bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hiding negative trials by pooling them: a secondary analysis of pooled-trials publication bias in FDA-registered antidepressant trials
Authors: de Vries Ymkje Anna , Roest Annelieke M. , Turner Erick H. , de Jonge Peter 
Published: September 2018

AbstractBackgroundPrevious studies on reporting bias generally examined whether trials were published in stand-alone publications. In this study, we investigated whether pooled-trials publications constitute a specific form of reporting bias. We assessed whether negative trials were more likely to be exclusively published in pooled-trials publications than positive trials and examined the research questions, individual trial results, and conclusions presented in these articles.MethodsData from a cohort of 105 randomized controlled trials of 16 antidepressants were extracted from earlier publications and the corresponding Food and Drug Administration (FDA) reviews. A systematic literature search was conducted to identify pooled-trials publications.ResultsWe found 107 pooled-trials publications that reported results of 23 (72%) of 32 trials not published in stand-alone publications. Only two (3.8%) of 54 positive trials were published exclusively in pooled-trials publications, compared with 21 (41.1%) of 51 negative trials (p < 0.001). Thirteen (12%) of 107 publications had as primary aim to present data on the trial's primary research question (drug efficacy compared with placebo). Only four of these publications, reporting on five (22%) trials, presented individual efficacy data for the primary research question. Additionally, only five (5%) of 107 pooled-trials publications had a negative conclusion.ConclusionsCompared with positive trials, negative trials of antidepressants for depression were much more likely to be reported exclusively in pooled-trials publications. Pooled-trials publications flood the evidence base with often-redundant articles that, instead of addressing the original primary research question, present (positive) results on secondary questions. Therefore, pooled-trials publications distort the apparent risk–benefit profile of antidepressants.
Child and adult spinal tuberculosis at tertiary hospitals in the Western Cape, South Africa: 4-year burden and trend
Authors: Mann T. N. , Schaaf H. S. , Dunn R. N. , Dix-Peek S. , du Preez K. , Lamberts R. P. , du Toit J. , Davis J. H. 
Published: September 2018

AbstractThe aim of this retrospective review was to assess the overall burden and trend in spinal tuberculosis (TB) at tertiary hospitals in the Western Cape Province of South Africa. All spinal TB cases seen at the province's three tertiary hospitals between 2012 and 2015 were identified and clinical records of each case assessed. Cases were subsequently classified as bacteriologically confirmed or clinically diagnosed and reported with accompanying clinical and demographic information. Odds ratios (OR) for severe spinal disease and corrective surgery in childvs.adult cases were calculated. A total of 393 cases were identified (319 adults, 74 children), of which 283 (72%) were bacteriologically confirmed. Adult cases decreased year-on-year (P= 0.04), however there was no clear trend in child cases. Kyphosis was present in 60/74 (81%) children and 243/315 (77%) adults with available imaging. Corrective spinal surgery was performed in 35/74 (47%) children and 80/319 (25%) adults (OR 2.7, 95% confidence interval 1.6–4.5,P= 0.0003). These findings suggest that Western Cape tertiary hospitals have experienced a substantial burden of spinal TB cases in recent years with a high proportion of severe presentation, particularly among children. Spinal TB remains a public health concern with increased vigilance required for earlier diagnosis, especially of child cases.
Course in Prehospital Major Incidents Management for Health Care Providers in Saudi Arabia
Authors: Bajow Nidaa A. , AlAssaf Wajdan I. , Cluntun Ameera A. 
Published: September 2018

AbstractIntroductionUnacceptable practices of health care providers during disasters have been observed because they work outside the scope of their daily practices and have inadequate training. A greater need for the involvement of health professionals in disaster management has been noted in Saudi Arabia. This study evaluates the efficacy of a training course in prehospital major incident management for health care providers in Saudi Arabia.MethodsAn interactive course for general principles in prehospital major incident management was developed with domains and core competencies. The course was designed according to the local context and was based on international standards. It was piloted over four days at the Officers Club of the Ministry of Interior (Riyadh, Saudi Arabia) and was sponsored by Mohammed Bin Naif Medical Center, King Fahd Security College in Riyadh, Saudi Arabia. The participants (n=29) were from different disciplines from main government health facilities in Riyadh. They completed a pre-test and a post-test.ResultsThe overall score was 55.1% on the pre-test and 68.4% on the post-test (Wilcoxon test for paired samples, P <.05). Three out of the four domains had significant difference between pre- and post-test results, as well as the overall total knowledge.Conclusion:Conducting inter-disciplinary and competency-based disaster medicine courses for health care providers can augment appropriate disaster preparedness for major incidents in Saudi Arabia.BajowNA,AlAssafWI,CluntunAA.Course in prehospital major incidents management for health care providers in Saudi Arabia.Prehosp Disaster Med.2018;33(6):587–595.
An investigation into the efficacy of a cognitive behavioural therapy group for low self-esteem in a primary care setting
Authors: Beattie Sarah , Beattie David 
Published: September 2018

