gebhart/patrepeval huggingface dataset:
Accumulation Profile of Frameshift Mutations During Development and Progression of Colorectal Cancer From Patients With Hereditary Nonpolyposis Colorectal Cancer (2006)

The present data suggest that the disruption of the transforming growth factor-beta super-family signaling pathway by the alteration of the ACVR2 and/or TGFbetaRII genes and the disruption of antiproliferative function by the PTHLH gene alteration contribute to the development of early colorectal cancer. Moreover, the further accumulation of alterations in the MARCKS, BAX, IGFIIR, and PTEN genes seem to be associated with progression from early to advanced colorectal cancer from patients with hereditary nonpolyposis colorectal cancer.
Directed Rotational Motion of Microscale Objects Using Interfacial Tension Gradients Continually Generated via Catalytic Reactions (2004)

Gearing up for the future: Continuous rotational motion of gear-like microscale objects is demonstrated via interfacial tension gradients generated through catalytic reactions (the picture shows one such gear with a diameter of ≈150 μm). Hydrophobicity of the surface adjacent to the catalyst is shown to be the key in the formation of the surface tension gradient.
Good features to track (1994)

No feature-based vision system can work unless good features can be identified and tracked from frame to frame. Although tracking itself is by and large a solved problem, selecting features that can be tracked well and correspond to physical points in the world is still hard. We propose a feature selection criterion that is optimal by construction because it is based on how the tracker works, and a feature monitoring method that can detect occlusions, disocclusions, and features that do not correspond to points in the world. These methods are based on a new tracking algorithm that extends previous Newton-Raphson style search methods to work under affine image transformations. We test performance with several simulations and experiments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Tumor-Specific Effector CD8+ T Cells That Can Establish Immunological Memory in Humans after Adoptive Transfer Are Marked by Expression of IL7 Receptor and c-myc (2015)

The optimal T-cell attributes for adoptive cancer immunotherapy are unclear. Recent clinical trials of ex vivo-expanded tumor-infiltrating lymphocytes indicated that differentiated T effector cells can elicit durable antitumor responses in some patients with cancer, with their antitumor activity tightly correlated with their persistence in the host. Thus, there is great interest in the definition of intrinsic biomarkers that can predict the conversion of short-lived tumor antigen-specific T effector cells into long-lived T memory cells. Long-term persistence of ex vivo-expanded tumor-specific CD8+ T effector clones has been reported in refractory metastatic melanoma patients after adoptive T-cell transfer. By using highly homogeneous clone populations from these preparations, we performed a comparative transcriptional profiling to define preinfusion molecular attributes that can be ascribed to an effector-to-memory transition. Through this route, we discovered that preinfusion T-cell clones that expressed the IL7 receptor (IL7R) and c-myc were more likely to persist longer after adoptive transfer to patients. The predictive value of these two biomarkers was strengthened by using IL7R protein, IL7-induced pSTAT5, and c-myc mRNA expression to prospectively identify human tumor-specific T effector clones capable of engraftment into immunodeficient mice. Overall, our findings reveal IL7R and c-myc expression as intrinsic biomarkers that can predict the fate of CD8+ T effector cells after adoptive transfer.
Comparative Genomic Analysis ofChlamydia trachomatisOculotropic and Genitotropic Strains (2005)

