bluuebunny/crossref_metadata_2025_split huggingface dataset:
Powerful differential expression analysis incorporating network topology for next-generation sequencing data
Authors: Dona Malathi S.I , Prendergast Luke A , Mathivanan Suresh , Keerthikumar Shivakumar , Salim Agus 
Published: February 2017

AbstractMotivationRNA-seq has become the technology of choice for interrogating the transcriptome. However, most methods for RNA-seq differential expression (DE) analysis do not utilize prior knowledge of biological networks to detect DE genes. With the increased availability and quality of biological network databases, methods that can utilize this prior knowledge are needed and will offer biologists with a viable, more powerful alternative when analyzing RNA-seq data.ResultsWe propose a three-state Markov Random Field (MRF) method that utilizes known biological pathways and interaction to improve sensitivity and specificity and therefore reducing false discovery rates (FDRs) when detecting differentially expressed genes from RNA-seq data. The method requires normalized count data (e.g. in Fragments or Reads Per Kilobase of transcript per Million mapped reads (FPKM/RPKM) format) as its input and it is implemented in an R package pathDESeq available from Github. Simulation studies demonstrate that our method outperforms the two-state MRF model for various sample sizes. Furthermore, for a comparable FDR, it has better sensitivity than DESeq, EBSeq, edgeR and NOISeq. The proposed method also picks more top Gene Ontology terms and KEGG pathways terms when applied to real dataset from colorectal cancer and hepatocellular carcinoma studies, respectively. Overall, these findings clearly highlight the power of our method relative to the existing methods that do not utilize prior knowledge of biological network.Availability and ImplementationAs an R package at https://github.com/MalathiSIDona/pathDESeqTo install the package typeinstall_github("MalathiSIDona/pathDESeq",build_vignettes = TRUE). After installation, type vignette("pathDESeq") to access the vignette.Supplementary informationSupplementary data are available at Bioinformatics online.
CircosVCF: circos visualization of whole-genome sequence variations stored in VCF files
Authors: Drori E , Levy D , Smirin-Yosef P , Rahimi O , Salmon-Divon M 
Published: February 2017

Abstract

Summary
Visualization of whole-genomic variations in a meaningful manner assists researchers in gaining new insights into the underlying data, especially when it comes in the context of whole genome comparisons. CircosVCF is a web based visualization tool for genome-wide variant data described in VCF files, using circos plots. The user friendly interface of CircosVCF supports an interactive design of the circles in the plot, and the integration of additional information such as experimental data or annotations. The provided visualization capabilities give a broad overview of the genomic relationships between genomes, and allow identification of specific meaningful SNPs regions.

Availability and Implementation
CircosVCF was implemented in JavaScript and is available at http://www.ariel.ac.il/research/fbl/software.

Supplementary information
Supplementary data are available at Bioinformatics online.
GLINT: a user-friendly toolset for the analysis of high-throughput DNA-methylation array data
Authors: Rahmani Elior , Yedidim Reut , Shenhav Liat , Schweiger Regev , Weissbrod Omer , Zaitlen Noah , Halperin Eran 
Published: February 2017

Abstract

Summary
GLINT is a user-friendly command-line toolset for fast analysis of genome-wide DNA methylation data generated using the Illumina human methylation arrays. GLINT, which does not require any programming proficiency, allows an easy execution of Epigenome-Wide Association Study analysis pipeline under different models while accounting for known confounders in methylation data.

Availability and Implementation
GLINT is a command-line software, freely available at https://github.com/cozygene/glint/releases. It requires Python 2.7 and several freely available Python packages. Further information and documentation as well as a quick start tutorial are available at http://glint-epigenetics.readthedocs.io.
Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants
Authors: Jo Jihoon , Oh Jooseong , Lee Hyun-Gwan , Hong Hyun-Hee , Lee Sung-Gwon , Cheon Seongmin , Kern Elizabeth M A , Jin Soyeong , Cho Sung-Jin , Park Joong-Ki , Park Chungoo 
Published: February 2017

