bluuebunny/crossref_metadata_2025 huggingface dataset:
Sharing of Data as It Relates to Human Subjects Issues and Data Management Plans
Authors: Warner Natasha
Published: November 2014

Researchers often wish to make knowledge publicly available, especially through publication, but may not wish to share their raw data. Human Subjects offices (IRBs) sometimes wish to keep all information private or even to have raw data destroyed. Funding agencies may hope for the data they finance collection of to be made publicly available to increase its impact. These motivations often conflict. This paper discusses how current Human Subjects regulations impact sharing of corpus data among researchers, how funding agencies influence this, and how researchers react to these forces. The paper also discusses potential future changes to the current outcomes, through changes to Human Subjects Protection regulations and changes to funding agency requirements on data sharing.
Archiving and Managing Sociolinguistic Data: The Problems of Portability, Access and Security, and Discoverability and Relevance
Authors: Kendall Tyler
Published: November 2014

In recent years, sociolinguists have become increasingly focused on and more explicit about ensuring the preservation, and accessibility, of their data. This increased focus on our data has involved new lines of work explicitly on data management and, in turn, has led to important (re)considerations of the nature of sociolinguistic data and the metadata of importance for sociolinguist research. While many of the papers in this special issue focus on issues having to do with specific metadata, in this paper, I consider archiving and sharing data more generally. I attend to three specific problem areas, portability access and security, and discoverability and relevance, providing advice as well as some ‘food for thought’ discussions for each.
The Role of Metadata in the Infrastructure for Archival Interoperation
Authors: Simons Gary F.
Published: November 2014

Sociolinguists want to be able to share and compare datasets, and they want to do so now and far into the future. Achieving this dream will require that sociolinguistic corpora are archived in a sustainable way and that those corpora are encoded in such a way that interoperation among them is possible. This paper first sets the stage by describing broadly the requirements for sustainable archiving. It then focuses on the role of metadata in constructing an infrastructure that will support the kind of interoperation that is envisioned – both corpus‐level metadata for facilitating the discovery of relevant corpora and observation‐level metadata for facilitating the comparison of observations that are comparable.
The Problem with Binaries: Coding for Gender and Sexuality
Authors: Eckert Penelope
Published: November 2014

Gender has emerged as the primary social constraint in variation, but the complexities of correlations with a gender binary make it clear that gender must be examined as it interacts with other social constraints (e.g. class). Recent interest in sexuality as a social variable has emerged similarly to that found in studies of gender, with a problematic focus on a binary based on gender choice of sexual partner. This paper examines the problems with the binary treatment of gender and sexuality in variation studies, and considers the consequences and options for the coding and use of large corpora.
Baculovirus‐induced tree‐top disease: how extended is the role ofegtas a gene for the extended phenotype?
Authors: Ros Vera I. D. , van Houte Stineke , Hemerik Lia , van Oers Monique M.
Published: November 2014

Many parasites alter host behaviour to enhance their chance of transmission. Recently, the ecdysteroidUDP‐glucosyl transferase (egt) gene from the baculovirusLymantria disparmultiple nucleopolyhedrovirus (LdMNPV) was identified to induce tree‐top disease inL. disparlarvae. Infected gypsy moth larvae died at elevated positions (hence the term tree‐top disease), which is thought to promote dissemination of the virus to lower foliage. It is, however, unknown whetheregthas a conserved role among baculoviruses in inducing tree‐top disease. Here, we studied tree‐top disease induced by the baculovirusAutographa californicamultiple nucleopolyhedrovirus (AcMNPV) in two different host insects,Trichoplusia niandSpodoptera exigua, and we investigated the role of the viralegtgene therein. AcMNPVinduced tree‐top disease in bothT. niandS. exigualarvae, although inS. exiguaa moulting‐dependent effect was seen. ThoseS. exigualarvae undergoing a larval moult during the infection process died at elevated positions, while larvae that did not moult after infection died at low positions. For bothT. niandS. exigua, infection with a mutant AcMNPVlackingegtdid not change the position where the larvae died. We conclude thategthas no highly conserved role in inducing tree‐top disease in lepidopteran larvae. The conclusion thategtis a ‘gene for an extended phenotype’ is therefore not generally applicable for all baculovirus–host interactions. We hypothesize that in some baculovirus–host systems (including LdMNPVinL. dispar), an effect ofegton tree‐top disease can be observed through indirect effects ofegton moulting‐related climbing behaviour.
Population genomics of natural and experimental populations of guppies (Poecilia reticulata)
Authors: Fraser Bonnie A. , Künstner Axel , Reznick David N. , Dreyer Christine , Weigel Detlef
Published: November 2014

