bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of in vitro measurable sperm attributes and their influence on electroejaculated bull semen with a fixed‐time artificial insemination protocol in AustralianBos indicuscattle
Authors: Satake N , Edwards SAA , Tutt D , McGowan MR , Boe‐Hansen GB 
Published: December 2017

ContentsIncreasing use of fixed‐time artificial insemination (FTAI) in beef cattle production has presented an opportunity for the use of fresh or chilled semen as an alternative to standard cryopreserved semen. The objective of this study was to examine in vitro sperm function and pregnancy rate of electroejaculated semen, chilled and stored for 48 hr, compared to conventionally cryopreserved semen with an optimizedFTAIprotocol in Brahman cattle. Semen from three Brahman bulls was collected, and aliquots were extended in either chilled (at 5°C) or frozen (LN2) in a Tris‐egg yolk extender base with 2.4% or 7.0% glycerol, respectively. Semen samples were assessed 48 hr after collection or post‐thaw and warming, for sperm motility, in vitro sperm function and fertilizing ability, and used in aFTAIprogramme. The overall pregnancy rates was significantly different (p < .01) afterFTAIwith frozen (n = 173; 53.2%) and chilled semen (n = 174; 31.6%). In contrast, the in vitro sperm assessment showed that the chilled semen had significantly faster motility (p < .05), a higher proportion of progressively motile spermatozoa (p < .05), with significantly higher proportions of acrosome intact, viable spermatozoa (p < .01). This study showed that reasonable pregnancy rates in Brahman cattle can be achieved usingFTAIwith chilled semen collected using electroejaculation and stored for up to 48 hr. However, improvements in semen extenders are required in consideration of semen collection method to improve the longevity of sperm fertilizing ability to significantly increaseFTAIoutput using chilled storage of bull semen.
A Spatio‐Temporal Exposure‐Hazard Model for Assessing Biological Risk and Impact
Authors: Walker Emily , Leclerc Melen , Rey Jean‐François , Beaudouin Rémy , Soubeyrand Samuel , Messéan Antoine 
Published: December 2017

AbstractWe developed a simulation model for quantifying the spatio‐temporal distribution of contaminants (e.g., xenobiotics) and assessing the risk of exposed populations at the landscape level. The model is a spatio‐temporal exposure‐hazard model based on (i) tools of stochastic geometry (marked polygon and point processes) for structuring the landscape and describing the exposed individuals, (ii) a dispersal kernel describing the dissemination of contaminants from polygon sources, and (iii) an (eco)toxicological equation describing the toxicokinetics and dynamics of contaminants in affected individuals. The model was implemented in the briskaR package (biological risk assessment with R) of the R software. This article presents the model background, the use of the package in an illustrative example, namely, the effect of genetically modified maize pollen on nontarget Lepidoptera, and typical comparisons of landscape configurations that can be carried out with our model (different configurations lead to different mortality rates in the treated example). In real case studies, parameters and parametric functions encountered in the model will have to be precisely specified to obtain realistic measures of risk and impact and accurate comparisons of landscape configurations. Our modeling framework could be applied to study other risks related to agriculture, for instance, pathogen spread in crops or livestock, and could be adapted to cope with other hazards such as toxic emissions from industrial areas having health effects on surrounding populations. Moreover, the R package has the potential to help risk managers in running quantitative risk assessments and testing management strategies.
An Integrated Framework for Environmental Multi‐Impact Spatial Risk Analysis
Authors: Ferretti Valentina , Montibeller Gilberto 
Published: December 2017

