bluuebunny/crossref_metadata_2025 huggingface dataset:
What Are Meaningful Social Interactions in Today’s Media Landscape? A Cross-Cultural Survey
Authors: Litt Eden , Zhao Siyan , Kraut Robert , Burke Moira
Published: August 2020

As we increasingly integrate technology into our lives, we need a better framework for understanding social interactions across the communication landscape. Utilizing survey data in which more than 4,600 people across the United States, India, and Japan described a recent social interaction, this article qualitatively and quantitatively explores what makes an interaction meaningful. A qualitative analysis of respondents’ own words finds that meaningful interactions are those with emotional, informational, or tangible impact that people believe enhance their lives, the lives of their interaction partners, or their personal relationships. A quantitative analysis predicting respondents’ ratings of recent interactions finds the attributes most likely to facilitate meaningfulness include strong ties (e.g., friends and family), community ties (e.g., neighbors), shared activities, and synchronicity; meaningful social interactions are also more likely to be planned in advance and memorialized with photos or videos. These attributes are consistent across cultures. Although popular rhetoric often juxtaposes people’s online lives against their offline lives, this research finds in-person interactions can be just as meaningful as technology-mediated interactions. We conclude with a new framework for thinking about social interactions more holistically.
On the Overlap of Systemic Events: Covid-19, Climate, and Journalism
Authors: Kunelius Risto
Published: August 2020

Covid-19 represents a systemic event—a state of emergency—that disrupts the routines of societies from the level of individuals to institutions, nations, and global interaction. Revealing the vulnerability of the intensively interconnected world suggests a juxtaposition with another systemic crisis: the climate emergency. Drawing on some key literature on the different aspects of “events”—as heightened political semiosis (Wagner-Pacifi), as (possible) transformation of social and symbolic structures (Sewell), and as moments where new horizons are opened (Arendt)—this essay suggests three intersecting themes where reactions to Covid-19 help to sharpen the crucial questions of future journalism: the role of “knowledge” and expertise, the power of national framing, and the challenge of covering the new imperatives and possibilities of everyday life.
The Rise of the Data Poor: The COVID-19 Pandemic Seen From the Margins
Authors: Milan Stefania , Treré Emiliano
Published: August 2020

Quantification is central to the narration of the COVID-19 pandemic. Numbers determine the existence of the problem and affect our ability to care and contribute to relief efforts. Yet many communities at the margins, including many areas of the Global South, are virtually absent from this number-based narration of the pandemic. This essay builds on critical data studies to warn against the universalization of problems, narratives, and responses to the virus. To this end, it explores two types of data gaps and the corresponding “data poor.” The first gap concerns the data poverty perduring in low-income countries and jeopardizing their ability to adequately respond to the pandemic. The second affects vulnerable populations within a variety of geopolitical and socio-political contexts, whereby data poverty constitutes a dangerous form of invisibility which perpetuates various forms of inequality. But, even during the pandemic, the disempowered manage to create innovative forms of solidarity from below that partially mitigate the negative effects of their invisibility.
An Exploratory Study to Understand Factors Associated with Health-related Quality of Life Among Uninsured/Underinsured Patients as Identified by Clinic Providers and Staff
Authors: Wippold Guillermo M. , Nmezi Nwakaego , Williams Jaime L. , Butler Jacqueline , Hodge Tanya M.
Published: August 2020

Since the release of Healthy People 2020, there has been extensive research understanding factors associated with health-related quality of life (HRQoL) among specific populations. Despite this growing body of research, little has been conducted to understand the factors associated with HRQoL among uninsured/underinsured Americans. The purposes of the present study were to assess clinic staff to determine: (1) whether there is a need to examine HRQoL among uninsured/underinsured individuals, (2) whether there is a need for tailored HRQoL-promoting interventions among uninsured/underinsured individuals, and (3) the factors associated with HRQoL among uninsured/underinsured individuals. A survey was sent to an association of 41 clinics that provides free medical services to uninsured/underinsured individuals. The majority of participants indicated that uninsured/underinsured individuals experience unique factors associated with HRQoL and that there was a need to implement tailored HRQoL-improving interventions among uninsured/underinsured individuals. The results also present the personal/contextual factors associated with HRQoL of uninsured/underinsured individuals.
Tricuspid Valve and Right Ventricular Function Throughout the Hybrid Palliation Strategy for Hypoplastic Left Heart Syndrome and Variants
Authors: Carrillo Sergio A. , Texter Karen M. , Phelps Christina , Tan Yubo , McConnell Patrick I. , Galantowicz Mark
Published: August 2020

Background:

Tricuspid valve (TV) and right ventricular (RV) function are major determinants of morbidity and mortality in patients with hypoplastic left heart syndrome (HLHS). We sought to retrospectively evaluate these parameters throughout the hybrid palliation strategy.

Methods:

From 2002 to 2018, 203 patients with HLHS and variants presented for hybrid stage I (HS1). Echocardiographic evaluation of tricuspid regurgitation (TR) and RV function was assessed at multiple time points. Clinical outcomes including tricuspid valvuloplasty, transplantation, and death were reviewed.

