bluuebunny/crossref_metadata_2025_split huggingface dataset:
HIV Populations Are Large and Accumulate High Genetic Diversity in a Nonlinear Fashion
Authors: Maldarelli Frank , Kearney Mary , Palmer Sarah , Stephens Robert , Mican JoAnn , Polis Michael A. , Davey Richard T. , Kovacs Joseph , Shao Wei , Rock-Kress Diane , Metcalf Julia A. , Rehm Catherine , Greer Sarah E. , Lucey Daniel L. , Danley Kristen , Alter Harvey , Mellors John W. , Coffin John M. 
Published: May 2013

ABSTRACTHIV infection is characterized by rapid and error-prone viral replication resulting in genetically diverse virus populations. The rate of accumulation of diversity and the mechanisms involved are under intense study to provide useful information to understand immune evasion and the development of drug resistance. To characterize the development of viral diversity after infection, we carried out an in-depth analysis of single genome sequences of HIVpro-polto assess diversity and divergence and to estimate replicating population sizes in a group of treatment-naive HIV-infected individuals sampled at single (n= 22) or multiple, longitudinal (n= 11) time points. Analysis of single genome sequences revealed nonlinear accumulation of sequence diversity during the course of infection. Diversity accumulated in recently infected individuals at rates 30-fold higher than in patients with chronic infection. Accumulation of synonymous changes accounted for most of the diversity during chronic infection. Accumulation of diversity resulted in population shifts, but the rates of change were low relative to estimated replication cycle times, consistent with relatively large population sizes. Analysis of changes in allele frequencies revealed effective population sizes that are substantially higher than previous estimates of approximately 1,000 infectious particles/infected individual. Taken together, these observations indicate that HIV populations are large, diverse, and slow to change in chronic infection and that the emergence of new mutations, including drug resistance mutations, is governed by both selection forces and drift.
Sequential rationality in cryptographic protocols
Authors: Gradwohl Ronen , Livne Noam , Rosen Alon 
Published: May 2013

Much of the literature on rational cryptography focuses on analyzing the strategic properties of cryptographic protocols. However, due to the presence of computationally-bounded players and the asymptotic nature of cryptographic security, a definition of sequential rationality for this setting has thus far eluded researchers.We propose a new framework for overcoming these obstacles, and provide the first definitions of computational solution concepts that guarantee sequential rationality. We argue that natural computational variants of subgame perfection are too strong for cryptographic protocols. As an alternative, we introduce a weakening called threat-free Nash equilibrium that is more permissive but still eliminates the undesirable “empty threats” of nonsequential solution concepts.To demonstrate the applicability of our framework, we revisit the problem of implementing a mediator for correlated equilibria [Dodis et al 2000], and propose a variant of their protocol that is sequentially rational for a nontrivial class of correlated equilibria. Our treatment provides a better understanding of the conditions under which mediators in a correlated equilibrium can be replaced by a stable protocol.
New Breast Cancer Risk Variant Discovered at 10q25 in East Asian Women
Authors: Shi Jiajun , Sung Hyuna , Zhang Ben , Lu Wei , Choi Ji-Yeob , Xiang Yong-Bing , Kim Mi Kyung , Iwasaki Motoki , Long Jirong , Ji Bu-Tian , Park Sue K. , Zheng Ying , Tsugane Shoichiro , Yoo Keun-Young , Wang Wenjing , Noh Dong-Young , Han Wonshik , Kim Sung-Won , Lee Min Hyuk , Lee Jong Won , Lee Jong-Young , Shen Chen-Yang , Matsuo Keitaro , Ahn Sei-Hyun , Gao Yu-Tang , Shu Xiao Ou , Cai Qiuyin , Kang Daehee , Zheng Wei 
Published: May 2013

