bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermodynamically consistent Navier–Stokes–Cahn–Hilliard models with mass transfer and chemotaxis
Authors: LAM KEI FONG , WU HAO
Published: October 2017

We derive a class of Navier–Stokes–Cahn–Hilliard systems that models two-phase flows with mass transfer coupled to the process of chemotaxis. These thermodynamically consistent models can be seen as the natural Navier–Stokes analogues of earlier Cahn–Hilliard–Darcy models proposed for modelling tumour growth, and are derived based on a volume-averaged velocity, which yields simpler expressions compared to models derived based on a mass-averaged velocity. Then, we perform mathematical analysis on a simplified model variant with zero excess of total mass and equal densities. We establish the existence of global weak solutions in two and three dimensions for prescribed mass transfer terms. Under additional assumptions, we prove the global strong well-posedness in two dimensions with variable fluid viscosity and mobilities, which also includes a continuous dependence on initial data and mass transfer terms for the chemical potential and the order parameter in strong norms.
A Simple SVD Algorithm for Finding Hidden Partitions
Authors: VU VAN
Published: October 2017

Finding a hidden partition in a random environment is a general and important problem which contains as subproblems many important questions, such as finding a hidden clique, finding a hidden colouring, finding a hidden bipartition,etc.

In this paper we provide a simple SVD algorithm for this purpose, addressing a question of McSherry. This algorithm is easy to implement and works for sparse graphs under optimal density assumptions. We also consider an approximating algorithm, which on one hand works under very mild assumptions, but on other hand can sometimes be upgraded to give the exact solution.
Colourings of Uniform Hypergraphs with Large Girth and Applications
Authors: KUPAVSKII ANDREY , SHABANOV DMITRY
Published: October 2017

This paper deals with a combinatorial problem concerning colourings of uniform hypergraphs with large girth. We prove that ifHis ann-uniform non-r-colourable simple hypergraph then its maximum edge degree Δ(H) satisfies the inequality$$ \Delta(H)\geqslant c\cdot r^{n-1}\ffrac{n(\ln\ln n)^2}{\ln n} $$for some absolute constantc> 0.

As an application of our probabilistic technique we establish a lower bound for the classical van der Waerden numberW(n, r), the minimum naturalNsuch that in an arbitrary colouring of the set of integers {1,. . .,N} withrcolours there exists a monochromatic arithmetic progression of lengthn. We prove that$$ W(n,r)\geqslant c\cdot r^{n-1}\ffrac{(\ln\ln n)^2}{\ln n}. $$
Uniformly Discrete Forests with Poor Visibility
Authors: ALON NOGA
Published: October 2017

We prove that there is a setFin the plane so that the distance between any two points ofFis at least 1, and for any positive ϵ < 1, and every line segment in the plane of length at least ϵ−1−o(1), there is a point ofFwithin distance ϵ of the segment. This is tight up to theo(1)-term in the exponent, improving earlier estimates of Peres, of Solomon and Weiss, and of Adiceam.
New Light on Early Mongol Islamisation: The Case of Arghun Aqa's Family
Authors: LANDA ISHAYAHU
Published: October 2017

The paper discusses the questions of the alleged conversion of Arghun Aqa, the powerful Mongol governor of great parts of Western Asia in the mid-13thcentury, to Islam, claimed by the famous Armenian historian Kirakos. While in the end dismissing the historicity of this claim, the paper uses a variety of archaeological, numismatic, epigraphic and literary sources in order to highlight the great role the Islamic beliefs and identity of the surrounding Persianised society played in the continuous Islamic acculturation of Arghun Aqa and his family since the earliest phases of their presence in Iran.
Food insecurity, social networks and symptoms of depression among men and women in rural Uganda: a cross-sectional, population-based study
Authors: Perkins Jessica M , Nyakato Viola N , Kakuhikire Bernard , Tsai Alexander C , Subramanian SV , Bangsberg David R , Christakis Nicholas A
Published: October 2017

Objective

To assess the association between food insecurity and depression symptom severity stratified by sex, and test for evidence of effect modification by social network characteristics.

Design

A population-based cross-sectional study. The nine-item Household Food Insecurity Access Scale captured food insecurity. Five name generator questions elicited network ties. A sixteen-item version of the Hopkins Symptom Checklist for Depression captured depression symptom severity. Linear regression was used to estimate the association between food insecurity and depression symptom severity while adjusting for potential confounders and to test for potential network moderators.

Setting

In-home survey interviews in south-western Uganda.

Subjects

All adult residents across eight rural villages; 96 % response rate (n1669).

Results

Severe food insecurity was associated with greater depression symptom severity (b=0·4, 95 % CI 0·3, 0·5,P<0·001 for women;b=0·3, 95 % CI 0·2, 0·4,P<0·001 for men). There was no evidence of effect modification by social network factors for women. However, for men who are highly embedded within in their village social network, and (separately) for men who have few poor contacts in their personal network, the relationship between severe food insecurity and depression symptoms was stronger than for men on the periphery of their village social network, and for men with many poor personal network contacts, respectively.

