bluuebunny/crossref_metadata_2025 huggingface dataset:
A Cone-Beam Computed Tomographic Study of Alveolar Bone Morphology in Patients With Unilateral Cleft Lip and Palate
Authors: Movahhedian Najmeh , Vossoughi Mehrdad , Hajati-Sisakht Mahtab
Published: September 2019

Objective:

To evaluate the bony support around the teeth adjacent to the unilateral cleft lip and palate (ULCLP) using cone-beam computed tomography.

Methods and Materials:

Cone-beam computed tomographies of 48 cleft-adjacent teeth (28 anterior and 20 posterior to the cleft) and 48 noncleft control teeth were evaluated. The alveolar bone thickness at 3 and 6 mm apical to the cement–enamel junction (CEJ), the distance between the alveolar crest and CEJ (Alv-CEJ), and the presence of fenestration were assessed in buccal, palatal, and proximal surfaces.

Results:

The alveolar bone on the buccal and palatal sides of the teeth anterior to the cleft was significantly thinner than the noncleft teeth (all P < .05). The Alv-CEJ was significantly greater on the buccal and distal surfaces of the teeth anterior to the cleft ( P < .001 and P = .010, respectively) and on the palatal and mesial surfaces of the teeth posterior to the cleft ( P = .024 and P = .003, respectively) when compared to the noncleft teeth. The frequency of reduced alveolar bone height (>2 mm) was higher than noncleft side for buccal and distal sides of the teeth anterior to the cleft ( P = .016 and .006, respectively) and the buccal and mesial sides of the teeth posterior to the cleft ( P = .008 and <.001, respectively). The teeth anterior to the cleft had a higher prevalence of fenestration ( P = .004).

Conclusion:

Reduced alveolar bone height is more common in the cleft side compared to the control side. The teeth anterior to the ULCLP have thinner alveolar bone support and higher frequency of fenestration.
Pierre Robin Sequence: Incidence of Speech-Correcting Surgeries and Fistula Formation
Authors: Gustafsson Charlotta , Vuola Pia , Leikola Junnu , Heliövaara Arja
Published: September 2019

Objective:

Children with Pierre Robin sequence (PRS) and cleft palate have a high rate of velopharyngeal insufficiency (VPI) following primary palatoplasty. Our purpose was to determine the long-term incidence of speech-correcting surgeries (SCSs) and fistula rates in PRS after primary palatoplasty and the influence of possible causal factors.

Design:

A retrospective single-center, observational chart review study.

Participants:

After exclusion, the study cohort comprised 78 nonsyndromic PRS children (48 females) born between 1990 and 2009 and treated at the Cleft Palate and Craniofacial Center of Helsinki University Hospital, Finland. Causal factors included gender, surgeon, age at primary palatoplasty, surgical technique, airway obstruction in infancy, and cleft severity. We analyzed the outcome at age 8 years and at data retrieval, with a median follow-up of 14 years (range: 8-27 years).

Results:

Thirty-four (43.6%) children received SCS by age 8 years, and of the 19 (24.4%) postoperative fistulas, 6 (7.7%) underwent closure. At data retrieval, 37 (47.4%) children had undergone SCS and 8 (10.3%) had a fistula closure. Median age at SCS was 6 years. The results showed no significant association for gender, surgeon, age at primary palatoplasty, surgical technique, cleft severity, or airway obstruction in infancy regarding incidence of SCS, fistulas, or repaired fistulas.

Conclusion:

Pierre Robin sequence in children is associated with a high incidence of SCS and fistula formation, which necessitates accurate clinical follow-up and observation of speech development. The development of VPI in PRS is complex and most likely involving multiple factors.
Preparation and The Real World of Education: How Prospective Teachers Grapple with Using Culturally Responsive Teaching Practices in the Age of Standardized Testing
Authors: Ramsay-Jordan Natasha
Published: September 2019

The most highlighted provision and consequence of the reauthorization of the 1965 Elementary and Secondary Education Act (ESEA), the No Child Left Behind (NCLB) Act of 2001, is obsessive practices of assessing students across the United States (U.S.). Despite newly named policies, including Every Student Succeed Act (ESSA) of 2015, which governs current U.S. K-12 education standards, concerns over NCLB’s unprecedented fixation on high stakes testing remain acute for many school districts. This manuscript examines the struggles of four preservice secondary mathematics teachers (PMTs) who grappled with enacting culturally responsive teaching practices at schools that aimed to meet accountability standards.
Midterm outcomes of total hip arthroplasty with a modular Birmingham head
Authors: Cushnie Duncan W , Lanting Brent A , McCalden Richard , Naudie Douglas DR , Howard James L
Published: September 2019

Introduction:

Birmingham Hip Resurfacing (BHR) implants may be combined with a conventional femoral stem to create a modular metal-on-metal total hip arthroplasty (BHR MoM THA). There is little outcome data regarding this construct. This study examines midterm outcomes of BHR MoM THA compared to oxidised zirconium total hip arthroplasty (THA).

