gebhart/patrepeval huggingface dataset:
Metagenome Fragment Classification Using N‐Mer Frequency Profiles (2008)

A vast amount of microbial sequencing data is being generated through large-scale projects in ecology, agriculture, and human health. Efficient high-throughput methods are needed to analyze the mass amounts of metagenomic data, all DNA present in an environmental sample. A major obstacle in metagenomics is the inability to obtain accuracy using technology that yields short reads. We construct the unique N-mer frequency profiles of 635 microbial genomes publicly available as of February 2008. These profiles are used to train a naive Bayes classifier (NBC) that can be used to identify the genome of any fragment. We show that our method is comparable to BLAST for small 25 bp fragments but does not have the ambiguity of BLAST's tied top scores. We demonstrate that this approach is scalable to identify any fragment from hundreds of genomes. It also performs quite well at the strain, species, and genera levels and achieves strain resolution despite classifying ubiquitous genomic fragments (gene and nongene regions). Cross-validation analysis demonstrates that species-accuracy achieves 90% for highly-represented species containing an average of 8 strains. We demonstrate that such a tool can be used on the Sargasso Sea dataset, and our analysis shows that NBC can be further enhanced.
Association Between Two Unlinked Loci at 8q24 and Prostate Cancer Risk Among European Americans (2007)

Three loci at 8q24 are independent genetic risk factors for prostate cancer.
Dual requirement in yeast DNA mismatch repair for MLH1 and PMS1, two homologs of the bacterial mutL gene. (1994)

We have identified a new Saccharomyces cerevisiae gene, MLH1 (mutL homolog), that encodes a predicted protein product with sequence similarity to DNA mismatch repair proteins of bacteria (MutL and HexB) and S. cerevisiae yeast (PMS1). Disruption of the MLH1 gene results in elevated spontaneous mutation rates during vegetative growth as measured by forward mutation to canavanine resistance and reversion of the hom3-10 allele. Additionally, the mlh1 delta mutant displays a dramatic increase in the instability of simple sequence repeats, i.e., (GT)n (M. Strand, T. A. Prolla, R. M. Liskay, and T. D. Petes, Nature [London] 365:274-276, 1993). Meiotic studies indicate that disruption of the MLH1 gene in diploid strains causes increased spore lethality, presumably due to the accumulation of recessive lethal mutations, and increased postmeiotic segregation at each of four loci, the latter being indicative of inefficient repair of heteroduplex DNA generated during genetic recombination. mlh1 delta mutants, which should represent the null phenotype, show the same mutator and meiotic phenotypes as isogenic pms1 delta mutants. Interestingly, mutator and meiotic phenotypes of the mlh1 delta pms1 delta double mutant are indistinguishable from those of the mlh1 delta and pms1 delta single mutants. On the basis of our data, we suggest that in contrast to Escherichia coli, there are two MutL/HexB-like proteins in S. cerevisiae and that each is a required component of the same DNA mismatch repair pathway.
Morphological Changes of Intraparenchymal Arterioles after Experimental Subarachnoid Hemorrhage in Dogs (1997)

These results suggest that constriction of intraparenchymal arterioles occurs after SAH and may contribute to delayed cerebral ischemia.
Association Between Stroke Risk and Metformin Use in Hemodialysis Patients With Diabetes Mellitus: A Nested Case–Control Study (2017)

This nested case-control study is the first to show that metformin use is associated with stroke risk in hemodialysis patients with DM. We suggest that metformin should not be used by hemodialysis patients with DM.
Adrenergic α2C-Receptors Modulate the Acoustic Startle Reflex, Prepulse Inhibition, and Aggression in Mice (1998)

