gebhart/patrepeval huggingface dataset:
Trehalose and Trehalose-based Polymers for Environmentally Benign, Biocompatible and Bioactive Materials (2008)

Trehalose is a non-reducing disaccharide that is found in many organisms but not in mammals. This sugar plays important roles in cryptobiosis of selaginella mosses, tardigrades (water bears), and other animals which revive with water from a state of suspended animation induced by desiccation. The interesting properties of trehalose are due to its unique symmetrical low-energy structure, wherein two glucose units are bonded face-to-face by 1-->1-glucoside links. The Hayashibara Co. Ltd., is credited for developing an inexpensive, environmentally benign and industrial-scale process for the enzymatic conversion of alpha-1,4-linked polyhexoses to alpha,alpha-D-trehalose, which made it easy to explore novel food, industrial, and medicinal uses for trehalose and its derivatives. Trehalosechemistry is a relatively new and emerging field, and polymers of trehalose derivatives appear environmentally benign, biocompatible, and biodegradable. The discriminating properties of trehalose are attributed to its structure, symmetry, solubility, kinetic and thermodynamic stability and versatility. While syntheses of trehalose-based polymer networks can be straightforward, syntheses and characterization of well defined linear polymers with tailored properties using trehalose-based monomers is challenging, and typically involves protection and deprotection of hydroxyl groups to attain desired structural, morphological, biological, and physical and chemical properties in the resulting products. In this review, we will overview known literature on trehalose's fascinating involvement in cryptobiology; highlight its applications in many fields; and then discuss methods we used to prepare new trehalose-based monomers and polymers and explain their properties.
DBSeer: Resource and Performance Prediction for Building a Next Generation Database Cloud (2013)

Cloud computing is characterized by shared infrastructure and a decoupling between its operators and tenants. These two characteristics impose new challenges to databases applications hosted in the cloud, namely: (i) how to price database services, (ii) how to isolate database tenants, and (iii) how to optimize database performance on this shared infrastructure. We argue that today’s solutions, based on virtual-machines, do not properly address these challenges. We hint at new research directions to tackle these problems and argue that these three challenges share a common need for accurate predictive models of performance and resource utilization. We present our approach, called DBSeer, with our initial results on predictive models for the important class of OLTP/Web workloads and show how they can be used to address these challenges. 1.
Spinal muscular atrophy disease: a literature review for therapeutic strategies. (2010)

Currently, there is no cure for the treatment of spinal muscular atrophy (SMA). Based on the available clinical and molecular findings, different therapeutic strategies were tested in vitro and in vivo and clinical trials are ongoing. The main therapeutic direction is focused on the enhancement of SMN expression by increasing the full-length (fl) SMN2 transcript levels, preventing the SMN exon 7 from skipping or from protein stabilizing. In addition, the action of neurotrophic, neuroprotective or anabolic agents is tested and stem cell and gene therapy approaches are in a promising development.
Effect of Allopurinol on the Survival of Hyperemic Island Skin Flaps (1984)

Allopurinol was investigated in 3 x 6 cm congested island skin flaps in rats. Eight hours of venous occlusion produced total flap necrosis. Pretreatment with systemic allopurinol, an inhibitor of xanthine oxidase, enhanced the survival rate of hyperemic skin flaps. Xanthine oxidase activities were demonstrated in skin, and these enzyme activities were noted to increase in skin flaps during ischemia and reperfusion. Much of this increase in enzyme activity was prevented by allopurinol treatment. The xanthine oxidase system appears to be one of the sources of the superoxide radical, which may be involved in ischemic and reperfusion injury in skin.
Tousled-like kinase regulates cytokine-mediated communication between cooperating cell types during collective border cell migration (2015)

