gebhart/patrepeval huggingface dataset:
Genetic polymorphisms in methylenetetrahydrofolate reductase and methionine synthase, folate levels in red blood cells, and risk of neural tube defects (1999)

Folic acid administration to women in the periconceptional period reduces the occurrence of neural tube defects (NTDs) in their offspring. A polymorphism in the gene encoding methylenetetrahydrofolate reductase (MTHFR), 677C-->T, is the first genetic risk factor for NTDs in man identified at the molecular level. The gene encoding another folate-dependent enzyme, methionine synthase (MTR), has recently been cloned and a common variant, 2756A-->G, has been identified. We assessed genotypes and folate status in 56 patients with spina bifida, 62 mothers of patients, 97 children without NTDs (controls), and 90 mothers of controls, to determine the impact of these factors on NTD risk. Twenty percent of cases and 18% of case mothers were homozygous for the MTHFR polymorphism, compared to 11% of controls and 11% of control mothers, indicating that the mutant genotype conferred an increased risk for NTDs. The risk was further increased if both mother and child had this genotype. The MTR polymorphism was associated with a decreased O.R. (O.R.); none of the cases and only 10% of controls were homozygous for this variant. Red blood cell (RBC) folate was lower in cases and in case mothers, compared to their respective controls. Having a RBC folate in the lowest quartile of the control distribution was associated with an O.R. of 2.56 (95% CI 1.28-5.13) for being a case and of 3.05 (95% CI 1.54-6.03) for being a case mother. The combination of homozygous mutant MTHFR genotype and RBC folate in the lowest quartile conferred an O.R. for being a NTD case of 13.43 (CI 2.49-72.33) and an O.R. for having a child with NTD of 3.28 (CI 0.84-12.85). We propose that the genetic-nutrient interaction--MTHFR polymorphism and low folate status--is associated with a greater risk for NTDs than either variable alone.
Synthesis of Photocleavable Linear Macromonomers by ATRP and Star Macromonomers by a Tandem ATRP−Click Reaction:  Precursors to Photodegradable Model Networks (2007)

Atom transfer radical polymerization (ATRP) and the copper-catalyzed azide−alkyne cycloaddition (CuAAC) were utilized for the synthesis of photodegradable polymeric materials by two complementary schemes. Linear azido-telechelic macromonomers possessing a photocleavable functionality at the center were synthesized by ATRP and subsequent end-group modification. These macromonomers were cross-linked with a tetrafunctional alkyne by CuAAC to form insoluble materials which degraded upon exposure to UV light of 350 nm to yield soluble star polymer products of defined molecular weight. Complementary to this approach, four-armed star polymers possessing photocleavable arms and terminal azides were prepared by a novel one-pot CuAAC/ATRP reaction followed by end-group modification. These star polymers were cross-linked with a linear, bifunctional alkyne to yield insoluble materials which, upon exposure to UV light, degraded to yield linear polymers of defined molecular weight.
Vascular Endothelial Growth Factor as a Therapeutic Target in Cancer (2004)

Inhibiting VEGF appears to be a valid therapeutic strategy and may prevent the growth of new tumor blood vessels, cause regression of the existing tumor vasculature, enhance the anti-tumor immune response, and normalize the vasculature (thereby improving the delivery of chemotherapy).
Oxidized Low-Density Lipoprotein Correlates Positively With Toll-Like Receptor 2 and Interferon Regulatory Factor-1 and Inversely With Superoxide Dismutase-1 Expression (2006)

Our data support the hypothesis that oxLDL is a proinflammatory stimulus that induces the expression of TLR2 and IRF1, 2 important gene regulators of innate immune response, and inhibits the expression of the antioxidant SOD1.
Absence of the Chemokine Receptor CCR2 Protects Against Cerebral Ischemia/Reperfusion Injury in Mice (2007)

These data suggest that inhibiting the CCL2/CCR2 axis affects brain reperfusion outcome by reducing brain edema, leukocyte infiltration, and inflammatory mediator expression.
Effect of Platelet-rich Plasma (PRP) on Regeneration of Rat Sciatic Nerve in a Silicone Chamber (2010)

Purpose: The purpose of this study is to determine the effect of platelet-rich plasma (PRP) on rat sciatic nerve regeneration in a 10 mm silicone chamber. Methods: A total of 6 inbred Lewis rats were used in this study. Bilateral sciatic neurectomy was performed on each rat. On one side, silicone chambers containing PRP solutions were implanted; on the contralateral side, the chambers without PRP were implanted as a control. In 12 weeks post-implantation, chambers were retrieved and both gastrocnemius muscles were excised. Nerves biopsy samples were examined under a light microscope after Masson trichrome staining. Results: Cross sections of the midpoints of PRP treated nerves were significantly larger and appeared more mature than those of controls. Conclusion: Based on morphological evidence, PRP has a positive effect on neural regeneration, and it may therefore be useful for treating peripheral nerve injuries.
Sensitive and Specific New Enzyme-Linked Immunosorbent Assay for N-ERC/Mesothelin Increases its Potential as a Useful Serum Tumor Marker for Mesothelioma (2008)

N-ERC/mesothelin is a very promising tumor marker for mesothelioma, especially epithelioid mesothelioma.
EFFECT OF PROTEASE INHIBITOR ON ISCHEMIA/REPERFUSION INJURY OF THE RAT LIVER (1993)

The purposes of this study were to clarify the role of neutrophilic proteases in the pathogenesis of hepatic ischemia/reperfusion injury and to determine whether urinary trypsin inhibitor (UTI) pretreatment attenuated liver ischemia/reperfusion injury in rats. Livers from male Sprague-Dawley rats were subjected to 90 min of no-flow warm ischemia followed by 120 min of reperfusion. Rats were divided into a UTI group and a control group. In the control group, 120-min reperfusion of the liver produced a significant increase in myeloperoxidase activity, a significant decrease in ATP and energy charge, and a marked increase in the serum aspartate aminotransferase, alanine aminotransferase, and lactic dehydrogenase levels. In the UTI group, the myeloperoxidase activity was significantly attenuated (P < 0.01), ATP and energy charge were significantly improved (P < 0.01 and P < 0.05, respectively), and the elevation in serum aspartate aminotransferase, alanine aminotransferase, and lactic dehydrogenase was also markedly suppressed (P < 0.05, P < 0.01, and P < 0.05, respectively) compared with the control group. Sections through the livers of control rats showed severe hepatocyte necrosis with neutrophil infiltration. In the UTI group, there was slight congestion and hepatocyte necrosis. The survival rate after 90-min liver ischemia was significantly improved compared with that in the control group (P < 0.05). The results of this study suggest that pretreatment with UTI significantly attenuates liver reperfusion injury, perhaps by inhibiting neutrophil proteases.
ChemInform Abstract: REACTION OF DIPHENYLCYCLOPROPENONE WITH GUANIDINES (1981)

Abstract Die Titelverbindung (I) reagiert mit den Guanidinen (II), (IV), (VIII), (IX), (XII) bzw. dem Aminobenzimidazol (XIII) zu den Produkten (III) (aufgrund der spektroskopischen Daten als Cyclomerocyanine im Sinne des Resonanzhybrids A 6B charakterisiert), (V) [nachfolgendes Erhitzen gibt die Isomeren (VIa), (VIb)] (VIC), (VIIa) [nachfolgendes Erhitzen ‐ Isomeres (VIIb)], (X), (XI) bzw. (XIV).
CODRA: A Novel Discriminative Framework for Rhetorical Analysis (2015)

Clauses and sentences rarely stand on their own in an actual discourse; rather, the relationship between them carries important information that allows the discourse to express a meaning as a whole beyond the sum of its individual parts. Rhetorical analysis seeks to uncover this coherence structure. In this article, we present CODRA— a COmplete probabilistic Discriminative framework for performing Rhetorical Analysis in accordance with Rhetorical Structure Theory, which posits a tree representation of a discourse. CODRA comprises a discourse segmenter and a discourse parser. First, the discourse segmenter, which is based on a binary classifier, identifies the elementary discourse units in a given text. Then the discourse parser builds a discourse tree by applying an optimal parsing algorithm to probabilities inferred from two Conditional Random Fields: one for intra-sentential parsing and the other for multi-sentential parsing. We present two approaches to combine these two stages of parsing effectively. By conducting a series of empirical evaluations over two different data sets, we demonstrate that CODRA significantly outperforms the state-of-the-art, often by a wide margin. We also show that a reranking of the k-best parse hypotheses generated by CODRA can potentially improve the accuracy even further.
Mitigating the risk of cytokine release syndrome in a Phase I trial of CD20/CD3 bispecific antibody mosunetuzumab in NHL: impact of translational system modeling (2020)

