bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation
Authors: Furukawa Ryohei , Hachiya Tsuyoshi , Ohmomo Hideki , Shiwa Yuh , Ono Kanako , Suzuki Sadafumi , Satoh Mamoru , Hitomi Jiro , Sobue Kenji , Shimizu Atsushi 
Published: May 2016

AbstractCytosine methylation at CpG dinucleotides is an epigenetic mechanism that affects the gene expression profiles responsible for the functional differences in various cells and tissues. Although gene expression patterns are dynamically altered in response to various stimuli, the intraindividual dynamics of DNA methylation in human cells are yet to be fully understood. Here, we investigated the extent to which DNA methylation contributes to the dynamics of gene expression by collecting 24 blood samples from two individuals over a period of 3 months. Transcriptome and methylome association analyses revealed that only ~2% of dynamic changes in gene expression could be explained by the intraindividual variation of DNA methylation levels in peripheral blood mononuclear cells and purified monocytes. These results showed that DNA methylation levels remain stable for at least several months, suggesting that disease-associated DNA methylation markers are useful for estimating the risk of disease manifestation.
Glucagon-like peptide 1 receptor activation regulates cocaine actions and dopamine homeostasis in the lateral septum by decreasing arachidonic acid levels
Authors: Reddy I A , Pino J A , Weikop P , Osses N , Sørensen G , Bering T , Valle C , Bluett R J , Erreger K , Wortwein G , Reyes J G , Graham D , Stanwood G D , Hackett T A , Patel S , Fink-Jensen A , Torres G E , Galli A 
Published: May 2016

AbstractAgonism of the glucagon-like peptide 1 (GLP-1) receptor (GLP-1R) has been effective at treating aspects of addictive behavior for a number of abused substances, including cocaine. However, the molecular mechanisms and brain circuits underlying the therapeutic effects of GLP-1R signaling on cocaine actions remain elusive. Recent evidence has revealed that endogenous signaling at the GLP-1R within the forebrain lateral septum (LS) acts to reduce cocaine-induced locomotion and cocaine conditioned place preference, both considered dopamine (DA)-associated behaviors. DA terminals project from the ventral tegmental area to the LS and express the DA transporter (DAT). Cocaine acts by altering DA bioavailability by targeting the DAT. Therefore, GLP-1R signaling might exert effects on DAT to account for its regulation of cocaine-induced behaviors. We show that the GLP-1R is highly expressed within the LS. GLP-1, in LS slices, significantly enhances DAT surface expression and DAT function. Exenatide (Ex-4), a long-lasting synthetic analog of GLP-1 abolished cocaine-induced elevation of DA. Interestingly, acute administration of Ex-4 reduces septal expression of the retrograde messenger 2-arachidonylglycerol (2-AG), as well as a product of its presynaptic degradation, arachidonic acid (AA). Notably, AA reduces septal DAT function pointing to AA as a novel regulator of central DA homeostasis. We further show that AA oxidation product γ-ketoaldehyde (γ-KA) forms adducts with the DAT and reduces DAT plasma membrane expression and function. These results support a mechanism in which postsynaptic septal GLP-1R activation regulates 2-AG levels to alter presynaptic DA homeostasis and cocaine actions through AA.
Evaluating the privacy properties of telephone metadata
Authors: Mayer Jonathan , Mutchler Patrick , Mitchell John C. 
Published: May 2016

Significance
Privacy protections against government surveillance are often scoped to communications content and exclude communications metadata. In the United States, the National Security Agency operated a particularly controversial program, collecting bulk telephone metadata nationwide. We investigate the privacy properties of telephone metadata to assess the impact of policies that distinguish between content and metadata. We find that telephone metadata is densely interconnected, can trivially be reidentified, enables automated location and relationship inferences, and can be used to determine highly sensitive traits.
Target shape dependence in a simple model of receptor-mediated endocytosis and phagocytosis
Authors: Richards David M. , Endres Robert G. 
Published: May 2016

