bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel application of multi‐event modeling to estimate class segregation in a highly migratory oceanic vertebrate
Authors: Chapple T. K. , Chambert T. , Kanive P. E. , Jorgensen S. J. , Rotella J. J. , Anderson S. D. , Carlisle A. B. , Block B. A. 
Published: September 2016

AbstractSpatial segregation of animals by class (i.e., maturity or sex) within a population due to differential rates of temporary emigration (TE) from study sites can be an important life history feature to consider in population assessment and management. However, such rates are poorly known; new quantitative approaches to address these knowledge gaps are needed. We present a novel application of multi‐event models that takes advantage of two sources of detections to differentiate temporary emigration from apparent absence to quantify class segregation within a study population of double‐marked (photo‐identified and tagged with coded acoustic transmitters) white sharks (Carcharodon carcharias) in central California. We use this model to test if sex‐specific patterns in TE result in disparate apparent capture probabilities (po) between male and female white sharks, which can affect the observed sex ratio. The best‐supported model showed a contrasting pattern of Pr(TE) from coastal aggregation sites between sexes (for males Pr[TE] = 0.015 [95% CI = 0.00, 0.31] and Pr[TE]= 0.57 [0.40, 0.72] for females), but not maturity classes. Additionally, by accounting for Pr(TE) and imperfect detection, we were able to estimate class‐specific values of true capture probability (p*) for tagged and untagged sharks. The best‐supported model identified differences between maturity classes but no difference between sexes or tagging impacts (tagged mature sharks p* = 0.55 (0.46–0.63) and sub‐adult sharks p* = 0.36 (0.25, 0.50); and untagged mature sharks p* = 0.50 (0.39–0.61) and sub‐adults p* = 0.18 (0.10, 0.31). Estimated sex‐based differences in po were linked to sex‐specific differences in Pr(TE) but not in p*; once the Pr(TE) is accounted for, the p* between sexes was not different. These results indicate that the observed sex ratio is not a consequence of unequal detectability and sex‐specific values of Pr(TE) are important drivers of the observed male‐dominated sex ratio. Our modeling approach reveals complex class‐specific patterns in Pr(TE) and p* in a mark‐recapture data set, and highlights challenges for the population modeling and conservation of white sharks in central California. The model we develop here can be used to estimate rates of temporary emigration and class segregation when two detection methods are used.
Stereodynamics of some pyridoxine derivatives
Authors: Rakhmatullin I. Z. , Galiullina L. F. , Balandina A. A. , Garipov M. R. , Strelnik A. D. , Galiullina A. S. , Shtyrlin Y. G. , Klochkov V. V. 
Published: September 2016

AbstractThe conformational properties of three pyridoxine derivatives were studied by 1H dynamic NMR spectroscopy. Conformational exchange caused by a rotation of 2‐nytrophenyl group around one single C–C bond, of 2,4‐dinitrophenyl substituent around two single C–O bonds, and twist‐twist transformations of the seven‐membered ketal cycle was observed by NMR experiments at low temperatures. Meanwhile, the conformational exchange of the acetal ring remains fast in the NMR timescale even at 198 K. The energy barriers for all observed conformational exchange processes were determined by the lineshape analysis of dynamic NMR spectra. The activation barriers of the 2‐nitrophenyl group rotation were almost the same for all studied compounds, about 40–41 kJ/mol. The energy barriers of the conformational exchange processes of the 2,4‐nitrophenyl group and the ketal cycle increased significantly up to 10 kJ/mol in comparison with previously studied compounds with similar structure. Copyright © 2016 John Wiley & Sons, Ltd.
Effects of a meal replacement system alone or in combination with phentermine on weight loss and food cravings
Authors: Moldovan Christina P. , Weldon Abby J. , Daher Noha S. , Schneider Louise E. , Bellinger Denise L. , Berk Lee S. , Hermé Alyson C. , Aréchiga Adam L. , Davis Willie L. , Peters Warren R. 
Published: September 2016

