15 iPS cells. The four transgenes (Oct3/4, Sox2, c-myc and Klf4) were strongly silenced in Nanog iPS cells. We obtained adult chimaeras from seven Nanog iPS cell clones, with one clone being transmitted through the germ line to the next generation. Approximately 20% of the offspring developed tumours attributable to reactivation of the c-myc transgene. Thus, iPS cells competent for germline chimaeras can be obtained from fibroblasts, but retroviral introduction of c-Myc should be avoided for clinical application.
The impact of Glu→Ala and Glu→Asp mutations on the crystallization properties of RhoGDI: the structure of RhoGDI at 1.3 Å resolution (2002)

It is hypothesized that surface residues with high conformational entropy, specifically lysines and glutamates, impede protein crystallization. In a previous study using a model system of Rho-specific guanine nucleotide dissociation inhibitor (RhoGDI), it was shown that mutating Lys residues to Ala results in enhanced crystallizability, particularly when clusters of lysines are targeted. It was also shown that one of these mutants formed crystals that yielded diffraction to 2.0 A, a significant improvement on the wild-type protein crystals. In the current paper, an analysis of the impact of surface mutations replacing Glu residues with Ala or Asp on the stability and crystallization properties of RhoGDI is presented. The Glu-->Ala (Asp) mutants are generally more likely to produce crystals of the protein than the wild-type and in one case the resulting crystals yielded a diffraction pattern to 1.2 A resolution. This occurs in spite of the fact that mutating surface Glu residues almost invariably affects the protein's stability, as illustrated by the reduced deltaG between folded and unfolded forms measured by isothermal equilibrium denaturation. The present study strongly supports the notion that rational surface mutagenesis can be an effective tool in overcoming problems stemming from the protein's recalcitrance to crystallization and may also yield dramatic improvements in crystal quality.
Automatic Brake Control for Trucks - What Good is It? (1968)

&lt;div class="htmlview paragraph"&gt;A review of benefits to be gained by automatically controlling the slip properties of truck tires indicates that up to 40% shorter stops and complete jackknife control when braking is possible. A simple all-mechanical device is described for use with air brakes which, from the data, shows 7-30% shorter stops, no tire degradation, and full steering control. Data is presented from full sized semi-trailer truck skid tests.&lt;/div&gt;
Familial Pyrimidinemia and Pyrimidinuria Associated with Severe Fluorouracil Toxicity (1985)

RAPIDLY growing tumor cells depend on a high rate of pyrimidine synthesis for the generation of RNA and DNA. Fluorouracil is a pyrimidine-base analogue that acts as an antimetabolite to block the synthesis of deoxythymidylic acid and to disrupt normal RNA function.1 , 2 This compound is frequently employed in combination with other chemotherapeutic drugs for the therapy of certain solid tumors, such as cancers of the breast, ovary, and gastrointestinal tract.3 4 5 The toxicity of fluorouracil can be severe and includes bone marrow suppression, mucosal ulceration, diarrhea, and less frequently, somnolence, upper motor-neuron signs, reversible cerebellar ataxia, and reversible symptoms like those . . .
SCAM: A Copy Detection Mechanism for Digital Documents (1995)

Copy detection in Digital Libraries may provide the necessary guarantees for publishers and newsfeed services to offer valuable on-line data. We consider the case for a registration server that maintains registered documents against which new documents can be checked for overlap. In this paper we present a new scheme for detecting copies based on comparing the word frequency occurrences of the new document against those of registered documents. We also report on an experimental comparison between our proposed scheme and COPS [6], a detection scheme based on sentence overlap. The tests involve over a million comparisons of netnews articles and show that in general the new scheme performs better in detecting documents that have partial overlap. Keywords: Copy Detection, Plagiarism, Registration Server, Databases. INTRODUCTION A Digital Library provides users with on-line access to digitized news articles, books, and other information. In this environment, a user may easily redistribut...
Structure-activity studies on gossypol in tumor cell lines (2000)

