gebhart/patrepeval huggingface dataset:
Cell Wall and Secreted Proteins ofCandida albicans: Identification, Function, and Expression (1998)

The cell wall is essential to nearly every aspect of the biology and pathogenicity of Candida albicans. Although it was initially considered an almost inert cellular structure that protected the protoplast against osmotic offense, more recent studies have demonstrated that it is a dynamic organelle. The major components of the cell wall are glucan and chitin, which are associated with structural rigidity, and mannoproteins. The protein component, including both mannoprotein and nonmannoproteins, comprises some 40 or more moieties. Wall proteins may differ in their expression, secretion, or topological location within the wall structure. Proteins may be modified by glycosylation (primarily addition of mannose residues), phosphorylation, and ubiquitination. Among the secreted enzymes are those that are postulated to have substrates within the cell wall and those that find substrates in the extracellular environment. Cell wall proteins have been implicated in adhesion to host tissues and ligands. Fibrinogen, complement fragments, and several extracellular matrix components are among the host proteins bound by cell wall proteins. Proteins related to the hsp70 and hsp90 families of conserved stress proteins and some glycolytic enzyme proteins are also found in the cell wall, apparently as bona fide components. In addition, the expression of some proteins is associated with the morphological growth form of the fungus and may play a role in morphogenesis. Finally, surface mannoproteins are strong immunogens that trigger and modulate the host immune response during candidiasis.
Very low threshold oxide-confined 1.3 /spl mu/m GaAs-based quantum dot laser (2000)

Summary form only given. Research on GaAs-based quantum dot (QD) lasers operating at 1.3 /spl mu/m wavelength has been rapidly advancing since the demonstrations of room-temperature operation in pulsed-mode and continuous wave (CW) operation. Native oxide confinement is of interest for this type of laser, similar to that used for quantum well edge-emitting lasers and quantum dot vertical cavity surface emitting lasers. The native oxide confinement is especially interesting due to the lateral "built-in" electronic confinement potentials that confine the current in lateral direction. We report on the room-temperature CW operation of oxide-confined single-layer InGaAs QD lasers with very low threshold current of 1.2 mA. The low threshold operation is achieved due to low optical waveguide loss of the native oxide.
Acute Lung Injury and Acute Kidney Injury Are Established by Four Hours in Experimental Sepsis and Are Improved with Pre, but Not Post, Sepsis Administration of TNF-α Antibodies (2013)

ALI and AKI occur together early in the course of sepsis and TNF-α plays a role in the early pathogenesis of both.
Differential effects of protein synthesis inhibitors on porcine oocyte activation (1995)

This study was designed to evaluate the effects of cycloheximide and puromycin on activation and protein synthesis of porcine oocytes. When matured oocytes were electrostimulated, then cultured in the presence of cycloheximide (5 micrograms/ml) for 6 or 24 hr, 92% of oocytes were activated as indicated by pronuclear formation, vs. 2.8% for untreated oocytes, 5.3% for oocytes not electrostimulated but cultured with cycloheximide, and 60.0% for those only electrostimulated. When cultured with L-[35S]methionine in the presence of cycloheximide, puromycin (100 micrograms/ml), or no protein synthesis inhibitor for 24 hr, oocytes had mean radiolabeled incorporation rates of 36.5, 2.21, and 32.0 fmol/4 hr/oocyte, respectively. Thus, cycloheximide had little effect on protein synthesis after 24 hr of culture. A 1D-SDS PAGE showed that oocytes cultured with puromycin or cycloheximide are not activated, while electrostimulated oocytes are activated, as characterized by the conversion of a 25-kDa polypeptide to a 22-kDa polypeptide. The radiolabeling experiment was repeated, except that oocytes were cultured for 4 or 24 hr. At 4 hr, mean incorporation rates were lower in the cycloheximide group (2.34 fmol/4 hr/oocyte), but similar in the puromycin (15.7 fmol/4 hr/oocyte) and control groups (18.9 fmol/4 hr/oocyte). At 24 hr, the puromycin group 5.73 fmol/4 hr/oocyte) had a lower rate of incorporation, while the cycloheximide (22.6 fmol/4 hr/oocyte) and control (26.0 fmol/4 hr/oocyte) groups were similar. Cycloheximide was more effective earlier during culture, while puromycin was more effective later. When combined with ES, puromycin did have a higher rate (P = 0.10) of activation (87.8%) than with electrostimulation alone (73.0%).(ABSTRACT TRUNCATED AT 250 WORDS)
Opportunities of Downhole Dielectric Heating in Venezuela: Three Case Studies Involving Medium, Heavy and Extra-Heavy Crude Oil Reservoirs (2002)

