bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adolescent Substance Use: Assessing the Knowledge, Attitudes, and Practices of a School-Based Health Center Workforce
Authors: Ramos Mary M. , Sebastian Rachel A. , Murphy Mary , Oreskovich Kristin , Condon Timothy P. 
Published: February 2017

Background: Recent attention has focused on the potential for school-based health centers (SBHCs) to provide access points for adolescent substance use care. In 2015, the University of New Mexico began screening, brief intervention, and referral to treatment (SBIRT) training for providers at New Mexico Department of Health (NMDOH)-funded SBHCs across the state. This study assesses baseline knowledge, attitudes, and practices of the New Mexico SBHC provider workforce regarding adolescent substance use and provision of services. Methods: In early 2015, the NMDOH administered an SBHC provider workforce survey ( N = 118) and achieved a 44.9% response rate. This descriptive analysis includes all survey respondents who self-identified as a primary care or behavioral health provider in an SBHC serving middle or high school students ( n = 52). Results: Among respondents, the majority (57.7%) were primary care providers, including nurse practitioners, physicians, and physician assistants. The remaining 42.3% of respondents were master's-level behavioral health providers. Only 44.2% of providers reported practicing the full SBIRT model at their SBHC, and 21.2% reported having received continuing education on SBIRT within the previous 3 years. Most respondents, 84.6%, agreed that it is the responsibility of SBHC providers to screen students for substance use using a standardized tool, and 96.2% agreed that it is the responsibility of the SBHC provider to assess for students’ readiness to change. A majority reported self-efficacy in helping students achieve change in their alcohol use, illicit drug use, and prescription drug misuse: 73.1%, 65.4%, and 63.5%, respectively. Conclusions: These results suggest that SBIRT training for New Mexico SBHC providers is timely. The authors identified gaps between recommended SBIRT practices and SBIRT delivery as well as discrepancies between reported provider self-efficacy and actual implementation of the SBIRT model. Further study will determine the effectiveness of efforts to address substance use and implement SBIRT in SBHCs.
fastMitoCalc: an ultra-fast program to estimate mitochondrial DNA copy number from whole-genome sequences
Authors: Qian Yong , Butler Thomas J , Opsahl-Ong Krista , Giroux Nicholas S , Sidore Carlo , Nagaraja Ramaiah , Cucca Francesco , Ferrucci Luigi , Abecasis Gonçalo R , Schlessinger David , Ding Jun 
Published: February 2017

Abstract
Mitochondrial DNA (mtDNA) copy number is tightly regulated in tissues, and is both a critical determinant of mitochondrial function and a potential biomarker for disease. We and other groups have shown that the mtDNA copy number per cell can be directly estimated from whole-genome sequencing. The computation is based on the rationale that sequencing coverage should be proportional to the underlying DNA copy number for autosomal and mitochondrial DNA, and most computing time is spent calculating the average autosomal DNA coverage across ∼3 billion bases. That makes analyzing tens of thousands of available samples very slow. Here we present fastMitoCalc, which takes advantage of the indexing of sequencing alignment files and uses a randomly selected small subset (0.1%) of the nuclear genome to estimate autosomal DNA coverage accurately. It is more than 100 times faster than current programs. fastMitoCalc also provides an option to estimate copy number using a single autosomal chromosome, which could also achieve high accuracy but is slower. Using fastMitoCalc, it becomes much more feasible now to conduct analyses on large-scale consortium data to test for association of mtDNA copy number with quantitative traits or nuclear variants.

Availability and Implementation
fastMitoCalc is available at https://lgsun.irp.nia.nih.gov/hsgu/software/mitoAnalyzer/index.html

Supplementary information
Supplementary data are available at Bioinformatics online.
P622 Efficacy of probiotics in inflammatory bowel disease: systematic review and meta-analysis
Authors: Derwa Y. , Gracie D.J. , Hamlin P.J. , Ford A.C. 
Published: February 2017