Chlamydia trachomatis infection is an important cause of preventable blindness and sexually transmitted disease (STD) in humans. C. trachomatis exists as multiple serovariants that exhibit distinct organotropism for the eye or urogenital tract. We previously reported tissue-tropic correlations with the presence or absence of a functional tryptophan synthase and a putative GTPase-inactivating domain of the chlamydial toxin gene. This suggested that these genes may be the primary factors responsible for chlamydial disease organotropism. To test this hypothesis, the genome of an oculotropic trachoma isolate (A/HAR-13) was sequenced and compared to the genome of a genitotropic (D/UW-3) isolate. Remarkably, the genomes share 99.6% identity, supporting the conclusion that a functional tryptophan synthase enzyme and toxin might be the principal virulence factors underlying disease organotropism. Tarp (translocated actin-recruiting phosphoprotein) was identified to have variable numbers of repeat units within the N and C portions of the protein. A correlation exists between lymphogranuloma venereum serovars and the number of N-terminal repeats. Single-nucleotide polymorphism (SNP) analysis between the two genomes highlighted the minimal genetic variation. A disproportionate number of SNPs were observed within some members of the polymorphic membrane protein (pmp) autotransporter gene family that corresponded to predicted T-cell epitopes that bind HLA class I and II alleles. These results implicate Pmps as novel immune targets, which could advance future chlamydial vaccine strategies. Lastly, a novel target for PCR diagnostics was discovered that can discriminate between ocular and genital strains. This discovery will enhance epidemiological investigations in nations where both trachoma and chlamydial STD are endemic.
Purification and properties of a single strand-specific endonuclease from mouse cell mitochondria (1986)

A nuclease was purified from mitochondria of the mouse plasmacytoma cell line, MCP-11 which acts on single-stranded DNA endonucleolytically and appears to have no activity upon native DNA. It degrades unordered RNA somewhat more effectively than it does DNA. The enzyme activity and the major detectable polypeptide migrate to a position corresponding to an Mr of 37,400 on denaturing polyacrylamide gels; in its native form the activity has an S value of 4.7, which corresponds to a molecular weight of roughly 73,000. The single-strand DNase activity has a pH optimum near 7.5, requires a divalent cation and is inhibited by EDTA, phosphate, KCl and NaCl. The enzyme is remarkably similar to fungal mitochondrial enzymes whose absence in various mutants correlates with defective DNA repair and recombination. It reacts weakly with antibody to a form of such an enzyme from Neurospora crassa.
Interpreting treatment effects in randomised trials (1998)

The need to measure the impact of treatments on health related quality of life has led to a rapid increase in the variety of instruments available and in their use as measures of outcome in clinical trials. One limitation of instruments that purport to measure health related quality of life is difficulty interpreting their results. In the past decade, investigators have progressed in making these questionnaire results interpretable. For example, we have shown that when questionnaires present response options in the form of seven point scales with verbal descriptions for each option (see box), the smallest difference that patients consider important is often approximately 0.5 per question. A moderate difference corresponds to a change of approximately 1.0 per question, and changes of greater than 1.5 can be considered large. Thus, for example, in a domain with four items, patients will consider a 1 point change in two or more items as important. This finding applies across different areas of function, including dyspnoea, fatigue, and emotional function in patients with chronic airflow limitation1; and symptoms, emotional function, and activity limitations in adults2 and children3 with asthma, parents of children with asthma,4 and adults with rhinoconjunctivitis.5 Initially, we used comparisons in the same patient to establish this difference, but more recently we have replicated this finding using differences between patients.6

#### Summary points

Several questionnaires on quality of life related to health are available, but interpreting their results may be difficult

For some questionnaires, we now know that the smallest change in score that patients consider important is 0.5

Even if the mean difference between a treatment and a control is appreciably less than the smallest change that is important, treatment may have an important impact on many patients

A method for estimating the proportion of patients who …
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics (2015)

A single TF often orchestrates the expression of multiple genes in response to environmental stimuli. It is not clear how different TF-binding sites within the regulon dictate the expression profile. Our studies of Escherichia coli PhoB, a response regulator that controls expression of a core set of phosphate assimilation genes in response to phosphate starvation, showed that expression levels of PhoB-regulated genes are under sophisticated control and do not follow a simple correlation with the binding affinity of PhoB~P to individual promoters. However, the expression timing correlates with the PhoB-binding affinity and gene functions. Genes involved in direct Pi uptake contain high-affinity sites and are transcribed earlier than genes involved in phosphorus scavenging. This illustrates an elaborate mechanism of temporally programmed gene expression, even for nondevelopmental pathways.
Continually evaluating similarity-based pattern queries on a streaming time series (2002)