Studies on animal models of stress, anxiety, aggression, and sensorimotor gating have linked specific monoamine neurotransmitter abnormalities to the cognitive and behavioral disturbances associated with many affective neuropsychiatric disorders. Although alpha2-adrenoceptors (alpha2-ARs) have been suggested to have a modulatory role in these disorders, the specific roles of each alpha2-AR subtype (alpha2A, alpha2B, and alpha2C) are largely unknown. The restricted availability of relevant animal models and the lack of subtype-selective alpha2-AR drugs have precluded detailed studies in this area. Therefore, transgenic mice were used to study the possible role of the alpha2C-AR subtype in two well established behavioral paradigms: prepulse inhibition (PPI) of the startle reflex and isolation-induced aggression. The alpha2C-AR-altered mice appear grossly normal, but subtle changes have been observed in their brain dopamine (DA) and serotonin (5-HT) metabolism. In this study, the mice with targeted inactivation of the gene encoding alpha2C-ARs (alpha2C-KO) had enhanced startle responses, diminished PPI, and shortened attack latency in the isolation-aggression test, whereas tissue-specific overexpression of alpha2C-ARs (alpha2C-OE) was associated with opposite effects. Correlation analyses suggested that both the magnitude of the startle response and its relative PPI (PPI%) were modulated by the mutations. In addition, the differences in PPI, observed between drug-naive alpha2C-OE mice and their wild-type controls, were abolished by treatment with a subtype nonselective alpha2-agonist and antagonist. Thus, drugs acting via alpha2C-ARs might have therapeutic value in disorders associated with enhanced startle responses and sensorimotor gating deficits, such as schizophrenia, attention deficit disorder, post-traumatic stress disorder, and drug withdrawal.
Real-time FEXT crosstalk identification in ADSL systems (2004)

FEXT crosstalk identification results in improved frequency spectrum utilization in ADSL systems. The accurate determination of the crosstalk transfer function is a demanding task that is affected by various system impairments. We investigate the performance of a real-time method that exploits the exchange of signaling information of a new activated ADSL line in order to determine the crosstalk function between this line and an existing operational line.
Designing an academic firewall: policy, practice, and experience with SURF (2002)

Corporate network firewalls are well-understood and are becoming commonplace. These firewalls establish a security perimeter that aims to block (or heavily restrict) both incoming and outgoing network communication. We argue that these firewalls are neither effective nor appropriate for academic or corporate research environments needing to maintain information security while still supporting the free exchange of ideas. In this paper we present the Stanford University Research Firewall (SURF), a network firewall design that is suitable for a research environment. While still protecting information and computing resources behind the firewall, this firewall is less restrictive of outward information flow than the traditional model; can be easily deployed; and can give internal users the illusion of unrestricted e-mail, anonymous FTP, and WWW connectivity to the greater Internet. Our experience demonstrates that an adequate firewall for a research environment can be constructed for minimal cost using off-the-shelf software and hardware components.
Simple Closed-Form Approximation to Ricean Sum Distributions (2009)

This letter focuses on the approximation of Ricean sum distributions of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</i> independent random variables. Although no closed-form expression is available for these exact distributions, a simple but accurate closed-form approximation is proposed. The expression is based on the Central Limit Theorem (CLT) for which an appropriate correction term is added. The result is a rather tight fit with the exact distribution for a wide range of input values and Ricean <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">K</i> -factors.
Tau Phosphorylation, Aggregation, and Cell Toxicity (2006)

Protein aggregation takes place in many neurodegenerative disorders. However, there is a controversy about the possible toxicity of these protein aggregates. In this review, this controversy is discussed, focussing on the tau aggregation that takes place in those disorders known as tauopathies.
Macrocirculation is not the sole determinant of respiratory induced variations in the reflection mode photoplethysmographic signal (2003)