Results:

The most prevalent HLHS subtype was aortic atresia/mitral atresia. The presence of significant TR and/or RV dysfunction was 14.78% and 9.36%, respectively, at the time of initial HS1. There were 185 survivors following HS1 (91.13%, n = 185/203), while 147 patients underwent comprehensive stage II or bidirectional Glenn shunt (72.41%, n = 147/203). Tricuspid valvuloplasty was undertaken in nine patients (4.86%, n = 9/185). Ultimately, 100 patients underwent the Fontan procedure. The odds of development of significant TR and/or RV dysfunction were not statistically different throughout the stages of palliation (TR: odds ratio [OR] = 0.14-0.25, P = .5260; RV dysfunction: OR = 0.02-0.13, P = .3992). However, the risk of death and/or transplant was 2.5- to 3.8-fold when either were present alone or in combination (TR: OR = 2.58, P = .0356; RV dysfunction: OR = 3.84, P = .0262). Transplant-free survival at 15 years was 44.8%.

Conclusion:

Following hybrid palliation for HLHS, the majority of survivors have normal RV and TV functions. Tricuspid valvuloplasty was required in few patients. Once significant TR and/or RV dysfunction ensues, there is a two- to three-fold risk of death and/or transplant.
Overview of Hofstede-Inspired Research Over the Past 40 Years: The Network Diversity Perspective
Authors: Zhou Yan , Kwon Jong-Wook
Published: August 2020

Hofstede’s cultural value framework has inspired many empirical studies in various fields. Scholars have advanced our understanding of how the Hofstede value model is used. However, there remain a number of underexplored areas regarding the ways in which Hofstede’s framework has been used over the last decade. Drawing on the co-authorship network and cultural diversity literature, we attempt to make a contribution that goes beyond the existing research by addressing underexplored areas, namely, the network diversity of institutions, authors, and countries engaged in Hofstede-inspired research. As a result, the cultural diversity and diversity of specialization of the networks of institutions, authors, and countries engaged in research incorporating the Hofstede framework are still too Western-based and psychology-oriented to acquire new research directions and increase innovation opportunities in new fields. We summarize the possible limitations of this study and provide some future research directions, including how to expand networks, the influence of author identity on networks, the appropriate number of authors and the diversity level of participants in a network, and the main motivations of author co-authorship networks.
Infection Recurrence in Instrumented Spinal Fusion in Children
Authors: Moyano Carlos A. , Tello Carlos A. , Piantoni Lucas , Wilson Ida A. Francheri , Galaretto Eduardo , Remondino Rodrigo G. , Bersusky Ernesto , Noël Mariano A.
Published: August 2020

Study Design:

Level 4 retrospective case series.

Objectives:

Surgical site infection (SSI) is one of the main complications of instrumented spinal fusion. The aim of our study was to evaluate infection recurrence (same bacteria) or reinfection (different bacteria) in posterior spinal fusion in children.

Methods:

A retrospective study was conducted to evaluate patients who were successfully treated for SSI after instrumented spinal fusion due to deformity, with irrigation and debridement (I&D) procedures, followed by antibiotic therapy, with a follow-up of at least 2 years.

Results:

Overall, 29 patients with a mean age of 14 + 3 years were evaluated. Preoperative diagnosis was nonidiopathic scoliosis in 23, idiopathic scoliosis in 5, and Scheuermann’s disease in 1 patient. The etiology was Gram-positive cocci (40.9%), Gram-negative bacilli (27.2%), and polymicrobial infection (31.8%). A mean of 1.5 (1-3) I&D procedures were performed. Intravenous antibiotic treatment was given for a mean of 15.8 (4-86) days, followed by oral treatment for a mean of 335.1 (0-1095) days. Mean follow-up was 5 + 2 years (2 to 14 + 7 years) during which 28 patients were cured (96.6%) and 1 patient developed reinfection (3.4%). This reinfection was treated with oral clindamycin for 6 months. After the infection persisted, the decision was to remove the implants.

Conclusions:

In this series of 29 pediatric patients who underwent instrumented spinal fusion due to deformity, we reported one case of reinfection (3.4%). Given that 96.6% of infections were resolved, we suggest treatment with I&D procedures with retention of implants to treat acute SSI.
Use of MACI (Autologous Cultured Chondrocytes on Porcine Collagen Membrane) in the United States: Preliminary Experience
Authors: Carey James L. , Remmers Ann E. , Flanigan David C.
Published: August 2020

Background:

In December 2016, MACI (autologous cultured chondrocytes on porcine collagen membrane) received approval from the US Food and Drug Administration for the treatment of symptomatic articular cartilage defects of the knee with or without bone involvement in adults.

Purpose:

To describe the cartilage defects and patient characteristics for 1000 adult patients treated with MACI for knee cartilage repair in the United States.

Study Design:

Case series; Level of evidence, 4.

Methods:

Data collected by Vericel for adult patients treated for articular cartilage defects of the knee were reconciled and summarized. Data were collected for 1000 consecutive patients starting on July 1, 2017, when Carticel (the prior generation of autologous cultured chondrocytes) was no longer available. Patient names were removed for confidentiality, and patients were identified by MACI lot number and surgery date. Safety data were derived from the pharmacovigilance database. Patient demographics, cartilage defect characteristics, concomitant surgical procedures, and adverse events were summarized with descriptive statistics.

