bluuebunny/crossref_metadata_2025 huggingface dataset:
Cross-linguistic influence in the interpretation of boundary crossing events in L2 acquisition
Authors: Alonso Rosa Alonso
Published: June 2016

This paper analyses the interpretation of boundary-crossing events in second language acquisition (SLA) to determine whether L2 learners are able to select the target-like option for the interpretation of motion events or whether, on the contrary, their choice reflects cross-linguistic influence (CLI) of their L1. The two groups participating in the study – thirty Spanish learners of L2 English and sixteen English first language (L1) speakers – were subjected to an experiment involving an interpretation task with L2 boundary-crossing events pictures. Findings indicate that Spanish L2 learners selected three possible constructions (manner verb + path satellite, path in verb + manner in satellite and a combination of both) in clear contrast to English L1 speakers who only selected one construction (manner verb + path satellite). CLI has also been found to regulate the type of boundary-crossing event selected, primarily in cases of motion INTO a bounded space in the horizontal axis.
Showing versus telling
Authors: Caballero Rosario
Published: June 2016

In this paper I provide a qualitative description of the verbs used to introduce Direct Speech (DS) in fictional narratives written in English and their Spanish translations in order to compare the way these two languages reconstruct speech events in texts by means of both speech verbs (e.g. say/decir, counter/argumentar, declare/manifestar) and non-speech verbs (e.g. grin/sonreír, scowl/fruncir el ceño). Using a corpus of popular fictional narrative genres and drawing upon typological research on motion after the work by Talmy (1985, 1988, 1991) and Slobin (1996a, 1996b, 2004, 2005, 2006). I look into the strategies used in English and Spanish for recreating speech events in order to explore whether the typological differences between these languages are replicated in the case of speech. The hypothesis is that, contrary to what happens with motion events, the differences between English and Spanish do not rest upon lexical availability but, rather, on the weight placed in different speech elements in agreement with two different agendas regarding speech events. While congruent with typological studies, this piece of research attempts to broaden their scope and explore a topic still underexplored.
Status after 5 Years of Survival Compliance Testing in the Federal Columbia River Power System (FCRPS)
Authors: Skalski John R. , Weiland Mark A. , Ham Kenneth D. , Ploskey Gene R. , McMichael Geoffrey A. , Colotelo Alison H. , Carlson Thomas J. , Woodley Christa M. , Eppard M. Brad , Hockersmith Eric E.
Published: June 2016

Survival studies of juvenile Pacific salmon Oncorhynchus spp. implanted with acoustic tags have been conducted at hydroelectric dams within the Federal Columbia River Power System in the Columbia and Snake rivers between 2010 and 2014 to assess compliance with the dam passage survival standards stipulated in the 2008 Biological Opinion. For juvenile yearling Chinook Salmon O. tshawytscha and steelhead O. mykiss that migrate downstream in the spring, dam passage survival (defined as survival from the upstream dam face to the tailrace mixing zone) must be ≥ 96%, and for subyearling Chinook Salmon that migrate downstream in summer, dam passage survival must be ≥ 93%. Precision requirement stipulates a standard error ≤ 1.5% (i.e., a 95% confidence interval of ± 3%). A total of 29 compliance tests have been conducted at six of eight main-stem dams in the Federal Columbia River Power System, using over 109,000 acoustic-tagged salmonid smolts. Of these 29 compliance studies, 23 met the survival standards and 26 met the precision requirements. Of the six dams evaluated to date, individual survival estimates range from 0.9597 to 0.9868 for yearling Chinook Salmon, from 0.9534 to 0.9952 for steelhead, and from 0.9076 to 0.9789 for subyearling Chinook Salmon. Averages across the six dams exceed the survival standards for all three migrant populations.

Received November 9, 2015; accepted February 16, 2016 Published online June 27, 2016
Modernising agriculture through a ‘new’ Green Revolution: the limits of the Crop Intensification Programme in Rwanda
Authors: Cioffo Giuseppe Davide , Ansoms An , Murison Jude
Published: June 2016

Over the past decade, African agriculture sectors have been the object of numerous initiatives advancing a ‘new’ Green Revolution for the continent. The low productivity of African smallholders is attributed to the low use of modern, improved agricultural inputs. In short, African countries are expected to catch up with the Green Revolution in other parts of the world. This paper is a contribution to the debate on the new African Green Revolution. We analyse the Rwandan Crop Intensification Programme (CIP) as a case study of the application of the African Green Revolution model. The paper is based on research at the macro, meso and micro levels. We argue that the CIP fails to draw lessons from previous Green Revolution experiences in terms of its effects on social differentiation, on ecological sustainability, and on knowledge exchange and creation.
Analysis of microbial community and nitrogen transition with enriched nitrifying soil microbes for organic hydroponics
Authors: Saijai Sakuntala , Ando Akinori , Inukai Ryuya , Shinohara Makoto , Ogawa Jun
Published: June 2016

