gebhart/patrepeval huggingface dataset:
Eph, a Protein Family Coming of Age: More Confusion, Insight, or Complexity? (2008)

Since the mid-1980s, Eph receptors have evolved from being regarded as orphan receptors with unknown functions and ligands to becoming one of the most complex "global positioning systems" that regulates cell traffic in multicellular organisms. During this time, there has been an exponentially growing interest in Ephs and ephrin ligands, coinciding with important advances in the way biological function is interrogated through mapping of genomes and manipulation of genes. As a result, many of the original concepts that used to define Eph signaling and function went overboard. Clearly, the need for progress in understanding Eph-ephrin biology and the underlying molecular principles involved has been compelling. Many cell-positioning programs during normal and oncogenic development-in particular, the patterning of skeletal, vascular, and nervous systems-are modulated in some way by Eph-ephrin function. Undeniably, the complexity of the underlying signaling networks is considerable, and it seems probable that systems biology approaches are required to further improve our understanding of Eph function.
On the performance of random vector quantization limited feedback beamforming in a MISO system (2007)

In multiple antenna wireless systems, beamforming is a simple technique for guarding against the negative effects of fading. Unfortunately, beamforming requires the transmitter to have knowledge of the forward-link channel which is often not available a priori. One way of overcoming this problem is to design the beamforming vector using a limited number of feedback bits sent from the receiver to the transmitter. In limited feedback beamforming, the beamforming vector is restricted to lie in a codebook that is known to both the transmitter and receiver. Random vector quantization (RVQ) is a simple approach to codebook design that generates the vectors independently from a uniform distribution on the complex unit sphere. This correspondence presents performance analysis results for RVQ limited feedback beamforming
Well-Defined Poly(sulfobetaine) Brushes Prepared by Surface-Initiated ATRP Using a Fluoroalcohol and Ionic Liquids as the Solvents (2010)

Surface-initiated atom transfer radical polymerization (ATRP) of 2-(N-2-methacryloyloxyethyl-N,N-dimethyl) ammonatoethanesulfonate) (MAES), 3-(N-2-methacryloyloxyethyl-N,N-dimethyl) ammonatopropanesulfonate) (MAPS), and 4-(N-2-methacryloyloxyethyl-N,N-dimethyl) ammonatobutanesulfonate) (MABS) was carried out in 2,2,2-trifluoroethanol (TFE) containing a small amount of 1-hexyl-3-methylimidazolium chloride at 60 °C to produce well-defined poly(sulfobetaine) brushes and the corresponding free polymers with predictable number-average molecular weight (Mn, 1 × 104 to 3 × 105 g mol−1) and narrow molecular weight distributions (Mw/Mn < 1.2). A first-order kinetic plot for ATRP of MAPS revealed a linear relationship between the monomer conversion index (ln([M]0/[M])) and polymerization time. The polymerization rates decreased with increasing ionic liquid concentration. The Mn of poly(MAPS) increased in proportion to the conversion. The sequential polymerization of MAPS initiated with the chain ends of poly(MAPS) produced the postpolymer with quantitative efficiency. The thickness of the polymer brush was controllable from 5 to 100 nm based on the Mn of the polymer. The polymer brush was cleaved from the silicon substrate under the acidic condition to measure the molecular weight by size exclusion chromatography equipped with a multiangle light scattering detector (SEC-MALS). We have confirmed that the molecular weight distribution of polymer brush was also narrow (Mn = 150 000, Mw/Mn =1.26) as well as the corresponding free polymer. These results suggest the successful control of the polymerization of sulfobetaine-type methacrylates owing to the TFE and ionic liquids. In particular, the high affinity of TFE for the sulfobetaine monomers and polymers yielded a homogeneous polymerization media to improve surface-initiated polymerization generating the polymer brushes on the substrate surface as well as the free polymers formed in the solution. The effect on ATRP of the chemical structure of ionic liquids and ligands for copper catalyst was also investigated.
Evolutionary implications of primate endogenous retroviruses (1991)

