bluuebunny/crossref_metadata_2025_split huggingface dataset:
Untangling mechanisms of crude oil toxicity: linking gene expression, morphology and PAHs at two developmental stages in a cold-water fish
Authors: Sørhus Elin , Donald Carey E. , da Silva Denis , Thorsen Anders , Karlsen Ørjan , Meier Sonnich 
Published: September 2020

AbstractEarly life stages of fish are highly sensitive to crude oil exposure and thus, short term exposures during critical developmental periods could have detrimental consequences for juvenile survival. Here we administered crude oil to Atlantic haddock (Melanogrammus aeglefinus) in short term (3-day) exposures at two developmental time periods: before first heartbeat, from gastrulation to cardiac cone stage (early), and from first heartbeat to one day before hatching (late). A frequent sampling regime enabled us to determine immediate PAH uptake, metabolite formation and gene expression changes. In general, the embryotoxic consequences of an oil exposure were more severe in theearlyexposure animals. Oil droplet fouling in the highest doses resulted in severe cardiac and craniofacial abnormalities. Gene expression changes of Cytochrome 1 a,b,c and d (cyp1a,b,c,d), Bone morphogenetic protein 10 (bmp10), ABC transporter b1 (abcb1) and Rh-associated G-protein (rhag) were linked to PAH uptake, occurrence of metabolites of phenanthrene and developmental and functional abnormalities. We detected circulation-independent, oil-induced gene expression changes and separated phenotypes linked to proliferation, growth and disruption of formation events at early and late developmental stages. Our study gives an increased knowledge about developmentally dependent effects of crude oil toxicity. Thus, providing more knowledge and detail to new and several existing adverse outcome pathways of crude oil toxicity.Graphical abstractHighlightsOil droplet fouling occurred in the whole water column and increased the oil toxicity.Early exposure resulted in higher PAH uptake due to lower metabolism resulting in more severe abnormalities.A rapid and circulation-indepenent regulation ofbmp10suggested a direct oil-induced effect on calcium homeostasis.Expression ofrhagindicated a direct oil-induced effect on osmoregulatory cells and osmoregulation.Severe eye abnormalities especially in the late exposure was linked to inappropriate overexpression ofcyp1bin the eyes.
DBFOLD: An efficient algorithm for computing folding pathways of complex proteins
Authors: Bitran Amir , Jacobs William M. , Shakhnovich Eugene 
Published: September 2020

AbstractAtomistic simulations can provide valuable, experimentally-verifiable insights into protein folding mechanisms, but existingab initiosimulation methods are restricted to only the smallest proteins due to severe computational speed limits. The folding of larger proteins has been studied using native-centric potential functions, but such models omit the potentially crucial role of non-native interactions.Here, we present an algorithm, entitled DBFOLD, which can predict folding pathways for a wide range of proteins while accounting for the effects of non-native contacts. In addition, DBFOLD can predict the relative rates of different transitions within a protein’s folding pathway. To accomplish this, rather than directly simulating folding, our method combines equilibrium Monte-Carlo simulations, which deploy enhanced sampling, withunfoldingsimulations at high temperatures. We show that under certain conditions, trajectories from these two types of simulations can be jointly analyzed to compute unknown folding rates from detailed balance. This requires inferring free energies from the equilibrium simulations, and extrapolating transition rates from the unfolding simulations to lower, physiologically-reasonable temperatures at which the native state is marginally stable. As a proof of principle, we show that our method can accurately predict folding pathways and Monte-Carlo rates for the well-characterized Streptococcal protein G. We then show that our method significantly reduces the amount of computation time required to compute the folding pathways of large, misfolding-prone proteins that lie beyond the reach of existing direct simulation methods. Our algorithm, which is available online, can generate detailed atomistic models of protein folding mechanisms while shedding light on the role of non-native intermediates which may crucially affect organismal fitness and are frequently implicated in disease.Author summaryMany proteins must adopt a specific structure in order to function. Computational simulations have been used to shed light on the mechanisms of protein folding, but unfortunately, realistic simulations can typically only be run for small proteins, due to severe limits in computational speed. Here, we present a method to solve this problem, whereby instead of directly simulating folding from an unfolded state, we run simulations that allow for computation of equilibrium folding free energies, alongside high temperature simulations to compute unfolding rates. From these quantities, folding rates can be computed using detailed balance. Importantly, our method can account for the effects of nonnative contacts which transiently form during folding and must be broken prior to adoption of the native state. Such contacts, which are often excluded from simple models of folding, may crucially affect real protein folding pathways and are often observed in folding intermediates implicated in disease.
Tracking individual honeybees among wildflower clusters with computer vision-facilitated pollinator monitoring
Authors: Ratnayake Malika Nisal , Dyer Adrian G , Dorin Alan 
Published: September 2020