Abstract
Background: Ulcerative colitis (UC) and Crohn's disease (CD) are inflammatory bowel diseases (IBD). Evidence implicates disturbances of the gastrointestinal microbiota in their pathogenesis. We performed a systematic review and meta-analysis to examine the efficacy of probiotics in IBD.
Methods: MEDLINE, EMBASE, and the Cochrane Controlled Trials Register were searched (up to November 2016). Eligible randomised controlled trials (RCTs) recruited adults with UC or CD, and compared probiotics with 5-aminosalicylates (5-ASAs) or placebo. Dichotomous symptom data were pooled to obtain a relative risk (RR) of failure to achieve remission in active IBD, or RR of relapse of disease activity in quiescent IBD, with 95% confidence intervals (CIs).
Results: The search identified 12,251 citations. Twenty-two RCTs were eligible. There was no benefit of probiotics over placebo in inducing remission in active UC (RR of failure to achieve remission = 0.86; 95% CI 0.68–1.08).
Figure 1. Forest plot of randomised controlled trials reporting the efficacy of probiotics versus placebo in inducing remission in active UC, or in preventing relapse in quiescent UC.
However, when only trials of VSL#3 were considered there appeared to be a benefit (RR =0.74; 95% CI 0.63–0.87). Probiotics appeared equivalent to 5-ASAs in preventing UC relapse (RR =1.02 (95% CI 0.85 to 1.23).
Figure 2. Forest plot of randomised controlled trials reporting the efficacy of probiotics versus 5-aminosalicylates in Inducing remission in active UC, or in preventing relapse in quiescent UC.
There was no benefit of probiotics in inducing remission of active CD, in preventing relapse of quiescent CD, or in preventing endoscopic or clinical relapse of CD after surgically induced remission.
Figure 3. Forest plot of randomised controlled trials reporting the efficacy of probiotics versus placebo in inducing remission in active CD, or in preventing relapse in quiescent CD.
Conclusions: VSL#3 appears to be effective in inducing remission in active UC, and probiotics may be as effective as 5-ASAs in preventing relapse of quiescent UC. However, the efficacy of probiotics in CD remains uncertain, and more evidence from RCTs is required before their utility is known.
Constitutional Interpretation
Authors: Chandrachud Chintan 
Published: February 2017

Abstract
This chapter examines the question of interpretation with regard to the Indian Constitution. It begins with an overview of two meta-judgments underlying constitutional interpretation, the first of which relates to the legitimate source of the Constitution’s authority and the second to the tools and techniques that can be relied upon in order to expound constitutional meaning. It then considers the three historical phases of the Indian Supreme Court’s interpretive philosophy: textualism, structuralism and ethicalism, and panchayati eclecticism. It also explains how the Court started deciding cases based on self-conceptions of its own role, resulting in the adoption of various interpretive approaches that are not only incongruent, but also often producing incoherent constitutional jurisprudence.
Law, Politics, and Constitutional Hegemony
Authors: Baxi Upendra 
Published: February 2017

Abstract
This chapter examines constitutional hegemony in relation to three forms of prudence: legisprudence, jurisprudence, and demosprudence. It considers how constitutional pluralism has influenced the making and working of the Indian Constitution, especially through the dynamics of the Supreme Court of India. In particular, it explores the notion of adjudicatory leadership and the concept of demosprudence in the context of the Indian Supreme Court, along with the changing relation between demosprudence and jurisprudence. The article first looks at the demosprudence of the Supreme Court of India, before discussing the concepts of organisational adjudicatory leadership, hermeneutic adjudicatory leadership, Social Action Litigation, and socially responsible criticism. It also analyses the politics and law of constitutional amendments.
Separation of Powers
Authors: Pal Ruma 
Published: February 2017

Abstract
This chapter examines how the issue of separation of powers is treated in the Indian Constitution. More specifically, it considers whether the separation of powers is a principle in the constitutional law of India and if so, what sort of doctrine of separation of powers is embraced by the Indian Constitution. The chapter begins with an overview of the three models of separation of powers articulated in the Indian Constitution, along with the constitutional provisions showing the functional overlap between the executive, legislature, and judiciary. It then turns to a discussion of the legislative branch’s judicial powers under the Constitution, as well as its control of the judiciary; the executive’s administration, legislative, and judicial functions; and the courts’ judicial power and independence. Finally, it looks at the allocation of powers relating to governance to autonomous bodies such as the Election Commission and the Comptroller and Auditor-General.
Legislature
Authors: Chauhan Sidharth 
Published: February 2017