Conclusions

In this population-based study from rural Uganda, food insecurity was associated with mental health for both men and women. Future research is needed on networks and food insecurity-related shame in relation to depression symptoms among food-insecure men.
Sociodemographic, anthropometric and behavioural risk factors for ultra-processed food consumption in a sample of 2–9-year-olds in Brazil
Authors: Mais Laís Amaral , Warkentin Sarah , Vega Juliana Bergamo , Latorre Maria do Rosário Dias de Oliveira , Carnell Susan , Taddei José Augusto de Aguiar Carrazedo
Published: October 2017

Objective

The present study aimed to identify food patterns among 2–9-year-olds and investigate sociodemographic, anthropometric and behavioural predictors of less healthy dietary patterns.

Design

Cross-sectional study. Parents of 2–9-year-olds completed an FFQ and factor analysis was applied to identify dietary patterns. Parents also completed questionnaires assessing sociodemographic, anthropometric and behavioural characteristics of parents and children, including parental feeding practices.

Setting

Participants were recruited from private schools of Campinas and São Paulo, SP, Brazil, between April and June 2014.

Subjects

Parents of 2–9-year-olds (n 929).

Results

Two dietary patterns emerged: ‘traditional food’ and ‘ultra-processed food’. Lower maternal education (OR=2·05, P=0·010) and higher maternal weight status (OR=1·43, P=0·044) were associated with a greater likelihood of the ultra-processed food pattern. Lower perceived parental responsibility for adequacy of food group intake (OR=2·41, P=0·020), and lower scores on the parental feeding practices of ‘Healthy Eating Guidance’ (OR=1·83, P<0·001) and ‘Monitoring’ (OR=2·52, P<0·001), were also associated with the presence of this pattern, as was higher child’s screen use during mealtimes (OR=1·61, P=0·004).

Conclusions

The present study is the first to evaluate associations between less healthy dietary patterns of Brazilian 2–9-year-olds and parental feeding practices. Our findings highlight sociodemographic, anthropometric and behavioural factors within families that could be used to target tailored policies to at-risk populations.
SFA intake among Japanese schoolchildren: current status and possible intervention to prevent excess intake
Authors: Asakura Keiko , Sasaki Satoshi
Published: October 2017

Objective

Although a high intake of fat, particularly SFA, is a well-known risk factor for CVD, fat intake in Japan has attracted relatively little attention from health professionals to date due to the low intake in the Japanese population. However, recent surveys have shown an increase in fat intake in younger Japanese populations. Here, we described the fat intake and dietary sources of SFA in Japanese schoolchildren. Also, we experimentally exchanged a high-SFA food with a low-SFA substitute in the data, and calculated the resulting changes in nutrient intakes.

Design

The study was conducted nationwide under a cross-sectional design. A non-consecutive, three-day diet record was performed on two school days and a non-school day.

Setting

Fourteen elementary and thirteen junior high schools.

Subjects

Elementary-school children (n 629) and junior high-school children (n 281).

Results

Prevalence of excess fat intake was 35·4 % in boys and 45·0 % in girls. Excess SFA intake was suspected in 97·7 % of boys and 99·4 % of girls when the dietary reference intake values for adults were applied. Major dietary sources of SFA were meat (26·4 % of total SFA intake), dairy products (25·7 %) and confectioneries (11·3 %).

Conclusions

Since one-third to nearly one-half of our Japanese schoolchildren consumed excess fat, careful monitoring of fat intake in the Japanese population should be continued. Adoption of low-fat milk and/or lean meat in daily meals might be a suitable means of reducing fat, particularly SFA intake, in schoolchildren.
Perceptions of primary health care service users regarding dental team practices in Brazil
Authors: Baumgarten Alexandre , Veiga Rochelle Santos Da , Bulgarelli Patricia Tavora , Diesel Vitor Motta , Bulgarelli Alexandre Favero
Published: October 2017

Background

The Unified Health System (SUS) is the Brazilian set of public health services that offers global access to health care and disease treatments for all citizens. These services have been evaluated by means of a national survey assessing the users’ perceptions.

Aim

To explore and characterize the SUS users’ perceptions regarding primary dental team practices in the five Brazilian geographical regions.

Methods

Descriptive study. The sample consisted of 37 262 subjects. Data were collected by means of the Ministry of Health survey, conducted between 2012 and 2014. Variables used in the present study are associated with SUS users’ perspectives of satisfaction, access, and use of services. The study utilized bivariate data analysis, and dichotomous variables were derived for analysis following 95% reliability.

Findings

This study observed similarities and proportionality of perceptions in the Brazilian territory. In most macro-regions, dental teams did not develop an active search for dental treatment absentees. However, the SUS users reported very good and good perceptions, which were homogeneously distributed across five Brazilian regions, thereby showing an overall positive perception of primary dental treatment.
A controlled trial of screening, brief intervention and referral for treatment (SBIRT) implementation in primary care in the United Arab Emirates
Authors: Matheson Catriona , Pflanz-Sinclair Christiane , Almarzouqi Amna , Bond Christine M , Lee Amanda J , Batieha Anwar , Al Ghaferi H , El Kashef A
Published: October 2017

Aim

This project evaluated the effectiveness of screening brief intervention and referral for treatment (SBIRT) in primary care in Abu Dhabi to manage patients with problematic substance use. This study aimed to determine whether: (i) training primary care physicians on the SBIRT model increased the identification of patients using substances at a harmful, hazardous or dependent level; (ii) training improved physicians’ knowledge, attitudes and beliefs in self-efficacy in managing substance use.

Background

Substance use is increasing in the United Arab Emirates yet there has been no formal primary care intervention. SBIRT was considered an appropriate model given its endorsement by the WHO.

