bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of the relation between species traits and extinction risk
Authors: Chichorro Filipe , Juslén Aino , Cardoso Pedro 
Published: September 2018

ABSTRACTBiodiversity is shrinking rapidly, and despite our efforts only a small part of it has been assessed for extinction risk. Identifying the traits that make species vulnerable might help us to predict the outcome for those less known. We gathered information on the relations of traits to extinction risk from 173 publications, across all taxa, spatial scales and biogeographical regions, in what we think it is the most comprehensive compilation to date. Vertebrates and the Palaearctic are the most studied taxon and region because of higher accumulation of data in these groups. Among the many traits that have been suggested to be good predictors, our meta-analyses were successful in identifying two as potentially useful in assessing risk for the lesser-known species: regardless of the taxon, species with small range and habitat breadth are more vulnerable to extinction. On the other hand, body size (the most studied trait) did not present a consistently positive or negative response. In line with recent research, we hypothesize that the relationship between body size and extinction risk is shaped by different aspects, namely body size is a proxy for different phenomena depending on the taxonomic group.
HIV-1 accessory protein Vpr interacts with REAF/RPRD2 to mitigate its antiviral activity
Authors: Gibbons Joseph M , Marno Kelly M , Pike Rebecca , Lee Wing-yiu Jason , Jones Christopher E , Ogunkolade Babatunji W , Pardieu Claire , Bryan Alexander , Fu Rebecca Menhua , Warnes Gary , Rowley Paul A , Sloan Richard D , McKnight Áine 
Published: September 2018

AbstractThe Human Immunodeficiency Virus type 1 (HIV-1) accessory protein Vpr enhances viral replication in both macrophages and in cycling T cells to a lesser extent. Virion packaged Vpr is released in target cells shortly after entry, suggesting its requirement in the early phase of infection. Previously, we described REAF (RNA-associated Early-stage Antiviral Factor, RPRD2), a constitutively expressed protein that potently restricts HIV replication at or during reverse transcription. Here, we show that a virus without intactvpris more highly restricted by REAF and, using delivery by VLPs, that Vpr alone is sufficient for REAF degradation in primary macrophages. REAF is more highly expressed in macrophages than in cycling T cells and we detect, by co-immunoprecipitation assay, an interaction between Vpr protein and endogenous REAF. Vpr acts very quickly during the early phase of replication and induces the degradation of REAF within 30 minutes of viral entry. Using Vpr F34I and Q65R viral mutants, we show that nuclear localisation and interaction with cullin4A-DBB1 (DCAF1) E3 ubiquitin ligase is required for REAF degradation by Vpr. In response to infection, cells upregulate REAF levels. This response is curtailed in the presence of Vpr. These findings support the hypothesis that Vpr induces the degradation of a factor, REAF, which impedes HIV infection in macrophages.ImportanceFor at least 30 years, it has been known that HIV-1 Vpr, a protein carried in the virion, is important for efficient infection of primary macrophages. Vpr is also a determinant of the pathogenic effects of HIV-1in vivo. A number of cellular proteins that interact with Vpr have been identified. So far, it has not been possible to associate these proteins with altered viral replication in macrophages, or to explain why Vpr is carried in the virus particle. Here we show that Vpr mitigates the antiviral effects of REAF, a protein highly expressed in primary macrophages and one which inhibits virus replication early during reverse transcription. REAF is degraded by Vpr within 30 minutes of virus entry, in a manner dependent on the nuclear localization of Vpr and its interaction with the cell’s protein degradation machinery.
CORnet: Modeling the Neural Mechanisms of Core Object Recognition
Authors: Kubilius Jonas , Schrimpf Martin , Nayebi Aran , Bear Daniel , Yamins Daniel L. K. , DiCarlo James J. 
Published: September 2018

AbstractDeep artificial neural networks with spatially repeated processing (a.k.a., deep convolutional ANNs) have been established as the best class of candidate models of visual processing in primate ventral visual processing stream. Over the past five years, these ANNs have evolved from a simple feedforward eight-layer architecture in AlexNet to extremely deep and branching NAS-Net architectures, demonstrating increasingly better object categorization performance and increasingly better explanatory power of both neural and behavioral responses. However, from the neuroscientist’s point of view, the relationship between such very deep architectures and the ventral visual pathway is incomplete in at least two ways. On the one hand, current state-of-the-art ANNs appear to be too complex (e.g., now over 100 levels) compared with the relatively shallow cortical hierarchy (4-8 levels), which makes it difficult to map their elements to those in the ventral visual stream and to understand what they are doing. On the other hand, current state-of-the-art ANNs appear to be not complex enough in that they lack recurrent connections and the resulting neural response dynamics that are commonplace in the ventral visual stream. Here we describe our ongoing efforts to resolve both of these issues by developing a “CORnet” family of deep neural network architectures. Rather than just seeking high object recognition performance (as the state-of-the-art ANNs above), we instead try to reduce the model family to its most important elements and then gradually build new ANNs with recurrent and skip connections while monitoring both performance and the match between each new CORnet model and a large body of primate brain and behavioral data. We report here that our current best ANN model derived from this approach (CORnet-S) is among the top models on Brain-Score, a composite benchmark for comparing models to the brain, but is simpler than other deep ANNs in terms of the number of convolutions performed along the longest path of information processing in the model. All CORnet models are available at github.com/dicarlolab/CORnet, and we plan to up-date this manuscript and the available models in this family as they are produced.
Prediction of Deleterious Single Nucleotide Polymorphisms in Human p53 Gene
Authors: Alam Saruar , Sayem Mohammad , Hasan Md. Kamrul , Sharmin Zinat , Pavel Mahmud Arif , Hossain Md. Faruk 
Published: September 2018

