bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV testing practices among New England college health centers
Authors: Patel Nilay , Rana Aadia , Thomas Alyssa , Barnhart John C , Flanigan Timothy P , van den Berg Jacob J , Chan Philip A 
Published: March 2013

Abstract

Background
The prevalence of human immunodeficiency virus (HIV) continues to increase among certain populations including young men who have sex with men (MSM). College campuses represent a potential setting to engage young adults and institute prevention interventions including HIV testing. The purpose of this study was to evaluate testing practices for HIV and other sexually transmitted infections (STIs) on college campuses.

Methods
Medical directors at four-year residential baccalaureate college health centers in New England were surveyed from June, 2011 to September, 2011. Thirty-one interviews were completed regarding experiences with HIV testing, acute HIV infection, other STI testing, and outreach efforts targeting specific at-risk groups such as MSM.

Results
Among schools that responded to the survey, less than five percent of students were tested for HIV at their local college health center in the past academic year (2010–2011). Significant barriers to HIV testing included cost and availability of rapid antibody testing. One-third of college health medical directors reported that their practitioners may not feel comfortable recognizing acute HIV infection.

Conclusions
Improved HIV testing practices are needed on college campuses. Programs should focus on outreach efforts targeting MSM and other at-risk populations.
Respiratory complex I is essential to induce a Warburg profile in mitochondria-defective tumor cells
Authors: Calabrese Claudia , Iommarini Luisa , Kurelac Ivana , Calvaruso Maria Antonietta , Capristo Mariantonietta , Lollini Pier-Luigi , Nanni Patrizia , Bergamini Christian , Nicoletti Giordano , De Giovanni Carla , Ghelli Anna , Giorgio Valentina , Caratozzolo Mariano Francesco , Marzano Flaviana , Manzari Caterina , Betts Christine M , Carelli Valerio , Ceccarelli Claudio , Attimonelli Marcella , Romeo Giovanni , Fato Romana , Rugolo Michela , Tullo Apollonia , Gasparre Giuseppe , Porcelli Anna Maria 
Published: March 2013

Abstract

Background
Aerobic glycolysis, namely the Warburg effect, is the main hallmark of cancer cells. Mitochondrial respiratory dysfunction has been proposed to be one of the major causes for such glycolytic shift. This hypothesis has been revisited as tumors appear to undergo waves of gene regulation during progression, some of which rely on functional mitochondria. In this framework, the role of mitochondrial complex I is still debated, in particular with respect to the effect of mitochondrial DNA mutations in cancer metabolism. The aim of this work is to provide the proof of concept that functional complex I is necessary to sustain tumor progression.

Methods
Complex I-null osteosarcoma cells were complemented with allotopically expressed complex I subunit 1 (MT-ND1). Complex I re-assembly and function recovery, also in terms of NADH consumption, were assessed. Clones were tested for their ability to grow in soft agar and to generate tumor masses in nude mice. Hypoxia levels were evaluated via pimonidazole staining and hypoxia-inducible factor-1α (HIF-1α) immunoblotting and histochemical staining. 454-pyrosequencing was implemented to obtain global transcriptomic profiling of allotopic and non-allotopic xenografts.

Results
Complementation of a truncative mutation in the gene encoding MT-ND1, showed that a functional enzyme was required to perform the glycolytic shift during the hypoxia response and to induce a Warburg profile in vitro and in vivo, fostering cancer progression. Such trigger was mediated by HIF-1α, whose stabilization was regulated after recovery of the balance between α-ketoglutarate and succinate due to a recuperation of NADH consumption that followed complex I rescue.

Conclusion
Respiratory complex I is essential for the induction of Warburg effect and adaptation to hypoxia of cancer cells, allowing them to sustain tumor growth. Differently from other mitochondrial tumor suppressor genes, therefore, a complex I severe mutation such as the one here reported may confer anti-tumorigenic properties, highlighting the prognostic values of such genetic markers in cancer.
Treatment of rheumatoid arthritis in the Medicare Current Beneficiary Survey
Authors: Solomon Daniel H , Yelin Edward , Katz Jeffrey N , Lu Bing , Shaykevich Tamara , Ayanian John Z 
Published: March 2013

Abstract
Introduction
Numerous studies across different health systems have documented that many patients with rheumatoid arthritis (RA) do not receive disease-modifying anti-rheumatic drugs (DMARDs). Relatively little is known about correlates of DMARD use and whether there are socioeconomic and demographic disparities. We examined DMARD use during 2001 to 2006 in the Medicare Current Beneficiary Survey (MCBS), a longitudinal US survey of randomly selected Medicare beneficiaries.