AbstractQuantitative risk analysis is being extensively employed to support policymakers and provides a strong conceptual framework for evaluating decision alternatives under uncertainty. Many problems involving environmental risks are, however, of a spatial nature, i.e., containing spatial impacts, spatial vulnerabilities, and spatial risk‐mitigation alternatives. Recent developments in multicriteria spatial analysis have enabled the assessment and aggregation of multiple impacts, supporting policymakers in spatial evaluation problems. However, recent attempts to conduct spatial multicriteria risk analysis have generally been weakly conceptualized, without adequate roots in quantitative risk analysis. Moreover, assessments of spatial risk often neglect the multidimensional nature of spatial impacts (e.g., social, economic, human) that are typically occurring in such decision problems. The aim of this article is therefore to suggest a conceptual quantitative framework for environmental multicriteria spatial risk analysis based on expected multi‐attribute utility theory. The framework proposes: (i) the formal assessment of multiple spatial impacts; (ii) the aggregation of these multiple spatial impacts; (iii) the assessment of spatial vulnerabilities and probabilities of occurrence of adverse events; (iv) the computation of spatial risks; (v) the assessment of spatial risk mitigation alternatives; and (vi) the design and comparison of spatial risk mitigation alternatives (e.g., reductions of vulnerabilities and/or impacts). We illustrate the use of the framework in practice with a case study based on a flood‐prone area in northern Italy.
Patellar tendinopathy with intratendinous alteration on MRI may be related to patellofemoral dysplasia
Authors: Tscholl P. M. , Biedert R. M. , Wanivenhaus F. , Fucentese S. F. 
Published: December 2017

Patellar tendinopathy (PT) is a frequent overuse injury of the extensor knee apparatus, whereas as up to 30% of the athletes might suffer from persisting symptoms during their entire career. In the present case‐control study, 47 patients (30.8 ± 11.4 years) with PT with intratendinous alteration (PTita) of a minimum of ≥25% of the axial surface on MRI and minimum Blazina score of II (pain during without limiting sports activity) were included; MR images were analyzed for trochlear geometry, patellar height/tilt, and tibial tubercle‐trochlear groove distance (TT‐TG). The control group (CG) comprised 87 age‐ and gender‐matched patients without history of anterior knee pain or lateral patellar instability. It was hypothesized that patients with PT might be related to patellofemoral dysplasia. It was found that the patella was significantly higher in patients with PT compared to the CG (patellotrochlear index [PT‐I]: 0.33 vs 0.37, P = .014; Insall‐Salvati index [InSa]: 1.18 vs 1.07, P = .004). PT‐I was above the cut‐off value in 10.6% of PT knees (CG 5.7%, P = .27), and InSa in 42.6% (CG 21.8%, P = .012). TT‐TG was significantly higher in patients with PT compared to CG (12.0 mm vs 9.9 mm, P = .002); however, TT‐TG was only pathologic (>20 mm) in one patient. The trochlear facet ratio was above the cut‐off value in 55.3% of PT patients and 23% of CG (P < .001), and was significantly greater in patients with PT (0.39 ± 0.09) than CG (0.48 ± 0.1, P < .001). Knees with PT have significantly more morphological characteristics of patellofemoral instability, which needs to be considered especially in recurrent or treatment‐refractive cases.
Genomic Insights into Colistin-Resistant Klebsiella pneumoniae from a Tunisian Teaching Hospital
Authors: Jaidane Nadia , Bonnin Rémy A. , Mansour Wejdene , Girlich Delphine , Creton Elodie , Cotellon Garance , Chaouch Cherifa , Boujaafar Noureddine , Bouallegue Olfa , Naas Thierry 
Published: December 2017