Nitrifying microbial consortia were enriched from bark compost in a water system by regulating the amounts of organic nitrogen compounds and by controlling the aeration conditions with addition of CaCO3 for maintaining suitable pH. Repeated enrichment showed reproducible mineralization of organic nitrogen via the conversion of ammonium ions () and nitrite ions () into nitrate ions (). The change in microbial composition during the enrichment was investigated by PCR-DGGE analysis with a focus on prokaryote, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and eukaryote cell types. The microbial transition had a simple profile and showed clear relation to nitrogen ions transition. Nitrosomonas and Nitrobacter were mainly detected during and oxidation, respectively. These results revealing representative microorganisms acting in each ammonification and nitrification stages will be valuable for the development of artificial simple microbial consortia for organic hydroponics that consisted of identified heterotrophs and autotrophic nitrifying bacteria.
Disciplinarity and sport science in Europe: A statistical and sociological study of ECSS conference abstracts
Authors: Champely Stéphane , Fargier Patrick , Camy Jean
Published: June 2016

Abstracts of European College of Sports Science conferences (1995–2014) are studied. The number of abstracts has been increasing regularly (+90 per year). This rise is in recent years largely due to extra‐European countries. The magnitude and accumulation of the different topics of discussion are examined. An operational criterion determines four stages of evolution of a topic: social network, cluster, specialty, and discipline. The scientific production can, therefore, be classified as disciplinary or non‐disciplinary. The disciplinary part is more important but has been less dynamic recently. The cognitive content of sport science is then explored through a multidimensional scaling of the topics based on the keywords used in the abstracts. Three areas are visible: social sciences and humanities, sports medicine and physiology, and biomechanics and neurophysiology. According to the field theory of Bourdieu (1975), three scientific habitus are distinguished. The logic of academic disciplinary excellence is the consequence of the autonomy of this scientific field, its closure, peer‐review process, and barriers to entry. The distribution of scientific capital and professional capital is unequal across the three areas. Basically, conservation strategies of academic disciplinary excellence are predicted in biomechanics and neurophysiology, subversion strategies of interdisciplinarity based on professional concerns can appear in the sports medicine and physiology area, and critical strategies of interdisciplinarity based on social utility in social sciences and humanities. Moreover, additional tensions within these areas are depicted. Lastly methods based on co‐citations of disciplines and boundary objects are proposed to find tangible patterns of multidisciplinarity confirming these strategies.
A Presenilin-2–ARF4 trafficking axis modulates Notch signaling during epidermal differentiation
Authors: Ezratty Ellen J. , Pasolli H. Amalia , Fuchs Elaine
Published: June 2016

How primary cilia impact epidermal growth and differentiation during embryogenesis is poorly understood. Here, we show that during skin development, Notch signaling occurs within the ciliated, differentiating cells of the first few suprabasal epidermal layers. Moreover, both Notch signaling and cilia disappear in the upper layers, where key ciliary proteins distribute to cell–cell borders. Extending this correlation, we find that Presenilin-2 localizes to basal bodies/cilia through a conserved VxPx motif. When this motif is mutated, a GFP-tagged Presenilin-2 still localizes to intercellular borders, but basal body localization is lost. Notably, in contrast to wild type, this mutant fails to rescue epidermal differentiation defects seen upon Psen1 and 2 knockdown. Screening components implicated in ciliary targeting and polarized exocytosis, we provide evidence that the small GTPase ARF4 is required for Presenilin basal body localization, Notch signaling, and subsequent epidermal differentiation. Collectively, our findings raise the possibility that ARF4-dependent polarized exocytosis acts through the basal body–ciliary complex to spatially regulate Notch signaling during epidermal differentiation.
Mitochondrial lipid transport and biosynthesis: A complex balance
Authors: Mesmin Bruno
Published: June 2016

Little is known about how mitochondrial lipids reach inner membrane–localized metabolic enzymes for phosphatidylethanolamine synthesis. Aaltonen et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201602007) and Miyata et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201601082) now report roles for two mitochondrial complexes, Ups2–Mdm35 and mitochondrial contact site and cristae organizing system, in the biosynthesis and transport of mitochondrial lipids.
Exosomes expand the sphere of influence of Eph receptors and ephrins
Authors: Pasquale Elena B.
Published: June 2016

Membrane-anchored Eph receptors and ephrins represent a ubiquitous intercellular communication system that typically engages at sites of cell–cell contact to initiate bidirectional signaling. Gong et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201601085) show that cells can deploy the EphB2 receptor on exosomes to activate ephrinB signaling and collapse the growth cones of distant neurons.
Rhodopsin kinase and arrestin binding control the decay of photoactivated rhodopsin and dark adaptation of mouse rods
Authors: Frederiksen Rikard , Nymark Soile , Kolesnikov Alexander V. , Berry Justin D. , Adler Leopold , Koutalos Yiannis , Kefalov Vladimir J. , Cornwall M. Carter
Published: June 2016