AbstractSelf-esteem refers to how an individual appraises themselves and is associated with good mental health. A number of studies have identified the efficacy of cognitive behavioural therapy (CBT) in the treatment of low self-esteem based on the formulation and treatment trajectory developed by Fennell (1999). However, there has been little empirical enquiry into the efficacy of the programme delivered in primary care. The current study investigated the effectiveness of a CBT programme for low self-esteem delivered within primary care. Fifty-four participants attended a 9-week ‘Boost Your Mood’ group programme. Paired sample t-tests were conducted on pre- and post-group scores on measures of depression, anxiety and self-esteem. Results indicated that there were statistically significant improvements in levels of depression, anxiety and self-esteem post-treatment. Findings are consistent with the suggestion that group CBT may be effective at increasing levels of self-esteem and reducing levels of depression and anxiety when delivered in a primary care setting.
Energy Conversion and Partition in the Asymmetric Reconnection Diffusion Region
Authors: Wang Shan , Chen Li‐Jen , Bessho Naoki , Hesse Michael , Yoo Jongsoo , Yamada Masaaki , Liu Yi‐Hsin , Gershman Danial J. , Giles Barbara L. , Moore Thomas E. 
Published: September 2018

AbstractWe investigate the energy conversion and partition in the asymmetric reconnection diffusion region using two‐dimensional particle‐in‐cell simulations and Magnetosphere Multiscale (MMS) mission observations. Under an upstream condition with equal temperatures in the two inflow regions, the simulation analysis indicates that the energy partition between ions and electrons depends on the distance from the X‐line. Within the central electron diffusion region (EDR), nearly all dissipated electromagnetic field energies are converted to electrons. From the EDR to the ion diffusion region (IDR) scales, the rate of the electron energy gain decreases to be lower than that of ions. A magnetopause reconnection event inside the IDR observed by MMS shows comparable ion and electron energy gains, consistent with the simulation result in the transition region from EDR to IDR. At the EDR scale, the electron energization is mainly by the reconnection electric field (Er); in‐plane electric fields (Exz) provide additional positive contributions near the X‐line and do negative work on electrons beyond the EDR. The guide field reduces the electron energization by both Er and Exz in the EDR. For ion energization, Er and Exz have comparable contributions near the time of the peak reconnection rate, while Exz dominants at later time. At the IDR scale, the guide field causes asymmetry in the amount of the energy gain and energization mechanisms between two exhausts but does not have significant effects on energy partition. Our study advances understanding of ion and electron energization in asymmetric reconnect IDRs.
A Comparison Study of NO Cooling Between TIMED/SABER Measurements and TIEGCM Simulations
Authors: Li Zheng , Knipp Delores , Wang Wenbin , Sheng Cheng , Qian Liying , Flynn Sierra 
Published: September 2018

AbstractWe investigate the latitudinal and longitudinal variations of thermospheric nitric oxide (NO) cooling rate from 2005 to 2016. We compare the maximum of the NO cooling rate and its altitude from measurements by the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on National Aeronautics and Space Administration (NASA)'s TIMED (Thermosphere‐Ionosphere‐Mesosphere Energetics and Dynamics) satellite and from simulations by the Thermosphere‐Ionosphere‐Electrodynamics General Circulation Model (TIEGCM). In both data and model, the maximum NO cooling rate varies with ~11‐year solar cycle, while the altitude of the peak value does not. At local noon, the maximum NO cooling rate from TIEGCM is significantly larger than that derived from SABER, especially in solar minimum. There are differences in the altitudes of the maximum NO cooling rates between the observations and simulations. The largest difference occurs at noon at low latitudes, with SABER values exceeding TIEGCM values by more than 10 km with a maximum difference of 16 km near solar maximum. Model sensitivity tests suggest that the biases are caused by a model temperature overestimation in the low thermosphere, and tides in the TIEGCM lower boundary play an important role in inducing the low‐latitude temperature overestimation by the model. In addition, SABER's height‐integrated cooling rate (NO flux) exceeds that from TIEGCM, primarily due to the lower cooling rates at 140–200 km in the model.
Variability and Long‐Term Trends in the Shelf Circulation Off Eastern Tasmania
Authors: Oliver Eric C. J. , Holbrook Neil J. 
Published: September 2018

