gebhart/patrepeval huggingface dataset:
Chemical Characterization of Biobinder from Swine Manure: Sustainable Modifier for Asphalt Binder (2011)

This paper presents the production, modification, and characterization of biobinder from swine manure. A hydrothermal process was used to convert swine manure to a bio-oil. The bio-oil was fractionated to extract water, solid residue, and some of the organic compounds. The sticky residue after fractionation was used as a replacement for asphalt binder. This paper presents production and chemical and rheological characterization of the biobinder as compared with petroleum-asphalt binder. Biobinder from swine manure was found to be a promising candidate for partial replacement for petroleum-asphalt binder. Considering the limitations imposed on growth of swine farms by manure management practices and environmental regulations and the increasing demand for asphalt binder for infrastructure rehabilitation, this sustainable development will result in major improvements in environmental and economical impacts in both the agricultural and construction sectors. Hence, this study offers a unique approach that simultaneously addresses the increased depletion of petroleum resources the growing swine manure pollution and released greenhouse gases and the development of sustainable alternative for petroleum-asphalt binder. The use of biobinder will improve petroleum-asphalt binder’s low temperature properties while reducing asphalt pavement construction costs; the cost of biobinder production is estimated to be $0.13/L ($0.54/gal.) and that of asphalt binder is $0.53/L ($2/gal).
Diagnosis of AIDS by Using a 12-Amino Acid Peptide Representing an Immunodominant Epitope of the Human Immunodeficiency Virus (1987)

We mapped an immunodominant domain of the human immunodeficiency virus (HIV). We selected hydrophilic amino acid sequences encoded by conserved regions of the gag, pol, and env genes of HIV as potential antigenic domains. Eighteen peptides representing these sequences were synthesized; the peptides elicited strong antibody responses in rabbits. Sera from 53 HIV-infected patients and 50 controls were tested against the synthetic peptides. Although no antibodies to peptides from gag, pol, or env gp120 proteins were present, antibodies to four of the six peptides from env gp41 were detected. Epitope mapping using overlapping peptides showed that sera from 53 (100%) of 53 HIV-infected patients (and from none of 50 controls) reacted with peptides aa584-609 and aa598-609 from gp41, sera from 32 (60%) of 53 patients reacted with peptide aa603-614, and sera from 19 (35%) of 53 patients reacted with peptides aa609-620. Thus, amino acid sequence LeuGlyIleTrpGlyCysSerGlyLysLeuIleCys (aa598-609) from the transmembrane glycoprotein is an immunodominant domain of HIV recognized by serum antibodies from HIV-infected patients.
Chronic Hyperglycemia Triggers Loss of Pancreatic β Cell Differentiation in an Animal Model of Diabetes (1999)

Differentiated pancreatic beta cells are unique in their ability to secrete insulin in response to a rise in plasma glucose. We have proposed that the unique constellation of genes they express may be lost in diabetes due to the deleterious effect of chronic hyperglycemia. To test this hypothesis, Sprague-Dawley rats were submitted to a 85-95% pancreatectomy or sham pancreatectomy. One week later, the animals developed mild to severe chronic hyperglycemia that was stable for the next 3 weeks, without significant alteration of plasma nonesterified fatty acid levels. Expression of many genes important for glucose-induced insulin release decreased progressively with increasing hyperglycemia, in parallel with a reduction of several islet transcription factors involved in beta cell development and differentiation. In contrast, genes barely expressed in sham islets (lactate dehydrogenase A and hexokinase I) were markedly increased, in parallel with an increase in the transcription factor c-Myc, a potent stimulator of cell growth. These abnormalities were accompanied by beta cell hypertrophy. Changes in gene expression were fully developed 2 weeks after pancreatectomy. Correction of blood glucose by phlorizin for the next 2 weeks normalized islet gene expression and beta cell volume without affecting plasma nonesterified fatty acid levels, strongly suggesting that hyperglycemia triggers these abnormalities. In conclusion, chronic hyperglycemia leads to beta cell hypertrophy and loss of beta cell differentiation that is correlated with changes in c-Myc and other key transcription factors. A similar change in beta cell differentiation could contribute to the profound derangement of insulin secretion in human diabetes.
Resistant Mechanism Study of Benzalkonium Chloride Selected Salmonella Typhimurium Mutants (2013)

