bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the taxonomic status of the Great White Heron (Ardea herodias occidentalis) using morphological, behavioral and genetic evidence
Authors: McGuire Heather L , Taylor Sabrina S , Sheldon Frederick H 
Published: June 2019

AbstractThe Great White Heron (GWH) has an all-white plumage and occurs in the Gulf of Mexico and Caribbean. Described originally as Ardea occidentalis, it is now considered a subspecies of Great Blue Heron (GBH; A. herodias). GWH and GBH meet in Florida Bay at the southern tip of Florida, providing the opportunity to evaluate their interaction and species status. To this end, we examined size variation and mate choice across their contact zone and genetic variation range-wide. Measurements of 7 morphological characters indicate trends, but not a significant difference, in size between GBH and GWH in southern Florida. GBH and GWH nest mainly in different places (mainland vs. islands) and at different peak times. In Florida Bay, mixed pairs occur, but white-white and blue-blue pairs are more common than in a randomly mating population. Assessing mating, however, is complicated because most, if not all, nesting blue birds are of mixed parentage. Microsatellite DNA analysis indicates that white and blue herons in Florida Bay and the outer Keys (outside Florida Bay) form a group distinct from blue forms on Florida Peninsula and elsewhere in North America. However, some gene flow occurs from white herons on the outer Keys to white and blue herons in Florida Bay, and from blue herons in Florida Bay to GBH on the Florida Peninsula. GWH alleles occur in all North American populations, but whether this is from gene flow or incomplete lineage sorting is unknown. Deciding GWH's species status is difficult. GWH and GBH meet in an ecotone where some gene flow occurs, but behavior and habitat largely isolate them. We argue in favor of splitting GWH from GBH. Regardless of how it is ultimately classified, the GWH's small population needs to be actively managed as an isolate in an extremely vulnerable environment.
Protein functional annotation of simultaneously improved stability, accuracy and false discovery rate achieved by a sequence-based deep learning
Authors: Hong Jiajun , Luo Yongchao , Zhang Yang , Ying Junbiao , Xue Weiwei , Xie Tian , Tao Lin , Zhu Feng 
Published: June 2019

Abstract
Functional annotation of protein sequence with high accuracy has become one of the most important issues in modern biomedical studies, and computational approaches of significantly accelerated analysis process and enhanced accuracy are greatly desired. Although a variety of methods have been developed to elevate protein annotation accuracy, their ability in controlling false annotation rates remains either limited or not systematically evaluated. In this study, a protein encoding strategy, together with a deep learning algorithm, was proposed to control the false discovery rate in protein function annotation, and its performances were systematically compared with that of the traditional similarity-based and de novo approaches. Based on a comprehensive assessment from multiple perspectives, the proposed strategy and algorithm were found to perform better in both prediction stability and annotation accuracy compared with other de novo methods. Moreover, an in-depth assessment revealed that it possessed an improved capacity of controlling the false discovery rate compared with traditional methods. All in all, this study not only provided a comprehensive analysis on the performances of the newly proposed strategy but also provided a tool for the researcher in the fields of protein function annotation.
Positive multistate protein design
Authors: Vucinic Jelena , Simoncini David , Ruffini Manon , Barbe Sophie , Schiex Thomas 
Published: June 2019

AbstractMotivationStructure-based computational protein design (CPD) plays a critical role in advancing the field of protein engineering. Using an all-atom energy function, CPD tries to identify amino acid sequences that fold into a target structure and ultimately perform a desired function. The usual approach considers a single rigid backbone as a target, which ignores backbone flexibility. Multistate design (MSD) allows instead to consider several backbone states simultaneously, defining challenging computational problems.ResultsWe introduce efficient reductions of positive MSD problems to Cost Function Networks with two different fitness definitions and implement them in the Pompd (Positive Multistate Protein design) software. Pompd is able to identify guaranteed optimal sequences of positive multistate full protein redesign problems and exhaustively enumerate suboptimal sequences close to the MSD optimum. Applied to nuclear magnetic resonance and back-rubbed X-ray structures, we observe that the average energy fitness provides the best sequence recovery. Our method outperforms state-of-the-art guaranteed computational design approaches by orders of magnitudes and can solve MSD problems with sizes previously unreachable with guaranteed algorithms.Availability and implementationhttps://forgemia.inra.fr/thomas.schiex/pompd as documented Open Source.Supplementary informationSupplementary data are available at Bioinformatics online.
Ovarian cancer and the evolution of subtype classifications using transcriptional profiling†
Authors: Cook David P , Vanderhyden Barbara C 
Published: June 2019

