gebhart/patrepeval huggingface dataset:
Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming (2005)

We study the problem of reconstructing haplotype configurations from genotypes on pedigree data with missing alleles under the Mendelian law of inheritance and the minimum-recombination principle, which is important for the construction of haplotype maps and genetic linkage/association analyses. Our previous results show that the problem of finding a minimum-recombinant haplotype configuration (MRHC) is in general NP-hard. This paper presents an effective integer linear programming (ILP) formulation of the MRHC problem with missing data and a branch-and-bound strategy that utilizes a partial order relationship and some other special relationships among variables to decide the branching order. Nontrivial lower and upper bounds on the optimal number of recombinants are introduced at each branching node to effectively prune the search tree. When multiple solutions exist, a best haplotype configuration is selected based on a maximum likelihood approach. The paper also shows for the first time how to incorporate marker interval distance into a rule-based haplotyping algorithm. Our results on simulated data show that the algorithm could recover haplotypes with 50 loci from a pedigree of size 29 in seconds on a Pentium IV computer. Its accuracy is more than 99.8% for data with no missing alleles and 98.3% for data with 20% missing alleles in terms of correctly recovered phase information at each marker locus. A comparison with a statistical approach SimWalk2 on simulated data shows that the ILP algorithm runs much faster than SimWalk2 and reports better or comparable haplotypes on average than the first and second runs of SimWalk2. As an application of the algorithm to real data, we present some test results on reconstructing haplotypes from a genome-scale SNP dataset consisting of 12 pedigrees that have 0.8% to 14.5% missing alleles.
Detergents in Water Supplies (1956)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDetergents in Water SuppliesJames C. Vaughn and Ralph F. FalkenthalCite this: Ind. Eng. Chem. 1956, 48, 2, 241–245Publication Date (Print):February 1, 1956Publication History Published online1 May 2002Published inissue 1 February 1956https://doi.org/10.1021/ie50554a027RIGHTS & PERMISSIONSArticle Views160Altmetric-Citations1LEARN 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 (503 KB) Get e-Alerts
An <i>O</i> (log <i>n</i> ) expected rounds randomized byzantine generals protocol (1987)

Byzantine Generals protocols enable processes to broadcast messages reliably in the presence of faulty processes. These protocols are run in a system that consists of n processes, t of which are faulty. The protocols are conducted in synchronous rounds of message exchange. It is shown that, in the absence of eavesdropping, without using cryptography, for any ε > 0 and t = n /(3 + ε), there is a randomized protocol with O (log n ) expected number of rounds. If cryptographic methods are allowed, then, for ε > 0 and t = n /(2 + ε), there is a randomized protocol with O (log n ) expected number of rounds. This is an improvement on the lower bound of t + 1 rounds required for deterministic protocols, and on a previous result of t /log n expected number of rounds for randomized noncryptographic protocols.
A Practical Device for the Recovery of Silver and Prolongation of Life of Fixing Baths (1956)

Recovery of silver from fixing baths and consequent prolongation of the useful life of solution can be accomplished by simple electrolysis using currents of 150–175 ma. These methods are ineffective in an installation processing large quantities of film because silver deposited in the solution soon exceeds the recovery rate. Various physical-chemical expedients, combined with electrolysis, were tried, these being such as would allow the use of higher currents while preserving the integrity of the thiosulfate ion. These tests have led to the development of a small, flexible and efficient silver recovery unit which makes possible significant savings in chemicals and recovered silver.
Damage Assessment from Social Media Imagery Data During Disasters (2017)

Rapid access to situation-sensitive data through social media networks creates new opportunities to address a number of real-world problems. Damage assessment during disasters is a core situational awareness task for many humanitarian organizations that traditionally takes weeks and months. In this work, we analyze images posted on social media platforms during natural disasters to determine the level of damage caused by the disasters. We employ state-of-the-art machine learning techniques to perform an extensive experimentation of damage assessment using images from four major natural disasters. We show that the domain-specific fine-tuning of deep Convolutional Neural Networks (CNN) outperforms other state-of-the-art techniques such as Bag-of-Visual-Words (BoVW). High classification accuracy under both event-specific and cross-event test settings demonstrate that the proposed approach can effectively adapt deep-CNN features to identify the severity of destruction from social media images taken after a disaster strikes.
Introduction to Lambda (1983)