ObjectiveTo examine the effects of phentermine combined with a meal replacement program on weight loss and food cravings and to investigate the relationship between food cravings and weight loss.MethodsIn a 12‐week randomized, double‐blind, placebo‐controlled clinical trial, 77 adults with obesity received either phentermine or placebo. All participants were provided Medifast® meal replacements, were instructed to follow the Take Shape for Life® Optimal Weight 5&1 Plan for weight loss, and received lifestyle coaching in the Habits of Health program. The Food Craving Inventory and the General Food Cravings State and Trait Questionnaires were used to measure food cravings.ResultsThe phentermine group lost 12.1% of baseline body weight compared with 8.8% in the placebo group. Cravings for all food groups decreased in both groups; however, there was a greater reduction in cravings for fats and sweets in the phentermine group compared with the placebo group. Percent weight loss correlated significantly with reduced total food cravings (r = 0.332, P = 0.009), cravings for sweets (r = 0.412, P < 0.000), and state food cravings (r = 0.320, P = 0.007).ConclusionsBoth phentermine combined with a meal replacement program and meal replacements alone significantly reduced body weight and food cravings; however, the addition of phentermine enhanced these effects.
The anti‐adipogenic effect of peripheral blood mononuclear cells is absent with PCSK9 loss‐of‐function variants
Authors: Gagnon AnneMarie , Ooi Teik C. , Cousins Marion , Favreau Colette , Henry Kathy , Landry Anne , Sorisky Alexander 
Published: September 2016

ObjectiveTo determine the effect of (1) an oral fat load and (2) pro‐protein convertase subtilisin/kexin type (PCSK) 9 loss‐of‐function (LOF) variant status on the ability of peripheral blood mononuclear cells (PBMC) to inhibit human adipogenesis.MethodsPBMC from subjects with one or more PCSK9 LOF variants versus non‐variant controls were compared in the fasting state and after an oral fat load.ResultsFasting triglyceride (TG) levels were lower in the LOF variant versus non‐variant group but rose to the same level after the oral fat load. Conditioned medium from PBMC was obtained in fasting (PBMC‐CM‐F) and 4‐h postprandial (PBMC‐CM‐PP) states. PBMC‐CM‐PP from non‐variant controls inhibited adipogenesis of human preadipocytes more than did PBMC‐CM‐F. In contrast, PBMC‐CM‐F or ‐PP from PCSK9 LOF variant subjects had no effect on adipogenesis. After the oral fat load, PBMC from PCSK9 LOF variant subjects showed significant increases in mRNA levels of interleukin‐1β, tumor necrosis factor‐α, sterol regulatory element binding protein‐1c, CD36, and monocyte chemoattractant protein‐1 (MCP‐1), only MCP‐1 mRNA levels increased in PBMC from non‐variant controls.ConclusionsThe absence of anti‐adipogenic action of PBMC from PCSK9 LOF variant subjects points to a novel role for PCSK9 in PBMC‐adipose cell interactions.
Advanced Glycation Endproducts Impair Endothelial Progenitor Cell Migration and Homing via Syndecan 4 Shedding
Authors: Xie Jun , Li Ran , Wu Han , Chen Jianzhou , Li Guannan , Chen Qinhua , Wei Zhonghai , He Guixin , Wang Lian , Ferro Albert , Xu Biao 
Published: September 2016

Abstract
Endothelial progenitor cells (EPCs) are a subtype of bone marrow–derived progenitor cells. Stromal cell-derived factor 1 (SDF-1)-mediated EPC mobilization from bone marrow to areas of ischemia plays an important role in angiogenesis. Previous studies have reported that advanced glycation endproducts (AGEs), which are important mediators of diabetes-related vascular pathology, may impair EPC migration and homing, but the mechanism is unclear. Syndecan-4 (synd4) is a ubiquitous heparan sulfate proteoglycan receptor on the cell surface, involved in SDF-1-dependent cell migration. The extracellular domain of synd4 (ext-synd4) is shed in the context of acute inflammation, but the shedding of ext-synd4 in response to AGEs is undefined. Here we investigated changes in ext-synd4 on EPCs in response to AGEs, focusing on the influence of impaired synd4 signaling on EPC migration and homing. We found decreased full length and increased residue of synd4 in cells incubated with AGEs, with concomitant increase in the soluble fragment of ext-synd4 in the cell medium. EPCs from patients with type 2 diabetes expressed less ext-synd4 as assessed by Western blotting. Flow cytometry analysis showed less ext-synd4 on circulating CD34+ peripheral blood mononuclear cells, of which EPCs form a subgroup. We then explored the role of synd4 in EPC migration and homing. Impaired migration of synd4-deficient EPCs was observed by a 2D-chemotaxis slide. Furthermore, poor homing of synd4−/− EPCs was observed in a mouse model of lower limb ischemia. This study demonstrates that the shedding of synd4 from EPCs plays a key role in AGE-mediated dysfunction of EPC migration and homing.
NIAGADS: The NIA Genetics of Alzheimer's Disease Data Storage Site
Authors: Kuzma Amanda , Valladares Otto , Cweibel Rebecca , Greenfest‐Allen Emily , Childress Daniel M. , Malamon John , Gangadharan Prabhakaran , Zhao Yi , Qu Liming , Leung Yuk Yee , Naj Adam C. , Stoeckert Christian J. , Schellenberg Gerard D. , Wang Li‐San 
Published: September 2016