Endogenous DNA sequences related to retroviruses are probably present in all primates. By using approaches based on the polymerase chain reaction, two separate studies have revealed the evolutionary history of some of these sequences. In the first study, a retrovirus-like reverse transcriptase (RT) sequence homologous to that of Baboon endogenous virus (BaEV) has been identified in both Old World monkeys and African apes, but not in humans or Asian apes. This RT sequence is highly conserved at the amino acid level, but not the nucleotide level, in the baboon, African green monkey, Java macaque, chimpanzee, and gorilla. The patterns of nucleotide substitution indicate functional conservation and suggest that this RT sequence was present in the primate germline before apes and Old World monkeys diverged about 30 million years ago. In the second study, a comparison of endogenous proviral DNAs and their adjacent sequences has been used to analyze the evolutionary history of three previously reported human endogenous retroviruses, HERV-E(4.14), HERV-R(3), and HERV-Ia. It is shown that these retroviruses have also been resident in the primate line since before the ape-Old World monkey divergence. The implications of the presence of functionally conserved RT genes in the germlines of primates, and the potential for using integration sites as tools for analyzing phylogenetic relationships among primates and their retroviruses, are discussed.
Family History and Serology Predict Crohn's Disease after Ileal Pouch-Anal Anastomosis for Ulcerative Colitis (2007)

Patients with ulcerative colitis and indeterminate colitis with a family history of Crohn's disease or preoperative anti-Saccharomyces cerevisiae immunoglobulin-A seropositivity are more likely to be diagnosed with Crohn's disease after ileal pouch-anal anastomosis.
Walking on a Graph with a Magnifying Glass: Stratified Sampling via Weighted Random Walks (2011)

Our objective is to sample the node set of a large unknown graph via crawling, to accurately estimate a given metric of interest. We design a random walk on an appropriately defined weighted graph that achieves high efficiency by preferentially crawling those nodes and edges that convey greater information regarding the target metric. Our approach begins by employing the theory of stratification to find optimal node weights, for a given estimation problem, under an independence sampler. While optimal under independence sampling, these weights may be impractical under graph crawling due to constraints arising from the structure of the graph. Therefore, the edge weights for our random walk should be chosen so as to lead to an equilibrium distribution that strikes a balance between approximating the optimal weights under an independence sampler and achieving fast convergence. We propose a heuristic approach (stratified weighted random walk, or S-WRW) that achieves this goal, while using only limited information about the graph structure and the node properties. We evaluate our technique in simulation, and experimentally, by collecting a sample of Facebook college users. We show that S-WRW requires 13-15 times fewer samples than the simple re-weighted random walk (RW) to achieve the same estimation accuracy for a range of metrics.
Medication Practices Among Chinese American Older Adults: A STUDY OF CULTURAL INFLUENCES (2004)

The magnitude and intensity of medication use in older individuals have been widely discussed. Yet, a paucity of research data exists on medication practices among community-dwelling Chinese American older adults. This study examined factors associated with medication practices in community-dwelling Chinese American older adults. Data were collected through a descriptive survey. Chinese American older adults (n = 165) from the greater Boston area participated in the survey. The study revealed that ethnocultural barriers and a lack of health insurance significantly influenced medication practices among Chinese American older adults. The study suggested three important implications. First, more ethnoculturally appropriate health services are needed. Secondly, communication between clients and health providers must be improved. Finally, culturally sensitive medication management programs are needed.
4-<i>N</i>-, 4-<i>S</i>-, and 4-<i>O</i>-Chloroquine Analogues: Influence of Side Chain Length and Quinolyl Nitrogen p<i>K</i><sub>a</sub> on Activity vs Chloroquine Resistant Malaria (2008)