Results:

A total of 1000 adults and 1010 knee joints were implanted with MACI by 372 surgeons. The male (49.6%)-to-female (50.4%) ratio was evenly split, and the mean age was 34.0 years. The majority of patients (68.1%) had a single cartilage defect treated, and the mean treated defect size was 4.7 cm2. The mean total treated lesion size, including multiple defects, was 5.8 cm2. The patella was the most commonly treated joint surface (32.7%), followed by the medial femoral condyle (31.3%). Most patients (92.4%) had concomitant surgical procedures at the time of cartilage biopsy acquisition. The most common concomitant procedures at the time of biopsy procurement included cartilage debridement (83.7%) and meniscal resection (11.3%). The most common planned concomitant surgeries at the time of MACI implantation were anterior tibial tubercleplasty (7.8%) and reconstruction of dislocating patella (5.5%). Few patients (2.6%) had adverse events.

Conclusion:

Patient age and mean total MACI-treated defect size in the United States are similar to the findings of the pivotal European SUMMIT (Superiority of MACI Implant Versus Microfracture Treatment) trial and other studies from outside the United States. Treatment of multiple cartilage defects is more frequent in the United States than elsewhere.
Treatment for Symptomatic Genu Recurvatum: A Systematic Review
Authors: Dean Robert S. , Graden Nathan R. , Kahat David H. , DePhillipo Nicholas N. , LaPrade Robert F.
Published: August 2020

Background:

Symptomatic genu recurvatum is a challenging condition to treat. Both osseous and soft tissue treatment options have been reported to address symptomatic genu recurvatum.

Purpose/Hypothesis:

The purpose of this article was to review the current literature on surgical treatment options for symptomatic genu recurvatum and to describe the associated clinical outcomes. We hypothesized that anterior opening-wedge proximal tibial osteotomy (PTO) would be the most common surgical technique described in the literature and that this intervention would allow for successful long-term management of symptomatic genu recurvatum.

Study Design:

Systematic review; Level of evidence, 4.

Methods:

A systematic review was performed according to PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, with the inclusion criterion of surgical treatment options for symptomatic genu recurvatum. Recurvatum secondary to polio, cerebrovascular accident, or cerebral palsy was excluded from this review.

Results:

A total of 311 studies were identified, of which 6 studies with a total of 80 patients met the inclusion criteria. Causes of genu recurvatum included physeal arrest; soft tissue laxity; and complications related to fractures, such as prolonged immobilization and malalignment. Mean follow-up times ranged from 1 to 14.5 years postoperatively. There were 5 studies that described anterior opening-wedge PTO, 2 of which used the Ilizarov distraction technique. All 3 studies that used PTO without the Ilizarov technique reported correction of recurvatum and increased posterior tibial slope; 2 of these studies also included subjective outcomes scores, reporting good or excellent outcomes in 70% (21/30) of patients. Of the studies that used the Ilizarov technique, both reported correction of recurvatum and increased posterior slope from preoperative to postoperative assessments. Both of these studies reported good or excellent subjective outcomes postoperatively in 89.5% (17/19) of patients. Additionally, 1 study successfully corrected recurvatum by performing a retensioning of the posterior capsule to address knee hyperextension, although follow-up was limited to 1 year postoperatively.

Conclusion:

Anterior opening-wedge PTO, with or without postoperative external fixation with progressive distraction, was found to be a reliable surgical treatment for symptomatic genu recurvatum. After surgical management with PTO, patients can expect to achieve correction of knee hyperextension, restoration of a more posterior tibial slope, and increased subjective outcome scores.
Challenges of Diagnosing Pediatric Posterior Reversible Encephalopathy Syndrome in Resource Poor Settings: A Narrative Review
Authors: Ndu Ikenna Kingsley , Ayuk Adaeze Chikaodinaka , Onukwuli Vivian Ozoemena
Published: August 2020

Posterior reversible encephalopathy syndrome (PRES) is a rare clinical syndrome that has been observed in different age groups, including pediatric patients. Identified triggers of PRES in both children and adults have included immunosuppressive and cytotoxic agents, organ transplantation, severe sepsis, blood transfusion, or evidence of human immunodeficiency virus-1 (HIV-1). Its clinical and radiological courses have been reported as mostly benign and reversible over days to weeks. Computed tomography (CT) scans are helpful in diagnosis, but magnetic resonance imaging (MRI) remains the gold standard. Unfortunately, because of the prohibitive costs of such medical equipment, diagnosis remains a challenge in developing countries. There is a dearth of information about pediatric PRES in resource–poor settings. This narrative aims to draw attention to the possible existence of PRES in children and to identify factors responsible for the difficulty in making the diagnosis. This review will hopefully increase awareness of PRES among pediatricians in order to make early diagnosis and institute appropriate management of this condition.
Posterior Segment Findings in Patients on Extracorporeal Membrane Oxygenation
Authors: Blegen Halward Martin John , Plaster Andrew Lemuel , Hobbs Samuel David , Reed Donovan Stephen , Santamaria Joseph Anthony , Heath Zachary George , Nelson Frederick David , Giles Gregory Bryant , Drayna Paul Michael
Published: August 2020

Purpose:

Extracorporeal membrane oxygenation (ECMO) is an established treatment modality for critically ill patients with cardiopulmonary failure, yet little is known of the ocular pathology in this population. The aim of this study is to characterize the posterior segment findings of ECMO patients.

