gebhart/patrepeval huggingface dataset:
Identification of large rearrangements in cancer genomes with barcode linked reads (2017)

Large genomic rearrangements involve inversions, deletions and other structural changes that span Megabase segments of the human genome. This category of genetic aberration is the cause of many hereditary genetic disorders and contributes to pathogenesis of diseases like cancer. We developed a new algorithm called ZoomX for analysing barcode-linked sequence reads-these sequences can be traced to individual high molecular weight DNA molecules (>50 kb). To generate barcode linked sequence reads, we employ a library preparation technology (10X Genomics) that uses droplets to partition and barcode DNA molecules. Using linked read data from whole genome sequencing, we identify large genomic rearrangements, typically greater than 200kb, even when they are only present in low allelic fractions. Our algorithm uses a Poisson scan statistic to identify genomic rearrangement junctions, determine counts of junction-spanning molecules and calculate a Fisher's exact test for determining statistical significance for somatic aberrations. Utilizing a well-characterized human genome, we benchmarked this approach to accurately identify large rearrangement. Subsequently, we demonstrated that our algorithm identifies somatic rearrangements when present in lower allelic fractions as occurs in tumors. We characterized a set of complex cancer rearrangements with multiple classes of structural aberrations and with possible roles in oncogenesis.
<title>Generalized sampling theory and applications to multiresolutions and wavelets of L<formula><inf><roman>2</roman></inf></formula></title> (1993)

We use approximation theory to generalize the classical sampling procedure of Shannon. We give a link between this theory and the theory of wavelet transforms. As an application, we give a general method for constructing scaling and wavelet functions with specifiable properties.
UN 장애인권리협약 이후 완전통합교육의 입장에서 바라본 독일의 공동체학교의 특성과 시사점 (2018)

연구목적: 본 연구의 목적은 UN 장애인권리협약 이후 독일이 어떠한 방법으로 완전통합교육을 실현해 나가는지를 알아보고자 하며, 그에 대한 개혁모델로서 공동체학교를 다루고 있다. 연구방법: 본 연구는 문헌연구로서 UN 장애인권리협약 이후의 독일의 통합교육현황 및 변화, 독일의 교육개혁의 방향 그리고 완전통합교육 입장에서 바라본 공동체학교의 특성과 시사점을 제시한다. 연구결과: 3월 30일 협약에 서명한 독일은 완전통합교육 요구에 직면하였으며, 이후 통합교육을 받는 비율은 꾸준히 증가하는 추세를 보이고 있다. 그러나 그러한 양적 수치와 별개로 그들은 기존 학제의 문제점을 지적하고 있다. 이에 독일은 학제개혁으로서 조기에 학생들을 계열별로 분리시키기보다는 함께 한 학교에서 교육받는 방향을 추진하고 있다. 특히 공동체학교는 기존 학교 간 합병을 기초로 한 2010년 이후 추진되고 있는 대표적인 개혁 모델로서 완전통합교육의 이념을 바탕으로 한다. 결론: 통합교육은 학교개혁과 함께 이루어질 때 그 효율성이 극대화된다. 또한 교육개혁의 연장선에서 추진되고 있는 독일 공동체학교의 통합교육 적용사례는 우리에게 하나의 단초가 될 수 있을 것으로 기대한다.
驰骋数字办公平台,提高商用计算应用 戴尔以OptiPlex GX520／620商用台式机诠释英特尔“数字办公”新理念 (2005)

从诞生的那一天起,商用计算就面临着稳定性、可 管理性及安全性等诸多挑战。今天,随着应用领域的不 断拓展与应用程度的曰趋深化,这些挑战正变得越来越 严峻——企业如何确保灵活地应对各种变化,以保持竞 争优势;如何让全球化、跨地域的员工通过计算和通信 技术实现无缝协作;如何应对黑客、病毒或者其它IT攻 击,以保障网络连接和内部数据的安全——都成为亟待 解决的问题。
ChemInform Abstract: Ring‐Closing Metathesis Strategy to Unsaturated γ‐ and δ‐Lactones: Synthesis of Hydroxyethylene Isostere for Protease Inhibitors. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Peptide YY3-36 and glucagon-like peptide-1 in functional dyspepsia. Secretion and role in symptom generation (2015)

