bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models
Authors: Bloom Jesse D. 
Published: January 2016

AbstractSites of positive selection are identified by comparing observed evolutionary patterns to those expected under a null model for evolution in the absence of such selection. For protein-coding genes, the most common null model is that nonsynonymous and synonymous mutations fix at equal rates; this unrealistic model has limited power to detect many interesting forms of selection. I describe a new approach that uses a null model based on high-throughput lab measurements of a gene's site-specific amino-acid preferences. This null model makes it possible to identify diversifying selection for amino-acid change and differential selection for mutations to amino acids that are unexpected given the measurements made in the lab. I show that this approach identifies sites of adaptive substitutions in four genes (lactamase, Gal4, influenza nucleoprotein, and influenza hemagglutinin) far better than a comparable method that simply compares the rates of nonsynonymous and synonymous substitutions. As rapid increases in biological data enable increasingly nuanced descriptions of the constraints on individual sites, approaches like the one here can improve our ability to identify many interesting forms of selection.
Statistics of Cellular Evolution in Leukemia: Allelic Variations in Patient Trajectories Based on Immune Repertoire Sequencing
Authors: Gao Hong , Wang Chunlin , Seok Junhee , Feldman Marcus W. , Xiao Wenzhong 
Published: January 2016

AbstractThe evolution of a cancer system consisting of cancer clones and normal cells is a complex dynamic process with multiple interacting factors including clonal expansion, somatic mutation, and sequential selection. As a typical example, in patients with chronic lymphocytic leukemia (CLL), a monoclonal population of transformed B cells expands to dominate the B cell population in the peripheral blood and bone marrow. This expansion of transformed B cells suggests that they might evolve through processes distinct from those of normal B cells. Recent advances in next generation sequencing enable the high-throughput identification and tracking of individual B cell clones through sequencing of the V-D-J junction segments of the immunoglobulin heavy chain (IGH). Here we developed a statistical approach to modeling cellular evolution of the immune repertoire. Adapting the infinitely many alleles model from population genetics, we studied abnormalities occurring in the immune repertoire of patients as substantial deviations from the null model. The Ewens sampling test (EST) distinguished the immune repertoires of CLL patients with imminent relapse from healthy controls and patients in sustained remission. Extensive simulations based on sequencing data showed that EST is sensitive in detecting cancer-related derangements of the IGH repertoire. In addition, we suggest two potentially useful parameters: the rate at which donor’s B cell clones enter the circulation and the average time to regenerate a transplanted immune repertoire, both of which help to distinguish relapsing CLL patients from those in sustained remission and provide additional information about the dynamics of immune reconstitution in the latter patients. We anticipate that our models and statistics will be useful in diagnosis and prognosis of leukemia, and may be adapted for application to other diseases related to adaptive immunity.
Multi-scale computational study of the mechanical regulation of cell mitotic rounding in epithelia
Authors: Nematbakhsh Ali , Sun Wenzhao , Brodskiy Pavel A. , Amiri Aboutaleb , Narciso Cody , Xu Zhiliang , Zartman Jeremiah J. , Alber Mark S 
Published: January 2016

