bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Authors: Ghurye Jay , Koren Sergey , Small Scott T , Redmond Seth , Howell Paul , Phillippy Adam M , Besansky Nora J 
Published: June 2019

Abstract

Background
Anopheles funestus is one of the 3 most consequential and widespread vectors of human malaria in tropical Africa. However, the lack of a high-quality reference genome has hindered the association of phenotypic traits with their genetic basis in this important mosquito.

Findings
Here we present a new high-quality A. funestus reference genome (AfunF3) assembled using 240× coverage of long-read single-molecule sequencing for contigging, combined with 100× coverage of short-read Hi-C data for chromosome scaffolding. The assembled contigs total 446 Mbp of sequence and contain substantial duplication due to alternative alleles present in the sequenced pool of mosquitos from the FUMOZ colony. Using alignment and depth-of-coverage information, these contigs were deduplicated to a 211 Mbp primary assembly, which is closer to the expected haploid genome size of 250 Mbp. This primary assembly consists of 1,053 contigs organized into 3 chromosome-scale scaffolds with an N50 contig size of 632 kbp and an N50 scaffold size of 93.811 Mbp, representing a 100-fold improvement in continuity versus the current reference assembly, AfunF1.

Conclusion
This highly contiguous and complete A. funestus reference genome assembly will serve as an improved basis for future studies of genomic variation and organization in this important disease vector.
Coastal migration patterns of the four largest Barents Sea Atlantic salmon stocks inferred using genetic stock identification methods
Authors: Svenning Martin-A , Falkegård Morten , Niemelä Eero , Vähä Juha-Pekka , Wennevik Vidar , Ozerov Mikhail , Prusov Sergey , Dempson J Brian , Power Michael , Fauchald Per 
Published: June 2019

AbstractCombining detailed temporal and spatial catch data, including catch per unit effort, with a high-resolution microsatellite genetic baseline facilitated the development of stock-specific coastal migration models for the four largest Atlantic salmon (Salmo salar) populations, Målselv, Alta, Tana and Kola rivers, contributing to the Barents Sea mixed-stock fishery. Målselv salmon displayed a restricted coastal movement with 85% of the fish captured within 20 km of their natal river. Kola salmon also demonstrated limited coastal movements in Norwegian waters, with most (&gt; 90%) caught in eastern Finnmark. Multi-sea-winter (MSW) Alta salmon were caught west of Alta fjord across a broader stretch of coast while one-sea-winter (1SW) fish migrated more extensively along the coast prior to river entry. Tana salmon, however, were detected over a broad expanse (600 km) of the North-Norwegian coast. For all populations MSW salmon dominating catches earlier in the season (May–June) while 1SW fish were more common from July to August. This study provides an example of how traditional catch and effort information may be combined with genetic methods to obtain insights into spatial and temporal changes in Atlantic salmon catch composition and their associated migration patterns in a mixed-stock coastal fishery.
Nontuberculous Mycobacteria and Heterologous Immunity to Tuberculosis
Authors: Shah Javeed A , Lindestam Arlehamn Cecilia S , Horne David J , Sette Alessandro , Hawn Thomas R 
Published: June 2019

AbstractDevelopment of an improved tuberculosis (TB) vaccine is a high worldwide public health priority. Bacillus Calmette-Guerin (BCG), the only licensed TB vaccine, provides variable efficacy against adult pulmonary TB, but why this protection varies is unclear. Humans are regularly exposed to non-tuberculous mycobacteria (NTM) that live in soil and water reservoirs and vary in different geographic regions around the world. Immunologic cross-reactivity may explain disparate outcomes of BCG vaccination and susceptibility to TB disease. Evidence supporting this hypothesis is increasing but challenging to obtain due to a lack of reliable research tools. In this review, we describe the progress and bottlenecks in research on NTM epidemiology, immunology and heterologous immunity to Mtb. With ongoing efforts to develop new vaccines for TB, understanding the effect of NTM on vaccine efficacy may be a critical determinant of success.
Influence of temperature on the occurrence and distribution of the sand shrimp Crangon septemspinosaSay, 1818 (Decapoda: Caridea: Crangonidae) in polyhaline lagoons in Maryland, USA
Authors: Chigbu Paulinus , Malinis Lauren , Malagon Hector , Doctor Steve 
Published: June 2019