Abstract The use of electromagnetic radiation, radiofrequency (RF) and microwaves (MW), for downhole dielectric heating has potential applications in enhanced/improved oil recovery processes (EOR). The Lambert’s equation was coupled to a commercial simulator in order to model reservoir dielectric heating. Using a MW heated (2.45 GHz) one-dimensional reactor, this mathematical model was validated in the presence of crude oil/sand cores. Three different conceptual reservoirs were evaluated which involved a medium crude oil (24°API), a shallow (1100 ft) Lake Maracaibo heavy oil (11°API) and a thin pay zone (20 ft) Orinoco Basin extraheavy crude (7.7°API). For all the cases evaluated, numerical simulation results showed an important acceleration in the oil production due to RF and MW heating which was attributed to reduction of crude viscosity coupled with favorable relative water-to-oil permeabilities. For example, in the shallow heavy oil case, RF heating led to an increase of 86% of the cumulative oil production in comparison with the cold production case, using 140 MHz at 50 kW over a ten-year period. Furthermore, calculated energy gains (measured as the ratio between the energy extracted as crude oil equivalent to energy added to the reservoir as electricity) were in the 8 to 20 range, indicating that the process is favorable from the thermodynamic point of view. These conceptual numerical simulation results indicate the high potential of dielectric heating technology for medium, heavy and extra-heavy EOR with possible field applications.
Protein Expression Analysis Using Quantitative Fluorescence Image Analysis on Tissue Microarray Slides (2002)

We have developed a tissue microarray (TMA)-based quantitative fluorescence image analysis (QFIA) method in which protein markers on TMA sections were labeled by immunofluorescence using tyramide signal amplification and a quantitative fluorescence detection system. Using this method, BRCA1 protein expression patterns were studied in the TMA sections of cell lines with known levels of BRCA1 expression and in a small group of human tissue samples obtained from sporadic epithelial ovarian cancers, their corresponding adjacent dysplastic fields, and distant non-tumor areas. We detected distinctive BRCA1 expression patterns in high-grade and low-grade sporadic epithelial ovarian cancers and their associated adjacent dysplastic fields. However, such patterns of expression could not be adequately detected by traditional immunohistochemical staining methods. TMA-QFIA provides a sensitive, automated, and quantitative measurement of protein expression on archived tissue and cell samples and will be a useful tool for protein-level molecular profiling analyses.
Non-Uniform Constellations for ATSC 3.0 (2016)

This paper introduces the concept of a non-uniform constellation (NUC) in contrast to conventional uniform quadrature-amplitude modulation (QAM) constellations. Such constellations provide additional shaping gain, which allows reception at lower signal-to-noise ratios. ATSC3.0 will be the first major broadcasting standard, which completely uses NUCs due to their outstanding properties. We will consider different kinds of NUCs and describe their performance: 2-D NUCs provide more shaping gain at the cost of higher demapping complexity, while 1-D NUCs allow low-complexity demapping at slightly lower shaping gains. These NUCs are well suited for very large constellations sizes, such as 1k and 4k QAM.
Binaural Interaction of a Beating Frequency-Following Response (1980)

Frequency-following responses to 500-Hz tone bursts presented to the left ear and 540-Hz tone bursts presented to the right ear were recorded from human subjects. Recordings were made both under monaural and binaural conditions. The responses summed over monaural conditions (for left and right ear stimulation) were larger than the responses obtained in the binaural condition. This binaural interaction shows that the frequency-following response reflects binaural processing probably occurring at or below the level of the inferior colliculi.
Conditioning of quasi-Newton methods for function minimization (1970)

Quasi-Newton methods accelerate the steepest-descent technique for function minimization by using computational history to generate a sequence of approximations to the inverse of the Hessian matrix. This paper presents a class of approximating matrices as a function of a scalar parameter. The problem of optimal conditioning of these matrices under an appropriate norm as a function of the scalar parameter is investigated. A set of computational results verifies the superiority of the new methods arising from conditioning considerations to known methods.
Initiation and Processing of Two Kappa Immunoglobulin Germ Line Transcripts in Mouse B Cells (1990)

