bluuebunny/crossref_metadata_2025_split huggingface dataset:
Doxycycline improves traumatic brain injury outcomes in a murine survival model
Authors: Malek Adil J. , Robinson Bobby D. , Hitt Angie R. , Shaver Courtney N. , Tharakan Binu , Isbell Claire L. 
Published: May 2020

BACKGROUNDTraumatic brain injury (TBI) has significant morbidity and cost implications. Primary treatment modalities aim to decrease intracranial pressure; however, therapies targeting the underlying pathophysiology of a TBI are limited. The TBI-induced microvascular leak and secondary injury are largely due to proteolysis of the blood-brain barrier (BBB) by matrix metalloproteinase-9. We previously observed doxycycline's inhibitory affinity on matrix metalloproteinase-9 resulting in preserved BBB integrity in nonsurvival murine studies. This study sought to determine the effect of doxycycline on functional motor and behavioral outcomes in the setting of a TBI murine survival model.METHODSC57BL/6J mice were assigned to a sham, TBI, or TBI with doxycycline arm. A moderate TBI was induced utilizing a controlled cortical impactor. The TBI with doxycycline cohort received a dose of doxycycline (20 mg/kg) 2 hours after injury and every 12 hours until postoperative day (POD) 6. All mice underwent preoperative testing for weight, modified neurological severity score, wire grip, and ataxia analysis (DigiGait). Postoperative testing was performed on POD 1, POD 3, and POD 6 for the same measures. SAS 9.4 was used for comparative analysis.RESULTSFifteen sham mice, 15 TBI mice, and 10 TBI with doxycycline mice were studied. Mice treated with doxycycline had significantly improved modified neurological severity score and wire grip scores at POD 1 (allp< 0.05). Mice treated with doxycycline had significantly improved ataxia scores by POD 3 and POD 6 (allp< 0.05). There was no significant difference in rate of weight change between the three groups.CONCLUSIONMice treated with doxycycline following TBI demonstrated improved behavioral and motor function suggesting doxycycline's role in preserving murine BBB integrity. Examining the role of doxycycline in human TBIs is warranted given the relative universal accessibility, affordability, and safety profile of doxycycline.
Correlation of ride sharing service availability and decreased alcohol-related motor vehicle collision incidence and fatality
Authors: Friedman Jessica , Hendrix Vera , Fustok Judy , Reza Tara , Madda Prathima , Smith Alison , Mayer Scott , Duchesne Juan , Greiffenstein Patrick , Schroll Rebecca 
Published: May 2020

BACKGROUND
Alcohol-related motor vehicle collisions (AR-MVCs) account for ~30% of all US traffic fatalities. Ride-sharing services (RSS) have existed since 2010, but few studies to date have investigated their impact on AR-MVCs. We hypothesized that the availability of RSS would be correlated with a decrease in AR-MVCs at an urban Level I trauma center.

METHODS
A retrospective chart review was conducted of all AR-MVC trauma activations at a Level I trauma center from 2012 to 2018. Additional data were gathered from regional governmental traffic and law enforcement databases, including crash incidence, fatalities, and demographics. Data were compared pre- and post-RSS and analyzed using an unpaired t test with p less than 0.05 considered significant.

RESULTS
There were 1,474 patients in AR-MVCs during the study period. There was a significant decrease in the annual average proportion of MVCs that were AR-MVCs pre- vs. post-RSS (39% vs. 29%, p = 0.02) as well as a decrease in the average annual incidence of fatal AR-MVCs (11.6 vs. 5, p = 0.02). Subset analysis showed a decrease in AR-MVC incidence in 18- to 29-year-olds (12.7% vs. 7.5%; p = 0.03), which was also demonstrated by data from a local law enforcement database. Availability of RSS was also correlated with a decreased proportion of nighttime AR-MVCs (14.7% vs. 7.6%, p = 0.03) and decreased number of driving while intoxicated (1198.0 ± 78.5 vs. 612.8 ± 137.6, p = <0.01).

CONCLUSION
We found that the incidence of both total AR-MVCs and fatal AR-MVCs presenting to our trauma center decreased after the introduction of RSS. Ride-sharing services may play a role in preventing AR-MVCs. Further research is needed to correlate AR-MVC incidence with granular proprietary RSS usage data and to account for any confounding factors. Future studies may identify ways to better utilize RSS availability as a targeted intervention for certain demographic groups to prevent AR-MVCs.

