gebhart/patrepeval huggingface dataset:
Identification of immunodominant epitopes in the filamentous hemagglutinin of<i>Bordetella pertussis</i> (1999)

The filamentous hemagglutinin (FHA) of Bordetella pertussis is a principal adhesin, which plays a key role in the colonization of the upper respiratory tract. FHA is also a protective antigen, which has been incorporated in the new generation of acellular vaccines against whooping cough. The protein is synthesized as a large 367-kDa precursor, which is then processed into a 220-kDa secreted polypeptide. To optimize the use of this protein for vaccine purposes it would be helpful to define the regions encompassing immunodominant epitopes. Twelve recombinant plasmids have been generated encoding fusion proteins between fragments of the matured-secreted 220-kDa form of FHA and the vector-encoded phage MS2 polymerase. Protein extracts of the resulting recombinant clones have been tested for reactivity with sera from 20 patients convalescent from whooping cough, and two human standard sera. The results indicate the presence of an immunodominant B cell epitope in the polypeptide coded by a 1-kb DNA fragment encompassing positions 5781-6800 of the published sequence. These results suggest that the identified fragment should be conserved in the formulation of vaccines against pertussis.
Predicted structure of agonist-bound glucagon-like peptide 1 receptor, a class B G protein-coupled receptor (2012)

The glucagon-like peptide 1 receptor (GLP1R) is a G protein-coupled receptor (GPCR) involved in insulin synthesis and regulation; therefore, it is an important drug target for treatment of diabetes. However, GLP1R is a member of the class B1 family of GPCRs for which there are no experimental structures. To provide a structural basis for drug design and to probe class B GPCR activation, we predicted the transmembrane (TM) bundle structure of GLP1R bound to the peptide Exendin-4 (Exe4; a GLP1R agonist on the market for treating diabetes) using the MembStruk method for scanning TM bundle conformations. We used protein-protein docking methods to combine the TM bundle with the X-ray crystal structure of the 143-aa N terminus coupled to the Exe4 peptide. This complex was subjected to 28 ns of full-solvent, full-lipid molecular dynamics. We find 14 strong polar interactions of Exe4 with GLP1R, of which 8 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions involve the N terminus (3 interactions found in the crystal structure). We also find 10 important hydrophobic interactions, of which 4 interactions are in the TM bundle (2 interactions confirmed by mutation studies) and 6 interactions are in the N terminus (6 interactions present in the crystal structure). Thus, our predicted structure agrees with available mutagenesis studies. We suggest a number of mutation experiments to further validate our predicted structure. The structure should be useful for guiding drug design and can provide a structural basis for understanding ligand binding and receptor activation of GLP1R and other class B1 GPCRs.
Convective-diffusion-based fluorescence correlation spectroscopy for detection of a trace amount of E coli in water (2003)

Fluorescence correlation spectroscopy (FCS) is adapted for a new procedure to detect trace amounts of Escherichia coli in water. The present concept is based on convective diffusion rather than Brownian diffusion and employs confocal microscopy as in traditional FCS. With this system it is possible to detect concentrations as small as 1.5 x 10(5) E. coli per milliliter (2.5 x 10(-16) M). This concentration corresponds to an approximately 1.0-nM level of Rhodamine 6G dyes. A detailed analysis of the optical system is presented, and further improvements for the procedure are discussed.
The epidemiology of infection with Entamoeba histolytica in The Gambia, West Africa (1977)

A country-wide stool survey of The Gambia showed the prevalence of Entamoeba histolytica cysts to range from 13.7% up-country in the dry season to 52.3% near the coast. A longitudinal survey showed a near 100% infection rate over one year and a sharp rise in prevalence as the rains commence with an equally sharp fall as the rains progress. Specific antibody levels are elevated and reasonably constant through the year. Carriers generally show no specific lymphocyte reactivity to amoebic antigen but consistently parasite-negative individuals tended to show elevated lymphocyte reactivity. Attempts to discover the presence of cysts in the environment of villages by cultivation of specimens of water, soil, food, flies and washing from clothes and hands generally failed though E. histolytica was recovered once from a well.
Analyzing the mechanical strengths of SMT attached solder joints (1990)

