bluuebunny/crossref_metadata_2025_split huggingface dataset:
Educational and health outcomes of children and adolescents receiving antidepressant medication: Scotland-wide retrospective record linkage cohort study of 766 237 schoolchildren
Authors: Fleming Michael , Fitton Catherine A , Steiner Markus F C , McLay James S , Clark David , King Albert , Mackay Daniel F , Pell Jill P 
Published: January 2020

AbstractBackgroundChildhood depression is relatively common, under-researched and can impact social and cognitive function and self-esteem.MethodsRecord linkage of routinely collected Scotland-wide administrative databases covering prescriptions [prescribing information system (PIS)], hospitalizations (Scottish Morbidity Records 01 and 04), maternity records (Scottish Morbidity Records 02), deaths (National Records of Scotland), annual pupil census, school absences/exclusions, special educational needs (Scottish Exchange of Educational Data; ScotXed), examinations (Scottish Qualifications Authority) and (un)employment (ScotXed) provided data on 766 237 children attending Scottish schools between 2009 and 2013 inclusively. We compared educational and health outcomes of children receiving antidepressant medication with their peers, adjusting for confounders (socio-demographic, maternity and comorbidity) and explored effect modifiers and mediators.ResultsCompared with peers, children receiving antidepressants were more likely to be absent [adjusted incidence rate ratio (IRR) 1.90, 95% confidence interval (CI) 1.85–1.95] or excluded (adjusted IRR 1.48, 95% CI 1.29–1.69) from school, have special educational needs [adjusted odds ratio (OR) 1.77, 95% CI 1.65–1.90], have the lowest level of academic attainment (adjusted OR 3.00, 95% CI 2.51–3.58) and be unemployed after leaving school (adjusted OR 1.88, 95% CI 1.71–2.08). They had increased hospitalization [adjusted hazard ratio (HR) 2.07, 95% CI 1.98–2.18] and mortality (adjusted HR 2.73, 95% CI 1.73–4.29) over 5 years’ follow-up. Higher absenteeism partially explained poorer attainment and unemployment. Treatment with antidepressants was less common among boys than girls (0.5% vs 1.0%) but the associations with special educational need and unemployment were stronger in boys.ConclusionsChildren receiving antidepressants fare worse than their peers across a wide range of education and health outcomes. Interventions to reduce absenteeism or mitigate its effects should be investigated.
Drug Resistance Assessment Following Administration of Respiratory Syncytial Virus (RSV) Fusion Inhibitor Presatovir to Participants Experimentally Infected With RSV
Authors: Stray Kirsten , Perron Michel , Porter Danielle P , Anderson Francisco , Lewis Sandra A , Perry Jason , Miller Michael , Cihlar Tomas , DeVincenzo John , Chien Jason W , Jordan Robert 
Published: January 2020

AbstractBackgroundPresatovir is an oral respiratory syncytial virus (RSV) fusion inhibitor targeting RSV F protein. In a double-blind, placebo-controlled study in healthy adults experimentally infected with RSV (Memphis-37b), presatovir significantly reduced viral load and clinical disease severity in a dose-dependent manner.MethodsViral RNA from nasal wash samples was amplified and the F gene sequenced to monitor presatovir resistance. Effects of identified amino acid substitutions on in vitro susceptibility to presatovir, viral fitness, and clinical outcome were assessed.ResultsTwenty-eight treatment-emergent F substitutions were identified. Of these, 26 were tested in vitro; 2 were not due to lack of recombinant virus recovery. Ten substitutions did not affect presatovir susceptibility, and 16 substitutions reduced RSV susceptibility to presatovir (2.9- to 410-fold). No substitutions altered RSV susceptibility to palivizumab or ribavirin. Frequency of phenotypically resistant substitutions was higher with regimens containing lower presatovir dose and shorter treatment duration. Participants with phenotypic presatovir resistance had significantly higher nasal viral load area under the curve relative to those without, but substitutions did not significantly affect peak viral load or clinical manifestations of RSV disease.ConclusionsEmergence of presatovir-resistant RSV occurred during therapy but did not significantly affect clinical efficacy in participants with experimental RSV infection.
Protection From Natural Immunity Against Enteric Infections and Etiology-Specific Diarrhea in a Longitudinal Birth Cohort
Authors: Rogawski McQuade Elizabeth T , Liu Jie , Kang Gagandeep , Kosek Margaret N , Lima Aldo A M , Bessong Pascal O , Samie Amidou , Haque Rashidul , Mduma Estomih R , Shrestha Sanjaya , Leite Jose Paulo , Bodhidatta Ladaporn , Iqbal Najeeha , Page Nicola , Kiwelu Ireen , Bhutta Zulfiqar , Ahmed Tahmeed , Houpt Eric R , Platts-Mills James A 
Published: January 2020

Abstract

Background
The degree of protection conferred by natural immunity is unknown for many enteropathogens, but it is important to support the development of enteric vaccines.

