bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell dynamic morphology classification using deep convolutional neural networks
Authors: Li Heng , Pang Fengqian , Shi Yonggang , Liu Zhiwen 
Published: May 2018

AbstractCell morphology is often used as a proxy measurement of cell status to understand cell physiology. Hence, interpretation of cell dynamic morphology is a meaningful task in biomedical research. Inspired by the recent success of deep learning, we here explore the application of convolutional neural networks (CNNs) to cell dynamic morphology classification. An innovative strategy for the implementation of CNNs is introduced in this study. Mouse lymphocytes were collected to observe the dynamic morphology, and two datasets were thus set up to investigate the performances of CNNs. Considering the installation of deep learning, the classification problem was simplified from video data to image data, and was then solved by CNNs in a self‐taught manner with the generated image data. CNNs were separately performed in three installation scenarios and compared with existing methods. Experimental results demonstrated the potential of CNNs in cell dynamic morphology classification, and validated the effectiveness of the proposed strategy. CNNs were successfully applied to the classification problem, and outperformed the existing methods in the classification accuracy. For the installation of CNNs, transfer learning was proved to be a promising scheme. © 2018 International Society for Advancement of Cytometry
An optimized protocol for large‐scale in situ sampling and analysis of volatile organic compounds
Authors: Nair Jyothi V. , Shanmugam Pragadheesh V. , Karpe Snehal D. , Ramakrishnan Uma , Olsson Shannon 
Published: May 2018

AbstractChemical ecology is an ever‐expanding field with a growing interest in population‐ and community‐level studies. Many such studies are hindered due to lack of an efficient and accelerated protocol for large‐scale sampling and analysis of chemical compounds. Here, we present an optimized protocol for such large‐scale study of volatiles. A large‐scale in situ study to understand role of semiochemicals in variation in mating success of lekking blackbuck was conducted. Suitable methods for sampling and statistical analysis were identified by testing and comparing the efficiencies of available techniques to reduce analysis time while retaining sensitivity and comprehensiveness. Solid‐phase extraction using polydimethylsiloxane, analysis using a semiautomated detection of retention time and base peak, and statistical analysis using random forest algorithm were identified as the most efficient methods for large‐scale in situ sampling and analysis of volatiles. The protocol for large‐scale volatile analysis can facilitate evolutionary and metaecological studies of volatiles in situ from all types of biological samples. The protocol has potential for wider application with the analysis and interpretation methods being suitable for all kinds of semiochemicals, including nonvolatile chemicals.
DNA methylation in adults and during development of the self‐fertilizing mangrove rivulus, Kryptolebias marmoratus
Authors: Fellous Alexandre , Labed‐Veydert Tiphaine , Locrel Mélodie , Voisin Anne‐Sophie , Earley Ryan L. , Silvestre Frederic 
Published: May 2018

AbstractIn addition to genetic variation, epigenetic mechanisms such as DNA methylation might make important contributions to heritable phenotypic diversity in populations. However, it is often difficult to disentangle the contributions of genetic and epigenetic variation to phenotypic diversity. Here, we investigated global DNA methylation and mRNA expression of the methylation‐associated enzymes during embryonic development and in adult tissues of one natural isogenic lineage of mangrove rivulus fish, Kryptolebias marmoratus. Being the best‐known self‐fertilizing hermaphroditic vertebrate affords the opportunity to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. Using the LUminometric Methylation Assay (LUMA), we described variable global DNA methylation at CpG sites in adult tissues, which differed significantly between hermaphrodite ovotestes and male testes (79.6% and 87.2%, respectively). After fertilization, an immediate decrease in DNA methylation occurred to 15.8% in gastrula followed by re‐establishment to 70.0% by stage 26 (liver formation). Compared to zebrafish, at the same embryonic stages, this reprogramming event seems later, deeper, and longer. Furthermore, genes putatively encoding DNA methyltransferases (DNMTs), Ten‐Eleven Translocation (TET), and MeCP2 proteins showed specific regulation in adult gonad and brain, and also during early embryogenesis. Their conserved domains and expression profiles suggest that these proteins play important roles during reproduction and development. This study raises questions about mangrove rivulus’ peculiar reprogramming period in terms of epigenetic transmission and physiological adaptation of individuals to highly variable environments. In accordance with the general‐purpose genotype model, epigenetic mechanisms might allow for the expression of diverse phenotypes among genetically identical individuals. Such phenotypes might help to overcome environmental challenges, making the mangrove rivulus a valuable vertebrate model for ecological epigenetic studies. The mangrove rivulus, Kryptolebias marmoratus, is the best‐known self‐fertilizing hermaphroditic vertebrate that allows to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. The reprogramming event is later, more dramatic and longer than in other described vertebrates. High evolutionary conservation and expression patterns of DNMT, TET, and MeCP2 proteins in K. marmoratus suggest biological roles for each member in gametogenesis and development.
Parallel evolution of site‐specific changes in divergent caribou lineages
Authors: Horn Rebekah L. , Marques Adam J. D. , Manseau Micheline , Golding Brian , Klütsch Cornelya F. C. , Abraham Ken , Wilson Paul J. 
Published: May 2018