Methods:

This study is a retrospective analysis of 20 ECMO patients evaluated by ophthalmology from September 2012 to May 2019 at a level 1 trauma center. Comprehensive examinations assessed for intraocular pathology. Demographic data, exam findings, and mortality were analyzed.

Results:

The sample size consisted of 20 patients; a majority were male (75%), and mean age was 37.4 years (interquartile range, 26.75-50 years). All patients received ECMO for care of acute respiratory distress syndrome (ARDS). Average duration of ECMO therapy was 9.6 ± 6.5 days. Eleven (55%) patients had acute retinal pathology, including Purtscher-like retinopathy (20%), intraocular hemorrhage (50%), and septic chorioretinitis (bacterial or fungal, 10%). Location of hemorrhage included the retina (40%), vitreous (30%), and optic disc (15%). Sixty percent (n = 12) of patients were unable to provide a subjective history on initial assessment. Ultimately, 5 out of 20 patients (25%) died of systemic illness during their hospital stay.

Conclusion:

This study demonstrates high rates of retinal pathology, most commonly vitreous and/or retinal hemorrhage alongside a Purtscher-like retinopathy. This is likely secondary to complications of anticoagulation, microthrombi, septicemia, and hemodynamic instability. We found a mortality rate slightly lower than that of prior ECMO studies. Prospective studies with pre-ECMO and post-ECMO fundus photography is warranted for better understanding of these medically complex patients.
Assessing the Educational Climate: Transgender Content in Medical Imaging Curricula
Authors: Custer Tanya , Sayles Harlan , Michael Kim
Published: August 2020

Objective:

The purpose of this mixed-methods study was to gather benchmark data on curricular content related to imaging of transgender patients. In addition, the intent was to explore program directors’ opinions on the need to include this content in the curriculum.

Material and Methods:

An online survey was emailed to all directors (n = 982) of accredited imaging programs in the United States.

Results:

In total, 331 (34%) program directors participated in the survey. Fifty-six percent currently do not include this content in their curriculum and 67% reported no discussion of adding the material. There was a modest and significant positive correlation between the program directors’ perceived level of knowledge, regarding imaging transgender patients, and their perceived importance of including this material in the curriculum ( r = 0.370; P < .001). Positive (55%), negative (7%), and neutral themes (38%) emerged from the qualitative data analysis.

Conclusion:

These findings were consistent with literature regarding a lack of curriculum specific to transgender patients. Program directors recognized the need to include this content, although barriers exist related to readiness to implement, limited faculty knowledge with the material, and lack of educational resources. Program directors are seeking strategies and resources to guide the integration of this material into the curriculum.
Parent and Youth Post-School Expectations: Students With Intellectual Disability in Rural Schools
Authors: Bouck Emily C. , Long Holly M. , Costello M. Patty
Published: August 2020

While research exists on parent expectations associated with post-school outcomes of youth with intellectual disability, limited research examines issues of parent—and youth—post-school expectations relative to issues of community, such as living in rural versus urban or suburban settings. Through a secondary analysis of the National Longitudinal Transition Study (NLTS) 2012, we examined parent and youth expectations regarding post-school outcomes for students with intellectual disability relative to school locale (i.e., rural, urban, and suburban) and severity of intellectual disability. Youth from rural schools reported high rates of positive post-school expectations with regard to independent living and being employed, and their rates relative to independent living exceeded parental expectations. However, across the different variables, school locale was only a factor in the binary or ordinal logistic regression analyses for two dependent variables: parental expectation for their child to support themselves financially and parental expectations of obtained level of education.
Economic consequences of migraine in Sweden and implications for the cost-effectiveness of onabotulinumtoxinA (Botox) for chronic migraine in Sweden and Norway
Authors: Hansson-Hedblom Amanda , Axelsson Isabelle , Jacobson Lena , Tedroff Joakim , Borgström Fredrik
Published: August 2020

Background

Migraine is a common and incapacitating condition, with severe impact on the quality of life (QoL) of the afflicted and their families, and negative economic consequences through decreased workforce participation, reduced functional ability and elevated healthcare costs. This study aimed to describe the economic consequences of migraine in Sweden using cost of illness survey data and, based on this data, assess the cost-effectiveness of onabotulinumtoxinA (Botox) for the treatment of chronic migraine in Sweden and Norway.

Methods

A survey study was conducted in Swedish migraine patients, with questions on patient characteristics, headache frequency and severity, effect on daily activities and work, QoL, health resource utilization, and medication use. Resulting costs were estimated as annual averages over subgroups of average monthly headache days. Some results were used to inform a Markov cost-effectiveness chronic migraine model. The model was adapted to Sweden and Norway using local data. The analysis perspective was semi-societal. Results’ robustness was tested using one-way, structural, and probabilistic sensitivity analyses.

