bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous Glucose Monitoring Adherence
Authors: de Bock Martin , Cooper Matthew , Retterath Adam , Nicholas Jennifer , Ly Trang , Jones Timothy , Davis Elizabeth 
Published: February 2016

Aims: This study reports continuous glucose monitoring (CGM) adherence patterns and contributing factors in patients who were part of a 6-month clinical trial using sensor augmented pump therapy with low glucose insulin suspension. Methods: CGM data from 38 patients using sensor augmented pump therapy for 6 months were analyzed. CGM adherence was defined by having a working sensor available and determined by the time it was switched on as a proportion of available time for the 6 month study period with allowance for practical CGM use. Age, gender, HbA1c, duration of diagnosis, capillary blood glucose testing frequency, sensor accuracy, and insulin pump alarm frequency were characterized and examined for an association with CGM adherence. Results: Overall CGM adherence was 75% (range: 35% to 96%), CGM adherence was demonstrated to fall after 9 to 11 weeks before reaching a steady rate. CGM adherence patterns showed substantial variation. Mean adherence differed ( P < .01) between age groups 72% (<12 years), 69% (12-18 years), and 88% (≥18 years). Sensor accuracy predicted adherence, where every 1% decline in mean absolute difference in a given week was associated with a 0.5% decline in sensor adherence ( P < .01). Gender, HbA1c, duration of diagnosis, capillary blood glucose testing frequency, and insulin pump alarm frequency were not associated with CGM adherence. Conclusions: CGM adherence and patterns of use are individualized. However, a predictable fall in adherence at 9 to 11 weeks may present an opportunity for timed interventions to increase CGM use. Adolescent age and sensor accuracy predict CGM adherence.
Genesis of smectite in siliciclastics and pyroclastics of the Eocene İslambeyli Formation in the Lalapaşa region, NW Thrace, Turkey
Authors: Ekіncі Şans B. , Esenlі F. , Kadir S. , Elliott W.C. 
Published: February 2016

AbstractThe Eocene İslambeyli Formation in the Lalapaşa region (NW Thrace, Turkey) consists predominantly of siliciclastic clayey clastics at the bottom and of claystone, tuff and tuffaceous claystone/ sandstone/limestone in the middle and uppermost parts of this formation. Some tuff-tuffaceous beds of the middle–upper parts of the formation are economically viable bentonite depoits. The İslambeyli Formation exhibits vertical variations in the mineralogy, elemental compositions, and smectite-forming processes. Smectite was formed by weathering and diagenetic processes in the fluvial-shore environments in the lower part and by diagenetic alteration in a shallow-marine environment in the middle–upper parts of the formation. Ca-smectite flakes were formed by two processes: direct precipitation; and by means of a dissolution-precipitation mechanism from feldspar and mica. Dissolution-precipitation was most prevalent in the siliciclastic lower part of the formation. The amounts of Al, Fe, Mg and Ca required to form smectite and accessory illite were supplied mainly from the alteration of feldspars, mica and glass shards. The origin of smectite can also be explained by the inferred solution compositions given the parent phases in this formation, and the devitrification of glass shards in pyroclastic-rich middle–upper parts of the formation. In the upper beds, the observed decrease of K and Fe in the smectite structure coincided with both the increase in the amount of smectite and the increase in solution pH suggesting that precipitation of smectite developed over a prolonged period and under arid conditions.
Sparse regressions for predicting and interpreting subcellular localization of multi-label proteins
Authors: Wan Shibiao , Mak Man-Wai , Kung Sun-Yuan 
Published: February 2016

Abstract
Background
Predicting protein subcellular localization is indispensable for inferring protein functions. Recent studies have been focusing on predicting not only single-location proteins, but also multi-location proteins. Almost all of the high performing predictors proposed recently use gene ontology (GO) terms to construct feature vectors for classification. Despite their high performance, their prediction decisions are difficult to interpret because of the large number of GO terms involved.