Methods
We used the Andersen-Gill extension of the Cox model to estimate the effects of previous infections on the incidence of subsequent subclinical infections and diarrhea in children under 2 using quantitative molecular diagnostics in the MAL-ED cohort. We used cross-pathogen negative control associations to correct bias due to confounding by unmeasured heterogeneity of exposure and susceptibility.

Results
Prior rotavirus infection was associated with a 50% lower hazard (calibrated hazard ratio [cHR], 0.50; 95% confidence interval [CI], 0.41–0.62) of subsequent rotavirus diarrhea. Strong protection was evident against Cryptosporidium diarrhea (cHR, 0.32; 95% CI, 0.20–0.51). There was also protection due to prior infections for norovirus GII (cHR against diarrhea, 0.67; 95% CI, 0.49–0.91), astrovirus (cHR, 0.62; 95% CI, 0.48–0.81), and Shigella (cHR, 0.79; 95% CI, 0.65–0.95). Minimal protection was observed for other bacteria, adenovirus 40/41, and sapovirus.

Conclusions
Natural immunity was generally stronger for the enteric viruses than bacteria, potentially due to less antigenic diversity. Vaccines against major causes of diarrhea may be feasible but likely need to be more immunogenic than natural infection.
Should they stay or should they go? Climate migrants and local conflicts
Authors: Bosetti Valentina , Cattaneo Cristina , Peri Giovanni 
Published: January 2020

Abstract
There is extensive evidence that higher temperatures increase the probability of local conflict. There is also evidence that emigration represents an important margin of adaptation to a warming climate. In this article, we analyse whether migration influences the link between warming and conflicts by either attenuating this connection in countries of origin and/or by exacerbating it in countries of destination. We find that in countries where the propensity to emigrate—as measured by past diaspora—is higher, increases in temperature have smaller effects on the probability of armed conflict, compared to countries with lower migration propensity. This is consistent with emigration functioning as ‘escape valve’ for local tensions. We find no evidence that climate-induced migration increased the probability of conflict in receiving countries.
Melanoma Prognosis: Accuracy of the American Joint Committee on Cancer Staging Manual Eighth Edition
Authors: Bajaj Shirin , Donnelly Douglas , Call Melissa , Johannet Paul , Moran Una , Polsky David , Shapiro Richard , Berman Russell , Pavlick Anna , Weber Jeffrey , Zhong Judy , Osman Iman 
Published: January 2020

Abstract

Background
The American Joint Committee on Cancer (AJCC) maintains that the eighth edition of its Staging Manual (AJCC8) has improved accuracy compared with the seventh (AJCC7). However, there are concerns that implementation may disrupt analysis of active clinical trials for stage III patients. We used an independent cohort of melanoma patients to test the extent to which AJCC8 has improved prognostic accuracy compared with AJCC7.

Methods
We analyzed a cohort of 1315 prospectively enrolled patients. We assessed primary tumor and nodal classification of stage I–III patients using AJCC7 and AJCC8 to assign disease stages at diagnosis. We compared recurrence-free (RFS) and overall survival (OS) using Kaplan-Meier curves and log-rank tests. We then compared concordance indices of discriminatory prognostic ability and area under the curve of 5-year survival to predict RFS and OS. All statistical tests were two-sided.

Results
Stage IIC patients continued to have worse outcomes than stage IIIA patients, with a 5-year RFS of 26.5% (95% confidence interval [CI] = 12.8% to 55.1%) vs 56.0% (95% CI = 37.0% to 84.7%) by AJCC8 (P = .002). For stage I, removing mitotic index as a T classification factor decreased its prognostic value, although not statistically significantly (RFS concordance index [C-index] = 0.63, 95% CI = 0.56 to 0.69; to 0.56, 95% CI = 0.49 to 0.63, P = .07; OS C-index = 0.48, 95% CI = 0.38 to 0.58; to 0.48, 95% CI = 0.41 to 0.56, P = .90). For stage II, prognostication remained constant (RFS C-index = 0.65, 95% CI = 0.57 to 0.72; OS C-index = 0.61, 95% CI = 0.50 to 0.72), and for stage III, AJCC8 yielded statistically significantly enhanced prognostication for RFS (C-index = 0.65, 95% CI = 0.60 to 0.70; to 0.70, 95% CI = 0.66 to 0.75, P = .01).