In epigastric pain syndrome, postprandial insulin secretion seems to be increased. Neither GLP-1 nor PYY3-36 secretion is altered in functional dyspepsia, but postprandial GLP-1 secretion seems to correlate with nausea and PYY3-36 to the sensation of fullness, and therefore, these hormones might be involved in symptom generation.
A VTK Algorithm for the Computation of the Hausdorff Distance (2011)

The Hausdorff distance is a measure of the distance between sets of points. There are many advantages to using this metric compared to other similarity measures. This document describes a VTK class for computing the Hausdorff Distance between two sets of points. The main contribution, compared to other implementations, lies in the definition of the distance not only to the closest point but to the closest point in the represented surface, which yields an accurate measure even between undersampled surfaces. This is achieved by implementing a point-to-cell distance instead of a point-to-point. Furthermore, a plugin for ParaView was implemented, which is also available with the code. After introducing the interest of this distance, the VTK code is explained and illustrated with some examples.
UNBS3157, a new amonafide derivative with improved in vivo efficacy and decreased toxicity (2006)

Abstract 1105
Strategies to Discover Unexpected Targets for Drugs Active at G Protein–Coupled Receptors (2011)

G protein-coupled receptors (GPCRs) are an evolutionarily conserved family of signaling molecules comprising approximately 2% of the human genome; this receptor family remains a central focus in basic pharmacology studies and drug discovery efforts. Detailed studies of drug action at GPCRs over the past decade have revealed existing and novel ligands that exhibit polypharmacology-that is, drugs with activity at more than one receptor target for which they were designed. These "off-target" drug actions can be a liability that causes adverse side effects; however, in several cases, drugs with less selectivity demonstrate better clinical efficacy. Here we review physical screening and cheminformatic approaches that define drug activity at the GPCR receptorome. In many cases, such profiling has revealed unexpected targets that explain therapeutic actions as well as off-targets underlying drug side effects. Such drug-receptor profiling has also provided new insights into mechanisms of action of existing drugs and has suggested directions for future drug development.
Ultrastructural modifications of intestinal and colonic mucosa induced by free or bound bile acids. (1981)

There is substantial evidence that bile acids may enhance the colon tumorigenesis induced by chemical carcinogens and that agents stimulating increased bile acid excretion may show similar promoting or enhancing activity. To test the premise that these agents might modify topographical ultrastructure of the small intestine and colon in the absence of carcinogens, rats were fed for 6 weeks on chemically defined diets containing 2% levels of three commercial bile acid sequestrants or 15% levels of wheat brain, cellulose, pectin, or alfalfa. Major qualitative and quantitative deviations from normal morphology were observed with each of the three sequestrants. Similar but less dramatic modifications occurred with diets containing alfalfa or pectin, both of which either "bind" bile acids in vitro or result in increased bile acid excretion. Bran and cellulose which neither "bind" bile acids nor increase their fecal excretion, were without significant effects on intestinal or colonic morphology. The morphological deviations observed with bile acid sequestrants were shown to be a direct response to free or bound bile acids by comparing the morphological modifications resulting from daily intracolonic infusions of free bile acids, sequestrant-bound bile acids, or the sequestrant alone.
Design, development and experiments of a high stroke-precision 2DoF (linear-angular) microsystem (2006)

This paper presents the design, the development and the experiments on a two degrees of freedom (2DoF) microsystem. The originality of the microsystem is its ability to do angular and linear motions independently with a very high stroke and a submicrometric precision. The target performances are first presented. Afterwards the stick-slip piezoelectric microactuators that are used are presented. Then, their integration inside the microsystem is detailed. Finally, results of experiments are given
Thermal-wave radar (2010)