AbstractThe parallel evolution of phenotypes or traits within or between species provides important insight into the basic mechanisms of evolution. Genetic and genomic advances have allowed investigations into the genetic underpinnings of parallel evolution and the independent evolution of similar traits in sympatric species. Parallel evolution may best be exemplified among species where multiple genetic lineages, descended from a common ancestor, colonized analogous environmental niches, and converged on a genotypic or phenotypic trait. Modern North American caribou (Rangifer tarandus) originated from three ancestral sources separated during the Last Glacial Maximum (LGM): the Beringian–Eurasian lineage (BEL), the North American lineage (NAL), and the High Arctic lineage (HAL). Historical introgression between the NAL and the BEL has been found throughout Ontario and eastern Manitoba. In this study, we first characterized the functional differentiation in the cytochrome‐b (cytB) gene by identifying nonsynonymous changes. Second, the caribou lineages were used as a direct means to assess site‐specific parallel changes among lineages. There was greater functional diversity within the NAL despite the BEL having greater neutral diversity. The patterns of amino acid substitutions occurring within different lineages supported the parallel evolution of cytB amino acid substitutions suggesting different selective pressures among lineages. This study highlights the independent evolution of identical amino acid substitutions within a wide‐ranging mammal species that have diversified from different ancestral haplogroups and where ecological niches can invoke parallel evolution.
2D Materials‐based Platforms for Electroanalysis Applications
Authors: Alarcon‐Angeles Georgina , Palomar‐Pardavé Manuel , Merkoçi Arben 
Published: May 2018

AbstractA new class of nanomaterials called “2D materials” (2DMs) is attracting recently the electrochemical sensing field due to the unique physicochemical properties associated to their chemical structure, formed by ultra‐thin layers. In this review, we summarize the recent advances in the electroanalysis area using 2DMs giving first a brief overview on the structure, synthesis and properties of these materials followed by the analysis of their advantages while used in the development of electrochemical sensors.
Effect of different concentrations of pulverized mesocarp of Citrus paradisi Macf. on the bromatological characteristics of spray‐dried lemon juice powder
Authors: Alcantara Marte Yanilka , Alcantara Marte Yulisa , Tejada Andrea Escotto , Ros Berruezo Gaspar 
Published: May 2018

AbstractThe aim of this research was to evaluate the effect of different concentrations of pulverized mesocarp of Citrus paradisi Macf. as a drying aid on the bromatological characteristics and yield of spray‐dried lemon juice powder. Five concentrations of grapefruit mesocarp encapsulant (0.4, 0.8, 1.2, 1.6, and 2.0% (w / w)) and maltodextrin DE 10 (1.2%, w / w) were evaluated as encapsulant agents. The highest yield (46.76%) was obtained with 1.2% of grapefruit encapsulant. Water activity and ash content were inversely proportional to the added encapsulant concentration. The highest moisture value was obtained with 0.4% and the highest soluble solids with 2.0%. For all treatments, the pH level did not change, except at 0.4% (it was lower). The concentrations of the encapsulants significantly affected the evaluated characteristics, except for the proteins.
Specifying the Dimensions of Aquatic Life Benchmark Values in Clear, Complete, and Justified Problem Formulations
Authors: Suter Glenn 
Published: May 2018