AbstractThis study investigates trends and interannual variability of the marine climate across the continental shelf off eastern Tasmania for 1993–2016. This region is a hotspot for global warming and biodiversity. Eastern Tasmania lies at the boundary between two ocean currents (the East Australian Current Extension, or EAC Extension, and the Zeehan Current, ZC) leading to the local marine climate exhibiting trends and variability from both boundary currents. A numerical ocean model is used to provide high‐resolution (∼2 km) estimates of the temperature, salinity, and circulation for the region. Results indicate significant positive trends in temperature, salinity, and southward flow over the shelf, consistent with an increasing EAC Extension. These trends are particularly strong in autumn, indicating a lengthening of the warm season. The interannual variability in the EAC Extension and ZC was quantified by a simple index, based on a modal analysis of surface circulation, indicating the relative dominance of each current. Strong EAC years were related to significantly more summertime marine heat wave days. Large‐scale remote drivers of variability were considered, and we found weak but significant links with El Niño–Southern Oscillation and Tasman Sea Blocking. El Niño–Southern Oscillation was found to modulate the EAC Extension in summer with a El Niño leading to enhanced southward flow and warming over the shelf. Tasman Sea Blocking was found to drive enhanced southward surface flow, particularly in winter. Nonetheless, large‐scale forcing modes explain less than 25% of the total variability in the EAC‐ZC system indicating that most of the variability is internally generated.
Evaluation of a Data Assimilation System for Land Surface Models Using CLM4.5
Authors: Fox Andrew M. , Hoar Timothy J. , Anderson Jeffrey L. , Arellano Avelino F. , Smith William K. , Litvak Marcy E. , MacBean Natasha , Schimel David S. , Moore David J. P. 
Published: September 2018

AbstractThe magnitude and persistence of land carbon (C) pools influence long‐term climate feedbacks. Interactive ecological processes influence land C pools and our understanding of these processes is imperfect so land surface models have errors and biases when compared to each other and to real observations. Here we implement an Ensemble Adjustment Kalman Filter (EAKF), a sequential state data assimilation technique to reduce these errors and biases. We implement the EAKF using the Data Assimilation Research Testbed coupled with the Community Land Model (CLM 4.5 in CESM 1.2). We assimilated simulated and real satellite observations for a site in central New Mexico, United States. A series of observing system simulation experiments allowed assessment of the data assimilation system without model error. This showed that assimilating biomass and leaf area index observations decreased model error in C dynamics forecasts (29% using biomass observations and 40% using leaf area index observations) and that assimilation in combination shows greater improvement (51% using both observation streams). Assimilating real observations highlighted likely model structural errors and we implemented an adaptive model‐variance‐inflation technique to allow the model to track the observations. Monthly and longer model forecasts using real observations were improved relative to forecasts without data assimilation. The reliable forecast lead‐time varied by model pool and is dependent on how tightly the C pool is coupled to meteorologically driven processes. The EAKF and similar state data assimilation techniques could reduce errors in projections of the land C sink and provide more robust forecasts of C pools and land‐atmosphere exchanges.
FIBP knockdown attenuates growth and enhances chemotherapy in colorectal cancer via regulating GSK3β-related pathways
Authors: Huang Yan-Feng , Niu Wen-Bo , Hu Rong , Wang Ling-Jun , Huang Zeng-Yan , Ni Shi-Hao , Wang Ming-Qing , Yang Yi , Huang Yu-Sheng , Feng Wen-Jun , Xiao Wei , Zhu Da-Jian , Xian Shao-Xiang , Lu Lu 
Published: September 2018