Analytic approaches to the pull strength and the shear strength of SMT (surface mount technology) attached solder joints are studied by mathematical models. The predicted pull/shear strength of leaded ceramic quad packages was correlated with the experimentally measured data. The predictive models have been used for defining the design guidelines for selecting the optimum lead/pad configurations, the minimum solder volume, and the maximum component misalignment for fine-pitch SMT assemblies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Current Status of Injectable Oxygen Carriers (1994)

In this review the current status of what commonly are termed "blood substitutes" is discussed. The term blood substitute is a misnomer because the formulations under development at this time transport respiratory gases but do not perform the metabolic, regulatory, and protective functions of blood. Either hemoglobin or a perfluorochemical form the base to transport oxygen; the advantages and disadvantages of each base are discussed. The availability of a blood substitute in the U.S. will require approval by the Food and Drug Administration (FDA) and, by law, both its efficacy and safety must be demonstrated prior to approval. Showing efficacy of any blood substitute is complicated by the oxygen reserve and the compensatory mechanisms to acute blood loss in man. The challenge is to prove that the administration of these formulations offer clinical advantages compared with replacement of volume alone. Several efficacy models, the most attractive among them being perioperative hemodilution, should provide data that would bring these formulations into clinical practice. When hemoglobin is not within the favorable environment of the red cell, whether the hemoglobin is derived from expression vectors developed through recombinant biotechnology or from lysed human red cells, it acquires a left-shifted oxygen disassociation curve. Further, because the tetramer disassociates when injected intravenously and the resulting dimers are cleared rapidly from the circulation by the kidneys, intravascular dwell time is brief. Hemoglobins have been modified chemically and linked intramolecularly, intermolecularly, and to macromolecules to correct these problems. While these manipulations have normalized the p50 and extended the dwell time significantly, some toxicity problems remain unresolved. The binding of nitric oxide to hemoglobin preparations and the presumably resultant systemic and pulmonary hypertension observed in animals may be the most difficult to overcome, although the implications of these reactions in man is poorly understood. Perfluorochemicals (PFC) provide a fundamentally different and simpler approach to oxygen transport than hemoglobin formulations. Typically, the PFCs used are liquids composed of 8 to 10 carbon atoms that dissolve oxygen and obey Henry's law. Thus, the recipient's inspired oxygen and cardiac output assume importance. Because they are insoluble in water, PFCs are administered as emulsions, that is, as small droplets about 0.1 to 0.2 microns in diameter. In this respect, they are very similar to the lipid emulsions widely used for parenteral nutrition. Egg yolk phospholipid and poloxamers are most commonly used as emulsifiers. PFCs are not metabolized and are excreted unchanged by the lungs, following temporary storage by the monocyte-macrophage system (MMS).(ABSTRACT TRUNCATED AT 400 WORDS)
[Stochastic resonance in weak signal detection by sensory systems]. (2004)

This work gives a proof that stochastic resonance is not only an epiphenomenon in sensory systems.
M$^2$S-Net: Multi-Modal Similarity Metric Learning based Deep Convolutional Network for Answer Selection (2016)

Recent works using artificial neural networks based on distributed word representation greatly boost performance on various natural language processing tasks, especially the answer selection problem. Nevertheless, most of the previous works used deep learning methods (like LSTM-RNN, CNN, etc.) only to capture semantic representation of each sentence separately, without considering the interdependence between each other. In this paper, we propose a novel end-to-end learning framework which constitutes deep convolutional neural network based on multi-modal similarity metric learning (M$^2$S-Net) on pairwise tokens. The proposed model demonstrates its performance by surpassing previous state-of-the-art systems on the answer selection benchmark, i.e., TREC-QA dataset, in both MAP and MRR metrics.
[Activity of serum angiotensin converting enzyme in pregnancy-induced hypertension]. (1991)

