gebhart/patrepeval huggingface dataset:
Smoking and Pancreatic Cancer in Men and Women (1997)

Most studies of smoking and pancreatic cancer have used male subjects or combined men and women together in statistical analyses. There is little information on the relative risk of smoking and pancreatic cancer in women. Because of the high case-fatality rate, many of these studies were also based on information gathered from proxy respondents, in which smoking habits may not be recalled with certainty. A hospital-based study of 484 male and female patients with pancreatic cancer and 954 control subjects was conducted based on direct interviews of incident cases. Compared to never smokers, the odds ratio (OR) for current cigarette smokers was 1.6 [95% confidence interval (CI), 1.1-2.4] for men and 2.3 (95% CI, 1.4-3.5) for women. In women, but not in men, there was a trend in the ORs with years of daily cigarette consumption (P < 0.01). Filter cigarettes offered no protective advantage compared to nonfilter cigarettes. Among men, the OR was 2.1 (95% CI, 1.2-3.8) for pipe/ cigar smokers and 3.6 (95% CI, 1.0-12.8) for tobacco chewers. Tobacco smoke causes pancreatic cancer when inhaled into the lungs. Tobacco juice may also cause pancreatic cancer when ingested or absorbed through the oral cavity. These data suggest that smoking is a cause of pancreatic cancer in women and that the risks for female smokers are comparable to male smokers. Nevertheless, the causes of most pancreatic cancers are unknown.
Minireview: Genomic Organization of the Human ERα Gene Promoter Region (2001)

The ERalpha gene has been intensively studied for more than a decade. During this long time, multiple promoters used in ERalpha expression have been discovered in several species. Although an already large body of literature describing various aspects of the regulation of ERalpha expression and utilization of different promoters is constantly growing, the inconsistent terminology used by individual authors makes the interpretation and comparison of data very difficult. Furthermore, completion of the human genome project now allows all known human ERalpha promoters to be placed on a physical map. This review describes promoters used in the generation of ERalpha transcripts in human and in other species and suggests a consistent nomenclature. The possible role of multiple promoters in the differential expression of ERalpha in tissues and during development is also discussed.
Structural understanding of stabilization patterns in engineered bispecific Ig‐like antibody molecules (2009)

Bispecific immunoglobulin-like antibodies capable of engaging multiple antigens represent a promising new class of therapeutic agents. Engineering of these molecules requires optimization of the molecular properties of one of the domain components. Here, we present a detailed crystallographic and computational characterization of the stabilization patterns in the lymphotoxin-beta receptor (LTbetaR) binding Fv domain of an anti-LTbetaR/anti-TNF-related apoptosis inducing ligand receptor-2 (TRAIL-R2) bispecific immunoglobulin-like antibody. We further describe a new hierarchical structure-guided approach toward engineering of antibody-like molecules to enhance their thermal and chemical stability.
Synthetic carbohydrate vaccines based on tumour-associated antigens (1995)

T. Toyokuni and A. K. Singhal, Chem. Soc. Rev., 1995, 24, 231 DOI: 10.1039/CS9952400231
A practical automatic polyhedral parallelizer and locality optimizer (2008)

We present the design and implementation of an automatic polyhedral source-to-source transformation framework that can optimize regular programs (sequences of possibly imperfectly nested loops) for parallelism and locality simultaneously. Through this work, we show the practicality of analytical model-driven automatic transformation in the polyhedral model -- far beyond what is possible by current production compilers. Unlike previous works, our approach is an end-to-end fully automatic one driven by an integer linear optimization framework that takes an explicit view of finding good ways of tiling for parallelism and locality using affine transformations. The framework has been implemented into a tool to automatically generate OpenMP parallel code from C program sections. Experimental results from the tool show very high speedups for local and parallel execution on multi-cores over state-of-the-art compiler frameworks from the research community as well as the best native production compilers. The system also enables the easy use of powerful empirical/iterative optimization for general arbitrarily nested loop sequences.
Molecular Pathways Involved in Loss of Kidney Graft Function with Tubular Atrophy and Interstitial Fibrosis (2008)

