bluuebunny/crossref_metadata_2025_split huggingface dataset:
Techniques for sperm evaluation using fluorescent probes
Authors: Cunha Andrielle Thainar Mendes , Carvalho José Oliveira , Dode Margot Alves Nunes 
Published: July 2016

<p> </p><p>A variety of laboratory tests were developed to obtain more reliable results of sperm evaluation and increase the accuracy of sperm fertility predictions. These tests detected damage of sperm specific compartments or organelles, which cannot be detected in routine sperm analysis. The use of fluorescent probes and detection using fluorescent microscopy or flow cytometry is an important tool but a more precise and accurate laboratory test is needed. Propidium iodide and 6-carboxyfluorescein diacetate are used for evaluations of plasmatic membrane integrity. Fluorescein isothiocyanate, associated with conjugated lecithin <em>Psium sativum </em>or <em>Arachis hypogaea</em>, are used for evaluations of acrosome integrity. Two probes, MitoTracker or Rhodamine123, are generally used to measure the absence or presence of mitochondrial potential. However, a better option is 5,5’; 6,6’ - tetrachloro - 1,1’; 3,3’ -tetraetilbenzimidazolil-carbocyanine (JC-1) dye, which assesses not only the presence of mitochondrial potential and distinguished spermatozoa with poorly and highly functional mitochondria. Two techniques, TUNEL or COMETA, and the Acridine Orange Test (AOT) dye are used to evaluate chromatin integrity. A fluorescence technique based on chlortetracycline (CTC) or Merocyanine 540 is used to estimate whether sperm pass by or through the capacitation process. This review focuses on the fluorescent probes that are most widely used to evaluate plasma membrane integrity, capacitation, acrosome integrity, chromatin integrity and mitochondrial potential.</p>
Apparent digestibility of pacu (Piaractus mesopotamicus) diets containing different levels of phosphorus
Authors: Nervis Juliana Alice Lösch , Feiden Aldi , Moro Evandro Bilha , Moreno Marlon Casarini , Klein Sidnei , Boscolo Wilson Rogério 
Published: July 2016

<p>The present study aimed to evaluate pacu (<em>Piaractus mesopotamicus</em>) diets and determine the apparent digestibility at different levels of phosphorus using the feces collection method with an intestinal dissection marker. A total of 320 pacu with average weights of 768.5±36.34 g were used, and they were distributed in four 5 m³ net cages. The fish were fed isonitrogenous (27%), isoenergetic (3000 kcal/kg) and isocalcium (1.50%) diets with total phosphorus levels of 0.6, 0.8, 1.0 and 1.2%. The fish were incised with lateral openings to allow for feces removal from the rectum, and the fish were then sent for carcass chemical composition analysis. Significant differences were observed (P&lt;0.01) between treatments for the apparent diet digestibility, apparent phosphorous digestibility, available phosphorus and residual phosphorus. There was a linear decrease in apparent diet digestibility and apparent phosphorus digestibility with increasing levels of phosphorous in the diet, and the highest values were observed for the diet with 0.6% total phosphorus. For available phosphorus and residual phosphorus, there was a linear increase based on total phosphorus levels in the diet. No significant differences were observed for the chemical composition of the pacu carcasses. Therefore, the greatest digestibility of total phosphorus in the diet obtained through dissection was observed in the diet containing 0.6% total phosphorus, and the different levels of phosphorus did not influence the chemical composition of the pacu carcasses. </p>
A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing
Authors: Duncavage Eric J. , Abel Haley J. , Merker Jason D. , Bodner John B. , Zhao Qin , Voelkerding Karl V. , Pfeifer John D. 
Published: July 2016

