bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic variation predicts regional and local intraspecific functional diversity in a perennial herb
Authors: Medrano Mónica , Herrera Carlos M. , Bazaga Pilar 
Published: September 2014

AbstractThe ecological significance of epigenetic variation has been generally inferred from studies on model plants under artificial conditions, but the importance of epigenetic differences between individuals as a source of intraspecific diversity in natural plant populations remains essentially unknown. This study investigates the relationship between epigenetic variation and functional plant diversity by conducting epigenetic (methylation‐sensitive amplified fragment length polymorphisms, MSAP) and genetic (amplified fragment length polymorphisms, AFLP) marker–trait association analyses for 20 whole‐plant, leaf and regenerative functional traits in a large sample of wild‐growing plants of the perennial herb Helleborus foetidus from ten sampling sites in south‐eastern Spain. Plants differed widely in functional characteristics, and exhibited greater epigenetic than genetic diversity, as shown by per cent polymorphism of MSAP fragments (92%) or markers (69%) greatly exceeding that for AFLP ones (41%). After controlling for genetic structuring and possible cryptic relatedness, every functional trait considered exhibited a significant association with at least one AFLP or MSAP marker. A total of 27 MSAP (13.0% of total) and 12 AFLP (4.4%) markers were involved in significant associations, which explained on average 8.2% and 8.0% of trait variance, respectively. Individual MSAP markers were more likely to be associated with functional traits than AFLP markers. Between‐site differences in multivariate functional diversity were directly related to variation in multilocus epigenetic diversity after multilocus genetic diversity was statistically accounted for. Results suggest that epigenetic variation can be an important source of intraspecific functional diversity in H. foetidus, possibly endowing this species with the capacity to exploit a broad range of ecological conditions despite its modest genetic diversity.
Mobile Impact Testing for Structural Flexibility Identification with only a Single Reference
Authors: Zhang J. , Guo S.L. , Zhang Q.Q. 
Published: September 2014

AbstractIn contrast to the traditional impact test method requiring a number of sensors to measure the entire structure, a mobile impact test method sequentially measuring segments of the structure and the related data processing strategy is proposed. Especially, only a single reference node is required when integrating measurements of the segments to identify the flexibility characteristic of the entire structure. Equations are first derived to adjust the magnitudes of mode shapes of the substructure to a same scaling level. Then the phase angle concept is utilized to determine the coherent signs of mode shapes for structural flexibility identification. The advantage of the proposed method is that it outputs the same flexibility identification results as the traditional impact test method, whereas it only requires a single reference no matter how many segments of the structure are divided, thus it significantly speeds up the impact test and makes it be an ideal approach for rapid testing of short/middle span bridges. Numerical and experiment examples investigated successfully verify the effectiveness of the proposed method for structural flexibility identification.
Experiences from the Brazilian Atlantic Forest: ecological findings and conservation initiatives
Authors: Joly Carlos A. , Metzger Jean Paul , Tabarelli Marcelo 
Published: September 2014

SummaryThe Brazilian Atlantic Forest hosts one of the world's most diverse and threatened tropical forest biota. In many ways, its history of degradation describes the fate experienced by tropical forests around the world. After five centuries of human expansion, most Atlantic Forest landscapes are archipelagos of small forest fragments surrounded by open‐habitat matrices. This ‘natural laboratory’ has contributed to a better understanding of the evolutionary history and ecology of tropical forests and to determining the extent to which this irreplaceable biota is susceptible to major human disturbances. We share some of the major findings with respect to the responses of tropical forests to human disturbances across multiple biological levels and spatial scales and discuss some of the conservation initiatives adopted in the past decade. First, we provide a short description of the Atlantic Forest biota and its historical degradation. Secondly, we offer conceptual models describing major shifts experienced by tree assemblages at local scales and discuss landscape ecological processes that can help to maintain this biota at larger scales. We also examine potential plant responses to climate change. Finally, we propose a research agenda to improve the conservation value of human‐modified landscapes and safeguard the biological heritage of tropical forests.

