bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effective freezing rate for semen cryopreservation in endangered Mediterranean brown trout (Salmo trutta macrostigma) inhabiting the Biferno river (South Italy)
Authors: Iaffaldano Nicolaia , Di Iorio Michele , Manchisi Angelo , Esposito Stefano , Gibertoni Pier Paolo 
Published: December 2015

SummaryThis study was designed to determine: (i) thein vitroeffects of different freezing rates on post-thaw semen quality of Mediterranean brown trout (Salmo trutta macrostigma) from the Biferno river; and (ii) thein vivofertilization and hatching percentage of freezing rate giving rise to the best post-thaw semen quality.Pooled semen samples were diluted 1:3 (v:v) in a freezing extender composed of 300 mM glucose, 10% egg yolk and 10% dimethyl sulfoxide (DMSO). The extended semen was packaged in 0.25 ml plastic straws and frozen at different heights above the liquid nitrogen surface (1, 5 or 10 cm) for 10 min to give three different freezing rates. Semen samples were thawed at 30°C for 10 s. The variables assessed after thawing were sperm motility, duration of motility and viability.Our results clearly indicate a significant effect of freezing rate on post-thaw semen quality. Semen frozen 5 cm above the liquid nitrogen surface showed the best quality after freezing/thawing. Based on thesein vitrodata, 2 groups of 200 eggs were fertilized with fresh semen or semen frozen 5 cm above the liquid nitrogen surface. Fertilization and hatching rates recorded for eggs fertilized with frozen semen were significantly lower (25.4% and 22.5%, respectively) than the ones obtained using fresh semen (87.8% and 75.5%, respectively). An effective freezing protocol will allow for the creation of a sperm cryobank to recover the original population of Mediterranean brown trout in the Biferno river.
Systemic rapamycin to prevent in-stent stenosis in peripheral pulmonary arterial disease: early clinical experience
Authors: Hallbergson Anna , Esch Jesse J. , Tran Trang X. , Lock James E. , Marshall Audrey C. 
Published: December 2015

AbstractObjectivesWe have taken a novel approach using oral rapamycin – sirolimus – as a medical adjunct to percutaneous therapy in patients with in-stent stenosis and high risk of right ventricular failure.BackgroundPeripheral pulmonary artery stenosis can result in right ventricular hypertension, dysfunction, and death. Percutaneous pulmonary artery angioplasty and stent placement acutely relieve obstructions, but patients frequently require re-interventions due to re-stenosis. In patients with tetralogy of Fallot or arteriopathy, the problem of in-stent stenosis contributes to the rapidly recurrent disease.MethodsRapamycin was administered to 10 patients (1.5–18 years) with peripheral pulmonary stenosis and in-stent stenosis and either right ventricular hypertension, pulmonary blood flow maldistribution, or segmental pulmonary hypertension. Treatment was initiated around the time of catheterisation and continued for 1–3 months. Potential side-effects were monitored by clinical review and blood tests.ResultsTarget serum rapamycin level (6–10 ng/ml) was accomplished in all patients; eight of the nine patients who returned for clinically indicated catheterisations demonstrated reduction in in-stent stenosis, and eight of the 10 patients experienced no significant side-effects. Among all, one patient developed diarrhoea requiring drug discontinuation, and one patient experienced gastrointestinal bleeding while on therapy that was likely due to an indwelling feeding tube and this patient tolerated rapamycin well following tube removal.ConclusionsOur initial clinical experience supports that patients with peripheral pulmonary artery stenosis can be safely treated with rapamycin. Systemic rapamycin may provide a novel medical approach to reduce in-stent stenosis.
Neuropsychological Correlates of Hazard Perception in Older Adults
Authors: McInerney Katalina , Suhr Julie 
Published: December 2015