AbstractMonitoring animals in their natural habitat is essential for advancement of animal behavioural studies, especially in pollination studies. Non-invasive techniques are preferred for these purposes as they reduce opportunities for research apparatus to interfere with behaviour. One potentially valuable approach is image-based tracking. However, the complexity of tracking unmarked wild animals using video is challenging in uncontrolled outdoor environments. Out-of-the-box algorithms currently present several problems in this context that can compromise accuracy, especially in cases of occlusion in a 3D environment. To address the issue, we present a novel hybrid detection and tracking algorithm to monitor unmarked insects outdoors. Our software can detect an insect, identify when a tracked insect becomes occluded from view and when it re-emerges, determine when an insect exits the camera field of view, and our software assembles a series of insect locations into a coherent trajectory. The insect detecting component of the software uses background subtraction and deep learning-based detection together to accurately and efficiently locate the insect among a cluster of wildflowers.We applied our method to track honeybees foraging outdoors using a new dataset that includes complex background detail, wind-blown foliage, and insects moving into and out of occlusion beneath leaves and among three-dimensional plant structures. We evaluated our software against human observations and previous techniques. It tracked honeybees at a rate of 86.6% on our dataset, 43% higher than the computationally more expensive, standalone deep learning model YOLOv2. We illustrate the value of our approach to quantify fine-scale foraging of honeybees. The ability to track unmarked insect pollinators in this way will help researchers better understand pollination ecology. The increased efficiency of our hybrid approach paves the way for the application of deep learning-based techniques to animal tracking in real-time using low-powered devices suitable for continuous monitoring.
Mechanical principles governing the shapes of dendritic spines
Authors: Alimohamadi H. , Bell M.K. , Halpain S. , Rangamani P. 
Published: September 2020

AbstractDendritic spines are small, bulbous protrusions along the dendrites of neurons and are sites of excitatory postsynaptic activity. The morphology of spines has been implicated in their function in synaptic plasticity and their shapes have been well-characterized, but the potential mechanics underlying their shape development and maintenance have not yet been fully understood. In this work, we explore the mechanical principles that could underlie specific shapes using a minimal biophysical model of membrane-actin interactions. Using this model, we first identify the possible force regimes that give rise to the classic spine shapes – stubby, filopodia, thin, and mushroom-shaped spines. We also use this model to investigate how the spine neck might be stabilized using periodic rings of actin or associated proteins. Finally, we use this model to predict that the cooperation between force generation and ring structures can regulate the energy landscape of spine shapes across a wide range of tensions. Thus, our study provides insights into how mechanical aspects of actin-mediated force generation and tension can play critical roles in spine shape maintenance.
A snapshot of food supply chain in Wuhan under the COVID-19 pandemic
Authors: Min Shi , Zhang Xiaoheng , Li Gucheng 
Published: September 2020

PurposeThe objective is to have a better understanding of the impacts of the COVID-19 pandemic on food supply chain in Wuhan.Design/methodology/approachThrough a simplified flow, the authors qualitatively analyze the impacts of the COVID-19 pandemic on food supply chain. Data was gathered through a telephone survey of food suppliers in Wuhan.FindingsThe prevention measures of the COVID-19 pandemic had negative impacts on food supply chain in Wuhan. About 83.1% of food suppliers experienced a decrease in revenues. This is influenced by factors including food category on sale, purchase channel of food, food supplier's household registration and the number of the COVID-19 patients in the located community.Research limitations/implicationsDue to the limitation of available data, there is a lack of quantitative analysis on the impact on food supply chain. The sample size of food suppliers is limited.Practical implicationsThis study identifies the challenges in the food supply chain resulting from the control measures implemented during the COVID-19 pandemic in Wuhan and provides a reference for the design of control measures in other regions.Originality/valueThis study supplements the literature regarding the impact of public health emergencies such as the COVID-19 pandemic on food supply chain, especially food suppliers' revenues.
Supply chain corruption practices circumventing sustainability standards: wolves in sheep's clothing
Authors: Silvestre Bruno S. , Viana Fernando Luiz E. , Sousa Monteiro Marcelo de 
Published: September 2020