Abstract
Background: Recently, 41 new genetic susceptibility loci for breast cancer risk were identified in a genome-wide association study (GWAS) conducted in European descendants. Most of these risk variants have not been directly replicated in Asian populations.
Methods: We evaluated nine of those nonreplication loci in East Asians to identify new risk variants for breast cancer in these regions. First, we analyzed single-nucleotide polymorphisms (SNP) in these regions using data from two GWAS conducted among Chinese and Korean women, including 5,083 cases and 4,376 controls (stage 1). In each region, we selected an SNP showing the strongest association with breast cancer risk for replication in an independent set of 7,294 cases and 9,404 controls of East Asian descents (stage 2). Logistic regression models were used to calculate adjusted ORs and 95% confidence intervals (CI) as a measure of the association of breast cancer risk and genetic variants.
Results: Two SNPs were replicated in stage 2 at P &lt; 0.05: rs1419026 at 6q14 [per allele OR, 1.07; 95% confidence interval (CI), 1.03–1.12; P = 3.0 × 10−4] and rs941827 at 10q25 (OR, 0.92, 95% CI, 0.89–0.96; P = 5.3 × 10−5). The association with rs941827 remained highly statistically significant after adjusting for the risk variant identified initially in women of European ancestry (OR, 0.88; 95% CI, 0.82–0.97; P = 5.3 × 10−5).
Conclusion: We identified a new breast cancer risk variant at 10q25 in East Asian women.
Impact: Results from this study improve the understanding of the genetic basis for breast cancer. Cancer Epidemiol Biomarkers Prev; 22(7); 1297–303. ©2013 AACR.
Genome-Wide Association Study Identifies Possible Genetic Risk Factors for Colorectal Adenomas
Authors: Edwards Todd L. , Shrubsole Martha J. , Cai Qiuyin , Li Guoliang , Dai Qi , Rex Douglas K. , Ulbright Thomas M. , Fu Zhenming , Delahanty Ryan H. , Murff Harvey J. , Smalley Walter , Ness Reid M. , Zheng Wei 
Published: May 2013

Abstract
Background: Colorectal cancer is the second leading cause of cancer-related death, and most colorectal cancer usually arises from colorectal adenomas. Removal of polyps reduces mortality from colorectal cancer. Colorectal adenomas are known to aggregate in families; however, the genetic determinants for risk of polyps are largely unknown.
Methods: In this study, we used data from the Tennessee Colorectal Polyp Study and the Tennessee-Indiana Adenoma Recurrence Study to conduct a GWAS of adenoma cases and controls. Our design consisted of discovery and replication phases for a total of 2,551 Caucasian adenoma cases and 3,285 Caucasian controls. We carried out logistic regression to test for association in both the discovery and replication phase and further examined the results with meta-analysis.
Results: No single nucleotide polymorphism (SNP) achieved a genome-wide significant P value; however, the most significantly associated SNPs were either previously associated with colorectal cancer in GWAS, such as rs10505477 in the gene POU5F1 [odds ratio (OR) = 0.87; 95% confidence interval (CI) 0.81–0.94; P = 4.4 × 10−4), or have been biologically linked to benign growths in other tissues, such as rs1919314 in the gene histone deacetylase 9 (OR = 1.32; 95% CI, 1.18–1.47; P = 1.1 × 10−6).
Conclusions: This study suggests that several SNPs may be related to adenoma risk and provides clues for future studies.
Impact: These results suggest that some known genetic risk factors of colorectal cancer are necessary but not sufficient for carcinogenesis. Cancer Epidemiol Biomarkers Prev; 22(7); 1219–26. ©2013 AACR.
Hormonal and Reproductive Risk Factors for Sporadic Microsatellite Stable and Unstable Endometrial Tumors
Authors: Amankwah Ernest K. , Friedenreich Christine M. , Magliocco Anthony M. , Brant Rollin , Speidel Thomas , Rahman Wahida , Cook Linda S. 
Published: May 2013

