bluuebunny/crossref_metadata_2025_split huggingface dataset:
Top-down, decoupled control of constitutive parameters in electromagnetic metamaterials with dielectric resonators of internal anisotropy
Authors: Koo Sukmo , Mason Daniel R. , Kim Yunjung , Park Namkyoo 
Published: February 2017

AbstractA meta-atom platform providing decoupled tuning for the constitutive wave parameters remains as a challenging problem, since the proposition of Pendry. Here we propose an electromagnetic meta-atom design of internal anisotropy (εr ≠ εθ), as a pathway for decoupling of the effective- permittivity εeff and permeability μeff. Deriving effective parameters for anisotropic meta-atom from the first principles, and then subsequent inverse-solving the obtained decoupled solution for a target set of εeff and μeff, we also achieve an analytic, top-down determination for the internal structure of a meta-atom. To realize the anisotropy from isotropic materials, a particle of spatial permittivity modulation in r or θ direction is proposed. As an application example, a matched zero index dielectric meta-atom is demonstrated, to enable the super-funneling of a 50λ-wide flux through a sub-λ slit; unharnessing the flux collection limit dictated by the λ-zone.
CENP-A chromatin disassembly in stressed and senescent murine cells
Authors: Hédouin Sabrine , Grillo Giacomo , Ivkovic Ivana , Velasco Guillaume , Francastel Claire 
Published: February 2017

AbstractCentromeres are chromosomal domains essential for genomic stability. We report here the remarkable transcriptional and epigenetic perturbations at murine centromeres in genotoxic stress conditions. A strong and selective transcriptional activation of centromeric repeats is detected within hours. This is followed by disorganization of centromeres with striking delocalization of nucleosomal CENP-A, the key determinant of centromere identity and function, in a mechanism requiring active transcription of centromeric repeats, the DNA Damage Response (DDR) effector ATM and chromatin remodelers/histone chaperones. In the absence of p53 checkpoint, activated transcription of centromeric repeats and CENP-A delocalization do not occur and cells accumulate micronuclei indicative of genomic instability. In addition, activated transcription and loss of centromeres identity are features of permanently arrested senescent cells with persistent DDR activation. Together, these findings bring out cooperation between DDR effectors and loss of centromere integrity as a safeguard mechanism to prevent genomic instability in context of persistent DNA damage signalling.
Multilocus sequence analyses reveal extensive diversity and multiple origins of fluconazole resistance in Candida tropicalis from tropical China
Authors: Wu Jin-Yan , Guo Hong , Wang Hua-Min , Yi Guo-Hui , Zhou Li-Min , He Xiao-Wen , Zhang Ying , Xu Jianping 
Published: February 2017

AbstractCandida tropicalis is among the most prevalent human pathogenic yeast species, second only to C. albicans in certain geographic regions such as East Asia and Brazil. However, compared to C. albicans, relatively little is known about the patterns of genetic variation in C. tropicalis. This study analyzed the genetic diversity and relationships among isolates of C. tropicalis from the southern Chinese island of Hainan. A total of 116 isolates were obtained from seven geographic regions located across the Island. For each isolate, a total of 2677 bp from six gene loci were sequenced and 79 (2.96%) polymorphic nucleotide sites were found in our sample. Comparisons with strains reported from other parts of the world identified significant novel diversities in Hainan, including an average of six novel sequences (with a range 1 to 14) per locus and 80 novel diploid sequence types. Most of the genetic variation was found within individual strains and there was abundant evidence for gene flow among the seven geographic locations within Hainan. Interestingly, our analyses identified no significant correlation between the diploid sequence types at the six loci and fluconazole susceptibility, consistent with multiple origins of fluconazole resistance in the Hainan population of C. tropicalis.
Gene Transfer of Prolyl Hydroxylase Domain 2 Inhibits Hypoxia-inducible Angiogenesis in a Model of Choroidal Neovascularization
Authors: Takei Anna , Ekström Malena , Mammadzada Parviz , Aronsson Monica , Yu Ma , Kvanta Anders , André Helder 
Published: February 2017