Photoactivation of vertebrate rhodopsin converts it to the physiologically active Meta II (R*) state, which triggers the rod light response. Meta II is rapidly inactivated by the phosphorylation of C-terminal serine and threonine residues by G-protein receptor kinase (Grk1) and subsequent binding of arrestin 1 (Arr1). Meta II exists in equilibrium with the more stable inactive form of rhodopsin, Meta III. Dark adaptation of rods requires the complete thermal decay of Meta II/Meta III into opsin and all-trans retinal and the subsequent regeneration of rhodopsin with 11-cis retinal chromophore. In this study, we examine the regulation of Meta III decay by Grk1 and Arr1 in intact mouse rods and their effect on rod dark adaptation. We measure the rates of Meta III decay in isolated retinas of wild-type (WT), Grk1-deficient (Grk1−/−), Arr1-deficient (Arr1−/−), and Arr1-overexpressing (Arr1ox) mice. We find that in WT mouse rods, Meta III peaks ∼6 min after rhodopsin activation and decays with a time constant (τ) of 17 min. Meta III decay slows in Arr1−/− rods (τ of ∼27 min), whereas it accelerates in Arr1ox rods (τ of ∼8 min) and Grk1−/− rods (τ of ∼13 min). In all cases, regeneration of rhodopsin with exogenous 11-cis retinal is rate limited by the decay of Meta III. Notably, the kinetics of rod dark adaptation in vivo is also modulated by the levels of Arr1 and Grk1. We conclude that, in addition to their well-established roles in Meta II inactivation, Grk1 and Arr1 can modulate the kinetics of Meta III decay and rod dark adaptation in vivo.
Patch-clamp fluorometry–based channel counting to determine HCN channel conductance
Authors: Liu Chang , Xie Changan , Grant Khade , Su Zhuocheng , Gao Weihua , Liu Qinglian , Zhou Lei
Published: June 2016

Counting ion channels on cell membranes is of fundamental importance for the study of channel biophysics. Channel counting has thus far been tackled by classical approaches, such as radioactive labeling of ion channels with blockers, gating current measurements, and nonstationary noise analysis. Here, we develop a counting method based on patch-clamp fluorometry (PCF), which enables simultaneous electrical and optical recordings, and apply it to EGFP-tagged, hyperpolarization-activated and cyclic nucleotide–regulated (HCN) channels. We use a well-characterized and homologous cyclic nucleotide–gated (CNG) channel to establish the relationship between macroscopic fluorescence intensity and the total number of channels. Subsequently, based on our estimate of the total number of HCN channels, we determine the single-channel conductance of HCN1 and HCN2 to be 0.46 and 1.71 pS, respectively. Such a small conductance would present a technical challenge for traditional electrophysiology. This PCF-based technique provides an alternative method for counting particles on cell membranes, which could be applied to biophysical studies of other membrane proteins.
Prethermalization and universal dynamics in near-integrable quantum systems
Authors: Langen Tim , Gasenzer Thomas , Schmiedmayer Jörg
Published: June 2016

We review the recent progress in the understanding of the relaxation of isolated near-integrable quantum many-body systems. Focusing on prethermalization and universal dynamics following a quench, we describe the experiments with ultracold atomic gases that illustrate these phenomena and summarize the essential theoretical concepts employed to interpret them. Our discussion highlights the key topics that link the different approaches to this interdisciplinary field, including the generalized Gibbs ensemble, non-thermal fixed points, critical slowing and universal scaling. Finally, we point to new experimental challenges demonstrating these fundamental features of many-body quantum systems out of equilibrium.
A Removable Long-arm Soft Cast to Treat Nondisplaced Pediatric Elbow Fractures: A Randomized, Controlled Trial
Authors: Silva Mauricio , Sadlik Gal , Avoian Tigran , Ebramzadeh Edward
Published: June 2016

Background:

The ideal type of immobilization for nondisplaced pediatric elbow fractures has not been established. We hypothesized that the use of a long-arm cylinder made of soft cast material will result in similar outcomes to those obtained with a traditional long-arm hard cast.

Methods:

We randomly assigned 100 consecutive children who presented with a closed, nondisplaced, type I supracondylar humeral fracture or an occult, closed, acute elbow injury, to 1 of 2 groups: group A (n=50) received a long-arm, traditional fiberglass (hard) cast. Group B (n=50) received a long-arm, soft fiberglass cast. After 4 weeks, the cast was removed in group A by a member of our staff using a cast saw, and in group B by one of the patient’s parents by rolling back the soft fiberglass material. We compared the amount of fracture displacement and/or angulation, recovery of range of motion, elbow pain, and patient satisfaction.

Results:

There were no instances of unplanned removal of the cast by the patient or parent. No evidence of fracture displacement or angulation was seen in either group. The final carrying angle of the affected elbow was nearly identical of that of the normal, contralateral elbow in both groups (P=0.64). At the latest follow-up appointment, elbows in groups A and B had a similar mean arc of motion (156 vs. 154 degrees; P=0.45), and had achieved identical relative arc of motion of 99.6% and 99.5% of that of the normal, contralateral side, respectively (P=0.94). Main pain scores were low and comparable over the study period. All patients in both groups reported the highest rate of satisfaction at the eighth week of follow-up.

Conclusions:

The results indicate that children with nondisplaced supracondylar humeral fractures can be successfully managed with the use of a removable long-arm soft cast, maintaining fracture alignment and resulting in comparable rates of range of motion, pain, and patient satisfaction. The use of a removable immobilization that can reliably maintain fracture alignment and result in similar outcomes, while minimizing the risk of noncompliance, could be advantageous. Although we elected to remove the soft cast during a scheduled follow-up, it appears that such immobilization could be removed easily and safely at home, potentially resulting in a lower number of patient visits, decreased health care costs, and higher patient/parent satisfaction.

