bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of Functional Results After Cross-Face Nerve Graft-, Spinal Accessory Nerve-, and Masseter Nerve-Innervated Gracilis for Facial Paralysis Reconstruction
Authors: Chuang David Chwei-Chin , Lu Johnny Chuieng-Yi , Chang Tommy Nai-Jen , Laurence Vincent G.
Published: April 2018

Background

Using functioning free muscle transplantation (FFMT) for facial paralysis and postparalysis facial synkinesis reconstruction is our preferred technique. Gracilis was the first choice of muscle. Three motor neurotizers: cross-face nerve graft (CFNG), spinal accessory nerve (XI) and masseter nerve (V3) have been used as neurotizers for different indications.

Methods

A total of 362 cases of facial reanimation with FFMT were performed between 1986 and 2015. Of these, 350 patients with 361 FFMT were enrolled: 272 (78%) patients were treated by CFNG-gracilis, 56 (15%) by XI-gracilis, and 22 (6%) by V3-gracilis. Smile excursion score, cortical adaptation stage with tickle test for spontaneous smile, facial synkinesis, satisfaction score by questionnaire, and functional facial grading were used for outcome assessment.

Results

The CFNG-gracilis in a 2-stage procedure achieved most natural and spontaneous smile when longer observation (≥2 years) was followed. The single-stage procedure using the XI-gracilis has proven a good alternative. V3-gracilis provided high smile excursion score in the shortest rehabilitation period, but never obtained spontaneous smile.

Conclusions

The CFNG-gracilis remains our first choice for facial paralysis reconstruction which can achieve natural and spontaneous smile. XI- or V3-gracilis can be selected as a save procedure when CFNG-gracilis fails. The V3-gracilis is indicated in some specific conditions, such as bilateral Möbius syndrome, older patients (age, >70 years), or patients with malignant disease.
TEG Lysis Shutdown Represents Coagulopathy in Bleeding Trauma Patients: Analysis of the PROPPR Cohort
Authors: Cardenas Jessica C. , Wade Charles E. , Cotton Bryan A. , George Mitchell J. , Holcomb John B. , Schreiber Martin A. , White Nathan J.
Published: April 2018

Background:

Thrombelastography (TEG) fibrinolysis shutdown after trauma is associated with increased mortality due to hypercoagulability-associated organ failure. However, a lack of mechanistic data has precluded the development of novel interventions to treat shutdown.

Objectives:

To define the pathophysiology of TEG shutdown in severely injured, bleeding patients through secondary analysis of the PROPPR trial.

Methods:

Fibrinolysis was characterized in PROPPR subjects using admission TEG lysis at 30 min (LY30) or plasmin-antiplasmin (PAP) levels. LY30 categories were low (<0.9%), moderate (0.9–2.9%), or high (≥ 3%). PAP was classified as low (<1,500 μg/L), moderate (1,500–20,000 μg/L), or high (>20,000 μg/L). Demographics, outcomes, admission TEG values, platelet count and function, standard coagulation tests, and coagulation proteins were compared.

Results:

Five hundred forty-seven patients had TEG data and 549 patients had PAP data available. Low LY30 was associated with reduced platelet count and aggregation, poorer TEG clot formation, prolonged clotting times, and reduced fibrinogen and alpha2 antiplasmin. Compared to moderate PAP, low PAP subjects had similar platelet parameters, TEG values, fibrinogen, and alpha2 antiplasmin, but reduced tPA, and elevated PAI-1. D-Dimer values increased as PAP increased, however patients with low LY30 had elevated D-Dimer compared with moderate LY30 patients. Most low LY30 deaths were due to TBI (45%) and hemorrhage (42%) versus one of each cause (TBI, hemorrhage, MOF) in low PAP patients.

Conclusions:

Low TEG LY30 does not reflect shutdown of enzymatic fibrinolysis with hypercoagulability, but rather a coagulopathic state of moderate fibrinolysis with fibrinogen consumption and platelet dysfunction that is associated with poor outcomes.
Phagocytosis by Fibrocytes as a Mechanism to Decrease Bacterial Burden and Increase Survival in Sepsis
Authors: Collins Dalis , Fry Christopher , Moore Bethany B. , Nemzek Jean A.
Published: April 2018

Fibrocytes are unique cells with innate and adaptive immune functions, but these mechanisms have not been fully explored. The aim of this study was to explain the mechanism by which adoptive transfer of exogenous fibrocytes improved bacterial clearance and increased sepsis survival. Initial flow cytometry-based, in vitro assays demonstrated phagocytosis by fibrocytes and intracellular bacterial killing was confirmed by direct plating of cell lysates after exposure to live bacteria. Intravenous adoptive transfer of fibrocytes at the time of cecal ligation and puncture (CLP) or 2 h after CLP in mice increased survivability. Decreased intraperitoneal bacterial burden was also observed. Quantification of peritoneal cell populations using flow cytometry demonstrated transferred and endogenous fibrocytes were significantly increased after CLP, while macrophage and neutrophil numbers were unchanged. To determine the impact in vivo, fluorescently labeled, killed bacteria were injected i.p. into mice 10 h after CLP or sham surgery ± adoptive transfer. Two hours later, flow cytometry of peritoneal cell populations after CLP alone revealed increased phagocytosis by macrophages, neutrophils, and endogenous fibrocytes. Transferred fibrocytes had significantly increased phagocytic activity in the septic peritoneum compared with sham and greater activity than any other cell type. Therefore, adoptive transfer may enhance bacterial clearance in early sepsis through the cumulative effects of endogenous and transferred fibrocytes rather than modulating the function of other endogenous phagocytes. Direct phagocytic activity coupled with previously described influences on T cell responses may explain the benefits of fibrocyte transfer in sepsis.
Chronic Alcohol Ingestion Worsens Survival and Alters Gut Epithelial Apoptosis and CD8+ T Cell Function After Pseudomonas Aeruginosa Pneumonia-Induced Sepsis
Authors: Klingensmith Nathan J. , Fay Katherine T. , Lyons John D. , Chen Ching-wen , Otani Shunsuke , Liang Zhe , Chihade Deena B. , Burd Eileen M. , Ford Mandy L. , Coopersmith Craig M.
Published: April 2018

