bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid brain responses to affective pictures indicate dimensions of trauma‐related psychopathology in adolescents
Authors: Sill Johanna , Popov Tzvetan , Schauer Maggie , Elbert Thomas
Published: February 2019

A variety of mental disorders are related to deviant brain activity, but these neural alterations do not validate psychiatric diagnostic categories. High symptom overlap and variable symptom patterns encourage a dimensional approach. Following the logic of the Research Domain Criteria (RDoC), we investigated trauma survivors for symptom clusters that might be associated with characteristics of ERPs, in particular with the early posterior negativity (EPN) elicited during affective picture processing. In rapid serial visual presentation, 90 adolescents (40 male/50 female, age M = 15.0 ± 2.5 years) who had been exposed to varying amounts of traumatic stress passively viewed a stream of high‐arousing positive and low‐arousing neutral pictures taken from the International Affective Picture System (IAPS). Using standardized interviews, symptoms of trauma‐related mental disorders were assessed (including those for PTSD, depression, borderline personality disorder, and behavioral problems). A principal component analysis was performed to derive potential dimensions of psychopathology. Multiple regression analysis confirmed a factor comprising problems concentrating, sleeping difficulties, and mistrust as a predictor of a larger EPN difference between high‐arousing positive and low‐arousing neutral IAPS pictures (β = 0.19, p < 0.05). Sex predicted the magnitude of the EPN (β = 0.45, p < 0.001). Male adolescents displayed a stronger EPN suppression than female adolescents. The result suggests that problems concentrating, sleeping difficulties, and mistrust seem to be trans‐diagnostic elements related to diminished early emotional discrimination represented by the EPN. Furthermore, our findings indicate that the EPN in response to emotional processing is modulated by sex.
Cheap and Dirty: The Effect of Contracting Out Cleaning on Efficiency and Effectiveness
Authors: Elkomy Shimaa , Cookson Graham , Jones Simon
Published: February 2019

Contracting out of public services, especially ancillary services, has been a key feature of New Public Management since the 1980s. By 2014, more than £100 billion of U.K. public services were being contracted out annually to the private sector. A number of high‐profile cases have prompted a debate about the value for money that these contracts provide. Value for money comprises both the cost and the quality of the services. This article empirically tests the contestability and quality shading hypotheses of contracting out in the context of cleaning services in the English National Health Service. Additionally, a new hypothesis of coupling is presented and tested: the effect of contracting of ancillary services on patient health outcomes, using the hospital‐acquired infection rate as our measure. Using data from 2010–11 to 2013–14 for 130 National Health Service trusts, the study finds that private providers are cheaper but dirtier than their in‐house counterparts.
Dog sperm swimming parameters analysed by computer‐assisted semen analysis of motility reveal major breed differences
Authors: Valverde Anthony , Arnau Sandra , García‐Molina Almudena , Bompart Daznia , Campos Marcos , Roldán Eduardo Raúl S. , Soler Carles
Published: February 2019

Contents

Dogs have undergone an intensive artificial selection process ever since the beginning of their relationship with humans. As a consequence, a wide variety of well‐defined breeds exist today. Due to the enormous variation in dog phenotypes and the unlikely chance of gene exchange between them, the question arises as to whether they should still be regarded as a single species or, perhaps, they be considered as different taxa that possess different reproductive traits. The aim of this study was therefore to characterize some male reproductive traits, focusing on kinematic characteristics of dog spermatozoa from several breeds. Thirty‐seven dogs from the following breeds were used: Staffordshire Bull Terrier, Labrador Retriever, Spanish Mastiff, Valencian Rat Hunting Dog, British Bulldog and Chihuahua. Semen samples were obtained via manual stimulation and diluted to a final sperm concentration of 50 million/ml, and they were subsequently analysed by the computer assisted semen analysis (CASA‐Mot) ISAS®v1 system. Eight kinematic parameters were evaluated automatically. All parameters showed significant different values among breeds and among individuals within each breed. The fastest sperm cells were those of Staffordshire Bull Terriers and the slowest were recorded in Chihuahuas. The intra‐male coefficient of variation (CV) was higher than the inter‐male CV for all breeds with the Staffordshire Bull Terrier showing the lowest values. When taking into consideration the cells by animal and breed, discriminant analyses showed a high capability to predict the breed. Cluster analyses showed a hierarchical classification very close to that obtained after phylogenetic studies with genome markers. In conclusion, future workers on dog spermatozoa should bear in mind major differences between breeds and realize that results cannot be extrapolated from one to another. Because sperm characteristics are associated with breed diversity, dogs may represent a good model to examine changes in reproductive parameters associated with selection processes.
Superovulation protocols for dairy cows bred with SexedULTRA™ sex‐sorted semen
Authors: Dell’Eva Giuliana , Bolognini Davide , Iacono Eleonora , Merlo Barbara
Published: February 2019

