bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of 1.5 °C and 2 °C global warming on regional rainfall and temperature change across India
Authors: Yaduvanshi Aradhana , Zaroug Modathir , Bendapudi Ramkumar , New Mark 
Published: October 2019

Abstract
The participating member nations in Paris at the 2015 convention of the United Nations Framework Convention on Climate Change (UNFCCC) resolved to maintain the rise in global average temperature to a level much less than 2.0 °C compared to pre-industrial levels. It was also committed that the parties would continue with all-out endeavor to limit warming to 1.5 °C. For a country like India with a primarily agrarian economy this leads to two key questions. Firstly, what does the global rise of mean annual temperature (1.5 °C and 2.0 °C) mean at the regional scale? Secondly, what are the implications of keeping warming at or below 1.5 °C for different sectors and in particular on agriculture and water resources? To address these questions we have examined the annual and seasonal impacts of 1.5 °C and 2 °C global temperature rise (GTR) on temperature and rainfall change over all the states of India under two Representative concentration pathways, RCP 8.5 and RCP 4.5, using all Coupled Model Inter Comparison Project CMIP5 Models. Rainfall is projected to increase over all the states with very low change in the western part of the country and highest change in the North eastern and southern region of the country under RCP 8.5. 35% of the country is projected to witness a temperature change equal to or lesser than global mean temperature of 1.5 °C and 2.0 °C whereas 65% is expected to show a greater rise in temperature. The most severe temperature change is expected to be witnessed by the presently colder Northern most states of India such as Jammu and Kashmir, Himachal Pradesh and Uttaranchal (2.0 °C to 2.2 °C at 1.5 °C and 2.5 °C to 2.8 °C at 2.0 °C) in both RCPs. There are opportunities and threats due to climate change and it is imperative for researchers and policy makers to recognize these in the context of the scenarios of 1.5 °C and 2.0 °C global temperature changes. It is essential for the current national and state action plan on climate change and adaptation to be more sensitive in strategizing an efficient response to the different scenarios at the global level (3 °C, 2 °C and 1.5 °C) in order to take more informed policy decisions at global level in synergy with the regional analysis to be able to develop strategies that benefit the local populace.
Neuropsychological Test Performances and Depression in Early-Stage De Novo Parkinson’s Disease
Authors: Honsey Blair N , Erickson Lauren O , Wyman-Chick Kathryn A 
Published: October 2019

Abstract

Objective
Evaluate neuropsychological test performance in depressed patients with early-stage Parkinson’s disease.

Method
Data from 422 participants from the Parkinson’s Progression Marker Initiative were examined. The Geriatric Depression Scale-15 was used to categorize depressed and non-depressed participants. Neuropsychological tests measured verbal learning/memory, processing speed, visuospatial ability, verbal fluency, and working memory. Demographic and clinical variables were compared using independent samples t tests and chi-square analyses.
Linear regression models were fit to adjust for age, years of education, and symptom duration.

Results
The non-depressed group (n = 280) was significantly older; t(246.08) = 2.25, p = .026 and had higher education; t(420) = 2.35, p = .019; and longer duration of PD symptoms; t(170.58) = −2.13, p = .035 than the depressed group (n = 142). The non-depressed group performed better on a working memory task than the depressed group, t(420) = 2.05, p = .041, but the results did not appear to be of clinical significance. There was no significant difference between other cognitive domains. The results were not influenced by age, education, or disease duration.

Conclusions
Among patients with early-stage, untreated Parkinson’s disease, depression does not appear to affect neuropsychological test performance. Clinicians should demonstrate caution in over-interpreting the influence of depression on cognition in this population.
3D flow field estimation and assessment for live cell fluorescence microscopy
Authors: Manandhar Sandeep , Bouthemy Patrick , Welf Erik , Danuser Gaudenz , Roudot Philippe , Kervrann Charles 
Published: October 2019

Abstract

Motivation
The revolution in light sheet microscopy enables the concurrent observation of thousands of dynamic processes, from single molecules to cellular organelles, with high spatiotemporal resolution. However, challenges in the interpretation of multidimensional data requires the fully automatic measurement of those motions to link local processes to cellular functions. This includes the design and the implementation of image processing pipelines able to deal with diverse motion types, and 3D visualization tools adapted to the human visual system.