Using predictions from heme-quinoline antimalarial complex structures, previous modifications of chloroquine (CQ), and hypotheses for chloroquine resistance (CQR), we synthesize and assay CQ analogues that test structure-function principles. We vary side chain length for both monoethyl and diethyl 4-N CQ derivatives. We alter the pKa of the quinolyl N by introducing alkylthio or alkoxy substituents into the 4 position and vary side chain length for these analogues. We introduce an additional titratable amino group to the side chain of 4-O analogues with promising CQR strain selectivity and increase activity while retaining selectivity. We solve atomic resolution structures for complexes formed between representative 4-N, 4-S, and 4-O derivatives vs mu-oxo dimeric heme, measure binding constants for monomeric vs dimeric heme, and quantify hemozoin (Hz) formation inhibition in vitro. The data provide additional insight for the design of CQ analogues with improved activity vs CQR malaria.
Phospholipid Metabolism Regulated by a Transcription Factor Sensing Phosphatidic Acid (2004)

Cells regulate the biophysical properties of their membranes by coordinated synthesis of different classes of lipids. Here, we identified a highly dynamic feedback mechanism by which the budding yeast Saccharomyces cerevisiae can regulate phospholipid biosynthesis. Phosphatidic acid on the endoplasmic reticulum directly bound to the soluble transcriptional repressor Opi1p to maintain it as inactive outside the nucleus. After the addition of the lipid precursor inositol, this phosphatidic acid was rapidly consumed, releasing Opi1p from the endoplasmic reticulum and allowing its nuclear translocation and repression of target genes. Thus, phosphatidic acid appears to be both an essential ubiquitous metabolic intermediate and a signaling lipid.
Transduction of a freshwater microbial community by a new <i>Pseudomonas aeruginosa</i> generalized transducing phage, UT1 (1994)

A pseudolysogenic, generalized transducing bacteriophage, UT1, isolated from a natural freshwater habitat, is capable of mediating the transfer of both chromosomal and plasmid DNA between strains of Pseudomonas aeruginosa. Several chromosomal alleles from three different P. aeruginosa strains were found to transduce at frequencies from 10(-8) to 10(-10) transductants per PFU at multiplicities of infection (MOI) between 0.1 and 1. Transduction frequencies of certain alleles increased up to 1000-fold as MOIs were decreased to 0.01. UT1 is also capable of transducing plasmid DNA to indigenous populations of microorganisms in natural lake-water environments. Data obtained in this study suggest that environmentally endemic bacteriophages such as UT1 are formidable transducers of naturally occurring microbial communities. It should be possible to develop model systems to test transduction in freshwater environments using components derived exclusively from these environments.
Diagnóstico das práticas da responsabilidade sócio-ambiental no setor de supermercado (2012)

Com o crescente desenvolvimento da atividade varejista ao redor do mundo, é notável a preocupação dos gestores, em relação aos impactos sócio-ambientais que podem ser causados por esse setor. Assim, deve-se atentar para a responsabilidade sócio-ambiental que essas empresas devem ter com a comunidade e o meio ambiente. O objetivo deste estudo é identificar as práticas de responsabilidade sócio-ambiental do setor de supermercado. Para isso, utilizou-se uma pesquisa descritiva de caráter exploratório, em cinco supermercados da cidade de Campina Grande, Estado da Paraíba, utilizando os indicadores de responsabilidade social proposto pelo Instituto ETHOS. De acordo com os resultados obtidos, percebe-se que a maioria das empresas se encontra regularmente enquadradas para o seu devido funcionamento, não incentivam a reciclagem de produtos, não possuem um sistema adequado de destinação para os resíduos de cada produto. Fica claro que muitos paradigmas ainda precisam ser quebrados para atender aos interesses da sociedade e do meio ambiente. Palavras-chave: Responsabilidade Sócioambiental; Varejo; Supermercado.
Identification of a Putative Microvascular Oxygen Sensor (1996)

