bluuebunny/crossref_metadata_2025_split huggingface dataset:
miR-146a and miR-196a-2 genes polymorphisms and its circulating levels in lung cancer patients
Authors: Mohamed Randa H , Pasha Heba F , Gad Doaa M , Toam Mostafa M 
Published: May 2019

AbstractRecently, MicroRNAs polymorphisms and their serum expression have been linked to increase risk of various cancers. The aim of this study was to elucidate the association between single nucleotide polymorphisms of miR-146a and miR-196a-2 and their serum expression and lung cancer risk. One hundred and twenty lung cancer patients and 120 health controls were included in this study. Genotyping and expression for miR-146a and miR-196a-2 were performed using polymerase chain reaction (PCR)-restriction fragment length polymorphism and quantitative real-time PCR. Individuals carrying miR-146a CG and CC genotypes had significantly increased risk for lung cancer than those carrying miR-146a GG genotype. MiR-146a expression significantly decreased in miR-146a CG and CC genotypes carriers as compared with GG genotype carriers. MiR-196a-2 CT and TT genotypes were significantly associated with increased lung cancer while the highest expression of MiR-196a-2 was detected in miR-196a-2 CC genotype carriers. Serum miR-146a was significantly decreased in lung cancer patients while serum miR-196a-2 expression was significantly increased in lung cancer patients. In conclusion, miR-146a and miR-196a-2 genes polymorphisms and their circulating levels were associated with lung cancer risk in Egyptians and may be helpful in early detection of lung cancer.
Minimally Important Differences for Interpreting EORTC QLQ-C30 Scores in Patients With Advanced Breast Cancer
Authors: Musoro Jammbe Z , Coens Corneel , Fiteni Frederic , Katarzyna Pogoda , Cardoso Fatima , Russell Nicola S , King Madeleine T , Cocks Kim , Sprangers Mirjam Ag , Groenvold Mogens , Velikova Galina , Flechtner Hans-Henning , Bottomley Andrew ,   EORTC Breast and Quality of Life Groups
Published: May 2019

Abstract

Background
We aimed to estimate the minimally important difference (MID) for interpreting group-level change over time, both within a group and between groups, for the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire core 30 (EORTC QLQ-C30) scores in patients with advanced breast cancer.

Methods
Data were derived from two published EORTC trials. Clinical anchors (eg, performance status [PS]) were selected using correlation strength and clinical plausibility of their association with a particular QLQ-C30 scale. Three change status groups were formed: deteriorated by one anchor category, improved by one anchor category, and no change. Patients with greater anchor changes were excluded. The mean change method was used to estimate MIDs for within-group change, and linear regression was used to estimate MIDs for between-group differences in change over time. For a given QLQ-C30 scale, MID estimates from multiple anchors were triangulated to a single value via a correlation-based weighted average.

Results
MIDs varied by QLQ-C30 scale, direction (improvement vs deterioration), and anchor. MIDs for within-group change ranged from 5 to 14 points (improvement) and −14 to −4 points (deterioration), and MIDs for between-group change over time ranged from 4 to 11 points and from −18 to −4 points. Correlation-weighted MIDs for most QLQ-C30 scales ranged from 4 to 10 points in absolute values.

Conclusions
Our findings aid interpretation of changes in EORTC QLQ-C30 scores over time, both within and between groups, and for performing more accurate sample size calculations for clinical trials in advanced breast cancer.
Long-term variability of Swift J1753.5−0127: X-ray spectral–temporal correlations during state transitions
Authors: Bu Qingcui , Tao Lian , Lu Yu , Zhang Shuangnan , Zhang Liang , Huang Yue , Chen Li , Qu Jinlu , Ma Xiang 
Published: May 2019

