bluuebunny/crossref_metadata_2025_split huggingface dataset:
LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism
Authors: Dromms Robert A. , Lee Justin Y. , Styczynski Mark P. 
Published: March 2020

AbstractBackgroundThe systems-scale analysis of cellular metabolites, “metabolomics,” provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Flux Balance Analysis (FBA), which makes assumptions that preclude direct integration of metabolomics data into the underlying models. Finding a way to retain the advantages of FBA’s linear structure while relaxing some of its assumptions could allow us to account for metabolite levels and metabolite-dependent regulation in strain design tools built from FBA, improving the accuracy of predictions made by these tools. We designed, implemented, and characterized a modeling strategy based on Dynamic FBA (DFBA), called Linear Kinetics-Dynamic Flux Balance Analysis (LK-DFBA), to satisfy these specifications. Our strategy adds constraints describing the dynamics and regulation of metabolism that are strictly linear. We evaluated LK-DFBA against alternative modeling frameworks using simulated noisy data from a small in silico model and a larger model of central carbon metabolism inE. coli, and compared each framework’s ability to recapitulate the original system.ResultsIn the smaller model, we found that we could use regression from a dynamic flux estimation (DFE) with an optional non-linear parameter optimization to reproduce metabolite concentration dynamic trends more effectively than an ordinary differential equation model with generalized mass action rate laws when tested under realistic data sampling frequency and noise levels. We observed detrimental effects across all tested modeling approaches when metabolite time course data were missing, but found these effects to be smaller for LK-DFBA in most cases. With theE. colimodel, we produced qualitatively reasonable results with similar properties to the smaller model and explored two different parameterization structures that yield trade-offs in computation time and accuracy.ConclusionsLK-DFBA allows for calculation of metabolite concentrations and considers metabolite-dependent regulation while still retaining many computational advantages of FBA. This provides the proof-of-principle for a new metabolic modeling framework with the potential to create genome-scale dynamic models and the potential to be applied in strain engineering tools that currently use FBA.
Genome-wide discovery, and computational and transcriptional characterization of an AIG gene family in the freshwater snail Biomphalaria glabrata, a vector for Schistosoma mansoni
Authors: Lu Lijun , Loker Eric S. , Zhang Si-Ming , Buddenborg Sarah K. , Bu Lijing 
Published: March 2020

Abstract
Background
The AIG (avrRpt2-induced gene) family of GTPases, characterized by the presence of a distinctive AIG1 domain, is mysterious in having a peculiar phylogenetic distribution, a predilection for undergoing expansion and loss, and an uncertain functional role, especially in invertebrates. AIGs are frequently represented as GIMAPs (GTPase of the immunity associated protein family), characterized by presence of the AIG1 domain along with coiled-coil domains. Here we provide an overview of the remarkably expanded AIG repertoire of the freshwater gastropod Biomphalaria glabrata, compare it with AIGs in other organisms, and detail patterns of expression in B. glabrata susceptible or resistant to infection with Schistosoma mansoni, responsible for the neglected tropical disease of intestinal schistosomiasis.

Results
We define the 7 conserved motifs that comprise the AIG1 domain in B. glabrata and detail its association with at least 7 other domains, indicative of functional versatility of B. glabrata AIGs. AIG genes were usually found in tandem arrays in the B. glabrata genome, suggestive of an origin by segmental gene duplication. We found 91 genes with complete AIG1 domains, including 64 GIMAPs and 27 AIG genes without coiled-coils, more than known for any other organism except Danio (with > 100). We defined expression patterns of AIG genes in 12 different B. glabrata organs and characterized whole-body AIG responses to microbial PAMPs, and of schistosome-resistant or -susceptible strains of B. glabrata to S. mansoni exposure. Biomphalaria glabrata AIG genes clustered with expansions of AIG genes from other heterobranch gastropods yet showed unique lineage-specific subclusters. Other gastropods and bivalves had separate but also diverse expansions of AIG genes, whereas cephalopods seem to lack AIG genes.

Conclusions
The AIG genes of B. glabrata exhibit expansion in both numbers and potential functions, differ markedly in expression between strains varying in susceptibility to schistosomes, and are responsive to immune challenge. These features provide strong impetus to further explore the functional role of AIG genes in the defense responses of B. glabrata, including to suppress or support the development of medically relevant S. mansoni parasites.
The structure, functional evolution, and evolutionary trajectories of the H+-PPase gene family in plants
Authors: Zhang Yiming , Feng Xue , Wang Lihui , Su Yanping , Chu Zhuodong , Sun Yanxiang 
Published: March 2020

Abstract
Background
The H+-PPase (pyrophosphatase) gene family is an important class of proton transporters that play key roles in plant development and stress resistance. Although the physiological and biochemical functions of H+-PPases are well characterized, the structural evolution and functional differentiation of this gene family remain unclear.