In many applications, local or remote sensors send in streams of data, and the system needs to monitor the streams to discover relevant events/patterns and deliver instant reaction correspondingly. An important scenario is that the incoming stream is a continually appended time series, and the patterns are time series in a database. At each time when a new value arrives (called a time position), the system needs to find, from the database, the nearest or near neighbors of the incoming time series up to the time position. This paper attacks the problem by using Fast Fourier Transform (FFT) to efficiently find the cross correlations of time series, which yields, in a batch mode, the nearest and near neighbors of the incoming time series at many time positions. To take advantage of this batch processing in achieving fast response time, this paper uses prediction methods to predict future values. FFT is used to compute the cross correlations of the predicted series (with the values that have already arrived) and the database patterns, and to obtain predicted distances between the incoming time series at many future time positions and the database patterns. When the actual data value arrives, the prediction error together with the predicted distances is used to filter out patterns that are not possible to be the nearest or near neighbors, which provides fast responses. Experiments show that with reasonable prediction errors, the performance gain is significant.
Use of Cutometer to assess epidermal hydration (2000)

Background/aims: The Cutometer equipped with a 2‐mm diameter suction probe is a device suitable for assessment of epidermal mechanics. The objectives of this study were to determine the sensitivity of Cutometer parameters to epidermal hydration, to evaluate the correlation between skin mechanical parameters and skin capacitance, and to study the role of pretension of the skin. Methods: In the first study, skin capacitance (Corneometer) and 10 mechanical parameters were determined before and 60 min after application of five different moisturizers on the volar forearm. In the second study, measurements of epidermal mechanics were made without and with 0.1 s presuction of the skin, before and 120 min after application of petrolatum and glycerin. Results: Hydration of the skin significantly increased the values of capacitance and all rheological parameters. Delayed distension ( U v ) and viscoelastic‐to‐elastic ratio ( U v / U e ) were the most sensitive Cutometer parameters. Significant correlations between skin capacitance and mechanical parameters were not found. Pretension of the skin did not significantly influence the values of skin mechanical parameters. Conclusions: The non‐invasive measurements of skin elasticity are appropriate for an objective and quantitative evaluation of the complex effect of different dermatological and cosmetic products on skin mechanics and hydration.
Boron-pyrazole chemistry. IV. Carbon- and boron-substituted poly[(1-pyrazolyl) borates] (1967)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBoron-pyrazole chemistry. IV. Carbon- and boron-substituted poly[(1-pyrazolyl) borates]Swiatoslaw. TrofimenkoCite this: J. Am. Chem. Soc. 1967, 89, 24, 6288–6294Publication Date (Print):November 1, 1967Publication History Published online1 May 2002Published inissue 1 November 1967https://pubs.acs.org/doi/10.1021/ja01000a053https://doi.org/10.1021/ja01000a053research-articleACS PublicationsRequest reuse permissionsArticle Views3622Altmetric-Citations327LEARN 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
Folate analogs. 35. Synthesis and biological evaluation of 1-deaza, 3-deaza, and bridge-elongated analogs of N10-propargyl-5,8-dideazafolic acid (1991)

Structural modifications at the pyrimidine ring and at the C9,N10-bridge region of the thymidylate synthase (TS) inhibitors N10-propargyl-5,8-dideazafolate (1; PDDF; CB 3717), 2-desamino-N10-propargyl-5,8-dideazafolate (2, DPDDF), and 2-desamino-2-methyl-N10-propargyl-5,8-dideazafolate (3, DMPDDF) have been carried out. Methods for the synthesis of 2-desamino-N10-propargyl-1,5,8-trideazafolate (4), 2-desamino-2-methyl-N10-propargyl-3,5,8-trideazafolate (5a), and 2-desamino-2-methyl-N10-propargyl-5,8-dideaza-1,2-dihydrofolate (6) have been developed. The bridge-extended analogues isohomo-PDDF (7) and isohomo-DMPDDF (8) contain an additional methylene group interposed between N10 and the phenyl ring of 1 and 3, respectively. All new compounds were evaluated as inhibitors of TS and the growth of tumor cells in culture. Selected analogues were tested as substrates of folylpolyglutamate synthetase (FPGS) and striking differences in substrate activity were observed among these compounds, indicating that structural modifications at the pyrimidine ring of classical antifolates profoundly influence their polyglutamylation. Enzyme inhibition data established that both N1 and N3-H of the pyrimidine ring are essential for efficient binding of quinazoline-type antifolates to human TS.
Agonists of MAS oncogene and angiotensin II type 2 receptors attenuate cardiopulmonary disease in rats with neonatal hyperoxia-induced lung injury (2013)