Collective cell migration is emerging as a major contributor to normal development and disease. Collective movement of border cells in the Drosophila ovary requires cooperation between two distinct cell types: four to six migratory cells surrounding two immotile cells called polar cells. Polar cells secrete a cytokine, Unpaired (Upd), which activates JAK/STAT signaling in neighboring cells, stimulating their motility. Without Upd, migration fails, causing sterility. Ectopic Upd expression is sufficient to stimulate motility in otherwise immobile cells. Thus regulation of Upd is key. Here we report a limited RNAi screen for nuclear proteins required for border cell migration, which revealed that the gene encoding Tousled-like kinase (Tlk) is required in polar cells for Upd expression without affecting polar cell fate. In the absence of Tlk, fewer border cells are recruited and motility is impaired, similar to inhibition of JAK/STAT signaling. We further show that Tlk in polar cells is required for JAK/STAT activation in border cells. Genetic interactions further confirmed Tlk as a new regulator of Upd/JAK/STAT signaling. These findings shed light on the molecular mechanisms regulating the cooperation of motile and nonmotile cells during collective invasion, a phenomenon that may also drive metastatic cancer.
The His‐probe method: Effects of histidine residues introduced into the complementarity‐determining regions of antibodies on antigen‐antibody interactions at different pH values (1992)

We examined the effects of histidine residues that were artificially introduced into complementarity-determining regions of antibodies on antigen-antibody interactions at different pH values. Using a monoclonal antibody specific for hen egg-white lysozyme and three mutant antibodies that contained a histidine residue, we measured binding constants for antibodies and lysozyme at different pH values (pH 5-8). No gross conformational changes were evident over this range of pH values, as determined by analysis of the spectra of circular dichroism. Since the charge on a histidine residue is the most likely factor that can vary over this range of pH values, differences on pH-dependent antigen-binding patterns observed between the wild-type and mutant antibodies should be due mainly to the effects of the charges on the histidine residues. The three mutant antibodies showed different and characteristic patterns of pH-dependent binding to lysozyme, which depended on the location of the artificially introduced histidine residues.
Electrical stimulation of the posterior and ventromedial hypothalamic nuclei causes specific activation of shivering and nonshivering thermogenesis (1994)

Experiments were designed to determine in the same animal whether electrical stimulation of the posterior hypothalamus and ventromedial hypothalamic nucleus could specifically evoke shivering and nonshivering (brown adipose tissue) thermogenesis, respectively, in anesthetized, normothermic rats. Urethane-anesthetized, male Long-Evans rats, kept at 37 degrees C, had colonic (Tc), gastrocnemius muscle (Tm), intrascapular brown adipose tissue (TIBAT), and tail (Tt) temperatures measured via thermistor probes, and electromyogram activity (differential multiunit activity from bipolar recording electrodes within gastrocnemius muscle) recorded, before and after unilateral electrical stimulation (monophasic 0.5-ms pulses of 200 microA at 50 Hz for 30 s) of the posterior hypothalamus and ventromedial hypothalamic nucleus (via stereotaxically implanted concentric stimulating electrodes). Each rat showed shivering (increased electromyogram activity) following posterior hypothalamic stimulation, which caused an immediate rise in Tm values with no change in TIBAT or Tt values. Electrical stimulation of the ventromedial hypothalamic nucleus of the same animals elicited no shivering activity, but significant increases in TIBAT values occurred with no change in Tm or Tt values. Results confirm that stimulation of the posterior and ventromedial hypothalamic nuclei in rodents specifically activates shivering and nonshivering (brown adipose tissue) effector mechanisms, respectively, to raise core temperature.
Vertical-Interval Encoding for the Recordable Laser Videodisc (1985)

The introduction of the recordable laser videodisc has brought the full process of videodisc technology into the user's hands. Along with the playback power of fast access on low-cost players, the user can now record the disc in his own facility in real time. The burden of properly formatting and encoding the material for disc is now in-house. The Laser Vision videodisc and an encoder/generator that encodes the vertical interval to the IEC specifications in the Laser Vision standard are described.
Formation of Lipid Bilayers on a New Amphiphilic Polymer Support (1999)