AbstractHormonal and reproductive factors modulate bioavailable estrogen to influence endometrial cancer risk. Estrogen affects the microsatellite status of tumors, but the relation between these estrogen-related factors and microsatellite instability (MSI) status of endometrial tumors is not known. We evaluated associations between hormonal and reproductive factors and risks of microsatellite stable (MSS) and MSI endometrial cancer among postmenopausal women (MSS cases = 258, MSI cases = 103, and controls = 742) in a population-based case–control study in Alberta, Canada (2002–2006). Polytomous logistic regression was used to estimate ORs and 95% confidence intervals (95% CI). We observed a significant trend in risk reduction for MSI (Ptrend = 0.005) but not MSS (Ptrend = 0.23) cancer with oral contraceptive use; with 5-year use or more, the risk reduction was stronger for MSI (OR = 0.42; 95% CI, 0.23–0.77) than for MSS cancer (OR = 0.80; 95% CI, 0.54–1.17; Pheterogeneity = 0.05). For more recent use (&lt;30 years), the risk reduction was stronger for MSI (OR = 0.36; 95% CI, 0.19–0.69) than for MSS cancer (OR = 0.77; 95% CI, 0.51–1.15; Pheterogeneity = 0.032). No differential risk associations were observed for menopausal hormone use, parity and age at menarche, menopause or first pregnancy. We found limited evidence for statistical heterogeneity of associations of endometrial cancer risk with hormonal and reproductive factors by MSI status, except with oral contraceptive use. This finding suggests a potential role for the MMR system in the reduction of endometrial cancer risk associated with oral contraceptive use, although the exact mechanism is unclear.This study shows for the first time that oral contraceptive use is associated with a reduced risk for MSI but not for MSS endometrial cancer. Cancer Epidemiol Biomarkers Prev; 22(7); 1325–31. ©2013 AACR.
Exome Sequencing and Systems Biology Converge to Identify Novel Mutations in the L-Type Calcium Channel,
CACNA1C
, Linked to Autosomal Dominant Long QT Syndrome
Authors: Boczek Nicole J. , Best Jabe M. , Tester David J. , Giudicessi John R. , Middha Sumit , Evans Jared M. , Kamp Timothy J. , Ackerman Michael J. 
Published: May 2013

Background—
Long QT syndrome (LQTS) is the most common cardiac channelopathy with 15 elucidated LQTS-susceptibility genes. Approximately 20% of LQTS cases remain genetically elusive.

Methods and Results—

We combined whole-exome sequencing and bioinformatic/systems biology to identify the pathogenic substrate responsible for nonsyndromic, genotype-negative, autosomal dominant LQTS in a multigenerational pedigree, and we established the spectrum and prevalence of variants in the elucidated gene among a cohort of 102 unrelated patients with “genotype-negative/phenotype-positive” LQTS. Whole-exome sequencing was used on 3 members within a genotype-negative/phenotype-positive family. Genomic triangulation combined with bioinformatic tools and ranking algorithms led to the identification of a
CACNA1C
mutation. This mutation, Pro857Arg-CACNA1C, cosegregated with the disease within the pedigree, was ranked by 3 disease-network algorithms as the most probable LQTS-susceptibility gene and involves a conserved residue localizing to the proline, gltamic acid, serine, and threonine (PEST) domain in the II-III linker. Functional studies reveal that Pro857Arg-CACNA1C leads to a gain of function with increased I
Ca,L
and increased surface membrane expression of the channel compared to wild type. Subsequent mutational analysis identified 3 additional variants within
CACNA1C
in our cohort of 102 unrelated cases of genotype-negative/phenotype-positive LQTS. Two of these variants also involve conserved residues within Ca
v
1.2’s PEST domain.

Conclusions—

This study provides evidence that coupling whole-exome sequencing and bioinformatic/systems biology is an effective strategy for the identification of potential disease-causing genes/mutations. The identification of a functional
CACNA1C
mutation cosegregating with disease in a single pedigree suggests that
CACNA1C
perturbations may underlie autosomal dominant LQTS in the absence of Timothy syndrome.
Development of sexual and socio-sexual behaviours in free-ranging juvenile male Japanese macaques, Macaca fuscata
Authors: Gunst Noëlle , Leca Jean-Baptiste , Vasey Paul L. 
Published: May 2013

The emergence of conceptive and non-conceptive sexual behaviours in mature individuals can be traced back to immature socio-sexual behavioural patterns. We tested the ‘needing-to-learn hypothesis’ in the development of sexual behaviours in the immature male Japanese macaques of Arashiyama, Japan. This hypothesis holds that juvenility serves to provide young individuals with a period in which to practice adult male-like sexual and socio-sexual behaviours and partner choice. Our cross-sectional focal data on mounting behaviour and partner choice in juvenile males (1–3 years) supported most of our predictions: (1) as they became older and learnt more effective patterns of sexual solicitations, juvenile males performed more demonstrative solicitations and less non-demonstrative solicitations, (2) the frequency of mounts performed by juvenile males increased with age and converged on a frequency of mounts typical of adult males, (3) the frequency of mounts reflecting underachievement (i.e., improperly oriented mounts and single/no foot-clasp mounts) decreased as juvenile males became older, (4) the double foot-clasp mounting posture became gradually more common in juvenile males over time, while other mounting postures became less common and (5) from two to three years old, the frequency of males’ sexual mounts directed to adult females increased. Such timelines of gradual increase in the frequency of effective adult-like behavioural patterns and gradual decrease in the frequency of less effective immature behavioural patterns are consistent with the ‘needing-to-learn hypothesis’ emphasizing the role of age and practice in the progressive acquisition of adult-like sexual behaviour, mounting skills, and partner age choice during male juvenility.
A Reconceptualisation of the Self in Humanistic Psychology: Heidegger, Foucault and the Sociocultural Turn
Authors: McDonald Matthew , Wearing Stephen 
Published: May 2013

