gebhart/patrepeval huggingface dataset:
Pairwise comparison between genomic sequences and optical-maps (2006)

With the development and improvement of high throughput experimental technologies, massive amount of biological data including genomic sequences and optical-maps have been collected for various species. Comparative techniques play a central role in investigating the adaptive significance of organismal traits and revealing evolutionary relations among organisms by comparing these biological data. This dissertation presents two efficient comparative analysis' tools used in comparative genomics and comparative optical-map study, respectively. 
A complete genome sequence of an organism can be viewed as its ultimate genetic map, in the sense that the heritable information are encoded within the DNA and the order of nucleotides along chromosomes is known. Comparative genomics can be applied to find functional sites by comparing genetic maps. Comparing vertebrate genomes requires efficient cross-species sequence alignment programs. The first tool introduced in this thesis is COMBAT (Clean Ordered Mer-Based Alignment Tool), a new mer-based method which can search rapidly for highly similar translated genomic sequences using the stable-marriage algorithm (SM) as an alignment filter. In experiments COMBAT is applied to comparative analysis between yeast genomes, and between the human genome and the recently published bovine genome. The homologous blocks identified by COMBAT are comparable with the alignments produced by BLASTP and BLASTZ. 
When genetic maps are not available, other genomic maps, including optical-maps, can be constructed. An optical map is an ordered enumeration of the restriction sites along with the estimated lengths of the restriction fragments between consecutive restriction sites. CAPO (Comparative Analysis and Phylogeny with Optical-Maps), introduced as a second technique in this thesis, is a tool for inferring phylogeny based on pairwise optical map comparison and bipartite graph matching. CAPO combines the stable matching algorithm with either the Unweighted Pair Group Method with Arithmetic Averaging (UPGMA) or the Neighbor-Joining (NJ) method for constructing phylogenetic trees. This new algorithm is capable of constructing phylogenetic trees in logarithmic steps and performs well in practice. Using optical maps constructed in silico and in vivo, our work shows that both UPGMA-flavored trees and the NJ-flavored trees produced by CAPO share substantial overlapping tree topology and are biologically meaningful.
Impact of Reduced Patient Life Expectancy on Potential Cancer Risks from Radiologic Imaging (2011)

The importance of radiation exposure in determining optimal imaging usage is much reduced for patients with markedly reduced life expectancies: Imaging justification and optimization criteria for patients with substantially reduced life expectancies should not necessarily be the same as for those with normal life expectancies.
Dichloro[1,1'-bis(diphenylphosphino)ferrocene]palladium(II): an effective catalyst for cross-coupling of secondary and primary alkyl Grignard and alkylzinc reagents with organic halides (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDichloro[1,1'-bis(diphenylphosphino)ferrocene]palladium(II): an effective catalyst for cross-coupling of secondary and primary alkyl Grignard and alkylzinc reagents with organic halidesTamio Hayashi, Mitsuo Konishi, Yuji Kobori, Makoto Kumada, Taiichi Higuchi, and Ken HirotsuCite this: J. Am. Chem. Soc. 1984, 106, 1, 158–163Publication Date (Print):January 1, 1984Publication History Published online1 May 2002Published inissue 1 January 1984https://pubs.acs.org/doi/10.1021/ja00313a032https://doi.org/10.1021/ja00313a032research-articleACS PublicationsRequest reuse permissionsArticle Views8790Altmetric-Citations696LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Early-life risk factors and the development of Alzheimer’s disease (2000)

The early-life childhood and adolescent environment is associated with the risk of AD.
Highly Efficient Ruthenium Catalysts for the Formation of Tetrasubstituted Olefins via Ring-Closing Metathesis (2007)