Significance
Most previous work on endocytosis (the way cells ingest particles) has focused on engulfment of spherical targets. However, this is rarely relevant outside the laboratory, where cells must engulf a huge variety of target shapes, from capped cylinders (like many bacteria) to hourglasses (such as dividing cells). Here, we map this problem to the well-studied physics problem of the freezing of water. This allows us to study a wide range of different, biologically relevant shapes. In particular, for the first time, to our knowledge, it allows us to examine the orientation dependence of phagocytosis, to explain the shape dependence of phagocytosis and receptor-meditated endocytosis, and to explain why nonspherical targets often engulf faster when the most highly-curved tip is engulfed first.
Receptor arrays optimized for natural odor statistics
Authors: Zwicker David , Murugan Arvind , Brenner Michael P. 
Published: May 2016

Significance
Natural odors typically consist of many molecules at different concentrations, which together determine the odor identity. This information is collectively encoded by olfactory receptors and then forwarded to the brain. However, it is unclear how the receptor activity can encode both the composition of the odor and the concentrations of its constituents. We study a simple model of the olfactory receptors from which we derive design principles for optimally communicating odor information in a given natural environment. We use these results to discuss biological olfactory systems, and we propose how they can be used to improve artificial sensor arrays.
A lead isotope perspective on urban development in ancient Naples
Authors: Delile Hugo , Keenan-Jones Duncan , Blichert-Toft Janne , Goiran Jean-Philippe , Arnaud-Godet Florent , Romano Paola , Albarède Francis 
Published: May 2016

SignificanceA well-dated sedimentary sequence from the ancient harbor of Naples sheds new light on an old problem: could the great AD 79 Vesuvius eruption have affected the water supply of the cities around the Bay of Naples? We here show, using Pb isotopes, that this volcanic catastrophe not only destroyed the urban lead pipe water supply network, but that it took the Roman administration several decades to replace it, and that the commissioning of the new system, once built, occurred nearly instantaneously. Moreover, discontinuities in the Pb isotopic record of the harbor deposits prove a powerful tool for tracking both Naples’ urbanization and later major conflicts at the end of the Roman period and in early Byzantine times.
In-drop capillary spooling of spider capture thread inspires hybrid fibers with mixed solid–liquid mechanical properties
Authors: Elettro Hervé , Neukirch Sébastien , Vollrath Fritz , Antkowiak Arnaud 
Published: May 2016

Significance
The spiraling capture threads of spider orb webs are covered with thousands of tiny glue droplets whose primary function is to entrap insects. In this paper we demonstrate that the function of the drops goes beyond that of gluing prey for they also play a role in the mechanical properties of these fibers—usually ascribed solely to the complex molecular architecture of the silk. Indeed, each of the droplets can spool and pack the core silk filament, thus keeping the thread and the whole web under tension. We demonstrate that this effect is the result of the interplay between elasticity and capillarity by making a fully artificial drops-on-fiber compound as extensible as capture thread is.
Structural characterization of the ternary complex that mediates termination of NF-κB signaling by IκBα
Authors: Mukherjee Sulakshana P. , Quintas Pedro O. , McNulty Reginald , Komives Elizabeth A. , Dyson H. Jane 
Published: May 2016

Significance
Rapid response to extracellular signals is promoted by the maintenance of the transcription factor NF-κB in resting cells in a stable complex with its inhibitor IκBα. Upon receipt of a signal, IκBα is degraded, allowing NF-κB to enter the nucleus. One of the downstream genes that is frequently transcribed in response to signals is that of IκBα. Newly synthesized IκBα enters the nucleus and strips NF-κB from the DNA, terminating the signal response by an unknown mechanism. Previous experiments provided evidence for formation of a ternary complex between DNA, NF-κB, and IκBα. Here we characterize this ternary complex by NMR and cryoelectron microscopy and show that it is a feasible intermediate in the termination process.
Reproductive Traits of Brown Trout in Two Contrasting Streams of Southeast Minnesota
Authors: Dieterman Douglas J. , Walker Thomas S. , Cochran Philip A. , Konsti Melissa 
Published: May 2016