Results
This paper proposes using sparse regressions to exploit GO information for both predicting and interpreting subcellular localization of single- and multi-location proteins. Specifically, we compared two multi-label sparse regression algorithms, namely multi-label LASSO (mLASSO) and multi-label elastic net (mEN), for large-scale predictions of protein subcellular localization. Both algorithms can yield sparse and interpretable solutions. By using the one-vs-rest strategy, mLASSO and mEN identified 87 and 429 out of more than 8,000 GO terms, respectively, which play essential roles in determining subcellular localization. More interestingly, many of the GO terms selected by mEN are from the biological process and molecular function categories, suggesting that the GO terms of these categories also play vital roles in the prediction. With these essential GO terms, not only where a protein locates can be decided, but also why it resides there can be revealed.

Conclusions
Experimental results show that the output of both mEN and mLASSO are interpretable and they perform significantly better than existing state-of-the-art predictors. Moreover, mEN selects more features and performs better than mLASSO on a stringent human benchmark dataset. For readers’ convenience, an online server called SpaPredictor for both mLASSO and mEN is available at http://bioinfo.eie.polyu.edu.hk/SpaPredictorServer/.
Structure-based Markov random field model for representing evolutionary constraints on functional sites
Authors: Jeong Chan-Seok , Kim Dongsup 
Published: February 2016

Abstract
Background
Elucidating the cooperative mechanism of interconnected residues is an important component toward understanding the biological function of a protein. Coevolution analysis has been developed to model the coevolutionary information reflecting structural and functional constraints. Recently, several methods have been developed based on a probabilistic graphical model called the Markov random field (MRF), which have led to significant improvements for coevolution analysis; however, thus far, the performance of these models has mainly been assessed by focusing on the aspect of protein structure.

Results
In this study, we built an MRF model whose graphical topology is determined by the residue proximity in the protein structure, and derived a novel positional coevolution estimate utilizing the node weight of the MRF model. This structure-based MRF method was evaluated for three data sets, each of which annotates catalytic site, allosteric site, and comprehensively determined functional site information. We demonstrate that the structure-based MRF architecture can encode the evolutionary information associated with biological function. Furthermore, we show that the node weight can more accurately represent positional coevolution information compared to the edge weight. Lastly, we demonstrate that the structure-based MRF model can be reliably built with only a few aligned sequences in linear time.

Conclusions
The results show that adoption of a structure-based architecture could be an acceptable approximation for coevolution modeling with efficient computation complexity.
MethPat: a tool for the analysis and visualisation of complex methylation patterns obtained by massively parallel sequencing
Authors: Wong Nicholas C. , Pope Bernard J. , Candiloro Ida L. , Korbie Darren , Trau Matt , Wong Stephen Q. , Mikeska Thomas , Zhang Xinmin , Pitman Mark , Eggers Stefanie , Doyle Stephen R. , Dobrovic Alexander 
Published: February 2016

Abstract
Background
DNA methylation at a gene promoter region has the potential to regulate gene transcription. Patterns of methylation over multiple CpG sites in a region are often complex and cell type specific, with the region showing multiple allelic patterns in a sample. This complexity is commonly obscured when DNA methylation data is summarised as an average percentage value for each CpG site (or aggregated across CpG sites). True representation of methylation patterns can only be fully characterised by clonal analysis. Deep sequencing provides the ability to investigate clonal DNA methylation patterns in unprecedented detail and scale, enabling the proper characterisation of the heterogeneity of methylation patterns. However, the sheer amount and complexity of sequencing data requires new synoptic approaches to visualise the distribution of allelic patterns.

Results
We have developed a new analysis and visualisation software tool “Methpat”, that extracts and displays clonal DNA methylation patterns from massively parallel sequencing data aligned using Bismark. Methpat was used to analyse multiplex bisulfite amplicon sequencing on a range of CpG island targets across a panel of human cell lines and primary tissues. Methpat was able to represent the clonal diversity of epialleles analysed at specific gene promoter regions. We also used Methpat to describe epiallelic DNA methylation within the mitochondrial genome.