Contents

The objective was to compare embryo yield and quality in lactating dairy cows superovulated (SO) with varying amounts of gonadotropins and FSH:LH ratios and inseminated with SexedULTRA™ sex‐sorted semen. The SO treatments (n = 77) involved 3 protocols: groups F700 and F1000 were given total doses of 700 and 1,000 IU of Folltropin (FSH:LH ratio 49:1), respectively, whereas group F700P300 was given 700 IU of Folltropin + 300 IU of Pluset (FSH:LH ratio 1:1). Cows were artificially inseminated 3 times over a 10‐hr interval with frozen‐thawed SexedULTRA™ sex‐sorted semen (total of 10 × 106 sex‐sorted sperm), starting 18 hr after onset of oestrus, with embryos/ova recovered 7 d after oestrus. Total number of recovered structures and transferable embryos were lower (p < 0.05) in F700 (4.7 ± 3.0 and 1.9 ± 1.7, respectively; mean ± SD) compared to F1000 (8.1 ± 3.8 and 4.4 ± 2.6) and F700P300 (8.5 ± 6.4 and 4.5 ± 3.3). Percentage of cows ovulating >50% of follicles ≥0.8 cm in diameter was lower (p < 0.05) in F700 (35.5%) than in F1000 (82.4%) and F700P300 (73.1%). Percentage of unfertilized oocytes was higher (p < 0.05) in F700 (45.0% vs. 27.7% for F1000 and 29.0% for F700P300) whereas percentage of morulae was higher (p < 0.05) in F1000 (19.3% vs. 8.7% for F700 and 12.2% for F700P300). Embryo quality was similar among groups (p > 0.05). In conclusion, embryo production in lactating dairy cows was improved by increasing total dose of gonadotropins from 700 to 1,000 IU, with SexedULTRA™ sex‐sorted semen yielding satisfactory fertilization rates and embryo quality.
ACCESS ALL AREAS: Electromagnetic navigation and the pulmonologist
Authors: Steinfort Daniel P.
Published: February 2019

See related Article
Having It All? Employment, Earnings, and Children*
Authors: Laun Tobias , Wallenius Johanna
Published: February 2019

We study the effect of family policies on female employment, fertility, and the gender wage gap. We develop a life‐cycle model of heterogeneous households featuring endogenous labor supply, human capital accumulation, fertility, and home production. Our results suggest that human capital accumulation is important in accounting for the widening of the gender wage gap following children. We find that, in aggregate, childcare subsidies promote maternal employment and fertility, although the effects are heterogeneous across couples. A subsidy on home goods increases female employment, but primarily later in life. Thus, it does not dampen the widening of the gender gap.
Discovery of a novel HLA‐DRB1*16 variant, HLA‐DRB1*16:53, in a Taiwanese hematopoietic stem cell donor
Authors: Yang Kuo‐Liang , Lin Py‐Yu
Published: February 2019

One nucleotide substitution at residue 344 of the HLA‐DRB1*16:02:01:01 results in a novel allele, HLA‐DRB1*16:53.
Dynamics of crustal overthrust versus underthrust in the continental collision zones: Numerical modelling
Authors: Huangfu Pengpeng , Li Zhong‐Hai , Fan Weiming , Shi Yaolin
Published: February 2019

Trans‐plate crustal overthrust and underthrust are two unusual crustal architectures in nature, the mechanisms of which remain debated. Here, we construct a series of 2D numerical models to investigate the dynamics of trans‐plate crustal overthrust and underthrust. Model results indicate that the favourable conditions of crustal overthrust include low convergence rate, plastically strong crust, rheologically strong upper crust and hot subducting plate, which meanwhile contribute to the formation of ‘crocodile’ crustal structure. In contrast, a combination of a strong and buoyant subducting plate with a hot overriding plate facilitates crustal underthrust. The development of crustal overthrust shows no correlation with the subduction mode of lithospheric mantle, whereas crustal underthrust normally occurs in an advancing subduction system. Development conditions and crustal structures of the modelled overthrust and underthrust are consistent, on the first order, with the natural Dinarides orogen and the southern Tibetan plateau respectively.
Naturally propped fractures caused by quartz cementation preserve oil reservoirs in basement rocks
Authors: Baba Mas'ud , Parnell John , Bowden Stephen A.
Published: February 2019

Much silica precipitation in oil reservoirs occurred in the presence of hydrocarbons, evidenced by the entrapment of oil fluid inclusions in quartz. Also, silica in sedimentary basins is commonly precipitated at oil‐window temperatures. This spatial and temporal relationship between oil and quartz precipitation aids the entry of oil into fractured reservoirs, including fractured basement. Where quartz is precipitated as fracture linings, the fractures are propped open by bridging quartz crystals, creating high fracture porosity and permeability. Evidence from fossil fractured reservoirs shows a large proportion of oil residue is in such propped open fractures.
Establishing a perinatal red blood cell transfusion risk evaluation model for obstetric patients: a retrospective cohort study
Authors: Xing Zhun , He Yanjing , Ji Chao , Xu Chang , Zhang Wen , Li Yunhui , Tan Xiangqian , Zhao Ping , Wang Qiushi , Zheng Liqiang
Published: February 2019

BACKGROUND

The ability to predict risk factors for blood transfusion after postpartum hemorrhage could enhance the performance of lifesaving procedures in patients who experience postpartum hemorrhage. Therefore, this study aimed to evaluate these risk factors and create a scoring system for blood transfusion evaluations and risk in obstetric patients.

STUDY DESIGN AND METHODS

Diagnosis and blood transfusion data of 14,112 women who delivered between January 1, 2015, and December 31, 2015, were analyzed. A binary logistic regression model was used. We conducted univariate analyses of each risk factor as well as multivariable logistic regression analysis. Data of obstetric patients in 2016 validated the receiver operating characteristic curve. A risk prediction score was generated from the transfusion risk factor β‐coefficients in the multivariable logistic regression model.

RESULTS

In total, 392 (2.94%) of 13,328 patients received transfusions. After multivariable adjustment, polyembryony, anemia, thrombocytopenia, preeclampsia, placenta previa, placental implantation, uterine scarring, uterine rupture, retained placenta, stillbirth, and HELLP syndrome (hemolysis, elevated liver enzymes, and low platelets) were significantly associated with perinatal transfusion. Heart disease and hemophilia were not related to transfusion risk. The blood transfusion risk evaluation table was well calibrated.