Photoplethysmography (PPG) is a non-invasive optical technique sensitive to variations in blood volume and perfusion in the tissue. Reflection mode PPG may have clinical advantages over transmission mode PPG. To improve clinical usefulness and further development of the reflection mode PPG, studies on factors that modify the signal are warranted. We studied the coherence between the respiratory induced intensity variations (RIIV) of the PPG signal and respiratory synchronous pressure variations in central venous pressure (CVP), peripheral venous pressure (PVP) and arterial blood pressure (ABP) during positive pressure ventilation on 12 patients under anaesthesia and on 12 patients with spontaneous breathing. During positive pressure ventilation the coherence between all signals was high. Inspiration was followed first by an increase in CVP, then by increases in ABP and PVP and lastly by RIIV indicating less back-scattered light. In spontaneously breathing patients the coherence was high, but the phases between the signals were changed. During inspiration, ABP decreased slightly before CVP, followed by a decrease in RIIV and PVP. The phase relation between RIIV and respiratory induced variation in macrocirculation changed with ventilatory mode, but not in a uniform way, indicating the influence of mechanisms other than macrocirculation involved in generating the RIIV signal.
Stereochemical course of phosphoanhydride synthesis (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStereochemical course of phosphoanhydride synthesisJohn P. Richard and Perry A. FreyCite this: J. Am. Chem. Soc. 1983, 105, 22, 6605–6609Publication Date (Print):October 1, 1983Publication History Published online1 May 2002Published inissue 1 October 1983https://doi.org/10.1021/ja00360a010Request reuse permissionsArticle Views107Altmetric-Citations16LEARN 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 InReddit PDF (658 KB) Get e-Alertsclose Get e-Alerts
The human tissue plasminogen activator gene. (1986)

The nucleotide sequence of the human tissue plasminogen activator (t-PA) gene has been established. A total of 36,594 base pairs (bp) was sequenced; this included 32,720 bp from the site of initiation of transcription to the polyadenylation site, in addition to 3,530 and 344 bp of 5' and 3' flanking DNA, respectively. Thirteen intervening sequences divide the gene into 14 coding regions; the size range for exons is 43-914 bp, while that for introns is 111-14,257 bp. The gene and 5' flanking region contain 28 copies of Alu repetitive DNA and a single KpnI repeat. The transcription initiation site was identified by S1 nuclease, exonuclease VII, and primer extension analysis as an A residue; "TATA" and "CAAT" boxes are located in the expected positions upstream of this proposed site. Results of the analysis of the gene sequence and its comparison with data banks are described. The protein and gene structures of tissue and urokinase plasminogen activator are compared; based on these features the evolutionary relationship of the two human plasminogen activators appears to be close.
Transcranial magnetic stimulation (2000)

1 Behavioral Neurology Unit, Laboratory for Magnetic Brain Stimulation, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, KS 450, Boston, MA 02215, USA Acknowledgements: Supported in part by grants from the National Institute of Mental Health (RO1MH57980, RO1MH60734), the National Eye Institute (RO1EY12091), and the General Clinical Research Center at Beth Israel Deaconess Medical Center (National Center for Research Resources. MO1RR01032).
Serum ionised calcium concentration: measurement versus calculation. (1978)

Four hundred and eighteen measurements of serum ionised calcium, total calcium, and protein concentrations were made from 47 normal volunteers, 104 patients with chronic renal failure (33 being treated conservatively and 71 with regular haemodialysis), and 83 renal transplant recipients. The serum ionised calcium concentration was measured with an Orion SS-20 meter and calculated from the total serum calcium and protein concentrations by using three formulae and a nomogram. In the normal subjects and patients undergoing regular haemodialysis, whose serum calcium concentrations were in or near the normal range, three of the calculations gave results similar to those obtained by direct measurement. In patients with conservatively treated chronic renal failure and those who had received renal transplants, however, there was poor aggrement between the methods. When patients with hypercalcaemia and hypocalcaemia from all the groups were considered separately there was again poor agreement between calculated and measured concentrations of serum ionised calcium. Of the patients whose measured concentrations of serum ionised calcium were high, 69-76% were classified as normal by the four indirect methods. We conclude that calculation of the serum ionised calcium concentrations is not an adequate substitute for direct measurement.
Adhesion molecules and tumor metastasis: an update. (1995)