Methods

A controlled trial (two intervention and two matched control clinics) was undertaken. Intervention physicians (n=17) were trained in SBIRT. Physicians’ attitudes were measured before and after training and eight months after implementation. Target recruitment was 900 patients. Inclusion criteria were: consenting UAE national, ⩾18 years, using the ‘walk-in’ primary care clinic. Patient data was collected by physician-administered questionnaire. Prevalence of drug use was measured through electronic patient records.

Findings

A total of 906 patients were screened, aged 18–82 years and 496 (55%) were female. Of these, 5.7% reported use of amphetamine, 3.9% alcohol, 3.3%, sedatives, 1.7% opioids and 1.1% cannabis. In all, 21 people had a moderate/high ASSIST score and received a brief intervention, but did not attend follow-up; three high-risk people were referred for specialist treatment. Physicians’ attitudes towards patients with problematic substance use and providing treatment improved after training, but returned to pre-training levels after eight months. Including the 21 individuals identified from intervention screening, the prevalence of substance use increased to 0.208% (95% CI 0.154–0.274), significantly higher than in control clinics (P<0.001).

In conclusion, physicians were generally positive towards SBIRT and SBIRT increased recorded drug related conditions at a practice level. However, poor patient attendance at follow-up requires investigation.
Perceived Stress and Intent to Die in Young Soldiers Who Attempt Suicide
Authors: Shelef Leah , Brunstein Klomek Anat , Yavnai Nirit , Shahar Golan
Published: October 2017

Abstract. Background: Intent to die is an important component of suicide risk assessment. The authors compared the predictive effect of two forms of stress – military and perceived – in intent to die by suicide among young adult Israeli soldiers with a history of suicide attempts. Depression, suicide ideation, and habituation/acquired capacity for suicidality served as covariates. Methods: Participants were 60 young adult soldiers in the Israeli Defense Force (ISF; aged 18–21 years), who made a suicide attempt during their military service. Study variables were assessed using self-report measures. Results: Intent to die by suicide correlated with suicide ideation, habituation/acquired capacity, depressive symptoms, and perceived stress. In a multiple regression analysis, perceived stress predicted intent to die (b = .44, p = .002) over and above the prediction by suicide ideation (b = .42, p = .013) and acquired capacity/habituation (b = .28, p = .023). Limitations: The cross-sectional design restricts causal inference. In addition, an exclusive reliance on self-report measures might have inflated shared method variance. Conclusions: Perceived stress captures a unique dimension of intent to die by suicide among young suicide attempters.
Protein and chemotherapy profiling of extracellular vesicles harvested from therapeutic induced senescent triple negative breast cancer cells
Authors: Kavanagh E L , Lindsay S , Halasz M , Gubbins L C , Weiner-Gorzel K , Guang M H Z , McGoldrick A , Collins E , Henry M , Blanco-Fernández A , O'Gorman P , Fitzpatrick P , Higgins M J , Dowling P , McCann A
Published: October 2017

Triple negative breast cancer (TNBC) is an aggressive subtype with relatively poor clinical outcomes and limited treatment options. Chemotherapy, while killing cancer cells, can result in the generation of highly chemoresistant therapeutic induced senescent (TIS) cells that potentially form stem cell niches resulting in metastases. Intriguingly, senescent cells release significantly more extracellular vesicles (EVs) than non-senescent cells. Our aim was to profile EVs harvested from TIS TNBC cells compared with control cells to identify a potential mechanism by which TIS TNBC cells maintain survival in the face of chemotherapy. TIS was induced and confirmed in Cal51 TNBC cells using the chemotherapeutic paclitaxel (PTX) (Taxol). Mass spectrometry (MS) analysis of EVs harvested from TIS compared with control Cal51 cells was performed using Ingenuity Pathway Analysis and InnateDB programs. We demonstrate that TIS Cal51 cells treated with 75 nM PTX for 7 days became senescent (senescence-associated β-galactosidase (SA-β-Gal) positive, Ki67-negative, increased p21 and p16, G2/M cell cycle arrest) and released significantly more EVs (P=0.0002) and exosomes (P=0.0007) than non-senescent control cells. Moreover, TIS cells displayed an increased expression of the multidrug resistance protein 1/p-glycoprotein. MS analysis demonstrated that EVs derived from senescent Cal51 cells contained 142 proteins with a significant increased fold change compared with control EVs. Key proteins included ATPases, annexins, tubulins, integrins, Rabs and insoluble senescence-associated secretory phenotype (SASP) factors. A fluorescent analogue of PTX (Flutax-2) allowed appreciation of the removal of chemotherapy in EVs from senescent cells. Treatment of TIS cells with the exosome biogenesis inhibitor GW4869 resulted in reduced SA-β-Gal staining (P=0.04). In summary, this study demonstrates that TIS cells release significantly more EVs compared with control cells, containing chemotherapy and key proteins involved in cell proliferation, ATP depletion, apoptosis and the SASP. These findings may partially explain why cancer senescent cells remain viable despite chemotherapeutic challenge.
Impaired p65 degradation by decreased chaperone-mediated autophagy activity facilitates epithelial-to-mesenchymal transition
Authors: Tang J , Zhan M-N , Yin Q-Q , Zhou C-X , Wang C-L , Wo L-L , He M , Chen G-Q , Zhao Q
Published: October 2017