CONCLUSIONS

Our retrospective analysis revealed that diagnoses including polyembryony, anemia, thrombocytopenia, preeclampsia, placenta previa, placenta implantation, uterine scarring, uterine rupture, retained placenta, stillbirth, and HELLP syndrome are significantly associated with perinatal transfusion and are risk factors for blood transfusion. The blood transfusion scoring system could be beneficial for evaluating blood transfusion risk.
An objective flow cytometry method to rapidly determine cord blood potency in cryopreserved units
Authors: Simard Carl , Bonnaure Guillaume , Fournier Diane , Néron Sonia
Published: February 2019

BACKGROUND

Cord blood banks have to determine the regenerative potential of cord blood units (CBUs) on a representative sample of the cryopreserved product before release to the transplant center. Potency can be measured by using a colony‐forming unit (CFU) method, which delays the release of CBU by 7 to 14 days. To accelerate CBU qualification, we have developed a rapid method to assess the response of CD34 cells to interleukin (IL)‐3. Flow cytometry was used to measure IL‐3–induced STAT5 phosphorylation within CD34‐cells. This IL‐3 test was compared to the CFU method, as well as the aldehyde dehydrogenase (ALDH) enzyme‐based assay.

STUDY DESIGN AND METHODS

Ten cryopreserved CBUs were analyzed for their contents in CD34 and CD45 viable cells, total CFUs, ADLHbright cells, and IL‐3–responsive CD34+ cells. Extreme and mild warming event scenarios were simulated on CBUs and used as poor‐quality samples. Segments, tubes, and bags from five CBUs were compared for their potency using IL‐3 and CFU methods.

RESULTS

The IL‐3 test was accurate in identifying the samples handled following standard operating procedures and those subjected to extreme warming events. Based on these results, a threshold of 55% of IL‐3–responsive CD34 cells was established to identify good‐quality samples. The IL‐3 test was also the most sensitive to detect samples subjected to milder warming events.

CONCLUSIONS

Our new method for determining CBU functionality is rapid, unbiased, and robust. The IL‐3 test described herein fulfills the requirements for validation, and we intend to implement this method in our cord blood bank facility.
Longitudinal transcriptomic and genetic landscape of radiotherapy response in canine melanoma
Authors: Giannuzzi Diana , Marconato Laura , Elgendy Ramy , Ferraresso Serena , Scarselli Elisa , Fariselli Piero , Nicosia Alfredo , Pegolo Sara , Leoni Guido , Laganga Paola , Leone Vito F. , Giantin Mery , Troise Fulvia , Dacasto Mauro , Aresu Luca
Published: February 2019

Canine malignant melanoma (MM) is a highly aggressive tumour with a low survival rate and represents an ideal spontaneous model for the human counterpart. Considerable progress has been recently obtained, but the therapeutic success for canine melanoma is still challenging. Little is known about the mechanisms beyond pathogenesis and melanoma development, and the molecular response to radiotherapy has never been explored before. A faster and deeper understanding of cancer mutational processes and developing mechanisms are now possible through next generation sequencing technologies. In this study, we matched whole exome and transcriptome sequencing in four dogs affected by MM at diagnosis and at disease progression to identify possible genetic mechanisms associated with therapy failure. According to previous studies, a genetic similarity between canine MM and its human counterpart was observed. Several somatic mutations were functionally related to MAPK, PI3K/AKT and p53 signalling pathways, but located in genes other than BRAF, RAS and KIT. At disease progression, several mutations were related to therapy effects. Natural killer cell‐mediated cytotoxicity and several immune‐system‐related pathways resulted activated opening a new scenario on the microenvironment in this tumour. In conclusion, this study suggests a potential role of the immune system associated to radiotherapy in canine melanoma, but a larger sample size associated with functional studies are needed.
Sub‐clinical dose of bone morphogenetic protein‐2 does not precipitate rampant, sustained inflammatory response in bone wound healing
Authors: Grey Zachary J. , Howie R. Nicole , Durham Emily L. , Hall Sarah Rose , Helke Kristi L. , Steed Martin B. , LaRue Amanda C. , Muise‐Helmericks Robin C. , Cray James J.
Published: February 2019

Large bone injuries, defects, and chronic wounds present a major problem for medicine. Several therapeutic strategies are used clinically to precipitate bone including a combination therapy delivering osteoinductive bone morphogenetic protein 2 (rhBMP‐2) via an osteoconductive scaffold (absorbable collagen sponge [ACS], i.e., INFUSE). Adverse side effects reportedly associated with rhBMP2 administration include rampant inflammation and clinical failures. Although acute inflammation is necessary for proper healing in bone, inflammatory cascade dysregulation can result in sustained tissue damage and poor healing. We hypothesized that a subclinical dose of rhBMP2 modeled in the murine calvarial defect would not precipitate alterations to inflammatory markers during acute phases of bone wound healing. We utilized the 5 mm critical size calvarial defect in C57BL6 wild‐type mice which were subsequently treated with ACS and a subclinical dose of rhBMP2 shown to be optimal for healing. Three and 7‐day postoperative time points were used to assess the role that rhBMP‐2 plays in modulating inflammation vs. ACS alone by cytokine array and histological interrogation. Data revealed that rhBMP‐2 delivery resulted in substantial modulation of several markers associated with inflammation, most of which decreased to levels similar to control by the 7‐day time point. Additionally, while rhBMP‐2 administration increased macrophage response, this peptide had a little noticeable effect on traditional markers of macrophage polarization (M1‐iNOS, M2‐Arg1). These results suggest that rhBMP‐2 delivered at a lower dose does not precipitate rampant inflammation. Thus, an assessment of dosing for rhBMP‐2 therapies may lead to better healing outcomes and less surgical failure.
Analysis on Identification Level of Football Fans with Their Teams in Eastern and Southeastern Anatolia Region
Authors: Karataş Özgür , Bingölbalı Abdullah
Published: February 2019