[reaction: see text] A series of ruthenium-based metathesis catalysts with N-heterocyclic carbene (NHC) ligands have been prepared in which the N-aryl groups have been changed from mesityl to mono-ortho-substituted phenyl (e.g., tolyl). These new catalysts offer an exceptional increase in activity for the formation of tetrasubstituted olefins via ring-closing metathesis (RCM), while maintaining high levels of activity in ring-closing metathesis (RCM) reactions that generate di- and trisubstituted olefins.
Quantitation of calcitonin gene‐related peptide mrna and neuronal cell death in facial motor nuclei following axotomy and 633 nm low power laser treatment (2002)

These findings demonstrate that 633 nm laser light upregulates CGRP mRNA and support the theory that laser irradiation increases the rate of regeneration, target reinnervation, and neuronal survival of the axotomized neuron.
Efficient Yb:KGW lasers end-pumped by high-power diode bars (2006)

The generation of 12.4 W of output power with optical-to-optical conversion efficiency of 47% and slope efficiency of 74% is demonstrated in Yb:KGW laser end-pumped with high-power diode bars. Thermal-lensing and laser tuning has been investigated.
Single current sensor technique in the DC link of three-phase PWM-VS inverters: a review and a novel solution (1997)

A review of the existing methods to determine the output currents in a pulsewidth modulation voltage-source (PWM-VS) inverter using a single current sensor in the DC link is presented, and a novel solution is proposed. The unique arrangement of the DC link allows full protection of the inverter from short circuits and overloads. Also, a new method of sampling the DC-link current is described that produces true values of the output currents at the centers of switching intervals. Results of investigation of an experimental setup have shown that full protection of the inverter has been accomplished and the output currents can accurately be determined within the whole operating area.
Nucleophilic-type radical cyclizations of indoles: conversion of 2-cyano 3-substituted indoles to spiro-annelated indolines and tetrahydrocarbazolones (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNucleophilic-type radical cyclizations of indoles: conversion of 2-cyano 3-substituted indoles to spiro-annelated indolines and tetrahydrocarbazolonesChau Chen Yang, Han Ting Chang, and Jim Min FangCite this: J. Org. Chem. 1993, 58, 11, 3100–3105Publication Date (Print):May 1, 1993Publication History Published online1 May 2002Published inissue 1 May 1993https://pubs.acs.org/doi/10.1021/jo00063a032https://doi.org/10.1021/jo00063a032research-articleACS PublicationsRequest reuse permissionsArticle Views806Altmetric-Citations36LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
V(D)J recombination in mammalian cell mutants defective in DNA double-strand break repair. (1993)

V(D)J recombination has been examined in several X-ray-sensitive and double-strand break repair-deficient Chinese hamster cell mutants. Signal joint formation was affected in four mutants (xrs 5, XR-1, V-3, and XR-V9B cells, representing complementation groups 1 through 4, respectively) defective in DNA double-strand break rejoining. Among these four, V-3 and XR-V9B were the most severely affected. Only in V-3 was coding joint formation also affected. Ataxia telangiectasia-like hamster cell mutants (V-E5 and V-G8), which are normal for double-strand break repair but are X ray sensitive, were normal for all aspects of the V(D)J recombination reaction, indicating that X-ray sensitivity is not the common denominator but that the deficiency in double-strand break repair appears to be. The abnormality at the signal joints consisted of an elevated incidence of nucleotide loss from each of the two signal ends. Interestingly, in complementation groups 1 (xrs 5) and 2 (XR-1), signal joint formation was within the normal range under some transfection conditions. This suggests that the affected gene products in these two complementation groups are not catalytic components. Instead, they may be either secondary or stochiometric components involved in the later stages of both the V(D)J recombination reaction and double-strand break repair. The fact that such factors can affect the precision of the signal joint has mechanistic implications for V(D)J recombination.
Part I: Modeling image curves using invariant 3-D object curve models-a path to 3-D recognition and shape estimation from image contours (1994)