Results
We identified 124 H+-PPase members from 27 plant species using complete genomic data obtained from algae to angiosperms. We found that all analyzed plants carried H+-PPase genes, and members were not limited to the two main types (type I and II). Differentiation of this gene family occurred early in evolutionary history, probably prior to the emergence of algae. The type I and II H+-PPase genes were retained during the subsequent evolution of higher plants, and their copy numbers increased rapidly in some angiosperms following whole-genome duplication (WGD) events, with obvious expression pattern differentiation among the new copies. We found significant functional divergence between type I and II H+-PPase genes, with both showing evidence for positive selection pressure. We classified angiosperm type I H+-PPases into subtypes Ia and non-Ia, which probably differentiated at an early stage of angiosperm evolution. Compared with non-Ia subtype, the Ia subtype appears to confer some advantage in angiosperms, as it is highly conserved and abundantly expressed, but shows no evidence for positive selection.

Conclusions
We hypothesized that there were many types of H+-PPase genes in the plant ancestral genome, and that different plant groups retained different types of these genes. In the early stages of angiosperm evolution, the type I H+-PPase genes differentiated into various subtypes. In addition, the expression pattern varied not only among genes of different types or subtypes, but also among copies of the same subtype. Based on the expression patterns and copy numbers of H+-PPase genes in higher plants, we propose two possible evolutionary trajectories for this gene family.
Barley ROP-Interactive Partner-a organizes into RAC1- and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1-dependent membrane domains
Authors: Hoefle Caroline , McCollum Christopher , Hückelhoven Ralph 
Published: March 2020

Abstract
Background
Small ROP (also called RAC) GTPases are key factors in polar cell development and in interaction with the environment. ROP-Interactive Partner (RIP) proteins are predicted scaffold or ROP-effector proteins, which function downstream of activated GTP-loaded ROP proteins in establishing membrane heterogeneity and cellular organization. Grass ROP proteins function in cell polarity, resistance and susceptibility to fungal pathogens but grass RIP proteins are little understood.

Results
We found that the barley (Hordeum vulgare L.) RIPa protein can interact with barley ROPs in yeast. Fluorescent-tagged RIPa, when co-expressed with the constitutively activated ROP protein CA RAC1, accumulates at the cell periphery or plasma membrane. Additionally, RIPa, locates into membrane domains, which are laterally restricted by microtubules when co-expressed with RAC1 and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1. Both structural integrity of MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1 and microtubule stability are key to maintenance of RIPa-labeled membrane domains. In this context, RIPa also accumulates at the interface of barley and invading hyphae of the powdery mildew fungus Blumeria graminis f.sp. hordei.

Conclusions
Data suggest that barley RIPa interacts with barley ROPs and specifies RAC1 activity-associated membrane domains with potential signaling capacity. Lateral diffusion of this RAC1 signaling capacity is spatially restricted and the resulting membrane heterogeneity requires intact microtubules and MICROTUBULE-ASSOCIATED ROP-GTPASE ACTIVATING PROTEIN 1. Focal accumulation of RIPa at sites of fungal attack may indicate locally restricted ROP activity at sites of fungal invasion.
Evaluating a screener to quantify PTSD risk using emergency care information: a proof of concept study
Authors:   International Consortium to Predict PTSD, van der Mei Willem F. , Barbano Anna C. , Ratanatharathorn Andrew , Bryant Richard A. , Delahanty Douglas L. , deRoon-Cassini Terri A. , Lai Betty S. , Lowe Sarah R. , Matsuoka Yutaka J. , Olff Miranda , Qi Wei , Schnyder Ulrich , Seedat Soraya , Kessler Ronald C. , Koenen Karestan C. , Shalev Arieh Y. 
Published: March 2020

Abstract
Background
Previous work has indicated that post-traumatic stress disorder (PTSD) symptoms, measured by the Clinician-Administered PTSD Scale (CAPS) within 60 days of trauma exposure, can reliably produce likelihood estimates of chronic PTSD among trauma survivors admitted to acute care centers. Administering the CAPS is burdensome, requires skilled professionals, and relies on symptoms that are not fully expressed upon acute care admission. Predicting chronic PTSD from peritraumatic responses, which are obtainable upon acute care admission, has yielded conflicting results, hence the rationale for a stepwise screening-and-prediction practice. This work explores the ability of peritraumatic responses to produce risk likelihood estimates of early CAPS-based PTSD symptoms indicative of chronic PTSD risk. It specifically evaluates the Peritraumatic Dissociative Experiences Questionnaire (PDEQ) as a risk-likelihood estimator.