Convergent evolution represents one of the best lines of evidence for adaptation, but few cases of phenotypic convergence are understood at the genetic level. Guppies inhabiting the Northern Mountain Range of Trinidad provide a classic example of phenotypic convergent evolution, where adaptation to low or high predation environments has been found for a variety of traits. A major advantage of this system is the possibility of long‐term experimental studies in nature, including transplantation from high to low predation sites. We used genome scans of guppies from three natural high and low predation populations and from two experimentally established populations and their sources to examine whether phenotypic convergent evolution leaves footprints at the genome level. We used population‐genetic modelling approaches to reconstruct the demographic history and migration among sampled populations. Naturally colonized low predation populations had signatures of increased effective population size since colonization, while introduction populations had signatures of decreased effective population size. Only a small number of regions across the genome had signatures of selection in all natural populations. However, the two experimental populations shared many genomic regions under apparent selection, more than expected by chance. This overlap coupled with a population decrease since introduction provides evidence for convergent selection occurring in the two introduced populations. The lack of genetic convergence in the natural populations suggests that convergent evolution is lacking in these populations or that the effects of selection become difficult to detect after a long‐time period.
The iron‐binding CyaY and IscX proteins assist the ISC‐catalyzed Fe‐S biogenesis in Escherichia coli
Authors: Roche Béatrice , Huguenot Allison , Barras Frédéric , Py Béatrice
Published: November 2014

In eukaryotes, frataxin deficiency (FXN) causes severe phenotypes including loss of iron‐sulfur (Fe‐S) cluster protein activity, accumulation of mitochondrial iron and leads to the neurodegenerative disease Friedreich's ataxia. In contrast, in prokaryotes, deficiency in the FXN homolog, CyaY, was reported not to cause any significant phenotype, questioning both its importance and its actual contribution to Fe‐S cluster biogenesis. Because FXN is conserved between eukaryotes and prokaryotes, this surprising discrepancy prompted us to reinvestigate the role of CyaY in Escherichia coli. We report that CyaY (i) potentiates E. coli fitness, (ii) belongs to the ISC pathway catalyzing the maturation of Fe‐S cluster‐containing proteins and (iii) requires iron‐rich conditions for its contribution to be significant. A genetic interaction was discovered between cyaY and iscX, the last gene of the isc operon. Deletion of both genes showed an additive effect on Fe‐S cluster protein maturation, which led, among others, to increased resistance to aminoglycosides and increased sensitivity to lambda phage infection. Together, these in vivo results establish the importance of CyaY as a member of the ISC‐mediated Fe‐S cluster biogenesis pathway in E. coli, like it does in eukaryotes, and validate IscX as a new bona fide Fe‐S cluster biogenesis factor.
The metabolic regulator CodY links Listeria monocytogenes metabolism to virulence by directly activating the virulence regulatory gene prfA
Authors: Lobel Lior , Sigal Nadejda , Borovok Ilya , Belitsky Boris R. , Sonenshein Abraham L. , Herskovits Anat A.
Published: November 2014

Metabolic adaptations are critical to the ability of bacterial pathogens to grow within host cells and are normally preceded by sensing of host‐specific metabolic signals, which in turn can influence the pathogen's virulence state. Previously, we reported that the intracellular bacterial pathogen Listeria monocytogenes responds to low availability of branched‐chain amino acids (BCAAs) within mammalian cells by up‐regulating both BCAA biosynthesis and virulence genes. The induction of virulence genes required the BCAA‐responsive transcription regulator, CodY, but the molecular mechanism governing this mode of regulation was unclear. In this report, we demonstrate that CodY directly binds the coding sequence of the L. monocytogenes master virulence activator gene, prfA, 15 nt downstream of its start codon, and that this binding results in up‐regulation of prfA transcription specifically under low concentrations of BCAA. Mutating this site abolished CodY binding and reduced prfA transcription in macrophages, and attenuated bacterial virulence in mice. Notably, the mutated binding site did not alter prfA transcription or PrfA activity under other conditions that are known to activate PrfA, such as during growth in the presence of glucose‐1‐phosphate. This study highlights the tight crosstalk between L. monocytogenes metabolism and virulence, while revealing novel features of CodY‐mediated regulation.
Enterococcus faecalis pCF10‐encoded surface proteins PrgA, PrgB (aggregation substance) and PrgC contribute to plasmid transfer, biofilm formation and virulence
Authors: Bhatty Minny , Cruz Melissa R. , Frank Kristi L. , Laverde Gomez Jenny A. , Andrade Fernando , Garsin Danielle A. , Dunny Gary M. , Kaplan Heidi B. , Christie Peter J.
Published: November 2014