The past decade has witnessed substantial progress in our understanding of the molecular mechanisms of tumor cell interactions with vascular endothelium and extracellular matrix, important events in the metastatic process. This progress has been made possible by the identification and functional characterization of a large number of adhesion molecules involved in tumor cell-vasculature interactions. Essentially, most of the adhesion receptor families so far reported, including integrins, cadherins, selectins, immunoglobulins, and proteoglycans, have been implicated in various stages of tumor progression and metastasis. Disseminating cancer cells often employ ectopic expression of certain adhesion molecules to facilitate their interaction with the vessel wall and matrix, typical examples being the expression of integrins alpha IIb beta 3 and alpha L beta 2 and immunoglobulin family members PECAM-1, ICAM-1, and N-CAM in solid tumor cells. The expression of adhesion molecules in cancer cells and vascular endothelial cells is spatiotemporally regulated, in a dynamic fashion, by a wide diversity of bioactive molecules such as eicosanoid 12(S)-HETE. Recent data indicate that most adhesion molecules, integrins in particular, participate in various signaling functions such as the induction of calcium fluctuation and protein tyrosine phosphorylation. The importance of adhesion molecules in tumor metastasis is also evidenced by their involvement in other important parameters of metastasis such as angiogenesis. Collectively, the accumulated literature suggests that interference with adhesion and signaling represent a future direction for the development of anticancer and antimetastasis therapeutic protocols.
Surface-Plasmon-Assisted Guiding of Broadband Slow and Subwavelength Light in Air (2005)

A class of axially uniform waveguides is introduced, employing a new mechanism to guide light inside a low-index dielectric material without the use of photonic band gap, and simultaneously exhibiting subwavelength modal size and very slow group velocity over an unusually large frequency bandwidth. Their basis is the presence of plasmonic modes on the interfaces between dielectric regions and the flat unpatterned surface of a bulk metallic substrate. These novel waveguides allow for easy broadband coupling and exhibit absorption losses limited only by the intrinsic loss of the metal.
Differentiation-Induced Internal Translation of c- sis mRNA: Analysis of the cis Elements and Their Differentiation-Linked Binding to the hnRNP C Protein (1999)

In previous reports we showed that the long 5' untranslated region (5' UTR) of c-sis, the gene encoding the B chain of platelet-derived growth factor, has translational modulating activity due to its differentiation-activated internal ribosomal entry site (D-IRES). Here we show that the 5' UTR contains three regions with a computer-predicted Y-shaped structure upstream of an AUG codon, each of which can confer some degree of internal translation by itself. In nondifferentiated cells, the entire 5' UTR is required for maximal basal IRES activity. The elements required for the differentiation-sensing ability (i.e., D-IRES) were mapped to a 630-nucleotide fragment within the central portion of the 5' UTR. Even though the region responsible for IRES activation is smaller, the full-length 5' UTR is capable of mediating the maximal translation efficiency in differentiated cells, since only the entire 5' UTR is able to confer the maximal basal IRES activity. Interestingly, a 43-kDa protein, identified as hnRNP C, binds in a differentiation-induced manner to the differentiation-sensing region. Using UV cross-linking experiments, we show that while hnRNP C is mainly a nuclear protein, its binding activity to the D-IRES is mostly nuclear in nondifferentiated cells, whereas in differentiated cells such binding activity is associated with the ribosomal fraction. Since the c-sis 5' UTR is a translational modulator in response to cellular changes, it seems that the large number of cross-talking structural entities and the interactions with regulated trans-acting factors are important for the strength of modulation in response to cellular changes. These characteristics may constitute the major difference between strong IRESs, such as those seen in some viruses, and IRESs that serve as translational modulators in response to developmental signals, such as that of c-sis.
In vivo effects of antibodies to immune response gene products: prevention of experimental allergic encephalitis. (1981)

Prevention of experimental allergic encephalitis in SJL/J [H-2s] mice was achieved with in vivo administration of antibody reactive with I-As gene products prior to immunization with spinal cord antigen. No protection was evident in animals that received antisera specific for I-Js gene products. Administration of antibody to I-As beginning 5 days after immunization with spinal cord antigen delayed, but did not prevent, the onset of experimental allergic encephalitis.
Anomalous transport properties of the half-metallic ferromagnets Co2TiSi, Co2TiGe and Co2TiSn (2011)