Contents

Summary
459

I.
Introduction
459

II.
The Atlantic Forest: a highly diverse, relevant and threatened forest
460

III.
Biotic homogenization and forest secondarization
462

IV.
Species persistence at larger scales
464

V.
Future threats: climate change impacts
466

VI.
Atlantic Forest conservation: integrating basic and applied research agendas
467

VII.
Concluding remarks
469

Acknowledgements
469

References
469
The unseen iceberg: plant roots in arctic tundra
Authors: Iversen Colleen M. , Sloan Victoria L. , Sullivan Patrick F. , Euskirchen Eugenie S. , McGuire A. David , Norby Richard J. , Walker Anthony P. , Warren Jeffrey M. , Wullschleger Stan D. 
Published: September 2014

SummaryPlant roots play a critical role in ecosystem function in arctic tundra, but root dynamics in these ecosystems are poorly understood. To address this knowledge gap, we synthesized available literature on tundra roots, including their distribution, dynamics and contribution to ecosystem carbon and nutrient fluxes, and highlighted key aspects of their representation in terrestrial biosphere models. Across all tundra ecosystems, belowground plant biomass exceeded aboveground biomass, with the exception of polar desert tundra. Roots were shallowly distributed in the thin layer of soil that thaws annually, and were often found in surface organic soil horizons. Root traits – including distribution, chemistry, anatomy and resource partitioning – play an important role in controlling plant species competition, and therefore ecosystem carbon and nutrient fluxes, under changing climatic conditions, but have only been quantified for a small fraction of tundra plants. Further, the annual production and mortality of fine roots are key components of ecosystem processes in tundra, but extant data are sparse. Tundra root traits and dynamics should be the focus of future research efforts. Better representation of the dynamics and characteristics of tundra roots will improve the utility of models for the evaluation of the responses of tundra ecosystems to changing environmental conditions.

Contents

Summary
34

I.
Arctic tundra and plant roots: an introduction
35

II.
A comprehensive literature review
35

III.
A brief history of fine‐root studies in tundra ecosystems
41

IV.
Distribution and dynamics of tundra plant roots: current knowledge and future directions
43

V.
Contribution of living plant roots to fluxes of CO2 and CH4 from tundra ecosystems to the atmosphere
49

VI.
The role of fine roots in tundra ecosystem nutrient cycling
50

VII.
Opportunities for improving the representation of root processes in arctic models
51

VIII.
Conclusions and priorities for future research
52

Acknowledgements
53

References
53
The Oral Surgery trainee perspective
Authors: Patel V. , Ormondroyd L. 
Published: September 2014

AbstractAimThis study aims to gather information about Oral Surgery training programmes by carrying out a survey of the trainees currently in post.Materials and methodsA web‐based questionnaire was sent to current Oral Surgery trainees. Questions about training environment, clinical exposure, examinations and future career aspirations were included.ResultsThirty of the 40 trainees contacted responded by part or fully completing the questionnaire. The mean time period of qualification from dental school to Oral Surgery training was 5.1 years. The majority, 80%, of trainees were on a 3‐year full‐time programme that entitled them to sit the Membership in Oral Surgery Examination (M Oral Surg) only. Four trainees who responded were eligible to sit both M Oral Surg and the Intercollegiate Specialty Fellowship Exam.ConclusionsThe questionnaire highlighted areas Oral Surgery trainees perceived to be important for their training and development. Identification of these issues will allow attention to be focused in addressing them.
Regression Analysis of Length‐biased and Right‐censored Failure Time Data with Missing Covariates
Authors: Hu Na , Chen Xuerong , Sun Jianguo 
Published: September 2014