Methods
Participants in MCBS with RA were included in the analyses, and DMARD use was based on an in-home assessment of all medications. Variables included as potential correlates of DMARD use in weighted regression models included race/ethnicity, insurance, income, education, rheumatology visit, region, age, gender, comorbidity index, and calendar year.

Results
The cohort consisted of 509 MCBS participants with a diagnosis code for RA. Their median age was 70 years, 72% were female, and 24% saw a rheumatologist. Rates of DMARD use ranged from 37% among those <75 years of age to 25% of those age 75 to 84 and 4% of those age 85 and older. The multivariable adjusted predictors of DMARD use include: visit with a rheumatologist in the prior year (odds ratio, OR, 7.74, 95% CI, 5.37, 11.1) and older patient age (compared with <75 years, ages 75 to 84, OR 0.58, 95% CI 0.37, 0.92, and 85 and over, OR 0.09, 95% CI 0.02, 0.31). In those without a rheumatology visit, lower income and older age were associated with a significantly reduced probability of DMARD use; no association of DMARD use with income or age was observed for subjects seen by rheumatologists. Race and ethnicity were not significantly associated with receipt of DMARDs.

Conclusions
Among individuals not seeing rheumatologists, lower income and older age were associated with a reduced probability of DMARD use.
Treatment of Children and Adolescents With Hodgkin Lymphoma Without Radiotherapy for Patients in Complete Remission After Chemotherapy: Final Results of the Multinational Trial GPOH-HD95
Authors: Dörffel Wolfgang , Rühl Ursula , Lüders Heike , Claviez Alexander , Albrecht Marion , Bökkerink Jos , Holte Harald , Karlen Jonas , Mann Georg , Marciniak Heinz , Niggli Felix , Schmiegelow Kjeld , Schwarze Ernst-Wilhelm , Pötter Richard , Wickmann Lutz , Schellong Günther 
Published: March 2013

PurposeTo minimize the risk of late effects in pediatric Hodgkin lymphoma (HL) by omitting radiotherapy (RT) in patients in complete remission (CR) after chemotherapy and reducing the standard radiation dose to 20 Gy in patients in incomplete remission.Patients and MethodsBetween 1995 and 2001, 925 patients with classical HL (cHL) were registered from seven European countries in German Society of Pediatric Oncology and Hematology Hodgkin Lymphoma Trial 95. Patients in treatment group 1 (TG1; early stages) received two cycles of vincristine, prednisone, procarbazine, and doxorubicin or vincristine, prednisone, etoposide, and doxorubicin chemotherapy; additional two or four cycles of cyclophosphamide, vincristine, prednisone, and procarbazine were added in TG2 (intermediate stages) or TG3 (advanced stages), respectively. Patients in CR (assessed by computed tomography or magnetic resonance imaging) did not undergo RT. Those with tumor volume reduction more than 75% received reduced involved-field RT with 20 Gy and an additional 10- or 15-Gy boost only for larger residuals.ResultsRates of overall survival, progression-free survival (PFS), and event-free survival at 10 years were (± SE) 96.3% ± 0.6%, 88.2% ± 1.1%, and 85.4% ± 1.3%, respectively. PFS for TG1 patients without or with RT was 97.0% ± 2.1% versus 92.2% ± 1.7% (P = .214) but was unsatisfactory for nonirradiated patients in TG2 (68.5% ± 7.4% v 91.4% ± 1.9%; P < .0001), with similar but not significant results in TG3 (82.6% ± 5.4% v 88.7% ± 2.0%, P = .259). Reduction of the standard radiation dose from 25 to 20 Gy did not increase failure rate.ConclusionRT can be omitted in early stage HL in so defined CR following this chemotherapy. RT with 20(−35) Gy proved to be sufficient in patients with incomplete remission following chemotherapy.
Theoretical Study on the Mechanism of Dioxygen Evolution in Photosystem II. I. Molecular and Electronic Structures at the S0, S1, and S2 States of Oxygen-Evolving Complex
Authors: Ichino Tomoya , Yoshioka Yasunori 
Published: March 2013

