gebhart/patrepeval huggingface dataset:
Complement Inhibitor of C5 Activation from the Soft Tick Ornithodoros moubata (2005)

Blood-feeding ticks must control C activation or be damaged by the host inflammatory response. We report the characterization and expression of a novel, relatively small, broad-acting C inhibitory protein (termed OmCI) from the soft tick Ornithodoros moubata. The native 17-kDa nonglycosylated protein inhibits both human and guinea pig classical and alternative C activation pathways. The IC50 values for each pathway were 12 and 27 nM, respectively, in hemolytic assays using human serum diluted 40-fold. The cDNA encodes a protein of 168 aa, including an 18-aa secretion signal sequence that is absent in the mature form. The inhibitor has 46% amino acid identity with moubatin, a platelet aggregation inhibitor also from O. moubata that is an outlying member of the lipocalin family. Native OmCI had no inhibitory effect on the addition of C8 and C9 to preformed C5b-C7 and C5b-C8 to form the membrane attack complex and no effect on the rate of C3a production by the C3 convertase enzymes C4bC2a, C3(H2O)Bb, or C3bBb. Both recombinant and native OmCI abolish production of C5a by human classical (C4bC3bC2a) and alternative (C3bC3bBb) C5 convertases. Addition of excess C5 but not C3 competes away the inhibitory activity of OmCI, indicating that OmCI targets C5 itself rather than inhibiting the C5 convertase C4bC3bC2a itself. Direct binding of OmCI to C5 was demonstrated by Western blotting and gel filtration chromatography using 125I-labeled proteins. OmCI is the first lipocalin family member shown to inhibit C and also the first natural inhibitor that specifically targets the C5 activation step.
Scheduling Cluster Tools for Concurrent Processing of Two Wafer Types (2014)

We examine a scheduling problem of cluster tools that concurrently process two wafer types in a cyclic operational sequence. Whereas the process steps for different wafer types are assigned to different processing modules (PMs), the wafer loading and unloading tasks at the PMs are performed by a single robot. For a given cycle plan, which is a mix of different wafers for each cycle, we wish to determine the robot task sequence so as to minimize the tool cycle time. When a single wafer type is processed, the backward and swap sequences are optimal for single-armed and dual-armed tools, respectively. They are being prevalently used because of their simplicity and robustness. To maintain such advantages in concurrent processing, we introduce and define the concurrent backward and swap sequences (CBSs and CSSs, respectively). We then develop conditions on process times, robot task times, and the number of wafers produced in a cycle for which such CBSs and CSSs are still optimal for concurrent processing. We also show that, for some special cases, the two wafer types can achieve their maximum throughput rates as if each wafer type exclusively uses the tool regardless of other wafer types in progress. When the developed conditions do not hold, an effective mixed integer programming (MIP) model based on the CBSs and CSSs is used for robot task sequencing. Finally, we experimentally verify its efficiency and effectiveness by comparing to the existing scheduling methods for optimal scheduling of cluster tools.
Enhanced anti-HIV-1 activity and altered chemotactic potency of NH2-terminally processed macrophage-derived chemokine (MDC) imply an additional MDC receptor. (1998)

Posttranslational processing of chemokines increases (IL-8) or decreases (monocyte chemotactic protein-1) their chemotactic potency. Macrophage-derived chemokine (MDC) attracts monocytes, dendritic cells, activated lymphocytes, and NK cells and has reportedly anti-HIV-1 activity. Here we report that truncation of MDC by deletion of two NH2-terminal residues resulted in impaired binding to CC chemokine receptor (CCR)4, the only identified MDC receptor so far. Truncated MDC(3-69) failed to desensitize calcium mobilization by MDC(1-69) or thymus- and activation-regulated chemokine (TARC), another CCR4 ligand. MDC(3-69) lacked HUT-78 T cell chemotactic activity but retained its capacity to attract monocytes and to desensitize chemotaxis. Compared with MDC(1-69), MDC(3-69) had weak but enhanced antiviral activity against M- and T-tropic HIV-1 strains. Furthermore, both MDC forms failed to signal through the orphan receptors Bonzo/STRL33 and BOB/GPR15 and to desensitize RANTES and stromal cell-derived factor (SDF)-1 responses in CCR5-transfected and CXC chemokine receptor (CXCR)4-transfected cells, respectively. These findings suggest that MDC recognizes another, yet unidentified, receptor. We conclude that minimal NH2-terminal truncation of MDC differentially affects its various immunologic functions.
Quantitative responsiveness of murine hemopoietic populations in vitro and in vivo to recombinant multi-CSF (IL-3). (1987)