In this work, the theoretical and experimental investigations of Co₂TiZ (Z=Si, Ge or Sn) compounds are reported. Half-metallic ferromagnetism is predicted for all three compounds with only two bands crossing the Fermi energy in the majority channel. The magnetic moments fulfil the Slater-Pauling rule and the Curie temperatures are well above room temperature. All compounds show a metallic-like resistivity for low temperatures up to their Curie temperature, above the resistivity changes to semiconducting-like behaviour. A large negative magnetoresistance (MR) of 55 per cent is observed for Co₂TiSn at room temperature in an applied magnetic field of μ(0)H=4T, which is comparable to the large negative MRs of the manganites. The Seebeck coefficients are negative for all three compounds and reach their maximum values at their respective Curie temperatures and stay almost constant up to 950 K. The highest value achieved is -52 μVK(-1) for Co₂TiSn, which is large for a metal. The combination of half-metallicity and the constant large Seebeck coefficient over a wide temperature range makes these compounds interesting materials for thermoelectric applications and further spincaloric investigations.
Mediators in the Pathogenesis of Toxic Shock Syndrome: Overview (1989)

Journal Article Mediators in the Pathogenesis of Toxic Shock Syndrome: Overview Get access Jeffrey Parsonnet Jeffrey Parsonnet Channing Laboratory Department of Medicine Brigham and Women's Hospital and Harvard Medical SchoolBoston, Massachusetts Please address requests for reprints to Dr. Jeffrey Parsonnet, Channing Laboratory, 180 Longwood Avenue, Boston, Massachusetts 02115. Search for other works by this author on: Oxford Academic PubMed Google Scholar Reviews of Infectious Diseases, Volume 11, Issue Supplement_1, January-February 1989, Pages S263–S269, https://doi.org/10.1093/clinids/11.Supplement_1.S263 Published: 01 January 1989
The Role of Cysteines and Charged Amino Acids in Extracellular Loops of the Human Ca2+Receptor in Cell Surface Expression and Receptor Activation Processes (2004)

The Ca(2+) receptor is a plasma-membrane bound G protein-coupled receptor stimulated by extracellular calcium [Ca(2+)](o) and other di- and poly-cations. We investigated the role in receptor activation of all the charged amino acid residues and cysteines in the three extracellular loops (EL1, 2, and 3) of the human Ca(2+) receptor by alanine-scanning mutagenesis. The mutant receptors were transiently expressed in HEK-293 cells, and cell surface expression patterns were analyzed by endoglycosidase-H digestion, immunoblotting, intact cell ELISA, and hydrolysis of phosphoinositides (PI) induced by [Ca(2+)](o.) The mutation of Cys677 and Cys765 located in EL1 and EL2, respectively, ablated PI hydrolysis completely, showed less than 5% cell surface expression of the wild-type receptor, and were not properly glycosylated. Replacement of the charged residues by using a single mutation or multiple alanine mutations in EL1, 2, and 3 produced only minor changes in receptor activation, except for Glu767 and Lys831. The E767A and K831A mutations in EL2 and EL3, respectively, showed gain-of-function by significantly enhancing apparent [Ca(2+)](o) affinity. E767A and K831A exhibited EC(50) values of 2.1 and 2.8 mm, respectively, for [Ca(2+)](o)-stimulated PI hydrolysis as opposed to EC(50) value of 4.2 mm for the wild-type receptor. Like E767A, substitutions of Glu767 with Gln and Lys was similarly activating, whereas Asp substitution displayed wild-type [Ca(2+)](o) sensitivity. Substitution of Lys831 with Glu but not with Gln showed similar activating effect as Ala replacement. A double-mutant E767K/K831E in which charged residues were switched positions showed impaired cell surface expression and failed to respond to [Ca(2+)](o.) Taken together, these results suggest that in ELs, two cysteines form critical disulfide links, and the side chains of Glu767 and Lys831 are probably involved in ionic interactions with other prospective oppositely charged residues. Some of these interactions could be important for receptor folding and also may contribute to keep the Ca(2+) receptor transmembrane helix bundle in an inactive conformation.