bluuebunny/crossref_metadata_2025 huggingface dataset:
BinSanity: Unsupervised Clustering of Environmental Microbial Assemblies Using Coverage and Affinity Propagation
Authors: Graham Elaina , Heidelberg John , Tully Benjamin
Published: August 2016

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage alone, removing potential composition based biases in clustering contigs, but requires a minimum of two samples. To increase fidelity, a refinement script was developed that uses composition data (tetranucleotide frequency and %G+C content) to refine bins containing multiple source organisms. This separation of composition and coverage based signatures reduces clustering bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that this implementation of AP lead to a higher precision, recall, and Adjusted Rand Index over five commonly implemented methods. When tested on a previously published infant gut metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes.
Genome-wide analysis of lncRNAs and mRNAs expression during the differentiation of abdominal preadipocytes in chicken
Authors: Zhang Tao , Zhang Xiangqian , Han Kunpeng , Zhang Genxi , Wang Jinyu , Xie Kaizhou , Xue Qian
Published: August 2016

lncRNAs regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in preadipocytes differentiation of chicken. Here, we identified lncRNAs in preadipocytes of different differentiation stages by RNA-sequencing using Jinghai Yellow chicken. A total of 1,300,074,528 clean reads and 27,023 lncRNAs were obtained from twenty samples. 3095 genes (1,336 lncRNAs and 1,759 mRNAs) were differentially expressed among different stages, of which the number of DEGs decreased with the differentiation, demonstrating that the early stage might be most important for chicken preadipocytes differentiation. Furthermore, 3,095 DEGs were clustered into 8 clusters with their expression patterns by K-means clustering. We identified six stage-specific modules related to A0, A2 and A6 stages using weighted co-expression network analysis. Many well-known/novel pathways associated with preadipocytes differentiation were found. We also identified highly connected genes in each module and visualized them by cytoscape. Many well-known genes related to preadipocytes differentiation were found such asIGFBP2andJUN. Yet, the majority of high connected genes were unknown in chicken preadipocytes. This study provides a valuable resource for chicken lncRNA study and contributes to batter understanding the biology of preadipocytes differentiation in chicken.
Frank-Starling law and Bowditch phenomenon may have the common theoretical grounds
Authors: Kamnev Yuri
Published: August 2016

The relationship between two different linear dimensions of the chamber (ventricle) and the two respective values of the force of contraction (which are applied to the imaginary piston in order to accelerate the initial venous inflow) is deduced as the ratio of forces which is equal to the ratio of squares of linear dimensions of the chamber; the equation is valid when the durations of both contractions (systoles) are identical. The relationship corresponds to Frank-Starling law (the right limb of parabola can be approximated to the direct proportionality of the law). When the durations of systoles are different the ratio of forces is equal to the inverse ratio of durations of systoles; the inverse proportionality permits to interpret the Bowditch phenomenon by means of the ascending asymptote of hyperbole. Stepwise shortening of systole is impossible due to extremely narrow range of variable (duration of systole), hence the shift of variable can be realized only as a leap; this leap is accompanied by the enormous rise of function (force of contraction) which can be accommodated to several contractions. Homoiometric regulation can be considered a safety device (presumably in the form of paroxysmal tachycardia with the shortened systole) in the case when heterometric regulation lacks to produce the adequate force of contraction in response to excessively distended chamber.
Changes in brain morphology and working memory capacity over childhood
Authors: Bathelt Joe , Gathercole Susan , Johnson Amy , Astle Duncan
Published: August 2016

1

Developmental improvements in working memory are important in the acquisition of new skills, like reading and maths. Current accounts of the brain systems supporting working memory rarely take development into account. However, understanding the development of these skills, and in turn where this development can go awry, will require more sophsiticated neuropsychological accounts that fully consider the role of development. The current study investigated how structural brain correlates of components of the working memory system change over developmental time. Verbal and visuospatial short-term and working memory were assessed in 153 children between 6 and 16 years and latent components of the working memory system were derived using principal component analysis. Further, fractional anisotropy and cortical thickness maps were derived from T1-weighted and diffusion-weighted MRI and processed using eigenanatomy decomposition, an advanced dimensionality reduction method for neuroimaging data. We were then able to explore how the structural brain correlates of working memory gradually shifted across childhood. Regression modelling indicated greater involvement of the corpus callosum and posterior temporal white matter in younger children for performance associated with the executive part of the working memory system, while thickness of the occipitotemporal cortex was more predictive in older children. These findings are consistent with an account in which increasing specialisation leads to shifts in the contribution of neural substrates over developmental time, from early reliance on a distributed system supported by long-range connections to later reliance on specialised local circuitry. Furthemore, our findings emphasise the importance of taking development into account when considering the neural systems that support complex cognitive skills, like working memory.
Statistical Association Mapping of Population-Structured Genetic Data
Authors: Najafi A. , Janghorbani S. , Motahari S. A. , Fatemizadeh E.
Published: August 2016