Conclusions
Compared with AJCC7, we demonstrate that AJCC8 enables more accurate prognosis for patients with stage III melanoma. Restaging a large cohort of patients can enhance the analysis of active clinical trials.
Trends in Late Mortality Among Adolescent and Young Adult Cancer Survivors
Authors: Anderson Chelsea , Nichols Hazel B 
Published: January 2020

Abstract

Background
Over the past several decades, treatment of cancer in adolescents and young adults (AYAs) has evolved substantially, leading to steady improvements in estimated 5-year survival at diagnosis. However, the impact on late mortality in this population is largely unexamined. We investigated temporal trends in mortality among 5-year AYA cancer survivors.

Methods
The Surveillance, Epidemiology, and End Results database was used to identify AYAs (age 15–39 years) diagnosed with cancer during 1975–2011 who survived at least 5 years beyond diagnosis. Survival months were accrued from 5 years postdiagnosis until death or the end of 2016. Cumulative mortality from all causes, the primary cancer, other cancers, and noncancer or nonexternal causes (ie, excluding accidents, suicide, homicide) were estimated according to diagnosis era.

Results
Among 282 969 five-year AYA cancer survivors, 5-year mortality (ie, from 5 through 10 years postdiagnosis) from all-causes decreased from 8.3% (95% confidence interval = 8.0% to 8.6%) among those diagnosed in 1975–1984 to 5.4% (95% confidence interval = 5.3% to 5.6%) among those diagnosed in 2005–2011. This was largely explained by decreases in mortality from the primary cancer (6.8% to 4.2%) between these periods. However, for specific cancer types, including colorectal, bone, sarcomas, cervical/uterine, and bladder, cumulative mortality curves demonstrated little improvement in primary cancer mortality over time. Some reduction in late mortality from noncancer or nonexternal causes was apparent for Hodgkin lymphoma, leukemia, kidney cancer, head and neck cancers, and trachea, lung, and bronchus cancers.

Conclusion
Over the past four decades, all-cause and cancer-specific mortality have decreased among 5-year AYA cancer survivors overall, but several cancer types have not shared in these improvements.
Symplasmic isolation marks cell fate changes during somatic embryogenesis
Authors: Godel-Jedrychowska Kamila , Kulinska-Lukaszek Katarzyna , Horstman Anneke , Soriano Mercedes , Li Mengfan , Malota Karol , Boutilier Kim , Kurczynska Ewa U 
Published: January 2020

AbstractCell-to-cell signalling is a major mechanism controlling plant morphogenesis. Transport of signalling molecules through plasmodesmata is one way in which plants promote or restrict intercellular signalling over short distances. Plasmodesmata are membrane-lined pores between cells that regulate the intercellular flow of signalling molecules through changes in their size, creating symplasmic fields of connected cells. Here we examine the role of plasmodesmata and symplasmic communication in the establishment of plant cell totipotency, using somatic embryo induction from Arabidopsis explants as a model system. Cell-to-cell communication was evaluated using fluorescent tracers, supplemented with histological and ultrastructural analysis, and correlated with expression of a WOX2 embryo reporter. We showed that embryogenic cells are isolated symplasmically from non-embryogenic cells regardless of the explant type (immature zygotic embryos or seedlings) and inducer system (2,4-dichlorophenoxyacetic acid or the BABY BOOM (BBM) transcription factor), but that the symplasmic domains in different explants differ with respect to the maximum size of molecule capable of moving through the plasmodesmata. Callose deposition in plasmodesmata preceded WOX2 expression in future sites of somatic embryo development, but later was greatly reduced in WOX2-expressing domains. Callose deposition was also associated with a decrease DR5 auxin response in embryogenic tissue. Treatment of explants with the callose biosynthesis inhibitor 2-deoxy-D-glucose supressed somatic embryo formation in all three systems studied, and also blocked the observed decrease in DR5 expression. Together these data suggest that callose deposition at plasmodesmata is required for symplasmic isolation and establishment of cell totipotency in Arabidopsis.
The Jewish Fusgeyer Migration Movement from Early Twentieth-Century Romania as Transcultural Rhetorical Tool in US Memorial Literary Culture
Authors: Mihăilescu Dana 
Published: January 2020