Context.—Most current proficiency testing challenges for next-generation sequencing assays are methods-based proficiency testing surveys that use DNA from characterized reference samples to test both the wet-bench and bioinformatics/dry-bench aspects of the tests. Methods-based proficiency testing surveys are limited by the number and types of mutations that either are naturally present or can be introduced into a single DNA sample.
Objective.—To address these limitations by exploring a model of in silico proficiency testing in which sequence data from a single well-characterized specimen are manipulated electronically.
Design.—DNA from the College of American Pathologists reference genome was enriched using the Illumina TruSeq and Life Technologies AmpliSeq panels and sequenced on the MiSeq and Ion Torrent platforms, respectively. The resulting data were mutagenized in silico and 26 variants, including single-nucleotide variants, deletions, and dinucleotide substitutions, were added at variant allele fractions (VAFs) from 10% to 50%. Participating clinical laboratories downloaded these files and analyzed them using their clinical bioinformatics pipelines.
Results.—Laboratories using the AmpliSeq/Ion Torrent and/or the TruSeq/MiSeq participated in the 2 surveys. On average, laboratories identified 24.6 of 26 variants (95%) overall and 21.4 of 22 variants (97%) with VAFs greater than 15%. No false-positive calls were reported. The most frequently missed variants were single-nucleotide variants with VAFs less than 15%. Across both challenges, reported VAF concordance was excellent, with less than 1% median absolute difference between the simulated VAF and mean reported VAF.
Conclusions.—The results indicate that in silico proficiency testing is a feasible approach for methods-based proficiency testing, and demonstrate that the sensitivity and specificity of current next-generation sequencing bioinformatics across clinical laboratories are high.
The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents
Authors: Dececchi T. Alexander , Larsson Hans C.E. , Habib Michael B. 
Published: July 2016

Background:Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping.Methods:Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground truthed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds.Results:None of these behaviours were found to meet the biomechanical threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa likeMicroraptorandArchaeopteryx.Discussion:Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this separation is critical for our understanding of the origin of powered flight and avian evolution.
Solar cycle variations in ion composition in the dayside ionosphere of Titan
Authors: Madanian H. , Cravens T. E. , Richard M. S. , Waite J. H. , Edberg N. J. T. , Westlake J. H. , Wahlund J.‐E. 
Published: July 2016

AbstractOne Titanian year spans over two complete solar cycles, and the solar irradiance has a significant effect on ionospheric densities. Solar cycle 24 has been one of the quietest cycles on record. In this paper we show data from the Cassini ion and neutral mass spectrometer (INMS) and the radio and plasma wave science Langmuir probe spanning the time period from early 2005, at the declining phase of solar cycle 23, to late 2015 at the declining phase of solar cycle 24. Densities of different ion species measured by the INMS show a consistent enhancement for high solar activity, particularly near the ionospheric peak. The density enhancement is best seen in primary ion species such as CH3+ rather than heavier ion species such as HCNH+. Unlike at Earth, where the ionosphere and atmosphere thermally expand at high solar activity, at Titan the altitude of the ionospheric peak decreases, indicating that the underlying neutral atmosphere was less extensive. Among the major ion species, CH5+ shows the largest decrease in peak altitude, whereas heavy ions such as C3H5+ show very little decrease. We also calculate the ion production rates using a theoretical model and a simple empirical model using INMS data and show that these effectively predict the increased ion production rates at high solar activity.
Impacts of sea spray geoengineering on ocean biogeochemistry
Authors: Partanen Antti‐Ilari , Keller David P. , Korhonen Hannele , Matthews H. Damon 
Published: July 2016

AbstractWe used an Earth system model of intermediate complexity to study the effects of Solar Radiation Management (SRM) by sea spray geoengineering on ocean biogeochemistry. SRM slightly decreased global ocean net primary productivity (NPP) relative to the control run. The lower temperatures in the SRM run decreased NPP directly but also indirectly increased NPP in some regions due to changes in nutrient availability resulting from changes in ocean stratification and circulation. Reduced light availability had a minor effect on global total NPP but a major regional effect near the nutrient‐rich upwelling region off the coast of Peru, where light availability is the main limiting factor for phytoplankton growth in our model. Unused nutrients from regions with decreased NPP also fueled NPP elsewhere. In the context of RCP4.5 simulation used here, SRM decreased ocean carbon uptake due to changes in atmospheric CO2 concentrations, seawater chemistry, NPP, temperature, and ocean circulation.
The Fonualei Rift and Spreading Center: Effects of ultraslow spreading and arc proximity on back‐arc crustal accretion
Authors: Sleeper Jonathan D. , Martinez Fernando , Arculus Richard 
Published: July 2016