Abstract
This chapter examines how the exercise of legislative privileges is treated in the Indian Constitution. More specifically, it considers whether the exercise of legislative privileges by members of the Indian Parliament is justiciable and if so, to what extent. While the courts have ruled in favour of limited judicial scrutiny, the broader principle of ‘separation of powers’ invites further debate. This article begins with an overview of the justifications for legislative privileges and prominent judgments related to their scope, along with some instances where their invocation has become the subject of political controversy but not litigated. In particular, it discusses the Indian Supreme Court’s lack of a clear position on press freedoms vs legislative privileges, as well as legal questions concerning the validity of invoking privileges against acts committed outside the legislatures and the permissibility of judicial review over them.
Fiscal Federalism
Authors: Singh Nirvikar 
Published: February 2017

Abstract
This chapter examines the fiscal aspects of federalism as enshrined in the Indian Constitution. It gives an overview of the original structures of fiscal federalism in India, including assignments of spending and revenue and mechanisms and institutions for making transfers across different government levels. It reviews constitutional amendments that have occurred since the adoption of the Constitution, from changes in expenditure and revenue authorities to the creation of a tier of local governments. It also considers the process of amending the Constitution, with particular emphasis on the intellectual and political drivers of change, and proceeds with a discussion of how the various constitutional provisions and amendments have been implemented in practice. Finally, it looks at legal cases concerning the constitutionality of fiscal federalism in India at various times, paying attention to institutions governing intergovernmental transfers, the distinction between taxes and fees, and the scope of authority of different levels of government.
Rights
Authors: Padmanabhan Ananth 
Published: February 2017

Abstract
This chapter examines the constitutional framework for fundamental rights in India. It considers three key issues raised by Part III: the application of fundamental rights to private actors (the ‘actor’ question); the applicability of fundamental rights to personal laws and to constitutional amendments (the ‘form’ question); and the effect of unconstitutionality on the validity of a law (the ‘effect’ question). The chapter focuses upon how the Supreme Court has interpreted the meaning of ‘State’ under Article 12, highlighting the structuralist understanding that it has provided, and also considering the contentious question of whether the judiciary should be regarded as ‘State’ for the purposes of Part III of the Constitution. It also examines the meaning of ‘law’ in Article 13 of the Constitution and concludes with an analysis of the doctrine of severability and the doctrine of eclipse.
Saving Clauses
Authors: Deva Surya 
Published: February 2017

Abstract
This chapter examines the drafting history, nature, scope, (mis)use, and relevance of the so-called ‘saving clauses’ of the Indian Constitution: Article 31A, Article 31B read with the Ninth Schedule, and Article 31C. They are designed to protect laws aimed at agrarian reforms or at implementing certain Directive Principles of State Policy (DPSPs) from a potential constitutional challenge on the ground of violating fundamental rights (FRs), andexceptionally allow certain laws to override FRs. This chapter offers an alternative reading of the saving clauses and discusses the Ninth Schedule, arguing that, despite being misused in the past, it might not be abused in the future, and that the Basic Structure doctrine is inappropriate to test the validity of laws inserted in the Ninth Schedule. It also suggests that the judiciary misconstrued their role with respect to the right to property as a FR, as well as the value of DPSPs relative to FRs.
Gender Equality
Authors: Kapur Ratna 
Published: February 2017

Abstract
This chapter examines gender equality in post-colonial India, particularly some of the structural and normative factors that make it difficult for women to bring constitutional challenges in their fight for greater equality. It considers efforts at using law, especially constitutional equality rights, to challenge laws promoting sex discrimination in India, along with the use of fundamental rights to equality as guaranteed by Articles 14, 15, and 16 of the Indian Constitution to challenge legal rules and provisions believed to discriminate against women. The chapter describes two different approaches to equality and gender difference through which the constitutional guarantees can be understood: a formal approach and a substantive approach. It then explores how familial ideology has influenced the judiciary’s approach to gender difference and provides examples to illustrate the impact of fundamental rights challenges on the very familial and legal discourses that have constituted women as different and subordinate.
Sovereign Immunity
Authors: Maitra Neel 
Published: February 2017

