bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Effect of Anchoring the Columellar Strut Graft to the Lateral Crural Steal Suture in Patients With a Low Nasal Tip: A New Technique
Authors: Cetiner Hasan 
Published: January 2019

Objective:
The achievement of consistently superior results in rhinoplasty is difficult. This study aimed to evaluate the effect of anchoring the columellar strut graft to the thread of the lateral crural steal for nasal tip projection and rotation.

Study Design:
A retrospective, case-control study.

Methods:
Two groups were created which consisted of patients who had a history of low nasal tip deformity according to the type of nasal tip surgery in rhinoplasty. In group 1, the lateral crural steal technique with the strut graft was used, whereas in group 2, a new technique, in which the strut graft was anchored to the thread of the lateral crural steal, was used. Patients with low nasal tip deformity due to intrinsic factors such as long lateral crura were included. The effects of the 2 different surgical approaches on facial parameters (the nasolabial angle, nasofacial angle, and Goode ratio) were statistically compared using the Mann–Whitney U test and Student t test, as applicable.

Results:
Sixty patients were enrolled: half of them were included in group 1 and the other half in group 2. Average postoperative increases of the nasolabial angle score were 10.9 ± 4.72° and 18.76 ± 6.30° in groups 1 and 2, respectively (P < 0.001). Average improvements of the nasofacial angle were 2.33 ± 2.12° and 3.50 ± 2.44° in groups 1 and 2, respectively (P = 0.053). Average postoperative increases of the Goode ratio were 0.02 ± 0.02 in group 1 and 0.04 ± 0.03 in group 2 (P = 0.028).

Conclusion:
The new technique provided a prominent nasal cephalic rotation with a strong effect on the nasolabial angle and a partial effect on nasal projection.
ModellingTERTregulation across 19 different cancer types based on the MIPRIP 2.0 gene regulatory network approach
Authors: Poos Alexandra M. , Kordaß Theresa , Kolte Amol , Ast Volker , Oswald Marcus , Rippe Karsten , König Rainer 
Published: January 2019

AbstractBackgroundReactivation of the telomerase reverse transcriptase geneTERTis a central feature for the unlimited proliferation potential of the majority of cancers but the underlying regulatory processes are only partly understood.ResultsWe assembled regulator binding information from different sources to construct a generic human and mouse regulatory network. Advancing our “Mixed Integer linear Programming based Regulatory Interaction Predictor” (MIPRIP) approach, we identified the most common and cancer-type specific regulators ofTERTacross 19 different human cancers. The results were validated by using the well-knownTERTregulation by the ETS1 transcription factor in a subset of melanomas with mutations in theTERTpromoter.ConclusionOur improved MIPRIP2 R-package and the associated generic regulatory networks are freely available athttps://github.com/network-modeling/MIPRIP. MIPRIP 2.0 identified both common as well as tumor type specific regulators ofTERT. The software can be easily applied to transcriptome datasets to predict gene regulation for any gene and disease/condition under investigation.
Neural Mediators of Altered Perceptual Choice and Confidence Using Social Information
Authors: Roy Tiasha Saha , Giri Bapun , Chowdhury Arpita Saha , Mazumder Satyaki , Das Koel 
Published: January 2019

AbstractUnderstanding how individuals utilize social information while making perceptual decisions and how it affects their decision confidence is crucial in a society. Till date, very little is known about perceptual decision making in humans under the influence of social cues and the associated neural mediators. The present study provides empirical evidence of how individuals get manipulated by social cues while performing a face/car identification task. Subjects were significantly influenced by what they perceived as decisions of other subjects while the cues in reality were manipulated independently from the stimulus. Subjects in general tend to increase their decision confidence when their individual decision and social cues coincide, while their confidence decreases when cues conflict with their individual judgments often leading to reversal of decision. Using a novel statistical model, it was possible to rank subjects based on their propensity to be influenced by social cues. This was subsequently corroborated by analysis of their neural data. Neural time series analysis revealed no significant difference in decision making using social cues in the early stages unlike neural expectation studies with predictive cues. Multivariate pattern analysis of neural data alludes to a potential role of frontal cortex in the later stages of visual processing which appeared to code the effect of social cues on perceptual decision making. Specifically medial frontal cortex seems to play a role in facilitating perceptual decision preceded by conflicting cues.
Capturing the Diversity of Subsurface Microbiota – Choice of Carbon Source for Microcosm Enrichment and Isolation of Groundwater Bacteria
Authors: Wu Xiaoqin , Spencer Sarah , Alm Eric J. , Voriskova Jana , Chakraborty Romy 
Published: January 2019