ABSTRACT
We studied the long-term evolution of the spectral–temporal correlated properties of the black hole candidate Swift J1753.5−0127 from the onset of its outburst until 2011 with the Rossi X-ray Timing Explorer (RXTE). The source stayed most of its lifetime during hard state, with occasionally transitioned to the hard intermediate state. Similar to typical black hole transients, Swift J1753.5−0127 traces a clear hard line in absolute rms–intensity diagram during the low hard state, with expected highest absolute rms, while shows a clear turn during the hard intermediate state, accompanied by lower absolute rms. Different from Cyg X-1, we found that frequency-dependent time lag increased significantly in the 0.02–3.2 Hz band during state transition in this source. The X-ray time lags in 0.02–3.2 Hz can therefore be used as indicators of state transition in this source. Type-C quasi-periodic oscillation frequency is positively related with its fractional rms and X-ray photon index, suggesting a moving inwards disc/corona scenario. We discussed the physical interpretation of our results in this paper.
BEERE: a web server for biomedical entity expansion, ranking and explorations
Authors: Yue Zongliang , Willey Christopher D , Hjelmeland Anita B , Chen Jake Y 
Published: May 2019

AbstractBEERE (Biomedical Entity Expansion, Ranking and Explorations) is a new web-based data analysis tool to help biomedical researchers characterize any input list of genes/proteins, biomedical terms or their combinations, i.e. ‘biomedical entities’, in the context of existing literature. Specifically, BEERE first aims to help users examine the credibility of known entity-to-entity associative or semantic relationships supported by database or literature references from the user input of a gene/term list. Then, it will help users uncover the relative importance of each entity—a gene or a term—within the user input by computing the ranking scores of all entities. At last, it will help users hypothesize new gene functions or genotype–phenotype associations by an interactive visual interface of constructed global entity relationship network. The output from BEERE includes: a list of the original entities matched with known relationships in databases; any expanded entities that may be generated from the analysis; the ranks and ranking scores reported with statistical significance for each entity; and an interactive graphical display of the gene or term network within data provenance annotations that link to external data sources. The web server is free and open to all users with no login requirement and can be accessed at http://discovery.informatics.uab.edu/beere/.
APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data
Authors: Leonard Simon , Meyer Sam , Lacour Stephan , Nasser William , Hommais Florence , Reverchon Sylvie 
Published: May 2019

AbstractSmall non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5′ and 3′ ends of all transcripts. Since sRNAs are about the same size as individual fragments (50–350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5′ UTR or 3′ UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO
Regulatory/inflammatory cellular response discrimination in operational tolerance
Authors: Carmona Priscila , Medina-Armenteros Yordanka , Cabral Amanda , Monteiro Sandra Maria , Gonçalves Fonseca Simone , Faria Ana Caetano , Lemos Francine , Saitovitch David , Noronha Irene L , Kalil Jorge , Coelho Verônica 
Published: May 2019

Abstract

Background
Antigen-specific cellular response is essential in immune tolerance. We tested whether antigen-specific cellular response is differentially modulated in operational tolerance (OT) in renal transplantation with respect to critical antigenic challenges in allotransplantation—donor antigens, pathogenic antigens and self-antigens.

Methods
We analysed the profile of immunoregulatory (REG) and pro-inflammatory (INFLAMMA) cytokines for the antigen-specific response directed to these three antigen groups, by Luminex.

Results
We showed that, in contrast to chronic rejection and healthy individuals, OT gives rise to an immunoregulatory deviation in the cellular response to donor human leucocyte antigen DR isotype peptides, while preserving the pro-inflammatory response to pathogenic peptides. Cellular autoreactivity to the N6 heat shock protein 60 (Hsp60) peptide also showed a REG profile in OT, increasing IL4, IL-5, IL-10 and IL-13.

Conclusions
The REG shift of donor indirect alloreactivity in OT, with inhibition of interleukin (IL)-1B, IL-8, IL-12, IL-17, granulocyte colony-stimulating factor, Interferon-γ and monocyte chemoattractant protein-1, indicates that this may be an important mechanism in OT. In addition, the differential REG profile of cellular response to the Hsp60 peptide in OT suggests that REG autoimmunity may also play a role in human transplantation tolerance. Despite cross-reactivity of antigen-specific T cell responses, a systemic functional antigen-specific discrimination takes place in OT.
Cannabis Use Is Associated With Increased Risk of Cigarette Smoking Initiation, Persistence, and Relapse Among Adults in the United States
Authors: Weinberger Andrea H , Delnevo Cristine D , Wyka Katarzyna , Gbedemah Misato , Lee Joun , Copeland Jan , Goodwin Renee D 
Published: May 2019

Abstract

Introduction
Despite increasing use of cannabis, it is unclear how cannabis use is related to cigarette transitions. This study examined cannabis use and smoking initiation, persistence, and relapse over 1 year among a nationally representative sample of US adults.