AbstractSand shrimp, Crangon septemspinosaSay, 1818, is one of the most abundant decapod crustaceans in estuaries and coastal waters of the northwestern Atlantic Ocean, though little is known about its population dynamics in polyhaline lagoons of the mid-Atlantic region. Seasonal and spatial patterns of abundance and distribution of C. septemspinosa were evaluated in relation to temperature, salinity, and dissolved oxygen in Maryland coastal bays (MCBs) using monthly data (April to October 1994 to 2012). We tested the hypothesis that temperature influences the occurrence and distribution of sand shrimp in the lagoons. A consistent pattern of high relative abundance of shrimp in spring and its scarcity in summer and early fall was observed. Shrimp abundance was highest in the northern bays and at sites closest to the Ocean City Inlet during April, but lowest at sites in the upper parts of Chincoteague Bay and MCBs tributaries. As mean temperature increased from April (12.2–17.1 oC) to June (21.8–26.7 oC), the relative abundance of the shrimp decreased substantially at most sites except at two sites where mean water temperature was comparatively low (21.8–23.3 oC). By July, when mean temperature was at its maximum (23.1–28.9 oC) in the bays, shrimp were rarely caught in trawls even in early fall in spite of the decline in temperature. It is likely that shrimp moved into nearshore waters with cooler temperature or suffered high mortality due to high temperature during this period. Generalized linear models suggest that temperature, and temperature and dissolved oxygen combined, were the most important abiotic factors examined that influenced the spatial distribution of C. septemspinosa in May and June, respectively. Considering their trophic importance, the spatio-temporal variations in the occurrence and abundance of the shrimp have implications for food web dynamics in the MCBs.
Precipitation and seasonality affect grazing impacts on herbage nutritive values in alpine meadows on the Qinghai-Tibet Plateau
Authors: Yao Xixi , Wu Jianping , Gong Xuyin 
Published: June 2019

AbstractAimsGrasslands used for animal husbandry are chosen depending on the nutritive values of dominant herbage species. However, the influence of grazing in combination with precipitation and growing season on the nutritive values of dominant species has not been explicated.MethodsTo unveil the influence of the different grazing intensities on the nutritional values, an ecological study was formulated, namely fencing (G0), light grazing (G1), moderate grazing (G2) and high grazing (G3). This ambitious study was undertaken on the nutritive values of the four dominant species of herbage in an alpine meadow on the Qinghai-Tibet Plateau (QTP) during growing season (June–September) for two successive years, namely 2015 (rainy year) and 2016 (droughty year).Important FindingsWe found that (i) the nutritive value of Kobresia capillifolia, Polygonum viviparum and Caragana sinica was noticeably increased by grazing, but negligible effect on Potentilla fruticosa nutritive value was recorded. (ii) During the rainy year (2015), compared with G0, Polygonum viviparum and Potentilla fruticosa displayed 5.4 and 1.5% increases in the crude protein (CP) content and 8.5 and 2.4% increases in vitro true digestibility (IVTD), respectively, while the neutral detergent fibre (NDF) decreased by 13.5 and 0.9%, respectively. During the droughty year (2016), compared with G0, C. sinica and Potentilla fruticosa showed increases in the CP content by 4.3 and 1.3% and increases in the IVTD by 10.7 and 0.4%, respectively, during G3, while the NDF decreased by 6.0 and 1.0%, respectively. (iii) The nutritive values of all species were higher in the years when the rains were good. However, the nutritive values suffered heavily during drought conditions. Besides, the highest and lowest values of nutrition were detected in June and in September, respectively. The inter-seasonal and the inter-annual changes in the nutritional values of species were higher for K. capillifolia and Polygonum viviparum than for Potentilla fruticosa and C. sinica, suggesting that Potentilla fruticosa and C. sinica had higher water-use efficiency. (iv) Grazing clearly reduced the drought tolerance of three species and showed no effects on Potentilla fruticosa. (v) Grazing clearly increased the inter-month variation in the nutritional value of K. capillifolia and Polygonum viviparum but showed no effects on Potentilla fruticosa or C. sinica. Evidently, the grazing effects impacting the nutritional value of the dominant species of herbage exhibited conspicuous inter-annual and seasonal variations with species-specific influences and responses. Our findings are expected to have far-reaching implications enabling the authorities to arrive at strategic decisions and designing of relevant policies for the efficient management of the ecosystems ensuring the speed restoration of the QTP under severe grazing and extreme climatic circumstances.
Trauma Resilience and Recovery Program: Addressing Mental Health in Pediatric Trauma Centers
Authors: Ridings Leigh E , Anton Margaret T , Winkelmann Jennifer , Davidson Tatiana M , Wray Lauren , Streck Christian J , Ruggiero Kenneth J 
Published: June 2019