AbstractObjectives:Hazard perception, the ability to identify and react to hazards while driving, is of growing importance in driving research, given its strong relationship to real word driving variables. Furthermore, although poor hazard perception is associated with novice drivers, recent research suggests that it declines with advanced age. In the present study, we examined the neuropsychological correlates of hazard perception in a healthy older adult sample.Methods:A total of 68 adults age 60 and older who showed no signs of dementia and were active drivers completed a battery of neuropsychological tests as well as a hazard perception task. Tests included the Repeatable Battery for the Assessment of Neuropsychological Status, Wechsler Test of Adult Reading, Trail Making Test, Block Design, Useful Field of View, and the Delis-Kaplan Executive Function System Color Word Interference Test.Results:Hazard perception errors were related to visuospatial/constructional skills, processing speed, memory, and executive functioning skills, with a battery of tests across these domains accounting for 36.7% of the variance in hazard perception errors. Executive functioning, particularly Trail Making Test part B, emerged as a strong predictor of hazard perception ability.Conclusions:Consistent with prior work showing the relationship of neuropsychological performance to other measures of driving ability, neuropsychological performance was associated with hazard perception skill. Future studies should examine the relationship of neuropsychological changes in adults who are showing driving impairment and/or cognitive changes associated with Mild Cognitive Impairment or dementia. (JINS, 2015,21, 332–340)
Carbonization in Titan Tholins: implication for low albedo on surfaces of Centaurs and trans-Neptunian objects
Authors: Giri Chaitanya , McKay Christopher P. , Goesmann Fred , Schäfer Nadine , Li Xiang , Steininger Harald , Brinckerhoff William B. , Gautier Thomas , Reitner Joachim , Meierhenrich Uwe J. 
Published: December 2015

AbstractAstronomical observations of Centaurs and trans-Neptunian objects (TNOs) yield two characteristic features – near-infrared (NIR) reflectance and low geometric albedo. The first feature apparently originates due to complex organic material on their surfaces, but the origin of the material contributing to low albedo is not well understood. Titan tholins synthesized to simulate aerosols in the atmosphere of Saturn's moon Titan have also been used for simulating the NIR reflectances of several Centaurs and TNOs. Here, we report novel detections of large polycyclic aromatic hydrocarbons, nanoscopic soot aggregates and cauliflower-like graphite within Titan tholins. We put forth a proof of concept stating the surfaces of Centaurs and TNOs may perhaps comprise of highly ‘carbonized’ complex organic material, analogous to the tholins we investigated. Such material would apparently be capable of contributing to the NIR reflectances and to the low geometric albedos simultaneously.
Hepatitis C virus utilizes VLDLR as a novel entry pathway
Authors: Ujino Saneyuki , Nishitsuji Hironori , Hishiki Takayuki , Sugiyama Kazuo , Takaku Hiroshi , Shimotohno Kunitada 
Published: December 2015

Significance
Hepatitis C virus (HCV) utilizes various host factors to enter host cells. During the process of HCV entry, cell surface-residing lipoprotein receptors such as scavenger receptor class B member 1 (SR-BI) play important roles through interactions with virus envelope protein E2 and virus-associated apolipoproteins such as apolipoprotein E (ApoE). CD81 plays a crucial role during this process in association with HCV. Here, we identified another pathway for HCV entry that does not use CD81. This pathway involves an association with the very-low-density lipoprotein receptor (VLDLR) and does not require previously reported host factors such as claudin, occludin, or CD81. This finding may shed new light on the process of HCV entry.
A linear relationship between wave power and erosion determines salt-marsh resilience to violent storms and hurricanes
Authors: Leonardi Nicoletta , Ganju Neil K. , Fagherazzi Sergio 
Published: December 2015

Significance
In recent years, there has been a flurry of restoration projects aimed at mitigating the impact of coastal storms using salt marshes and vegetated surfaces (called “living shorelines”). Based on a large dataset of salt marsh erosion and wave measurements collected all around the world, we find that erosion rates of marsh boundaries and incident wave energy collapse into a unique linear relationship. Our result clearly shows that long-term salt marsh deterioration is dictated by average wave conditions, and it is, therefore, predictable. Violent storms and hurricanes contribute less than 1% to long-term salt marsh erosion rates. This result is of high value for coastal restoration projects and the use of living shorelines to mitigate storms effect.
Surface expression, peptide repertoire, and thermostability of chicken class I molecules correlate with peptide transporter specificity
Authors: Tregaskes Clive A. , Harrison Michael , Sowa Anna K. , van Hateren Andy , Hunt Lawrence G. , Vainio Olli , Kaufman Jim 
Published: December 2015

