bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anogenital distance as a marker of androgen exposure in humans
Authors: Thankamony A. , Pasterski V. , Ong K. K. , Acerini C. L. , Hughes I. A. 
Published: February 2016

SummaryAbnormal foetal testis development has been proposed to underlie common disorders of the male reproductive system such as cryptorchidism, hypospadias, reduced semen quality and testicular germ cell tumour, which are regarded as components of a ‘testicular dysgenesis syndrome’. The increasing trends and geographical variation in their incidence have been suggested to result from in utero exposure to environmental chemicals acting as endocrine disruptors. In rodents, the anogenital distance (AGD), measured from the anus to the base of genital tubercle, is a sensitive biomarker of androgen exposure during a critical embryonic window of testis development. In humans, several epidemiological studies have shown alterations in AGD associated with prenatal exposure to several chemicals with potential endocrine disrupting activity. However, the link between AGD and androgen exposure in humans is not well‐defined. This review focuses on the current evidence for such a relationship. As in rodents, a clear gender difference is detected during foetal development of the AGD in humans which is maintained thereafter. Reduced AGD in association with clinically relevant outcomes of potential environmental exposures, such as cryptorchidism or hypospadias, is in keeping with AGD as a marker of foetal testicular function. Furthermore, AGD may reflect variations in prenatal androgen exposure in healthy children as shorter AGD at birth is associated with reduced masculine play behaviour in preschool boys. Several studies provide evidence linking shorter AGD with lower fertility, semen quality and testosterone levels in selected groups of adults attending andrology clinics. Overall, the observational data in humans are consistent with experimental studies in animals and support the use of AGD as a biomarker of foetal androgen exposure. Future studies evaluating AGD in relation to reproductive hormones in both infants and adults, and to gene polymorphisms, will help to further delineate the effect of prenatal and postnatal androgen exposures on AGD.
Making Space for Energy: Wasteland Development, Enclosures, and Energy Dispossessions
Authors: Baka Jennifer 
Published: February 2016

AbstractThis paper analyzes why and how wasteland development narratives persist through an evaluation of wasteland development policies in India from 1970 to present. Integrating critical scholarship on environmental narratives and enclosures, I find that narratives of wastelands as “empty” spaces available for “improvement” continue because they are metaphors for entrenched struggles between the government's shifting visions of “improvement” and communities whose land use practices contradict these logics. Since the 1970s, “improvement” has meant establishing different types of tree plantations on wastelands to ostensibly provide energy security. These projects have dispossessed land users by enclosing common property lands and by providing forms of energy incommensurate with local needs, a trend I term “energy dispossessions”. Factors enabling energy dispossessions include the government's increased attempts to establish public–private partnerships to carry out “improvement” and a “field of observation” constructed to obscure local livelihoods. Unveiling these logics will help to problematize and contest future iterations of wasteland development.
Problematic Internet use was more common in Turkish adolescents with major depressive disorders than controls
Authors: Alpaslan Ahmet Hamdi , Soylu Nusret , Kocak Ugur , Guzel Halil Ibrahim 
Published: February 2016

AbstractAimThis study compared problematic Internet use (PIU) rates in 12‐ to 18‐year‐olds with major depressive disorder (MDD) and healthy controls and explored potential links between PIU and suicide among patients with MDD.MethodsThe study sample consisted of 120 patients with MDD (62.5% girls) and 100 controls (58% girls) with a mean age of 15. Suicide ideation and suicide attempts were evaluated, and sociodemographic data were collected. In addition, the Children's Depression Inventory, Young Internet Addiction Test and Suicide Probability Scale were applied.ResultsThe results showed that PIU rates were significantly higher in the MDD cases than the controls (p < 0.001). The analysis of covariance results showed that there was no relationship between potential suicide and the Young Internet Addiction Test score in MDD cases. However, the hopelessness subscale scores of the MDD patients with PIU were significantly higher than the scores of those without PIU.ConclusionOur results show that PIU was higher in adolescents with MDD and hopelessness was more prevalent among MDD patients with PIU, but no links with potential suicide were found. As this study was a cross‐sectional one, it did not allow us to infer a causality relationship between PIU and MDD.
Review article: sarcopenia in cirrhosis – aetiology, implications and potential therapeutic interventions
Authors: Sinclair M. , Gow P. J. , Grossmann M. , Angus P. W. 
Published: February 2016