In this paper we present a way to build up tether supported lipid bilayers. First we synthesized novel amphiphilic polymers with an adjustable hydrophilicity. This was achieved by introducing ionic groups together with disulfide and lipid anchor groups in polyacrylamides or N,N-dimethylacrylamides. The self-assembly of these polymers on a gold surface was monitored by surface plasmon spectroscopy and was characterized by contact angle measurements and swelling experiments. The contact angle decreased linearly with the percent of ionic groups in the polymer, resulting in a more hydrophilic surface. Swelling experiments demonstrated the greater hydrophilicity of the charged polymers. To build up tether supported lipid bilayers, we fused phospholipid vesicles onto the prepared thin polymer films. The charged polymers initiated a vesicle fusion on the thin polymer films and resulted in a supported lipid bilayer.
Alkyl and Aryl Neoalkanamides: Highly Effective Insect Repellents (1992)

Alkyl and aryl neoalkanamides with a total carbon number between 11 and 14, or within a molecular weight range between 185 and 227, were highly effective repellents of male German cockroaches, Blattella germanica (L.). Comparison with known repellents showed that members of this unique family of secondary amides are among the most effective and long-lasting repellents of cockroaches examined to date. In assays with females and nymphs of the German cockroach, male American cockroaches, Periplaneta americana (L.), and carpenter ant workers, Camponotus pennsylvanicus (De Geer) methyl neodecanamide, propyl neodecanamide, and methyl neotridecanamide were found highly repellent. Because of their broad spectrum of activity, longevity, and safety, these compounds, along with several other members of this family, have important applications as repellents of nuisance pests and of arthropods of public health importance.
Characterization of 298 Patients with Lung Cancer Harboring MET Exon 14 Skipping Alterations (2016)

Diverse targetable METex14 alterations were identified in patients with NSCLC across age groups, including elderly patients, and in all major NSCLC histologic subtypes with an overall frequency of 2.7%. These findings support the use of hybrid capture-based molecular profiling across NSCLC subtypes to identify patients who will potentially benefit from MET TKIs.
Dietary fish oils containing eicosapentaenoic acid and the prevention of atherosclerosis and thrombosis. (1988)

Recent epidemiologic studies have shown that rates of cardiovascular disease are lower in populations such as the Greenland Eskimos than in those that do not eat seafood, even though the levels of dietary fat intake are often similar. Dietary fish oils are rich in eicosapentaenoic acid (EPA), a polyunsaturated fatty acid of the omega-3 series. EPA has been shown to prolong bleeding time and to decrease platelet aggregation and blood viscosity. EPA inhibits the production of prostaglandins from endogenous arachidonic acid, which is associated with the formation of thromboxane A2 and may also dampen cyclo-oxygenase and lipoxygenase metabolites involved in mediating endothelial cell proliferation. Dietary fish oils are now available in the form of EPA-enriched capsules. Short-term trials in humans have shown that EPA significantly reduces the levels of plasma triglycerides and may increase the levels of high-density lipoproteins; however, no consistent effect on serum cholesterol levels has been shown. The results of evaluations of EPA's use in patients with renal disorders, mild hypertension, inflammatory disorders or hyperlipidemia have been promising. On the basis of the epidemiologic and biologic evidence dietary fish oils warrant further study in extensive clinical trials.
EFFECTIVENESS OF TWO PINE OILS FOR PROTECTING LODGEPOLE PINE FROM ATTACK BY MOUNTAIN PINE BEETLE (COLEOPTERA: SCOLYTIDAE) (1985)

The mountain pine beetle, Dendroctonus ponderosae Hopkins, is one of the most destructive bark beetles found on pine in western North America (McCambridge et al. 1979), particularly in forests of lodgepole pine, Pinus contorta Douglas var. latifolia (Furniss and Carolin 1977). The treatment registered in the United States for the protection of high-value trees in residential areas and recreational areas is 2% carbaryl applied to the bole of the tree with a hydraulic sprayer. Recently, pine oil, a derivative of paper pulp waste, was found to be an effective non-insecticidal repellent against several species of bark beetles (Nijholt et al. 1981).
Correction: Corrigendum: N-acetyl ornithine deacetylase is a moonlighting protein and is involved in the adaptation of Entamoeba histolytica to nitrosative stress (2017)