Methods:

A retrospective institutional review identified all patients receiving BHR MoM THA between April 2005 and February 2011 and a matched control cohort of zirconium THA patients. Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC), Harris Hip Score (HHS), and SF-12 Health status scores were obtained. Revisions and complications were collected from clinical records. Radiographs were assessed for evidence of component malposition, loosening, osteolysis, or heterotopic ossification.

Results:

63 modular BHR MoM THA were identified in 61 patients (36 with BHR cups, 27 with R3 cups) and 63 zirconium THA in 58 matched controls. Mean follow-up was 58 months. 14 BHR MoM THA hips (22.2%) were revised (4 infections, 1 dislocation, 9 soft tissue reactions) compared to 3 (4.8%) zirconium THA (all infections). At latest follow-up, 18.4% of surviving BHR MoM THA hips were painful compared to 0.5% of zirconium THA controls ( p < 0.001). WOMAC, HHS, and SF-12 did not differ significantly between surviving members of the 2 groups.

Discussion:

BHR MoM THA demonstrated a high revision rate, largely for adverse local soft tissue reaction and pain. Among those not revised, many reported some residual pain despite similar quality of life measures to those who received zirconium THA.
Shifting sands: The reconfiguration of neoliberal youth penality
Authors: Gray Patricia , Smith Roger
Published: September 2019

This article begins by tracing the emergence of ‘therapeutic surveillance’ as a new formula for neoliberal disciplinary power. It maps and interrogates the reconfiguration of a hybrid array of neoliberal rationalities and technologies for the penal governance of young people who offend. It then engages with the challenges posed by critical realists to the governmentality position by questioning how human agency can contest, subvert and resist the dystopian reach of ‘therapeutic surveillance’ in action. While ‘therapeutic surveillance’ is steeped in a disciplinary logic of individualization and responsibilization, we argue that it also opens the space for a more transformative youth penality to be articulated; one which challenges the constraints of structural disadvantage in the pursuit of social justice. The article concludes by arguing that newly emerging youth justice configurations which have appeared in response to dramatic cuts in public spending offer a plausible or transformative challenge to the regulatory logic of neoliberal youth penality.
Transient dynamic finite element simulation for prediction of surface integrity induced by waterjet peening
Authors: Amri Rihem , Laamouri Adnen , Manchoul Sondes , Fathallah Raouf
Published: September 2019

This paper aims to develop and validate the transient dynamic finite element three-dimensional simulation of a waterjet peening process to predict surface properties (residual stresses, plastic strains, surface roughness, and superficial damage). The finite-element model considers an impingement of multisets of droplets, which strike the treated surface by impact pressures over the corresponding contact regions at high velocities. The impact pressures and their durations are modelled by using the liquid impact theory combined with an impact velocity law depending on the main parameters of the process. The behavior law of the material is an elastoviscoplastic law coupled to the Johnson–Cook damage criterion. The effectiveness of this simulation is discussed in two cases: (i) a linear mono-set of droplets and (ii) multisets of droplets using the experimental results of a waterjet-peened Al7075-T6 aluminum alloy. The predictive results of surface properties obtained by simulation with multi-sets of droplets appear more realistic than those obtained by simulation with a single set of droplets and more close to the experimental surface properties.
Noise radiated by an open cavity at low Mach number: Effect of the cavity oscillation mode
Authors: Martin Rocio , Soria Manel , Lehmkuhl Oriol , Gorobets Andrey , Duben Alexey
Published: September 2019

The present work focuses on the study of noise generation and radiation of an infinite open three-dimensional cavity at low Mach number with laminar upstream conditions that is of interest to understand noise generation mechanisms in wall-bounded separated flows. A particular feature of this configuration is the oscillatory mode: shear layer mode or wake mode. For the parameters considered in the present study it is seen that while in shear layer mode the flow shows a two-dimensional behavior, in the wake mode the flow is three-dimensional, resulting in significantly different sound sources. The influence of the acoustic feedback mechanism in the shear layer mode has also been investigated comparing the results between different momentum thickness values at the cavity inlet. This paper presents results of sound radiated by a three-dimensional infinite open cavity with aspect ratio L/ D =  4 at Reynolds number based on the cavity depth of ReD = 1500 and Mach number of M =  0.15, both for shear layer ( L/ θ = 67) and wake ( L/ θ = 84) oscillation modes. To do so, Curle integral evaluated as a post-process of an incompressible solution will be used. The results are compared with the resulting Curle post-process of a two-dimensional incompressible simulation.
Rule violations by SMEs: The influence of conduct within the industry, company culture and personal motives
Authors: Peeters Marlijn , Denkers Adriaan , Huisman Wim
Published: September 2019

