bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semi‐automated scoring of triple‐probe FISH in human sperm using confocal microscopy
Authors: Branch Francesca , Nguyen GiaLinh , Porter Nicholas , Young Heather A. , Martenies Sheena E. , McCray Nathan , Deloid Glen , Popratiloff Anastas , Perry Melissa J. 
Published: July 2017

AbstractStructural and numerical sperm chromosomal aberrations result from abnormal meiosis and are directly linked to infertility. Any live births that arise from aneuploid conceptuses can result in syndromes such as Kleinfelter, Turners, XYY and Edwards. Multi‐probe fluorescence in situ hybridization (FISH) is commonly used to study sperm aneuploidy, however manual FISH scoring in sperm samples is labor‐intensive and introduces errors. Automated scoring methods are continuously evolving. One challenging aspect for optimizing automated sperm FISH scoring has been the overlap in excitation and emission of the fluorescent probes used to enumerate the chromosomes of interest. Our objective was to demonstrate the feasibility of combining confocal microscopy and spectral imaging with high‐throughput methods for accurately measuring sperm aneuploidy. Our approach used confocal microscopy to analyze numerical chromosomal abnormalities in human sperm using enhanced slide preparation and rigorous semi‐automated scoring methods. FISH for chromosomes X, Y, and 18 was conducted to determine sex chromosome disomy in sperm nuclei. Application of online spectral linear unmixing was used for effective separation of four fluorochromes while decreasing data acquisition time. Semi‐automated image processing, segmentation, classification, and scoring were performed on 10 slides using custom image processing and analysis software and results were compared with manual methods. No significant differences in disomy frequencies were seen between the semi automated and manual methods. Samples treated with pepsin were observed to have reduced background autofluorescence and more uniform distribution of cells. These results demonstrate that semi‐automated methods using spectral imaging on a confocal platform are a feasible approach for analyzing numerical chromosomal aberrations in sperm, and are comparable to manual methods. © 2017 International Society for Advancement of Cytometry
Characterization of companion animal pluripotent stem cells
Authors: Paterson Y.Z. , Kafarnik C. , Guest D.J. 
Published: July 2017

AbstractPluripotent stem cells have the capacity to grow indefinitely in culture and differentiate into derivatives of the three germ layers. These properties underpin their potential to be used in regenerative medicine. Originally derived from early embryos, pluripotent stem cells can now be derived by reprogramming an adult cell back to a pluripotent state. Companion animals such as horses, dogs, and cats suffer from many injuries and diseases for which regenerative medicine may offer new treatments. As many of the injuries and diseases are similar to conditions in humans the use of companion animals for the experimental and clinical testing of stem cell and regenerative medicine products would provide relevant animal models for the translation of therapies to the human field. In order to fully utilize companion animal pluripotent stem cells robust, standardized methods of characterization must be developed to ensure that safe and effective treatments can be delivered. In this review we discuss the methods that are available for characterizing pluripotent stem cells and the techniques that have been applied in cells from companion animals. We describe characteristics which have been described consistently across reports as well as highlighting discrepant results. Significant steps have been made to define the in vitro culture requirements and drive lineage specific differentiation of pluripotent stem cells in companion animal species. However, additional basic research to compare pluripotent stem cell types and define characteristics of pluripotency in companion animal species is still required. © 2017 International Society for Advancement of Cytometry
Switching from monoculture to polyculture farming benefits birds in oil palm production landscapes: Evidence from mist netting data
Authors: Yahya Muhammad S. , Syafiq Muhamad , Ashton‐Butt Adham , Ghazali Amal , Asmah Siti , Azhar Badrul 
Published: July 2017