AbstractMitotic rounding during cell division is critical for preventing daughter cells from inheriting an abnormal number of chromosomes, a condition that occurs frequently in cancer cells. Cells must significantly expand their apical area and transition from a polygonal to circular apical shape to achieve robust mitotic rounding in epithelial tissues, which is where most cancers initiate. However, how cells mechanically regulate robust mitotic rounding within packed tissues is unknown. Here, we analyze mitotic rounding using a newly developed multi-scale subcellular element computational model that is calibrated using experimental data. Novel biologically relevant features of the model include separate representations of the sub-cellular components including the apical membrane and cytoplasm of the cell at the tissue scale level as well as detailed description of cell properties during mitotic rounding. Regression analysis of predictive model simulation results reveals the relative contributions of osmotic pressure, cell-cell adhesion and cortical stiffness to mitotic rounding. Mitotic area expansion is largely driven by regulation of cytoplasmic pressure. Surprisingly, mitotic shape roundness within physiological ranges is most sensitive to variation in cell-cell adhesivity and stiffness. An understanding of how perturbed mechanical properties impact mitotic rounding has important potential implications on, amongst others, how tumors progressively become more genetically unstable due to increased chromosomal aneuploidy and more aggressive.Author SummaryMitotic rounding (MR) during cell division which is critical for the robust segregation of chromosomes into daughter cells, plays important roles in tissue growth and morphogenesis, and is frequently perturbed in cancerous cells. Mechanisms of MR have been investigated in individual cultured cells, but mechanisms regulating MR in tissues are still poorly understood. We developed and calibrated an advanced subcellular element-based computational model called Epi-Scale that enables quantitative testing of hypothesized mechanisms governing epithelial cell behavior within the developing tissue microenvironment. Regression analysis of predictive model simulation results reveals the relative contributions of osmotic pressure, cell-cell adhesion and cortical stiffness to mitotic rounding and establishes a novel mechanism for ensuring robustness in mitotic rounding within densely packed epithelia.
Gathering Data for Archival, Field, Survey, and Experimental Accounting Research
Authors: BLOOMFIELD ROBERT , NELSON MARK W. , SOLTES EUGENE 
Published: January 2016

ABSTRACTIn the published proceedings of the first Journal of Accounting Research Conference, Vatter [1966] lamented that “Gathering direct and original facts is a tedious and difficult task, and it is not surprising that such work is avoided.” For the fiftieth JAR Conference, we introduce a framework to help researchers understand the complementary value of seven empirical methods that gather data in different ways: prestructured archives, unstructured (“hand‐collected”) archives, field studies, field experiments, surveys, laboratory studies, and laboratory experiments. The framework spells out five goals of an empirical literature and defines the seven methods according to researchers’ choices with respect to five data gathering tasks. We use the framework and examples of successful research studies in the financial reporting literature to clarify how data gathering choices affect a study's ability to achieve its goals, and conclude by showing how the complementary nature of different methods allows researchers to build a literature more effectively than they could with less diverse approaches to gathering data.
The mediating role of leader–member exchange: a study of job satisfaction and turnover intentions in temporary work
Authors: Flickinger Miriam , Allscher Marcel , Fiedler Marina 
Published: January 2016

AbstractThis paper focuses on turnover intentions in temporary work. Specifically, we analyse whether job satisfaction and leader–member exchange (LMX) play the same role as antecedents of turnover intentions for both temporary and permanent employees. Results from a total‐effects moderation model based on a survey of 593 individuals placed by a temporary work agency suggest that temporary work lessens the impact that high job satisfaction has in terms of reducing turnover intentions. Furthermore, while for permanent employees, high‐quality LMX relationships play a central role in the link between job satisfaction and turnover intentions; for temporary employees, job satisfaction is less important in the formation of high‐quality LMX relationships. Therefore, we contribute to knowledge on turnover intentions in temporary work by showing that within this context, turnover intentions cannot be directly remedied by high job satisfaction and that temporary work inhibits LMX's reinforcing role in the relationship between job satisfaction and turnover intentions.
Multimodal Interventions to Enhance Adherence to Secondary Preventive Medication after Stroke: A Systematic Review and Meta‐Analyses
Authors: Al AlShaikh Sukainah , Quinn Terry , Dunn William , Walters Matthew , Dawson Jesse 
Published: January 2016

