gebhart/patrepeval huggingface dataset:
Comparative genomics of xylose-fermenting fungi for enhanced biofuel production (2011)

Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.
A Vicious Cycle Involving Release of Heat Shock Protein 60 from Injured Cells and Activation of Toll-Like Receptor 4 Mediates Neurodegeneration in the CNS (2008)

Infection, ischemia, trauma, and neoplasia elicit a similar inflammatory response in the CNS characterized by activation of microglia, the resident CNS monocyte. The molecular events leading from CNS injury to the activation of innate immunity is not well understood. We show here that the intracellular chaperone heat shock protein 60 (HSP60) serves as a signal of CNS injury by activating microglia through a toll-like receptor 4 (TLR4)-dependent and myeloid differentiation factor 88 (MyD88)-dependent pathway. HSP60 is released from CNS cells undergoing necrotic or apoptotic cell death and specifically binds to microglia. HSP60-induced synthesis of neurotoxic nitric oxide by microglia is dependent on TLR4. HSP60 induces extensive axonal loss and neuronal death in CNS cultures from wild-type but not TLR4 or MyD88 loss-of-function mutant mice. This is the first evidence of an endogenous molecular pathway common to many forms of neuronal injury that bidirectionally links CNS inflammation with neurodegeneration.
A new viewpoint on the operation principles of the reflection type cavity-stablized gunn oscillator (1989)

As one of the three types of cavity-stablized oscillators (CSO), the reflection-type CSO has found ride applications. Its operation principle and structure features have bean discussed in many papers.
Preinduction of heat shock proteins protects cardiac and hepatic functions following trauma and hemorrhage (2000)

Although studies have shown that induction of the heat shock proteins (HSPs), such as HSP-70, has various beneficial effects after ischemia-reperfusion, it remains unknown whether prior induction of HSP-70 has any salutary effects on cardiovascular and hepatocellular functions after trauma-hemorrhage and resuscitation. Male rats were exposed to heat stress (41 degrees C, 15 min) and then allowed to recover for 24 h at room temperature (21 degrees C). The rats then underwent laparotomy (i.e., trauma induced) and were bled to and maintained at a mean arterial pressure of 40 mmHg until 40% of the maximal shed blood volume was returned in the form of Ringer lactate. Animals were then resuscitated with four times the volume of shed blood with Ringer lactate over 60 min. The maximal rate of the left ventricular pressure increase or decrease was measured up to 4 h after resuscitation. Cardiac output, hepatocellular function, plasma levels of tumor necrosis factor-alpha (TNF-alpha), and interleukin-6 (IL-6) were determined at 4 h after resuscitation. Cardiac and hepatic tissue were examined for HSP-70 by Western blot analysis. Left ventricular performance, cardiac output, and hepatocellular function decreased significantly following trauma-hemorrhage. Plasma levels of TNF-alpha and IL-6 were also significantly increased. However, prior heat stress attenuated cardiovascular and hepatocellular dysfunction, decreased circulating levels of proinflammatory cytokines following trauma-hemorrhage, and was associated with an increased abundance of HSP-70 in the heart and liver. Our data, therefore, suggest that preinduction of HSP-70 protects cardiovascular and hepatocellular functions following trauma-hemorrhage and resuscitation.
Whooping Cough Caused by <EMPH TYPE="ITAL">Bordetella pertussis</EMPH> and <EMPH TYPE="ITAL">Bordetella parapertussis</EMPH> in an Immunized Population (1998)

Bordetella infections are common in an immunized population, and B parapertussis infections apparently are more prevalent than previously documented.
Transgene Expression and Host Cell Responses to Replication-Defective, Single-Cycle, and Replication-Competent Adenovirus Vectors (2017)