Abstract
Since the early 1970s humanistic psychology has struggled to remain a relevant force in the social and psychological sciences, we attribute this in part to a conceptualisation of the self rooted in theoretically outmoded thinking. In response to the issue of relevancy a sociocultural turn has been called for within humanistic psychology, which draws directly and indirectly on the conceptual insights of Michel Foucault. However, this growing body of research lacks a unifying conceptual base that is able to encompass its new perspectives (its call for a sociocultural turn) and the movement’s theoretical antecedents (the actualising tendency). This analysis suggests a way forward by offering a potential reconceptualisation of the self in humanistic psychology through the existential-phenomenology of Martin Heidegger. We argue that Heidegger’s conception of the self takes account of subjectivities produced in discourse and institutional practice, while acknowledging the human capacity for actualisation in his concept of the authentic-self.
A Study of the Serpent Incantation KTU2 1.82: 1–7 and its Contributions to Ugaritic Mythology and Religion
Authors: Miglio Adam E. 
Published: May 2013

Abstract
This article treats KTU2 1.82: 1–7, an Ugaritic incantation. It deals, first, with matters of epigraphy, philology, morpho-syntax and lexicography. Thereafter, it discusses the contributions of this incantation to understanding Ugaritic mythology and religion. In particular, it assesses the relationship of KTU2 1.82: 1–7 to the Ugaritic Baʕlu Cycle.
Preparation and microwave absorbing properties of polyaniline-modified silicon carbide composites
Authors: Li Sha , Gan Mengyu , Ma Li , Yan Jun , Tang Jihai , Fu Dandan , Li Zhitao , Bai Youqian 
Published: May 2013

Polyaniline (PANI)/silicon carbide (SiC) composites were prepared by emulsion polymerization using sodium dodecylbenzene sulfonate and ammonium persulfate as emulsifier and oxidant, respectively. The structure and morphology of the composites were characterized by Fourier transform infrared (FTIR) spectroscopy, x-ray diffraction (XRD), and scanning electron microscopy (SEM). The FTIR and XRD results indicated that there existed an interaction between PANI molecules and SiC particles. The SEM results indicated that SiC particles were covered with the conducting PANI. Microwave absorbing properties were investigated by measuring complex permittivity and complex permeability at 26.5–40 GHz. The results showed that the reflection loss (RL) properties of PANI/SiC composites exhibited significant improvements compared with pure SiC. A maximum RL of −36.3 dB was observed at 38.6 GHz with a thickness of 0.9 mm for the composites and the effective absorption band under −10 dB reached 6.2 GHz.
Physical and chemical stability of reconstituted and diluted dexrazoxane infusion solutions
Authors: Zhang Yan-Ping , Myers Alan L , Trinh Van A , Kawedia Jitesh D , Kramer Mark A , Benjamin Robert S , Tran Hai T 
Published: May 2013

Background and purpose Dexrazoxane is used clinically to prevent anthracycline-associated cardiotoxicity. Hydrolysis of dexrazoxane prior to reaching the cardiac membranes severely hampers its mode of action; therefore, degradation during the preparation and administration of intravenous dexrazoxane admixtures demands special attention. Moreover, the ongoing national shortage of one dexrazoxane formulation in the United States has forced pharmacies to dispense other commercially available dexrazoxane products. However, the manufacturers’ limited stability data restrict the flexibility of dexrazoxane usage in clinical practice. The aims of this study are to determine the physical and chemical stability of reconstituted and diluted solutions of two commercially available dexrazoxane formulations. Methods The stability of two dexrazoxane products, brand and generic name, in reconstituted and intravenous solutions stored at room temperature without light protection in polyvinyl chloride bags was determined. The concentrations of dexrazoxane were measured at predetermined time points up to 24 h using a validated reversed phase high-performance liquid chromatography with ultraviolet detection assay. Results Brand (B-) and generic (G-) dexrazoxane products, reconstituted in either sterile water or 0.167 M sodium lactate (final concentration of 10 mg/mL), were found stable for at least to 8 h. Infusion solutions of B-dexrazoxane, prepared according to each manufacturer’s directions, were stable for at least 24 h and 8 h at 1 mg/mL and 3 mg/mL, respectively. Infusion solutions of G-dexrazoxane, prepared in either 5% dextrose or 0.9% sodium chloride following the manufacturer’s guidelines, were also stable for at least 24 h and 8 h at 1 mg/mL and 3 mg/mL, respectively. All tested solutions were found physically stable up to 24 h at room temperature. Conclusion The stability of dexrazoxane infusion solutions reported herein permits advance preparation of dexrazoxane intravenous admixtures, facilitating pharmacy workflow and clinical operations. However, due to the potential risks of fluid overload when these intravenous solutions are administered to patients, caution is advised to ensure patient safety.
Frontal Network Syndrome Testing
Authors: Hoffmann Michael 
Published: May 2013

