bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pervasive introgression of MHC genes in newt hybrid zones
Authors: Dudek K. , Gaczorek T. S. , Zieliński P. , Babik W. 
Published: July 2019

AbstractVariation in the vertebrate major histocompatibility complex (MHC) genes is crucial for fighting pathogen assault. Because new alleles confer a selective advantage, MHC should readily introgress between species, even under limited hybridization. Using replicated transects through two hybrid zones between strongly reproductively isolated newts, we demonstrated recent and ongoing MHC introgression. Its extent correlated with the age of contact. In the older zone, MHC similarity between species within transects exceeded that of between transects within species, implying pervasive introgression – a massive exchange of MHC genes, not limited to specific variants. In simulations, the observed pattern emerged under the combined action of balancing selection and hybridization, but not when these processes acted separately. Thus, massive introgression at advanced stages of divergence can introduce novel and restore previously lost MHC variation, boosting the adaptive potential of hybridizing taxa. In consequence, MHC genes may be the last to stop introgressing between incipient species.
Comparing the selective landscape of TLR7 and TLR8 across primates reveals unique sites under positive selection inAlouatta
Authors: Torosin Nicole S. , Argibay Hernan , Webster Timothy H. , Corneli Patrice Showers , Knapp Leslie A. 
Published: July 2019

AbstractAmong primates, susceptibility to yellow fever (YFV), a single-stranded (ss) RNA virus, ranges from complete resistance to high susceptibility. Howler monkeys (genusAlouatta) are the most susceptible to YFV. In order to identifyAlouatta-specific genetic factors that may be responsible for their susceptibility, we collected skin samples from howler monkey museum specimens of the speciesA. carayaandA. guariba clamitans. We compared the rate of nonsynonymous to synonymous (dN/dS) changes of Toll-like receptor (TLR) 7 and TLR8, the two genes responsible for detecting all ssRNA viruses, across the Primate order. Overall, we found that the TLR7 gene is under stronger purifying selection in howler monkeys compared to other New World and Old World primates, but TLR8 is under the same selective pressure. When we evaluateddN/dSat each codon, we found six codons under positive selection inAlouattaTLR8 and two codons under positive selection in TLR7. The changes in TLR7 are unique toA. guariba clamitansand are found in functionally important regions likely to affect detection of ssRNA viruses by TLR7/TLR8, as well as downstream signaling. These amino acid differences inA. guariba clamitansmay play a role in YFV susceptibility. These results have implications for identifying genetic factors affecting YFV susceptibility in primates.
Validating Minimally Invasive Laser Doppler Flowmetry for Serial Bone Perfusion Measurements in Mice
Authors: Hanne Nicholas J. , Easter Elizabeth D. , Cole Jacqueline H. 
Published: July 2019

AbstractIn vivo laser Doppler flowmetry (LDF) has previously been used to quantify blood perfusion accurately at a single timepoint in the murine tibial metaphysis. However, this procedure entailed substantial disruption to soft tissues overlying the bone and caused notable localized inflammation for several weeks after the procedure, impeding serial measurements in the same mouse. In this study, we tested a less invasive technique to measure perfusion in the tibia with LDF and validated that it can be used serially in the same mouse without causing inflammation or gait perturbations. Twenty 14-week-old C57Bl/6J mice were evenly divided into groups that either had daily treadmill exercise or remained sedentary. Within these activity groups, mice were evenly subdivided into groups that received LDF measurements either weekly or only once at the study endpoint. Bone perfusion was measured with LDF in the anteromedial region of the right tibial metaphysis. Serum concentrations of interleukin 6, incision site wound area, and interlimb coordination during gait were measured weekly for four weeks. Tibial perfusion did not differ significantly between exercise and sedentary groups within the weekly or endpoint-only LDF groups at any timepoint. Perfusion was significantly increased in the third week in the weekly LDF group relative to measurements in the second and fourth weeks. Ligation of the femoral artery caused consistent, rapid reductions in tibial perfusion, validating that LDF is sensitive to changes in tibial blood supply. Weekly LDF procedures did not adversely affect gait, as interlimb coordination during treadmill locomotion was similar between weekly and endpoint-only LDF groups at every timepoint. Images of the incision site show wound closure within one week, and serum concentrations of interleukin 6 were not significantly different between weekly and endpoint-only groups. Together, these findings demonstrate that our minimally invasive LDF technique can be used for serial in vivo measurements of intraosseous blood perfusion without inducing localized inflammation or negatively affecting gait patterns in mice.HighlightsModified, minimally invasive laser Doppler flowmetry (LDF) technique was validated for serial measures of tibial perfusion in mice.Weekly LDF procedures did not induce inflammation or alter gait patterns that could confound metrics of interest in bone studies.Ligation of the femoral artery confirmed the LDF technique measures functional perfusion within the bone.
Temporo-nasally biased moving grating selectivity in mouse primary visual cortex
Authors: Tolkiehn Marie , Schultz Simon R. 
Published: July 2019