SummaryIntroductionNonadherence to secondary preventative medications after stroke is common and is associated with poor outcomes. Numerous strategies exist to promote adherence. We performed a systematic review and meta‐analysis to describe the efficacy of strategies to improve adherence to stroke secondary prevention.MethodsWe created a sensitive search strategy and searched multiple electronic databases (MEDLINE, EMBASE, CINAHL, PsycINFO, CENTRAL, and Web of Knowledge) for studies of interventions that aimed to enhance adherence to secondary preventative medication after stroke. We assessed quality of included studies using the Cochrane tool for assessing risk of bias. We performed narrative review and performed meta‐analysis where data allowed.ResultsFrom 12,237 titles, we included seventeen studies in our review. Eleven studies were considered to have high risk of bias, 3 with unclear risk, and 3 of low risk. Meta‐analysis of available data suggested that these interventions improved adherence to individual medication classes (blood pressure‐lowering drugs – OR, 2.21; 95% CI (1.63, 2.98), [P < 0.001], lipid‐lowering drugs – OR, 2.11; 95% CI (1.00, 4.46), [P = 0.049], and antithrombotic drugs – OR, 2.32; 95% CI (1.18, 4.56, [P = 0.014]) but did not improve adherence to an overall secondary preventative medication regimen (OR, 1.96; 95% CI (0.50, 7.67), [P = 0.332]).ConclusionInterventions can lead to improvement in adherence to secondary preventative medication after stroke. However, existing data is limited as several interventions, duration of follow‐up, and various definitions were used. These findings need to be interpreted with caution.
Violet and blue light‐induced green fluorescence emissions from dental caries
Authors: Shakibaie F , Walsh LJ 
Published: January 2016

AbstractBackgroundThe objective of this laboratory study was to compare violet and visible blue LED light‐elicited green fluorescence emissions from enamel and dentine in healthy or carious states.MethodsMicroscopic digital photography was undertaken using violet and blue LED illumination (405 nm and 455 nm wavelengths) of tooth surfaces, which were photographed through a custom‐made stack of green compensating filters which removed the excitation light and allowed green fluorescence emissions to pass. Green channel pixel data were analysed.ResultsDry sound enamel and sound root surfaces showed strong green fluorescence when excited by violet or blue lights. Regions of cavitated dental caries gave lower green fluorescence, and this was similar whether the dentine in the lesions was the same colour as normal dentine or was darkly coloured. The presence of saliva on the surface did not significantly change the green fluorescence, while the presence of blood diluted in saliva depressed green fluorescence.ConclusionsUsing violet or blue illumination in combination with green compensating filters could potentially aid in the assessment of areas of mineral loss.
Single institution experience of paediatric melanoma in Victoria, Australia
Authors: Le Quynh , Norris Diana , McClean Catriona A , Mcguiness Myra , Meani Rowena , Kelly John W , Pan Yan 
Published: January 2016

AbstractBackground/ObjectivesPaediatric melanoma is an uncommon presentation of melanoma that accounts for 3% of all paediatric cancers. The objective was to describe a series of paediatric melanoma cases presenting to a state‐wide tertiary referral service over the past 19 years.MethodsA search of the Victorian Melanoma Service database was performed to identify all patients under the age of 20 years diagnosed with melanoma from 1994 to 2013. Histological, demographic and phenotypical information for each patient was collected. Patients were matched against the Victorian Death Registry to identify those who had died. Fisher's exact test was used to examine associations. Melanoma‐specific survival was estimated using the Kaplan–Meier method.ResultsA total of 65 paediatric melanoma patients were included for analysis, in whom 72.3% of melanomas were diagnosed when they were 16–19 years of age with a mean age at diagnosis of 16 years. The mean Breslow thickness was 1.4 mm. It was greatest (3.4 mm) in the youngest age group (< 12 years of age). Ten patients developed nodal metastatic disease, eight of which progressed to visceral metastatic disease. The 5‐year melanoma‐specific survival rate was 96.8%.ConclusionThis is the first descriptive epidemiological study of paediatric melanoma in Victoria. Further large, population‐based, multi‐institutional studies of paediatric melanoma are warranted to provide a clearer understanding of this group of melanoma patients.
The Multifaceted Actions of Leukaemia Inhibitory Factor in Mediating Uterine Receptivity and Embryo Implantation
Authors: Rosario Gracy Xavier , Stewart Colin L 
Published: January 2016