Abstract

Nations that develop water quality benchmark values have relied primarily on standard data and methods. However, experience with chemicals such as Se, ammonia, and tributyltin has shown that standard methods do not adequately address some taxa, modes of exposure, and effects. Development of benchmark values that are protective requires an explicit description of the issues, a problem formulation. In particular, the assessment endpoints and other dimensions should be specified for each chemical so that the necessary data will be obtained and appropriate analyses will be performed. Assessment endpoints specify the entity and attribute to be protected. In addition, the level of protection, including the magnitude of effect and the proportion effected, is specified. Magnitude and proportion are included because they are used to calculate the benchmark concentration. If uncertainty is considered in the benchmark, the proportion of the uncertainty distribution that is protected should be specified. Because effects are related to the duration of exposure and time for recovery, temporal dimensions should be specified. Clearly described exposure metrics are also needed because the relevant exposure parameter is not always total aqueous concentration. Finally, the benchmark may be applicable to particular geographic or climatological areas, water chemistries, taxa, or habitat types. Considering and justifying all the dimensions is likely to result in protective and more easily communicated benchmarks. Integr Environ Assess Manag 2018;14:631–638. Published 2018. This article is a US Government work and is in the public domain in the USA.

Key Points
Benchmark values for aquatic life are based on standard methods. Problem formulation provides an opportunity to identify conditions that make the standard method unsuitable. Problem formulation can be more effective if each of the dimensions of a benchmark value is formally characterized by weighing available evidence. The dimensions relate to the assessment endpoint, the level of protection, temporal dimensions, exposure metrics, and limits of applicability.
Comparison of materno‐fetal predictors and short‐term outcomes between early and late onset pre‐eclampsia in the low‐income setting of Douala, Cameroon
Authors: Nguefack Charlotte T. , Ako Mangwi A. , Dzudie Anastase T. , Nana Théophile N. , Tolefack Paul N. , Mboudou Emile 
Published: May 2018

AbstractObjectiveTo describe and compare materno‐fetal predictors and short‐term outcomes of early onset pre‐eclampsia (EOPE) and late onset pre‐eclampsia (LOPE) in Douala, Cameroon.MethodsThe present prospective hospital‐based cross‐sectional study included women with pre‐eclampsia attending obstetric units at four hospitals in Douala between December 1, 2016, and April 30, 2017. To determine maternal predictors, sociodemographic and medical data were recorded using a pretested questionnaire. Pregnancy outcomes, and maternal and fetal adverse events were recorded. Univariate and multivariate logistic regression analyses were used to examine associations.ResultsOf 170 participants, 58 (34.1%) had EOPE and 112 (65.9%) had LOPE. EOPE was associated with higher incidences of chronic hypertension (P=0.027) and history of pre‐eclampsia (P=0.003) compared with LOPE. Higher incidences of nulliparity and a different partner from prior pregnancy (P=0.024) were associated with LOPE. Women with EOPE had higher odds of acute kidney injury (odds ratio [OR] 6.67, 95% confidence interval [CI] 1.73–25.73) and HELLP (hemolysis, elevated liver enzyme, low platelets) syndrome (OR 10.47, 95% CI 1.19–91.9), and lower odds of deliveries without perinatal adverse events (OR 0.19, 95% CI 0.09–0.38), compared with patients with LOPE.ConclusionIn the low‐income setting of Douala, there was a higher rate of LOPE than EOPE. Factors associated with EOPE and LOPE varied, and outcomes were worse for women with EOPE.
Appreciating local variations in standardising health care data collection processes and tools: A case of health management information system in Tanzania
Authors: Mahundi Masoud Hussein , Chaula Hassani Badi , Igira Faraja 
Published: May 2018

AbstractThe need for integration of health information systems as realised in the 90s by the developing countries resulted into deliberate standardisation initiatives. Software systems, human resources, procedures, and data collection tools were all subjected to standardisation. This standardisation, however, has been so absolute that the local and permanent variations were not taken into consideration. This study sought to find out how the local variations within the health care provision units can be taken into consideration in the design of health care data collection processes and tools. It employed qualitative, case study design and had 3 data collection techniques: observations, semi‐structured interviews, and documents review. The study found out that success in standardising data collection tools and processes in health care settings can be achieved if standards are put into clusters as it is unrealistic to subject the different health facility types into the same standards. The study proposes 3 clusters of standards. The dispensary cluster which accounts for the majority of all health facilities and the hospital cluster which accounts for all advanced diagnosis and treatment facilities and the third, specialised hospital cluster which accounts for specialised services.
Host heme oxygenase‐1: Friend or foe in tackling pathogens?
Authors: Singh Nisha , Ahmad Zeeshan , Baid Navin , Kumar Ashwani 
Published: May 2018

