bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal shifts in the mycobiome structure and network architecture associated with a rat (Rattus norvegicus) deep partial-thickness cutaneous burn
Authors: Sanjar Fatemeh , Weaver Alan J , Peacock Trent J , Nguyen Jesse Q , Brandenburg Kenneth S , Leung Kai P 
Published: March 2019

Abstract
With a diverse physiological interface to colonize, mammalian skin is the first line of defense against pathogen invasion and harbors a consortium of microbes integral in maintenance of epithelial barrier function and disease prevention. While the dynamic roles of skin bacterial residents are expansively studied, contributions of fungal constituents, the mycobiome, are largely overlooked. As a result, their influence during skin injury, such as disruption of skin integrity in burn injury and impairment of host immune defense system, is not clearly delineated. Burn patients experience a high risk of developing hard-to-treat fungal infections in comparison to other hospitalized patients. To discern the changes in the mycobiome profile and network assembly during cutaneous burn-injury, a rat scald burn model was used to survey the mycobiome in healthy (n = 30) (sham-burned) and burned (n = 24) skin over an 11-day period. The healthy skin demonstrated inter-animal heterogeneity over time, while the burned skin mycobiome transitioned toward a temporally stabile community with declining inter-animal variation starting at day 3 post-burn injury. Driven primarily by a significant increase in relative abundance of Candida, fungal species richness and abundance of the burned skin decreased, especially in days 7 and 11 post-burn. The network architecture of rat skin mycobiome displayed community reorganization toward increased network fragility and decreased stability compared to the healthy rat skin fungal network. This study provides the first account of the dynamic diversity observed in the rat skin mycobiome composition, structure, and network assembly associated with postcutaneous burn injury.
Coccidioidomycosis Among American Indians and Alaska Natives, 2001–2014
Authors: McCotter Orion , Kennedy Jordan , McCollum Jeffrey , Bartholomew Michael , Iralu Jonathan , Jackson Brendan R , Haberling Dana , Benedict Kaitlin 
Published: March 2019

Abstract

Background
American Indians and Alaska Natives (AI/ANs) may be uniquely vulnerable to coccidioidomycosis given the large population residing in the Southwestern United States. We describe coccidioidomycosis-associated hospitalizations and outpatient visits during 2001–2014 in the Indian Health Service (IHS) system and compare hospitalizations with data from the Agency for Healthcare Research and Quality’s National (Nationwide) Inpatient Sample (NIS).

Methods
We identified hospitalizations in the IHS and the NIS and outpatient visits in the IHS using International Classification of Diseases, 9th Revision, Clinical Modification (ICD-9-CM) codes 114.0–114.9. We calculated average annual hospitalization and outpatient visit rates per 1 000 000 population and used Poisson regression to calculate rate ratios (RRs) and 95% confidence intervals (CIs). We used multivariable logistic regression to assess factors associated with IHS hospitalization.

Results
AI/ANs had the highest average annual hospitalization rate (58.0; 95% CI, 49.5–66.6) of any racial/ethnic group in the NIS, compared with 13.4 (95% CI, 12.7–14.2) for non-Hispanic whites. IHS data showed a hospitalization rate of 37.0; the median length of stay (interquartile range) was 6 (3–10) days. The average annual outpatient visit rate in IHS was 764.2, and it increased from 529.9 in 2001 to 845.9 in 2014. Male sex, age ≥65 years, diabetes, and extrapulmonary or progressive coccidioidomycosis were independently associated with increased risk for hospitalization. Twenty-four percent of patients had ICD-9-CM codes for community-acquired pneumonia in the 3 months before coccidioidomycosis diagnosis.