Using matched-filtering principles and linear frequency modulation a powerful photothermal depth-profilometry method is introduced. Unlike FD-PTR, in thermal-wave radar (TWR) the frequency of the optical excitation increases linearly within the chirp period, enabling the method to scan a depth range in a single iteration. Simulations and experimental results suggest a significant improvement in the dynamic range when using TWR instead of conventional PTR. Analytical solutions to the TWR heat diffusion problem for both opaque and transparent solids are provided.
Improved liposome immunomigration strip assay for alachlor determination (1995)

The feasibility of a simple, single-use immunomigration strip assay for alachlor was previously demonstrated. In the device, capillary action caused alachlor and alachlor-tagged, dye-containing liposomes to migrate through an anti-alachlor antibody zone, on a plastic-backed nitrocellulose strip, where competitive binding occurred. Unbound liposomes continued migration to a liposome capture zone, where they were quantified by densitometry. The amount of liposome-entrapped dye measured in this zone was directly proportional to the alachlor concentration in the sample. This report describes modifications to various components of the system, leading to improvement in the sensitivity of the assay to the point where the maximum contaminant level of alachlor, 2 ppb, can be easily detected. Measurements of liposome size and antibody cross-reactivity are also presented. The new methodology involves acid treatment of the antibody and the use of preincubation of the analyte-tagged liposomes, free analyte and anti-alachlor before initiating migration. This results in strong interactions between the anti-alachlor, liposome and strip such that liposomes that have bound to antibody do not migrate. This inhibition of migration is reversed by free analyte, which competes with the liposome for the available antibody binding sites. As in the previous assay, unbound liposomes migrate to a capture zone where they can be quantified, and the color intensity of this zone is directly proportional to the amount of analyte present. This technique produces an assay capable of detecting alachlor at levels down to 1 ppb.
Identity management and trusted interaction in Internet and mobile computing (2013)

The convergence of the Internet and mobile computing enables personalised access to online services anywhere and anytime. This potent access capability creates opportunities for new business models which stimulates vigorous investment and rapid innovation. Unfortunately, this innovation also produces new vulnerabilities and threats, and the new business models also create incentives for attacks, because criminals will always follow the money. Unless the new threats are balanced with appropriate countermeasures, growth in the Internet and mobile services will encounter painful setbacks. Security and trust are two fundamental factors for sustainable development of identity management in online markets and communities. The aim of this study is to present an overview of the central aspects of identity management in the Internet and mobile computing with respect to security and trust.
Accessibility evaluation based on machine learning technique (2006)

Presentation documents are used in several situations. However, there is no tool to sufficiently check the accessibility level of a presentation document. Traditional rule-based checking has limitations in checking semantic criteria. This paper describes a new approach to evaluate the accessibility of presentation documents using machine learning with a model built from features of a presentation's appearance. A prototype system was implemented, and an exploratory experiment was conducted.
Retinal damage in macaque after white light exposures lasting ten minutes to twelve hours. (1989)

We induced photochemical damage in small parts of the retinas of anesthetized macaques after light exposures of varying intensity, lasting between 10 min and 12 hr. Damage was assessed both with funduscopy and densitometry at several periods after exposure. Damage was most extensive 2 days post-exposure, with similar thresholds for both methods. Reciprocity between exposure time and irradiance was found for all exposures at a threshold irradiant dose of 230 J/cm2. This is in good agreement with part of the literature data on monkeys, yet contradicts another report (Sykes et al) in which a much lower threshold dose was found. The latter data probably concern a different class of damage. It remains unclear what critical factors distinguish the two classes. Observations more than 70 days post-exposure show a divergence between funduscopic and densitometric thresholds. Although the appearance of funduscopic lesions had changed, the threshold dose remained 230 J/cm2. Densitometry showed full recovery of the amount of visual pigment for doses below 600 J/cm2.
p38α Mitogen-Activated Protein Kinase Is Activated by CD28-Mediated Signaling and Is Required for IL-4 Production by Human CD4+CD45RO+ T Cells and Th2 Effector Cells (1999)