Enterococcus faecalis pCF10 transfers at high frequencies upon pheromone induction of the prgQ transfer operon. This operon codes for three cell wall‐anchored proteins – PrgA, PrgB (aggregation substance) and PrgC – and a type IV secretion system through which the plasmid is delivered to recipient cells. Here, we defined the contributions of the Prg surface proteins to plasmid transfer, biofilm formation and virulence using the Caenorhabditis elegans infection model. We report that a combination of PrgB and extracellular DNA (eDNA), but not PrgA or PrgC, was required for extensive cellular aggregation and pCF10 transfer at wild‐type frequencies. In addition to PrgB and eDNA, production of PrgA was necessary for extensive binding of enterococci to abiotic surfaces and development of robust biofilms. However, although PrgB is a known virulence factor in mammalian infection models, we determined that PrgA and PrgC, but not PrgB, were required for efficient killing in the worm infection model. We propose that the pheromone‐responsive, conjugative plasmids of E. faecalis have retained Prg‐like surface functions over evolutionary time for attachment, colonization and robust biofilm development. In natural settings, these biofilms are polymicrobial in composition and constitute optimal environments for signal exchange, mating pair formation and widespread lateral gene transfer.
Rice stripe tenuivirus p2 may recruit or manipulate nucleolar functions through an interaction with fibrillarin to promote virus systemic movement
Authors: Zheng Luping , Du Zhenguo , Lin Chen , Mao Qianzhuo , Wu Kangcheng , Wu Jianguo , Wei Taiyun , Wu Zujian , Xie Lianhui
Published: November 2014

Rice stripe virus (RSV) is the type species of the genus Tenuivirus and represents a major viral pathogen affecting rice production in East Asia. In this study, RSV p2 was fused to yellow fluorescent protein (p2‐YFP) and expressed in epidermal cells of Nicotiana benthamiana. p2‐YFP fluorescence was found to move to the nucleolus initially, but to leave the nucleolus for the cytoplasm forming numerous distinct bright spots there at later time points. A bimolecular fluorescence complementation (BiFC) assay showed that p2 interacted with fibrillarin and that the interaction occurred in the nucleus. Both the nucleolar localization and cytoplasmic distribution of p2‐YFP fluorescence were affected in fibrillarin‐silenced N. benthamiana. Fibrillarin depletion abolished the systemic movement of RSV, but not that of Tobacco mosaic virus (TMV) and Potato virus X (PVX). A Tobacco rattle virus (TRV)‐based virus‐induced gene silencing (VIGS) method was used to diminish RSV NS2 (encoding p2) or NS3 (encoding p3) during RSV infection. Silencing of NS3 alleviated symptom severity and reduced RSV accumulation, but had no obvious effects on virus movement and the timing of symptom development. However, silencing of NS2 abolished the systemic movement of RSV. The possibility that RSV p2 may recruit or manipulate nucleolar functions to promote virus systemic infection is discussed.
Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant
Authors: Sanchez‐Puerta M. Virginia , Zubko Mikhajlo K. , Palmer Jeffrey D.
Published: November 2014

The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants.

We conducted the first study in which the organellar genomes of a cybrid – between Nicotiana tabacum and Hyoscyamus niger – were sequenced and compared to those of its parents.

This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes.

Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double‐strand break repair and/or break‐induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene – and genome – transfer in angiosperm mitochondrial DNAs.
Novel ITGB6 mutation in autosomal recessive amelogenesis imperfecta
Authors: Seymen F , Lee K‐E , Koruyucu M , Gencay K , Bayram M , Tuna EB , Lee ZH , Kim J‐W
Published: November 2014

Objective

Hereditary defects in tooth enamel formation, amelogenesis imperfecta (AI), can be non‐syndromic or syndromic phenotype. Integrins are signaling proteins that mediate cell–cell and cell–extracellular matrix communication, and their involvement in tooth development is well known. The purposes of this study were to identify genetic cause of an AI family and molecular pathogenesis underlying defective enamel formation.

Materials and Methods

We recruited a Turkish family with isolated AI and performed mutational analyses to clarify the underlying molecular genetic etiology.

Results

Autozygosity mapping and exome sequencing identified a novel homozygous ITGB6 transversion mutation in exon 4 (c.517G>C, p.Gly173Arg). The glycine at this position in the middle of the βI‐domain is conserved among a wide range of vertebrate orthologs and human paralogs. Clinically, the enamel was generally thin and pitted with pigmentation. Thicker enamel was noted at the cervical area of the molars.

Conclusions

In this study, we identified a novel homozygous ITGB6 mutation causing isolated AI, and this advances the understanding of normal and pathologic enamel development.
Non‐consumptive effects of avian predators on fish behavior and cascading indirect interactions in seagrasses
Authors: Hill Jennifer M. , Heck Kenneth L.
Published: November 2014