Aberrant activation of nuclear factor-κB (NF-κB) has been observed in a wide range of human cancers and is thought to promote tumorigenesis and metastasis. As a central component of NF-κB pathway, p65 protein level is tightly regulated and could be subjected to proteasome degradation. Here we demonstrated that p65 can bind to HSC70 with four consensus recognition motif in its RHD domain and be constitutively transported to the lysosome membrane to bind with lysosome-associated membrane protein type 2A and degraded within the lysosome in two epithelial cell lines, proposing that p65 can be degraded by chaperone-mediated autophagy (CMA). Of great importance, there is a decreased CMA activity together with impaired degradation of p65 in a process of epithelial–mesenchymal transition (EMT). The resulted accumulation of p65 leads to higher NF-κB activity and contributes to the progression and maintenance of the EMT program. Taken together, our results define a novel regulatory mechanism for the important transcription factor p65, and these findings would shed new light on the inhibition of EMT, as well as metastasis of cancer cells.
BAD-LAMP controls TLR9 trafficking and signalling in human plasmacytoid dendritic cells
Authors: Combes Alexis , Camosseto Voahirana , N’Guessan Prudence , Argüello Rafael J. , Mussard Julie , Caux Christophe , Bendriss-Vermare Nathalie , Pierre Philippe , Gatti Evelina
Published: October 2017

Toll-like receptors (TLR) are essential components of the innate immune system. Several accessory proteins, such as UNC93B1, are required for transport and activation of nucleic acid sensing Toll-like receptors in endosomes. Here, we show that BAD-LAMP (LAMP5) controls TLR9 trafficking to LAMP1+ late endosomes in human plasmacytoid dendritic cells (pDC), leading to NF-κB activation and TNF production upon DNA detection. An inducible VAMP3+/LAMP2+/LAMP1− endolysosome compartment exists in pDCs from which TLR9 activation triggers type I interferon expression. BAD-LAMP-silencing enhances TLR9 retention in this compartment and consequent downstream signalling events. Conversely, sustained BAD-LAMP expression in pDCs contributes to their lack of type I interferon production after exposure to a TGF-β-positive microenvironment or isolation from human breast tumours. Hence, BAD-LAMP limits interferon expression in pDCs indirectly, by promoting TLR9 sorting to late endosome compartments at steady state and in response to immunomodulatory cues.
Erratum: Symmetry-based indicators of band topology in the 230 space groups
Authors: Po Hoi Chun , Vishwanath Ashvin , Watanabe Haruki
Published: October 2017

A correction to this article has been published and is linked from the HTML version of this article.
Citizen science provides a reliable and scalable tool to track disease-carrying mosquitoes
Authors: Palmer John R. B. , Oltra Aitana , Collantes Francisco , Delgado Juan Antonio , Lucientes Javier , Delacour Sarah , Bengoa Mikel , Eritja Roger , Bartumeus Frederic
Published: October 2017

Recent outbreaks of Zika, chikungunya and dengue highlight the importance of better understanding the spread of disease-carrying mosquitoes across multiple spatio-temporal scales. Traditional surveillance tools are limited by jurisdictional boundaries and cost constraints. Here we show how a scalable citizen science system can solve this problem by combining citizen scientists’ observations with expert validation and correcting for sampling effort. Our system provides accurate early warning information about the Asian tiger mosquito (Aedes albopictus) invasion in Spain, well beyond that available from traditional methods, and vital for public health services. It also provides estimates of tiger mosquito risk comparable to those from traditional methods but more directly related to the human–mosquito encounters that are relevant for epidemiological modelling and scalable enough to cover the entire country. These results illustrate how powerful public participation in science can be and suggest citizen science is positioned to revolutionize mosquito-borne disease surveillance worldwide.
Counteracting structural errors in ensemble forecast of influenza outbreaks
Authors: Pei Sen , Shaman Jeffrey
Published: October 2017

For influenza forecasts generated using dynamical models, forecast inaccuracy is partly attributable to the nonlinear growth of error. As a consequence, quantification of the nonlinear error structure in current forecast models is needed so that this growth can be corrected and forecast skill improved. Here, we inspect the error growth of a compartmental influenza model and find that a robust error structure arises naturally from the nonlinear model dynamics. By counteracting these structural errors, diagnosed using error breeding, we develop a new forecast approach that combines dynamical error correction and statistical filtering techniques. In retrospective forecasts of historical influenza outbreaks for 95 US cities from 2003 to 2014, overall forecast accuracy for outbreak peak timing, peak intensity and attack rate, are substantially improved for predicted lead times up to 10 weeks. This error growth correction method can be generalized to improve the forecast accuracy of other infectious disease dynamical models.
Optical conversion of pure spin currents in hybrid molecular devices
Authors: Wheeler May C. , Ma’Mari Fatma Al , Rogers Matthew , Gonçalves Francisco J. , Moorsom Timothy , Brataas Arne , Stamps Robert , Ali Mannan , Burnell Gavin , Hickey B. J. , Cespedes Oscar
Published: October 2017

