bluuebunny/crossref_metadata_2025 huggingface dataset:
PV power conditioning system using a three‐phase multilevel pulse width modulation inverter employing cascaded Scott transformers
Authors: Fernão Pires Vitor , Foito Daniel , Cordeiro Armando
Published: October 2018

Voltage source inverters (VSIs) are power converters that are considered essential in grid connected photovoltaic (PV) generators. There are several types of topologies for these converters. However, from the point of view of high‐quality AC output voltage, multilevel inverters are considered the most adequate. Under this context, this study proposes a new structure for the three‐phase DC−AC conversion stage for a grid‐connected PV system. It consists of two four‐leg two‐level voltage source inverters that are connected to two PV generators. These inverters are associated with two Scott transformers. The secondary windings of the transformer are connected in a way that allows a series connection. Due to this, a multilevel operation will be achieved. The performance of the proposed power conditioning system will be verified through simulation and experimental results.
Frequency‐coupled admittance modelling of grid‐connected voltage source converters for the stability evaluation of subsynchronous interaction
Authors: Liu Wei , Lu Zongxiang , Wang Xiongfei , Xie Xiaorong
Published: October 2018

Recently, subsynchronous interaction (SSI), a type of stability issue caused by interactionsbetween power electronic converters and weak grids, has attracted greatconcerns. Many efforts have been made to use impedance/admittance‐based methodsfor its modelling and analysis. However, most impedance/admittance models(IM/AMs) are aimed at higher‐frequency dynamics and do not reflect the couplingeffects between sub‐ and super‐synchronous frequencies or the outer controlloops, which, as indicated in this work, have significant impacts on thecharacteristics of SSI. To fill the gap, this study derives the explicitfrequency‐coupled AM for a typical grid‐tied voltage‐sourced converter by takingthe coupling effects and outer‐loop controls into full account and furtherinvestigates their impacts on the subsynchronous stability. The model itself andits effectiveness in predicting the stability of SSI have been validated withdetailed electromagnetic transient simulations.
Total rotational velocity estimation in a multistatic ISAR system
Authors: Phan An , Brisken Stefan , Ng Brian W.‐H. , Tran Hai‐Tan
Published: October 2018

In this study, the authors report on a novel method to estimate the total rotational velocity of a non‐cooperative moving target in a multi‐static Inverse Synthetic Aperture Radar (ISAR) system. The method requires a system with at least four receivers spatially distributed such that their line‐of‐sight vectors are not coplanar. By using least squares optimisation, estimates of the magnitude of the effective rotational velocity ‘seen’ by each receiver and trackfile information on the target trajectory and translational velocity are combined to determine the component due purely to the target's own rotational motion; an estimate for the total rotational velocity can thus be obtained, which can be useful for automatic target recognition. The multi‐static nature of the system allows the technique to take into account the translational motion component of the total rotational velocity with some levels of robustness, which is not the case with other approaches. Simulated data results demonstrate the feasibility of the proposed method.
Frequency rising sub-THz emission from solar flare ribbons
Authors: Kontar E. P. , Motorina G. G. , Jeffrey N. L. S. , Tsap Y. T. , Fleishman G. D. , Stepanov A. V.
Published: October 2018

Observations of solar flares at sub-THz frequencies (millimetre and sub-millimetre wavelengths) over the last two decades often show a spectral component rising with frequency. Unlike a typical gyrosynchrotron spectrum decreasing with frequency or a weak thermal component from hot coronal plasma, the observations can demonstrate a high flux level (up to ∼104 solar flux units at 0.4 THz) and fast variability on sub-second timescales. Although, many models have been put forward to explain the puzzling observations, none of them has clear observational support. Here we propose a scenario to explain the intriguing sub-THz observations. We show that the model, based on free-free emission from the plasma of flare ribbons at temperatures 104 − 106 K, is consistent with all existing observations of frequency-rising sub-THz flare emission. The model provides a temperature diagnostic of the flaring chromosphere and suggests fast heating and cooling of the dense transition region plasma.
Systematic Review of Pulmonary Function and Cognition in Aging
Authors: Duggan Emily Clare , Graham Raquel B , Piccinin Andrea M , Jenkins Natalie D , Clouston Sean , Muniz-Terrera Graciela , Hofer Scott M
Published: October 2018

Background

Substantial research is dedicated to understanding the aging-related dynamics among individual differences in level, change, and variation across physical and cognitive abilities. Evaluating replicability and synthesizing findings has been limited by differences in measurements, samples, study design, and statistical analyses that confound between-person differences with within-person changes. Here, we systematically reviewed longitudinal results on the aging-related dynamics linking pulmonary function and cognitive performance.

Methods

Preferred Reporting Items for Systematic Review and Meta-Analyses guidelines were used to systematically review longitudinal studies of pulmonary function and cognition.

Results

Only four studies thoroughly investigating cognitive and pulmonary longitudinal associations (three or more measurement occasions) were identified. Expanded review criteria identified three studies reporting two measurement occasions, and seven studies reporting one measurement of pulmonary function or cognition and two or more measurements of the other. We identified numerous methodological quality and risk for bias issues across studies.