The literature suggests many different variables that may explain rule violations by companies. These can be categorized into variables at the industry level, such as the degree of rule violations, at the company level, such as the organizational culture, and at the individual level, such as personal or social norms. From the Dutch Tax Administration’s (2009) registration data, industries were selected with relatively low and relatively high tax correction rates. Within these industries, small and medium-sized enterprises (SMEs) with 20–150 employees were selected that either had received no (or negative) corrections or had received large positive corrections, resulting in a population of 1558 companies. In 194 of these SMEs, both the director and an employee were interviewed about violations of administrative, environmental and tax obligations, about their personal motives and about the ethical organizational culture. The results of the study show that all three levels of variables explain intentions to comply or to violate the rules. Ethical culture contributes to explaining the compliance intentions of both directors and employees. However, in contrast to previous research, about half of the SMEs cannot be characterized by a coherent ethical culture.
The Killing: The Gender Politics of the Nordic Noir Crime Drama and Its American Remake
Authors: Pinedo Isabel
Published: September 2019

How does the depiction of female subjectivity and agency change when a Danish public broadcasting serial is adapted for an American commercial network? I compare Forbrydelsen (DR1, 2007–2012) with its remake, The Killing (AMC 2011–2013, Netflix 2014), to draw out the significance of postfeminism and neoliberalism as interpretive grids that limit feminist progress in the United States. Despite similar narrative and aesthetic strategies that center a strong female protagonist, female agency is undermined in The Killing through the postfeminist “bad mother” trope, which supplants Forbrydelsen’s Nordic noir left-wing critique of global capitalism and gender issues. This analysis illustrates that the cultural milieux of societies that are as egalitarian as Scandinavian states convey indirect feminist creative influence on cultural production, even when there is limited direct female creative input, an influence that may outweigh greater direct female creative control in the anti-egalitarian cultural context of a neoliberal and postfeminist United States.
Experimental investigation and multi-conditions identification method of centrifugal pump using Fisher discriminant ratio and support vector machine
Authors: Qiu Guangqi , Huang Si , Gu Yingkui
Published: September 2019

For identifying the operation situations of centrifugal pumps by artificial intelligence, we performed an experiment on multi-flow conditions. The multi-flow conditions were simulated by adjusting an automatic flow-regulating valve installed on outlet pipe, and the vertical vibration signals of 20 flow points at the bearing house were collected by the test system. By time-domain analysis, frequency-domain analysis, information entropy, empirical modal decomposition, and wavelet packet decomposition methods, a comprehensive feature space was constructed. In addition, the optimal features were selected by Fisher discriminant ratio, and the dimensionality of the selected optimal features was reduced with principal component analysis. Finally, support vector machine algorithm was employed to identify the real-time flow condition, and the hyper-parameters of support vector machine classifier model were optimized by a grid search technique. Results show that the vibration test can effectively simulate the operation situation of centrifugal pumps under multi-flow conditions, and the proposed multi-flow conditions identification method has achieved a good identification performance.
Press freedom and corruption: An examination of the relationship
Authors: Hamada Basyouni Ibrahim , Abdel-Salam Abdel-Salam G , Elkilany Elsayed Abdelwahed
Published: September 2019

Are countries with a free press less corrupt than countries where the press is partly or completely unfree? Our empirical investigation finds evidence of a significant relationship between higher levels of press freedom and lower levels of corruption with other variables being equal. Furthermore, we provide evidence that while democracy deters corruption only in countries that enjoy press freedom, rule of law reduces corruption whether the press is free or unfree. Press freedom and democracy are complements rather than substitutes in the fight against corruption.
Agenda-setting in the realm of popular culture: The case of the Korean Wave in East Asia
Authors: Jung Hyeri
Published: September 2019

The spread of South Korean popular culture across the globe, known as the Korean Wave, has signalled a significant challenge towards the traditional one-way flow of media culture. This study applies agenda-setting effect, which has been largely applied to political communication, to the domain of mass-produced popular culture. It explores how Korean media’s news coverage of the popularity of Korean TV drama in China influences not only the first and second agenda-setting effect but also Koreans’ perception of Chinese audiences. The findings suggest that the Korean Wave could serve as a form of reversed cultural diplomacy by promoting soft power in East Asia.
Genetic and nongenetic factors explaining metabolically healthy and unhealthy phenotypes in participants with excessive adiposity: relevance for personalized nutrition
Authors: Ramos-Lopez Omar , Riezu-Boj Jose I. , Milagro Fermin I. , Cuervo Marta , Goni Leticia , Martinez J. Alfredo
Published: September 2019

Background:

Different genetic and environmental factors can explain the heterogeneity of obesity-induced metabolic alterations between individuals. In this study, we aimed to screen factors that predict metabolically healthy (MHP) and unhealthy (MUP) phenotypes using genetic and lifestyle data in overweight/obese participants.

Methods:

In this cross-sectional study we enrolled 298 overweight/obese Spanish adults. The Adult Treatment Panel III criteria for metabolic syndrome were used to categorize MHP (at most, one trait) and MUP (more than one feature). Blood lipid and inflammatory profiles were measured by standardized methods. Body composition was determined by dual-energy X-ray absorptiometry. A total of 95 obesity-predisposing single-nucleotide polymorphisms (SNPs) were genotyped by a predesigned next-generation sequencing system. SNPs associated with a MUP were used to compute a weighted genetic-risk score (wGRS). Information concerning lifestyle (dietary intake and physical activity level) was collected using validated questionnaires.