Carbon-based molecules offer unparalleled potential for THz and optical devices controlled by pure spin currents: a low-dissipation flow of electronic spins with no net charge displacement. However, the research so far has been focused on the electrical conversion of the spin imbalance, where molecular materials are used to mimic their crystalline counterparts. Here, we use spin currents to access the molecular dynamics and optical properties of a fullerene layer. The spin mixing conductance across Py/C60 interfaces is increased by 10% (5 × 1018 m−2) under optical irradiation. Measurements show up to a 30% higher light absorbance and a factor of 2 larger photoemission during spin pumping. We also observe a 0.15 THz slowdown and a narrowing of the vibrational peaks. The effects are attributed to changes in the non-radiative damping and energy transfer. This opens new research paths in hybrid magneto-molecular optoelectronics, and the optical detection of spin physics in these materials.
Entanglement of photons in their dual wave-particle nature
Authors: Rab Adil S. , Polino Emanuele , Man Zhong-Xiao , Ba An Nguyen , Xia Yun-Jie , Spagnolo Nicolò , Lo Franco Rosario , Sciarrino Fabio
Published: October 2017

Wave-particle duality is the most fundamental description of the nature of a quantum object, which behaves like a classical particle or wave depending on the measurement apparatus. On the other hand, entanglement represents nonclassical correlations of composite quantum systems, being also a key resource in quantum information. Despite the very recent observations of wave-particle superposition and entanglement, whether these two fundamental traits of quantum mechanics can emerge simultaneously remains an open issue. Here we introduce and experimentally realize a scheme that deterministically generates entanglement between the wave and particle states of two photons. The elementary tool allowing this achievement is a scalable single-photon setup which can be in principle extended to generate multiphoton wave-particle entanglement. Our study reveals that photons can be entangled in their dual wave-particle behavior and opens the way to potential applications in quantum information protocols exploiting the wave-particle degrees of freedom to encode qubits.
DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells
Authors: Roost Matthias S. , Slieker Roderick C. , Bialecka Monika , van Iperen Liesbeth , Gomes Fernandes Maria M. , He Nannan , Suchiman H. Eka D. , Szuhai Karoly , Carlotti Françoise , de Koning Eelco J. P. , Mummery Christine L. , Heijmans Bastiaan T. , Chuva de Sousa Lopes Susana M.
Published: October 2017

Determining cell identity and maturation status of differentiated pluripotent stem cells (PSCs) requires knowledge of the transcriptional and epigenetic trajectory of organs during development. Here, we generate a transcriptional and DNA methylation atlas covering 21 organs during human fetal development. Analysis of multiple isogenic organ sets shows that organ-specific DNA methylation patterns are highly dynamic between week 9 (W9) and W22 of gestation. We investigate the impact of reprogramming on organ-specific DNA methylation by generating human induced pluripotent stem cell (hiPSC) lines from six isogenic organs. All isogenic hiPSCs acquire DNA methylation patterns comparable to existing hPSCs. However, hiPSCs derived from fetal brain retain brain-specific DNA methylation marks that seem sufficient to confer higher propensity to differentiate to neural derivatives. This systematic analysis of human fetal organs during development and associated isogenic hiPSC lines provides insights in the role of DNA methylation in lineage commitment and epigenetic reprogramming in humans.
Role of the orbital degree of freedom in iron-based superconductors
Authors: Yi Ming , Zhang Yan , Shen Zhi-Xun , Lu Donghui
Published: October 2017

Almost a decade has passed since the serendipitous discovery of the iron-based high temperature superconductors (FeSCs) in 2008. The fact that, as in the copper oxide high temperature superconductors, long-range antiferromagnetism in the FeSCs arises in proximity to superconductivity immediately raised the question of the degree of similarity between the two. Despite the great resemblance in their phase diagrams, there exist important differences between the FeSCs and the cuprates that need to be considered in order to paint a full picture of these two families of high temperature superconductors. One of the key differences is the multi-orbital multi-band nature of the FeSCs, which contrasts with the effective single-band nature of the cuprates. Systematic studies of orbital related phenomena in FeSCs have been largely lacking. In this review, we summarize angle-resolved photoemission spectroscopy (ARPES) measurements across various FeSC families that have been reported in literature, focusing on the systematic trends of orbital dependent electron correlations and the role of different Fe 3d orbitals in driving the nematic transition, the spin-density-wave transition, and superconductivity.
Touching is believing: interrogating halide perovskite solar cells at the nanoscale via scanning probe microscopy
Authors: Li Jiangyu , Huang Boyuan , Nasr Esfahani Ehsan , Wei Linlin , Yao Jianjun , Zhao Jinjin , Chen Wei
Published: October 2017

Halide perovskite solar cells based on CH3NH3PbI3 and related materials have emerged as the most exciting development in the next generation photovoltaic technologies, yet the microscopic phenomena involving photo-carriers, ionic defects, spontaneous polarization, and molecular vibration and rotation interacting with numerous grains, grain boundaries, and interfaces are still inadequately understood. In fact, there is still need for an effective method to interrogate the local photovoltaic properties of halide perovskite solar cells that can be directly traced to their microstructures on one hand and linked to their device performance on the other hand. In this perspective, we propose that scanning probe microscopy (SPM) techniques have great potential to realize such promises at the nanoscale, and highlight some of the recent progresses and challenges along this line of investigation toward local probing of photocurrent, work function, ionic activities, polarization switching, and chemical degradation. We also emphasize the importance of multi-modality imaging, in-operando scanning, big data analysis, and multidisciplinary collaboration for further studies toward fully understanding of these complex systems.
A comparison of passive and active estimates of sleep in a cohort with schizophrenia
Authors: Staples Patrick , Torous John , Barnett Ian , Carlson Kenzie , Sandoval Luis , Keshavan Matcheri , Onnela Jukka-Pekka
Published: October 2017