Association mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the disease-causing sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease causal factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability distribution of the model parameters. We have implemented our proposed framework on a software package whose performance is extensively evaluated on a number of synthetic datasets, and compared to some of the well-known existing methods such as STRUCTURE. It has been shown that in extreme scenarios, up to 10 – 15% of improvement in the inference accuracy is achieved with a moderate increase in computational complexity.
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Authors: Huang Yi-Fei , Gulko Brad , Siepel Adam
Published: August 2016

Across many species, a large fraction of genetic variants that influence phenotypes of interest is located outside of protein-coding genes, yet existing methods for identifying such variants have poor predictive power. Here, we introduce a new computational method, called LINSIGHT, that substantially improves the prediction of noncoding nucleotide sites at which mutations are likely to have deleterious fitness consequences, and which therefore are likely to be phenotypically important. LINSIGHT combines a simple neural network for functional genomic data with a probabilistic model of molecular evolution. The method is fast and highly scalable, enabling it to exploit the “Big Data” available in modern genomics. We show that LINSIGHT outperforms the best available methods in identifying human noncoding variants associated with inherited diseases. In addition, we apply LINSIGHT to an atlas of human enhancers and show that the fitness consequences at enhancers depend on cell-type, tissue specificity, and constraints at associated promoters.
The large majority of intergenic sites in bacteria are selectively constrained, even when known regulatory elements are excluded
Authors: Thorpe Harry A. , Bayliss Sion , Hurst Laurence D. , Feil Edward J.
Published: August 2016

There are currently no broad estimates of the overall strength and direction of selection operating on intergenic variation in bacteria. Here we address this using large whole genome sequence datasets representing six diverse bacterial species; Escherichia coli, Staphylococcus aureus, Salmonella enterica, Streptococcus pneumoniae, Klebsiella pneumoniae, and Mycobacterium tuberculosis. Excluding M. tuberculosis, we find that a high proportion (62%-79%; mean 70%) of intergenic sites are selectively constrained, relative to synonymous sites. Non-coding RNAs tend to be under stronger selective constraint than promoters, which in turn are typically more constrained than rho-independent terminators. Even when these regulatory elements are excluded, the mean proportion of constrained intergenic sites only falls to 69%; thus our current understanding of the functionality of intergenic regions (IGRs) in bacteria is severely limited. Consistent with a role for positive as well as negative selection on intergenic sites, we present evidence for strong positive selection in Mycobacterium tuberculosis promoters, underlining the key role of regulatory changes as an adaptive mechanism in this highly monomorphic pathogen.
Transcriptomic Signatures for Ovulation in Vertebrates
Authors: Liu Dongteng , Brewer Michael S. , Chen Shixi , Hong Wanshu , Zhu Yong
Published: August 2016

Recently, we found anovulation in nuclear progestin receptor (Pgr) knockout (Pgr-KO) zebrafish, which offers a new model for examining Pgr regulated genes and pathways that are important for ovulation and fertility. In this study, we examined expression of all transcripts using RNA-Seq in pre-ovulatory follicular cells collected after the final oocyte maturation, but prior to ovulation, from wild-type (WT) or Pgr-KO fish. Differential expression analysis revealed 2,888 genes significantly differentially expressed between WT and Pgr-KO fish. Among those, 1,230 gene transcripts were significantly more expressed, while 1,658 genes were significantly less expressed in WT than those in Pgr-KO. We then retrieved and compared transcriptional data from online databases and further identified 661 conserved genes in fish, mice, and humans, that showed similar levels of high (283 genes) or low (387) expression in animals that were ovulating compared to those with no ovulation. For the first time, ovulatory genes and their involved biological processes and pathways were also visualized using Enrichment Map and Cytoscape. Intriguingly, enrichment analysis indicated the genes with higher expression were involved in multiple ovulatory pathways and processes such as inflammatory response, angiogenesis, cytokine production, cell migration, chemotaxis, MAPK, focal adhesion, and cytoskeleton reorganization. In contrast, the genes with lower expression were mainly involved DNA replication, DNA repair, DNA methylation, RNA processing, telomere maintenance, spindle assembling, nuclear acid transport, catabolic processes, nuclear and cell division. Our results indicate that a large set of genes (>3,000) are differentially regulated in the follicular cells in zebrafish prior to ovulation, terminating programs including growth and proliferation, and beginning processes including the inflammatory response and apoptosis. Further studies are required to establish relationships among these genes and an ovulatory circuit in zebrafish model.
A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland
Authors: Raven Kathy E. , Reuter Sandra , Reynolds Rosy , Brodrick Hayley J. , Russell Julie E. , Török M. Estée , Parkhill Julian , Peacock Sharon J.
Published: August 2016