Stimulation of MAS oncogene receptor (MAS) or angiotensin (Ang) receptor type 2 (AT2) may be novel therapeutic options for neonatal chronic lung disease (CLD) by counterbalancing the adverse effects of the potent vasoconstrictor angiotensin II, consisting of arterial hypertension (PAH)-induced right ventricular hypertrophy (RVH) and pulmonary inflammation. We determined the cardiopulmonary effects in neonatal rats with CLD of daily treatment during continuous exposure to 100% oxygen for 10 days with specific ligands for MAS [cyclic Ang-(1-7); 10-50 μg·kg(-1)·day(-1)] and AT2 [dKcAng-(1-7); 5-20 μg·kg(-1)·day(-1)]. Parameters investigated included lung and heart histopathology, fibrin deposition, vascular leakage, and differential mRNA expression in the lungs of key genes involved in the renin-angiotensin system, inflammation, coagulation, and alveolar development. We investigated the role of nitric oxide synthase inhibition with N(ω)-nitro-l-arginine methyl ester (25 mg·kg(-1)·day(-1)) during AT2 agonist treatment. Prophylactic treatment with agonists for MAS or AT2 for 10 days diminished cardiopulmonary injury by reducing alveolar septum thickness and medial wall thickness of small arterioles and preventing RVH. Both agonists attenuated the pulmonary influx of inflammatory cells, including macrophages (via AT2) and neutrophils (via MAS) but did not reduce alveolar enlargement and vascular alveolar leakage. The AT2 agonist attenuated hyperoxia-induced fibrin deposition. In conclusion, stimulation of MAS or AT2 attenuates cardiopulmonary injury by reducing pulmonary inflammation and preventing PAH-induced RVH but does not affect alveolar and vascular development in neonatal rats with experimental CLD. The beneficial effects of AT2 activation on experimental CLD were mediated via a NOS-independent mechanism.
Guidelines for Protein Design: The Energetics of β Sheet Side Chain Interactions (1995)

To determine the interaction energy between cross-strand pairs of side chains on an antiparallel beta sheet, pairwise amino acid substitutions were made on the solvent-exposed face of the B1 domain of streptococcal protein G. The measured interaction energies were substantial (1.8 kilocalories per mole) and comparable to the magnitude of the beta sheet propensities. The experimental results paralleled the statistical frequency with which the residue pairs are found in beta sheets of known structure.
Moderate pH, Potassium, Polymer-Treated Mud Reduces Washout (1986)

ABSTRACT In the past, borehole stability and preventing hole washout have been major problems on many wells drilled in the Gulf Coast. Both of these problems have major influences on drilling efficiency and drilling cost. Two objectives were established to investigate these problems and possible solutions: To build and maintain an inhibitive mud system. To minimize washout by contributing to borehole stability. It is the intent of this paper to show that selected water soluble polymers and potassium hydroxide additives improve bore-hole stability and hole washout by reducing the water adsorption rate at the borehole-drilling fluid interface. Before implementation of the fluid system on, Well #A-2, Main Pass 77, Block 151 some guidelines were established. To gauge the degree of success, directionally drilled Well #A-2 was compared with the #1 Wildcat that was drilled as a straight hole five years earlier. The section of the wells used for comparison was the 8 1/2″ hole approximately 1100 feet in length. These sections were correlated using the D-5 and D-10 sands and divided into fourteen intervals. The two wells were compared as to washout, mud cost to drill, hours spent drilling, hours spent washing and reaming, and total circulating time (excluding drilling). Comparisons were also made using annular velocity, jet velocity, pH, pm and pf. The fluid system is being applied to other wells and the results are encouraging.
HIV‐1 neutralizing antibodies: understanding nature's pathways (2013)