AbstractBack‐arc spreading center characteristics reflect interactions between plate‐driven mantle advection and melting and slab‐driven hydrous melting and buoyant upwelling in the mantle wedge. At the Fonualei Rift and Spreading Center (FRSC) in the Lau Basin, spreading rates decrease from slow to ultraslow, providing an opportunity to examine crustal accretion as the plate‐driven component is minimized. A new Lau Basin kinematic analysis predicts FRSC spreading rates of ~32–8 mm/yr southward, much slower than previous estimates of ~95–47 mm/yr. Here we examine FRSC morphology and geophysical characteristics as it approaches the Tofua arc volcanic front southward and spreading rates decrease, minimizing the plate‐driven component of mantle advection and maximizing buoyant hydrous flux melting. Axial morphology changes abruptly from a deep, flat, faulted axis ~100 km away from the arc to a volcanic ridge that shoals and increases in relief southward. Within ~50 km of the arc at the south end, the volcanic ridge is abruptly replaced by isolated volcanic cones bisected by volcanic rift zones and surrounded by anomalously deep seafloor. These morphologic changes likely reflect along‐axis focusing of mantle upwelling and melting similar to that seen at ultraslow mid‐ocean ridges, causing the change in morphology from a segmented ridge to spaced axial cones. We propose that as opening rates slow and the ridge approaches the arc, more of the inherently three‐dimensional pattern of hydrous flux melting and buoyant upwelling in the mantle wedge is expressed volcanically. With faster opening, two‐dimensional plate‐driven mantle advection dominates melt production, favoring ridges over point‐source features.
Outcome Expectations and Osteoarthritis: Association of Perceived Benefits of Exercise With Self‐Efficacy and Depression
Authors: Marszalek Jolanta , Price Lori Lyn , Harvey William F. , Driban Jeffrey B. , Wang Chenchen 
Published: July 2016

ObjectiveOutcome expectancy is recognized as a determinant of exercise engagement and adherence. However, little is known about which factors influence outcome expectations for exercise among people with knee osteoarthritis (OA). This is the first study to examine the association of outcome expectations for exercise with demographic, physical, and psychosocial outcomes in individuals with knee OA.MethodsWe performed a cross‐sectional analysis of the baseline data from a randomized trial of tai chi versus physical therapy in participants with symptomatic knee OA. Knee pain was evaluated using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC). Outcome expectations for exercise, self‐efficacy, depression, anxiety, stress, and social support were measured using standard instruments. Logistic regression models were utilized to determine associations with outcome expectations.ResultsThere were 262 participants, with a mean age of 59.8 years and a mean body mass index of 32.1 kg/m2; 69.1% of the participants were female, 51.5% were white, the mean disease duration was 8.6 years, and the mean WOMAC knee pain and function scores were 260.8 and 906.8, respectively. Higher outcome expectations for exercise were associated with greater self‐efficacy (odds ratio [OR] 1.25 [95% confidence interval (95% CI) 1.11–1.41]; P = 0.0004), as well as with fewer depressive symptoms (OR 0.84 for each 5‐point increase [95% CI 0.73–0.97]; P = 0.01). Outcome expectancy was not significantly associated with sex, race, education, pain, function, radiographic severity, social support, anxiety, or stress.ConclusionOur results suggest significant associations between outcome expectations for exercise and self‐efficacy and depression. Future studies should examine how these relationships longitudinally affect long‐term clinical outcomes of exercise‐based treatment for knee OA.
Nationwide Trends in Hospitalizations and In‐Hospital Mortality in Granulomatosis With Polyangiitis (Wegener's)
Authors: Wallace Zachary S. , Lu Na , Miloslavsky Eli , Unizony Sebastian , Stone John H. , Choi Hyon K. 
Published: July 2016

