bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions
Authors: Hill W. D. , Davies G. , Harris S. E , Hagenaars S. P. ,   The neuroCHARGE Cognitive Working group, Liewald D. C. , Penke L. , Gale C. R. , Deary Ian 
Published: July 2016

AbstractDifferences in general cognitive function have been shown to be partly heritable and to show genetic correlations with a several psychiatric and physical disease states. However, to date few single nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium and UK Biobank, to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~ 40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions.
A correlation between Long noncoding RNA and unpaired DNA silencing in Drosophila
Authors: Pal-Bhadra Manika , Bag Indira , Pushpavalli Sreerangam N.C. L.V , Surolia Avadhesha , Bhadra Utpal 
Published: July 2016

SUMMARYHybrid transgenes are often recognized as foreign genetic material by cell surveillance mechanisms and are repressed in expression inversely to their copy numbers. Here, we compare the expression of multipleAdh-promoter-whitereporter (Adh-w) inserts in paired and unpaired configurations inDrosophilasomatic cells. The unpaired copies exhibit a clear repression at the transcriptional level relative to paired gene dosage effect, which is dependent upon long noncoding RNA,Polycombandpiwi. Deficiency mapping usingAdh-wconstructs showed that a minimal sequence of 532 bp of theAdhpromoter is required for unpaired DNA silencing. Long noncoding RNA detected from this region of theAdhpromoter is abundant in the unpaired condition. It serves as a docking site for at least two proteins POLYCOMB and Piwi that are essential for active transcriptional silencing. The lesser abundance of noncoding RNAs in the paired configuration only allows PC binding. An active RNA-Protein complex binds to unpaired copies. The loss-of-functionpiwimutation relieves transcriptional silencing even in association with POLYCOMB. It suggests that functional RNA-Piwi complex might create a silencing driven chromatin configuration by accumulating histone modifying enzymes at theAdh-wpromoter target. This distinct transcriptional silencing that is stronger for unpaired DNA represents a novel mechanism to repress new transposon and foreign DNA insertions for protection of genome integrity.
A massively parallel strategy for STR marker development, capture, and genotyping
Authors: Kistler Logan , Johnson Stephen M. , Irwin Mitchell T. , Louis Edward E. , Ratan Aakrosh , Perry George H. 
Published: July 2016

AbstractShort tandem repeat (STRs or microsatellites) variants, are highly polymorphic markers that facilitate powerful, high-precision population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic flux. However, STR marker development and analysis by conventional PCR-based methods imposes a workflow bottleneck and is suboptimal for noninvasive sampling strategies such as fecal DNA recovery. While massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery, here we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without requiring a reference genome assembly, and a methodological approach for highly parallel recovery of enriched STR loci. We first employed our approach to design and capture a panel of 5,000 STR loci from a test group of diademed sifakas (Propithecus diadema, n=3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3-99.6% of STRs characterized with ≥10x non-redundant coverage. Second, we tested our STR capture strategy on aP. diademafecal DNA preparation, and report robust initial results and methodological suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from regions flanking the STR loci. Our method provides a cost-effective and highly scalable solution for rapid recovery of large STR and SNP datasets in any species without need for a reference genome, and can be used even with suboptimal DNA, which is more easily acquired in conservation and ecological genetic studies.Data DepositionRaw sequencing data are available under Study Accession numbers SRP073167 (genomic shotgun data for Oberon and Tatiana) and SRP076225 (targeted re-sequencing data) from the NCBI Sequence Read Archive. BaitSTR software is available at Github (core BaitSTR programs:https://github.com/aakrosh/BaitSTR; BaitSTR_type.pl companion script for genotyping and block manipulation:https://github.com/lkistler/BaitSTR_type).
Pre‐discharge home visits by occupational therapists completed for patients following hip fracture
Authors: Lockwood Kylee J. , Taylor Nicholas F. , Boyd Jude N. , Harding Katherine E. 
Published: July 2016