Purpose: The purpose of this study is to analyze the identification level of football fans with their teams in Eastern and Southeastern Anatolia Region.Material and method: General screening model, which is one of the descriptive methods, was used in the research. The research contains 944 people being the fans of 7 football teams (Yeni Malatyaspor in the Super League, Büyükşehir Belediye Erzurumspor, Elazığspor, Gaziantepspor, Gazişehir Gaziantepspor in the 1st League and Amed sportif faaliyetler, Şanlıurfaspor in the 2nd League) in Eastern and Southeastern Anatolia Region playing in Super League, 1st League and 2nd League during 2017-2018 football season. As the data collection tool of the study, ‘Sports Fan Identification Scale’ developed by Wann and Branscompe (1993) and translated into Turkish by Günay and Tiryaki (2003) with validity and reliability studies performed was used. 0.88 value was found as the Cronbach Alpha coefficient of the Sports Fan Identification Scale. The significance level was adopted as α=0.05.Findings: It has been determined that there are significant differences between the variables of age, marital status and the teams supported and the mean scores on identification level of fans with their teams (p<0.05) while no significant difference has been ascertained between the variables of education, job and income level and the mean scores on identification level of fans with their teams (p>0.05).Conclusion: It has been concluded that mean scores of fans on their identification level with their teams playing in high leagues are high and the fans’ level of identification with the teams has decreased as the lower leagues are considered.
On the Assessment of a Numerical Weather Prediction Model for Solar Photovoltaic Power Forecasts in Cities
Authors: Gamarro Harold , Gonzalez Jorge E. , Ortiz Luis E.
Published: February 2019

Recent developments in the weather research and forecasting (WRF) model have made it possible to accurately estimate incident solar radiation. This study couples the WRF-solar modifications with a multilayer urban canopy and building energy model (BEM) to create a unified WRF forecasting system called urban WRF–solar (uWRF-solar). This paper tests the integrated approach in the New York City (NYC) metro region as a sample case. Hourly forecasts are validated against ground station data collected at ten different sites in and around the city. Validation is carried out independently for clear, cloudy, and overcast sky conditions. Results indicate that the uWRF-solar model can forecast solar irradiance considerably well for the global horizontal irradiance (GHI) with an R2 value of 0.93 for clear sky conditions, 0.61 for cloudy sky conditions, and finally, 0.39 for overcast conditions. Results are further used to directly forecast solar power production in the region of interest, where evaluations of generation potential are done at the city scale. Outputs show a gradient of power generation produced by the potential available solar energy on the entire uWRF-solar grid. In total, the city has a city photovoltaic (PV) potential of 118 kWh/day/m2 and 3.65 MWh/month/m2.
Molecular mechanisms of atomic layer etching of cobalt with sequential exposure to molecular chlorine and diketones
Authors: Konh Mahsa , He Chuan , Lin Xi , Guo Xiangyu , Pallem Venkateswara , Opila Robert L. , Teplyakov Andrew V. , Wang Zijian , Yuan Bo
Published: February 2019

The mechanism of thermal dry etching of cobalt films is discussed for a thermal process utilizing sequential exposures to chlorine gas and a diketone [either 1,1,1,5,5,5-hexafluoro-2,4-pentanedione (hexafluoroacetylacetone, hfacH) or 2,4-pentanedione (acetylacetone, acacH)]. The process can be optimized experimentally to approach atomic layer etching (ALE); a sequential exposure to Cl2 and hfacH dry etchants at 140 °C is shown to proceed efficiently. The use of acacH as a diketone does not result in ALE with chlorine even at 180 °C, but the decrease of surface chlorine concentration and chemical reduction of cobalt is noted. However, thermal desorption analysis suggests that the reaction of chlorinated cobalt surface exposed to the ambient conditions (oxidized) with hfacH does produce volatile Co-containing products within the desired temperature range and the products contain Co3+. The effect of adsorption of ligands on the energy required to remove surface cobalt atoms is evaluated using the density functional theory.
NG-Test Carba 5 for Rapid Detection of Carbapenemase-Producing Enterobacterales from Positive Blood Cultures
Authors: Takissian Julie , Bonnin Rémy A. , Naas Thierry , Dortet Laurent
Published: February 2019

The immunochromatographic assay, NG-test Carba 5 (NG Biotech), has been evaluated for detection of carbapenemase-producing
Enterobacterales
(CPE) from spiked blood cultures (
n
 = 205). It detected and discriminated in less than 30 minutes KPC, IMP, VIM, NDM, and OXA-48-like producers with a sensitivity and specificity of 97.7% and 96.1%, respectively.
Measuring Antimicrobial Efficacy against Biofilms: a Meta-analysis
Authors: Stewart Philip S. , Parker Albert E.
Published: February 2019

Through a statistical meta-analysis of published data on antimicrobial efficacy against biofilms formed by two common bacterial species, it was concluded that the particular experimental method used is the most important factor determining the outcome of the test. An expected dose-response relationship (greater killing with higher doses or longer treatment times) was observed for data sets derived from a single method but was not observed when data from multiple studies using diverse methods were pooled.
Whole-Genome Sequencing Analysis of Multidrug-Resistant Serotype 15A Streptococcus pneumoniae in Japan and the Emergence of a Highly Resistant Serotype 15A-ST9084 Clone
Authors: Nakano Satoshi , Fujisawa Takao , Ito Yutaka , Chang Bin , Matsumura Yasufumi , Yamamoto Masaki , Suga Shigeru , Ohnishi Makoto , Nagao Miki
Published: February 2019