AbstractCellular responses to hypoxia are mediated by the hypoxia-inducible factors (HIF). In normoxia, HIF-α proteins are regulated by a family of dioxygenases, through prolyl and asparagyl hydroxylation, culminating in proteasomal degradation and transcriptional inactivation. In hypoxia, the dioxygenases become inactive and allow formation of HIF transcription factor, responsible for upregulation of hypoxia genes. In ocular neoangiogenic diseases, such as neovascular age-related macular degeneration (nAMD), hypoxia seems pivotal. Here, we investigate the effects of HIF regulatory proteins on the hypoxia pathway in retinal pigment epithelium (RPE) cells, critically involved in nAMD pathogenesis. Our data indicates that, in ARPE-19 cells, prolyl hydroxylase domain (PHD)2 is the most potent negative-regulator of the HIF pathway. The negative effects of PHD2 on the hypoxia pathway were associated with decreased HIF-1α protein levels, and concomitant decrease in angiogenic factors. ARPE-19 cells stably expressing PHD2 impaired angiogenesis in vitro by wound healing, tubulogenesis, and sprouting assays, as well as in vivo by iris-induced angiogenesis. Gene transfer of PHD2 in vivo resulted in mitigation of HIF-mediated angiogenesis in a mouse model of nAMD. These results may have implications for the clinical treatment of nAMD patients, particularly regarding the use of gene therapy to negatively regulate neoangiogenesis.
Imaging Spectrum of Unusual Pineal Region Masses: A Short Series of Four Cases
Authors: Dhar Anandamoyee , Jain Ruchi , Walia Bipin , Mukherjee Urmi , Aggarwal Bharat 
Published: February 2017

AbstractPineal tumors are rare intracranial neoplasm with germ cell tumors and pineal parenchymal tumors being the predominant type, seen in 80 to 90% of cases. Only a few cases of glioblastomas have been reported. The incidence of astrocytoma and meningioma is also low in this region. In this article, we will discuss the key imaging features and diagnostic dilemmas in four rare types of pineal region tumors including pineal parenchymal tumor of intermediate differentiation, pineal astrocytoma, falcotentorial junction meningioma, and glioblastoma with subependymal spread.
Kanaloplastik ab interno – eine minimalinvasive Alternative
Authors: Körber N. 
Published: February 2017

Zusammenfassung
Zweck Beschreibung und Bewertung der Wirksamkeit der Kanaloplastik ab interno (ABiC) bei Patienten mit primärem Offenwinkelglaukom (POAG).
Methoden In diese monozentrische konsekutive Fallstudienreihe wurden Patienten mit Katarakt und Offenwinkelglaukom (kombiniertes Verfahren) und pseudophake Patienten (Durchschnittsalter: 78 Jahre, Bereich: 66–90 Jahre) mit POAG aufgenommen und einer ABiC mit dem iTrack™ 250-Mikron-Mikrokatheter (Ellex Medical Lasers Pty Ltd, Adelaide, Australien) unterzogen, um den Schlemm-Kanal zirkumferenziell zu viskodilatieren und zu intubieren, ohne eine Spannnaht anzubringen. Die primären Endpunkte waren der mittlere Augeninnendruck (IOP) und die mittlere Anzahl Glaukommedikamente bis 1, 3, 6, 9 und 12 Monate nach der Operation.
Ergebnisse 23 Patienten (23 Augen) wurden in die Studie aufgenommen. Der mittlere IOP ohne Wash-out sank von 18,8 ± 5,63 mmHg vor der Operation auf jeweils 14,9 ± 2,90 mmHg (n = 22), 13,82 ± 2,98 (n = 19), 14,69 ± 2,36 mmHg (n = 13), 16,0 ± 2,09 (n = 11) und 14,73 ± 2,97 (n = 11) bis 1, 3, 6, 9 und 12 Monate nach der Operation. Die mittlere Anzahl Medikamente wurde reduziert von 1,69 vor der Operation auf 0,21 bei der letzten Follow-up-Visite. Es gab eine Komplikation mit begrenzter Descemetolyse nahe dem Limbus.
Schlussfolgerung Die ABiC war bei dieser Patientengruppe einfach in der Durchführung und brachte nur minimale Komplikationen mit sich. Erste Ergebnisse in dieser Studie weisen darauf hin, dass die ABiC den IOP und somit auch die Abhängigkeit von Medikamenten vergleichbar zur konventionellen Kanaloplastik senkt.
Wann wird heute noch gelasert?
Authors: Enders P. , Schaub F. , Fauser S. 
Published: February 2017