Top–down impacts of avian predators are often overlooked in marine environments despite evidence from other systems that birds significantly impact animal distribution and behavior; instead, birds are typically recognized for the impacts of their nutrient rich guano. This is especially true in shallow seagrass meadows where restoration methods utilize bird perches or stakes to attract birds as a passive fertilizer delivery system that promotes the regrowth of damaged seagrasses. However, this method also increases the local density of avian piscivores that may have multiple unexplored non‐consumptive effects on fish behavior and indirect impacts to seagrass communities. We utilized laboratory and field experiments to investigate whether visual cues of avian predators impacted the behavior of the dominant demersal fish in seagrass habitats, the pinfish Lagodon rhomboides, and promoted cascading interactions on seagrass‐associated fauna and epiphytes. In laboratory mesocosms, pinfish displayed species specific responses to models of avian predators, with herons inducing the greatest avoidance behaviors. Avoidance patterns were confirmed in field seagrass meadows where heron models significantly reduced the number of fish caught in traps. In a long term field experiment, we investigated whether avian predators caused indirect non‐consumptive effects on seagrass communities by monitoring fish abundances, invertebrate epiphyte grazers, and the seagrass epiphytes in response to heron models, bird exclusions, and bird stakes. On average, more fish were recovered under bird exclusions and fewer fish under heron models. However, we found no evidence of cascading effects on invertebrate grazers or epiphytes. Bird stake treatments only displayed a simple nutrient effect where higher bird abundances resulted in higher epiphyte biomass. Our results indicate that although birds and their visual cues can affect fish and epiphyte abundance through non‐consumptive effects and nutrient enrichment, these impacts do not propagate beyond one trophic level, most likely because of dampening by omnivory and larger scale processes.
Flying with diverse passengers: greater richness of parasitic nematodes in migratory birds
Authors: Koprivnikar Janet , Leung Tommy L. F.
Published: November 2014

Environmental changes are simultaneously affecting parasitic diseases and animal migrations, making it important to understand the disease dynamics of migratory species, including their range of infections and investment into defences. There is an urgent need for such knowledge because migratory animals, especially birds, are important for pathogen transmission and also particularly sensitive to environmental changes. Here we compare the nematode species richness and relative immune investment (via relative spleen size) of almost 200 migratory and non‐migratory species within three diverse groups of birds (Anseriformes, Accipitriformes and Turdidae) with worldwide distributions and varied ecology. Our results provide the first large‐scale demonstration that migratory birds face greater challenge from macroparasites as they have significantly dissimilar nematode fauna and higher nematode species richness compared to non‐migratory species. Even though birds with relatively large spleens had more nematode species, there was no difference in relative spleen size between migratory and non‐migratory bird species. The physiological stress of migration can be exacerbated by the potential range of pathologies induced by their richer nematode communities, particularly in combination with environmental perturbations. Altered migration stemming from global changes can also have important consequences for nematode transmission.

Synthesis

Most studies on parasites of migratory birds versus non‐migratory birds focus upon blood parasites; here we compared the diversity of another important parasite group – nematodes (roundworms) in three orders of birds. We found for any given order, migratory species and species with proportionally larger spleens generally have a wider range of nematodes. It is unclear why migratory species harbour more nematode species. Global climate change is expected to influence both bird migration patterns and infectious diseases, which may increase host susceptibility to parasitism and also introduce diverse nematodes to new areas and potential hosts.
Synovial cyst of the temporomandibular joint: a case report with surgical management and long‐term follow‐up
Authors: Verma S. , Chambers I.
Published: November 2014

Synovial cysts of the temporomandibular joint (TMJ) are rare, with only 10 cases reported in the literature. They may present with pain, swelling or trismus and can be a diagnostic dilemma for the clinician. With reference to the literature, this case report describes the presentation, investigation and management of a rare synovial cyst of the TMJ, presenting as a painful preauricular swelling in a 33‐year‐old woman. The long‐term follow‐up of this patient is discussed. We explore different modes of imaging of such disorders, as well as the histological features and the reported treatment modalities of temporomandibular synovial cysts.
C2 Nerve Dysfunction Associated with C1 Lateral Mass Screw Fixation
Authors: Huang Da‐geng , Hao Ding‐jun , Li Guang‐lin , Guo Hao , Zhang Yu‐chen , He Bao‐rong
Published: November 2014

The C1 lateral mass screw technique is widely used for atlantoaxial fixation. However, C2 nerve dysfunction may occur as a complication of this procedure, compromising the quality of life of affected patients. This is a review of the topic of C2 nerve dysfunction associated with C1 lateral mass screw fixation and related research developments. The C2 nerve root is located in the space bordered superiorly by the posterior arch of C1, inferiorly by the C2 lamina, anteriorly by the lateral atlantoaxial joint capsule, and posteriorly by the anterior edge of the ligamentum flavum. Some surgeons suggest cutting the C2 nerve root during C1 lateral mass screw placement, whereas others prefer to preserve it. The incidence, clinical manifestations, causes, management, and prevention of C2 nerve dysfunction associated with C1 lateral mass screw fixation are reviewed. Sacrifice of the C2 nerve root carries a high risk of postoperative numbness, whereas postoperative nerve dysfunction can occur when it has been preserved. Many surgeons have been working hard on minimizing the risk of postoperative C2 nerve dysfunction associated with C1 lateral mass screw fixation.
Corrections of Lower Limb Deformities in Patients with Diastrophic Dysplasia
Authors: Al Kaissi Ali , Kenis Vladimir , Melchenko Eugeniy , Chehida Farid Ben , Ganger Rudolf , Klaushofer Klaus , Grill Franz
Published: November 2014

Objective

Accurate understanding of the cause of the underlying pathology in children with diastrophic dysplasia would help in designing targeted management of their locomotion.