SummaryBackgroundSarcopenia (loss of muscle mass) is common in cirrhosis and is associated with poor outcomes. Current teaching recommends the use of protein supplementation and exercise, however, this fails to address many other factors which contribute to muscle loss in this setting.AimsTo summarise existing knowledge regarding the aetiology of sarcopenia in cirrhosis, diagnostic modalities and the clinical significance of this condition. In addition to discuss recent research findings that may allow the development of more effective treatments.MethodsWe conducted a Medline and PubMed search using the search terms ‘sarcopenia’, ‘muscle’, ‘body composition’, ‘cirrhosis’, ‘liver’ and ‘malnutrition’ from inception to October 2015.ResultsCirrhotic patients with sarcopenia have reduced survival, experience increased rates of infection and have worse outcomes following liver transplantation. The aetiology of this condition is more complex than simple protein and calorie malnutrition. Cirrhosis also results in depleted glycogen stores and metabolic alterations that cause excessive protein catabolism, increased activation of the ubiquitin–proteasome pathway and inappropriate muscle autophagy. Satellite cell differentiation and proliferation is also reduced due to a combination of elevated myostatin levels, reducedIGF‐1 and hypogonadism. Although there is some evidence supporting the use of late evening snacks, branched chain amino acid supplementation and high protein/high calorie diets, well designed clinical trials addressing the effects of treatment on body composition in cirrhosis are lacking.ConclusionSarcopenia in cirrhosis has a complex pathogenesis and simple dietary interventions are insufficient. Improved understanding of the multiple mechanisms involved should allow the development of more effective therapies, which target the specific underlying metabolic derangements.
Estimation of Sparse Directed Acyclic Graphs for Multivariate Counts Data
Authors: Han Sung Won , Zhong Hua 
Published: February 2016

Summary
The next-generation sequencing data, called high-throughput sequencing data, are recorded as count data, which are generally far from normal distribution. Under the assumption that the count data follow the Poisson -normal distribution, this article provides an -penalized likelihood framework and an efficient search algorithm to estimate the structure of sparse directed acyclic graphs (DAGs) for multivariate counts data. In searching for the solution, we use iterative optimization procedures to estimate the adjacency matrix and the variance matrix of the latent variables. The simulation result shows that our proposed method outperforms the approach which assumes multivariate normal distributions, and the -transformation approach. It also shows that the proposed method outperforms the rank-based PC method under sparse network or hub network structures. As a real data example, we demonstrate the efficiency of the proposed method in estimating the gene regulatory networks of the ovarian cancer study.
The outcome of Chronic lymphocytic leukaemia patients with 97% IGHV gene identity to germline is distinct from cases with <97% identity and similar to those with 98% identity
Authors: Davis Zadie , Forconi Francesco , Parker Anton , Gardiner Anne , Thomas Peter , Catovsky Daniel , Rose‐Zerilli Matthew , Strefford Jonathan C , Oscier David 
Published: February 2016

