gebhart/patrepeval huggingface dataset:
Author's Response: Low Levels of Endogenous Androgens Increase the Risk of Atherosclerosis in Elderly Men—Further Supportive Data (2003)

We have read the interesting paper "Hyperglycemia: An Independent Marker of In-Hospital Mortality in Patients with Undiagnosed Diabetes" by Umpierrez et al. (1), which is one of the few studies on this issue conducted on a satisfactory number of patients.
Extended Amplification In Vitro and Replicative Senescence: Key Factors Implicated in the Success of Human Myoblast Transplantation (2003)

The limited success of human myoblast transplantation has been related to immune rejection, poor survival, and limited spread of injected myoblasts after transplantation. An important issue that has received little attention, but is nevertheless of fundamental importance in myoblast transplantation protocols, is the proliferative capacity of human satellite cells. Previous studies from our laboratory have demonstrated that the maximum number of divisions that a population of satellite cells can make decreases with age during the first two decades of life then stabilizes in adulthood. These observations indicate that when satellite cells are used as vectors in myoblast transplantation protocols it is important to consider donor age and the number of divisions that the cells have made prior to transplantation as limiting factors in obtaining an optimal number of donor derived muscle fibers. In this study, myoblasts derived from donors of different ages (newborn, 17 years old, and 71 years old) were isolated and amplified in culture. Their potential to participate in in vivo muscle regeneration in RAG2(-/-)/gamma(c)/C5 triple immunodeficient hosts after implantation was evaluated at 4 and 8 weeks postimplantation. Our results demonstrate that prolonged amplification in culture and the approach to replicative senescence are both important factors that may condition the success of myoblast transplantation protocols.
Transannular peroxides as radiation sensitizers. (1973)

A member of a potential new class of radiation sensitizers which act by radiation induced oxygen release, 9,10-di (p-carboxyphenyl) anthracene-9,10-endoperoxide, a transannular peroxide, has been synthesized and evaluated in bacteria, Escherichia coli (B/r). This material acts as a sensitizer in air apparently by virtue of its high reactivity with water radicals to produce a transient but highly toxic material. In the absence of air, a small and qualitatively different effect is found which may be due to release of oxygen either in its normal state or in an excited singlet state.
Follicular thyroid lesions, elements that affect both diagnosis and prognosis (2005)

The precise diagnosis of follicular thyroid lesions is frequently debated because of the subjective nature of capsular invasion as well as both the histological and cytological characteristics. Furthermore, several different prognostic indices have been devised to examine prognosis associated with thyroid cancer. Herein, we describe how these confounding elements can affect the ability to accurately predict prognosis for patients with follicular thyroid lesions.
Two New Cytotoxic Naphthoquinones from Mendoncia cowanii from the Rainforest of Madagascar (2006)

Bioassay-guided fractionation of the root and stem extracts of Mendoncia cowanii led to the isolation of two new and two known naphthoquinones. The structures of the new compounds, avicequinones D and E (1 and 2), were determined using 1D and 2D NMR spectroscopy and by chemical conversion of compound 1 to 2. The new compounds were active in the A2780 human ovarian cancer cell line with IC50 values of 7.4 - 50 microM, respectively, and 1, 3, and 4 were subsequently found to be weakly active in an assay for inhibition of the kinase Akt.
Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation (2015)

DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues within DNMT1's KG linker. This intermolecular interaction is required for USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine residues impair DNMT1-USP7 interaction and promote the degradation of DNMT1. Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and decreased total DNMT1 protein. This negative correlation is observed in differentiated neuronal cells and pancreatic cancer cells. Our studies reveal that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide a structural basis for the design of inhibitors, targeting the DNMT1-USP7 interaction surface for therapeutic applications.
A New Metric for Torque Nonuniformity (1983)

&lt;div class="htmlview paragraph"&gt;This paper presents a new metric for the nonuniformity of the torque random process of a reciprocating internal combustion engine. The proposed metric is derived from the torque 2N extrema which occur within each engine cycle for an N-cylinder engine. A 2N-dimensional vector is obtained for each cycle, which represents torque nonuniformity. The proposed metric is either the 1&lt;sub&gt;1&lt;/sub&gt; or 1&lt;sub&gt;2&lt;/sub&gt;, norm for this vector. It is shown in this paper that this metric satisfies several properties which are desirable for quantitatively representing torque nonuniformity. Moreover, this metric is computed once each engine cycle and is, therefore, a quasi-real time measure of torque nonuniformity. This metric has several potential applications in electronic engine control systems.&lt;/div&gt;
Geodesic star convexity for interactive image segmentation (2010)