Conclusions
AI/ANs experience high coccidioidomycosis-associated hospitalization rates, high morbidity, and possible missed opportunities for earlier diagnosis. Yearly trends in IHS data were similar to the general increase in hospitalizations and reported cases nationwide in the same period.
Membership and fundamental parameters of the intermediate-age open clusters NGC 2281 and NGC 2539 based on Gaia-DR2
Authors: Gao Xin-Hua 
Published: March 2019

AbstractThis paper presents an investigation on the two intermediate-age open clusters NGC 2281 and NGC 2539 based on Gaia Data Release 2 (Gaia-DR2). A combined machine-learning method is used to identify likely cluster members of the two clusters, taking into account the astrometric and photometric data of Gaia-DR2. It is found that NGC 2281 and NGC 2539 each have more than 600 likely cluster members, which are highly suitable for further investigation of the fundamental parameters of the two clusters. Robust estimates of the distances, proper motions, and radial velocities for the two clusters are obtained via a Monte Carlo simulation technique. NGC 2281 is found to have a distance of 522$\, \pm \,$12 pc, a proper motion of (〈μαcos δ〉, 〈μδ〉) = ($-2.947\, \pm \,$0.014, $-8.344\, \pm \,$0.014) mas yr−1, and a radial velocity of $+20.0\, \pm \,$0.7 km s−1. The distance, proper motion, and radial velocity of NGC 2539 are determined to be 1271$\, \pm \,$70 pc, (〈μαcos δ〉, 〈μδ〉) = ($-2.335\, \pm \,$0.007, $-0.583\, \pm \,$0.006) mas yr−1, and $+29.6\, \pm \,$0.4 km s−1, respectively. We find that NGC 2281 has a core radius of ${8{^{\prime}_{.}}89}$$\, \pm \,$${0{^{\prime}_{.}}27}$ (1.3 pc) and a limiting radius of ${79{^{\prime}_{.}}26}$$\, \pm \,$${2{^{\prime}_{.}}86}$ (12.0 pc). The core and limiting radius of NGC 2539 are determined to be ${5{^{\prime}_{.}}62}$$\, \pm \,$${0{^{\prime}_{.}}28}$ (2.1 pc) and ${33{^{\prime}_{.}}65}$$\, \pm \,$${1{^{\prime}_{.}}96}$ (12.4 pc), respectively. In addition, we find strong evidence for the existence of mass segregation in the two clusters.
Robot Reinforcement and Error-Based Movement Learning in Infants With and Without Cerebral Palsy
Authors: Kolobe Thubi H A , Fagg Andrew H 
Published: March 2019

AbstractBackgroundProne mobility, central to development of diverse psychological and social processes that have lasting effects on life participation, is seldom attained by infants with cerebral palsy (CP) and has no tested interventions. Reinforcement learning (RL) and error-based movement learning (EBL) offer novel intervention possibilities.ObjectiveThis study examined movement learning strategies in infants with or at risk for CP using RL and EBL during acquisition of prone locomotion.DesignThe study was a randomized trial that used repeated measures.SettingThe study setting was a university physical therapy clinic in the United States.PatientsThirty infants aged 4.5 to 6.5 months participated in the study: 24 had or were at risk for CP, and 6 were typically developing.InterventionInfants with and at risk for CP were randomly assigned to a combination of RL and EBL (SIPPC-RE), or RL only (SIPPC-R) conditions. Infants with typical development comprised the RL-only reference group (SIPPC-TD). Infants trained in prone locomotion with the Self-Initiated Prone Progression Crawler (SIPPC) robotic system for three 5-minute trials, twice a week for 12 weeks in their homes or child care. All training sessions were videotaped for behavioral coding.MeasurementsThe SIPPC gathered robot and infant trunk/limb movement data. Randomized 2-way analysis of variance with repeated measures and Pearson r to analyze the data was used.ResultsResults included the number of arm movements and trial-and-error activity distinguished between the SIPPC-RE and SIPPC-R groups. The mean change in arm movements from baseline for the SIPPC-RE and SIPPC-R groups was 4.8 m and −7.0 m, respectively. The mean differences in rotational amplitude (trial and error) from baseline to the end of the study were 278 degrees and 501 degrees, respectively. These changes were correlated with distance traveled and goal-directed movements. The latter increased over the 12 weeks for the SIPPC-RE and SIPPC-TD groups, but not the SIPPC-R group.LimitationsThe CP groups were unequal due to reassignment and did not include a typically developing comparison group of a combination of RL and EBL.ConclusionThese findings suggest movement learning and retention in infants with CP is differentially affected by the use of RL and EBL, with a combination of both showing more promise than RL alone. The findings also implicate cognition, type of brain insult, emergence of reaching, and muscle force production, which must be explored in future studies.
Cost of behavioral weight loss programs implemented in clinical practice: The POWER trial at Johns Hopkins
Authors: Daumit Gail L , Janssen Ellen M , Jerome Gerald J , Dalcin Arlene T , Charleston Jeanne , Clark Jeanne M , Coughlin Janelle W , Yeh Hsin-Chieh , Miller Edgar R , Durkin Nowella , Louis Thomas A , Frick Kevin D , Wang Nae-Yuh , Appel Lawrence J 
Published: March 2019