AbstractObjectiveApproximately 225,000 children sustain injuries requiring hospitalization annually. Posttraumatic stress disorder (PTSD) and depression are prevalent among pediatric patients and caregivers post-injury. Most U.S. trauma centers do not address patients’ mental health needs. Better models of care are needed to address emotional recovery. This article describes the engagement and recovery trajectories of pediatric patients enrolled in the Trauma Resilience and Recovery Program (TRRP), a stepped-care model to accelerate emotional recovery following hospitalization.MethodsTRRP is designed to (a) provide in-hospital education about post-injury emotional recovery and assess child and caregiver distress; (b) track mental health symptoms via a 30-day text-messaging program; (c) complete 30-day PTSD and depression phone screens; and (d) provide evidence-based treatment via telehealth or in-person services or referrals, if needed. All 154 families approached were offered TRRP services, 96% of whom agreed to enroll in TRRP. Most patients were boys (59.8%), and average age was 9.12 years [standard deviation (SD) = 5.42]. Most injuries (45.8%) were sustained from motor vehicle accidents.ResultsIn hospital, 68.5% of caregivers and 78.3% of children reported clinically significant distress levels. Over 60% of families enrolled in the texting service. TRRP re-engaged 40.1% of families for the 30-day screen, 35.5% of whom reported clinically significant PTSD (M = 13.90, SD = 11.42) and/or depression (M = 13.35, SD = 11.16). Most (76%) patients with clinically significant symptomology agreed to treatment.ConclusionsOur intervention model was feasible and increased reach to families who needed services. Efforts to improve follow-up engagement are discussed, as are initial successes in implementing this model in other pediatric trauma centers.
Trial Registration and Outcome Reporting in Child and Pediatric Psychology: A Systematic Review
Authors: Hildenbrand Aimee K , Conour Cecily , Straus Jacob A , Moufarrej Sacha , Palermo Tonya M 
Published: June 2019

Abstract

Objective
To examine rate of registration for randomized controlled trials (RCTs) published in the Journal of Pediatric Psychology (JPP) and Journal of Clinical Child & Adolescent Psychology (JCCAP). Secondary aims were to investigate associations between trial characteristics and registration status and compare registered and published primary outcomes.

Methods
RCTs published in JPP or JCCAP between January 1, 2007 and December 31, 2017 were included. Secondary analyses of previously published RCTs, meta-analytic, systematic, and narrative reviews, and articles reporting primary aims related to intervention acceptability, feasibility, and/or cost-effectiveness were excluded. Trial registration status, primary registered and published outcomes, dates of registration, participant enrollment and publication, sample size, and country where the trial was conducted were extracted from articles and trial registries.

Results
Of 61 RCTs included, 48% were registered. Among registered trials, only 14% were registered before participant enrollment began. Most were registered late (i.e., retrospectively; 86%) in ClinicalTrials.gov (90%). Registration status did not differ based on journal, study sample size, or geographic region where the study was conducted. A greater proportion of trials published in 2013–2017 were registered (61%) relative to those published in 2007–2012 (32%), p = .03. Among registered trials, 57% had discrepancies between registered and published primary outcomes.

Conclusions
Findings reveal low rates of prospective registration and considerable risk for incomplete or selective outcome reporting among RCTs published in JPP and JCCAP. Coordinated efforts from all stakeholders involved in the conduct and reporting of clinical child and pediatric psychology research are needed to improve transparent reporting of clinical trials.
Linking gas and galaxies at high redshift: MUSE surveys the environments of six damped Lyα systems at z ≈ 3
Authors: Mackenzie Ruari , Fumagalli Michele , Theuns Tom , Hatton David J , Garel Thibault , Cantalupo Sebastiano , Christensen Lise , Fynbo Johan P U , Kanekar Nissim , Møller Palle , O’Meara John , Prochaska J Xavier , Rafelski Marc , Shanks Tom , Trayford James 
Published: June 2019