Since the introduction of pneumococcal conjugate vaccines (PCVs), an increase in the incidence of disease attributable to serotype 15A-ST63 (sequence type 63) pneumococci has been observed in many regions worldwide. We conducted a nationwide pediatric pneumococcal infection surveillance study between 2012 and 2014 in Japan.
Zinc Toxicity and Iron-Sulfur Cluster Biogenesis in
Escherichia coli
Authors: Li Jianghui , Ren Xiaojun , Fan Bingqian , Huang Zhaoyang , Wang Wu , Zhou Huaibin , Lou Zhefeng , Ding Huangen , Lyu Jianxin , Tan Guoqiang
Published: February 2019

Zinc toxicity has been implicated in causing various human diseases. High concentrations of zinc can also inhibit bacterial cell growth. However, the underlying mechanism has not been fully understood. Here, we report that zinc overload in
Escherichia coli
cells inhibits iron-sulfur cluster biogenesis by targeting specific iron-sulfur cluster assembly proteins. Because iron-sulfur proteins are involved in diverse physiological processes, the zinc-mediated inhibition of iron-sulfur cluster biogenesis could be largely responsible for the zinc-mediated cytotoxicity. Our finding provides new insights on how intracellular zinc overload may inhibit cellular functions in bacteria.
Low Temperature and Neutral pH Define “
Candidatus
Nitrotoga sp.” as a Competitive Nitrite Oxidizer in Coculture with Nitrospira defluvii
Authors: Wegen Simone , Nowka Boris , Spieck Eva
Published: February 2019

“
Ca.
Nitrotoga” is a NOB of high environmental relevance, but physiological data exist for only a few representatives. Initially, it was detected in specialized niches of low temperature and low nitrite concentrations, but later on, its ubiquitous distribution revealed its critical role for N removal in engineered systems like WWTPs. In this study, we analyzed the competition between
Nitrotoga
and
Nitrospira
in bioreactors and identified conditions where the
K
strategist
Ns. defluvii
was almost replaced by
Nitrotoga
sp. BS. We show that the pH value is an important factor that regulates the composition of the nitrite-oxidizing enrichment with a dominance of
Nitrotoga
sp. BS versus
Ns. defluvii
at a neutral pH of 7.4 in combination with a temperature of 17°C. The physiological diversity of novel
Nitrotoga
cultures improves our knowledge about niche differentiation of NOB with regard to functional nitrification under suboptimal conditions.
Prebiotic Supplementation of
In Vitro
Fecal Fermentations Inhibits Proteolysis by Gut Bacteria, and Host Diet Shapes Gut Bacterial Metabolism and Response to Intervention
Authors: Wang Xuedan , Gibson Glenn R. , Costabile Adele , Sailer Manuela , Theis Stephan , Rastall Robert A.
Published: February 2019

Dietary protein intake is high in Western populations, which could result in potentially harmful metabolites in the gut from proteolysis. In an
in vitro
fermentation model, the addition of prebiotics reduced the negative consequences of high protein levels. Supplementation with a prebiotic resulted in a reduction of proteolytic metabolites in the model. A difference was seen in protein fermentation between omnivore and vegetarian gut microbiotas: bacteria from vegetarian donors grew more on soy and Quorn than on meat and casein, with reduced ammonia production. Bacteria from vegetarian donors produced less branched-chain fatty acids (BCFA).
Farm Stage, Bird Age, and Body Site Dominantly Affect the Quantity, Taxonomic Composition, and Dynamics of Respiratory and Gut Microbiota of Commercial Layer Chickens
Authors: Ngunjiri John M. , Taylor Kara J. M. , Abundo Michael C. , Jang Hyesun , Elaish Mohamed , KC Mahesh , Ghorbani Amir , Wijeratne Saranga , Weber Bonnie P. , Johnson Timothy J. , Lee Chang-Won
Published: February 2019

The poultry industry is faced with numerous challenges associated with infectious diseases and suboptimal performance of flocks. As microbiome research continues to grow, it is becoming clear that poultry health and production performance are partly influenced by nonpathogenic symbionts that occupy different habitats within the bird. This study has defined the baseline composition and overlaps between respiratory and gut bacteria in healthy, optimally performing chicken layers across all stages of the commercial farm sequence. Consequently, the study has set the groundwork for the development of interventions that seek to enhance production performance and to prevent and control infectious diseases through the modulation of gut and respiratory bacteria.
Interferon Lambda Inhibits Bacterial Uptake during Influenza Superinfection
Authors: Rich Helen E. , McCourt Collin C. , Zheng Wen Quan , McHugh Kevin J. , Robinson Keven M. , Wang Jieru , Alcorn John F.
Published: February 2019

Influenza kills 30,000 to 40,000 people each year in the United States and causes 10 times as many hospitalizations. A common complication of influenza is bacterial superinfection, which exacerbates morbidity and mortality from the viral illness.
Neutrophils Dampen Adaptive Immunity in Brucellosis
Authors: Mora-Cartín Ricardo , Gutiérrez-Jiménez Cristina , Alfaro-Alarcón Alejandro , Chaves-Olarte Esteban , Chacón-Díaz Carlos , Barquero-Calvo Elías , Moreno Edgardo
Published: February 2019