Results:

The prevalence of MHP and MUP was 44.3% and 55.7%, respectively, in this sample. Overall, 12 obesity-related genetic variants were associated with the MUP. Multiple logistic regression analyses revealed that wGRS (OR = 4.133, p < 0.001), total dietary fat [odds ratio (OR) = 1.105, p = 0.002], age (OR = 1.064, p = 0.001), and BMI (OR = 1.408, p < 0.001) positively explained the MUP, whereas female sex (OR = 0.330, p = 0.009) produced a protective effect. The area under the receiver operating characteristic curve using the multivariable model was high (0.8820). Interestingly, the wGRS was the greatest contributor to the MUP (squared partial correlation = 0.3816, p < 0.001).

Conclusions:

The genetic background is an important factor explaining MHP and MUP related to obesity, in addition to lifestyle variables. This information could be useful to metabolically categorize individuals, as well as for the design/implementation of personalized nutrition interventions aimed at promoting metabolic health and nutritional wellbeing.
Etiology and Outcomes of Spinal Cord Infarct: A Case Series From a Level 1 Trauma Center
Authors: Ge Laurence , Arul Karan , Stoner Michael , Mesfin Addisu
Published: September 2019

Study Design:

Retrospective study.

Objectives:

To evaluate the demographics, prevalence, etiology, severity, and outcomes of spinal cord injuries (SCIs) resulting from ischemic infarction.

Methods:

All patients with SCI and a diagnosis of cord infarct who were admitted to the inpatient rehabilitation unit at a level 1 trauma center from January 2003 to January 2014 were identified using an administrative billing database. Outcomes measures were evaluated.

Results:

Among 685 unique SCI patients who were identified, 30 (4.4%) had SCI due to spinal ischemic infarction. The mean age was 59 years (range 17-80 years). Fifty percent of patients had ASIA (American Spinal Injury Association) A and B severity. Most common causes were the following: 6 (20%) abdominal aortic aneurysm (AAA) repairs, 6 (20%) arteriovenous fistulas, and 6 (20%) with an unknown cause. Surgical complications led to 4 (13.3%) cord infarcts and was associated with a higher severity of injury ( P = .02) compared with other etiologies. Other causes included systemic hypotension, AAA rupture, trauma, diabetic ketoacidosis, and after radiation therapy. At follow-up, 6 (20%) of patients were able to ambulate normally without assistance, 7 (23.3%) were ambulating with assistance, and 17 (56.7%) were still wheelchair bound. Clinical improvement in ambulatory status was noted in 6 (20%) patients and was associated with less severe initial injury ( P = .02).

Conclusions:

While the existing literature associates spinal cord infarction with aortic pathologies and surgery, these caused less than 30% of cases, while nonaortic surgical complications were associated with the most severe injuries. Outcomes were worse than previously reported in the literature.
Does transforaminal lumbar interbody fusion produce leg pain?—Results from a RCT
Authors: Høy Kristian , Grycel Blazej , Andersen Thomas , Bünger Cody
Published: September 2019

Background:

Transforaminal lumbar interbody fusion (TLIF) is presently the most used method to achieve lumbar interbody fusion worldwide. The special preparation and cage insertion imply a risk of an undesirable side effect in the form of residual neurogenic pain. This issue has not been investigated prior in a randomized clinical trial (RCT) set up.

Aim:

To test whether TLIFs had a higher incidence of leg pain in comparison to a common instrumented posterolateral fusion (PLF) and to test whether a higher occurrence of leg pain on the ipsilateral side in the TLIF group was present.

Methods:

One hundred patients included in a RCT comparing TLIF and PLF fulfilled pain drawings and numeric rating scale (NRS) scale from 0 to 10 preoperatively, after 1 year, and after 2 years. Difference in pain appearance, type, localization, and intensity was compared between groups.

Results:

A slightly higher number of patients in the TLIF group reported leg pain at 2 years follow-up: no leg pain, 47% (PLF) and 37% (TLIF); unilateral leg pain, 31% (PLF) and 25% (TLIF); bilateral leg pain, 22% (PLF) and 37% (TLIF), p = 0.270. Numbness and pins and needles on the anterior aspect of the lower leg were marked by 10% and 12% of TLIF patients compared to 6% and 4% in PLF patients p = 0.498/0.197. The ipsilateral side of cage insertion in the TLIF group was not a place for new leg pain compared to the contralateral side.

Conclusion:

The special surgical preparation used in TLIFs does not result in the development of new ipsilateral leg pain. However, a higher percentage of the patients in the TLIF group had new leg pain in comparison to PLF after 2 years.
The modified anterior ellipsoidal cap titanium cable tension band for comminuted patellar fractures
Authors: Wang Fasheng , Luo Tianyi David , Chen Chunyong , Xie Yun , Lin Zhangxiong , Zeng Da , Lin Jianhua , Ye Junjian
Published: September 2019

Purpose:

The purpose of this study was to assess the outcomes in a series of patients, who underwent cerclage and figure-of-eight tension band wiring using a single titanium cable for comminuted patellar fractures.