The splicing patterns and sequences of two processed kappa immunoglobulin germ line mRNAs are presented. A 1.1-kilobase (kb) mRNA appeared to be derived from splicing of the previously characterized 8.4-kb germ line transcript, while a 0.8-kb mRNA was the splice product of a second 4.7-kb germ line transcript that initiated 50 base pairs upstream of J kappa 1. The interaction of the two kappa germ line promoters with nuclear binding factors is also examined. The potential role of these germ line transcripts in establishing the rearrangement potential of the locus is discussed.
Treatment with a C5aR Antagonist Decreases Pathology and Enhances Behavioral Performance in Murine Models of Alzheimer’s Disease (2009)

Alzheimer's disease (AD) is an age-related dementia, characterized by amyloid plaques, neurofibrillary tangles, neuroinflammation, and neuronal loss in the brain. Components of the complement system, known to produce a local inflammatory reaction, are associated with the plaques and tangles in AD brain, and thus a role for complement-mediated inflammation in the acceleration or progression of disease has been proposed. A complement activation product, C5a, is known to recruit and activate microglia and astrocytes in vitro by activation of a G protein-coupled cell-surface C5aR. Here, oral delivery of a cyclic hexapeptide C5a receptor antagonist (PMX205) for 2-3 mo resulted in substantial reduction of pathological markers such as fibrillar amyloid deposits (49-62%) and activated glia (42-68%) in two mouse models of AD. The reduction in pathology was correlated with improvements in a passive avoidance behavioral task in Tg2576 mice. In 3xTg mice, PMX205 also significantly reduced hyperphosphorylated tau (69%). These data provide the first evidence that inhibition of a proinflammatory receptor-mediated function of the complement cascade (i.e., C5aR) can interfere with neuroinflammation and neurodegeneration in AD rodent models, suggesting a novel therapeutic target for reducing pathology and improving cognitive function in human AD patients.
[The regulatory effect of endogenous hydrogen sulfide on acute asthma]. (2007)

Endogenous H(2)S is involved in the pathogenesis of asthma in this animal model. Exogenously applied H(2)S can attenuate inflammation of asthma and exert protective effect from asthma.
Fusion of the transcription factor TFE3 gene to a novel gene, PRCC , in t(X;1)(p11;q21)-positive papillary renal cell carcinomas (1996)

The (X;1)(p11;q21) translocation is a recurrent chromosomal abnormality in a subset of human papillary renal cell carcinomas, and is sometimes the sole cytogenetic abnormality present. Via positional cloning, we were able to identify the genes involved. The translocation results in a fusion of the transcription factor TFE3 gene on the X chromosome to a novel gene, designated PRCC, on chromosome 1. Through this fusion, reciprocal translocation products are formed, which are both expressed in papillary renal cell carcinomas. PRCC is ubiquitously expressed in normal adult and fetal tissues and encodes a putative protein of 491 aa with a relatively high content of prolines. No relevant homologies with known sequences at either the DNA or the protein level were found.
Screening serum biomarkers of fatty liver disease using proteomic technology (2008)

AIM:To analyze the serum proteomic pattern of the fatty liver disease(FLD)patients,to build a diagnostic model and to evaluate its clinic significance using magnetic bead and MALDI-TOF-MS.METHODS:WCX magnetic bead and MALDI-TOF-MS were used to detect the serum pro-teomic patterns of 95 modest FLD patients,76mild FLD patients and 99 healthy persons(HP).Biomarker Wizard software was used to ana-lyze protein peaks for significant difference.The model was then built by Biomarker Patterns Software and was further evaluated in blind test for reliability.RESULTS:A diagnostic pattern for modest FLD from HP using m/z 7626.2,24147.7,6118.2 was established with 90.2% sensitivity and 93.9% specificity.A sensitivity of 90.9% and a specific-ity of 92.0% in blind test were obtained.One diagnostic pattern using m/z 7626.2,3286.0,2760.7,2543.1,2746.1 was established to differen-tiate mild from modest FLD;the other diagnos-tic pattern using m/z 7626.2,11721.0,24141.7,8529.1,9042.7 was established to differentiate mild FLD from HP.CONCLUSION:Proteomic technology can sig-nificantly identify novel significant biomarkers in the serum.The diagnostic pattern consisting of three differential protein peaks can discrimi-nate the modest FLD from HP.The diagnostic pattern consisting of five specific differential protein peaks can differentiate mild from mod-est FLD as well as mild FLD from HP.
Host cell protein dynamics in recombinant CHO cells (2013)