AbstractImproved and innovative enrichment/isolation techniques that yield to relevant isolates representing the true diversity of environmental microbial communities would significantly advance exploring the physiology of ecologically important taxa in ecosystems. Traditionally, either simple organic carbon (C) or yeast extract is used as C source in culture medium for microbial enrichment/isolation in laboratory. In natural environment, however, microbial population and evolution are greatly influenced by the property and composition of natural organic C. In this study, 8 types of organic C sources were fed to intrinsic groundwater microbes collected at Oak Ridge Reservation Field Research Center (ORR-FRC) background site for a 30-day incubation period to investigate the response of indigenous bacterial communities to different C sources. The tested C sources included simple organic C (glucose, acetate, benzoate, oleic acid, and cellulose) that are either traditionally used as C source in bacterial culture medium or present in natural environments; naturally occurring undefined complex C (bacterial cell lysate and sediment-derived natural organic matter (NOM)); as well as vitamin mixture which is a commonly used ingredient in culture medium. Our results clearly indicate that natural complex C substrates served better in enriching diverse bacteria compared to other C sources. Microcosms amended with small organic C (glucose, acetate, benzoate, or oleic acid) showed significantly lower biodiversity than control groups, dominated by only a few phyla of bacteria such as Proteobacteria and Bacteroidetes which are commonly isolated and already have diverse representative isolates, while those amended with natural complex C (cell lysate or NOM) displayed significantly higher biodiversity than control groups, in which three phyla (Verrucomicrobia, Planctomycetes, and Armatimonadetes) that are poorly represented in published culture collections were abundantly enriched. Further isolation of pure bacterial strains from complex C-amended enrichments led to 51 species representing 4 phyla, 13 orders. Furthermore, 5 isolates with low similarities to published strains were considered to be novel. Results from this study will aid in the design of better cultivation and isolation strategy for maximize the diversity of organisms recovered from subsurface environment.
Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification
Authors: Argelaguet Ricard , Mohammed Hisham , Clark Stephen J , Stapel L Carine , Krueger Christel , Kapourani Chantriolnt-Andreas , Xiang Yunlong , Hanna Courtney , Smallwood Sebastien , Ibarra-Soria Ximena , Buettner Florian , Sanguinetti Guido , Krueger Felix , Xie Wei , Rugg-Gunn Peter , Kelsey Gavin , Dean Wendy , Nichols Jennifer , Stegle Oliver , Marioni John C , Reik Wolf 
Published: January 2019

AbstractFormation of the three primary germ layers during gastrulation is an essential step in the establishment of the vertebrate body plan. Recent studies employing single cell RNA-sequencing have identified major transcriptional changes associated with germ layer specification. Global epigenetic reprogramming accompanies these changes, but the role of the epigenome in regulating early cell fate choice remains unresolved, and the coordination between different epigenetic layers is unclear. Here we describe the first single cell triple-omics map of chromatin accessibility, DNA methylation and RNA expression during the exit from pluripotency and the onset of gastrulation in mouse embryos. We find dynamic dependencies between the different molecular layers, with evidence for distinct modes of epigenetic regulation. The initial exit from pluripotency coincides with the establishment of a global repressive epigenetic landscape, followed by the emergence of local lineage-specific epigenetic patterns during gastrulation. Notably, cells committed to mesoderm and endoderm undergo widespread coordinated epigenetic rearrangements, driven by loss of methylation in enhancer marks and a concomitant increase of chromatin accessibility. In striking contrast, the epigenetic landscape of ectodermal cells is already established in the early epiblast. Hence, regulatory elements associated with each germ layer are either epigenetically primed or epigenetically remodelled prior to overt cell fate decisions during gastrulation, providing the molecular logic for a hierarchical emergence of the primary germ layers.HighlightsFirst map of mouse gastrulation using comprehensive single cell triple-omic analysis.Exit from pluripotency is associated with a global repressive epigenetic landscape, driven by a sharp gain of DNA methylation and a gradual decrease of chromatin accessibility.DNA methylation and chromatin accessibility changes in enhancers, but not in promoters, are associated with germ layer formation.Mesoderm and endoderm enhancers become open and demethylated upon lineage commitment.Ectoderm enhancers are primed in the early epiblast and protected from the global repressive dynamics, supporting a default model of ectoderm commitmentin vivo.
Molecular Genetic Analysis ofRB1gene among Sudanese children with Retinoblastoma
Authors: Ibrahim Nada O. , Saleem Mahgoub , Eltayeb Entesar , Mekki Salwa , Elnaim Elteleb G. , Idris Abeer Babiker , Bashir Sanaa , Salim Mohammed A. , Hassan Mohamed A. 
Published: January 2019