The bacteriophages form a diverse collection of viruses that multiply in bacterial cells. This book describes the variety called λ and some of its relatives, which multiply in Escherichia coli. Chapter 1 presents general characteristics of the λ group, and explains how λ came to be the subject of intensive study. The classical phages destroy their host cells by lysis. Lambda causes lysis too, but can also propagate in a form that permits joint multiplication of phage and host. Phages possessing this added potentiality are called temperate, in distinction from the broad class of intemperate or virulent species, which cannot reproduce without destroying their host cells. Lambda is also one of a few well known genetic elements, called episomes, that are able to multiply in the cell either autonomously or as part of the bacterial chromosome. In fact λ and the fertility agent F of E. coli are historical prototypes of the class. Campbell (1969) presents the comparative biology of episomes. For newcomers to phage research, Stent’s Molecular Biology of Bacterial Viruses (1963) can be recommended as a source book. THE LIFE CYCLE Lambda phage particles are about half protein and half DNA. Each contains one double-stranded DNA molecule encapsulated in an icosahedral head, 0.05 μ in diameter, from which projects a tubular tail, 0.15 μ long (Chapter 14). The DNA molecule is made from the usual four bases and weighs about 31 million daltons. Phage particles can be prepared in milligram quantities for analysis of various sorts. Lambda is...
Binding Properties of Insulin-Like Growth Factor Binding Protein-3 (IGFBP-3), IGFBP-3 N- and C-Terminal Fragments, and Structurally Related Proteins mac25 and Connective Tissue Growth Factor Measured Using a Biosensor (2002)

We measured the binding of IGF-I and IGF-II to recombinant human N-terminal [residues 1-97; recombinant human IGF-binding protein-3(1-97) (rhIGFBP-3(1-97))] and C-terminal (residues 98-264; rhIGFBP-3(98-264)) IGFBP-3 fragments and compared it with IGF binding to intact IGFBP-3 using biosensor analysis. Experiments were carried out in different configurations, either with binding protein or fragment immobilized or with IGF immobilized. These experiments showed that IGF-I and IGF-II bind to IGFBP-3 with affinities of 4-5 x 10(9) M(-1) and similar binding kinetics. The affinities of both rhIGFBP-3(1-97) and rhIGFBP-3(98-264) for IGF proteins were approximately 3 orders of magnitude less than that of full-length IGFBP-3. These results further support the concept that high affinity binding of IGF to IGF-binding proteins results from a two-site interaction of IGF with both the N- and C-terminal regions of the binding protein. Binding of insulin to IGFBP-3 and its N- and C-terminal fragments and of IGF-I and IGF-II to the structurally related proteins mac25 and connective tissue growth factor was also investigated. Weak insulin binding to full-length IGFBP-3 could be demonstrated in a few experiments, but we found that binding of IGF-I, IGF-II, and insulin to mac25 or connective tissue growth factor was below the detection limit of the biosensor instrument.
Advances in Boundary Elements (1989)

These proceedings review the latest developments in boundary element methods and point out new advances and future trends. Rapid progress in these methods and applications makes it essential to discuss these developments every year. The emphasis in these volumes is on engineering advances, applications in practical problems, new directions in boundary element research and fundamentals of the method. The volumes also include a series of invited lectures given by boundary element researchers at the forefront of advanced application and a few review lectures to summarize boundary element progress in a particular field.
CGS 35601 and its Orally Active Prodrug CGS 37808 as Triple Inhibitors of Endothelin-converting Enzyme-1, Neutral Endopeptidase 24.11, and Angiotensin-converting Enzyme (2004)