Conclusions
Methpat can summarise and visualise epiallelic DNA methylation results from targeted amplicon, massively parallel sequencing of bisulfite converted DNA in a compact and interpretable format. Unlike currently available tools, Methpat can visualise the diversity of epiallelic DNA methylation patterns in a sample.
Systematic evaluation of the impact of ChIP-seq read designs on genome coverage, peak identification, and allele-specific binding detection
Authors: Zhang Qi , Zeng Xin , Younkin Sam , Kawli Trupti , Snyder Michael P. , Keleş Sündüz 
Published: February 2016

Abstract
Background
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) experiments revolutionized genome-wide profiling of transcription factors and histone modifications. Although maturing sequencing technologies allow these experiments to be carried out with short (36–50 bps), long (75–100 bps), single-end, or paired-end reads, the impact of these read parameters on the downstream data analysis are not well understood. In this paper, we evaluate the effects of different read parameters on genome sequence alignment, coverage of different classes of genomic features, peak identification, and allele-specific binding detection.

Results
We generated 101 bps paired-end ChIP-seq data for many transcription factors from human GM12878 and MCF7 cell lines. Systematic evaluations using in silico variations of these data as well as fully simulated data, revealed complex interplay between the sequencing parameters and analysis tools, and indicated clear advantages of paired-end designs in several aspects such as alignment accuracy, peak resolution, and most notably, allele-specific binding detection.

Conclusions
Our work elucidates the effect of design on the downstream analysis and provides insights to investigators in deciding sequencing parameters in ChIP-seq experiments. We present the first systematic evaluation of the impact of ChIP-seq designs on allele-specific binding detection and highlights the power of pair-end designs in such studies.
V3DM+: BIM interactive collaboration system for facility management
Authors: Lee Wan-Li , Tsai Meng-Han , Yang Cheng-Hsuan , Juang Jhih-Ren , Su Jui-Yu 
Published: February 2016

AbstractBackgroundFacility management (FM) is an important phase in the building lifecycle. Although building information modeling (BIM) technology has been widely used in the design and construction phase, efforts to transfer information to the FM phase are still in the nascent stage. A good BIM-to-FM tool should be able to inherit and integrate the building information built in the design and construction phase as well as be able to provide a platform for managers to browse the information, discuss potential problems, and arrange maintenance work.MethodsIn this research, a BIM interactive collaboration system for FM is designed and implemented. Two modules were developed for optimizing the BIM system in the FM phase: the data arrangement module, which has functionalities of data importing and processing, and the data presentation module, which provides functionalities of data revealing and collaboration.ResultFrom the results of an accessibility analysis, we verified that the developed system, V3DM+, can be implemented on real projects. Managers can use V3DM+ to support operation and maintenance of buildings. Moreover, a web-based platform allows users to manage facilities intuitively without investing on professionals or specialized software.ConcludingThe proposed system, V3DM+, provides a data arrangement module to integrate building information constructed by various types of commercial software and present them in a visual manner. The user can find the required information, initiate a discussion on an issue, or arrange operation and maintenance tasks directly on this system.
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
Authors: Huntemann Marcel , Ivanova Natalia N. , Mavromatis Konstantinos , Tripp H. James , Paez-Espino David , Tennessen Kristin , Palaniappan Krishnaveni , Szeto Ernest , Pillay Manoj , Chen I-Min A. , Pati Amrita , Nielsen Torben , Markowitz Victor M. , Kyrpides Nikos C. 
Published: February 2016

AbstractThe DOE-JGI Metagenome Annotation Pipeline (MAP v.4) performs structural and functional annotation for metagenomic sequences that are submitted to the Integrated Microbial Genomes with Microbiomes (IMG/M) system for comparative analysis. The pipeline runs on nucleotide sequences provided via the IMG submission site. Users must first define their analysis projects in GOLD and then submit the associated sequence datasets consisting of scaffolds/contigs with optional coverage information and/or unassembled reads in fasta and fastq file formats. The MAP processing consists of feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNAs, as well as CRISPR elements. Structural annotation is followed by functional annotation including assignment of protein product names and connection to various protein family databases.
Silychristin, a Flavonolignan Derived From the Milk Thistle, Is a Potent Inhibitor of the Thyroid Hormone Transporter MCT8
Authors: Johannes Jörg , Jayarama-Naidu Roopa , Meyer Franziska , Wirth Eva Katrin , Schweizer Ulrich , Schomburg Lutz , Köhrle Josef , Renko Kostja 
Published: February 2016