Most adenovirus (Ad) vectors are E1 gene deleted replication defective (RD-Ad) vectors that deliver one transgene to the cell and all expression is based on that one gene. In contrast, E1-intact replication-competent Ad (RC-Ad) vectors replicate their DNA and their transgenes up to 10,000-fold, amplifying transgene expression markedly higher than RD-Ad vectors. While RC-Ad are more potent, they run the real risk of causing adenovirus infections in vector recipients and those that administer them. To gain the benefits of transgene amplification, but avoid the risk of Ad infections, we developed "single cycle" Ad (SC-Ad) vectors. SC-Ads amplify transgene expression and generated markedly stronger and more persistent immune responses than RD-Ad as expected. However, they also unexpectedly generated stronger immune responses than RC-Ad vectors. To explore the basis of this potency here, we compared gene expression and the cellular responses to infection to these vectors in vitro and in vivo. In vitro, in primary human lung epithelial cells, SC- and RC-Ad amplified their genomes more than 400-fold relative to RD-Ad with higher replication by SC-Ad. This replication translated into higher green fluorescent protein (GFP) expression for 48 h by SC- and RC-Ad than by RD-Ad. In vitro, in the absence of an immune system, RD-Ad expression became higher by 72 h coincident with cell death mediated by SC- and RC-Ad and release of transgene product from the dying cells. When the vectors were compared in human THP-1 Lucia- interferon-stimulated gene (ISG) cells, which are a human monocyte cell line that have been modified to quantify ISG activity, RC-Ad6 provoked significantly stronger ISG responses than RD- or SC-Ad. In mice, intravenous or intranasal injection produced up to 100-fold genome replication. Under these in vivo conditions in the presence of the immune system, luciferase expression by RC and SC-Ad was markedly higher than that by RD-Ad. In immunodeficient mice, SC-Ad drove stronger luciferase expression than RC- or RD-Ad. These data demonstrate better transgene expression by SC- and RC-Ad in vitro and in vivo than RD-Ad. This higher expression by the replicating vectors results in a peak of expression within 1 to 2 days followed by cell death of infected cells and release of transgene products. While SC- and RC-Ad expression were similar in mice and in Syrian hamsters, RC-Ad provoked much stronger ISG induction which may explain in part SC-Ad's ability to generate stronger and more persistent immune responses than RC-Ad in Ad permissive hamsters.
On the effectiveness of secret key extraction from wireless signal strength in real environments (2009)

We evaluate the effectiveness of secret key extraction, for private communication between two wireless devices, from the received signal strength (RSS) variations on the wireless channel between the two devices. We use real world measurements of RSS in a variety of environments and settings. Our experimental results show that (i) in certain environments, due to lack of variations in the wireless channel, the extracted bits have very low entropy making these bits unsuitable for a secret key, (ii) an adversary can cause predictable key generation in these static environments, and (iii) in dynamic scenarios where the two devices are mobile, and/or where there is a significant movement in the environment, high entropy bits are obtained fairly quickly. Building on the strengths of existing secret key extraction approaches, we develop an environment adaptive secret key generation scheme that uses an adaptive lossy quantizer in conjunction with Cascade-based information reconciliation [7] and privacy amplification [14]. Our measurements show that our scheme, in comparison to the existing ones that we evaluate, performs the best in terms of generating high entropy bits at a high bit rate. The secret key bit streams generated by our scheme also pass the randomness tests of the NIST test suite [21] that we conduct.
Affinity purification of the novel cysteine proteinase papaya proteinase IV, and papain from papaya latex (1989)

A procedure is described for the purification of a previously undetected cysteine proteinase, which we have called papaya proteinase IV, from spray-dried latex of the papaya (Carica papaya) plant. The purification involves affinity chromatography on Gly-Phe-aminoacetonitrile linked to CH-Sepharose 4B, with elution by 2-hydroxyethyl disulphide at pH 4.5. The product thus obtained is a mixture of almost fully active papain and papay proteinase IV, which are then separated by cation-exchange chromatography. A preliminary characterization of papaya proteinase IV showed it to be very similar to chymopapain in both molecular size and charge. However, the new enzyme is immunologically distinct from the previously characterized cysteine proteinases of papaya latex. It also differs in its lack of activity against the synthetic substrates of the other papaya proteinases, in its narrow specificity against protein substrates and its lack of inhibition by chicken cystatin. Papaya proteinase IV is abundant, contributing almost 30% of the protein in spray-dried papaya latex, and contamination of chymopapain preparations with this enzyme may account for some of the previously reported heterogeneity of chymopapain.
El abrazo transatlántico. La Guerra Civil Española en la íntima lejanía de América (2016)