Abstract
The Japanese sea cucumber (Apostichopus japonicus Selenka 1867) is an economically important species as a source of seafood and ingredient in traditional medicine. It is mainly found off the coasts of northeast Asia. Recently, substantial exploitation and widespread biotic diseases in A. japonicus have generated increasing conservation concern. However, the genomic knowledge base and resources available for researchers to use in managing this natural resource and to establish genetically based breeding systems for sea cucumber aquaculture are still in a nascent stage. A total of 312 Gb of raw sequences were generated using the Illumina HiSeq 2000 platform and assembled to a final size of 0.66 Gb, which is about 80.5% of the estimated genome size (0.82 Gb). We observed nucleotide-level heterozygosity within the assembled genome to be 0.986%. The resulting draft genome assembly comprising 132 607 scaffolds with an N50 value of 10.5 kb contains a total of 21 771 predicted protein-coding genes. We identified 6.6–14.5 million heterozygous single nucleotide polymorphisms in the assembled genome of the three natural color variants (green, red, and black), resulting in an estimated nucleotide diversity of 0.00146. We report the first draft genome of A. japonicus and provide a general overview of the genetic variation in the three major color variants of A. japonicus. These data will help provide a comprehensive view of the genetic, physiological, and evolutionary relationships among color variants in A. japonicus, and will be invaluable resources for sea cucumber genomic research.
Indian Constitutionalism
Authors: Mehta Uday S. 
Published: February 2017

Abstract
This chapter examines the background conditions, or ideas, that informed the Indian Constituent Assembly (1946–49) as it reflected on the country’s future identity, and how that identity has been shaped by the Constitution. Constitutions, including the Indian Constitution, have been associated with concrete events that are saturated in terms of context and are often interpreted as the product of a historical process. This article begins with an overview of how constitutions respond to imperatives in relation to the logic of historical causation. It then considers the ways in which crisis and anarchy inform constitutional founding moments, along with social issues that have pervaded the Constituent Assembly debates and the Constitution. The chapter also discusses the significance of national unity/disunity and the idea of the future for the Constitution and the vision of country it put in place.
Citizenship
Authors: Jayal Niraja Gopal 
Published: February 2017

Abstract
This chapter examines the question of citizenship in the Indian Constitution. It first considers the debate in the Indian Constituent Assembly over jus soli vs jus sanguinis citizenship, along with the constitutional settlement of citizenship and the key issues that are most contested—and remain central to—citizenship jurisprudence. It then turns to a discussion of four terms whose interpretation has been central to the case law on citizenship: domicile, intention, migrant, and passport. It also analyses the main provisions of the Citizenship Act 1955 and the amendments to this piece of legislation from the mid-1980s to the present. The rest of the chapter explores the gradual shift from a jus soli conception of citizenship to one based on the principle of jus sanguinis, as well as the patterns of change and continuity in the constitutional and post-constitutional law of citizenship in India.
Emergency Powers
Authors: Sagar Rahul 
Published: February 2017

Abstract
This chapter examines constitutional provisions regarding emergency powers in India. It begins with an overview of the emergency provisions enumerated in Part XVIII of the Indian Constitution, with particular emphasis on three types of extraordinary situations. It then considers a curious feature of Part XVIII, the inclusion of Articles 356 and 360, which address failures of constitutional machinery in the States as well as threats to financial stability and credit. It also explores how Articles 352 and 356 have been interpreted over time, focusing on the extent of the executive power once an emergency has been proclaimed and whether the presidential proclamation is subject to judicial review. The chapter concludes by suggesting that the safeguards found in Part XVIII of the Indian Constitution may not be as resilient as they seem.
Constitutional Amendment
Authors: Khosla Madhav 
Published: February 2017

Abstract
This chapter examines the formal method for constitutional amendment provided for in Article 368 of the Indian Constitution. It first reviews the early cases that gave rise to the Basic Structure doctrine, which placed substantive restrictions upon the power of amendment, before exploring subsequent developments and the application of the doctrine. It considers how Indian courts have addressed the idea of an unconstitutional constitutional amendment, with particular emphasis on the architectural framework that the courts have envisioned the Constitution to have. It explains how the Basic Structure doctrine has been used to understand the principles on which constitutionalism must depend.
Executive
Authors: Dam Shubhankar 
Published: February 2017