Sleep abnormalities are considered an important feature of schizophrenia, yet convenient and reliable sleep monitoring remains a challenge. Smartphones offer a novel solution to capture both self-reported and objective measures of sleep in schizophrenia. In this three-month observational study, 17 subjects with a diagnosis of schizophrenia currently in treatment downloaded Beiwe, a platform for digital phenotyping, on their personal Apple or Android smartphones. Subjects were given tri-weekly ecological momentary assessments (EMAs) on their own smartphones, and passive data including accelerometer, GPS, screen use, and anonymized call and text message logs was continuously collected. We compare the in-clinic assessment of sleep quality, assessed with the Pittsburgh Sleep Questionnaire Inventory (PSQI), to EMAs, as well as sleep estimates based on passively collected accelerometer data. EMAs and passive data classified 85% (11/13) of subjects as exhibiting high or low sleep quality compared to the in-clinic assessments among subjects who completed at least one in-person PSQI. Phone-based accelerometer data used to infer sleep duration was moderately correlated with subject self-assessment of sleep duration (r = 0.69, 95% CI 0.23–0.90). Active and passive phone data predicts concurrent PSQI scores for all subjects with mean average error of 0.75 and future PSQI scores with a mean average error of 1.9, with scores ranging from 0–14. These results suggest sleep monitoring via personal smartphones is feasible for subjects with schizophrenia in a scalable and affordable manner.
Evidence of local and regional freshening of Northeast Greenland coastal waters
Authors: Sejr Mikael K. , Stedmon Colin A. , Bendtsen Jørgen , Abermann Jakob , Juul-Pedersen Thomas , Mortensen John , Rysgaard Søren
Published: October 2017

The supply of freshwater to fjord systems in Greenland is increasing as a result of climate change-induced acceleration in ice sheet melt. However, insight into the marine implications of the melt water is impaired by lack of observations demonstrating the fate of freshwater along the Greenland coast and providing evaluation basis for ocean models. Here we present 13 years of summer measurements along a 120 km transect in Young Sound, Northeast Greenland and show that sub-surface coastal waters are decreasing in salinity with an average rate of 0.12 ± 0.05 per year. This is the first observational evidence of a significant freshening on decadal scale of the waters surrounding the ice sheet and comes from a region where ice sheet melt has been less significant. It implies that ice sheet dynamics in Northeast Greenland could be of key importance as freshwater is retained in southward flowing coastal currents thus reducing density of water masses influencing major deep water formation areas in the Subarctic Atlantic Ocean. Ultimately, the observed freshening could have implications for the Atlantic meridional overturning circulation.
Oxidative and anti-oxidative status in muscle of young rats in response to six protein diets
Authors: Zhu Jing , Li Xiao , Qi Hao , Gu Zetong , Song Shangxin , Yang Xiangli , Zhou Guanghong , Li Chunbao
Published: October 2017

We investigated the impact of six protein diets on oxidation and anti-oxidation status in the muscle of young rats. Rats were fed six protein diets for 14 days, including casein (control), and proteins isolated from soy, fish, chicken, pork and beef. Grx1, Trx1 and other oxidative metabolic indices in muscle were quantified. Compared with the casein diet, the soy protein diet had a similar oxidation level, but higher GSH and lower SOD activities. The chicken and fish protein groups had lower GSH and higher SOD activities, the pork protein group showed lower Grx1 levels than the casein group and the beef protein group showed the highest GSH, Grx1 and Trx1 levels as reflected by RT-PCR, Western blotting and immunohistochemistry analyses. Intake of meat proteins showed higher ROS and T-AOC but lower MDA levels than non-meat proteins, which may be due to the increase in Grx1 and Trx1 expression and other antioxidants. Meat proteins are more conducive to muscle of growing rats.
Risk of Sarcopenia and Osteoporosis in Male Tuberculosis Survivors: Korea National Health and Nutrition Examination Survey
Authors: Choi Chang-Jin , Choi Whan-Seok , Kim Churl-Min , Lee Sook-Young , Kim Kyung-Soo
Published: October 2017

Short-term prospective studies have suggested that pulmonary tuberculosis (TB) preludes permanent loss of lean tissue and fat mass even when TB treatment is effective. The aim of this study was to estimate the risk of sarcopenia and osteoporosis among Korean male TB survivors. Data of the population-based, Korea National Health and Nutrition Examination Survey (KNHANES) (2008–2011) were analyzed, including 3,228 males aged 50 years or older who underwent chest X-ray (CXR) and dual-energy x-ray absorptiometry (DEXA). TB survivors having both medical history and TB scars on CXR had increased risk of sarcopenia (odds ratio [OR] 3.44, 95% confidence interval [CI] 1.79–6.68) and osteoporosis (OR 1.75, 95% CI 1.04–2.95) after adjusting for age, height, smoking, alcohol, physical activity, serum 25-hydroxyvitamin D, parathyroid hormone level, education, and fat mass index. Having TB scars on CXR without medical history of TB was an independent risk factor of sarcopenia (OR 2.05, 95% CI 1.05–4.00), but not a risk factor of osteoporosis. Sarcopenia and low bone mineral density are prevalent in pulmonary TB survivors with TB scars on CXR. Medical history of TB with TB scars on CXR is an independent risk factor for sarcopenia and osteoporosis.
Self-organisation of small-world networks by adaptive rewiring in response to graph diffusion
Authors: Jarman Nicholas , Steur Erik , Trengove Chris , Tyukin Ivan Y. , van Leeuwen Cees
Published: October 2017