Loss of kidney graft function with tubular atrophy (TA) and interstitial fibrosis (IF) causes most kidney allograft losses. We aimed to identify the molecular pathways involved in IF/TA progression. Kidney biopsies from normal kidneys (n = 24), normal allografts (n = 6), and allografts with IF/TA (n = 17) were analyzed using high-density oligonucleotide microarray. Probe set level tests of hypotheses tests were conducted to identify genes with a significant trend in gene expression across the three groups using Jonckheere-Terpstra test for trend. Interaction networks and functional analysis were used. An unsupervised hierarchical clustering analysis showed that all the IF/TA samples were associated with high correlation. Gene ontology classified the differentially expressed genes as related to immune response, inflammation, and matrix deposition. Chemokines (CX), CX receptor (for example, CCL5 and CXCR4), interleukin, and interleukin receptor (for example, IL-8 and IL10RA) genes were overexpressed in IF/TA samples compared with normal allografts and normal kidneys. Genes involved in apoptosis (for example, CASP4 and CASP5) were importantly overexpressed in IF/TA. Genes related to angiogenesis (for example, ANGPTL3, ANGPT2, and VEGF) were downregulated in IF/TA. Genes related to matrix production-deposition were upregulated in IF/TA. A distinctive gene expression pattern was observed in IF/TA samples compared with normal allografts and normal kidneys. We were able to establish a trend in gene expression for genes involved in different pathways among the studied groups. The top-scored networks were related to immune response, inflammation, and cell-to-cell interaction, showing the importance of chronic inflammation in progressive graft deterioration.
Pathogenic role of Demodex mites in blepharitis (2010)

Demodex blepharitis is a common but overlooked external eye disease. The pathogenesis of Demodex blepharitis in eliciting ocular surface inflammation has been further clarified. The modified eyelash sampling and counting method makes it easier and more accurate to diagnose Demodex infestation. Tea tree oil shows promising potential to treat Demodex blepharitis by reducing Demodex counts with additional antibacterial, antifungal, and anti-inflammatory actions.
The mechanical properties of the rubber elastic polymer polydimethylsiloxane for sensor applications (1997)

Polydimethylsiloxane (PDMS) is a commercially available physically and chemically stable silicone rubber. It has a unique flexibility with a shear elastic modulus due to one of the lowest glass transition temperatures of any polymer . Further properties of PDMS are a low change in the shear elastic modulus versus temperature , virtually no change in G versus frequency and a high compressibility. Because of its clean room processability, its low curing temperature, its high flexibility, the possibility to change its functional groups and the very low drift of its properties with time and temperature, PDMS is very well suited for micromachined mechanical and chemical sensors, such as accelerometers (as the spring material) and ISFETs (as the ion selective membrane). It can also be used as an adhesive in wafer bonding, as a cover material in tactile sensors and as the mechanical decoupling zone in sensor packagings.
Management and Treatment of Patients With Cirrhosis and Portal Hypertension: Recommendations From the Department of Veterans Affairs Hepatitis C Resource Center Program and the National Hepatitis C Program (2009)

Cirrhosis represents the end stage of any chronic liver disease. Hepatitis C and alcohol are currently the main causes of cirrhosis in the United States. Although initially cirrhosis is compensated, it eventually becomes decompensated, as defined by the presence of ascites, variceal hemorrhage, encephalopathy, and/or jaundice. These management recommendations are divided according to the status, compensated or decompensated, of the cirrhotic patient, with a separate section for the screening, diagnosis, and management of hepatocellular carcinoma (HCC), as this applies to patients with both compensated and decompensated cirrhosis. In the compensated patient, the main objective is to prevent variceal hemorrhage and any practice that could lead to decompensation. In the decompensated patient, acute variceal hemorrhage and spontaneous bacterial peritonitis are severe complications that require hospitalization. Hepatorenal syndrome is also a severe complication of cirrhosis but one that usually occurs in patients who are already in the hospital and, as it represents an extreme of the hemodynamic alterations that lead to ascites formation, it is placed under treatment of ascites. Recent advances in the pathophysiology of the complications of cirrhosis have allowed for a more rational management of cirrhosis and also for the stratification of patients into different risk groups that require different management. These recommendations are based on evidence in the literature, mainly from randomized clinical trials and meta-analyses of these trials. When few or no data exist from well-designed prospective trials, emphasis is given to results from large series and consensus conferences with involvement of recognized experts. A rational management of cirrhosis will result in improvements in quality of life, treatment adherence, and, ultimately, in outcomes.
Sequence analysis reveals homology between two proteins of the flagellar radial spoke. (1992)

Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. We have sequenced the genes for radial spoke protein 4 (RSP4) and RSP6, two of the five proteins that make up the radial spoke head in Chlamydomonas reinhardtii. The two genes, which are tightly linked genetically (B. Huang, G. Piperno, Z. Ramanis, and D.J.L. Luck, J. Cell Biol. 88:80-88, 1981), are separated by only 435 bp. They encode proline-rich polypeptides of 49.8 kDa (RSP4) and 48.8 kDa (RSP6), which are 48% identical to each other but do not resemble any previously sequenced proteins. The transcription start sites of these genes and an additional radial spoke protein gene, that for RSP3, were determined, and patterns of mRNA accumulation during flagellar regeneration were examined for the three radial spoke protein genes. These studies provide the molecular tools for a detailed analysis of radial spoke head function and assembly and for a determination of the mechanism by which the genes required to build a complex organelle are regulated.
PEAKS: powerful software for peptide de novo sequencing by tandem mass spectrometry (2003)

A number of different approaches have been described to identify proteins from tandem mass spectrometry (MS/MS) data. The most common approaches rely on the available databases to match experimental MS/MS data. These methods suffer from several drawbacks and cannot be used for the identification of proteins from unknown genomes. In this communication, we describe a new de novo sequencing software package, PEAKS, to extract amino acid sequence information without the use of databases. PEAKS uses a new model and a new algorithm to efficiently compute the best peptide sequences whose fragment ions can best interpret the peaks in the MS/MS spectrum. The output of the software gives amino acid sequences with confidence scores for the entire sequences, as well as an additional novel positional scoring scheme for portions of the sequences. The performance of PEAKS is compared with Lutefisk, a well-known de novo sequencing software, using quadrupole-time-of-flight (Q-TOF) data obtained for several tryptic peptides from standard proteins.
Improvement of signal reproducibility and matrix/comatrix effects in MALDI analysis (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImprovement of signal reproducibility and matrix/comatrix effects in MALDI analysisArkady I. Gusev, William R. Wilkinson, Andrew. Proctor, and David M. HerculesCite this: Anal. Chem. 1995, 67, 6, 1034–1041Publication Date (Print):March 15, 1995Publication History Published online1 May 2002Published inissue 15 March 1995https://pubs.acs.org/doi/10.1021/ac00102a003https://doi.org/10.1021/ac00102a003research-articleACS PublicationsRequest reuse permissionsArticle Views1467Altmetric-Citations190LEARN 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
Discovery of 4-Substituted Methoxybenzoyl-aryl-thiazole as Novel Anticancer Agents: Synthesis, Biological Evaluation, and Structure−Activity Relationships (2009)

A series of 4-substituted methoxybenzoyl-aryl-thiazoles (SMART) have been discovered and synthesized as a result of structural modifications of the lead compound 2-arylthiazolidine-4-carboxylic acid amides (ATCAA). The antiproliferative activity of the SMART agents against melanoma and prostate cancer cells was improved from muM to low nM range compared with the ATCAA series. The structure-activity relationship was discussed from modifications of "A", "B", and "C" rings and the linker. Preliminary mechanism of action studies indicated that these compounds exert their anticancer activity through inhibition of tubulin polymerization.
GaN-Based Light Emitting Diodes with Tunnel Junctions (2001)