AbstractMonoculture farming is pervasive in industrial oil palm agriculture, including those RSPO plantations certified as sustainably managed. This farming practice does not promote the maintenance of farmland biodiversity. However, little scientific attention has been given to polyculture farming in oil palm production landscapes. Polyculture farming is likely to increase the floristic diversity and stand structural complexity that underpins biodiversity. Mist nets were used to sample birds at 120 smallholdings in Peninsular Malaysia. At each site, 12 vegetation structure characteristics were measured. We compared bird species richness, abundance, and composition between monoculture and polyculture smallholdings and used predictive models to examine the effects of habitat quality on avian biodiversity. Bird species richness was significantly greater in polyculture than that of monoculture smallholdings. The number of fallen and standing, dead oil palms were also important positive predictors of species richness. Bird abundance was also strongly increased by standing and dead oil palms and decreased with oil palm stand height. Our results indicate that polyculture farming can improve bird species richness in oil palm production landscapes. In addition, key habitat variables that are closely associated with farming practices, such as the removal of dead trees, should and can be managed by oil palm growers in order to promote biodiversity. To increase the sustainability of oil palm agriculture, it is imperative that stakeholders modify the way oil palms are currently planted and managed. Our findings can guide policy makers and certification bodies to promote oil palm production landscapes that will function more sustainably and increase existing biodiversity of oil palm landscapes.
Logical Genetic Programming (LGP) Development for Irrigation Water Supply Hedging Under Climate Change Conditions
Authors: Ashofteh Parisa‐Sadat , Bozorg‐Haddad Omid , Loáiciga Hugo A. 
Published: July 2017

AbstractTraditional genetic programming (TGP) is herein enhanced by the addition of logical operators to form logical genetic programming (LGP). The LGP approach is applied to calculate hedging reservoir‐operation rules for the Aidoghmoush single‐purpose reservoir (north‐eastern Iran) to supply irrigation water during a 14‐year baseline operation period (1987–2000) and a climatically changed condition (2026–2039). The objective function of the hedging rule is to minimize the long‐term shortage ratio (LSR). Our results show that the LGP‐obtained hedging rule compares favourably with that obtained with the TGP approach, so that the former approach's objective function is 25 and 6% better than the latter's approach with the baseline and climate change conditions, respectively. The results obtained concerning the reliability, vulnerability and resiliency of water supply indicate that the LGP hedging operating rule decreases the water supply reliability by 34%, increases the vulnerability by 58%, and decreases the resiliency by 29% during climate change conditions compared with baseline conditions. Copyright © 2017 John Wiley & Sons, Ltd.
Population Pharmacokinetic Analysis of Vaginally and Intravenously Administered Oxytocin in Postmenopausal Women
Authors: Nielsen Elisabet I. , Al‐Saqi Shahla H. , Jonasson Aino F. , Uvnäs‐Moberg Kerstin 
Published: July 2017

AbstractOxytocin is a neuropeptide hormone used clinically for more than 50 years due to its ability to induce uterine contractions and milk ejection. Vagitocin is a vaginal oxytocin gel developed as a potential treatment of vaginal atrophy in postmenopausal women. The aim of this study was to characterize the oxytocin pharmacokinetics following vaginal and intravenous administration in postmenopausal women. Data from 33 participants enrolled in 2 clinical studies were used in the analysis, with a total of 651 observed oxytocin plasma concentrations, of which 78 were baseline observations, 178 observations following intravenous administration (10 IU), and 395 observations following vaginal administration (100 or 400 IU). The population pharmacokinetics of oxytocin was described using a 2‐compartment disposition model with a flexible parallel absorption model accounting for double‐peak profiles following vaginal administration. The clearance, volume of distribution at steady state, distribution half‐life, and terminal half‐life were estimated to be 27 L/h, 15 L, 5.5 minutes, and 1.2 hours, respectively. The bioavailability following vaginal administration was estimated to be 2.5% for the typical patient, but with considerable variability both between individuals (interindividual variability of 374%) and between occasions (interoccasion variability of 79%). The data and the developed model add new and important information as to the clinical pharmacokinetics of oxytocin.
Moving In and Moving Up? Labor Conditions and China's Changing Development Model
Authors: Yang Yujeong , Gallagher Mary 
Published: July 2017

