gebhart/patrepeval huggingface dataset:
Matching and indexing sequences of different lengths (1997)

Article Matching and indexing sequences of different lengths Share on Authors: Tolga Bozkaya Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OH Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OHView Profile , Nasser Yazdani Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OH Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OHView Profile , Meral Özsoyoğlu Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OH Department of Computer Engineering and Science, Case Western Reserve University, Cleveland, OHView Profile Authors Info & Claims CIKM '97: Proceedings of the sixth international conference on Information and knowledge managementJanuary 1997 Pages 128–135https://doi.org/10.1145/266714.266880Online:01 January 1997Publication History 48citation595DownloadsMetricsTotal Citations48Total Downloads595Last 12 Months15Last 6 weeks2 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Bayesian analysis of complex traits in pedigreed plant populations (2007)

A Bayesian approach to analyze complex traits is presented that can help plant eneticists and breeders in exploiting the marker and phenotypic data on pedigreed populations as available from ongoing breeding programs. The statistical model for the quantitative trait may include non-genetic and genetic components. The latter component can be divided into QTL on known marker linkage groups, major genes and a polygenic component. The full probability model, prior assumptions on model variables are presented and criterion for model selection and posterior inferences are given. Simulated data on a known pedigreed population structure of the EU project HiDRAS was used to illustrate the use of the Bayesian approach to analyze complex traits. It was shown that estimates for QTL parameters were more accurate when non-genetic factors were included in the model and when a polygenic component was included when not all linkage groups were analyzed simultaneously. The Bayesian approach has been implemented into the software package FlexQTL and allows plant breeders explore their pedigreed populations for segregating QTL alleles that are relevant in their breeding program.
Electromagnetic Response of Weyl Semimetals (2013)

It has been suggested recently, based on subtle field-theoretical considerations, that the electromagnetic response of Weyl semimetals and the closely related Weyl insulators can be characterized by an axion term θE·B with space and time dependent axion angle θ(r,t). Here we construct a minimal lattice model of the Weyl medium and study its electromagnetic response by a combination of analytical and numerical techniques. We confirm the existence of the anomalous Hall effect expected on the basis of the field theory treatment. We find, contrary to the latter, that chiral magnetic effect (that is, ground state charge current induced by the applied magnetic field) is absent in both the semimetal and the insulator phase. We elucidate the reasons for this discrepancy.
Interactions of a photoaffinity analog of GTP with the proteins of microtubules. (1977)

Tubulin dimers isolated from brain contain two GTP binding sites, a nonexchangeable site and an exchangeable site. To localize the exchangeable site, we used a photoaffinity analog of GTP, 8-azidoguanosine triphosphate (8-N3GTP), which supports tubulin polymerization in the absence of activating light. Photolysis of tubulin polymerized in the presence of 0.01 to 0.1 mM [beta, gamma-32P]8-N3GTP resulted in covalent incorporation of radioactivity only onto the beta monomer. Photolysis with 8-N3GTP also prevented any further repolymerization of the tubulin whereas like treatment in the presence of GTP had no effect. Preincubation of tubulin with GTP prevented photo-incorporation of [beta, gamma-32P]8-N3GTP whereas preincubation with ATP did not.
Promising efficacy and acceptable safety of venetoclax plus bortezomib and dexamethasone in relapsed/refractory MM (2017)

