bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human genome-wide repair map of DNA damage caused by the cigarette smoke carcinogen benzo[a]pyrene
Authors: Li Wentao , Hu Jinchuan , Adebali Ogun , Adar Sheera , Yang Yanyan , Chiou Yi-Ying , Sancar Aziz 
Published: June 2017

Significance
Benzo[a]pyrene (BaP) is a widespread potent carcinogen found in food, coal tar, cigarette smoke, and industrial smoke. Cigarette smoking is the leading cause of lung cancer, and the mutagenesis in smoking-associated lung cancer is determined by multiple factors, including nucleotide excision repair. We have developed a general method for genome-wide mapping of nucleotide excision repair at single-nucleotide resolution and applied it to generate repair maps of UV- and BaP-induced DNA damage in human. Results show a novel sequence specificity of BaP diol epoxide-deoxyguanosine repair. This general method can be used to study repair of all types of DNA damages that undergo nucleotide excision repair.
Intraoperative assessment of tumor margins during glioma resection by desorption electrospray ionization-mass spectrometry
Authors: Pirro Valentina , Alfaro Clint M. , Jarmusch Alan K. , Hattab Eyas M. , Cohen-Gadol Aaron A. , Cooks R. Graham 
Published: June 2017

Significance
Gliomas infiltrate into surrounding healthy brain tissue. Microsurgical resection aims for maximal tumor resection while minimizing morbidity. Surgical margins are defined based on the surgeon’s experience, visual observation, and neuronavigation. Surgical margin assessment is rarely undertaken intraoperatively due to time constraints and unreliability of such evaluation. Routine, pathologic intraoperative examination provides no molecular information. Molecular measurements using mass spectrometry can be made rapidly on tissue during surgery to identify tissue types, estimate tumor infiltration, and recognize the presence of prognostic mutations by monitoring oncometabolites and phospholipids. This intraoperative study demonstrates the power of mass spectrometry in assessing diagnostic and prognostic information on discrete surgeon-defined points along the resection margins to improve tumor resection, even in regions without MRI contrast enhancement.
WSF-P-1, a novel AMPK activator, promotes adiponectin multimerization in 3T3-L1 adipocytes
Authors: Wang Yao , Zhang Yudian , Wang Yunyun , Peng Han , Rui Jian , Zhang Zhijie , Wang Shifa , Li Zhen 
Published: June 2017

Abstract
Adiponectin, an adipokine with insulin-sensitizing effect, is secreted from adipocytes into circulation as high, medium, and low molecular weight forms (HMW, MMW, and LMW). The HMW adiponectin oligomers possess the most potent insulin-sensitizing activity. WSF-P-1(N-methyl-1,2,3,4,5,6-hexahydro-1,1,5,5-tetramethyl-7H-2,4α-methanonaphthalen-7-amine) is derived from natural sesquiterpene longifolene by chemical modifications. We found that WSF-P-1 activates AMPK in both 3T3-L1 adipocytes and 293T cells in this study. Activation of AMPK by WSF-P-1 promotes the assembly of HMW adiponectin and increases the HMW/total ratio of adiponectin in 3T3-L1 adipocytes. We demonstrated that the Ca2+-dependent CaMKK signaling pathway is involved in WSF-P-1-induced AMPK activation and adiponectin multimerization. WSF-P-1 also activates GLUT1-mediated glucose uptake in 3T3-L1 adipocytes, making it a potential drug candidate for the treatment of type 2 diabetes, obesity, and other obesity-related metabolic diseases.
Metoprolol Increases Uric Acid and Risk of Gout in African Americans With Chronic Kidney Disease Attributed to Hypertension
Authors: Juraschek Stephen P , Appel Lawrence J , Miller Edgar R 
Published: June 2017

Abstract

BACKGROUND
There is little evidence guiding selection of nondiuretic, antihypertensive agents with a goal of lowering uric acid (SUA) and minimizing gout risk.