AbstractOrientation tuning in mouse primary visual cortex (V1) has long been reported to have a random or “salt-and-pepper” organisation, lacking the structure found in cats and primates. Laminar in-vivo multi-electrode array recordings here reveal previously elusive structure in the representation of visual patterns in the mouse visual cortex, with temporo-nasally drifting gratings eliciting consistently highest neuronal responses across cortical layers and columns, whilst upward moving gratings reliably evoked the lowest activities. We suggest this bias in direction selectivity to be behaviourally relevant as objects moving into the visual field from the side or behind may pose a predatory threat to the mouse whereas upward moving objects do not. We found furthermore that direction preference and selectivity was affected by stimulus spatial frequency, and that spatial and directional tuning curves showed high signal correlations decreasing with distance between recording sites. In addition, we show that despite this bias in direction selectivity, it is possible to decode stimulus identity and that spatiotemporal features achieve higher accuracy in the decoding task whereas spike count or population counts are sufficient to decode spatial frequencies implying different encoding strategies.Significance statementWe show that temporo-nasally drifting gratings (i.e. opposite the normal visual flow during forward movement) reliably elicit the highest neural activity in mouse primary visual cortex, whereas upward moving gratings reliably evoke the lowest responses. This encoding may be highly behaviourally relevant, as objects approaching from the periphery may pose a threat (e.g. predators), whereas upward moving objects do not. This is a result at odds with the belief that mouse primary visual cortex is randomly organised. Further to this biased representation, we show that direction tuning depends on the underlying spatial frequency and that tuning preference is spatially correlated both across layers and columns and decreases with cortical distance, providing evidence for structural organisation in mouse primary visual cortex.
Investigation of a New Superhydrophobic, Oleophobic-Coated Biliary Duct Stent and its Preventive Effect on Biliary Mud in Vitro
Authors: Zhang Wei Xing , Ji Ya Li , Qian Yue Qin , Wan Xin Jian , Xu Zheng Jie 
Published: July 2019

AbstractBackground and AimA new type of superhydrophobic, oleophobic-coated biliary stent was created, and its characteristics and preventive effect on biliary mud deposition in vitro are studied herein.MethodsThe observational experiment included a bare stent group and coated stent group, with 10 stents per group. The groups were used in a model of the extracorporeal biliary perfusion system with bacterial infection, and the experiment was terminated when the stent was completely blocked. Changes of bile characteristics before and after the experiment, patency time, and amount of bile sludge deposition were compared between the groups. The t-test and analysis of variance were used to analyze the data.ResultsIn the bare stent group, contact angles of bile were about 80.4 degrees and 79.8 degrees before and after the experiment, respectively. There was no change in the effect of bile aversion after the experiment between the groups (P < 0.05). In the coated stent group, contact angles of bile changed from 143.3 degrees before the experiment to 135.7 degrees after the experiment; the effect of the coating decreased significantly after the experiment (P > 0.05). The patency times were 8 weeks and 23 weeks in the bare and coated stent groups, respectively (P > 0.05). Depositions of biliary mud were 47 mg and 13 mg in the bare and coated stent groups, respectively (P > 0.05).ConclusionThe superhydrophobic, oleophobic-coated biliary stent can repel bile better and play a role in preventing bile sludge deposition in the extracorporeal biliary perfusion system.
Exploring midwives’ understanding of respectful and non-abusive maternal care in Kumasi, Ghana: Qualitative Inquiry
Authors: Millicent Dzomeku Veronica , Bemah Bonsu Adwoa , Emmanuel Nakua Kweku , Pascal Agbadi , Jody Lori R. , Peter Donkor 
Published: July 2019

AbstractBackgroundVarious aspects of disrespect and abusive maternity care have received scholarly attention because of frequent reports of the phenomenon in most healthcare facilities globally, especially in low- and middle-income countries. However, the perspectives of skilled providers on respectful maternal care have not been extensively studied. Midwives’ knowledge of respectful maternity care is critical in designing any interventive measures to address the menace of disrespect and abuse in maternity care. Therefore, the present study sought to explore the views of midwives on respectful maternity care at a Teaching Hospital in Kumasi, Ghana.MethodsPhenomenological qualitative research design was employed in the study. Data were generated through individual in-depth interviews, which were audio-recorded and transcribed verbatim. Data saturation was reached with fifteen midwives. Open Code 4.03 was used to manage and analyse the data.FindingsThe midwives’ understanding of respectful maternity care was comprised of the following components: non-abusive care, consented care, confidential care, non-violation of childbearing women’s basic human rights, and non-discriminatory care. Probing questions to solicit midwives’ opinions on an evidenced-based component of respectful maternity care generated little information, suggesting that the midwives have a gap in knowledge regarding this component of respectful maternity care.ConclusionMidwives reported an understanding of most components of respectful maternity care, but their gap in knowledge on evidenced-based care requires policy attention and in-service training. To understand the extent to which this gap in knowledge can be generalized for midwives across Ghana to warrant a redesign of the national midwifery curriculum, the authors recommend a nationwide cross-sectional quantitative study.
CLEC-2 suppresses calcification in cultured osteoblasts
Authors: Kanai Takenori , Sawa Yoshihiko , Takara Kenyo , Kajiwara Koichiro , Fujita Takahiro , Sawa Naruhiko , Yamashita Junro , Sato Yoshiaki 
Published: July 2019