Methods:

We describe a modified tension band technique using a single titanium cable to create an ellipsoidal cap structure that combines the circumferential and figure-of-eight wrapping in the fixation of closed Association for the Study of Internal Fixation/Orthopaedic Trauma Association 34C2 and 34C3 patellar fractures. We retrospectively reviewed 25 patients (16 males and 9 females, mean age 54 years) who underwent the described fixation technique between 2015 and 2017. Postoperative function was evaluated using the Böstman score.

Results:

At the mean follow-up of 25 months (range 17–39 months), the mean Böstman score was 27.3 ± 2.6 points (range 23–30). Eighteen patients (72%) had excellent results (score ≥28); seven patients (28%) had good results (score 20–27); and no patients had an unsatisfactory result (score < 20). All surgical incisions healed without major wound complications. Two patients reported minor complications (soft tissue irritation, cellulitis). No patients demonstrated loss of reduction or implant failure during the follow-up period.

Conclusion:

The modified anterior ellipsoidal cap tension band using a single titanium cable created an effective tension band structure in the treatment of comminuted patella fractures. It is a simple operative technique that produced a stable fixation construct, which allowed early functional rehabilitation and weight-bearing with a high rate of excellent outcomes at 2 years after surgery.
Automatic discovery of 100-miRNA signature for cancer classification using ensemble feature selection
Authors: Lopez-Rincon Alejandro , Martinez-Archundia Marlet , Martinez-Ruiz Gustavo U. , Schoenhuth Alexander , Tonda Alberto
Published: September 2019

Background

MicroRNAs (miRNAs) are noncoding RNA molecules heavily involved in human tumors, in which few of them circulating the human body. Finding a tumor-associated signature of miRNA, that is, the minimum miRNA entities to be measured for discriminating both different types of cancer and normal tissues, is of utmost importance. Feature selection techniques applied in machine learning can help however they often provide naive or biased results.

Results

An ensemble feature selection strategy for miRNA signatures is proposed. miRNAs are chosen based on consensus on feature relevance from high-accuracy classifiers of different typologies. This methodology aims to identify signatures that are considerably more robust and reliable when used in clinically relevant prediction tasks. Using the proposed method, a 100-miRNA signature is identified in a dataset of 8023 samples, extracted from TCGA. When running eight-state-of-the-art classifiers along with the 100-miRNA signature against the original 1046 features, it could be detected that global accuracy differs only by 1.4%. Importantly, this 100-miRNA signature is sufficient to distinguish between tumor and normal tissues. The approach is then compared against other feature selection methods, such as UFS, RFE, EN, LASSO, Genetic Algorithms, and EFS-CLA. The proposed approach provides better accuracy when tested on a 10-fold cross-validation with different classifiers and it is applied to several GEO datasets across different platforms with some classifiers showing more than 90% classification accuracy, which proves its cross-platform applicability.

Conclusions

The 100-miRNA signature is sufficiently stable to provide almost the same classification accuracy as the complete TCGA dataset, and it is further validated on several GEO datasets, across different types of cancer and platforms. Furthermore, a bibliographic analysis confirms that 77 out of the 100 miRNAs in the signature appear in lists of circulating miRNAs used in cancer studies, in stem-loop or mature-sequence form. The remaining 23 miRNAs offer potentially promising avenues for future research.
Phylogenomics resolves major relationships and reveals significant diversification rate shifts in the evolution of silk moths and relatives
Authors: Hamilton C. A. , St Laurent R. A. , Dexter K. , Kitching I. J. , Breinholt J. W. , Zwick A. , Timmermans M. J. T. N. , Barber J. R. , Kawahara A. Y.
Published: September 2019

Background

Silkmoths and their relatives constitute the ecologically and taxonomically diverse superfamily Bombycoidea, which includes some of the most charismatic species of Lepidoptera. Despite displaying spectacular forms and diverse ecological traits, relatively little attention has been given to understanding their evolution and drivers of their diversity. To begin to address this problem, we created a new Bombycoidea-specific Anchored Hybrid Enrichment (AHE) probe set and sampled up to 571 loci for 117 taxa across all major lineages of the Bombycoidea, with a newly developed DNA extraction protocol that allows Lepidoptera specimens to be readily sequenced from pinned natural history collections.

Results

The well-supported tree was overall consistent with prior morphological and molecular studies, although some taxa were misplaced. The bombycid Arotros Schaus was formally transferred to Apatelodidae. We identified important evolutionary patterns (e.g., morphology, biogeography, and differences in speciation and extinction), and our analysis of diversification rates highlights the stark increases that exist within the Sphingidae (hawkmoths) and Saturniidae (wild silkmoths).