AbstractFrom 1900 to 1907, a so-called fusgeyer phenomenon was the most salient characteristic of Jewish emigration from Romania, given the high number of impoverished, desperate Jews who were on the brink of starvation and started to go on foot in the attempt to leave the country. My essay considers the literary representation of this fusgeyer movement over time as a conduit upholding transcultural networks of memory work in the United States. To that end, I will examine the representation of fusgeyers in the literature produced by immigrant fusgeyers to the United States immediately after emigration (M. E. Ravage’s 1917 An American in the Making: The Life Story of an Immigrant and Jacob Finkelstein’s 1942 “Memoirs of a Fusgeyer from Romania to America”) and in the literature created in contemporary times in the United States (Stuart Tower’s 2003 historical novel The Wayfarers). In my analysis, I rely on Astrid Erll’s demonstration that literature can be a powerful conduit of cultural memory by its use of “four modes of a ‘rhetoric of collective memory’: the experiential, the mythical, the antagonistic, and the reflexive mode.” I will show which of these modes of rhetoric apply to the literary works I consider and how they highlight a dynamic movement toward a transcultural type of rhetoric shaping Jewish memory forms in contemporary US literature.
Mass determinations of the three mini-Neptunes transiting TOI-125
Authors: Nielsen L D , Gandolfi D , Armstrong D J , Jenkins J S , Fridlund M , Santos N C , Dai F , Adibekyan V , Luque R , Steffen J H , Esposito M , Meru F , Sabotta S , Bolmont E , Kossakowski D , Otegi J F , Murgas F , Stalport M , Rodler F , Díaz M R , Kurtovic N T , Ricker G , Vanderspek R , Latham D W , Seager S , Winn J N , Jenkins J M , Allart R , M. Almenara J , Barrado D , Barros S C C , Bayliss D , Berdiñas Z M , Boisse I , Bouchy F , Boyd P , Brown D J A , Bryant E M , Burke C , Cochran W D , Cooke B F , Demangeon O D S , Díaz R F , Dittman J , Dorn C , Dumusque X , García R A , González-Cuesta L , Grziwa S , Georgieva I , Guerrero N , Hatzes A P , Helled R , Henze C E , Hojjatpanah S , Korth J , Lam K W F , Lillo-Box J , Lopez T A , Livingston J , Mathur S , Mousis O , Narita N , Osborn H P , Palle E , Rojas P A Peña , Persson C M , Quinn S N , Rauer H , Redfield S , Santerne A , dos Santos L A , Seidel J V , Sousa S G , Ting E B , Turbet M , Udry S , Vanderburg A , Van Eylen V , Vines J I , Wheatley P J , Wilson P A 
Published: January 2020

ABSTRACT
The Transiting Exoplanet Survey Satellite, TESS, is currently carrying out an all-sky search for small planets transiting bright stars. In the first year of the TESS survey, a steady progress was made in achieving the mission’s primary science goal of establishing bulk densities for 50 planets smaller than Neptune. During that year, the TESS’s observations were focused on the southern ecliptic hemisphere, resulting in the discovery of three mini-Neptunes orbiting the star TOI-125, a V = 11.0 K0 dwarf. We present intensive HARPS radial velocity observations, yielding precise mass measurements for TOI-125b, TOI-125c, and TOI-125d. TOI-125b has an orbital period of 4.65 d, a radius of 2.726 ± 0.075 RE, a mass of 9.50 ± 0.88 ME, and is near the 2:1 mean motion resonance with TOI-125c at 9.15 d. TOI-125c has a similar radius of 2.759 ± 0.10 RE and a mass of 6.63 ± 0.99 ME, being the puffiest of the three planets. TOI-125d has an orbital period of 19.98 d and a radius of 2.93 ± 0.17 RE and mass 13.6 ± 1.2 ME. For TOI-125b and d, we find unusual high eccentricities of 0.19 ± 0.04 and $0.17^{+0.08}_{-0.06}$, respectively. Our analysis also provides upper mass limits for the two low-SNR planet candidates in the system; for TOI-125.04 (RP = 1.36 RE, P = 0.53 d), we find a 2σ upper mass limit of 1.6 ME, whereas TOI-125.05 ($R_P=4.2^{+2.4}_{-1.4}$ RE, P = 13.28 d) is unlikely a viable planet candidate with an upper mass limit of 2.7 ME. We discuss the internal structure of the three confirmed planets, as well as dynamical stability and system architecture for this intriguing exoplanet system.
Global Site Selection for Astronomy
Authors: Aksaker N , Yerli S K , Erdoğan M A , Kurt Z , Kaba K , Bayazit M , Yesilyaprak C 
Published: January 2020