SummaryIGHV gene mutational status has prognostic significance in chronic lymphocytic leukaemia (CLL) but the percentage of mutations that correlates best with clinical outcome remains controversial. We initially studied 558 patients from diagnosis and found significant differences in median time to first treatment (TTFT) among Stage A patients and in overall survival (OS) for the whole cohort, between cases with <97% and 97–98·99% identity and between cases with 97–98·99% and ≥99% identity, when cases from the IGHV3‐21 Stereotype Subset #2 were excluded. A significant difference in progression‐free survival (PFS) and OS between those with <97% and 97–98·99% identity, but not between those with 97–98·99% and ≥99% identity was also observed in a validation cohort comprising 460 patients in the UK CLL4 trial. Cox Regression analyses in the Stage A cohort revealed that a model which incorporated <97%, 97–98·99% and ≥99% identity as subgroups, was a better predictor of TTFT in CLL than using the 98% cut‐off. Multivariate analysis selected the three mutational subgroups as independent predictors of TTFT in Stage A patients, and of OS in the diagnostic cohort. This study highlights that cases with 97% identity should not be considered to have the same prognosis as other cases with mutated IGHV genes defined as <98% identity to germline.
Lenalidomide in combination with R‐ESHAP in patients with relapsed or refractory diffuse large B‐cell lymphoma: a phase 1b study from GELTAMO group
Authors: Martín Alejandro , Redondo Alba M. , Dlouhy Iván , Salar Antonio , González‐Barca Eva , Canales Miguel , Montes‐Moreno Santiago , Ocio Enrique M. , López‐Guillermo Armando , Caballero Dolores ,   the Grupo Español de Linfomas y Trasplante Autólogo de Médula Ósea (GELTAMO)
Published: February 2016

SummaryDiffuse large B‐cell lymphoma (DLBCL) patients failing rituximab‐containing therapy have a poor outcome with the current salvage regimens. We conducted a phase 1b trial to determine the maximum tolerated dose (MTD) of lenalidomide in combination with R‐ESHAP (rituximab, etoposide, cisplatin, cytarabine, methylprednisolone) (LR‐ESHAP) in patients with relapsed or refractory DLBCL. Efficacy data were collected as a secondary objective. Subjects received 3 cycles of lenalidomide at escalating doses (5, 10 or 15 mg) given on days 1–14 of every 21‐day cycle, in combination with R‐ESHAP. Responding patients received BEAM (carmustine, etoposide, cytarabine, melphalan) followed by autologous stem‐cell transplantation. Lenalidomide 10 mg/d was identified as the MTD because, in the 15 mg cohort, one patient experienced dose‐limiting toxicity (grade 3 angioedema) and two patients had mobilization failure. A total of 19 patients (3, 12 and 4 in the 5, 10 and 15 mg cohorts, respectively) were evaluable. All toxicities occurring during LR‐ESHAP cycles resolved appropriately and no grade 4–5 non‐haematological toxicities were observed. The complete remission and overall response rates were 47·4% and 78·9%, respectively. With a median follow‐up of 24·6 (17·4–38·2) months, the 2‐year progression‐free survival and overall survival were 44% and 63%, respectively. In conclusion, the LR‐ESHAP regimen is feasible and yields encouraging outcomes.
Relationships among multiple aspects of agriculture's environmental impact and productivity: a meta‐analysis to guide sustainable agriculture
Authors: German Richard N. , Thompson Catherine E. , Benton Tim G. 
Published: February 2016

ABSTRACTGiven the pressures on land to produce ever more food, doing it ‘sustainably’ is growing in importance. However, ‘sustainable agriculture’ is complex to define, not least because agriculture impacts in many different ways and it is not clear how different aspects of sustainability may be in synergy or trade off against each other. We conducted a meta‐analysis to assess the relationships between multiple measures of sustainability using novel analytical methods, based around defining the efficiency frontier in the relationship between variables, as well as using correlation analysis. We define 20 grouped variables of agriculture's impact (e.g. on soil, greenhouse gas, water, biodiversity) and find evidence of both strong positive and negative correlations between them. Analysis based on the efficiency frontier suggests that trade‐offs can be ‘softened’ by exploiting the natural between‐study variation that arises from a combination of farming best practice and context. Nonetheless, the literature provides strong evidence of the relationship between yields and the negative externalities created by farming across a range of measures.
Functional Connectivity of Vim Nucleus in Tremor‐ and Akinetic‐/Rigid‐Dominant Parkinson's Disease
Authors: Zhang Jia‐Rong , Feng Tao , Hou Ya‐Nan , Chan Piu , Wu Tao 
Published: February 2016