BACKGROUNDRetinoblastoma (RB), the commonest early childhood intraocular tumor, is most often related to mutations in theRB1gene with an incidence of 3% of all pediatric tumors. It has good prognosis if diagnosed early but it is life-threatening when diagnosed late.OBJECTIVETo study the Molecular Genetic Analysis of Retinoblastoma (RB) in Sudanese families.METHODSThirty one (n=31) clinically and histopathologically diagnosed cases of RB attending Makkah Eye Complex (MEC) Orbit clinic (Khartoum, Sudan) were included in this Molecular Genetic RB Analysis. Fresh blood samples extracted from seven RB patients and 15 close families for DNA extraction and PCR were sent for Genetic Sequencing andIn silicoapproach for “Exon 18 mutations” which is one of the highly mutated exons worldwide.RESULTSThe majority of patients (41.9%) were below five years old. Females were 58.1%, males were 41.9%. Leukocoria was the commonest sign at presentation (41.9%). RB Unilaterality were in (77.4%) while Bilaterality in 19.4%. Both eyes were equally affected 50% each. The age at diagnosis time ranged from 0.02 to five years. Consanguinity of parents was very high (85.7%), the 1stdegree cousins were less (28.6%) while the 2nddegree was high (57.1%). The patients’ ethnic background and geographical area were from seven different tribes; all belong to the Western Sudan. The molecular genetic study showed that exon 18 was free of mutation among the seven patients + their three relatives. The Functional Analysis and (SNPs) prediction study of exon 18 from NCBI data base showed that the various computational approaches used (SIFT, PolyPhen-2, I-mutantandProject hope) identified 16 reported mutations worldwide, three of which (rs137853292, rs375645171 and rs772068738) are major nsSNPs (non-synonymous) which might contribute to nativeRB1protein malfunction and ultimately causing carcinoma.CONCLUSIONRB mainly affected children under five years and both sexes are equally affected. Unilaterality was predominant. Consanguinity plays a role in inheritance and the majority of patients were from Western Sudan. The most commonly detected deleterious mutations worldwide in exon 18 were not found in the Sudanese studies samples. Further screening for the highly reported mutations in exons 8, 10 and 14 or Next Generation Sequencing (NGS) are recommended.In silicotools are useful in studying the functional analysis of SNPs.
A comprehensive evaluation of long read error correction methods
Authors: Zhang Haowen , Jain Chirag , Aluru Srinivas 
Published: January 2019

AbstractBackgroundThird-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstream analysis. This difficulty has motivated the development of many long read error correction tools, which tackle this problem through sampling redundancy and/or leveraging accurate short reads of the same biological samples. Existing studies to asses these tools use simulated data sets, and are not sufficiently comprehensive in the range of software covered or diversity of evaluation measures used.ResultsIn this paper, we present a categorization and review of long read error correction methods, and provide a comprehensive evaluation of the corresponding long read error correction tools. Leveraging recent real sequencing data, we establish benchmark data sets and set up evaluation criteria for a comparative assessment which includes quality of error correction as well as run-time and memory usage. We study how trimming and long read sequencing depth affect error correction in terms of length distribution and genome coverage post-correction, and the impact of error correction performance on an important application of long reads, genome assembly. We provide guidelines for practitioners for choosing among the available error correction tools and identify directions for future research.ConclusionsDespite the high error rate of long reads, the state-of-the-art correction tools can achieve high correction quality. When short reads are available, the best hybrid methods outperform non-hybrid methods in terms of correction quality and computing resource usage. When choosing tools for use, practitioners are suggested to be careful with a few correction tools that discard reads, and check the effect of error correction tools on downstream analysis. Our evaluation code is available as open-source at https://github.com/haowenz/LRECE.
Genotype-by-environment interactions inferred from genetic effects on phenotypic variability in the UK Biobank
Authors: Wang Huanwei , Zhang Futao , Zeng Jian , Wu Yang , Kemper Kathryn E. , Xue Angli , Zhang Min , Powell Joseph E. , Goddard Michael E. , Wray Naomi R. , Visscher Peter M. , McRae Allan F. , Yang Jian 
Published: January 2019