AbstractOvarian cancer is a complex disease with multiple subtypes, each having distinct histopathologies and variable responses to treatment. This review highlights the technological milestones and the studies that have applied them to change our definitions of ovarian cancer. Over the past 50 years, technologies such as microarrays and next-generation sequencing have led to the discovery of molecular alterations that define each of the ovarian cancer subtypes and has enabled further subclassification of the most common subtype, high-grade serous ovarian cancer (HGSOC). Improvements in mutational profiling have provided valuable insight, such as the ubiquity of TP53 mutations in HGSOC tumors. However, the information derived from these technological advances has also revealed the immense heterogeneity of this disease, from variation between patients to compositional differences within single masses. In looking forward, the emerging technologies for single-cell and spatially resolved transcriptomics will allow us to better understand the cellular composition and structure of tumors and how these contribute to the molecular subtypes. Attempts to incorporate the complexities ovarian cancer has resulted in increasing sophistication of model systems, and the increased precision in molecular profiling of ovarian cancers has already led to the introduction of inhibitors of poly (ADP-ribose) polymerases as a new class of treatments for ovarian cancer with DNA repair deficiencies. Future endeavors to define increasingly accurate classification strategies for ovarian cancer subtypes will allow for confident prediction of disease progression and provide important insight into potentially targetable molecular mechanisms specific to each subtype.
Testicular endothelial cells promote self-renewal of spermatogonial stem cells in rats†
Authors: Kim Yong-Hee , Oh Myeong-Geun , Bhang Dong Ha , Kim Bang-Jin , Jung Sang-Eun , Kim Seok-Man , Dohr Gottfried , Kim Sun-Uk , Ryeom Sandra , Ryu Buom-Yong 
Published: June 2019

AbstractSpermatogonial stem cells (SSCs) are the basis of spermatogenesis in male due to their capability to multiply in numbers by self-renewal and subsequent meiotic processes. However, as SSCs are present in a very small proportion in the testis, in vitro proliferation of undifferentiated SSCs will facilitate the study of germ cell biology. In this study, we investigated the effectiveness of various cell lines as a feeder layer for rat SSCs. Germ cells enriched for SSCs were cultured on feeder layers including SIM mouse embryo-derived thioguanine and ouabain-resistant cells, C166 cells, and mouse and rat testicular endothelial cells (TECs) and their stem cell potential for generating donor-derived colonies and offspring was assessed by transplantation into recipient testes. Rat germ cells cultured on TECs showed increased mRNA and protein levels of undifferentiated spermatogonial markers. Rat SSCs derived from these germ cells underwent spermatogenesis and generated offspring when transplanted into recipients. Collectively, TECs can serve as an effective feeder layer that enhances the proliferative and self-renewal capacity of cultured rat SSCs while preserving their stemness properties.
Learning for Transdisciplinary Leadership: Why Skilled Scholars Coming Together Is Not Enough
Authors: Barrett M J , Alphonsus Khrisha B , Harmin Matt , Epp Tasha , Hoessler Carolyn , McIntyre Danielle , Reeder Bruce , Singh Baljit 
Published: June 2019

Abstract
Transdisciplinary research is an emerging new normal for many scientists in applied research fields, including One Health, planetary health, and sustainability. However, simply bringing highly skilled students (and faculty members) together to generate real-world solutions and policy recommendations for complex problems often fails to consistently create the desired results in transdisciplinary settings. Our research goal was to improve understanding and applications of transdisciplinary learning processes within a One Health graduate education program. This qualitative study analyzes 5 years of action research data, identifying four transdisciplinary leadership skills and four conditions required for consistent skill development. Combining Vygotsky's theory of proximal development with identified transdisciplinary skills, we explain why educational scaffolding is needed to enable more successful design and delivery of transdisciplinary learning, particularly in One Health educational programs.
Making the Connection Between Theories of Policy Change and Policy Practice: A New Conceptualization
Authors: Feldman Guy 
Published: June 2019