Level of Evidence:

Level I.
Reproductive and gynecologic care of women with fragile X primary ovarian insufficiency (FXPOI)
Authors: Hipp Heather S. , Charen Krista H. , Spencer Jessica B. , Allen Emily G. , Sherman Stephanie L.
Published: June 2016

Objective:

Approximately 20% of women with a premutation in the FMR1 gene experience primary ovarian insufficiency (POI). We explored diagnostic patterns, frequency of appropriate hormone replacement, obstetric outcomes, fertility treatment, reproductive decisions, and counseling of women with fragile X-associated POI (FXPOI).

Methods:

Semistructured interviews with 79 women with FXPOI were conducted by a single interviewer. FMR1 cytosine-guanine-guanine repeat size was determined from a blood, saliva, or buccal sample.

Results:

The median age of POI onset for women in our study was 33 years. Seventy-two percent of the women had an FMR1 cytosine-guanine-guanine repeat length of 80 to 100. Mean length of time from symptom onset to POI diagnosis was 1.12 years, longer in women with a younger age of POI onset and shorter in women who knew they were carriers. After diagnosis, 52% of women never took hormone therapy, started it years after POI diagnosis, or stopped it before 45 years of age. Forty-nine percent of the women had infertility, but 75% had had at least one genetically related child. Obstetric outcomes were similar to the general population. Forty-six percent of women had a diagnosis of low bone mineral density or osteoporosis, and an additional 19% had never had a bone density assessment.

Conclusions:

Women with FXPOI are at significant risk for delayed POI diagnosis and undertreatment with hormone therapy. Although approximately 50% of women had infertility, most were able to conceive at least one child and had no elevated risk of adverse obstetric outcomes.
Prescribing of FDA-approved and compounded hormone therapy differs by specialty
Authors: Constantine Ginger D. , Archer David F. , Graham Shelli , Bernick Brian A. , Mirkin Sebastian
Published: June 2016

Objective:

To determine the prescribing patterns of general practitioners (GPs), obstetrician/gynecologists (OB/GYNs), and wellness physicians (WPs) of menopausal hormone therapy (HT) for both compounded (CHT) and Food and Drug Administration (FDA)-approved products, using a survey of US physicians.

Methods:

Nine thousand one US physicians were invited to participate in a survey to report on their HT-prescribing patterns. Physicians were eligible if they prescribed HT for at least six patients per month.

Results:

The survey was completed by 440 eligible physicians (893 responded of 9,001 invited) including 171 GPs, 170 OB/GYNs, and 84 WPs. Physicians prescribed HT for 15% to 30% of their female patients, with WPs numerically most likely to prescribe HT. Menopausal symptoms were the leading reason for HT prescriptions among all specialties. WPs seemed more likely to prescribe HT for general/cardiovascular health (28%), and for shorter durations, than other specialties. WPs prescribed proportionally more compounded (vs FDA-approved) estrogens/progestogens than GPs or OB/GYNs, but OB/GYNs seemed to prescribe more compounded dehydroepiandrosterone and testosterone (prescribed alone) than did others. OB/GYNs seemed least likely to consider CHT being more safe or effective than FDA-approved HT. Symptom relief was the main determinant of efficacy for all specialties; WPs also used blood (61%) or saliva testing (25%) for dose adjustment.

Conclusions:

Although all physician specialties surveyed prescribed HT, differences in prescribing CHT versus FDA-approved formulations by medical specialty/practice seemed to exist. Of those surveyed, OB/GYNs and GPs prescribed proportionally more FDA-approved HT, whereas WPs, similarly, prescribed more CHT. More discussion is needed concerning physicians’ decisions to prescribe CHT versus FDA-approved formulations.
Pituitary stalk interruption syndrome: cause, clinical manifestations, diagnosis, and management
Authors: Voutetakis Antonis , Sertedaki Amalia , Dacou-Voutetakis Catherine
Published: June 2016

Purpose of review

Pituitary stalk interruption syndrome (PSIS) is characterized by a thin or absent pituitary stalk, hypoplasia of the adenohypophysis, and ectopic neurohypophysis. PSIS manifestations include a wide spectrum of clinical phenotypes and pituitary hormone deficiencies of variable degree and timing of onset. In this review, recent advances with respect to the cause of PSIS, clinical characteristics leading to earlier diagnosis, and management are outlined.

Recent findings

Diagnosis of PSIS is often delayed probably because clinical findings such as neonatal hypoglycemia, cholestasis, and/or micropenis as well as decreasing growth velocity are not appropriately and timely validated. Recently, molecular defects in various genes have been associated with PSIS albeit in a small number of cases. These findings suggest that PSIS belongs to the spectrum of holoprosencephaly-related defects. Phenotype–genotype discordance and the existence of asymptomatic carriers of a given molecular aberration indicate that penetrance may be modified favorably or unfavorably by the presence of other genetic and/or environmental factors.

