gebhart/patrepeval huggingface dataset:
The New Cratylus (2013)

The philologist and biblical critic John William Donaldson (1811–61) published this pioneering work in 1839. It is an attempt to apply the principles of comparative philology to ancient Greek, elucidating the grammar and syntax of the language by comparing it with actual or conjectural cognate languages. As well as producing a great deal of original research on the subject, Donaldson was the first British philologist to bring the work of continental scholars to the attention of English readers. In the book's first section, he gives a history of philology, surveys its present state and expounds a philosophy of language. Here he sets Greek in the context of other Indo-European languages, and outlines a theory of the Greek alphabet and its origins. In the second section, he examines pronouns, numerals, prepositions and particles before considering the noun in the third section, and finally the various tenses and moods of the verb in the fourth section.
Myeloproliferative sarcoma virus directed expression of beta-galactosidase following retroviral transduction of murine hematopoietic cells. (1995)

The introduction of genetic sequences into hematopoietic stem cells (HSC) has allowed study of HSC proliferation in vivo by proviral-sequence molecular analysis in the DNA of progeny. Analysis of HSC proliferation could be enhanced by development of a retroviral vector that encodes a reporter gene that allows sensitive detection of transduced cells. We developed a recombinant retrovirus vector encoding the reporter gene lacZ under the transcriptional control of the myeloproliferative sarcoma virus long-terminal repeat (LTR). Bone marrow cells from C3H mice were co-cultured on retrovirus producer cell lines and cultured for growth of colony-forming unit granulocyte/macrophage (CFU-GM) and high proliferative potential colony-forming cells (HPP-CFC) in semisolid media or were transplanted into irradiated recipients. In other experiments, recombinant retrovirus was injected in vivo into the liver of developing fetal rat pups, and circulating hematopoietic cells of the postnatal rats were analyzed for evidence of proviral integration and expression of beta-galactosidase. Expression of lacZ was detected in both CFU-GM and HPP-CFC that were cultured immediately following in vitro infection of mouse bone marrow. Beta-galactosidase activity from the retrovirus was also detected in both marrow cells isolated from reconstituted mice 22 weeks following transplantation as well as in blood cells of postnatal rats transduced in utero with the recombinant retrovirus. This strategy may be especially useful for characterizing proliferation of transduced populations of hematopoietic cells and in the development of protocols for somatic gene therapy.
Changes in Salivary Flow Rate and pH in Stressful Conditions (2001)

타액은 그 양과 조성 등에 있어 많은 인자들의 영향을 받는다. 타액분비 감소는 구강의 자정작용, 완충능, 치아우식저항성 등 타액의 고유한 기능을 변화시켜서 구강건조감, 구강작열감, 다발성 치아우식증 등의 소인이 된다. 이에 저자는 심리적 요인이 구강내 환경에 미치는 영향을 평가하고자 타액선질환을 포함한 전신질환이 없는 전북대학교 치과대학생 20명을 대상으로 일상생활시와 시험 직전의 비자극성 전타액을 5분간 추출하여, 그 유출량과 수소이온농도를 측정, 비교, 평가하였다. 타액유출량은 25㎖의 메스실린더를 사용하였고, 수소이온농도는 pH/SEmeter(ORION, 720A model)를 이용하여 측정하였다. 평가 결과 남성의 비자극성 타액유출량과 수소이온농도는 3.68±1.31㎖/5min와 7.63±0.17이었고, 여성에서는 각각 4.93±1.47㎖/5min와 7.43±0.29로서성별간 유의한 차이가 없었다. 그리고 일상생활시의 성인의 5분간 수집된 비자극성 타액유출량은 4.18±1.48㎖/5min였고, 스트레스하에서의 양은 2.20±0.95㎖/5min로 나타나 스트레스시 타액유출량이 감소하는 것으로 나타났다 (p 이상의 결과로 보아 스트레스는 타액유출량을 감소시키고 구강내를 보다 산성화시킨다고 사료된다.
The regulation of inflammation by interferons and their STATs (2013)