AbstractOver the past few decades, powerful economic, political and cultural forces have restructured the welfare state and social work practice. In response, there have been calls in recent years for the re-politicisation of the social work profession. One of the main ways in which social work has been re-politicised is through the emphasis on social workers’ involvement in the policy arena, commonly referred to as ‘policy practice’ in the literature. Although policy practice has recently received close attention in social work debates, it has remained relatively under-theorised. This article introduces social work scholars and practitioners to the theoretical work on policy change and elaborates its implications for how social workers can influence policy. Drawing on diverse literatures from the fields of political science and sociology, the article circumscribes to four influential theories of policy change that provide support for informed action in the policy arena: neo-institutional theory, elite theory, resource mobilisation theory and interdependent power theory. Drawing on these theories, the article develops a conceptualisation of four different types of policy practice: institutional policy practice, elite policy practice, resource-based policy practice and radical policy practice.
Neurotechnology-aided interventions for upper limb motor rehabilitation in severe chronic stroke
Authors: Coscia Martina , Wessel Maximilian J , Chaudary Ujwal , Millán José del R , Micera Silvestro , Guggisberg Adrian , Vuadens Philippe , Donoghue John , Birbaumer Niels , Hummel Friedhelm C 
Published: June 2019

AbstractUpper limb motor deficits in severe stroke survivors often remain unresolved over extended time periods. Novel neurotechnologies have the potential to significantly support upper limb motor restoration in severely impaired stroke individuals. Here, we review recent controlled clinical studies and reviews focusing on the mechanisms of action and effectiveness of single and combined technology-aided interventions for upper limb motor rehabilitation after stroke, including robotics, muscular electrical stimulation, brain stimulation and brain computer/machine interfaces. We aim at identifying possible guidance for the optimal use of these new technologies to enhance upper limb motor recovery especially in severe chronic stroke patients. We found that the current literature does not provide enough evidence to support strict guidelines, because of the variability of the procedures for each intervention and of the heterogeneity of the stroke population. The present results confirm that neurotechnology-aided upper limb rehabilitation is promising for severe chronic stroke patients, but the combination of interventions often lacks understanding of single intervention mechanisms of action, which may not reflect the summation of single intervention’s effectiveness. Stroke rehabilitation is a long and complex process, and one single intervention administrated in a short time interval cannot have a large impact for motor recovery, especially in severely impaired patients. To design personalized interventions combining or proposing different interventions in sequence, it is necessary to have an excellent understanding of the mechanisms determining the effectiveness of a single treatment in this heterogeneous population of stroke patients. We encourage the identification of objective biomarkers for stroke recovery for patients’ stratification and to tailor treatments. Furthermore, the advantage of longitudinal personalized trial designs compared to classical double-blind placebo-controlled clinical trials as the basis for precise personalized stroke rehabilitation medicine is discussed. Finally, we also promote the necessary conceptual change from ‘one-suits-all’ treatments within in-patient clinical rehabilitation set-ups towards personalized home-based treatment strategies, by adopting novel technologies merging rehabilitation and motor assistance, including implantable ones.
Locus coeruleus imaging as a biomarker for noradrenergic dysfunction in neurodegenerative diseases
Authors: Betts Matthew J , Kirilina Evgeniya , Otaduy Maria C G , Ivanov Dimo , Acosta-Cabronero Julio , Callaghan Martina F , Lambert Christian , Cardenas-Blanco Arturo , Pine Kerrin , Passamonti Luca , Loane Clare , Keuken Max C , Trujillo Paula , Lüsebrink Falk , Mattern Hendrik , Liu Kathy Y , Priovoulos Nikos , Fliessbach Klaus , Dahl Martin J , Maaß Anne , Madelung Christopher F , Meder David , Ehrenberg Alexander J , Speck Oliver , Weiskopf Nikolaus , Dolan Raymond , Inglis Ben , Tosun Duygu , Morawski Markus , Zucca Fabio A , Siebner Hartwig R , Mather Mara , Uludag Kamil , Heinsen Helmut , Poser Benedikt A , Howard Robert , Zecca Luigi , Rowe James B , Grinberg Lea T , Jacobs Heidi I L , Düzel Emrah , Hämmerer Dorothea 
Published: June 2019