Mortality is higher in septic patients with a history of alcohol use disorder than in septic patients without a history of chronic alcohol usage. We have previously described a model of chronic alcohol ingestion followed by sepsis from cecal ligation and puncture in which alcohol-fed septic mice have higher mortality than water-fed septic mice, associated with altered gut integrity and increased production of TNF and IFNγ by splenic CD4+ T cells without alterations in CD8+ T cell function. The purpose of this study was to determine whether this represents a common host response to the combination of alcohol and sepsis by creating a new model in which mice with chronic alcohol ingestion were subjected to a different model of sepsis. C57Bl/6 mice were randomized to receive either alcohol or water for 12 weeks and then subjected to Pseudomonas aeruginosa pneumonia. Mice were sacrificed either 24 hours after the onset of sepsis or followed for survival. Alcohol-fed septic mice had significantly higher 7-day mortality than water-fed septic mice (96% vs 58%). This was associated with a 5-fold increase in intestinal apoptosis in alcohol-fed septic animals, accompanied by an increase in the pro-apoptotic protein Bax. Serum IL-6 levels were higher and IL-2 levels were lower in alcohol-fed septic mice. In contrast, CD8+ T cell frequency was lower in alcohol-fed mice than water-fed septic mice, associated with increased production of IFNγ and TNF in stimulated splenocytes. No significant differences were noted in CD4+ T cells, lung injury or bacteremia. Mice with chronic alcohol ingestion thus have increased mortality regardless of their septic insult, associated with changes in both the gut and the immune system.
The Effects of Genetic 3-Mercaptopyruvate Sulfurtransferase Deficiency in Murine Traumatic-Hemorrhagic Shock
Authors: Gröger Michael , Wepler Martin , Wachter Ulrich , Merz Tamara , McCook Oscar , Kress Sandra , Lukaschewski Britta , Hafner Sebastian , Huber-Lang Markus , Calzia Enrico , Georgieff Michael , Nagahara Noriyuki , Szabó Csaba , Radermacher Peter , Hartmann Clair
Published: April 2018

Introduction:

Hemorrhagic shock is a major cause of death after trauma. An additional blunt chest trauma independently contributes to mortality upon the development of an acute lung injury (ALI) by aggravating pathophysiological consequences of hemorrhagic shock. The maintenance of hydrogen sulfide availability is known to play an important role during hemorrhage and ALI. We therefore tested the impact of a genetic 3-mercaptopyruvate sulfurtransferase mutation (Δ3-MST) in a resuscitated murine model of traumatic-hemorrhagic shock.

Methods:

Anesthetized wild-type (WT) and Δ3-MST mice underwent hemorrhagic shock with/without blunt chest trauma. Hemorrhagic shock was implemented for 1 h followed by retransfusion of shed blood and intensive care therapy for 4 h, including lung-protective mechanical ventilation, fluid resuscitation, and noradrenaline titrated to maintain a mean arterial pressure at least 50 mmHg. Systemic hemodynamics, metabolism, and acid-base status were assessed together with lung mechanics and gas exchange. Postmortem tissue samples were analyzed for immunohistological protein expression and mitochondrial oxygen consumption.

Results:

3-MST-deficient mice showed similar results in parameters of hemodynamics, gas exchange, metabolism, acid base status, and survival compared with the respective WT controls. Renal albumin extravasation was increased in Δ3-MST mice during hemorrhagic shock, together with a decrease of LEAK respiration in heart tissue. In contrast, mitochondrial oxygen consumption in the uncoupled state was increased in kidney and liver tissue of Δ3-MST mice subjected to the combined trauma.

Conclusions:

In summary, in a resuscitated murine model of traumatic-hemorrhagic shock, 3-MST deficiency had no physiologically relevant impact on hemodynamics and metabolism, which ultimately lead to unchanged mortality regardless of an additional blunt chest trauma.
Effect of Prehospital Red Blood Cell Transfusion on Mortality and Time of Death in Civilian Trauma Patients
Authors: Rehn Marius , Weaver Anne , Brohi Karim , Eshelby Sarah , Green Laura , Røislien Jo , Lockey David J.
Published: April 2018

Background:

Current management principles of hemorrhagic shock after trauma emphasize earlier transfusion therapy to prevent dilution of clotting factors and correct coagulopathy. London's Air Ambulance (LAA) was the first UK civilian prehospital service to routinely offer prehospital red blood cell (RBC) transfusion (phRTx). We investigated the effect of phRTx on mortality.

