gebhart/patrepeval huggingface dataset:
Recursive Clipping and Filtering With Bounded Distortion for PAPR Reduction (2007)

Repeated clipping and filtering (RCF) is a simple method for reducing the peak-to-average power ratio (PAPR) of the signal in the orthogonal frequency-division modulation (OFDM) system. We propose to modify RCF by limiting the distortion on each tone of the OFDM so that both low PAPR and low error can be achieved
Rituximab in autoimmune bullous diseases: mixed responses and adverse effects (2006)

Adjuvant B-cell depletion by rituximab is effective in otherwise therapy-resistant bullous autoimmune disorders but may be associated with substantial adverse effects including fatal outcomes.
A detailed inventory of DNA copy number alterations in four commonly used Hodgkin's lymphoma cell lines (2007)

aCGH was performed on four cHL cell lines leading to the improved delineation of known chromosomal imbalances and the detection of 35 hitherto undetected aberrations. More specifically, our results highlight STAT6 as a potential transcriptional target and identified RGMA, CHD2 and CYLD as candidate tumor suppressors in cHL.
Improving bioinformatic pipelines for exome variant calling (2012)

Exome sequencing analysis is a cost-effective approach for identifying variants in coding regions. However, recognizing the relevant single nucleotide variants, small insertions and deletions remains a challenge for many researchers and diagnostic laboratories typically do not have access to the bioinformatic analysis pipelines necessary for clinical application. The Atlas2 suite, recently released by Baylor Genome Center, is designed to be widely accessible, runs on desktop computers but is scalable to computational clusters, and performs comparably with other popular variant callers. Atlas2 may be an accessible alternative for data processing when a rapid solution for variant calling is required.See research article http://www.biomedcentral.com/1471-2105/13/8.
Initiation of Precocious Sexual Maturation in the Immature Rat Treated with Dehydroepiandrosterone1 (1975)

Administration of dehydroepiandrosterone (DHA) to immature female rats on day 27 for 3 days resulted in an increase in uterine weight within 6 h of injection and a surge of FSH, LH and prolactin occurred on day 30 resulting in premature ovulation. Increase in ovarian weight and vaginal patency also occurred on day 30. Ovulations occurred at various times on day 30 and some as late as day 33 and these could be synchronized by the administration of pregnant mare serum gonadotropin (PMSG). The gonadotropin surge resulting in ovulation could be blocked by central nervous system blocking agents like phenobarbital and reserpine. The action of DHA in inducing precocious ovulation appeared to be mediated through conversion to estrogens because DHA and testosterone both of which can be aromatized to estrogens at appropriate dose elvels caused potentiation of the effect of PMSG on the secretion of gonadotropins. They also induced vaginal patency in the castrated immature rat. Dihydrotestosterone, an androgen not aromatized to estrogens did not induce precocious ovulation, vaginal patency or potentiation of the effect of PMSG in the release of gonadotropins. Furthermore, cyanoketone an inhibitor of 3beta-hydroxysteroid dehydrogenase and thus the conversion of DHA to estrogens, prevented vaginal patency and DHA-induced precocious ovulation.
Cytidine 5′-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2 -C -methylerythritol (1999)

2-C-methylerythritol 4-phosphate has been established recently as an intermediate of the deoxyxylulose phosphate pathway used for biosynthesis of terpenoids in plants and in many microorganisms. We show that an enzyme isolated from cell extract of Escherichia coli converts 2-C-methylerythritol 4-phosphate into 4-diphosphocytidyl-2-C-methylerythritol by reaction with CTP. The enzyme is specified by the hitherto unannotated ORF ygbP of E. coli. The cognate protein was obtained in pure form from a recombinant hyperexpression strain of E. coli harboring a plasmid with the ygbP gene under the control of a T5 promoter and lac operator. By using the recombinant enzyme, 4-diphosphocytidyl-[2-(14)C]2-C-methylerythritol was prepared from [2-(14)C]2-C-methylerythritol 4-phosphate. The radiolabeled 4-diphosphocytidyl-2-C-methylerythritol was shown to be efficiently incorporated into carotenoids by isolated chromoplasts of Capsicum annuum. The E. coli ygbP gene appears to be part of a small operon also comprising the unannotated ygbB gene. Genes with similarity to ygbP and ygbB are present in the genomes of many microorganisms, and their occurrence appears to be correlated with that of the deoxyxylulose pathway of terpenoid biosynthesis. Moreover, several microorganisms have genes specifying putative fusion proteins with ygbP and ygbB domains, suggesting that both the YgbP protein and the YgbB protein are involved in the deoxyxylulose pathway. A gene from Arabidopsis thaliana with similarity to ygbP carries a putative plastid import sequence, which is well in line with the assumed localization of the deoxyxylulose pathway in the plastid compartment of plants.
An Adenovirus–Epstein-Barr Virus Hybrid Vector That Stably Transforms Cultured Cells with High Efficiency (1999)

