bluuebunny/crossref_metadata_2025 huggingface dataset:
Antenatal staging of congenital lower urinary tract obstruction
Authors: Fontanella F. , van Scheltema P. N. Adama , Duin L. , Cohen‐Overbeek T. E. , Pajkrt E. , Bekker M. N. , Willekes C. , Oepkes D. , Bilardo C. M.
Published: July 2018

Objective

To propose a staging system for congenital lower urinary tract obstruction (LUTO) capable of predicting the severity of the condition and its prognosis.

Methods

This was a national retrospective study carried out at the eight Academic Hospitals in The Netherlands. We collected prenatal and postnatal data of fetuses at high risk of isolated LUTO that were managed conservatively. Postnatal renal function was assessed by the estimated glomerular filtration rate (eGFR), calculated using the Schwartz formula, considering the length of the infant and the creatinine nadir in the first year after birth. Receiver–operating characteristics (ROC) curve analysis, univariate analysis and multivariate logistic regression analysis with stepwise backward elimination were performed in order to identify the best antenatal predictors of perinatal mortality and postnatal renal function.

Results

In total, 261 fetuses suspected of having LUTO and managed conservatively were included in the study. The pregnancy was terminated in 110 cases and perinatal death occurred in 35 cases. Gestational age at appearance of oligohydramnios showed excellent accuracy in predicting the risk of perinatal mortality with an area under the ROC curve of 0.95 (P < 0.001) and an optimal cut‐off at 26 weeks' gestation. Fetuses with normal amniotic fluid (AF) volume at 26 weeks' gestation presented with low risk of poor outcome and were therefore defined as cases with mild LUTO. In fetuses referred before the 26th week of gestation, the urinary bladder volume (BV) was the best unique predictor of perinatal mortality. ROC curve analysis identified a BV of 5.4 cm3 and appearance of oligohydramnios at 20 weeks as the best threshold for predicting an adverse outcome. LUTO cases with a BV ≥ 5.4 cm3 or abnormal AF volume before 20 weeks' gestation were defined as severe and those with BV < 5.4 cm3 and normal AF volume at the 20 weeks' scan were defined as moderate. Risk of perinatal mortality significantly increased according to the stage of severity, from mild to moderate to severe stage, from 9% to 26% to 55%, respectively. Similarly, risk of severely impaired renal function increased from 11% to 31% to 44%, for mild, moderate and severe LUTO, respectively.

Conclusions

Gestational age at appearance of oligo‐ or anhydramnios and BV at diagnosis can accurately predict mortality and morbidity in fetuses with LUTO. Our proposed staging system can triage reliably fetuses with LUTO and predict the severity of the condition and its prognosis. Copyright © 2018 ISUOG. Published by John Wiley & Sons Ltd.
Climate history of Russia and the Soviet Union
Authors: Bruno Andy
Published: July 2018

Russia and the Soviet Union bear great significance for global climate history, but scholarship on this region is still only beginning to develop as a field. While the historiographies of other geographical locations have matured over the past decade, works concerning Russia thus far have appeared in a piecemeal and somewhat disconnected fashion, not yet cohering in a systematic way. Instead, there exist several insightful threads in the environmental history literature on climate. Scholars have examined the history of climate science in Russia, extending from the research of the Academy of Sciences in the eighteenth century to the global thinking about climate change in the late twentieth century. Social scientists have explored the historical roots of Russia's contemporary climate policy. Disasters related to climate have long attracted the attention of historians, though newer works are more in tune with contemporary scholarship on vulnerability and risk. There has also been movement to analyze the varied experiences of the cold in Russia over the long haul. Making an asset out of its apparent lower stage of development, the field of Russian climate history has an opportunity to directly enter advanced scholarly conversations by focusing on the ubiquitous human experiences with climate. Doing so could allow Russian climate history to acquire a position as an innovator among global climate histories.

This article is categorized under:

Climate, History, Society, Culture > World Historical Perspectives
New physics opportunities for long-lived particles at electron-proton colliders
Authors: Curtin David , Deshpande Kaustubh , Fischer Oliver , Zurita José
Published: July 2018

Abstract

Future electron-proton collider proposals like the LHeC or the FCC-eh can supply ab−1of collisions with a center-of-mass energy in the TeV range, while maintaining a clean experimental environment more commonly associated with lepton colliders. We point out that this makese−pcolliders ideally suited to probe BSM signatures with final states that look like “hadronic noise” in the high-energy, pile-up-rich environment ofppcolliders. We focus on the generic vector boson fusion production mechanism, which is available for all BSM particles with electroweak charges at mass scales far above the reach of most lepton colliders. This is in contrast to previous BSM studies at these machines, which focused on BSM processes with large production rates from the asymmetric initial state. We propose to exploit the unique experimental environment in the search for long-lived particle signals arising from Higgsinos or exotic Higgs decays. Ate−pcolliders, the soft decay products of long-lived Higgsino can be explicitly reconstructed (“displaced single pion”), and very short lifetimes can be probed. We find thate−pcolliders can explore significant regions of BSM parameter space inaccessible to other collider searches, with important implications for the design of such machines.
Judicial Remedies for Forced Slum Evictions in Bangladesh: An Analysis of the Structural Injunction
Authors: NAZNIN S M Atia , ALAM Shawkat
Published: July 2018

