bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ecological drivers of variation in global language diversity
Authors: Hua Xia , Greenhill Simon J. , Cardillo Marcel , Schneemann Hilde , Bromham Lindell 
Published: September 2018

AbstractLanguage diversity is distributed unevenly over the globe. Why do some areas have so many different languages and other areas so few? Intriguingly, patterns of language diversity resemble biodiversity patterns, leading to suggestions that similar mechanisms may underlie both linguistic and biological diversification. Here we present the first global analysis of language diversity that identifies the relative importance of two key ecological mechanisms suggested to promote language diversification - isolation and ecological risk - after correcting for spatial autocorrelation and phylogenetic non-independence. We find significant effects of climate on language diversity consistent with the ecological risk hypothesis that areas of high year-round productivity lead to more languages by supporting human cultural groups with smaller distributions. Climate has a much stronger effect on language diversity than landscape features that might contribute to isolation of cultural groups, such as altitudinal variation, river density, or landscape roughness. The association between biodiversity and language diversity appears to be an incidental effect of their covariation with climate, rather than a causal link between the two. While climate and landscape provide strong explanatory signal for variation in language diversity, we identify a number of areas of high unexplained language diversity, with more languages than would be predicted from environmental features alone; notably New Guinea, the Himalayan foothills, West Africa, and Mesoamerica. Additional processes may be at play in generating higher than expected language diversity in these regions.
Mapping DNA replication with nanopore sequencing
Authors: Hennion Magali , Arbona Jean-Michel , Cruaud Corinne , Proux Florence , Tallec Benoît Le , Novikova Elizaveta , Engelen Stefan , Lemainque Arnaud , Audit Benjamin , Hyrien Olivier 
Published: September 2018

ABSTRACTWe have harnessed nanopore sequencing to study DNA replication genome-wide at the single-molecule level. Using in vitro prepared DNA substrates, we characterized the effect of bromodeoxyuridine (BrdU) substitution for thymidine on the MinION nanopore electrical signal. Using a neural-network basecaller trained on yeast DNA containing either BrdU or thymidine, we identified BrdU-labelled tracts in yeast cells synchronously entering S phase in the presence of hydroxyurea and BrdU. As expected, the BrdU-labelled tracts coincided with previously identified early-firing, but not late-firing, replication origins. These results open the way to high-throughput, high-resolution, single-molecule analysis of DNA replication in many experimental systems.
The Structure of Oxalate Decarboxylase at its Active pH
Authors: Burg M. J. , Goodsell J. L. , Twahir U. T. , Bruner S. D. , Angerhofer A. 
Published: September 2018

AbstractOxalate decarboxylase catalyzes the redox-neutral unimolecular disproportionation reaction of oxalic acid. The pH maximum for catalysis is ~4.0 and activity is negligible above pH7. Here we report on the first crystal structure of the enzyme in its active pH range at pH4.6, and at a resolution of 1.45 Å, the highest to date. The fundamental tertiary and quaternary structure of the enzyme does not change with pH. However, the low pH crystals are heterogeneous containing both a closed and open conformation of a flexible loop region which gates access to the N-terminal active site cavity. Residue E162 in the closed conformation points away from the active-site Mn ion owing to the coordination of a buffer molecule, acetate. Since the quaternary structure of the enzyme appears unaffected by pH many conclusions drawn from the structures taken at high pH remain valid. Density functional theory calculations of the possible binding modes of oxalate to the N-terminal Mn ion demonstrate that both mono- and bi-dentate coordination modes are possible in the closed conformation with an energetic preference for the bidentate binding mode. The simulations suggest that R92 plays an important role as a guide for positioning the substrate in its catalytically competent orientation. A strong hydrogen bond is seen between the bi-dentate bound substrate and E101, one of the coordinating ligands for the N-terminal Mn ion. This suggests a more direct role of E101 as a transient base during the first step of catalysis.
Sequence effects on size, shape, and structural heterogeneity in Intrinsically Disordered Proteins
Authors: Baul Upayan , Chakraborty Debayan , Mugnai Mauro L. , Straub John E. , Thirumalai D. 
Published: September 2018