Purified, bacterially synthesized, recombinant Multi-CSF (rMulti-CSF) exhibited in vitro proliferative effects identical to those of native Multi-CSF on a broad range of progenitor cells from normal murine bone marrow and on the continuous cell line FD-CP1. The injection into normal adult mice of 6-200 ng purified rMulti-CSF three times daily for six days induced dose-related rises in peritoneal macrophages, neutrophils, and eosinophils, and in the spleen weight and content of megakaryocytes, mast cells, and progenitor cells, some responses being detectable with the lowest dose injected. No Multi-CSF was detected in the serum, organ extracts, or organ-conditioned medium from normal or endotoxin-injected mice. While the data indicate that even small doses of injected rMulti-CSF can produce detectable hemopoietic changes in normal adult mice, the pattern of these changes and the failure to detect Multi-CSF in vivo raise doubts that Multi-CSF plays a significant role as a regulator of hemopoiesis in normal adult life.
MEME: discovering and analyzing DNA and protein sequence motifs (2006)

MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel 'signals' in sets of biological sequences. Applications include the discovery of new transcription factor binding sites and protein domains. MEME works by searching for repeated, ungapped sequence patterns that occur in the DNA or protein sequences provided by the user. Users can perform MEME searches via the web server hosted by the National Biomedical Computation Resource (http://meme.nbcr.net) and several mirror sites. Through the same web server, users can also access the Motif Alignment and Search Tool to search sequence databases for matches to motifs encoded in several popular formats. By clicking on buttons in the MEME output, users can compare the motifs discovered in their input sequences with databases of known motifs, search sequence databases for matches to the motifs and display the motifs in various formats. This article describes the freely accessible web server and its architecture, and discusses ways to use MEME effectively to find new sequence patterns in biological sequences and analyze their significance.
Droplet microfluidics for microbiology: techniques, applications and challenges (2016)

Droplet microfluidics has rapidly emerged as one of the key technologies opening up new experimental possibilities in microbiology. The ability to generate, manipulate and monitor droplets carrying single cells or small populations of bacteria in a highly parallel and high throughput manner creates new approaches for solving problems in diagnostics and for research on bacterial evolution. This review presents applications of droplet microfluidics in various fields of microbiology: i) detection and identification of pathogens, ii) antibiotic susceptibility testing, iii) studies of microbial physiology and iv) biotechnological selection and improvement of strains. We also list the challenges in the dynamically developing field and new potential uses of droplets in microbiology.
Fractal analysis of the signal scattered from the sea surface (1999)

This paper deals with the problem of the electromagnetic scattering from a sea fractal surface. The paper demonstrates that the sea-scattered signal retains some fractal characteristic of the sea surface. In detail, we analyze the signal scattered from a sea surface modeled by the one-dimensional (1-D) sea-surface fractal profile proposed by Berizzi, Mese, Pinelli and Andreoli (see Inst. Electr. Eng. Proc. Radar Sonar, Navigat., vol.146, p.55-66, 1999). The results show the graphs of the in-phase and quadrature components of the received signal are fractal curves with box-counting fractal dimension equal to the one of the sea profile. These results are validated by presenting and discussing some numerical examples.
Polymorphisms in Platelet Glycoprotein 1bα and Factor VII and Risk of Ischemic Stroke (2008)