Zusammenfassung
Hintergrund Die Laserbehandlung ist eine Therapieoption bei retinalen, bevorzugt vaskulären Pathologien. Meist kommen destruktive Verfahren zum Einsatz. Durch das Hinzukommen der intravitrealen Applikation von Antikörper(fragmenten) gegen den Wachstumsfaktor „vascular endothelial growth factor“ (VEGF) muss jedoch bei einigen Indikationen der Einsatz der Laserbehandlung als First-Line-Therapie kritisch hinterfragt werden. Neue Strategien und Behandlungskonzepte sollen erläutert werden.
Material und Methoden Zusammenfassung der Literatur aus PubMed sowie relevanter Leitlinien und Stellungnahmen.
Ergebnisse und Schlussfolgerung Das Anwendungsspektrum der retinalen Laserphotokoagulation ist vielfältig. Trotz und neben neuen, vielversprechenden medikamentösen Therapieansätzen stellt die retinale Laserbehandlung auch heute noch eine unverzichtbare Therapieoption insbesondere bei der proliferativen diabetischen Retinopathie, venösen ischämischen Verschlüssen und selteneren Erkrankungen wie Retinopathia praematurorum oder Morbus Coats dar.
Development of an Enzyme-Linked Immunosorbent Assay for Determination Of Miroestrol Using an Anti-miroestrol Monoclonal Antibody
Authors: Kitisripanya Tharita , Krittanai Supaluk , Udomsin Orapin , Jutathis Kamonthip , Komaikul Jukrapun , Juengwatanatrakul Thaweesak , Sakamoto Seiichi , Tanaka Hiroyuki , Morimoto Satoshi , Putalun Waraporn 
Published: February 2017

AbstractMiroestrol is a chromene with potent estrogenic activity present in Pueraria candollei, commonly known as White Kwao Krua. Although this compound is only present in low amounts in the plant, it plays an important role in the estrogenic action of P. candollei products. As a tool for further studies about the efficacy and safety of P. candollei as a phytoestrogenic supplement, we generated a novel monoclonal antibody against miroestrol. This anti-miroestrol monoclonal antibody was used to develop an immunoassay for the determination of miroestrol content, which can be used for quality control purposes of P. candollei. The developed ELISA against miroestrol has a calibration range of 10–780 ng/mL miroestrol, a limit of detection of 3.5 ng/mL, and a limit of quantitation of 12.2 ng/mL. According to the validation analysis, the established ELISA is precise, accurate, specific, and sensitive for miroestrol detection in plants. Furthermore, the anti-miroestrol monoclonal antibody was used to prepare an immunoaffinity column for the isolation of miroestrol from the tuberous root of P. candollei. The column provides a simple procedure for miroestrol isolation, with a capacity of 3.91 µg of miroestrol per 1 mL of immunogel.
Effects of Mangifera indica (Careless) on Microcirculation and Glucose Metabolism in Healthy Volunteers
Authors: Buchwald-Werner Sybille , Schön Christiane , Frank Sonja , Reule Claudia 
Published: February 2017