This paper and its companion are concerned with the problems of 3-D object recognition and shape estimation from image curves using a 3-D object curve model that is invariant to affine transformation onto the image space, and a binocular stereo imaging system. The objects of interest here are the ones that have markings (e.g., characters, letters, special drawings and symbols, etc.) on their surfaces. The 3-D curves on the object are modeled as B-splines, which are characterized by a set of parameters (the control points) from which the 3-D curve can be totally generated. The B-splines are invariant under affine transformations. That means that the affine projected object curve onto the image space is a B-spline whose control points are related to the object control points through the affine transformation. Part I deals with issues relating to the curve modeling process. In particular, the authors address the problems of estimating the control points from the data curve, and of deciding on the "best" order B-spline and the "best" number of control points to be used to model the image or object curve(s). A minimum mean-square error (mmse) estimation technique which is invariant to affine transformations is presented as a noniterative, simple, and fast approach for control point estimation. The "best" B-spline is decided upon using a Bayesian selection rule. Finally, we present a matching algorithm that allocates a sample curve to one of p prototype curves when the sample curve is an a priori unknown affine transformation of one of the prototype curves stored in the data base. The approach is tried on a variety of images of real objects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Induced systemic resistance against three foliar diseases of Agrostis stolonifera by (2R,3R)‐butanediol or an isoparaffin mixture (2010)

Induced systemic resistance (ISR) is a type of plant defence mechanism typically activated by non‐pathogenic root‐associated micro‐organisms and systemic priming of gene expression in response to subsequent pathogen challenge. ISR was found to be activated by PC1, a mixture of food‐grade synthetic isoparaffins and (2 R ,3 R )‐butanediol, a volatile organic compound produced by bacteria. In controlled environment tests, application of PC1 or (2 R ,3 R )‐butanediol to the soil reduced the diseased leaf area of Agrostis stolonifera by 20–40% for the fungal pathogens, Microdochium nivale , Rhizoctonia solani or Sclerotinia homoeocarpa compared to the water control. In A. stolonifera , expression of the jasmonate synthesis‐related genes, AsAOS1 , encoding an allene oxide synthase, and AsOPR4 , encoding a 12‐oxo‐phytodienoic acid reductase, and expression of a pathogenesis‐related protein gene, AsGns5 , encoding an acidic β ‐1,3‐glucanase, were primed for increased expression by PC1 or (2 R ,3 R )‐butanediol when M. nivale was inoculated 7 days later. However, the compounds differed in their ability to induce expression prior to pathogen challenge. PC1 induced AsAOS1 expression upon treatment, whereas (2 R ,3 R )‐butanediol induced expression of AsOPR4 and AsGns5 upon treatment. These results indicate that both (2 R ,3 R )‐butanediol and PC1 can produce ISR in A. stolonifera but may do so through different mechanisms.
Morphological and biochemical characterization of a human liver in a uPA‐SCID mouse chimera†‡ (2005)

A small animal model harboring a functional human liver cell xenograft would be a useful tool to study human liver cell biology, drug metabolism, and infections with hepatotropic viruses. Here we describe the repopulation, organization, and function of human hepatocytes in a mouse recipient and the infections with hepatitis B virus (HBV) and hepatitis C virus (HCV) of the transplanted cells. Homozygous urokinase plasminogen activator (uPA)-SCID mice underwent transplantation with primary human hepatocytes, and at different times animals were bled and sacrificed to analyze plasma and liver tissue, respectively. The plasma of mice that were successfully transplanted contained albumin and an additional 21 human proteins. Liver histology showed progressive and massive replacement of diseased mouse tissue by human hepatocytes. These cells were accumulating glycogen but appeared otherwise normal and showed no signs of damage or death. They formed functional bile canaliculi that connected to mouse canaliculi. Besides mature hepatocytes, human hepatic progenitor cells that were differentiating into mature hepatocytes could be identified within liver parenchyma. Infection of chimeric mice with HBV or HCV resulted in an active infection that did not alter the liver function and architecture. Electron microscopy showed the presence of viral and subviral structures in HBV infected hepatocytes. In conclusion, human hepatocytes repopulate the uPA(+/+)-SCID mouse liver in a very organized fashion with preservation of normal cell function. The presence of human hepatic progenitor cells in these chimeric animals necessitates a critical review of the observations and conclusions made in experiments with isolated "mature" hepatocytes. Supplementary material for this article can be found on the HEPATOLOGY website (http://www.interscience.wiley.com/jpages/0270-9139/suppmat/index.html).
Eicosapentaenoic acid reduces membrane fluidity, inhibits cholesterol domain formation, and normalizes bilayer width in atherosclerotic-like model membranes (2016)