Vancomycin-resistant Enterococcus faecium (VREfm) is an important cause of healthcare-associated infections worldwide. We undertook whole-genome sequencing (WGS) of 495 E. faecium bloodstream isolates from 2001–2011 in the United Kingdom and Ireland (UK&I) and 11 E. faecium isolates from a reference collection. Comparison between WGS and multilocus sequence typing (MLST) identified major discrepancies for 17% of isolates, with multiple instances of the same sequence type (ST) being located in genetically distant positions in the WGS tree. This confirms that WGS is superior to MLST for evolutionary analyses and is more accurate than current typing methods used during outbreak investigations. E. faecium has been categorized as belonging to three clades (Clades A1, hospital-associated; A2, animal-associated; and B, community-associated). Phylogenetic analysis of our isolates replicated the distinction between Clade A (97% of isolates) and Clade B but did not support the subdivision of Clade A into Clade A1 and A2. Phylogeographic analyses revealed that Clade A had been introduced multiple times into each hospital referral network or country, indicating frequent movement of E. faecium between regions that rarely share hospital patients. Numerous genetic clusters contained highly related vanA-positive and -negative E. faecium, which implies that control of vancomycin-resistant enterococci (VRE) in hospitals also requires consideration of vancomycin-susceptible E. faecium. Our findings reveal the evolution and dissemination of hospital-associated E. faecium in the UK&I and provide evidence for WGS as an instrument for infection control.
Development of a speckle-based portable device forin situmetrology of synchrotron X-ray mirrors
Authors: Kashyap Yogesh , Wang Hongchang , Sawhney Kawal
Published: August 2016

A portable device forin situmetrology of synchrotron X-ray mirrors based on the near-field speckle scanning technique has been developed. Ultra-high angular sensitivity is achieved by scanning a piece of abrasive paper or filter membrane in the X-ray beam. In addition to the compact setup and ease of implementation, a user-friendly graphical user interface has been developed to ensure that optimizing active X-ray mirrors is simple and fast. The functionality and feasibility of this device have been demonstrated by characterizing and optimizing X-ray mirrors.
Cooperative Jahn–Teller effect and the role of strain in the tetragonal-to-cubic phase transition in MgxCu1 − xCr2O4
Authors: Tarantino Serena C. , Giannini Mattia , Carpenter Michael A. , Zema Michele
Published: August 2016

Temperature and composition dependences of theI41/amd→ Fd\bar 3m phase transition in the MgxCu1 − xCr2O4spinel solid solution, due to the melting of the cooperative Jahn–Teller distortion, have been studied by means of single-crystal X-ray diffraction. Crystals withx= 0, 0.10, 0.18, 0.43, 0.46, 0.53, 1 were grown by flux decomposition methods. All crystals have been refined in the tetragonalI41/amdspace group except for the Mg end-member, which has cubic symmetry. In MgxCu1 − xCr2O4the progressive substitution of the Jahn–Teller,d9Cu2+cation with spherical and closed-shell Mg2+has a substantial effect on the crystal structure, such that there is a gradual reduction of the splitting ofaandcunit-cell parameters and flattening of the tetrahedra. Single-crystal diffraction data collectedin situup toT= 1173 K show that the tetragonal-to-cubic transition temperature decreases with increasing Mg content. The strength of the Cu—Cu interaction is, in effect, modulated by varying the Cu/Mg ratio. Structure refinements of diffraction data collected at different temperatures reveal that heating results in a gradual reduction in the tetrahedron compression, which remains significant until near the transition temperature, however, at which point the distortion of the tetrahedra rapidly vanishes. The spontaneous strain arising in the tetragonal phase is large, amounting to 10% shear strain,et, and ∼ 1% volume strain,Vs, in the copper chromite end-member at room temperature. Observed strain relationships are consistent with pseudoproper ferroelastic behaviour (e_{\rm t}^2 ∝Vs∝ q_{\rm JT}^2, whereqJTis the order parameter). TheI41/amd→ Fd\bar 3m phase transition is first order in character for Cu-rich samples and then evolves towards second-order character. Although a third order term is permitted by symmetry in the Landau expansion, this behaviour appears to be more accurately represented by a 246 expansion with a change from negative to positive values of the fourth-order coefficient with progressive dilution of the Jahn–Teller cation.
Crystal structure of bis(η2-ethylene)(η5-pentamethylcyclopentadienyl)cobalt
Authors: Ramful Chandika D. , Robertson Katherine N. , Ylijoki Kai E. O.
Published: August 2016

The title compound, [Co(C10H15)(C2H4)2], was prepared by Na/Hg reduction of [Co2(C10H15)2(μ-Cl)2] in THF under an ethylene atmosphere and crystallized from pentane at 193 K. The Co—C(olefin) bonds have an average length of 2.022 (2) Å, while the Co—C(pentadienyl) bonds average 2.103 (19) Å. The olefin C=C bonds are 1.410 (1) Å. The dihedral angle between the planes defined by the cyclopentadienyl ligand and the two olefin ligands is 0.25 (12)°. In the crystal, molecules are linked into chains by C—H...π interactions.
A two-dimensional CdII coordination polymer: poly[diaqua[μ3-5,6-bis(pyridin-2-yl)pyrazine-2,3-dicarboxylato-κ5
O
2:O
3:O
3,N
4,N
5]cadmium]
Authors: Alfonso Monserrat , Stoeckli-Evans Helen
Published: August 2016