The development of an effective vaccine has been hindered by the enormous diversity of human immunodeficiency virus-1 (HIV-1) and its ability to escape a myriad of host immune responses. In addition, conserved vulnerable regions on the HIV-1 envelope glycoprotein are often poorly immunogenic and elicit broadly neutralizing antibody responses (BNAbs) in a minority of HIV-1-infected individuals and only after several years of infection. All of the known BNAbs demonstrate high levels of somatic mutations and often display other unusual traits, such as a long heavy chain complementarity determining region 3 (CDRH3) and autoreactivity that can be limited by host tolerance controls. Nonetheless, the demonstration that HIV-1-infected individuals can make potent BNAbs is encouraging, and recent progress in isolating such antibodies and mapping their immune pathways of development is providing new strategies for vaccination.
Isolation and Characterization of a Hormone-binding Polypeptide from Pig Posterior Pituitary Powder (1969)

A large polypeptide has been isolated from acetone powder of pig posterior pituitary tissue by the methods of percolation, gel filtration on Sephadex G-25 and G-50, and ion exchange chromatography on diethylaminoethyl cellulose. The purified polypeptide appears to be homogeneous by the criteria of electrophoresis on paper and starch gel, column and paper chromatography, ultracentrifugation, and amino acid analysis. It consists of 89 amino acid residues with a molecular weight of 9170. The purified peptide contains all of the usual amino acids except histidine and tryptophan. There are 14 glycyl, 13 glutamyl, 7 seryl, 7 alanyl, 7 leucyl, 6 prolyl, 6 cystinyl, 5 argininyl, 5 aspartyl, 3 phenylalanyl, and 1 or 2 of each of the other residues. Its isoelectric point is estimated to be about pH 5.8. It is devoid of pressor and oxytocic activity but has the ability to bind lysine vasopressin, oxytocin, and synthetic analogues of oxytocin. However, the performic acid-oxidized polypeptide fails to bind either lysine vasopressin or oxytocin.
Efficient CdSe/CdS Quantum Dot Light-Emitting Diodes Using a Thermally Polymerized Hole Transport Layer (2006)

We report multilayer nanocrystal quantum dot light-emitting diodes (QD-LEDs) fabricated by spin-coating a monolayer of colloidal CdSe/CdS nanocrystals on top of thermally polymerized solvent-resistant hole-transport layers (HTLs). We obtain high-quality QD layers of controlled thickness (down to submonolayer) simply by spin-coating QD solutions directly onto the HTL. The resulting QD-LEDs exhibit narrow ( approximately 30 nm, fwhm) electroluminescence from the QDs with virtually no emission from the organic matrix at any voltage. Using multiple spin-on HTLs improves the external quantum efficiency of the QD-LEDs to approximately 0.8% at a brightness of 100 cd/m(2) (with a maximum brightness over 1,000 cd/m(2)). We conclude that QD-LEDs could be made more efficient by further optimization of the organic semiconductors.
Caveolins, Liquid-Ordered Domains, and Signal Transduction (1999)

Caveolae were originally identified as flask-shaped invaginations of the plasma membrane in endothelial and epithelial cells (14). Prior to the development of biochemical methods for their purification, caveolae were thought to principally mediate the transcellular movement of molecules (101, 145). Recently, the development of novel purification procedures has greatly expanded our knowledge regarding the putative functions of caveolae in vivo. In this review, we seek to update the working definition of caveolae, describe the functional roles of the caveolin gene family, and summarize the evidence that supports a role for caveolae as mediators of a number of cellular signaling processes.
Learning and memory in pain pathways (2000)

Department of Physiology and Pathophysiology, University of Heidelberg, Im Neuenheimer Feld 326, D-69120 Heidelberg, Germany *Tel.: +49-6221-544052; fax: +49-6221-544047 E-mail: [email protected] Received 18 August 2000; accepted 18 September 2000.