Methods
Data were from US adults (≥18 years) who completed two waves of longitudinal data from the Population Assessment of Tobacco and Health Study (Wave 1, 2013–2014; Wave 2, 2014–2015; n = 26 341). Logistic regression models were used to calculate the risk of Wave 2 incident smoking among Wave 1 never-smokers, smoking cessation among Wave 1 smokers, and smoking relapse among Wave 1 former smokers by Wave 1 cannabis use. Analyses were adjusted for age, gender, race/ethnicity, income, and education.

Results
Among Wave 1 never-smokers, cannabis use was associated with increased odds of initiation of nondaily (adjusted odds ratio [AOR] = 5.50, 95% confidence limits [CL] = 4.02–7.55) and daily cigarette smoking (AOR = 6.70, 95% CL = 4.75–9.46) 1 year later. Among Wave 1 daily smokers, cannabis use was associated with reduced odds of smoking cessation (AOR = 0.36, 95% CL = 0.20–0.65). Among Wave 1 former smokers, cannabis use was associated with increased odds of relapse to daily and nondaily cigarette smoking (daily AOR = 1.90, 95% CL = 1.11–3.26; nondaily AOR = 2.33, 95% CL = 1.61–3.39).

Conclusions
Cannabis use was associated with increased cigarette smoking initiation, decreased smoking cessation, and increased smoking relapse among adults in the United States. Increased public education about the relationship between cannabis use and cigarette smoking transitions may be needed as cannabis use becomes more common among US adults.

Implications
As cannabis use increases in the United States and other countries, an evaluation of the relationships of cannabis use to other health-related behaviors (eg, cigarette smoking) is needed to understand the population-level impact of legalization. Little is known about associations between cannabis use and cigarette smoking transitions (1) using recent longitudinal data, (2) among adults, and (3) examining transitions other than smoking initiation (eg, smoking relapse). Our results suggest that among US adults, cannabis use was associated with increased cigarette smoking initiation among never-smokers, decreased cigarette smoking cessation among current smokers, and increased cigarette smoking relapse among former smokers.
Evaluating current definitions of low disease activity in psoriatic arthritis using ultrasound
Authors: Bosch Philipp , Husic Rusmir , Ficjan Anja , Gretler Judith , Lackner Angelika , Graninger Winfried B , Duftner Christina , Hermann Josef , Dejaco Christian 
Published: May 2019

Abstract

Objective
To evaluate low disease activity (LDA) cut-offs in psoriatic arthritis (PsA) using ultrasound.

Methods
Eighty-three PsA patients underwent clinical and ultrasound examinations at two visits. LDA was assessed using the Disease Activity index for Psoriatic Arthritis (DAPSA ⩽ 14), the Psoriatic ArthritiS Disease Activity Score (PASDAS ⩽ 3.2), the Composite Psoriatic Disease Activity Index ⩽ 4, the DAS28-CRP ⩽ 2.8 and the minimal disease activity criteria. Ultrasound was performed at 68 joints and 14 entheses. Minimal ultrasound disease activity (MUDA-j/e) was defined as a Power Doppler score ⩽ 1, respectively at joints, paratendinous tissue, tendons and entheses. A global ultrasound score was calculated by summing Grey Scale and Power Doppler information (GUIS-j/e).

Results
LDA was present in 33.7–65.0% at baseline and in 44.3–80.6% at follow-up, depending on the criteria used. MUDA-j/e was observed in 16.9% at baseline and in 30% at follow-up. GUIS-j/e was significantly higher in patients with moderate/high disease activity vs LDA according to DAPSA and PASDAS at baseline and DAPSA, PASDAS, Composite Psoriatic Disease Activity Index and minimal disease activity at follow-up. Patients in moderate/high disease activity had MUDA-j/e in 8.1–21.4% at baseline and in 8.3–20.0% at follow-up, depending on the applied clinical composite. MUDA-j/e patients with moderate/high disease activity had higher levels of pain and pain-related items than those with LDA.