The adoption of weak remedies, such as declarations or recommendations by the Bangladesh Supreme Court in litigations on state-induced forced slum evictions, significantly contributes to the tardy implementation of court orders. In this context, there is a growing global consensus on the structural injunction—a remedy that enables judges to monitor and bring about governmental compliance with judicial orders of social rights litigation. The Bangladesh Supreme Court faces several real and compelling challenges relating to its constitutional authority and institutional capacity that hinder remedial innovation. Through examining relevant constitutional provisions, judicial approach, and comparative examples, this article argues that the court has the capacity to overcome these constraints. Thus, it advocates judicial reform in Bangladesh to offset the state’s often arbitrary interference with the basic necessity of housing of the slum dwellers.
Building diverse careers in clinical and translational research: Evaluation of a certificate program in translational research
Authors: Comeau Dawn L. , Alvarez Jessica A. , Bhatti Pamela , Paulsen Douglas F. , Quarshie Alexander , Escoffery Cam , Ofotukun Igho , Eisen Hannah , Ziegler Thomas R. , Blumberg Henry M.
Published: July 2018

Introduction

The Certificate Program in Translational Research (CPTR) at the Georgia Clinical and Translational Science Alliance provides Ph.D. students, postdoctoral fellows and faculty with didactic, mentored, and experiential training in clinical and translational research.

Methods

Quantitative evaluation includes tracking trainee competency, publications, grants and careers in clinical and translational research. Qualitative evaluation includes interviews with trainees about program experiences.

Results

The CPTR provided knowledge and skills in clinical and translational research through coursework, clinical rotations, and collaboration with interdisciplinary scientists. Trainees reported increased confidence in 22 program competencies. Trainees have published more than 290 peer-reviewed articles and received over $4 million in grants from the NIH, over $15 million from the U.S. Department of Defense, and more than $300,000 from foundations. Trainees who completed the program remained in clinical and translational research.

Conclusions

Programs like the CPTR are needed to train investigators to advance biomedical discoveries into population health.
Effect of Herbicide Management Practices Used by Invasive Plant Managers onBerteroa incana(Hoary Alyssum) Seed Biology and Control
Authors: Menalled Uriel D. , Davis Stacy C. , Mangold Jane M.
Published: July 2018

Hoary alyssum [Berteroa incana(L.) DC.] is a nonnative invasive forb that is noxious in California, Idaho, Michigan, Montana, Oregon, Washington, Wyoming, Alberta, British Columbia, and Saskatchewan. ManagingB. incanais difficult, because it has an extended flowering period, during which plants simultaneously flower and produce seeds. Consequently, poorly timed herbicide applications may killB. incanaflowers but not prevent viable seed production. We examined how different herbicide management practices used by invasive plant managers affectedB. incanaseed production and viability the year of application as well as population density 1 yr after application. Professional invasive plant managers sprayedB. incanawith various herbicides as part of their current management practices at six sites in southwestern Montana in summer 2016. We collectedB. incanaplants at 4 wk postapplication for seed biology analyses. Across the six sites, nonsprayedB. incanaproduced 5 to 1,855 seeds plant−1and averaged 429 seeds plant−1. Seed production was reduced by 64% to 99% with 7 of the 11 herbicide applications.Berteroa incanaseed viability in nonsprayed areas averaged 53% and ranged from 36% to 73% across the sites. Nine of the 10 herbicide applications used by invasive plant managers reduced seed viability 49% to 100%. Few of the herbicide management practices reducedB. incana’s population density the following growing season, suggesting that managers should expect reoccurring infestations at least 1 yr after application. Our results show that invasive plant managers can reduceB. incanaviable seed production even when spraying plants that have flowered and formed seed pods. However, sites may need to be monitored for additional years to treat reoccurring infestations.
Resting-State Functional Brain Connectivity Best Predicts the Personality Dimension of Openness to Experience
Authors: Dubois Julien , Galdi Paola , Han Yanting , Paul Lynn K. , Adolphs Ralph
Published: July 2018

Personality neuroscience aims to find associations between brain measures and personality traits. Findings to date have been severely limited by a number of factors, including small sample size and omission of out-of-sample prediction. We capitalized on the recent availability of a large database, together with the emergence of specific criteria for best practices in neuroimaging studies of individual differences. We analyzed resting-state functional magnetic resonance imaging (fMRI) data from 884 young healthy adults in the Human Connectome Project database. We attempted to predict personality traits from the “Big Five,” as assessed with the Neuroticism/Extraversion/Openness Five-Factor Inventory test, using individual functional connectivity matrices. After regressing out potential confounds (such as age, sex, handedness, and fluid intelligence), we used a cross-validated framework, together with test-retest replication (across two sessions of resting-state fMRI for each subject), to quantify how well the neuroimaging data could predict each of the five personality factors. We tested three different (published) denoising strategies for the fMRI data, two intersubject alignment and brain parcellation schemes, and three different linear models for prediction. As measurement noise is known to moderate statistical relationships, we performed final prediction analyses using average connectivity across both imaging sessions (1 hr of data), with the analysis pipeline that yielded the highest predictability overall. Across all results (test/retest; three denoising strategies; two alignment schemes; three models), Openness to experience emerged as the only reliably predicted personality factor. Using the full hour of resting-state data and the best pipeline, we could predict Openness to experience (NEOFAC_O:r=.24,R2=.024) almost as well as we could predict the score on a 24-item intelligence test (PMAT24_A_CR:r=.26,R2=.044). Other factors (Extraversion, Neuroticism, Agreeableness, and Conscientiousness) yielded weaker predictions across results that were not statistically significant under permutation testing. We also derived two superordinate personality factors (“α” and “β”) from a principal components analysis of the Neuroticism/Extraversion/Openness Five-Factor Inventory factor scores, thereby reducing noise and enhancing the precision of these measures of personality. We could account for 5% of the variance in the β superordinate factor (r=.27,R2=.050), which loads highly on Openness to experience. We conclude with a discussion of the potential for predicting personality from neuroimaging data and make specific recommendations for the field.
Lost in Space: Geolocation in Event Data
Authors: Lee Sophie J. , Liu Howard , Ward Michael D.
Published: July 2018