LEVEL OF EVIDENCE
Therapeutic/Care Management, Level IV.
Obesity and impaired barrier function after shock: A biomimetic in vitro model using microfluidics
Authors: Diebel Lawrence N. , Peraino Nicholas , Westrick Judy , Shinki Kazuhiko , Liberati David M. 
Published: May 2020

BACKGROUND
Impaired microvascular perfusion in the obese patient has been linked to chronic adverse health consequences. The impact on acute illnesses including trauma, sepsis, and hemorrhagic shock (HS) is uncertain. Studies have shown that endothelial glycocalyx and vascular endothelial derangements are causally linked to perfusion abnormalities. Trauma and HS are also associated with impaired microvascular perfusion in which glycocalyx injury and endothelial dysfunction are sentinel events. We postulate that obesity may impact the adverse consequences of HS on the vascular barrier. This was studied in vivo in a biomimetic model of HS using microfluidic technology.

METHODS
Human umbilical vein endothelial cell monolayers were established in a microfluidic device. Cells were exposed to standard or biomimetic shock conditions (hypoxia plus epinephrine) followed by perfusion from plasma obtained from obese or nonobese subjects. Endothelial glycocalyx and endothelial cellular injury were then determined.

RESULTS
Plasma from nonobese patients completely reversed glycocalyx and endothelial vascular barrier injury. Plasma from obese patients was only partially protective and was associated with differences in adipokines and other substances in the plasma of these patients.

CONCLUSION
Our study supports that obesity impairs HS resuscitation. This may be due to microrheological differences between nonobese and obese individuals and may contribute to the poorer outcome in this patient population.
Safety and Feasibility Report of Robotic-assisted Left Lateral Sectionectomy for Pediatric Living Donor Liver Transplantation: A Comparative Analysis of Learning Curves and Mastery Achieved With the Laparoscopic Approach
Authors: Troisi Roberto I. , Elsheikh Yasser , Alnemary Yasir , Zidan Ahmed , Sturdevant Mark , Alabbad Saleh , Algoufi Talal , Shagrani Mohammed , Broering Dieter C. 
Published: May 2020

Background.
There is a growing interest in left lateral sectionectomy for donor hepatectomy. No data are available concerning the safety of the robotic (ROB) approach.

Methods.
A retrospective comparative study was conducted on 75 consecutive minimally invasive donor hepatectomies. The first 25 ROB procedures performed from November 2018 to July 2019 were compared with our first (LAP1) and last 25 (LAP2) laparoscopic cases performed between May 2013 and October 2018. Short-term donors and recipients’ outcomes were analyzed.

Results.
No conversions were noticed in ROB whereas 2 conversions (8%) were recorded in LAP1 and none in LAP2. Blood loss was significantly less in ROB compared with LAP1 (P ≤ 0.001) but not in LAP2. Warm ischemia time was longer in ROB (P ≤ 0.001) with respect to the other groups. Operative time was similar in the 3 groups (P = 0.080); however, the hospital stay was shorter in ROB (P = 0.048). The trend in operative time in ROB was significantly shorter compared to LAP1 and LAP2: linear R2 0.478, P≤0.001; R2 0.012, P = 0.596; R3 0.004, P = 0.772, respectively. Donor morbidity was nihil in ROB, similar in LAP1 and LAP2 (n=3%–12%; P = 0.196). ROB procedures required less postoperative analgesia (P = 0.002). Recipient complications were similar for all groups (P = 0.274), and no early retransplantations were recorded.

Conclusions.
Robotic left lateral sectionectomy for donor hepatectomy is a safe procedure with results comparable to the laparoscopy in terms of donor morbidity and overall recipients’ outcome when the procedure is performed by experts. Certainly, its use is currently very limited.
The Impact of Environmental Risk Factors on Delirium and Benefits of Noise and Light Modifications: A Scoping Review
Authors: Hashemighouchani Haleh , Cupka Julie , Lipori Jessica , Ruppert Matthew M , Ingersent Elizabeth , Ozrazgat-Baslanti Tezcan , Rashidi Parisa , Bihorac Azra 
Published: May 2020