The vascular response to changes in oxygen levels in the blood and tissue is a highly adaptive physiological response that functions to match tissue oxygen supply to metabolic demand. Defining the cellular mechanisms that can sense physiologically relevant changes in PO2 and adjust vascular diameter are vital to our understanding of this process. A cytochrome P450 (P450) enzyme of the 4A family of omega-hydroxylases was localized in renal microvessels, renal cortex, and a striated muscle microvascular bed (cremaster) of the rat. In the presence of molecular oxygen, this P450 enzyme catalyzes formation of 20-HETE from arachidonic acid (AA). Prior studies have shown that 20-HETE potently contracts renal and cerebral arteries and arterioles. The present study demonstrates that 20-HETE constricts striated muscle arterioles as well. In both intact renal microvessels and enriched renal cortical microsomal enzyme preparations, the formation of 20-HETE was linearly dependent on PO2 between 20 and 140 mm Hg. Homogenates of cremaster tissue produced 20-oxygen HETE when incubated with AA. They also expressed message for P450 4A enzyme, as determined by Southern and Western blots. Administration of 17-octadecynoic acid (17-ODYA), which is a P450 4A inhibitor, attenuated the constriction of third-order cremasteric arterioles in response to elevation of superfusion solution PO2 from approximately equal to 3 to 5 mm Hg to approximately equal to 35 mm Hg. 17-ODYA had no effect on basal vascular tone or response of cremaster arterioles to vasoactive compounds. These results demonstrate the existence of P450 omega-hydroxylase activity and 20-HETE formation in the vasculature and parenchyma of at least two microvascular beds. Our data suggest that a P450 enzyme of the 4A family has the potential to function as an oxygen sensor in mammalian microcirculatory beds and to regulate arteriolar caliber by generating 20-HETE in an oxygen-dependent manner.
High‐Throughput Molecular Detection of Hemorrhagic Fever Virus Threats with Applications for Outbreak Settings (2007)

Within the past dozen years, outbreaks of filoviral hemorrhagic fever within the human population have been occurring with increasing frequency, with an average of 1 epidemic now occurring every 1-2 years. Many of the outbreaks have been large (involving >150 cases), necessitating rapid responses from the international community to help implement infection control and surveillance. This increased activity, combined with today's climate of bioterrorism threats, has heightened the need for high-throughput methodologies for specific detection of these high-hazard viruses in sophisticated laboratory setups and mobile field laboratory situations. Using Zaire Ebola virus as an example, we describe here the development of a high-throughput protocol for RNA extraction and quantitative reverse-transcription polymerase chain reaction analysis that is safe, fast, and reliable. Furthermore, the applicability of this method to an outbreak setting was demonstrated by correct analysis of >500 specimens at a field laboratory established during a recent outbreak of Marburg hemorrhagic fever in Angola.
COLD-PCR Amplification of Bisulfite-Converted DNA Allows the Enrichment and Sequencing of Rare Un-Methylated Genomic Regions (2014)

Aberrant hypo-methylation of DNA is evident in a range of human diseases including cancer and diabetes. Development of sensitive assays capable of detecting traces of un-methylated DNA within methylated samples can be useful in several situations. Here we describe a new approach, fast-COLD-MS-PCR, which amplifies preferentially un-methylated DNA sequences. By employing an appropriate denaturation temperature during PCR of bi-sulfite converted DNA, fast-COLD-MS-PCR enriches un-methylated DNA and enables differential melting analysis or bisulfite sequencing. Using methylation on the MGMT gene promoter as a model, it is shown that serial dilutions of controlled methylation samples lead to the reliable sequencing of un-methylated sequences down to 0.05% un-methylated-to-methylated DNA. Screening of clinical glioma tumor and infant blood samples demonstrated that the degree of enrichment of un-methylated over methylated DNA can be modulated by the choice of denaturation temperature, providing a convenient method for analysis of partially methylated DNA or for revealing and sequencing traces of un-methylated DNA. Fast-COLD-MS-PCR can be useful for the detection of loss of methylation/imprinting in cancer, diabetes or diet-related methylation changes.
Adaptive Control of Space Truss Structures by Piezoelectric Actuator (1992)

Control/structure interaction problems are much concerned with the atti tude stability of space structures and the accuracies of on-board instruments as the sizes and flexibilities of structures increase. In this paper, an attempt to integrate collocated actuators and sensors into truss structures and to suppress the vibration or to adjust the truss geometry is investigated. For both functions of vibration suppression and shape adjustment, piezoelectric actuator Type-I was manufactured. And, for the purpose of increasing the abilities of vibration suppression, another type of actuator (Type-II) was designed. Some experimental results and analyses show the capabilities of vibration sup pression and precise adjustment of truss geometry by these piezoelectric actuators.
Precise client-side protection against DOM-based cross-site scripting (2014)