PurposeA growing number of private, voluntary and mandatory sustainability standards have recently emerged. However, supply chain corruption practices as mechanisms to circumvent sustainability standards have also grown and occur regularly. This paper strives to elaborate theory on the intersection of institutional theory, business corruption and the sustainability standards literature by investigating factors that influence the emergence of supply chain corruption practices.Design/methodology/approachBased on secondary data, four in-depth case studies of supply chain corruption practices are investigated through the use of adaptive theory and the method of constant comparisons to elaborate theory on this important phenomenon.FindingsThe paper suggests that although sustainability standards can improve supply chain sustainability performance, if they are adopted only symbolically and not substantively, unanticipated outcomes such as supply chain corruption may occur. The study proposes a typology of supply chain corruption practices, further explores the symbolic adoption of sustainability standards in supply chains and proposes the novel construct of “social isomorphism for corruption.” Since focal companies play central roles in leading supply chain corruption practices, we reason that they can also play a pivotal role in preventing supply chain corruption practices by promoting the substantive adoption of sustainability standards across their supply chains.Originality/valueThis paper elaborates theory on the challenging phenomenon of corruption in supply chains by linking the supply chain management literature to the corruption and the sustainability discourses and offers important insights to aid our understanding on the topic. It generates six propositions and four contributions to the sustainable supply chain management theory, practice and policy.
Net gains: a comparison of competitive balance between the ANZ Championship and Suncorp Super Netball
Authors: Wetherall Henry E.T. , Stewart Mark F. , Trinh Trong Anh 
Published: September 2020

PurposeCompetitive balance is critical for the survival of athletic leagues. A relationship between “uncertainty of outcome” and fan interest has been found in many sports all over the world. This paper examines competitive balance in professional netball in Australia and New Zealand by contrasting two competitions: the ANZ Championship, an elite Australasian competition that began in 2008 but was disbanded in 2016 as there was a perception of dominance by the Australian teams over their New Zealand rivals; and its Australian domestic replacement, Suncorp Super Netball, which started in 2017.Design/methodology/approachCompetitive balance is gauged in three broad ways: match result concentration, which looks at the evenness of each season; team dominance, where comparisons are made across several seasons; and within game equality, which examines the results of individual games.FindingsSeveral methods are used under each heading, with the results surprisingly showing that measured competitive balance was similar in the two competitions.Originality/valueIn sports management, quantitative analysis or sports economics, there are few published papers on netball. This is the first research to examine competitive balance in netball, and the findings have important ramifications for this women-only game, as it competes against other purveyors of professional sport.
Proposing student support model for postgraduate research education
Authors: Ahmad Tashfeen 
Published: September 2020

PurposeMany start pursuing graduate or postgraduate research based education, however few complete on time. The purpose of this paper is to conceptualize a postgraduate student support model which will facilitate students to complete their studies successfully and on time.Design/methodology/approachThe model was designed using authors viewpoint on this issue which was informed by literature and first-hand interactions with post graduate students and supervisors.FindingsAhmad's Student Support Model for Postgraduate Research Training proposes that students need support on three major dimension (Financial, Technical and Publishing) to complete degree on time. University and supervisor play critical role in this as they provide administrative and emotional support as they create learning environment for students. The model illustrates their role.Originality/valueThe model is useful for universities to ensure they provide students with all elements proposed. New supervisors can get ideas how to play their role in facilitating students to complete their degrees on time. Students can evaluate an institution before enrolling in research education if the institution has the elements proposed in the model.
Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation
Authors: Kaptan Damla , Penkov Sider , Zhang Xingyu , Gade Vamshidhar R. , Raghuraman Bharath Kumar , Galli Roberta , Sampaio Júlio L. , Haase Robert , Koch Edmund , Shevchenko Andrej , Zaburdaev Vasily , Kurzchalia Teymuras V. 
Published: September 2020

AbstractThe dauer larva of Caenorhabditis elegans, destined to survive long periods of food scarcity and harsh environment, does not feed and has a very limited exchange of matter with the exterior. It was assumed that the survival time is determined by internal energy stores. Here, we show that ethanol can provide a potentially unlimited energy source for dauers by inducing a controlled metabolic shift that allows it to be metabolized into carbohydrates, amino acids, and lipids. Dauer larvae provided with ethanol survive much longer and have greater desiccation tolerance. On the cellular level, ethanol prevents the deterioration of mitochondria caused by energy depletion. By modeling the metabolism of dauers of wild‐type and mutant strains with and without ethanol, we suggest that the mitochondrial health and survival of an organism provided with an unlimited source of carbon depends on the balance between energy production and toxic product(s) of lipid metabolism.
The analysis of surgical prognostic factors and molecular typing of locally advanced lung squamous cell carcinomas
Authors: Dong Ming , Liu Jinghao , Gong Hao , Li Xin , Song Zuoqing , Zhao Honglin , Wei Sen , Chen Gang , Zhou Qinghua , Liu Hongyu , Chen Jun 
Published: September 2020