In this paper we introduce a new shape constraint for interactive image segmentation. It is an extension of Veksler's star-convexity prior, in two ways: from a single star to multiple stars and from Euclidean rays to Geodesic paths. Global minima of the energy function are obtained subject to these new constraints. We also introduce Geodesic Forests, which exploit the structure of shortest paths in implementing the extended constraints. The star-convexity prior is used here in an interactive setting and this is demonstrated in a practical system. The system is evaluated by means of a “robot user” to measure the amount of interaction required in a precise way. We also introduce a new and harder dataset which augments the existing Grabcut dataset with images and ground truth taken from the PASCAL VOC segmentation challenge.
Outsourcing multi-version key-value stores with verifiable data freshness (2014)

In the age of big data, key-value data updated by intensive write streams is increasingly common, e.g., in social event streams. To serve such data in a cost-effective manner, a popular new paradigm is to outsource it to the cloud and store it in a scalable key-value store while serving a large user base. Due to the limited trust in third-party cloud infrastructures, data owners have to sign the data stream so that the data users can verify the authenticity of query results from the cloud. In this paper, we address the problem of verifiable freshness for multi-version key-value data. We propose a memory-resident digest structure that utilizes limited memory effectively and can have efficient verification performance. The proposed structure is named IncBM-Tree because it can INCrementally build a Bloom filter-embedded Merkle Tree. We have demonstrated the superior performance of verification under small memory footprints for signing, which is typical in an outsourcing scenario where data owners and users have limited resources.
Declining Incidence of Hepatocellular Carcinoma in Osaka, Japan, from 1990 to 2003 (2008)

The incidence of HCC in Osaka started to decrease by 2000, mainly because of decreased HCV-related HCC.
Targeted mitochondrial therapy using MitoQ shows equivalent renoprotection to angiotensin converting enzyme inhibition but no combined synergy in diabetes (2017)

Mitochondrial dysfunction is a pathological mediator of diabetic kidney disease (DKD). Our objective was to test the mitochondrially targeted agent, MitoQ, alone and in combination with first line therapy for DKD. Intervention therapies (i) vehicle (D); (ii) MitoQ (DMitoQ;0.6 mg/kg/day); (iii) Ramipril (DRam;3 mg/kg/day) or (iv) combination (DCoAd) were administered to male diabetic db/db mice for 12 weeks (n = 11-13/group). Non-diabetic (C) db/m mice were followed concurrently. No therapy altered glycaemic control or body weight. By the study end, both monotherapies improved renal function, decreasing glomerular hyperfiltration and albuminuria. All therapies prevented tubulointerstitial collagen deposition, but glomerular mesangial expansion was unaffected. Renal cortical concentrations of ATP, ADP, AMP, cAMP, creatinine phosphate and ATP:AMP ratio were increased by diabetes and mostly decreased with therapy. A higher creatine phosphate:ATP ratio in diabetic kidney cortices, suggested a decrease in ATP consumption. Diabetes elevated glucose 6-phosphate, fructose 6-phosphate and oxidised (NAD+ and NADP+) and reduced (NADH) nicotinamide dinucleotides, which therapy decreased generally. Diabetes increased mitochondrial oxygen consumption (OCR) at complex II-IV. MitoQ further increased OCR but decreased ATP, suggesting mitochondrial uncoupling as its mechanism of action. MitoQ showed renoprotection equivalent to ramipril but no synergistic benefits of combining these agents were shown.
Endovascular repair of aortic aneurysms, arteriovenous fistulas, and false aneurysms. (1995)

The diagnosis of abdominal aortic aneurysms (AAA) has been established with increasing frequency during the past two decades. This is probably due to the aging of the population as well as to the extensive use of ultrasonography and computerized tomography (CT) scanning for different pathologies. Although AAA may occasionally cause distal embolization, rupture remains the most common and deadly complication. Elective replacement with a synthetic graft has proved to be the most appropriate method to prevent AAA rupture for nearly 40 years, and at respected medical centers, it has been associated with a postoperative mortality of less than 5%. Non-fatal complications occur with some regularity irrespective of the setting in which the operation is performed. Increasingly, vascular surgeons are encountering older patients with severe co-morbid conditions. This can increase operative morbidity and may even elevate mortality of aortic surgery to a figure in excess of 60%. It seems inevitable that every vascular surgeon will, with some frequency, encounter patients who represent a prohibitive risk for conventional graft replacement, yet alternative forms of treatment (such as axillofemoral bypass in conjunction with induced AAA thrombosis) generally have been abandoned despite preliminary reports of their initial success.
Left-handed Z-DNA binding by the recA protein of Escherichia coli. (1987)

