bluuebunny/crossref_metadata_2025_split huggingface dataset:
Current Risk Stratification Systems Are Not Generalizable across Surgical Technique in Midline Ventral Hernia Repair
Authors: Fligor Jennifer E. , Lanier Steven T. , Dumanian Gregory A. 
Published: March 2017

Background:
Current ventral hernia repair risk estimation tools focus on patient comorbidities with the goal of improving clinical outcomes through improved patient selection. However, their predictive value remains unproven.

Methods:
Outcomes of patients who underwent midline ventral hernia repair with retrorectus placement of mid-weight soft polypropylene mesh between 2010 and 2015 were retrospectively reviewed and compared with predicted wound-related complication risk from 3 tools in the literature: Carolinas Equation for Determining Associated Risk, the Ventral Hernia Working Group (VHWG) grade, and a modified VHWG grade.

Results:
A total of 101 patients underwent hernia repair. Mean age was 56 years and mean body mass index was 29 m/kg2 (range, 18–51 m/kg2). We found no significant relationship between the risk estimated by Carolinas Equation for Determining Associated Risk (B = 1.45, P = 0.61) and actual wound-related complications. VHWG grades >1 were not statistically different with regard to rate of wound complication compared with VHWG grade 1 (grade 2: B = 0.05, P = 0.95; grade 3: B = −0.21, P = 0.86; grade 4: B = 2.57, P = 0.10). Modified VHWG grades >1 were not statistically different with regard to rate of wound complication compared with modified VHWG grade 1 (grade 2: B = 0.20, P = 0.80; grade 3: B = 1.03, P = 0.41).

Conclusions:
Current risk stratification tools overemphasize patient factors, ignoring the importance of technique in minimizing complications and recurrence. We attribute our low complication rate to retrorectus placement of a narrow, macroporous polypropylene mesh with up to 45 suture fixation points for force distribution in contrast to current strategies that employ wide meshes with minimal fixation.
Pediatric Melanoma: A 35-year Population-based Review
Authors: Dean Paige H. , Bucevska Marija , Strahlendorf Caron , Verchere Cynthia 
Published: March 2017

Background:
Melanoma is a rare neoplasm in the pediatric population. Recent publications suggest a possible increase in incidence over the past few decades. The purpose of this study was to analyze trends in pediatric patients diagnosed with malignant melanoma in British Columbia (BC) in the past 35 years.

Methods:
A retrospective review was performed. All patients in BC diagnosed with melanoma before 18 years of age from 1979 to 2014 were included. Patient demographics, melanoma description, treatment details, and survival data were collected.

Results:
Seventy-eight subjects were identified for the study. Patients were equally distributed by sex. Sixty-one (78%) of the subjects were diagnosed in the postpubertal age (≥12 years old). The most common sites of occurrence were the extremities (n = 33) and the trunk (n = 27), with the location on the trunk showing the highest mortality rate (22%). All patients were surgically treated and some had additional chemotherapy (12) and/or radiotherapy (12). Fatal outcome was recorded in 12 of the 78 subjects, 10 of whom had postpubertal diagnosis. The average time from date of diagnosis to date of death was 9.3 years.

Conclusions:
The incidence of melanoma in the pediatric population remains exceedingly rare: less than 2.5 per million children younger than 18 years. The diagnosis is rarely made before puberty; the incidence is equal in males and females and has not changed over a 35-year time period in BC. Our study shows 85% survival with the majority of patients having had surgical excision only.
Brief Report: Randomized, Double-Blind Comparison of Tenofovir Alafenamide (TAF) vs Tenofovir Disoproxil Fumarate (TDF), Each Coformulated With Elvitegravir, Cobicistat, and Emtricitabine (E/C/F) for Initial HIV-1 Treatment: Week 144 Results
Authors: Arribas José R. , Thompson Melanie , Sax Paul E. , Haas Bernhard , McDonald Cheryl , Wohl David A. , DeJesus Edwin , Clarke Amanda E. , Guo Susan , Wang Hui , Callebaut Christian , Plummer Andrew , Cheng Andrew , Das Moupali , McCallister Scott 
Published: March 2017