Results

Results from the cost of illness analysis (n = 454) indicated a clear correlation between decreased QoL and increased costs with increasing monthly headache days. Total annual costs ranged from EUR 6221 in patients with 0–4 headache days per month, to EUR 57,832 in patients with 25–31. Indirect costs made up the majority of costs, ranging from 82% of total costs in the 0–4 headache days group, to 91% in 25–31 headache days. The cost-effectiveness analyses indicated that in Sweden, Botox was associated with 0.223 additional QALYs at an additional cost of EUR 4126 compared to placebo, resulting in an incremental cost-effectiveness ratio (ICER) of EUR 18,506. In Norway, Botox was associated with 0.216 additional QALYs at an additional cost of EUR 4301 compared to placebo, resulting in an ICER of EUR 19,954.

Conclusions

In people with migraine, an increase in monthly headache days is clearly related to lower QoL and higher costs, indicating considerable potential costs-savings in reducing the number of headache days. The main cost driver for migraine is indirect costs. Botox reduces headache days and is a cost-effective treatment for chronic migraine in Sweden and Norway.
The status and high risk factors of severe psychological distress in migraine patients during nCOV-2019 outbreak in Southwest China: a cross-sectional study
Authors: Ma Mengmeng , Fang Jinghuan , Li Changling , Bao Jiajia , Zhang Yang , Chen Ning , Guo Jian , He Li
Published: August 2020

Background

Psychological distress is highly prevalent among migraineurs during public health emergencies. The coronavirus disease 2019 (nCOV-2019) has created mass panic in China due to its highly contagious by contact and aerosols and lack of effective treatment. However, the emotion status of migraineurs stayed unclear during the nCOV-2019 outbreak.

Objective

To understand psychological distress of migraineurs by comparing with common population and identify potential high-risk factors of severe psychological distress among migraine patients.

Method

We enrolled the migraineurs treated at the department of Neurology of West China Hospital and healthy controls with age- and sex-matched to migraineurs. Data on clinicodemographics and psychological distress in the month of February 2020 (during in the nCOV-2019 outbreak in China) were collected. We used the Kessler 6-item (K-6) scale to assess psychological distress. Potential risk factors of severe psychological distress were identified using univariate and multivariate logistic regression.

Results

The 144 migraineurs and 150 controls were included in the study. Migraineurs showed significantly higher K-6 scores than controls (P < 0.001). Migraine attack frequency in previous 30 days and time spent paying attention to outbreak showed significant in multivariate logistic regression with respective odds ratios of 2.225 (95%CI 1.361–3.628,P = 0.001) and 1.589 (95% 1.117–2.26,P = 0.01).

Conclusion

During public health outbreaks, healthcare professionals should focus not only on controlling and reducing migraine attack but also on mental health of migraineurs, especially those with high frequency migraine attack.
Development of a relational workplace social capital scale for Japanese nurses
Authors: Norikoshi Kensuke , Kobayashi Toshio , Tabuchi Keiji , Oriyama Sanae
Published: August 2020

Background

Although nurses’ workplace social capital for a healthy work environment has received considerable attention, few scales about nurses’ workplace social capital are based on the attributes of clinical settings in Japan. This study aims to develop a Relational Workplace Social Capital Scale for Japanese Nurses (RWSCS-JN), which includes bonding, linking, and bridging social capital and assessing its reliability and validity.

Methods

We assessed its reliability and validity using questionnaire survey data collected from 309 nurses in the first survey and 105 nurses in the second survey in four hospitals in Japan. First, we determined the number of factors and items for the RWSCS-JN through the parallel and factor analyses after conducting the item analysis. Then, we confirmed the omega coefficients and intraclass correlation coefficients (ICC) of the RWSCS-JN. Finally, we examined the Pearson product-moment correlation coefficient between the RWSCS-JN score and other variables, including an existing measurement of workplace social capital, work engagement, and turnover intention.

Results

The newly developed RWSCS-JN contained 15 items, comprising three factors as follows: bonding social capital, linking social capital, and bridging social capital. The omega coefficient and the ICC of the RWSCS-JN were 0.90 and 0.85, respectively. The Pearson product-moment correlation coefficient between the RWSCS-JN and the existing scale of the workplace social capital was 0.88 (p < 0.01). Furthermore, the Pearson product-moment correlation coefficient between the RWSCS-JN and work engagement was 0.36 (p < 0.01) and that of the RWSCS-JN and turnover intention was − 0.40 (p < 0.01).

Conclusions

This study suggests that the RWSCS-JN could be sufficiently useful for a healthy work environment in a clinical setting.
X chromosome variants are associated with male fertility traits in two bovine populations
Authors: Fortes Marina R. S. , Porto-Neto Laercio R. , Satake Nana , Nguyen Loan T. , Freitas Ana Claudia , Melo Thaise P. , Scalez Daiane Cristina Becker , Hayes Ben , Raidan Fernanda S. S. , Reverter Antonio , Boe-Hansen Gry B.
Published: August 2020

Background

Twenty-five phenotypes were measured as indicators of bull fertility (1099 Brahman and 1719 Tropical Composite bulls). Measurements included sperm morphology, scrotal circumference, and sperm chromatin phenotypes such as DNA fragmentation and protamine deficiency. We estimated the heritability of these phenotypes and carried out genome-wide association studies (GWAS) within breed, using the bovine high-density chip, to detect quantitative trait loci (QTL).