AbstractA commercial Mangifera indica fruit powder (Careless) showed beneficial acute effects on microcirculation in a randomized, double-blind, crossover pilot study. Here, long-term effects on microcirculation and glucose metabolism were investigated in a double-blind, randomized, placebo-controlled, 3-arm parallel-design study in healthy individuals. A daily dose of 100 mg or 300 mg of the fruit powder was compared to placebo after supplementation for 4 weeks. Microcirculation and endothelial function were assessed by the Oxygen-to-see System and pulse amplitude tonometry, respectively. Glucose metabolism was assessed under fasting and postprandial conditions by capillary glucose and HbA1c values.Microcirculatory reactive hyperemia flow increased, especially in the 100 mg group (p = 0.025). The 300 mg of the M. indica fruit preparation reduced postprandial glucose levels by trend if compared to placebo (p = 0.0535) accompanied by significantly lower HbA1c values compared to baseline. Furthermore, 300 mg intake significantly improved postprandial endothelial function in individuals with decreased endothelial function after high-dose glucose intake (p = 0.0408; n = 11).In conclusion, the study suggests moderate beneficial effects of M. indica fruit preparation on microcirculation, endothelial function, and glucose metabolism.
Protective Effects of Ellagic Acid on Cardiovascular Injuries Caused by Hypertension in Rats
Authors: Jordão Juliana , Porto Hellen , Lopes Flávio , Batista Aline , Rocha Matheus 
Published: February 2017

AbstractEllagic acid is described as having antioxidant and antiproliferative properties. Hence, it was hypothesized that ellagic acid could improve cardiovascular damage caused by hypertension. In this work, hypertension was induced in rats with Nω-Nitro-L-arginine methyl ester hydrochloride (60 mg/kg/day in drinking water) for 6 weeks. Ellagic acid was coadministered (10 or 30 mg/kg/day by gavage) between the second and sixth week. Blood pressure was recorded every week by tail-cuff plethysmography. After 6 weeks, the rats were sacrificed, the hearts and kidneys were weighed, and blood was collected. Aortas were isolated and set up to isometric recordings in an organ bath for histological assay and measuring of calcium content. Hypertension (233.6 ± 9.5 mmHg) was reduced (p < 0.01) by treatment with ellagic acid 10 or 30 mg/kg. The blood levels of nitrate/nitrite were reduced in hypertensive rats and the ellagic acid restored these levels. While the vascular relaxations to acetylcholine and sodium nitoprusside and the contraction to phenylephrine were impaired in the hypertensive group, they were improved after ellagic acid treatment. The alkaline phosphatase activity was increased by hypertension and returned to control levels after ellagic acid treatment. In the aorta, the administration of ellagic acid resulted in less aortic wall thickening and less calcification. In conclusion, ellagic acid attenuates hypertension, possibly improving nitric oxide bioavailability. The vascular response to acetylcholine, sodium nitroprusside, and phenylephrine was impaired by hypertension and improved after treatment with ellagic acid. Moreover, plasmatic alkaline phosphatase activity, calcium content, and hypertrophy in vascular tissues during hypertension were attenuated by treatment with ellagic acid.
Biomechanics of judo backward breakfall for different throwing techniques in novice judokas
Authors: Koshida Sentaro , Ishii Takanori , Matsuda Tadamitsu , Hashimoto Toshihiko 
Published: February 2017

AbstractIt is generally accepted that proper learning of the breakfall technique during early judo training is essential for attenuating the risk of judo‐related head injury. Therefore, it is critical to understand the kinematics and head injury risks of breakfall motion to design a more safe and effective judo teaching paradigm that results in reduction of injury risk. We aimed to investigate the biomechanics of judo backward breakfalls by comparing osoto‐gari and ouchi‐gari in novice judokas. Twelve male novice judokas (age: 21.3 years, SD = 0.6 years; height: 1.74 m, SD = 0.04 m; body weight: 71.3, SD = 6.4 kg; body mass index: 23.5, SD = 2.3) volunteered to participate in this study. The kinematic data of the breakfall motion for both osoto‐gari and ouchi‐gari were collected using a three‐dimensional motion analysis technique (200 Hz). We observed significant differences between the movement patterns for the two techniques, especially in the lower extremity movements. In addition, a significantly greater peak extension momentum (osoto‐gari: 1.29, SD = 0.23 kg m2 s−1; ouchi‐gari: 0.84, SD = 0.29 kg m2 s−1) and lower head position along the vertical axis (osoto‐gari: 0.18, SD = 0.05 m; ouchi‐gari: 0.31, SD = 0.08 m) with a large effect size were found in the breakfall for osoto‐gari. Our results suggest that a different paradigm is needed for effectively teaching each breakfall technique that will enable us to substantially lower the risk of judo‐related head injuries in novice judokas.
Kollector: transcript-informed, targeted de novo assembly of gene loci
Authors: Kucuk Erdi , Chu Justin , Vandervalk Benjamin P , Hammond S Austin , Warren René L , Birol Inanc 
Published: February 2017