ObjectiveGranulomatosis with polyangiitis (Wegener's) (GPA) is a type of antineutrophil cytoplasmic antibody–associated vasculitis that often entails severe end‐organ damage and treatment‐related complications that frequently lead to hospitalization and death. Nationwide trends in hospitalizations and in‐hospital mortality over the past 2 decades are unknown and were evaluated in this study.MethodsUsing the National Inpatient Sample, the largest all‐payer inpatient database in the US, trends in hospitalizations with a discharge diagnosis of GPA (formerly Wegener's granulomatosis; International Classification of Disease, Ninth Revision, Clinical Modification code 446.4) between 1993 and 2011 were studied. Analyses were performed using hospital‐level sampling weights to obtain US national estimates.ResultsFrom 1993 to 2011, the annual hospitalization rate for patients with a principal diagnosis of GPA increased by 24%, from 5.1 to 6.3 per 1 million US persons (P < 0.0001 for trend); however, in‐hospital deaths in this group declined by 73%, from 9.1% to 2.5% (P < 0.0001 for trend), resulting in a 66% net reduction in the annual in‐hospital mortality rate. The median length of stay declined by 20%, from 6.9 days in 1993 to 5.5 days in 2011 (P = 0.0002 for trend). Infection was the most common principal discharge diagnosis when GPA was a secondary diagnosis, including among those who died during hospitalization.ConclusionThe findings from these nationally representative, contemporary inpatient data indicate that the in‐hospital mortality of GPA has declined substantially over the past 2 decades, while the overall hospitalization rate for GPA increased slightly. Infection remains a common principal hospitalization diagnosis among GPA patients, including hospitalizations resulting in mortality.
Symptom Recognition and Perceived Urgency of Help‐Seeking for Rheumatoid Arthritis and Other Diseases in the General Public: A Mixed Method Approach
Authors: Simons Gwenda , Belcher John , Morton Chris , Kumar Kanta , Falahee Marie , Mallen Christian D. , Stack Rebecca J. , Raza Karim 
Published: July 2016

ObjectiveClinical outcomes in rheumatoid arthritis (RA) are improved if the disease is treated early. However, treatment is often significantly delayed as a result of delayed help‐seeking by patients who fail to recognize its symptoms or the need for rapid medical attention. Two studies were conducted to investigate the role of symptom recognition in help‐seeking for the symptoms of RA, and compared this to symptom recognition and help‐seeking in angina and bowel cancer.MethodsA qualitative interview study with 31 individuals and a survey of 1,088 members of the general public (all without RA) were conducted. Both studies used vignettes describing the symptoms of RA, bowel cancer, and angina. Participants made causal attributions and rated the perceived seriousness of the symptoms and the urgency with which they would seek medical help if confronted with these symptoms.ResultsOnly a small proportion of participants in both studies recognized the symptoms of RA, whereas the symptoms of bowel cancer and angina were readily recognized by many participants and considered to be more serious and to require more rapid medical attention (Z = 14.7–34.2, P < 0.001).ConclusionAccurate symptom attribution and the perception that symptoms are indicative of a serious underlying condition are both important drivers for rapid help‐seeking. In the case of angina and bowel cancer, recent campaigns have promoted not only recognition of symptoms and their seriousness, but also emphasized the consequences of not seeking timely help. Our results suggest that these consequences should also be addressed in any public health campaign for RA.
Clinical Risk Factors for the Presence and Development of Vertebral Fractures in Patients With Ankylosing Spondylitis
Authors: Maas Fiona , Spoorenberg Anneke , van der Slik Boukje P. G. , van der Veer Eveline , Brouwer Elisabeth , Bootsma Hendrika , Bos Reinhard , Wink Freke R. , Arends Suzanne 
Published: July 2016