Results

Our analyses suggested that both sperm DNA fragmentation and sperm protamine deficiency are heritable (h2 from 0.10 to 0.22). To confirm these first estimates of heritability, further studies on sperm chromatin traits, with larger datasets are necessary. Our GWAS identified 12 QTL for bull fertility traits, based on at least five polymorphisms (P < 10−8) for each QTL. Five QTL were identified in Brahman and another seven in Tropical Composite bulls. Most of the significant polymorphisms detected in both breeds and nine of the 12 QTL were on chromosome X. The QTL were breed-specific, but for some traits, a closer inspection of the GWAS results revealed suggestive single nucleotide polymorphism (SNP) associations (P < 10−7) in both breeds. For example, the QTL for inhibin level in Braham could be relevant to Tropical Composites too (many polymorphisms reached P < 10−7 in the same region). The QTL for sperm midpiece morphological abnormalities on chromosome X (QTL peak at 4.92 Mb, P < 10−17) is an example of a breed-specific QTL, supported by 143 significant SNPs (P < 10−8) in Brahman, but absent in Tropical Composites. Our GWAS results add evidence to the mammalian specialization of the X chromosome, which during evolution has accumulated genes linked to spermatogenesis. Some of the polymorphisms on chromosome X were associated to more than one genetically correlated trait (correlations ranged from 0.33 to 0.51). Correlations and shared polymorphism associations support the hypothesis that these phenotypes share the same underlying cause, i.e. defective spermatogenesis.

Conclusions

Genetic improvement for bull fertility is possible through genomic selection, which is likely more accurate if the QTL on chromosome X are considered in the predictions. Polymorphisms associated with male fertility accumulate on this chromosome in cattle, as in humans and mice, suggesting its specialization.
Bias and accuracy of dairy sheep evaluations using BLUP and SSGBLUP with metafounders and unknown parent groups
Authors: Macedo Fernando L. , Christensen Ole F. , Astruc Jean-Michel , Aguilar Ignacio , Masuda Yutaka , Legarra Andrés
Published: August 2020

Background

Bias has been reported in genetic or genomic evaluations of several species. Common biases are systematic differences between averages of estimated and true breeding values, and their over- or under-dispersion. In addition, comparing accuracies of pedigree versus genomic predictions is a difficult task. This work proposes to analyse biases and accuracies in the genetic evaluation of milk yield in Manech Tête Rousse dairy sheep, over several years, by testing five models and using the estimators of the linear regression method. We tested models with and without genomic information [best linear unbiased prediction (BLUP) and single-step genomic BLUP (SSGBLUP)] and using three strategies to handle missing pedigree [unknown parent groups (UPG), UPG with QP transformation in the $${\mathbf{H}}$$
H
matrix (EUPG) and metafounders (MF)].

Methods

We compared estimated breeding values (EBV) of selected rams at birth with the EBV of the same rams obtained each year from the first daughters with phenotypes up to 2017. We compared within and across models. Finally, we compared EBV at birth of the rams with and without genomic information.

Results

Within models, bias and over-dispersion were small (bias: 0.20 to 0.40 genetic standard deviations; slope of the dispersion: 0.95 to 0.99) except for model SSGBLUP-EUPG that presented an important over-dispersion (0.87). The estimates of accuracies confirm that the addition of genomic information increases the accuracy of EBV in young rams. The smallest bias was observed with BLUP-MF and SSGBLUP-MF. When we estimated dispersion by comparing a model with no markers to models with markers, SSGBLUP-MF showed a value close to 1, indicating that there was no problem in dispersion, whereas SSGBLUP-EUPG and SSGBLUP-UPG showed a significant under-dispersion. Another important observation was the heterogeneous behaviour of the estimates over time, which suggests that a single check could be insufficient to make a good analysis of genetic/genomic evaluations.

Conclusions

The addition of genomic information increases the accuracy of EBV of young rams in Manech Tête Rousse. In this population that has missing pedigrees, the use of UPG and EUPG in SSGBLUP produced bias, whereas MF yielded unbiased estimates, and we recommend its use. We also recommend assessing biases and accuracies using multiple truncation points, since these statistics are subject to random variation across years.
Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum
Authors: Luo Ying , Zhang Xiujie , Xu Jiahong , Zheng Yao , Pu Shouqin , Duan Zhizhen , Li Zhihao , Liu Guodao , Chen Jinhui , Wang Zhiyong
Published: August 2020

Background

Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. secundatum, limiting its application and development as a crop. Here, to provide a theoretical basis for further conservation, utilization, and classification of S. secundatum germplasm resources, we used phenotypic and molecular markers (single-nucleotide polymorphisms, SNPs; sequence-related amplified polymorphism, SRAP; inter-simple sequence repeat, ISSR) to analyze the genetic diversity of 49 S. secundatum accessions.