AbstractPodoplanin is the only counter-receptor of platelet CLEC-2 and is expressing on mature osteoblast, but there is no report on the role of podoplanin and CLEC-2 in calcification. This study aimed to investigate the role of podoplanin binding to CLEC-2 in the calcification of osteoblasts carrying homozygously deletedPdpnalleles (PdpnΔ/Δ) by heterozygously expressing collagen type I alpha 1 promoter (Col1a)-drivenCrerecombinase. There were no macroscopic abnormalities in the bone and dentin ofCol1a11-Cre;PdpnΔ/Δmice but the coccygeal bone medullary cavity was very narrow. In the quantitative analysis for alizarin red-stained products and alkaline phosphatase activities on the cultured calvarial osteoblasts, the amounts of calcified products and alkaline phosphatase activity of calvarial osteoblasts of bothPdpnfl/flandCol1a11-Cre;PdpnΔ/Δmice were significantly higher in the calcification medium than in the α-mem. Both the amounts of calcified products and alkaline phosphatase activity of calvarial osteoblasts fromPdpnfl/flmice were significantly lower in the calcification medium with CLEC-2 than without CLEC-2 while there were no significant differences in the amounts of calcified products and alkaline phosphatase activities of calvarial osteoblasts fromCol1a11-Cre;PdpnΔ/Δmice with CLEC-2. Platelet CLEC-2 may play a role in regulating the calcification via binding to podoplanin on mature osteoblasts expressing podoplanin in the medullary cavity of a part of the bone.
Evaluation of Model Fit of Inferred Admixture Proportions
Authors: Garcia-Erill Genís , Albrechtsen Anders 
Published: July 2019

AbstractModel based methods for genetic clustering of individuals such as those implemented instructureor ADMIXTURE allow to infer individual ancestries and study population structure. The underlying model makes several assumptions about the demographic history that shaped the analysed genetic data. One assumption is that all individuals are a result of K homogeneous ancestral populations that are all well represented in the data, while another assumption is that no drift happened after the admixture event. The histories of many real world populations do not conform to that model, and in that case taking the inferred admixture proportions at face value might be misleading. We propose a method to evaluate the fit of admixture models based on estimating the correlation of the residual difference between the true genotypes and the genotypes predicted by the model. When the model assumptions are not violated, the residuals from a pair of individuals are not correlated. In case of a bad fit, individuals with similar demographic histories have a positive correlation of their residuals. Using simulated and real data, we show how the method is able to detect a bad fit of inferred admixture proportions due to using an insufficient number of clusters K or to demographic histories that deviate significantly from the admixture model assumptions, such as admixture from ghost populations, drift after admixture events and non-discrete ancestral populations. We have implemented the method as an open source software that can be applied to both unphased genotypes and next generation sequencing data.
PyIOmica: Longitudinal Omics Analysis and Classification
Authors: Domanskyi Sergii , Piermarocchi Carlo , Mias George I. 
Published: July 2019

AbstractSummaryPyIOmica is an open-source Python package focusing on integrating longitudinal multiple omics datasets, characterizing, and classifying temporal trends. The package includes multiple bioinformatics tools including data normalization, annotation, classification, visualization, and enrichment analysis for gene ontology terms and pathways. Additionally, the package includes an implementation of visibility graphs to visualize time series as networks.Availability and implementationPyIOmica is implemented as a Python package (pyiomica), available for download and installation through the Python Package Index (PyPI) (https://pypi.python.org/pypi/pyiomica), and can be deployed using the Python import function following installation. PyIOmica has been tested on Mac OS X, Unix/Linux and Microsoft Windows. The application is distributed under an MIT license. Source code for each release is also available for download on Zenodo (https://doi.org/10.5281/zenodo.3342612).Contactgmias@msu.edu
The nemesis who stood tall: a tale of governance and leadership
Authors: Saha Arindam 
Published: July 2019

Learning outcomes
After a thorough briefing, classroom discussions and de-briefing, the students should be able to appreciate issues of leadership; understand challenges related to managing an organisation; and understand the aspects of organisational politics and power.