Brucellaorganisms are intracellular stealth pathogens of animals and humans. The bacteria overcome the assault of innate immunity at early stages of an infection.
Sortase-Dependent Proteins Promote Gastrointestinal Colonization by Enterococci
Authors: Banla Leou Ismael , Pickrum Adam M. , Hayward Michael , Kristich Christopher J. , Salzman Nita H.
Published: February 2019

The human gastrointestinal tract (GIT) is inhabited by a dense microbial community of symbionts. Enterococci are among the earliest members of this community and remain core members of the GIT microbiota throughout life.
Identification of Redox Partners of the Thiol-Disulfide Oxidoreductase SdbA in Streptococcus gordonii
Authors: Jalal Naif A. , Davey Lauren , Halperin Scott A. , Lee Song F.
Published: February 2019

Streptococcus gordonii
is a commensal bacterium of the human dental plaque. Previously, we identified an enzyme, SdbA, that forms disulfide bonds in substrate proteins and plays a role in a number of cellular processes in
S. gordonii
. Here, we identified the redox partners of SdbA. We showed that SdbA has multiple redox partners, SdbB and CcdA2, forming a complex oxidative protein-folding pathway. This pathway is essential for autolysis, bacteriocin production, genetic competence, and extracellular DNA (eDNA) release in
S. gordonii
. These cellular processes are considered to be important for the success of
S. gordonii
as a dental plaque organism. This is the first example of an oxidative protein-folding pathway in Gram-positive bacteria that consists of an enzyme that uses multiple redox partners to function.
Vaccinia Virus BBK E3 Ligase Adaptor A55 Targets Importin-Dependent NF-κB Activation and Inhibits CD8
+
T-Cell Memory
Authors: Pallett Mitchell A. , Ren Hongwei , Zhang Rui-Yao , Scutts Simon R. , Gonzalez Laura , Zhu Zihan , Maluquer de Motes Carlos , Smith Geoffrey L.
Published: February 2019

NF-κB is a critical transcription factor in the innate immune response to infection and in shaping adaptive immunity. The identification of host and virus proteins that modulate the induction of immunological memory is important for improving virus-based vaccine design and efficacy. In viruses, the expression of BTB-BACK Kelch-like (BBK) proteins is restricted to poxviruses and conserved within them, indicating the importance of these proteins for these medically important viruses. Using vaccinia virus (VACV), the smallpox vaccine, we report that the VACV BBK protein A55 dysregulates NF-κB signaling by disrupting the p65-importin interaction, thus preventing NF-κB translocation and blocking NF-κB-dependent gene transcription. Infection with VACV lacking A55 induces increased VACV-specific CD8
+
T-cell memory and better protection against VACV challenge. Studying viral immunomodulators therefore expands not only our understanding of viral pathogenesis and immune evasion strategies but also of the immune signaling cascades controlling antiviral immunity and the development of immune memory.
Right-angled vessels in macular telangiectasia type 2
Authors: Tzaridis Simone , Heeren Tjebo , Mai Clarissa , Thiele Sarah , Holz Frank G , Charbel Issa Peter , Herrmann Philipp
Published: February 2019

Purpose

To evaluate the role of right-angled vessels (RAVs) during disease progression in macular telangiectasia type 2 (MacTel).

Methods

In this study, 100 eyes of 52 patients and 52 eyes of 26 age-related controls were examined using fundus photography, spectral-domain optical coherence tomography (SD-OCT), OCT angiography (OCT-A) and fundus fluorescein angiography (FFA). Two masked readers graded fundus photographs of patients’ eyes into five disease stages according to Gass and Blodi, and evaluated all eyes for the presence of RAVs. If RAVs were present, their course and origin (arterial vs venous) was evaluated with OCT-A and FFA, respectively. Additionally, we looked for morphological correlates of these vessels on SD-OCT scans. Neovascular eyes were analysed for the presence of RAVs and for morphological changes on formation of neovascularisations (NVs).

Results

In OCT-A, RAVs were already detectable in eyes with early stages (1 to 2), could be tracked from superficial to outer retinal layers and were shown to form anastomoses in the outer retina with disease progression. These vessels were of both arterial and venous origin as shown by early phase FFA. Dilated capillaries and RAVs in OCT-A corresponded to hyper-reflective alterations of the outer retina on SD-OCT scans. In 19/19 eyes, NVs were associated with the presence of RAVs, and RAVs were shown to directly connect to neovascular complexes and to undergo morphological changes upon NV formation.

Conclusions

The results emphasise the role of RAVs during disease progression from an early stage on and demonstrate their involvement in the development of secondary NVs in MacTel.
Post hoc analyses of surrogate markers of non-alcoholic fatty liver disease (NAFLD) and liver fibrosis in patients with type 2 diabetes in a digitally supported continuous care intervention: an open-label, non-randomised controlled study
Authors: Vilar-Gomez Eduardo , Athinarayanan Shaminie J , Adams Rebecca N , Hallberg Sarah J , Bhanpuri Nasir H , McKenzie Amy L , Campbell Wayne W , McCarter James P , Phinney Stephen D , Volek Jeff S , Chalasani Naga
Published: February 2019

Objective

One year of comprehensive continuous care intervention (CCI) through nutritional ketosis improves glycosylated haemoglobin(HbA1c), body weight and liver enzymes among patients with type 2 diabetes (T2D). Here, we report the effect of the CCI on surrogate scores of non-alcoholic fatty liver disease (NAFLD) and liver fibrosis.

Methods

This was a non-randomised longitudinal study, including adults with T2D who were self-enrolled to the CCI (n=262) or to receive usual care (UC, n=87) during 1 year. An NAFLD liver fat score (N-LFS) >−0.640 defined the presence of fatty liver. An NAFLD fibrosis score (NFS) of >0.675 identified subjects with advanced fibrosis. Changes in N-LFS and NFS at 1 year were the main endpoints.