Abstract
Obesity presents an important public health problem that affects more than a third of the U.S. adult population and that is associated with increased morbidity, mortality, and costs. Previously, we documented that two primary care-based weight loss interventions were clinically effective. To encourage the implementation of and reimbursement for these interventions, we evaluated their relative cost-effectiveness. We performed a cost analysis of the Practice-based Opportunities for Weight Reduction (POWER) trial, a three-arm trial that enrolled 415 patients with obesity from six primary care practices. Trial participants were randomized to a control arm, an in-person support intervention, or a remote support intervention; in the two intervention arms, behavioral interventions were delivered over 24 months, in two phases. Weight loss was measured at 6, 12, and 24 months. Using timesheets and empirical data, we evaluated the cost of the in-person and remote support interventions from the perspective of a health care system delivering the interventions. A univariate sensitivity analysis was conducted to evaluate uncertainty around model assumptions. All comparisons were tested using independent t-tests. Cost of the in-person intervention was higher at 6 months ($113 per participant per month and $117 per kg lost) than the remote support intervention ($101 per participant per month and $99 per kg lost; p &lt; .001). Costs were also higher for the in-person support intervention at 24 months ($73 per participant per month and $342 per kg lost) than for the remote support intervention ($53 per participant per month and $275 per kg lost; p &lt; .001). In the sensitivity analyses, cost ranged from $274/kg lost to $456/kg lost for the in-person support intervention and from $218/kg to $367/kg lost for the remote support intervention. A primary care weight loss intervention administered remotely was relatively more cost-effective than an in-person intervention. Expanding the scope of reimbursable programs to include other cost-effective interventions could help ensure that a broader range of patients receive the type of support needed.
General practitioner endorsement of mail-out colorectal cancer screening: The perspective of nonparticipants
Authors: Goodwin Belinda C , Crawford-Williams Fiona , Ireland Michael J , March Sonja 
Published: March 2019

Abstract
Despite the health and economic benefits associated with mail-out colorectal cancer (CRC) screening, participation in programs across the world is suboptimal. A letter from the recipient’s general practitioner (GP) endorsing program participation has been shown to have a consistent, but modest, effect on screening uptake; however, the mechanisms by which GP endorsement is effective have not been investigated. The purpose of the present study was to evaluate the potential utility of GP endorsement letters or SMS in the context of facilitating bowel cancer screening in previous nonparticipants and to identify mechanisms underlying responses. A cross-section of nonparticipants in the Australian National Bowel Cancer Screening Program (N = 110) was randomly assigned to view a letter or SMS from a GP endorsing participation via an online survey. Ordinal responses reflecting effectiveness of, and influences on, GP endorsement were collected along with open questions regarding other potential endorsers. Percentages, means, and 95% confidence intervals were calculated and compared. Fifty-two percent of the sample agreed that GP endorsement would encourage their future participation. Responses did not differ between SMS and letter formats. Trust in the GP had significantly more influence on response to GP endorsement than the credibility or medical knowledge. Other health professionals and cancer survivors were commonly suggested as alternative sources of endorsement. Interventions to improve CRC screening participation could benefit from the routine implementation of GP endorsement from GPs, other trusted health professionals, or cancer survivors, particularly by encouraging people who forget or procrastinate over collecting a stool sample.
Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells
Authors: Chen Pei-Hsuan , Cai Ling , Huffman Kenneth , Yang Chendong , Kim Jiyeon , Faubert Brandon , Boroughs Lindsey , Ko Bookyung , Sudderth Jessica , McMillan Elizabeth A. , Girard Luc , Peyton Michael , Shields Misty D. , Shames David , Kim Hyun Seok , Timmons Brenda , Sekine Ikuo , Britt Rebecca , Weber Stephanie , Byers Lauren A. , Heymach John V. , White Michael A. , Minna John D. , Xiao Guanghua , DeBerardinis Ralph J. 
Published: March 2019

SummaryIntermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes including signal transduction and gene expression patterns arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here we quantified over 100 metabolic features, mostly from 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.
Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels
Authors: Salehin M. , Li B. , Tang M. , Katz E. , Song L. , Ecker J. R. , Kliebenstein D. , Estelle M. 
Published: March 2019

AbstractA detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.One Sentence SummaryAux/IAA proteins promote drought tolerance by regulating glucosinolate levels.
Symbiont community diversity is more constrained in holobionts that tolerate diverse stressors
Authors: Howe-Kerr Lauren I. , Bachelot Benedicte , Wright Rachel M. , Kenkel Carly D. , Bay Line K. , Correa Adrienne M.S. 
Published: March 2019

AbstractCoral reefs are experiencing global declines as climate change and other stressors cause environmental conditions to exceed the physiological tolerances of host organisms and their microbial symbionts (collectively termed the holobiont). To assess the role of symbiont community composition in holobiont stress tolerance, diversity metrics and abundances of obligate dinoflagellate endosymbionts (Family: Symbiodiniaceae) were quantified from eight Acropora millepora coral colonies (hereafter called genets) that thrived under or responded poorly to various stressors. Four ‘best performer’ coral genets were selected for analysis because they survived 10 days of high temperature, high pCO2, bacterial addition, or combined stressors, whereas four ‘worst performer’ coral genets were analyzed because they experienced significant mortality under these stressors. At the end of the experimental period, seven of eight coral genets mainly hosted Cladocopium symbionts, but also contained Brevolium, Durusdinium, and/or Gerakladinium symbionts at lower abundances (<0.1% of the total community). After 10 days of stress, symbiont communities varied significantly among host genets, but not stress treatments, based on alpha and beta diversity metrics. A generalized joint attribute model (GJAM) also predicted that symbiont communities were primarily sensitive to host genet at regional scales. Indicator species analysis and the regional GJAM model identified significant associations among particular symbionts and host genet performance. Specifically, Cladocopium 3k contributed to the success of best performer host genets under various stressful conditions, whereas Durusdinium glynnii and Durusdinium trenchii were significantly associated with one worst performer genet. Cladocopium 3k dominance should be more broadly investigated as a potential predictor of stress resistance in Acropora millepora populations across their geographic range. Symbiodiniaceae communities exhibited higher richness and variance (beta diversity) in the worst performing genets. These findings highlight that symbiont community diversity metrics may be important indicators of resilience in hosts central to diverse disciplines, from agriculture to medicine.
Modularity in the Microcircuitry of the Mouse Inferior Colliculus Yields Dual Processing Streams for Auditory and Multisensory Information
Authors: Lesicko Alexandria M. H. , Llano Daniel A. 
Published: March 2019

ABSTRACTThe lateral cortex of the inferior colliculus (LCIC) is parcellated into two neurochemical compartments: one that comprises periodic neurochemical modules rich in GABAergic and cholinergic terminals and an extramodular matrix rich in calretinin neurons. We recently found that projections from auditory structures (auditory cortex and central nucleus of the IC) target the extramodular matrix, while somatosensory structures (somatosensory cortex and dorsal column nuclei) target the modules. What is peculiar about this finding of segregated inputs is that previous work has found that many LCIC neurons respond to both auditory and somatosensory stimuli. To investigate how these pathways interact, here we use laser photostimulation of caged glutamate to interrogate local LCIC circuits in brain slices from mouse. We found that most cell types in the LCIC receive inputs only from their home domain, but that GABAergic neurons in the modules serve as a bridge between modules and extramodular space. Further, we found that residence in- or out-of a module strongly predicted the output connectivity of that cell. These data suggest that distinct processing streams are seen in the LCIC and that GABAergic cells in modules serve to link these streams.
Motor context coordinates visually guided walking inDrosophila
Authors: Cruz Tomás , Fujiwara Terufumi , Varela Nélia , Mohammad Farhan , Claridge-Chang Adam , Chiappe M Eugenia 
Published: March 2019