Improving geolocation accuracy in text data has long been a goal of automated text processing. We depart from the conventional method and introduce a two-stage supervised machine-learning algorithm that evaluates each location mention to be either correct or incorrect. We extract contextual information from texts, i.e., N-gram patterns for location words, mention frequency, and the context of sentences containing location words. We then estimate model parameters using a training data set and use this model to predict whether a location word in the test data set accurately represents the location of an event. We demonstrate these steps by constructing customized geolocation event data at the subnational level using news articles collected from around the world. The results show that the proposed algorithm outperforms existing geocoders even in a case added post hoc to test the generality of the developed algorithm.
DIFFERENTIALS IN SEXUAL AND REPRODUCTIVE
HEALTH KNOWLEDGE AMONG EAST MALAYSIAN
ADOLESCENTS
Authors: Awang Halimah , Low Wah Yun , Tong Wen Ting , Tan Lih Yoong , Cheah Whye Lian , Benedict Lasimbang Helen , Mohd Hassan Hamizah
Published: July 2018

The aim of this study was to assess the knowledge of
East Malaysian adolescents on sexual and
reproductive health issues. Data were collected in
March–July 2015 from 2858 adolescents aged 13–18
years from selected East Malaysian secondary schools
using a self-administered questionnaire. Twelve
items relating to sexual and reproductive health
were used to measure respondents’ knowledge based on
their responses ‘True’, ‘False’ or ‘Don’t know’,
with the proportion of correct answers being the
variable of interest. Cronbach’s alpha for the
twelve items was 0.761 and the mean knowledge score
was 6.8. While the majority of the respondents knew
that a woman can get pregnant if she has sex with a
man and that HIV and AIDS can be transmitted through
sexual intercourse, knowledge about Malaysia’s
abortion laws, that a woman can get pregnant if she
has sex only once and that people with sexually
transmitted infections may look healthy was poor.
Older respondents and those from urban schools
reported significantly higher knowledge than younger
respondents and those from rural schools,
respectively. More emphasis should be given in
schools to the specific topics for which low levels
of sexual and reproductive health knowledge were
found, with greater attention being given to younger
adolescents and those in rural areas.
On the iteration of quasimeromorphic mappings
Authors: WARREN LUKE
Published: July 2018

The Fatou–Julia theory for rational functions has been extended both to transcendental meromorphic functions and more recently to several different types of quasiregular mappings in higher dimensions. We extend the iterative theory to quasimeromorphic mappings with an essential singularity at infinity and at least one pole, constructing the Julia set for these maps. We show that this Julia set shares many properties with those for transcendental meromorphic functions and for quasiregular mappings of punctured space.
Sacubitril/Valsartan: potential treatment for paediatric heart failure
Authors: Das Bibhuti B. , Scholl Frank , Vandale Breanna , Chrisant Maryanne
Published: July 2018

The Prospective comparison of angiotensin receptor antagonist Valsartan and neprilysin inhibitor Sacubitril with angiotensin-converting enzyme inhibitor (enalapril) to determine impact on Global Mortality and Morbidity in Heart Failure trial has demonstrated that Sacubitril/Valsartan is superior to Enalapril in reducing the risks of both sudden cardiac death and death from worsening heart failure. This novel combination, Sacubitril/Valsartan, is also shown to reduce the risk of hospitalisation and progression of heart failure in adults. However, the benefit of Sacubitril/Valsartan in paediatric heart failure patients is unknown. In this review, we discuss the similarities and differences in pathophysiology of heart failure in children versus adults, and the potential role of Sacubitril/Valsartan in paediatric heart failure patients.
Language background affects online word order processing in a second language but not offline
Authors: ANDERSSON ANNIKA , SAYEHLI SUSAN , GULLBERG MARIANNE
Published: July 2018