We have demonstrated hole injection through a tunnel junction embedded in the GaN-based light emitting diode structure. The tunnel junction consists of 30 nm GaN:Si ++ and 15 nm InGaN:Mg ++ grown on a GaN–InGaN quantum well heterostructure. The forward voltage of the light emitting diode, including the voltage drop across the reverse-biased tunnel junction, is 4.1 V at 50 A/cm 2 , while that of a standard light emitting diode with a conventional contact structure is 3.5 V. The light output of the diode with the tunnel junction is comparable to that of the standard device. This tunnel junction eliminates the need for a highly resistive p-AlGaN cladding layer in short-wavelength laser diodes and the semi-transparent electrode required for current spreading in conventional GaN-based light emitting diodes.
Structural basis for selective targeting of leishmanial ribosomes: aminoglycoside derivatives as promising therapeutics (2015)

Leishmaniasis comprises an array of diseases caused by pathogenic species of Leishmania, resulting in a spectrum of mild to life-threatening pathologies. Currently available therapies for leishmaniasis include a limited selection of drugs. This coupled with the rather fast emergence of parasite resistance, presents a dire public health concern. Paromomycin (PAR), a broad-spectrum aminoglycoside antibiotic, has been shown in recent years to be highly efficient in treating visceral leishmaniasis (VL)-the life-threatening form of the disease. While much focus has been given to exploration of PAR activities in bacteria, its mechanism of action in Leishmania has received relatively little scrutiny and has yet to be fully deciphered. In the present study we present an X-ray structure of PAR bound to rRNA model mimicking its leishmanial binding target, the ribosomal A-site. We also evaluate PAR inhibitory actions on leishmanial growth and ribosome function, as well as effects on auditory sensory cells, by comparing several structurally related natural and synthetic aminoglycoside derivatives. The results provide insights into the structural elements important for aminoglycoside inhibitory activities and selectivity for leishmanial cytosolic ribosomes, highlighting a novel synthetic derivative, compound 3: , as a prospective therapeutic candidate for the treatment of VL.
Optimization of Optical Wavelength Conversion in SOI Waveguide (2011)

In this paper the wavelength conversion in a 1cm long silicon-on-insulator (SOI) waveguide has been investigated numerically. The wavelength conversion efficiency is optimized by analyzing free carriers absorption (FCA) loss generated by two-photon-absorption (TPA). The free carriers life time is focused while other factors influencing noise figure are also considered.
Effect of Whole-Body Hyperthermia on AIDS Patients with Kaposi's Sarcoma: A Pilot Study (1996)

The safety and possible efficacy of extracorporeal whole-body hyperthermia (WBHT) were evaluated in the first FDA-approved feasibility study of WBHT in persons with AIDS. Six gay men, aged 20-50 years, CDC class C-3, underwent 1 h of WBHT at either 40 degrees C or 42 degrees C, employing a system that minimizes the physiological and biochemical changes that occur during WBHT. All subjects had Kaposi's sarcoma (KS), were free of opportunistic infections, and had significant elevations of plasma HIV RNA. During the treatment, there were no adverse side effects and all subjects tolerated WBHT without problems. KS lesions partially regressed immediately following WBHT in all subjects but returned to pretreatment status in five of six patients at 1 week. In subjects treated at 40 degrees C, CD4 counts decreased during the 8-week follow-up period; they remained unchanged, however, following 42 degrees C WBHT. Viral load remained unchanged following WBHT in subjects treated at 40 degrees C. Treatment at 42 degrees C resulted in an immediate reduction in HIV RNA that was not sustained at 1 week post-WBHT. We conclude that WBHT is safe in subjects with advanced HIV disease and that it may have a role in treating HIV infection. A larger controlled trial involving two treatments in less immunocompromised subjects is currently in progress to test this hypothesis.
Early Career Researchers between Predatory Publishing and Academic Excellence: The Views and Behaviours of the Millennials (2021)