Conclusion
The LDA cut-offs of DAPSA, PASDAS, Composite Psoriatic Disease Activity Index, minimal disease activity, but not DAS28-CRP are capable of distinguishing between high and low ultrasound activity. Pain and pain-related items are the main reason why PsA patients without signs of ultrasound inflammation are classified with higher disease activity.
Spinal-pelvic orientation: potential effect on the diagnosis of spondyloarthritis
Authors: Carvajal Alegria Guillermo , Deloire Lucile , Herbette Marion , Garrigues Florent , Gossec Laure , Simon Alexandre , Feydy Antoine , Reijnierse Monique , van der Heijde Désirée , Loeuille Damien , Claudepierre Pascal , Marhadour Thierry , Saraux Alain 
Published: May 2019

Abstract

Objective
To assess associations of spinal-pelvic orientation with clinical and imaging-study findings suggesting axial SpA (axSpA) in patients with recent-onset inflammatory back pain.

Methods
Spinal-pelvic orientation was assessed in DESIR cohort patients with recent-onset inflammatory back pain and suspected axSpA, by using lateral lumbar-spine radiographs to categorize sacral horizontal angle (&lt;40° vs ⩾40°), lumbosacral angle (&lt;15° vs ⩾15°) and lumbar lordosis (LL, &lt;50° vs ⩾50°). Associations between these angle groups and variables collected at baseline and 2 years later were assessed using the χ2 test (or Fisher's exact) and the Mann–Whitney test. With Bonferroni’s correction, P &lt; 0.001 indicated significant differences.

Results
Of 362 patients, 358, 356 and 357 had available sacral horizontal angle, lumbosacral angle and LL values, respectively; means were 39.3°, 14.6° and 53.0°, respectively. The prevalence of sacroiliitis on both radiographs and MRI was higher in the LL &lt; 50° group than in the LL ⩾50° group, but the difference was not statistically significant. Clinical presentation and confidence in a diagnosis of axSpA did not differ across angle groups. No significant differences were identified for degenerative changes according to sacral horizontal angle, lumbosacral angle or LL.

Conclusion
Spinal-pelvic balance was not statistically associated with the clinical or imaging-study findings suggesting axSpA in patients with recent-onset inflammatory back pain.
The association of insomnia and sleep apnea with deployment and combat exposure in the entire population of US army soldiers from 1997 to 2011: a retrospective cohort investigation
Authors: Caldwell John A , Knapik Joseph J , Shing Tracie L , Kardouni Joseph R , Lieberman Harris R 
Published: May 2019

AbstractSince 2001, the United States has been engaged in the longest and most expensive overseas conflict in its history. Sleep disorders, especially insomnia and obstructive sleep apnea (OSA), are common in service members and appear related to deployment and combat exposure, but this has not been systematically examined. Therefore, the incidence of clinically diagnosed insomnia and OSA from 1997 to 2011 in the entire population of US Army soldiers was determined and associations of these disorders with deployment and combat exposure examined. This observational retrospective cohort study linked medical, demographic, deployment, and combat casualty data from all active duty US Army soldiers serving from 1997 to 2011 (n = 1 357 150). The mediating effects of multiple known comorbid conditions were considered. From 2003 to 2011, there were extraordinary increases in incidence of insomnia (652%) and OSA (600%). Factors increasing insomnia risk were deployment (risk ratio [RR] [deployed/not deployed] = 2.06; 95% confidence interval [CI], 2.04–2.08) and combat exposure (RR [exposed/not exposed] = 1.20; 95% CI, 1.19–1.22). Risk of OSA was increased by deployment (RR [deployed/not deployed] = 2.14; 95% CI, 2.11–2.17), but not combat exposure (RR [exposed/not exposed] = 1.00; 95% CI, 0.98–1.02). These relationships remained after accounting for other factors in multivariable analyses. A number of comorbid medical conditions such as posttraumatic stress disorder and traumatic brain injury mediated a portion of the association between the sleep disorders and deployment. It is essential to determine underlying mechanisms responsible for these very large increases in insomnia and OSA and introduce effective preventive measures.
Opioid Prescribing In-Hospital: Time for Innovative Approaches to Help Combat the Opioid Crisis
Authors: Parmar Gurjit , Ti Lianping , Nolan Seonaid 
Published: May 2019

ABSTRACT
Inappropriate opioid prescribing has been well recognized as a major contributor to North America's current opioid epidemic. Despite this, hospitals have largely been overlooked as a potential setting responsible for the development and management of opioid use disorder. This commentary examines acute care settings as a risk environment associated with opioid use disorder and discusses several innovative strategies to address existing challenges in hospital environments.