Conclusions

Despite documented correlational associations between pulmonary function and cognition, these results show there is very limited research thoroughly investigating their longitudinal associations. This highlights the need for longitudinal data, rigorous methodological design including key covariates, and clear communication of methods and analyses to facilitate replication across an array of samples. We recommend systematic study of outcome measures and covariates, inclusion of multiple measures (e.g., peak expiratory flow, forced expiratory volume in 1 s, and forced vital capacity), as well as application of the same analytic approach across multiple datasets.
Density Forecast Evaluations via a Simulation-Based Dynamic Probability Integral Transformation*
Authors: Yun Jaeho
Published: October 2018

This paper presents simulation-based density forecast evaluation methods using particle filters. The simulation-based dynamic probability integral transformation or log-likelihood evaluation method is combined with the existing density forecast evaluation methods. This methodology is applicable to various density forecast models, such as log stochastic volatility models and affine jump diffusion (AJD) models, for which the probability integral transform or likelihood computation is difficult due to the presence of latent stochastic volatilities. This methodology is applied to the daily S&P 500 stock index. The empirical results show that the AJD models with jumps perform the best for out-of-sample evaluations.
Restrictive Transfusion Strategy Is More Effective in Massive Burns: Results of the TRIBE Multicenter Prospective Randomized Trial
Authors: Palmieri Tina L , Holmes James H , Arnoldo Brett , Peck Michael , Cochran Amalia , King Booker T , Dominic William , Cartotto Robert , Bhavsar Dhaval , Tredget Edward , Stapelberg Francois , Mozingo David , Friedman Bruce , Sen Soman , Taylor Sandra L , Pollock Brad H
Published: October 2018

Objectives

Studies suggest that a restrictive transfusion strategy is safe in burns, yet the efficacy of a restrictive transfusion policy in massive burn injury is uncertain. Our objective: compare outcomes between massive burn (≥60% total body surface area (TBSA) burn) and major (20–59% TBSA) burn using a restrictive or a liberal blood transfusion strategy.

Methods

Patients with burns ≥20% were block randomized by age and TBSA to a restrictive (transfuse hemoglobin <7 g/dL) or liberal (transfuse hemoglobin <10 g/dL) strategy throughout hospitalization. Data collected included demographics, infections, transfusions, and outcomes.

Results

Three hundred and forty-five patients received 7,054 units blood, 2,886 in massive and 4,168 in restrictive. Patients were similar in age, TBSA, and inhalation injury. The restrictive group received less blood (45.57 ± 47.63 vs. 77.16 ± 55.0, p < 0.03 massive; 11.0 ± 16.70 vs. 16.78 ± 17.39, p < 0.001) major). In massive burn, the restrictive group had fewer ventilator days (p < 0.05). Median ICU days and LOS were lower in the restrictive group; wound healing, mortality, and infection did not differ. No significant outcome differences occurred in the major (20–59%) group (p > 0.05).

Conclusions:

A restrictive transfusion strategy may be beneficial in massive burns in reducing ventilator days, ICU days and blood utilization, but does not decrease infection, mortality, hospital LOS or wound healing.
Treatment of Hypertrophic Scars Using Laser-Assisted Corticosteroid Versus Laser-Assisted 5-Fluorouracil Delivery
Authors: Waibel Jill S. , Wulkan Adam J. , Rudnick Ashley , Daoud Alexander
Published: October 2018

BACKGROUND

As the mortality of individuals suffering severe cutaneous injuries decreases, there is an increased need to improve the methods by which physicians treat the resultant scars. Fractional lasers, which create zones of ablation at variable depths, provide a powerful tool in the management of scar complications and deformities. After disruption of the normal skin barrier, these zones may be used to deliver drugs that may enhance scar resolution.

OBJECTIVE

To determine the differences in clinical outcome for hypertrophic scars treated with laser-assisted corticosteroid delivery, as compared to laser-assisted 5-fluorouracil delivery.

METHODS

In this prospective, double-blinded, single-subject study of 20 individuals with hypertrophic scars, subjects underwent 3 treatment sessions at 1-month intervals consisting of fractional ablative laser treatment, followed by postoperative application of either topical triamcinolone acetonide (20 mg/mL) or topical 5-fluorouracil (50 mg/mL).

RESULTS

Three sessions of laser-assisted triamcinolone acetonide and 5-fluorouracil delivery both produced reductions in overall scar area. When compared with one another, there were no statistically significant differences in area reduction between the 2 modalities (p = .603). However, scars treated with 5-fluorouracil were not associated with side effects seen with corticosteroid therapy, such as dermal atrophy or telangiectasia formation.