SummaryWork in the past 10 years has greatly expanded our understanding of Alzheimer's disease (AD) genetics, with more than 20 susceptibility genetic loci discovered in large genome‐wide association and sequencing studies. The NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) is funded by National Institute on Aging to serve as a one‐stop portal for the community to access research data and findings generated from AD genetics projects. In this article, we describe the mission of NIAGADS, available resources, and data sets including the Alzheimer's Disease Sequencing Project, and how researchers may apply for access to genetic data.
Concordance of immune checkpoints within tumor immune contexture and their prognostic significance in gastric cancer
Authors: Dai Congqi , Geng Ruixuan , Wang Chenchen , Wong Angela , Qing Min , Hu Jianjun , Sun Yu , Lo A.W.I. , Li Jin 
Published: September 2016

AbstractCheckpoint blockade therapy has emerged as a novel approach for cancer immunotherapy in several malignancies. However, patient prognosis and disease progression relevant to immune checkpoints in gastric tumor microenvironment are not defined. This study aims to investigate the expression and prognostic significance of immune checkpoints within gastric cancer. In the study, a cohort of 398 cancer tissues from stage I to IV gastric cancer patients were assessed for programmed cell death 1 ligand 1 (PD‐L1) expression and tumor‐infiltrating lymphocyte (TIL) infiltration using immunohistochemistry to ascertain their survival correlation. The data revealed that higher TIL density correlated with less risk of disease progression, and exhibited survival benefits in gastric cancer patients, and PD‐L1 positivity showed a significant association with the presence of high TIL infiltration. Furthermore, real‐time quantitative polymerase chain reaction was performed to detect expression of multiple immune checkpoints with the relation to clinical outcome in 139 samples randomly selected from the same cohort, and higher messenger RNA levels of most immune checkpoints were associated with favorable outcome, while consistently showing a positive correlation with interferon gamma levels. In situ hybridization was used to determine the localization of Epstein–Barr virus (EBV) in 97 specimens, and showed EBV‐positive gastric cancer samples correlated with PD‐L1 expression and increased TIL density. These results suggest that induction of immune checkpoint within gastric cancer patients reflects a high immune infiltration density, especially in those with EBV‐associated gastric cancer, which may direct patient selection for checkpoint blockade therapy.
Neurotensin stimulates sortilin and mTOR in human microglia inhibitable by methoxyluteolin, a potential therapeutic target for autism
Authors: Patel Arti B. , Tsilioni Irene , Leeman Susan E. , Theoharides Theoharis C. 
Published: September 2016

Significance
Human microglia, the resident immune cells of the brain, express only the neurotensin (NT) receptor-3/sortilin. NT significantly increases microglia synthesis and release of proinflammatory cytokine IL-1β and chemokine (C-X-C motif) ligand 8 (CXCL8), chemokine (C-C motif) ligand 2 (CCL2), and CCL5 via NTR3/sortilin. A soluble form of this receptor is secreted from stimulated microglia and is increased in the serum of children with autism spectrum disorders (ASD). These responses and the NT-stimulated increases in microglia numbers are mediated via mammalian target of rapamycin (mTOR) activation and are inhibitable by the natural flavonoids luteolin and methoxyluteolin.
Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark
Authors: Klein Max , Sharma Rati , Bohrer Chris H , Avelis Cameron M , Roberts Elijah 
Published: September 2016

Abstract

Summary
Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology.

Availability and Implementation
Source code is licensed under the Apache 2.0 open source license and is available at the project website: https://www.assembla.com/spaces/roberts-lab-public/wiki/Biospark