Résumé
La prescription d’opioïdes inappropriés a été largement reconnue comme étant l’une des principales causes de l’épidémie actuelle d’opioïdes en Amérique du Nord. Malgré cela, les hôpitaux ont été largement négligés en tant que cadre potentiel responsable du développement et de la gestion du trouble de l’usage des opioïdes (TLUO). Ce commentaire examine les établissements de soins de courte durée en tant qu’environnement de risque associé aux TLUO et examine plusieurs stratégies novatrices pour relever les défis existants en milieu hospitalier.
Morphologic Forms and Classification of Dermal Mitotic Figure Density in Primary Cutaneous Melanoma: A Retrospective Study
Authors: Marsch Amanda F. , McKee Ryan M. , Hinds Brian R. 
Published: May 2019

Abstract:New American Joint Committee on Cancer eighth edition staging parameters have removed mitotic rate as a stage T1 category criterion, but it remains embedded in the synopsis of primary cutaneous melanoma (CM). A paucity of data is available, characterizing atypical mitotic forms in CM. In this study, we classify the various morphologic forms of atypical mitoses, characterize mitotic figure density, and examine the correlation between atypical mitotic figures and Breslow depth. We performed a retrospective study of 185 thick (>0.8 mm) and thin (<0.8 mm) CM specimens. Metaphase mitotic figures represented the highest percentage of total mitotic figures in cases of thick melanoma (40%) and were the second most common in thin melanoma (18%). The average Breslow depth for melanoma harboring starburst mitoses was 2.85 mm, compared with the average Breslow depth of all thick melanoma cases, 1.88 mm. The average thickness of melanoma cases containing tripolar mitoses was 2.28 mm. Breslow depth correlated with the number of atypical mitotic figures in both thick and thin melanomas (the Pearson correlation test, r = +0.18,P< 0.01). Metaphase and prophase mitoses are a common finding in both thick and thin melanomas. Although atypical mitoses were indiscriminate, starburst and tripolar (ie, multipolar) mitoses were only inherent to cases of thick melanoma (stage T3). In sum, our study reveals a parallel relationship between the density of atypical mitotic figures and Breslow depth.
Are We Prepared for the Inevitable? A Survey on Defining and Managing Failure in Face Transplantation
Authors: Lee Z-Hye , Lopez Christopher D. , Plana Natalie M. , Caplan Arthur L. , Rodriguez Eduardo D. 
Published: May 2019

Background:
Facial transplantation (FT) experience has grown but success in this innovative and complex field has yet to be defined. The purpose of this study is to determine attitudes regarding the failures in FT and the appropriate management of these failures.

Methods:
An anonymous, 20-question survey elicited opinions regarding FT failure management. This survey was administered to attendees of 2 FT-focused national meetings. Demographics included sex, age, and personal/institutional FT experience. Attitudes related to FT recipient education, definition of FT failure, and management of complications were gathered.

Results:
Eighty of 271 attendees completed the survey (29.5%). Respondents were predominantly male (81.3%) and 50 years of age or younger (80.5%). Thirty-eight percentage previously performed an FT and 53.8% were a part of an institution with a vascularized composite allotransplantation (VCA)-related Institutional Review Board (IRB). Respondents almost unanimously agreed it was “absolutely essential” to discuss possibility of FT failure (93.8%), mortality (91.1%), and treatment for chronic rejection (78.8%). However, uncertainty of failure rate existed, with 56.4% citing failure rate as unknown, 25.6% citing <25% and 18.0% citing >25%. 51.2% of those with direct FT experience lacked clear criteria for defining FT success or an institutional protocol for managing chronic rejection. 78.8% believed failed FT patients should be considered for retransplantation, but only about 25% cited functional concerns or esthetic dissatisfaction as appropriate indications.

Conclusion:
There is a lack of consensus regarding definition of FT failure and rates mortality amongst experts. Even institutions with FT experience lack protocols for managing chronic rejection. Expert consensus and institutional regulations surrounding these issues are warranted.