CONCLUSION

As 5-fluorouracil was associated with fewer adverse events, these findings support the use of a nonsteroidal agent in the management of traumatic scars by laser-assisted therapy.
Competition for space induces cell elimination through compaction-driven ERK downregulation
Authors: Moreno Eduardo , Valon Léo , Levillayer Florence , Levayer Romain
Published: October 2018

The plasticity of developing tissues relies on the adjustment of cell survival and growth rate to environmental cues. This includes the effect of mechanical cues on cell survival. Accordingly, compaction of an epithelium can lead to cell extrusion and cell death. This process was proposed to contribute to tissue homeostasis but also to facilitate the expansion of pretumoral cells through the compaction and elimination of the neighbouring healthy cells. However we know very little about the pathways than can trigger apoptosis upon tissue deformation and the contribution of compaction driven death to clone expansion was never assessedin vivo. Using theDrosophilapupal notum and a new live sensor of ERK, we show that tissue compaction induces cell elimination through the downregulation of EGFR/ERK pathway and the upregulation of the pro-apoptotic protein Hid. Those results suggest that the sensitivity of EGFR/ERK pathway to mechanics could play a more general role in the fine tuning of cell elimination during morphogenesis and tissue homeostasis. Secondly, we assessedin vivothe contribution of compaction driven death to pretumoral cell expansion. We found that the activation of the oncogene Ras in clones can also downregulate ERK and activate apoptosis in the neighbouring cells through their compaction, which contributes to Ras clone expansion. The mechanical modulation of EGFR/ERK during growth-mediated competition for space may contribute to tumour progression.
Integrated epigenome, exome and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids
Authors: George Jitu W. , Fan Huihui , Johnson Benjamin K. , Chatterjee Anindita , Patterson Amanda L. , Koeman Julie , Adams Marie , Madaj Zachary B. , Chesla David W. , Marsh Erica E. , Triche Timothy J. , Shen Hui , Teixeira Jose M.
Published: October 2018

Uterine fibroids are benign myometrial smooth muscle tumors of unknown etiology that when symptomatic are the most common indication for hysterectomy in the USA. We conducted an integrated analysis of fibroids and adjacent normal myometria by whole exome sequencing, Infinium MethylationEPIC array, and RNA-sequencing. Unsupervised clustering by DNA methylation segregated normal myometria from fibroids, and further separated the fibroids into subtypes marked byMED12mutation,HMGA2activation (HMGA2hi) andHMGA1activation (HMGA1hi). Upregulation ofHMGA2expression inHMGA2hi fibroids did not always appear to be dependent on translocation, as has been historically described, and was associated with hypomethylation in theHMGA2gene body. Furthermore, we found that expression ofHOXA13was highly upregulated in fibroids and that overexpression ofHOXA13in a myometrial cell line induced expression of genes classically associated with uterine fibroids. Transcriptome analyses of the most differentially expressed genes between cervix and myometrium also showed that uterine fibroids and normal cervix clustered together and apart from normal myometria. Together, our integrated analysis shows a role for epigenetic modification in fibroid biology and strongly suggests that homeotic transformation of myometrium cells to a more cervical phenotype is important for the etiology of the disease.
Ecological and evolutionary insights into pathogenic and non-pathogenic rice associatedXanthomonas
Authors: Bansal Kanika , Midha Samriti , Kumar Sanjeet , Kaur Amandeep , Sonti Ramesh V. , Patil Prabhu B.
Published: October 2018

Xanthomonas oryzaeis a devastating pathogen of rice worldwide, however,X. sontiiandX. maliensisare its non-pathogenic counterparts from the same host. So far, these non-pathogenic isolates were overlooked due to their less economic importance and lack of genomic information. We have carried out detailed ecological and evolutionary study focusing on diverse lifestyles of these strains. Phylogenomic analysis revealed two major lineages corresponding toX. sontii(ML-I) andX. oryzae(ML-II) species. Interestingly, one of the non-pathogenicXanthomonasstrains belonging toX. maliensisis intermediary to both the major lineages/species suggesting on-going diversification and selection. Accordingly, pangenome analysis revealed large number of lifestyle specific genes with atypical GC content indicating role of horizontal gene transfer in genome diversification. Our comprehensive comparative genomic investigation of major lineages has revealed that impact of recombination is more forX. sontiias compared toX. oryzae. Acquisition of type III secretion system and its effectome along with a type VI secretion system also seem to have played a major role in the pathogenic lineage. Other known key pathogenicity clusters or genes like biofilm forming cluster, cellobiohydrolase and non-fimbrial adhesin (yapH)are exclusive to pathogenic lineage. However, commonality of loci encoding exopolysacharide,rpfsignalling molecule, iron-uptake, xanthomonadin pigment, etc. suggests their essentiality in host adaptation. Overall, this study reveals evolutionary history of pathogenic and non-pathogenic strains and will further open up a new avenue for better management of pathogenic strains for sustainable cultivation of a major staple food crop.
Structure reveals mechanism of CRISPR RNA-guided nuclease recruitment and anti-CRISPR viral mimicry
Authors: Rollins MaryClare F. , Chowdhury Saikat , Carter Joshua , Golden Sarah M. , Miettinen Heini M. , Santiago-Frangos Andrew , Faith Dominick , Lawrence C. Martin , Lander Gabriel C. , Wiedenheft Blake
Published: October 2018