Methods
We used individual participant data (IPD) from five acute care studies that used both the PDEQ and the CAPS (n = 647). Logistic regression calculated the probability of having CAPS scores ≥ 40 between 30 and 60 days after trauma exposure across the range of initial PDEQ scores, and evaluated the added contribution of age, sex, trauma type, and prior trauma exposure. Brier scores, area under the receiver-operating characteristic curve (AUC), and the mean slope of the calibration line evaluated the accuracy and precision of the predicted probabilities.

Results
Twenty percent of the sample had CAPS ≥ 40. PDEQ severity significantly predicted having CAPS ≥ 40 symptoms (p < 0.001). Incremental PDEQ scores produced a reliable estimator of CAPS ≥ 40 likelihood. An individual risk estimation tool incorporating PDEQ and other significant risk indicators is provided.

Conclusion
Peritraumatic reactions, measured here by the PDEQ, can reliably quantify the likelihood of acute PTSD symptoms predictive of chronic PTSD and requiring clinical attention. Using them as a screener in a stepwise chronic PTSD prediction strategy may reduce the burden of later CAPS-based assessments. Other peritraumatic metrics may perform similarly and their use requires similar validation.

Trial registration
Jerusalem Trauma Outreach and Prevention Study (J-TOPS): NCT00146900.
Effects of simultaneous cognitive and aerobic exercise training on dual-task walking performance in healthy older adults: results from a pilot randomized controlled trial
Authors: Raichlen David A. , Bharadwaj Pradyumna K. , Nguyen Lauren A. , Franchetti Mary Kathryn , Zigman Erika K. , Solorio Abigail R. , Alexander Gene E. 
Published: March 2020

AbstractBackgroundThe ability to walk and perform cognitive tasks simultaneously is a key aspect of daily life. Performance declines in these dual-tasks may be associated with early signs of neurodegenerative disease and increased risk of falls. Thus, interventions to improve dual-task walking performance are of great interest for promoting healthy aging. Here, we present results of a pilot randomized controlled trial (RCT) to evaluate the effects of a simultaneous aerobic exercise and cognitive training intervention on dual-task walking performance in healthy older adults.MethodsCommunity-dwelling, healthy older adults were recruited to participate in a 12-week RCT. Participants were randomized into one of four groups (n = 74): 1) cognitive training (COG), 2) aerobic exercise (EX), 3) combined aerobic exercise and cognitive training (EXCOG), and 4) video-watching control (CON). The COG and EXCOG groups both used a tablet-based cognitive training program that challenged aspects of executive cognitive function, memory, and processing speed. Performance on a dual-task walking test (DTWT; serial subtraction during two-minute walk) was assessed by researchers blinded to groupings before the intervention, and at 6 and 12 weeks. We included all participants randomized with baseline measurements in an intention to treat analysis using linear mixed effects models.ResultsWe found a significant group by time interaction for cognitive performance on the DTWT (p = 0.039). Specifically, participants in the EXCOG, EX, and COG groups significantly improved on the cognitive aspect of the DTWT following the full 12-week intervention (p = 3.5e-7,p = 0.048,p = 0.048, respectively). The improvements in EXCOG were twice as large as in the other groups, and were significant at 6 weeks (p = 0.019). The CON group did not show a significant change in cognitive performance on the DTWT, and no group significantly altered dual-task gait measures following the intervention.ConclusionsA simultaneous aerobic exercise and cognitive training intervention significantly improved cognitive performance during a DTWT in healthy older adults. Despite no change in DTWT gait measures, significant improvements in cognitive performance indicate that further investigation in a larger RCT is warranted.Trial registrationClinicaltrials.gov,NCT04120792, Retrospectively Registered 08 October 2019.
Identification of differentially expressed miRNAs and mRNAs in synovial of osteoarthritis via RNA-sequencing
Authors: Zhou Yu , Wang Zhicong , Chen Xi , Zhang Jianjun , Yang Ling , Liu Shuping , Liu Yuehong 
Published: March 2020

Abstract
Background
Osteoarthritis (OA) is the most common form of arthritis and a leading cause of disability. This study attempted to investigate the key mRNAs and miRNAs related to OA.

Patients and methods
From April 17th, 2018 to May 17th, 2018, five patients with OA and three normal controls were enrolled in this present study. To identify the differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) between patients with OA and normal controls, RNA-sequencing was performed. Then, DEmiRNA-target DEmRNAs analysis and functional annotation of DEmiRNA-target DEmRNAs were performed. To validate the RNA-sequencing results, quantitative real time-PCR (RT-PCR) and western blot analysis were performed as well.