Abstract
Thyroid hormones (THs) are charged and iodinated amino acid derivatives that need to pass the cell membrane facilitated by thyroid hormone transmembrane transporters (THTT) to exert their biological function. The importance of functional THTT is affirmed by the devastating effects of mutations in the human monocarboxylate transporter (MCT) 8, leading to a severe form of psychomotor retardation. Modulation of THTT function by pharmacological or environmental compounds might disturb TH action on a tissue-specific level. Therefore, it is important to identify compounds with relevant environmental exposure and THTT-modulating activity. Based on a nonradioactive TH uptake assay, we performed a screening of 13 chemicals, suspicious for TH receptor interaction, to test their potential effects on THTT in MCT8-overexpressing MDCK1-cells. We identified silymarin, an extract of the milk thistle, to be a potent inhibitor of T3 uptake by MCT8. Because silymarin is a complex mixture of flavonolignan substances, we further tested its individual components and identified silychristin as the most effective one with an IC50 of approximately 100 nM. The measured IC50 value is at least 1 order of magnitude below those of other known THTT inhibitors. This finding was confirmed by T3 uptake in primary murine astrocytes expressing endogenous Mct8 but not in MCT10-overexpressing MDCK1-cells, indicating a remarkable specificity of the inhibitor toward MCT8. Because silymarin is a frequently used adjuvant therapeutic for hepatitis C infection and chronic liver disease, our observations raise questions regarding its safety with respect to unwanted effects on the TH axis.
Mechanisms of Action of Liraglutide in Patients With Type 2 Diabetes Treated With High-Dose Insulin
Authors: Vanderheiden Anna , Harrison Lindsay B. , Warshauer Jeremy T. , Adams-Huet Beverley , Li Xilong , Yuan Qing , Hulsey Keith , Dimitrov Ivan , Yokoo Takeshi , Jaster Adam W. , Pinho Daniella F. , Pedrosa Ivan , Lenkinski Robert E. , Pop Laurentiu M. , Lingvay Ildiko 
Published: February 2016

Abstract

Context:
The mechanisms of action of incretin mimetics in patients with long-standing type 2 diabetes (T2D) and high insulin requirements have not been studied.

Objective:
To evaluate changes in β-cell function, glucagon secretion, and fat distribution after addition of liraglutide to high-dose insulin.

Design:
A single-center, randomized, double-blind, placebo-controlled trial.

Setting:
University of Texas Southwestern and Parkland Memorial Hospital clinics.

Patients:
Seventy-one patients with long-standing (median, 17 years) T2D requiring high-dose insulin treatment (&gt;1.5 U/kg/d; average, 2.2 ± 0.9 U/kg/d).

Intervention:
Patients were randomized to liraglutide 1.8 mg/d or matching placebo for 6 months.

Main Outcome Measures:
We measured changes in insulin and glucagon secretion using a 4-hour mixed-meal challenge test. Magnetic resonance-based techniques were used to estimate sc and visceral fat in the abdomen and ectopic fat in the liver and pancreas.

Results:
Glycosylated hemoglobin improved significantly with liraglutide treatment, with an end-of-trial estimated treatment difference between groups of −0.9% (95% confidence interval, −1.5, −0.4%) (P = .002). Insulin secretion improved in the liraglutide group vs placebo, as measured by the area under the curve of C-peptide (P = .002) and the area under the curves ratio of C-peptide to glucose (P = .003). Insulin sensitivity (Matsuda index) and glucagon secretion did not change significantly between groups. Liver fat and sc fat decreased in the liraglutide group vs placebo (P = .0006 and P = .01, respectively), whereas neither visceral nor pancreatic fat changed significantly.