Embryo implantation is mediated by the combined actions of the ovarian hormones E2 and P4 on the uterus. In addition, the pro‐inflammatory cytokine, leukaemia inhibitory factor (LIF), plays a pivotal role in regulating uterine receptivity. LIF is expressed in the endometrial glands and has a robust action on the uterine luminal epithelium (LE). In mice, LIF is induced by nidatory E2 and functions to convert the LE from a non‐receptive to an embryo‐responsive state. LIF mediates its actions by activating the JAK‐STAT pathway specifically in the LE. Activation of JAK‐STAT pathway results in the induction of many additional pathways, including some 40 + transcription factors, many of which initiate a cascade of changes affecting epithelial polarity, epithelial–mesenchymal interactions, angiogenesis, stromal cell decidualization, and inhibiting cell proliferation. This review discusses the role of LIF and the recent analysis of its action on the uterine LE in regulating endometrial receptivity and implantation.
On the classification and evolution of endogenous retrovirus: human endogenous retroviruses may not be ‘human’ after all
Authors: Escalera‐Zamudio Marina , Greenwood Alex D. 
Published: January 2016

Retroviruses, as part of their replication cycle, become integrated into the genome of their host. When this occurs in the germline the integrated proviruses can become an endogenous retrovirus (ERV) which may eventually become fixed in the population. ERVs are present in the genomes of all vertebrates including humans, where more than 50 groups of human endogenous retrovirus (HERVs) have been described within the last 30 years. Despite state‐of‐the‐art genomic tools available for retroviral discovery and the large number of retroviral sequences described to date, there are still gaps in understanding retroviral macroevolutionary patterns and host–retrovirus interactions and a lack of a coherent systematic classification particularly for HERVs. Here, we discuss the current knowledge on ERV (and HERV) classification, distribution and origins focusing on the role of cross‐species transmission in retroviral diversity.
The place of viscoelastic testing in clinical practice
Authors: Hans Gregory A. , Besser Martin W. 
Published: January 2016

SummaryHellmut Hartert was the first person to exploit the viscoelastic properties of clotting blood to measure blood coagulation in 1948. Since then, the technology has improved, allowing these analyses to be performed as point‐of‐care tests with immediately‐available results. The addition of several activators and inhibitors to the original assay creates a panel of tests able to quantify the different aspects of blood clotting that can rival conventional laboratory assays. However, although much progress has been made, the standardization and validation of these tests still need improvement. Viscoelastic analyses of blood coagulation are mainly used to guide haemostatic therapy in bleeding patients and have proven superior to standard clotting tests in some circumstances. There is potential to extend their use to other areas, such as drug monitoring, and diagnosis and management of congenital bleeding disorders. The forthcoming cartridge‐based assays are expected to improve the reliability and usability of viscoelastic assays of blood coagulation but high quality clinical trials remain urgently needed to determine their exact place, benefit and cost effectiveness.
Generalist Species Have a Central Role In a Highly Diverse Plant–Frugivore Network
Authors: Palacio Rubén Darío , Valderrama‐Ardila Carlos , Kattan Gustavo H. 
Published: January 2016

AbstractAnalysis of plant–frugivore interactions provides a quantitative framework for integrating community structure and ecosystem function in terms of how the roles and attributes of individual species contribute to network structure and resilience. In this study, we used centrality metrics to rank and detect the most important species in a mutualistic network of fruit‐eating birds and plants in a cloud forest in the Colombian Andes. We identified a central core of ten bird and seven plant species in a network of 135 species that perform dual roles as local hubs and connectors. The birds were mostly large forest frugivores, such as cracids, cotingas, and toucans, which consume fruits of all sizes. The plants were species of intermediate successional stages with small‐ to medium‐sized seeds that persist in mature forest or forest borders (e.g., Miconia, Cecropia, Ficus). We found the resilience of our network depends on super‐generalist species, because their elimination makes the network more prone to disassemble than random extinctions, potentially disrupting seed‐dispersal processes. At our study site, extirpation of large frugivores has already been documented, and if this continues, the network might collapse despite its high diversity. Our results suggest that generalist species play critical roles in ecosystem function and should be incorporated into conservation and monitoring programs.
Using geovisualization to assess lead sediment contamination in Lake St. Clair
Authors: Forsythe K. Wayne , Marvin Chris H. , Valancius Christine J. , Watt James P. , Swales Stephen J. , Aversa Joseph M. , Jakubek Daniel J. 
Published: January 2016