Bacteria and archaea have evolved sophisticated adaptive immune systems that rely on CRISPR RNA (crRNA)-guided detection and nuclease-mediated elimination of invading nucleic acids. Here we present the cryo-EM structure of the type I-F CRISPR RNA-guided surveillance complex (Csy complex) from Pseudomonas aeruginosa bound to a double-stranded DNA target. Comparison of this structure to previously determined structures of this complex reveals a Ȉ180-degree rotation of the C-terminal helical bundle on the “large” Cas8f subunit. We show that the dsDNA-induced conformational change in Cas8f exposes a Cas2/3 “nuclease recruitment helix” that is structurally homologous to a virally encoded anti-CRISPR protein (AcrIF3). Structural homology between Cas8f and AcrIF3 suggests that AcrIF3 is a mimic of the Cas8f “nuclease recruitment helix”, implying that cas genes may sometimes serve as genetic fodder for the evolution of anti-CRISPRs.
Highly Predictive Transdiagnostic Features Shared across Schizophrenia, Bipolar Disorder, and ADHD Identified Using a Machine Learning Based Approach
Authors: Liu Yuelu , Mellem Monika S. , Gonzalez Humberto , Kollada Matthew , Mahableshwarkar Atul R. , Madrid Annette , Martin William J. , Ahammad Parvez
Published: October 2018

The Diagnostic and Statistical Manual of Mental Disorders (DSM) is the standard for diagnosing psychiatric disorders in the United States. However, evidence has suggested that symptoms in psychiatric disorders are not restricted to the boundaries between DSM categories, implying an underlying latent transdiagnostic structure of psychopathology. Here, we applied an importance-guided machine learning technique for model selection to item-level data from self-reported instruments contained within the Consortium for Neuropsychiatric Phenomics dataset. From 578 questionnaire items, we identified a set of features which consisted of 85 items that were shared across diagnoses of schizophrenia (SCZ), bipolar disorder (BD), and attention deficit/hyperactivity disorder (ADHD). A classifier trained on the transdiagnostic features reliably distinguished the patient group as a whole from healthy controls (classification AUC = 0.95) and only 10 items were needed to attain the performance level of AUC being 0.90. A sum score created from the items produced high separability between patients and healthy controls (Cohen’s d = 2.85), and it outperformed predefined sum scores and sub-scores within the instruments (Cohen’s d ranging between 0.13 and 1.21). The transdiagnostic features comprised both symptom domains (e.g. dysregulated mood, attention deficit, and anhedonia) and personality traits (e.g. neuroticism, impulsivity, and extraversion). Moreover, by comparing the features that were common across the three patient groups with those that were most predictive of a single patient category, we can describe the unique features for each patient group superimposed on the transdiagnostic feature structure. Overall, our results reveal a latent transdiagnostic symptom/behavioral phenotypic structure shared across SCZ, BD, and ADHD and present a new perspective to understand insights offered by self-report psychiatric instruments.
Are protein-ligand complexes robust structures?
Authors: Majewski Maciej , Ruiz-Carmona Sergio , Barril Xavier
Published: October 2018

The predominant view in structure-based drug design is that small-molecule ligands, once bound to their target structures, display a well-defined binding mode. While this is convenient from a design perspective, it ignores the fact that structural stability (robustness) is not necessary for thermodynamic stability (binding affinity). In fact, any potential benefit of a rigid binding mode will have to be balanced against the entropic penalty that it entails. Surprisingly, little is known about the causes, consequences and real degree of robustness of protein-ligand complexes. Here we investigate two diverse sets of structures, comprising 79 drug-like and 27 fragment ligands, respectively. We focus on hydrogen bond interactions (469 in total), as they have been described as essential for structural stability. We find that 75% of complexes are anchored by at least one robust hydrogen bond, the remaining 25% either form loose complexes or are constrained by other interactions types. The first type of complexes generally combine a single anchoring point with looser regions, thus balancing order and disorder. Completely constricted protein-ligand complexes are rare and seem to fulfil a functional necessity. Structural stability analysis reveals a hidden layer of complexity in protein-ligand complexes that should be considered in ligand design.
Caribbean golden orbweaving spiders maintain gene flow with North America
Authors: Čandek Klemen , Agnarsson Ingi , Binford Greta J. , Kuntner Matjaž
Published: October 2018

The Caribbean archipelago offers one of the best natural arenas for testing biogeographic hypotheses. The intermediate dispersal model of biogeography (IDM) predicts variation in species richness among lineages on islands to relate to their dispersal potential. To test this model, one would need background knowledge of dispersal potential of lineages, which has been problematic as evidenced by our prior biogeographic work on the Caribbean tetragnathid spiders. In order to investigate the biogeographic imprint of an excellent disperser, we study the AmericanTrichonephila, a nephilid genus that contains globally distributed species known to overcome long, overwater distances. Our results reveal that the AmericanT. clavipesshows a phylogenetic and population genetic structure consistent with a single species over the Caribbean, but not over the entire Americas. Haplotype network suggests that populations maintain lively gene flow between the Caribbean and North America. Combined with prior evidence from spider genera of different dispersal ability, these patterns coming from an excellent disperser (Trichonephila) that is species poor and of a relatively homogenous genetic structure, support the IDM predictions.
Dendritic spikes expand the range of well-tolerated population noise structures
Authors: Poleg-Polsky Alon
Published: October 2018

The brain operates surprisingly well despite the noisy nature of individual neurons. The central mechanism for noise mitigation in the nervous system is thought to involve averaging over multiple noise-corrupted inputs. Subsequently, there has been considerable interest recently to identify noise structures that can be integrated linearly in a way that preserves reliable signal encoding. By analyzing realistic synaptic integration in biophysically accurate neuronal models, I report a complementary de-noising approach that is mediated by focal dendritic spikes. Dendritic spikes might seem to be unlikely candidates for noise reduction due to their miniscule integration compartments and poor averaging abilities. Nonetheless, the extra thresholding step introduced by dendritic spike generation increases neuronal performance for a broad category of computational tasks, including analog and binary discrimination, as well as for a range of correlated and uncorrelated noise structures, some of which cannot be adequately resolved with averaging. This property of active dendrites compensates for compartment size constraints and expands the repertoire of brain states and presynaptic population activity dynamics can be reliably de-noised by biologically-realistic neurons.