AbstractIntrinsically disordered proteins (IDPs) lack well-defined three-dimensional structures, thus challenging the archetypal notion of structure-function relationships. Determining the ensemble of conformations that IDPs explore under physiological conditions is the first step towards understanding their diverse cellular functions. Here, we quantitatively characterize the structural features of IDPs as a function of sequence and length using coarse-grained simulations. For diverse IDP sequences, with the number of residues (NT) ranging from 24 to 441, our simulations not only reproduce the radii of gyration (Rg) obtained from experiments, but also predict the full scattering intensity profiles in very good agreement with Small Angle X-ray Scattering experiments. TheRgvalues are well-described by the standard Flory scaling law,, withv≈ 0.588, making it tempting to assert that IDPs behave as polymers in a good solvent. However, clustering analysis reveals that the menagerie of structures explored by IDPs is diverse, with the extent of heterogeneity being highly sequence-dependent, even though ensemble-averaged properties, such as the dependence ofRgon chain length, may suggest synthetic polymer-like behavior in a good solvent. For example, we show that for the highly charged Prothymosin-α, a substantial fraction of conformations is highly compact. Even if the sequence compositions are similar, as is the case forα-Synuclein and a truncated construct from the Tau protein, there are substantial differences in the conformational heterogeneity. Taken together, these observations imply that metrics based on net charge or related quantities alone, cannot be used to anticipate the phases of IDPs, either in isolation or in complex with partner IDPs or RNA. Our work sets the stage for probing the interactions of IDPs with each other, with folded protein domains, or with partner RNAs, which are critical for describing the structures of stress granules and biomolecular condensates with important cellular functions.Graphical TOC Entry
Structural brain alterations in youth with psychosis and bipolar spectrum symptoms
Authors: Jalbrzikowski Maria , Freedman David , Hegarty Catherine E. , Mennigen Eva , Karlsgodt Katherine H. , Loohuis Loes M. Olde , Ophoff Roel A. , Gur Raquel E. , Bearden Carrie E. 
Published: September 2018

AbstractObjectiveAdults with established diagnoses of serious mental illness (bipolar disorder and schizophrenia) exhibit structural brain abnormalities, yet less is known about how such abnormalities manifest earlier in development.MethodsWe analyzed the data publicly available from the Philadelphia Neurodevelopmental Cohort (PNC). Structural magnetic resonance neuroimaging data (sMRI) were collected on a subset of the PNC (N=989, ages 9-22 years old). We calculated measures of cortical thickness (CT) and surface area (SA), along with subcortical volumes. Study participants were assessed for psychiatric symptomatology via structured interview and the following groups were created: typically developing (TD, N=376), psychosis spectrum (PS, N=113), bipolar spectrum (BP, N=117), and BP + PS (N=109). We examined group and developmental differences in sMRI measures. We also examined to what extent any structural aberration was related to neurocognition, global functioning, and clinical symptomatology.ResultsIn comparison to all other groups, PS youth exhibited significantly reduced SA in orbitofrontal, cingulate, precentral, and postcentral regions. PS youth also exhibited reduced thalamic volume in comparison to all other groups. Strongest effects for precentral and posterior cingulate SA reductions were seen during early adolescence (ages 13-15) in PS youth. Strongest effects for reductions in thalamic volume and orbitofrontal and postcentral SA were observed in mid-adolescence (16-18 years) in PS youth. Across groups, better overall functioning was associated with increased lateral orbitofrontal SA. Increased postcentral SA was associated with better executive cognition and less severe negative symptoms in the entire sample.ConclusionIn a community-based sample, we found that reduced cortical SA and thalamic volume are present early in adolescent development in youth with psychosis spectrum symptoms, but not in youth with bipolar spectrum symptoms, or with both bipolar and psychosis spectrum symptoms. These findings point to potential biological distinctions between psychosis and bipolar spectrum conditions, which may suggest additional biomarkers relevant to early identification.
The augmentation of retinogeniculate communication during thalamic burst mode
Authors: Alitto Henry , Rathbun Daniel L. , Vandeleest Jessica J. , Alexander Prescott C. , Usrey W. Martin 
Published: September 2018

AbstractRetinal signals are transmitted to cortex via neurons in the lateral geniculate nucleus (LGN), where they are processed in burst or tonic response mode. Burst mode occurs when LGN neurons are sufficiently hyperpolarized for T-Type Ca2+ channels to de-inactivate, allowing them to open in response to a depolarization which can trigger a high-frequency sequence of Na+-based spikes (i.e. burst). In contrast, T-type channels are inactivated during tonic mode and do not contribute to spiking. Although burst mode is commonly associated with sleep and the disruption of retinogeniculate communication, bursts can also be triggered by visual stimulation, thereby transforming the retinal signals relayed to the cortex.To determine how burst mode affects retinogeniculate communication, we made recordings from monosynaptically connected retinal ganglion cells and LGN neurons in the cat during visual stimulation. Our results reveal a robust augmentation of retinal signals within the LGN during burst mode. Specifically, retinal spikes were more effective and often triggered multiple LGN spikes during periods likely to have increased T-Type Ca2+ activity. Consistent with the biophysical properties of T-Type Ca2+ channels, analysis revealed that effect magnitude was correlated with the duration of the preceding thalamic interspike interval and occurred even in the absence of classically defined bursts. Importantly, the augmentation of geniculate responses to retinal input was not associated with a degradation of visual signals. Together, these results indicate a graded nature of response mode and suggest that, under certain conditions, bursts facilitate the transmission of visual information to the cortex by amplifying retinal signals.SignificanceThe thalamus is the gateway for retinal information traveling to the cortex. The lateral geniculate nucleus (LGN), like all thalamic nuclei, has two classically defined categories of spikes—tonic and burst—that differ in their underlying cellular mechanisms. Here we compare retinogeniculate communication during burst and tonic response modes. Our results show that retinogeniculate communication is enhanced during burst mode and visually evoked thalamic bursts, thereby augmenting retinal signals transmitted to cortex. Further, our results demonstrate that the influence of burst mode on retinogeniculate communication is graded and can be measured even in the absence of classically defined thalamic bursts.
Microbial communities of the Mediterranean rocky coast: ecology and biotechnological potential
Authors: Tanner Kristie , Molina-Menor Esther , Vidal-Verdú Àngela , Peretó Juli , Porcar Manuel 
Published: September 2018