Results
Here, we describe a new method for 3D motion estimation that addresses the aforementioned issues. We integrate 3D matching and variational approach to handle a diverse range of motion without any prior on the shape of moving objects. We compare different similarity measures to cope with intensity ambiguities and demonstrate the effectiveness of the Census signature for both stages. Additionally, we present two intuitive visualization approaches to adapt complex 3D measures into an interpretable 2D view, and a novel way to assess the quality of flow estimates in absence of ground truth.

Availability and implementation
https://team.inria.fr/serpico/data/3d-optical-flow-data/

Supplementary information
Supplementary data are available at Bioinformatics online.
Topological data analysis quantifies biological nano-structure from single molecule localization microscopy
Authors: Pike Jeremy A , Khan Abdullah O , Pallini Chiara , Thomas Steven G , Mund Markus , Ries Jonas , Poulter Natalie S , Styles Iain B 
Published: October 2019

Abstract

Motivation
Localization microscopy data is represented by a set of spatial coordinates, each corresponding to a single detection, that form a point cloud. This can be analyzed either by rendering an image from these coordinates, or by analyzing the point cloud directly. Analysis of this type has focused on clustering detections into distinct groups which produces measurements such as cluster area, but has limited capacity to quantify complex molecular organization and nano-structure.

Results
We present a segmentation protocol which, through the application of persistence-based clustering, is capable of probing densely packed structures which vary in scale. An increase in segmentation performance over state-of-the-art methods is demonstrated. Moreover we employ persistent homology to move beyond clustering, and quantify the topological structure within data. This provides new information about the preserved shapes formed by molecular architecture. Our methods are flexible and we demonstrate this by applying them to receptor clustering in platelets, nuclear pore components, endocytic proteins and microtubule networks. Both 2D and 3D implementations are provided within RSMLM, an R package for pointillist-based analysis and batch processing of localization microscopy data.

Availability and implementation
RSMLM has been released under the GNU General Public License v3.0 and is available at https://github.com/JeremyPike/RSMLM. Tutorials for this library implemented as Binder ready Jupyter notebooks are available at https://github.com/JeremyPike/RSMLM-tutorials.

Supplementary information
Supplementary data are available at Bioinformatics online.
Theorizing social media and activism: where is community development?
Authors: McCabe Angus , Harris Kevin 
Published: October 2019

AbstractThere is a growing public and academic debate on the societal impacts of the internet and, in particular, social media. For its proponents, social media is a force for change, which can challenge entrenched hierarchies, redistribute power, democratize information, support mass mobilization and contribute to the building of global movements. Increasingly such positivist arguments are being questioned. Critics argue that it has become a sinister force, facilitating the spread of ‘fake news’, providing an instrument for citizen surveillance and re-enforcing neoliberal hegemony. The community development literature has barely engaged in those debates around social media that appear urgent in other disciplines. Social media has been seen as a value-free tool for broadcasting and dissemination, and neither evaluated as a force for change nor examined as an instrument of neoliberal intents. Although there is a community development literature on neoliberalism and globalization, it often accepts these, rather than critiques them, as the contexts within which community development operates. Challenging established power imbalances and enhancing citizen participation in democratic processes are purposes central to community development values. Analysis of wider literature raises questions with regard to the values embedded in the technologies from which enhanced levels of participation and engagement are expected to flow. It also raises questions about who benefits most from the affordances of these technologies. This article, drawing on an extensive literature review, presents the case for community development values to be asserted in these debates.
Isoniazid Preventive Therapy and Pregnancy Outcomes in Women Living With Human Immunodeficiency Virus in the Tshepiso Cohort
Authors: Salazar-Austin Nicole , Cohn Silvia , Lala Sanjay , Waja Ziyaad , Dooley Kelly E , Hoffmann Christopher J , Chaisson Richard E , Martinson Neil 
Published: October 2019

Abstract

Background
Both pregnancy and human immunodeficiency virus (HIV) increase the risk of tuberculosis disease, which results in poor maternal, pregnancy, and infant outcomes. Isoniazid preventive therapy (IPT) reduces mortality among individuals living with HIV in high-burden settings but has recently been associated with adverse pregnancy outcomes when initiated during pregnancy.