Interferons (IFN) are subdivided into type I IFN (IFN-I, here synonymous with IFN-α/β), type II (IFN-γ) and type III IFN (IFN-III/IFN-λ) that reprogram nuclear gene expression through STATs 1 and 2 by forming STAT1 dimers (mainly IFN-γ) or the ISGF3 complex, a STAT1-STAT2-IRF9 heterotrimer (IFN-I and IFN-III). Dominant IFN activities in the immune system are to protect cells from viral replication and to activate macrophages for enhanced effector function. However, the impact of IFN and their STATs on the immune system stretches far beyond these activities and includes the control of inflammation. The goal of this review is to give an overview of the different facets of the inflammatory process that show regulatory input by IFN/STAT.
Post-Transcriptional and Translational Controls of Gene Expression in Eukaryotes (1978)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Inhibition of Mannose-Binding Lectin Reduces Postischemic Myocardial Reperfusion Injury (2001)

The lectin complement pathway is activated after myocardial ischemia-reperfusion and leads to tissue injury. Blockade of the lectin pathway with inhibitory mAbs protects the heart from ischemia-reperfusion by reducing neutrophil infiltration and attenuating proinflammatory gene expression.
Biotransformation of Hexahydro-1,3,5-trinitro-1,3,5-triazine Catalyzed by a NAD(P)H:  Nitrate Oxidoreductase from Aspergillus niger (2002)

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) can be efficiently mineralized with anaerobic domestic sludge, but the initial enzymatic processes involved in its transformation are unknown. To test the hypothesis that the initial reaction involves reduction of nitro group(s), we designed experiments to test the ability of a nitrate reductase (EC 1.6.6.2) to catalyze the initial reaction leading to ring cleavage and subsequent decomposition. A nitrate reductase from Aspergillus niger catalyzed the biotransformation of RDX most effectively at pH 7.0 and 30 degrees C under anaerobic conditions using NADPH as electron donor. LC/MS (ES-) chromatograms showed the formation of hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine (MNX) and methylenedinitramine as key initial products of RDX, but neither the dinitroso neither (DNX) nor trinitroso (TNX) derivatives were observed. None of the above detected products persisted, and their disappearance was accompanied by the accumulation of nitrous oxide (N20), formaldehyde (HCHO), and ammonium ion (NH4+). Stoichiometric studies showed that three NADPH molecules were consumed, and one molecule of methylenedinitramine was produced per RDX molecule. The carbon and nitrogen mass balances were 96.14% and 82.10%, respectively. The stoichiometries and mass balance measurements supported a mechanism involving initial transformation of RDX to MNX via a two-electron reduction mechanism. Subsequent reduction of MNX followed by rapid ring cleavage gave methylenedinitramine which in turn decomposed in water to produce quantitatively N2O and HCHO. The results clearly indicate that an initial reduction of a nitro group by nitrate reductase is sufficient for the decomposition of RDX.
Synthesis of Symmetrical and Unsymmetrical Ureas Using Unsymmetrical Diaryl Carbonates (1996)

Abstract Appropriately substituted unsymmetrical diaryl carbonates react smoothly with primary amines to give the carbamates derived by nucleophilic displacement of the less electron rich aromatic substituent. Subsequent treatment of the carbamates with primary and secondary amines gives either symmetrical or unsymmetrical ureas in excellent yield and the overall process can be carried out as a “one pot” operation. Acetonitrile is the preferred solvent and addition of DBU facilitates the carbamate → urea transformation.
Chromosome 11q13 and atopic asthma (1999)

Asthma is a complex syndrome in which bronchial inflammation and smooth muscle hyperactivity lead to labile airflow obstruction. The commonest form of asthma is that due to atopy, which is an immune disorder where production of IgE to inhaled antigens leads to bronchial mucosal inflammation. The ultimate origins of asthma are interactive environmental and genetic factors. The genetics is acknowledged to be heterogeneous, and one chromosomal region of interest and controversy has been 11q13. To clarify the nature of the chromosome 11q13 effect in atopy and asthma, we conducted a genetic association study in subjects with marked atopic asthma and matched controls, which incorporated the study of 13 genetic variants over a distance of 10-12 cM and which took account of detailed immune and clinical phenotyping. Association with high IgE levels was limited to the interval flanked by D11S1335 and CD20 in a 0.8-Mb interval and was greatest for variants of Fc epsilonRIbeta and HTm4; these variants also associated with asthma (recurrent wheeze with labile airflow obstruction and need for regular inhaler treatment). At the more telomeric marker, D11S480, variants associated with asthma, but not with high IgE levels. The data might support the possibility of multiple loci relevant to atopic asthma on chromosome 11q13.
Compaction Experiences with Bulk-Format Switchgrass in Commercial Transfer Systems (2011)

