bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historical factors shaped species diversity and composition of Salix in eastern Asia
Authors: Wang Qinggang , Su Xiangyan , Shrestha Nawal , Liu Yunpeng , Wang Siyang , Xu Xiaoting , Wang Zhiheng 
Published: February 2017

AbstractAmbient energy, niche conservatism, historical climate stability and habitat heterogeneity hypothesis have been proposed to explain the broad-scale species diversity patterns and species compositions, while their relative importance have been controversial. Here, we assessed the relative contributions of contemporary climate, historical climate changes and habitat heterogeneity in shaping Salix species diversity and species composition in whole eastern Asia as well as mountains and lowlands using linear regressions and distance-based redundancy analyses, respectively. Salix diversity was negatively related with mean annual temperature. Habitat heterogeneity was more important than contemporary climate in shaping Salix diversity patterns, and their relative contributions were different in mountains and lowlands. In contrast, the species composition was strongly influenced by contemporary climate and historical climate change than habitat heterogeneity, and their relative contributions were nearly the same both in mountains and lowlands. Our findings supported niche conservatism and habitat heterogeneity hypotheses, but did not support ambient energy and historical climate stability hypotheses. The diversity pattern and species composition of Salix could not be well-explained by any single hypothesis tested, suggesting that other factors such as disturbance history and diversification rate may be also important in shaping the diversity pattern and composition of Salix species.
Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids
Authors: Pan Yang , Yan Cheng , Hu Yu , Fan Yu , Pan Qing , Wan Quan , Torcivia-Rodriguez John , Mazumder Raja 
Published: February 2017

AbstractSingle nucleotide variations (SNVs) can result in loss or gain of protein functional sites. We analyzed the effects of SNVs on enzyme active sites, ligand binding sites, and various types of post translational modification (PTM) sites. We found that, for most types of protein functional sites, the SNV pattern differs between germline and somatic mutations as well as between synonymous and non-synonymous mutations. From a total of 51,138 protein functional site affecting SNVs (pfsSNVs), a pan-cancer analysis revealed 142 somatic pfsSNVs in five or more cancer types. By leveraging patient information for somatic pfsSNVs, we identified 17 loss of functional site SNVs and 60 gain of functional site SNVs which are significantly enriched in patients with specific cancer types. Of the key pfsSNVs identified in our analysis above, we highlight 132 key pfsSNVs within 17 genes that are found in well-established cancer associated gene lists. For illustrating how key pfsSNVs can be prioritized further, we provide a use case where we performed survival analysis showing that a loss of phosphorylation site pfsSNV at position 105 in MEF2A is significantly associated with decreased pancreatic cancer patient survival rate. These 132 pfsSNVs can be used in developing genetic testing pipelines.
Multistable states in a system of coupled phase oscillators with inertia
Authors: Yuan Di , Lin Fang , Wang Limei , Liu Danyang , Yang Junzhong , Xiao Yi 
Published: February 2017

AbstractWe investigate the generalized Kuramoto model of globally coupled oscillators with inertia, in which oscillators with positive coupling strength are conformists and oscillators with negative coupling strength are contrarians. We consider the correlation between the coupling strengths of oscillators and the distributions of natural frequencies. Two different types of correlations are studied. It is shown that the model supports multistable synchronized states such as different types of travelling wave states, π state and another type of nonstationary state: an oscillating π state. The phase distribution oscillates in a confined region and the phase difference between conformists and contrarians oscillates around π periodically in the oscillating π state. The different types of travelling wave state may be characterized by the speed of travelling wave and the effective frequencies of oscillators. Finally, the bifurcation diagrams of the model in the parameter space are presented.
Association between cytokine response, the LRINEC score and outcome in patients with necrotising soft tissue infection: a multicentre, prospective study
Authors: Hansen Marco Bo , Rasmussen Lars Simon , Svensson Mattias , Chakrakodi Bhavya , Bruun Trond , Madsen Martin Bruun , Perner Anders , Garred Peter , Hyldegaard Ole , Norrby-Teglund Anna ,   INFECT study group, Nekludov Michael , Arnell Per , Rosén Anders , Oscarsson Nicklas , Karlsson Ylva , Oppegaard Oddvar , Skrede Steinar , Itzek Andreas , Wahl Anna Mygind , Hedetoft Morten , Bærnthsen Nina Falcon , Müller Rasmus , Nedrebø Torbjørn 
Published: February 2017