Results
A total of 1068 DEmRNAs, 21 DEmiRNAs and 395 DEmiRNA-DEmRNA pairs were identified in synovial tissues of patients with OA. The functional annotation of DEmiRNA-target DEmRNAs revealed that Pathways in cancer and PI3K-Akt signaling pathway were significantly enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. QRT-PCR and western blot results revealed that except for TLR7, the expression level of the others was consistent with the RNA-sequencing results, generally.

Conclusion
The findings of this present study may provide new clues for the roles of DEmRNAs and DEmiRNAs in the pathogenesis of OA.
How addicted are newly admitted undergraduate medical students to smartphones?: a cross-sectional study from Chitwan medical college, Nepal
Authors: Karki Sirisa , Singh Jaya Prasad , Paudel Gita , Khatiwada Sushma , Timilsina Sameer 
Published: March 2020

Abstract
Background
Increasing smartphone use among adolescents in todays’ world has made this handy device an indispensable electronic tool, however, it comes at a price of problematic overuse or addiction. We aim to investigate the prevalence of smartphone addiction among undergraduate medical students and explore its association with various demographic and personal factors.

Methods
A pool of 250 undergraduate students completed a survey composed of socio-demographics information, smartphone-use related variables and 10-point Smartphone Addiction Scale-Short Version in February 2019.

Results
Smartphone addiction among medical students was estimated at around 36.8% with higher percentage of male smartphone addicts. Phubbing was reported by 37.6% participants with more than 60% reporting overuse. Statistically significant association was observed between smartphone addiction and gender and overuse. Self-acknowledgement of addiction was found to be the biggest predictor of smartphone addiction.

Conclusion
This study provides preliminary insights into smartphone use, smartphone addiction and various factors predicting smartphone addiction among early undergraduate medical students from Nepal, which should be extended in future studies. Education policymakers and educators need to develop some strategies encouraging student’s smartphone utilization to enhance academic performance.
Trans-hiatal repair for Oesophageal and Junctional perforation: a case series
Authors: Lee Adele H. H. , Kweh Barry T. S. , Gillespie Carla , Johnson Mary Ann 
Published: March 2020

AbstractBackgroundOesophageal perforation is a life-threatening condition that requires urgent intervention. Surgical repair is recommended within 24 h of onset to minimise mortality risk, traditionally via an open thoracotomy or a laparotomy. Primary oesophageal repair via a laparoscopic trans-hiatal approach has been seldomly reported due to concerns of inadequate eradication of soilage in the mediastinum and pleural space, as well as poor access and an increased operative time in an unwell population.Case presentationWe report a case series of 3 oesophageal and junctional perforations with varying presentations, demonstrating how the laparoscopic trans-hiatal approach can be used successfully to manage oesophageal perforations.ConclusionsLaparoscopic trans-hiatal repair is an attractive option for oesophageal and junctional perforations, in haemodynamically stable surgical candidates, in the absence of gross contamination of the thoracic cavity.
A systematic review of patient access to medical records in the acute setting: practicalities, perspectives and ethical consequences
Authors: D’Costa Stephanie N. , Kuhn Isla L. , Fritz Zoë 
Published: March 2020

Abstract
Background
Internationally, patient access to notes is increasing. This has been driven by respect for patient autonomy, often recognised as a primary tenet of medical ethics: patients should be able to access their records to be fully engaged with their care. While research has been conducted on the impact of patient access to outpatient and primary care records and to patient portals, there is no such review looking at access to hospital medical records in real time, nor an ethical analysis of the issues involved in such a change in process.

Methods
This study employed a systematic review framework in two stems, to integrate literature identified from two searches: Medline, CINAHL and Scopus databases were conducted, (for (1) hospitalised patients, patient access to records and its effects on communication and trust within the doctor-patient relationship; and (2) patient access to medical records and the ethical implications identified). The qualitative and quantitative results of both searches were integrated and critically analysed.

Results
3954 empirical and 4929 ethical studies were identified; 18 papers representing 16 studies were identified for review (12 empirical and 6 ethical). The review reveals a consensus that our current approach to giving information to patients – almost exclusively verbally – is insufficient; that patient access to notes is a welcome next step for patient-centred care, but that simply allowing full access, without explanation or summary, is also insufficient. Several ethical implications need to be considered: increased information could improve patient trust and knowledge but might transfer an (unwelcome) sense of responsibility to patients; doctors and patients have conflicting views on how much information should be shared and when; sharing written information might increase the already significant disparity in access to health care, and have unforeseen opportunity costs. The impact on medical practice of sharing notes in real time will also need to be evaluated.

Conclusions
The review presents encouraging data to support patient access to medical notes. However, sharing information is a critical part of clinical practice; changing how it is done could have significant empirical and ethical impacts; any changes should be carefully evaluated.