Supply chain efficiencies must be improved for lignocellulosic biomass to become an economically viable energy feedstock. Switchgrass round bales require labor-intensive unit handling and de-baling processes that are not readily scalable, so a bulk-chopped format was investigated to improve handling efficiencies throughout the harvest, transportation, and storage systems. However, low loose-filled bulk density of chopped switchgrass presented challenges for long distance transportation to the end user. Increasing biomass bulk density with minimal time and energy inputs was achieved using waste transfer equipment. A commercial-grade compactor was used to compress size-reduced switchgrass into a 57 m3 reinforced, ejector-style transfer trailer. Pressure relief setting on the compactor was 20,684 kPa, corresponding with a compactor ram face pressure of 347 kPa. The compactor was cycled until the pressure relief setting was reached, and the truck was weighed to determine the compacted bulk density of the switchgrass. The trailer was then offloaded using the hydraulic-powered ejector ram. Observations were made regarding the compatibility of chopped switchgrass with existing equipment. Particle size distribution was determined according to ASABE S424.1, and moisture content was determined according to ASABE S358.2. Results indicated in-bulk compaction as a promising method to improve transportation efficiencies of loose chopped biomass as a means of increasing low bulk densities of low-moisture switchgrass feedstock by a factor of about 2x.
Gastrointestinal-related arthritis and psoriatic arthritis (1991)

Psoriatic arthritis and the enteropathic arthropathies are included among the seronegative spondyloarthropathies. The concept of psoriatic arthritis as a specific entity continues to be challenged by some investigators, while others report on additional findings in this condition, such as temporomandibular joint disease. The etiopathogenesis of the condition continues to be investigated by the exploration of genetic and immunologic factors. Treatment options include dietary manipulations. The prevalence of arthritis among patients with bowel disease seems to be increasing, while the presence of gut lesions among patients with spondyloarthropathy is noted to be associated with disease activity.
Platelets adhere to and translocate on von Willebrand factor presented by endothelium in stimulated veins (2000)

With the use of intravital microscopy, a new type of platelet–endothelial interaction in mouse mesenteric venules at low shear (80-100 seconds−1) is described. Stimulation of these vessels with calcium ionophore A23187, a known secretagogue of Weibel-Palade bodies, induced immediate platelet adhesion (within 15 seconds) and translocation without the formation of aggregates. This stop-and-go process reached a maximum in approximately 1 minute, when approximately 25 000 platelets adhered/mm2·s, and then adhesion progressively decreased. This adhesion process was dependent on von Willebrand factor (vWF) and independent of P-selectin. Immunohistologic analysis showed that the venules were not denuded withA23187 treatment, suggesting that platelets adhered to vWF secreted on the luminal face of the endothelial cells. Histamine treatment induced a similar adhesion phenomenon. Platelet adhesion was not abolished in β3-deficient mice or when the platelets were treated with inhibitory antibodies to PECAM-1 or PSGL-1, indicating that these molecules are not required for platelet–endothelium interaction at low shear. The adhesion was mediated by platelet glycoprotein Ibα (GPIbα) because the adhesion of murine platelets expressing exclusively the human GPIbα could be prevented by a pretreatment with mocarhagin, a snake venom protease that cleaves human GPIbα. The results indicate that vWF released from Weibel-Palade bodies can dramatically increase the concentration of platelets along the vessel wall through an interaction with GPIbα. It is proposed that this process may rapidly recruit platelets to sites of injury or inflammation in veins.
Evaluation of the Acute Electrophysiologic Effects of Intravenous Dronedarone, an Amiodarone-Like Agent, with Special Emphasis on Ventricular Repolarization and Acquired Torsade de Pointes Arrhythmias (1999)