Cholesterol crystalline domains characterize atherosclerotic membranes, altering vascular signaling and function. Omega-3 fatty acids reduce membrane lipid peroxidation and subsequent cholesterol domain formation. We evaluated non-peroxidation-mediated effects of eicosapentaenoic acid (EPA), other TG-lowering agents, docosahexaenoic acid (DHA), and other long-chain fatty acids on membrane fluidity, bilayer width, and cholesterol domain formation in model membranes. In membranes prepared at 1.5:1 cholesterol-to-phospholipid (C/P) mole ratio (creating pre-existing domains), EPA, glycyrrhizin, arachidonic acid, and alpha linolenic acid promoted the greatest reductions in cholesterol domains (by 65.5%, 54.9%, 46.8%, and 45.2%, respectively) compared to controls; other treatments had modest effects. EPA effects on cholesterol domain formation were dose-dependent. In membranes with 1:1 C/P (predisposing domain formation), DHA, but not EPA, dose-dependently increased membrane fluidity. DHA also induced cholesterol domain formation without affecting temperature-induced changes in-bilayer unit cell periodicity relative to controls (d-space; 57Å-55Å over 15-30°C). Together, these data suggest simultaneous formation of distinct cholesterol-rich ordered domains and cholesterol-poor disordered domains in the presence of DHA. By contrast, EPA had no effect on cholesterol domain formation and produced larger d-space values relative to controls (60Å-57Å; p<0.05) over the same temperature range, suggesting a more uniform maintenance of lipid dynamics despite the presence of cholesterol. These data indicate that EPA and DHA had different effects on membrane bilayer width, membrane fluidity, and cholesterol crystalline domain formation; suggesting omega-3 fatty acids with differing chain length or unsaturation may differentially influence membrane lipid dynamics and structural organization as a result of distinct phospholipid/sterol interactions.
Mitochondrial dysfunction and apoptosis in neurodegenerative diseases (2006)

近年，脳虚血，アルツハイマー病およびパーキンソン病などの神経脱落疾患においてアポトーシスが関与することが見いだされ，病態機構の解明ならびに新しい治療法を開発するうえで，中枢神経系のアポトーシスの役割ならびにその発現制御機構の解明が重要な課題と考えられている．アポトーシスの実行には，カスパーゼと呼ばれるプロテアーゼの連鎖的活性化が中心的役割を果たしており，その活性化に，細胞膜に存在する細胞死受容体，ミトコンドリアおよび小胞体を介するシグナル経路の関与が知られている．本総説では，筆者らの成果を中心に，脳虚血-再灌流障害およびアルツハイマー病におけるアポトーシスとミトコンドリア機能変化との関連について述べた．脳虚血-再灌流障害に関しては，脳の主要グリア細胞であるアストロサイトにおいて，インビボ脳虚血-再灌流時の細胞外Ca2+濃度変化を反映するパラドックス負荷により遅発性アポトーシスが発現することを示し，本アポトーシスに，活性酸素の産生増加，ミトコンドリアからのチトクロムc遊離ならびにカスパーゼ-3活性化といったミトコンドリア機能変化によるアポトーシスシグナル経路の活性化が関与することを示した．本アポトーシスに対して，cGMP-ホスホジエステラーゼ阻害薬，cGMPアナログおよび一酸化窒素産生薬は，cGMP依存性プロテインキナーゼを介するミトコンドリア膜透過性遷移孔抑制作用により保護効果を示す．また，アルツハイマー病に関しては，神経細胞において，ミトコンドリア内におけるアミロイドβタンパク（Aβ）とAβ結合アルコール脱水素酵素（ABAD）との相互作用が，チトクロムc酸化酵素活性，ATP産生，ミトコンドリア膜電位の低下といったミトコンドリア障害を引き起こし，アポトーシスを誘導することを示した．これらの知見は，ミトコンドリアの機能異常が脳虚血-再灌流障害およびアルツハイマー病におけるアポトーシスの発現において重要な働きをもつことを示唆する．
Excise, Ablate or Observe: The Small Renal Mass Dilemma—A Meta-Analysis and Review (2008)