ABSTRACTPurposeTo explore existing literature on the association between environmental risk factors with delirium and to investigate the effectiveness of environmental modifications on prevention or management of delirium.Materials and MethodsThis is a scoping review of peer-reviewed studies in Pubmed and the reference lists of reviewed articles. Observational studies reporting the effect of noise, light, and circadian rhythm on delirium and interventional studies assessing delirium in modified environments were reviewed.ResultsThirty eight studies were included, of which, 21 evaluated impact of environment on delirium, and 16 studied the interventions. Interventions targeted reducing noise exposure, improving light exposure to follow circadian rhythm, and promoting sleep. Mixed findings of the reviewed studies yielded to inconclusive results; however quiet-time protocols, earplugs, and bright light therapy might benefit prevention, or management of delirium.ResultsThirty seven studies were included, 21 of which evaluated the impact of environment on delirium and 16 studied possible solutions to mitigate those impacts. Mixed findings of the reviewed studies yielded inconclusive results; a clearly delineated association between high noise levels, abnormal amounts of light exposure, and sleep disruption with delirium could not be established. Interventions targeted reducing noise exposure, improving day-time and mitigating night-time light exposure to follow circadian rhythm, and promoting sleep. The overall evidence supporting effectiveness of environmental interventions was also of a low confidence; however, quiet-time protocols, earplugs, and bright light therapy showed a benefit for prevention or management of delirium.ConclusionEnvironmental modifications are non-invasive, risk-free, and low-cost strategies that may be beneficial in preventing and managing delirium, especially when used as part of a multi-component plan. However, given the limited evidence-based conclusions, further high-quality and larger studies focusing on environmental modifications and delirium outcomes are strongly recommended.
Transcription factor TGA2 is essential for UV-B stress tolerance controlling oxidative stress in Arabidopsis
Authors: Herrera-Vásquez Ariel , Fonseca Alejandro , Ugalde José Manuel , Lamig Liliana , Seguel Aldo , Moyano Tomás C. , Gutiérrez Rodrigo A. , Salinas Paula , Vidal Elena A. , Holuigue Loreto 
Published: May 2020

AbstractPlants possess a diversity of Reactive Oxygen Species (ROS)-processing enzymes involved in sensing and controlling ROS levels under basal and stressful conditions. There is little information on the transcriptional regulators that control the expression of these ROS-processing enzymes, particularly at the onset of the defense response to abiotic stress. Filling this gap, this paper reports a critical role for Arabidopsis TGA class II factors (TGA2, TGA5, and TGA6) in the tolerance response to UV-B light and photooxidative stress, by activating the expression of genes with antioxidative roles. We identified two clusters of genes responsive to UV-B and activated by TGA2/5/6 were identified using RNAseq and clustering analysis. The GSTU gene family, which encodes glutathione transferase enzymes from the Tau subclass, was overrepresented in these clusters. We corroborated the TGA2-mediated activation in response to UV-B for three model genes (GSTU7, GSTU8, and GSTU25) using RT-qPCR and ChIP analyses. Interestingly, using tga256 mutant and TGA2- and GSTU7-complemented mutant plants, we demonstrated that TGA2-mediated induction of GSTU genes is essential to control ROS levels and oxidative damage after UV-B and MeV treatments. This evidence positions TGA class II factors, particularly TGA2, as a key players in the redox signaling network of Arabidopsis plants.HighlightArabidopsis TGA2 transcription factor is part of the redox-signaling network controlling ROS levels and oxidative damage in tolerance response to UV-B and photooxidative stress, via activation of antioxidant GSTU genes.
Alignment-free Comparison of Metagenomics Sequences via Approximate String Matching
Authors: Chen Jian , Yang Le , Li Lu , Goodison Steve , Sun Yijun 
Published: May 2020

AbstractQuantifying pairwise sequence similarities is a key step in metagenomics studies. Alignment-free methods provide a computationally efficient alternative to alignment-based methods for large-scale sequence analysis. Several neural network-based methods have recently been developed for this purpose. However, existing methods do not perform well on sequences of varying lengths and are sensitive to the presence of insertions and deletions. In this paper, we describe the development of a new method, referred to as AsMac, that addresses the aforementioned issues. We proposed a novel neural network structure for approximate string matching for the extraction of pertinent information from biological sequences and developed an efficient gradient computation algorithm for training the constructed neural network. We performed a large-scale benchmark study using real-world data that demonstrated the effectiveness and potential utility of the proposed method. The open-source software for the proposed method and trained neural-network models for some commonly used metagenomics marker genes were developed and are freely available atwww.acsu.buffalo.edu/~yijunsun/lab/AsMac.html.
Acibenzolar-S-methyl activates stomatal-based defense systemically in Japanese radish by inducing peroxidase-dependent reactive oxygen species production
Authors: Sakata Nanami , Ishiga Takako , Taniguchi Shizuku , Ishiga Yasuhiro 
Published: May 2020