Abstract
Brown Trout Salmo trutta are widely distributed fish that display substantial interpopulation variation in fundamental reproductive traits due to differences in local environmental conditions. This wide variation necessitates regional determination of key traits to aid local management efforts. In addition, several populations demonstrate a trade-off between fecundity and egg size, often as a function of growth history in response to environmental conditions. To determine these traits in the Driftless Area of the Upper Midwest, we identified two streams with contrasting environmental conditions and quantified reproductive traits just prior to the fall-spawning period in 2012. Reproductive traits included growth, length- and age-at-maturity, gonadosomatic index, and female fecundity and egg size. Environmental conditions were considered harsher at one site based on warmer water temperatures, more sand substrate, less adult fish cover, and presence of more potential interspecific competitors than at the other site. At both sites, Brown Trout of both sexes were short-lived; few Brown Trout older than age 3 were collected, and both sexes matured at age 2. Length-at-maturity ranged from 226 to 230 mm TL for males and from 214 to 238 mm TL for females. Fecundity and egg size were both positively related to female size, and females produced up to about 800 eggs. Ovaries represented a maximum of about 15% of female body weight. Female Brown Trout growth differed between the two sites, but most reproductive traits and growth of males did not. There was no evidence of a trade-off between fecundity and egg size, but length-adjusted egg sizes were significantly larger at the site with harsher environmental conditions. Differences in egg size probably were not due to the presence of competitors but may have been due to warmer water temperatures. Collectively, these fundamental reproductive data will prove useful for future population modeling efforts to support evaluation of several management strategies.
Received August 10, 2015; accepted December 16, 2015 Published online May 16, 2016
Population Dynamics of Fish Species in a Marine Ecosystem: A Case Study in the Bohai Sea, China
Authors: Shan Xiujuan , Jin Xianshi , Dai Fangqun , Chen Yunlong , Yang Tao , Yao Jianping 
Published: May 2016

Abstract
There were rapid shifts of the dominant species in the Bohai Sea from the 1950s to the 1990s, with large-sized, high-valued species (e.g., Small Yellow Croaker Larimichthys polyactis and Largehead Hairtail Trichiurus lepturus) being replaced by small-sized, low-valued species (e.g., Japanese Anchovy Engraulis japonicus and Hairfin Anchovy Setipinna taty). From the 1990s to the present, the Small Yellow Croaker and some of the small-sized species (Hairfin Anchovy and Dotted Gizzard Shad Konosirus punctatus) have become the dominant species. The food web is now simple, with species from relatively low trophic levels controlling the energy flow within the fishery ecosystem. Along with the shift in community structure, the abundance of dominant species changed, the diversity of fish species and species number density decreased, and interannual and seasonal variations in species number density were found. Fish abundance had a decreasing trend and fish interannual and seasonal distribution greatly changed. Variation in the sizes of the ecological niches of the dominant species regulated the succession of the fish community, and the alteration of ecological niches caused changes in the fishery community.
Received August 11, 2014; accepted September 30, 2015
PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances
Authors: Tang Zheng-Zheng , Chen Guanhua , Alekseyenko Alexander V. 
Published: May 2016