AbstractLung squamous cell carcinoma (LSCC) is a common subtype of non‐small cell lung cancer (NSCLC), accounts for about 30% of all lung cancer, and has unique clinical and histologic characteristics. The predominant treatment of LSCC is surgical intervention. The purpose of this study was to explore the survival rates of the patients with primary LSCC after surgical treatment and the factors affecting prognosis. And also to analyze the molecular typing of local advanced LSCC of patients with various survival periods. We retrospectively evaluated the files of 170 patients with squamous NSCLC who were treated at the Department of Lung Cancer Surgery, Tianjin Medical University General Hospital, between January 2008 and December 2011. Univariate (Cox regression analysis) and multivariate (likelihood ratio) analyses were carried out for overall survival (OS) and the median survival duration. A P‐value of < .05 was defined as significant. And then, we detected the mutation of 56 genes related to lung cancer by next‐generation sequencing for two groups of lung squamous cell cancer patients, in which the OS was more than 3 years in one group and less than 1 year in the other group. In addition, we analysis the relationship between the molecular typing and the survival period. Next, we used the Cancer Genome Atlas (TCGA) database to compare the different patients’ clinical information with the genes, which have been analyzed in our patients’ tumor tissue samples.
Anti‐HBcand hepatitis B virusDNAamongHBsAg‐negative blood donors from the main central blood bank units in Eastern Libya
Authors: El‐Nabi Sobhy Hassab , El‐Garawani Islam , Ismail Faisal , Abdelsameea Eman 
Published: September 2020

SummaryBackgroundPost‐transfusion hepatitis B virus (PTHB) infection is still a public health problem in the world. In many developed countries, nucleic acid testing (NAT) for detection of Hepatitis B Virus (HBV)‐DNA has been implemented to enhance blood donation safety. In Libya, however, the testing for HBV infection is limited to the detection of HBV surface antigen (HBsAg) only.ObjectivesTo determine the frequency of anti‐Hepatitis B core antibody (HBc) and HBV‐DNA in HBsAg‐negative, anti‐HBc‐positive blood donors in the main Central Blood Bank Units (CBBUs) in eastern Libya.MethodsOne thousand blood samples were obtained from healthy blood donors at the five main CBBUs in eastern Libya. The samples were screened for HBsAg and anti‐HBc. Real‐time polymerase chain reaction (PCR) was carried out to detect HBV‐DNA in all anti‐HBc‐positive samples.ResultsA total of 94 (9.4%) donors were positive for anti‐HBc. Of the 94 anti‐HBc‐positive samples, 9 samples (9.5%) tested positive for HBV‐DNA by real‐time PCR.ConclusionThe rate of anti‐HBc among blood donors in this study (9.4%) was similar to that reported from other regions in the country. In the absence of advanced tests for the detection of HBV infection in blood donors, such as NAT, anti‐HBc should be routinely tested for, at least for first‐time donors.
The Multi Wavelength Arrayed Flexible PPG Sensing Patch for to Estimate Heart Rate and Blood Oxygen
Authors: Chen Yu-Ting , Tu Tse-Yi , Chao Paul C.-P. 
Published: September 2020

Abstract
This study aims to develop the Photoplethysmography (PPG) sensor patch for to estimate the heart rate (HR) and blood oxygen (SpO2). A newly developed multi wavelength arrayed flexible OLED-OPD PPG sensing patch elevates the performance of motion artifact for not only for heart rate estimation but also blood oxygen estimation. The PPG sensing patch ensures the long-time continuous monitoring of the PPG signal from the wrist artery during sleeping, walking and cycling. The accuracy of the HRs is 92% and the accuracy of SpO2 is 95%.
Qualitative research study on addressing barriers to healthy diet among low-income individuals at an urban, safety-net hospital
Authors: Cahill Erin , Schmidt Stacie R , Henry Tracey L , Kumar Gayathri , Berney Sara , Bussey-Jones Jada , Girard Amy Webb 
Published: September 2020

BackgroundSome American households experience food insecurity, where access to adequate food is limited by lack of money and other resources. As such, we implemented a free 6-month Fruit and Vegetable Prescription Program within a large urban safety-net hospital .Methods32 participants completed a baseline and postintervention qualitative evaluation about food-related behaviour 6 months after study completion. Deductive codes were developed based on the key topics addressed in the interviews; inductive codes were identified from analytically reading the transcripts. Transcripts were coded in MAXQDA V.12 (Release 12.3.2).ResultsThe information collected in the qualitative interviews highlights the many factors that affect dietary habits, including the environmental and individual influences that play a role in food choices people make. Participants expressed very positive sentiments overall about their programme participation.ConclusionsA multifaceted intervention that targets individual behaviour change, enhances nutritional knowledge and skills, and reduces socioeconomic barriers to accessing fresh produce may enhance participant knowledge and self-efficacy around healthy eating. However, socioeconomic factors remain as continual barriers to sustaining healthy eating over the long term. Ongoing efforts that address social determinants of health may be necessary to promote sustainability of behaviour change.