Methods
In this secondary analysis, we used multivariable logistic regression to evaluate the association between IPT exposure and adverse pregnancy outcomes (fetal demise, prematurity, low birth weight, congenital anomaly) in pregnant women living with HIV enrolled as controls in the Tshepiso study, a prospective observational cohort of pregnant women living with HIV with and without tuberculosis disease in Soweto, South Africa, from 2011–2014.

Results
There were 151 women enrolled with known pregnancy outcomes; 69 (46%) reported IPT initiation during pregnancy. Of the 69 IPT-exposed women, 11 (16%) had an adverse pregnancy outcome compared with 23 (28%) IPT-unexposed women. The adjusted odds of having an adverse pregnancy outcome was 2.5 (95% confidence interval, 1.0–6.5; P = .048) times higher in IPT-unexposed women compared with IPT-exposed women after controlling for maternal age, CD4 count, viral load, antiretroviral regimen, body mass index, and anemia.

Conclusions
IPT exposure during pregnancy was not negatively associated with pregnancy outcomes after controlling for demographic, clinical, and HIV-related factors. These results provide some reassurance that IPT can be safely used in the second or third trimester of pregnancy. Additional research is needed to evaluate the safety of IPT and new short-course tuberculosis preventive therapies during pregnancy.
Longitudinal Evidence for the Effects of Social Group Engagement on the Cognitive and Mental Health of Chinese Retirees
Authors: Lam Ben C P , Haslam Catherine , Steffens Niklas K , Yang Jie , Haslam S Alexander , Cruwys Tegan , Pachana Nancy A 
Published: October 2019

Abstract

Background
Research investigating the health benefits of social group participation in the retirement transition has provided little insight into the longitudinal effects on cognitive health and the generalizability of these relationships to non-Western samples. The present paper addresses these issues by examining the effects of social group engagement on the cognitive performance and depression symptoms of Chinese older adults followed over 4 years in their transition to retirement.

Methods
Using the China Health and Retirement Longitudinal Study (CHARLS) data, a sample of 1,297 Chinese seniors transitioning to retirement were followed between 2011 and 2013, and then 2 years later (in 2015) after retirement. Group-based social engagement was used to predict retiree cognitive performance and depression symptoms across time.

Results
After controlling for established demographic covariates and close relationship factors at baseline, social group engagement at baseline positively predicted overall cognitive performance and depression symptoms. Moreover, positive change in group engagement was associated with reduced decline in cognitive performance over the 4-year retirement transition period.

Discussion
The current findings demonstrate the generalizability of the health benefits of social group engagement to cognitive health and to a non-Western (Chinese) sample of retirees.
Improvements in seismic resolution and current limitations in the Global Seismographic Network
Authors: Ringler A T , Steim J , Wilson D C , Widmer-Schnidrig R , Anthony R E 
Published: October 2019

SUMMARYStation noise levels play a fundamental limitation in our ability to detect seismic signals. These noise levels are frequency-dependent and arise from a number of physically different drivers. At periods greater than 100 s, station noise levels are often limited by the self-noise of the instrument as well as the sensitivity of the instrument to non-seismic noise sources. Recently, station operators in the Global Seismographic Network (GSN) have deployed several Streckeisen STS-6A very broad-band borehole seismometers. These sensors provide a potential replacement for the no-longer-produced Streckeisen STS-1 seismometer and the GeoTech KS-54 000 borehole seismometer. Along with showing some of the initial observational improvements from installing modern very broad-band seismometers at depth, we look at current limitations in the seismic resolution from earth tide periods 100 000 s (0.01 mHz) to Nyquist at most GSN sites (0.02 s or 50 Hz). Finally, we show the potential for improved observations of continuously excited horizontal Earth hum as well as the splitting of very long-period torsional modes. Both of these observations make use of the low horizontal noise levels which are obtained by installing very broad-band borehole seismometers at depth.
Conventional and High-Sensitivity Malaria Rapid Diagnostic Test Performance in Two Transmission Settings: Haiti 2017
Authors: Rogier Eric , Hamre Karen E S , Joseph Vena , Plucinski Mateusz M , Presume Jacquelin , Romilus Ithamare , Mondelus Gina , Elisme Tamara , van den Hoogen Lotus , Lemoine Jean Frantz , Drakeley Chris , Ashton Ruth A , Chang Michelle A , Existe Alexandre , Boncy Jacques , Stresman Gillian , Druetz Thomas , Eisele Thomas P 
Published: October 2019