La Guerra Civil Española ha sido estudiada en sus múltiples facetas. Algo similar puede decirse de su literatura: las novelas, los relatos, los poemas y todas las formas literarias generadas a partir del conflicto armado (tanto por intelectuales españoles como extranjeros) han sido en general comentados de forma minuciosa por parte de la crítica académica de las dos orillas del Atlántico. Sin embargo, han sido menos numerosos los enfoques que hayan situado en el centro de su discurso crítico la importancia del conflicto español en América, su absoluta relevancia como parte de un fenómeno que es también americano.
Phosphatidylcholine formation by LPCAT1 is regulated by Ca2+ and the redox status of the cell (2012)

Unsaturated fatty acids are susceptible to oxidation and damaged chains are removed from glycerophospholipids by phospholipase A2. De-acylated lipids are then re-acylated by lysophospholipid acyltransferase enzymes such as LPCAT1 which catalyses the formation of phosphatidylcholine (PC) from lysoPC and long-chain acyl-CoA. Activity of LPCAT1 is inhibited by Ca2+, and a Ca2+-binding motif of the EF-hand type, EFh-1, was identified in the carboxyl-terminal domain of the protein. The residues Asp-392 and Glu-403 define the loop of the hairpin structure formed by EFh-1. Substitution of D392 and E403 to alanine rendered an enzyme insensitive to Ca2+, which established that Ca2+ binding to that region negatively regulates the activity of the acyltransferase amino-terminal domain. Residue Cys-211 of the conserved motif III is not essential for catalysis and not sufficient for sensitivity to treatment by sulfhydryl-modifier agents. Among the several active cysteine-substitution mutants of LPCAT1 generated, we identified one to be resistant to treatment by sulfhydryl-alkylating and sulfhydryl-oxidizer agents. Mutant forms of LPCAT1 that are not inhibited by Ca2+ and sulfhydryl-alkylating and –oxidizing agents will provide a better understanding of the physiological function of a mechanism that places the formation of PC, and the disposal of the bioactive species lysoPC, under the control of the redox status and Ca2+ concentration of the cell.
Development of a CMOS-compatible PCR chip: comparison of design and system strategies (2004)

Altres ajuts: this work was partly funded by the Consejo Superior de Investigaciones Científicas (CSIC), by grant TIC97-0569 from the Comision Interministerial de Ciencia y Tecnología (CICYT).
Masticatory Function and Bite Force in Stroke Patients (2010)

Orofacial functions are frequently affected by stroke, but little is known on the nature and extent of the impairment of mastication, which is investigated in this observational study. Thirty-one stroke patients, aged 69.0 ± 12.7 yrs, presenting with a hemi-syndrome with facial palsy, were recruited. Chewing efficiency, maximum bite and restraining lip forces were tested. Stroke severity (National Institutes of Health Stroke Scale) and dental state were recorded. The control group was similar in age, gender, and dental state (n = 24). The chewing efficiency was significantly lower in the stroke group (p ≤ 0.0001) and was related to both the dental state and the lip forces measured with small and medium-sized labial plates. The maximum bite force proved to be not significantly different between sides or groups (n.s.), whereas lip force was significantly lower in the stroke group (p ≤ 0.05). Chewing efficiency is severely affected by stroke; thus, rehabilitation protocols should aim to restore the strength and co-ordination of the orofacial muscles.
Cytological feature of adenomatous hyperplasia of the endometrium. (1991)

腺腫性増殖症 (腺増殖) 31例およびコントロールとした正常増殖期20例より得られたEndocyte採取による内膜細胞標本を比較して, 腺増殖が細胞診断可能かどうかにつき検討した. 腺増殖で高頻度に認められた所見項目は, 集塊に関しては半島状突出, 乳頭状突出, 不整形小集塊, 最外層細胞の突出, 腺構造の増強・腺上皮の重層化の5項目, 核所見については腫大・大小不同, 不整形, 核縁肥厚, クロマチン増加, 核小体の出現, 配列不整の6項目, および背景の汚染を含めた合計12項目であった. これらの項目の陽性数から, 8項目以上を含む38.7%は腺増殖との推定診断が, 5～7項目を含む41.9%は細胞標本からスクリーニング可能と想定された. 一方, 4項目以下であった19.4%では検出不能と思われた. 12項目のうち8項目はx2検定にて有意と判定され, これらの陽性数から, 45.2%は推定診断が, また41.9%はスクリーニング可能と想定された.
Thyroid Hormone Receptor Mutations that Interfere with Transcriptional Activation also Interfere with Receptor Interaction with a Nuclear Protein (1991)