AbstractGenotype-by-environment interaction (GEI) is a fundamental component in understanding complex trait variation. However, it remains challenging to identify genetic variants with GEI effects in humans largely because of the small effect sizes and the difficulty of monitoring environmental fluctuations. Here, we demonstrate that GEI can be inferred from genetic variants associated with phenotypic variability in a large sample without the need of measuring environmental factors. We performed a genome-wide variance quantitative trait locus (vQTL) analysis of ~5.6 million variants on 348,501 unrelated individuals of European ancestry for 13 quantitative traits in the UK Biobank, and identified 75 significant vQTLs with P<2.0×10−9 for 9 traits, especially for those related to obesity. Direct GEI analysis with five environmental factors showed that the vQTLs were strongly enriched with GEI effects. Our results indicate pervasive GEI effects for obesity-related traits and demonstrate the detection of GEI without environmental data.
GWAS identifies nine nephrolithiasis susceptibility loci related with metabolic metabolic and crystallization pathways
Authors: Tanikawa Chizu , Kamatani Yoichiro , Terao Chikashi , Usami Masayuki , Takahashi Atsushi , Momozawa Yukihide , Suzuki Kichiya , Ogishima Soichi , Shimizu Atsushi , Satoh Mamoru , Matsuo Keitaro , Mikami Haruo , Naito Mariko , Wakai Kenji , Yamaji Taiki , Sawada Norie , Iwasaki Motoki , Tsugane Shoichiro , Kohri Kenjiro , Yasui Takahiro , Murakami Yoshinori , Kubo Michiaki , Matsuda Koichi 
Published: January 2019

ABSTRACTNephrolithiasis is a common urological trait disorder with acute pain. Although previous studies have identified various genetic variations associated with nephrolithiasis, the host genetic factors remain largely unidentified. To identify novel nephrolithiasis loci in the Japanese population, we performed large-scale GWAS (Genome wide association study) using 11,130 cases and 187,639 controls, followed by a replication analysis using 2,289 cases and 3,817 controls. The analysis identified 14 significant loci, including 9 novel loci on 2p23.2-3, 6p21.2, 6p12.3, 6q23.2, 16p12.3, 16q12.2, 17q23.2, 19p13.12, and 20q13.2. Interestingly, 10 of the 14 regions showed a significant association with any of 16 quantitative traits, including metabolic, kidney-related, and electrolyte traits, suggesting a common genetic background among nephrolithiasis patients and these quantitative traits. Four novel loci are related to the metabolic pathway, while the remaining 10 loci are associated with the crystallization pathway. Our findings demonstrate the crucial roles of genetic variations in the development of nephrolithiasis.SIGNIFICANCE STATEMENTNephrolithiasis is a common urothelial disorders with frequent recurrence rate, but its genetic background is largely remained unidentified. Previous GWAS identified 6 genetic factors in total. Here we performed a GWAS using more than 200,000 samples in the Japanese populations, and identified 14 significant loci and nine of them are novel. We also found that 10 of the 14 loci showed a significant association with any of 16 quantitative traits, including metabolic, kidney-related, and electrolyte traits (BMI, eGFR, UA, Ca etc). All 14 significant loci are associate with either metabolic or crystallization pathways. Thus, our findings elucidated the underlying molecular pathogenesis of nephrolithiasis.
Structural basis of HMCES interactions with DNA reveals multivalent substrate recognition
Authors: Halabelian Levon , Ravichandran Mani , Li Yanjun , Zheng Hong , Aravind L. , Rao Anjana , Arrowsmith Cheryl H 
Published: January 2019