AbstractMicrobial communities from harsh environments hold great promise as sources of biotechnologically-relevant strains. In the present work, we have deeply characterized the microorganisms from three different rocky locations of the Mediterranean coast, an environment characterised by being subjected to harsh conditions such as high levels of irradiation and large temperature and salinity fluctuations. Through culture-dependent and culture-independent techniques, we have retrieved a complete view of the ecology and functional aspects of these communities and assessed the biotechnological potential of the cultivable microorganisms. A culture-independent approach through high-throughput 16S rRNA amplicon sequencing revealed that all three locations display very similar microbial communities, suggesting that there is a stable community associated to the sampled region, withStanieria cyanosphaera, Rubrobactersp. and the families Flammeovirgaceae, Phyllobacteriaceae, Rhodobacteraceae and Trueperaceae being the most abundant taxa. Furthermore, shotgun metagenomic sequencing results were in concordance with the high-thoughput 16S rRNA, and allowed a description of the eukaryotic and archaeal members of the community, which were abundant in Ascomycota and halotolerant archaea, respectively. The culture-dependent approach yielded a collection of 100 isolates (mainly pigmented), out of which 12 displayed high antioxidant activities, as proved with twoin vitro(hydrogen peroxide and DPPH) and anin vivo(model organismC. elegans) assays.
The Swiss mental healthcare system for people with intellectual disabilities
Authors: Georgescu Dan , Styp von Rekowski Anne 
Published: September 2018

Purpose
The purpose of this paper is to describe the mental healthcare system for people with intellectual disabilities (ID) in Switzerland. It covers the current provision of mental healthcare services as well as educational and research aspects, and summarises both the historical development and the current data on demography, health economics, legislation and national policy.

Design/methodology/approach
The authors performed an extensive literature research and evaluated the (very sparse) literature, conducted some interviews with recognised experts and carried out extensive internet-based research on the topic.

Findings
There are numerous, well-funded, well-staffed and well-equipped facilities for people with ID. These facilities have highly trained special education teachers and social education workers. Legislation, the insurance system as well as the policies and strategies on a national level are basically in line with people’s with ID needs. On the other hand, there are too few specialist physicians and psychologists, not enough training centres and too few specialist psychiatric services, both inpatient and outpatient. Medical and psychological research in this field is also insufficient.

Practical implications
In Switzerland, the development of treatment facilities typically does not start with a decision by a central authority to implement a policy in a top-down process. Usually, these organisations develop on the basis of some local initiatives and spread throughout the country. The process is likely to be similar in the case of services for people with mental health and intellectual disabilities (MHID), and the situation can be expected to be much better throughout the country within a few years. Furthermore, specific training programmes are expected to be created for physicians and psychologists of various disciplines, to promote an interdisciplinary approach.

Originality/value
This review fills a gap in that there are very few published reviews on the provision of MHID services in Switzerland.
Permanent magnet shaping for cogging torque and torque ripple reduction of PMSM
Authors: Ladghem Chikouche Brahim , Boughrara Kamel , Ibtiouen Rachid 
Published: September 2018

Purpose
This paper aims to the improvement of permanent magnet shape in the popular permanent magnet synchronous machine (PMSM) is proposed in this paper in view to mitigate cogging torque magnitude and torque ripple.

Design/methodology/approach
A two-dimensional exact analytical approach of magnetic field distribution is established for the PMSM considering magnet shape and slot opening. The optimal magnet shape is constituted of small number of layers stacked radially. The thickness of each magnet layer is considered equal to about one mm or more; however, a parametric study was performed to determine pole pitch ratio value. The finite element method is used to validate the analytical results.

Findings
Cogging torque peaks and torque ripples can be mitigated significantly more than 90 per cent compared to results issued from machine having classical magnet shape. Raising the number of magnet layers can give better results. The results of this paper are compared also with those issued from the machine having sinusoidal magnet shape and give a good solution.