This study examines possible crosslinguistic influence on basic word order processing in a second language (L2). Targeting Swedish V2 word order we investigate adult German learners (+V2 in the L1) and English learners (-V2 in the L1) of Swedish who are matched for proficiency. We report results from two offline behavioural tasks (written production, metalinguistic judgements), and online processing as measured by event-related potentials (ERPs). All groups showed sensitivity to word order violations behaviourally and neurocognitively. Behaviourally, the learners differed from the native speakers only on judgements. Crucially, they did not differ from each other. Neurocognitively, all groups showed a similar increased centro-parietal P600 ERP-effect, but German learners (+V2) displayed more nativelike anterior ERP-effects than English learners (-V2). The results suggest crosslinguistic influence in that the presence of a similar word order in the L1 can facilitate online processing in an L2 – even if no offline behavioural effects are discerned.
SERIES SOLUTION OF LAPLACE PROBLEMS
Authors: TREFETHEN LLOYD N.
Published: July 2018

At the ANZIAM conference in Hobart in February 2018, there were several talks on the solution of Laplace problems in multiply connected domains by means of conformal mapping. It appears to be not widely known that such problems can also be solved by the elementary method of series expansions with coefficients determined by least-squares fitting on the boundary. (These are not convergent series; the coefficients depend on the degree of the approximation.) Here we give a tutorial introduction to this method, which converges at an exponential rate if the boundary data are sufficiently well-behaved. The mathematical foundations go back to Runge in 1885 and Walsh in 1929. One of our examples involves an approximate Cantor set with up to 2048 components.
Party politics at the water’s edge: contestation of military operations in Europe
Authors: Wagner Wolfgang , Herranz-Surrallés Anna , Kaarbo Juliet , Ostermann Falk
Published: July 2018

This paper contributes to current debates on the politicization of international politics by examining party-political contestation of peace and security missions. It is guided by two inter-related questions, (a) to what extent deployment decisions are contested amongst political parties and (b) what drives such contestation. We examine data from a new data set on parliamentary votes on deployment decisions in France, Germany, Spain, and the United Kingdom and from the Chapel Hill Expert Survey. Against conventional wisdom and in an effort to address the often-overlooked role of political parties, we find that military deployments have been systematically contested amongst political parties across Europe. Further, we find that contestation is driven by the left/right axis, as opposed to newer cleavages captured here by the so-called gal/tan axis. We also find evidence that patterns of contestation depend on parties’ positions in government or opposition, a factor we relate to bureaucratic and international pressures on the parties in office, and to political opportunities for opposition parties.
Transnational REDD+Rule Making: The Regulatory Landscape for REDD+ Implementation in Latin America
Authors: Recio María Eugenia
Published: July 2018

REDD+ – an incentive mechanism to reduce deforestation and associated greenhouse gas emissions in developing countries – was developed under the United Nations Framework Convention on Climate Change (UNFCCC) and subsequently included in the Paris Agreement. Its early implementation activities have highlighted the role of certain intergovernmental actors: REDD+financing initiatives, including the World Bank’s Forest Carbon Partnership Facility and Forest Investment Programme, and UN-REDD, a collaborative programme involving three agencies of the United Nations. By setting conditions for the provision of support for REDD+, these initiatives have actively and influentially engaged in REDD+rule making. This article focuses on the regulatory landscape for REDD+and examines rules developed under the UNFCCC and elaborated by the REDD+financing initiatives, using examples from the Latin American region. The analysis shows that informal lawmaking plays a more relevant role in REDD+rule making than international formal law, and has demonstrated legal and practical effects. However, informality can also tilt power relations between donor and recipient countries, which could jeopardize the legitimacy of transnational rule making.
Carotid Artery Atherosclerosis: A Review on Heritability and Genetics
Authors: Forgo Bianka , Medda Emanuela , Hernyes Anita , Szalontai Laszlo , Tarnoki David Laszlo , Tarnoki Adam Domonkos
Published: July 2018

Carotid atherosclerosis (CAS) is associated with increased cardiovascular risk, and therefore, assessing the genetic versus environmental background of CAS traits is of key importance. Carotid intima-media-thickness and plaque characteristics seem to be moderately heritable, with remarkable differences in both heritability and presence or severity of these traits among ethnicities. Although the considerable role of additive genetic effects is obvious, based on the results so far, there is an important emphasis on non-shared environmental factors as well. We aimed to collect and summarize the papers that investigate twin and family studies assessing the phenotypic variance attributable to genetic associations with CAS. Genes in relation to CAS markers were overviewed with a focus on genetic association studies and genome-wide association studies. Although the role of certain genes is confirmed by studies conducted on large populations and meta-analyses, many of them show conflicting results. A great focus should be on future studies elucidating the exact pathomechanism of these genes in CAS in order to imply them as novel therapeutic targets.
How Consistent are Genetic Factors in Explaining Leisure-Time Physical Activity and Sport Participation? The Portuguese Healthy Families Study
Authors: Pereira Sara , Katzmarzyk Peter T. , Gomes Thayse N. , Elston Robert , Maia José
Published: July 2018