CGS 35601 is a potent triple inhibitor of endothelin-converting enzyme-1, neutral endopeptidase 24.11, and angiotensin-converting enzyme. It inhibited the activities of these three enzymes with IC50 values of 55, 2 and 22 nM, respectively. In conscious rats, CGS 35601 suppressed the big endothelin-1-induced pressor response by 82% and 72% at 30 and 120 minutes, respectively, following injection at a dose of 10 mg/kg, intravenously. At the same dose, CGS 35601 increased plasma atrial natriuretic peptide (ANP) immunoreactivity by 170% for up to 4 hours in conscious rats infused with ANP, and it inhibited the angiotensin I-induced pressor response by 74-94% within the first 2 hours after dosing. Similar in vivo activities were also observed with its orally active prodrug, CGS 37808. This compound blocked the big endothelin-1- induced pressor response by 71% and 67% at 30 and 120 minutes, respectively, after an oral dose of 10 mgEq/kg in conscious rats. It also increased plasma ANP immunoreactivity by 103% for up to 4 hours and inhibited the angiotensin I-induced pressor response by an average of 49% within the first 4 hours after the same dosing regimen. By suppressing the biosyntheses of endothelin-1 and angiotensin II, two potent vasoconstrictors, while simultaneously potentiating the circulating levels of ANP, a vasorelaxant and diuretic, CGS 35601 and CGS 37808 may represent novel agents for the treatment of cardiovascular and renal diseases.
Analysis of Nucleotide Sequence Variations by Solid-Phase Minisequencing (2003)

The Sanger dideoxy-nucleotide sequencing method has been simplified by a number of methodological improvements, such as the use of the polymerase chain reaction (PCR) technique for generating DNA templates in sufficient quantities for sequencing, the use of affinity-capture techniques for convenient and efficient purification of the PCR fragments for sequencing, the development of laboratory robots for carrying out the sequencing reactions, and the development of instruments for automatic on-line analysis of fluorescent products of the sequencing reactions. Despite these technical improvements, the requirement for gel electrophoretic separation remains an obstacle when sequence analysis of large numbers of samples are needed, as in DNA diagnosis, or in the analysis of sequence variation for genetic, evolutionary, or epidemiological studies.
Mutual repression between steroid and xenobiotic receptor and NF- B signaling pathways links xenobiotic metabolism and inflammation (2006)

While it has long been known that inflammation and infection reduce expression of hepatic cytochrome P450 (CYP) genes involved in xenobiotic metabolism and that exposure to xenobiotic chemicals can impair immune function, the molecular mechanisms underlying both of these phenomena have remained largely unknown. Here we show that activation of the nuclear steroid and xenobiotic receptor (SXR) by commonly used drugs in humans inhibits the activity of NF-kappaB, a key regulator of inflammation and the immune response. NF-kappaB target genes are upregulated and small bowel inflammation is significantly increased in mice lacking the SXR ortholog pregnane X receptor (PXR), thereby demonstrating a direct link between SXR and drug-mediated antagonism of NF-kappaB. Interestingly, NF-kappaB activation reciprocally inhibits SXR and its target genes whereas inhibition of NF-kappaB enhances SXR activity. This SXR/PXR-NF-kappaB axis provides a molecular explanation for the suppression of hepatic CYP mRNAs by inflammatory stimuli as well as the immunosuppressant effects of xenobiotics and SXR-responsive drugs. This mechanistic relationship has clinical consequences for individuals undergoing therapeutic exposure to the wide variety of drugs that are also SXR agonists.
Fusion of Yeast Protoplasts (1977)

Journal Article Fusion of Yeast Protoplasts Get access Masahiro Yamamoto, Masahiro Yamamoto The Institute of Applied Microbiology, The University of Tokyo, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Sakuzo Fukui Sakuzo Fukui The Institute of Applied Microbiology, The University of Tokyo, Tokyo, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 41, Issue 9, 1 September 1977, Pages 1829–1830, https://doi.org/10.1080/00021369.1977.10862772 Published: 01 September 1977 Article history Received: 04 July 1977 Published: 01 September 1977
Shared Cognitive–Emotional–Interactional Platforms: Markers and Conditions for Successful Interdisciplinary Collaborations (2015)