Mosunetuzumab, a T-cell dependent bispecific antibody that binds CD3 and CD20 to drive T-cell mediated B-cell killing, is currently being tested in non-Hodgkin lymphoma. However, potent immune stimulation with T-cell directed therapies poses the risk of cytokine release syndrome, potentially limiting dose and utility. To understand mechanisms behind safety and efficacy and explore safety mitigation strategies, we developed a novel mechanistic model of immune and antitumor responses to the T-cell bispecifics (mosunetuzumab and blinatumomab), including the dynamics of B- and T-lymphocytes in circulation, lymphoid tissues, and tumor. The model was developed and validated using mosunetuzumab nonclinical and blinatumomab clinical data. Simulations delineated mechanisms contributing to observed cell and cytokine (IL6) dynamics and predicted that initial step-fractionated dosing limits systemic T-cell activation and cytokine release without compromising tumor response. These results supported a change to a step-fractionated treatment schedule of mosunetuzumab in the ongoing Phase I clinical trial, enabling safer administration of higher doses.
Optimal pruning with applications to tree-structured source coding and modeling (1989)

An algorithm introduced by L. Breiman et al. (1984) in the context of classification and regression trees is reinterpreted and extended to cover a variety of applications in source coding and modeling in which trees are involved. These include variable-rate and minimum-entropy tree-structured vector quantization, minimum expected cost decision trees, variable-order Markov modeling, optimum bit allocation, and computer graphics and image processing using quadtrees. A concentration on the first of these and a detailed analysis of variable-rate tree-structured vector quantization are provided. It is found that variable-rate tree-structured vector quantization outperforms not only the fixed-rate variety but also full-search vector quantization. The successive approximation character of variable-rate tree-structured vector quantization permits it to degrade gracefully if the rate is reduced at the encoder. This has applications to the problem of buffer overflow.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A benzothiadiazole derivative induces systemic acquired resistance in tobacco (1996)

Summary Systemic acquired resistance (SAR) is a pathogen‐induced disease resistance response in plants that is characterized by broad spectrum disease control and an associated coordinate expression of a set of SAR genes. Benzo(1,2,3)‐thiadiazole‐7‐carbothioic acid S‐methyl ester (BTH) is a novel synthetic chemical capable of inducing disease resistance in a number of dicotyledenous and monocotyledenous plant species. In this report, the response of tobacco plants to BTH treatment is characterized and the fact that it controls disease by activating SAR is demonstrated. BTH does not cause an accumulation of salicylic acid (SA), an intermediate in the SAR signal transduction pathway. As BTH also induces disease resistance and gene expression in transgenic plants expressing the nahG gene, it appears to activate the SAR signal transduction pathway at the site of or downstream of SA accumulation. BTH, SA and TMV induce the PR‐1a promoter using similar cis ‐acting elements and gene expression is blocked by cycloheximide treatment. Thus, BTH induces SAR based on all of the physiological and biochemical criteria that define SAR in tobacco.
Heat to H2: Using Waste Heat for Hydrogen Production through Reverse Electrodialysis (2019)

This work presents an integrated hydrogen production system using reverse electrodialysis (RED) and waste heat, termed Heat to H 2 . The driving potential in RED is a concentration difference over alternating anion and cation exchange membranes, where the electrode potential can be used directly for water splitting at the RED electrodes. Low-grade waste heat is used to restore the concentration difference in RED. In this study we investigate two approaches: one water removal process by evaporation and one salt removal process. Salt is precipitated in the thermally driven salt removal, thus introducing the need for a substantial change in solubility with temperature, which KNO 3 fulfils. Experimental data of ion conductivity of K + and NO 3 − in ion-exchange membranes is obtained. The ion conductivity of KNO 3 in the membranes was compared to NaCl and found to be equal in cation exchange membranes, but significantly lower in anion exchange membranes. The membrane resistance constitutes 98% of the total ohmic resistance using concentrations relevant for the precipitation process, while for the evaporation process, the membrane resistance constitutes over 70% of the total ohmic resistance at 40 ∘ C. The modelled hydrogen production per cross-section area from RED using concentrations relevant for the precipitation process is 0.014 ± 0.009 m 3 h − 1 (1.1 ± 0.7 g h − 1 ) at 40 ∘ C, while with concentrations relevant for evaporation, the hydrogen production per cross-section area was 0.034 ± 0.016 m 3 h − 1 (2.6 ± 1.3 g h − 1 ). The modelled energy needed per cubic meter of hydrogen produced is 55 ± 22 kWh (700 ± 300 kWh kg − 1 ) for the evaporation process and 8.22 ± 0.05 kWh (104.8 ± 0.6 kWh kg − 1 ) for the precipitation process. Using RED together with the precipitation process has similar energy consumption per volume hydrogen produced compared to proton exchange membrane water electrolysis and alkaline water electrolysis, where the energy input to the Heat to H 2 -process comes from low-grade waste heat.
Human -galactosidase A: characterization of the N-linked oligosaccharides on the intracellular and secreted glycoforms overexpressed by Chinese hamster ovary cells (1998)