Background/aimHome visits by occupational therapists are a routine part of practice, but there remains little understanding about factors that are associated with the decision to complete a home visit. The aim of this study was to investigate the rate of pre‐discharge home visits by occupational therapists for patients following hip fracture and explore factors associated with their occurrence.MethodsA retrospective cohort study including 293 patients admitted to a metropolitan health service following hip fracture. Multi‐variate logistic regression was used to identify significant variables associated with receiving a home visit.ResultsHome visits were conducted by occupational therapists for 28% of patients admitted from a private residence, and for less than 5% of patients admitted from low‐level residential care facilities. The variables significantly associated with receiving a home visit at a private residence were older age and being admitted to a rehabilitation ward, but the model only explained between 9% and 13% of the variance. Other clinical and socio‐demographic variables evaluated were not associated with the provision of a home visit.ConclusionsAbout one in four people admitted to hospital from a private residence following hip fracture receive a home visit. The results suggest that whether or not a patient receives a home visit has little to do with socio‐demographic or clinical factors at the time of admission to hospital. There remains much unexplained variation in whether or not a patient receives a home visit and this study highlights the diversity that exists in clinical practice.
School‐age children enjoyed good respiratory health and fewer allergies despite having lung disease after preterm birth
Authors: Ronkainen Eveliina , Kaukola Tuula , Marttila Riitta , Hallman Mikko , Dunder Teija 
Published: July 2016

AbstractAimThis study explored the under‐researched area of whether preterm birth or bronchopulmonary dysplasia (BPD) affected hospitalisation rates, allergies or health‐related quality of life (HRQoL).MethodsWe studied 88 schoolchildren born preterm at a mean gestational age of 28.8 weeks (range 24.1–31.9) and matched term‐born controls at the mean age of 11 years (range 8–14). Hospitalisations after the first discharge were recorded, skin prick allergy tests were performed and HRQoL was assessed with a parental questionnaire.ResultsPreterm children were hospitalised more than controls (64% versus 39%, p = 0.001), mostly before two years of age. The adjusted odds ratios (OR) for two‐year‐old preterm‐born children being hospitalised for wheezing was 8.2 (95% CI 2.0–34.1). BPD affected 56% of the preterm children, but did not influence hospitalisations, and the positive skin prick rate was similar between the preterm and term‐born children (35% versus 48%, p = 0.126). Preterm BPD children had fewer positive skin prick tests than those without BPD. HRQoL was lower in preterm than term children (81.25 ± 10.84 versus 86.80 ± 9.60, p = 0.001).ConclusionMost health problems experienced by preterm‐born schoolchildren occurred before two years of age and were mainly wheezing disorders. BPD decreased atopy but had no influence on hospitalisation rates.
4D in vivo imaging of glomerular barrier function in a zebrafish podocyte injury model
Authors: Siegerist F. , Zhou W. , Endlich K. , Endlich N. 
Published: July 2016

AbstractAimZebrafish larvae with their simplified pronephros are an ideal model to study glomerular physiology. Although several groups use zebrafish larvae to assess glomerular barrier function, temporary or slight changes are still difficult to measure. The aim of this study was to investigate the potential of in vivo two‐photon microscopy (2‐PM) for long‐term imaging of glomerular barrier function in zebrafish larvae.MethodsAs a proof of principle, we adapted the nitroreductase/metronidazole model of targeted podocyte ablation for 2‐PM. Combination with a strain, which expresses eGFP‐vitamin D‐binding protein in the blood plasma, led to a strain that allowed induction of podocyte injury with parallel assessment of glomerular barrier function. We used four‐dimensional (4D) 2‐PM to assess eGFP fluorescence over 26 h in the vasculature and in tubules of multiple zebrafish larvae (5 days post‐fertilization) simultaneously.ResultsBy 4D 2‐PM, we observed that, under physiological conditions, eGFP fluorescence was retained in the vasculature and rarely detected in proximal tubule cells. Application of metronidazole induced podocyte injury and cell death as shown by TUNEL staining. Induction of podocyte injury resulted in a dramatic decrease of eGFP fluorescence in the vasculature over time (about 50% and 90% after 2 and 12 h respectively). Loss of vascular eGFP fluorescence was paralleled by an endocytosis‐mediated accumulation of eGFP fluorescence in proximal tubule cells, indicating proteinuria.ConclusionWe established a microscopy‐based method to monitor the dynamics of glomerular barrier function during induction of podocyte injury in multiple zebrafish larvae simultaneously over 26 h.
‘She was like a mother and a father to me’: searching for the ideal mentor for youth in care
Authors: Sulimani‐Aidan Yafit 
Published: July 2016