METHODS
In the African American Study of Kidney Disease and Hypertension (AASK) trial, African Americans with chronic kidney disease were randomly assigned to metoprolol (a beta-blocker), ramipril (an angiotensin-converting enzyme inhibitors [ACEi]), or amlodipine (a dihydropyridine calcium-channel blocker). SUA was measured at baseline and 12 months. Gout-related hospitalizations were based on ICD9 codes. Gout-related medication use (GRMs) was based on active prescriptions of allopurinol, colchicine, or probenecid during the baseline visit of the AASK cohort phase. We examined the effect of drug assignment on 12-month SUA (linear regression), gout-related hospitalization (Cox regression), and GRM (logistic regression).

RESULTS
Of the 630 participants, 40% were female with a mean age of 55 years (SD, 10), mean SUA of 8.2 mg/dl (2.0), and mean serum creatinine of 1.8 mg/dl (0.6). After 12 months, metoprolol increased SUA by 0.3 mg/dl, while ramipril or amlodipine had no effect on SUA. Compared to ramipril, metoprolol significantly increased 12-month SUA (0.40; 0.10, 0.70 mg/dl; P = 0.009), nonsignificantly increased risk of gout-related hospitalization (hazard ratio: 3.87; 0.82, 18.26; P = 0.09), and significantly increased the odds of GRM (odds ratio: 1.62; 1.03, 2.54; P = 0.04). While metoprolol was associated with a higher 12-month SUA compared with amlodipine (0.57; 0.18, 0.95; P = 0.004), there was no difference in gout-related hospitalizations or GRM.

CONCLUSIONS
Metoprolol increased SUA and GRM in African American adults. Health professionals treating patients with kidney disease at risk for gout should avoid metoprolol and possibly consider an ACEi.

CLINICAL TRIALS REGISTRATION
Trial Number NCT00582777.
StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data
Authors: Stavrovskaya Elena D , Niranjan Tejasvi , Fertig Elana J , Wheelan Sarah J , Favorov Alexander V , Mironov Andrey A 
Published: June 2017

Abstract

Motivation
Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required.

Results
Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features. These features may represent high-throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. We apply our method to numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicability. We observe the changes in the correlation between epigenomic features across developmental trajectories of several tissue types consistent with known biology and find a novel spatial correlation of CAGE clusters with donor splice sites and with poly(A) sites. These analyses provide examples for the broad applicability of StereoGene for regulatory genomics.

Availability and implementation
The StereoGene C ++ source code, program documentation, Galaxy integration scripts and examples are available from the project homepage http://stereogene.bioinf.fbb.msu.ru/

Supplementary information
Supplementary data are available at Bioinformatics online.
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
Authors: Mallet Ludovic , Bitard-Feildel Tristan , Cerutti Franck , Chiapello Hélène 
Published: June 2017

Abstract

Motivation
Genome sequencing projects sometimes uncover more organisms than expected, especially for complex and/or non-model organisms. It is therefore useful to develop software to identify mix of organisms from genome sequence assemblies.

Results
Here we present PhylOligo, a new package including tools to explore, identify and extract organism-specific sequences in a genome assembly using the analysis of their DNA compositional characteristics.

Availability and implementation
The tools are written in Python3 and R under the GPLv3 Licence and can be found at https://github.com/itsmeludo/Phyloligo/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Generating prosperity, creating crisis: impacts of resource development on diverse groups in northern communities
Authors: Stienstra Deborah , Manning Susan M , Levac Leah , Baikie Gail 
Published: June 2017

AbstractNorthern Canada illustrates the contradictory dynamics in resource development – at once generating prosperity and inclusion within some communities and for some people, and creating or perpetuating crisis in some communities and exclusion for some people. Existing literature related to resource extraction and development focuses on the impacts on the environment and government regulatory mechanisms. Few authors or policy makers pay attention to how multiple and diverse groups within communities are affected by resource development. Building from research in a community-university research alliance, the authors argue that these competing dynamics are initiated and sustained through resource development projects and have disproportionate effects on historically marginalized groups within northern communities. This article presents the results of a comprehensive scoping review of the literature related to the social and economic impacts of resource extraction in Northern Canada. Some of the impacts of resource extraction clearly generate prosperity, while others can move communities towards crises and some do both. Using intersectionality, we argue that policy makers, especially those responsible for community development and regulating resource development projects, require a multilayered analysis to understand and redress the unequal effects of resource development on northern communities.
Loneliness, Social Integration, and Incident Dementia Over 6 Years: Prospective Findings From the English Longitudinal Study of Ageing
Authors: Rafnsson Snorri Bjorn , Orrell Martin , d’Orsi Eleonora , Hogervorst Eef , Steptoe Andrew 
Published: June 2017

Abstract

Objectives
Social relationships are important for the maintenance of cognitive function at older ages, with both objective features of social networks and perceived social connections (loneliness) being relevant. There is limited evidence about how different aspects of social experience predict diagnosed dementia.