AbstractColorectal cancer stem cells (CSCs), characterized by self-renewal ability and high expression of proliferative genes, contribute to the chemoresistance of colorectal cancer (CRC). We aimed to identify the molecular mechanisms underlying CRC chemoresistance through comprehensive bioinformatics screenings and experimental confirmation of gene functions. We found that high expression of FGF1 intracellular binding protein (FIBP) was correlated with chemoresistance and poor prognosis in CRC patients. Therefore, the chemoresistant CRC cell line HCT116-CSC with high expression of the stem cell markers CD44 and CD133 was established for further phenotypic tests. FIBP knockdown inhibited proliferation, enhanced chemotherapy effects, and attenuated the stemness markers of CRC cells in vivo and in vitro. Through RNA-seq and gene set enrichment analysis, we identified cyclin D1 as a key downstream target in FIBP-regulated cell cycle progression and proliferation. Moreover, FIBP bound to GSK3β, inhibited its phosphorylation at Tyr216, and activated β-catenin/TCF/cyclin D1 signaling in HCT116-CSCs. Additional GSK3β knockdown reversed the FIBP silencing-induced inhibition of proliferation and decreased stemness marker expression in HCT116-CSCs. Furthermore, DNA methylation profiling suggested that FIBP regulated the stemness of CRC cells via methylation activity that was dependent on GSK3β but independent of β-catenin signaling. Our data illuminate the potential of FIBP as a novel therapeutic target for treating chemoresistant CRC through inhibition of GSK3β-related signaling.
Atomic cobalt as an efficient electrocatalyst in sulfur cathodes for superior room-temperature sodium-sulfur batteries
Authors: Zhang Bin-Wei , Sheng Tian , Liu Yun-Dan , Wang Yun-Xiao , Zhang Lei , Lai Wei-Hong , Wang Li , Yang Jianping , Gu Qin-Fen , Chou Shu-Lei , Liu Hua-Kun , Dou Shi-Xue 
Published: September 2018

AbstractThe low-cost room-temperature sodium-sulfur battery system is arousing extensive interest owing to its promise for large-scale applications. Although significant efforts have been made, resolving low sulfur reaction activity and severe polysulfide dissolution remains challenging. Here, a sulfur host comprised of atomic cobalt-decorated hollow carbon nanospheres is synthesized to enhance sulfur reactivity and to electrocatalytically reduce polysulfide into the final product, sodium sulfide. The constructed sulfur cathode delivers an initial reversible capacity of 1081 mA h g−1 with 64.7% sulfur utilization rate; significantly, the cell retained a high reversible capacity of 508 mA h g−1 at 100 mA g−1 after 600 cycles. An excellent rate capability is achieved with an average capacity of 220.3 mA h g−1 at the high current density of 5 A g−1. Moreover, the electrocatalytic effects of atomic cobalt are clearly evidenced by operando Raman spectroscopy, synchrotron X-ray diffraction, and density functional theory.
High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites
Authors: Mihailovic Mia K. , Vazquez-Anderson Jorge , Li Yan , Fry Victoria , Vimalathas Praveen , Herrera Daniel , Lease Richard A. , Powell Warren B. , Contreras Lydia M. 
Published: September 2018

AbstractHerein we introduce a high-throughput method, INTERFACE, to reveal the capacity of contiguous RNA nucleotides to establish in vivo intermolecular RNA interactions for the purpose of functional characterization of intracellular RNA. INTERFACE enables simultaneous accessibility interrogation of an unlimited number of regions by coupling regional hybridization detection to transcription elongation outputs measurable by RNA-seq. We profile over 900 RNA interfaces in 71 validated, but largely mechanistically under-characterized,Escherichia colisRNAs in the presence and absence of a global regulator, Hfq, and find that two-thirds of tested sRNAs feature Hfq-dependent regions. Further, we identify in vivo hybridization patterns that hallmark functional regions to uncover mRNA targets. In this way, we biochemically validate 25 mRNA targets, many of which are not captured by typically tested, top-ranked computational predictions. We additionally discover direct mRNA binding activity within the GlmY terminator, highlighting the information value of high-throughput RNA accessibility data.
Large-scale transcriptome-wide association study identifies new prostate cancer risk regions
Authors: Mancuso Nicholas , Gayther Simon , Gusev Alexander , Zheng Wei , Penney Kathryn L. , Kote-Jarai Zsofia , Eeles Rosalind , Freedman Matthew , Haiman Christopher , Pasaniuc Bogdan ,   The PRACTICAL consortium, Henderson Brian E. , Benlloch Sara , Schumacher Fredrick R. , Olama Ali Amin Al , Muir Kenneth , Berndt Sonja I. , Conti David V. , Wiklund Fredrik , Chanock Stephen , Stevens Victoria L. , Tangen Catherine M. , Batra Jyotsna , Clements Judith , Gronberg Henrik , Pashayan Nora , Schleutker Johanna , Albanes Demetrius , Weinstein Stephanie , Wolk Alicja , West Catharine , Mucci Lorelei , Cancel-Tassin Géraldine , Koutros Stella , Sorensen Karina Dalsgaard , Maehle Lovise , Neal David E. , Hamdy Freddie C. , Donovan Jenny L. , Travis Ruth C. , Hamilton Robert J. , Ingles Sue Ann , Rosenstein Barry , Lu Yong-Jie , Giles Graham G. , Kibel Adam S. , Vega Ana , Kogevinas Manolis , Park Jong Y. , Stanford Janet L. , Cybulski Cezary , Nordestgaard Børge G. , Brenner Hermann , Maier Christiane , Kim Jeri , John Esther M. , Teixeira Manuel R. , Neuhausen Susan L. , De Ruyck Kim , Razack Azad , Newcomb Lisa F. , Lessel Davor , Kaneva Radka , Usmani Nawaid , Claessens Frank , Townsend Paul A. , Gago-Dominguez Manuela , Roobol Monique J. , Menegaux Florence , Khaw Kay-Tee , Cannon-Albright Lisa , Pandha Hardev , Thibodeau Stephen N. , Hunter David J. , Kraft Peter 
Published: September 2018