Human alpha-galactosidase A (alpha-Gal A) is the lysosomal glycohydrolase that cleaves the terminal alpha-galactosyl moieties of various glycoconjugates. Overexpression of the enzyme in Chinese hamster ovary (CHO) cells results in high intracellular enzyme accumulation and the selective secretion of active enzyme. Structural analysis of the N -linked oligosaccharides of the intracellular and secreted glycoforms revealed that the secreted enzyme's oligosaccharides were remarkably heterogeneous, having high mannose (63%), complex (30%), and hybrid (5%) structures. The major high mannose oligosaccharides were Man5-7GlcNAc2 species. Approximately 40% of the high mannose and 30% of the hybrid oligosaccharides had phosphate monoester groups. The complex oligosaccharides were mono-, bi-, 2,4-tri-, 2,6-tri- and tetraantennary with or without core-region fucose, many of which had incomplete outer chains. Approximately 30% of the complex oligosaccharides were mono- or disialylated. Sialic acids were mostly N -acetylneuraminic acid and occurred exclusively in alpha2, 3-linkage. In contrast, the intracellular enzyme had only small amounts of complex chains (7.7%) and had predominantly high mannose oligosaccharides (92%), mostly Man5GlcNAc2 and smaller species, of which only 3% were phosphorylated. The complex oligosaccharides were fucosylated and had the same antennary structures as the secreted enzyme. Although most had mature outer chains, none were sialylated. Thus, the overexpression of human alpha-Gal A in CHO cells resulted in different oligosaccharide structures on the secreted and intracellular glycoforms, the highly heterogeneous secreted forms presumably due to the high level expression and impaired glycosylation in the trans- Golgi network, and the predominately Man5-7GlcNAc2 cellular glycoforms resulting from carbohydrate trimming in the lysosome.
Akt, a Target of Phosphatidylinositol 3-Kinase, Inhibits Apoptosis in a Differentiating Neuronal Cell Line (1998)

Phosphatidylinositol (PI) 3-kinase has been suggested to mediate cell survival. Consistent with this possibility, apoptosis of conditionally (simian virus 40 Tts) immortalized rat hippocampal H19-7 neuronal cells was increased in response to wortmannin, an inhibitor of PI 3-kinase. Downstream effectors of PI 3-kinase include Rac1, protein kinase C, and the serine-threonine kinase Akt (protein kinase B). Here, we show that activation of Akt is one mechanism by which PI 3-kinase can mediate survival of H19-7 cells during serum deprivation or differentiation. While ectopic expression of wild-type Akt (c-Akt) does not significantly enhance survival in H19-7 cells, expression of activated forms of Akt (v-Akt or myristoylated Akt) results in enhanced survival which can be comparable to that conferred by Bcl-2. Conversely, expression of a dominant-negative mutant of Akt accelerates cell death upon serum deprivation or differentiation. Finally, the results indicate that Akt can transduce a survival signal for differentiating neuronal cells through a mechanism that is independent of induction of Bcl-2 or Bcl-XL or inhibition of Jun kinase activity.
Nanofabrication of photonic lattice structures in GaAs/AlGaAs (1993)

The nanofabrication of two-dimensional photonic lattice structures in GaAs/AlGaAs is reported. The nanofabrication procedure combines direct-write electron-beam lithography and reactive-ion-beam etching to achieve etched features as small as 50 nm. The lattice comprises a hexagonal array of air cylinders etched into a semiconductor surface with a refractive index contrast of 3.54. A range of air volume fractions from 14% to 84% was investigated. The lithographic, masking, and etching processes necessary to fabricate the lattice are described along with practical limitations to achieving a lattice of arbitrary air volume fraction. Initial results from optical characterization of the lattice are also presented.
Exploitation of a Tuned Oxidation with N-Haloimides in the Synthesis of Caulibugulones A–D (2013)