Abstract:
In 2 double-blind phase 3 trials, 1733 antiretroviral-naive adults were randomized to tenofovir alafenamide (TAF) or tenofovir disoproxil fumarate (TDF), each coformulated with elvitegravir/cobicistat/emtricitabine (E/C/F). At 144 weeks, TAF was superior to TDF in virologic efficacy, with 84.2% vs 80.0% having HIV-1 RNA <50 copies/mL (difference 4.2%; 95% confidence interval: 0.6% to 7.8%). TAF had less impact than TDF on bone mineral density and renal biomarkers. No participants on TAF had renal-related discontinuations vs 12 on TDF (P < 0.001), with no cases of proximal tubulopathy for TAF vs 4 for TDF. There were greater increases in lipids with TAF vs TDF, with no difference in the total cholesterol to high-density lipoprotein ratio. For initial HIV therapy, E/C/F/TAF is superior to E/C/F/TDF in efficacy and bone and renal safety.
A Comprehensive Assessment of the Genetic Determinants inSalmonellaTyphimurium for Resistance to Hydrogen Peroxide Using Proteogenomics
Authors: Karash Sardar , Liyanage Rohana , Qassab Abdullah , Lay Jackson O. , Kwon Young Min 
Published: March 2017

AbstractSalmonellais an intracellular pathogen that infects a wide range of hosts and can survive in macrophages. An essential mechanism uses by the macrophages to eradicateSalmonellais production of reactive oxygen species. Here, we used proteogenomics to determine the candidate genes and proteins that have a role in resistance ofS.Typhimurium to H2O2. For Tn-seq, a highly saturated Tn5 insertion library was grownin vitrounder either 2.5 (H2O2L) or 3.5 mM H2O2(H2O2H). We identified two sets of overlapping genes that are required for resistance ofS. Typhimurium to H2O2L and H2O2H, and the results were validated via phenotypic evaluation of 50 selected mutants. The enriched pathways for resistance to H2O2included DNA repair, aromatic amino acid biosynthesis (aroBK), Fe-S cluster biosynthesis, iron homeostasis and a putative iron transporter system (ybbKLM), flagellar genes (fliBC), H2O2scavenging enzymes, and DNA adenine methylase. Proteomics revealed that the majority of essential proteins, including ribosomal proteins, were downregulated upon exposure to H2O2. A subset of proteins identified by Tn-seq were analyzed by targeted proteomics, and 70% of them were upregulated upon exposure to H2O2. The identified candidate genes will deepen our understanding about mechanisms ofS. Typhimurium survival in macrophages, and can be exploited to develop new antimicrobial drugs.
Multiple reference genome sequences of hot pepper reveal the massive evolution of plant disease resistance genes by retroduplication
Authors: Kim Seungill , Park Jieun , Yeom Seon-In , Kim Yong-Min , Seo Eunyoung , Kim Ki-Tae , Kim Myung-Shin , Lee Je Min , Cheong Kyeongchae , Shin Ho-Sub , Kim Saet-Byul , Han Koeun , Lee Jundae , Park Minkyu , Lee Hyun-Ah , Lee Hye-Young , Lee Young-sill , Oh Soohyun , Lee Joo Hyun , Choi Eunhye , Choi Eunbi , Lee So Eui , Jeon Jongbum , Kim Hyunbin , Choi Gobong , Song Hyeunjeong , Lee JunKi , Lee Sang-Choon , Kwon Jin-Kyung , Lee Hea-Young , Koo Namjin , Hong Yunji , Kim Ryan W. , Kang Won-Hee , Huh Jin Hoe , Kang Byoung-Cheorl , Yang Tae-Jin , Lee Yong-Hwan , Bennetzen Jeffrey L. , Choi Doil 
Published: March 2017