Activity of serum angiotensin converting enzyme (SACE) was measured in serum of 33 pregnant women with normal blood pressure or pregnancy induced hypertension (PIH), using sensitive Hippurate colorimetric micromethod. The mean level of SACE activity in 17 PIH patients (73.25 +/- 18.81 U/ml) was significantly higher than that in normotensive pregnant women (16 cases) ( 52.36 +/- 9.91 U/ml) (P less than 0.01). The mean arterial blood pressure showed a positive correlation with the level of SACE activity in all pregnant women (Y = 69.089 + 0.494x, r = 0.562, P less than 0.01). In PIH patients, the gestosis index and degree of edema also had statistically significant correlation with the level of SACE activity (Y = -0.560 + 0.056x, r = 0.549, P less than 0.01) (Y = -1.760 + 0.043x, r = 0.629, P less than 0.05). The amount of 24h urinary protein was independent of the level of SACE activity. It suggests that disturbance in regulation of ACE activity may be one of the factors responsible for the development of PIH.
Comparison of atmospheric aqueous glycerol and steam explosion pretreatments of wheat straw for enhanced enzymatic hydrolysis (2008)

Abstract BACKGROUND: The oversupply of cheap glycerol by the oleochemicals industry together with problems occurring in low‐boiling‐point organosolv pretreatments, has generated an interest in the use of glycerol in the organosolv pretreatment of lignocellulosic biomass. Atmospheric aqueous glycerol autocatalytic organosolv pretreatment (AAGAOP) is a promising strategy that can effectively enhance enzymatic hydrolysis of lignocellulosic biomass. As a cost‐effective technique, steam explosion pretreatment (SEP) is being adopted in industrial applications. Accordingly, work has been carried out to investigate how AAGAOP enhanced enzymatic hydrolysis of lignocellulosic biomass compares with the SEP method. RESULTS: Under controlled laboratory conditions, based on ≥ 90% cellulose recovery, AAGAOP removed ≥ 60% hemicellulose and ≥ 60% lignin from wheat straw while SEP led to ∼80% hemicellulose and 10% lignin removal. Enzymatic hydrolysis yields of AAGAOP and SEP reached ∼90% and ∼70%, respectively. Physical‐chemical structural characterization by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT‐IR), helped explain the above results. The two methods gave priority to dissociating the guaiacyl lignin and had a relatively small effect on syringyl units. However, AAGAOP exhibited a superior performance. CONCLUSION: The two methods enhanced the enzymatic hydrolysis of lignocellulosic biomass by removing and/or altering physical‐chemical structural impediments. The AAGAOP technique, with some special advantages, was more effective than SEP in enhancing the recovery and enzymatic digestibility of cellulose. Copyright © 2008 Society of Chemical Industry
Ascendency of the black bottle (activated charcoal). (1987)

Previous well-established guidelines for the management of poisonous ingestions in children are undergoing significant change. The time-honored practice of syrup of ipecac-induced vomiting as the primary means of gastrointestinal decontamination now frequently yields to the administration of activated charcoal. Practitioners and emergency room physicians who are increasingly relying on advice from and participation in treatment by regional poison control centers need to understand the rationale behind what many consider contradictions to accepted teaching. A case in point was a recent letter to the American Academy of Pediatrics from a pediatrician questioning the treatment of an ingestion of poison in a toddler.
A cyclin-dependent kinase-activating kinase regulates differentiation of root initial cells in <i>Arabidopsis</i> (2000)

Cell division and differentiation continue throughout the plant life cycle without significant loss of control. However, little is known about the mechanisms that allow the continuous development of meristems. Cell division is controlled by a family of cyclin-dependent kinases (CDKs). CDK-activating kinases (CAKs) are known to phosphorylate and activate almost all CDKs and thus may have a crucial role in controlling CDK activities in each cell of the meristems. Here, we show that overexpression of sense or antisense gene for Cak1At in Arabidopsis by using the glucocorticoid-mediated transcriptional induction system resulted in a reduction of CDK activities. After 14–24 h of glucocorticoid treatment, starch granules appeared in columellar initials in the root meristem, and cortical initials were periclinally divided into cortical and endodermal cells. Accumulation of the cyclin∷β-glucuronidase fusion protein ceased after 72 h of glucocorticoid treatment. Our results indicate that a change of Cak1At activity leads to differentiation of initial cells, followed by cessation of cell division. Therefore, we propose that differentiation of initial cells is controlled by Cak1At but is maintained independent of cell division.
Detection of DOPA 4,5-Dioxygenase (DOD) Activity Using Recombinant Protein Prepared from Escherichia coli Cells Harboring cDNA Encoding DOD from Mirabilis jalapa (2009)