Marine alkaloids caulibugulones A-D were synthesized in six steps starting from the readily available 2,5-dimethoxybenzaldehyde. Pomeranz-Fritsch reaction of N-(2,5-dimethoxybenzyl)-N-(2,2-dimethoxyethyl)-2-nitrobenzenesulfonamide proceeded smoothly to give 5,8-dimethoxyisoquinoline, which was oxidized to isoquinolinediones by a tunable oxidation reaction with N-haloimides. Therefore, NBS furnished direct conversion to the isoquinoline-5,8-dione; alternatively, N-haloimides of cyanuric acid provided both oxidation and halogenation generating 6,7-dihaloisoquinoline-5,8-diones. Aminolyses of these isoquinolinediones with methylamine or ethanolamine produced the isoquinolinedione alkaloids caulibugulones A-D in 24-57% overall yield.
Structures and Properties of Gellan Polymers Produced bySphingomonas paucimobilisATCC 31461 from Lactose Compared with Those Produced from Glucose and from Cheese Whey (1999)

The dairy industry produces large quantities of whey as a by-product of cheese production and is increasingly looking for new ways to utilize this waste product. Gellan gum is reliably produced by Sphingomonas paucimobilis in growth media containing lactose, a significant component of cheese whey, as a carbon source. We studied and compared polysaccharide biosynthesis by S. paucimobilis ATCC 31461 in media containing glucose, lactose (5 to 30 g/liter), and sweet cheese whey. We found that altering the growth medium can markedly affect the polysaccharide yield, acyl substitution level, polymer rheological properties, and susceptibility to degradation. Depression of gellan production from lactose compared with gellan production from glucose (approximately 30%) did not appear to occur at the level of synthesis of sugar nucleotides, which are the donors of monomers used for biosynthesis of the repetitive tetrasaccharide unit of gellan. The lactose-derived biopolymer had the highest total acyl content; the glucose- and whey-derived gellans had similar total acyl contents but differed markedly in their acetate and glycerate levels. Rheological studies revealed how the functionality of a gellan polysaccharide is affected by changes in the acyl substitution.
Effect of somatostatin combined with TPN in malignant bowel obstruction due to inoperable gastrointestinal carci-noma (2009)

Objective To investigate the effects of somatostatin combined with total parenteral nutrition(TPN) on malignant bowel obstruction(MBO) due to inoperable gastrointestiinal carcinoma. Methods From Jan. 2003 to Jun. 2008, 29 patients with MBO due inoperable gastrointestinal carcinoma were randomly divided into two groups:the control group(only TPN group) 11 cases and the treatment group(somatostatin combined with TPN) 18 cases(octreotide, 100 μg, subcutaneous injection, tid, for two weeks). The effects were compared between the two groups. Resuits After the treatment, the clinical symptoms of abdominal distention and abdominal pain were relieved significantly (83.33% to 45.45%), the echaust of anus was 66.67% to 27.27%. The average volume of gastroenteral decom-pression reduced more efficiently. Qaality of life, evaluated with Karnofsky score, was improved significantly, the KPS of 88.9% treatment group were higher than 60. Conclusions The administration of somatostatin combined with TPN is effective in the MBO due to inoperable gastrointestinal carcinoma. It can obviously relieve the symptoms of MBO and improve the quality of life in patients.

Key words: 
Somatostatin;  Malignant bowel obstruction;  Gastrointestinal carcinoma
Plasma RNA Integrity Analysis (2006)

The detection of cell-free RNA in plasma and serum of human subjects has found increasing applications in the field of medical diagnostics. However, many questions regarding the biology of circulating RNA remain to be addressed. One issue concerns the molecular nature of these circulating RNA species. We have recently developed a simple and quantitative method to investigate the integrity of plasma RNA. Our results have suggested that cell-free RNA in plasma is generally present as fragmented molecules instead of intact transcripts, with a predominance of 5' fragments. In this article, we summarize the basic principles in the experimental design for plasma RNA integrity analysis and highlight some of the important technical considerations for this type of investigation.