ABSTRACT
We present results from a survey of galaxies in the fields of six z ≥ 3 damped Lyman α (Lyα) systems (DLAs) using the Multi Unit Spectroscopic Explorer (MUSE) at the Very Large Telescope (VLT). We report a high detection rate of up to ${\approx } 80{{\ \rm per\ cent}}$ of galaxies within 1000 km s−1 from DLAs and with impact parameters between 25 and 280 kpc. In particular, we discovered five high-confidence Lyα emitters associated with three DLAs, plus up to nine additional detections across five of the six fields. The majority of the detections are at relatively large impact parameters (>50 kpc) with two detections being plausible host galaxies. Among our detections, we report four galaxies associated with the most metal-poor DLA in our sample (Z/Z⊙ = −2.33 ± 0.22), which trace an overdense structure resembling a filament. By comparing our detections with predictions from the Evolution and Assembly of GaLaxies and their Environments (EAGLE) cosmological simulations and a semi-analytic model designed to reproduce the observed bias of DLAs at z > 2, we conclude that our observations are consistent with a scenario in which a significant fraction of DLAs trace the neutral regions within haloes with a characteristic mass of $M_{\rm h} \approx 10^{11}-10^{12}~\rm M_\odot$, in agreement with the inference made from the large-scale clustering of DLAs. We finally show how larger surveys targeting ≈25 absorbers have the potential of constraining the characteristic masses of haloes hosting high-redshift DLAs with sufficient accuracy to discriminate between different models.
Spliceosome disassembly factors ILP1 and NTR1 promote miRNA biogenesis in Arabidopsis thaliana
Authors: Wang Junli , Chen Susu , Jiang Ning , Li Ning , Wang Xiaoyan , Li Zhongpeng , Li Xu , Liu Hongtao , Li Lin , Yang Yu , Ni Ting , Yu Chaoyi , Ma Jinbiao , Zheng Binglian , Ren Guodong 
Published: June 2019

Abstract
The intron-lariat spliceosome (ILS) complex is highly conserved among eukaryotes, and its disassembly marks the end of a canonical splicing cycle. In this study, we show that two conserved disassembly factors of the ILS complex, Increased Level of Polyploidy1-1D (ILP1) and NTC-Related protein 1 (NTR1), positively regulate microRNA (miRNA) biogenesis by facilitating transcriptional elongation of MIRNA (MIR) genes in Arabidopsis thaliana. ILP1 and NTR1 formed a stable complex and co-regulated alternative splicing of more than a hundred genes across the Arabidopsis genome, including some primary transcripts of miRNAs (pri-miRNAs). Intriguingly, pri-miRNAs, regardless of having introns or not, were globally down-regulated when the ILP1 or NTR1 function was compromised. ILP1 and NTR1 interacted with core miRNA processing proteins Dicer-like 1 and Serrate, and were required for proper RNA polymerase II occupancy at elongated regions of MIR chromatin, without affecting either MIR promoter activity or pri-miRNA decay. Our results provide further insights into the regulatory role of spliceosomal machineries in the biogenesis of miRNAs.
Complex distribution and velocity field of molecular gas in NGC 1316 as revealed by the Morita Array of ALMA
Authors: Morokuma-Matsui Kana , Serra Paolo , Maccagni Filippo M , For Bi-Qing , Wang Jing , Bekki Kenji , Morokuma Tomoki , Egusa Fumi , Espada Daniel , Miura Rie E , Nakanishi Kouichiro , Koribalski Bärbel S , Takeuchi Tsutomu T 
Published: June 2019

Abstract
We present the results of 12CO(J = 1–0) mosaicing observations of the cD galaxy NGC 1316 at kiloparsec resolution performed with the Morita Array of the Atacama Large Millimeter/submillimeter Array (ALMA). We reveal the detailed distribution of the molecular gas in the central region for the first time: a shell structure in the northwest, a barely resolved blob in the southeast of the center, and some clumps between them. The total molecular gas mass obtained with a standard Milky Way CO-to-H2 conversion factor is $(5.62 \pm 0.53) \times 10^{8}\, M_{\odot }$, which is consistent with previous studies. The disturbed velocity field of the molecular gas suggests that the molecular gas was injected very recently (&lt;1 Gyr) if it has an external origin, and is in the process of settling into a rotating disk. Assuming that a low-mass gas-rich galaxy has accreted, the gas-to-dust ratio and H2-to-H i ratio are unusually low (∼28) and high (∼5.6), respectively. To explain these ratios additional processes should be taken into account, such as effective dust formation and conversion from atomic to molecular gas during the interaction. We also discuss the interaction between the nuclear jet and the molecular gas.
Detection of a new methylamine (CH3NH2) source: Candidate for future glycine surveys
Authors: Ohishi Masatoshi , Suzuki Taiki , Hirota Tomoya , Saito Masao , Kaifu Norio 
Published: June 2019