Abstract

Motivation
Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time-consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene-centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment-free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes—properties that makes it especially useful for researchers working on non-model eukaryotic organisms.

Results
We demonstrate the performance of Kollector for assembling complete or near-complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time- and memory-efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications.

Availability and Implementation
Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector

Supplementary information
Supplementary data are available at Bioinformatics online.
VALORATE: fast and accurate log-rank test in balanced and unbalanced comparisons of survival curves and cancer genomics
Authors: Treviño Victor , Tamez-Pena Jose 
Published: February 2017

Abstract

Summary
The association of genomic alterations to outcomes in cancer is affected by a problem of unbalanced groups generated by the low frequency of alterations. For this, an R package (VALORATE) that estimates the null distribution and the P-value of the log-rank based on a recent reformulation is presented. For a given number of alterations that define the size of survival groups, the log-rank density is estimated by a weighted sum of conditional distributions depending on a co-occurrence term of mutations and events. The estimations are accurately accelerated by sampling across co-occurrences allowing the analysis of large genomic datasets in few minutes. In conclusion, the proposed VALORATE R package is a valuable tool for survival analysis.

Availability and Implementation
The R package is available in CRAN at https://cran.r-project.org and in http://bioinformatica.mty.itesm.mx/valorateR.

Supplementary information
Supplementary data are available at Bioinformatics online.
FELLS: fast estimator of latent local structure
Authors: Piovesan Damiano , Walsh Ian , Minervini Giovanni , Tosatto Silvio C.E 
Published: February 2017

Abstract

Motivation
The behavior of a protein is encoded in its sequence, which can be used to predict distinct features such as secondary structure, intrinsic disorder or amphipathicity. Integrating these and other features can help explain the context-dependent behavior of proteins. However, most tools focus on a single aspect, hampering a holistic understanding of protein structure. Here, we present Fast Estimator of Latent Local Structure (FELLS) to visualize structural features from the protein sequence. FELLS provides disorder, aggregation and low complexity predictions as well as estimated local propensities including amphipathicity. A novel fast estimator of secondary structure (FESS) is also trained to provide a fast response. The calculations required for FELLS are extremely fast and suited for large-scale analysis while providing a detailed analysis of difficult cases.

Availability and Implementation
The FELLS web server is available from URL: http://protein.bio.unipd.it/fells/. The server also exposes RESTful functionality allowing programmatic prediction requests. An executable version of FESS for Linux can be downloaded from URL: protein.bio.unipd.it/download/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Binning_refiner: improving genome bins through the combination of different binning programs
Authors: Song Wei-Zhi , Thomas Torsten 
Published: February 2017

Abstract

Summary
Microbial genomes have recently been reconstructed from metagenomic datasets using binning approaches. Inconsistent binning results are however often observed between different binning programs, likely due to the different algorithms or statistical models used. We present Binning_refiner, a pipeline that merges the results of different binning programs. Our results demonstrated that Binning_refiner can significantly reduce the contamination level of genome bins and increase the total size of contamination-free and ‘good-quality’ genome bins. Binning_refiner is thus an useful tool to improve the quality of genome bins derived from metagenomic data.

Availability and Implementation
Binning_refiner is implemented in Python3 and is freely available at: https://github.com/songweizhi/Binning_refiner.

Supplementary information
Supplementary data are available at Bioinformatics online.