This study investigates how consistent genetic factors are, as measured by heritability estimates (h2), in the leisure-time physical activity index (LTPAI) and sport participation index (SPI) from early (10–14 yrs) to late adolescence (15–19 yrs). The sample comprises 12,385 subjects from 3,378 Portuguese nuclear families. Height and weight were measured and body mass index (BMI) was calculated, and the LTPAI and SPI were estimated by questionnaire. Socioeconomic status (SES) was assessed by parental occupation. Analyses were done using S.A.G.E. software. Our results showed that h2 estimates for the LTPAI and SPI in the two age groups (10–14 yrs and 15–19 yrs) were stable: for the LTPAI, h2 = 0.297 and 0.322, respectively; and for the SPI, h2 = 0.413 and 0.428, respectively. Sibling correlations and environmental correlations are higher in the younger age group for both the LTPAI and the SPI. Spousal correlations are higher in the younger age group for the LTPAI and lower for the SPI than the older group. Parent–offspring correlations are similar in both age groups for the LTPAI and SPI. In conclusion, the influence of genetic factors on physical activity and sport participation remains stable across age in adolescence. However, variation in sibling correlations — in particular, environmental correlations — was observed. These findings suggest that shared/non-shared environmental factors express different degrees of importance across age. Future intervention programs aiming to promote change in behaviors need to consider these results to bring about positive changes in physical activity and sport participation behaviors within the family setting.
Atmospheric Modeling of 137Cs Plumes From the Fukushima Daiichi Nuclear Power Plant—Evaluation of the Model Intercomparison Data of the Science Council of Japan
Authors: Kitayama K. , Morino Y. , Takigawa M. , Nakajima T. , Hayami H. , Nagai H. , Terada H. , Saito K. , Shimbori T. , Kajino M. , Sekiyama T. T. , Didier D. , Mathieu A. , Quélo D. , Ohara T. , Tsuruta H. , Oura Y. , Ebihara M. , Moriguchi Y. , Shibata T.
Published: July 2018

Since the Fukushima Daiichi Nuclear Power Plant (FDNPP) accident in March 2011, atmospheric simulation models have improved our understanding of the atmospheric behavior of radionuclides. Model intercomparisons provide valuable and useful information for evaluating the validity and variability of individual model results. In this study, we compared results of seven atmospheric transport models used to simulate 137Cs released from the FDNPP to the atmosphere. All model results used in this analysis had been submitted for a model intercomparison project of the Science Council of Japan (2014, http://www.scj.go.jp/en/report/index.html). Here we assessed model performance by comparing model results with observed hourly atmospheric concentrations of 137Cs, with a particular focus on nine plumes over the Tohoku and Kanto regions. The intercomparison results showed that model performance in reproducing 137Cs concentrations was highly variable among different models and plumes. In general, models better reproduced plumes that passed over many observation stations. The performance among the models was consistent with the simulated wind fields and the source terms used. We also assessed model performance in relation to accumulated 137Cs deposition. Simulated areas of high 137Cs deposition were consistent with the simulated 137Cs plume pathways, though the models that best simulated atmospheric 137Cs concentrations were different from those that best simulated deposition. The ensemble mean of all models consistently reproduced atmospheric 137Cs concentrations and deposition well, suggesting that use of a multimodel ensemble results in more effective and consistent model performance.
Microfluidic-based flexible reflective multicolor display
Authors: Kobayashi Kazuhiro , Onoe Hiroaki
Published: July 2018

This paper describes a microfluidic-based flexible reflective display constructed using dyed water droplets and air gaps as pixel elements. Our display is composed of a flexible polydimethylsiloxane sheet with a connected pixel-patterned microchannel. Several types of dyed water droplets and air gaps are sequentially introduced to the microchannel through a suction process to display a multicolor image. The displayed image is stable and can be retained without an energy supply. To ensure that images are displayed correctly, the geometric parameters of the dot pixel design and minimum differential pressure necessary to drive the water droplets are evaluated. As a demonstration, we successfully display three-color dot-matrix reflective images and bitmap characters in the microchannel. Our proposed method can be applied to energy-less and color-changeable displays for use in future daily-life accessories, such as bags, shoes, and clothes, and can change the surface color and pattern of these accessories.
Network-based approach to prediction and population-based validation of in silico drug repurposing
Authors: Cheng Feixiong , Desai Rishi J. , Handy Diane E. , Wang Ruisheng , Schneeweiss Sebastian , Barabási Albert-László , Loscalzo Joseph
Published: July 2018

Here we identify hundreds of new drug-disease associations for over 900 FDA-approved drugs by quantifying the network proximity of disease genes and drug targets in the human (protein–protein) interactome. We select four network-predicted associations to test their causal relationship using large healthcare databases with over 220 million patients and state-of-the-art pharmacoepidemiologic analyses. Using propensity score matching, two of four network-based predictions are validated in patient-level data: carbamazepine is associated with an increased risk of coronary artery disease (CAD) [hazard ratio (HR) 1.56, 95% confidence interval (CI) 1.12–2.18], and hydroxychloroquine is associated with a decreased risk of CAD (HR 0.76, 95% CI 0.59–0.97). In vitro experiments show that hydroxychloroquine attenuates pro-inflammatory cytokine-mediated activation in human aortic endothelial cells, supporting mechanistically its potential beneficial effect in CAD. In summary, we demonstrate that a unique integration of protein-protein interaction network proximity and large-scale patient-level longitudinal data complemented by mechanistic in vitro studies can facilitate drug repurposing.
Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR
Authors: Wang Jiaxu , Yuan Zenglin , Cui Yaqi , Xie Rong , Yang Guang , Kassab Muzaffer A. , Wang Mengxi , Ma Yinliang , Wu Chen , Yu Xiaochun , Liu Xiuhua
Published: July 2018