Significance Statement

Noise, or random variability, is a prominent feature of the neuronal code and poses a fundamental challenge for information processing. To reconcile the surprisingly accurate output of the brain with the inherent noisiness of biological systems, previous work examined signal integration in idealized neurons. The notion that emerged from this body of work is that accurate signal representation relies largely on input averaging in neuronal dendrites. In contrast to the prevailing view, I show that de-noising in simulated neurons with realistic morphology and biophysical properties follows a different strategy: dendritic spikes act as classifiers that assist in extracting information from a variety of noise structures that have been considered before to be particularly disruptive for reliable brain function.
Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells
Authors: Khetchoumian Konstantin , Balsalobre Aurélio , Mayran Alexandre , Christian Helen , Chénard Valérie , St-Pierre Julie , Drouin Jacques
Published: October 2018

Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the physiological UPR pathway prevents triggering the protein stress response. The pituitary differentiation factor Tpit activates Creb3l2 expression, the Creb3l2-dependent regulatory network as well as the physiological UPR pathway. Thus, Creb3l2 implements high basal translation levels through direct targeting of translation effector genes acting downstream of signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins.
PS membrane asymmetry influences the folding and insertion of a transmembrane helix
Authors: Scott Haden L. , Heberle Frederick A. , Katsaras John , Barrera Francisco N.
Published: October 2018

The plasma membrane (PM) contains an asymmetric distribution of lipids between the inner and outer leaflets of its bilayer. A lipid of special interest in eukaryotic cells is the negatively charged phosphatidylserine (PS). In healthy cells, PS is actively sequestered to the inner leaflet of the PM but can redistribute to the outer leaflet when the cell is damaged or at the onset of apoptosis. The influence of PS asymmetry and its loss on membrane protein structure and organization have not been widely addressed. Marginally hydrophobic membrane proteins contain acidic residues in their transmembrane sequence, which can enable topological transitions after membrane association. The pH low insertion peptide (pHLIP), which undergoes a topological reorientation and inserts into the membrane at acidic pH – as its name implies, is a useful and well-characterized model for studying these transitions. Although it is known that the inclusion of PS in symmetric vesicles affects the membrane insertion process of pHLIP by lowering the pH midpoint of insertion, it is unclear how PS asymmetry influences these topological transitions. Here, we studied pHLIP’s topology using freely-floating asymmetric phosphatidylcholine (PC)/PS vesicles with PS enriched in the inner leaflet. We developed a modified protocol to create asymmetric vesicles containing PS and employed Annexin V labeled with an Alexa 568 fluorophore as a new probe to quantifying PS asymmetry. For pHLIP, membrane insertion was affected by the surface charge difference between bilayer leaflets caused by the asymmetric distribution of charged lipids between the leaflets. We thus conclude that lipid asymmetry can have consequences for the behavior of membrane-associated proteins. A corollary is that model studies using symmetric bilayers to mimic the PM may fail to capture important aspects of protein-membrane interactions.
fruitlessfunctions downstream ofdoublesexto promote sexual dimorphism of the gonad stem cell niche
Authors: Zhou Hong , Whitworth Cale , Pozmanter Caitlin , Neville Megan C. , Van Doren Mark
Published: October 2018

Background

doublesex(dsx) andfruitless(fru) are the two downstream transcription factors that actuateDrosophilasex determination. Whiledsxassistsfruto regulate sex-specific behavior, whetherfrucollaborates withdsxin regulating other aspects of sexual dimorphism remains unknown. One important aspect of sexual dimorphism is found in the gonad stem cell (GSC) niches, where male and female GSCs are regulated to create large numbers of sperm and eggs.

Results

Here we report that Fru is expressed male-specifically in the GSC niche and plays important roles in the development and maintenance of these cells. Unlike previously studied regulation of sex-specific Fru expression, which is regulated by alternative splicing by Transformer (Tra), we show that male-specific expression offruis regulated downstream ofdsx, and is independent of Tra. Regulation offrubydsxalso occurs in the nervous system.frugenetically interacts withdsxto support maintenance of the hub throughout development. Ectopic expression offruinhibited female niche formation and partially masculinized the ovary.fruis also required autonomously for cyst stem cell maintenance and cyst cell survival. Finally, we identified a conserved Dsx binding site upstream offrupromoter P4 that regulatesfruexpression in the hub, indicating thatfruis likely a direct target for transcriptional regulation by Dsx.