Methods:

Retrospective trauma database study comparing mortality before implementation with after implementation of phRTx in exsanguinating trauma patients. Univariate logistic regression was performed for the unadjusted association between phRTx and mortality was performed, and multiple logistic regression adjusting for potential confounders.

Results:

We identified 623 subjects with suspected major hemorrhage. We excluded 84 (13.5%) patients due to missing data on survival status. Overall 187 (62.3%) patients died in the before phRTx period and 143 (59.8%) died in the after phRTx group. There was no significant improvement in overall survival after the introduction of phRTx (P = 0.554). Examination of prehospital mortality demonstrated 126 deaths in the pre-phRTx group (42.2%) and 66 deaths in the RBC administered group (27.6%). There was a significant reduction in prehospital mortality in the group who received RBC (P < 0.001).

Conclusions:

phRTx was associated with increased survival to hospital, but not overall survival. The “delay death” effect of phRTx carries an impetus to further develop inhospital strategies to improve survival in severely bleeding patients.
Pancreatic Neuroendocrine Neoplasms: A Role of Laparoscopy in Surgical Treatment: Review
Authors: Szeliga Jacek , Jackowski Marek
Published: April 2018

Pancreatic neuroendocrine neoplasms (PNENs) are extremely rare neoplasms of the pancreas. They originate from pancreatic islet cells, and from the very beginning, cancer cells may or may not show hormone hypersecretion. Currently, surgical treatment is the only therapeutic method that significantly prolongs life expectancy, and in such cases it is a method of choice. In the paper, a review of literature based on the Medline database and including mainly the period of 2013 to 2017 was performed. In each case an operating surgeon is responsible for selection of a method used for surgical treatment. There is no unanimous consensus with regard to selection of a surgical method. With regard to surgeries performed in PNEN cases a laparoscopic approach can be used in almost all procedures to treat PNENs. The analysis of oncological outcomes of resection surgeries is still incomplete, but a video approach has a strong position in PNEN surgery, and according to current knowledge its therapeutic effects are equivalent to those of traditional surgery, and it offers general benefits associated with a minimally invasive approach.
Occupational exposure during emergency department thoracotomy: A prospective, multi-institution study
Authors: Nunn Andrew , Prakash Priya , Inaba Kenji , Escalante Alvarez , Maher Zoë , Yamaguchi Seiji , Kim Dennis Y. , Maciel James , Chiu William C. , Drumheller Byron , Hazelton Joshua P. , Mukherjee Kaushik , Luo-Owen Xian , Nygaard Rachel M. , Marek Ashley P. , Morse Bryan C. , Fitzgerald Caitlin A. , Bosarge Patrick L. , Jawa Randeep S. , Rowell Susan E. , Magnotti Louis J. , Ong Adrian W. , Brahmbhatt Tejal S. , Grossman Michael D. , Seamon Mark J.
Published: April 2018

BACKGROUND

Occupational exposure is an important consideration during emergency department thoracotomy (EDT). While human immunodeficiency virus/hepatitis prevalence in trauma patients (0–16.8%) and occupational exposure rates during operative trauma procedures (1.9–18.0%) have been reported, exposure risk during EDT is unknown. We hypothesized that occupational exposure risk during EDT would be greater than other operative trauma procedures.

METHODS

A prospective, observational study at 16 US trauma centers was performed (2015–2016). All bedside EDT resuscitation providers were surveyed with a standardized data collection tool and risk factors analyzed with respect to the primary end point, EDT occupational exposure (percutaneous injury, mucous membrane, open wound, or eye splash). Provider and patient variables and outcomes were evaluated with single and multivariable logistic regression analyses.

RESULTS

One thousand three hundred sixty participants (23% attending, 59% trainee, 11% nurse, 7% other) were surveyed after 305 EDTs (gunshot wound, 68%; prehospital cardiopulmonary resuscitation, 57%; emergency department signs of life, 37%), of which 15 patients survived (13 neurologically intact) their hospitalization. Overall, 22 occupational exposures were documented, resulting in an exposure rate of 7.2% (95% confidence interval [CI], 4.7–10.5%) per EDT and 1.6% (95% CI, 1.0–2.4%) per participant. No differences in trauma center level, number of participants, or hours worked were identified. Providers with exposures were primarily trainees (68%) with percutaneous injuries (86%) during the thoracotomy (73%). Full precautions were utilized in only 46% of exposed providers, while multiple variable logistic regression determined that each personal protective equipment item utilized during EDT correlated with a 34% decreased risk of occupational exposure (odds ratio, 0.66; 95% CI, 0.48–0.91; p = 0.010).

CONCLUSIONS

Our results suggest that the risk of occupational exposure should not deter providers from performing EDT. Despite the small risk of viral transmission, our data revealed practices that may place health care providers at unnecessary risk of occupational exposure. Regardless of the lifesaving nature of the procedure, improved universal precaution compliance with personal protective equipment is paramount and would further minimize occupational exposure risks during EDT.