ABSTRACT
A global site selection for astronomy was performed with 1 km spatial resolution (∼1 gigapixel in size) using long-term and up-to-date datasets to classify the entire terrestrial surface of the Earth. Satellite instruments are used to get the following datasets of geographical information system (GIS) layers: cloud coverage, digital elevation model, artificial light, precipitable water vapour, aerosol optical depth, wind speed, and land use and land cover. A multi-criteria decision analysis (MCDA) technique is applied to these datasets, creating four different series where each layer will have a specific weight. We introduce for the first time a suitability index for astronomical sites (SIAS). This index can be used to find suitable locations and to compare different sites or observatories. The midwestern Andes in South America and the Tibetan Plateau in western China were found to be the best in all SIAS series. Considering all the series, less than 3 per cent of all terrestrial surfaces are found to be the best regions to establish an astronomical observatory. In addition to this, only approximately 10 per cent of all current observatories are located in good locations in all SIAS series. Amateurs, institutions or countries aiming to construct an observatory could create a shortlist of potential site locations using a layout of SIAS values for each country without spending time and budget. The outcomes and datasets of this study have been made available through a website, the Astro GIS Database, at www.astrogis.org.
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Authors: Minh Bui Quang , Schmidt Heiko A , Chernomor Olga , Schrempf Dominik , Woodhams Michael D , von Haeseler Arndt , Lanfear Robert 
Published: January 2020

AbstractIQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.
Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA
Authors: Boivin Vincent , Reulet Gaspard , Boisvert Olivier , Couture Sonia , Elela Sherif Abou , Scott Michelle S 
Published: January 2020

Abstract
The study of RNA expression is the fastest growing area of genomic research. However, despite the dramatic increase in the number of sequenced transcriptomes, we still do not have accurate estimates of the number and expression levels of non-coding RNA genes. Non-coding transcripts are often overlooked due to incomplete genome annotation. In this study, we use annotation-independent detection of RNA reads generated using a reverse transcriptase with low structure bias to identify non-coding RNA. Transcripts between 20 and 500 nucleotides were filtered and crosschecked with non-coding RNA annotations revealing 111 non-annotated non-coding RNAs expressed in different cell lines and tissues. Inspecting the sequence and structural features of these transcripts indicated that 60% of these transcripts correspond to new snoRNA and tRNA-like genes. The identified genes exhibited features of their respective families in terms of structure, expression, conservation and response to depletion of interacting proteins. Together, our data reveal a new group of RNA that are difficult to detect using standard gene prediction and RNA sequencing techniques, suggesting that reliance on actual gene annotation and sequencing techniques distorts the perceived architecture of the human transcriptome.
Cooperation of the NEIL3 and Fanconi anemia/BRCA pathways in interstrand crosslink repair
Authors: Li Niu , Wang Jian , Wallace Susan S , Chen Jing , Zhou Jia , D’Andrea Alan D 
Published: January 2020

AbstractThe NEIL3 DNA glycosylase is a base excision repair enzyme that excises bulky base lesions from DNA. Although NEIL3 has been shown to unhook interstrand crosslinks (ICL) in Xenopus extracts, how NEIL3 participants in ICL repair in human cells and its corporation with the canonical Fanconi anemia (FA)/BRCA pathway remain unclear. Here we show that the NEIL3 and the FA/BRCA pathways are non-epistatic in psoralen-ICL repair. The NEIL3 pathway is the major pathway for repairing psoralen-ICL, and the FA/BRCA pathway is only activated when NEIL3 is not present. Mechanistically, NEIL3 is recruited to psoralen-ICL in a rapid, PARP-dependent manner. Importantly, the NEIL3 pathway repairs psoralen-ICLs without generating double-strand breaks (DSBs), unlike the FA/BRCA pathway. In addition, we found that the RUVBL1/2 complex physically interact with NEIL3 and function within the NEIL3 pathway in psoralen-ICL repair. Moreover, TRAIP is important for the recruitment of NEIL3 but not FANCD2, and knockdown of TRAIP promotes FA/BRCA pathway activation. Interestingly, TRAIP is non-epistatic with both NEIL3 and FA pathways in psoralen-ICL repair, suggesting that TRAIP may function upstream of the two pathways. Taken together, the NEIL3 pathway is the major pathway to repair psoralen-ICL through a unique DSB-free mechanism in human cells.