SummaryTransposable elements (TEs) provide major evolutionary forces leading to new genome structure and species diversification. However, the role of TEs in the expansion of disease resistance gene families has been unexplored in plants. Here, we report high-qualityde novogenomes for two peppers (Capsicum baccatumandC. chinense) and an improved reference genome (C. annuum). Dynamic genome rearrangements involving translocations among chromosome 3, 5 and 9 were detected in comparison betweenC. baccatumand the two other peppers. The amplification ofathilaLTR-retrotransposons, members of thegypsysuperfamily, led to genome expansion inC. baccatum.In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs exhibited great abundance across the angiosperms, with most cases lineage-specific and thus recent events. Our study revealed that retroduplication has played key roles in the emergence of new disease-resistance genes in plants.
Maintaining maximal metabolic flux by gene expression control
Authors: Planqué Robert , Hulshof Josephus , Teusink Bas , Hendriks Johan , Bruggeman Frank J. 
Published: March 2017

SummaryMany evolutionarily successful bacteria attain high growth rates across growth-permissive conditions. They express metabolic networks that synthesise all cellular components at a high rate. Metabolic reaction rates are bounded by the concentration of the catalysing enzymes and cells have finite resources available for enzyme synthesis. Therefore, bacteria that grow fast should express needed metabolic enzymes at precisely tuned concentrations. To maintain fast growth in a dynamic environment, cells should adjust gene expression of metabolic enzymes. The activity of many of the associated transcription factors is regulated by their binding to intracellular metabolites. We study optimal metabolite-mediated regulation of metabolic-gene expression that preserves maximisation of metabolic fluxes across varying conditions. We logically derive the underlying control logic of this type of optimal regulation, which we term ‘Specific Flux (q) Optimization by Robust Adaptive Control’ (qORAC), and illustrate it with several examples. We show that optimal metabolic flux can be maintained in the face ofKchanging parameters only if the number of transcription-factor-binding metabolites is at least equal toK.qORAC-regulation of metabolism can generally be achieved with basic biochemical interactions, indicating that metabolism can operate close to optimality. The theory that we present is directly applicable to synthetic biology, biotechnology and fundamental studies of the regulation of metabolism.
“I feel proud we are moving forward”: safeguarding mindfulness for vulnerable student and teacher wellbeing in a community college
Authors: Burrows Leigh 
Published: March 2017

Purpose
The purpose of this paper is to report on a study conducted for the purpose of learning more about the mindfulness experiences of college students and their teachers. To assist in developing a more inclusive approach to the teaching of mindfulness tailored to the individual needs of more vulnerable students and to inform teacher training and curriculum development.

Design/methodology/approach
This three-phase phenomenological study involved face-to-face and online contact with community college students and teachers involved in courses that incorporated mindfulness meditation. The findings from interviews with students in phase 1 were shared with teachers in phase 2 along with suggestions for safeguarding in phase 3 but initial results are promising as a number of safeguards have already been put into place.

Findings
This study found that mindfulness meditation is not necessarily a positive experience for vulnerable college students and their teachers and that there was a need for more teacher training, knowledge and ongoing support about the effects of some mindfulness meditations on some vulnerable students and how to adjust their intensity.

Research limitations/implications
While this is a small qualitative study, the majority of students interviewed reported unusual experiences. This this is not well known in the literature on mindfulness in higher education, and a search of the clinical literature supports the findings that significant safeguards and adjustments are needed for mindfulness meditation for vulnerable students in educational, non-clinical settings. Further research is needed.

Practical implications
An implication of this study is that mindfulness meditation in its current form is likely to be unsuitable for vulnerable students. Practical recommendations for safeguarding mindfulness in higher education are already being trialed, as mentioned in this paper and will be the subject of more extensive exploration in another paper.

Social implications
There are significant implications in these findings that the potential harmful effects of mindfulness may be overlooked and may be more commonly experienced than is currently realized especially for individuals with a history of trauma, with addictions, mental health difficulties or self-harm.

Originality/value
An innovation in this study is its methodology which drew out students’ and teachers’ own experience of mindfulness meditation in their own words when most mindfulness studies are quantitative and tend to focus on outcomes before understanding. In addition, the findings were presented directly to teachers making it possible to see how little they knew about their students’ experiences. This created an opening and a willingness to adopt safeguarding recommendations.
Negotiating meaning – the experience of community aged care
Authors: Doyle Susanna 
Published: March 2017

Purpose
A framework for achieving what Heidegger referred to as a “fusion of horizons” of understanding, was developed during a study into the experience of a group of older adults receiving care. The paper aims to discuss this issue.