The antiapoptotic proteins BCL-2 and myeloid cell leukemia sequence 1 (MCL-1) promote multiple myeloma (MM) cell survival. Venetoclax is a selective, orally bioavailable small-molecule BCL-2 inhibitor; bortezomib can indirectly inhibit MCL-1. In preclinical studies, venetoclax enhanced bortezomib activity, suggesting that cotargeting of BCL-2 and MCL-1 could be an effective treatment strategy in myeloma. This phase 1b trial studied patients with relapsed/refractory MM receiving daily venetoclax (50-1200 mg per designated dose cohort; 800 mg in safety expansion) in combination with bortezomib and dexamethasone. A total of 66 patients were enrolled (54 in the dose-escalation cohorts and 12 in the safety expansion). Patients had received a median of 3 prior therapies (range, 1-13); 26 (39%) were refractory to prior bortezomib and 35 (53%) to lenalidomide; 39 (59%) had prior stem cell transplant. The combination was generally well tolerated, and common adverse events included mild gastrointestinal toxicities (diarrhea [46%], constipation [41%], and nausea [38%]) and grade 3/4 cytopenias (thrombocytopenia [29%] and anemia [15%]). The overall response rate (ORR) was 67% (44/66); 42% achieved very good partial response or better (≥VGPR). Median time to progression and duration of response were 9.5 and 9.7 months, respectively. ORR of 97% and ≥VGPR 73% were seen in patients not refractory to bortezomib who had 1 to 3 prior therapies. Patients with high <i>BCL2</i> expression had a higher ORR (94% [17/18]) than patients with low <i>BCL2</i> expression (59% [16/27]). This novel combination of venetoclax with bortezomib and dexamethasone has an acceptable safety profile and promising efficacy in patients with relapsed/refractory MM. This trial was registered at www.clinicaltrials.gov as #NCT01794507.
Attenuating Ischemia-Reperfusion Injury in Kidney Transplantation by Perfusing Donor Organs With siRNA Cocktail Solution (2016)

In conclusion, this is the first demonstration that perfusing donor organs with an siRNA cocktail solution can induce gene silencing in the kidney and prevent kidneys from extended cold I/R injury in kidney transplantation, highlighting the promise of the clinical application of siRNA-based therapies in the preservation of donor organs.
Growth of LNCaP human prostate cancer cells is stimulated by estradiol via its own receptor. (1995)

We report that growth of LNCaP human prostate cancer cells is significantly stimulated (up to 120% above control) by physiological estradiol (E2) concentrations. This growth increase appears to be comparable to that induced by either testosterone or dihydrotestosterone, as also reported by others. This paper presents novel illustrative evidence for estrogen-binding proteins and messenger RNA transcripts in LNCaP cells. In fact, 1) the reverse transcriptase-polymerase chain reaction system documented normal messenger RNA for estrogen receptors (ER); 2) the radioligand binding assay allowed the detection of high affinity, reduced capacity binding sites in both soluble and nuclear cell fractions; and 3) the immunocytochemical analysis showed a consistently intensive staining for both ER and progesterone receptors. Compared to other human estrogen-responsive mammary cancer cells, MCF7 and ZR75-1, ER expression in LNCaP cells was not significantly lower, as shown by levels of the ER transcripts, number of sites per cell, or femtomoles per mg DNA as well as the percentage and intensity of immunocytochemical staining. A relative estimate of ER expression obtained by matching LNCaP with another human prostate cancer cell line, PC3, always displayed significantly and consistently higher levels in LNCaP cells. The detection of relatively high type I ER content in either cell compartment of LNCaP cells was paralleled by a highly intensive staining for progesterone receptors. In addition, evidence that the synthetic androgen R1881 did not compete for type I binding of E2 and that any E2-induced growth was completely reversed by the pure antiestrogen ICI-182,780, but unaffected by the antiandrogen Casodex, clearly suggests that the biological response of LNCaP cells to E2 is mediated via its own receptor.
Tissue factor-positive microparticles in blood associated with coagulopathy in cancer (2007)

Editorial Focus: Tissue factor-positive microparticles in blood associated with coagulopathy in cancer -
Percussion drilling of metals using bursts of nanosecond pulses (2011)

The effect of ns bursting on percussion drilling of metal is investigated experimentally and analytically, and compared with the efficiency and quality of drilling using single ns pulses. Key advantages are demonstrated, correlating well with the results from a thermal theoretical model. The 1064 nm bursts contain up to 14 pulses of various pulse widths and spacing, and at frequencies of tens of MHz within the burst. The individual pulses have pulse widths of 10 to 200 ns, and up to 12 kW peak power. Burst repetition frequency is single shot to 500 kHz.
Interactions between LAS and nonionic surfactants (1985)