The reaction of 5,6-bis(pyridin-2-yl)pyrazine-2,3-dicarboxylic acid with cadmium dichloride leads to the formation of the title two-dimensional coordination polymer, [Cd(C16H8N4O4)(H2O)2]
n
. The metal atom is sevenfold coordinated by one pyrazine and one pyridine N atom, two water O atoms, and by two carboxylate O atoms, one of which bridges two CdII atoms to form a Cd2O2 unit situated about a centre of inversion. Hence, the ligand coordinates to the cadmium atom in an N,N′,O-tridentate and an O-monodentate manner. Within the polymer network, there are a number of O—H...O hydrogen bonds present, involving the water molecules and the carboxylate O atoms. There are also C—H...N and C—H...O hydrogen bonds present. In the crystal, the polymer networks lie parallel to the bc plane. They are aligned back-to-back along the a axis with the non-coordinating pyridine rings directed into the space between the networks.
mer-Trichloridotris(tetrahydrothiophene-κS)iridium(III): preparation and comparison with other mer-trichloridotris(tetrahydrothiophene-κS)metal complexes
Authors: Brown Loren C. , DuChane Christine M. , Merola Joseph S.
Published: August 2016

The title complex, [IrCl3(C4H8S)3], was prepared according to a literature method. A suitable crystal was obtained by diffusion of pentane into a dichloromethane solution and analyzed by single-crystal X-ray diffraction at 100 K. The title complex is isotypic with mer-trichloridotris(tetrahydrothiophene-κS)rhodium(III). However, the orientation of the tetrahydrothiophene rings is different from an earlier report of mer-trichloridotris(tetrahydrothiophene-κS)iridium(III) deposited in the Cambridge Structural Database. The IrS3Cl3 core shows a nearly octahedral structure with various bond angles within 1–2° of the perfect 90 or 180° expected for an octahedron. The structure of the title compound is compared with the previous iridium complex as well as the rhodium and other octahedral metal tris-tetrahydrothiophene compounds previously structurally characterized. DFT calculations were performed, which indicate the mer isomer is significantly lower in energy than the fac isomer by 50.1 kJ mol−1, thereby accounting for all compounds in the CSD being of the mer geometry. Powder X-ray diffraction of the bulk material showed that the preparation method yielded only the isomorph reported in this communication.
Tris(4-methoxyphenyl)phosphine selenide
Authors: Raymundo Melina , Padgett Clifford W. , Lynch Will E.
Published: August 2016

The title compound, C21H21O3PSe, is comprised of a P atom in a distorted tetrahedral environment, attached to the Se atom and three C atoms of the phenyl rings. The P—Se bond length is 2.1214 (12) Å. All three methoxy groups are near coplanar with their respective phenyl rings, with the angles between the phenyl ring and the C—O bond of the methoxy groups being 5.7 (2), 1.5 (4), and 5.7 (3)°. The torsion angles of the phenyl rings relative to the P=Se bond are 35.62 (10), 35.07 (13), and 44.50 (11)°. No strong intermolecular interactions were observed, but that in addition to van der Waals forces, there are C—H...π and C—H...Se close contacts.
2-(2-Amino-1,3-thiazol-4-yl)acetohydrazide
Authors: Pallavi G. B. , Gowda Ramakrishna , Gowda K. V. Arjuna , Basanagouda Mahantesha , Latha A. L.
Published: August 2016

In the title compound, C5H8N4OS, the dihedral angle between the acetohydrazide moiety and the thiazole ring is 80.96 (8)°. In the crystal, molecules are linked by N—H...O and N—H...N hydrogen bonds generating (010) sheets.
(Biphenyl-2,2′-diyl)[1,3-bis(diphenylphosphanyl)propane-κ2P,P′]platinum(II)
Authors: Rillema D. Paul , Moore Curtis , Jehan Ali
Published: August 2016

The C2P2donor set in the title compound, [Pt(C12H8)(C27H26P2)], defines a distorted planar coordination environment about the PtIIatom with small deviations from planarity. The bidentate nature of the biphenyl dianionic ligand results in a C—Pt—C bond angle of 79.94 (16)° and a P—Pt—P bond angle of 93.40 (4)°. The average Pt—C bond length is 2.083 (3) Å [range 2.081 (4)–2.085 (4) Å]; the average Pt—P bond length is 2.308 (8) Å [range 2.3030 (11)–2.3136 (11) Å].
Making the case for gender sensitive climate policy – lessons from South Asia/IGP
Authors: Jafry Tahseen
Published: August 2016

Purpose

The purpose of this paper is to provide an overview of gender and social inequality in the agricultural sector of South Asia with a focus on wheat as a major staple crop, which underpins the breadbasket of the Indo-Gangetic Plains (IGP). It provides new insights, as examined through a climate justice lens, into the status of women and socially excluded groups in the region and, based on this, calls for re-thinking both politically and practically on how to shape future initiatives to be more gender and socially inclusive, thereby supporting the rights of the neediest.