Supplementary information
Supplementary data are available at Bioinformatics online.
Large X-ray flares on stars detected with MAXI/GSC: A universal correlation between the duration of a flare and its X-ray luminosity
Authors: Tsuboi Yohko , Yamazaki Kyohei , Sugawara Yasuharu , Kawagoe Atsushi , Kaneto Soichiro , Iizuka Ryo , Matsumura Takanori , Nakahira Satoshi , Higa Masaya , Matsuoka Masaru , Sugizaki Mutsumi , Ueda Yoshihiro , Kawai Nobuyuki , Morii Mikio , Serino Motoko , Mihara Tatehiro , Tomida Hiroshi , Ueno Shiro , Negoro Hitoshi , Daikyuji Arata , Ebisawa Ken , Eguchi Satoshi , Hiroi Kazuo , Ishikawa Masaki , Isobe Naoki , Kawasaki Kazuyoshi , Kimura Masashi , Kitayama Hiroki , Kohama Mitsuhiro , Kotani Taro , Nakagawa Yujin E. , Nakajima Motoki , Ozawa Hiroshi , Shidatsu Megumi , Sootome Tetsuya , Sugimori Kousuke , Suwa Fumitoshi , Tsunemi Hiroshi , Usui Ryuichi , Yamamoto Takayuki , Yamaoka Kazutaka , Yoshida Atsumasa 
Published: September 2016

Abstract
Twenty-three giant flares from thirteen active stars (eight RS CVn systems, one Algol system, three dMe stars, and one young stellar object) were detected during the first two years of our all-sky X-ray monitoring with the gas propotional counters (GSC) of the Monitor of All-sky X-ray Image (MAXI). The observed parameters of all these MAXI/GSC flares are found to be at the upper ends for stellar flares with the luminosity of 1031–34 erg s−1 in the 2–20 keV band, the emission measure of 1054–57 cm−3, the e-folding time of 1 hr to 1.5 d, and the total radiative energy released during the flare of 1034–39 erg. Notably, the peak X-ray luminosity of $5^{+4}_{-2} \times 10^{33}\:$erg s−1 in the 2–20 keV band was detected in one of the flares on II Peg, which is one of the, or potentially the, largest-ever-observed in stellar flares. X-ray flares were detected from GT Mus, V841 Cen, SZ Psc, and TWA-7 for the first time in this survey. Whereas most of our detected sources are multiple-star systems, two of them are single stars (YZ CMi and TWA-7). Among the stellar sources within 100 pc distance, the MAXI/GSC sources have larger rotation velocities than the other sources. This suggests that the rapid rotation velocity may play a key role in generating large flares. Combining the X-ray flare data of nearby stars and the sun, taken from literature and our own data, we discovered a universal correlation of $\tau \propto L_{\rm X}^{0.2}$ for the flare duration τ and the intrinsic X-ray luminosity LX in the 0.1–100 keV band, which holds for 5 and 12 orders of magnitude in τ and LX, respectively. The MAXI/GSC sample is located at the highest ends of the correlation.
Surgical Consideration for Adolescents and Young Adults With Cervical Chordoma
Authors: Zhong Nanzhe , Yang Xinghai , Yang Jian , Meng Tong , Yang Cheng , Yan Wangjun , Xiao Jianru 
Published: September 2016

Study Design.
Retrospective study.

Objective.
The aim of this study was to compare the clinical outcomes between adolescent and young adult (AYA) patients and old adult patients with cervical chordoma who were treated surgically and present the surgical consideration for adolescents and young adults with cervical chordoma.

Summary of Background Data.
With predominance in senior patients, chordoma is distinctively rare in AYAs. Because of the rarity of AYA chordoma, individual case report represents most of the literature on this disease entity on mobile spine and lack of long-term follow up, which leads to the paucity of clinical evidence for treatment planning and prognosis prediction.

Methods.
A retrospective study was conducted to investigate the prognosis of AYA patients with cervical chordoma who were treated surgically. We collected the clinical data of these patients and their older counterparts, and further compared the prognosis of the patients in different age groups. To estimate survival curves, Kaplan-Meier method was used, and significance was assessed using a log-rank test.

Results.
Forty consecutive patients with chordoma of the cervical spine treated in our institution were included in the study. Two groups were identified according to age. Group 1 comprised children and adolescents (age ≤ 25 yrs; n = 9) and Group 2 comprised adults (age > 25 years; n = 31). In comparison, Group 1 was featured by significantly higher rate of recurrence and shorter overall survival, although no difference found in the surgical modality between two groups.

Conclusion.
There is a dismal prognosis in young patients with chordoma, and thus support the notion that as radical a total en bloc spondylectomy (TES) of the lesions as possible may benefit the overall survival of these young patients. Although the ensuing neurological deficits may be devastating, it will be worth sacrificing if the life expectancy of these young patients is prolonged.

Levels of Evidence: 4
Long-term Outcome of Surgical Treatment for Superior Cluneal Nerve Entrapment Neuropathy
Authors: Morimoto Daijiro , Isu Toyohiko , Kim Kyongsong , Chiba Yasuhiro , Iwamoto Naotaka , Isobe Masanori , Morita Akio 
Published: September 2016

Study Design.
Prospective observational cohort study.