Abstract Physicochemical interactions between linear alkylbenzene sulfonate (LAS) and various linear alcohol nonionics (NI) have been investigated. The effect of adding nonionic to LAS on critical micelle concentration (cmc), surface tension, water hardness sensitivity and detergency performance depends on both hydrophobe and hydrophile structure. The addition of low levels of a lauryl range‐high EO nonionic surfactant significantly lowers cmc and causes the formation of micelles containing predominantly nonionic molecules. These mixed micelles improve hard water performance by acting as a sink for LAS and free calcium. Nonionic surfactant enhances LAS hard water performance by preventing the loss of LAS via Ca(LAS) 2 precipitation, not by its own soil removal capabilities. Nonionic surfactant acts as a micelle promotion agent, while LAS remains responsible for surface and interfacial properties.
Autosomal <i>P[ovo</i> <i>D1</i> <i>]</i> dominant female-sterile insertions in <i>Drosophila</i> and their use in generating germ-line chimeras (1993)

The 'dominant female-sterile' technique used to generate germ-line mosaics in Drosophila is a powerful tool to determine the tissue specificity (germ line versus somatic) of recessive female-sterile mutations as well as to analyze the maternal effect of recessive zygotic lethal mutations. This technique requires the availability of germ-line-dependent, dominant female-sterile (DFS) mutations that block egg laying but do not affect viability. To date only one X-linked mutation, ovoD1 has been isolated that completely fulfills these criteria. Thus the 'DFS technique' has been largely limited to the X-chromosome. To extend this technique to the autosomes, we have cloned the ovoD1 mutation into a P-element vector and recovered fully expressed P[ovoD1] insertions on each autosomal arm. We describe the generation of these P[ovoD1] strains as well as demonstrate their use in generating germ-line chimeras. Specifically, we show that the Gap1 gene, which encodes a Drosophila homologue of mammalian GTPase-activating protein, is required in somatic follicle cells for embryonic dorsoventral polarity determination.
<i>Pichia pastoris</i> as a host for secretion of toxic saporin chimeras (2009)

Most of the targeting moieties, such as antibody fragments or growth factor domains, used to construct targeted toxins for anticancer therapy derive from secretory proteins. These normally fold in the oxidative environment of the endoplasmic reticulum, and hence their folding in bacterial cells can be quite inefficient. For instance, only low amounts of properly folded antimetastatic chimera constituted by the amino-terminal fragment of human urokinase (ATF) fused to the plant ribosome-inactivating protein saporin could be recovered. ATF-saporin was instead secreted efficiently when expressed in eukaryotic cells protected from autointoxication with neutralizing anti-saporin antibodies. Pichia pastoris is a microbial eukaryotic host where these domains can fold into a transport-competent conformation and reach the extracellular medium. We show here that despite some host toxicity codon-usage optimization greatly increased the expression levels of active saporin but not those of an active-site mutant SAP-KQ in GS115 (his4) strain. The lack of any toxicity associated with expression of the latter confirmed that toxicity is due to saporin catalytic activity. Nevertheless, GS115 (his4) cells in flask culture secreted 3.5 mg/L of a histidine-tagged ATF-saporin chimera showing an IC(50) of 6 x 10(-11) M against U937 cells, thus demonstrating the suitability of this expression platform for secretion of toxic saporin-based chimeras.
Development of antifouling surfaces to reduce bacterial attachment (2013)