AbstractWith a variety of accessible Single Nucleotide Polymorphisms (SNPs) data on human p53 gene, this investigation is intended to deal with detrimental SNPs in p53 gene by executing diverse valid computational tools, including Filter, SIFT, PredictSNP, Fathmm, UTRScan, ConSurf, Phyre, Tm-Adjust, I-Mutant, Task Seek after practical and basic appraisal, dissolvable openness, atomic progression, and analysing the energy minimization. Of 581 p53 SNPs, 420 SNPs are found to be missense or non-synonymous and 435 SNPs are in the 3 prime UTR and 112 SNPs are of every 5 prime UTR from which 16 non synonymous SNPs (nsSNPs) as non-tolerable while PredictSNP package predicted 14 (taking consideration SNP colored green by two or more than 2 analyses is neutral). By concentrating on six bioinformatics tools of various dimensions a combined output is generated where 14 nsSNPs are prone to exert a deleterious effect. By using diverse SNP analysing tools we have found 5 missense SNPs in the 3 crucial amino acids position in the DNA binding domain. The underlying discoveries are fortified by I-Mutant and Project HOPE. The ExPASy-PROSITE tools characterized whether the mutations located in the functional part of the protein or not. This study provides a decisive outcome concluding the accessible SNPs information by recognizing the five harming nsSNPs: rs28934573 (S241F), rs11540652 (R248Q), rs121913342 (R248W), rs121913343 (R273C) and rs28934576 (R273H). The findings of this investigation recognize the detrimental nsSNPs which enhance the danger of various kinds of oncogenesis in patients of different populations’ in genome-wide studies (GWS).
Identification of rare-disease genes in diverse undiagnosed cases using whole blood transcriptome sequencing and large control cohorts
Authors: Frésard Laure , Smail Craig , Smith Kevin S. , Ferraro Nicole M. , Teran Nicole A. , Kernohan Kristin D. , Bonner Devon , Li Xin , Marwaha Shruti , Zappala Zachary , Balliu Brunilda , Davis Joe R. , Liu Boxiang , Prybol Cameron J. , Kohler Jennefer N. , Zastrow Diane B. , Fisk Dianna G. , Grove Megan E. , Davidson Jean M. , Hartley Taila , Joshi Ruchi , Strober Benjamin J. , Utiramerur Sowmithri ,   Care4Rare Canada Consortium,   Undiagnosed Diseases Network, Lind Lars , Ingelsson Erik , Battle Alexis , Bejerano Gill , Bernstein Jonathan A. , Ashley Euan A. , Boycott Kym M. , Merker Jason D. , Wheeler Matthew T. , Montgomery Stephen B. 
Published: September 2018

AbstractRNA sequencing (RNA-seq) is a complementary approach for Mendelian disease diagnosis for patients in whom exome-sequencing is not informative. For both rare neuromuscular and mitochondrial disorders, its application has improved diagnostic rates. However, the generalizability of this approach to diverse Mendelian diseases has yet to be evaluated. We sequenced whole blood RNA from 56 cases with undiagnosed rare diseases spanning 11 diverse disease categories to evaluate the general application of RNA-seq to Mendelian disease diagnosis. We developed a robust approach to compare rare disease cases to existing large sets of RNA-seq controls (N=1,594 external and N=31 family-based controls) and demonstrated the substantial impacts of gene and variant filtering strategies on disease gene identification when combined with RNA-seq. Across our cohort, we observed that RNA-seq yields a 8.5% diagnostic rate. These diagnoses included diseases where blood would not intuitively reflect evidence of disease. We identified RARS2 as an under-expression outlier containing compound heterozygous pathogenic variants for an individual exhibiting profound global developmental delay, seizures, microcephaly, hypotonia, and progressive scoliosis. We also identified a new splicing junction in KCTD7 for an individual with global developmental delay, loss of milestones, tremors and seizures. Our study provides a broad evaluation of blood RNA-seq for the diagnosis of rare disease.
CNVkit-RNA: Copy number inference from RNA-Sequencing data
Authors: Talevich Eric , Shain A. Hunter 
Published: September 2018