Results

At baseline, NAFLD was present in 95% of patients in the CCI and 90% of patients in the UC. At 1 year, weight loss of ≥5% was achieved in 79% of patients in the CCI versus 19% of patients in UC (p<0.001). N-LFS mean score was reduced in the CCI group (−1.95±0.22, p<0.001), whereas it was not changed in the UC (0.47±0.41, p=0.26) (CCI vs UC, p<0.001). NFS was reduced in the CCI group (−0.65±0.06, p<0.001) compared with UC (0.26±0.11, p=0.02) (p<0.001 between two groups). In the CCI group, the percentage of individuals with a low probability of advanced fibrosis increased from 18% at baseline to 33% at 1 year (p<0.001).

Conclusions

One year of a digitally supported CCI significantly improved surrogates of NAFLD and advanced fibrosis in patients with T2D.

Trial registration number

NCT02519309; Results.
Statins reduce the progression of non-advanced adenomas to colorectal cancer: a postcolonoscopy study in 187 897 patients
Authors: Cheung Ka-Shing , Chen Lijia , Chan Esther W , Seto Wai-Kay , Wong Ian C K , Leung Wai K
Published: February 2019

Background and aims

Postcolonoscopy colorectal cancer (PCCRC) accounts for up to 9% of all CRCs. Statins have been shown to be associated with a lower CRC risk. We aimed to investigate whether PCCRC risk was also lower among statin users.

Methods

This is a retrospective cohort study using a territory-wide electronic healthcare database in Hong Kong including patients aged 40 years or above who had undergone colonoscopies between 2005 and 2013. Exclusion criteria included prior colorectal cancer (CRC), inflammatory bowel disease, prior colectomy and CRC detected within 6 months of index colonoscopy. We defined statin use as at least 90-day use before index colonoscopy. Medication use was traced up to 5 years before index colonoscopy. PCCRC-3y was defined as cancer diagnosed between 6 and 36 months after index colonoscopy. Sites of CRC were categorised as proximal (proximal to splenic flexure) and distal cancer. The subdistribution HR (SHR) of PCCRC-3y with statin use was derived by propensity score matching based on covariates (including patient factors, concurrent medication use and endoscopy centre’s performance).

Results

Of 187 897 eligible subjects, 854 (0.45%) were diagnosed with PCCRC-3y. Statin use was associated with a lower PCCRC-3y risk (SHR: 0.72; 95% CI 0.55 to 0.95; p=0.018). Subgroup analysis shows that SHRs were 0.50 (95% CI 0.28 to 0.91; p=0.022) for proximal and 0.80 (95% CI 0.59 to 1.09; p=0.160) for distal cancer. Older (>60 years) patients, women and those without diabetes mellitus or polyps appeared to benefit more from statins.

Conclusions

Statins were associated with a lower PCCRC risk, particularly for proximal cancer.
Probabilistic seismic slope stability analysis and design
Authors: Burgess Jesse , Fenton Gordon A. , Griffiths D.V.
Published: February 2019

Deterministic seismic slope stability design charts for cohesive–frictional ([Formula: see text]) soils are traditionally used by geotechnical engineers to include the effects of earthquakes on slopes. These charts identify the critical seismic load event that is sufficient to bring the slope to a state of limit equilibrium, but they do not specify the probability of this event. In this paper, the probabilistic seismic stability of slopes, modeled using a two-dimensional spatially random [Formula: see text] soil, is examined for the first time using the random finite element method (RFEM). Slope stability design aids for seismic loading, which consider spatial variability of the soil, are provided to allow informed geotechnical seismic design decisions in the face of geotechnical uncertainties. The paper also provides estimates of the probability of slope failure without requiring computer simulations. How the design aids may be used is demonstrated with an example of slope remediation cost analysis and risk-based design.
Mercury bioaccumulation in relation to changing physicochemical and ecological factors across a large and undisturbed boreal watershed
Authors: Lescord Gretchen L. , Johnston Thomas , Branfireun Brian A. , Gunn John M.
Published: February 2019

Within a drainage basin, the position of a lake or river can greatly affect its limnological and ecological characteristics. These properties influence the cycling of mercury (Hg), a neurotoxic and bioaccumulative metal prevalent in remote northern watersheds. In this study, we examined how 43 physical, chemical, and ecological endpoints change across 58 lake and river sites within an undisturbed boreal watershed in Ontario, Canada, and assessed the influence of these endpoints on aqueous and biotic Hg concentrations ([Hg]). We found that several physicochemical parameters, but few ecological factors, varied in systematic patterns across the watershed. Overall, [Hg] in water and some fish increased in systems with decreasing landscape positions. Aqueous and biotic [Hg] were strongly related to dissolved organic carbon and nutrient concentrations. Biotic [Hg] was lower in higher-nutrient systems, potentially due to biodilution, but higher in systems with more nitrates + nitrites, suggesting an indirect relationship between Hg and nitrogen cycling. This study is the first to assess patterns of [Hg] across an entire intact watershed and provides valuable results for a region anticipating substantial industrial development.
The spinless relativistic Hellmann problem
Authors: Lucha Wolfgang , Schöberl Franz F.
Published: February 2019