It is well documented that bacterial adhesion to surfaces is mediated by the physical and chemical properties of the substrate, as well as the surface characteristics of the organism. Topographical features that limit cell–surface interactions have been shown to reduce surface colonization and biofilm formation. In this study, bacterial attachment to medically relevant materials was evaluated. Our data show that Escherichia coli attachment to glass, silicone, and titanium surfaces was most affected by the surface energy of these materials, as determined by water contact angle. The inherent roughness of the surface, however, was not correlated with cell attachment density. To study the effect of engineered surface roughness on bacterial attachment, topographical features, including arrays of holes and repeating lines/trenches, were formed from silicon wafers and then used as a template to imprint silicone-based polydimethylsiloxane (PDMS). Patterned silicone surfaces were then used in static and microfluidic flow-based experiments to evaluate cellular settlement and attachment. Cell attachment was observed to be strongly dependent upon the topographical features under both static and microfluidic flow conditions. The highest attachment density was observed on flat, un-patterned surfaces, while linear patterned surfaces showed greatly reduced cell attachment. Moreover, surfaces consisting of arrays of holes further reduced cell attachment as compared to linear patterns. These results demonstrate that the size, spacing, and shape of surface features play a significant role in cell–surface attachment and provide insight for the design of surfaces with antifouling properties.
Mobile web searching (2002)

Searching the Web on a mobile device such as a cell phone poses unique problems for the user that cannot be easily overcome through the interface. Given the restricted display of current wireless devices, users cannot efficiently examine search results when they are presented as a long list. In our system, Hyponym, we organize search results into topics and allow the user to explore relevant resources within each topic. The data to support this kind of analysis are drawn from sequences of Web pages that users have visited while searching. We have found that queries that lead users to request similar pages tend to be topically related. From this simple observation, we form clusters or groups of queries that are used to structure the search display. Hyponym can be thought of as a collaborative filtering application that takes as its input navigation data from previous Web-searching tasks. Because of this, the lists that we return within each topic or query group tend to be much more accurate than those recommended by standard search engines. In fact, Hyponym can significantly cut the number of pages a user visits while searching the Web. We are currently extending the Hyponym framework to support personalization and location-specific information.3
www.annals.org (2000)

Editorials4 January 2000www.annals.orgFrank Davidoff, MDFrank Davidoff, MDEditor (Davidoff)Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-132-1-200001040-00016 SectionsAboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail As dedicated Annals readers know, the full text of many, but not all, articles in the journal has been available on the Web for some years, tucked away in the Web site of our publisher, the American College of Physicians-American Society of Internal Medicine, at www.acponline.org. But as befits this new year, this new century, and this (almost) new millennium, an entirely new electronic version of Annals is currently under development and will be up and running several months from now.What will be new about the new e-journal? Nearly everything, including a Web address (URL) of its own: www.annals.org. ... Author, Article, and Disclosure InformationAffiliations: Editor (Davidoff) PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetailsSee AlsoSuppose There Were No Printers Frank Davidoff Metrics Cited ByAnnals of Internal Medicine at Age 75: Reflections on the Past 25 YearsEdward J. Huth, MD and Kathleen Case, MSAuthors, Editors, and Readers in the Brave New (Electronic) WorldFrank Davidoff, MD, EditorSuppose There Were No PrintersFrank Davidoff, MD 4 January 2000Volume 132, Issue 1Page: 92KeywordsDrugsInformation technologyRunning Issue Published: 4 January 2000 CopyrightCopyright © 2000 by American College of Physicians. All Rights Reserved.PDF DownloadLoading ...
Using electronic biology based platform to predict flu vaccine efficacy for 2018/2019 (2018)

<ns4:p>Flu epidemics and potential pandemics pose great challenges to public health institutions, scientists and vaccine producers. Creating right vaccine composition for different parts of the world is not trivial and has been historically very problematic. This often resulted in decrease in vaccinations and reduced trust in public health officials. To improve future protection of population against flu we urgently need new methods for vaccine efficacy prediction and vaccine virus selection.</ns4:p>
Design Method of Single Flux Quantum Logic Circuits Using Dynamically Reconfigurable Logic Gates (2014)