Complex networks emerging in natural and human-made systems tend to assume small-world structure. Is there a common mechanism underlying their self-organisation? Our computational simulations show that network diffusion (traffic flow or information transfer) steers network evolution towards emergence of complex network structures. The emergence is effectuated through adaptive rewiring: progressive adaptation of structure to use, creating short-cuts where network diffusion is intensive while annihilating underused connections. With adaptive rewiring as the engine of universal small-worldness, overall diffusion rate tunes the systems’ adaptation, biasing local or global connectivity patterns. Whereas the former leads to modularity, the latter provides a preferential attachment regime. As the latter sets in, the resulting small-world structures undergo a critical shift from modular (decentralised) to centralised ones. At the transition point, network structure is hierarchical, balancing modularity and centrality - a characteristic feature found in, for instance, the human brain.
Oxygen isotope anomaly in tropospheric CO2 and implications for CO2 residence time in the atmosphere and gross primary productivity
Authors: Liang Mao-Chang , Mahata Sasadhar , Laskar Amzad H. , Thiemens Mark H. , Newman Sally
Published: October 2017

The abundance variations of near surface atmospheric CO2isotopologues (primarily16O12C16O,16O13C16O,17O12C16O, and18O12C16O) represent an integrated signal from anthropogenic/biogeochemical processes, including fossil fuel burning, biospheric photosynthesis and respiration, hydrospheric isotope exchange with water, and stratospheric photochemistry. Oxygen isotopes, in particular, are affected by the carbon and water cycles. Being a useful tracer that directly probes governing processes in CO2biogeochemical cycles, Δ17O (=ln(1 + δ17O) − 0.516 × ln(1 + δ18O)) provides an alternative constraint on the strengths of the associated cycles involving CO2. Here, we analyze Δ17O data from four places (Taipei, Taiwan; South China Sea; La Jolla, United States; Jerusalem, Israel) in the northern hemisphere (with a total of 455 measurements) and find a rather narrow range (0.326 ± 0.005‰). A conservative estimate places a lower limit of 345 ± 70 PgC year−1on the cycling flux between the terrestrial biosphere and atmosphere and infers a residence time of CO2of 1.9 ± 0.3 years (upper limit) in the atmosphere. A Monte Carlo simulation that takes various plant uptake scenarios into account yields a terrestrial gross primary productivity of 120 ± 30 PgC year−1and soil invasion of 110 ± 30 PgC year−1, providing a quantitative assessment utilizing the oxygen isotope anomaly for quantifying CO2cycling.
Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes
Authors: Zapata Luis , Susak Hana , Drechsel Oliver , Friedländer Marc R. , Estivill Xavier , Ossowski Stephan
Published: October 2017

Tumors are composed of an evolving population of cells subjected to tissue-specific selection, which fuels tumor heterogeneity and ultimately complicates cancer driver gene identification. Here, we integrate cancer cell fraction, population recurrence, and functional impact of somatic mutations as signatures of selection into a Bayesian model for driver prediction. We demonstrate that our model, cDriver, outperforms competing methods when analyzing solid tumors, hematological malignancies, and pan-cancer datasets. Applying cDriver to exome sequencing data of 21 cancer types from 6,870 individuals revealed 98 unreported tumor type-driver gene connections. These novel connections are highly enriched for chromatin-modifying proteins, hinting at a universal role of chromatin regulation in cancer etiology. Although infrequently mutated as single genes, we show that chromatin modifiers are altered in a large fraction of cancer patients. In summary, we demonstrate that integration of evolutionary signatures is key for identifying mutational driver genes, thereby facilitating the discovery of novel therapeutic targets for cancer treatment.
Plasmodium falciparum specific helicase 3 is nucleocytoplasmic protein and unwinds DNA duplex in 3′ to 5′ direction
Authors: Chauhan Manish , Tarique Mohammed , Tuteja Renu
Published: October 2017

Plasmodium falciparum is responsible for most dangerous and prevalent form of malaria. The emergence of multi drug resistant parasite hindered the prevention of malaria burden worldwide. Helicases are omnipresent enzymes, which play important role in nucleic acid metabolism and can be used as potential targets for development of novel therapeutics. The genome wide analysis of P. falciparum 3D7 strain revealed some novel parasite specific helicases, which are not present in human host. Here we report the detailed biochemical characterization of P. falciparum parasite specific helicase 3 (PfPSH3). The characteristic ATPase and helicase activities of PfPSH3 reside in its N-terminal region (PfPSH3N) as it contains all the conserved signature motifs whereas the C-terminal does not show any detectable biochemical activity. PfPSH3N also shows DNA helicase activity in the 3′–5′ direction. The immunofluorescence microscopy results show that PSH3 is localized in nucleus as well as in cytoplasm during different stages such as trophozoite and early schizont stages of intraerythrocytic development. This report sets the foundation for further study of parasite specific helicases and will be helpful in understanding the parasite biology.
Adolescent Ethanol Exposure Enhances NMDA Receptor-Mediated Currents in Hippocampal Neurons: Reversal by Gabapentin
Authors: Swartzwelder H. S. , Park Maeng-Hee , Acheson Shawn
Published: October 2017