LEVEL OF EVIDENCE

Therapeutic/care management study, level III.
αB-crystallin inhibits amyloidogenesis by disassembling aggregation nuclei
Authors: Tkachenko Olga , Benesch Justin L.P. , Baldwin Andrew J.
Published: April 2018

Amyloid formation is implicated in a range of neurodegenerative conditions including Alzheimer’s and Parkinson’s diseases. The small heat-shock protein αB-crystallin (αBC) is associated with both, and directly inhibits amyloid formation in vitro and its toxicity in cells. Studying the mechanism of aggregation inhibition is challenging owing to sample heterogeneity and the dynamic nature of the process. Here, by means of NMR spectroscopy and chemical kinetics, we establish the mechanism by which the protein α-lactalbumin aggregates and forms amyloid, and how this is inhibited by αBC. In particular, we characterise the lifetime of the unstable aggregation nucleus, and determine that this species is specifically destabilised by αBC. This mechanism allows the chaperone to delay the onset of aggregation, although it is overwhelmed on longer timescales. The methodology we present provides a mechanistic understanding of how αBC reduces the toxicity of amyloids, and is widely applicable to other complex mixtures.
A prior-based approach for hypothesis comparison and its utility to discern among temporal scenarios of divergence
Authors: Zarza Eugenia , O’Hara Robert B. , Klussmann-Kolb Annette , Pfenninger Markus
Published: April 2018

One of the major problems in evolutionary biology is to elucidate the relationships between historical events and the tempo and mode of lineage divergence. The development of relaxed molecular clock models and the increasing availability of DNA sequences resulted in more accurate estimations of taxa divergence times. However, finding the link between competing historical events and divergence is still challenging. Here we investigate assigning constrained-age priors to nodes of interest in a time-calibrated phylogeny as a means of hypothesis comparison. These priors are equivalent to historic scenarios for lineage origin. The hypothesis that best explains the data can be selected by comparing the likelihood values of the competing hypotheses, modelled with different priors. A simulation approach was taken to evaluate the performance of the prior-based method and to compare it with an unconstrained approach. We explored the effect of DNA sequence length and the temporal placement and span of competing hypotheses (i.e. historic scenarios) on selection of the correct hypothesis and the strength of the inference. Competing hypotheses were compared applying a posterior simulation analogue of the Akaike Information Criterion and Bayes factors (obtained after calculation of the marginal likelihood with three estimators: Harmonic Mean, Stepping Stone and Path Sampling). We illustrate the potential application of the prior-based method on an empirical data set to compare competing geological hypotheses explaining the biogeographic patterns inPleurodelesnewts. The correct hypothesis was selected on average 89% times. The best performance was observed with DNA sequence length of 3500-10000 bp. The prior-based method is most reliable when the hypotheses compared are not temporally too close. The strongest inferences were obtained when using the Stepping Stone and Path Sampling estimators. The prior-based approach proved effective in discriminating between competing hypotheses when used on empirical data. The unconstrained analyses performed well but it probably requires additional computational effort. Researchers applying this approach should rely only on inferences with moderate to strong support. The prior-based approach could be applied on biogeographical and phylogeographical studies where robust methods for historical inferences are still lacking.
Rules Governing Perception of Multiple Phosphenes by Human Observers
Authors: Bosking William , Foster Brett , Sun Ping , Beauchamp Mike , Yoshor Daniel
Published: April 2018

Stimulation of single sites in primary visual cortex results in the perception of a small flash of light known as a phosphene. Little is known about how phosphenes from multiple electrodes can be combined to form perception of coherent patterns. Here we examine the percepts reported by human observers as various spatial configurations of 2 to 5 electrodes in visual cortex were stimulated simultaneously. When two electrodes were stimulated simultaneously, subjects reliably perceived either one or two phosphenes depending on the physical distance separating the electrodes. In cases where two phosphenes were perceived, they were located in the same visual field location as when the two electrodes were stimulated separately. Adding a third electrode produced similar results. In several subjects, we obtained combination of 4 to 5 electrodes that generated individual phosphenes when stimulated concurrently. Subjects were able to reliably discriminate between different multiple electrode stimulation patterns that were presented in random order. These results demonstrate that simple pattern information can be conveyed to subjects with surface electrodes spaced at millimeters apart on the cortex.
HIR-1 Mediates Response to Hypoxia-Induced Extracellular Matrix Remodeling
Authors: Vozdek Roman , Long Yong , Ma Dengke K.
Published: April 2018

Inadequate tissue oxygen, or hypoxia, is a central concept in pathophysiology of ischemic disorders and cancer. Hypoxia promotes extracellular matrix (ECM) remodeling, cellular metabolic adaptation and metastasis. To determine how cells respond to hypoxia-induced ECM remodeling, we performed a large-scale forward genetic screen inC.elegans. We identified a previously uncharacterized receptor tyrosine kinase (RTK) named HIR-1 as a key mediator in a pathway that orchestrates transcriptional responses to hypoxia-induced ECM remodeling. Impaired ECM integrity caused by hypoxia or deficiency of the oxygen-dependent procollagen hydroxylases, heme peroxidases or cuticular collagens activates gene expression through inhibition of HIR-1. Genetic suppressor screens identified NHR-49 and MDT-15 as transcriptional regulators downstream of HIR-1. Cellular responses through HIR-1 maintain ECM homeostasis and promote animal adaptation to severe hypoxia. We propose thatC.elegansHIR-1 defines an unprecedented type of RTK that mediates responses to hypoxia-induced ECM remodeling by mechanisms that are likely conserved in other organisms.