53BP1 performs essential functions in DNA double-strand break (DSB) repair and it was recently reported that Tudor interacting repair regulator (TIRR) negatively regulates 53BP1 during DSB repair. Here, we present the crystal structure of the 53BP1 tandem Tudor domain (TTD) in complex with TIRR. Our results show that three loops from TIRR interact with 53BP1 TTD and mask the methylated lysine-binding pocket in TTD. Thus, TIRR competes with histone H4K20 methylation for 53BP1 binding. We map key interaction residues in 53BP1 TTD and TIRR, whose mutation abolishes complex formation. Moreover, TIRR suppresses the relocation of 53BP1 to DNA lesions and 53BP1-dependent DNA damage repair. Finally, despite the high-sequence homology between TIRR and NUDT16, NUDT16 does not directly interact with 53BP1 due to the absence of key residues required for binding. Taken together, our study provides insights into the molecular mechanism underlying TIRR-mediated suppression of 53BP1-dependent DNA damage repair.
Publisher Correction: Computational identification of specific genes for glioblastoma stem-like cells identity
Authors: Fiscon Giulia , Conte Federica , Licursi Valerio , Nasi Sergio , Paci Paola
Published: July 2018

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.
An account of solvent accessibility in protein-RNA recognition
Authors: Mukherjee Sunandan , Bahadur Ranjit Prasad
Published: July 2018

Protein–RNA recognition often induces conformational changes in binding partners. Consequently, the solvent accessible surface area (SASA) buried in contact estimated from the co-crystal structures may differ from that calculated using their unbound forms. To evaluate the change in accessibility upon binding, we compare SASA of 126 protein-RNA complexes between bound and unbound forms. We observe, in majority of cases the interface of both the binding partners gain accessibility upon binding, which is often associated with either large domain movements or secondary structural transitions in RNA-binding proteins (RBPs), and binding-induced conformational changes in RNAs. At the non-interface region, majority of RNAs lose accessibility upon binding, however, no such preference is observed for RBPs. Side chains of RBPs have major contribution in change in accessibility. In case of flexible binding, we find a moderate correlation between the binding free energy and change in accessibility at the interface. Finally, we introduce a parameter, the ratio of gain to loss of accessibility upon binding, which can be used to identify the native solution among the flexible docking models. Our findings provide fundamental insights into the relationship between flexibility and solvent accessibility, and advance our understanding on binding induced folding in protein-RNA recognition.
Novel Interplay Between Smad1 and Smad3 Phosphorylation via AGE Regulates the Progression of Diabetic Nephropathy
Authors: Ono Hiroyuki , Abe Hideharu , Sakurai Akiko , Ochi Arisa , Tominaga Tatsuya , Tamaki Masanori , Kishi Seiji , Murakami Taichi , Nagai Kojiro , Kohashi Masayuki , Doi Toshio
Published: July 2018

Diabetic nephropathy (DN) is the major cause of end-stage renal failure and is associated with increased morbidity and mortality compared with other causes of renal diseases. We previously found that Smad1 plays a critical role in the development of DN both in vitro and in vivo. However, functional interaction between Smad1 and Smad3 signaling in DN is unclear. Here, we addressed the molecular interplay between Smad1 and Smad3 signaling under a diabetic condition by using Smad3-knockout diabetic mice. Extracellular matrix (ECM) protein overexpression and Smad1 activation were observed in the glomeruli of db/db mice but were suppressed in the glomeruli of Smad3+/−; db/db mice. Smad3 activation enhanced the phosphorylation of Smad1 C-terminal domain but decreased the phosphorylation of linker domain, thus regulating Smad1 activation in advanced glycation end product-treated mesangial cells (MCs). However, forced phosphorylation of the Smad1 linker domain did not affect Smad3 activation in MCs. Phosphorylation of the Smad1 linker domain increased in Smad3+/−; db/db mice and probucol-treated db/db mice, which was consistent with the attenuation of ECM overproduction. These results indicate that Smad3 expression and activation or probucol treatment alters Smad1 phosphorylation, thus suggesting new molecular mechanisms underlying DN development and progression.
Switchable plasmonic routers controlled by external magnetic fields by using magneto-plasmonic waveguides
Authors: Ho Kum-Song , Im Song-Jin , Pae Ji-Song , Ri Chol-Song , Han Yong-Ha , Herrmann Joachim
Published: July 2018

We analytically and numerically investigate magneto-plasmons in metal films surrounded by a ferromagnetic dielectric. In such waveguide using a metal film with a thickness exceeding the Skin depth, an external magnetic field in the transverse direction can induce a significant spatial asymmetry of mode distribution. Superposition of the odd and the even asymmetric modes over a distance leads to a concentration of the energy on one interface which is switched to the other interface by the magnetic field reversal. The requested magnitude of magnetization is exponentially reduced with the increase of the metal film thickness. Based on this phenomenon, we propose a waveguide-integrated magnetically controlled switchable plasmonic routers with 99-%-high contrast within the optical bandwidth of tens of THz. This configuration can also operate as a magneto-plasmonic modulator.
Wnt4 is significantly upregulated during the early phases of cisplatin-induced acute kidney injury
Authors: He Yi-Xin , Diao Tian-Tian , Song Shu-Min , Wang Cen-Cen , Wang Yu , Zhou Chun-Lan , Bai Yi-Bing , Yu Shan-Shen , Mi Xuan , Yang Xin-Yu , Wei Qiu-Ju , Li Bing
Published: July 2018