This analysis provides strong evidence that the Factor VII R353Q gene polymorphism is not associated with ischemic stroke, that the Thr/Met polymorphism of GP1balpha is associated with ischemic stroke in a dominant genetic model, and that the Kozak sequence polymorphism of GP1balpha may be close to another causative locus that is associated with ischemic stroke.
Esterification of substituted O-benzoylbenzoic acids / (1965)

A nhydride (XVH) P r e p a r a tio n o f o -B e n z o y lb e n z o ic N ,N -D im eth ylcarb on ic Anhydride (X V H I) P y
Rapid enumeration of microorganisms in foods by the direct epifluorescent filter technique (1982)

Filtration of "stomachered" food suspensions through nylon filters (pore size, 5 microns) removed most of the food debris without affecting the recovery of microorganisms. Two to ten milliliters of these prefiltered suspensions could be filtered in the direct epifluorescent filter technique (DEFT). The technique takes less than 30 min to complete and has a lower sensitivity of less than 60,000 microorganisms per g for all products examined. Vegetative bacterial cells, spores, fungal hyphae, and yeasts could be distinguished with the technique. For fresh meat and fish, the DEFT count of prefiltered suspensions agreed well with the plate count of unfiltered suspensions over the range of 10(4) to 10(10)/g (correlation coefficient of 0.91). For frozen meat and fish and frozen vegetables, the two counting methods had correlation coefficients of 0.87 and 0.66, respectively. The poor correlation for frozen vegetables was due to the inclusion in the DEFT count of nonviable bacteria killed by the blanching process used to inactivate enzymes. Good agreement was obtained between the prefiltered DEFT count and unfiltered plate count for cooked meats, cream doughnut, and whole peppers. Possible reasons for the poor agreement between the DEFT count and plate count for certain products are discussed.
A general and efficient method for finding cycles in 3D curve networks (2013)

Generating surfaces from 3D curve networks has been a longstanding problem in computer graphics. Recent attention to this area has resurfaced as a result of new sketch based modeling systems. In this work we present a new algorithm for finding cycles that bound surface patches. Unlike prior art in this area, the output of our technique is unrestricted, generating both manifold and non-manifold geometry with arbitrary genus. The novel insight behind our method is to formulate our problem as finding local mappings at the vertices and curves of our network, where each mapping describes how incident curves are grouped into cycles. This approach lends us the efficiency necessary to present our system in an interactive design modeler, whereby the user can adjust patch constraints and change the manifold properties of curves while the system automatically re-optimizes the solution.
Release of Alzheimer Amyloid Precursor Derivatives Stimulated by Activation of Muscarinic Acetylcholine Receptors (1992)

Altered processing of the amyloid precursor protein (APP) is a central event in the formation of amyloid deposits in the brains of individuals with Alzheimer's disease. To investigate whether cellular APP processing is controlled by cell-surface neurotransmitter receptors, human embryonic kidney (293) cell lines were transfected with the genes for human brain muscarinic acetylcholine receptors. Stimulation of m1 and m3 receptor subtypes with carbachol increased the basal release of APP derivatives within minutes of treatment, indicating that preexisting APP is released in response to receptor activation. Receptor-activated APP release was blocked by staurosporine, suggesting that protein kinases mediate neurotransmitter receptor-controlled APP processing.
Targeting Voltage-Gated Calcium Channels for Neuropathic Pain Management (2009)

Voltage-gated calcium channels (VGCC) play obligatory roles in diverse physiological functions. Pathological conditions leading to changes in their biophysical properties and expression levels may cause malfunctions of VGCC-mediated activities, resulting in disease states. It is believed that changes in VGCC properties under pain-inducing conditions may play a causal role in the development of chronic pain, including nerve injury-induced pain or neuropathic pain. For the past several decades, preclinical and clinical research in developing VGCC blockers or modulators for chronic pain management has been fruitful, leading to some U.S. Food and Drug Administration-approved drugs currently available for chronic pain management. However, their efficacy in pain relief is limited in some patients, and their long-term use is limited by their side-effect profiles. Certainly, there is room for improvement in developing more subtype-specific VGCC blockers or modulators for chronic pain conditions. In this review, we summarized the most recent preclinical and clinical studies related to chronic pain medications acting on the VGCC. We also included clinical trials aiming to expand the application of approved VGCC drugs to different pain states derived from various pathological conditions, as well as drug combination therapies trying to improve the efficacies and side-effect profiles of current pain medications.
Platelet-Derived Growth Factor Three isoforms that bind to two distinct cell surface receptors (1989)