AbstractAcibenzolar-S-methyl (ASM) is a well-known plant activator, which is a synthetic analog of salicylic acid (SA). Recently, copper fungicides and antibiotics are major strategies for controlling bacterial diseases. However, resistant strains have already been found. Therefore, there is an increasing demand for sustainable new disease control strategies. We investigated the ASM disease control effect againstPseudomonas cannabinapv.alisalensis(Pcal), which causes bacterial blight on Japanese radish. In this study, we demonstrated that ASM effectively suppressedPcaldisease symptom development associated with reduced bacterial populations on Japanese radish leaves. Interestingly, we also demonstrated that ASM activated systemic acquired resistance (SAR), including stomatal-based defense, not only on ASM treated leaves, but also on untreated upper and lower leaves. Reactive oxidative species (ROS) are essential second messengers in stomatal-based defense. We found that ASM induced stomatal closure by inducing ROS production through peroxidase. These results indicate that stomatal closure induced by ASM treatment is effective for preventingPcalpathogen invasion into plants, and in turn reduction of disease development.
A framework forin situmolecular characterization of coral holobionts using nanopore sequencing
Authors: Carradec Quentin , Poulain Julie , Boissin Emilie , Hume Benjamin CC , Voolstra Christian R , Ziegler Maren , Engelen Stefan , Cruaud Corinne , Planes Serge , Wincker Patrick 
Published: May 2020

AbstractMolecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires bulky instruments and controlled laboratory conditions which are impractical for environmental experiments in remote areas. Recent advances in sequencing technologies now permit rapid sequencing in the field; however, development of specific protocols and pipelines for the effective processing of complex microbial systems are currently lacking. Here, we used a combination of 3 marker genes targeting the coral animal host, its symbiotic alga, and the associated bacterial microbiome to characterize 60 coral colonies collected and processedin situ, during theTaraPacific expedition. We used Oxford Nanopore Technologies to sequence marker gene amplicons and developed bioinformatics pipelines to analyze nanopore reads on a laptop, obtaining results in less than 24 hours. Reef scale network analysis of coral-associated bacteria reveals broadly distributed taxa, as well as host-specific associations. Protocols and tools used in this work may be applicable for rapid coral holobiont surveys, immediate adaptation of sampling strategy in the field, and to make informed and timely decisions in the context of the current challenges affecting coral reefs worldwide.
Haplotype tagging reveals parallel formation of hybrid races in two butterfly species
Authors: Meier Joana I. , Salazar Patricio A. , Kučka Marek , Davies Robert William , Dréau Andreea , Aldás Ismael , Power Olivia Box , Nadeau Nicola J. , Bridle Jon R. , Rolian Campbell , Barton Nicholas H. , McMillan W. Owen , Jiggins Chris D. , Chan Yingguang Frank 
Published: May 2020

AbstractGenetic variation segregates as linked sets of variants, or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. And yet, genomic data often lack haplotype information, due to constraints in sequencing technologies. Here we present “haplotagging”, a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius eratoandH. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species the geographic clines for the major wing pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.One-sentence summaryHaplotagging, a novel linked-read sequencing technique that enables whole genome haplotyping in large populations, reveals the formation of a novel hybrid race in parallel hybrid zones of two co-mimickingHeliconiusbutterfly species through strikingly parallel divergences in their genomes.
LoxTnSeq: Random Transposon insertions combined with cre/lox recombination and counterselection to generate large random genome reductions
Authors: Shaw Daniel , Miravet-Verde Samuel , Pinero Carlos , Serrano Luis , Lluch-Senar Maria 
Published: May 2020

AbstractThe removal of unwanted genetic material is a key aspect in many synthetic biology efforts, and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deep-sequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via cre recombinase, catalogued via deep-sequencing. When LoxTnSeq was applied to the naturally genome reduced bacteriumMycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from >50 bp to 28 Kb, which represent 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions.
The effect of dispersal and preferential mating on the genetic control of mosquitoes
Authors: Khamis Doran , El Mouden Claire , Kura Klodeta , Bonsall Michael B. 
Published: May 2020

AbstractMosquito-borne diseases cause significant social and economic damage across much of the globe. New biotechnologies that utilise manipulations of the mosquito genome have been developed to combat disease. The successful implementation of genetic mosquito control technologies may depend upon ecological, evolutionary and environmental factors, as well as the specifications of the chosen technology. Understanding the influence of these external factors will help inform how best to deploy a chosen technology to control vectors of infectious diseases. We use a continuous-time stochastic spatial network model of a mosquito life-cycle coupled to population genetics models to investigate the impact of releasing seven types of genetic control technology: a self-limiting lethal gene, two underdominance threshold gene drives, two homing gene drives and twoWolbachiasystems. We apply the mathematical framework to understand control interventions of two archetypes of mosquito species: a short-range dispersingAedes aegyptiand comparatively longer-range dispersingAnopheles gambiae. We show that mosquito dispersal behaviour is an extremely important factor in determining the outcome of a release programme. Assortative mating – where the mating success of genetically modified males is lower than their wild counterparts – can facilitate the spatial containment of gene drives. The rapid evolution of strong mating preference can damage the efficacy of control efforts for all control technologies. We suggest that there cannot be a one-size-fits-all approach to regulation and implementation of vector control; there must be application-specific control plans that take account of understudied ecological, evolutionary and environmental factors.