SummaryFor the last decade, a large contingent of manufacturing firms in developmental zones on China's coast has moved to inland provinces. What are the implications of this move inland for Chinese workers? Research on labor conditions in the current period of economic globalization and mobile capital debates the existence of a “race to the bottom” in labor standards through the pressures of international capital mobility. These theories predict that as inland China develops and attracts a larger amount of foreign and domestic capital, inland governments will compete by offering cheap labor and lower or unenforced standards. Our argument in this paper is contrarian in that we propose the possibility of a positive relationship between the movement inland and labor conditions. We argue that the movement of manufacturing to inland China is not primarily about cheaper workers, but instead signals the beginning of a fundamental shift in the development model through the employment of a localized workforce. Having more workers from within the province, local governments in inland provinces will be more inclined to develop inclusive social policies and improve labor conditions. Local governments in coastal provinces that inherit fundamentally different demographic structures are less likely to pursue this governance style. We use audit data from Apple corporation suppliers (2007–2013), supplementary survey data, and in‐depth interviews to discuss the relationship between localized production and better labor conditions. Copyright © 2017 John Wiley & Sons, Ltd.
Clear cell and endometrioid carcinomas: are their differences attributable to distinct cells of origin?
Authors: Cochrane Dawn R , Tessier‐Cloutier Basile , Lawrence Katherine M , Nazeran Tayyebeh , Karnezis Anthony N , Salamanca Clara , Cheng Angela S , McAlpine Jessica N , Hoang Lien N , Gilks C Blake , Huntsman David G 
Published: July 2017

AbstractEndometrial epithelium is the presumed tissue of origin for both eutopic and endometriosis‐derived clear cell and endometrioid carcinomas. We had previously hypothesized that the morphological, biological and clinical differences between these carcinomas are due to histotype‐specific mutations. Although some mutations and genomic landscape features are more likely to be found in one of these histotypes, we were not able to identify a single class of mutations that was exclusively present in one histotype and not the other. This lack of genomic differences led us to an alternative hypothesis that these cancers could arise from distinct cells of origin within endometrial tissue, and that it is the cellular context that accounts for their differences. In a proteomic screen, we identified cystathionine γ‐lyase (CTH) as a marker for clear cell carcinoma, as it is expressed at high levels in clear cell carcinomas of the ovary and endometrium. In the current study, we analysed normal Müllerian tissues, and found that CTH is expressed in ciliated cells of endometrium (both eutopic endometrium and endometriosis) and fallopian tubes. We then demonstrated that other ciliated cell markers are expressed in clear cell carcinomas, whereas endometrial secretory cell markers are expressed in endometrioid carcinomas. The same differential staining of secretory and ciliated cells was demonstrable in a three‐dimensional organoid culture system, in which stem cells were stimulated to differentiate into an admixture of secretory and ciliated cells. These data suggest that endometrioid carcinomas are derived from cells of the secretory cell lineage, whereas clear cell carcinomas are derived from, or have similarities to, cells of the ciliated cell lineage. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Multi‐pronged proteomic analysis to study the glioma pathobiology using cerebrospinal fluid samples
Authors: Gahoi Nikita , Malhotra Darpan , Moiyadi Aliasgar , Varma Santosh G , Gandhi Mayuri N , Srivastava Sanjeeva 
Published: July 2017

PurposeGliomas are one of the most aggressive and lethal brain tumors arising from neoplastic transformation of astrocytes and oligodendrocytes. A comprehensive quantitative analysis of proteome level differences in cerebrospinal fluid (CSF) across different grades of gliomas for a better understanding of glioma pathobiology is carried out.Experimental designGlioma patients are diagnosed by radiology and histochemistry‐based analyses. Differential proteomic analysis of high (n = 12) and low (n = 8) grade gliomas, and control (n = 3) samples is performed by using two complementary quantitative proteomic approaches; 2D‐DIGE and iTRAQ. Further, comparative analysis of three IDH wild‐type and five IDH mutants is performed to identify the proteome level differences between these two sub‐classes.ResultsLevel of several proteins including haptoglobin, transthyretin, osteopontin, vitronectin, complement factor H and different classes of immunoglobulins are found to be considerably increased in CSF of higher grades of gliomas. Subsequent bioinformatics analysis indicated that many of the dysregulated CSF proteins are associated with metabolism of lipids and lipoproteins, complement and coagulation cascades and extracellular matrix remodeling in gliomas. Intriguingly, CSF of glioma patients with IDH mutations exhibite increased levels of multiple proteins involved in response to oxidative stress.Conclusion and clinical relevanceTo the best of our knowledge, this is the foremost proteome level investigation describing comprehensive proteome profiles of different grades of gliomas using proximal fluid (CSF); and thereby providing insights into disease pathobiology, which aided in identification of grade and sub‐type specific alterations. Moreover, if validated in larger clinical cohorts, a panel of differentially abundant CSF proteins may serve as potential disease monitoring and prognostic markers for gliomas.
Effect of social interactions on hippocampal protein expression in animal dominant and submissive model of behavioral disorders
Authors: Borovok Natalia , Nesher Elimelech , Reichenstein Michal , Tikhonova Tatiana , Levin Yishai , Pinhasov Albert , Michaelevski Izhak 
Published: July 2017