AbstractLength‐biased and right‐censored failure time data arise from many fields, and their analysis has recently attracted a great deal of attention. Two examples of the areas that often produce such data are epidemiological studies and cancer screening trials. In this paper, we discuss regression analysis of such data in the presence of missing covariates, for which no established inference procedure seems to exist. For the problem, we consider the data arising from the proportional hazards model and propose two inverse probability weighted estimation procedures. The asymptotic properties of the resulting estimators are established, and the extensive simulation study conducted for the evaluation of the proposed methods suggests that they work well for practical situations.
Comparison of equine endometrial cytology samples collected with uterine swab, uterine brush, and low‐volume lavage from healthy mares
Authors: Bohn Andrea A. , Ferris Ryan A. , McCue Patrick M. 
Published: September 2014

BackgroundThere have been no studies evaluating and comparing the quality of equine endometrial cytology samples obtained via the 3 most common sampling techniques from healthy mares.ObjectivesThe objective was to compare the quality and contents of equine endometrial samples obtained by 3 different sampling techniques: double‐guarded uterine swab, double‐guarded uterine brush, and low‐volume lavage (LVL), all collected from clinically healthy mares.MethodsSamples were collected from 24 healthy mares in early estrus. In 19 mares, samples were obtained in a sequential manner, first with the swab, then with the brush, followed by LVL. Cytologic evaluation included estimates of quality, cellularity, and presence of inflammatory cells. The clinical pathologist performing the evaluations was blinded to the collection technique. The Friedman test with Dunn's multiple comparisons was used to compare rankings of quality, cellularity, and the presence or absence of inflammatory cells. Observed cytologic differences were described.ResultsAll techniques provided diagnostic samples, but swabs yielded the lowest quality sample. In our hands, the uterine brush provided the highest quality sample. Low‐volume lavage samples contained higher numbers of neutrophils, although, in general, < 1 neutrophil/400× field is expected for all endometrial sampling techniques in healthy mares.ConclusionsAll sampling techniques can be adequate methods for endometrial cytology, but the brush technique consistently provided the best sample. Sample contamination or poor slide quality can adversely affect interpretation. The most accurate criteria for determining what constitutes mild endometritis in mares have yet to be established.
Physiological links between circadian rhythms, metabolism and nutrition
Authors: Johnston Jonathan D. 
Published: September 2014

New Findings
What is the topic of this review?
This review provides a discussion of the links between circadian, metabolic and nutritional physiology, with a particular focus on mouse and human studies.
What advances does it highlight?
Links between circadian biology and metabolism exist from the molecular level through to whole‐organism physiology. Advances highlighted include the following: interactions between circadian clock genes/proteins and intracellular metabolic pathways; identification of the function of clocks in specific peripheral tissues; effects of timed feeding; and the variable effect of obesity on rhythms.
Circadian rhythms, metabolism and nutrition are closely interlinked. A great deal of recent research has investigated not only how aspects of metabolic physiology are driven by circadian clocks, but also how these circadian clocks are themselves sensitive to metabolic change. At the cellular level, novel feedback loops have been identified that couple circadian ‘clock genes’ and their proteins to expression of nuclear receptors, regulation of redox state and other major pathways. Using targeted disruption of circadian clocks, mouse models are providing novel insight into the role of tissue‐specific clocks in glucose homeostasis and body weight regulation. The relationship between circadian rhythms and obesity appears complex, with variable alteration of rhythms in obese individuals. However, it is clear from animal studies that the timing and nutritional composition of meals can regulate circadian rhythms, particularly in peripheral tissues. Translation of these findings to human physiology now represents an important goal.
The role of gut endocrine cells in control of metabolism and appetite
Authors: Parker Helen E. , Gribble Fiona M. , Reimann Frank 
Published: September 2014