AbstractRecent studies of youth in out‐of‐home placements have indicated that a successful mentoring relationship in care is associated with better emotional, educational and behavioural outcomes in adulthood. The goal of this exploratory qualitative study is to describe the profile of a staff member who is able to establish a meaningful relationship with youth in care through the perspectives of 20 young adults aged 21–26 who left care in Israel. Findings revealed that the staff member who formed meaningful relationships with youth was the staff member who was available to the youth and familiar with their personal backgrounds, who was able to see them as positive and trustworthy and to provide guidance and support from a non‐judgmental approach. One of the study's conclusions is that staff members who were able to transform their connection with the youth into mentoring relationships were those who were able to make the youth feel as if they were the staff member's own children, and as a result feel cared for deeply and loved. The discussion addresses the barriers in forming a mentoring relationship with a formal professional and the ways to utilize these mentoring relationship components more effectively within the care system.
Fracture resistance of implant‐supported screw‐retained zirconia‐based molar restorations
Authors: Honda Junichi , Komine Futoshi , Kamio Shingo , Taguchi Kohei , Blatz Markus B. , Matsumura Hideo 
Published: July 2016

AbstractObjectivesThe objective of this in vitro study was to investigate fracture loads of screw‐retained zirconia‐based molar restorations (hybrid abutment crown) fabricated with different restorative materials and designs.Material and methodsForty‐four screw‐retained zirconia‐based molar restorations were fabricated on dental implants and divided into four groups (n = 11): porcelain‐layered zirconia‐based restorations (PLZ), indirect composite‐layered zirconia‐based restorations (ILZ), metal–ceramic restorations (MC), and monolithic zirconia restorations (MONO). The zirconia‐based restorations in the PLZ, ILZ, and MONO groups were adhesively bonded on implant abutments with a dual‐polymerized resin material. All restorations were tightened on implant bodies with titanium screws and were tested for fracture resistance. The Kruskal–Wallis test and Steel–Dwass test were used to evaluate differences in fracture loads (α = 0.05).ResultsAs compared with the other groups, the MONO specimens had a significantly higher mean fracture resistance (7.54 kN); no significant differences were found among the PLZ (1.96 kN), ILZ (1.80 kN), and MC (1.45 kN) groups (P > 0.05). For the PLZ, ILZ, and MC groups, all specimens fractured within the layering materials. In contrast, the fracture mode for the MONO group was complete fracture of the restorations.ConclusionsAll restorations withstood the masticatory forces. Fracture loads were significantly higher for screw‐retained implant‐supported monolithic zirconia restorations than for screw‐retained bilayered restorations. For the screw‐retained bilayered zirconia‐based restorations, the fracture resistance of ILZ restorations was comparable to that of PLZ restorations and MC restorations.
Single‐center experience of living donor liver transplantation in patients with portal vein thrombosis
Authors: Song Sanghyun , Kwon Choon Hyuck David , Kim Jong Man , Joh Jae‐Won , Lee Suk‐Koo 
Published: July 2016

AbstractBackgroundPortal vein thrombosis (PVT) is a relative contraindication in living donor liver transplantation (LDLT). We investigated the long‐term outcome of adult patients with PVT in LDLT.MethodsBetween 2004 and 2009, 471 cases of adult LDLT were performed and 56 patients had PVT (11.8%). Thrombectomy was attempted using a modified eversion technique. We evaluated the outcome of patients with PVT according to grade and compared with no‐PVT patients.ResultsThere was no difference in terms of age, gender, Child‐Pugh score, MELD score, proportion of malignance, operation time, and total amount of transfused blood. Complete thrombectomy was successful in 73.2% (41/56), partial thrombectomy in 26.8% (15/56), and one case needed jump graft for portal vein reconstruction. Among patients with partial thrombectomy, when the PV velocity was above 20 cm/s, the remnant thrombus disappeared in 46%. The rate of PV complication was statistically not different (8.9% vs 3.4%, P=.062). Five‐year survival of mild PVT was 69.3%, 60.6% for severe PVT, and 80.4% for no‐PVT (P=.059).ConclusionsEversion thrombectomy by modified technique is feasible in most cases of PVT. Good long‐term outcome may be expected in LDLT with PVT.
Reconstruction of the historical distribution of sturgeons (Acipenseridae) in the eastern North Atlantic based on ancientDNAand bone morphology of archaeological remains: implications for conservation and restoration programmes
Authors: Nikulina Elena A. , Schmölcke Ulrich 
Published: July 2016