PurposePsychiatric conditions, in many cases, arise from social interactions necessary for optimal mental functioning. Dominance and submissiveness are two opposite poles of behavior, stemming from processes of social interactions between members inside one group or species. Extreme dominance and submissiveness expressions in humans is accompanied by mental impairments, including mania and depression. Here, taking advantage of animals bred selectively for traits of dominance and submissiveness, we assess protein expression profiles in dominant and submissive mice in the context of social interaction.Experimental designProteins extracted from hippocampi of naïve and social interaction subjected dominant, submissive and wild type mice (15 mice per each group) are quantified using label‐free quantitative LC/MS/MS analysis. Complexity of social interaction‐related protein expression is resolved by factor analysis and enriched with GO and protein‐protein interaction functional network analyses.ResultsIn total, 1146 proteins exhibiting expression changes in the wild type mice, as well as dominant and submissive mice are enriched in protein datasets responsible for: 1) socially triggered dominance (90 proteins), 2) inherent submissiveness (75 proteins), 3) socially triggered submissiveness (117 proteins), and 4) social interaction triggered protein expression changes, related to resilience/adaptation to stress (69 proteins). Among the most enriched categories, extensive changes are found in proteins related to presynaptic release, ion channel regulation, circadian rhythm, MAPK, ErbB and NF‐kB pathways.
ConclusionData extracted from this first extensive proteomic study of a social interaction paradigm may facilitate decoding of molecular mechanisms responsible for pathogenesis of psychiatric disorders.
A new Dienerian (Early Triassic) brachiopod fauna from South China and implications for biotic recovery after the Permian–Triassic extinction
Authors: Wang Fengyu , Chen Jing , Dai Xu , Song Haijun 
Published: July 2017

AbstractBrachiopods suffered severe extinction during the Permian–Triassic crisis, such that their diversity dropped to extremely low levels in the Early Triassic. Here we describe a new brachiopod fauna from the Dienerian of Lichuan, South China. This fauna consists of three monospecific genera, including one new genus and one new species: Lichuanorelloides lichuanensis gen. et sp. nov., Lissorhynchia sp. and Crurithyris sp. These brachiopods co‐occur with the ammonoids Ussuridiscus, Jieshaniceras, Hubeitoceras and Vishnuites, suggesting an early Dienerian age. The geographical distribution of brachiopods in family Norellidae during the Early Triassic suggests that a migration took place towards higher latitudes, which may have been caused by the extreme climate warming that prevailed during the Dienerian.
Physico‐chemical and Spectroscopic Approach to Analyse the Behaviour of Surface‐Active Ionic Liquid and Conventional Surfactant in Aqueous Glycine
Authors: Chauhan Suvarcha , Kumar Ashish , Kaur Maninder , Chauhan M. S. 
Published: July 2017

AbstractThe present work reports a comparison of direct or indirect (water‐mediated) interactions of surface active ionic liquid SAIL, tetrabutylammonium dodecylsulphate (TBADS) in aqueous solutions of glycine with those of sodium dodecylsulphate (SDS) in same solvent system, by employing techniques like conductivity, fluorescence, UV–Vis probe studies and clouding phenomenon. High hydrophobicity and penetrating ability of TBA+ counterions and most significant salting‐out effect due to the preferential hydration of glycine molecules accounts for the enhanced micellization and better surface activity of TBADS as compared to its conventional analogue SDS. Further, driving force for the micellization in both the cases is the hydrophobic interactions, whereas in the case of SDS, London dispersion interactions as alternative forces also contribute considerably at higher temperatures. In addition, the decrease in the cloud point () of aqueous TBADS solutions in the presence of glycine is attributed to the dehydration of hydrophilic head groups of micelles, resulting in their collapse and hence phase separation.
Polygonumnolides A1–B3, minor dianthrone derivatives from the roots of Polygonum multiflorum Thunb
Authors: Yang Jianbo , Yan Zheng , Ren Jin , Dai Zhong , Ma Shuangcheng , Wang Aiguo , Su Yalun 
Published: July 2017