Methods

Diastrophic dysplasia was diagnosed in twelve patients (nine girls and three boys; age range 1–14 years), all of whom presented with small stature and apparent short extremities. Club foot (mostly talipes equinovarus) was the most frequent and consistent abnormality. Concomitant abnormalities such as hip flexion contracture, flexion contractures of the knees with excessive valgus deformity and lateral patellar subluxation, were also encountered. Muscle ultrasound and muscle magnetic resonance imaging imaging showed no myopathic changes and muscle biopsies and the respiratory chain were normal. Serum choline kinase and plasma lactate concentrations were normal.

Results

Surgical correction of the foot and ankle in patients with diastrophic dysplasia is extremely difficult because of the markedly distorted anatomy. In all of these children, plantigrade foot was achieved along with the improved function of the locomotor system. Mutations of the diastrophic dysplasia sulfate transporter (also known as solute carrier family 26 member 2) were encountered.

Conclusion

Arthrogryposis multiplex is the usual terminology used to describe the abnormality in infants with multiple contractures. Diligent orthopaedic care should be provided based on an accurate understanding of the associated syndromes in such children.
RNAi‐based GM plants: food for thought for risk assessors
Authors: Ramon Matthew , Devos Yann , Lanzoni Anna , Liu Yi , Gomes Ana , Gennaro Andrea , Waigmann Elisabeth
Published: November 2014

RNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi‐based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here.
AlfRoss on the Concept of a Legal Right
Authors: Spaak Torben
Published: November 2014

In this article, I discussAlfRoss's claim that the concept of a legal right is best understood as a technical tool of presentation, which ties together a disjunction of operative facts and a conjunction of legal consequences, and that rights statements render the content of a number of legal norms in a convenient manner. I argue that whileRoss's analysis is appealing, it is problematic in at least three respects. I also argue, however, that despite these difficulties Ross's analysis deserves our continued attention, because the fundamental idea—that the concept of a legal right must be understood functionally—is sound.
Dutch ('t) schijnt and german scheint(')s: on the grammaticalization of evidential particles
Authors: Van Bogaert Julie , Leuschner Torsten
Published: November 2014

This paper presents a contrastive study of on the one hand('t) schijnt(‘it seems’), a form of the Dutch verb of appearanceschijnen(‘seem’), and on the other hand, a similar use of the German cognatescheinen, viz.scheint(')s(lit. ‘seems it’). On the basis of corpus data, using a mainly qualitative methodology, we argue that these forms ofschijnenandscheinenhave grammaticalized into evidential particles. We demonstrate that('t) schijntandscheint(')sevolved via distinct grammaticalization paths, the former via the path outlined by matrix‐clause hypothesis and the latter via that of the parataxis hypothesis, and that('t) schijnthas reached a higher degree of grammaticalization thanscheint(')s.
Time to initiation of multidrug‐resistant tuberculosis treatment and its relation with outcome in a high incidence district in Lima, Peru
Authors: Otero L. , De Orbegoso A. , Navarro A. F. , Ríos J. , Párraga T. , Gotuzzo E. , Seas C. , Van der Stuyft P.
Published: November 2014

Objective

To determine the time from diagnosis to start of multidrug resistant tuberculosis (MDR TB) treatment in Lima, Peru.

Methods

We studied new smear‐positive TB adults that were started on MDR TB treatment or that were switched to it between June 2008 and December 2011.

Results

Time from the first positive smear to MDR‐TB treatment was >30 days in 35% (13/37) of patients. Among the 27% (24/88) of patients that switched to MDR‐TB treatment, time from the last dose of a drug‐susceptible regimen was >30 days.

Conclusion

Start of and switching to MDR TB treatment is still delayed.
Getting the basic rights – the role of water, sanitation and hygiene in maternal and reproductive health: a conceptual framework
Authors: Campbell Oona M. R. , Benova Lenka , Gon Giorgia , Afsana Kaosar , Cumming Oliver
Published: November 2014

Objective

To explore linkages between water, sanitation and hygiene (WASH) and maternal and perinatal health via a conceptual approach and a scoping review.

Methods

We developed a conceptual framework iteratively, amalgamating three literature‐based lenses. We then searched literature and identified risk factors potentially linked to maternal and perinatal health. We conducted a systematic scoping review for all chemical and biological WASH risk factors identified using text and MeSH terms, limiting results to systematic reviews or meta‐analyses. The remaining 10 complex behavioural associations were not reviewed systematically.