Originality/value
A new technique for cogging torque and torque ripple mitigation is proposed in this paper by changing permanent magnet shape. The proposed final magnet shape is constituted of a set of stacked and well-dimensioned layers relative to the opening angle.
Social eating patterns, identity and the subjective well-being of Chinese teenagers
Authors: Veeck Ann , Yu Hongyan , Zhang Hongli , Zhu Hong , Yu Fang (Grace) 
Published: September 2018

PurposeThe purpose of this study is to explore the association between eating patterns, social identity and the well-being of adolescents via a mixed methods study of Chinese teenagers. The specific research questions presented in this study are as follows: What is the relationship between social eating and well-being? How is the relationship between social eating and well-being mediated by social identity?Design/methodology/approachThis study is based on a sequential mixed methods study, including interviews with 16 teenage–parent dyads, and a large-scale survey of over 1,000 teenagers on their eating patterns, conducted with the support of public schools. A model that tests relationships among social eating, social identity and subjective well-being is developed and tested.FindingsThe results show that dining with family members leads to improved subjective well-being for teenagers, through a partial mediator of stronger family identity. However, dining with peers is not found to influence subjective well-being.Research limitations/implicationsThe privileged position of family meals demonstrated through this study may be an artifact of the location of this study in one Chinese city. Further research is needed related to the connections among social identity, objective well-being and the social patterns of teenagers’ food consumption behavior.Practical implicationsTo improve the subjective well-being of teenagers, families, public policy-makers and food marketers should support food consumption patterns that promote family meals.Originality/valueWhile many food-related consumer studies focus on the individual, social and environmental influences of food choices of adolescents, few studies address how eating patterns affect overall well-being. These results reinforce the importance of understanding the effect of the social context of teenagers’ eating patterns on health and well-being.
The electric energy stored in PEDOT:PSS capacitors integrated on textile substrate
Authors: Odhiambo Sheilla Atieno , Fiszer Piotr , De Mey Gilbert , Hertleer Carla , Nuramdhani Ida , Van Langenhove Lieva , Napieralski Andrzej 
Published: September 2018

Purpose
The purpose of this paper is to develop a capacitor fully integrated into a wearable textile fabric for the application on smart clothing.

Design/methodology/approach
A small capacitor with stainless steel yarns as the electrodes and poly-(3,4–ethylenedioxythiophene): polystryrene sulphonate (PEDOT:PSS) as the dielectric material has been made, integrated into a textile fabric. The electric performance of the capacitor was analyzed and compared with other kinds of electric capacitors.

Findings
The fabricated small, PEDOT:PSS capacitor could finally power a calculator for 37 s with the energy stored in it.

Originality/value
This finding is of an important significance for a further development on the capacitor with a better performance.
Learners’ perceptions on online library resources at Namibian College of Open Learning
Authors: Matheus Elizabeth , Abankwah Ruth 
Published: September 2018

PurposeThe purpose of this paper is to determine the learners’ perceptions on the use of online resources at the Namibian College of Open Learning (NAMCOL) Yetu Yama Resource Center.Design/methodology/approachThis study used a mixed methods research approach which was also used by other researchers such as Hamutumwa (2014). It enabled the researchers to delve into the topic under study by conducting a survey using self-administered questionnaires to collect data from learners, and a semi-structured interview guide, to collect data from the Librarian, the Director and tutors. The target population for the study was Grade 12 distance learners registered with NAMCOL for the academic year 2016, librarians and tutors. Convenient sampling was used to select 200 Grade 12 distance NAMCOL learners: one Director, one Librarian and five tutors were purposeful selected as they manage the Yetu Yama Resource Centre. The Statistical Package for the Social Sciences (SPSS) was used to generate descriptive data, while qualitative data were manually analysed using content analysis. This approach enabled the researcher to identify key themes which emerged from the interviews.FindingsAlmost all the learners (159) opted for printed materials. The challenges experienced by learners included slow internet, as indicated by 78 (39 per cent); limited facilities, 60 (30 per cent); and inability to find relevant information, 46 (23 per cent), coupled with lack of proper guidance on the use of e-resources as indicated by 16 (8 per cent) learners.Research limitations/implicationsThis study was limited to Yetu Yama Resource Center. The results cannot be generalised to all distance learners in Namibia.Practical implicationsThe results of this study could guide librarians in Namibia when planning and/or upgrading e-resources.Social implicationsOnce the learners are equipped with the required skills, they will make optimum use of the e-resources which are provided by NAMCOL.Originality/valueThis is the first study to be conducted at NAMCOL, and it is hoped that the results will be applied to other tertiary institutions which offer distance education in Namibia.