Abstract
Seven new dianthrone glycosides, named polygonumnolides A1–B3 (1–7), were isolated from the 70 % EtOH extract of the dried roots of Polygonum multiflorum Thunb. using column chromatography and preparative high-performance liquid chromatography. Their structures were determined by 1D and 2D NMR and mass spectroscopy. The isolated compounds were evaluated for their cytotoxic effects against KB tumor cell lines and compounds 1–4 showed moderate cytotoxicity.
Volumetric and morphological characteristics of the hippocampus are associated with progression to schizophrenia in patients with first-episode psychosis
Authors: Sauras R. , Keymer A. , Alonso-Solis A. , Díaz A. , Molins C. , Nuñez F. , Rabella M. , Roldán A. , Grasa E. , Alvarez E. , Portella M.J. , Corripio I. 
Published: July 2017

AbstractBackground:Abnormalities in the hippocampus have been implicated in the pathophysiology of psychosis. However, it is still unclear whether certain abnormalities are a pre-existing vulnerability factor, a sign of disease progression or a consequence of environmental factors. We hypothesized that first-episode psychosis patients who progress to schizophrenia after one year of follow up will display greater volumetric and morphological changes from the very beginning of the disorder.Methods:We studied the hippocampus of 41 patients with a first-episode psychosis and 41 matched healthy controls. MRI was performed at the time of the inclusion in the study. After one year, the whole sample was reevaluated and divided in two groups depending on the diagnoses (schizophrenia vs. non-schizophrenia).Results:Patients who progressed to schizophrenia showed a significantly smaller left hippocampus volume than control group and no-schizophrenia group (F = 3.54; df = 2, 77; P = 0.03). We also found significant differences in the morphology of the anterior hippocampus (CA1) of patients with first-episode psychosis who developed schizophrenia compared with patients who did not.Conclusions:These results are consistent with the assumption of hyperfunctioning dopaminergic cortico-subcortical circuits in schizophrenia, which might be related with an alteration of subcortical structures, such as the hippocampus, along the course of the disease. According with these results, hippocampus abnormalities may serve as a prognostic marker of clinical outcome in patients with a first-episode psychosis.
On the instabilities of a potential vortex with a free surface
Authors: Mougel J. , Fabre D. , Lacaze L. , Bohr T. 
Published: July 2017

In this paper, we address the linear stability analysis of a confined potential vortex with a free surface. This particular flow has been recently used by Tophøj et al. (Phys. Rev. Lett., vol. 110(19), 2013, article 194502) as a model for the swirling flow of fluid in an open cylindrical container, driven by rotating the bottom plate (the rotating bottom experiment) to explain the so-called rotating polygons instability (Vatistas J. Fluid Mech., vol. 217, 1990, pp. 241–248; Jansson et al., Phys. Rev. Lett., vol. 96, 2006, article 174502) in terms of surface wave interactions leading to resonance. Global linear stability results are complemented by a Wentzel–Kramers–Brillouin–Jeffreys (WKBJ) analysis in the shallow-water limit as well as new experimental observations. It is found that global stability results predict additional resonances that cannot be captured by the simple wave coupling model presented in Tophøj et al. (2013). Both the main resonances (thought to be at the root of the rotating polygons) and these secondary resonances are interpreted in terms of over-reflection phenomena by the WKBJ analysis. Finally, we provide experimental evidence for a secondary resonance supporting the numerical and theoretical analysis presented. These different methods and observations allow to support the unstable wave coupling mechanism as the physical process at the origin of the polygonal patterns observed in free-surface rotating flows.