Abstract
Based on the structure at 1.9 Å resolved OEC (PDBid=3ARC), geometries and electronic structures of the S0, S1, and S2 states in the Kok cycle have been theoretically investigated by the broken-symmetry B3LYP method. The exchange coupling constants of spins in three states were also estimated. The oxidation states of four manganese atoms at the S0 state are Mn4[III, III, IV, III]. It was found that the hydrogen-bonding patterns of water molecules are influenced by the electronic structure of the CaMn4O5 core. At the S1 state, the oxidation states are Mn4[III, IV, IV, III]. The hydrogen-bonding pattern of the lowest state is similar to that of the higher energy state of the S0 state. The H2O molecule coordinated to the Mn4 atom loses a proton to yield an OH− anion. At the S2 state, the oxidation states are Mn4[III, IV, IV, IV]. For S0 → S1 → S2 states, the released electrons have the same direction of spins. Only Mn atoms are oxidized not the substrate (H2O). Our theoretical results are consistent with the observed results.
Synthesis of Substituted Sumanenes by Aromatic Electrophilic Substitution Reactions
Authors: Shrestha Binod Babu , Karanjit Sangita , Panda Gautam , Higashibayashi Shuhei , Sakurai Hidehiro 
Published: March 2013

Abstract
Electrophilic substitution reactions of sumanene were studied. Mono-, di-, and trisubstituted sumanenes were selectively prepared with the separation of all regioisomers. The regioselectivity was predicted well by the HOMO density values determined by DFT calculations.
Ionic liquid catalyzed one-pot synthesis of spiropyran derivatives via three-component reaction in water
Authors: Jin Shuai-Shuai , Ding Mao-Hua , Guo Hong-Yun 
Published: March 2013

Abstract
The ionic liquid [H3N+CH2CH2OH][CH3COO-] (HEAA) catalyzes a three-component, one-pot condensation of malononitrile/ethyl cyanoacetate, 1,3-dicarbonyl compound/enol, and quinone or ninhydrin in water to afford a spiropyran derivative. This method has advantages of mild reaction conditions, short reaction time, and environmental friendliness.
Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing
Authors: Tilgner Hagen , Raha Debasish , Habegger Lukas , Mohiuddin Mohammed , Gerstein Mark , Snyder Michael 
Published: March 2013

AbstractPrecise identification of RNA-coding regions and transcriptomes of eukaryotes is a significant problem in biology. Currently, eukaryote transcriptomes are analyzed using deep short-read sequencing experiments of complementary DNAs. The resulting short-reads are then aligned against a genome and annotated junctions to infer biological meaning. Here we use long-read complementary DNA datasets for the analysis of a eukaryotic transcriptome and generate two large datasets in the human K562 and HeLa S3 cell lines. Both data sets comprised at least 4 million reads and had median read lengths greater than 500 bp. We show that annotation-independent alignments of these reads provide partial gene structures that are very much in-line with annotated gene structures, 15% of which have not been obtained in a previous de novo analysis of short reads. For long-noncoding RNAs (i.e., lncRNA) genes, however, we find an increased fraction of novel gene structures among our alignments. Other important aspects of transcriptome analysis, such as the description of cell type-specific splicing, can be performed in an accurate, reliable and completely annotation-free manner, making it ideal for the analysis of transcriptomes of newly sequenced genomes. Furthermore, we demonstrate that long read sequence can be assembled into full-length transcripts with considerable success. Our method is applicable to all long read sequencing technologies.
Resource Allocation for Maximizing Prediction Accuracy and Genetic Gain of Genomic Selection in Plant Breeding: A Simulation Experiment
Authors: Lorenz Aaron J 
Published: March 2013