ABSTRACT

The emergence of colistin-resistant
Klebsiella pneumoniae
(CoR
Kp
) is a public health concern, since this antibiotic has become the last line of treatment for infections caused by multidrug-resistant (MDR) Gram negatives. In this study, we have investigated the molecular basis of colistin resistance in 13 MDR
K. pneumoniae
strains isolated from 12 patients in a teaching hospital in Sousse, Tunisia. Whole-genome sequencing (WGS) was used to decipher the molecular mechanism of colistin resistance and to identify the resistome of these CoR
Kp
isolates. It revealed a genome of ca. 5.5 Mbp in size with a G+C content of 57%, corresponding to that commonly observed for
K. pneumoniae
. These isolates belonged to the 5 different sequence types (ST11, ST15, ST101, ST147, and ST392), and their resistome was composed of acquired β-lactamases, including extended-spectrum beta-lactamase and carbapenemase genes (
bla
CTX-M-15
,
bla
OXA-204
,
bla
OXA-48
, and
bla
NDM-1
genes), aminoglycoside resistance genes [
aac
(
6
′)
Ib-cr
,
aph
(
3
″)-
Ib
,
aph
(
6
)-
Id
, and
aac
(
3
)-
IIa
], and fosfomycin (
fosA
), fluoroquinolone (
qnr
-like), chloramphenicol, trimethoprim, and tetracycline resistance genes. All of the isolates were identified as having a mutated
mgrB
gene. Mapping reads with reference sequences of the most common genes involved in colistin resistance revealed several modifications in
mgrB
,
pmr
, and
pho
operons (deletions, insertions, and substitutions) likely affecting the function of these proteins. It is worth noting that among the 12 patients, 10 were treated with colistin before the isolation of CoR
Kp
. No plasmid encoding
mcr-1
to
mcr-5
genes was found in these isolates. This study corresponds to the first molecular characterization of a collection of CoR
Kp
strains in Tunisia and highlights that the small-transmembrane protein MgrB is a main mechanism for colistin resistance in
K. pneumoniae
.
Suppression of Reactive Oxygen Species Accumulation Accounts for Paradoxical Bacterial Survival at High Quinolone Concentration
Authors: Luan Gan , Hong Yuzhi , Drlica Karl , Zhao Xilin 
Published: December 2017

ABSTRACT

When bacterial cells are exposed to increasing concentrations of quinolone-class antibacterials, survival drops, reaches a minimum, and then recovers, sometimes to 100%. Despite decades of study, events underlying this paradoxical high-concentration survival remain obscure. Since reactive oxygen species (ROS) have been implicated in antimicrobial lethality, conditions generating paradoxical survival were examined for diminished ROS accumulation.
Escherichia coli
cultures were treated with various concentrations of nalidixic acid, followed by measurements of survival, rate of protein synthesis, and ROS accumulation. The last measurement used a dye (carboxy-H2DCFDA) that fluoresces in the presence of ROS; fluorescence was assessed by microscopy (individual cells) and flow cytometry (batch cultures). High, nonlethal concentrations of nalidixic acid induced lower levels of ROS than moderate, lethal concentrations. Sublethal doses of exogenous hydrogen peroxide became lethal and eliminated the nalidixic acid-associated paradoxical survival. Thus, quinolone-mediated lesions needed for ROS-executed killing persist at high, nonlethal quinolone concentrations, thereby implicating ROS as a key factor in cell death. Chloramphenicol suppressed nalidixic acid-induced ROS accumulation and blocked lethality, further supporting a role for ROS in killing. Nalidixic acid also inhibited protein synthesis, with extensive inhibition at high concentrations correlating with lower ROS accumulation and paradoxical survival. A catalase deficiency, which elevated ROS levels, overcame the inhibitory effect of chloramphenicol on nalidixic acid-mediated killing, emphasizing the importance of ROS. The data collectively indicate that ROS play a dominant role in the lethal action of narrow-spectrum quinolone-class compounds; a drop in ROS levels accounted for the quinolone tolerance observed at very high concentrations.
Topical Antibiotic Use Coselects for the Carriage of Mobile Genetic Elements Conferring Resistance to Unrelated Antimicrobials in Staphylococcus aureus
Authors: Carter Glen P. , Schultz Mark B. , Baines Sarah L. , Gonçalves da Silva Anders , Heffernan Helen , Tiong Audrey , Pham Peter H. , Monk Ian R. , Stinear Timothy P. , Howden Benjamin P. , Williamson Deborah A. 
Published: December 2017