PSIS constitutes an antenatal anatomical defect. Neonatal hypoglycemia, cholestasis, and/or micropenis with or without growth deficit should raise the possibility of combined pituitary hormone deficiency, a life-threatening condition in cases of coexisting cortisol deficiency. It is important to search for molecular defects in all PSIS cases, as precise identification of the cause is a prerequisite for genetic counseling.
The Conundrum in the Diagnosis and Management of Atypical Fulminant Measles in a Leukemia Survivor on Maintenance Chemotherapy
Authors: Huang James Guoxian , Yeoh Allen Eng Juh , Tambyah Paul Anantharajah , Suhaila Mas Bte Isa
Published: June 2016

We report the diagnostic and therapeutic challenges in an unusually fulminant presentation of measles, presenting as severe necrotizing bronchiolitis with secondary hemophagocytic lymphohistiocytosis (HLH) in the absence of classical clinical features in an immunocompromised host on maintenance chemotherapy. Our patient had presented with features of a viral pneumonitis without the classical exanthem, in combination with HLH. Although rhinovirus-induced HLH was highly unusual, the positive rhinovirus swab result had distracted us from the eventual diagnosis. This calls for greater impetus to increase awareness and public education to improve vaccination rates and herd immunity to curb outbreaks and protect the immunocompromised patients.
Effects of Local Low-Dose Alendronate Injections Into the Distraction Gap on New Bone Formation and Distraction Rate on Distraction Osteogenesis
Authors: Alp Yunus Emre , Taskaldiran Alper , Onder Mustafa Ercument , Karahan Siyami , Kocyigit Ismail Doruk , Atil Fethi , Tekin Umut
Published: June 2016

Bisphosphonates that constrain bone resorption have a direct effect on osteoclast function. In this experimental study, the effects of low-dose local alendronate injections on the distraction gap (DG) in rabbit mandible at 2 different rates were evaluated.

The experimental study was conducted on 20 male, New Zealand white rabbits. The animals were divided into 3 experimental groups and 1 control group. Group 1 consisted of animals with distraction at the rate of 1 mm/day, receiving postoperative local low-dose alendronate local injections into the DG. Group 2 consisted of animals with distraction at the rate of 2 mm/day, receiving postoperative 0.75 μg/kg of alendronate local injections into the DG. Group 3 consisted of animals with distraction at the rate of 2 mm/day, receiving postoperative 0.2 mL local saline injections into the DG. Group 4 consisted of animals with distraction at the rate of 1 mm/day, receiving postoperative 0.2 mL local saline injections into the DG. All the injections were performed immediately postoperatively and for all groups at 1, 2, 3, and 4 weeks following surgery. The distraction zones were evaluated using dual-energy X-ray absorptiometry and histological analysis.

Histologically, bone healing was found to be significantly accelerated in Groups 1 and 4 compared with Groups 2 and 3 (P < 0.05). Bone healing was superior in Group 1 and the difference was statistically significant compared with Group 4. There was a significant increase in mean bone mineral density in the 1 mm daily rate groups (Groups 1 and 4) compared with the 2 mm daily rate groups (Groups 2 and 3) (P < 0.05).

Local low-dose alendronate injections could be an effective way for improving bone formation in distraction osteogenesis. Furthermore, the results of this study did not support the hypothesis that injections of local low-dose alendronate may allow 2 mm/day instead of 1 mm/day of elongation in the rabbit mandible.
Bayesian identification of bacterial strains from sequencing data
Authors: Sankar Aravind , Malone Brandon , Bayliss Sion C. , Pascoe Ben , Méric Guillaume , Hitchings Matthew D. , Sheppard Samuel K. , Feil Edward J. , Corander Jukka , Honkela Antti
Published: June 2016

Rapidly assaying the diversity of a bacterial species present in a sample obtained from a hospital patient or an environmental source has become possible after recent technological advances in DNA sequencing. For several applications it is important to accurately identify the presence and estimate relative abundances of the target organisms from short sequence reads obtained from a sample. This task is particularly challenging when the set of interest includes very closely related organisms, such as different strains of pathogenic bacteria, which can vary considerably in terms of virulence, resistance and spread. Using advanced Bayesian statistical modelling and computation techniques we introduce a novel pipeline for bacterial identification that is shown to outperform the currently leading pipeline for this purpose. Our approach enables fast and accurate sequence-based identification of bacterial strains while using only modest computational resources. Hence it provides a useful tool for a wide spectrum of applications, including rapid clinical diagnostics to distinguish among closely related strains causing nosocomial infections. The software implementation is available at https://github.com/PROBIC/BIB.
No evidence for phylostratigraphic bias impacting inferences on patterns of gene emergence and evolution
Authors: Domazet-Lošo Tomislav , Carvunis Anne-Ruxandra , Albà M.Mar , Sebastijan Šestak Martin , Bakarić Robert , Neme Rafik , Tautz Diethard
Published: June 2016