SignificanceMajor histocompatibility complex (MHC) molecules play crucial roles in the immune response to pathogens and tumors by presenting protein fragments (peptides) to T lymphocytes. Recently, it has become clear that the breadth of peptide presentation by MHC class I molecules is inversely correlated with the level of cell surface expression, a relationship that is correlated with resistance to Marek’s disease in chickens and with progression to AIDS in humans. In this article, evidence is presented that class I molecules vary in a suite of correlated properties, including thermostability, that are influenced, at least in part, by the breadth of peptide translocation by the transporters for antigen presentation (TAPs) that pump peptides to be loaded.
Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs
Authors: Marsden Clare D. , Ortega-Del Vecchyo Diego , O’Brien Dennis P. , Taylor Jeremy F. , Ramirez Oscar , Vilà Carles , Marques-Bonet Tomas , Schnabel Robert D. , Wayne Robert K. , Lohmueller Kirk E. 
Published: December 2015

SignificanceDogs have an integral role in human society, and recent evidence suggests they have a unique bond that elicits a beneficial hormonal response in both dogs and human handlers. Here, we show this relationship has a dark side. Small population size during domestication and strong artificial selection for breed-defining traits has unintentionally increased the numbers of deleterious genetic variants. Our findings question the overly typological practice of breeding individuals that best fit breed standards, a Victorian legacy. This practice does not allow selection to remove potentially deleterious variation associated with genes responsible for breed-specific traits.
Transplantation of human embryonic stem cell-derived retinal tissue in two primate models of retinal degeneration
Authors: Shirai Hiroshi , Mandai Michiko , Matsushita Keizo , Kuwahara Atsushi , Yonemura Shigenobu , Nakano Tokushige , Assawachananont Juthaporn , Kimura Toru , Saito Koichi , Terasaki Hiroko , Eiraku Mototsugu , Sasai Yoshiki , Takahashi Masayo 
Published: December 2015

Significance
We first confirmed the ability of human embryonic stem cell-derived retina (hESC-retina) to form structured mature photoreceptor layers after transplantation into nude rats. We then developed two monkey models of retinal degeneration and evaluated their utility as host models for transplantation studies. Finally, we performed a pilot study of hESC-retina transplantation in the developed models and conducted in vivo monitoring studies using clinical devices and subsequently confirmed structured graft maturation and the potential formation of synaptic contacts between graft and host cells. This study demonstrates the competency of hESC-retina as a graft source and the eligibility of two newly developed monkey models that may be useful in future, long-term, functional studies of retinal transplantation.
Nuclear deformability and telomere dynamics are regulated by cell geometric constraints
Authors: Makhija Ekta , Jokhun D. S. , Shivashankar G. V. 
Published: December 2015

Significance
Physical properties of the cell nucleus are important for various cellular functions. However, the role of cell geometry and active cytoskeletal forces in regulating nuclear dynamics and chromatin dynamics is not well understood. Our results show cells with reduced matrix constraints have short actomyosin structures. These dynamic structures together with lower lamin A/C levels, resulting in softer nuclei, may provide the driving force for nuclear fluctuations. Furthermore, we observed increased dynamics of heterochromatin and telomere structures under such reduced cell–matrix interactions. We conclude that extracellular matrix signals alter cytoskeletal organization and lamin A/C expression levels, which together lead to nuclear and chromatin dynamics. These results highlight the importance of matrix constraints in regulating gene expression and maintaining genome integrity.
Cold season emissions dominate the Arctic tundra methane budget
Authors: Zona Donatella , Gioli Beniamino , Commane Róisín , Lindaas Jakob , Wofsy Steven C. , Miller Charles E. , Dinardo Steven J. , Dengel Sigrid , Sweeney Colm , Karion Anna , Chang Rachel Y.-W. , Henderson John M. , Murphy Patrick C. , Goodrich Jordan P. , Moreaux Virginie , Liljedahl Anna , Watts Jennifer D. , Kimball John S. , Lipson David A. , Oechel Walter C. 
Published: December 2015