Betalains are synthesized in flowers, fruits and other tissues of the plant order Caryophyllales. Betalamic acid is the chromophore of betalain pigments synthesized by a ring-cleaving enzyme reaction on l-dihydroxyphenylalanine (DOPA). Although reverse genetic evidence has proven that DOPA 4,5-dioxygenase (DOD) is a key enzyme of betalain biosynthesis, all attempts to detect recombinant plant DOD activity in vitro have failed. Here, we report on the formation of betalamic acid from DOPA under suitable assay conditions using recombinant MjDOD produced by Escherichia coli. This is the first report showing biochemical evidence for DOD activity in vitro.
Genome wide analysis of pathogenic SH2 domain mutations (2008)

The authors have made a genome-wide analysis of mutations in Src homology 2 (SH2) domains associated with human disease. Disease-causing mutations have been detected in the SH2 domains of cytoplasmic signaling proteins Bruton tyrosine kinase (BTK), SH2D1A, Ras GTPase activating protein (RasGAP), ZAP-70, SHP-2, STAT1, STAT5B, and the p85alpha subunit of the PIP3. Mutations in the BTK, SH2D1A, ZAP70, STAT1, and STAT5B genes have been shown to cause diverse immunodeficiencies, whereas the mutations in RASA1 and PIK3R1 genes lead to basal carcinoma and diabetes, respectively. PTPN11 mutations cause Noonan sydrome and different types of cancer, depending mainly on whether the mutation is inherited or sporadic. We collected and analyzed all known pathogenic mutations affecting human SH2 domains by bioinformatics methods. Among the investigated protein properties are sequence conservation and covariance, structural stability, side chain rotamers, packing effects, surface electrostatics, hydrogen bond formation, accessible surface area, salt bridges, and residue contacts. The majority of the mutations affect positions essential for phosphotyrosine ligand binding and specificity. The structural basis of the SH2 domain diseases was elucidated based on the bioinformatic analysis.
The emerging role of lysine demethylases in DNA damage response: dissecting the recruitment mode of KDM4D/JMJD2D to DNA damage sites (2015)

KDM4D is a lysine demethylase that removes tri- and di- methylated residues from H3K9 and is involved in transcriptional regulation and carcinogenesis. We recently showed that KDM4D is recruited to DNA damage sites in a PARP1-dependent manner and facilitates double-strand break repair in human cells. Moreover, we demonstrated that KDM4D is an RNA binding protein and mapped its RNA-binding motifs. Interestingly, KDM4D-RNA interaction is essential for its localization on chromatin and subsequently for efficient demethylation of its histone substrate H3K9me3. Here, we provide new data that shed mechanistic insights into KDM4D accumulation at DNA damage sites. We show for the first time that KDM4D binds poly(ADP-ribose) (PAR) in vitro via its C-terminal region. In addition, we demonstrate that KDM4D-RNA interaction is required for KDM4D accumulation at DNA breakage sites. Finally, we discuss the recruitment mode and the biological functions of additional lysine demethylases including KDM4B, KDM5B, JMJD1C, and LSD1 in DNA damage response.
Liquefaction of Biomass by Supercritical Gas Extraction (2001)

Verbascum and sunflower stalks mill were converted to liquid products by using organic solvents (methanol, ethanol, and acetone) with catalysts (% 10 NaOH) and without catalysts in an autoclave at temperatures of 533 and 573 K for verbascum and 523 and 563 K for sunflower The liquid products were extracted by liquid-liquid extraction (benzene and diethyl ether). The yields from supercritical methanol, ethanol, and acetone conversions were 44.4. 43.3, and 60.5 (at 573 K for verbascum stalk) and 40.0, 45.6 and 47.8% (at 563 K for sunflower stalk), respectively. In the catalytic runs with methanol and ethanol. extracts were 52.4 and 44.8 (at 553 K for verbascum stalk) and 58.5 and 54.2% (at 563 K for sunflower stalk), respectively.
Magnetorheological landing gear: 1. A design methodology (2007)

Aircraft landing gears are subjected to a wide range of excitation conditions, which result in conflicting damping requirements. A novel solution to this problem is to implement semi-active damping using magnetorheological (MR) fluids. This paper presents a design methodology that enables an MR landing gear to be optimized, both in terms of its damping and magnetic circuit performance, whilst adhering to stringent packaging constraints. Such constraints are vital in landing gear, if MR technology is to be considered as feasible in commercial applications.
Predominantly sensory neuropathy in patients with AIDS and AIDS‐related complex (1988)

The most common type of peripheral neuropathy associated with human immunodeficiency virus (HIV) infection, predominantly sensory neuropathy, affects 10-30% of patients with acquired immunodeficiency syndrome (AIDS). From 40 individuals with peripheral neuropathy and HIV infection, we have identified 26 patients with this syndrome. All had constitutional symptoms when neuropathic symptoms developed; 20 had AIDS and six had AIDS-related complex. The most common complaint was pain on the soles. Paresthesias were frequent and usually involved the entire foot. Signs of peripheral neuropathy were present in all; the most frequent finding was absent or reduced ankle reflexes. Electrophysiologic studies revealed abnormal sensory and motor conduction, studies suggesting a dying-back axonopathy. Over time, the neuropathy progressed in all except one patient with ARC, who had spontaneous subjective improvement. Tricyclic antidepressants provided partial symptomatic relief. In three patients, the neuropathy did not change during azidothymidine treatment. Predominantly sensory neuropathy in HIV infection appears to be a distal axonal degeneration primarily involving sensory neurons. The mechanism is unknown, but the neuropathy is associated with the late manifestations of HIV infection.
ChemInform Abstract: REACTION OF TERTIARY ARSINE SULFIDES WITH ALKYL CHLOROCARBONATES (1977)

Abstract Das Arsinsulfid (II) und der Ester (III) reagieren bei 25°C in 2 Richtungen; einmal zum Arsoniumchlorid (I) oder zum Alkylaryl‐carbomethoxyarsinsulfid (IV).
Stability of austenitic 316L steel against martensite formation during cyclic straining (2011)

Solution-annealed AISI 316L steel was fatigued with constant plastic strain amplitudes at room temperature and under various conditions at depressed temperatures down to 113 K to reveal its stability against deformation-induced martensite formation. Microstructural changes induced by fatigue were characterized by transmission electron microscopy (TEM), electron channeling contrast imaging (ECCI) and electron backscattering diffraction (EBSD) techniques. Neutron diffraction and magnetic induction method were adopted for quantification of martensite content. Deformation-induced martensite formation in the bulk of material was evidenced for low temperature cyclic straining under various conditions. Room temperature cycling, even with high plastic strain amplitudes, results in a local very limited martensite formation in areas closely linked with the long fatigue crack growth.
Chromatographic Profiles and Identification of New Phenolic Components of <i>Ginkgo biloba</i> Leaves and Selected Products (2008)

Ginkgo biloba leaves and their extracts are one of the most widely used herbal products and/or dietary supplements in the world. A systematic study of the phenolic compounds is necessary to establish quality parameters. A modified LC-DAD-ESI/MS method was used to obtain chromatographic profiles for the flavonoids and terpene lactones of Ginkgo biloba leaves. The method was used to identify 45 glycosylated flavonols and flavones, 3 flavonol aglycones, catechin, 10 biflavones, a dihydroxybenzoic acid, and 4 terpene lactones in an aqueous methanol extract of the leaves. The extracted G. biloba leaf products contained the same flavonoids as the raw leaves except for the lack of biflavones. The detected glycosylated flavonol contents were equal to or more than 0.0008% of the dry plant material. This is the first report of the presence of more than 20 of these flavonoids in G. biloba.
Improving value communication for thread-level speculation (2004)

Thread-level speculation (TLS) allows us to automatically parallelize general-purpose programs by supporting parallel execution of threads that might not actually be independent. In this paper, we show that the key to good performance ties in the three different ways to communicate a value between speculative threads: speculation, synchronization and prediction. The difficult part is deciding how and when to apply each method. This paper shows how we can apply value prediction, dynamic synchronization and hardware instruction prioritization to improve value communication and hence performance in several SPECint benchmarks that have been automatically transformed by our compiler to exploit TLS. We find that value prediction can be effective when properly throttled to avoid the high costs of mis-prediction, while most of the gains of value prediction can be more easily achieved by exploiting silent stores. We also show that dynamic synchronization is quite effective for most benchmarks, while hardware instruction prioritization is not. Overall, we find that these techniques have great potential for improving the performance of TLS.