Methods
The sample comprised 6,677 dementia-free individuals at baseline (2004) from the English Longitudinal Study of Ageing. Baseline information on loneliness, number of close relationships, marital status, and social isolation (contact with family and friends and participation in organizations) was analyzed in relation to incident dementia over an average 6.25 years using Cox regression, controlling for potential confounding factors.

Results
Two hundred twenty participants developed dementia during follow-up. In multivariable analyses, dementia risk was positively related to greater loneliness (hazard ratio 1.40, 95% confidence interval 1.09–1.80, p = .008), and inversely associated with number of close relationships (p &lt; .001) and being married (p = .018). Sensitivity analyses testing for reverse causality and different criteria for diagnosing dementia confirmed the robustness of these findings. There was no association with social isolation.

Discussion
Dementia risk is associated with loneliness and having fewer close relationships in later life. The underlying mechanisms remain to be elucidated, but efforts to enhance older peoples’ relationship quality may be relevant to dementia risk.
Hepatitis E Virus–Associated Meningoencephalitis in a Lung Transplant Recipient Diagnosed by Clinical Metagenomic Sequencing
Authors: Murkey Jamie A. , Chew Kara W. , Carlson Margrit , Shannon Chelsea L. , Sirohi Deepika , Sample Hannah A. , Wilson Michael R. , Vespa Paul , Humphries Romney M. , Miller Steve , Klausner Jeffrey D. , Chiu Charles Y. 
Published: June 2017

Abstract
Hepatitis E virus (HEV) infection uncommonly causes chronic hepatitis and neurologic disease. We describe a case of genotype 3a HEV meningoencephalitis diagnosed by metagenomic next-generation sequencing, illustrating the power of an unbiased molecular approach to microbial testing and the first reported case of HEV infection presumably acquired through lung transplantation.
Evaluation of a Clinical Protocol to Assess and Diagnose Neuropathic Pain During Acute Hospital Admission
Authors: Bélanger Lise M.A. , Umedaly Hamed S. , Noonan Vanessa K. , Park So Eyun , Prince Jennifer , Thorogood Nancy P. , Shen Tian , Townson Andrea F. , Street John T. , Dvorak Marcel F. , Negraeff Michael 
Published: June 2017

Objectives:
A clinical protocol was developed for clinicians to routinely assess and initiate treatment for patients with neuropathic pain (NP) in an acute care setting. The objectives of this study were to: (1) determine the incidence and onset of NP in patients with traumatic spinal cord injury during acute care and (2) describe how the implementation of a clinical protocol impacts the assessment and diagnosis of NP.

Materials and Methods:
The study was a cohort analysis with a pre-post-test utilizing a historical control. Data were retrospectively collected from a patient registry and charts. Participants were randomly selected in cohort 1 (control) and cohort 2 (NP clinical protocol).

Results:
The incidence of NP was 56% without significant difference between the cohorts (P=0.3). Onset of NP was 8 days (SD=14) across the study and >85% of the participants with NP were diagnosed within 2 weeks. Participants with incomplete injuries had a significant earlier onset than participants with complete injuries (6.2±12.8, 10.9±15.8 d; P=0.003). The mean number of days from hospital admission to initial assessment decreased with use of the NP clinical protocol (3.7±5.7 d; P=0.02).

Discussion:
This study demonstrates a high incidence and early onset of NP in traumatic spinal cord injury during acute hospital care, with an earlier emergence in participants with incomplete injury. The NP clinical protocol ensured continuous assessment and documentation of NP while decreasing the time to an initial screen, but did not impact diagnosis.
OTA/AO Classification Is Highly Predictive of Acute Compartment Syndrome After Tibia Fracture: A Cohort of 2885 Fractures
Authors: Beebe Michael J. , Auston Darryl A. , Quade Jonathan H. , Serrano-Riera Rafael , Shah Anjan R. , Watson David T. , Sanders Roy W. , Mir Hassan R. 
Published: June 2017

Objective:
To determine the correlation between the OTA/AO classification of tibia fractures and the development of acute compartment syndrome (ACS).