SummaryAimsThe aim of this study was to investigate the involvement of the ventral intermediate nucleus of thalamus (Vim) in the tremor‐ and akinetic‐/rigid‐related networks in Parkinson's disease (PD).MethodsTremor‐dominant (TD) and akinetic‐/rigid‐dominant (ARD) PD patients were recruited and scanned by resting‐state functional MRI. Functional connectivity from the Vim nucleus was analyzed.ResultsIn the TD patients, the Vim nucleus exhibited increased connectivity with the cerebellum/dentate nucleus, primary motor cortex (M1), supplementary motor area (SMA), premotor cortex, thalamus, globus pallidus, putamen, and parietal cortex compared with the controls, while the connections between the Vim nucleus and M1 and cerebellum/dentate nucleus had positive correlations with the tremor scores. In the ARD patients, the Vim nucleus only showed enhanced connectivity with the globus pallidus and limbic lobe compared with the controls, and no connectivity showed correlation against the akinetic–rigidity scores. TD patients had increased connectivity with the Vim nucleus in the cerebellum, M1, SMA, thalamus, globus pallidus, putamen, and parietal cortex compared with ARD patients.ConclusionsThis study demonstrates that the Vim nucleus has an important role in the tremor‐related network, but not in the akinetic‐/rigid‐related network. Our finding is helpful to explain the selective effect of Vim deep brain stimulation in PD.
Metabarcoding reveals strong spatial structure and temporal turnover of zooplankton communities among marine and freshwater ports
Authors: Chain Frédéric J. J. , Brown Emily A. , MacIsaac Hugh J. , Cristescu Melania E. 
Published: February 2016

AbstractAimThe urgent need for large‐scale spatio‐temporal assessments of biodiversity in the face of rapid environmental change prompts technological advancements in species identification and biomonitoring such as metabarcoding. The high‐throughput DNA sequencing of bulk samples offers many advantages over traditional morphological identification for describing community composition. Our objective was to evaluate the applicability of metabarcoding to identify species in taxonomically complex samples, evaluate biodiversity trends across broad geographical and temporal scales and facilitate cross‐study comparisons.LocationMarine and freshwater ports along Canadian coastlines (Pacific, Arctic and Atlantic) and the Great Lakes.MethodsWe used metabarcoding of bulk zooplankton samples to identify species and profile biodiversity across habitats and seasons in busy commercial ports. A taxonomic assignment approach circumventing sequence clustering was implemented to provide increased resolution and accuracy compared to pre‐clustering.ResultsTaxonomic classification of over seven million sequences identified organisms spanning around 400 metazoan families and complements previous surveys based on morphological identification. Metabarcoding revealed over 30 orders that were previously not reported, while certain taxonomic groups were underrepresented because of depauperate reference databases. Despite the limitations of assigning metabarcoding data to the species level, zooplankton communities were distinct among coastlines and significantly divergent among marine, freshwater and estuarine habitats even at the family level. Furthermore, biodiversity varied substantially across two seasons reaching a beta diversity of 0.9 in a sub‐Arctic port exposed to high vessel traffic.Main ConclusionsMetabarcoding offers a powerful and sensitive approach to conduct large‐scale biodiversity surveys and allows comparability across studies when rooted in taxonomy. We highlight ways of overcoming current limitations of metabarcoding for identifying species and assessing biodiversity, which has important implications for detecting organisms at low abundance such as endangered species and early invaders. Our study conveys pertinent and timely considerations for future large‐scale monitoring surveys in relationship to environmental change.
Stress During Adolescence Shapes Performance in Adulthood: Context‐Dependent Effects on Foraging and Vigilance
Authors: Chaby Lauren E. , Sheriff Michael J. , Cavigelli Sonia A. , Hirrlinger Amy M. , Lim James , Braithwaite Victoria A. 
Published: February 2016