Abstract
This chapter examines the place and role of the executive within India’s constitutional scheme. It begins with an overview of the office of the President of India and the Governor that heads each State, before turning to a discussion of the council of ministers, the role of the Prime Minister and the chief ministers, and their terms of office. It then considers the principal offices that comprise the executive, along with their appointments, powers, and functions, and the relationship between the formal and real heads of the executive. It also outlines the powers and functions of the executive and the range of discretionary powers vested in the President and Governors, as well as their effect, if any, on parliamentary credentials.
Jurisdiction
Authors: Vakil Raeesa 
Published: February 2017

Abstract
This chapter explores how the jurisdiction of the Indian Supreme Court has evolved as an appellate court, a constitutional court, and a ‘final’ court. It begins by reviewing the four kinds of appeal that may be heard by the Supreme Court as specified in the Indian Constitution: civil, criminal, questions of constitutional interpretation, and appeals by special leave of the Court. It then considers the uncertainty and expansion in the Supreme Court’s appellate jurisdiction, with particular emphasis on the imbalance in jurisdictional reforms, the absence of guidelines for the exercise of discretion, and inconsistency in implementing constitutional provisions. It also discusses the Court’s advisory jurisdiction, adjudication of federal disputes, and jurisdiction to interpret the Constitution, along with its power to enforce justice and its claim to inherent powers. The chapter concludes by outlining some of the challenges faced by the Court today.
Horizontal Effect
Authors: Gardbaum Stephen 
Published: February 2017

Abstract
This chapter examines the applicability of Part III of the Indian Constitution to non-State actors and the horizontal effect of fundamental rights. More specifically, it considers the extent to which the actions of private actors deemed not to be ‘the State’ for purposes of Article 12 of the Constitution are subject to the Constitution’s fundamental rights provisions. It begins with an overview of the distinction between the direct and indirect effect of constitutional rights on non-State actors. It then explores the Indian Supreme Court’s use of its writ petition jurisdiction to approach the issue of the fundamental rights contained in Part III of the Constitution applying horizontally.
Directive Principles of State Policy
Authors: Bhatia Gautam 
Published: February 2017

Abstract
This chapter examines the Directive Principles of State Policy (DPSPs) and their controversial place in the Indian Constitution. It first reviews the origins of DPSPs and the notion that fundamental rights must be interpreted in light of the DPSPs. It then considers the role played by the DPSPs in judicial inquiries by focusing on the Indian Supreme Court’s jurisprudence in the aftermath of the Re Kerala Education Bill case. After discussing the DPSPs as markers of reasonableness, the chapter explores whether it is possible to ground the DPSPs within a coherent intellectual vision, one that is justified both constitutionally and philosophically. It also analyses the Supreme Court’s evolving understanding of the place of Part IV within the constitutional scheme, and concludes by outlining the distinct roles played by DPSPs in judicial interpretation.
Equality
Authors: Khaitan Tarunabh 
Published: February 2017

Abstract
This chapter examines the grounds of legislative review under the general constitutional guarantee of the right to equality as embodied in Article 14 of the Indian Constitution. It first provides an overview of the traditional narrative on the transformation of Article 14, before turning to a discussion of two doctrines that have evolved to test the constitutionality of a measure when faced with an Article 14 challenge: the ‘classification test’ or the ‘old doctrine’ (‘unreasonable comparison’) and the ‘arbitrariness test’ or the ‘new doctrine’ (‘non-comparative unreasonableness’). It examines differences between the nature and application of these two tests, and current shortcomings within India’s equality framework.
Personal Laws
Authors: Agnes Flavia 
Published: February 2017

Abstract
This chapter examines the legal framework for personal laws in India. It begins with an overview of the legal system introduced for personal laws during colonial rule, along with the evolution of legislation for such laws. It then considers Hindu law reforms following Independence and goes on to discuss the manner in which the courts have tackled the challenges to the constitutionality of personal laws. In particular, it explores two approaches used by the courts to test personal laws on the touchstone of fundamental rights: the non-interventionist approach and the scrutinising approach. The chapter concludes by assessing Article 44 of the Indian Constitution and the debate over the Uniform Civil Code.
Minority Educational Institutions
Authors: Reddy K. Vivek 
Published: February 2017