Benzalkonium chloride is one of the invaluable biocides that is extensively used in healthcare settings as well as in the food processing industry. After exposing wild-type Salmonella Typhimurium 14028s or its AcrAB inactivation mutant to gradually increasing levels of benzalkonium chloride, resistance mutants S-41, S-150, S-AB-23, S-AB-38, and S-AB-73 were selected and these mutants also showed a 2-64-fold stable minimum inhibitory concentration (MIC) increase to chloramphenicol, ciprofloxacin, nalidixic acid, and tetracycline. In S-41 and S-150, the expression of acrB was increased 2.7- and 7.6-fold, and ΔtolC or ΔacrAB mutants of S-41 and S-150 showed the same MICs to all tested antimicrobials as the equivalent Salmonella Typhimurium 14028s mutants. However, in S-AB-23, S-AB-38, and S-AB-73, the expression of acrF was increased 96-, 230-, and 267-fold, respectively, and ΔtolC or ΔacrEF mutants of S-AB-23, S-AB-38, and S-AB-73 showed the similar MICs to all tested antimicrobials as the ΔtolC mutant of Salmonella Typhimurium 14028s. Our data showed that constitutively over-expressed AcrAB working through TolC was the main resistance mechanism in ST14028s benzalkonium chloride resistance mutants. However, after AcrAB had been inactivated, benzalkonium chloride-resistant mutants could still be selected and constitutively over-expressed, AcrEF became the dominant efflux pump working through TolC and being responsible for the increasing antimicrobial resistance. These data indicated that different mechanisms existed for acrB and acrF constitutive over-expression. Since exposure to benzalkonium chloride may lead to Salmonella mutants with a decreased susceptibility to quinolones, which is currently one of the drugs of choice for the treatment of life-threatening salmonelosis, research into the pathogenesis and epidemiology of the benzalkonium chloride resistance mutants will be of increasing importance.
Gastric cancers overexpress S100A calcium-binding proteins. (2002)

Serial analysis of gene expression provides quantitative and comprehensive expression profiling in a given cell population. In our efforts to define the genes overexpressed in carcinoma of the stomach, we performed serial analysis of gene expression analyses on dissected neoplastic and normal gastric epithelia. We identified 91,334 expressed tags, including 26,633 that were unique. The 20 most up-regulated genes (P < 0.01) in gastric cancer (GC) compared with normal gastric epithelia included several keratins that are specific for epithelial cells such as keratin 6A, 13, and 17. Interestingly, five calcium-binding proteins (S100A2, S100A7, S100A8, S100A9, and S100A10) were overexpressed. Quantitative real-time PCR on primary GC samples demonstrated overexpression of S100A2 in 18 of 20 tumors (90%). The other calcium-binding proteins were overexpressed in 25-45% of the GC samples that we studied. Our results indicate that S100A proteins may be important for gastric tumorigenesis. Additional investigations are required to elucidate the biological role of calcium-binding proteins in cancer.
Treatment of Hepatocellular Carcinoma with Traditional Chinese Medicine: Possible Molecular Mechanisms (2012)

Hepatocellular carcinoma (HCC) is one of the most frequent malignancies worldwide, and it has the highest prevalence in Asia and Africa countries. Most symptomatic HCCs have a low surgical respectability and the disease usually progresses rapidly and has a very poor prognosis. The constant searching for the molecular and genetic mechanisms involved in the development of HCC is necessary for the development of more effective therapeutic strategies against this cancer. Over the last few years, many alternative approaches have been explored in the management of HCC. The possible therapeutic role of traditional Chinese medicine (TCM) against HCC has been extensively studied, and some showed promising results, but the underlying molecular mechanisms involved in the TCM against HCC remain largely unknown. In this review article, we aim to elucidate the possible molecular mechanisms of TCM in HCC therapy. Based on preliminary basic and clinical studies, TCM is able to induce apoptosis, inhibit cell proliferation, strengthen the host immune functions, and suppress the invasion and metastasis of HCC.
Document image understanding: geometric and logical layout (1994)