Case overview/synopsis
This real-life case study is based on a leading management institution of central India. The institute was quite successful in establishing its brand central India during 2011-2017 and is still going strong. The case here captures a change of leadership and the challenges/opportunities it posed to faculty and staff members. The case also intends to address the power struggle that ensued in later years of its functioning. The case is also about how the present leader would finally deal with it all. Students would be able to generate insights in leadership style, power and politics, employee retention, organisational decision-making and concerns in recruiting culturally fit employees.

Complexity academic level
Graduate level.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 1: Accounting and Finance
To do or not to do: the real state of real estate
Authors: Solangi Rukhman , Umrani Waheed Ali , Solangi Iqra , Memon Mumtaz Ali 
Published: July 2019

Learning outcomes
This case will enable students to develop an understanding of starting a single proprietorship business focusing on the real estate; understand the possible challenges that an entrepreneur faces in the beginning; apply ethical decision-making frame works when faced in ethically conflicting situation; andlook at the career anchoring theory.

Case overview/synopsis
The case study takes a look at the ways and means of starting a small business depending on the owner managers experience, capabilities and skills including networking which are germane to success. It also highlights the ethical issues that small business proprietors have to face in order to make money and grow. The setting of the case is a town in Sindh province of Pakistan, which setting generally represent the arena where such business (Single Proprietorship) develop and get involved in the economic development of a backward area. Finally, the case study highlights the significant but realistic expose of career anchor theory, which stipulates that people normally start with a job but switch jobs over their working life.

Complexity academic level
Graduate and undergraduate.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 3: Entrepreneurship.
Numerical identification of temperature dependent thermal conductivity using least squares method
Authors: Ivanova Anna , Migorski Stanislaw , Wyczolkowski Rafal , Ivanov Dmitry 
Published: July 2019

Purpose
This paper aims to considered the problem of identification of temperature-dependent thermal conductivity in the nonstationary, nonlinear heat equation. To describe the heat transfer in the furnace charge occupied by a homogeneous porous material, the heat equation is formulated. The inverse problem consists in finding the heat conductivity parameter, which depends on the temperature, from the measurements of the temperature in fixed points of the material.

Design/methodology/approach
A numerical method based on the finite-difference scheme and the least squares approach for numerical solution of the direct and inverse problems has been recently developed.

Findings
The influence of different numerical scheme parameters on the accuracy of the identified conductivity coefficient is studied. The results of the experiment carried out on real measurements are presented. Their results confirm the ones obtained earlier by using other methods.

Originality/value
Novelty is in a new, easy way to identify thermal conductivity by known temperature measurements. This method is based on special finite-difference scheme, which gives a resolvable system of algebraic equations. The results sensitivity on changes in the method parameters was studies. The algorithms of identification in the case of a purely mathematical experiment and in the case of real measurements, their differences and the practical details are presented.
Catastrophic health expenditure and its determinants in households with gastrointestinal cancer patients: evidence from new health system reform in Iran
Authors: Piroozi Bakhtiar , Zarei Bushra , Ghaderi Bayazid , Safari Hossein , Moradi Ghobad , Rezaei Satar , Ghaderi Mahfooz , Amirhosseini Shina , Mohamadi-Bolbanabad Amjad 
Published: July 2019

Purpose
The right to health for all people means that everyone should have access to the needed healthcare services without suffering from severe financial hardship. The purpose of this paper is to investigate the prevalence as well as the effective factors on facing catastrophic health expenditures (CHE) among gastrointestinal cancer patients and families in Kurdistan province in west of Iran after the implementation of Health Transformation Plan (HTP).

Design/methodology/approach
A cross-sectional study was carried out on 189 households with gastrointestinal cancer patients in Kurdistan province in 2018. Data were collected using World Health Survey questionnaire. A method developed by World Health Organization with the threshold of 40 percent household’s capacity to pay was used in order to measure the proportion of households facing CHE. Also, logistic regression was applied for identifying the effective factors on household’s exposure to CHE. Data were analyzed using STATA version 13.

Findings
Almost 73 percent (72.7 percent) of the households (n=117) faced the CHE. Not having supplementary health insurance (adjusted odds ratio (AOR): 3.8; 95% confidence interval: 1.3–10.8 (and having low socio-economic status (AOR: 7.1; 95% CI: 1.8–28.1) were the significant factors affecting the households’ exposure to CHE. In total, 57 and 1 percent of the studied households reported that having a gastrointestinal cancer patient at home had a significant effect on refraining from using health services by other family members.

Originality/value
The proportion of the studied households facing CHE was very high. This may indicate the weakness of health system as well as health insurance or the weakness of HTP in financial protection of fragile population.