EBV episomes are nuclear plasmids that are stably maintained through multiple cell divisions in primate and canine cells (J. L. Yates, N. Warren, and B. Sugden, Nature 313:812-815, 1985). In this report, we describe the construction and characterization of an E1-deleted recombinant adenovirus vector system that delivers an EBV episome to infected cells. This adenovirus-EBV hybrid vector system utilizes Cre-mediated, site-specific recombination to excise an EBV episome from a target recombinant adenovirus genome. We demonstrate that this vector system efficiently delivers the EBV episome and stably transforms a large fraction of infected canine D-17 cells. Using a colony-forming assay, we demonstrate stable transformation of 37% of cells that survive the infection. However, maximal transformation efficiency is achieved at doses of the E1-deleted recombinant adenoviruses that are toxic to the infected cells. Consequently, E1-deleted vector toxicity imposes a limitation on our current vector system.
Temporal variation in natural methane seep rate due to tides, Coal Oil Point area, California (2001)

Two large steel tents (each 30 m by 30 m), open at the bottom to the seafloor, capture ∼16,800 m 3 d −1 (594 MCF) of primarily methane from a large natural hydrocarbon seep, occurring a kilometer offshore in 67 m of water. The gas is piped to shore where it is metered and processed. The seep flow rate was monitored hourly for 9 months. Our results show that the tidal forcing causes the flow rate to vary by 4–7% around the mean. These results are the first quantitative documentation of the effect of tides on natural gas seepage in relatively deep water. Time series analyses of the 9 month record clearly show four principal tidal components with periods of 12.0, 12.4, 23.9, and 25.8 hours. High tide correlates with reduced flow, and low tide correlates with increased flow. The correlation indicates that each meter increase of sea height results in a decrease of 10–15 m 3 hr −1 or 1.5–2.2% of the hourly flow rate. The observed changes are best accounted for by a pore activation model, whereby gas is released from small pores at low pressures but is inhibited at higher pressure. Pressure‐dependent gas solubility changes are a less likely cause of flow variation. Our study implies that sea level differences, on a tidal timescale, can significantly change the gas seepage rate from sediments. Lower sea level in the last hundred thousand years would presumably allow higher gas loss from the sediment, assuming sufficient gas present, because of reduced hydrostatic pressure at the sediment‐sea interface. The magnitude of this long‐term change cannot be extrapolated from our tidal data.
Fourier spectrum of halftone images (1975)

An analytic expression has been developed that can be used for computing the Fourier spectrum of any halftone image as a function of the original continuous-tone image and the halftone process. This result takes into account the nonlinear effects of the threshold step in the halftone process. Although the result is general and can be applied to any original image, in some cases of periodic images the Fourier components of the halftone image are particularly easy to compute. We show important differences between spectra of halftone images and scanned or sampled images. In halftone images, significant image detail is maintained at spatial frequencies greater than half of the screen frequency and aliasing or moiré patterns depend upon object contrast and upon the halftone function differently from similar patterns which occur in scanned or sampled imagery.
ALGORITHM FOR REMOTE SENSING OF TROPOSPHERIC AEROSOL FROM MODIS (1998)