Results

Based on seven types of phenotypic data, the 49 S. secundatum accessions could be divided into three classes with great variation. We identified 1,280,873 SNPs in the 49 accessions, among which 66.22% were transition SNPs and 33.78% were transversion SNPs. Among these, C/T was the most common (19.12%) and G/C the least common (3.68%). Using 28 SRAP primers, 267 polymorphic bands were detected from the 273 bands amplified. In addition, 27 ISSR markers generated 527 amplification bands, all of which were polymorphic. Both marker types revealed a high level of genetic diversity, with ISSR markers showing a higher percentage of polymorphic loci (100%) than SRAP markers (97.8%). The genetic diversity of the accessions based on SRAP markers (h = 0.47, I = 0.66) and ISSR markers (h = 0.45, I = 0.64) supports the notion that the S. secundatum accessions are highly diverse. S. secundatum could be divided into three classes based on the evaluated molecular markers.

Conclusions

Phenotypic and molecular marker analysis using SNP, SRAP, and ISSR markers revealed great genetic variation among S. secundatum accessions, which were consistently divided into three classes. Our findings provide a theoretical basis for the genetic diversity and classification of S. secundatum. Our results indicate that SNP, SRAP and ISSR markers are reliable and effective for analyzing genetic diversity in S. secundatum. The SNPs identified in this study could be used to distinguish S. secundatum accessions.
Population analysis of the Korean native duck using whole-genome sequencing data
Authors: Lee Daehwan , Lee Jongin , Heo Kang-Neung , Kwon Kisang , Moon Youngbeen , Lim Dajeong , Lee Kyung-Tai , Kim Jaebum
Published: August 2020

Background

Advances in next-generation sequencing technologies have provided an opportunity to perform population-level comparative genomic analysis to discover unique genomic characteristics of domesticated animals. Duck is one of the most popular domesticated waterfowls, which is economically important as a source of meat, eggs, and feathers. The objective of this study is to perform population and functional analyses of Korean native duck, which has a distinct meat flavor and texture phenotype, using whole-genome sequencing data. To study the distinct genomic features of Korean native duck, we conducted population-level genomic analysis of 20 Korean native ducks together with 15 other duck breeds.

Results

A total of 15.56 million single nucleotide polymorphisms were detected in Korean native duck. Based on the unique existence of non-synonymous single nucleotide polymorphisms in Korean native duck, a total of 103 genes related to the unique genomic characteristics of Korean native duck were identified in comparison with 15 other duck breeds, and their functions were investigated. The nucleotide diversity and population structures among the used duck breeds were then compared, and their phylogenetic relationship was analyzed. Finally, highly differentiated genomic regions among Korean native duck and other duck breeds were identified, and functions of genes in those regions were examined.

Conclusions

This is the first study to compare the population of Korean native duck with those of other duck breeds by using whole-genome sequencing data. Our findings can be used to expand our knowledge of genomic characteristics of Korean native duck, and broaden our understanding of duck breeds.
S-layer associated proteins contribute to the adhesive and immunomodulatory properties of Lactobacillus acidophilus NCFM
Authors: Klotz Courtney , Goh Yong Jun , O’Flaherty Sarah , Barrangou Rodolphe
Published: August 2020

Background

Surface layers (S-layers) are two-dimensional crystalline arrays of repeating proteinaceous subunits that form the outermost layer of many bacterial cell envelopes. Within theLactobacillusgenus, S-layer presence is frequently associated with probiotic-relevant properties such as improved adherence to host epithelial cells and modulation of the immune response. However, recent studies have demonstrated that certain S-layer functions may be supplemented by a novel subset of proteins embedded within its lattice, termed S-layer associated proteins (SLAPs). In the following study, fourLactobacillus acidophilusNCFM SLAPs (LBA0046, LBA0864, LBA1426, and LBA1539) were selected for in silico and phenotypic assessment.

Results

Despite lacking any sequence similarity or catalytic domains that may indicate function, the genes encoding the four proteins of interest were shown to be unique to S-layer-forming, host-adapted lactobacilli species. Likewise, their corresponding deletion mutants exhibited broad, host-relevant phenotypes including decreased inflammatory profiles and reduced adherence to Caco-2 intestinal cells, extracellular matrices, and mucin in vitro.

Conclusions

Overall, the data presented in this study collectively links several previously uncharacterized extracellular proteins to roles in the underlying host adaptive mechanisms ofL. acidophilus.
Differences between predicted outer membrane proteins of genotype 1 and 2 Mannheimia haemolytica
Authors: Clawson Michael L. , Schuller Gennie , Dickey Aaron M. , Bono James L. , Murray Robert W. , Sweeney Michael T. , Apley Michael D. , DeDonder Keith D. , Capik Sarah F. , Larson Robert L. , Lubbers Brian V. , White Brad J. , Blom Jochen , Chitko-McKown Carol G. , Brichta-Harhay Dayna M. , Smith Timothy P. L.
Published: August 2020

Background

Mannheimia haemolytica strains isolated from North American cattle have been classified into two genotypes (1 and 2). Although members of both genotypes have been isolated from the upper and lower respiratory tracts of cattle with or without bovine respiratory disease (BRD), genotype 2 strains are much more frequently isolated from diseased lungs than genotype 1 strains. The mechanisms behind the increased association of genotype 2 M. haemolytica with BRD are not fully understood. To address that, and to search for interventions against genotype 2 M. haemolytica, complete, closed chromosome assemblies for 35 genotype 1 and 34 genotype 2 strains were generated and compared. Searches were conducted for the pan genome, core genes shared between the genotypes, and for genes specific to either genotype. Additionally, genes encoding outer membrane proteins (OMPs) specific to genotype 2 M. haemolytica were identified, and the diversity of their protein isoforms was characterized with predominantly unassembled, short-read genomic sequences for up to 1075 additional strains.