Abstract
Pathological alterations to the locus coeruleus, the major source of noradrenaline in the brain, are histologically evident in early stages of neurodegenerative diseases. Novel MRI approaches now provide an opportunity to quantify structural features of the locus coeruleus in vivo during disease progression. In combination with neuropathological biomarkers, in vivo locus coeruleus imaging could help to understand the contribution of locus coeruleus neurodegeneration to clinical and pathological manifestations in Alzheimer’s disease, atypical neurodegenerative dementias and Parkinson’s disease. Moreover, as the functional sensitivity of the noradrenergic system is likely to change with disease progression, in vivo measures of locus coeruleus integrity could provide new pathophysiological insights into cognitive and behavioural symptoms. Locus coeruleus imaging also holds the promise to stratify patients into clinical trials according to noradrenergic dysfunction. In this article, we present a consensus on how non-invasive in vivo assessment of locus coeruleus integrity can be used for clinical research in neurodegenerative diseases. We outline the next steps for in vivo, post-mortem and clinical studies that can lay the groundwork to evaluate the potential of locus coeruleus imaging as a biomarker for neurodegenerative diseases.
Automated Canine Scent-Detection Apparatus: Technical Description and Training Outcomes
Authors: Edwards Timothy L 
Published: June 2019

Abstract
To date, laboratory scent-detection work with dogs has been a manual process whereby some or all aspects of the procedures are mediated by researchers. Automation of this process would eliminate issues associated with cuing, subjectivity in data collection, and reinforcement delivery. Herein, I describe an automated apparatus that can accommodate almost any type of sample that can be brought into the laboratory. The apparatus consists of a 17-segment carousel that rotates behind a panel. Dogs can access a single sample at a time through a port in the panel. Infrared beams are used to detect sample observations and indications, and a dog-activated switch is used to advance the carousel to the next sample. Correct indications are reinforced with an automated feeder. After screening 12 dogs, 5 dogs were selected and trained to use the apparatus to classify samples containing amyl acetate. All dogs achieved hit rates and correct rejection rates at or near 100% in fewer than 25 half-days of training (mean: 19.6, range: 12–24). These data suggest that the apparatus can be used to obtain accurate sample classification without excessive training requirements. Future improvements to the apparatus and training protocols may reduce the training requirements further.
Ionic Liquid-based Hollow Fiber Liquid–Liquid–Liquid Microextraction Combined with Capillary Electrophoresis for the Determination of Sulfonamides in Aquaculture Waters
Authors: Wu Youyi , Zhou Jingwen , Wang Xuedong , Zhang Zhanen , Gao Shiqian 
Published: June 2019

Abstract
Ionic liquid-based hollow-fiber liquid–liquid–liquid microextraction (IL-HF-LLLME) coupled to capillary electrophoresis (CE) has been developed for the determination of six sulfonamides (SAs) in aquaculture waters. A series of extraction parameters was optimized to enhance the extraction efficiency, which included type and pore size of hollow fiber, type and composition of extraction solvent, pH value of donor phase, the concentration of acceptor phase and the mass ratio of donor phase to acceptor phase along with extraction temperature and time. Under optimal conditions, the IL-HF-LLLME-CE method provided a wide liner range for six SAs from 2 to 1,000 μg L−1 (r2 ≥ 0.9995), the limits of the detection from 0.25 to 0.48 and the enrichment factors from 122 to 230, respectively. Relative standard deviations for intra- and interday precision were 1.4–5.3% and 1.8–7.5% (n = 5), respectively. The proposed method was successfully applied for the determination of trace-level SAs in seven real-world aquaculture water samples with good recoveries (80.4–100.7%). Also, sulfamerazine and sulfamethoxazole were detected at the level of 0.52–1.60 μg L−1 in two water samples. Due to its good sensitivity, simple operation, short analysis time and eco-friendliness, the developed method has a great application potential in analysis of trace SA residues in aquaculture waters.
(Re)membering Sara Baartman, Venus, and Aphrodite
Authors: Derbew Sarah 
Published: June 2019