Conclusions

These findings demonstrate thatfruacts outside the nervous system to influence sexual dimorphism and reveal a new mechanism for regulating sex-specific expression offruthat is regulated at the transcriptional level by Dsx, rather than by alternative splicing by Tra.
Identifying Emerging Phenomenon in Plant Long Temporal Phenotyping Experiments
Authors: Peng Jiajie , Lu Junya , Hoh Donghee , Dina Ayesha S , Shang Xuequn , Kramer David M , Chen Jin
Published: October 2018

The rapid improvement of phenotyping capability, accuracy, and throughput have greatly increased the volume and diversity of phenomics data. A remaining challenge is an efficient way to identify phenotypic patterns to improve our understanding of the quantitative variation of complex phenotypes, and to attribute gene functions. To address this challenge, we developed a new algorithm to identify emerging phenomena from large-scale temporal plant phenotyping experiments. An emerging phenomenon is defined as a group of genotypes who exhibit a coherent phenotype pattern during a relatively short time. Emerging phenomena are highly transient and diverse, and are dependent in complex ways on both environmental conditions and development. Identifying emerging phenomena may help biologists to examine potential relationships among phenotypes and genotypes in a genetically diverse population and to associate such relationships with the change of environments or development. We present an emerging phenomenon identification tool called Temporal Emerging Phenomenon Finder (TEP-Finder). Using large-scale longitudinal phenomics data as input, TEP-Finder first encodes the complicated phenotypic patterns into a dynamic phenotype network. Then, emerging phenomena in different temporal scales are identified from dynamic phenotype network using a maximal clique based approach. Meanwhile, a directed acyclic network of emerging phenomena is composed to model the relationships among the emerging phenomena. The experiment that compares TEP-Finder with two state-of-art algorithms shows that the emerging phenomena identified by TEP-Finder are more functionally specific, robust, and biologically significant. The source code, manual, and sample data of TEP-Finder are all available at:http://phenomics.uky.edu/TEP-Finder/.
Why do a PhD in geography? A sympathetic response to ‘the career aspirations and expectations of geography students’
Authors: Sigler Thomas , Lieske Scott N. , Charles‐Edwards Elin , Corcoran Jonathan
Published: October 2018

This article provides commentary on the changing nature of the geography PhD. Taking as a point of departure Rae Dufty‐Jones's article on the career aspirations and expectations of geography doctoral students published in this journal earlier this year, we frame the paper around a series of propositions that prospective higher degree candidates may find useful. We buttress Dufty‐Jones's argument with numerical evidence that the “supply” of Australian PhDs outstrips “demand” by any reasonable measure. This evidence brings to light the question of whether a PhD in geography is meant to serve its traditional function as a threshold for an academic career and whether those pursuing non‐academic pathways should invest their time and effort in what may have become a “gladiatorial” pursuit. While the challenges facing PhD candidates are not insurmountable, they are not trivial. To optimise the experience and outcomes of a PhD, the needs and aspirations of candidates must be balanced, therefore, against the levels of support provided by universities. Candidates thus need to understand how such professional and personal aspirations fit in the contemporary higher education landscape and to appreciate what value a PhD holds—both to the individual and to society more broadly. We suggest two solutions to the pessimism of neoliberalisation and “massification”: greater emphasis on a terminal master's degree in geography and insistence that geographers promote disciplinary visibility to the greatest extent possible, with the hope that geographical approaches to problem‐solving are increasingly recognised across industry and government.
Unsafe drinking water quality in remote Western Australian Aboriginal communities
Authors: Rajapakse Jay , Rainer‐Smith Semone , Millar Graeme J. , Grace Peter , Hutton Allison , Hoy Wendy , Jeffries‐Stokes Christine , Hudson Brian
Published: October 2018

Chronic kidney disease (CKD) is important in the fields of public health and health geography because of its heavy burden on the health system and high cost of treatment in its advanced stages. The causes of CKD are associated with diabetes and hypertension, but in some parts of the world, the disease occurs in the absence of these factors. Researchers identify this condition as CKD of “unknown” causes (CKDu). CKDu is a multi‐factored health problem and one suspected causal factor is contaminated drinking water. The disease occurs globally but is found in particularly high concentrations among people of certain ethnic and disadvantaged social groups living in very different locations around the world. CKD has become endemic in Western Australia where hospital admissions for Aboriginal people requiring renal dialysis or treatment for diabetes are much higher than for the general population. The possible proportions of CKDu cases among the CKD patients are unknown. This study examines the drinking water quality among communities such as these. Water chemistry analysis in these areas indicates that the nitrate and uranium content greatly exceed officially recommended levels. Most of these communities rely on raw groundwater to supply their domestic needs, and it is very likely that the people are unwittingly ingesting high levels of nitrates and uranium, probably including uranyl nitrates. Very few such remote communities have access to treated drinking water, and cost‐effective water treatment systems are required to provide potable water at the local scale.
The effect of dexmedetomidine on delirium and agitation in patients in intensive care: systematic review and meta‐analysis with trial sequential analysis
Authors: Ng K. T. , Shubash C. J. , Chong J. S.
Published: October 2018