Abstract
Accurate malaria diagnosis is foundational for control and elimination, and Haiti relies on HRP2-based rapid diagnostic tests (RDTs) identifying Plasmodium falciparum in clinical and community settings. In 2017, one household and two easy-access group (EAG) surveys tested all participants (N=32,506) by conventional and high-sensitivity RDTs (cRDT/hsRDT). A subset of blood samples (n=1,154) were laboratory tested for HRP2 by bead-based immunoassay and for P. falciparum 18S rDNA by PET-PCR. Both RDT types detected low concentrations of HRP2 with sensitivity estimates between 2.6 and 14.6 ng/mL. Compared to the predicate HRP2 laboratory assay,, RDT sensitivity ranged from 86.3% to 96.0% between tests and settings, and specificity from 90.0% to 99.6%. In the household survey, the hsRDT provided a significantly higher number of positive tests, but this represented a very small proportion (<0.2%) of all participants. These data show an hsRDT may have limited utility in a malaria elimination setting like Haiti.
Evolution of Antibodies to Epitopes of PE_PGRS51 in the Spectrum of Active Pulmonary Tuberculosis
Authors: Sakamuri Rama Murthy , Ryndak Michelle B , Singh Krishna Kumar , Laal Suman 
Published: October 2019

Abstract

Background
Intrafamily homology has impeded correlation of expression of individual PE_PGRS proteins with stage of tuberculosis (TB). We investigated the in vivo expression of PE_PGRS51, which has 3 unique regions.

Methods
Sera from patients across the spectrum of TB were used to screen peptide arrays spanning PE_PGRS51.

Results
Antibodies against a subset of conserved “core epitopes” within PE/PGRS domains are elicited during early TB. The epitope repertoire expands to adjacent regions with disease progression. Antiunique region antibodies appear only during cavitary TB.

Conclusions
Elicitation of antiunique region antibodies can serve as markers for in vivo expression of PE_PGRS proteins.
Forgotten metal stent (3 years) presenting with a high burden of intra- and extra-hepatic ducts stones and cholangitis
Authors: Lesetedi Chiapo , Motsumi Mpapho Joseph 
Published: October 2019

Abstract
Forgotten stents may lead to serious complications. We present a case report of a forgotten common bile duct (CBD) fully covered metal stent presenting with recurrent cholangitis. A 79-years-old female patient presented with a history of recurrent cholangitis. Past surgical history was notable for open cholecystectomy for symptomatic cholelithiasis in 2016. Subsequently, she was found to have retained CBD stones in the same year. She had endoscopic retrograde cholangiopancreatography (ERCP), during which a complete clearance of the stone was not achieved and she was stented with a completely covered metal stent. She was lost to follow-up until 2019. A differential diagnosis of cholangitis secondary to a blocked stent was made. At ERCP, she had intra- and extra-hepatic stones, which could not be removed. A plastic stent was deployed. She later had an open bile duct exploration with Roux-en-Y hepaticojejunostomy. Forgotten stents can lead to serious complications. An electronic stent follow-up registry is recommended.
Detection of the nearest Jupiter analogue in radial velocity and astrometry data
Authors: Feng Fabo , Anglada-Escudé Guillem , Tuomi Mikko , Jones Hugh R A , Chanamé Julio , Butler Paul R , Janson Markus 
Published: October 2019