Wnt4 is a secreted growth factor associated with renal tubulogenesis. Our previous studies identified that renal and urinary Wnt4 are upregulated following ischemia-reperfusion injury in mice, but the roles of Wnt4 in other forms of acute kidney injury (AKI) remain unclear. Here, we investigated the changes in Wnt4 expression using a cisplatin-induced AKI model. We found that renal and urinary Wnt4 expression increased as early as 12 hours, peaked at day 4 following cisplatin-induced AKI and was closely correlated with histopathological alterations. By contrast, the serum creatinine level was significantly elevated until day 3, indicating that Wnt4 is more sensitive to early tubular injury than serum creatinine. In addition, renal Wnt4 was co-stained with aquaporin-1 and thiazide-sensitive NaCl cotransporter, suggesting that Wnt4 can detect both proximal and distal tubular injuries. These data were further confirmed in a clinical study. Increased urinary Wnt4 expression was detected earlier than serum creatinine and eGFR in patients with contrast-induced AKI after vascular intervention. This study is the first to demonstrate that increased expression of renal and urinary Wnt4 can be detected earlier than serum creatinine after drug-induced AKI. In particular, urinary Wnt4 can potentially serve as a noninvasive biomarker for monitoring patients with tubular injury.
Enhancing the systems productivity and water use efficiency through coordinated soil water sharing and compensation in strip-intercropping
Authors: Chen Guodong , Kong Xuefu , Gan Yantai , Zhang Renzhi , Feng Fuxue , Yu Aizhong , Zhao Cai , Wan Sumei , Chai Qiang
Published: July 2018

In arid areas, water shortage is threating agricultural sustainability, and strip-intercropping may serve as a strategy to alleviate the challenge. Here we show that strip-intercropping enhances the spatial distributions of soil water across the 0–110 cm rooting zones, improves the coordination of soil water sharing during the co-growth period, and provides compensatory effect for available soil water. In a three-year (2009–2011) experiment, shorter-season pea (Pisum sativum L.) was sown in alternate strips with longer-season maize (Zea mays L.) without or with an artificially-inserted root barrier (a solid plastic sheet) between the strips. The intercropped pea used soil water mostly in the top 20-cm layers, whereas maize plants were able to absorb water from deeper-layers of the neighboring pea strips. After pea harvest, the intercropped maize obtained compensatory soil water from the pea strips. The pea-maize intercropping without the root barrier increased grain yield by 25% and enhanced water use efficiency by 24% compared with the intercropping with the root barrier. The improvement in crop yield and water use efficiency was partly attributable to the coordinated soil water sharing between the inter-strips and the compensatory effect from the early-maturing pea to the late-maturing maize.
Microemulsion formulation of a new biopesticide to control the diamondback moth (Lepidoptera: Plutellidae)
Authors: Shao Hainan , Xi Na , Zhang Yalin
Published: July 2018

This study was designed to develop a microemulsion formulation of norcantharidin for the control of the diamondback moth (DBM), Plutella xylostella (Linnaeus), a notorious pest of brassica crops worldwide. The oil phase was screened and selected based on norcantharidin solubility while the surfactants were selected on the basis of their efficiency to form microemulsion. Optimized batches were selected using pseudo ternary phase diagrams. The microemulsion system were stabilized using mixtures composed of norcantharidin, surfactants (Tx13 and Tw80), and cosurfactant (ethanol). Its physicochemical characteristics were also demonstrated to have a higher cloud point than 72 °C as well as good thermodynamic and dilution stability. In additon, a subsequent insecticidal bioassay indicated that the acute LC50 for norcantharidin microemulsion to P. xylostella was estimated to be 12.477 mg/L (11.58–13.41, 95% CL). Our results provide an environment-friendly promising alternative to control P. xylostella and possibly contribute to ameliorating any pesticide resistance in P. xylostella.
Sexual ancestors generated an obligate asexual and globally dispersed clone within the model diatom species Thalassiosira pseudonana
Authors: Koester Julie A. , Berthiaume Chris T. , Hiranuma Naozumi , Parker Micaela S. , Iverson Vaughn , Morales Rhonda , Ruzzo Walter L. , Armbrust E. Virginia
Published: July 2018

Sexual reproduction roots the eukaryotic tree of life, although its loss occurs across diverse taxa. Asexual reproduction and clonal lineages persist in these taxa despite theoretical arguments suggesting that individual clones should be evolutionarily short-lived due to limited phenotypic diversity. Here, we present quantitative evidence that an obligate asexual lineage emerged from a sexual population of the marine diatom Thalassiosira pseudonana and rapidly expanded throughout the world’s oceans. Whole genome comparisons identified two lineages with characteristics expected of sexually reproducing strains in Hardy-Weinberg equilibrium. A third lineage displays genomic signatures for the functional loss of sexual reproduction followed by a recent global colonization by a single ancestral genotype. Extant members of this lineage are genetically differentiated and phenotypically plastic, potentially allowing for rapid adaptation when they are challenged by natural selection. Such mechanisms may be expected to generate new clones within marginal populations of additional unicellular species, facilitating the exploration and colonization of novel environments, aided by exponential growth and ease of dispersal.
Tunable double-Weyl Fermion semimetal state in the SrSi2 materials class
Authors: Singh Bahadur , Chang Guoqing , Chang Tay-Rong , Huang Shin-Ming , Su Chenliang , Lin Ming-Chieh , Lin Hsin , Bansil Arun
Published: July 2018