Key Messages

Geovisualization of contaminated sediment patterns is improved when bathymetry data are included.
Lead contamination in Lake St. Clair decreased from 1970 to 2001.
Visual interpretation of 3D surfaces highlights contaminated areas and provides additional information that could be used for remediation planning.
The adsorption performance of Vat Scarlet R on natural superfine needle down particles
Authors: Chen Fengxiang , Liu Xin , Liu Keshuai , Xiao Xinfang , Zhang Chunhua , Cheng Fan , Xia Liangjun , Zhou Yinshan , Dong Binghai , Wan Li , Wang Shimin , Xu Weilin 
Published: January 2016

Natural superfine needle down particles were successfully prepared on a self‐made machine and applied to remove hazardous dye Vat Scarlet R from aqueous solution. The adsorbent was characterised by scanning electron microscopy and Fourier transform infrared spectroscopy. The effects of contact time, pH, adsorbent dosage, initial dye concentration, and temperature on dye adsorption on natural superfine needle down particles were discussed. Equilibrium adsorption studies revealed that the Langmuir isotherm model gave the best fit to experimental data, which indicates monolayer adsorption on a homogeneous surface. The monolayer adsorption capacity increased with increasing temperature in the range 298–318 K for Vat Scarlet R adsorption, and the maximum obtained adsorption capacity was 76.823 mg g−1 at 318 K. The present study suggested that natural superfine needle down particles could be used as a good and cheaper adsorbent for dye effluent treatment.
Insights on How Museum Objects Mediate Recall of Nostalgic Life Episodes at a Shōwa Era Museum in Japan
Authors: Anderson David , Shimizu Hiroyuki , Campbell Chris 
Published: January 2016

AbstractUnderstanding visitors' nostalgic experiences in museums as they make connections between museum objects and their life histories is of considerable interest to the museum field. This study employed a qualitative multiple‐case narrative approach to understand the common characteristic themes about the nature of visitors' nostalgic recall, mediated though exhibits at a Shōwa era social history museum in Aichi Prefecture, Japan. Five sustaining characteristic themes about visitors' nostalgic recall are exemplified through five visitor cases in this study, including, a) Objects tied to collective identity and values perceived to be lost; b) Objects used or consumed as part of visitors' life‐scripts; c) Objects associated with individuals dear to the visitor; d) Objects associated with childhood; and e) Objects that invoke vicarious nostalgia. The outcomes of this study contribute to the broader understandings of the power of museum objects to incite strong nostalgic recollections and more broadly to our understanding of visitors' long‐term memories through their encounters with museum objects.
Biomarker value and pitfalls of serum S100B in the follow‐up of high‐risk melanoma patients
Authors: Gebhardt Christoffer , Lichtenberger Ramtin , Utikal Jochen 
Published: January 2016

SummaryBackground and objectivesSerum levels of S100B are standard in monitoring advanced malignant melanoma patients in order to discriminate progressive from non‐progressive disease. False‐positive results lead to distress among patients and increase the amount of cost‐intensive diagnostics. We therefore analyzed reported comorbid diseases as putative sources of excessive S100B release.Patients and methodsHere, we report a single‐center experience on serum S100B levels in 2,664 blood samples from 1,113 stage IB to IV melanoma patients (AJCC) who presented for follow‐up examinations over a period of 24 months.ResultsOverall, 295 (11 %) of patients developed disease progression. In patients with a high tumor load, the rate of false‐negative results was 30/185 (16 %). The rate of false‐positive results was 247/2369 (12 %). One hundred and six false‐positive results (69 %) compared to 46 true‐positive results (31 %) were found in patients with cardiovascular diseases such as arrhythmia (50/32) or previous myocardial infarction (22/14). Moreover, obesity (85/14), liver cirrhosis (31/10), migraine (18/2), chronic kidney disease (13/2), and previous stroke (11/1) were found to be associated with false‐positive S100B levels.ConclusionsSerum S100B is a useful quantitative biomarker in routine follow‐up of high‐risk melanoma patients. While false‐negative results are frequent in patients with low tumor load, false‐positive results are associated with several comorbid diseases and warrant careful reevaluation.