recA binding to left-handed Z-DNA was measured using nitrocellulose filter binding assays with four DNA polymers with defined nucleotide sequences and four recombinant plasmids. Two to 7-fold preferential binding of recA to Z-DNA polymers was observed. Left-handed Z-DNA polymer binding by recA required ATP or its nonhydrolyzable analog, ATP(gamma S), while ADP inhibited binding. Complex formation with both B- and Z-forms was influenced by polymer length; recA bound longer DNAs better. recA binding to recombinant plasmids containing supercoil-stabilized Z-DNA was essentially similar to that found for the control vector; thus, no preferential binding of recA to the Z-form was observed. Comparative experiments with the rec1 protein of Ustilago maydis and the Escherichia coli recA protein were performed. In our hands, recA and rec1 have a similar capacity for binding left-handed Z-DNA polymers and for binding recombinant plasmids containing B- and/or Z-regions. recA contains a left-handed Z-DNA-stimulated ATPase activity. This activity differs from the right-handed B-DNA-stimulated activity since it is less sensitive to increasing pH. The kinetics of ATP hydrolysis in B-DNA/Z-DNA mixing experiments showed that the turnover of the Z-DNA recA complex was slower than for B-DNA suggesting that left-handed Z-DNA is more stably bound by recA. Our results are consistent with the postulate that left-handed Z-DNA is involved in genetic recombination.
Dextran-Induced Changes in Fibrin Fiber Size and Density Based on Wavelength Dependence of Gel Turbidity (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDextran-Induced Changes in Fibrin Fiber Size and Density Based on Wavelength Dependence of Gel TurbidityMarcus E. Carr and Don A. GabrielCite this: Macromolecules 1980, 13, 6, 1473–1477Publication Date (Print):November 1, 1980Publication History Published online1 May 2002Published inissue 1 November 1980https://pubs.acs.org/doi/10.1021/ma60078a022https://doi.org/10.1021/ma60078a022research-articleACS PublicationsRequest reuse permissionsArticle Views258Altmetric-Citations57LEARN 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
Probing RNA hairpins with cobalt(III)hexammine and electrospray ionization mass spectrometry (2006)

In this work, electrospray ionization mass spectrometry (ESI MS) was employed to study the interactions of cobalt(III) hexammine, Co(NH3)63+, with five RNA hairpins representing the 790 loop of 16S ribosomal RNA and 1920 loop of 23S ribosomal RNA. The RNAs varied in mismatch identity (G±U versus A±C) and level of base modification (pseudouridine versus uridine). Co(NH3)63+ binding was observed with the four RNA hairpins that contained a G±U wobble pair in the stem region. ESI MS revealed 1:1 and 1:2 complex formation with all RNAs. Weaker binding was observed with the fifth RNA hairpin that contained an A±C wobble pair in the stem region. The effects of pH on Co(NH3)63+ binding were also examined.
Two Putative c -Type Multiheme Cytochromes Required for the Expression of OmcB, an Outer Membrane Protein Essential for Optimal Fe(III) Reduction in Geobacter sulfurreducens (2006)

Deletion of two homologous Geobacter sulfurreducens c-type cytochrome genes, omcG and omcH, decreased the rate of Fe(III) reduction and decreased the level of an outer membrane cytochrome critical for Fe(III) reduction, OmcB, without affecting its transcription. Expression of either gene restored Fe(III) reduction and OmcB expression, suggesting functional similarity.
Genome Analysis of F. nucleatum sub spp vincentii and Its Comparison With the Genome of F. nucleatum ATCC 25586 (2003)

We present the draft genome sequence and its analysis for Fusobacterium nucleatum sub spp. vincentii (FNV), and compare that genome with F. nucleatum ATCC 25586 (FN). A total of 441 FNV open reading frames (ORFs) with no orthologs in FN have been identified. Of these, 118 ORFs have no known function and are unique to FNV, whereas 323 ORFs have functional orthologs in other organisms. In addition to the excretion of butyrate, H2S and ammonia-like FN, FNV has the additional capability to excrete lactate and aminobutyrate. Unlike FN, FNV is likely to incorporate galactopyranose, galacturonate, and sialic acid into its O-antigen. It appears to transport ferrous iron by an anaerobic ferrous transporter. Genes for eukaryotic type serine/threonine kinase and phosphatase, transpeptidase E-transglycosylase Pbp1A are found in FNV but not in FN. Unique ABC transporters, cryptic phages, and three types of restriction-modification systems have been identified in FNV. ORFs for ethanolamine utilization, thermostable carboxypeptidase, gamma glutamyl-transpeptidase, and deblocking aminopeptidases are absent from FNV. FNV, like FN, lacks the classical catalase-peroxidase system, but thioredoxin/glutaredoxin enzymes might alleviate oxidative stress. Genes for resistance to antibiotics such as acriflavin, bacitracin, bleomycin, daunorubicin, florfenicol, and other general multidrug resistance are present. These capabilities allow Fusobacteria to survive in a mixed culture in the mouth.
The role of alcohol in oral carcinogenesis with particular reference to alcohol‐containing mouthwashes (2008)