AbstractRNA-sequencing is most commonly used to measure gene expression, but it is possible to extract genotypic information from RNA-sequencing data, too. Point mutations and translocations can be detected when they occur in expressed genes, however, there are few software solutions to infer copy number information from RNA-sequencing data. This is because a gene’s expression is dictated by a number of variables, including, but not limited to, copy number variation. Here, we report new functionalities within the software package CNVkit that enable copy number inference from RNA-sequencing data. First, CNVkit removes technical variation in gene expression associated with GC-content and transcript length. Next, CNVkit assigns a weight, dictated by several variables, to each transcript with the net effect of preferentially inferring copy number from highly and stably expressed genes. We benchmarked our approach on 105 melanomas from The Cancer Genome Atlas project and observed a high degree of concordance (R = 0.739) between our estimates and those from array comparative genomic hybridization (aCGH) on the same samples. After initial configuration, the software requires few inputs, is able to process a batch of up to 100 samples in less than ten minutes, and can be used in conjunction with pre-existing features of CNVkit, including visualization tools. Overall, we present a rapid, user-friendly software solution to infer copy number information from gene expression data.
Hydrogen exchange protection factors can be extracted from sparse HDX-MS data
Authors: Skinner S. , Radou G. , Tuma R. , Houwing-Duistermaat J. J. , Paci E. 
Published: September 2018

AbstractHydrogen/deuterium exchange (HDX) monitored by mass spectrometry (MS) is a promising technique for rapidly fingerprinting structural and dynamical properties of proteins. The time dependent change in mass of any fragment of the polypeptide chain depends uniquely on the rate of exchange of its amide hydrogens but determining the latter from the former is generally not possible. Here we show that, if time-resolved measurements are available for a number of overlapping peptides that cover the whole sequence, rate constants for each amide hydrogen exchange (or equivalently, their protection factors) can be predicted. In most cases, the solution may not be unique, so a number of solutions have to be considered. Such analysis always provides meaningful constraints on protection factors and thus can be used in situations where obtaining more refined data is impractical, e.g., high throughput structure and interaction fingerprinting. It also provides a systematic way to improve data collection strategies in order to obtain unambiguous information at single residue level, e.g. for assessing protein structure predictions at atomistic level.
Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I
Authors: Gomez-Ospina Natalia , Scharenberg Sam Glynne , Mostrel Nathalie , Bak Rasmus O. , Mantri Sruthi , Quadros Rolen M. , Gurumurthy Channabasavaiah B. , Lee Ciaran , Bao Gang , Aurelian Laure , Porteus Matthew H. 
Published: September 2018

SummaryLysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR/Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can correct biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. Our studies provide support for the development of human, genome-edited CD34+ hematopoietic stem and progenitor cells for the treatment of a multi-systemic lysosomal storage disorder. Our safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes, exemplifying a potential new paradigm for the treatment of these diseases.
Hermeneutics as innovative method to design the brand identity of a nanotechnology company
Authors: Settembre-Blundo Davide , Fernández del Hoyo Alfonso Pedro , García-Muiña Fernando Enrique 
Published: September 2018

Purpose
The purpose of this paper is to develop an innovative branding method based on the hermeneutical approach and interpretive theory, to respond to the need of a simple and effective tool to build corporate identity through an industrial brand identity design and, being a new business, has been considered the brand perception of their stakeholders as the main input to analyze.

Design/methodology/approach
The case study of a small- and medium-sized enterprise (SME), that produces nanomaterials for the business-to-business (B2B) industrial market, is used to design the new hermeneutic branding method. The methodology process has been structured in four phases that have marked the investigation and that correspond to four different levels of knowledge that, in succession, between them, constituted the so-called hermeneutic circle.

Findings
This new approach allowed us to understand the social phenomenon related to the brand: its characteristic, context and the brand itself. Though hermeneutic analysis has confirmed that business strategy is only part of a more complex system of brand management, it must also consider the competitive environment and the views of the stakeholders.

Practical implications
This paper contributes to research on industrial branding by adopting the hermeneutical approach in managerial practice. This paper is the first of its kind in detail modelling the design phases of a B2B brand, providing an operational tool for marketing specialists.

Originality/value
There is a lack of research studies in the methods for designing industrial brands. The contribution of this paper lies in proposing a new interpretative approach that, acknowledging the different expectations of the stakeholder in the supply chain, allows to draw a B2B brand that communicates the system values of the product and company.
Efficiency analysis for nonprofit organizations using DEA
Authors: Kim Hyunsoo , Lee Chang Won 
Published: September 2018

Purpose
The purpose of this study is to provide models to analyze the efficiency of programs and efficiency of fundraising to apply the models to non-profit organizations (NPOs) in Korea and to draw out improvement points of inefficiency using data envelopment analysis (DEA).