Abstract
Interstellar glycine (NH2CH2COOH), the simplest amino acid, has long been sought in studying a possible relation between the Universe and origin of life. In the last 40 or so years all surveys of glycine have failed; an alternative strategy would be to search for precursor(s) to glycine. Such studies of precursors would be crucial prior to conducting sensitive surveys with ALMA. Laboratory studies have suggested that CH3NH2 is a possible precursor to glycine. Further theoretical study also suggests that the CH2NH2 radical that can be formed from CH3NH2 through photodissociation can be a good precursor to glycine. Thus, we have looked for CH3NH2 towards several hot core sources using the Nobeyama 45 m radio telescope, and succeeded in finding a new CH3NH2 source, G10.47+0.03, with a fractional abundance of 1.5 ± 1.1 × 10−8; at the time of writing, this source is the most abundant source of CH3NH2 ever known. We found that the observed abundance of CH3NH2 agrees fairly well with the theoretical value predicted by R. T. Garrod (2013, ApJ, 765, 60). The detectability of interstellar glycine is discussed.
Can topic models be used in research evaluations? Reproducibility, validity, and reliability when compared with semantic maps
Authors: Hecking Tobias , Leydesdorff Loet 
Published: June 2019

AbstractWe replicate and analyze the topic model which was commissioned to King’s College and Digital Science for the Research Evaluation Framework (REF 2014) in the United Kingdom: 6,638 case descriptions of societal impact were submitted by 154 higher-education institutes. We compare the Latent Dirichlet Allocation (LDA) model with Principal Component Analysis (PCA) of document-term matrices using the same data. Since topic models are almost by definition applied to text corpora which are too large to read, validation of the results of these models is hardly possible; furthermore the models are irreproducible for a number of reasons. However, removing a small fraction of the documents from the sample—a test for reliability—has on average a larger impact in terms of decay on LDA than on PCA-based models. The semantic coherence of LDA models outperforms PCA-based models. In our opinion, results of the topic models are statistical and should not be used for grant selections and micro decision-making about research without follow-up using domain-specific semantic maps.
Neglected bodily senses in women living with vertebral fracture: a focus group study
Authors: Drew Sarah , Clark Emma , Al-Sari Usama , Moore Andrew , Gooberman-Hill Rachael 
Published: June 2019

Abstract

Objective
Older women are at particular risk of osteoporosis. Among women with osteoporosis, fractures of the vertebra (vertebral fracture) are common, hard to detect and associated with risk of further fracture. Identifying vertebral fracture in a timely manner allows instigation of preventive measures to reduce the risk of further fracture. Although detection of vertebral fracture requires spinal radiograph, many women do not receive referral. To begin development of a screening tool to identify women in need of referral we undertook a qualitative study to characterize women’s experiences of vertebral fracture, using Eccleston’s ‘Ten Neglected Bodily Senses’.

Methods
Four qualitative focus groups were conducted with women who had been diagnosed with vertebral fracture (n = 19, age 60–91 years). Data were audio-recorded, transcribed and analysed thematically using the ‘Ten Neglected Bodily Senses’.

Results
Women’s experiences of vertebral fractures related to seven senses: pain, movement, fatigue, balance, pressure, appetite and breathing. Pain was the dominant sense and all participants explained how pain increased with activity, reaching a crescendo, and described strategies to minimize this disruption. Most participants had become physically shorter, making some feel ‘squashed’, putting pressure on other body parts. Some described appetite loss or a sense of restricted breathing. Participants experienced a sense of being ‘pulled’ forwards, impacting on balance and exacerbating fear of falling.

Conclusion
The study found senses that have not been previously described in the experiences of women with vertebral fracture. These will be used to inform the design of a new screening tool for use in primary care.