ONE-SENTENCE SUMMARY

A regulatory pathway for ECM homeostasis underlies adaptation to hypoxia and re-oxygenation
DraftAphaenogastergenomes expand our view of ant genome size variation across climate gradients
Authors: Lau Matthew K. , Ellison Aaron M. , Nguyen Andrew D. , Penick Clint , DeMarco Bernice , Gotelli Nicholas J. , Sanders Nathan J. , Dunn Robert R. , Cahan Sara Helms
Published: April 2018

Given the abundance, broad distribution, and diversity of roles that ants play in many ecosystems, they are an ideal group to serve as ecosystem indicators of climatic change. At present, only a few whole-genome sequences of ants are available (19 of>16,000 species), mostly from tropical and sub-tropical species. To address this limited sampling, we sequenced genomes of temperate-latitude species from the genusAphaenogaster, a genus with important seed dispersers. In total, we sampled seven colonies of six species:A. ashmeadi,A. floridana,A. fulva,A. miamiana,A. picea, andA. rudis. The geographic ranges of these species collectively span eastern North America from southern Florida to southern Canada, which encompasses a latitudinal gradient in which many climatic variables are changing rapidly. For the six genomes, we assembled an average of 271,039 contigs into 47,337 scaffolds. The mean genome size was 370.5 Mb, ranging from 310.3 to 429.7, which is comparable to that of other sequenced ant genomes (212.8 to 396.0 Mb) and flow cytometry estimates (210.7 to 690.4 Mb). In an analysis of currently sequenced ant genomes and the newAphaenogastersequences, we found that after controlling for both spatial autocorrelation and phylogenetics ant genome size was marginally correlated with sample site climate similarity. Of all examined climate variables, minimum temperature showed the strongest correlation with genome size, with ants from locations with colder minimum temperatures having larger genomes. These results suggest that temperature extremes could be a selective force acting on ant genomes and point to the need for more extensive sequencing of ant genomes.
A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes
Authors: Koganebuchi Kae , Gakuhari Takashi , Takeshima Hirohiko , Sato Kimitoshi , Fujii Kiyotaka , Kumabe Toshihiro , Kasagi Satoshi , Sato Takehiro , Tajima Atsushi , Shibata Hiroki , Ogawa Motoyuki , Oota Hiroki
Published: April 2018

To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome region with substantial length.
Mode of Growth and Temperature Dependence on Expression of Atrazine-degrading Genes inPseudomonassp. strain ADP Biofilms
Authors: Delcau Michael A. , Henry Victoria A. , Pattee Emily R. , Peeples Tonya L.
Published: April 2018

Bacterial strainPseudomonassp. strain ADP is capable of metabolizing atrazine, a synthetic herbicide, and uses atrazine as a sole nitrogen source for growth. The microbe completely mineralizes the substrate in a catabolic pathway comprised of six enzymatic steps. All enzymes, AtzA-AtzF, encoded by corresponding genes,AtzA-AtzF, are located on a self-transmissible plasmid, pADP-1. (Souza, M. L., Wackett, L.P., and Sadowsky, M.JAppl. and Environ. Microbiol. 64(6): 2323-2326, 1998) RT-qPCR was used to differentiate gene expression in atrazine-degrading genes inPseudomonassp. strain ADP cells grown as suspended cells and as biofilms. Relative gene expression was also evaluated for biofilms grown at 25°C, 30°C, and 37°C. Complementary atrazine kinetic data was collected using GC-MS for both modes of growth and temperature variance. No significant difference in expression was observed for all atrazine-degrading genes in biofilm-mediated cells relative to planktonic cells, suggesting neither decreased or increased catabolic activity at the mRNA level. In contrasting experiments concerning biofilm growth, expression was downregulated at 37°C for genes AtzA,AtzB, andAtzCand upregulated for genesAtzD, AtzE, AtzF, signifyingPseudomonassp. strain ADP biofilms catabolic activity may change in response to substantial temperature changes. Gradual decreases in atrazine concentration were apparent in cells grown in shake flasks, while biofilm-mediated cells showed transient increases and decreases in reactor effluent. The complex extracellular matrix components, quorum sensing, and genetic transfer may account for accumulation and rapid degradation of atrazine. The data collected suggest biofilm-mediated bioremediation may give insight into catabolic activity and atrazine degradation potential.

Importance

Atrazine is the second most applied herbicide in the United States. It is applied to crops including sorghum, corn, and sugarcane to prevent the growth of broad-leaved weeds. Once used, it can permeate the soil and contaminate proximal groundwater sources, which provide drinking water for over 90-million people. The Environmental Protection Agency sets the maximum contaminant level at 3 parts per billion for atrazine in drinking water, however this is frequently exceeded in rural regions which presents a public safety concern. Atrazine is an endocrine disruptor compound and a suspected teratogen in humans and freshwater species, respectively. This research is significant in evaluating the use an atrazine-degrading strain,Pseudomonassp. strain ADP, grown in a biofilm mode of growth to increase the degradation potential compared to suspended cells. Our results concerning expression and kinetics will aid the development of biofilm reactors forex situbioremediation and understanding environmental biofilms.
Development and validation of a phenotypic high-content imaging assay for assessing the antiviral activity of small-molecule inhibitors targeting the Zika virus
Authors: Bernatchez Jean A. , Yang Zunhua , Coste Michael , Li Jerry , Beck Sungjun , Liu Yan , Clark Alex E. , Zhu Zhe , Luna Lucas A. , Sohl Christal D. , Purse Byron W. , Li Rongshi , de Siqueira-Neto Jair L.
Published: April 2018