In this study, we designed and tested dynamically reconfigurable AND/OR and NAND/NOR single flux quantum (SFQ) logic gates. The measured dc bias margins at low frequency were 99%-126% and 121%-144% for AND/OR and NAND/NOR gates, respectively. The experimentally confirmed maximum operating frequencies of the AND/OR and NAND/NOR gates were 36 and 24 GHz, respectively. We investigated a circuit design method that enables the efficient design of SFQ logic circuits by using dynamically reconfigurable SFQ logic gates. The logic circuits were designed with a small number of gates using the input data pattern dependence of the Boolean function and reconfiguring the dynamically reconfigurable SFQ logic gates. As a case study, we designed and tested a bit-serial SFQ full adder using the investigated circuit design method. Compared with the conventional bit-serial SFQ full adder, the delay of the proposed full adder was reduced by 27%, assuming a clock frequency of 20 GHz. We confirmed correct operation of the adder with a low-speed test.
Increased toxicity of <i>Bacillus thuringiensis</i> Cry3Aa against <i>Crioceris quatuordecimpunctata</i>, <i>Phaedon brassicae</i> and <i>Colaphellus bowringi</i> by a <i>Tenebrio molitor</i> cadherin fragment (2011)

The application of rTmCad1p to enhance Cry3Aa insecticidal activity has potential for use in increasing range and activity levels against coleopteran pests displaying low susceptibility to Bt-based biopesticides.
High-frequency noncontact ultrasonic analysis of materials: introduction and applications (2001)

High frequency Non-Contact Ultrasonic (NCU) analysis of materials has been a persistent dream of materials engineers and scientists. However, a natural impediment to NCU is the exorbitant acoustic impedance mismatch between air and the test materials. The magnitude of this obstacle is further exacerbated in the Megahertz frequencies, necessary for high resolution, detectability, and sensitivity. This air- material acoustic impedance barrier has been successfully broken by virtue of our phenomenally high transduction piezoelectric transducers (from 100 kHz to 5 MHz) and equally high sensitivity non-contact analyzer (> 150 dB dynamic range and nano-second time-of-flight accuracy). It is now possible to transmit ultrasound in virtually all materials and all states of matter (with the exception of vacuum) without any contact with them. Unlike the conventional contact ultrasound, with NCU, characterization of materials is easy in the early stages of their formation and processing. This includes powders, green ceramics, consolidated powder metals, composite pre-pregs, and polymerization process. In this paper we provide a systematic introduction to the significant of materials characterization, NCU transducers and an analyzer. Also provided are a number of examples of NCU analysis of a wide range of materials, including their internal and surface characteristics. Materials are characterized for thickness, velocity (density and mechanical properties), microstructure, delaminations, defects, etc.
Electrostatic discharge in semiconductor devices: protection techniques (2000)

Electrostatic discharges (ESDs) are everywhere-in our homes and businesses. Even the manufacturers of the electronics experience ESD failures in their factories. Electronic devices are sensitive to ESD. ESD results in failure of our computers, calculators, and car phones. There are ways to protect these sensitive components. This paper looks at ESD protection from a two-pronged approach: reducing the likelihood of having an ESD event and improving the robustness of the devices themselves. The first approach focuses on reducing the amount of charge that is developed and controlling the redistribution of any charges that are developed The second approach reviews ways to improve the circuit robustness by improving individual circuit elements and by adding additional elements for charge flow control and voltage clamping.
Iminium carbonic acid derivative salts. <b>VIII</b>. Electrophilic reactions of 2‐methylthio‐5,6‐dihydro‐1,3‐thiazinium iodides, 2‐methylthio‐5,6‐dihydrothiazolium iodides and 5‐methyl‐2‐methylthiothiazolium iodides. Part <b>II</b>. With active methylene compounds (1997)

Abstract The title compounds 1a‐c and 2 werre reacted with several doubly activated methylene components to yield the cyclic ketene S,N ‐acetals 3‐10 .