Conclusions

Our study establishes a backbone for future evolutionary, comparative, and taxonomic studies of Bombycoidea. We postulate that the rate shifts identified are due to the well-documented bat-moth “arms race”. Our research highlights the flexibility of AHE to generate genomic data from a wide range of museum specimens, both age and preservation method, and will allow researchers to tap into the wealth of biological data residing in natural history collections around the globe.
Alternative methods improve the accuracy of genomic prediction using information from a causal point mutation in a dairy sheep model
Authors: Oget Claire , Teissier Marc , Astruc Jean-Michel , Tosser-Klopp Gwenola , Rupp Rachel
Published: September 2019

Background

Genomic evaluation is usually based on a set of markers assumed to be linked with causal mutations. Selection and precise management of major genes and the remaining polygenic component might be improved by including causal polymorphisms in the evaluation models. In this study, various methods involving a known mutation were used to estimate prediction accuracy. TheSOCS2gene, which influences body growth, milk production and somatic cell scores, a proxy for mastitis, was studied as an example in dairy sheep.

Methods

The data comprised 1,503,148 phenotypes and 9844 54K SNPs genotypes. TheSOCS2SNP was genotyped for 4297 animals and imputed in the above 9844 animals. Breeding values and their accuracies were estimated for each of nine traits by using single-step approaches. Pedigree-based BLUP, single-step genomic BLUP (ssGBLUP) involving the 54K ovine SNPs chip, and four weighted ssGBLUP (WssGBLUP) methods were compared. In WssGBLUP methods, weights are assigned to SNPs depending on their effect on the trait. The ssGBLUP and WssGBLUP methods were again tested after including theSOCS2causal mutation as a SNP. Finally, the Gene Content approach was tested, which uses a multiple-trait model that considers theSOCS2genotype as a trait.

Results

EBV accuracies were increased by 14.03% between the pedigree-based BLUP and ssGBLUP methods and by 3.99% between ssGBLUP and WssGBLUP. Adding theSOCS2SNP to ssGBLUP methods led to an average gain of 0.26%. Construction of the kinship matrix and estimation of breeding values was generally improved by placing emphasis on SNPs in regions with a strong effect on traits. In the absence of chip data, the Gene Content method, compared to pedigree-based BLUP, efficiently accounted for partial genotyping information onSOCS2as accuracy was increased by 6.25%. This method also allowed dissociation of the genetic component due to the major gene from the remaining polygenic component.

Conclusions

Causal mutations with a moderate to strong effect can be captured with conventional SNP chips by applying appropriate genomic evaluation methods. The Gene Content method provides an efficient way to account for causal mutations in populations lacking genome-wide genotyping.
Uncovering sperm metabolome to discover biomarkers for bull fertility
Authors: Menezes E. B. , Velho A. L. C. , Santos F. , Dinh T. , Kaya A. , Topper E. , Moura A. A. , Memili E.
Published: September 2019

Background

Subfertility decreases the efficiency of the cattle industry because artificial insemination employs spermatozoa from a single bull to inseminate thousands of cows. Variation in bull fertility has been demonstrated even among those animals exhibiting normal sperm numbers, motility, and morphology. Despite advances in research, molecular and cellular mechanisms underlying the causes of low fertility in some bulls have not been fully elucidated. In this study, we investigated the metabolic profile of bull spermatozoa using non-targeted metabolomics. Statistical analysis and bioinformatic tools were employed to evaluate the metabolic profiles high and low fertility groups. Metabolic pathways associated with the sperm metabolome were also reported.

Results

A total of 22 distinct metabolites were detected in spermatozoa from bulls with high fertility (HF) or low fertility (LF) phenotype. The major metabolite classes of bovine sperm were organic acids/derivatives and fatty acids/conjugates. We demonstrated that the abundance ratios of five sperm metabolites were statistically different between HF and LF groups including gamma-aminobutyric acid (GABA), carbamate, benzoic acid, lactic acid, and palmitic acid. Metabolites with different abundances in HF and LF bulls had also VIP scores of greater than 1.5 and AUC- ROC curves of more than 80%. In addition, four metabolic pathways associated with differential metabolites namely alanine, aspartate and glutamate metabolism, β-alanine metabolism, glycolysis or gluconeogenesis, and pyruvate metabolism were also explored.

Conclusions

This is the first study aimed at ascertaining the metabolome of spermatozoa from bulls with different fertility phenotype using gas chromatography-mass spectrometry. We identified five metabolites in the two groups of sires and such molecules can be used, in the future, as key indicators of bull fertility.
Signatures of selection in the genome of Swedish warmblood horses selected for sport performance
Authors: Ablondi Michela , Viklund Åsa , Lindgren Gabriella , Eriksson Susanne , Mikko Sofia
Published: September 2019

Background

A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits.

Results

The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (FSTand XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses.

Conclusions

Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.
Α de novo 3.8-Mb inversion affecting the EDA and XIST genes in a heterozygous female calf with generalized hypohidrotic ectodermal dysplasia
Authors: Escouflaire Clémentine , Rebours Emmanuelle , Charles Mathieu , Orellana Sébastien , Cano Margarita , Rivière Julie , Grohs Cécile , Hayes Hélène , Capitan Aurélien
Published: September 2019

Background

In mammals, hypohidrotic ectodermal dysplasia (HED) is a genetic disorder that is characterized by sparse hair, tooth abnormalities, and defects in cutaneous glands. Only four genes,EDA,EDAR,EDARADDandWNT10Aaccount for more than 90% of HED cases, andEDA, on chromosome X, is involved in 50% of the cases. In this study, we explored an isolated case of a female Holstein calf with symptoms similar to HED.