Zika virus (ZIKV) has been linked to the development of microcephaly in newborns, as well as Guillain-Barré syndrome. There are currently no drugs available to treat infection, and accordingly there is an unmet medical need for discovery of new therapies. High-throughput drug screening efforts focusing on indirect readouts of cell viability are prone to a higher frequency of false positives in cases where the virus is viable in the cell but the cytopathic effect is reduced or delayed. Here, we describe a fast and label-free phenotypic high-content imaging assay used to detect cells affected by the viral-induced cytopathic effect (CPE) using automated imaging and analysis. Protection from CPE correlates with a decrease in viral antigen production as observed by immunofluorescence. We trained our assay using a collection of nucleoside analogues against ZIKV; the previously reported antiviral activities of 2’-C-methylribonucleosides and ribavirin against the Zika virus in Vero cells were confirmed using our developed method. Profiling of a novel library of 24 natural product derivatives using our assay revealed compound 1 as an inhibitor of ZIKV-induced cytopathic effect; activity of the compound was confirmed in human fetal neural stem cells (NSCs). The described technique can be easily leveraged as a primary screening assay for profiling large compound libraries against ZIKV, and can be expanded to other ZIKV strains and other cell lines displaying morphological changes upon ZIKV infection.
The lipid environment determines the activity of theE. coliammonium transporter, AmtB
Authors: Mirandela Gaëtan Dias , Tamburrino Giulia , Hoskisson Paul A. , Zachariae Ulrich , Javelle Arnaud
Published: April 2018

The movement of ammonium across biological membranes is a fundamental process in all living organisms and is mediated by the ubiquitous Amt/Mep/Rh family of transporters. Recent structural analysis and coupled mass spectrometry studies have shown that theEscherichia coliammonium transporter, AmtB, specifically binds phosphatidylglycerol (PG). Upon PG binding, several residues of AmtB undergo a small conformational change, which stabilizes the protein against unfolding. However, no studies have so far been conducted to explore if PG binding to AmtB has functional consequences. Here, we used an invitroexperimental assay with purified components together with molecular dynamics simulations to characterise the relation between PG binding and AmtB activity. Firstly, our results indicate that the function of Amt in archaebacteria and eubacteria may differ. Secondly, we show that PG is an essential cofactor for AmtB activity and that in the absence of PG AmtB cannot complete the full translocation cycle. Furthermore, our simulations reveal previously undiscovered PG binding sites on the intracellular side of the lipid bilayer between the AmtB subunits. The possible molecular mechanisms explaining the functional role of PG are discussed.
A discontinuous Galerkin model for fluorescence loss in photobleaching of intracellular polyglutamine protein aggregates
Authors: Hansen Christian Valdemar , Schroll Hans J , Wüstner Daniel
Published: April 2018

Background: Intracellular phase separation and aggregation of proteins with extended poly-glutamine (polyQ) stretches are hallmarks of various age-associated neurodegenerative diseases. Progress in our understanding of such processes heavily relies on quantitative fluorescence imaging of suitably tagged proteins. Fluorescence loss in photobleaching (FLIP) is particularly well-suited to study the dynamics of protein aggregation in cellular models of Chorea Huntington and other polyQ diseases, as FLIP gives access to the full spatio-temporal profile of intensity changes in the cell geometry. In contrast to other methods, also dim aggregates become visible during time evolution of fluorescence loss in cellular compartments. However, methods for computational analysis of FLIP data are sparse, and transport models for estimation of transport and diffusion parameters from experimental FLIP sequences are missing.
Results: In this paper, we present a computational method for analysis of FLIP imaging experiments of intracellular polyglutamine protein aggregates also called inclusion bodies (IBs). By this method, we are able to determine the diffusion constant and nuclear membrane permeability coefficients of polyQ proteins as well as the exchange rates between aggregates and the cytoplasm. Our method is based on a reaction-diffusion multi-compartment model defined on a mesh obtained by segmentation of the cell images from the FLIP sequence. The discontinuous Galerkin (DG) method is used for numerical implementation of our model in FEniCS, which greatly reduces the computing time. The method is applied to representative experimental FLIP sequences, and consistent estimates of all transport parameters are obtained.
Conclusions: By directly estimating the transport parameters from live-cell image sequences using our new computational FLIP approach surprisingly fast exchange dynamics of mutant Huntingtin between cytoplasm and dim IBs could be revealed. This is likely relevant also for other polyQ diseases. Thus, our method allows for quantifying protein dynamics at different stages of the protein aggregation process in cellular models of neurodegeneration.
Structure-guided disruption of pseudopilus tip inhibits Type II secretion in Pseudomonas aeruginosa
Authors: Jia Zongchao , Zhang Yichen , Faucher Frederick , Zhang Wenwen , Wang Shu , Neville Nolan , Poole Keith , Zheng Jun
Published: April 2018