AbstractInfectious diseases are a major challenge in management of human health worldwide. Recent literature suggests that host immune system could be modulated to ameliorate the pathogenesis of infectious disease. Heme oxygenase (HMOX1) is a key regulator of cellular signaling and it could be modulated using pharmacological reagents. HMOX1 is a cytoprotective enzyme that degrades heme to generate carbon monoxide (CO), biliverdin, and molecular iron. CO and biliverdin (or bilirubin derived from it) can restrict the growth of a few pathogens. Both of these also induce antioxidant pathways and anti‐inflammatory pathways. On the other hand, molecular iron can induce proinflammatory pathway besides making the cellular environment oxidative in nature. Since microbial infections often induce oxidative stress in host cells/tissues, role of HMOX1 has been analyzed in the pathogenesis of number of infections. In this review, we have described the role of HMOX1 in pathogenesis of bacterial infections caused by Mycobacterium species, Salmonella and in microbial sepsis. We have also provided a succinct overview of the role of HMOX1 in parasitic infections such as malaria and leishmaniasis. In the end, we have also elaborated the role of HMOX1 in viral infections such as AIDS, hepatitis, dengue, and influenza. © 2018 IUBMB Life, 70(9):869–880, 2018
PRKAR2B promotes prostate cancer metastasis by activating Wnt/β‐catenin and inducing epithelial‐mesenchymal transition
Authors: Sha Jianjun , Han Qing , Chi Chenfei , Zhu Yinjie , Pan Jiahua , Dong Baijun , Huang Yiran , Xia Weiliang , Xue Wei 
Published: May 2018

AbstractCastration‐resistant prostate cancers (CRPC) that occur after the failure of androgen‐blocking therapies cause most of the deaths in prostate cancer (PCa) patients. In a previous study we identified that PRKAR2B expression is upregulated in CRPC and possesses potentials to develop CRPC. Here we further investigated the underlying mechanism of PRKAR2B in regulating prostate cancer metastasis. We established an androgen‐independent LNCaPcell line (LNCaP‐AI), and investigated the function of PRKAR2B on regulating cell invasion in vitro and in vivo. We found that PRKAR2B expression was markedly increased in LNCaP‐AI cells and metastatic CRPC (mCRPC) tissues compared to LNCaP cells and primary PCa specimens, respectively. PRKAR2B level was significantly correlated with the Gleason score and lymph nodes metastasis in PCa. In vitro, PRKAR2B overexpression promoted cell invasion, whereas knockdown of PRKAR2B in CRPC cells inhibited cell invasion. PRKAR2B overexpression also promoted tumor metastasis in vivo. PRKAR2B resulted in a decreased expression of E‐cadherin and an increased expression of Vimentin, N‐cadherin, Fibronectin, indicating that PRKAR2B induced epithelial‐mesenchymal transition (EMT). PRKAR2B activated Wnt/β‐catenin signaling in CRPC cells. More important, inhibition of Wnt/β‐catenin attenuated PRKAR2B‐induced EMT and cancer cells invasion. Our results provided novel insights to PRKAR2B‐driven CRPC cell invasion and indicated that PRKAR2B might be served as a potential target for CRPC therapy.
Identification of problems in search strategies in Cochrane Reviews
Authors: Franco Juan Víctor Ariel , Garrote Virginia Laura , Escobar Liquitay Camila Micaela , Vietto Valeria 
Published: May 2018