Design/methodology/approach
The interpretive hermeneutic phenomenological methodology provided strategies for enabling a researcher to shift his or her understanding to be closer to that of the older adult receiving care, to better understand the experience of receiving care from the perspective of a recipient. Older adults participated in research exploring their everyday lived experiences, and contributed to the researcher’s understanding of the personal impact of care.

Findings
The older adults in this study perceived care in essentially relational terms, and raised the importance of maintaining personal autonomy and relationships as central to maintain meaning in daily life. This framework for successfully achieving a “fusion of horizons” during research is discussed and proposed as a potential strategy for also supporting active participation by adults in their own care provision.

Originality/value
This strategy might be used as a way of enhancing the engagement, safety and satisfaction of older adults, thereby also assisting to protect them from potentially negative influences of power differentials impacting on their care experience.
Breaking white silences in South African-Dutch collaboration in higher education
Authors: Kamsteeg Frans , Wels Harry 
Published: March 2017

PurposeThe purpose of this paper is to show the complex positionality and the complexity that comes with the study of whiteness in South African higher education by Dutch, white academics. This complexity stems from the long-standing relationship between Dutch universities, the Vrije Universiteit Amsterdam (VUA) in particular, with their South African counterparts, which predominantly supported apartheid with reference to a shared religious (Protestant) background.Design/methodology/approachThe paper rests upon a literature review of the development of South African higher education, and an assessment of the prominent role played by the Dutch Vrije Universiteit in support of the all-white, Afrikaans Potchefstroom University (presently North-West University). The authors, who are both involved in the institutional cooperation between Vrije Universiteit and South African universities, reflect on the complexity of this relationship by providing auto-ethnographic evidence from their own (religious) biography.FindingsThe paper reflects the ambiguous historical as well as contemporary contexts and ties that bind Vrije Universiteit to South African universities, especially formerly Afrikaans-speaking ones. The ambiguity is about the comfort of sharing an identity with formerly Afrikaans-speaking universities, on the one hand, and the discomfort of historical and political complicities in a (still) segregated South African society on the other hand.Originality/valueThis auto-ethnographic paper breathes an atmosphere of a “coming out” that is not very common in academic writing. It is a reflection and testimony of a lifelong immersion in VUA-South African academic research relations in which historical, institutional, and personal contexts intermingle and lead to a unique positionality leading to “breaking silences” around these complex relations.
Measurement artefacts lead to false positives in the study of birdsong in noise
Authors: Brumm Henrik , Zollinger Sue Anne , Niemelä Petri T. , Sprau Philipp 
Published: March 2017

SummaryNumerous studies over the past decade have reported correlations between elevated levels of anthropogenic noise and a rise in the minimum frequency of acoustic signals of animals living in noisy habitats. This pattern appears to be occurring globally, and higher pitched signals have been hypothesized to be adaptive changes that reduce masking by low‐frequency traffic noise. However, the sound analysis methods most often used in these studies are prone to measurement errors that can result in false positives. In addition, the commonly used method of measuring frequencies visually from spectrograms might also lead to observer‐expectancy biases that could exacerbate measurement errors.We conducted an experiment to (i) quantify the size and type of errors that result from ‘eye‐balling’ frequency measurements with cursors placed manually on spectrograms of signals recorded in noise and no‐noise conditions, and (ii) to test whether observer expectations lead to significant errors in frequency measurements. We asked 54 volunteers, blind to the true intention of our study, to visually measure the minimum frequency of a variety of natural and synthesized bird sounds, recorded either in noise, or no‐noise conditions. Test subjects were either informed or uninformed about the hypothesized results of the measurements.Our results demonstrate that inappropriate methodology in acoustic analysis can yield false positives with effect sizes as large, or even larger, than those reported in published studies. In addition to these measurement artefacts, psychological observer biases also led to false positives – when observers expected signals to have higher minimum frequencies in noise, they measured significantly higher minimum frequencies than uninformed observers, who had not been primed with any expectation.The use of improper analysis methods in bioacoustics can lead to the publication of spurious results. We discuss alternative methods that yield unbiased frequency measures and we caution that it is imperative for researchers to familiarize themselves both with the functions and limitations of their sound analysis programmes. In addition, observer‐expectancy biases are a potential source of error not only in the field of bioacoustics, but in any situation where measurements can be influenced by human subjectivity.
Spermatogenesis associated 22 is required for DNA repair and synapsis of homologous chromosomes in mouse germ cells
Authors: Hays E. , Majchrzak N. , Daniel V. , Ferguson Z. , Brown S. , Hathorne K. , La Salle S. 
Published: March 2017