Phylostratigraphy is a computational framework for dating the emergence of sequences (usually genes) in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny andde novogene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have raised concerns about the ability of BLAST to detect remote homologues and its impact on phylostratigraphic inferences. These simulations called into question some of our previously published work on patterns of gene emergence and evolution inferred from phylostratigraphy. Here, we re-assessed these simulations and found major problems including unrealistic parameter choices, irreproducibility, statistical flaws and partial representation of results. We found that, even with a possible overall BLAST false negative rate between 5-15%, the large majority (>74%) of sequences assigned to a recent evolutionary origin by phylostratigraphy is unaffected by technical concerns about BLAST. Where the results of the simulations did cast doubt on our previous findings, we repeated our analyses but now excluded all questionable sequences. The originally described patterns remained essentially unchanged. These new analyses strongly support our published inferences, including: genes that emerged after the origin of eukaryotes are more likely to be expressed in the ectoderm than in the endoderm or mesoderm inDrosophila, and thede novoemergence of protein-coding genes from non-genic sequences occurs through proto-gene intermediates in yeast. We conclude that BLAST is an appropriate and sufficiently sensitive tool in phylostratigraphic analysis.
Sustainability in facilities management: an overview of current research
Authors: Nielsen Susanne Balslev , Sarasoja Anna-Liisa , Galamba Kirsten Ramskov
Published: June 2016

Purpose

Climate adaptation, energy efficiency, sustainable development and green growth are societal challenges for which the Facilities Management (FM) profession can develop solutions and make positive contributions on the organisational level and with societal-level effects. To base the emerging sub-discipline of sustainable facilities management (SFM) on research, an overview of current studies is needed. The purpose of this literature review is to provide exactly this overview.

Design/methodology/approach

This article identifies and examines current research studies on SFM through a comprehensive and systematic literature review. The literature review included screening of 85 identified scientific journals and almost 20,000 articles from the period of 2007-2012. Of the articles reviewed, 151 were identified as key articles and categorised according to topic.

Findings

The literature review indicated that the current research varies in focus, methodology and application of theory, and it was concluded that the current research primary addresses environmental sustainability, whereas the current research which takes an integrated strategic approach to SFM is limited. The article includes lists of reviewed journals and articles to support the further development of SFM in research and practice.

Research limitations/implications

The literature review includes literature from 2007 to 2012, to manage the analytical process within the project period. However, with the current categorisation and the access to the reviewed journals and articles, it is possible to continue with the latest literature.

Practical implications

The article provides an overview of theoretical and practical knowledge which can guide: how to document and measure the performance of building operations in terms of environmental, social and economical impacts? How to improve the sustainability performance of buildings? What are the potentials for and barriers to integrating sustainability into FM on strategic, tactical and operational levels?

Originality/value

The paper presents the most comprehensive literature study on SFM so far, and represents an important knowledge basis which is likely to become a key reference point for pioneers and scholars in the emerging sub-discipline of SFM.
Evaluating the effectiveness and practicality of a cooling vest across four industries in Hong Kong
Authors: Chan Albert P.C. , Yi Wen , Wong Francis K.W.
Published: June 2016

Purpose

Extreme hot environments are prevalent in many occupational settings, and facilities management workers are no exception. Wearing suitable cooling garment is a useful means to alleviate heat strain and improving performance at heat exposure. This paper aims to evaluate the effectiveness and applicability of the cooling vest across four selected fields (i.e. construction, outdoor cleaning and horticulture, kitchen work and work involved manual handling at the airport) and identify the shortcomings of the cooling vest used by the participating workers.

Design/methodology/approach

This study adopted a two-phase design: a quantitative questionnaire survey followed by qualitative in-depth interviews.

Findings

A remarkable physical strain alleviation (PSA) of 21.1 per cent (14.8 per cent in construction, 18.8 per cent in horticulture and cleaning, 27.4 per cent in kitchen and catering and 26.5 per cent in airport apron service) is achieved by the use of cooling vest in four industries. Despite the success of PSA, several shortcomings of the cooling vest were identified: easily stained color, heavy weight, short cooling time, inflexibility that presents a hazard around moving equipment, lack of industry-specific design, nondurable and thick fabric with poor permeability.

Originality/value

The findings of the current study do not only confirm the effectiveness of the cooling vest in alleviating heat strain and physical strain but also identify the major shortcomings upon which further improvements can be made.
The retail distribution review
Authors: Ring Patrick
Published: June 2016

Purpose

The purpose of this paper is to review the effect of reforms to the UK’s retail advice sector as a result of the Retail Distribution Review (RDR).

Design/methodology/approach

The paper takes the form of a review of the RDR in the context of the Financial Advice Market Review (FAMR).

Findings

There is a lack of clarity, experienced by both consumers and financial advisers, concerning the nature of “advice”. This results from the use of an array of regulatory and non-regulatory terms. Whilst enhancing professionalisation and reducing commission bias, the RDR is failing to address the needs of many financial consumers – identified by many as an “advice gap”. It is argued that the focus of the RDR, and previous reforms, on addressing market failures may be misplaced.

Practical implications

The paper provides an analysis designed to help in the process of developing a retail advice sector that meets the needs of consumers, in the context policy reforms placing more emphasis on the responsibilities of individuals for financial planning.

Social implications

The study has the potential of better outcomes for consumers and reputational returns for the financial services sector.