New Findings
What is the topic of this review?
Gut hormones, especially glucagon‐like peptide‐1 (GLP‐1), have beneficial effects in diabetes and obesity. Recent research addresses the underlying mechanisms of the secretion and action of GLP‐1.
What advances does it highlight?
The development of transgenic reporter mice with fluorescently tagged GLP‐1‐secreting cells has helped to characterize the molecular mechanisms underlying hormone secretion and has challenged the traditional classification of enteroendocrine cells by hormone expression alone. Recent adoption of this strategy to label GLP‐1‐receptor‐positive cells has highlighted that peripheral and centrally released GLP‐1 acts on a number of different targets, including a variety of neurons. Evidence for their role in glucose homeostasis and appetite control is discussed.
After food is ingested, nutrients pass through the gastrointestinal tract, stimulating the release of a range of peptide hormones. Among their many local, central and peripheral actions, these hormones act to mediate glucose metabolism and satiety. Indeed, it is the modification of gut hormone secretion that is considered partly responsible for the normalization of glycaemic control and the reduction in appetite seen in many patients after certain forms of bariatric surgery. This review describes recent developments in our understanding of the secretion and action of anorexigenic gut hormones, primarily concentrating on glucagon‐like peptide‐1 (GLP‐1).
Ball Python Nidovirus: a Candidate Etiologic Agent for Severe Respiratory Disease in
Python regius
Authors: Stenglein Mark D. , Jacobson Elliott R. , Wozniak Edward J. , Wellehan James F. X. , Kincaid Anne , Gordon Marcus , Porter Brian F. , Baumgartner Wes , Stahl Scott , Kelley Karen , Towner Jonathan S. , DeRisi Joseph L. 
Published: September 2014

ABSTRACT

A severe, sometimes fatal respiratory disease has been observed in captive ball pythons (
Python regius
) since the late 1990s. In order to better understand this disease and its etiology, we collected case and control samples and performed pathological and diagnostic analyses. Electron micrographs revealed filamentous virus-like particles in lung epithelial cells of sick animals. Diagnostic testing for known pathogens did not identify an etiologic agent, so unbiased metagenomic sequencing was performed. Abundant nidovirus-like sequences were identified in cases and were used to assemble the genome of a previously unknown virus in the order
Nidovirales
. The nidoviruses, which were not previously known to infect nonavian reptiles, are a diverse order that includes important human and veterinary pathogens. The presence of the viral RNA was confirmed in all diseased animals (
n
= 8) but was not detected in healthy pythons or other snakes (
n
= 57). Viral RNA levels were generally highest in the lung and other respiratory tract tissues. The 33.5-kb viral genome is the largest RNA genome yet described and shares canonical characteristics with other nidovirus genomes, although several features distinguish this from related viruses. This virus, which we named ball python nidovirus (BPNV), will likely establish a new genus in
Torovirinae
subfamily. The identification of a novel nidovirus in reptiles contributes to our understanding of the biology and evolution of related viruses, and its association with lung disease in pythons is a promising step toward elucidating an etiology for this long-standing veterinary disease.

IMPORTANCE
Ball pythons are popular pets because of their diverse coloration, generally nonaggressive behavior, and relatively small size. Since the 1990s, veterinarians have been aware of an infectious respiratory disease of unknown cause in ball pythons that can be fatal. We used unbiased shotgun sequencing to discover a novel virus in the order
Nidovirales
that was present in cases but not controls. While nidoviruses are known to infect a variety of animals, this is the first report of a nidovirus recovered from any reptile. This report will enable diagnostics that will assist in determining the role of this virus in the causation of disease, which would allow control of the disease in zoos and private collections. Given its evolutionary divergence from known nidoviruses and its unique host, the study of reptile nidoviruses may further our understanding of related diseases and the viruses that cause them in humans and other animals.
Critical Glycosylated Residues in Exon Three of Erythrocyte Glycophorin A Engage Plasmodium falciparum EBA-175 and Define Receptor Specificity
Authors: Salinas Nichole D. , Paing May M. , Tolia Niraj H. 
Published: September 2014