We discuss first-principles topological electronic structure of noncentrosymmetric SrSi2 materials class based on the hybrid exchange-correlation functional. Topological phase diagram of SrSi2 is mapped out as a function of the lattice constant with focus on the semimetal order. A tunable double-Weyl Fermion state in Sr1−xCaxSi2 and Sr1−xBaxSi2 alloys is identified. Ca doping in SrSi2 is shown to yield a double-Weyl semimetal with a large Fermi arc length, while Ba doping leads to a transition from the topological semimetal to a gapped insulator state. Our study indicates that SrSi2 materials family could provide an interesting platform for accessing the unique topological properties of Weyl semimetals.
Reference values for white blood-cell-based inflammatory markers in the Rotterdam Study: a population-based prospective cohort study
Authors: Fest Jesse , Ruiter Rikje , Ikram M. Arfan , Voortman Trudy , van Eijck Casper H. J. , Stricker Bruno H.
Published: July 2018

Novel prognostic inflammatory markers of cancer survival and cardiovascular disease are; the neutrophil-to-lymphocyte ratio (NLR), the platelet-to-lymphocyte ratio (PLR) and the systemic immune-inflammation index (SII). As normal values for these markers are unknown, our objective was to obtain reference values in the general population. We obtained data from a population-based prospective cohort study of individuals aged 45 years and over between 2002 and 2014. Absolute blood counts were used to calculate the NLR, PLR and SII. All inflammatory indices followed a log-normal distribution. We calculated the mean and 95% reference intervals in an unselected population. Furthermore we studied whether the inflammatory markers differed between age categories and gender. In total 8,711 participants (57.1% female; mean age 65.9 years, standard deviation 10.5 years) were included. Mean values and corresponding 95% reference intervals for the NLR were: 1.76 (0.83–3.92), for PLR: 120 (61–239) and for SII: 459 (189–1168). The inflammatory markers increased with age. The PLR and SII were higher in females, whilst the NLR was higher in males. In conclusion, we provided reference values for new inflammatory markers. All increase with age and vary with gender. This provides context that allows for proper interpretation of their potential value in future clinical practice and research.
High speed error correction for continuous-variable quantum key distribution with multi-edge type LDPC code
Authors: Wang Xiangyu , Zhang Yichen , Yu Song , Guo Hong
Published: July 2018

Error correction is a significant step in postprocessing of continuous-variable quantum key distribution system, which is used to make two distant legitimate parties share identical corrected keys. We propose an experiment demonstration of high speed error correction with multi-edge type low-density parity check (MET-LDPC) codes based on graphic processing unit (GPU). GPU supports to calculate the messages of MET-LDPC codes simultaneously and decode multiple codewords in parallel. We optimize the memory structure of parity check matrix and the belief propagation decoding algorithm to reduce computational complexity. Our results show that GPU-based decoding algorithm greatly improves the error correction speed. For the three typical code rate, i.e., 0.1, 0.05 and 0.02, when the block length is 106 and the iteration number are 100, 150 and 200, the average error correction speed can be respectively achieved to 30.39 Mbits/s (over three times faster than previous demonstrations), 21.23 Mbits/s and 16.41 Mbits/s with 64 codewords decoding in parallel, which supports high-speed real-time continuous-variable quantum key distribution system.
The tomato subtilase family includes several cell death-related proteinases with caspase specificity
Authors: Reichardt Sven , Repper Dagmar , Tuzhikov Alexander I. , Galiullina Raisa A. , Planas-Marquès Marc , Chichkova Nina V. , Vartapetian Andrey B. , Stintzi Annick , Schaller Andreas
Published: July 2018

Phytaspases are Asp-specific subtilisin-like plant proteases that have been likened to animal caspases with respect to their regulatory function in programmed cell death (PCD). We identified twelve putative phytaspase genes in tomato that differed widely in expression level and tissue-specific expression patterns. Most phytaspase genes are tandemly arranged on tomato chromosomes one, four, and eight, and many belong to taxon-specific clades, e.g. the P69 clade in the nightshade family, suggesting that these genes evolved by gene duplication after speciation. Five tomato phytaspases (SlPhyts) were expressed in N. benthamiana and purified to homogeneity. Substrate specificity was analyzed in a proteomics assay and with a panel of fluorogenic peptide substrates. Similar to animal caspases, SlPhyts recognized an extended sequence motif including Asp at the cleavage site. Clear differences in cleavage site preference were observed implying different substrates in vivo and, consequently, different physiological functions. A caspase-like function in PCD was confirmed for five of the seven tested phytaspases. Cell death was triggered by ectopic expression of SlPhyts 2, 3, 4, 5, 6 in tomato leaves by agro-infiltration, as well as in stably transformed transgenic tomato plants. SlPhyts 3, 4, and 5 were found to contribute to cell death under oxidative stress conditions.