Abstract T cell proliferation and cytokine production usually require stimulation via both the TCR/CD3 complex and the CD28 costimulatory receptor. Using purified human CD4+ peripheral blood T cells, we show that CD28 stimulation alone activates p38α mitogen-activated protein kinase (p38α). Cell proliferation induced by CD28 stimulation alone, a response attributed to CD4+CD45RO+ memory T cells, was blocked by the highly specific p38 inhibitors SB 203580 (IC50 = 10–80 nM) and RWJ 67657 (IC50 = 0.5–4 nM). In contrast, proliferation induced by anti-CD3 plus anti-CD28 mAbs was not blocked. Inhibitors of p38 also blocked CD4+ T cell production of IL-4 (SB 203580 IC50 = 20–100 nM), but not IL-2, in response to CD3 and CD28 stimulation. IL-5, TNF-α, and IFN-γ production were also inhibited, but to a lesser degree than IL-4. IL-4 production was attributed to CD4+CD45RO+ T cells, and its induction was suppressed by p38 inhibitors at the mRNA level. In polarized Th1 and Th2 cell lines, SB 203580 strongly inhibited IL-4 production by Th2 cells (IC50 = 10–80 nM), but only partially inhibited IFN-γ and IL-2 production by Th1 cells (&amp;lt;50% inhibition at 1 μM). In both Th1 and Th2 cells, CD28 signaling activated p38α and was required for cytokine production. These results show that p38α plays an important role in some, but not all, CD28-dependent cellular responses. Its preferential involvement in IL-4 production by CD4+CD45RO+ T cells and Th2 effector cells suggests that p38α may be important in the generation of Th2-type responses in humans.
Overcoming technical variation and biological variation in quantitative proteomics (2003)

Quantitative proteomics investigates physiology at the molecular level by measuring relative differences in protein expression between samples under different experimental conditions. A major obstacle to reliably determining quantitative changes in protein expression is to overcome error imposed by technical variation and biological variation. In drug discovery and development the issue of biological variation often rises in concordance with the developmental stage of research, spanning from in vitro assays to clinical trials. In this paper we present case studies to raise awareness to the issues of technical variation and biological variation and the impact this places on applying quantitative proteomics. We defined the degree of technical variation from the process of two-dimensional electrophoresis as 20-30% coefficient of variation. On the other hand, biological variation observed experiment-to-experiment showed a broader degree of variation depending upon the sample type. This was demonstrated with case studies where variation was monitored across experiments with bacteria, established cell lines, primary cultures, and with drug treated human subjects. We discuss technical variation and biological variation as key factors to consider during experimental design, and offer insight into preparing experiments that overcome this challenge to provide statistically significant outcomes for conducting quantitative proteomic research.
ChemInform Abstract: A Simple and Direct Method for Converting Thioamides into Thioesters. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Multimedia document models-sealed fate or setting out for new shores? (2003)

Existing multimedia document models like HTML, MHEG, SMIL and HyTime lack appropriate modeling primitives to fit the needs of next generation multimedia applications which bring up requirements like reusability of multimedia content in different presentations and contexts, and adaptation to user preferences. We motivate and present new requirements stemming from advanced multimedia applications and the resulting consequences for multimedia document models. Along these requirements, we discuss HTML, HyTime, MHEG, SMIL, and ZyX, a new model that has been developed with special focus on reusability and adaptation. The analysis and comparison of the models show the limitations of existing models, point the way to the need for new flexible multimedia document models, and throw light on the many implications on authoring systems, multimedia content management and presentation.
Device model approximation using 2/sup N/ trees (1990)