AbstractThis article analyses the Black diasporic reception of Venus in the figure of Sara Baartman, a South African woman who performed under the name ‘Hottentot Venus’ in the early nineteenth century, and her theatrical persona in Suzan-Lori Parks’s play Venus [1990] (1997). Through her sophisticated characterization of Sara Baartman, Parks provides insight into the complex performativity of Black femalehood in conjunction with an overwritten Greco-Roman divinity. Parks’s play presents Sara Baartman as a person who forces her audiences, both theatrical and historical, to contend with their own complicit role in her objectification. More broadly, this cross-cultural dialogue attempts to recuperate the Black female subject from lopsided archives. It also contributes to a larger dismantling of the perceived boundaries between Greco-Roman art, African history, and African American literature.
Altererythrobacter rubellus sp. nov., a marine alphaproteobacterium isolated from seawater
Authors: Yoon Jaewoo , Ryu Jaewon 
Published: June 2019

ABSTRACT
The phylogenetic and taxonomic status of an alphaproteobacterium isolated from seawater, collected in the Republic of Korea, was elucidated based on a polyphasic method. Strain KMU-45T was Gram-stain-negative, strictly aerobic, rod-shaped, non-motile and chemoheterotrophic. Phylogenetic investigation based on the 16S rRNA gene sequence demonstrated that the novel marine isolate belongs to the family Erythrobacteraceae, of the class Alphaproteobacteria, and that it possessed the highest (98.7%) sequence similarity with Altererythrobacter ishigakiensis ATCC BAA-2084T. DNA–DNA hybridization values between strains KMU-45T and A. ishigakiensis KCTC 42446T were 31.4% ± 8.4%. The major isoprenoid quinone of the novel isolate was ubiquinone-10 (Q-10) and the major (&gt;10%) cellular fatty acids were C17:1 ω8c, C17:1 ω6c and C18:1 ω7c. The genomic DNA G + C content of strain KMU-45T was 57.7 mol%. The polar lipid profile of the strain KMU-45T comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, an unidentified phospholipid and an unidentified lipid. From the polyphasic taxonomic results in this study, the bacterium can be considered to represent a new species of the genus Altererythrobacter, for which the name Altererythrobacter rubellus sp. nov. is proposed. The type species is A. rubellus sp. nov., with the type strain KMU-45T (= KCCM 90270T = NBRC 112769T).
Evaluation of a PGP3 ELISA for surveillance of the burden of Chlamydia infection in women from Australia and Samoa
Authors: Mazraani Rami , Timms Peter , Hill Philip C , Suaalii-Sauni Tamaailau , Niupulusu Tavita , Temese Seiuli V A , Iosefa-Siitia Liai , Auvaa Leveti , Tapelu Siuomatautu A , Motu Maauga F , Righarts Antoinette , Walsh Michael S , Rombauts Luk , Allan John A , Horner Patrick , Huston Wilhelmina M 
Published: June 2019

ABSTRACT
Serological assays can be used to investigate the population burden of infection and potentially sequelae from Chlamydia. We investigated the PGP3 ELISA as a sero-epidemiological tool for infection or sub-fertility in Australian and Samoan women. The PGP3 ELISA absorbance levels were compared between groups of women with infertility, fertile, and current chlamydial infections. In the Australian groups, women with chlamydial tubal factor infertility had significantly higher absorbance levels in the PGP3 ELISA compared to fertile women (P &lt; 0.0001), but not when compared to women with current chlamydial infection (P = 0.44). In the Samoan study, where the prevalence of chlamydial infections is much higher there were significant differences in the PGP3 ELISA absorbance levels between chlamydial sub-fertile women and fertile women (P = 0.003). There was no difference between chlamydial sub-fertile women and women with a current infection (P = 0.829). The results support that the PGP3 assay is effective for sero-epidemiological analysis of burden of infection, but not for evaluation of chlamydial pathological sequelae such as infertility.