Adolescent intermittent ethanol (AIE) exposure compromises neural function into adulthood. We have reported that astrocyte-secreted thrombospondins, and their target neuronal receptors (α2δ−1) are upregulated in the hippocampus in adulthood after AIE, suggesting aberrant excitatory synaptogenesis and hyperexcitability in memory-related circuits. Gabapentin antagonizes the interaction of thrombospondins (TSPs) with the α2δ−1 receptor, and thus may reverse or ameliorate the effects of AIE on hippocampal function. Adolescent rats were exposed to AIE or vehicle. In adulthood, hippocampal slices were prepared. Half of the slices from each animal were pre-incubated in normal artificial cerebrospinal fluid (aCSF) while half were pre-incubated in aCSF containing gabapentin. Whole-cell voltage clamp recordings were then made from CA1 pyramidal cells in normal aCSF. Evoked, N-methyl-D-aspartate (NMDA) receptor-mediated currents were recorded at baseline, and after application of the GluN2B antagonist, RO25–6981. Current amplitudes were higher in neurons from AIE-exposed animals. However, no amplitude increase was observed in neurons from slices that had been pre-incubation in gabapentin. GluN2B antagonism reduced NMDA receptor-mediated currents more efficaciously in cells from AIE-exposed animals, an effect that was also reversed by pre-incubation in gabapentin. These findings identify a mechanism underlying the enduring effects of AIE, and a clinically-utilized agent that may ameliorate those effects.
Transgenic Nicotiana benthamiana plants expressing a hairpin RNAi construct of a nematode Rs-cps gene exhibit enhanced resistance to Radopholus similis
Authors: Li Yu , Wang Ke , Lu Qisen , Du Juan , Wang Zhenyue , Wang Desen , Sun Bingjian , Li Honglian
Published: October 2017

Burrowing nematodes (Radopholus similis) cause severe harm in many agronomic and horticultural crops and are very difficult to manage. Cathepsin S is one of the most important cysteine proteinases and plays key roles in nematodes and many other parasites. To evaluate the effect of in planta RNAi on the control of this nematode, a specific fragment from the protease gene, cathepsin S (Rs-cps), was cloned into the binary vector pFGC5941 in the forward and reverse orientations to construct recombinant plant RNAi vectors. Transgenic Nicotiana benthamiana plants expressing Rs-cps dsRNA were obtained and studied. The transcript abundance of Rs-cps dsRNA appeared to be diverse in the different transgenic lines. Moreover, the bioassay results revealed that Rs-cps transgenic N. benthamiana plants were resistant to R. similis and the transcription level of Rs-cps in R. similis was drastically decreased. In addition, the reproduction and hatching rate of R. similis isolated from the Rs-cps transgenic plants were also significantly reduced. Our results suggest that Rs-cps is essential for the reproduction and pathogenicity of R. similis. This is the first study to employ in planta RNAi approach to target the Rs-cps gene for the control of plant parasitic nematodes.
Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits
Authors: Naziga Emmanuel B. , Wereszczynski Jeff
Published: October 2017

Pili are elongated structures that protrude from bacteria and increase their virulence. TheStreptococcus pnuenomaepilus island 1 pili are composed of three subunits, RrgA, RrgB, and RrgC, and are assembled by three class C sortase C (SrtC) enzymes: SrtC-1, SrtC-2, and SrtC-3. Pilin subunits are recognized by SrtC proteins through a pentapeptide sorting signal, and while previous studies have sought to characterize the selectivities of SrtC isoforms for these subunits, the molecular mechanisms underlying these interactions remain unclear. Here, we report a series of molecular dynamics simulations of each SrtC enzyme with the sorting signals of RrgA, RrgB, and RrgC to determine the structural and thermodynamic basis of pilin recognition. Results show that, in accordance with previous studies, both SrtC-1 and SrtC-3 are selective for RrgB, while SrtC-2 is selective for RrgA. This specificity is tuned by the sorting signal binding conformation in which the first two residue sidechains complement hydrophobic residues around the active site, while the third residue projects away from the catalytic triad and makes specific interactions based on its charge and reach. Together, these results provided atomic-scale descriptions of the SrtC substrate selectivity mechanisms and extend the emerging model of pilin construction inS. pnuenomae.
Objective-lens-free Fiber-based Position Detection with Nanometer Resolution in a Fiber Optical Trapping System
Authors: Ti Chaoyang , Ho-Thanh Minh-Tri , Wen Qi , Liu Yuxiang
Published: October 2017

Position detection with high accuracy is crucial for force calibration of optical trapping systems. Most existing position detection methods require high-numerical-aperture objective lenses, which are bulky, expensive, and difficult to miniaturize. Here, we report an affordable objective-lens-free, fiber-based position detection scheme with 2 nm spatial resolution and 150 MHz bandwidth. This fiber based detection mechanism enables simultaneous trapping and force measurements in a compact fiber optical tweezers system. In addition, we achieved more reliable signal acquisition with less distortion compared with objective based position detection methods, thanks to the light guiding in optical fibers and small distance between the fiber tips and trapped particle. As a demonstration of the fiber based detection, we used the fiber optical tweezers to apply a force on a cell membrane and simultaneously measure the cellular response.