Design:
Retrospective review of prospectively collected database.

Setting:
Single Level 1 academic trauma center.

Patients:
All patients with a tibia fracture from 2006 to 2016 were reviewed for this study. Three thousand six hundred six fractures were initially identified. Skeletally mature patients with plate or intramedullary fixation managed from initial injury through definitive fixation at our institution were included, leaving 2885 fractures in 2778 patients.

Methods:
After database and chart review, univariate analyses were conducted using independent t tests for continuous data and χ2 tests of independence for categorical data. A simultaneous multivariate binary logistic regression was developed to identify variables significantly associated with ACS.

Results:
ACS occurred in 136 limbs (4.7%). The average age was 36.2 years versus 43.3 years in those without (P < 0.001). Men were 1.7 times more likely to progress to ACS than women (P = 0.012). Patients who underwent external fixation were 1.9 times more likely to develop ACS (P = 0.003). OTA/AO 43 injuries were at least 4.0 times less likely to foster ACS versus OTA/AO 41 or 42 injuries (P < 0.007). OTA/AO 41-C injuries were 5.5 times more likely to advance to ACS compared with OTA/AO 41-A (P = 0.03). There was a significantly higher rate of ACS in OTA/AO 42-B (P = 0.005) and OTA/AO 42-C (P = 0.002) fractures when compared with OTA/AO 42-A fractures. In the distal segment, fracture type did not predict the risk of ACS (P > 0.15). Group 1 fractures had a lower rate of ACS compared with group 2 (P = 0.03) and group 3 (P = 0.003) fractures in the middle segment only. Bilateral tibia fractures had a 2.7 times lower rate of ACS (P = 0.04). Open injury, multiple segment injury, fixation type, and concurrent pelvic or femoral fractures did not predict ACS.

Conclusions:
In this large cohort of tibia fractures, we found that the age, sex, and OTA/AO classification were highly predictive for the development of ACS.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Surgery for patients with newly diagnosed advanced ovarian cancer: which patient, when and extent?
Authors: Eggink Florine A. , Koopmans Corine M. , Nijman Hans W. 
Published: June 2017

Purpose of review
Cytoreduction to no residual disease is the mainstay of primary treatment for advanced epithelial ovarian cancer (AdvEOC). This review addresses recent insights on optimal patient selection, timing, and extent of surgery, intended to optimize cytoreduction in patients with AdvEOC.

Recent findings
Clinical guidelines recommend primary cytoreductive surgery (PCS) for AdvEOC patients with a high likelihood of achieving complete cytoreduction with acceptable morbidity. In line with this, preoperative prediction markers such as cancer antigen-125, histologic and genomic factors, innovative imaging modalities, and the performance of a diagnostic laparoscopy have been suggested to improve clinical decision-making with regard to optimal timing of cytoreductive surgery. To determine whether these strategies should be incorporated into clinical practice validation in randomized clinical trials is essential.

Summary
The past decade has seen a paradigm shift in the number of AvdEOC patients that are being treated with upfront neoadjuvant chemotherapy instead of PCS. However, although neoadjuvant chemotherapy may reduce morbidity at the time of interval cytoreductive surgery, no favorable impact on survival has been demonstrated and it may induce resistance to chemotherapy. Therefore, optimizing patient selection for PCS is crucial. Furthermore, surgical innovations in patients diagnosed with AvdEOC should focus on improving survival outcomes.
Collagen Anomalies as Clues for Diagnosis: Part 2
Authors: Santos-Alarcón Sergio , López-López Omar Francisco , Flores-Terry Miguel Ángel , Villamil-Cerda Dante , Allemant-Ortiz Luis Jesús , Ríos-Martín Juan José , Alegría Victoria , Requena Luis 
Published: June 2017

Background:
Collagen is the most abundant protein in the body and the main structural component of the skin.