Abstract
This chapter examines the right of religious and linguistic minorities to ‘establish and administer educational institutions of their choice’ as embodied in the Indian Constitution. Before discussing India’s constitutional experience with minority educational institutions, it considers the reasons that fuel the debate over the right of educational institutions under Article 30(1), including the Indian Supreme Court’s failure to provide an appropriate constitutional framework for the protection of such right. It explores whether, under Article 30, the right to establish and administer educational institutions is exclusive to religious and linguistic minorities or can be extended to other communities. It argues that the constitutional promise of Article 30(1) is yet to be fully understood and fulfilled.
Property
Authors: Wahi Namita 
Published: February 2017

Abstract
This chapter examines the fundamental right to property as an important, albeit contentious, provision in the Indian Constitution. It considers Article 19(1)(f) of the Constitution, which guaranteed to all citizens the fundamental right to ‘acquire, hold and dispose of property’. It considers the shifts and continuities concerning this right in India, in both colonial and Independent India. It analyses case law relating to agrarian reform under the First, Fourth, and Seventeenth Amendments (Article 31(4) and (6), Articles 31A and 31B). It also assesses the laws within the scope of Article 31(2) needed to satisfy the requirements of public purpose and compensation. It concludes by commenting on the abolition of the fundamental right to property through the Forty-fourth Constitutional Amendment, as well as attempts to reinstate this right in the Indian Constitution.
Density and metallicity of the Milky Way circumgalactic gas
Authors: Troitsky Sergey 
Published: February 2017

Abstract
The halo of the Milky Way circumgalactic gas extends up to the virial radius of the Galaxy, ∼250 kpc. The halo properties may be deduced from X-ray spectroscopic observations and from studies of the ram-pressure stripping of satellite dwarf galaxies. The former method is more precise, but its results depend crucially on the assumed metallicity of the circumgalactic gas; the latter one does not need these assumptions. Here, the information from both approaches is combined to constrain observationally the gas metallicity and density as functions of the galactocentric distance. It is demonstrated that the two kinds of data could be reconciled if the metallicity decreased to Z ∼ 0.1 Z⊙ in the outer parts of the extended halo. The corresponding gas density profile is rather flat, falling as r−(0.45–0.75) at large galactocentric distances r.
Increasing Incidence, Cost, and Seasonality in Patients Hospitalized for Cellulitis
Authors: Peterson Ryan A. , Polgreen Linnea A. , Cavanaugh Joseph E. , Polgreen Philip M. 
Published: February 2017

Abstract
Using data from the National Inpatient Sample, 1998–2013, we show that hospitalizations for cellulitis have approximately doubled. Costs increased by 118% to $3.74 billion annually. In addition, hospitalizations for cellulitis are highly seasonal, peaking in summer months: incidence during the peak month of July is 35% higher than in February.
A hard-to-soft state transition of Aquila X-1 observed with Suzaku
Authors: Ono Ko , Makishima Kazuo , Sakurai Soki , Zhang Zhongli , Yamaoka Kazutaka , Nakazawa Kazuhiro 
Published: February 2017

Abstract
The recurrent soft X-ray transient Aquila X-1 was observed with Suzaku for a gross duration of 79.9 ks, on 2011 October 21 when the object was in a rising phase of an outburst. During the observation, the source exhibited a clear spectral transition from the hard state to the soft state, on a time scale of ∼30 ks. Across the transition, the 0.8–10 keV X-Ray Imaging Spectrometer count rate increased by a factor ∼3, that of Hard X-ray Detector PIN (HXD-PIN) in 15–60 keV decreased by a similar factor, and the unabsorbed 0.1–100 keV luminosity increased from 3.5 × 1037 erg s−1 to 5.1 × 1037 erg s−1. The broadband spectral shape changed continuously, from a power-law-like one with a high-energy cut-off to a more convex one. Throughout the transition, the 0.8–60 keV spectra were successfully described with a model consisting of a multi-color blackbody and a Comptonized blackbody, which are considered to arise from a standard accretion disk and a closer vicinity of the neutron star, respectively. All the model parameters were confirmed to change continuously, from those typical in the hard state to those typical of the soft state. More specifically, the inner disk radius decreased from 31 km to 18 km, the effects of Comptonization on the blackbody photons weakened, and the electron temperature of Comptonization decreased from 10 keV to 3 keV. The derived parameters imply that the Comptonizing corona shrinks towards the final soft state, and/or the radial infall velocity of the corona decreases. These results reinforce the view that the soft and hard states of Aql X-1 (and of similar objects) are described by the same “disk plus Comptonized blackbody” model, but with considerably different parameters.
Celestial polarization patterns sufficient for Viking navigation with the naked eye: detectability of Haidinger's brushes on the sky versus meteorological conditions
Authors: Horváth Gábor , Takács Péter , Kretzer Balázs , Szilasi Szilvia , Száz Dénes , Farkas Alexandra , Barta András 
Published: February 2017