Given the growing centrality of interdisciplinarity to scientific research, gaining a better understanding of successful interdisciplinary collaborations has become imperative. Drawing on extensive case studies of nine research networks in the social, natural, and computational sciences, we propose a construct that captures the multidimensional character of such collaborations, that of a shared cognitive–emotional–interactional (SCEI) platform. We demonstrate its value as an integrative lens to examine markers of and conditions for successful interdisciplinary collaborations as defined by researchers involved in these groups. We show that (1) markers and conditions embody three different dimensions: cognitive, emotional, and interactional; (2) these dimensions are present in all networks, albeit to different degrees; (3) the dimensions are intertwined and mutually constitutive; and (4) they operate in conjunction with institutional conditions created by funders. We compare the SCEI platforms to available frame-works for successful interdisciplinary work.
Glutathione and ascorbic acid in spinach (<i>Spinacia oleracea</i>) chloroplasts. The effect of hydrogen peroxide and of Paraquat (1983)

The stroma of spinach chloroplasts contains ascorbic acid and glutathione at millimolar concentrations. [Reduced glutathione]/[oxidized glutathione] and [ascorbate]/[dehydroascorbate] ratios are high under both light and dark conditions and no evidence for a role of oxidized glutathione or dehydroascorbate in the dark-deactivation of fructose bisphosphatase could be obtained. Addition of H2O2 to chloroplasts in the dark decreases the above ratios, an effect that is reversed on illumination. Addition of Paraquat to illuminated chloroplasts caused a rapid oxidation of reduced glutathione and ascorbate, and apparent loss of dehydroascorbate. Paraquat rapidly inactivated fructose bisphosphatase activity, as assayed under physiological conditions.
<title>Content-based searching of multimedia databases using approximate digital signatures</title> (2002)

We propose the use of approximate digital signatures of selected multimedia feature vectors for fast content based retrieval in very large multimedia databases. We adapt and extend the Approximate Message Authentication Code (AMAC), introduced by some of the authors recently in the area of message authentication, to the multimedia searching problem. An AMAC is a binary signature with the ability to reflect changes in the message it represents. The hamming distance between two AMACs is used to measure the degree of the similarity between multimedia objects. We develop a method to compress AMAC signatures to create a direct lookup table that allows fast searching of a database. The color histogram is used as the example feature space to show how the signature is applied. Experimental results show that the performance of the proposed method is comparable with existing methods based on other popular metrics, but significantly decreases search time.
Dose-effects of 8-methoxypsoralen and UVA in cultured human lymphocytes (1978)

Cultures of human lymphocytes were incubated with 8-methoxypsoralen (8-MOP) and irradiated with long wave ultraviolet light (UVA). Subsequently the mitogenic response to PHA was determined by 3H-thymidine incorporation. The minimal effective dosages of drug and light for the partial suppression of lymphocyte PHA-responsiveness were found to be 0.1 microgram/ml 8-MOP and 0.5 J/cm2 UVA. While an increase in the concentration of 8-MOP revealed a comparatively small rise in phototoxicity, a marked inhibition of 3H-thymidine uptake was obtained by increasing the UVA dosage. Cell viability of non-stimulated lymphocytes was similarly affected by the combined treatment.
Reprocessing of flexible endoscopes and endoscopic accessories used in gastrointestinal endoscopy: Position Statement of the European Society of Gastrointestinal Endoscopy (ESGE) and European Society of Gastroenterology Nurses and Associates (ESGENA) – Update 2018 (2018)

This Position Statement from the European Society of Gastrointestinal Endoscopy (ESGE) and the European Society of Gastroenterology Nurses and Associates (ESGENA) sets standards for the reprocessing of flexible endoscopes and endoscopic devices used in gastroenterology. An expert working group of gastroenterologists, endoscopy nurses, chemists, microbiologists, and industry representatives provides updated recommendations on all aspects of reprocessing in order to maintain hygiene and infection control.
Contemporary application-domain taxonomies (1995)