Results

Clinical examination confirmed the diagnosis. The affected female showed homogeneous hypotrichosis and oligodontia as previously observed in bovineEDARhomozygous andEDAhemizygous mutants. Under light microscopy, the hair follicles were thinner and located higher in the dermis of the frontal skin in the affected animal than in the control. Moreover, the affected animal showed a five-fold increase in the number of hair follicles and a four-fold decrease in the diameter of the pilary canals. Pedigree analysis revealed that the coefficient of inbreeding of the affected calf (4.58%) was not higher than the average population inbreeding coefficient (4.59%). This animal had ten ancestors in its paternal and maternal lineages. By estimating the number of affected cases that would be expected if any of these common ancestors carried a recessive mutation, we concluded that, if they existed, other cases of HED should have been reported in France, which is not the case. Therefore, we assumed that the causal mutation was dominant and de novo. By analyzing whole-genome sequencing data, we identified a large chromosomal inversion with breakpoints located in the first introns of theEDAandXISTgenes. Genotyping by PCR-electrophoresis the case and its parents allowed us to demonstrate the de novo origin of this inversion. Finally, using various sources of information we present a body of evidence that supports the hypothesis that this mutation is responsible for a skewed inactivation of X, and that only the normal X can be inactivated.

Conclusions

In this article, we report a unique case of X-linked HED affected Holstein female calf with an assumed full inactivation of the normal X-chromosome, thus leading to a severe phenotype similar to that of hemizygous males.
Evolution of resistance mechanisms and biological characteristics of rifampicin-resistant Staphylococcus aureus strains selected in vitro
Authors: Wang Chong , Fang Renchi , Zhou Beibei , Tian Xuebin , Zhang Xiucai , Zheng Xiangkuo , Zhang Siqin , Dong Guofeng , Cao Jianming , Zhou Tieli
Published: September 2019

Background

We aimed to determine the evolutionary pathways of rifampicin resistance in Staphylococcus aureus, and the impact of resistance mutations in the rpoB gene on fitness.

Methods

Three clinical strains and one reference strain were used to select for rifampicin-resistant S. aureus variants. The mutations responsible for rifampicin resistance in all of the selected isolates in vitro were investigated by polymerase chain reaction (PCR) and DNA sequencing. To compare the fitness cost of rpoB mutations against their corresponding original isolates, we performed bacterial growth curve assays, static biofilm assays, in vitro competition experiments and an infection model of Galleria mellonella larvae.

Results

We obtained four rifampicin-resistant S. aureus isolates that showed high levels of resistance to rifampicin with a minimal inhibitory concentration (MIC) of 128 mg/L, and all isolates had a mutation at position 481 (H481F/Y) in RpoB. A broth microdilution assay indicated that mutation of H481F/Y did not affect susceptibility to common antibacterial drugs but slightly increased the vancomycin MIC. To identify the pathways involved in the development of rifampicin resistance, 32 variants (eight mutants for each strain) and four original isolates were selected for gene sequencing. Different generations of isolates were found to harbor various mutations sites. Compared with the corresponding original isolates, an in vitro fitness assay of the variant isolates showed that growth and virulence were reduced, with a statistically significantly decreased fitness, whereas the capacity for biofilm formation was elevated.

Conclusions

Our findings suggested that the acquisition of rifampicin resistance in S. aureus was dynamic and was associated with a significant fitness cost.
QTL and candidate genes associated with leaf anion concentrations in response to phosphate supply in Arabidopsis thaliana
Authors: El-Soda Mohamed , Neris Moreira Charles , Goredema-Matongera Nakai , Jamar Diaan , Koornneef Maarten , Aarts Mark G. M.
Published: September 2019

Background

Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability.

Results

Recombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions ofArabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped toPP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other toSIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found inSULTR2;1,encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped toFMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of theSUL2locus.

Conclusion

We identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
Prophylactic HIPEC with radical D2 gastrectomy improves survival and peritoneal recurrence rates for locally advanced gastric cancer: personal experience from a randomized case control study
Authors: Beeharry Maneesh Kumarsing , Zhu Zheng-Lun , Liu Wen-Tao , Yao Xue-Xin , Yan Min , Zhu Zheng-Gang
Published: September 2019

Background

To investigate the implications of prophylactic intraoperative Hyperthermic Intraperitoneal Chemotherapy (HIPEC) with D2 radical gastrectomy for locally advanced Gastric Cancer (AGC) in a randomized case control study.

Method

Eighty consecutive patients with locally AGC were randomly separated into 2 groups: HIPEC group (Curative Resection + intraoperative HIPEC with cisplatin 50 mg/m2 at 42.0 ± 1.0 °C for 60 min) and Control group (Curative Resection only). Intraoperative and post-operative events, clinical recovery, morbidity and the disease-free survival (DFS) rates were closely monitored.