Originality/value

This paper is a review of the current regulatory issues facing financial advisers and retail consumers in the context of the RDR and FAMR.
Black engineering students’ motivation for PhD attainment: passion plus purpose
Authors: McGee Ebony O. , White Devin T. , Jenkins Akailah T. , Houston Stacey , Bentley Lydia C. , Smith William J. , Robinson William H.
Published: June 2016

Purpose

Much of the extant research, practice and policy in engineering education has focused on the limited persistence, waning interest and lack of preparation among Black students to continue beyond the post-secondary engineering pipeline. However, this research suggests that many Black PhD students persist and succeed in engineering, fueled by various motivational strengths. To better understand the motivations of Black students in engineering doctoral programs, this study aims to explore the factors that influence their decision to enroll in either an engineering or a computing doctoral program.

Design/methodology/approach

This paper uses an intrinsic and extrinsic motivational framework to investigate the inspiration of 44 Black engineering doctoral students in PhD engineering programs in 11 engineering schools across the country.

Findings

Results show that the participants’ motivation to pursue a PhD in engineering comes from several distinct factors, including the following: an unyielding passion for their particular discipline, a sense of responsibility to serve marginalized peoples and society, a path toward autonomy, pre-PhD mentorship and research opportunities and family and prior work experience.

Research limitations/implications

Based on this study’s findings, a reconceptualization of graduate engineering education that incorporates the importance of “being Black” and its relationships with motivating and, potentially, retaining Black science, technology, engineering and mathematics (STEM) students is also offered.

Originality/value

This paper seeks to expose particular constructs and behaviors surrounding Black students’ motivation to learn and achieve in engineering at the highest academic levels, offering a more nuanced perspective than currently is found in traditional engineering education literature.
Descubriendo mi lugar
Authors: Williams Pichon Henrietta
Published: June 2016

Purpose

The purpose of this quantitative study is to explore the differences and relations among how Black science, technology, engineering and mathematics-life and health sciences (STEM-H) and non-STEM-H students develop a sense of belonging and community at a Hispanic serving institution (HSI).

Design/methodology/approach

This paper used findings from a survey that collected both numeric and string data. Surveys were administered via e-mail.

Findings

There were a limited number of significant findings related to STEM-H students believing that faculty would be sensitive to their needs and that they would be part of the community. String data provide more data about positive and negative experiences related to belonging and community.

Research limitations/implications

It was a single-institution study in New Mexico. Therefore, it may not mirror other HSIs across the country. Also, there were only 84 participants. This number is relatively low compared to the 465 Black students identified at the institutions. Thus, it is clear that not all voices are heard in this study. Finally, this study used preexisting scales to measure a sense of belonging and a sense of community. Because of this, the questions were not customized to the region.

Originality/value

This study introduces STEM-H as a viable area of study. It examines Black STEM-H students enrolled at an HSI using two scales for sense of belonging and sense of community.
Melanoma diagnosed in lesions previously treated by laser therapy
Authors: Delker Sarah , Livingstone Elisabeth , Schimming Tobias , Schadendorf Dirk , Griewank Klaus G.
Published: June 2016

Laser therapy has become a routine procedure in dermatological practice and is frequently also used for pigmented lesions. Few reports exist of melanomas diagnosed in lesions previously treated by laser therapy. Between 2007 and 2014, we identified 11 patients who presented to our department with a melanoma diagnosed in a region previously treated by laser therapy. The course of events until the diagnosis of melanoma was assessed as well as patient outcome including treatment for disease progression. No histological assessment had been performed prior to laser therapy in nine of 11 (82%) cases. Benign melanocytic lesions had been diagnosed by biopsy prior to laser therapy in the other two cases. Time from laser therapy to diagnosis of melanoma ranged from less than 1 to 10 years. Stage of disease at diagnosis varied from stage IA to IIIC. Four patients progressed to stage IV disease, of whom at least one died of melanoma. We conclude that laser treatment of pigmented lesions can complicate the diagnosis of melanoma and lead to diagnosis delay with potentially fatal consequences. Considering this risk, we believe laser therapy for pigmented lesions should either be avoided entirely or at a minimum performed only after prior histological assessment.
Presence of anti‐phosphatidylserine–prothrombin complex antibodies and anti‐moesin antibodies in patients with polyarteritis nodosa
Authors: Okano Tatsuro , Takeuchi Sora , Soma Yoshinao , Suzuki Koya , Tsukita Sachiko , Ishizu Akihiro , Suzuki Kazuo , Kawakami Tamihiro
Published: June 2016