The paper draws on evidence of predatory publishing obtained from the 4 year-long Harbingers research study of the changing scholarly communication attitudes and behaviour of early career researchers (ECRs). The project featured longitudinal interviews for its first 3 years with 116 ECRs researching science and social sciences who came from China, France, Malaysia, Poland, Spain, UK and USA. The interview data provided the building blocks for a questionnaire survey in the 4th year, which obtained 1600 responses from a global audience, which included arts and humanities ECRs and those from Russia. These studies investigated predatory publishing as part of general questioning about scholarly communications, in other words, in context. The main finding from the interview study were:1) ECRs generally do not publish in predatory journals; 2) they only allude to them lightly and mainly in the context of open access publishing; 3) they no longer acquaint all open access publishing with predatory journals. The questionnaire found that, as in the case of the interviews, complaints that open access is low quality publishing are diminishing, however, this positivity has been partly offset by increased concerns about the dangers of predatory journals.
Evaluation of systemic blood NO dynamics by EPR spectroscopy: HbNO as an endogenous index of NO (2003)

The measurement of hemoglobin-nitric oxide (NO) adduct (HbNO) in whole blood by the electron paramagnetic resonance (EPR) method seems relevant for the assessment of systemic NO levels. However, ceruloplasmin and unknown radical species overlap the same magnetic field as that of HbNO. To reveal the EPR spectrum of HbNO, we then introduced the EPR signal subtraction method, which is based on the computer-assisted subtraction of the digitized EPR spectrum of HbNO-depleted blood from that of sample blood using the software. Rats were treated with N(omega)-nitro-L-arginine methyl ester (L-NAME; 120 mg. kg-1. day-1) for 1 wk to obtain HbNO-depleted blood. When this method was applied to the analysis of untreated fresh whole blood, the five-coordinate state of HbNO was observed. HbNO concentration in pentobarbital-anesthetized rats was augmented (change in [HbNO] = 1.6-5.5 microM) by infusion of L-arginine (0.2-0.6 g/kg) but not D-arginine. Using this method, we attempted to evaluate the effects of temocapril on HbNO dynamics in an L-NAME-induced rat endothelial dysfunction model. The oral administration of L-NAME for 2 wk induced a serious hypertension, and the HbNO concentration was reduced (change in [HbNO] = 5.7 microM). Coadministration of temocapril dose dependently improved both changes in blood pressure and the systemic HbNO concentration. In this study, we succeeded in measuring the blood HbNO level as an index of NO by the EPR HbNO signal subtraction method. We also demonstrated that temocapril improves abnormalities of NO dynamics in L-NAME-induced endothelial dysfunction rats using the EPR HbNO signal subtraction method.
Mo:Y multilayer mirror technology utilized to image the near-field output of a Ni-like Sn laser at 119nm (2003)

Although bright x-ray sources exist at shorter wavelengths, the development of sophisticated diagnostics with x-ray laser sources has been restricted to wavelengths longer than 12.5 nm because of the limitations of the widely used Mo:Si multilayer mirrors. With the novel Mo:Y multilayer mirrors that we present, many x-ray laser applications can be extended to the 7-12-nm range. We demonstrate this new capability by imaging the near-field output of the Ni-like Sn laser at 11.9 nm.
Lysyl Oxidase as a Potential Therapeutic Target (2008)

Lysyl oxidase (LOX) is a copper-dependent amine oxidase that catalyzes the covalent cross-link of collagens and elastin in the extracellular environment, thereby determining the mechanical properties of extracellular matrix (ECM) and connective tissues. ECM remodeling is a common feature of diverse pathologic processes. Therefore, dysregulation of LOX could underlie the onset and progression of multiple pathologies affecting connective tissue, such as fibrotic processes, tumor progression and metastasis and neurodegenerative and cardiovascular diseases. Here we review clinical and experimental evidence that supports a role for LOX in the pathophysiology of those processes and point out LOX as a potential therapeutic target.