AbstractCourse control is critical for the acquisition of spatial information during exploration and navigation, and it is thought to rely on neural circuits that process locomotive-related multimodal signals. However, which circuits underlie this control, and how multimodal information contributes to the control system are questions poorly understood. We used Virtual Reality to examine the role of self-generated visual signals (visual feedback) on the control of exploratory walking in flies. Exploratory flies display two distinct motor contexts, characterized by low speed and fast rotations, or by high speed and slow rotations, respectively. Flies use visual feedback to control body rotations, but in a motor-context specific manner, primarily when walking at high speed. Different populations of visual motion-sensitive cells estimate body rotations via congruent, multimodal inputs, and drive compensatory rotations. However, their effective contribution to course control is dynamically tuned by a speed-related signal. Our data identifies visual networks with a multimodal circuit mechanism for adaptive course control and suggests models for how visual feedback is combined with internal signals to guide exploratory course control.
Comprehensive Classification of the RNase H-like domain-containing Proteins in Plants
Authors: Li Shuai , Liu Kunpeng , Sun Qianwen 
Published: March 2019

AbstractBackgroundR-loop is a nucleic acid structure containing an RNA-DNA hybrid and a displaced single-stranded DNA. Recently, accumulated evidence showed that R-loops widely present in various organisms’ genomes and are involved in many physiological processes, including DNA replication, RNA transcription, and DNA repair. RNase H-like superfamily (RNHLS) domain-containing proteins, such as RNase H enzymes, are essential in restricting R-loop levels. However, little is known about the function and relationship of other RNHLS proteins on R-loop regulation, especially in plants.ResultsIn this study, we characterized 6193 RNHLS proteins from 13 representative plant species and clustered these proteins into 27 clusters, among which reverse transcriptases and exonucleases are the two largest groups. Moreover, we found 691 RNHLS proteins in Arabidopsis with a conserved catalytic alpha-helix and beta-sheet motif. Interestingly, each of the Arabidopsis RNHLS proteins is composed of not only an RNHLS domain but also another different protein domain. Additionally, the RNHLS genes are highly expressed in different meristems and metabolic tissues, which indicate that the RNHLS proteins might play important roles in the development and maintenance of these tissues.ConclusionsIn summary, we systematically analyzed RNHL proteins in plants and found that there are mainly 27 subclusters of them. Most of these proteins might be implicated in DNA replication, RNA transcription, and nucleic acid degradation. We classified and characterized the RNHLS proteins in plants, which may afford new insights into the investigation of novel regulatory mechanisms and functions of R-loops.
An equilibrium binding model for CpG DNA-dependent dimerization of Toll-like receptor 9
Authors: Reikine Stephanie , McLaughlin Stephen H. , Johnson Christopher M. , Modis Yorgo 
Published: March 2019

AbstractMicrobial nucleic acids in the extracellular milieu are recognized in vertebrates by Toll-like receptors (TLRs), one of the most important families of innate immune receptors. TLR9 recognizes single-stranded unmethylated CpG DNA in endosomes. DNA binding induces dimerization of TLR9 and activation of a potent inflammatory response. To provide insights on how DNA ligands induce TLR9 dimerization, we developed a detailed theoretical equilibrium ligand binding model. Light scattering and fluorescence polarization assays performed with a recombinant TLR9 ectodomain fragment and a panel of agonistic and antagonistic DNA ligands provide data that restrain the binding parameters in our binding model. This work brings us one step closer to establishing a rigorous biochemical understanding of how TLRs are activated by their ligands.