ABSTRACTHMCES can covalently crosslink to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the HMCES SRAP domain in complex with DNA-damage substrates, revealing interactions with both single-stranded and duplex segments of 3’ overhang DNA. HMCES may also bind gapped DNA and 5’ overhang structures to align single stranded abasic sites for crosslinking to the conserved Cys2 of its catalytic triad.
TooManyCells identifies and visualizes relationships of single-cell clades
Authors: Schwartz Gregory W. , Petrovic Jelena , Fasolino Maria , Zhou Yeqiao , Cai Stanley , Xu Lanwei , Pear Warren , Vahedi Golnaz , Faryabi Robert B. 
Published: January 2019

AbstractTranscriptional programs contribute to phenotypic and functional cell states. While elucidation of cell state heterogeneity and its role in biology and pathobiology has been advanced by studying single cell level measurements, the underlying assumptions of current analytical methods limit the identification and exploration of cell clades. Unlike other methods, which produce a single uni-layer partition of cells ignoring echelons of cell states, we presentTooManyCells, a software consisting of a suite of graph-based tools for efficient, global, and unbiased identification and visualization of cell clades while maintaining and presenting the relationship between cell states.TooManyCellsprovides a set of tools based on a matrix-free efficient divisive hierarchical spectral clustering algorithm wholly different from the prevalent Louvain-based methods.BirchBeer, the visualization component ofTooManyCells, introduces a new approach for single cell analysis that is built on a concept intentionally orthogonal to the widely used dimensionality reduction methods. Together, this suite of tools provide a paradigm shift in the analysis and interpretation of single cell data by enabling simultaneous comparisons of cell states at context-and application-dependent scales. A byproduct of this shift is the immediate detection and visualization of rare populations that outperforms previous algorithms as demonstrated by applying these tools to existing single cell RNA-seq data sets from various mouse organs.
Single-Cell Transcriptomic Evidence for Dense Intracortical Neuropeptide Networks
Authors: Smith Stephen J , Sümbül Uygar , Graybuck Lucas , Collman Forrest , Seshamani Sharmishtaa , Gala Rohan , Gliko Olga , Elabbady Leila , Miller Jeremy A. , Bakken Trygve , Rossier Jean , Yao Zizhen , Lein Ed , Zeng Hongkui , Tasic Bosiljka , Hawrylycz Michael 
Published: January 2019

SummarySeeking new insights into the homeostasis, modulation and plasticity of cortical synaptic networks, we have analyzed results from a single-cell RNA-seq study of 22,439 mouse neocortical neurons. Our analysis exposes transcriptomic evidence for dozens of molecularly distinct neuropeptidergic modulatory networks that directly interconnect all cortical neurons. This evidence begins with a discovery that transcripts of one or more neuropeptide precursor (NPP) and one or more neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes are highly abundant in all, or very nearly all, cortical neurons. Individual neurons express diverse subsets of NP signaling genes from palettes encoding 18 NPPs and 29 NP-GPCRs. These 47 genes comprise 37 cognate NPP/NP-GPCR pairs, implying the likelihood of local neuropeptide signaling. Here we use neuron-type-specific patterns of NP gene expression to offer specific, testable predictions regarding 37 peptidergic neuromodulatory networks that may play prominent roles in cortical homeostasis and plasticity.ImpactSingle-cell mRNA sequencing data from mouse neocortex expose evidence for peptidergic neuromodulatory networks that locally interconnect every cortical neuronData HighlightsAt least 97% of mouse neocortical neurons express one or more of 18 neuropeptide precursor proteins (NPP) genes at very high levelsAt least 98% of cortical neurons express one or more of 29 neuropeptide-selective G-protein-coupled receptor (NP-GPCR) genes cognate to the 18 highly expressed NPP genesNeocortical expression of these 18 NPP and 29 NP-GPCR genes is highly neuron-type-specific and their expression patterns differentiate transcriptomic neuron types with exceptional powerNeuron-type taxonomy and type-specific expression of 37 cognate NPP / NP-GPCR gene pairs generate testable predictions of at least 37 local intracortical neuromodulation networks