Pseudomonas aeruginosa utilizes the Type II secretion system (T2SS) to translocate a wide range of large, structured protein virulence factors through the periplasm to the extracellular environment for infection. In the T2SS, five pseudopilins assemble into the pseudopilus that acts as a piston to extrude exoproteins out of cells. Through structure determination of the pseudopilin complexes of XcpVWX and XcpVW and function analysis, we have confirmed that two minor pseudopilins, XcpV and XcpW, constitute a core complex indispensable to the pseudopilus tip. The absence of either XcpV or -W resulted in the non-functional T2SS. Our small-angle X-ray scattering experiment for the first time revealed the architecture of the entire pseudopilus tip and established the working model. Based on the interaction interface of complexes, we have developed inhibitory peptides. The structure-based peptides not only disrupted of the XcpVW core complex and the entire pseudopilus tip in vitro but also inhibited the T2SS in vivo. More importantly, these peptides effectively reduced the virulence of P. aeruginosa towards Caenorhabditis elegans.
In situ structures of periplasmic flagella reveal a distinct cytoplasmic ATPase complex inBorrelia burgdorferi
Authors: Qin Zhuan , Manne Akarsh , Tu Jiagang , Yu Zhou , Lees Kathryn , Yerke Aaron , Lin Tao , Li Chunhao , Norris Steven J. , Motaleb Md A. , Liu Jun
Published: April 2018

Periplasmic flagella are essential for the distinct morphology and motility of spirochetes. A flagella-specific Type III secretion system (fT3SS) composed of a membrane-bound export apparatus and a cytosolic ATPase complex is responsible for the assembly of the periplasmic flagella. Here, we combine cryo-electron tomography and mutagenesis approaches to characterize the fT3SS machine in the Lyme disease spirocheteBorrelia burgdorferi. We define the fT3SS machine by systematically characterizing mutants lacking key component genes. We discover that a distinct cytosolic ATPase complex is attached to the flagellar C-ring through multiple spoke-like linkers. The ATPase complex not only strengthens structural rigidity of the C-ring, but also undergoes conformational changes in concert with flagellar rotation. Our studies provide structural framework to uncover the unique mechanisms underlying assembly and rotation of the periplasmic flagella and may provide the bases for the development of novel therapeutic strategies against several pathogenic spirochetes.
The spatial and temporal dynamics of the nuclear RNAi-targeted RNA transcripts inCaenorhabditis elegans
Authors: Ni Julie Zhouli , Kalinava Natallia , Mendoza Sofia Galindo , Gu Sam Guoping
Published: April 2018

Small RNA-guided chromatin silencing, also referred to as nuclear RNAi, plays an essential role in genome surveillance in eukaryotes and provides a unique paradigm to explore the complexity in RNA-mediated chromatin regulation and transgenerational epigenetics. A well-recognized paradox in this research area is that transcription of the target loci is necessary for the initiation and maintenance of the silencing at the same loci. How the two opposing activities (transcriptional activation and repression) are coordinated during animal development is poorly understood. To resolve this gap, we took single-molecule RNA imaging, deep-sequencing, and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two exemplary endogenous germline nuclear RNAi targets inC. elegans, Cer3 and Cer8 LTR retrotransposons. By examining the wild type and a collection of mutant strains, we found that transcription and silencing cycle of Cer3 and Cer8 is tightly coupled with the early embryogenesis and germline mitotic and meiotic cell cycles. Strikingly, Cer3 and Cer8 transcripts are exclusively localized in the nuclei of germ cells in both wild type and germline nuclear RNAi-defective mutant animals. RNA-sequencing analysis found that this nuclear enrichment feature is a general feature for the endogenous targets of the germline nuclear RNAi pathway. In addition, the germline and somatic repressions of Cer3 have different genetic requirement for the three H3K9 histone methyltransferases, MET-2, SET-25, and SET-32, in conjunction with the nuclear Argonaute protein WAGO-9/HRDE-1. These results provide a first comprehensive cellular and developmental characterization of the nuclear RNAi-targeted endogenous targets throughout animal reproductive cycle. Altogether, these results support a model in which (1) both the transcriptional activation and repression steps of the germline nuclear RNAi pathway are tightly coupled with animal development, (2) the endogenous targets exhibit a hallmark of nuclear enrichment of their transcripts, and (3) different heterochromatin enzymes play distinct roles in somatic and germline silencing of the endogenous targets.
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
Authors: Zhu Anqi , Ibrahim Joseph G. , Love Michael I.
Published: April 2018

In RNA-seq differential expression analysis, investigators aim to detect genes with changes in expression across conditions, despite technical and biological variability. A common task is to accurately estimate the effect size. When the counts are low or highly variable, the simple effect size estimate has high variance, leading to poor ranking of genes by effect size. Here we propose apeglm, which uses a heavy-tailed Cauchy prior distribution for effect sizes, resulting in lower bias than previous shrinkage estimators, while still reducing variance. apeglm is available at http://bioconductor.org/packages/apeglm, and can be used from within the DESeq2 software.
1,3-Bis(2,6-diisopropylphenyl)imidazolium perchlorate
Authors: Minaker Samuel A. , Wang Ruiyao , Aquino Manuel A. S.
Published: April 2018