AbstractMotivation: Recent advances in sequencing technology have made it possible to obtain high-throughput data on the composition of microbial communities and to study the effects of dysbiosis on the human host. Analysis of pairwise intersample distances quantifies the association between the microbiome diversity and covariates of interest (e.g. environmental factors, clinical outcomes, treatment groups). In the design of these analyses, multiple choices for distance metrics are available. Most distance-based methods, however, use a single distance and are underpowered if the distance is poorly chosen. In addition, distance-based tests cannot flexibly handle confounding variables, which can result in excessive false-positive findings.Results: We derive presence-weighted UniFrac to complement the existing UniFrac distances for more powerful detection of the variation in species richness. We develop PERMANOVA-S, a new distance-based method that tests the association of microbiome composition with any covariates of interest. PERMANOVA-S improves the commonly-used Permutation Multivariate Analysis of Variance (PERMANOVA) test by allowing flexible confounder adjustments and ensembling multiple distances. We conducted extensive simulation studies to evaluate the performance of different distances under various patterns of association. Our simulation studies demonstrate that the power of the test relies on how well the selected distance captures the nature of the association. The PERMANOVA-S unified test combines multiple distances and achieves good power regardless of the patterns of the underlying association. We demonstrate the usefulness of our approach by reanalyzing several real microbiome datasets.Availability and Implementation: miProfile software is freely available at https://medschool.vanderbilt.edu/tang-lab/software/miProfile .Contact: z.tang@vanderbilt.edu or g.chen@vanderbilt.eduSupplementary information: Supplementary data are available at Bioinformatics online.
The effect of superfluid hydrodynamics on pulsar glitch sizes and waiting times
Authors: Haskell B. 
Published: May 2016

Abstract
Pulsar glitches, sudden jumps in frequency observed in many radio pulsars, may be the macroscopic manifestation of superfluid vortex avalanches on the microscopic scale. Small-scale quantum mechanical simulations of vortex motion in a decelerating container have shown that such events are possible and predict power-law distributions for the size of the events, and exponential distributions for the waiting time. Despite a paucity of data, this prediction is consistent with the size and waiting time distributions of most glitching pulsars. Nevertheless, a few object appear to glitch quasi-periodically, and exhibit many large glitches, while a recent study of the Crab pulsar has suggested deviations from a power-law distribution for smaller glitches. In this Letter, we incorporate the results of quantum mechanical simulations in a macroscopic superfluid hydrodynamics simulation. We show that the effect of vortex coupling to the neutron and proton fluids in the star naturally leads to deviations from power-law distributions for sizes, and from exponential distributions for waiting times, and we predict a cutoff in the size distribution for small glitches.
Intraoperative Indocyanine Green Laser Angiography in Pediatric Autologous Ear Reconstruction
Authors: Martins Deborah B. , Farias-Eisner Gina , Mandelbaum Rachel S. , Hoang Han , Bradley James P. , Lee Justine C. 
Published: May 2016

Summary:
Skin flap vascularity is a critical determinant of aesthetic results in autologous ear reconstruction. In this study, we investigate the use of intraoperative laser-assisted indocyanine green angiography (ICGA) as an adjunctive measure of skin flap vascularity in pediatric autologous ear reconstruction. Twenty-one consecutive pediatric patients undergoing first-stage autologous total ear reconstruction were retrospectively evaluated. The first 10 patients were treated traditionally (non-ICGA), and the latter 11 patients were evaluated with ICGA intraoperatively after implantation of the cartilage construct and administration of suction. Relative and absolute perfusion units in the form of contour maps were generated. Statistical analyses were performed using independent sample Student t test. Statistically significant differences in exposure and infection were not found between the 2 groups. However, decreased numbers of surgical revisions were required in cases with ICGA versus without ICGA (P = 0.03), suggesting that greater certainty in skin flap perfusion correlated with a reduction in revision surgeries. In cases of exposure, we found an average lowest absolute perfusion unit of 14.3, whereas cases without exposure had an average of 26.1 (P = 0.02), thereby defining objective parameters for utilizing ICGA data in tailoring surgical decision making for this special population of patients. Defined quantitative parameters for utilizing ICGA in evaluating skin flap vascularity may be a useful adjunctive technique in pediatric autologous ear reconstruction.
A RARE COMPLICATION OF POSTERIOR SUBTENON INJECTION
Authors: Mourya Deepesh , Balamurugan S. , Khanal Roshija 
Published: May 2016

Purpose:
To report a case of posterior ciliary artery occlusion after posterior subtenon injection.

Methods:
Clinical examination and fundus fluorescein angiography was performed to confirm diagnosis. A 49-year-old female who was on treatment for bilateral chronic sclerokeratouveitis was given posterior subtenon injection for cystoid macular edema.