ABSTRACT

Erythrocyte invasion is an essential step in the pathogenesis of malaria. The erythrocyte binding-like (EBL) family of
Plasmodium falciparum
proteins recognizes glycophorins (Gp) on erythrocytes and plays a critical role in attachment during invasion. However, the molecular basis for specific receptor recognition by each parasite ligand has remained elusive, as is the case with the ligand/receptor pair
P. falciparum
EBA-175 (PfEBA-175)/GpA. This is due largely to difficulties in producing properly glycosylated and functional receptors. Here, we developed an expression system to produce recombinant glycosylated and functional GpA, as well as mutations and truncations. We identified the essential binding region and determinants for PfEBA-175 engagement, demonstrated that these determinants are required for the inhibition of parasite growth, and identified the glycans important in mediating the PfEBA-175–GpA interaction. The results suggest that PfEBA-175 engages multiple glycans of GpA encoded by exon 3 and that the presentation of glycans is likely required for high-avidity binding. The absence of exon 3 in GpB and GpE due to a splice site mutation confers specific recognition of GpA by PfEBA-175. We speculate that GpB and GpE may have arisen due to selective pressure to lose the PfEBA-175 binding site in GpA. The expression system described here has wider application for examining other EBL members important in parasite invasion, as well as additional pathogens that recognize glycophorins. The ability to define critical binding determinants in receptor-ligand interactions, as well as a system to genetically manipulate glycosylated receptors, opens new avenues for the design of interventions that disrupt parasite invasion.

IMPORTANCE
Plasmodium falciparum
uses distinct ligands that bind host cell receptors for invasion of red blood cells (RBCs) during malaria infection. A key entry pathway involves
P. falciparum
EBA-175 (PfEBA-175) recognizing glycophorin A (GpA) on RBCs. Despite knowledge of this protein-protein interaction, the complete mechanism for specific receptor engagement is not known. PfEBA-175 recognizes GpA but is unable to engage the related RBC receptor GpB or GpE. Understanding the necessary elements that enable PfEBA-175 to specifically recognize GpA is critical in developing specific and potent inhibitors of PfEBA-175 that disrupt host cell invasion and aid in malaria control. Here, we describe a novel system to produce and manipulate the host receptor GpA. Using this system, we probed the elements in GpA necessary for engagement and thus for host cell invasion. These studies have important implications for understanding how ligands and receptors interact and for the future development of malaria interventions.
Outcomes of full-term infants with bilious vomiting: observational study of a retrieved cohort
Authors: Mohinuddin Syed , Sakhuja Pankaj , Bermundo Benjie , Ratnavel Nandiran , Kempley Stephen , Ward Harry C , Sinha Ajay 
Published: September 2014

Bilious vomiting in a neonate may be a sign of intestinal obstruction often resulting in transfer requests to surgical centres. The aim of this study was to assess the use of clinical findings at referral in predicting outcomes and to determine how often such patients have a time-critical surgical condition (eg, volvulus, where a delay in treatment is likely to compromise gut viability).Methods4-year data and outcomes of all term newborns aged ≤7 days with bilious vomiting transferred by a regional transfer service were analysed. Specificity, sensitivity, likelihood ratios, correlations, prior and posterior probability of clinical findings in predicting newborns with surgical diagnosis were calculated.ResultsOf 163 neonates with bilious vomiting, 75 (46%) had a surgical diagnosis and 23 (14.1%) had a time-critical surgical condition. The diagnosis of a surgical condition in neonates with bilious vomiting was significantly associated with abdominal distension (χ2=5.17, p=0.023), abdominal tenderness (χ2=5.90, p=0.015) and abnormal abdominal X-ray findings (χ2=5.68, p=0.017) but not with palpation findings of a soft as compared with a tense abdomen (χ2=3.21, p=0.073). Abnormal abdominal X-ray, abdominal distension and tenderness had 97%, 74% and 62% sensitivity, respectively, with regard to association with an underlying surgical diagnosis. Normal abdominal X-ray reduced the posterior probability of surgical diagnosis from 50% to 16%. Overall, clinical findings at referral did not differentiate between infants with or without surgical or time-critical condition.ConclusionsWe recommend that term neonates with bilious vomiting referred for transfer are prioritised as time critical.