gebhart/patrepeval huggingface dataset:
A modified parallel BFGS method for nonconvex functions (2011)

Compared to sequential BFGS method, in this paper an asynchronous parallel BFGS method for nonconvex functions is presented. Suppose that there are q p  processors, which are divided into two groups, the first group has p processors, the second group has q processors. The two groups are asynchronous. If the objective function is Lipschitz continuously, the iteration converge globally to the solution is proved. At last, the numerical result of this algorithm is given. The experimental results show that the proposed algorithm performs very well.
Counterinsurgency and the M‐VICO System: Human Relations Area Files and anthropology's dual‐use legacy (2012)

Over the past decade, ANTHROPOLOGY TODAY has published a number of features covering the relationship between anthropology and the security state. Here, David Price draws attention to an aborted counterinsurgency project, known as the M‐VICO project. Building on the categories and structures employed in the Human Relation Area Files (HRAF), this project relied on anthropologists to encode data cross‐culturally on all forms of behaviour in as many strategic localities as possible, which the security services subsequently scrutinize and probe for possible weaknesses that could be exploited. In this article, David Price shows that, in the secrecy that often surrounds the financing and precise purposes of its projects, anthropology is not all that different from many other disciplines, with some projects serving what he calls ‘dual‐use’ ends. Since civilian researchers are not supposed to have full knowledge of these ends, research into these semi‐covert purposes is particularly challenging.
Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH (2010)

The discovery of complex structural variations that exist within individual genomes has prompted a need to visualize chromosomes at a higher resolution than previously possible. To address this concern, we established a robust, high-resolution fluorescence in situ hybridization (FISH) method that utilizes probes derived from high complexity libraries of long oligonucleotides (>150 mers) synthesized in massively parallel reactions. In silico selected oligonucleotides, targeted to only the most informative elements in 18 genomic regions of interest, eliminated the need for suppressive hybridization reagents. Because of the inherent flexibility in our probe design methods, we readily visualized regions as small as 6.7 kb with high specificity on human metaphase chromosomes, resulting in an overall success rate of 94%. Two-color FISH over a 479-kb duplication, initially reported as being identical in 2 individuals, revealed distinct 2-color patterns representing direct and inverted duplicons, demonstrating that visualization by high-resolution FISH provides further insight in the fine-scale complexity of genomic structures. The ability to design FISH probes for any sequenced genome along with the ease, reproducibility, and high level of accuracy of this technique suggests that it will be powerful for routine analysis of previously difficult genomic regions and structures.
Linear plasmids of Borrelia burgdorferi have a telomeric structure and sequence similar to those of a eukaryotic virus (1991)

Spirochetes of the genus Borrelia have double-stranded linear plasmids with covalently closed ends. The physical nature of the terminal connections was determined for the 16-kb linear plasmid of the B31 strain of the Lyme disease agent Borrelia burgdorferi. Native telomeric fragments representing the left and right ends of this plasmid were isolated and subjected to Maxam-Gilbert sequence analysis. At the plasmid ends the two DNA strands formed an uninterrupted, perfectly palindromic, AT-rich sequence. This Borrelia linear plasmid consisted of a continuous polynucleotide chain that is fully base paired except for short single-stranded hairpin loops at each end. The left and right telomeres of the 16-kb plasmid were identical for 16 of the first 19 nucleotide positions and constituted an inverted terminal repeat with respect to each other. The left telomere of the 49-kb plasmid of strain B31 was identical to the corresponding telomere of the 16-kb plasmid. Different-sized plasmids of other strains of B. burgdorferi also contained sequences homologous to the left end of the 16-kb plasmid. When the borrelia telomeres were compared with telomeric sequences of other linear double-stranded DNA replicons, sequence similarities were noted with poxviruses and particularly with the iridovirus agent of African swine fever. The latter virus and a Borrelia sp. share the same tick vector. These findings suggest that the novel linear plasmids of Borrelia originated through a horizontal genetic transfer across kingdoms.
The impact of autophagic processes on the intracellular fate of<i><i>Helicobacter pylori</i></i> (2013)

Helicobacter pylori is a Gram-negative pathogen that colonizes the gastric epithelium of 50-60% of the world's population. Approximately one-fifth of the infected individuals manifest severe diseases such as peptic ulcers or gastric cancer. H. pylori infection has proven difficult to cure despite intensive antibiotic treatment. One possible reason for the relatively high resistance to antimicrobial therapy is the ability of H. pylori to reside inside host cells. Although considered by most as an extracellular pathogen, H. pylori can invade both gastric epithelial cells and immunocytes to some extent. The intracellular survival of H. pylori has been implicated in its ability to persist in the stomach, evade host immune responses and resist eradication by membrane-impermeable antibiotics. Interestingly, recent evidence suggests that macroautophagy, a cellular self-degradation process characterized by the formation of double-membraned autophagosomes, plays an important role in determining the intracellular fate of H. pylori. Detailed understanding of the interaction between H. pylori and host cell autophagic processes is anticipated to provide novel insights into the molecular mechanisms of macroautophagy and H. pylori pathogenesis, opening new avenues for the therapeutic intervention of autophagy-related and H. pylori-related disorders.
Human hair follicle organ culture: theory, application and perspectives (2015)

For almost a quarter of a century, ex vivo studies of human scalp hair follicles (HFs) have permitted major advances in hair research, spanning diverse fields such as chronobiology, endocrinology, immunology, metabolism, mitochondrial biology, neurobiology, pharmacology, pigmentation and stem cell biology. Despite this, a comprehensive methodological guide to serum-free human HF organ culture (HFOC) that facilitates the selection and analysis of standard HF biological parameters and points out both research opportunities and pitfalls to newcomers to the field is still lacking. The current methods review aims to close an important gap in the literature and attempts to promote standardisation of human HFOC. We provide basic information outlining the establishment of HFOC through to detailed descriptions of the analysis of standard read-out parameters alongside practical examples. The guide closes by pointing out how serum-free HFOC can be utilised optimally to obtain previously inaccessible insights into human HF biology and pathology that are of interest to experimental dermatologists, geneticists, developmental biologists and (neuro-) endocrinologists alike and by highlighting novel applications of the model, including gene silencing and gene expression profiling of defined, laser capture-microdissected HF compartments.
Molecular Abnormalities in Oocytes from Women with Polycystic Ovary Syndrome Revealed by Microarray Analysis (2006)

These analyses demonstrated that normal and PCOS oocytes that are morphologically indistinguishable and of high quality exhibit different gene expression profiles. Promoter analysis suggests that androgens and other activators of nuclear receptors may play a role in differential gene expression in the PCOS oocyte. Likewise, annotation of the differentially expressed genes suggests that defects in meiosis or early embryonic development may contribute to reduced developmental competency of PCOS oocytes.
<i>In vitro</i>cultivation of human fetal pancreatic ductal stem cells and their differentiation into insulin-producing cells (2004)

The human fetal pancreatic ductal stem cells are capable of proliferation in vitro. These cells have multidifferentiation potential and can be induced by glucose and differentiated into insulin-producing cells in vitro.
Production of ethanol by immobilized <i>Saccharomyces bayanus</i> in an extractive fermentation system (1987)

Abstract An extractive fermentation system using immobilized yeast cells was developed to study the ethanol production at high sugar concentrations. Organic acids were used as extracting solvents of ethanol and their toxicity was tested in free and k ‐carrageenan entrapped cell preparations. Immobilization seems to protect cells against solvent toxicity, when long‐chain organic acids, e.g., oleic acid, were used, probably due to steric and diffusional limitations, the free cells not being viable at high oleic acid concentrations. The entrapped cells also present a higher metabolic activity than their free counterparts at high glucose concentrations. A solution of 300 g/L of glucose was totally fermented by the immobilized yeast cells, which when free cannot normally convert more than 200 g/L. In situ recovery of ethanol by oleic acid in a batch immobilized cell system led to higher ethanol productivities and to the fermentation of 400 g/L, when an oleic acid/medium ratio of 5 was used.
Reducing the Number of Channels for an Ambulatory Patient-Specific EEG-based Epileptic Seizure Detector by Applying Recursive Feature Elimination (2006)

We are building an ambulatory version of a patient-specific epileptic seizure detector based on scalp EEG signals. Since patients have to wear the electrodes all the time, it is desirable to use the minimum number of electrodes needed to achieve good performance. In this paper, we describe a method that uses recursive feature elimination (RFE) to design detectors that use small numbers of electrodes. We also present results that indicate that the appropriate number of electrodes varies across patients. It is frequently the case that a surprisingly small number of electrodes, sometimes as few as two, suffices to construct a detector with expected performance comparable to that of detectors that use a full twenty-one-channel montage.
Azole-Based Energetic Salts (2011)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTAzole-Based Energetic SaltsHaixiang Gao*† and Jean'ne M. Shreeve*‡View Author Information† Department of Applied Chemistry, China Agricultural University, Beijing, 100193 China‡ Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United StatesE-mail: [email protected] (H.G.); [email protected] (J.M.S.).Cite this: Chem. Rev. 2011, 111, 11, 7377–7436Publication Date (Web):August 12, 2011Publication History Received31 January 2011Published online12 August 2011Published inissue 9 November 2011https://pubs.acs.org/doi/10.1021/cr200039chttps://doi.org/10.1021/cr200039creview-articleACS PublicationsCopyright © 2011 American Chemical SocietyRequest reuse permissionsArticle Views10662Altmetric-Citations1020LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Anions,Cations,Explosives,Materials,Salts Get e-Alerts
Stratification of a population of intracranial aneurysms using blood flow metrics (2014)

Indices of the intra-aneurysm hemodynamic environment have been proposed as potentially indicative of their longitudinal outcome. To be useful, the indices need to be used to stratify large study populations and tested against known outcomes. The first objective was to compile the diverse hemodynamic indices reported in the literature. Furthermore, as morphology is often the only patient-specific information available in large population studies, the second objective was to assess how the ranking of aneurysms in a population is affected by the use of steady flow simulation as an approximation to pulsatile flow simulation, even though the former is clearly non-physiological. Sixteen indices of aneurysmal hemodynamics reported in the literature were compiled and refined where needed. It was noted that, in the literature, these global indices of flow were always time-averaged over the cardiac cycle. Steady and pulsatile flow simulations were performed on a population of 198 patient-specific and 30 idealised aneurysm models. All proposed hemodynamic indices were estimated and compared between the two simulations. It was found that steady and pulsatile flow simulations had a strong linear dependence (r ≥ 0.99 for 14 indices; r ≥ 0.97 for 2 others) and rank the aneurysms in an almost identical fashion (ρ ≥ 0.99 for 14 indices; ρ ≥ 0.96 for other 2). When geometry is the only measured piece of information available, stratification of aneurysms based on hemodynamic indices reduces to being a physically grounded substitute for stratification of aneurysms based on morphology. Under such circumstances, steady flow simulations may be just as effective as pulsatile flow simulation for estimating most key indices currently reported in the literature.
Symptomatic Pelvic Organ Prolapse (2007)

Symptomatic prolapse is less common among African-American women and more common among women with a prior vaginal delivery, poor health status, constipation, or irritable bowel syndrome. Nearly one half of women with symptomatic prolapse are substantially bothered by their symptoms.
rf resistance and inductance of massively parallel single walled carbon nanotubes: Direct, broadband measurements and near perfect 50Ω impedance matching (2008)

We report using dielectrophoresis to accumulate hundred to thousands of solubilized single walled carbon nanotubes in parallel to achieve impedance values very close to 50Ω. This allows us to clearly measure the real (resistive) and imaginary (inductive) impedance over a broad frequency range. We find a negligible to mild frequency dependent resistance for the devices and an imaginary impedance that is significantly smaller then the resistance over the range of dc to 20GHz. This clearly and unambiguously demonstrates that kinetic inductance is not the major issue facing nanotube array interconnects, when compared to the real impedance (the resistance).
Crystallization and preliminary crystallographic analysis of trypanothione reductase from <i>Trypanosoma cruzi</i>, the causative agent of Chagas' disease (1993)

Trypanothione reductase from Trypanosoma cruzi is the most promising target molecule for the rational design of a specific drug against Chagas' disease. The recombinant protein was purified in a single chromatographic step and crystallized. Two crystal forms suitable for X-ray diffraction analysis were obtained. Tetragonal crystals (a = b = 87.4 A, c = 152.3 A) were grown from 30% polyethylene glycol (average M(r) = 8,000) in the presence of 0.2% beta-n-octylglucoside (space group either P4(2) with one dimer or P4(2)22 with one monomer in the asymmetric unit). Monoclinic crystals (space group P2, a = 136.3 A, b = 91.1 A, c = 126.0 A, beta = 94 degrees) were grown from 1.2 M sodium citrate in the presence of 2% octanoyl-N-methyl-glucamide. They contain two dimers of the enzyme in the asymmetric unit; both crystal forms diffract to 3 A resolution.
Behaviour of indicators of exposure and effect after cessation of occupational exposure to lead. (1981)

The behaviour of blood lead (PbB) and of some indicators of effect (erythrocyte protoporphyrin IX (EP), delta-aminolaevulinic acid dehydratase activity of erythrocytes (ALAD), and urinary delta-aminolaevulinic acid (ALAU)) were studied in subjects who had ceased working with inorganic lead for at least one year. Relations between these indices and chelatable lead (PbU-EDTA (lead in urine after injection of CaNa2 EDTA 1 g intravenously)), a test that is used to evaluate the lead deposits in the body, were also analysed. As a comparison, a group of subjects currently exposed was studied. In the workers with past exposure the PbB values were significantly lower, at the same PbU-EDTA levels, than those found in subjects at work. The relation between EP and PbU-EDTA shows that, corresponding levels of chelatable lead, the values of the erythrocyte metabolite are identical in the two groups. Considering the EP-PbB relation, however, at the same PbB levels the protoporphyrin values appear distinctly more altered in the subjects with past exposure. Similar results were obtained from a study of the relations between ALAD and PbU-EDTA and between ALAD and PbB. The relation between ALAU and PbU-EDTA, however, shows that, at the same PbU-EDTA levels the urinary metabolic in past-exposed subjects is distinctly lower than in subjects at work, while the relation between ALAU and PbB shows that, for similar blood lead values, the ALAU levels are identical. On the basis of the results obtained it is concluded that in subjects with past exposure, EP and ALAD can be used in establishing the persistence and extent of an "active deposit" of lead in the organism, while PbB is of very limited use.
Environmental Risk Factors for Attention Deficit Hyperactivity Disorder and Implications for Clinical Practice (2011)

In this review, we have provided an overview of the environmental risk factors for attention deficit hyperactivity disorder (ADHD), focusing on the major environmental toxicants related to the disorder. Researchers have indicated that since the characteristics of ADHD are complex, the disorder’s etiology involves multiple genes of moderate effect interacting with environmental factors. The possible roles of prenatal and perinatal exposure have been the main focus of research on environmental risk factors for ADHD. Among environmental toxicants, we reviewed the potential effects on the development of ADHD of exposure to lead, nicotine, alcohol, polychlorinated biphenyls (PCBs), and dioxin. Further, for the each neurotoxicant, clinical prevention or intervention strategies aimed at reducing a child’s risk from environmental toxic insults have been presented.
Vasodilative Effect of Adrenomedullin in Isolated Arteries of the Dog (1995)

Adrenomedullin is known to induce profound hypotension in vivo, but the direct effect of this peptide on isolated arteries has not been demonstrated. This study estimated the vasodilative effects of adrenomedullin in comparison with those of calcitonin gene-related peptide (CGRP) in basilar, mesenteric, coronary, renal and femoral arteries isolated from the dog. Adrenomedullin (3 to 100 nM) and CGRP (1 to 30 nM) induced concentration-dependent relaxation of these arteries with and without endothelium, and the relaxing effects were slightly greater in endothelium-intact arteries than in denuded ones. The vasodilative potency of adrenomedullin relative to CGRP was smaller in the femoral artery than in basilar, mesenteric, coronary and renal arteries.
Autoencoder-based detection of near-surface defects in ultrasonic testing (2021)

Defect detection during pulse-echo ultrasonic testing (UT) is challenging when defects are located in a dead zone where the echoes from the defects are overshadowed by disturbances from the initial ringing signal of the UT transducer. The time-gate method is one of the most widely used approaches in UT to filter out such unwanted components, but defects in the dead zone are virtually impossible to detect using conventional methods. This paper proposes an autoencoder-based end-to-end ultrasonic testing method to detect defects within the dead zone of a transducer. The autoencoder is designed to predict the normal behavior of ultrasonic signals including disturbances, thus enabling the identification of even subtle deviations made by defects. To advance the performance of the autoencoder further with a limited amount of training data, a two-step training procedure is presented, involving training using pure normal signals measured from a defect-free specimen and re-training using pseudo-normal samples identified by the autoencoder with a smart thresholding strategy. This two-step procedure enables us to develop an adaptive autoencoder model that can be effectively employed to process the newly measured ultrasonic signals. For a demonstration of the proposed method, UT-based B-scan inspections of aluminum blocks with near-surface defects are conducted. The results suggest that the proposed method outperforms the conventional gate-based inspection approach with regard to its ability to identify the sizes and locations of near-surface defects.
Purification and characterization of casein kinase I from broccoli (1993)

Casein kinase I from broccoli was purified approximately 65,000-fold by chromatography on phosphocellulose, phenyl-Sepharose, CM-Sephacel, and affinity chromatography on N-(2-aminoethyl)-5-chloroisoquinolone-8-sulphonamide (CKI-7)-Sepharose. The catalytic subunit of casein kinase I was identified as a 36-38 kDa polypeptide doublet by using the technique of activity gel assay after SDS/PAGE with casein as a gel-incorporated substrate. A silver-stained polypeptide doublet of the same molecular mass constituted at least 95% of the protein in the final preparation, corresponding to a specific activity of approximately 1800 nmol/min per mg of protein. The enzyme was found to be a monomer by gel filtration and glycerol gradient sedimentation; the native molecular mass was calculated to be 34.2 kDa. These characteristics, as well as other essential features of plant casein kinase I activity, such as substrate specificity and sensitivity to inhibitors, were found to be similar to those established for animal casein kinase I. Broccoli casein kinase I showed weak immunological cross-reactivity with antibodies raised against bovine casein kinase I.
Hereditary proctalgia fugax and constipation: report of a second family. (1995)

A second family with hereditary proctalgia fugax and internal anal sphincter hypertrophy associated with constipation is described. Anorectal ultrasonography, manometry, and sensory tests were conducted in two symptomatic and one asymptomatic subjects within the same family and further clinical information was obtained from other family members. The inheritance would correspond to an autosomal dominant condition with incomplete penetration, presenting after the second decade of life. Physiological studies showed deep, ultraslow waves and an absence of internal anal sphincter relaxation on rectal distension in the two most severely affected family members, suggesting the possibility of a neuropathic origin. Both of these patients had an abnormally high blood pressure. After treatment with a sustained release formulation of the calcium antagonist, nifedipine, their blood pressure returned to normal, anal tone was reduced, and the frequency and intensity of anal pain was suppressed. These together improved the quality of the patients' sleep, which had previously been very troubled because of night time attacks of anal pain.