Design/methodology/approach

An overview of research and evidence is conducted on how gender and social inequality is currently being addressed in the agricultural sector through an analysis of peer reviewed and grey literature. This is followed by a synthesis which is presented as directions and recommendations for future initiatives developed through a climate justice lens.

Findings

Gender and social inequality issues are rife across the IGP. This may be for many reasons including poor targeting, little capacity, lack of strategic positioning in programme and project design – all of which have enormous implications for the poorest and most marginalised communities and, especially, women. The need to conduct more gender-inclusive and socially inclusive research to enhance gender equity and equal opportunities for women and men is highlighted. The need to include a human rights-based approach to safeguarding the rights of the most vulnerable affected by climate change is indicated through the gender analysis; the finding provides some guiding principles in moving towards the new 2015 climate agreement and Post 2015 Development Goals.

Originality/value

The results provide a foundation which stimulates thinking around climate justice, and the contribution this approach can make to better inform future agricultural initiatives/policies to be more gender-inclusive and socially inclusive.
A gender justice approach to eliminating Sudan’s Savannah belt’s vulnerability to climate change
Authors: Ahmed Mey Eltayeb
Published: August 2016

Purpose

Arguing that a gendered invisibility surrounding climate justice contributes to the overall vulnerability and burden placed upon the ability of women from disadvantaged communities, the purpose of this paper is to demonstrate the importance of developing a participative gender framework for climate justice with the potential to address the policy and programme vulnerability gap within climate change and conflict in Sudan’s Savannah Belt.

Design/methodology/approach

In utilising gender responsive discourse analysis, along with setting out the history of gender engagement within social forestry, this paper examines both the method of Sudan’s reducing emissions from deforestation and forest degradation (REDD+) development and its content.

Findings

The paper’s findings demonstrate that the REDD+ programme in Sudan provides ample evidence of the importance of integrating climate justice and gender approaches to policy, programming and projects through ensuring women and local community participation at all levels and interaction within policy and programme development, along with its implementation.

Research limitations/implications

The paper is theoretical in nature but did draw upon case studies and consultations, and the author was involved in some of the research.

Originality/value

The paper provides a positive and arguably original example of social forestry within the Savannah Belt and its utilisation as a best practice that has fed into Sudan’s REDD+ Proposal/Policy Document so as to potentially drive and streamline similar such initiatives across Sudan.
The role of rights, risks and responsibilities in the climate justice debate
Authors: Shaw Christopher
Published: August 2016

Purpose

This paper aims to use the results of a synthesis of six social science fellowships to explore how alternative framings of the climate justice debate can support fairer climate policies.

Design/methodology/approach

The original fellowships drew on sociology, economics, geography, psychology and international relations. Cross-cutting themes of rights, risks and responsibilities were identified following a series of workshops. Results of these workshops were discussed in a number of policy fora. Analysis of the feedback from that fora is used to propose the case for a rights, risks and responsibilities approach to building a more accessible climate justice debate.

Findings

Existing climate policy unjustly displaces a) responsibility for emission reductions, b) risks from climate impacts and c) loss of rights. Foundational questions of acceptable risk have been ignored and a just climate policy requires procedurally just ways of revisiting this first-order question.

Research limitations/implications

The contribution a rights, risks and responsibilities framework can bring to a process of educating for climate stewardship is at this stage theoretical. It is only through trialling a rights, risks and responsibilities approach to climate justice debates with the relevant stakeholders that its true potential can be assessed.

Practical implications

Policy actors expressed strong resistance to the idea of overhauling current decision-making processes and policy frameworks. However, moving forward from this point with a more nuanced and tactical understanding of the dialectical relationship between rights, risks and responsibilities has the potential to improve those processes.

Social implications

Educating for climate stewardship will be more effective if it adopts an approach which seeks a co-production of knowledge. Beginning with the foundational question of what counts as an acceptable level of climate risk offers an inclusive entry point into the debate.

Originality/value

Reveals limits to public engagement with climate policy generated by a ‘justice’ framing.
“Crowd logistics”: the contribution of social crowds in logistics activities
Authors: Mladenow Andreas , Bauer Christine , Strauss Christine
Published: August 2016

Purpose

The paper aims to provide the necessary basis for a novel interdisciplinary research field. Various types and implementations of crowdsourcing have emerged in the market; many of them are related to logistics. While we can identify plenty of crowd logistics applications using information technology capabilities and information sharing in practice, theories behind this phenomenon have received only limited attention. This paper accounts for filling this research gap by analyzing the crowd’s contributions in logistics of goods and information.