Background: Dementia diagnosis and the various subtypes are challenging in the absence of biomarkers. Aim: To examine available tests and neuroimaging procedures that may help distinguish these disorders. Methods: Alzheimer’s disease (AD), cognitive vascular disorder (CVD), and Frontotemporal lobe disorders (FTLD) were tested with a hierarchical neuropsychological battery that included the Frontal Systems Behavior Scale, Mini-Mental State Examination, Montreal Cognitive Assessment Test, and subtests. All patients had multimodality magnetic resonance imaging and 18F fluorodeoxyglucose-positron emission tomography (FDG-PET) brain scans. Results: Of the 161 patients evaluated for dysmemory and cognitive impairment, 31 satisfied the full protocol. The mean T scores for the 3 principal frontal system syndromes for the AD group were all abnormal save disinhibition. For the CVD and FTLD groups, all the 4 subcategory scores were abnormal. Disinhibition differed significantly between the AD and FTD group (analysis of variance [ANOVA], P = .02) and there was a strong association between the memory for 5 words test and a significant difference in the word list generation test score among the 3 groups (ANOVA, P = .0233). There was a strong association between the FDG-PET and the disease subtype ( P < .0001). Conclusion: Evaluation for disinhibition, word list generation, 5-word memory testing and PET brain imaging may help distinguish the 3 most common dementia subtypes.
The gut in iron homeostasis: role of HIF-2 under normal and pathological conditions
Authors: Mastrogiannaki Maria , Matak Pavle , Peyssonnaux Carole 
Published: May 2013

AbstractAlthough earlier, seminal studies demonstrated that the gut per se has the intrinsic ability to regulate the rates of iron absorption, the spotlight in the past decade has been placed on the systemic regulation of iron homeostasis by the hepatic hormone hepcidin and the molecular mechanisms that regulate its expression. Recently, however, attention has returned to the gut based on the finding that hypoxia inducible factor-2 (HIF-2α) regulates the expression of key genes that contribute to iron absorption. Here we review the current understanding of the molecular mechanisms that regulate iron homeostasis in the gut by focusing on the role of HIF-2 under physiological steady-state conditions and in the pathogenesis of iron-related diseases. We also discuss implications for adapting HIF-2–based therapeutic strategies in iron-related pathological conditions.
Adenosine production by human B cells and B cell–mediated suppression of activated T cells
Authors: Saze Zenichiro , Schuler Patrick J. , Hong Chang-Sook , Cheng Dongmei , Jackson Edwin K. , Whiteside Theresa L. 
Published: May 2013

Key PointsProducts of ATP hydrolysis, 5′AMP, and adenosine orchestrate the dual regulatory activity of B cells. B cells emerge as a key regulatory component of T cell–B cell interactions, which are under environmental control.
Cytokine release syndrome after blinatumomab treatment related to abnormal macrophage activation and ameliorated with cytokine-directed therapy
Authors: Teachey David T. , Rheingold Susan R. , Maude Shannon L. , Zugmaier Gerhard , Barrett David M. , Seif Alix E. , Nichols Kim E. , Suppa Erica K. , Kalos Michael , Berg Robert A. , Fitzgerald Julie C. , Aplenc Richard , Gore Lia , Grupp Stephan A. 
Published: May 2013

Key Points
Cytokine release syndrome caused by T cell-directed therapies may be driven by abnormal macrophage activation and hemophagocytic syndrome. Cytokine-directed therapy can be effective against life-threatening cytokine release syndrome.