Delirium is common in intensive care patients. Dexmedetomidine is increasingly used for sedation in this setting, but its effect on delirium remains unclear. The primary aim of this review was to examine whether dexmedetomidine reduces the incidence of delirium and agitation in intensive care patients. We sought randomised clinical trials in MEDLINE, EMBASE, PubMed and CENTRAL from their inception until June 2018. Observational studies, case reports, case series and non‐systematic reviews were excluded. Twenty‐five trials including 3240 patients were eligible for inclusion in the data synthesis. In the patients who received dexmedetomidine (eight trials, 1425 patients), delirium was reduced, odds ratio (95%CI) 0.36 (0.26–0.51), p < 0.001 and high quality of evidence. The use of dexmedetomidine was associated with a reduced incidence of agitation, OR (95%CI) 0.34 (0.20–0.59), p < 0.001, moderate quality of evidence. Patients who were randomly assigned to dexmedetomidine had a significantly higher incidence of bradycardia, OR (95%CI) 2.18 (1.46–3.24), p < 0.001, moderate quality of evidence; and hypotension, OR (95%CI) 1.89 (1.48–2.41), p < 0.001, high quality of evidence. We found no evidence of an effect on mortality, OR (95%CI) 0.86 (0.66–1.10), p = 0.23, moderate quality of evidence. The trial sequential analyses for the incidence of delirium, bradycardia and hypotension was conclusive but not for the incidence of agitation and mortality. In summary, this meta‐analysis suggests that dexmedetomidine reduces the incidence of delirium and agitation in intensive care patients. The general quality of evidence ranged from moderate to high.
The impact of emergency department patient‐controlled analgesia (PCA) on the incidence of chronic pain following trauma and non‐traumatic abdominal pain
Authors: Rockett M. , Creanor S. , Squire R. , Barton A. , Benger J. , Cocking L. , Ewings P. , Eyre V. , Smith J. E.
Published: October 2018

The effect of patient‐controlled analgesia during the emergency phase of care on the prevalence of persistent pain is unkown. We studied individuals with traumatic injuries or abdominal pain 6 months after hospital admission via the emergency department using an opportunistic observational study design. This was conducted using postal questionnaires that were sent to participants recruited to the multi‐centre pain solutions in the emergency setting study. Patients with prior chronic pain states or opioid use were not studied. Questionnaires included the EQ5D, the Brief Pain Inventory and the Hospital Anxiety and Depression scale. Overall, 141 out of 286 (49% 95%CI 44–56%) patients were included in this follow‐up study. Participants presenting with trauma were more likely to develop persistent pain than those presenting with abdominal pain, 45 out of 64 (70%) vs. 24 out of 77 (31%); 95%CI 24–54%, p < 0.001. There were no statistically significant associations between persistent pain and analgesic modality during hospital admission, age or sex. Across both abdominal pain and traumatic injury groups, participants with persistent pain had lower EQ5D mobility scores, worse overall health and higher anxiety and depression scores (p < 0.05). In the abdominal pain group, 13 out of 50 (26%) patients using patient‐controlled analgesia developed persistent pain vs. 11 out of 27 (41%) of those with usual treatment; 95%CI for difference (control – patient‐controlled analgesia) −8 to 39%, p = 0.183. Acute pain scores at the time of hospital admission were higher in participants who developed persistent pain; 95%CI 0.7–23.6, p = 0.039. For traumatic pain, 25 out of 35 (71%) patients given patient‐controlled analgesia developed persistent pain vs. 20 out of 29 (69%) patients with usual treatment; 95%CI −30 to 24%, p = 0.830. Persistent pain is common 6 months after hospital admission, particularly following trauma. The study findings suggest that it may be possible to reduce persistent pain (at least in patients with abdominal pain) by delivering better acute pain management. Further research is needed to confirm this hypothesis.
Risk of preterm birth, low birthweight and small‐for‐gestational‐age infants in pregnancies with adenomyosis: A cohort study of the Japan Environment and Children's Study
Authors: Yamaguchi Akiko , Kyozuka Hyo , Fujimori Keiya , Hosoya Mitsuaki , Yasumura Seiji , Yokoyama Tadahiko , Sato Akiko , Hashimoto Koichi ,   The Japan Environment and Children's Study Group
Published: October 2018

Introduction

This study evaluated the risk of preterm birth, low birthweight and small‐for‐gestational‐age neonates born to mothers with adenomyosis during pregnancy.

Material and methods

We used the results of a Japanese nationwide prospective birth cohort study, identifying 93 668 singleton deliveries from 2011 to 2014. We identified 314 pregnancies with adenomyosis using self‐reported questionnaires. Multiple logistic regression analyses were conducted to examine whether adenomyosis was associated with adverse pregnancy outcome. Maternal age, smoking status, method of conception, history of parity, fibroids, endometriosis and body mass index before pregnancy were analyzed as confounding factors.

Results

Multiple logistic regression analysis showed that pregnancy with adenomyosis was a risk factor for preterm birth at less than 37 weeks (adjusted odds ratio [aOR: 2.49, 95% confidence interval [CI] 1.89‐3.41), preterm birth at less than 34 weeks (aOR 1.91, 95% CI 1.02‐3.55), low birthweight <2500 g (aOR 1.83, 95% CI 1.36‐2.45), low birthweight <1500 g (aOR 2.39, 95% CI 1.20‐4.77) and small‐for‐gestational‐age neonates (aOR 1.68, 95% CI 1.13‐2.51).