If a human looks at the clear blue sky from which light with high enough degree of polarization
d
originates, an 8-shaped bowtie-like figure, the yellow Haidinger's brush can be perceived, the long axis of which points towards the sun. A band of high
d
arcs across the sky at 90° from the sun. A person can pick two points on that band, observe the yellow brushes and triangulate the position of the sun based on the orientation of the two observed brushes. This method has been suggested to have been used on the open sea by Viking navigators to determine the position of the invisible sun occluded by cloud or fog. Furthermore, Haidinger's brushes can also be used to locate the sun when it is below the horizon or occluded by objects on the horizon. To determine the position of the sun using the celestial polarization pattern, the
d
of the portion of the sky used must be greater than the viewer's degree of polarization threshold
d
* for perception of Haidinger's brushes. We studied under which sky conditions the prerequisite
d
>
d
* is satisfied. Using full-sky imaging polarimetry, we measured the
d
-pattern of skylight in the blue (450 nm) spectral range for 1296 different meteorological conditions with different solar elevation angles
θ
and per cent cloud cover
ρ
. From the measured
d
-patterns of a given sky we determined the proportion
P
of the sky for which
d
>
d
*. We obtained that
P
is the largest at low solar elevations
θ
≈ 0° and under totally or nearly clear skies with cloud coverage
ρ
= 0%, when the sun's position is already easily determined. If the sun is below the horizon (−5° ≤
θ
< 0°) during twilight,
P
= 76.17 ± 4.18% for

d

min

∗

=
23
%

under clear sky conditions. Consequently, the sky-polarimetric Viking navigation based on Haidinger's brushes is most useful after sunset and prior to sunrise, when the sun is not visible and large sky regions are bright, clear and polarized enough for perception of Haidinger's brushes.
Tex19.1Regulates Acetylated SMC3 Cohesin and Prevents Aneuploidy in Mouse Oocytes
Authors: Reichmann Judith , Dobie Karen , Lister Lisa M. , Best Diana , Crichton James H. , MacLennan Marie , Read David , Raymond Eleanor S. , Hung Chao-Chun , Boyle Shelagh , Shirahige Katsuhiko , Cooke Howard J. , Bickmore Wendy A. , Herbert Mary , Adams Ian R. 
Published: February 2017

AbstractAge-dependent oocyte aneuploidy, a major cause of Down syndrome, is associated with declining sister chromatid cohesion in postnatal oocytes. Here we show that cohesion in postnatal mouse oocytes is regulated byTex19.1. We show thatTex19.1-/-oocytes have defects in the maintenance of chiasmata, mis-segregate their chromosomes during meiosis, and transmit aneuploidies to the next generation. By reconstituting aspects of this pathway in mitotic somatic cells, we show thatTex19.1regulates an acetylated SMC3-marked subpopulation of cohesin by inhibiting the activity of the E3 ubiquitin ligase UBR2 towards specific substrates, and that UBR2 itself has a previously undescribed role in negatively regulating acetylated SMC3. Lastly, we show that acetylated SMC3 is associated with meiotic chromosome axes in oocytes, but that this is reduced in the absence ofTex19.1. These findings indicate thatTex19.1maintains acetylated SMC3 and sister chromatid cohesion in postnatal oocytes, and prevents aneuploidy in the female germline.