In the anesthetized dog with complete chronic AV block (CAVB), we evaluated and compared the acute electrophysiologic effects of dronedarone i.v. (Dron, 2 times 2.5 mg/kg/10 min) and amiodarone i.v. (Amio, 2 times 5 mg/kg/10 min). This canine model with a high sensitivity for acquired torsade de pointes (TdP) provides an ideal substrate to evaluate ventricular repolarization abnormalities. Six ECG leads and two endocardial monophasic action potential (MAP) recordings in the left and right ventricle (LV and RV) were simultaneously recorded to measure QT time, action-potential duration (APD), interventricular dispersion (deltaAPD = LV(APD) - RV(APD)), early afterdepolarizations (EADs), ectopic beats (EBs), and TdP. Measurements were made at the spontaneous idioventricular rhythm (IVR) and 1,000-ms steady-state pacing. To investigate its short-term, antiarrhythmic properties, Dron was given after almokalant (0.12 mg/kg)-induced TdP. Furthermore, in another set of experiments, oral Dron (20 mg/kg, b.i.d) was given for 3 weeks to conscious CAVB dogs. Dron, i.v., shortened ventricular repolarization (QT, 435 +/- 60 to 360 +/- 55; LV(APD) 395 +/- 75 to 335 +/- 60 ms; p < 0.05), whereas IVR and ventricular effective refractory period (VERP, 225 +/- 30 to 230 +/- 30 ms) remained similar. Therefore the VERP/QT ratio increased (0.55 +/- 0.04 to 0.61 +/- 0.03; p < 0.05). Similar results were obtained with Amio, i.v.. Almokalant-induced TdP was characterized by an increased repolarization duration, deltaAPD, and EADs. Dron, i.v., suppressed the EADs, EBs, and TdP by a reduction and homogenization of repolarization (LV(APD), 505 +/- 110 to 455 +/- 80 ms, and deltaAPD, 110 +/- 55 to 65 +/- 40 ms). Long-term oral Dron increased the PP interval, CL-IVR, and QT(c) time. In contrast to oral treatment, Dron i.v. shortens ventricular repolarization parameters, resulting in suppression of EAD-dependent acquired TdP. The increased VERP/QT ratio after Dron i.v. may indicate an important second antiarrhythmic property.
Bacterial formate dehydrogenase. Increasing the enzyme thermal stability by hydrophobization of alpha‐helices (1999)

NAD+-dependent formate dehydrogenase (EC 1.2.1.2, FDH) from methylotrophic bacterium Pseudomonas sp.101 exhibits the highest stability among the similar type enzymes studied. To obtain further increase in the thermal stability of FDH we used one of general approaches based on hydrophobization of protein alpha-helices. Five serine residues in positions 131, 160, 168, 184 and 228 were selected for mutagenesis on the basis of (i) comparative studies of nine FDH amino acid sequences from different sources and (ii) with the analysis of the ternary structure of the enzyme from Pseudomonas sp.101. Residues Ser-131 and Ser-160 were replaced by Ala, Val and Leu. Residues Ser-168, Ser-184 and Ser-228 were changed into Ala. Only Ser/Ala mutations in positions 131, 160, 184 and 228 resulted in an increase of the FDH stability. Mutant S168A was 1.7 times less stable than the wild-type FDH. Double mutants S(131,160)A and S(184,228)A and the four-point mutant S(131,160,184,228)A were also prepared and studied. All FDH mutants with a positive stabilization effect had the same kinetic parameters as wild-type enzyme. Depending on the position of the replaced residue, the single point mutation Ser/Ala increased the FDH stability by 5-24%. Combination of mutations shows near additive effect of each mutation to the total FDH stabilization. Four-point mutant S(131,160,184,228)A FDH had 1.5 times higher thermal stability compared to the wild-type enzyme.
Hierarchical Bayesian Noise Inference for Robust Real-time Probabilistic Object Classification (2016)

Robust environment perception is essential for decision-making on robots operating in complex domains. Principled treatment of uncertainty sources in a robot's observation model is necessary for accurate mapping and object detection. This is important not only for low-level observations (e.g., accelerometer data), but for high-level observations such as semantic object labels as well. This paper presents an approach for filtering sequences of object classification probabilities using online modeling of the noise characteristics of the classifier outputs. A hierarchical Bayesian approach is used to model per-class noise distributions, while simultaneously allowing sharing of high-level noise characteristics between classes. The proposed filtering scheme, called Hierarchical Bayesian Noise Inference (HBNI), is shown to outperform classification accuracy of existing methods. The paper also presents real-time filtered classification hardware experiments running fully onboard a moving quadrotor, where the proposed approach is demonstrated to work in a challenging domain where noise-agnostic filtering fails.
Sphingosine Kinase-1 Expression Correlates With Poor Survival of Patients With Glioblastoma Multiforme: Roles of Sphingosine Kinase Isoforms in Growth of Glioblastoma Cell Lines (2005)