A 20 amino acid segment within the ligand-binding domain of the rat beta 1-thyroid hormone receptor (T3R; amino acids 286-305) is conserved in all members of the erbA superfamily. Mutations in this region impair T3 induction of reporter gene expression in a transfection system without impairing T3 binding or nuclear localization of the receptors. We postulate that a nuclear protein may need to interact with this domain for full transcriptional activity and provide evidence for the existence of this putative protein. Specifically, a JEG-3 cell protein (denoted TRAP, T3R auxiliary protein) interacts with wild-type T3R-beta 1 to increase binding of the receptor to T3 response elements in vitro. Mutations within amino acids 286-305 impair the ability of TRAP to enhance T3R binding to hormone response elements. Cross-linking studies indicate that TRAP has an apparent mol wt of 63 kDa. Surprisingly, TRAP does not enhance binding of erbA-alpha 2 and v-erbA to DNA, even though these proteins contain highly conserved versions of the 20-amino acid beta 1 T3R sequence under study. TRAP or a similar protein, however, does enhance binding of retinoic acid receptor-beta to a hormone response element. We conclude that the inability of T3Rs with mutations in this domain to fully activate transcription may be due to an inability of these proteins to fully interact with TRAP. We postulate that TRAP or related proteins may be important regulators of ligand-dependent transcriptional activation for other members of the erbA family in addition to the T3R.
Classic and atypical fibrodysplasia ossificans progressiva (FOP) phenotypes are caused by mutations in the bone morphogenetic protein (BMP) type I receptor ACVR1 (2008)

Fibrodysplasia ossificans progressiva (FOP) is an autosomal dominant human disorder of bone formation that causes developmental skeletal defects and extensive debilitating bone formation within soft connective tissues (heterotopic ossification) during childhood. All patients with classic clinical features of FOP (great toe malformations and progressive heterotopic ossification) have previously been found to carry the same heterozygous mutation (c.617G>A; p.R206H) in the glycine and serine residue (GS) activation domain of activin A type I receptor/activin-like kinase 2 (ACVR1/ALK2), a bone morphogenetic protein (BMP) type I receptor. Among patients with FOP-like heterotopic ossification and/or toe malformations, we identified patients with clinical features unusual for FOP. These atypical FOP patients form two classes: FOP-plus (classic defining features of FOP plus one or more atypical features) and FOP variants (major variations in one or both of the two classic defining features of FOP). All patients examined have heterozygous ACVR1 missense mutations in conserved amino acids. While the recurrent c.617G>A; p.R206H mutation was found in all cases of classic FOP and most cases of FOP-plus, novel ACVR1 mutations occur in the FOP variants and two cases of FOP-plus. Protein structure homology modeling predicts that each of the amino acid substitutions activates the ACVR1 protein to enhance receptor signaling. We observed genotype-phenotype correlation between some ACVR1 mutations and the age of onset of heterotopic ossification or on embryonic skeletal development.
On the Pathogenic Role of Brain-Sequestered αβ CD8+ T Cells in Experimental Cerebral Malaria (2002)

Cerebral malaria (CM) develops in a small proportion of persons infected with Plasmodium falciparum and accounts for a substantial proportion of the mortality due to this parasite. The actual pathogenic mechanisms are still poorly understood, and in humans investigations of experimental CM are unethical. Using an established Plasmodium berghei-mouse CM model, we have investigated the role of host immune cells at the pathological site, the brain. We report in this study the detailed quantification and characterization of cells, which migrated and sequestered to the brain of mice with CM. We demonstrated that CD8(+) alphabeta T cells, which sequester in the brain at the time when neurological symptoms appear, were responsible for CM mortality. These observations suggest a mechanism which unifies disparate observations in humans.
Synthesis of Fully Substituted Pyrazoles via Regio- and Chemoselective Metalations (2009)