Worldwide, oral cancer represents approximately 5 per cent of all malignant lesions, with over 800 new intra-oral squamous cell carcinomas registered in Australia each year. Despite recent advances in therapy, the five-year survival rate remains around 50 per cent and the sequelae of treatment can be seriously debilitating. It has been long established that smoking and alcohol consumption are risk factors linked to the development of oral cancer. This review assesses the epidemiological evidence, supportive in vitro studies and mechanism by which alcohol is involved in the development of oral cancer. Further, we review the literature that associates alcohol-containing mouthwashes and oral cancer. On the basis of this review, we believe that there is now sufficient evidence to accept the proposition that alcohol-containing mouthwashes contribute to the increased risk of development of oral cancer and further feel that it is inadvisable for oral healthcare professionals to recommend the long-term use of alcohol-containing mouthwashes.
Coexpression of the maize delta-zein and beta-zein genes results in stable accumulation of delta-zein in endoplasmic reticulum-derived protein bodies formed by beta-zein. (1997)

Zeins, the major seed storage proteins of maize, are of four distinct types: alpha, beta, delta, and gamma. They are synthesized on the rough endoplasmic reticulum (ER) in a sequential manner and deposited in ER-derived protein bodies. We investigated the potential for producing sulfur-rich beta-zein and delta-zein proteins in leaf and seed tissues by expressing the corresponding genes in a constitutive manner in transgenic tobacco. The delta-zein and beta-zein, when synthesized individually, were stable in the vegetative tissues and were deposited in unique, zein-specific ER-derived protein bodies. Coexpression of delta-zein and beta-zein genes, however, showed that delta-zein was colocalized in beta-zein-containing protein bodies and that the level of delta-zein was fivefold higher in delta-/beta-zein plants than in delta-zein plants. We conclude that delta-zein interacts with beta-zein and that the interaction has a stabilizing effect on delta-zein.
MATCHTM: a tool for searching transcription factor binding sites in DNA sequences (2003)

Match is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match is closely interconnected and distributed together with the TRANSFAC database. In particular, Match uses the matrix library collected in TRANSFAC and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team. A public version of the Match tool is available at: http://www.gene-regulation.com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called Match Professional is available at http://www.biobase.de.
Anti-dengue Vaccines: From Development to Clinical Trials (2020)

<i>Dengue Virus</i> (DENV) is an arbovirus (arthropod-borne virus). Four serotypes of DENV are responsible for the infectious disease called dengue that annually affects nearly 400 million people worldwide. Although there is only one vaccine formulation licensed for use in humans, there are other vaccine formulations under development that apply different strategies. In this review, we present information about anti-dengue vaccine formulations regarding development, pre-clinical tests, and clinical trials. The improvement in vaccine development against dengue is much needed, but it should be considered that the correlate of protection is still uncertain. Neutralizing antibodies have been proposed as a correlate of protection, but this ignores the key role of T-cell mediated immunity in controlling DENV infection. It is important to confirm the accurate correlate of protection against DENV infection, and also to have other anti-dengue vaccine formulations licensed for use.
Reversible Vesicle Restraint in Response to Spatiotemporally Controlled Electrical Signals:  A Bridge between Electrical and Chemical Signaling Modes (2006)

Microelectronic devices employ electrons for signaling whereas the nervous system signals using ions and chemicals. Bridging these signaling differences would benefit applications that range from biosensing to neuroprosthetics. Here, we report the use of localized electrical signals to perform an operation common to chemical signaling in the nervous system. Specifically, we employ electrical signals to restrain vesicles reversibly. We perform this operation using the stimuli-responsive aminopolysaccharide chitosan that is able to electrodeposit onto cathode surfaces in response to localized electrical stimuli. We show that surfactant-vesicles and liposomes can be co-deposited with chitosan and are entrapped (i.e., restrained) within the deposited film's matrix. Vesicle co-deposition could be controlled spatially and temporally using microfabricated wafers with independent electrode addresses. Finally, we show that vesicles restrained within the deposited chitosan matrix can be mobilized under mildly acidic conditions (pH <6.5) that resolubilize chitosan. Potentially, the ability to restrain and mobilize chemical signals that are segregated within vesicles may allow microfluidic systems to access the rich diversity offered by chemical signaling.