Several isoforms of the platelet-derived growth factor (PDGF) have been identified and purified to date. The functional effects of the PDGF isoforms differ, due to their different interactions with at least two distinct cell surface receptors. Thus, PDGF constitutes an example of an expanding growth factor family, characterized by possibilities for fine-tuned regulation of action. In this manuscript, we describe the structural features of the PDGF isoforms as well as their receptors.
Redirection of drug metabolism using antisense technology. (2001)

The cytochrome P450 (CYP) family is the most catalytically versatile component of the phase I oxidation metabolic pathway and participates in the metabolism of a large majority of drugs used in clinical practice. The inhibition of specific enzymes of this family can significantly alter the disposition and toxicity of substrate drugs by reducing and/or redirecting their metabolism. This review discusses the approaches available for CYP inhibition, with particular emphasis on the potential use of antisense phosphorodiamidate morpholino oligonucleotide strategies to inhibit human CYP3A4. Inter-individual variations of 10- to 50-fold have been reported in the activity of CYP3A4 enzyme, which contributes to the metabolism of more than half of all clinically relevant drugs. The application of antisense technology for inhibition of specific CYP enzymes can provide significant therapeutic benefits, including: (i) reduction of first-pass drug metabolism; (ii) reduction in drug dosage; (iii) selective reduction of toxic metabolites; and (iv) increased oral/topical drug bioavailability. The use of antisense morpholino oligonucleotide strategies to target CYP enzymes may result in safer and more uniform therapeutic applications.
Serum levels of brain-derived neurotrophic factor and thiobarbituric acid reactive substances in chronically medicated schizophrenic patients: a positive correlation (2008)

The positive correlation between brain-derived neurotrophic factor and thiobarbituric acid reactive substances suggests the need of further investigation on intracellular interactions of neurotrophins, antioxidant enzymes and oxidative markers. In addition, this opens a venue for investigation on treatments for the prevention of neurotoxicity along the course of schizophrenia.
Improvement of Sexual Function in Men with Late-Onset Hypogonadism Treated with Testosterone Only (2007)

Restoring testosterone levels to normal in men with proven subnormal testosterone levels improves libido in most subjects, and erectile function in more than 50% of these men. It may take 12-24 weeks before the effects of testosterone become manifest.
Gonococcal MinD Affects Cell Division in Neisseria gonorrhoeae and Escherichia coli and Exhibits a Novel Self-Interaction (2001)