Results

The main ways poor WASH could lead to adverse outcomes are via two non‐exclusive categories: 1. ‘In‐water’ associations: (a) Inorganic contaminants, and (b) ‘water‐system’ related infections, (c) ‘water‐based’ infections, and (d) ‘water borne’ infections. 2. ‘Behaviour’ associations: (e) Behaviours leading to water‐washed infections, (f) Water‐related insect‐vector infections, and (g‐i) Behaviours leading to non‐infectious diseases/conditions. We added a gender inequality and a life course lens to the above framework to identify whether WASH affected health of mothers in particular, and acted beyond the immediate effects. This framework led us to identifying 77 risk mechanisms (67 chemical or biological factors and 10 complex behavioural factors) linking WASH to maternal and perinatal health outcomes.

Conclusion

WASH affects the risk of adverse maternal and perinatal health outcomes; these exposures are multiple and overlapping and may be distant from the immediate health outcome. Much of the evidence is weak, based on observational studies and anecdotal evidence, with relatively few systematic reviews. New systematic reviews are required to assess the quality of existing evidence more rigorously, and primary research is required to investigate the magnitude of effects of particular WASH exposures on specific maternal and perinatal outcomes. Whilst major gaps exist, the evidence strongly suggests that poor WASH influences maternal and reproductive health outcomes to the extent that it should be considered in global and national strategies.
Risk factors for Chagas disease among pregnant women in El Salvador
Authors: Sasagawa Emi , Aiga Hirotsugu , Corado Edith Y. , Cuyuch Blanca L. , Hernández Marta A. , Guevara Ana V. , Romero José E. , Ramos Hector M. , Cedillos Rafael A. , Misago Chizuru , Kita Kiyoshi
Published: November 2014

Objectives

To determine the seroprevalence of Chagas disease among pregnant women and estimate the risk factors for Chagas disease during pregnancies.

Methods

Community‐based serological tests on Trypanosoma cruzi and structured interviews on socio‐demographic and socio‐economic status were conducted with pregnant women registered at three health centres in Sonsonate province, El Salvador.

Results

Of 797 pregnant women participating in the study, 29 (3.6%) were infected with Chagas disease. None had clinical symptoms. The results of bivariate analyses showed the significant association between seropositivity and maternal age ≥35 years, anaemia, illiteracy, having no formal school education and having knowledge on Chagas disease (P < 0.05). The results of multivariate analysis indicate that age ≥35 years and anaemia were significantly associated with being infected with Chagas disease among pregnant women (OR = 3.541 and 5.197, respectively).

Conclusion

We recommend that the national Chagas disease control programme be better coordinated with the national maternal and child health programme to introduce blood screening for T. cruzi during antenatal visits. If financial constraint allows systematic blood screening to be only partially implemented, resources should be focused on pregnant women ≥35 years and women who have anaemia.
The joint effects of water and sanitation on diarrhoeal disease: a multicountry analysis of the Demographic and Health Surveys
Authors: Fuller James A. , Westphal Joslyn A. , Kenney Brooke , Eisenberg Joseph N. S.
Published: November 2014

Objectives

To assess whether the joint effects of water and sanitation infrastructure, are acting antagonistically (redundant services preventing the same cases of diarrhoeal disease), independently, or synergistically; and to assess how these effects vary by country and over time.

Methods

We used data from 217 Demographic and Health Surveys conducted in 74 countries between 1986 and 2013. We used modified Poisson regression to assess the impact of water and sanitation infrastructure on the prevalence of diarrhoea among children under 5.

Results

The impact of water and sanitation varied across surveys, and adjusting for socio‐economic status drove these estimates towards the null. Sanitation had a greater effect than water infrastructure when all 217 surveys were pooled; however, the impact of sanitation diminished over time. Based on survey data from the past 10 years, we saw no evidence for benefits in improving drinking water or sanitation alone, but we estimated a 6% reduction of both combined (prevalence ratio = 0.94, 95% confidence limit 0.91–0.98).

Conclusions

Water and sanitation interventions should be combined to maximise the number of cases of diarrhoeal disease prevented in children under 5. Further research should identify the sources of variability seen between countries and across time. These national surveys likely include substantial measurement error in the categorisation of water and sanitation, making it difficult to interpret the roles of other pathways.
Rerouting of Plant Late Endocytic Trafficking Toward a Pathogen Interface
Authors: Bozkurt Tolga O. , Belhaj Khaoula , Dagdas Yasin F. , Chaparro‐Garcia Angela , Wu Chih‐Hang , Cano Liliana M. , Kamoun Sophien
Published: November 2014