Abstract
This chapter examines the doctrine of sovereign immunity and the related ‘Sovereign Functions’ doctrine in India. It begins with an overview of the text of Article 300 of the Indian Constitution and proceeds with a brief survey of the case law on sovereign immunity that preceded the adoption of the Constitution. It then revisits some early attempts to revise the law on sovereign immunity in the post-Independence period, before discussing the judicial treatment of sovereign immunity and how the Indian Supreme Court has dealt with the constraints imposed by its own precedents, along with the Court’s difficulties in providing a coherent account of sovereign immunity. In particular, it considers the Supreme Court’s attempt to bypass the constraints that it had placed upon itself through the evolution of new doctrines in fundamental rights cases.
The Indian Constitution Seen from Outside
Authors: Tushnet Mark 
Published: February 2017

Abstract
This chapter considers some aspects of the Indian Constitution and its judicial interpretation, as seen from abroad. To this end, it discusses a number of topics that compare India’s constitutional experience with those of other countries, beginning with unconstitutional constitutional amendments and the ‘Basic Structure’ doctrine. It then explores public interest litigation, affirmative action and reservations, and finally the mechanisms by which judicial independence has been secured in India. It also comments on the contentious relationship between constitutional courts and political elites in other institutions. The chapter concludes by noting how constitutional developments, including the growth of constitutional doctrine, are intertwined with a nation’s overall political system, especially the party system in place.
Pulsing ULXs: tip of the iceberg?
Authors: King Andrew , Lasota Jean-Pierre , Kluźniak Włodek 
Published: February 2017

Abstract
We consider the three currently known pulsing ultraluminous X-ray sources (PULXs). We show that in one of them the observed spin-up rate requires super-Eddington accretion rates at the magnetospheric radius, even if magnetar-strength fields are assumed. In the two other systems, a normal-strength neutron star field implies super-Eddington accretion at the magnetosphere. Adopting super-Eddington mass transfer as the defining characteristic of ULX systems, we find the parameters required for self-consistent simultaneous fits of the luminosities and spin-up rates of the three pulsed systems. These imply near equality between their magnetospheric radii RM and the spherization radii Rsph where radiation pressure becomes important and drives mass-loss from the accretion disc. We interpret this near equality as a necessary condition for the systems to appear as pulsed, since if it is violated the pulse fraction is small. We show that as a consequence all PULXs must have spin-up rates $\dot{\nu }\gtrsim 10^{-10}\, {\rm s^{-2}}$, an order of magnitude higher than in any other pulsing neutron-star binaries. The fairly tight conditions required for ULXs to show pulsing support our earlier suggestion that many unpulsed ULX systems must actually contain neutron stars rather than black holes.
Ayub Khan Ommaya (1930-2008): Legacy and Contributions to Neurosurgery
Authors: Dossani Rimal Hanif , Kalakoti Piyush , Thakur Jai Deep , Nanda Anil 
Published: February 2017

Abstract
Ayub Khan Ommaya (1930-2008) was a pioneering neurosurgeon of Pakistani origin who is widely known for inventing the Ommaya reservoir, a ventricular catheter with a mushroom-shaped dome for administration of intraventricular therapies. As a Rhodes Scholar at Oxford, Ommaya developed an early interest in studying traumatic brain injury. Over the course of his career, Ommaya employed subhuman primate models to better understand mechanisms underlying human cerebral concussion. His work on traumatic brain injury led to the creation of the National Center for Injury Prevention and Control, a center for injury prevention research at the Center for Disease Control. This historical paper visits Ommaya's life story and recounts his key contributions to neurosurgery.
Lateral Orbitotomy Approach for Lesions Involving the Middle Fossa: A Retrospective Review of Thirteen Patients
Authors: Chabot Joseph D. , Gardner Paul A. , Stefko S. Tonya , Zwagerman Nathan T. , Fernandez- Miranda Juan Carlos 
Published: February 2017

Abstract

BACKGROUND: Classically used for treatment of orbital lesions, the lateral orbitotomy with cantholysis can be combined with a temporal craniectomy for lesions involving the middle cranial fossa.

OBJECTIVE: To present a single-center experience with the lateral orbitotomy approach for lesions involving the middle fossa.