Nephron sparing surgery, ablation and surveillance are viable strategies for small renal masses based on short-term and intermediate term oncological outcomes. However, a significant selection bias exists in the application of these techniques. While long-term data have demonstrated durable outcomes for nephron sparing surgery, extended oncological efficacy is lacking for ablation and surveillance strategies. The extent to which treatment alters the natural history of small renal masses is not yet established.
Expression of NTPDase1 and NTPDase2 in murine kidney: relevance to regulation of P2 receptor signaling (2005)

The regulation of renal function by extracellular nucleotides encompasses alterations in glomerular hemodynamics, microvascular function, tubuloglomerular feedback, tubular transport, cell growth or apoptosis, and transport of water and solutes in the medullary collecting duct. Nearly all cells can release ATP or other nucleotides that are then rapidly hydrolyzed in the extracellular milieu. However, little information is available on the cellular expression of ectoenzymes that hydrolyze extracellular nucleotides within the kidney. Nucleoside triphosphate diphosphohydrolases (NTPDases) are plasma membrane-bound ectonucleotidases. NTPDase1 has identity with CD39, a B lymphocyte activation marker, and hydrolyzes extracellular ATP and ADP to AMP within the vasculature, whereas NTPDase2/CD39L(ike)1 preferentially converts ATP to ADP outside of blood vessels. Using immunohistochemical and in situ hybridization approaches, we localized the protein and mRNA of NTPDase1 and 2 in murine renal tissues. In the renal cortex, NTPDase1 is expressed by vascular smooth muscle cells and endothelium in interlobular arteries, afferent glomerular arterioles, and peritubular capillaries. In the inner medulla, NTPDase1 is expressed in ascending thin limbs of Henle's loop, ducts of Bellini, and in the pelvic wall. In contrast, NTPDase2 is expressed in Bowman's capsule, glomerular arterioles, adventitia of blood vessels, and pelvic wall. Thus the distribution patterns of NTPDases have parallels to the known distribution of P2 receptors within the kidney. NTPDases may modulate regulatory effects of ATP and degradation products within the vasculature and other sites and thereby potentially influence physiological as well as multiple pathological events in the kidney.
What is the shape of pores in natural rocks? (2002)

The geometry of the internal space of porous media determines transport properties at all scales. We demonstrate an experimental scheme to quantify the body-to-throat ratio and the shape of the pores through direct measurements of geometrical quantities. We used a constant-rate mercury injection measurement to obtain the throat size and the pore-body volume, and an NMR method (DDIF) to obtain the pore size distribution in a Berea sandstone. This approach uniquely identifies the pore throats and bodies and enables a quantification of their sizes. Our results show that the pore bodies in Berea sandstone is likely to be described by a very much elongated cavity.
Friction effects on force measurements with an atomic force microscope (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFriction effects on force measurements with an atomic force microscopeJan H. Hoh and Andreas EngelCite this: Langmuir 1993, 9, 11, 3310–3312Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/la00035a089https://doi.org/10.1021/la00035a089research-articleACS PublicationsRequest reuse permissionsArticle Views717Altmetric-Citations119LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts