bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bidirectional Associations of Momentary Affect with Physical Activity and Sedentary Behaviors in Working Adults
Authors: Kim Jinhyuk , Conroy David E , Smyth Joshua M 
Published: October 2019

AbstractBackgroundAffective experiences and movement-based behaviors form a system that has been shown to influence exercise adherence and mental health outcomes. Little is known about the naturalistic dynamics of the reciprocal associations in this system.PurposeWe examined the time intervals at which momentary affect precedes and follows movement-based behaviors in everyday life.MethodsA community sample of working adults (n = 111) completed ecological momentary assessments (EMA) asking about current affect states (sad, happy, tired, and interested) six times a day for three consecutive days. Ratings were used to generate scores for momentary affective arousal and valence. Participants also wore an activity monitor. Total activity counts and sedentary duration in the shorter to longer time intervals (5–120 min) before or after EMA were used as indicators of movement-based behaviors.ResultsMultilevel modeling showed that current affective arousal predicted higher subsequent activity counts in the longer time intervals (120 min) and less subsequent sedentary behavior in the shorter to longer time intervals (5, 60, and 120 min). For the reversed sequence, neither movement-based behavior predicted subsequent momentary arousal or valence. Affective valence was unrelated to movement-based behaviors in either temporal direction.ConclusionsSome naturally occurring affective experiences (i.e., arousal) might precede, rather than follow, movement-based behaviors. Understanding affective arousal may contribute to improved management of subsequent movement-based behaviors in everyday life.
Death Caused by Vaginal Injection of Hyaluronic Acid and Collagen: A Case Report
Authors: Yang Yang , Sheng Hengwei , Gu Qinmei , Su Lei , Tong Huasheng , Chen Jianwu , Qi Xiangdong 
Published: October 2019

Abstract
With the expanding utilization of hyaluronic acid (HA) and collagen as cosmetic fillers in plastic and reconstructive surgery, complications due to their excessive use and/or irregular procedures warrant great caution. Recently, a fatal case occurred caused by a poorly regulated procedure of vaginal injection of HA and collagen. A 33-year-old female was admitted to the emergency department 3 hours after the operation with a chief complaint of dyspnea, which initiated 5 to 10 minutes after the operation. Her blood pressure remained low while dopamine pressor and fluid replacement were used. Computed tomography of the chest showed local exudation in the lower lobe of the left lung, enlargement of right atrium and ventricle, and uneven development of the bilateral inferior lobar artery with filling defects. Pulmonary computed tomography angiography and three-dimensional reconstruction showed continuous interruption of pulmonary artery branches of the posterior basal segment of the right lower lobe. Unfortunately, the clinical symptoms caused by vaginal injection aggravated rapidly and could not be effectively controlled. The patient died 9 hours after injection. Pulmonary complications after injection of cosmetic fillers are scarcely reported. Thus far, only 2 cases of HA-related pulmonary complications after vaginal injection have been described. The present case emphasizes that surgeons and other healthcare providers must be aware of the risk of serious pulmonary complications and even death associated with these 2 widely utilized injectable fillers.
Level of Evidence: 5
Tools for fundamental analysis functions of TCR repertoires: a systematic comparison
Authors: Zhang Yanfang , Yang Xiujia , Zhang Yanxia , Zhang Yan , Wang Minhui , Ou Jin Xia , Zhu Yan , Zeng Huikun , Wu Jiaqi , Lan Chunhong , Zhou Hong-Wei , Yang Wei , Zhang Zhenhai 
Published: October 2019

Abstract
The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.
Matched Forest: supervised learning for high-dimensional matched case–control studies
Authors: Shomal Zadeh Nooshin , Lin Sangdi , Runger George C 
Published: October 2019

Abstract

Motivation
Matched case–control analysis is widely used in biomedical studies to identify exposure variables associated with health conditions. The matching is used to improve the efficiency. Existing variable selection methods for matched case–control studies are challenged in high-dimensional settings where interactions among variables are also important. We describe a quite different method for high-dimensional matched case–control data, based on the potential outcome model, which is not only flexible regarding the number of matching and exposure variables but also able to detect interaction effects.

Results
We present Matched Forest (MF), an algorithm for variable selection in matched case–control data. The method preserves the case and control values in each instance but transforms the matched case–control data with added counterfactuals. A modified variable importance score from a supervised learner is used to detect important variables. The method is conceptually simple and can be applied with widely available software tools. Simulation studies show the effectiveness of MF in identifying important variables. MF is also applied to data from the biomedical domain and its performance is compared with alternative approaches.

Availability and implementation
R code for implementing MF is available at https://github.com/NooshinSh/Matched_Forest.

Supplementary information
Supplementary data are available at Bioinformatics online.
Increased Mortality After Tuberculosis Treatment Completion in Persons Living With Human Immunodeficiency Virus in Latin America
Authors: Koenig Serena P , Kim Ahra , Shepherd Bryan E , Cesar Carina , Veloso Valdilea , Cortes Claudia P , Padgett Denis , Crabtree-Ramírez Brenda , Gotuzzo Eduardo , McGowan Catherine C , Sterling Timothy R , Pape Jean W 
Published: October 2019

Abstract
We assessed the association between cured tuberculosis (TB) and mortality among persons living with human immunodeficiency virus (HIV) in Latin America. We compared survival among persons with and without TB at enrollment in HIV care, starting 9 months after clinic enrollment. In multivariable analysis, TB was associated with higher long-term mortality (hazard ratio, 1.57; 95% confidence interval, 1.25–1.99).
The effect of natriuretic C-type peptide and its change over time on mortality in patients on haemodialysis or haemodiafiltration
Authors: de Roij van Zuijdewijn Camiel L M , van Gastel Lieke H A , ter Wee Piet M , Bots Michiel L , Blankestijn Peter J , van den Dorpel Marinus A , Fouque Denis , Nubé Menso J , Grooteman Muriel P C 
Published: October 2019

Abstract

Background
C-type natriuretic peptide (CNP) and its co-product N-terminal proCNP (NTproCNP) have been associated with beneficial effects on the cardiovascular system. In prevalent dialysis patients, however, a relation between NTproCNP and mortality has not yet been investigated. Furthermore, as a middle molecular weight substance, its concentration might be influenced by dialysis modality.

Methods
In a cohort of patients treated with haemodialysis (HD) or haemodiafiltration (HDF), levels of NTproCNP were measured at baseline and 6, 12, 24 and 36 months. The relation between serum NTproCNP and mortality and the relation between the 6-month rate of change of NTproCNP and mortality were analysed using Cox regression models. For the longitudinal analyses, linear mixed models were used.

Results
In total, 406 subjects were studied. The median baseline serum NTproCNP was 93 pmol/L and the median follow-up was 2.97 years. No relation between baseline NTproCNP or its rate of change over 6 months and mortality was found. NTproCNP levels remained stable in HD patients, whereas NTproCNP decreased significantly in HDF patients. The relative decline depended on the magnitude of the convection volume.

Conclusions
In our study, levels of NTproCNP appear strongly elevated in prevalent dialysis patients. Second, while NTproCNP remains unaltered in HD patients, its levels decline in individuals treated with HDF, with the decline dependent on the magnitude of the convection volume. Third, NTproCNP is not related to mortality in this population. Thus NTproCNP does not seem to be a useful marker for mortality risk in dialysis patients.
Impact of cardiology follow-up care on treatment and outcomes of patients with new atrial fibrillation discharged from the emergency department
Authors: Hawkins Nathaniel M , Scheuermeyer Frank X , Youngson Erik , Sandhu Roopinder K , Ezekowitz Justin A , Kaul Padma , McAlister Finlay A 
Published: October 2019

Abstract

Aims
The first presentation of atrial fibrillation (AF) is often to an emergency department (ED). We evaluated the association of subsequent specialist care with morbidity and mortality.

Methods and results
Retrospective cohort study of all adults in Alberta, Canada, with a new primary diagnosis of AF treated and released during an index ED visit between 2009 and 2015. Types of physician follow-up within 3 months of ED visit was analysed using Cox proportional hazards models with time-varying covariates. Outcomes were evaluated at 1 year. Of 7986 patients, 476 (6.0%) had no physician follow-up within 3 months, whereas 2730 (34.2%) attended a non-specialist only, 1277 (16.0%) an internal medicine specialist, and 3503 (43.9%) cardiology. An increasing gradient of cardiac investigations occurred across these groups. Cardiology compared with non-cardiologist care was associated with approximately two-fold greater electrophysiology interventions and revascularization, and increased use of beta-blockers (48.9% vs. 43.0%, P &lt; 0.0001), statins (31.4% vs. 26.7%, P &lt; 0.0001), and oral anticoagulation in patients with CHADS2 scores ≥1 (53.7% vs. 43.6%, P &lt; 0.0001). In the subsequent year, cardiology care was associated with fewer deaths [adjusted hazard ratio (aHR) 0.72, 95% confidence interval (CI) 0.55–0.93], strokes (aHR 0.60, 95% CI 0.37–0.96), or major bleeds (aHR 0.69, 95% CI 0.53–0.89). No differences in the risk of hospitalization or ED visits were associated with cardiology care.

Conclusion
Cardiology care after an ED visit for symptomatic new-onset AF is associated with better prognosis. The benefit may be mediated through more intensive investigation, identification, and treatment of cardiovascular risk factors and disease.
Intrinsic role of bacterial secretion systems in phylogenetic niche conservation of Bradyrhizobium spp.
Authors: Banerjee Goutam , Basak Swarnendu , Roy Tathagato , Chattopadhyay Pritam 
Published: October 2019

ABSTRACT
Bradyrhizobium is a biologically important bacterial genus. Different Bradyrhizobium strains exhibit distinct niche selection like free living, root nodular and stem nodular. The present in-silico study was undertaken to identify the role of bacterial secretome in the phylogenetic niche conservation (PNC) of Bradyrhizobium sp. Analysis was carried out with the publicly available 19 complete genome assembly and annotation reports. A protocol was developed to screen the secretome related genes using three different database, viz. genome, proteome and gene ortholog. This resulted into 139 orthologs that include type secretion systems (T1SS-T6SS) along with flagella (Flg), type IV pili (T4P) and tight adherence (Tad) systems. Multivariate analysis using bacterial secretome was undertaken to find out the role of these secretion systems in PNC. In free living strains, T3SS, T4SS and T6SS were completely absent. Whereas, in the stem nodulating strains, T3SS and T6SS were absent, but T4SS was found to be present. On the other hand, the T3SS was found to be present only in the root-nodulating strains. The present investigation clearly demonstrated a pattern of PNC based on the distribution of secretion system components. To the best of our knowledge, this is the first report on PNC of Bradyrhizobium using the multivariate analysis of secretome.
Unique Shine–Dalgarno Sequences in Cyanobacteria and Chloroplasts Reveal Evolutionary Differences in Their Translation Initiation
Authors: Wei Yulong , Xia Xuhua 
Published: October 2019

AbstractMicroorganisms require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A prominent feature that facilitates translation initiation in bacteria is the Shine–Dalgarno (SD) sequence. However, there is much debate over its conservation in Cyanobacteria and in chloroplasts which presumably originated from endosymbiosis of ancient Cyanobacteria. Elucidating the utilization of SD sequences in Cyanobacteria and in chloroplasts is therefore important to understand whether 1) SD role in Cyanobacterial translation has been reduced prior to chloroplast endosymbiosis or 2) translation in Cyanobacteria and in plastid has been subjected to different evolutionary pressures. To test these alternatives, we employed genomic, proteomic, and transcriptomic data to trace differences in SD usage among Synechocystis species, Microcystis aeruginosa, cyanophages, Nicotiana tabacum chloroplast, and Arabidopsis thaliana chloroplast. We corrected their mis-annotated 16S rRNA 3′ terminus using an RNA-Seq-based approach to determine their SD/anti-SD locational constraints using an improved measurement DtoStart. We found that cyanophages well-mimic Cyanobacteria in SD usage because both have been under the same selection pressure for SD-mediated initiation. Whereas chloroplasts lost this similarity because the need for SD-facilitated initiation has been reduced in plastids having much reduced genome size and different ribosomal proteins as a result of host-symbiont coevolution. Consequently, SD sequence significantly increases protein expression in Cyanobacteria but not in chloroplasts, and only Cyanobacterial genes compensate for a lack of SD sequence by having weaker secondary structures at the 5′ UTR. Our results suggest different evolutionary pressures operate on translation initiation in Cyanobacteria and in chloroplast.
A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona
Authors: Satou Yutaka , Nakamura Ryohei , Yu Deli , Yoshida Reiko , Hamada Mayuko , Fujie Manabu , Hisata Kanako , Takeda Hiroyuki , Satoh Noriyuki 
Published: October 2019

Abstract
Since its initial publication in 2002, the genome of Ciona intestinalis type A (Ciona robusta), the first genome sequence of an invertebrate chordate, has provided a valuable resource for a wide range of biological studies, including developmental biology, evolutionary biology, and neuroscience. The genome assembly was updated in 2008, and it included 68% of the sequence information in 14 pairs of chromosomes. However, a more contiguous genome is required for analyses of higher order genomic structure and of chromosomal evolution. Here, we provide a new genome assembly for an inbred line of this animal, constructed with short and long sequencing reads and Hi-C data. In this latest assembly, over 95% of the 123 Mb of sequence data was included in the chromosomes. Short sequencing reads predicted a genome size of 114–120 Mb; therefore, it is likely that the current assembly contains almost the entire genome, although this estimate of genome size was smaller than previous estimates. Remapping of the Hi-C data onto the new assembly revealed a large inversion in the genome of the inbred line. Moreover, a comparison of this genome assembly with that of Ciona savignyi, a different species in the same genus, revealed many chromosomal inversions between these two Ciona species, suggesting that such inversions have occurred frequently and have contributed to chromosomal evolution of Ciona species. Thus, the present assembly greatly improves an essential resource for genome-wide studies of ascidians.
Financial Stress and Risk for Entry into Medicaid Among Older Adults
Authors: Willink Amber , Wolff Jennifer L , Mulcahy John , Davis Karen , Kasper Judith D 
Published: October 2019

Abstract

Background and Objectives
Spending in the Medicaid program is a significant concern to both state and federal policy makers. Medicaid spending is driven by program enrollment and services use. Older adults with high health care needs incur a disproportionate proportion of program spending. This analysis identifies factors that place older Medicare beneficiaries at increased risk for entering into Medicaid.

Research Design and Methods
We use multinomial logistic regression and the 2011–2017 National Health and Aging Trends Study (NHATS) to examine the risks among older Medicare beneficiaries for entering into Medicaid over a 6-year follow-up period. We examine both time-invariant and time-varying factors to measure the impact of social and health and functioning changes at older ages.

Results
The risk of entry into Medicaid was higher for older adults who relocated to a nursing home (relative risk ratio [RRR]: 7.75; 95% confidence interval [CI]: 5.33–11.26) or other residential care setting (RRR: 1.36; 95% CI: 0.96–1.92) compared to those who remained in traditional community settings. Older adults who reported skipping a meal in the last month because there was not enough money to buy food were 2.4 times (95% CI: 1.10–5.21) more likely to enter Medicaid than those who did not. Similarly, older adults who reported not having enough money to pay household utility bills in the last year were 1.89 times (95% CI: 1.08–3.30) more likely to enter Medicaid.