Design/methodology/approach

This paper is part of an ongoing research endeavor in the field of location-based crowdsourcing. It represents conceptual work that builds on a literature review enriched with an in-depth analysis of real-world examples in the field of crowd logistics. Using a scoring method, we provide an example how a company may evaluate the alternatives of crowd logistics. The main approach is an analysis of variants of how the social crowd may be integrated in logistics processes. The work is conceptual in its core. Thereby, we use real-world examples of crowdsourcing applications to underpin the evaluated variants of crowd logistics.

Findings

The paper presents relevant theoretical background on crowd logistics. The authors differentiate between variants of crowd logistics with their flow of materials, goods and information. Thereby they zoom in the type, significance and process flow of the crowd’s contributions. They discuss potential advantages and challenges of logistics with the performing crowd and deeply discuss opportunities and challenges from a business and from an individual’s perspective. Finally, they highlight a route map for future research directions in this novel interdisciplinary research field.

Research limitations/implications

As this work is conceptual in its core, generalizations may be drawn only with great care. Still, we are in a position to propose a route map for further research in this area in this paper. Also the integration of an analysis of a scale of real-world applications allows us to highlight our research’s practical relevance and implications.

Originality/value

The main contribution of this paper is an in-depth analysis and consolidation of innovative crowd logistics applications to provide an overview on recent implementations. The authors propose a categorization scheme and contribute with a route map for further research in the field of crowd logistics.
Application of ICD‐PM to preterm‐related neonatal deaths in South Africa and United Kingdom
Authors: Allanson ER , Vogel JP , Tunçalp Ӧ , Gardosi J , Pattinson RC , Francis A , Erwich JJHM , Flenady VJ , Frøen JF , Neilson J , Quach A , Chou D , Mathai M , Say L , Gülmezoglu AM
Published: August 2016

Objective

We explore preterm‐related neonatal deaths using the WHO application of the International Classification of Disease (ICD‐10) to deaths during the perinatal period: ICD‐PM as an informative case study, where ICD‐PM can improve data use to guide clinical practice and programmatic decision‐making.

Design

Retrospective application of ICD‐PM.

Setting

South Africa, and the UK.

Population

Perinatal death databases.

Methods

Descriptive analysis of neonatal deaths and maternal conditions present.

Main outcome measures

Causes of preterm neonatal mortality and associated maternal conditions.

Results

We included 98 term and 173 preterm early neonatal deaths from South Africa, and 956 term and 3248 preterm neonatal deaths from the UK. In the South African data set, the main causes of death were respiratory/cardiovascular disorders (34.7%), low birthweight/prematurity (29.2%), and disorders of cerebral status (25.5%). Amongst preterm deaths, low birthweight/prematurity (43.9%) and respiratory/cardiovascular disorders (32.4%) were the leading causes. In the data set from the UK, the leading causes of death were low birthweight/prematurity (31.6%), congenital abnormalities (27.4%), and deaths of unspecified cause (26.1%). In the preterm deaths, the leading causes were low birthweight/prematurity (40.9%) and deaths of unspecified cause (29.6%). In South Africa, 61% of preterm deaths resulted from the maternal condition of preterm spontaneous labour. Among the preterm deaths in the data set from the UK, no maternal condition was present in 36%, followed by complications of placenta, cord, and membranes (23%), and other complications of labour and delivery (22%).

Conclusions

ICD‐PM can be used to appraise the maternal and newborn conditions contributing to preterm deaths, and can inform practice.

Tweetable abstract

ICD‐PM can be used to appraise maternal and newborn contributors to preterm deaths to improve quality of care.
Effects of Freeze‐Dried Vegetable Products on the Technological Process and the Quality of Dry Fermented Sausages
Authors: Eisinaite Viktorija , Vinauskiene Rimante , Viskelis Pranas , Leskauskaite Daiva
Published: August 2016

The aim of this study was to compare the chemical composition of freeze‐dried vegetable powders: celery, celery juice, parsnip and leek. The effect of different freeze‐dried vegetables onto the ripening process and the properties of dry fermented sausages was also evaluated. Vegetable products significantly (p < 0.05) differed in their chemical composition: celery products contained higher amounts of nitrates, total phenolic compounds and lower amounts of sucrose, parsnip had higher concentration of proteins, leek was rich in fat. The analysis of pH, water activity, lactic acid bacteria, coagulase‐positive staphylococci and coliforms content showed that the incorporation of freeze‐dried vegetables had no negative effect on the fermentation and ripening process of dry fermented sausages. In addition, the color parameters for sausages with the added lyophilised celery products were considerable (p < 0.05) more stable during these processes. At the end of the ripening process the sausages made with lyophilised celery juice were characterised by higher lightness and lower hardness than those made with the addition of other vegetable products and control. Freeze‐dried celery, celery juice, parsnip and leek have some potential for the usage as a functional ingredient or as a source for indirect addition of nitrate in the production of fermented sausages.
Drinking Motives Predict Subjective Effects of Alcohol and Alcohol Wanting and Liking During Laboratory Alcohol Administration: A Mediated Pathway Analysis
Authors: Wardell Jeffrey D. , Ramchandani Vijay A. , Hendershot Christian S.
Published: August 2016

Background

Motivational models of alcohol use suggest that individual differences in sensitivity to the acute subjective effects of alcohol play an important role in motivational pathways to alcohol use. However, few studies have examined the link between drinking motives and subjective responses to alcohol. This study investigated the associations of coping and enhancement drinking motives with subjective stimulant and sedative effects during a laboratory alcohol administration session. We also examined whether stimulation and sedation following alcohol administration mediated the relationships between drinking motives and postalcohol ratings of alcohol wanting and liking.