AbstractAlthough genome-wide association studies (GWAS) for prostate cancer (PrCa) have identified more than 100 risk regions, most of the risk genes at these regions remain largely unknown. Here we integrate the largest PrCa GWAS (N = 142,392) with gene expression measured in 45 tissues (N = 4458), including normal and tumor prostate, to perform a multi-tissue transcriptome-wide association study (TWAS) for PrCa. We identify 217 genes at 84 independent 1 Mb regions associated with PrCa risk, 9 of which are regions with no genome-wide significant SNP within 2 Mb. 23 genes are significant in TWAS only for alternative splicing models in prostate tumor thus supporting the hypothesis of splicing driving risk for continued oncogenesis. Finally, we use a Bayesian probabilistic approach to estimate credible sets of genes containing the causal gene at a pre-defined level; this reduced the list of 217 associations to 109 genes in the 90% credible set. Overall, our findings highlight the power of integrating expression with PrCa GWAS to identify novel risk loci and prioritize putative causal genes at known risk loci.
Selective prebiotic conversion of pyrimidine and purine anhydronucleosides into Watson-Crick base-pairing arabino-furanosyl nucleosides in water
Authors: Roberts Samuel J. , Szabla Rafał , Todd Zoe R. , Stairs Shaun , Bučar Dejan-Krešimir , Šponer Jiří , Sasselov Dimitar D. , Powner Matthew W. 
Published: September 2018

AbstractPrebiotic nucleotide synthesis is crucial to understanding the origins of life on Earth. There are numerous candidates for life’s first nucleic acid, however, currently no prebiotic method to selectively and concurrently synthesise the canonical Watson–Crick base-pairing pyrimidine (C, U) and purine (A, G) nucleosides exists for any genetic polymer. Here, we demonstrate the divergent prebiotic synthesis of arabinonucleic acid (ANA) nucleosides. The complete set of canonical nucleosides is delivered from one reaction sequence, with regiospecific glycosidation and complete furanosyl selectivity. We observe photochemical 8-mercaptopurine reduction is efficient for the canonical purines (A, G), but not the non-canonical purine inosine (I). Our results demonstrate that synthesis of ANA may have been facile under conditions that comply with plausible geochemical environments on early Earth and, given that ANA is capable of encoding RNA/DNA compatible information and evolving to yield catalytic ANA-zymes, ANA may have played a critical role during the origins of life.
DNA damage sensitivity of SWI/SNF-deficient cells depends on TFIIH subunit p62/GTF2H1
Authors: Ribeiro-Silva Cristina , Aydin Özge Z. , Mesquita-Ribeiro Raquel , Slyskova Jana , Helfricht Angela , Marteijn Jurgen A. , Hoeijmakers Jan H. J. , Lans Hannes , Vermeulen Wim 
Published: September 2018

AbstractMutations in SWI/SNF genes are amongst the most common across all human cancers, but efficient therapeutic approaches that exploit vulnerabilities caused by SWI/SNF mutations are currently lacking. Here, we show that the SWI/SNF ATPases BRM/SMARCA2 and BRG1/SMARCA4 promote the expression of p62/GTF2H1, a core subunit of the transcription factor IIH (TFIIH) complex. Inactivation of either ATPase subunit downregulates GTF2H1 and therefore compromises TFIIH stability and function in transcription and nucleotide excision repair (NER). We also demonstrate that cells with permanent BRM or BRG1 depletion have the ability to restore GTF2H1 expression. As a consequence, the sensitivity of SWI/SNF-deficient cells to DNA damage induced by UV irradiation and cisplatin treatment depends on GTF2H1 levels. Together, our results expose GTF2H1 as a potential novel predictive marker of platinum drug sensitivity in SWI/SNF-deficient cancer cells.