The title salt, C27H37N2
+·ClO4
−, arose as an unexpected oxidation product of the carbene 1,3-bis(2,6-diisopropylphenyl)-1,3-dihydro-2H-imidazol-2-ylidene in methanol. The five-membered cationic imidazolium ring is planar by symmetry and the complete cation is generated by a crystallographic twofold axis passing through the central N-bonded C atom and the mid-point of the C=C bond; the Cl atom of the perchlorate anion also lies on the rotation axis. The phenyl rings of the 2,6-diisopropylphenyl groups are each perpendicular to the imidazolium ring [dihedral angle = 90.0 (3)°]. In the crystal, weak C—H...O and bifurcated C—H...(O,O) interactions between the imidazolium ring H atoms and the perchlorate O atoms lead to [001] chains.
What is the post-2015 development agenda? A look from the underlying disaster risk drivers
Authors: Sarmiento Juan Pablo
Published: April 2018

Purpose

The purpose of this paper is to explore the current and projected impacts of the three post-2015 development agendas on the underlying disaster risk drivers (UDRD): the Sendai Framework for Disaster Risk Reduction, the Sustainable Development Goals, and the Paris COP21 Agreement.

Design/methodology/approach

The methodology is based on an ontological process, understood as an exhaustive analysis of the properties and relationships of an entity or subject of study.

Findings

The process characterized and linked the objectives proposed in the three agendas through the impact of the expected results on the underlying risk drivers. First, elements related to disaster risk within each agenda were identified. Then, in following the theory of change, a series of tools were used to identify domains of change, pathways, breakthroughs, and incremental outcomes that counteract the construction of disaster risk by acting on the underlying causes. It is essential that there be coherence, complementarity, and interdependence between the three agendas analyzed in order to transcend beyond the desired economic growth, and thus underpin true sustainable development by focusing on the UDRD.

Originality/value

Applying the theory of change constitutes a novel approach to identify the pathways or domains of change needed to integrate the three 2015 development agendas.
Fire resistance of concrete walls with light aggregate
Authors: Hertz Kristian
Published: April 2018

Purpose

The purpose of this paper is to present the design methods for fire-exposed concrete columns and walls. In addition, it presents analyses and tests showing that the methods are applicable for designing columns and walls of lightweight aggregate concrete based on expanded clay aggregate as well as heavy normal weight concrete and that the methods fit smoothly with cold design, when the fire exposure varies towards no fire.

Design/methodology/approach

During the 1990s, some of these design methods were included in the Eurocode as “the zone method”. They are still a part of the code. The rest of the methods, which were not included, served in practice, teaching and research. The present paper derives calculation methods proving their connection with common design for load cases without fire exposure. Furthermore, the paper presents full-scale tests proving the validation of the design methods for structural members of light aggregate concrete in addition to the full-scale tests of heavy concrete members.

Findings

The design methods give correct estimates of the load-bearing capacity of eccentric loaded concrete columns. An extended version of the methods estimates load-bearing capacity for walls with fire exposure on one side with sufficient accuracy for the purpose of design.

Originality/value

The author developed the main parts of the design methods in the 1980s and 1990s and others have from time to time referred to some parts of them mainly the minor parts published in the Eurocodes. However, owing to work overload, the author has not published the derivation and verification of them before. This paper provides in particular a verification against full-scale tests of light-aggregate concrete walls not published before.
A mechanistic framework to explain the immunosuppressive effects of neurotoxic pesticides on bees
Authors: Pamminger Tobias , Botías Christina , Goulson Dave , Hughes William O. H.
Published: April 2018

There is growing concern that declines in some managed and wild bee pollinator populations threaten biodiversity, the functioning of vital ecological processes and sustainable food production on a global scale.

In recent years, there has been increasing evidence that sublethal exposure to the neurotoxic class of insecticides (neonicotinoids) can undermine pollinator immunocompetence and amplify the effects of diseases, which have been suspected to be one of the drivers of pollinator declines. However, exactly how neonicotinoids might inhibit pollinator immunity remains elusive.

Here, we put forward a mechanistic framework to explain the effects of neurotoxic pesticides on insect immunocompetence. We propose that there is a close ontogenetic connection between the cellular arm (haemocytes) of the insect immune and nervous systems and that this connection makes the immune system of pollinators and other insects inherently susceptible to interference by neurotoxins such as neonicotinoids at sublethal doses.

Investigation of this connection is urgently needed to confirm the validity of this framework and develop a clear, mechanistically informed understanding of the interplay between neonicotinoids and disease ecology in pollinators. This in turn may enable us to develop strategies to mitigate impacts of neurotoxins on pollinators and/or enhance their impacts on pests.

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Innovative Behaviour, Trust and Perceived Workplace Performance
Authors: Hughes Mathew , Rigtering J. P. Coen , Covin Jeffrey G. , Bouncken Ricarda B. , Kraus Sascha
Published: April 2018

Building on theories of social exchange, enactment and trust, we provide a theorization of innovative work behaviour at the individual (IB) and team (IBT) levels and explain how desirable performance returns occur for individuals and teams. We further propose that horizontal (between team members) and vertical (between teams and their supervisor) team trust moderate the relationship between IBTand team performance. The results, based on surveys conducted at two points in time in a large insurance company in the Netherlands, show that employees’ IB is positively associated with perceived workplace performance at the individual and team levels and that the effects vary based on the forms of trust at play. Our findings offer important new knowledge about the consequences of entrepreneurship and innovation in the workplace and the significant role that trust plays in enabling such behaviour to promote perceived workplace performance, particularly in the vital financial services sector.