AbstractAimIn the 19th/early 20th century, overfishing caused a drastic decline and finally extinction of the local sturgeon populations in the eastern Atlantic. To date, it is not known whether it wasAcipenser sturioor the primarily North AmericanAcipenser oxyrinchusthat occurred here. The aim of the study was to show the historical pattern of sturgeon distribution and their diversity in this area over the last 2500 years. This question is essential for international restoration programmes.LocationNorth‐east Atlantic.MethodsThe study is based on 438 archaeological sturgeon remains from the estuaries of the rivers Rhine, Ems, Weser, Elbe and Eider. All bones were analysed morphologically and in 38 cases genetically by the amplification of two mitochondrialDNAfragments.ResultsThe data from the bones older than 1000 years show that only 1.4% derive fromA. sturio. In the south, this species was slightly more frequent. From the Elbe northwards,A. oxyrinchuswas for a long time by far the dominant sturgeon species.Main conclusionsThe genetic identification of the oldest sturgeon bone showsA. oxyrinchusoccurred in the north‐eastern Atlantic already 6000 years ago. Consequently, the immigration of this species from North America to Europe occurred even earlier, potentially during the last glacial. The north–south occurrence of the two sturgeon species suggests that the distribution was the result of interspecific competition under different and changing environmental conditions. As previously published, genetic data from about 100‐ to 200‐year‐old museum specimens show strong dominance ofA. sturioin the North Sea area, obviouslyA. oxyrinchushas been replaced in the time between 1000 and 200 years ago. Therefore, the Holocene distribution of sturgeons in the north‐east Atlantic had a complex pattern. Determining the ecological bases of this distribution is important for the justification and success of restoration programmes.
Fatigue and depression predict quality of life in patients with early multiple sclerosis: a longitudinal study
Authors: Nourbakhsh B. , Julian L. , Waubant E. 
Published: July 2016

Background and purpose
The clinical predictors of health‐related quality of life (HRQoL) in multiple sclerosis (MS) have mainly been studied in patients with long‐standing disease. The objective of this study was to investigate the longitudinal association among HRQoL and clinical characteristics in early MS.
Methods
Relapsing MS patients within 12 months of clinical onset were enrolled in a neuroprotection trial of riluzole versus placebo as an add‐on to weekly interferon with up to 36 months of follow‐up. Serial clinical measures included Short Form‐36 (SF‐36) as the measure of HRQoL, MS Functional Composite (as a measure of disability), Modified Fatigue Impact Scale, Patient Health Questionnaire‐9 (as a measure of depression) and a cognitive battery. Multivariable linear regression analyses assessed cross‐sectional associations. Mixed model regressions with mutual adjustments were used to assess the longitudinal association of HRQoL components and clinical, cognitive and demographic variables.
Results
Forty‐three patients were enrolled within 7.5 ± 4.9 months of clinical onset (72% female, mean age 36 years). The baseline severity of fatigue and depression predicted subsequent changes in SF‐36 Physical Component Summary (PCS) (P values of 0.001 and 0.021, respectively). In longitudinal analyses, changes in disability and depression were associated with changes in SF‐36 PCS (P values of 0.002 and 0.009, respectively), whereas changes in cognitive function and fatigue were associated with changes in SF‐36 Mental Component Summary (P values of 0.037 and 0.001, respectively). A 1‐unit increase in MS Functional Composite was associated with a 7.1‐point increase in SF‐36 PCS (95% CI, 2.6–11.6).
Conclusions
Fatigue, depression, cognition and disability are independently associated with HRQoL in early MS.
Reefs of tomorrow: eutrophication reduces coral biodiversity in an urbanized seascape
Authors: Duprey Nicolas N. , Yasuhara Moriaki , Baker David M. 
Published: July 2016