The Min proteins are involved in determining cell division sites in bacteria and have been studied extensively in rod-shaped bacteria. We have recently shown that the gram-negative coccus Neisseria gonorrhoeae contains a min operon, and the present study investigates the role of minD from this operon. A gonococcal minD insertional mutant, CJSD1, was constructed and exhibited both grossly abnormal cell division and morphology as well as altered cell viability. Western blot analysis verified the absence of MinD from N. gonorrhoeae (MinD(Ng)) in this mutant. Hence, MinD(Ng) is required for maintaining proper cell division and growth in N. gonorrhoeae. Immunoblotting of soluble and insoluble gonococcal cell fractions revealed that MinD(Ng) is both cytosolic and associated with the insoluble membrane fraction. The joint overexpression of MinC(Ng) and MinD(Ng) from a shuttle vector resulted in a significant enlargement of gonococcal cells, while cells transformed with plasmids encoding either MinC(Ng) or MinD(Ng) alone did not display noticeable morphological changes. These studies suggest that MinD(Ng) is involved in inhibiting gonococcal cell division, likely in conjunction with MinC(Ng). The alignment of MinD sequences from various bacteria showed that the proteins are highly conserved and share several regions of identity, including a conserved ATP-binding cassette. The overexpression of MinD(Ng) in wild-type Escherichia coli led to cell filamentation, while overexpression in an E. coli minD mutant restored a wild-type morphology to the majority of cells; therefore, gonococcal MinD is functional across species. Yeast two-hybrid studies and gel-filtration and sedimentation equilibrium analyses of purified His-tagged MinD(Ng) revealed a novel MinD(Ng) self-interaction. We have also shown by yeast two-hybrid analysis that MinD from E. coli interacts with itself and with MinD(Ng). These results indicate that MinD(Ng) is required for maintaining proper cell division and growth in N. gonorrhoeae and suggests that the self-interaction of MinD may be important for cell division site selection across species.
Clinical and Biomarker Changes in Dominantly Inherited Alzheimer's Disease (2012)

We found that autosomal dominant Alzheimer's disease was associated with a series of pathophysiological changes over decades in CSF biochemical markers of Alzheimer's disease, brain amyloid deposition, and brain metabolism as well as progressive cognitive impairment. Our results require confirmation with the use of longitudinal data and may not apply to patients with sporadic Alzheimer's disease. (Funded by the National Institute on Aging and others; DIAN ClinicalTrials.gov number, NCT00869817.).
Recent Advances in Egg Products Research and Development (1998)

Total egg consumption has basically become level with perhaps a slight increase in the last 3 or 4 years. Although shell egg consumption has declined, the growth of value added egg products has been very encouraging. In 1982, 12 % of the total egg consumption was in the form of further processed or value added egg products.Today,
Prevention of fat-induced insulin resistance by salicylate (2001)

Insulin resistance is a major factor in the pathogenesis of type 2 diabetes and may involve fat-induced activation of a serine kinase cascade involving IKK-beta. To test this hypothesis, we first examined insulin action and signaling in awake rats during hyperinsulinemic-euglycemic clamps after a lipid infusion with or without pretreatment with salicylate, a known inhibitor of IKK-beta. Whole-body glucose uptake and metabolism were estimated using [3-(3)H]glucose infusion, and glucose uptake in individual tissues was estimated using [1-(14)C]2-deoxyglucose injection during the clamp. Here we show that lipid infusion decreased insulin-stimulated glucose uptake and activation of IRS-1-associated PI 3-kinase in skeletal muscle but that salicylate pretreatment prevented these lipid-induced effects. To examine the mechanism of salicylate action, we studied the effects of lipid infusion on insulin action and signaling during the clamp in awake mice lacking IKK-beta. Unlike the response in wild-type mice, IKK-beta knockout mice did not exhibit altered skeletal muscle insulin signaling and action following lipid infusion. In summary, high-dose salicylate and inactivation of IKK-beta prevent fat-induced insulin resistance in skeletal muscle by blocking fat-induced defects in insulin signaling and action and represent a potentially novel class of therapeutic agents for type 2 diabetes.
Providing soft real-time QoS guarantees for Java threads (2001)

The Java platform has many characteristics that make it very desirable for integrated continuous media processing. Unfortunately, it lacks the necessary CPU resource management facility to support quality of service guarantees for soft real-time multimedia tasks. In this paper, we present our new Java Virtual Machine, Q-JVM, which brings CPU resource management to the Java platform. Q-JVM is based on Sun's JVM version 1.1.5. It implements an enhanced version or the MTR-LS algorithm in its thread scheduler. Combined with admission control that could be implemented in an application-level resource manager, it is able to support QoS parameters such as fairness, bandwidth partitioning and delay bound guarantees, as well as the cumulative service guarantee. Our test results show that Q-JVM is backward compatible with the standard JVM from Sun, has low scheduling overhead, and is able to provide QoS guarantees as specified.