In recent years it has become clear that application-independent techniques and tools must be supplemented with an application-specific approach. We begin to identify the foundations needed for application-specific software research by examining the role and nature of current application taxonomies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Catalytic Reactions Promoted by Homogeneous Catalysts Attached to Polystyrene Matrices. (1978)

Styrene-divinylbenzene resins have been functionalized with phosphine ligands and these phosphinated resins have been used to immobilize Rh(I), Ir(I), and Pd(O) catalysts. The selectivity of Rh(I)-catalyzed hydroformylations and the optical yields in styrene hydroformylations have been examined as a function of ligand loading and P/Rh ratios. The rates of Ir(I)-catalyzed hydrogenations of 1,5-cyclooctadienes and Pd(O)-catalyzed butadiene dimerization-methoxylations were studied. In all cases the resin-catalyzed reactions were compared to their homogeneously catalyzed analogs. All the results appear to be explained in terms of the influence of the resin matrix on metal-ligand equilibria which play important roles in the reaction mechanisms. (Author)
The Blood-Brain Barrier and Blood-Cerebral Spinal Fluid Barrier (2006)

An intact blood-brain barrier and normal production, circulation, and absorption of cerebrospinal fluid are critical for normal brain function. Minor disruptions of barrier function are without clinical consequences. Major disruptions accompany most significant acute brain injuries. The anatomic location of the blood-brain barrier is the endothelial cells of arterioles, capillaries, veins, and the epithelial cell surface of the choroid plexus. However, endothelial cells require the presence of glial cells to maintain barrier function. During cardiopulmonary bypass, several factors may result in a temporary disruption of the barrier; the most important are systemic inflammatory response and focal ischemia due to emboli. Lacking a lymphatic system, the brain depends on the circulation of cerebrospinal fluid to remove the products of metabolism, and the circulation of cerebrospinal fluid depends on a vascular systolic pulse wave to drive this fluid antegrade along the brain paravascular spaces. Although it is not possible to identify this paravascular space histologically, its presence is confirmed by tracer methods.
A few factors contributing to the mechanical strength of collagen fibres. (1975)

A knowledge of the influence of several factors on the stability and properties of collagen and preparations thereof precedes their industrial application. The results of such a study are reported in this paper. The mechanical properties of skin samples vary significantly with location and direction of cutting. The properties of isolated fibres from these locations, however, did not differ significantly, in a single animal. Collagen fibres from tendons and skins of several mammalian and other species exhibited under identical conditions of testing differences in their physical properties. The influence of factors like composition, shrinkage temperature, non-collagenous components, fibril width and age, on the properties is discussed individually. A slight increase in strength was observed in deaminated and deguanidinated collagen fibres while all the other treatments studied, viz. modification of side chains, crosslinking, tanning and irradiation with gamma-rays decreased the strength. An inverse correlation was observed between shrinkage temperature and strength of treated collagen fibres. The strength was also found to be influenced by the morphological structure of collagen. Irradiation with gamma-rays caused a reduction of not only the strength and shrinkage temperature of collagen but also caused severe destruction of the fibrillar structure at the X-ray and electronmicroscopic levels. The degradation was progressive with dosage. Non-hydrolytic scission of the polypeptide chains seemed to be responsible for the changes observed, which were also species specific.
A note on "On single-scanline camera calibration" [and reply] (1995)

In this correspondence, the single-scanline camera model proposed in the original paper (R. Horaud, R. Mohr and B. Lorecki, ibid., vol. 8, no. 1, p. 71-5, 1993) is modified to include a lens distortion coefficient. The authors say that, by this modification, the calibration approach presented will become more practical. The original authors accept that the improvement is sensible but say that the argument is not rigorous and suggest better approaches to some aspects.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Requirement of<i>NeuroD</i>for Photoreceptor Formation in the Chick Retina (2003)

The data suggest a specific and an essential role of neuroD in photoreceptor formation in the chick retina.