Scientific Reports 6: Article number: 36323; published online: 03 November 2016; updated: 05 April 2017 The original version of this Article contained errors in the spelling of the author Sharon Baumel-Alterzon, which was incorrectly given as Sharon Alterzon-Baumel. These errors have now been corrected in the PDF and HTML versions of the Article.
High-precision, fast current source for large-area current-programmed a-Si flat panels (2006)

Although current-programmed pixel circuits lead to a highly stable amorphous silicon (a-Si) active matrix backplane, they are prone to a long settling time due to the large parasitic capacitance coupled with the low mobility of a-Si thin film transistors (TFTs). This paper presents a fast-current source that can significantly improve the settling time of the a-Si active matrix. Also, to reduce the effect of mismatches a differential offset cancellation technique is introduced.
Volume haptization (1993)

The authors describe haptic representation of volume data. Volume visualization is a powerful tool in the field of scientific visualization. However, visual representation of full three-dimensional volume is hard to comprehend because of occlusion. Higher-dimensional and multi-parameter data sets are also difficult to present by visual image. The authors propose methods for presentation of volume data by force sensation. A six degree-of-freedom force reflective master manipulator is used for haptization. The manipulator is combined to real-time visual image of volume data. Methods of haptic representation of scalar, vector, and tensor data are discussed. Recognition performance tests of scalar and multiparameter volume data are examined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of Bacillus subtilis strain IS53 for the production of Bacillus anthracis protective antigen (1994)

An asporogenous strain of Bacillus subtilis, IS53, transformed with plasmid pPA102, produces the protective antigen (PA) component of the tripartite toxin of B. anthracis. Addition of yeast extract was required to support growth and PA production in all the media examined. Protective antigen expression was down-regulated during exponential growth and extracellular proteases caused marked degradation of the mature protein.
Supramolecular self-assemblies as functional nanomaterials (2013)

In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.
Teleportation of Continuous Quantum Variables (1998)

Quantum teleportation is analyzed for states of dynamical variables with continuous spectra, in contrast to previous work with discrete (spin) variables. The entanglement fidelity of the scheme is computed, including the roles of finite quantum correlation and nonideal detection efficiency. A protocol is presented for teleporting the wave function of a single mode of the electromagnetic field with high fidelity using squeezed-state entanglement and current experimental capability.
Phosphatidylcholine treatment to induce lipolysis (2005)

The medicine Lipostabil N has been in widespread use in Europe since 2002 by doctors working in the field of esthetics to achieve a reduction in the volume of smaller fat deposits by means of injections into the subcutaneous fatty tissue. The lipases released from the adipocytes by means of phosphatidylcholine produce a local breakdown of fat that is then discharged over the liver and metabolized via beta-oxidation. The medicine has been authorized for intravenous use in the prophylaxis and therapy of fat embolisms and liver diseases.
Evidence for Peroxynitrite Formation in the Vasculature of Women With Preeclampsia (1999)