Abstract
Allocating resources between population size and replication affects both genetic gain through phenotypic selection and quantitative trait loci detection power and effect estimation accuracy for marker-assisted selection (MAS). It is well known that because alleles are replicated across individuals in quantitative trait loci mapping and MAS, more resources should be allocated to increasing population size compared with phenotypic selection. Genomic selection is a form of MAS using all marker information simultaneously to predict individual genetic values for complex traits and has widely been found superior to MAS. No studies have explicitly investigated how resource allocation decisions affect success of genomic selection. My objective was to study the effect of resource allocation on response to MAS and genomic selection in a single biparental population of doubled haploid lines by using computer simulation. Simulation results were compared with previously derived formulas for the calculation of prediction accuracy under different levels of heritability and population size. Response of prediction accuracy to resource allocation strategies differed between genomic selection models (ridge regression best linear unbiased prediction [RR-BLUP], BayesCπ) and multiple linear regression using ordinary least-squares estimation (OLS), leading to different optimal resource allocation choices between OLS and RR-BLUP. For OLS, it was always advantageous to maximize population size at the expense of replication, but a high degree of flexibility was observed for RR-BLUP. Prediction accuracy of doubled haploid lines included in the training set was much greater than of those excluded from the training set, so there was little benefit to phenotyping only a subset of the lines genotyped. Finally, observed prediction accuracies in the simulation compared well to calculated prediction accuracies, indicating these theoretical formulas are useful for making resource allocation decisions.
Cell-Cycle Perturbations Suppress the Slow-Growth Defect ofspt10ΔMutants inSaccharomyces cerevisiae
Authors: Chang Jennifer S , Winston Fred 
Published: March 2013

AbstractSpt10 is a putative acetyltransferase of Saccharomyces cerevisiae that directly activates the transcription of histone genes. Deletion of SPT10 causes a severe slow growth phenotype, showing that Spt10 is critical for normal cell division. To gain insight into the function of Spt10, we identified mutations that impair or improve the growth of spt10 null (spt10Δ) mutants. Mutations that cause lethality in combination with spt10Δ include particular components of the SAGA complex as well as asf1Δ and hir1Δ. Partial suppressors of the spt10Δ growth defect include mutations that perturb cell-cycle progression through the G1/S transition, S phase, and G2/M. Consistent with these results, slowing of cell-cycle progression by treatment with hydroxyurea or growth on medium containing glycerol as the carbon source also partially suppresses the spt10Δ slow-growth defect. In addition, mutations that impair the Lsm1-7−Pat1 complex, which regulates decapping of polyadenylated mRNAs, also partially suppress the spt10Δ growth defect. Interestingly, suppression of the spt10Δ growth defect is not accompanied by a restoration of normal histone mRNA levels. These findings suggest that Spt10 has multiple roles during cell division.
Nectocaridid ecology, diversity, and affinity: early origin of a cephalopod-like body plan
Authors: Smith Martin R. 
Published: March 2013

Nectocaridids are soft-bodied early to middle Cambrian organisms known from Burgess Shale-type deposits in Canada, China, and Australia. Originally described as unrelated species, they have recently been interpreted as a clade; their flexible tentacles, camera-type eyes, lateral fins, internal gills, axial cavity, and funnel point to a relationship with the cephalopods. However, aspects of this reinterpretation, including the relevance of the group to cephalopod evolution, have been called into question.Here, I examine new and existing nectocaridid material, including a large new form that may represent a sexual dimorph ofNectocaris pteryx. Differences between existing taxa largely represent taphonomic variation between sites and specimens—which provides further constraint on the organisms' anatomy. I revise the morphology of the tentacles and fins, and describe mouthparts and phosphatized gills for the first time. A mathematical analysis supports the presence of the earliest known camera-type eyes, and fluid mechanical considerations suggest that the funnel is optimized for efficient jet propulsion in a low Reynolds number flow regime.Nectocaridids closely resemble coleoid cephalopods, but a position deeper within Cephalopoda raises fewer stratigraphic challenges. Whether its coleoid-like construction reflects common ancestry or profound convergence, theNectocarisbody plan adds substantially to Cambrian disparity, demonstrating the rapid colonization of nektobenthic niches after the Cambrian explosion.
Multicriteria Risk Assessment of Permian Basin Tank-Battery Facilities Using GIS
Authors: Pierce Timothy L. , Wills Grant K. 
Published: March 2013

Abstract
The development of a multicriteria, GIS-based model provides a systematic tool for assessing comprehensive risk for Permian Basin tank-battery facilities. Input variables include maximum saturated soil hydraulic conductivity, surface-water proximity, water-well proximity, depth to groundwater, public-road proximity, maximum HsS concentration, maximum reading of naturally occurring radioactive materials (NORM), total tank capacity, and average daily oil production. Raw values for these variables are derived from many different source datasets that undergo a wide range of formatting and geoprocessing.
Through a weighted linear combination (WLC) method coupled with the Analytic Hierarchy Process (AHP), raw variable scores are converted to a common, normalized scale and weighted according to relative importance. The weighted, normalized criteria scores are then summed to yield the overall risk score for each facility. The intention of the model is to identify facilities for which HSE incidents may have greater negative impact so that proactive measures can be taken in ensuring these higher-risk facilities receive additional inspections, maintenance, etc.
We apply the model to 122 facilities in a study area straddling Midland and Glasscock Counties in West Texas. Preliminary results yield a low overall risk range and suggest heavier weights on environmental criteria may produce a more useful score range while also recognizing spills as the most prevalent hazard associated with these facilities. Regardless of the overall score range, the model can be useful in defining relative risk among facilities for relative prioritization. Testing and expansion of the model into other areas and adding new criteria will continue to improve its applicability to current and future risk-based projects in the Permian Basin.
MultiObjective Genetic Modified Algorithm (MOGMA)
Authors: Vandeva Elica 
Published: March 2013