A number of plant pathogenic and symbiotic microbes produce specialized cellular structures that invade host cells where they remain enveloped by host‐derived membranes. The mechanisms underlying the biogenesis and functions of host–microbe interfaces are poorly understood. Here, we show that plant late endocytic trafficking is diverted toward the extrahaustorial membrane (EHM); a host–pathogen interface that develops in plant cells invaded by Irish potato famine pathogen Phytophthora infestans. A late endosome and tonoplast marker protein Rab7 GTPase RabG3c, but not a tonoplast‐localized sucrose transporter, is recruited to the EHM, suggesting specific rerouting of vacuole‐targeted late endosomes to a host–pathogen interface. We revealed the dynamic nature of this process by showing that, upon activation, a cell surface immune receptor traffics toward the haustorial interface. Our work provides insight into the biogenesis of the EHM and reveals dynamic processes that recruit membrane compartments and immune receptors to this host–pathogen interface.
Finite Time Convergence Guidance Law Accounting for Missile Autopilot
Authors: Qu Pingping , Shao Chuntao , Zhou Di
Published: November 2014

A guidance law with finite time convergence is designed using the sliding mode control method and finite time convergence control theory, accounting for the missile autopilot as second-order dynamics. The high-order derivatives of the line of sight (LOS) angle are avoided in the expression of guidance law such that it can be implemented in practical applications. The designed guidance law is effective in compensating the bad influence of the autopilot dynamics on guidance accuracy. In simulations of intercepting a non maneuvering target or a maneuvering target, respectively, the designed guidance law is compared with the adaptive sliding mode guidance (ASMG) law in the presence of missile autopilot lag. Simulation results show that the designed guidance law is able to guide a missile to accurately intercept a nonmaneuvering target or a maneuvering target with finite time, even if it escapes in a great and fast maneuver and the autopilot has a relatively large lag.
A Control Strategy of a Two Degrees-of-Freedom Heavy Duty Parallel Manipulator
Authors: Wu Jun , Wang Dong , Wang Liping
Published: November 2014

The motion accuracy of a heavy duty parallel manipulator is usually low due to time lag and the difficulty to real-time measure the position of the end-effector. In this paper, a dynamic modeling of this system with consideration of the link flexible deformation is proposed, and a double-feedforward control is presented. The link deformation is considered in the kinematic model. Taking link deformation into account, the dynamic model is derived for real-time application, and the inverse dynamic compensator is designed. The zero phase error tracking controller (ZPETC) is introduced as the second compensator. The system stability is investigated by simulations. The control method is compared with the kinematic-based control without consideration of link deformation. The results show that the maximum contouring error reduces from 7.5mm to 10μm. Thus, the tracking performance is improved when using the method proposed in this paper.
Surface Micropatterning of Pure Titanium for Biomedical Applications Via High Energy Pulse Laser Peening
Authors: Shen Ninggang , Ding Hongtao , Bowers Robert , Yu Yin , Pence Chelsey N. , Ozbolat Ibrahim T. , Stanford Clark M.
Published: November 2014

Pure titanium is an ideal material for biomedical implant applications for its superior biocompatibility, but it lacks of the mechanical strength required in these applications compared with titanium alloys. This research is concerned with an innovative laser peening-based material process to improve the mechanical strength and cell attachment property of pure titanium in biomedical applications. Evidence has shown that engineered surface with unsmooth topologies will contribute to the osteoblast differentiation in human mesenchymal pre-osteoblastic cells, which is helpful to avoid long-term peri-abutment inflammation issues for the dental implant therapy with transcutaneous devices. However, surface quality is difficult to control or mechanical strength is not enhanced using conventional approaches. In this paper, a novel high energy pulse laser peening (HEPLP) process is proposed to both improve the mechanical strength and introduce a micropattern into the biomedical implant material of a commercially pure Titanium (cpTi). The strong shock wave generated by HEPLP presses a stainless steel grid, used as a stamp, on cpTi foils to imprint a micropattern. To understand the basic science during the process, the HEPLP induced shock wave pressure profile and history are modeled by a multiphysics hydrodynamic numerical analysis. The micropatterns and strength enhancement are then simulated using a dislocation density-based finite element (FE) framework. Finally, cell culture tests are conducted to investigate the biomedical performance of the patterned surface.
Improved (G'/G)-Expansion Method for the Time-Fractional Biological Population Model and Cahn–Hilliard Equation
Authors: Baleanu Dumitru , Uğurlu Yavuz , Inc Mustafa , Kilic Bulent
Published: November 2014

In this paper, we used improved (G'/G)-expansion method to reach the solutions for some nonlinear time-fractional partial differential equations (fPDE). The fPDE is reduced to an ordinary differential equation (ODE) by means of Riemann–Liouille derivative and a basic variable transformation. Various types of functions are obtained for the time-fractional biological population model (fBPM) and Cahn–Hilliard (fCH) equation.
A Dimensionless Scaling Parameter for Thermal Effects on Cavitation in Turbopump Inducers
Authors: Ehrlich Daniel A. , Murdock John W.
Published: November 2014