SummaryAnalysis of the N‐ethyl‐N‐nitrosourea (ENU)‐induced repro42 mutation previously identified spermatogenesis associated 22 (Spata22) as a gene required for meiotic progression and fertility in both male and female mice, but its specific contribution to the process was unclear. Here, we report on a novel, null allele of Spata22 (Spata22Gt) and confirm its requirement for germ cell development. Similar to repro42 mutant mice, histological and mating analyses indicate that gametogenesis is profoundly affected in Spata22Gt/Gt males and females, resulting in infertility. Cytological examination confirms that germ cells do not progress beyond zygonema and meiotic arrest is linked to impairment of both synapsis and DNA repair. Analysis of SPATA22 distribution reveals that it localizes to foci associated with meiotic chromosomes during prophase I and that the number of foci peaks at zygonema; there are also more SPATA22 foci in oocytes than in spermatocytes. Furthermore, SPATA22 co‐localizes with a number of proteins involved in meiotic recombination, including RAD51, DMC1, and MLH1, and is present until mid‐pachynema, suggesting a role in resolution of recombination intermediates. In fact, SPATA22 co‐localizes with MLH1 in more than 20% of foci at pachynema. Analysis of Spata22Gt/Gt meiocytes confirms that SPATA22 is required for localization of MEIOB but not RPA (two proteins known to interact with SPATA22), and immunoblotting corroborates that production of MEIOB is indeed decreased in the absence of SPATA22. Together, these data suggest that SPATA22 is required for both meiotic recombination and synapsis during meiosis in mice.
Application of a Lumped Parameter Model to Study the Feasibility of Simultaneous Implantation of a Continuous Flow Ventricular Assist Device (VAD) and a Pulsatile Flow VAD in BIVAD Patients
Authors: Di Molfetta Arianna , Ferrari Gianfranco , Iacobelli Roberta , Filippelli Sergio , Fresiello Libera , Guccione Paolo , Toscano Alessandra , Amodeo Antonio 
Published: March 2017

AbstractThe aim of this work is to develop and test a lumped parameter model of the cardiovascular system to simulate the simultaneous use of pulsatile (P) and continuous flow (C) ventricular assist devices (VADs) on the same patient. Echocardiographic and hemodynamic data of five pediatric patients undergoing VAD implantation were retrospectively collected and used to simulate the patients' baseline condition with the numerical model. Once the baseline hemodynamic was reproduced for each patient, the following assistance modalities were simulated: (a) CVAD assisting the right ventricle and PVAD assisting the left ventricle (RCF + LPF), (b) CVAD assisting the left ventricle and PVAD assisting the right ventricle (LCF + RPF). The numerical model can well reproduce patients’ baseline. The cardiac output increases in both assisted configurations (RCF + LPF: +17%, LCF + RPF: +21%, P = ns), left (right) ventricular volumes decrease more evidently in the configuration LCF + RPF (RCF + LPF), left (right) atrial pressure decreases in the LCF + RPF (RCF + LPF) modality. The pulmonary arterial pressure slightly decreases in the configuration LCF + RPF and it increases with RCF + LPF. Left and right ventricular external work increases in both configurations probably because of the total cardiac output increment. However, left and right artero‐ventricular coupling improves especially in the LCF + RPF (−36% for the left ventricle and −21% for the right ventricle, P = ns). The pulsatility index decreases by 8.5% in the configuration LCF + RPF and increases by 6.4% with RCF + LPF (P = 0.0001). A numerical model could be useful to tailor on patients the choice of the VAD that could be implanted to improve the hemodynamic benefits. Moreover, a model could permit to simulate extreme physiological conditions and innovative configurations, as the implantation of both CVAD and PVAD on the same patient.