Gossypol [(2,2'-binaphthalene)-8,8'-dicarboxaldehyde-1,1',6,6',7,7'-hexahydroxy-5,5'-diisopropyl-3,3'-dimethyl] 1a is a naturally occurring compound extracted from the cotton plant and has been extensively studied as an oral male contraceptive. Its favorable toxicity profile, and the more recent demonstration of anti-tumor activity in animals and humans, prompted us to investigate the role of the aldehyde groups in a structure-activity study in cultured tumor cells. Four racemic compounds were evaluated: gossypol 1a, gossypolone 2, the bis Schiff's base of L-phenylalanine methyl ester with gossypol (bis Schiff's base) 1c and apogossypol 1b. The former two compounds both retain the aldehyde functional groups at positions 8 and 8' of the molecule whilst in the latter two compounds the aldehydes are blocked or absent, respectively. In addition, the l- and d-isomers of gossypol 1a, the bis Schiff's base 1c and the half Schiff's base 1d (one aldehyde blocked) were tested. The cell lines studied included melanoma (SK-mel-19), cervix (Sihas), small cell lung (H69) and myelogenous leukemia (K562). Cytotoxicity was measured using the MTT and flow cytometric viability assays. Racemic gossypol 1a and gossypolone 2 induced similar dose-dependent decreases in cell viability in all the cell lines with IC50 values of 23-46 and 28-50 microM, respectively. In contrast, the racemic bis Schiff's base derivative of gossypol 1c and apogossypol 1b showed minimal activity in any cell line up to 50 microM. The l-enantiomer of gossypol 1a was significantly more active than the d-enantiomer (IC50 of 20 versus > 50 microM, respectively). When one aldehyde of either enantiomer was blocked 1d cytoxicity was comparable to the l-enantiomer of gossypol. The data suggest that only one aldehyde group is required for the cytotoxicity of gossypol 1a, irrespective of the stereoconfiguration.
The initial phase of orthodontic root resorption incident to local compression of the periodontal ligament (1993)

The present light microscopic investigation was undertaken in order to study the initial phase of orthodontic root resorption in areas of pressure and, more specifically, to focus on the first cells that penetrate the root surface. Twenty-one upper first molars (rats) and 31 lower first molars (mice) were moved mesially by a fixed orthodontic appliance. The experimental periods were 1, 2, 3, 4, and 5 days in rats, and 1, 2, 3, 4, 5, 6, 7, and 8 days in mice. Tartrate-resistant acid phosphatase (TRAP) and Haematoxylin Eosin (H&E) stains were used. Root resorption related to a hyalinized zone showed a consistent pattern: Root resorption started in the circumference of the necrotic hyalinized tissue. In the central parts of the hyalinized zone frontal root resorption occurred 3-4 days later than in the periphery. Indications that the mechanisms for circumferential and central resorption differed was the reason for presenting only the periphery stage in this paper. The initial penetration of cells into precementum/cementum occurred at the peripheries or at a short distance from the peripheries of the hyalinized zone. These cells were TRAP-negative, indicating that they were not clasts or clast precursors. Before this happened TRAP-negative macrophage-like cells were observed at the borderline between the hyalinized tissue and vital periodontal membrane (PM). TRAP-positive cells were first observed in the bone marrow spaces. During the later stages mono- and multi-nucleated TRAP-positive cells were participating in active removal of the hyalinized tissue toward the root surface, and in resorption of cementum and dentine.
High reflectivity airgap distributed Bragg reflectors realized by wet etching of AlInN sacrificial layers (2009)

The authors report on the achievement of a vertically oriented three pair airgap/GaN distributed Bragg reflector realized by controlled oxidation and wet-chemical etching of AlInN sacrificial layers. Microreflectivity measurements exhibit high peak reflectivity values of 87% around 500 nm after the oxidation process and 90% around 600 nm after the etching process in overall good agreement with simulations. The broad stopband of airgap/GaN mirrors, about 250 nm wide, results from the strong refractive index contrast between air and GaN layers.
A rare genotype of Cryptococcus gattii caused the cryptococcosis outbreak on Vancouver Island (British Columbia, Canada) (2004)