To characterize cryogenic pump performance, at least one parameter in addition to flow coefficient and cavitation number is required. This parameter arises because the heat of vaporization and other physical parameters change along the saturation line of liquids and results in a thermal effect on cavitation that has been observed and studied by previous researchers over a range of operating conditions and working fluids. These previous efforts have defined both dimensionless and dimensional parameters governing thermal effects in pumps. In the present work, a dimensionless parameter (DB) scaling thermal effects in a cavitating pump across different tip diameters, rotational speeds, and working fluids is derived using a model of bubble growth in a time-varying pressure field. Although the derivation is somewhat different than others have used, the result is similar and in some cases identical to that of others. Careful testing is carried out to experimentally validate this parameter with (deaerated) variable temperature water and with variable pump speed. The results show that within the accuracy of the data, the same head fall-off curve is obtained when either the water temperature or the pump speed is used to set the DBs. This suggests the proposed parameter can thermally scale cryogenic pumping conditions for suction performance when testing in hot water. Also examined is the effect of thermodynamics on inducer cavitation instabilities. The quasi-steady, dynamic environments at the pump inlet are compared in cold and superheated water. The cavitation instabilities of the test inducer are found to be dramatically changed by thermal effects. These findings emphasize the importance of considering both fluid mechanical and thermal scaling when designing a test program to evaluate the suction performance of a cryogenic pump.
A Generalized Method for the Analysis of Planar Biaxial Mechanical Data Using Tethered Testing Configurations
Authors: Zhang Will , Feng Yuan , Lee Chung-Hao , Billiar Kristen L. , Sacks Michael S.
Published: November 2014

Simulation of the mechanical behavior of soft tissues is critical for many physiological and medical device applications. Accurate mechanical test data is crucial for both obtaining the form and robust parameter determination of the constitutive model. For incompressible soft tissues that are either membranes or thin sections, planar biaxial mechanical testing configurations can provide much information about the anisotropic stress–strain behavior. However, the analysis of soft biological tissue planar biaxial mechanical test data can be complicated by in-plane shear, tissue heterogeneities, and inelastic changes in specimen geometry that commonly occur during testing. These inelastic effects, without appropriate corrections, alter the stress-traction mapping and violates equilibrium so that the stress tensor is incorrectly determined. To overcome these problems, we presented an analytical method to determine the Cauchy stress tensor from the experimentally derived tractions for tethered testing configurations. We accounted for the measured testing geometry and compensate for run-time inelastic effects by enforcing equilibrium using small rigid body rotations. To evaluate the effectiveness of our method, we simulated complete planar biaxial test configurations that incorporated actual device mechanisms, specimen geometry, and heterogeneous tissue fibrous structure using a finite element (FE) model. We determined that our method corrected the errors in the equilibrium of momentum and correctly estimated the Cauchy stress tensor. We also noted that since stress is applied primarily over a subregion bounded by the tethers, an adjustment to the effective specimen dimensions is required to correct the magnitude of the stresses. Simulations of various tether placements demonstrated that typical tether placements used in the current experimental setups will produce accurate stress tensor estimates. Overall, our method provides an improved and relatively straightforward method of calculating the resulting stresses for planar biaxial experiments for tethered configurations, which is especially useful for specimens that undergo large shear and exhibit substantial inelastic effects.
Turning a surface superrepellent even to completely wetting liquids
Authors: Liu Tingyi “Leo” , Kim Chang-Jin “CJ”
Published: November 2014

Superhydrophobic and superoleophobic surfaces have so far been made by roughening a hydrophobic material. However, no surfaces were able to repel extremely-low-energy liquids such as fluorinated solvents, which completely wet even the most hydrophobic material. We show how roughness alone, if made of a specific doubly reentrant structure that enables very low liquid-solid contact fraction, can render the surface of any material superrepellent. Starting from a completely wettable material (silica), we micro- and nanostructure its surface to make it superomniphobic and bounce off all available liquids, including perfluorohexane. The same superomniphobicity is further confirmed with identical surfaces of a metal and a polymer. Free of any hydrophobic coating, the superomniphobic silica surface also withstands temperatures over 1000°C and resists biofouling.
The new frontier of genome engineering with CRISPR-Cas9
Authors: Doudna Jennifer A. , Charpentier Emmanuelle
Published: November 2014

The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.
Simulation as a tool for biopolymers design
Authors: Suppes Galen J.
Published: November 2014

New materials made from biobased raw materials can be formulated faster with computer simulation of their reaction chemistry
China supersizes its underground physics lab
Authors: Normile Dennis
Published: November 2014

Planned expansion could pave way for “ultimate dark matter experiment.”
Disentangling global soil fungal diversity
Authors: Wardle David A. , Lindahl Björn D.
Published: November 2014

A worldwide sampling effort reveals the global drivers of soil fungal biodiversity

[Also see Research Article by

Tedersoo
et al.

]
How quickly we forget
Authors: Rubin David C.
Published: November 2014

Why do we recall some things better than others?

[Also see Report by
Roediger and DeSoto
]
Big data meets public health
Authors: Khoury Muin J. , Ioannidis John P. A.
Published: November 2014

Human well-being could benefit from large-scale data if large-scale noise is minimized