AbstractExposure to chronic stress during adolescence can shape behaviour, cognition and physiology in adulthood, but the consequences of these long‐term changes remain unclear. Prior studies reporting altered performance following exposure to stress in adolescence have generally interpreted lasting changes as impairments. However, we have recently shown that exposure to chronic unpredictable stress during adolescence (from post‐natal days 30–70) can enhance performance in a context‐dependent manner during a foraging task. Increases in foraging performance, (previously measured by the number of rewards obtained), are often associated with trade‐offs in other behaviours, such as vigilance. Here, we examined the effect of stress exposure in adolescence on adult foraging in male Sprague Dawley rats to determine (1) whether the increase in foraging performance exhibited by animals exposed to stress in adolescence is balanced by a decrease in vigilance, and (2) whether stress in adolescence alters time allocation between foraging and vigilance behaviours in low‐ and high‐threat conditions. We found no evidence of a trade‐off between foraging and vigilance; under low‐threat conditions, rats exposed to stress in adolescence spent more time being vigilant compared with unstressed rats, suggesting that exposure to stress in adolescence enhances anticipation of threat in adulthood. Under high‐threat conditions, adolescent‐stressed and unstressed rats did not differ in foraging and vigilance behaviours. Given that we have previously found that rats exposed to stress in adolescence nearly double food intake under high‐threat, and we now show that high‐performing rats do not spend more time foraging, it appears that stress exposure in adolescence may enhance foraging efficiency (food consumed/time) under high‐threat conditions rather than time allocation between foraging and competing behaviours. We also examined the relationship, at the level of the individual, between foraging performance and foraging and vigilance behaviours. We found that changes in individual foraging performance between low‐ and high‐threat conditions were independent of behavioural changes (i.e. both highly and poorly performing rats were equally active and contacted a similar number of patches). This suggests that the ability to obtain many rewards under high‐threat conditions may be related to efficiency, rather than the frequency of foraging and effort‐related behaviours.
Learning and Memory in Juvenile Zebrafish: What makes the Difference – Population or Rearing Environment?
Authors: Roy Tamal , Bhat Anuradha 
Published: February 2016

AbstractThe ability to learn and remember about the surrounding environment is crucial for the survival of organisms in their natural habitats. Adults of numerous fish species have been shown to display sophisticated behaviour related to learning and memory. This study deals with testing learning abilities among juveniles (10 wks old) of zebrafish (Danio rerio) through a simple task of finding food. We compared the performance of juveniles from two populations, a wild collected from a natural habitat and an aquarium‐bred purchased from a pet shop, reared in bare environment (lacking visual cues). Additionally, we also tested the effect of early habitat enrichment on the performance among juveniles of the aquarium‐bred population. The experiments involved training fishes to solve a simple maze (with a food reward at the end) and testing their memory. Learning was measured based on the time taken to complete the task (performance time) of finding food in the maze‐arena across repeated trials. Our results showed that juveniles from the two populations possessed significantly different learning abilities. There were population differences in exploratory tendency and time taken to accomplish the task. However, when memory was tested based on performance time between training and test day, individuals (from both populations) were found to be poor at memorizing learnt tasks. On the other hand, juveniles (belonging to aquarium‐bred population) reared in spatially complex environments displayed higher rates of learning and were capable of remembering learnt tasks better than their counterparts from bare environments. This study thus demonstrates the importance of rearing conditions and natural ecology in ontogenetic development of learning and memory functions among zebrafish.
Inside the Great Recession: University Products and Regional Economic Development
Authors: Lendel Iryna , Qian Haifeng 
Published: February 2016

AbstractThis article investigates the role of universities in the economic development of American metropolitan regions during the Great Recession (2007–2009) and the growth period prior to it (2001–2007). It develops a supply‐side conceptual framework on the role of universities in technology‐led regional economic development. Specifically, this framework highlights three “university products” that can be explicitly defined and measured: educational services, business services, and new knowledge or technology. The empirical test of this conceptual framework finds that the presence of universities is positively associated with regional economic performance during the Great Recession, mainly via the educational services product. Findings indicate that regions with a higher level of university science, technology, engineering, and mathematics graduates are more resilient to the economic recession.