Objective:
To provide a review of the histopathology of collagen alterations and to propose a classification with the most important types of collagen anomalies in dermatopathology. The authors describe some of the main morphological clues of collagen anomalies for specific diagnosis of some cutaneous inflammatory and neoplastic conditions.

Methods:
The authors review histopathologic collagen anomalies, concerning both morphology and disposition in some inflammatory and neoplastic cutaneous conditions, and they review previous terminology and proposed a classification of the most important types of collagen anomalies that can be seen in dermatopathological practice.

Results:
Collagen anomalies in skin can be classified into lamellar fibrosis, sclerosis, and “balls” and “rings” of collagen. Lamellar fibrosis presents as long and thin collagen bundles forming a delicate network, which can be disposed in a parallel pattern, onion-bulb-like pattern, and storiform pattern. Sclerosis is characterized by large, thick, and eosinophilic bundles of collagen, which may present as a homogenous-diffuse pattern or as individual thick bundles of collagen with few or abundant number of fibroblasts between them. Finally, the authors propose the terms “balls” and “rings” of collagen. The term “balls” of collagen stands for thick, homogenous, eosinophilic, globular collagen bundles, with no distinguishable individual composing fibers, which include the floating sign and the free-floating sign. The term “rings” of collagen is characterized by sclerotic collagen arranged in a homogenous rimming pattern around vessels without independent fibers in its composition.

Conclusions:
Collagen anomalies may be important clues to establish specific clues for specific diagnoses in dermatopathology.
Association between menopause and lumbar disc degeneration: an MRI study of 1,566 women and 1,382 men
Authors: Lou Chao , Chen Hongliang , Mei Liangwei , Yu Weiyang , Zhu Kejun , Liu Feijun , Chen Zhenzhong , Xiang Guangheng , Chen Minjiang , Weng Qiaoyou , He Dengwei 
Published: June 2017

Abstract

Objective:
The aim of this study was to revisit and further investigate the association between menopause and disc degeneration in the lumbar spine using a magnetic resonance imaging-based eight-level grading system.

Methods:
This study cohort comprised of 1,566 women and 1,382 age-matched men who were admitted for low back pain from June 2013 to October 2016. Data on age, weight, height, body mass index, age at natural menopause, and years since menopause (YSM) were obtained. Lumbar disc degeneration was assessed using a magnetic resonance imaging-based eight-level grading system.

Results:
After adjustment for the confounding factors of age, height, and weight, young age-matched men were more susceptible to disc degeneration than premenopausal women (P < 0.05). However, after menopause, postmenopausal women had a significant tendency to develop more severe disc degeneration than their age-matched men (P < 0.05), and also compared with premenopausal and perimenopausal women (P < 0.01). Postmenopausal women were divided into nine subgroups by every 5 YSM. When YSM was less than 15 years, a positive trend was observed between YSM and severity of disc degeneration, respectively, at L1/L2 (r = 0.241), L2/L3 (r = 0.193), L3/L4 (r = 0.191), L4/L5 (r = 0.165), L5/S1 (r = 0.153), and all lumbar discs (r = 0.237) (P < 0.05 or 0.01). The analysis of covariance indicated a significant difference in each disc level (P < 0.05 or 0.01) between every two groups. When YSM was more than 15 years, the significant difference, however, disappeared in each disc level (P > 0.05).

Conclusions:
Menopause is associated with lumbar disc degeneration. The association occurred in the first 15 YSM, suggesting estrogen deficiency might be a risk factor of disc degeneration of the lumbar spine. Further studies need to be carried out for deciding whether age or menopause plays a more important role in the progression of disc degeneration in the lumbar spine.
Androgens in postmenopausal women: a review
Authors: Shifren Jan L. , Davis Susan R. 
Published: June 2017

Abstract
There is significant interest in the use of androgen therapy for postmenopausal women. This review provides background on endogenous androgens in women, describes factors that affect circulating androgen concentrations, and examines the relationship between low levels of androgens and sexual problems. Possible effects of androgens in postmenopausal women beyond sexual function also are discussed. Clinical trials of androgen therapy for the treatment of hypoactive sexual desire disorder are reviewed, with a discussion of potential risks. A practical approach to using androgens to treat low sexual desire with associated distress is presented, accompanied by an illustrative case.