METHODS: Twenty-five patients underwent lateral orbitotomies from April 2012 to July 2015. Excluding patients with solely intraorbital pathologies, 13 patients’ clinical and radiographic records were retrospectively reviewed.

RESULTS: Signs/symptoms in the 13 patients (ages 28-81) included proptosis (69%), decreased visual acuity (31%), diplopia (54%), and afferent pupillary defect (69%). Pathologies were meningioma (8), esthesioneuroblastoma, lymphoma, chordoma, Ewing's sarcoma, and squamous cell carcinoma. Surgical goals were maximal safe resection in 8 patients, palliative debulking in 3 patients, and cavernous sinus biopsy in 2 patients. In 8 patients for whom maximal resection was the goal, 2 had gross total resection, while 6 had near-total resection. All patients (3) for whom palliation was the goal had symptomatic improvement. Both cavernous sinus biopsies obtained diagnostic tissue without complications. All patients with proptosis (n = 9) and diplopia (n = 7), and 2 of 4 patients with decreased visual acuity had improvement in their symptoms. No patient reported worsening of their symptoms. Mean follow-up was 12 mo (2-30 mo). Complications included oculorrhea (1), pseudomeningocele (2), transient ptosis (2), and forehead numbness (1).

CONCLUSION: The lateral orbitotomy is a promising approach for carefully selected lesions with involvement of both the lateral orbit and middle cranial fossa. It provides minimally invasive access for biopsy, decompression, or resection.
Genetic Basis of Melanin Pigmentation in Butterfly Wings
Authors: Zhang Linlin , Martin Arnaud , Perry Michael W. , van der Burg Karin R.L. , Matsuoka Yuji , Monteiro Antónia , Reed Robert D. 
Published: February 2017

AbstractDespite the variety, prominence, and adaptive significance of butterfly wing patterns surprisingly little known about the genetic basis of wing color diversity. Even though there is intense interest in wing pattern evolution and development, the technical challenge of genetically manipulating butterflies has slowed efforts to functionally characterize color pattern development genes. To identify candidate wing pigmentation genes we used RNA-seq to characterize transcription across multiple stages of butterfly wing development, and between different color pattern elements, in the painted lady butterflyVanessa cardui. This allowed us to pinpoint genes specifically associated with red and black pigment patterns. To test the functions of a subset of genes associated with presumptive melanin pigmentation we used CRISPR/Cas9 genome editing in four different butterfly genera.pale,Ddc, andyellowknockouts displayed reduction of melanin pigmentation, consistent with previous findings in other insects. Interestingly, however,yellow-d,ebony, andblackknockouts revealed that these genes have localized effects on tuning the color of red, brown, and ochre pattern elements. These results point to previously undescribed mechanisms for modulating the color of specific wing pattern elements in butterflies, and provide an expanded portrait of the insect melanin pathway.
The Rosetta all-atom energy function for macromolecular modeling and design
Authors: Alford Rebecca F. , Leaver-Fay Andrew , Jeliazkov Jeliazko R. , O'Meara Matthew J. , DiMaio Frank P. , Park Hahnbeom , Shapovalov Maxim V. , Renfrew P. Douglas , Mulligan Vikram K. , Kappel Kalli , Labonte Jason W. , Pacella Michael S. , Bonneau Richard , Bradley Philip , Dunbrack Roland L. , Das Rhiju , Baker David , Kuhlman Brian , Kortemme Tanja , Gray Jeffrey J. 
Published: February 2017

AbstractOver the past decade, the Rosetta biomolecular modeling suite has informed diverse biological questions and engineering challenges ranging from interpretation of low-resolution structural data to design of nanomaterials, protein therapeutics, and vaccines. Central to Rosetta’s success is the energy function: amodel parameterized from small molecule and X-ray crystal structure data used to approximate the energy associated with each biomolecule conformation. This paper describes the mathematical models and physical concepts that underlie the latest Rosetta energy function,beta_nov15. Applying these concepts,we explain how to use Rosetta energies to identify and analyze the features of biomolecular models.Finally, we discuss the latest advances in the energy function that extend capabilities from soluble proteins to also include membrane proteins, peptides containing non-canonical amino acids, carbohydrates, nucleic acids, and other macromolecules.