Objective.
The objective of this study was to present the long-term surgical outcomes of operative treatment for superior cluneal nerve (SCN) entrapment neuropathy (SCNEN) and to analyze the causes of poor results and further treatment required.

Summary of Background Data.
There are a few reports of the outcomes of surgical treatment for SCNEN, and most studies describe results for operations conducted under general anesthesia with short follow-up periods.

Methods.
Surgery was performed for SCNEN in 52 consecutive patients on 79 sides, excluding patients who had undergone previous surgery on the lumbar spine. Entrapment was unilateral in 25 patients and bilateral in 27. The mean postoperative follow-up period was 41.3 months (range, 29–58 months). All patients had received conservative treatment without improvements, and operations were performed under local anesthesia.

Results.
Twenty-three cases (44%) involved only low-back pain (LBP), and 31 cases (60%) involved LBP associated with leg numbness or pain. The mean number of SCN branches decompressed in the operative field at the first operation was 1.4 (range, 1–4 branches). There were no local or systemic complications during or after the operation. All patients reported symptom improvement, but LBP caused by SCNEN recurrence was reported for 10 sides (13%) in seven patients who subsequently underwent repeat surgery. In the second surgery, the number of additionally treated SCN branches was 2.0 (range, 1–5). Additional surgeries were performed in two cases for lumbar disorders. All patients showed significant improvement at the last follow-up visit (P < 0.05), including those who developed recurrence.

Conclusion.
Long-term outcomes of surgical treatment for SCNEN were satisfactory. For prevention of recurrence, as many SCN branches as possible should be decompressed in the operation field during the first operation.

Level of Evidence: 4
Vascular Supply of the Auricle: Anatomical Study and Applications to External Ear Reconstruction
Authors: Hénoux Michaël , Espitalier Florent , Hamel Antoine , Dréno Brigitte , Michel Guillaume , Malard Olivier 
Published: September 2016

BACKGROUND
Reliable reconstructive flaps require convenient vascular supply. Thus, precise description of the vascular patterns of external ear is not completely elucidated.

OBJECTIVE
This anatomical study aims to provide comprehensive data of the arterial network of the auricular region, anastomosis, and patterns of arterial dependence regarding external ear subunits.

MATERIALS AND METHODS
After dyed latex injections in the external carotid artery, eleven auricles have been carefully dissected to examine the vascular network of the auricular region.

RESULTS
In all cases, the posterior auricular artery (PAA) supplied the cranial side of the auricle, as well as the concha on the lateral side through consistent perforating branches. The superficial temporal artery (STA) network supplied the upper third of the lateral aspect of the auricle. The authors' dissections showed a clear dominance of the PAA supply. However, the two arteries consistently developed anastomoses particularly in the cranial upper third of the auricle.

CONCLUSION
Consistent branches and anastomoses between the PAA and the STA network provide reliable pedicles for auricular and facial reconstruction.
CONGENITAL CONTRACTILE PERIPAPILLARY STAPHYLOMA WITH RHEGMATOGENOUS RETINAL DETACHMENT
Authors: Cao Xu Sheng , Peng Xiao Yan , You Qi Sheng , Jiang Li Bin , Jonas Jost B. 
Published: September 2016

Purpose:
To describe the occurrence of a congenital contractile peripapillary staphyloma in association with a rhegmatogenous retinal detachment.

Methods:
The clinical course of a 17-year-old patient with a contractile peripapillary staphyloma and undergoing pars plana vitrectomy for repair of an associated retinal detachment was studied.

Results:
The left eye showed a peripapillary staphyloma which during the ophthalmoscopical examination revealed contractile movements after the presentation of a light stimulus to either eye. The contraction of the peripapillary staphyloma was not correlated with a Valsalva maneuver, neck venous compression, forced lid closure, or respiratory movements. Because of a retinal detachment involving the inferior, nasal, and temporal retina, best-corrected visual acuity was 20/100. During pars plana vitrectomy under systemic anesthesia, the contractions of the peripapillary staphyloma subsided in the early phase of surgery, and reoccurred at approximately 80 minutes after the start of general anesthesia, when the posterior pole was touched with an aspiration syringe.

Conclusion:
The etiology of the movements of the congenital peripapillary staphyloma in our patient may include a misbalance between intraocular pressure and orbital cerebrospinal fluid pressure or contractions of extraocular muscles. The observations may give information about the physiology and pathophysiology of the optic nerve head.