Discussion and Implications
Study findings suggest that trouble paying for basic needs increases the risk of entry into Medicaid. Further research is required to examine whether addressing these needs through improved access to social services that enable older adults to live safely in their home may delay or mitigate entry into Medicaid.
Multitasking and Dual Motivational Systems: A Dynamic Longitudinal Study
Authors: Xu Shan , Wang Zheng , Woods Kelsey 
Published: October 2019

AbstractThis study further explores the myth of media multitasking: that is, why people increasingly media multitask despite its known harmful effects on performance. Building on previous research on the emotional gratifications of media multitasking and guided by the dynamic motivational activation (DMA) approach, this study specifies emotional gratifications in terms of positive and negative emotions, as well as their underlying appetitive and aversive motivational changes. Using a dynamic panel analysis of longitudinal experience sampling data collected from 71 adolescents (ages 11–17; 61% girls) over 2 weeks, this study identifies several dynamic reciprocal impacts of media multitasking and the dual motivational systems. As predicted by DMA, media multitasking coactivates both the appetitive and aversive motivational systems, and increases both positive and negative emotions; interestingly, only the appetitive system goes on to determine subsequent media multitasking.
Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis
Authors: Yang Xue , Bayat Vafa , DiDonato Nataliya , Zhao Yang , Zarnegar Brian , Siprashvili Zurab , Lopez-Pajares Vanessa , Sun Tao , Tao Shiying , Li Chenjian , Rump Andreas , Khavari Paul , Lu Bingwei 
Published: October 2019

AbstractMissense mutations in the RNA exosome component exosome component 2 (EXOSC2), also known as ribosomal RNA-processing protein 4 (RRP4), were recently identified in two unrelated families with a novel syndrome known as Short stature, Hearing loss, Retinitis pigmentosa and distinctive Facies (SHRF, #OMIM 617763). Little is known about the mechanism of the SHRF pathogenesis. Here we have studied the effect of mutations in EXOSC2/RRP4 in patient-derived lymphoblasts, clustered regularly interspaced short palindromic repeats (CRISPR)-generated mutant fetal keratinocytes and Drosophila. We determined that human EXOSC2 is an essential gene and that the pathogenic G198D mutation prevents binding to other RNA exosome components, resulting in protein and complex instability and altered expression and/or activities of critical genes, including those in the autophagy pathway. In parallel, we generated multiple CRISPR knockouts of the fly rrp4 gene. Using these flies, as well as rrp4 mutants with Piggy Bac (PBac) transposon insertion in the 3′UTR and RNAi flies, we determined that fly rrp4 was also essential, that fly rrp4 phenotypes could be rescued by wild-type human EXOSC2 but not the pathogenic form and that fly rrp4 is critical for eye development and maintenance, muscle ultrastructure and wing vein development. We found that overexpression of the transcription factor MITF was sufficient to rescue the small eye and adult lethal phenotypes caused by rrp4 inhibition. The autophagy genes ATG1 and ATG17, which are regulated by MITF, had similar effect. Pharmacological stimulation of autophagy with rapamycin also rescued the lethality caused by rrp4 inactivation. Our results implicate defective autophagy in SHRF pathogenesis and suggest therapeutic strategies.
Genetic and biophysical modelling evidence of generational connectivity in the intensively exploited, Western North Atlantic red grouper (Epinephelus morio)
Authors: Bernard Andrea M , Johnston Matthew W , Pérez-Portela Rocío , Oleksiak Marjorie F , Coleman Felicia C , Shivji Mahmood S 
Published: October 2019

AbstractUnderstanding the connectivity of reef organisms is important to assist in the conservation of biological diversity and to facilitate sustainable fisheries in these ecosystems. Common methods to assess reef connectivity include both population genetics and biophysical modelling. Individually, these techniques can offer insight into population structure; however, the information acquired by any singular analysis is often subject to limitations, underscoring the need for a multi-faceted approach. To assess the connectivity dynamics of the red grouper (Epinephelus morio), an economically important reef fish species found throughout the Gulf of Mexico and USA western Atlantic, we utilized two sets of genetic markers (12 microsatellite loci and 632 single nucleotide polymorphisms) to resolve this species’ population genetic structure, along with biophysical modelling to deliver a spatial forecast of potential larval “sources” and “sinks” across these same regions and spatial scale. Our genetic survey indicates little, if any, evidence of population genetic structure and modelling efforts indicate the potential for ecological connectivity between sampled regions over multiple generations. We offer that using a dual empirical and theoretical approach lessens the error associated with the use of any single method and provides an important step towards the validation of either of these methodologies.