Sphingosine-1-phosphate is a bioactive lipid that is mitogenic for human glioma cell lines by signaling through its G protein-coupled receptors. We investigated the role of sphingosine-1-phosphate receptors and the enzymes that form sphingosine-1-phosphate, sphingosine kinase (SphK)-1, and -2 in human astrocytomas. Astrocytomas of various histologic grades expressed three types of sphingosine-1-phosphate receptors, S1P1, S1P2, and S1P3; however, no significant correlation with histologic grade or patient survival was detected. Expression of SphK1, but not SphK2, in human astrocytoma grade 4 (glioblastoma multiforme) tissue correlated with short patient survival. Patients whose tumors had low SphK1 expression survived a median 357 days, whereas those with high levels of SphK1 survived a median 102 days. Decreasing SphK1 expression using RNA interference or pharmacologic inhibition of SphK significantly decreased the rate of proliferation of U-1242 MG and U-87 MG glioblastoma cell lines. Surprisingly, RNA interference to knockdown SphK2 expression inhibited glioblastoma cell proliferation more potently than did SphK1 knockdown. SphK knockdown also prevented cells from exiting G1 phase of the cell cycle and marginally increased apoptosis. Thus, SphK isoforms may be major contributors to growth of glioblastoma cells in vitro and to aggressive behavior of glioblastoma multiforme.
The primary structure of a halorhodopsin from Natronobacterium pharaonis. Structural, functional and evolutionary implications for bacterial rhodopsins and halorhodopsins. (1990)

We cloned and sequenced the gene coding for the polypeptide of a halorhodopsin in Natronobacterium pharaonis (named here pharaonis halorhodopsin). Peptide sequencing of cyanogen bromide fragments, and immunoreactions of the protein and synthetic peptides derived from the COOH-terminal gene sequence, confirmed that the open reading frame is the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences, as well as those for other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences (mutations/nucleotide at codon positions which do not result in amino acid changes) were calculated. These indicate very considerable evolutionary distance between each pair of genes. In spite of this, the three protein sequences show extensive similarities, indicating strong selective pressures. Conserved and conservatively replaced amino acid residues in all three proteins identify general features essential for ion-motive bacterial rhodopsins, responsible for overall structure and chromophore properties. Comparison of the bacteriorhodopsin sequence with those of the two halorhodopsins, on the other hand, identifies features involved in their specific (proton and chloride ion) transport functions.
Highly Efficient Gluten Degradation by Lactobacilli and Fungal Proteases during Food Processing: New Perspectives for Celiac Disease (2007)

Presently, the only effective treatment for celiac disease is a life-long gluten-free diet. In this work, we used a new mixture of selected sourdough lactobacilli and fungal proteases to eliminate the toxicity of wheat flour during long-time fermentation. Immunological (R5 antibody-based sandwich and competitive enzyme-linked immunosorbent assay [ELISA] and R5 antibody-based Western blot), two-dimensional electrophoresis, and mass spectrometry (matrix-assisted laser desorption ionization-time of flight, strong-cation-exchange-liquid chromatography/capillary liquid chromatography-electrospray ionization-quadrupole-time of flight [SCX-LC/CapLC-ESI-Q-TOF], and high-pressure liquid chromatography-electrospray ionization-ion trap mass spectrometry) analyses were used to determine the gluten concentration. Assays based on the proliferation of peripheral blood mononuclear cells (PBMCs) and gamma interferon production by PBMCs and intestinal T-cell lines (iTCLs) from 12 celiac disease patients were used to determine the protein toxicity of the pepsin-trypsin digests from fermented wheat dough (sourdough). As determined by R5-based sandwich and competitive ELISAs, the residual concentration of gluten in sourdough was 12 ppm. Albumins, globulins, and gliadins were completely hydrolyzed, while ca. 20% of glutenins persisted. Low-molecular-weight epitopes were not detectable by SCX-LC/CapLC-ESI-Q-TOF mass spectrometry and R5-based Western blot analyses. The kinetics of the hydrolysis of the 33-mer by lactobacilli were highly efficient. All proteins extracted from sourdough activated PBMCs and induced gamma interferon production at levels comparable to the negative control. None of the iTCLs demonstrated immunoreactivity towards pepsin-trypsin digests. Bread making was standardized to show the suitability of the detoxified wheat flour. Food processing by selected sourdough lactobacilli and fungal proteases may be considered an efficient approach to eliminate gluten toxicity.