-Preeclampsia is a multisystemic disorder of pregnancy in which the normal vascular adaptations to pregnancy are compromised. Oxidative stress as well as endothelial cell dysfunction have been implicated as pathophysiological features of preeclampsia. Endothelial cells produce the vasorelaxant nitric oxide (NO). However, NO is also known to react with superoxide anions (produced under conditions of oxidative stress), yielding peroxynitrite that may impair vascular function. Our objective was to use immunohistochemical techniques to determine whether there is evidence of peroxynitrite formation in the maternal systemic vasculature of women with preeclampsia. Vessels were obtained from a biopsy of subcutaneous fat at the time of cesarean section from normal pregnant (n=7) and preeclamptic (n=7) women or at the time of hysterectomy from nonpregnant women (n=5). There were significantly more vessels staining with greater intensity for nitrotyrosine and endothelial NO synthase in the endothelium of vessels from women with preeclampsia compared with that of normal pregnant women or nonpregnant women. Both endothelial and smooth muscle cells from all vessels showed evidence for the presence of superoxide dismutase (SOD), an enzyme that scavenges superoxide anions. However, the intensity of staining for SOD in the endothelium was significantly lower in the preeclamptic and nonpregnant women than in normal pregnant women. These data of increased endothelial NO synthase, decreased SOD, and increased nitrotyrosine immunostaining in the maternal vasculature of women with preeclampsia suggest increased peroxynitrite formation. We speculate that peroxynitrite is involved in endothelial cell dysfunction in preeclamptic women and contributes to the pathophysiology of this pregnancy disorder.
An Enzymatic TMPRSS2 Assay for Assessment of Clinical Candidates and Discovery of Inhibitors as Potential Treatment of COVID-19 (2020)

SARS-CoV-2 is the viral pathogen causing the COVID19 global pandemic. Consequently, much research has gone into the development of preclinical assays for the discovery of new or repurposing of FDA-approved therapies. Preventing viral entry into a host cell would be an effective antiviral strategy. One mechanism for SARS-CoV-2 entry occurs when the spike protein on the surface of SARS-CoV-2 binds to an ACE2 receptor followed by cleavage at two cut sites ("priming") that causes a conformational change allowing for viral and host membrane fusion. TMPRSS2 has an extracellular protease domain capable of cleaving the spike protein to initiate membrane fusion. A validated inhibitor of TMPRSS2 protease activity would be a valuable tool for studying the impact TMPRSS2 has in viral entry and potentially be an effective antiviral therapeutic. To enable inhibitor discovery and profiling of FDA-approved therapeutics, we describe an assay for the biochemical screening of recombinant TMPRSS2 suitable for high throughput application. We demonstrate effectiveness to quantify inhibition down to subnanomolar concentrations by assessing the inhibition of camostat, nafamostat, and gabexate, clinically approved agents in Japan. Also, we profiled a camostat metabolite, FOY-251, and bromhexine hydrochloride, an FDA-approved mucolytic cough suppressant. The rank order potency for the compounds tested are nafamostat (IC<sub>50</sub> = 0.27 nM), camostat (IC<sub>50</sub> = 6.2 nM), FOY-251 (IC<sub>50</sub> = 33.3 nM), and gabexate (IC<sub>50</sub> = 130 nM). Bromhexine hydrochloride showed no inhibition of TMPRSS2. Further profiling of camostat, nafamostat, and gabexate against a panel of recombinant proteases provides insight into selectivity and potency.
Development of the yeast Pichia pastoris as a model organism for a genetic and molecular analysis of peroxisome assembly (1992)

We describe the isolation of mutants of the yeast Pichia pastoris that are deficient in peroxisome assembly (pas). These mutants of P. pastoris can be identified solely by their inability to grow on methanol and oleic acid, the utilization of which requires peroxisomal enzymes, and are defined by the absence of normal peroxisomes as judged by electron microscopy and biochemical fractionation experiments. These mutants are the result of genetic defects at single loci and represent at least eight different complementation groups. The isolation of pas mutants of P. pastoris by a simple screen for mutants unable to use methanol and oleic acid represents a significantly more efficient method for identification of pas mutants than is possible in other organisms. To exploit this advantage fully we also developed new reagents for the genetic and molecular manipulation of P. pastoris. These include a set of auxotrophic strains with an essentially wild-type genetic background, plasmids that act as Escherichia coli-P. pastoris shuttle vectors, and genomic DNA libraries for isolation of P. pastoris genes by functional complementation of mutants or by nucleic acid hybridization. The availability of numerous pas mutants and the reagents necessary for their molecular analysis should lead to the isolation and characterization of genes involved in peroxisome assembly.