We measured both serum anti‐phosphatidylserine–prothrombin complex (anti‐PSPT) antibodies and anti‐moesin antibodies, as well as various cytokines (interleukin [IL]‐2, IL‐4, IL‐5, IL‐10, IL‐13, IL‐17, granulocyte macrophage colony‐stimulating factor, γ‐interferon, tumor necrosis factor‐α) levels in polyarteritis nodosa (PAN) patients with cutaneous manifestations. All patients showed the presence of a histological necrotizing vasculitis in the skin specimen. They were treated with i.v. cyclophosphamide pulse therapy (IV‐CY) and prednisolone therapy or steroid pulse therapy. The immunological assessments were performed on sera collected prior to and after treatment with IV‐CY or steroid pulse therapy. We found a significant positive correlation between serum anti‐moesin antibodies and both clinical Birmingham Vasculitis Activity Scores and Vasculitis Damage Index. Anti‐PSPT antibody and IL‐2 levels after treatment in PAN patients were significantly lower than before treatment. In contrast, anti‐moesin antibody levels were higher following IV‐CY or steroid pulse therapy compared with the pretreatment levels. In the treatment‐resistant PAN patients (n = 8), anti‐PSPT antibody levels after treatment were significantly lower than before treatment. In contrast, anti‐moesin antibody levels after treatment in the patients were significantly higher compared with the pretreatment levels. Immunohistochemical staining revealed moesin overexpression in mainly fibrinoid necrosis of the affected arteries in the PAN patients. We suggest that measurement of serum anti‐PSPT antibody levels could serve as a marker for PAN and aid in earlier diagnosis of PAN. We also propose that elevated serum anti‐moesin antibodies could play some role of the exacerbation in patients with PAN.
Fine‐tuned production of hydrogen peroxide promotes biofilm formation of Streptococcus parasanguinis by a pathogenic cohabitant Aggregatibacter actinomycetemcomitans
Authors: Duan Dingyu , Scoffield Jessica A. , Zhou Xuedong , Wu Hui
Published: June 2016

Balanced bacterial biofilm communities help to maintain host health. Disturbance of such balance can lead to bacterial dysbiosis and pathogenesis. However, complex and dynamic bacterial interactions within the biofilm communities are poorly understood. In this study, we used a dual‐species biofilm consisting of the periodontal pathogen Aggregatibacter actinomycetemcomitans, and a commensal Streptococcus parasanguinis to investigate bacterial interactions since the two organisms have been found to coexist during the development of localized aggressive periodontal disease. We report that A. actinomycetemcomitans promoted biofilm formation of S. parasanguinis in vitro and in vivo. Protein profiling of S. parasanguinis co‐cultured with A. actinomycetemcomitans revealed a significant decrease in the protein level of pyruvate oxidase(PoxL), an enzyme required for the generation of hydrogen peroxide (H2O2). Consistently, the H2O2 concentration was concurrently decreased. However, the complete removal of H2O2 impaired the biofilm formation. H2O2 at a low concentration range regulated by A. actinomycetemcomitans enhanced the biofilm formation. These results demonstrate that A. actinomycetemcomitans promotes the S. parasanguinis biofilm formation through modulating the production of H2O2 by fine‐tuning the expression of poxL, indicating that H2O2 functions as a signaling molecule. Taken together, this report revealed a previously unknown bacteria‐bacteria interaction mechanism.
Direct‐geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms
Authors: Barrero‐Canosa Jimena , Moraru Cristina , Zeugner Laura , Fuchs Bernhard M. , Amann Rudolf
Published: June 2016

Although fluorescence in situ hybridization (FISH) with specific ribosomal RNA (rRNA)‐targeted oligonucleotides is a standard method to detect and identify microorganisms, the specific detection of genes in bacteria and archaea, for example by using geneFISH, requires complicated and lengthy (> 30 h) procedures. Here we report a much improved protocol, direct‐geneFISH, which allows specific gene and rRNA detection within less than 6 h. For direct‐geneFISH, catalyzed amplification reporter deposition (CARD) steps are removed and fluorochrome‐labelled polynucleotide gene probes and rRNA‐targeted oligonucleotide probes are hybridized simultaneously. The protocol allows quantification of gene copy numbers per cell and the signal of the directly labelled probes enables a subcellular localization of the rRNA and target gene. The detection efficiencies of direct‐geneFISH were first evaluated on Escherichia coli carrying the target gene on a copy‐control vector. We could show that gene copy numbers correlated to the geneFISH signal within the cells. The new protocol was then applied for the detection of the sulfate thiolhydrolase (soxB) genes in cells of the gammaproteobacterial clade SUP05 in Lake Rogoznica, Croatia. Cell and gene detection efficiencies by direct‐geneFISH were statistically identical to those obtained with the original geneFISH, demonstrating the suitability of the simpler and faster protocol for environmental samples.
Food Grain Policies in India and their Implications for Stocks and Fiscal Costs: A Dynamic Partial Equilibrium Analysis
Authors: Kozicka Marta , Kalkuhl Matthias , Brockhaus Jan
Published: June 2016

We analyse current and possible future reforms of the Indian food policies for the most important staple grains, wheat and rice, within a two‐commodity dynamic partial equilibrium model with stochastic shocks. The model is empirically grounded and reproduces past values well. It uses a new reduced‐form approach to capture private storage dynamics. We evaluate the implementation of the National Food Security Act (NFSA) under several policy measures with the current regime as well as two scenarios with a regime change – implementation of cash transfers and deficiency payments. Implications for market fundamentals and fiscal costs are simulated in the medium term – until 2020/21. The NFSA puts a high pressure on fiscal costs and public stocks. Relying on imports with low support prices results in low fiscal costs and stable, but higher domestic and international prices, and a high risk of zero stocks. A policy strategy to manipulate procurement prices in order to maintain public stocks close to the norms leads to slightly higher fiscal costs with lower, but more volatile prices. The highest domestic price volatility occurs under a strategy which uses export bans in order to maintain sufficient public stocks. A cash‐based regime can bring considerable savings and curb fiscal costs, particularly if targeted to the poor, and would leave sufficient stocks due to higher private stocks.