Methods

Heavy episodic drinkers (n = 147, ages 19 to 25) at 2 sites participated in an intravenous alcohol administration session in which blood alcohol concentration was raised to a target of 80 mg% over 20 minutes. Participants completed measures of stimulation and sedation at baseline and 20 minutes and also rated alcohol liking and wanting at 20 minutes. Drinking motives and alcohol use were assessed during a previous laboratory visit.

Results

A path analysis controlling for baseline stimulation and sedation showed that enhancement motives were positively associated with postalcohol stimulation and negatively associated with postalcohol sedation. In contrast, coping motives were positively associated with postalcohol sedation. In turn, postalcohol stimulation, but not sedation, was associated with alcohol wanting and liking. Further, indirect pathways from enhancement motives to postalcohol wanting and liking mediated through postalcohol stimulation were statistically significant. Coping motives, on the other hand, were directly associated with increased postalcohol wanting and liking.

Conclusions

The results demonstrate that drinking motives are linked with individual differences in sensitivity to the effects of alcohol, which may serve as a mechanism underlying alcohol reinforcement and the motivation to consume more alcohol during a drinking episode.
Effects of long‐term fire exclusion and frequent fire on plant community composition: A case study from semi‐arid shrublands
Authors: Knuckey Chris G. , Van Etten Eddie J.B. , Doherty Tim S.
Published: August 2016

Time since last fire and fire frequency are strong determinants of plant community composition in fire‐prone landscapes. Our study aimed to establish the influence of time since last fire and fire frequency on plant community composition and diversity of a south‐west Australian semi‐arid shrubland. We employed a space‐for‐time approach using four fire age classes: ‘young’, 8–15 years since last fire; ‘medium’, 16–34; ‘old’, 35–50; and ‘very old’, 51–100; and three fire frequency classes: burnt once, twice and three times within the last 50 years. Species diversity was compared using one‐way ANOVA and species composition using PERMANOVA. Soil and climatic variables were included as covariables to partition underlying environmental drivers. We found that time since last fire influenced species richness, diversity and composition. Specifically, we recorded a late successional transition from woody seeders to long‐lived, arid‐zone, resprouting shrub species. Fire frequency did not influence species richness and diversity but did influence species composition via a reduction in cover of longer‐lived resprouter species – presumably because of a reduced ability to replenish epicormic buds and/or sufficient starch stores. The distinct floristic composition of old and very old habitat, and the vulnerability of these areas to wildfires, indicate that these areas are ecologically important and management should seek to preserve them.
The remarkable Australian rove beetle genus Myotyphlus: its cryptic diversity and significance for exploring mutualism among insects and mammals (Coleoptera: Staphylinidae)
Authors: Solodovnikov Alexey , Jenkins Shaw Josh
Published: August 2016

Myotyphlus jansoni (Matthews ) a rare and the only rove beetle species from the subtribe Amblyopinina (Staphylininae) in Australia that occurs in the fur of small mammals, is revised. Examination of the male genitalia of this species leads to identification of three distinct species: M. jansoni from Tasmania, Myotyphlus newtoni sp. nov. and Myotyphlus wurra sp. nov. described as new from mainland south‐eastern Australia. Distribution, bionomics and host associations are summarised for all three species with the conclusion that at least M. newtoni also occurs in bat guano in caves, or on the ground. Probably, none of the Myotyphlus species is specific to a particular mammal species although M. wurra is only known from one species of Rattus, while the genus as a whole occurs on several species of Rattus, on Pseudomys higginsi and on Antechinus swainsonii. Myotyphlus seems not as strongly associated with its host mammals as the more diverse Neotropical mammal‐associated genera of Amblyopinina, which is consistent with the shorter time period of those respective mammals' presence in Australia. Reviewed in the broad context of insect–mammal mutualisms, the ecology and putative sister‐group relationships of Myotyphlus suggest an independent origin for the mammal‐associated lifestyle in Myotyphlus and Neotropical Amblyopinina, respectively.
FTDP‐17 with Pick body‐like inclusions associated with a novel tau mutation, p.E372G
Authors: Tacik Pawel , DeTure Michael A. , Carlomagno Yari , Lin Wen‐Lang , Murray Melissa E. , Baker Matthew C. , Josephs Keith A. , Boeve Bradley F. , Wszolek Zbigniew K. , Graff‐Radford Neill R. , Parisi Joseph E. , Petrucelli Leonard , Rademakers Rosa , Isaacson Richard S. , Heilman Kenneth M. , Petersen Ronald C. , Dickson Dennis W. , Kouri Naomi
Published: August 2016