Results

Faster recovery of bowel function (43 ± 5 h vs 68 ± 7, P < 0.05) and shorter postoperative stay (8d vs 14d, P < 0.05) were noted in the HIPEC group. Among the 40 HIPEC group patients, the highest intracranial temperature recorded during the procedure was 38.2 °C but the patient made an eventless recovery. Mild renal dysfunction, hyperbilirubinemia and mild liver dysfunction were recorded in the HIPEC group but their incidences were found to be statistically insignificant when compared with the control group (P > 0.05). The 3 year DFS rate analysis showed that the prophylactic HIPEC group had a higher DFS rate (93% vs 65%, P = 0.0054). The peritoneal recurrence rate was lower in the HIPEC group (3% vs 23%, P < 0.05).

Conclusion

Prophylactic HIPEC with radical D2 Gastrectomy improves survival and peritoneal recurrence rates for AGC with favorable post-operative recovery at low and acceptable morbidity.
Mothers with and without bipolar disorder and their infants: group differences in mother-infant interaction patterns at three months postpartum
Authors: Anke Teija M. S. , Slinning Kari , Moe Vibeke , Brunborg Cathrine , Siqveland Torill S. , Skjelstad Dag Vegard
Published: September 2019

Background

Women with bipolar disorder (BD) have a high risk of illness relapse postpartum. The risk coincides with the period when mother-infant interactions are evolving. We compared mother-infant interactions in dyads where the mothers have BD with dyads where the mothers have no mental disorder. The association between concurrent affective symptoms of BD mothers and interaction quality was investigated.

Methods

Twenty-six women with BD and 30 comparison women with infants were included. The Parent-Child Early Relational Assessment (PCERA) was used to assess maternal behaviour, infant behaviour and dyadic coordination in interactions at 3 months postpartum. The Inventory of Depressive Symptomatology and Young Mania Rating Scale were used to assess affective symptoms of BD mothers at the time of interaction.

Results

There were significant group differences with medium to large effect sizes (0.73–1.32) on five of six subscales within the three interactional domains. Most interactional concerns were identified in dyadic coordination. No significant associations were found between maternal symptom load and interaction quality within the BD sample. Forty-six percent of the BD mothers experienced a mood episode within 0–3 months postpartum.

Conclusions

The present study identified challenges for mothers with BD and their infants in “finding” each other in interaction at 3 months postpartum. If sustained, this interaction pattern may have a long-term impact on children’s development. We suggest interventions specifically focusing on sensitising and supporting mothers to read infants’ cues on a micro-level. This may help them to respond contingently and improve dyadic coordination and synchronicity.
Process evaluation of the Getting it Right study and acceptability and feasibility of screening for depression with the aPHQ-9
Authors:   on behalf of the Getting it Right Investigators, Farnbach Sara , Gee Graham , Eades Anne-Marie , Evans John Robert , Fernando Jamie , Hammond Belinda , Simms Matty , DeMasi Karrina , Glozier Nick , Brown Alex , Hackett Maree L.
Published: September 2019

Background

The Getting it Right study determined the validity, sensitivity, specificity and acceptability of the culturally adapted 9-item Patient Health Questionnaire (aPHQ-9) as a screening tool for depression in Aboriginal and Torres Strait Islander (hereafter referred to as Indigenous) people. In this process evaluation we aimed to explore staff perceptions about whether Getting it Right was conducted per protocol, and if the aPHQ-9 was considered an acceptable and feasible screening tool for depression in primary healthcare. This process evaluation will provide information for clinicians and policy makers about the experiences of staff and patients with Getting it Right and what they thought about using the aPHQ-9.

Methods

Process evaluation using grounded theory approaches. Semi-structured interviews with primary healthcare staff from services participating in Getting it Right were triangulated with feedback (free-text and elicited) from participants collected during the validation study and field notes. Data were thematically analysed according to the Getting it Right study protocol to identify the acceptability and feasibility of the aPHQ-9.

Results

Primary healthcare staff (n = 36) and community members (n = 4) from nine of the ten participating Getting it Right services and Indigenous participants (n = 500) from the ten services that took part. Most staff reported that the research was conducted according to the study protocol. Staff from two services reported sometimes recruiting opportunistically (rather than recruiting consecutive patients attending the service as outlined in the main study protocol), when they spoke to patients who they knew from previous interactions, because they perceived their previous relationship may increase the likelihood of patients participating. All Getting it Right participants responded to at least six of the seven feedback questions and 20% provided free-text feedback. Most staff said they would use the aPHQ-9 and most participants said that the questions were easy to understand (87%), the response categories made sense (89%) and that they felt comfortable answering the questions (91%).

Conclusion

Getting it Right was predominantly conducted according to the study protocol. The aPHQ-9, the first culturally adapted, nationally validated, freely available depression screening tool for use by Indigenous people, appears to be acceptable and feasible to use.

Trial registration

Australian New Zealand Clinical Trial Registry ANZCTR12614000705684, 03/07/2014.