ABSTRACT
The presence of Jupiter is crucial to the architecture of the Solar system and models underline this to be a generic feature of planetary systems. We find the detection of the difference between the position and motion recorded by the contemporary astrometric satellite Gaia and its precursor Hipparcos can be used to discover Jupiter-like planets. We illustrate how observations of the nearby star ϵ Indi A giving astrometric and radial velocity data can be used to independently find the orbit of its suspected companion. The radial velocity and astrometric data provide complementary detections which allow for a much stronger solution than either technique would provide individually. We quantify ϵ Indi A b as the closest Jupiter-like exoplanet with a mass of 3 MJup on a slightly eccentric orbit with an orbital period of 45 yr. While other long-period exoplanets have been discovered, ϵ Indi A b provides a well-constrained mass and along with the well-studied brown dwarf binary in orbit around ϵ Indi A means that the system provides a benchmark case for our understanding of the formation of gas giant planets and brown dwarfs.
A semi-analytical model for secular dynamics of test particles in hierarchical triple systems
Authors: Lei Hanlun 
Published: October 2019

ABSTRACT
In this work, a semi-analytical model is formulated up to an arbitrary order in the semimajor axis ratio of the inner and outer binaries to describe the long-term (secular) dynamics of test particles in hierarchical triple systems. The third-body disturbing function is expressed as a Fourier series, where the harmonic arguments are linear combinations of the perturber’s mean anomaly, and the test particle’s mean anomaly, longitude of the ascending node, and argument of pericentre. Based on the series expansion, it is straightforward to arrive at the secular equations of motion by directly eliminating those terms that are irrelevant to the long-term dynamics. When the perturbations are so strong that the system’s hierarchy is no longer high, the conventional double-averaged model fails to predict the long-term behaviours of test particles. To overcome the difficulty, we develop a corrected double-averaged model by taking into account the short-term effects within the orbital periods of the inner and outer binaries. The resulting averaged model is applied to Jupiter’s irregular satellites, and simulation results show that the corrected model can reproduce the behaviours on time-scales much longer than the orbital periods. Moreover, we retrieve a triple-averaged model and discuss the associated dynamics in the phase space. It is found that the Kozai resonance in the corrected model occurs at a higher inclination than that in the conventional model.
The H i bias during the Epoch of Reionization
Authors: Xu Wenxiao , Xu Yidong , Yue Bin , Iliev Ilian T , Trac Hy , Gao Liang , Chen Xuelei 
Published: October 2019

ABSTRACT
The neutral hydrogen (H i) and its 21 cm line are promising probes to the reionization process of the intergalactic medium (IGM). To use this probe effectively, it is imperative to have a good understanding on how the neutral hydrogen traces the underlying matter distribution. Here, we study this problem using seminumerical modelling by combining the H i in the IGM and the H i from haloes during the epoch of reionization (EoR), and investigate the evolution and the scale dependence of the neutral fraction bias as well as the 21 cm line bias. We find that the neutral fraction bias on large scales is negative during reionization, and its absolute value on large scales increases during the early stage of reionization and then decreases during the late stage. During the late stage of reionization, there is a transition scale at which the H i bias transits from negative on large scales to positive on small scales, and this scale increases as the reionization proceeds to the end.
Effects of metallicity on high-mass X-ray binary formation
Authors: Ponnada S , Brorby M , Kaaret P 
Published: October 2019

ABSTRACT
The heating of the intergalactic medium in the early, metal-poor Universe may have been partly due to radiation from high-mass X-ray binaries (HMXBs). Previous investigations on the effect of metallicity have used galaxies of different types. To isolate the effects of metallicity on the production of HMXBs, we study a sample consisting only of 46 blue compact dwarf galaxies covering metallicity in the range 12+log(O/H) of 7.15–8.66. To test the hypothesis of metallicity dependence in the X-ray luminosity function (XLF), we fix the XLF form to that found for near-solar metallicity galaxies and use a Bayesian method to constrain the XLF normalization as a function of star formation rate for three different metallicity ranges in our sample. We find an increase by a factor of 4.45 ± 2.04 in the XLF normalization between the metallicity ranges 7.1–7.7 and 8.2–8.66 at a statistical significance of 99.79 per cent. Our results suggest that HMXB production is enhanced at low metallicity, and consequently that HMXBs may have contributed significantly to the reheating of the early Universe.