Significance
Arctic ecosystems are major global sources of methane. We report that emissions during the cold season (September to May) contribute ≥50% of annual sources of methane from Alaskan tundra, based on fluxes obtained from eddy covariance sites and from regional fluxes calculated from aircraft data. The largest emissions were observed at the driest site (<5% inundation). Emissions of methane in the cold season are linked to the extended “zero curtain” period, where soil temperatures are poised near 0 °C, indicating that total emissions are very sensitive to soil climate and related factors, such as snow depth. The dominance of late season emissions, sensitivity to soil conditions, and importance of dry tundra are not currently simulated in most global climate models.
Modeling the status, trends, and impacts of wild bee abundance in the United States
Authors: Koh Insu , Lonsdorf Eric V. , Williams Neal M. , Brittain Claire , Isaacs Rufus , Gibbs Jason , Ricketts Taylor H. 
Published: December 2015

SignificanceIn 2014, a presidential memorandum called for an assessment of the nation’s pollinators, in response to growing awareness of their economic importance and recent declines. We assess, for the first time to our knowledge, the status and trends of wild bee abundance and their potential impacts on pollination services across the United States. We develop national maps of wild bee abundance, report land-use–driven changes over time, and relate them to trends in agricultural demand for pollination. We estimate uncertainty in the findings, so future research can target the least-understood regions and topics. Our findings can also help focus conservation efforts where declines in bee abundance are most certain, especially where agricultural demand for pollination services is growing.
From convection rolls to finger convection in double-diffusive turbulence
Authors: Yang Yantao , Verzicco Roberto , Lohse Detlef 
Published: December 2015

Significance
Double-diffusive convection occurs in many natural flows with fluid density determined by two scalar components, such as the thermohaline convection in the ocean. It plays a crucial role in mixing and scalar transport. Here we report a systematic study of such flow under a destabilizing salinity gradient and a stabilizing temperature gradient. Counterintuitively, applying an extra stabilizing temperature gradient may enhance the salinity transfer even though the velocity becomes smaller. This happens when large-scale convection rolls are replaced by well-organized salt fingers. We identify the parameter ranges for different flow regimes and demonstrate that the Grossmann–Lohse theory can accurately predict the salinity transfer rate for a wide range of control parameters.
Limitations of GCTA as a solution to the missing heritability problem
Authors: Krishna Kumar Siddharth , Feldman Marcus W. , Rehkopf David H. , Tuljapurkar Shripad 
Published: December 2015

Significance
The genetic contribution to a phenotype is frequently measured by heritability, the fraction of trait variation explained by genetic differences. Hundreds of publications have found DNA polymorphisms that are statistically associated with diseases or quantitative traits [genome-wide association studies (GWASs)]. Genome-wide complex trait analysis (GCTA), a recent method of analyzing such data, finds high heritabilities for such phenotypes. We analyze GCTA and show that the heritability estimates it produces are highly sensitive to the structure of the genetic relatedness matrix, to the sampling of phenotypes and subjects, and to the accuracy of phenotype measurements. Plausible modifications of the method aimed at increasing stability yield much smaller heritabilities. It is essential to reevaluate the many published heritability estimates based on GCTA.
Age, Growth, and Reproduction in Two Coastal Populations of Longnose Gars
Authors: Smylie Meredith , Shervette Virginia , McDonough Chris 
Published: December 2015

AbstractMeasurements of age, growth, and reproduction are excellent tools for determining the ecological role and impact of a species within an ecosystem. Longnose Gar Lepisosteus osseus is a large, ubiquitous top predator in fresh and saline waters of the eastern United States. Even though the species is common, their basic biology has been largely uncharacterized in brackish and marine waters. Specimens were collected from two estuaries: Winyah Bay and Charleston Harbor, South Carolina, from May 2012 through July 2013 to examine age, growth, and reproduction in tidally influenced systems. This species is fairly long‐lived, with maximum ages of 17 and 25 years for males and females, respectively. The von Bertalanffy growth model yielded significantly higher growth rates for males than for females. Reproductive histology and the gonadosomatic index indicated that Longnose Gars exhibit determinate fecundity and spawn in late spring following a long development period during fall and winter. These life history parameters provide valuable insight into the basic biology of Longnose Gars and into how they function in estuarine environments. Further research on the precise timing and location of spawning movement, as well as daily movement patterns of this species, would provide a more comprehensive knowledge of Longnose Gar reproductive biology.
The State of Medical Student Performance Evaluations: Improved Transparency or Continued Obfuscation?
Authors: Hom Jason , Richman Ilana , Hall Philip , Ahuja Neera , Harman Stephanie , Harrington Robert , Witteles Ronald 
Published: December 2015

Purpose
The medical student performance evaluation (MSPE), a letter summarizing academic performance, is included in each medical student’s residency application. The extent to which medical schools follow Association of American Medical Colleges (AAMC) recommendations for comparative and transparent data is not known. This study’s purpose was to describe the content, interpretability, and transparency of MSPEs.