Design/methodology/approach
Using DEA, this study analyzed the program efficiency and fundraising efficiency of 22 Korean NPOs in the field of humanitarian assistance.

Findings
Of 22 NPOs, 15 were identified as being efficient in the program efficiency and 7 of 15 NPOs were found efficient in the fundraising efficiency. In all, four organizations were found efficient in both the program and the fundraising efficiency. Using CCR and BCC model, this study proposed the cause of inefficiency and state of returns of scale.

Practical implications
This study presents non-profit efficiency evaluation models regarding program efficiency and fundraising efficiency. This study provides the inefficient DMUs with their reference set of efficient DMUs to improve efficiency and the cause of inefficiency, whether the inefficiency is because of the pure technical inefficiency or the scale inefficiency. This study also indicates the state of variable returns to scale to propose the way of improving inefficiency by controlling the scale of inputs. The methods and the results of this study can serve as a model for researchers and practitioners to follow when evaluating efficiency in the NPOs.

Originality/value
This study has the value of performing the empirical studies of efficiency analysis of Korean NPOs and providing non-profits with the model of efficiency analysis in programs and fundraising activities and basis for establishing strategies to improve both efficiencies.
Innovative capability, strategic goals and financial performance of SMEs in Ghana
Authors: Donkor Jacob , Donkor George Nana Agyekum , Kankam-Kwarteng Collins , Aidoo Eunice 
Published: September 2018

PurposeThis paper aims to investigate the moderating role of innovation capability and strategic goals in the financial performance of small- and medium-scale enterprises (SMEs) in Ghana.Design/methodology/approachInnovative capabilities and strategic goals in SMEs and their influence on financial performance were recognized and briefly debated according to the existing literature. Hypotheses were tested on research data on 340 SMEs in Ghana, which were conveniently selected. Finally, quantitative analysis was done, followed by a discussion of the research findings.FindingsResults from the study have proved that strategic goals have a strong positive relationship with financial performance. Also, there is a strong, positive and highly significant impact innovative capacity has on financial performance. Finally, the study found that innovative capability moderates the relationship between strategic goals and financial performance. It showed that at high levels of innovative capacity, high levels of strategic goals boost financial performance massively.Research limitations/implicationsThe findings are limited to SMEs in Ghana. Researchers should study why SMEs may not pursue any innovation capability activities as they have positive impact on their financial performance. They may also focus on strategic goals and financial performance.Practical implicationsThe study shows a necessity for longer-term innovation perspectives and a higher level of the importance of the application and assessment of strategic goals. Business owners and caretakers need greater awareness about the importance of innovation capability and strategic goals and their influence on the overall financial performance of SMEs. This will help them to adopt right innovate procedures for their businesses.Originality/valueOne of few research works to examine innovation capability and strategic goals on the financial performance of SMEs in a developing country.
Farm size and production efficiency in Chinese agriculture: output and profit
Authors: Yan Jiao , Chen Chunlai , Hu Biliang 
Published: September 2018

Purpose
The purpose of this paper is to analyze the relationship between farm size and agricultural production efficiency from the aspects of output and profit in order to find an optimal farm size that achieves both output and profit efficiency in agricultural production in China.

Design/methodology/approach
This study uses the 2012 China Family Panel Studies survey data and employs the stochastic frontier analysis (SFA) models to investigate empirically the relationship between farm size and agricultural production efficiency.

Findings
The study finds that there is an inverted-U curve relationship between farm size and output efficiency and a U-shaped curve relationship between farm size and profit efficiency in agricultural production in China. Based on the empirical results, the study estimates that the appropriate farm size is around 10–40 mu and the optimal farm size is around 20–40 mu both in terms of output efficiency and profit efficiency in Chinese agricultural production under the current agricultural technology and land management system.

Practical implications
The findings of this study suggest that appropriate land consolidation will bring more benefits to farmer households and agricultural production efficiency. There are some policy implications. First, governments should give long term and more stable land using rights to farmers through extending the period of land contract and verifying land using rights. Second, governments should encourage transfers of land using rights and promote land consolidation. But the implementation of this policy should consider regional differences and not be used for blindly pursuing increasing land size. Third, land consolidation should be accompanied with the development of specialized agricultural services.

Originality/value
The paper makes two major contributions to the literature. First, the authors use the SFA model to investigate the relationship between land size and agricultural production efficiency. Second, the authors establish two SFA models – the stochastic frontier output analysis model and the stochastic frontier profit analysis model – to estimate the optimal land size to achieve both output and profit efficiency of agricultural production in China.