IntroductionTo investigate the prevalence and incidence of radiographic vertebral fractures and the association with patient characteristics, clinical assessments, and medication use in a large prospective cohort of patients with ankylosing spondylitis (AS) in daily clinical practice.MethodsConsecutive AS patients from the Groningen Leeuwarden AS (GLAS) cohort with baseline and 2‐year lateral radiographs of the thoracic and lumbar spine were included. Radiographs were scored for vertebral fractures by 2 readers according to the method of Genant et al. Differences in baseline characteristics between patients with and without radiographic vertebral fractures were explored.ResultsOf 292 included AS patients, 59 (20%) had radiographic vertebral fractures at baseline, 15 (6%) developed new fractures, and 7 (2%) showed an increase in the severity of existing fractures during 2 years of follow‐up. Most fractures were mild and located in the midthoracic and thoracolumbar region of the spine. The presence of vertebral fractures was significantly associated with older age, higher body mass index, longer smoking duration, larger occiput‐to‐wall distance, more spinal radiographic damage, and lower hip bone mineral density (BMD). The development of new or progressive vertebral fractures was also associated with older age and low BMD. Patients using nonsteroidal antiinflammatory drugs (NSAIDs) at baseline showed less prevalent and incident vertebral fractures.ConclusionIn this large AS cohort in daily clinical practice, radiographic vertebral fractures were frequently present in AS, especially in older patients with more advanced disease, low hip BMD, and a less healthy lifestyle. Interestingly, NSAID use was associated with a reduced vertebral fractures risk.
Depression and Progression of Subclinical Cardiovascular Disease in Systemic Lupus Erythematosus
Authors: Jorge April , Lertratanakul Apinya , Lee Jungwha , Pearce William , McPherson David , Thompson Trina , Barinas‐Mitchell Emma , Ramsey‐Goldman Rosalind 
Published: July 2016

ObjectiveWomen with systemic lupus erythematosus (SLE) have an increased incidence of premature cardiovascular disease (CVD). A relationship between depression and increased inflammation leading to CVD has been proposed. The aim of this study was to evaluate the relationship between depression and the progression of subclinical atherosclerosis in women with SLE.MethodsIn this prospective case–control study, 149 participants with SLE and 126 controls were followed over 5 years. Evaluation included laboratory studies, assessment of CVD risk factors, depression screening, ultrasound evaluations of carotid intima‐media thickness (CIMT) and carotid plaque, and assessment of SLE disease activity for the SLE cases.ResultsThe SLE group had a higher rate of depression: 29% compared with 11% in the control group (P = 0.003). When controlling for traditional CVD risk factors, the presence of baseline depression correlated with increased progression of CIMT in the SLE group, but not in the control group. The mean increase in CIMT was 0.026 mm in the SLE group without depression versus 0.064 mm in the depressed SLE group (P = 0.0096). There was no association between depression and carotid plaque in either group, with a calculated odds ratio for plaque progression in the depressed SLE group of 1.118 (95% confidence interval 0.476, 2.623) in the adjusted model.ConclusionWomen with SLE and concomitant depression have an increased risk of developing subclinical atherosclerosis, as measured by CIMT, but not by carotid plaque. The data suggest that depression, a potentially modifiable risk factor, may contribute to the increased risk of subclinical atherosclerosis in women with SLE.
A Typical Metal‐Ion‐Responsive Color‐Tunable Emitting Insulated π‐Conjugated Polymer Film
Authors: Hosomi Takuro , Masai Hiroshi , Fujihara Tetsuaki , Tsuji Yasushi , Terao Jun 
Published: July 2016

AbstractWe report the synthesis of an insulated π‐conjugated polymer containing 2,2′‐bipyridine moieties as metal coordination sites. Metal coordination to the polymer enabled easy and reversible tuning of the luminescent color without changes to the main chain skeleton. The permethylated α‐cyclodextrin (PM α‐CD)‐based insulation structure allowed the metalated polymers to demonstrate efficient emission even in the solid state, with identical spectral shapes to the dilute solutions. In addition, the coordination ability of the metal‐free polymer was maintained in the solid state, resulting in reversible changes in the luminescent color in response to the metal ions. The synthesized polymer is expected to be suitable for application in recyclable luminescent sensors to distinguish different metal ions.