Mutations in microtubule‐associated protein tau gene (MAPT) cause frontotemporal dementia with parkinsonism linked to chromosome 17 (FTDP‐17). Here, we describe a patient with FTDP‐17 and a novel missense mutation in exon 13 of MAPT, p.E372G. We compare clinicopathologic features of this patient to two previously unreported patients with another exon 13 mutation, p.G389R. The patient with the p.E372G mutation was a 40‐year‐old man with behavioral variant frontotemporal dementia (bvFTD), who subsequently developed agrammatic speech and parkinsonism. One of the FTDP‐17 patients with p.G389R mutation presented at age 24 with agrammatic variant of primary progressive aphasia, and subsequently behavioral dysfunction. The other presented at age 53 with bvFTD, followed by agrammatic speech and corticobasal syndrome. Neuropathologic features of FTDP‐17 due to p.E372G were similar to those of p.G389R, including tau‐immunoreactive Pick body‐like neuronal inclusions and swollen, tapering thread‐like processes in white matter immunoreactive for 3‐repeat and 4‐repeat tau. Biochemical analysis of insoluble tau showed similar isoform compositions in p.E372G and p.G389R. Functional studies of the p.E372G mutation showed marked increase in tau filament formation and its reduced ability to promote microtubule assembly. Together these findings indicate that p.E372G is a pathogenic MAPT mutation that causes FTDP‐17 similar to p.G389R.
Faulty splicing and cytoskeleton abnormalities in Huntington's disease
Authors: Fernández‐Nogales Marta , Santos‐Galindo María , Hernández Ivó H. , Cabrera Jorge R. , Lucas José J.
Published: August 2016

Huntington's disease (HD) is caused by a CAG‐repeat encoding a polyglutamine (polyQ) tract in the huntingtin protein. There is plenty of evidence of polyQ‐driven toxicity. However, CAG repeat RNA‐driven alteration of splicing has recently been proposed in analogy to CUG‐repeat diseases. Here we review the reported alteration of the CAG‐repeat associated splicing factor SRSF6 in brains of HD patients and mouse models and how this correlates with altered splicing of, at least, two microtubule‐associated proteins in HD, namely MAPT (tau) and MAP2. Regarding tau, altered splicing of exon 10 has been reported, along with increased levels and 4R/3R‐tau ratio and detection of tau in a new nuclear rod‐shaped histopathological hallmark termed tau nuclear rod (TNR) or tau nuclear indentation (TNI). These findings, together with an attenuation of HD phenotype in R6/1 mice with tau deficiency and subsequent studies showing increased phosphorylation in mouse models and increased levels in CSF of patients, has led to proposing HD as a tauopathy. Regarding MAP2, an increase in its juvenile form and a decrease in total MAP2 together with redistribution from dendrites to soma is observed in HD patients, which may contribute to the dendritic atrophy in HD. Furthermore, MAP2 positive structures filling nuclear indentations have occasionally been found and co‐localized with tau. Therefore, altered MAP function with imbalance in tau/MAP2 content could contribute to HD striatal atrophy and dysfunction. Besides, TNIs might be indicative of such MAP abnormalities. TNIs are also found in early pathology Alzheimer's disease and in tauopathy mice over‐expressing mutant 4R‐tau. This indicates that tau alteration is sufficient for TNI detection, which becomes a marker of increased total tau and/or altered 4R/3R‐tau ratio and reporter of pathology‐associated nuclear indentations. Altogether, these recent studies suggest that correcting the SRSF6‐driven missplicing and/or microtubule‐associated imbalance might be of therapeutic value in HD.
Cognitive dysfunction in Huntington's disease: mechanisms and therapeutic strategies beyond BDNF
Authors: Puigdellívol Mar , Saavedra Ana , Pérez‐Navarro Esther
Published: August 2016

One of the main focuses in Huntington's disease (HD) research, as well as in most neurodegenerative diseases, is the development of new therapeutic strategies, as currently there is no treatment to delay or prevent the progression of the disease. Neuronal dysfunction and neuronal death in HD are caused by a combination of interrelated pathogenic processes that lead to motor, cognitive and psychiatric symptoms. Understanding how mutant huntingtin impacts on a plethora of cellular functions could help to identify new molecular targets. Although HD has been classically classified as a neurodegenerative disease affecting voluntary movement, lately cognitive dysfunction is receiving increased attention as it is very invalidating for patients. Thus, an ambitious goal in HD research is to find altered molecular mechanisms that contribute to cognitive decline. In this review, we have focused on those findings related to corticostriatal and hippocampal cognitive dysfunction in HD, as well as on the underlying molecular mechanisms, which constitute potential therapeutic targets. These include alterations in synaptic plasticity, transcriptional machinery and neurotrophic and neurotransmitter signaling.