Results

The pan genome of the 69 sequenced M. haemolytica strains consisted of 3111 genes, of which 1880 comprised a shared core between the genotypes. A core of 112 and 179 genes or gene variants were specific to genotype 1 and 2, respectively. Seven genes encoding predicted OMPs; a peptidase S6, a ligand-gated channel, an autotransporter outer membrane beta-barrel domain-containing protein (AOMB-BD-CP), a porin, and three different trimeric autotransporter adhesins were specific to genotype 2 as their genotype 1 homologs were either pseudogenes, or not detected. The AOMB-BD-CP gene, however, appeared to be truncated across all examined genotype 2 strains and to likely encode dysfunctional protein. Homologous gene sequences from additional M. haemolytica strains confirmed the specificity of the remaining six genotype 2 OMP genes and revealed they encoded low isoform diversity at the population level.

Conclusion

Genotype 2 M. haemolytica possess genes encoding conserved OMPs not found intact in more commensally prone genotype 1 strains. Some of the genotype 2 specific genes identified in this study are likely to have important biological roles in the pathogenicity of genotype 2 M. haemolytica, which is the primary bacterial cause of BRD.
Development and evaluation of an up-converting phosphor technology-based lateral flow assay for rapid and quantitative detection of Coxiella burnetii phase I strains
Authors: Zhang Pingping , Jiao Jun , Zhao Yong , Fu Mengjiao , Wang Jin , Song Yajun , Zhou Dongsheng , Wang Yongqiang , Wen Bohai , Yang Ruifu , Xiong Xiaolu
Published: August 2020

Background

Coxiella burnetiiis an obligate intracellular Gram-negative bacterium that causes a zoonotic disease commonly called Q fever globally. In this study, an up-converting phosphor technology-based lateral flow (UPT-LF) assay was established for the rapid and specific detection of phase I strains ofC. burnetii.

Results

Specific monoclonal antibodies (10B5 and 10G7) againstC. burnetiiphase I strains were prepared and selected for use in the UPT-LF assay by the double-antibody-sandwich method. The detection sensitivity of theCoxiella-UPT-LF was 5 × 104GE/ml for a purifiedC. burnetiiphase I strain and 10 ng/ml for LPS ofC. burnetiiNine Mile phase I (NMI). Good linearity was observed forC. burnetiiphase I and NMI LPS quantification (R2 ≥ 0.989). The UPT-LF assay also exhibited a high specificity toC. burnetii, without false-positive results even at 108GE/ml of non-specific bacteria, and good inclusivity for detecting different phase I strains ofC. burnetii. Moreover, the performance of theCoxiella-UPT-LF assay was further confirmed using experimentally and naturally infected samples.

Conclusions

Our results indicate thatCoxiella-UPT-LF is a sensitive and reliable method for rapid screening ofC. burnetii,suitable for on-site detection in the field.
Evaluation of approaches for multiple imputation of three-level data
Authors: Wijesuriya Rushani , Moreno-Betancur Margarita , Carlin John B. , Lee Katherine J.
Published: August 2020

Background

Three-level data arising from repeated measures on individuals who are clustered within larger units are common in health research studies. Missing data are prominent in such longitudinal studies and multiple imputation (MI) is a popular approach for handling missing data. Extensions of joint modelling and fully conditional specification MI approaches based on multilevel models have been developed for imputing three-level data. Alternatively, it is possible to extend single- and two-level MI methods to impute three-level data using dummy indicators and/or by analysing repeated measures in wide format. However, most implementations, evaluations and applications of these approaches focus on the context of incomplete two-level data. It is currently unclear which approach is preferable for imputing three-level data.

Methods

In this study, we investigated the performance of various MI methods for imputing three-level incomplete data when the target analysis model is a three-level random effects model with a random intercept for each level. The MI methods were evaluated via simulations and illustrated using empirical data, based on a case study from the Childhood to Adolescence Transition Study, a longitudinal cohort collecting repeated measures on students who were clustered within schools. In our simulations we considered a number of different scenarios covering a range of different missing data mechanisms, missing data proportions and strengths of level-2 and level-3 intra-cluster correlations.

Results

We found that all of the approaches considered produced valid inferences about both the regression coefficient corresponding to the exposure of interest and the variance components under the various scenarios within the simulation study. In the case study, all approaches led to similar results.

Conclusion

Researchers may use extensions to the single- and two-level approaches, or the three-level approaches, to adequately handle incomplete three-level data. The two-level MI approaches with dummy indicator extension or the MI approaches based on three-level models will be required in certain circumstances such as when there are longitudinal data measured at irregular time intervals. However, the single- and two-level approaches with the DI extension should be used with caution as the DI approach has been shown to produce biased parameter estimates in certain scenarios.