The current generation of client-side Cross-Site Scripting filters rely on string comparison to detect request values that are reflected in the corresponding response's HTML. This coarse approximation of occurring data flows is incapable of reliably stopping attacks which leverage nontrivial injection contexts. To demonstrate this, we conduct a thorough analysis of the current state-of-the-art in browser-based XSS filtering and uncover a set of conceptual shortcomings, that allow efficient creation of filter evasions, especially in the case of DOM-based XSS. To validate our findings, we report on practical experiments using a set of 1,602 real-world vulnerabilities, achieving a rate of 73% successful filter bypasses. Motivated by our findings, we propose an alternative filter design for DOM-based XSS, that utilizes runtime taint tracking and taint-aware parsers to stop the parsing of attacker-controlled syntactic content. To examine the efficiency and feasibility of our approach, we present a practical implementation based on the open source browser Chromium. Our proposed approach has a low false positive rate and robustly protects against DOM-based XSS exploits.
Effect of Menthol and Related Terpenes on the Percutaneous Absorption of Propranolol across Excised Hairless Mouse Skin (1997)

The potential use of terpenes/terpenoids as penetration enhancers in the transdermal delivery of propranolol hydrochloride (PL) was investigated. PL was chosen for the reasons of its extensive first-pass metabolism and short elimination half-life. The terpenes studied included L-menthol, (+)-limonene, (+/-)-linalool, and carvacrol at 1%, 5%, and 10% w/v concentrations. The diffusion of PL across excised hairless mouse skin was determined using side-by-side diffusion cells. Flux, permeability coefficient (Pm), and lag time (tL) were calculated. PL showed comparable lag times with menthol at all three concentration levels. At a 1% level of carvacrol, PL exhibited a 2.4- and 2.2-fold increase in lag time compared with 5 and 10% levels of enhancer, respectively. In the presence of limonene, PL had shown maximum lag time (between 3.0 and 3.3 h) at all three levels. In the case of linalool, the lag times for PL with 5 and 10% levels of enhancer were 7.0- and 5.2-fold less compared with 1% level. A significant (p < 0.05) concentration effect was observed only with linalool. Hydrogel-based patches were formulated with or without menthol as enhancer. Release profiles from the hydrogel formulations obeyed zero-order kinetics. The permeability of propranolol was significantly higher (p < 0.05) from the test patch than the control (no enhancer) patch across the mouse skin. The mechanism of permeation enhancement of menthol could involve its distribution preferentially into the intercellular spaces of stratum corneum and the possible reversible disruption of the intercellular lipid domain. The results suggest the potential use of menthol as effective penetration enhancer in the delivery of significant amounts of PL through skin.
A Systematic Approach to the Optimization of Substrate-Based Inhibitors of the Hepatitis C Virus NS3 Protease:  Discovery of Potent and Specific Tripeptide Inhibitors (2004)

The inadequate efficacy and tolerability of current therapies for the infectious liver disease caused by the hepatitis C virus have warranted significant efforts in the development of new therapeutics. We have previously reported competitive peptide inhibitors of the NS3 serine protease based on the N-terminal cleavage products of peptide substrates. A detailed study of the interactions of these substrate-based inhibitors with the different subsites of the serine protease active site led to the discovery of novel residues that increased the affinity of the inhibitors. In this paper, we report the combination of the best binding residues in a tetrapeptide series that resulted in extremely potent inhibitors that bind exquisitely well to this enzyme. A substantial increase in potency was obtained with the simultaneous introduction of a 7-methoxy-2-phenyl-4-quinolinoxy moiety at the gamma-position of the P2 proline and a tert-leucine as a P3 residue. The increase in potency allowed for the further truncation and led to the identification of tripeptide inhibitors. Structure activity relationship studies on this inhibitor series led to the identification of carbamate-containing tripeptides that are able to inhibit replication of subgenomic HCV RNA in cell culture with potencies below 1 microM. This inhibitor series has the potential of becoming antiviral agents for the treatment of HCV infections.