ObjectiveSearch strategies are essential for the adequate retrieval of studies in a systematic review (SR). Our objective was to identify problems in the design and reporting of search strategies in a sample of new Cochrane SRs first published in The Cochrane Library in 2015.Study design and settingWe took a random sample of 70 new Cochrane SRs of interventions published in 2015. We evaluated their design and reporting of search strategies using the recommendations from the Cochrane Handbook for Systematic Reviews of Interventions, the Methodological Expectations of Cochrane Intervention Reviews, and the Peer Review of Electronic Search Strategies evidence‐based guideline.ResultsMost reviews complied with the reporting standards in the Cochrane Handbook and the Methodological Expectations of Cochrane Intervention Reviews; however, 8 SRs did not search trials registers, 3 SRs included language restrictions, and there was inconsistent reporting of contact with individuals and searches of the gray literature. We found problems in the design of the search strategies in 73% of reviews (95% CI, 60‐84%) and 53% of these contained problems (95% CI, 38‐69%) that could limit both the sensitivity and precision of the search strategies.ConclusionWe found limitations in the design and reporting of search strategies. We consider that a greater adherence to the guidelines could improve their quality.
Initiation of adjuvant therapy following surgical resection of pancreatic ductal adenocarcinoma (PDAC): Are patients from rural, remote areas disadvantaged?
Authors: Bertens Kimberly A. , Massman John D. , Helton Scott , Garbus Samuel , Mandelson Margaret M. , Lin Bruce , Picozzi Vincent J. , Biehl Thomas , Alseidi Adnan A. , Rocha Flavio G. 
Published: May 2018

Background and ObjectivesAlthough race and socioeconomic status have been shown to affect outcomes in pancreatic ductal adenocarcinoma (PDAC), the impact of rural residence on the delivery of adjuvant therapy (AT) has not been studied.MethodsPatients with resected PDAC were identified using the National Cancer Database (NCDB). Individuals were classified as living in a metro area, urban/rural adjacent to a metro area (URA), and urban/rural remote (URR) area. Multivariate logistic regression was used to assess geographic inhabitance as a predictor of receiving AT.ResultsA total of 32 521 individuals who underwent pancreatectomy for PDAC were identified. Univariate analysis demonstrated individuals in URR areas were less likely to receive adjuvant chemotherapy (ACT) than those living in URA or metro areas (55.3% vs 55.6% vs 58.8%, P = 0.011). However on multivariate analysis URR inhabitance was no longer a predictor of ACT (OR = 0.911 P = 0.125) or ART (OR = 0.953 P = 0.462). Cox proportional hazard modeling demonstrated URR inhabitance remained independently associated with poor OS (HR 1.076; 95% CI [1.008, 1.149], P < 0.029).ConclusionsURR inhabitance does not impact access to AT, however it is independently associated with a decreased OS. Attention must be focused on optimizing oncologic care to patients with disparate access to healthcare.
Upregulation of the adipokine genes ADIPOR1 and SPP1 is related to poor survival outcomes in colorectal cancer
Authors: Choe Eun K. , Yi Jin W. , Chai Young J. , Park Kyu J. 
Published: May 2018

BackgroundObesity is closely associated with colorectal cancer (CRC), but the underlying mechanism is unclear. We thus evaluated the expression of the adipokine gene family in CRC tissues and its clinicopathological implications.MethodsCorrelations between the mRNA expression levels of the adipokine gene family (ADIPOQ, ADIPOR1/2, LEP, LEPR, RETN, RETNLB, RBP4, SFRP5, NAMPT, and SPP1) in CRC tissue and clinicopathologic factors were analyzed using data from The Cancer Genome Atlas database.ResultsTissue samples from 369 patients were analyzed, and 82 deaths occurred during follow‐up (median, 670 days). Overall, mortality was associated with positive venous invasion, higher TNM stage, and increased ADIPOR1 (adiponectin receptor 1 gene) and SPP1 (secreted phosphoprotein gene 1) mRNA expression. Higher ADIPOR1 (odds ratio [OR]: 3.29, 95% confidence interval [CI]: 1.33‐8.13) and SPP1 (OR: 2.31, 95%CI: 1.49‐3.59) levels were independently associated with increased mortality. A Kaplan‐Meier survival analysis showed shorter overall survival times in patients with higher ADIPOR1 (P = 0.006) and SPP1 (P < 0.001) expression.ConclusionsUpregulation of ADIPOR1 and SPP1, among the adipokine gene family, in cancer tissue is associated with poor survival in CRC, suggesting a potential mechanism linking obesity and CRC. ADIPOR1 and SPP1 expression could become useful prognostic indicators after further validation.