Conclusions

This study found that pregnancy with adenomyosis was associated with preterm birth, low birthweight and small‐for‐gestational‐age neonates.
Effects of bifocals on visual acuity in children with Down syndrome: a randomized controlled trial
Authors: de Weger Christine , Boonstra Nienke , Goossens Jeroen
Published: October 2018

Purpose

Children with Down syndrome (DS) typically have reduced visual acuity (VA) and accommodation lag, but it is unclear whether prescribed glasses should correct both distance VA (DVA) and near VA (NVA) due to the lack of RCTs. We therefore conducted a multicentre RCT to compare the effects of bifocals designed to correct both DVA and NVA with distance‐correcting unifocal glasses in children with DS.

Methods

A total of 119 children with DS, aged 2–16, were randomly allocated for bifocal or unifocal glasses (with full correction of refraction error in cycloplegia) in 14 Dutch hospitals and followed during 1 year. VA data were analysed in relation to baseline VA with ancova.

Results

Treatment groups showed no differences at baseline. Shortly after receiving new corrections (~6 weeks), uncrowded NVA (bifocals 0.18 ± 0.33 LogMar; unifocals 0.09 ± 0.19 LogMar) and crowded NVA with bifocals (bifocals 0.13 ± 0.36 LogMar; unifocals 0.08 ± 0.33 LogMar) were significantly better than at baseline, but these short‐term improvements in NVA were not significantly different between the two treatments (p > 0.151). The 1‐year treatment differences were as follows: significantly larger improvement for bifocals compared to unifocals in both uncrowded NVA (bifocals 0.23 ± 0.29 LogMar, unifocals 0.12 ± 0.30 LogMar, p = 0.045) and crowded NVA (bifocals 0.31 ± 0.28 LogMar; unifocals 0.16 ± 0.30 LogMar, p = 0.017). Improvements in DVA were comparable (bifocals 0.07 ± 0.21 LogMar, unifocals 0.08 ± 0.22 LogMar, p = 0.565). Children with poor baseline VA improved more. Accommodation lag stayed unchanged.

Conclusion

After one year, bifocals with full correction of ametropia led to significantly larger improvement of both uncrowded NVA and crowded NVA in children with DS with accommodation lag compared to unifocals.
Effects of teaching planning strategies to first‐grade writers
Authors: Arrimada María , Torrance Mark , Fidalgo Raquel
Published: October 2018

Background

Traditionally writing instruction at the start of school has focused on developing students’ ability to spell and handwrite. Teaching children explicit self‐regulatory strategies for developing content and structure for their text has proved effective for students in later grades of primary (elementary) education.

Aims

The present study aims to determine whether first‐grade students benefit from learning higher‐level self‐regulating strategies for explicit planning of content and structure.

Sample

Five mixed‐ability Spanish first‐grade classes were randomly assigned either to an experimental condition that received strategy‐focused instruction (three classes, N = 62), or to a practice‐matched control condition (two classes, N = 39).

Method

Over 10, 50‐min sessions, the intervention taught strategies for writing stories. Writing performance was assessed prior to intervention, immediately after intervention and 7 weeks post‐intervention, in terms of both text features associated with written narratives and by holistic quality ratings.

Results

Students who received the intervention subsequently produced texts with better structure, coherence, and quality, and a larger number of features associated with narrative texts. These effects remained at follow‐up and were not present in the control condition.

Conclusion

Our findings indicate that teaching explicit strategies for planning text content and structure benefits young writers even when spelling and handwriting skills are not yet well established.
Classroom identification in ethnic minority and majority students: Effects of relationships and ethnic composition
Authors: Thijs Jochem , Keim Abigail C. , Geerlings Jolien
Published: October 2018

Background

Many studies have shown that school belonging is crucial for students’ school adjustment, but the construct has been operationalized in different ways. Moreover, most research has focused on adolescents and not compared its antecedents for ethnic minority versus majority students.

Aims

Based on Goodenow and Grady's (1993) seminal paper, we examined classroom identification as a central aspect of school belonging in minority and majority preadolescents, and predicted it from relationships with peers and teachers, taking into account classroom ethnic composition and perceived multicultural teaching.

Sample

Participants were 485 grade 4–6 students from 39 classrooms in Dutch primary schools. Of these children, 68 had a Turkish background, 72 had a Moroccan background, and 345 had a native Dutch background.

Methods

Participants completed questionnaires at two waves (4.5 months apart). We used self‐reports to measure classroom identification at both waves, and student–teacher relationship closeness and conflict, multicultural teaching, and peer friendship and rejection at Wave 1. We conducted multilevel analyses to predict classroom identification at Wave 2, while controlling for classroom identification at Wave 1.

Results

Children of all ethnicities reported more classroom identification over time if they were less rejected by their peers and had more co‐ethnic classmates. For minority children, both closeness and conflict with the teacher predicted less identification, but the effect of conflict appeared to result from their ethnic underrepresentation in the classroom.

Conclusions

Negative peer relationships can undermine classroom identification, and the student–teacher relationship has special significance for ethnic minority students.