Conclusions:
Treatment with liraglutide significantly improved insulin secretion, even in patients with long-standing T2D requiring high-dose insulin treatment. Liraglutide also decreased liver and sc fat, but it did not alter glucagon secretion.
Adrenocorticotropic hormone gel in the treatment of systemic lupus erythematosus: A retrospective study of patients.
Authors: Li Xiao , Golubovsky Josh , Hui-Yuen Joyce , Shah Ummara , Olech Ewa , Lomeo Rosalia , Singh Vijay , Busch Howard , Strandberg Mary Jane , Strandberg Kayla , Horowitz Leslie , Askanase Anca 
Published: February 2016

Objectives: Acthar Gel is a long-acting formulation of adrenocorticotropic hormone (ACTH) with anti-inflammatory effects thought to be mediated in part through melanocortin receptor activation. This study was initiated to understand the role of Acthar Gel in SLE treatment in rheumatology practices.Methods: This is a retrospective case series of nine adult female patients treated with Acthar Gel for at least six months at five academic centers. Treating physicians completed a one-page questionnaire on lupus medications, disease activity, and outcomes. Clinical response was defined using SLEDAI 2K and improvement in the clinical manifestation(s) being treated.Results: The most common clinical SLE manifestations/indications requiring therapy with Acthar Gel were arthritis, rash, and inability to taper corticosteroids. The mean SLEDAI 2K score at baseline was 5.8 ± 5.0 (range 0-16). Six patients were concomitantly treated with corticosteroids (mean dose 18.3mg/day). All patients were on background SLE medications including immunosuppressives. Seven of nine patients had an overall improvement, with a decrease in SLEDAI 2K from 5.8 ± 5.0 at baseline to 3.5 ± 2.7 (range 0-8); four of five patients had improvement or resolution in arthritis, and one of two patients had resolution of inflammatory rash. Four patients discontinued corticosteroids and one patient tapered below 50% of the initial dose by 3 months of treatment with Acthar Gel. No adverse events were reported.Conclusions: This study suggests a role for Acthar Gel as an alternative to corticosteroids in the treatment of SLE. Acthar Gel appears to be safe and well-tolerated after 6 months of treatment, with a significant reduction in disease activity.
(Im)possibility of practice: Satirical objectification and essaying projects
Authors: Robbins Felix 
Published: February 2016

Abstract
This article develops the notion of ‘tipping points’ with respect to the gaps and slippages in my architectural practice, and the consequences when considered in terms of projecting for architecture as opposed to the production of architecture. It adopts as a ‘starting point’ the insecurities of the discipline and the predominance of ‘models of’ architecture conceived as a ‘problem-solving’ exercise. It adopts a sceptical reflection on the premise of the discipline, and the value of its product – suggesting that the perpetuation of positions to justify a product merely exacerbate the impossibility of practice. The ‘objectification’ of the discipline is contrasted with the potential dynamics of ‘projection’ – exploring a shift in emphasis towards ‘projecting’ as a means to enable complex and dynamic ‘models for’ architecture. This shift is investigated through my ongoing design research that moves within the contradictions, translations and uncertainties of historical and projective slippages of ‘reconstructions’ and ‘parts’ of houses. My projects speculate on the contingent opportunities of inhabiting an open sequence of a ‘problematic situation’, rather than the singular limitations of a ‘solution’ to a ‘problem’. My research moves towards considering the liberating potential of acknowledging that contradiction is the architectural project, rather than perpetually conceiving of contradiction as an obstacle to be repositioned or removed by the construction of an architectural product. This shift in emphasis is considered as an open sequence of ‘tipping points’ that continue to evolve within the contradictions of practice as models for projecting architecture, rather than a singular ‘tipping point’ that simply reconstructs the same model of architectural product in different terms. The tipping point in my research is ultimately an acknowledgement of the (im)possibility of practice – the inherent contradiction in projecting an architectural project that by necessity is initiated by the belief in a transformative and ameliorative quality to ‘projecting’, but also necessarily without the capacity to articulate what that quality is.
This curious device: Allurer of abundance
Authors: Withers Simon 
Published: February 2016

Abstract
Far away and over the River lie the Maritime Complexities, where laws of exuberance and pleasures of imagination are so gloriously made manifest, at the heart of which exists the Vista Land. A place of curiosity, invention and combination. ‘This curious device’ is an enquiry into something of the extraordinary ingenuity, discovery, mutation, enlightenment and joy that evolved from the Maritime Complexities. An abundance of information at all scales, given shape, a spatial infinity. A place that also grew dark over time, a dark mirror with which to see our times. Of abundance appropriated and misused, of hope become cold, frozen by myriad small orthodoxies.