AbstractAlthough the impacts of nutrient pollution on coral reefs are well known, surprisingly, no statistical relationships have ever been established between water quality parameters, coral biodiversity and coral cover. Hong Kong provides a unique opportunity to assess this relationship. Here, coastal waters have been monitored monthly since 1986, at 76 stations, providing a highly spatially resolved water quality dataset including 68 903 data points. Moreover, a robust coral species richness (S) dataset is available from more than 100 surveyed locations, composed of 3453 individual colonies' observations, as well as a coral cover (CC) dataset including 85 sites. This wealth of data provides a unique opportunity to test the hypothesis that water quality, and in particular nutrients, drives coral biodiversity. The influence of water quality on S and CC was analyzed using GIS and multiple regression modeling. Eutrophication (as chlorophyll‐a concentration; CHLA) was negatively correlated with S and CC, whereas physicochemical parameters (DO and salinity) had no significant effect. The modeling further illustrated that particulate suspended matter, dissolved inorganic nitrogen (DIN) and dissolved inorganic phosphorus (DIP) had a negative effect on S and on CC; however, the effect of nutrients was 1.5‐fold to twofold greater. The highest S and CC occurred where CHLA <2 μg L−1, DIN < 2 μm and DIP < 0.1 μm. Where these values were exceeded, S and CC were significantly lower and no live corals were observed where CHLA > 15 μg L−1, DIN > 9 μm and DIP > 0.33 μm. This study demonstrates the importance of nutrients over other water quality parameters in coral biodiversity loss and highlights the key role of eutrophication in shaping coastal coral reef ecosystems. This work also provides ecological thresholds that may be useful for water quality guidelines and nutrient mitigation policies.
Comparative clinicopathological study of biliary intraductal papillary neoplasms and papillary cholangiocarcinomas
Authors: Fujikura Kohei , Fukumoto Takumi , Ajiki Tetsuo , Otani Kyoko , Kanzawa Maki , Akita Masayuki , Kido Masahiro , Ku Yonson , Itoh Tomoo , Zen Yoh 
Published: July 2016

AimsThe aim of this study was to achieve a better definition of intraductal papillary neoplasms of the bile duct (IPNBs).Methods and resultsBiliary tumours that showed predominantly intraductal papillary growth were provisionally classified as IPNBs (n = 25) and papillary cholangiocarcinomas (n = 27). IPNB was defined as a neoplasm that is confined to the epithelium or is regularly arranged in a high‐papillary architecture along thin fibrovascular stalks, whereas the term ‘papillary cholangiocarcinoma’ was used for tumours with more complex papillary structures (e.g. irregular papillary branching or mixed with solid–tubular growth). In our consecutive cohort of biliary neoplasms, 5% were classified as IPNBs, and 10% as papillary cholangiocarcinomas. IPNBs differed from papillary cholangiocarcinomas by less advanced invasion, gross mucin overproduction (72% versus 7%), and their prevalent location (84% of IPNBs in intrahepatic/hilar ducts; 70% of papillary cholangiocarcinomas in extrahepatic ducts). Gastric‐type and oncocytic‐type tumours were only detected in IPNBs. Expression of mucin core proteins and cytokeratin 20 significantly differed between the two groups. KRAS and GNAS were wild‐type genotypes in all but one case of KRAS‐mutated IPNB. Patients with IPNB had better recurrence‐free survival than those with papillary cholangiocarcinoma (P = 0.007). In multivariate analysis, in which several other prognostic factors (e.g. stromal invasion and lymph node metastasis) were applied, the classification of the two papillary tumours was an independent prognostic factor (P = 0.040).ConclusionsGiven the significant contrast in clinicopathological features between IPNBs and papillary cholangiocarcinomas, it may be more appropriate to use the diagnostic term ‘IPNB’ for selected tumours that show regular papillary growth, separately from papillary cholangiocarcinomas.