This document describes the algorithms for simultaneous remote sensing of aerosol from EOS-MODIS over land and ocean. The algorithm will be used to monitor the aerosol optical thickness (proportional to the aerosol total loading) and size distribution (integrated on the vertical column) of the ambient (undisturbed) aerosol, over most of the globe (oceans and the moist parts of the continents) on a daily basis. The size distribution will be derived only over the oceans. These aerosol products will be used to monitor the aerosol mass concentration, optical properties, and radiative forcing.
Bile-acid-mediated decrease in endoplasmic reticulum stress: a potential contributor to the metabolic benefits of ileal interposition surgery in UCD-T2DM rats (2012)

Post-operative increases in circulating bile acids have been suggested to contribute to the metabolic benefits of bariatric surgery; however, their mechanistic contributions remain undefined. We have previously reported that ileal interposition (IT) surgery delays the onset of type 2 diabetes in UCD-T2DM rats and increases circulating bile acids, independently of effects on energy intake or body weight. Therefore, we investigated potential mechanisms by which post-operative increases in circulating bile acids improve glucose homeostasis after IT surgery. IT, sham or no surgery was performed on 2-month-old weight-matched male UCD-T2DM rats. Animals underwent an oral fat tolerance test (OFTT) and serial oral glucose tolerance tests (OGTT). Tissues were collected at 1.5 and 4.5 months after surgery. Cell culture models were used to investigate interactions between bile acids and ER stress. IT-operated animals exhibited marked improvements in glucose and lipid metabolism, with concurrent increases in postprandial glucagon-like peptide-1 (GLP-1) secretion during the OFTT and OGTTs, independently of food intake and body weight. Measurement of circulating bile acid profiles revealed increases in circulating total bile acids in IT-operated animals, with a preferential increase in circulating cholic acid concentrations. Gut microbial populations were assessed as potential contributors to the increases in circulating bile acid concentrations, which revealed proportional increases in Gammaproteobacteria in IT-operated animals. Furthermore, IT surgery decreased all three sub-arms of ER stress signaling in liver, adipose and pancreas tissues. Amelioration of ER stress coincided with improved insulin signaling and preservation of β-cell mass in IT-operated animals. Incubation of hepatocyte, adipocyte and β-cell lines with cholic acid decreased ER stress. These results suggest that postoperative increases in circulating cholic acid concentration contribute to improvements in glucose homeostasis after IT surgery by ameliorating ER stress.
The Effect of pH, Germinants and Temperature on the Germination of Spores of Clostridium bifermentans (1974)

SUMMARY: The germination rate of Clostridium bifermentans spores and the manner in which it is influenced by pH, sodium ion concentration and temperature differ according to the organic germinant used. Only l-alanine initiated germination when present alone. The germination rate with optimal l-alanine was increased by l-phenylalanine, l-arginine, l-histidine or l-lysine but not by other common amino acids or l-lactate. With suboptimal concentrations of l-alanine, addition of l-lactate, l-arginine or l-phenylalanine increased the germination rate more than an equal concentration of l-alanine. The mechanisms whereby l-phenylalanine and l-arginine stimulate germination appear to be different from those involved when l-alanine or l-lactate are the germinants.
Ultrastructural study of surface components of Streptococcus suis (1990)

The presence of capsular material on cells of nine reference strains of Streptococcus suis representing serotypes 1 to 8 and 1/2 was determined by transmission electron microscopy after polycationic ferritin labeling, immunostabilization, or fixation with a combination of glutaraldehyde and lysine. All the cells of the reference strains examined were covered with a layer of capsular material whose thickness varied between 20 to 30 nm and 350 to 375 nm when examined by immunostabilization. Capsular material from cells exposed to homologous antiserum was usually thicker than that from polycationic ferritin-labeled cells or cells fixed with glutaraldehyde-lysine. Negative staining revealed detectable surface structures on S. suis strains. All strains carried peritichous, thin, and flexible fimbriae with a diameter of approximately 2 nm and a length of up to 250 nm. This study indicated that morphological differences of surface structure exist among S. suis reference strains.
In Situ Transcription: Specific Synthesis of Complementary DNA in Fixed Tissue Sections (1988)