The application of 2/sup N/ trees to device model approximation is described. The domain of the device model function is partitioned using a 2/sup N/ tree, with smaller partitions where the function is more nonlinear. The function value associated with each corner of each partition is precomputed, and the function is evaluated by a given point by interpolation over the smallest partition that includes that point. This technique has the advantage that highly nonlinear functions can be modeled with modest space and time requirements. Exponential functions, such as the subthreshold behavior of FETs, can be accurately modeled. Accuracy levels of 1% are possible down to currents of 10/sup -11/ A. Table generation time is small; it is only a few minutes for a MOSFET model including subthreshold effects. This algorithm is especially suited for application to a hardware-accelerated device model evaluator. The design of a prototype that is capable of performing a device model evaluation of a SPICE level-2 model including subthreshold effects in 1 mu s is described. Less detailed models, such as timing simulator models, can be evaluated in as little as 0.2 mu s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Microtubule Structure at Improved Resolution (2001)

Microtubule architecture can vary with eukaryotic species, with different cell types, and with the presence of stabilizing agents. For in vitro assembled microtubules, the average number of protofilaments is reduced by the presence of sarcodictyin A, epothilone B, and eleutherobin (similarly to taxol) but increased by taxotere. Assembly with a slowly hydrolyzable GTP analogue GMPCPP is known to give 96% 14 protofilament microtubules. We have used electron cryomicroscopy and helical reconstruction techniques to obtain three-dimensional maps of taxotere and GMPCPP microtubules incorporating data to 14 Å resolution. The dimer packing within the microtubule wall is examined by docking the tubulin crystal structure into these improved microtubule maps. The docked tubulin and simulated images calculated from “atomic resolution” microtubule models show tubulin heterodimers are aligned head to tail along the protofilaments with the β subunit capping the microtubule plus end. The relative positions of tubulin dimers in neighboring protofilaments are the same for both types of microtubule, confirming that conserved lateral interactions between tubulin subunits are responsible for the surface lattice accommodation observed for different microtubule architectures. Microtubules with unconventional protofilament numbers that exist in vivo are likely to have the same surface lattice organizations found in vitro. A curved “GDP” tubulin conformation induced by stathmin-like proteins appears to weaken lateral contacts between tubulin subunits and could block microtubule assembly or favor disassembly. We conclude that lateral contacts between tubulin subunits in neighboring protofilaments have a decisive role for microtubule stability, rigidity, and architecture.
Geofences on the Blockchain: Enabling Decentralized Location-Based Services (2018)

A decentralized ride-or carsharing application is among the early proposals of what smart contracts on blockchains may enable in the future. To facilitate use cases in the field of location-based services (LBS), smart contracts need to receive trustworthy positioning information, and be able to process them. We propose an approach on how geofences can be defined in smart contracts, and how supplied positions can be evaluated on whether they are contained in the geofence or not. The approach relies on existing location encoding systems like Geohashes and S2 cells that can transform polygons into a grid of cells. These can be stored in a smart contract to represent a geofence. An oracle run by a mobile network provider can submit network-based positioning information to the contract, that compares it with the geofence. We evaluate the location encoding systems on their ability to model city geofences and mobile network cell position estimates and analyze the costs associated with storing and evaluating received oracle-positions in an Ethereum-based smart contract implementation. Our results show that S2 encodings perform better than Geohashes, that the one-time cost of geofence definition corresponds linearly with the number of grid cells used, and that the evaluation of oracle-submitted locations does not incur high costs.
Supplementary Table 1 from Constitutive Short Telomere Length of Chromosome 17p and 12q but not 11q and 2p Is Associated with an Increased Risk for Esophageal Cancer (2023)

Supplementary Table 1 from Constitutive Short Telomere Length of Chromosome 17p and 12q but not 11q and 2p Is Associated with an Increased Risk for Esophageal Cancer
Prevention by Polyhydroxysteroids and Saponins ofAsterina pectiniferaof the Desquamation of Stratum Corneum Cells (2002)

Two polyhydroxysteroids and three steroidal saponins (pectiniosides A, B and C) were isolated as bioactive substances from Asterina pectinifera. These compounds inhibited the release of guinea-pig skin stratum corneum cells by 48-67% (control, 0%) at 2 mg/ml. It is suggested that the bioactivity of these compounds is connected with the remedial and preventive effects of an aqueous extract of A. pectinifera on rough human skin.