Document image understanding encompasses the technology required to make paper documents equivalent to other computer exchange media like floppies, tapes, and CDROMs. The physical reader of the paper document is the scanner just like the physical reader of the floppy is the floppy drive and the physical reader of the tape cartridge is the tape cartridge drive, and the physical reader of the CDROM is the CDROM drive. In the survey presented, we restrict ourselves to documents such as business letters, forms, and scientific and technical articles such as those found in archival journals and technical conferences. Understanding such documents involves estimating the rotation skew of each document page, determining the geometric page layout, labeling blocks as text or non-text, determining the read order for text blocks, recognizing the text of text blocks through an OCR system, determining the logical page layout, and formatting the data and information of the document in a suitable way for use by a word processing system or by an information retrieval system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Synthetic or natural surfactants (1997)

Surfactant replacement therapy is one of the most studied interventions in neonatal medicine, with many thousands of infants having been enrolled in randomized clinical trials. It is clear that surfactant therapy reduces neonatal mortality and the risk of pulmonary air leaks in babies with or at risk of developing respiratory distress syndrome. Yet some doubts linger over other aspects of this therapy, despite it having been an acceptable and proven therapy for the past 7-10 years. As regards timing of treatment, the earlier the better, with true prophylaxis being reserved for babies of less than 28 week's gestation. Natural surfactant preparations containing surfactant proteins B and C act more rapidly than their synthetic protein-free counterparts and probably also have a greater impact on reducing neonatal mortality and pulmonary air leaks. Fears raised about immunological effects, prion transmission and chemical contamination of natural surfactants have not been substantiated. Long-term follow-up studies do not show any differences in outcome between treated and non-treated infants, except that the incidence and severity of retinopathy of prematurity might be reduced by treatment with natural surfactant. Further research is needed and this will include more detailed follow-up studies, newer indications for surfactant therapy and the testing of newer preparations with synthetic peptides or protein analogues added.
A Data Model Based on Service and Process Abstractions for Management of Systems (2002)

In the crystal of the title compound, the quinone fragment of the host (1) participates in weak D-A interactions with a neighboring naphthalene moiety of 1 and with the guest molecule via fairly short intermolecular face-to-face contacts. An intermolecular electrostatic interaction between a quinone-oxygen atom and a neighboring quinone ring is suggested by short O...C contacts. There exist several C-H...O hydrogen bonds, one of which seems to contribute to the formation of a centrosymmetric dimer of 1.
Prevalence of Cognitive Impairment, Depression, and Anxiety Symptoms Among Older Adults With Glaucoma (2011)

The results from this study indicate that cognitive impairment may be common in older patients with glaucoma. This has implications for treatment adherence, as difficulties in remembering information may significantly impede the ability to follow instructions from a physician. It is imperative that physicians and caregivers are aware of the prevalence of such conditions, as they are among the first to interact with such individuals. Given the high prevalence of cognitive impairment and depressive symptoms, future research should examine the impact of such factors on glaucoma treatment adherence.
Irritable bowel syndrome (1990)

June Thompson looks at causes, incidence and symptoms of irritable bowel syndrome, the most common disorder of the intestines, which affects one in seven of the population.
Mounting a Targeted Strike on Unwanted Immune esponses (1992)

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Armed Antibodies Targeting the Mucin Repeats of the Ovarian Cancer Antigen, MUC16, Are Highly Efficacious in Animal Tumor Models (2007)

MUC16 is a well-validated cell surface marker for serous adenocarcinomas of the ovary and other gynecologic malignancies that is distinguished by highly repetitive sequences ("mucin repeats") in the extracellular domain (ECD). We produced and compared two monoclonal antibodies: one (11D10) recognizing a unique, nonrepeating epitope in the ECD and another (3A5) that recognizes the repeats and binds multiple sites on each MUC16 protein. 3A5 conjugated to cytotoxic drugs exhibited superior toxicity against tumor cells in vitro and in tumor xenograft models compared with antibody-drug conjugates of 11D10. Importantly, drug conjugates of 3A5 were well tolerated in primates at levels in excess of therapeutic doses. Additionally, the presence of circulating CA125 in a rat model did not exacerbate the toxicity of 3A5 drug conjugates. We conclude that targeting the repeat MUC16 domains, thereby increasing cell-associated levels of drug-conjugated antibody, provides superior efficacy in vitro and in vivo without compromising safety.
Identification of the second cluster of ligand-binding repeats in megalin as a site for receptor–ligand interactions (1997)

Megalin is a large cell surface receptor that mediates the binding and internalization of a number of structurally and functionally distinct ligands from the lipoprotein and protease:protease inhibitor families. To begin to address how megalin is able to bind ligands with unique structurally properties, we have mapped a binding site for apolipoprotein E (apoE)-beta very low density lipoprotein (beta VLDL), lipoprotein lipase, aprotinin, lactoferrin, and the receptor-associated protein (RAP) within the primary sequence of the receptor. RAP is known to inhibit the binding of all ligands to megalin. We identified a ligand-binding site on megalin by raising mAb against purified megalin, selected for a mAb whose binding to megalin is inhibited by RAP, and mapped the epitope for this mAb. mAb AC10 inhibited the binding of apoE-beta VLDL, lipoprotein lipase, aprotinin, and lactoferrin to megalin in a concentration-dependent manner. When cDNA fragments encoding the four cysteine-rich ligand-binding repeats in megalin were expressed in a baculovirus system and immunoblotted with AC10, it recognized only the second cluster of ligand-binding repeats. The location of the epitope recognized by mAb AC10 within this domain was pinpointed to amino acids 1111-1210. From these studies we conclude that the binding of apoE-beta VLDL, lactoferrin, aprotinin, lipoprotein lipase, and RAP to megalin is either competitively or sterically inhibited by mAb AC10 suggesting that these ligands bind to the same or closely overlapping sites within the second cluster of ligand-binding repeats.
On-chip three-dimensional cell culture in phaseguides improves hepatocyte functions in vitro (2015)

The in vitro study of liver functions and liver cell specific responses to external stimuli deals with the problem to preserve the in vivo functions of primary hepatocytes. In this study, we used the biochip OrganoPlate(TM) (MIMETAS) that combines different advantages for the cultivation of hepatocytes in vitro: (1) the perfusion flow is achieved without a pump allowing easy handling and placement in the incubator; (2) the phaseguides allow plating of matrix-embedded cells in lanes adjacent to the perfusion flow without physical barrier; and (3) the matrix-embedding ensures indirect contact of the cells to the flow. In order to evaluate the applicability of this biochip for the study of hepatocyte's functions, Matrigel(TM)-embedded HepG2 cells were cultured over three weeks in this biochip and compared to a static Matrigel culture (3D) and a monolayer culture (2D). Chip-cultured cells grew in spheroid-like structures and were characterized by the formation of bile canaliculi and a high viability over 14 days. Hepatocyte-specific physiology was achieved as determined by an increase in albumin production. Improved detoxification metabolism was demonstrated by strongly increased cytochrome P450 activity and urea production. Additionally, chip-cultured cells displayed increased sensitivity to acetaminophen. Altogether, the OrganoPlate seems to be a very useful alternative for the cultivation of hepatocytes, as their behavior was strongly improved over 2D and static 3D cultures and the results were largely comparable and partly superior to the previous reports on biochip-cultured hepatocytes. As for the low technical needs, this platform has the appearance of being highly applicable for further studies of hepatocytes' responses to external stimuli.
Synthesis and Structure−Activity Relationships of 3,7-Dimethyl-1-propargylxanthine Derivatives, A2A-Selective Adenosine Receptor Antagonists (1997)

A series of 8-substituted derivatives of 3,7-dimethyl-1-propargylxanthine (DMPX) was synthesized and investigated as A2A adenosine receptor antagonists. Different synthetic strategies for the preparation of DMPX derivatives and analogues were explored. A recently developed synthetic procedure starting from 3-propargyl-5,6-diaminouracil proved to be the method of choice for the preparation of this type of xanthine derivatives. The novel compounds were investigated in radioligand binding studies at the high-affinity adenosine receptor subtypes A1 and A2A and compared with standard A2A adenosine receptor antagonists. Structure−activity relationships were analyzed in detail. 8-Styryl-substituted DMPX derivatives were identified that exhibit high affinity and selectivity for A2A adenosine receptors, including 8-(m-chlorostyryl)-DMPX (CS-DMPX, Ki A2A = 13 nM, 100-fold selective), 8-(m-bromostyryl)-DMPX (BS-DMPX, Ki A2A = 8 nM, 146-fold selective), and 8-(3,4-dimethoxystyryl)-DMPX (Ki A2A = 15 nM, 167-fold selective). These and other novel compounds are superior to the standard A2A adenosine receptor antagonists KF17837 (4) and CSC (5) with respect to A2A affinity and/or selectivity.
High speed carrier-depletion modulators with 14V-cm V_πL integrated on 025μm silicon-on-insulator waveguides (2010)

We demonstrate a very efficient high speed silicon modulator with an ultralow pi-phase-shift voltage-length product V(pi)L = 1.4V-cm. The device is based on a Mach-Zehnder interferometer (MZI) fabricated using 0.25microm thick silicon-on-insulator (SOI) waveguide with offset lateral PN junctions. Optimal carrier-depletion induced index change has been achieved through the optimization of the overlap region of carriers and photons. The 3dB bandwidth of a typical 1mm long device was measured to be more than 12GHz. An eye-diagram taken at a transmission rate of 12.5Gb/s confirms the high speed capability of the device.
Folding and stability of a tryptophan-containing mutant of ubiquitin (1993)

To provide a fluorescence probe for equilibrium and kinetic folding studies on ubiquitin, cassette mutagenesis in an Escherichia coli expression plasmid was used to replace the largely buried Phe 45 by a tryptophan. Under native conditions, the tryptophan fluorescence spectrum of this F45W mutant exhibits a blue-shifted emission maximum at 336 nm indicative of a largely solvent-shielded tryptophan environment. In contrast, the unfolded protein in 6 M guanidine hydrochloride (GuHCl) shows a 4-fold more intense emission band at 353 nm matching that of free tryptophan. The two-dimensional 1H NMR spectrum of F45W ubiquitin was assigned by comparison with published assignments of the wild type. The mutation results in only limited chemical shift changes for residues in the immediate vicinity of residue 45. The structural similarity of F45W with wild-type ubiquitin was confirmed by a preliminary analysis of the nuclear Overhauser spectrum. NMR and circular dichroism measurements of the reversible GuHCl-induced unfolding transition show that the F45W mutation lowers the stability of the folded ubiquitin structure by less than 0.4 kcal/mol. The biological activity of the mutant was found to be indistinguishable from that of wild-type in terms of its reaction with the ubiquitin activating enzyme E1 and an in vitro assay of ATP-dependent protein degradation. The kinetics of folding and unfolding of F45W ubiquitin was studied at two temperatures (8 and 25 degrees C) in a series of fluorescence-detected stopped-flow measurements over a wide range of GuHCl concentrations (0.5-6 M). The measurements at 25 degrees C are consistent with a two-state model with strongly denaturant-dependent folding and unfolding rates above about 2 M GuHCl. However, at lower denaturant concentrations, the rate of the major folding phase becomes GuHCl-independent, and up to 60% of the total fluorescence change occurs during the 2-ms dead time of the stopped-flow measurement. These observations provide clear evidence for the formation of an early folding intermediate during the first few milliseconds of refolding with a partially developed hydrophobic core involving Trp 45. The sigmoid denaturant dependence of the initial amplitude with an apparent midpoint of 1.3 M GuHCl suggests the presence of a discrete state that is destabilized at higher denaturant concentrations. In contrast, there is no evidence for an early intermediate in the folding kinetics at 8 degrees C. The destabilization of the intermediate at low temperature is consistent with a collapsed state stabilized primarily by hydrophobic interactions.