ABSTRACT

Topical antibiotics, such as mupirocin and fusidic acid, are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, the widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains. New Zealand (NZ) has some of the highest globally recorded rates of topical antibiotic usage and resistance. Using a combination of Pacific Biosciences single-molecule real-time (SMRT) whole-genome sequencing, Illumina short-read sequencing, and Bayesian phylogenomic modeling on 118 new multilocus sequence type 1 (ST1) community
Staphylococcus aureus
isolates from New Zealand and 61 publically available international ST1 genome sequences, we demonstrate a strong correlation between the clinical introduction of topical antibiotics and the emergence of MDR ST1
S. aureus
. We also provide
in vitro
experimental evidence showing that exposure to topical antibiotics can lead to the rapid selection of MDR
S. aureus
isolates carrying plasmids that confer resistance to multiple unrelated antibiotics, from within a mixed population of competitor strains. These findings have important implications regarding the impact of the indiscriminate use of topical antibiotics.
High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
Authors: Loh John T. , Beckett Amber C. , Scholz Matthew B. , Cover Timothy L. 
Published: December 2017

ABSTRACT

Helicobacter pylori
infection and high dietary salt intake are risk factors for the development of gastric adenocarcinoma. One possible mechanism by which a high-salt diet could influence gastric cancer risk is by modulating
H. pylori
gene expression. In this study, we utilized transcriptome sequencing (RNA-seq) methodology to compare the transcriptional profiles of
H. pylori
grown in media containing different concentrations of sodium chloride. We identified 118 differentially expressed genes (65 upregulated and 53 downregulated in response to high-salt conditions), including multiple members of 14 operons. Twenty-nine of the differentially expressed genes encode proteins previously shown to undergo salt-responsive changes in abundance, based on proteomic analyses. Real-time reverse transcription (RT)-PCR analyses validated differential expression of multiple genes encoding outer membrane proteins, including adhesins (SabA and HopQ) and proteins involved in iron acquisition (FecA2 and FecA3). Transcript levels of
sabA
,
hopA
, and
hopQ
are increased under high-salt conditions, whereas transcript levels of
fecA2
and
fecA3
are decreased under high-salt conditions. Transcription of
sabA
,
hopA
,
hopQ
, and
fecA3
is derepressed in an
arsS
mutant strain, but salt-responsive transcription of these genes is not mediated by the ArsRS two-component system, and the CrdRS and FlgRS two-component systems do not have any detectable effects on transcription of these genes. In summary, these data provide a comprehensive view of
H. pylori
transcriptional alterations that occur in response to high-salt environmental conditions.
Scapular dyskinesis increases the risk of future shoulder pain by 43% in asymptomatic athletes: a systematic review and meta-analysis
Authors: Hickey Darren , Solvig Veronica , Cavalheri Vinicius , Harrold Meg , Mckenna Leanda 
Published: December 2017

BackgroundIt is unclear whether the presence of scapular dyskinesis increases the risk of developing shoulder pain in asymptomatic athletes.ObjectivesTo determine whether the presence of scapular dyskinesis in asymptomatic athletes increases the risk of developing shoulder pain by systematic review and meta-analysis.MethodsA systematic search was conducted in the Cochrane Library, Embase, PubMed, Cumulative Index to Nursing and Allied Health Literature, Allied and Complementary Medicine Database and SPORTDiscus. Prospective studies that assessed athletes for scapular dyskinesis and recorded incidents of shoulder pain were included. Study quality was assessed using the Downs and Black checklist. Meta-analysis was conducted to derive a pooled risk ratio (RR) for the development of shoulder pain in athletes with scapular dyskinesis compared with those without scapular dyskinesis.ResultsFive studies were included with a total of 419 athletes. Of the athletes with scapular dyskinesis, 35% (56/160) experienced shoulder pain during the follow-up, whereas 25% (65/259) of athletes without scapular dyskinesis experienced symptoms. The presence of scapular dyskinesis at baseline indicated a 43% increased risk of a shoulder pain event over a 9 to 24 months follow-up (RR=1.43, 95% CI 1.05 to 1.93).ConclusionsAthletes with scapular dyskinesis have 43% greater risk of developing shoulder pain than those without scapular dyskinesis.
New Zealand policy experts’ appraisal of interventions to reduce smoking in young adults: a qualitative investigation
Authors: Ball Jude , Hoek Janet , Tautolo El Shadan , Gifford Heather 
Published: December 2017