Method
This cross-sectional study examined one randomly selected MSPE from every Liaison Committee on Medical Education–accredited U.S. medical school from which at least one student applied to the Stanford University internal medical residency program during the 2013–2014 application cycle. The authors described the number, distribution, and range of key words and clerkship grades used in the MSPEs and the proportions of schools with missing or incomplete data.

Results
The sample included MSPEs from 117 (89%) of 131 medical schools. Sixty schools (51%) provided complete information about clerkship grade and key word distributions. Ninety-six (82%) provided comparative data for clerkship grades, and 71 (61%) provided complete key word data. Key words describing overall performance were extremely heterogeneous, with a total of 72 used and great variation in the assignment of the top designation (median: 24% of students; range: 1%–60%). There was also great variation in the proportion of students awarded the top internal medicine clerkship grade (median: 29%; range: 2%–90%).

Conclusions
The MSPE is a critical component of residency applications, yet data contained within MSPEs are incomplete and variable. Approximately half of U.S. medical schools do not follow AAMC guidelines for MSPEs.
OPTOMAP WIDEFIELD IMAGING OF THE ARGUS II RETINAL PROSTHESIS IN PATIENTS WITH RETINITIS PIGMENTOSA
Authors: Israelsen Paul E. , Sadda SriniVas R. , Dorn Jessy D. , Humayun Mark S. , Olmos de Koo Lisa C. 
Published: December 2015

Purpose:
To explore the utility of using ultra-widefield imaging to visualize the Argus II implant in the eyes of three patients with retinitis pigmentosa.

Methods:
Case series of three patients with retinitis pigmentosa who were implanted with the Argus II Retinal Prosthesis System; two of whom were enrolled in the Argus II clinical trial and one received the implant after the commercial release of the device. Optomap widefield fundus autofluorescence and color images of both eyes were taken in all three patients by an experienced technician using the Optos 200Tx imaging system. Analysis focused on fundus autofluorescence images of the implanted eyes and consisted of assessing the location and configuration of the Argus II electrode array and cable, and also the condition of the surrounding retina. Analysis was led by an experienced vitreoretinal surgeon.

Results:
Optos fundus autofluorescence images of the implanted eyes in all 3 patients gave a wide-angle view of the retina, with the electrode array and cable clearly visible. The status of the array and cable was able to be determined without difficulty. All 3 cases showed an appropriate mild-to-moderate bowing of the cable, and also the electrode array being positioned on or near the macula with a superotemporal tilt. Other features, such as “bone spicules,” were also clearly seen. Optos color images were not as useful in the analysis because of an exaggerated green light artifact seen in the implanted versus the nonimplanted eyes.

Conclusion:
Optomap fundus autofluorescence widefield images are useful in determining the configuration of the Argus II cable and the position of the electrode array on the retina and therefore are a useful component of the postoperative surveillance of patients implanted with the device. Using autofluorescence avoids the generation of a light reflection artifact often seen with Optos color imaging.
Absence of Maternal Microchimerism in Regional Lymph Nodes of Children With Biliary Atresia
Authors: Engelmann Carsten , Maelzer Madeleine , Kreyenberg Hermann 
Published: December 2015

ABSTRACTObjective:Maternal lymphocytes have been cited as a potential cause of infantile biliary atresia (BA). When hepatoportoenterostomy is performed, locoregional lymphadenopathy is frequently encountered.Methods:We screened enlarged nodes from 6 consecutive nonsyndromatic BA patients (age: 68 days ± 18.9 days) for maternal elements using DNA fingerprinting with short tandem repeat analysis and quantitative real‐time polymerase chain reaction for allelic (single nucleotide) sequence polymorphisms.Results:Although being partly positive in infants’ peripheral blood, no maternal microchimerism could be demonstrated in any of the lymph nodes.Conclusion:This result challenges the hypothesis that maternal cells play a role in hilar lymphadenopathy of children with BA.