A technique, in situ transcription, is described, in which reverse transcription of mRNAs is achieved within fixed tissue sections. An oligonucleotide complementary to proopiomelanocortin (POMC) mRNA was used as a primer for the specific synthesis of radiolabeled POMC cDNA in fixed sections of rat pituitary, thus permitting the rapid anatomical localization of POMC mRNA by autoradiography. Intermediate lobe signal intensities were sensitive to dopaminergic drugs, demonstrating that the method can be used for studies of mRNA regulation. The transcripts may also be eluted from tissue sections for a variety of uses, including the identification and cloning of autoradiographically localized cDNAs from small amounts of tissue.
Design and Synthesis of a Homogeneous Erythropoietin Analogue with Two Human Complex‐Type Sialyloligosaccharides: Combined Use of Chemical and Bacterial Protein Expression Methods (2009)

Highly expressive: Cell proliferation was observed with concentrations of an erythropoietin (EPO) analogue above 50 pg mL−1. The EPO analogue has two human complex-type sialyloligosaccharides (see picture) and was formed by the combined use of chemical synthesis and protein expression in E. coli. Both the 24- and 30-positions are glycosylated, but the two sialyloligosaccharides do not interfere with binding of the EPO analogue to a receptor. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
3,3‘-Bimorpholine Derivatives as a New Class of Organocatalysts for Asymmetric Michael Addition (2006)

New N-alkyl-3,3'-bimorpholine derivatives (iPBM) were revealed to be efficient organocatalysts for the asymmetric direct Michael addition of aldehydes to nitroolefins and a vinyl sulfone. In these transformations using iPBM, 1,4-adducts were afforded in high yields, with good to high levels of diastereo- and enantioselectivity. The stereochemical outcome of the reaction could be explained by an acyclic synclinal model. [reaction: see text]
Protective effect of arachidonic acid on glutamate neurotoxicity in rat retinal ganglion cells. (2002)

Low concentrations of AA can reduce glutamate neurotoxicity to RGCs by the inhibition of non-NMDA ionotropic receptors. These results suggest that endogenous or exogenous AA may be used to protect RGCs from glutamate neurotoxicity and that AA may be one potential treatment for RGC loss in a variety of eye diseases, including glaucoma.
X-ray/Neutron Diffraction and Electrochemical Studies of Lithium De/Re-Intercalation in Li1-xCo1/3Ni1/3Mn1/3O2 (x = 0 → 1) (2006)

X-ray and neutron diffraction studies were carried out on highly ordered (2−3% Li/Ni exchange) layered Li1-xCo1/3Ni1/3Mn1/3O2 [(1 − x) = 1.0; 0.8, 0.6, 0.45, 0.30, 0.04] prepared by chemical delithiation and relithiation. The studies reveal that the initial R3̄m phase (O3) is maintained up to extraction of 0.70−0.75 Li and exhibits only ∼1% change in volume over the range of composition. Additional extraction of Li results in the appearance of the O1 phase (trigonal; P3̄m1), which displays a strong contraction in the c axis by 5.3% and a volume decrease of 7.2%. Oxygen vacancies were not evident in the completely delithiated material. Re-intercalation of lithium in this phase was relatively irreversible, however, resulting in poorly defined mixtures of the O3 and O1 structures that exhibited a large fraction of stacking faults. In contrast, materials that were not delithiated beyond x = 0.30 resulted in fully reversible reformation of the original crystalline O3 phase on re-intercalation. Electrochemical cycling under different cutoff voltages were in accord with these observations and suggest an optimum upper cutoff voltage of 4.3−4.4 V.
The Intratumoral Balance between Metabolic and Immunologic Gene Expression Is Associated with Anti–PD-1 Response in Patients with Renal Cell Carcinoma (2016)