Results:
Posterior ciliary artery occlusion occurred after posterior subtenon injection.

Conclusion:
Choroidal vascular occlusion is a rare complication of posterior subtenon injection.
Regression and Progression Predictors of CIN2 in Women Younger Than 25 Years
Authors: Loopik Diede L. , Doucette Steve , Bekkers Ruud L.M. , Bentley James R. 
Published: May 2016

Objective
The purpose of this study was to review the management and outcome of cervical intraepithelial neoplasia 2 (CIN2) in women younger than 25 years.

Methods
A retrospective review was performed, investigating women younger than 25 years at the time of diagnosis with biopsy-proven CIN2 between January 1, 2010, and December 31, 2014, who were seen in the colposcopy clinic at the Queen Elizabeth II Hospital in Halifax, Nova Scotia, Canada. The regression, persistence, and progression rate of CIN2 in conservative managed women were evaluated, and potential risk factors were examined. Colposcopy, cytologic, and histopathologic findings were compared with women with immediate treatment (<6 months).

Results
Of the 319 women included in the study, 108 women received immediate treatment, and 211 women were managed conservatively; of these, 144 women remained untreated, and 67 women received treatment 6 months or greater. From the women managed conservatively, 150 women (71.1%) showed regression, 26 women (12.3%) had persistent disease, and 35 women (16.6%) progressed, with a median follow-up of 15.1 months. None of the women included in the study progressed to invasive cancer. The hazard ratio for time to progression was 2.40 for women who smoked (p = 0.006).

Conclusions
A conservative approach of CIN2 is the preferred management option for women younger than 25 years. Smoking was identified as a risk factor for progression.
Subclinical Ascites Does Not Affect the Long-term Prognosis in Hepatitis B Virus–related Cirrhosis Patients Receiving Antivirals
Authors: Yim Sun Young , Lee Jeong-Hoon , Ahn Hongkeun , Kim Seung Up , Kim Sang Gyune , Kim Young Seok , Kim Jeong Han , Choe Won Hyeok , Kim Tae Yeob , Jung Young Kul , Suh Sang Jun , Suk Ki Tae , An Hyunggin , Yim Hyung Joon , Seo Yeon Seok , Um Soon Ho 
Published: May 2016

Background and Aims:
This study evaluated the clinical significance of subclinical ascites in patients with hepatitis B virus–related cirrhosis treated with lamivudine (LMV) or entecavir (ETV).

Methods:
This multicenter retrospective study involved 8 hospitals. Patients were classified by degree of ascites: (1) no ascites (no ascites on imaging, no diuretics), (2) subclinical ascites (small amount of ascites on imaging, no diuretics), and (3) clinical ascites (moderate to severe ascites or diuretics).

Results:
Out of 501 patients, 336 (68%), 51 (10%), and 114 (23%) patients were classified as no-ascites, subclinical ascites, and clinical ascites, respectively. In all, 100 (20%) and 401 (80%) were treated with LMV and ETV, respectively. Over 58±24 months of follow-up, 105 patients (21%) developed hepatocellular carcinoma. The cumulative incidence of hepatocellular carcinoma did not differ between LMV-treated and ETV-treated patients (P=0.61); it was higher in the clinical-ascites group than the no-ascites (P=0.054) and subclinical-ascites (P=0.03) groups, but it was comparable between the latter 2 (P=0.225). Forty-five patients (9%) died during follow-up. Survival was significantly shorter in the clinical-ascites group than the other 2 (both P<0.005), but it was comparable between no-ascites and subclinical-ascites groups (P=0.444). Multivariate analysis showed that mortality was significantly associated with prothrombin time [hazard ratio (HR)=2.42; 95% confidence interval (CI), 1.59-3.70], serum albumin (HR=0.54; 95% CI, 0.29-0.99), and presence of clinical ascites (HR=3.58; 95% CI, 1.54-8.30).

Conclusions:
Subclinical ascites did not affect prognosis in patients with hepatitis B virus–related cirrhosis receiving antiviral treatment.