Abstract
Multiobjective optimization based on genetic algorithms and Pareto based approaches in solving multiobjective optimization problems is discussed in the paper. A Pareto based fitness assignment is used − non-dominated ranking and movement of a population towards the Pareto front in a multiobjective optimization problem. A MultiObjective Genetic Modified Algorithm (MOGMA) is proposed, which is an improvement of the existing algorithm.
Sexual Coercion Risk and Women’s Sport Participation
Authors: Brown Elise , Spiller Laura , Stiles Beverly , Kilgore Lon 
Published: March 2013

Abstract Sexual coercion affects approximately 58% of college-age females. Victims of sexual coercion often share similar characteristics, such as lower self-esteem, lower assertiveness, higher depressive symptoms, higher alcohol use, increased number of sexual partners, more romantic relationships, prior victimization, and relationship insecurity. Female athletes, on the other hand, have in common such protective factors as higher self-esteem, higher assertiveness, lower alcohol use, and fewer sexual partners. These, then, are assumed to guard against sexual coercion. The purpose of this study was to determine if female athletes were at a lower risk for sexual coercion and whether differences existed in levels of assertiveness, sexual assertiveness, self-esteem, sexual esteem, alcohol use, and the number of sexual partners. Participants included 174 college females (aged 19.94 ± 1.87 years). Participants were identified as an athlete if they reported a history of at least three years of athl iation etic involvement and described themselves as either a high school athlete or having participated in competitive sports (n=125). From among all the participants, 49 were classified as non-athletes. Data demonstrated no differences in either forced or coerced sexual contact history. Athletes and nonathletes differed neither in global nor sexual self-esteem, nor did they differ in global or sexual assertiveness. There was a significant difference across the groups in alcohol use: athletes scored higher on the AUDIT than non-athletes. The number of years of sport involvement positively correlated with the level of alcohol use. Athletes and non-athletes reported similar numbers of sexual partners. The findings of this study imply that athletics may indirectly place females at risk for sexual coercion through an assocwith higher alcohol use.
Microorganisms Associated with Valencia Peanut Affected by Pod Rot in New Mexico
Authors: Sanogo S. , Puppala N. 
Published: March 2013

Abstract
Pod rot of peanut is a disease that occurs worldwide. Soilborne pathogens typically causing pod rot include Rhizoctonia solani, Sclerotium rolfsii, and Pythium spp. Although pod rot is known to occur in New Mexico, no etiological study has been conducted on this disease. In 2005 and 2006, 14 Valencia peanut fields were surveyed in eastern New Mexico where the majority of Valencia peanut is produced. The primary focus of the study was to isolate and identify microorganisms associated with pod rot. The secondary focus of the study was to characterize microorganisms from roots and stems from the same plants selected for pod rot assessment. Peanut plants were collected and processed for isolation of microorganisms by plating seeds, pieces of hull, root, and stem on acidified potato dextrose agar. In both years, the average incidence of pods with hull discoloration or pod rot symptoms varied from 55–60 to over 90%, and disease severity ranged from 5 to over 90% across all fields surveyed. A diverse group of microorganisms representing more than 10 fungal and Oomycete genera were recovered from all plant part tissues, with R. solani as the most predominantly isolated mycelial microorganism. Rhizoctonia solani was found in all fields with average frequency of isolation from approximately 20 to 27% for pod tissue, 19 to 36% for root, and 20 to 27% for stem. In controlled-environment studies, all isolates of R. solani from different plant parts were shown to be pathogenic to Valencia peanut. This etiological study is the first in New Mexico to provide an insight into microorganisms associated with peanut affected by pod rot. Breeding Valencia peanuts for resistance to Rhizoctonia pod rot should be a priority.