ObjectivesReducing smoking in young adults, particularly young Māori and Pacific, is vital for reducing tobacco harm and health inequalities in New Zealand (NZ). We investigated how NZ policy experts appraised the feasibility and likely effectiveness of interventions designed to reduce smoking prevalence among 18–24 year olds.DesignWe used a qualitative design, conducting semistructured interviews and applying thematic analysis.ParticipantsWe interviewed 15 key informants, including politicians, senior policy analysts and leading tobacco control advocates. Participant selection was based on seniority and expertise and ensuring diverse perspectives were represented.InterventionsWe examined nine interventions that could either promote greater mindfulness or introduce barriers impeding smoking uptake: smoke-free outdoor dining and bars; no tobacco sales where alcohol is sold; social marketing campaigns; real life stories (testimonials); life skills training; raise purchase age to 21; tobacco-free generation; smokers’ licence; make tobacco retail premises R18.ResultsThe policies perceived as more effective denormalised tobacco; made it less convenient to access and use; highlighted immediate disadvantages (eg, impact on fitness); aligned with young people’s values; and addressed the underlying causes of smoking (eg, stress). Participants highlighted some political barriers and noted concerns that some interventions might widen ethnic disparities. Exceptions were social marketing campaigns and extending smoke-free regulations to include outdoor areas of cafes and bars, which participants saw as politically feasible and likely to be effective.ConclusionsOur findings suggest the merit of an approach that combines social marketing with regulation that makes accessing and using tobacco less convenient for young adults; however, political barriers may limit the regulatory options available in the short term. Strategies to support self-determination and address the underlying causes of smoking in young people warrant further investigation. Determining policy acceptability to Māori and Pacific, and likely effectiveness for these populations, should be key priorities.
A Framework to Design, Develop, and Evaluate Immersive and Collaborative Serious Games in Cultural Heritage
Authors: Andreoli Roberto , Corolla Angela , Faggiano Armando , Malandrino Delfina , Pirozzi Donato , Ranaldi Mirta , Santangelo Gianluca , Scarano Vittorio 
Published: December 2017

Video games and their design are complex in nature, given the variety of aspects and challenges to face and the different areas of expertise involved. Furthermore, serious games have an even tougher challenge, since the knowledge acquisition has the same importance and relevance as entertainment and pleasure for the players. Serious games in cultural heritage require additional effort to introduce immersivity and collaboration among players.This article introduces a framework, named FRACH, to conceive, design, and evaluate immersive and collaborative serious games in cultural heritage. In particular, FRACH provides a design framework with steps to follow during the whole process that is from the early design phase to the evaluation phase of a serious game.We assessed the efficacy of our framework, with a specific case study in cultural heritage, by implementing a section of a serious game namedHippocraticaCivitasGame, where players were allowed to visit the thermae of the historical site of San Pietro a Corte and Palazzo Fruscione in the city of Salerno, Italy, and to solve a given puzzle. Results of the game evaluation showed that the game was effective in terms of knowledge acquisition, the participants enjoyed the game, were highly involved in the immersive experience, and, finally, positively rated the idea of using the game for educational learning in the field of cultural heritage.
Bit-Precise Procedure-Modular Termination Analysis
Authors: Chen Hong-Yi , David Cristina , Kroening Daniel , Schrammel Peter , Wachter Björn 
Published: December 2017

Non-termination is the root cause of a variety of program bugs, such as hanging programs and denial-of-service vulnerabilities. This makes an automated analysis that can prove the absence of such bugs highly desirable. To scale termination checks to large systems, an interprocedural termination analysis seems essential. This is a largely unexplored area of research in termination analysis, where most effort has focussed on small but difficult single-procedure problems.
We present a modular termination analysis for C programs using template-based interprocedural summarisation. Our analysis combines a context-sensitive, over-approximating forward analysis with the inference of under-approximating preconditions for termination. Bit-precise termination arguments are synthesised over lexicographic linear ranking function templates. Our experimental results show the advantage of interprocedural reasoning over monolithic analysis in terms of efficiency, while retaining comparable precision.