Pretreatment tumor PD-L1 expression has been shown to correlate with response to anti-PD-1/PD-L1 therapies. Yet, most patients with PD-L1(+) tumors do not respond to treatment. The current study was undertaken to investigate mechanisms underlying the failure of PD-1-targeted therapies in patients with advanced renal cell carcinoma (RCC) whose tumors express PD-L1. Formalin-fixed, paraffin-embedded pretreatment tumor biopsies expressing PD-L1 were derived from 13 RCC patients. RNA was isolated from PD-L1(+) regions and subjected to whole genome microarray and multiplex quantitative (q)RT-PCR gene expression analysis. A balance between gene expression profiles reflecting metabolic pathways and immune functions was associated with clinical outcomes following anti-PD-1 therapy. In particular, the expression of genes involved in metabolic and solute transport functions such as UGT1A family members, also found in kidney cancer cell lines, was associated with treatment failure in patients with PD-L1(+) RCC. Conversely, tumors from responding patients overexpressed immune markers such as BACH2, a regulator of CD4(+) T-cell differentiation, and CCL3 involved in leukocyte migration. These findings suggest that tumor cell-intrinsic metabolic factors may contribute to treatment resistance in RCC, thus serving as predictive markers for treatment outcomes and potential new targets for combination therapy regimens with anti-PD-1. Cancer Immunol Res; 4(9); 726-33. ©2016 AACRSee related Spotlight by Ohashi, p. 719.
Extracellular Antigens fromSalmonella enteritidisInduce Effective Immune Response in Mice after Oral Vaccination (2002)

We have studied polyacryl starch microparticles as an adjuvant in oral vaccination in mice. Secreted antigens from Salmonella enterica serovar Enteritidis were administered covalently conjugated to microparticles, or as free antigens, orally or intramuscularly and evaluated for their immunogenicity and ability to elicit protective immune response against an oral challenge with live serovar Enteritidis. The highest immunoglobulin M (IgM)-plus-IgG titers were obtained in the groups immunized with antigen-conjugated microparticles. The subclass profile switched to a stronger Th1 influence in the oral groups after booster, while the intramuscular group showed a constant Th1/Th2 profile. A strong specific IgA response was seen in feces in the oral groups, which was further confirmed in an enzyme-linked immunospot assay. The delayed-type hypersensitivity test, as a measure of the cellular response, showed a significant increase in ear thickness in all the immunized groups, except for the group that received free antigen orally, compared to the nonimmunized group. The cytokines released from in vitro-stimulated spleens showed a strong gamma interferon response in all immunized groups. A significant reduction in CFU in liver and spleen was seen in the orally immunized groups compared to the nonimmunized group after oral challenge with serovar Enteritidis. Western blotting analysis with both sera and feces revealed that antibodies against three bands, 53, 56, and 60 kDa, dominated the oral groups, and an electrospray-mass spectroscopy analysis of these bands showed amino acid sequences coinciding with those of phase-1 flagellin and hook-associated protein 2.
Immunokinetics of autoreactive CD4 T cells in blood: a reporter for the “hit-and-run” autoimmune attack on pancreas and diabetes progression (2004)

Little is known about the fate of autoreactive CD4 T cells in blood. Using a mouse model for spontaneous autoimmune diabetes we demonstrated that the status of the autoimmune process in pancreas could be pictured through the frequency and phenotype of autoreactive CD4 T cells in the blood. Early during the prediabetic stage, the frequency of these cells in blood decreased as a consequence of their recruitment in the pancreas. This was followed by an imbalance between CD4(+)CD25(+) and CD4(+)CD69(+) T cells in the pancreas that was mirrored in the phenotype of autoreactive T cells in the blood. Waves of activated CD4(+)CD69(+) T cells in blood preceded the disease onset suggesting that the autoimmune attack on pancreas is a discontinuous "hit-and-run" rather than a continuous process. Tracking autoreactive CD4 T cells in blood may help in identifying prediabetic humans and monitoring the disease progression during therapeutic interventions.
ILIAD as an Expert Consultant to Teach Differential Diagnosis (1988)

A program (ILIAD) is described which uses knowledge frames representing diseases encountered in internal medicine to teach medical students about differential diagnosis. ILIAD consultant utilizes a number of sophisticated inferencing mechanisms to mimic the strategy of a medical expert in working up a patient. Its knowledge is represented in both Bayesean and Boolean frames which permit use of sensitivities and specificities to describe the relationship of a disease to its manifestations and provide a basis for explaining its conclusions. In addition to differential diagnosis, ILIAD provides advice regarding the most appropriate information to seek at each stage of the workup. ILIAD's knowledge base is also used to simulate patient cases and evaluate the problem solving performance of medical apprentices. It is presently being used by third year medical clerks on the wards of three hospitals and beta tested at eight additional sites.