The full functionalization of the pyrazole ring was achieved by successive regioselective metalations using TMPMgCl x LiCl and TMP(2)Mg x 2 LiCl. Trapping with various electrophiles led to trisubstituted pyrazoles. An application to the synthesis of the acaricide Tebufenpyrad is reported.
Nonreturn Rates of Dairy Cattle Following Uterine Body or Cornual Insemination (1990)

In the dairy cattle industry, uncertainty still remains regarding the most desirable site of inseminate deposition to maximize AI conception rates. The effect of site of inseminate deposition on nonreturn rates was determined from 2195 cornual and 2428 uterine body-bred dairy cattle. Twelve technicians from various areas of Pennsylvania and New York were chosen on the basis of their accuracy of semen deposition in retraining sessions, average nonreturn rates, and their willingness to cooperate in the study. For a 3-mo period (June, July, and August 1988), technicians alternated weeks of cornual and uterine breeding on all dairy cattle inseminated. One-half (.25 ml) of each semen unit was deposited approximately 5.1 cm into each uterine horn for cornual insemination. No significant difference in nonreturn rates was found between horn-bred (70.8%) and body-bred (69.5%) cows. The range of differences in percent nonreturn rates for technicians was 19 and 30% for body and cornual inseminations, respectively. A significant difference in nonreturn rates was found between technicians and between months with significantly higher average nonreturn rates (6.8%) in June. Cornual and uterine body deposition of semen yielded similar results; therefore, depositing an inseminate in the uterine horns to maximize fertility is unnecessary.
Expression of the Cry1Ab Protein in Genetically Modified Sugarcane for the Control of Diatraea saccharalis (Lepidoptera: Crambidae) (2003)

Previously, we genetically modified two Brazilian commercial sugarcane (Saccharum sp.) varieties (SP80-3280 and SP80-1842) for resistance to the sugarcane borer Diatraea saccharalis by co-bombardment transformation with three plasmids: pCIB4421 containing the Bacillus thuringiensis gene cry1Ab regulated by a maize phosphoenol-pyruvate carboxylase promoter, pCIB4426 carrying cry1Ab controlled by a pith promoter, and pHA9 with the neo antibiotic resistance gene. The genetically modified plants were submitted to molecular characterization and insect feeding bioassays. Plants also were screened in the field for insect infestation and had their phenotypic characteristics and quantitative traits evaluated. This study presents evidence that the B. thuringiensis cry1Ab gene can be efficiently expressed in sugarcane plants over an extended growing period, and can confer resistance to the sugarcane borer under field conditions, while not measurably altering numerous material traits of the crop.
Initiation of DNA replication in nuclei from quiescent cells requires permeabilization of the nuclear membrane. (1994)

We have investigated the replication capacity of intact nuclei from quiescent cells using Xenopus egg extract. Nuclei, with intact nuclear membranes, were isolated from both exponentially growing and contact-inhibited BALB/c 3T3 fibroblasts by treatment of the cells with streptolysin-O. Flow cytometry showed that > 90% of all contact-inhibited cells and approximately 50% of the exponential cells were in G0/G1-phase at the time of nuclear isolation. Intact nuclei were assayed for replication in the extract by incorporation of [alpha-32P]dATP or biotin-dUTP into nascent DNA. Most nuclei from exponential cells replicated in the egg extract, consistent with previous results showing that intact G1 nuclei from HeLa cells replicate in this system. In contrast, few nuclei from quiescent cells replicated in parallel incubations. However, when the nuclear membranes of these intact quiescent nuclei were permeabilized with lysophosphatidylcholine prior to addition to the extract, nearly all the nuclei replicated under complete cell cycle control in a subsequent incubation. The ability of LPC-treated quiescent nuclei to undergo DNA replication was reversed by resealing permeable nuclear membranes with Xenopus egg membranes prior to extract incubation demonstrating that the effect of LPC treatment is at the level of the nuclear membrane. These results indicate that nuclei from G1-phase cells lose their capacity to initiate DNA replication following density-dependent growth arrest and suggest that changes in nuclear membrane permeability may be required for the initiation of replication upon re-entry of the quiescent cell into the cell cycle.