Cryptococcus gattii causes life-threatening infection of the pulmonary and central nervous systems in hosts with normal immunity and traditionally has been considered to be restricted geographically to tropical and subtropical climates. The recent outbreak of C. gattii in the temperate climate of Vancouver Island, BC, Canada, led to a collaborative investigation. The objectives of the current study were to ascertain the environmental source of the outbreak infections, survey the molecular types of the outbreak and environmental cryptococcal isolates, and determine the extent of genetic diversity among the isolates. PCR-fingerprinting and amplified fragment length polymorphism (AFLP) were used to examine the genotypes, and mating assays were performed to determine the mating type of the isolates. All outbreak and environmental isolates belonged to C. gattii. Concordant results were obtained by using PCR-fingerprinting and AFLP analysis. The vast majority of clinical and veterinary infections were caused by isolates of the molecular type VGII/AFLP6, but two were caused by molecular type VGI/AFLP4. All environmental isolates belonged to molecular type VGII/AFLP6. Two or three subtypes were observed within VGII/AFLP6 among outbreak and environmental isolates. All mating-competent isolates were of the alpha-mating type. The emergence of this usually tropical pathogen on Vancouver Island highlights the changing distribution of this genotype and emphasizes the importance of an ongoing collaborative effort to monitor the global epidemiology of this yeast.
Multimodality Treatment of Lung Cancer (2000)

Introduction Molecular and Cellular Biological Abnormalities in Lung Cancer and the Potential for Novel Therapeutics Ravi Salgia and Arthur T. Skarin Chemoprevention of Lung Cancer Fadlo R. Khuri, Lamya R. Tannous-Khuri, and Waun Ki Hong Radiologic Staging of Lung Cancer Kitt Shaffer Non-Small-Cell Lung Cancer Surgical Staging Raja M. Flores, Jose J. Norberto, Michael T. Jaklitsch, and David J. Sugarbaker Non-Small-Cell Lung Cancer Role of Video-Assisted Thoracic Surgery in the Diagnosis and Treatment of Non-Small-Cell Lung Cancer Steven J. Mentzer Non-Small-Cell Lung Cancer: Surgery for Stage I and II Disease Malcolm M. DeCamp, Jr. and Raja M. Flores Randomized Trials in Stage I and II Non-Small-Cell Lung Cancer Victoria J. Dorr and Michael C. Perry Superior Pulmonary Sulcus Tumors Harold C. Urschel, Jr. Surgery for Advanced Lung Cancer Raphael Bueno Multimodality Therapy for Stage IIIA and IIIB Non-Small-Cell Lung Cancer Gary M. Strauss and Elizabeth H. Baldini Multimodality Therapy of Stage IIIB Non-Small-Cell Lung Cancer Scott J. Swanson Chemotheraphy of Advanced Non-Small-Cell Lung Cancer Nam H. Dang, Roy S. Herbst, and Arthur T. Skarin Multimodality Therapy for Non-Small-Cell Cancer Metastases to the Brain Rodolfo Hakim, Eben Alexander III, Peter McL. Black, and Jay S. Loeffler Laboratory Models to Evaluate New Agents for the Systemic Treatment of Lung Cancer Beverly A. Teicher and Emil Frei III Small-Cell Lung Cancer Surgery for Small-Cell Lung Cancer Dean M. Donahue and Douglas J. Mathisen Role of Thoracic Radiation Therapy and Prophylactic Cranial Irradiation in the Management of Small-Cell Lung Cancer Parvesh Kumar Chemotherapy of Small-Cell Lung Cancer Anthony L. Boral and Thomas J. Lynch, Jr. High-Dose Therapy for Small-Cell Lung Cancer with Stem Cell Support Anthony D. Elias
Quantification of tissue‐engineered trachea performance with computational fluid dynamics (2018)

NA. Laryngoscope, E272-E279, 2018.