During the production of recombinant protein products, such as monoclonal antibodies, manufacturers must demonstrate clearance of host cell impurities and contaminants to appropriate levels prior to use in the clinic. These include host cell DNA and RNA, product related contaminants such as aggregates, and importantly host cell proteins (HCPs). Despite the importance of HCP removal, the identity and dynamics of these proteins during cell culture and downstream processing (DSP) are largely unknown. Improvements in technologies such as SELDI-TOF mass spectrometry alongside the gold standard technique of ELISA has allowed semi-quantification of the total HCPs present. However, only recently have techniques been utilized in order to identify those HCPs present and align this with the development of approaches to monitor the dynamics of HCPs during both fermentation and downstream processing. In order to enable knowledge based decisions with regards to improving HCP clearance it is vital to identify potential problematic HCPs on a cell line and product specific basis. Understanding the HCP dynamics will in the future help provide a platform to rationally manipulate and engineer and/or select suitable recombinant CHO cell lines and downstream processing steps to limit problematic HCPs.
Composition, in vitro Anti-inflammatory, Antioxidant and Antimicrobial Activities of the Leaf Essential Oil of Machilus konishii from Taiwan (2016)

The chemical composition and in vitro anti-inflammatory, antioxidant and antimicrobial activities of the leaf essential oil of Machils konishii has been investigated. The essential oil was isolated using hydrodistillation in a Clevenger-type apparatus, and characterized by GC-FID and GC-MS. Sixty-six compounds were identified, representing 100% of the oil. The main components identified were a-pinene (33.9%), α-pinene (13.9%), and thymol (12.0%); The leaf oil was able to reduce nitric oxide production by lipopolysaccharide-activated murine macrophages RAW 264.7 without reducing the cell viability. In addition, the leaf oil showed strong antioxidant and antimicrobial activities. The major ingredient of the oil that was responsible for the anti-inflammatory, antioxidant and antimicrobial activities was thymol.
Mutation of the TGD1 Chloroplast Envelope Protein Affects Phosphatidate Metabolism inArabidopsis (2005)

Phosphatidate (PA) is a central metabolite of lipid metabolism and a signaling molecule in many eukaryotes, including plants. Mutations in a permease-like protein, TRIGALACTOSYLDIACYLGLYCEROL1 (TGD1), in Arabidopsis thaliana caused the accumulation of triacylglycerols, oligogalactolipids, and PA. Chloroplast lipids were altered in their fatty acid composition consistent with an impairment of lipid trafficking from the endoplasmic reticulum (ER) to the chloroplast and a disruption of thylakoid lipid biosynthesis from ER-derived precursors. The process mediated by TGD1 appears to be essential as mutation of the protein caused a high incidence of embryo abortion. Isolated tgd1 mutant chloroplasts showed a decreased ability to incorporate PA into galactolipids. The TGD1 protein was localized to the inner chloroplast envelope and appears to be a component of a lipid transporter. As even partial disruption of TGD1 function has drastic consequences on central lipid metabolism, the tgd1 mutant provides a tool to explore regulatory mechanisms governing lipid homeostasis and lipid trafficking in plants.
Knock-down of OsDCL2 in Rice Negatively Affects Maintenance of the Endogenous dsRNA Virus, Oryza sativa Endornavirus (2009)