We compile some easily deducible information on the discrete eigenvalue spectra of spinless Salpeter equations encompassing, besides a relativistic kinetic term, interactions which are expressible as superpositions of an attractive Coulomb potential and an either attractive or repulsive Yukawa potential and, hence, generalizations of the Hellmann potential employed in several areas of science. These insights should provide useful guidelines to all attempts of finding appropriate descriptions of bound states by (semi-)relativistic equations of motion.
Towards a multiscale vision of active particles
Authors: Bellomo N. , Brezzi F.
Published: February 2019

The aim of this paper is first to provide a presentation of the papers published in a special issue devoted to modeling, qualitative analysis, control and simulations of large systems of living entities, viewed as active particles, related to real-life applications, and subsequently to present some prospective ideas on possible future research programs for the development of mathematical tools to model living systems.
Methods for computation of flow-driven string dynamics in a pump and residence time
Authors: Kanai Taro , Takizawa Kenji , Tezduyar Tayfun E. , Komiya Kenji , Kaneko Masayuki , Hirota Kyohei , Nohmi Motohiko , Tsuneda Tomoki , Kawai Masahito , Isono Miho
Published: February 2019

We present methods for computation of flow-driven string dynamics in a pump and related residence time. The string dynamics computations help us understand how the strings carried by a fluid interact with the pump surfaces, including the blades, and get stuck on or around those surfaces. The residence time computations help us to have a simplified but quick understanding of the string behavior. The core computational method is the Space–Time Variational Multiscale (ST-VMS) method, and the other key methods are the ST Isogeometric Analysis (ST-IGA), ST Slip Interface (ST-SI) method, ST/NURBS Mesh Update Method (STNMUM), a general-purpose NURBS mesh generation method for complex geometries, and a one-way-dependence model for the string dynamics. The ST-IGA with NURBS basis functions in space is used in both fluid mechanics and string structural dynamics. The ST framework provides higher-order accuracy. The VMS feature of the ST-VMS addresses the computational challenges associated with the turbulent nature of the unsteady flow, and the moving-mesh feature of the ST framework enables high-resolution computation near the rotor surface. The ST-SI enables moving-mesh computation of the spinning rotor. The mesh covering the rotor spins with it, and the SI between the spinning mesh and the rest of the mesh accurately connects the two sides of the solution. The ST-IGA enables more accurate representation of the pump geometry and increased accuracy in the flow solution. The IGA discretization also enables increased accuracy in the structural dynamics solution, as well as smoothness in the string shape and fluid dynamics forces computed on the string. The STNMUM enables exact representation of the mesh rotation. The general-purpose NURBS mesh generation method makes it easier to deal with the complex geometry we have here. With the one-way-dependence model, we compute the influence of the flow on the string dynamics, while avoiding the formidable task of computing the influence of the string on the flow, which we expect to be small.
Space–time Isogeometric flow analysis with built-in Reynolds-equation limit
Authors: Kuraishi Takashi , Takizawa Kenji , Tezduyar Tayfun E.
Published: February 2019

We present a space–time (ST) computational flow analysis method with built-in Reynolds-equation limit. The method enables solution of lubrication fluid dynamics problems with a computational cost comparable to that of the Reynolds-equation model for the comparable solution quality, but with the computational flexibility to go beyond the limitations of the Reynolds-equation model. The key components of the method are the ST Variational Multiscale (ST-VMS) method, ST Isogeometric Analysis (ST-IGA), and the ST Slip Interface (ST-SI) method. The VMS feature of the ST-VMS serves as a numerical stabilization method with a good track record, the moving-mesh feature of the ST framework enables high-resolution flow computation near the moving fluid–solid interfaces, and the higher-order accuracy of the ST framework strengthens both features. The ST-IGA enables more accurate representation of the solid-surface geometries and increased accuracy in the flow solution in general. With the ST-IGA, even with just one quadratic NURBS element across the gap of the lubrication fluid dynamics problem, we reach a solution quality comparable to that of the Reynolds-equation model. The ST-SI enables moving-mesh computation when the spinning solid surface is noncircular. The mesh covering the solid surface spins with it, retaining the high-resolution representation of the flow near the surface, and the SI between the spinning mesh and the rest of the mesh accurately connects the two sides of the solution. We present detailed 2D test computations to show how the method performs compared to the Reynolds-equation model, compared to finite element discretization, at different circumferential and normal mesh refinement levels, when there is an SI in the mesh, and when the no-slip boundary conditions are weakly-enforced.
Binary-fluid–solid interaction based on the Navier–Stokes–Korteweg equations
Authors: Shokrpour Roudbari M. , van Brummelen E. H.
Published: February 2019

We consider a computational model for binary-fluid–solid interaction based on an arbitrary Lagrangian–Eulerian formulation of the Navier–Stokes–Korteweg equations, and we assess the predictive capabilities of this model. Due to the presence of two distinct fluid components, the stress tensor in the binary-fluid exhibits a capillary component in addition to the pressure and viscous-stress components. The distinct fluid–solid surface energies of the fluid components moreover lead to preferential wetting at the solid substrate. Compared to conventional FSI problems, the dynamic condition coupling the binary-fluid and solid subsystems incorporates an additional term associated with the binary-fluid–solid surface tension. We consider a formulation of the Navier–Stokes–Korteweg equations in which the free energy associated with the standard van-der Waals equation of state is replaced by a polynomial double-well function to provide better control over the diffuse-interface thickness and the surface tension. For the solid subsystem, we regard a standard hyperelastic model. We explore the main properties of the binary-fluid–solid interaction problem and establish a dissipation relation for the aggregated system. In addition, we present numerical results based on a fully monolithic approach to the complete nonlinear system. To validate the computational model, we consider the elasto-capillary interaction of a sessile droplet on a soft solid substrate and compare the numerical results with a corresponding solid model with fabricated fluid loads and with experimental data.