An endogenous double-stranded RNA (dsRNA), which has recently been recognized as the dsRNA virus Oryza sativa endornavirus (OsEV), is found in many strains of cultivated rice (Oryza sativa). Small RNAs derived from OsEV dsRNA were detected, indicating that the RNA silencing machinery recognizes OsEV dsRNA. The existence of OsEV in knock-down (KD) lines of five genes of RNA-dependent RNA polymerase (OsRDR1-OsRDR5) or two genes of Dicer-like protein (OsDCL2 or OsDCL3a) was examined to characterize the relationship between the host RNA silencing system and the propagation of this dsRNA virus. OsEV was not detected in OsRDR4-KD or OsDCL2-KD T(1) lines. We attempted to introduce OsEV into these KD lines by crossing them with OsEV-carrying plants because of the efficient transmission of OsEV to F(1) plants via pollen or ova. All OsRDR4-KD but only some OsDCL2-KD F(1) plants contained OsEV. Some OsDCL2-KD F(1) plants consisted of OsEV-carrying and OsEV-free cells. These results suggest that the maintenance of OsEV is unstable in OsDCL2-KD plants. Furthermore, the amount of OsEV-derived small interfering RNA (vsiRNA) in the OsDCL2-KD plants increased relative to the wild type. This increased level of vsiRNA may cause OsEV instability during cell division.
Ethylene Production, 1-Aminocyclopropane-l-Carboxylic Acid Content and Its Conversion to Ethylene in Axial Segments of Dormant and Nondormant Cocklebur Seeds (1983)

Journal Article Ethylene Production, 1-Aminocyclopropane-l-Carboxylic Acid Content and Its Conversion to Ethylene in Axial Segments of Dormant and Nondormant Cocklebur Seeds Get access Shigeru Satoh, Shigeru Satoh Department of Biological Science, Tohoku UniversityKawauchi, Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Yohji Esashi Yohji Esashi Department of Biological Science, Tohoku UniversityKawauchi, Sendai 980, Japan Search for other works by this author on: Oxford Academic Google Scholar Plant and Cell Physiology, Volume 24, Issue 5, July 1983, Pages 883–887, https://doi.org/10.1093/oxfordjournals.pcp.a076591 Published: 01 July 1983 Article history Received: 17 December 1982 Accepted: 30 April 1983 Published: 01 July 1983
A new approach to the study of haematopoietic development in the yolk sac and embryoid bodies (1995)

To understand the mechanisms that control the differentiation of uncommitted mesoderm precursors into haematopoietic stem cells (HSCs) and the activation of haematopoiesis, we conducted a study to identify genes expressed at the earliest stages of both in vivo and in vitro haematopoietic development. Our strategy was to utilize Differential Display by means of the Polymerase Chain Reaction (DD-PCR) to compare patterns of gene expression between mRNA populations representing different levels of haematopoietic activity obtained from the mouse embryo, embryoid bodies (EBs) and mouse cell lines. We report the molecular cloning of two groups of genes expressed in the yolk sac: a group of genes expressed in the day-8.5 yolk sac at higher levels than in the day-8.5 embryo proper and up-regulated during EB development, and another group of day-8.5 yolk sac genes not expressed in the day-8.5 embryo proper or in EBs. Specifically, we describe the molecular cloning of the first nucleobase permease gene to be found in vertebrates, yolk sac permease-like molecule 1 (Ysp11). The Ysp11 gene has the unique property of encoding both intracellular, transmembrane and extracellular protein forms, revealing novel aspects of nucleotide metabolism that may be relevant during mammalian development.
<title>Use of multiple data types in time-resolved optical absorption and scattering tomography</title> (1993)

In Time-resolved Optical Absorption and Scattering Tomography (TOAST) the imaging problem is to reconstruct the coefficients of absorption (mu)<SUB>a</SUB> and scattering (mu)<SUB>s</SUB> of light in tissue given the time-dependent photon flux at the surface of the subject, resulting from ultrafast laser input pulses. This inverse problem is mathematically similar to the Electrical Impedance problem (EIT) but presents some unique features. In particular the necessity of searching in two solution spaces requires the use of multiple data types that are maximally uncorrelated with respect to the solution spaces. We developed an algorithm for TOAST that uses an iterative non-linear gradient descent method to minimize an appropriate error norm. The algorithm can work on multiple types of data and an important topic is the choice of the best data format to use. Usually the choice is integrated intensity and mean time- of-flight for the temporal domain data. In this paper we compare these data types with the use of higher order moments of the temporal distribution (variance, skew, kurtosis). We show that reliable results must take detailed account of the confidence limits on each data point. We demonstrate how the probability distribution function for photon propagation can be calculated so that the variance of any given measurement type can be derived.
Dimethyl fumarate (2004)

Di­methyl fumarate, C6H8O4, crystallizes in the fully stretched planar conformation. The mol­ecule is located on a crystallographic inversion centre and has local symmetry 2/m. The fumarate mol­ecules aggregate in layers coinciding with the (1\overline 11) lattice planes.