AbstractEarly assessment of necrotising soft tissue infection (NSTI) is challenging. Analysis of inflammatory markers could provide important information about disease severity and guide decision making. For this purpose, we investigated the association between cytokine levels and the Laboratory Risk Indicator for Necrotising Fasciitis (LRINEC)-score, disease severity and mortality in NSTI patients. In 159 patients, plasma was analysed for IL-1β, IL-6, IL-10 and TNF-α upon admission. The severity of NSTI was assessed by SAPS, SOFA score, septic shock, microbial aetiology, renal replacement therapy and amputation. We found no significant difference in cytokine levels according to a LRINEC- score above or below 6 (IL-1β: 3.0 vs. 1.3; IL-6: 607 vs. 289; IL-10: 38.4 vs. 38.8; TNF-α: 15.1 vs. 7.8 pg/mL, P > 0.05). Patients with β-haemolytic streptococcal infection had higher level of particularly IL-6. There was no difference in mortality between patients with a LRINEC-score above or below 6. In the adjusted analysis assessing 30-day mortality, the association was strongest for IL-1β (OR 3.86 [95% CI, 1.43-10.40], P = 0.008) and IL-10 (4.80 [1.67-13.78], P = 0.004). In conclusion, we found no significant association between the LRINEC-score and cytokine levels on admission. IL-6 was consistently associated with disease severity, whereas IL-1β had the strongest association with 30-day mortality.
Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development
Authors: Gui Heng , Hyde Kevin , Xu Jianchu , Mortimer Peter 
Published: February 2017

AbstractAlthough there is a growing amount of evidence that arbuscular mycorrhizal fungi (AMF) influence the decomposition process, the extent of their involvement remains unclear. Therefore, given this knowledge gap, our aim was to test how AMF influence the soil decomposer communities. Dual compartment microcosms, where AMF (Glomus mosseae) were either allowed access (AM+) to or excluded (AM−) from forest soil compartments containing litterbags (leaf litter from Calophyllum polyanthum) were used. The experiment ran for six months, with destructive harvests at 0, 90, 120, 150, and 180 days. For each harvest we measured AMF colonization, soil nutrients, litter mass loss, and microbial biomass (using phospholipid fatty acid analysis (PLFA)). AMF significantly enhanced litter decomposition in the first 5 months, whilst delaying the development of total microbial biomass (represented by total PLFA) from T150 to T180. A significant decline in soil available N was observed through the course of the experiment for both treatments. This study shows that AMF have the capacity to interact with soil microbial communities and inhibit the development of fungal and bacterial groups in the soil at the later stage of the litter decomposition (180 days), whilst enhancing the rates of decomposition.
Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets
Authors: Ray Rajyavardhan , Kumar Sanjeev 
Published: February 2017

AbstractWe show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications.
How I Do It: The Role of Flexible Hand-held 2μ-Thulium Laser Fiber in Microsurgical Removal of Acoustic Neuromas
Authors: Cacciotti Guglielmo , Roperto Raffaele , Tonelli Maria , Carpineta Ettore , Mastronardi Luciano 
Published: February 2017

Aims We performed a retrospective nonrandomized study to analyze the results of microsurgery of acoustic neuromas (AN) using 2μ-thulium flexible hand-held laser fiber (Revolix jr).
Methods From September 2010 to September 2015, 89 patients suffering from AN have been operated on with microsurgical technique via retrosigmoid approach. In 37 cases, tumor resection was performed with the assistance of 2μ-thulium flexible hand-held laser fiber (L-group). Eight cases operated on with the assistance of CO2 hand-held flexible laser fiber were excluded from this study. A total of 44 patients, operated on without laser assistance during the same period, were used as comparison group (C-group) (matched pair technique). Facial nerve function was assessed with the House–Brackmann (HB) scale preoperatively, and 1 week and 6 months postoperatively.
Results Overall time from incision to skin suture changed in relation to size of tumor (165–575 minutes) and was not affected by the use of laser. In 7 out of 81 cases, a preoperative facial nerve palsy HB2 and in 1 case, HB4 (permanent) were observed. In the remaining 80 cases, at 6-month follow-up, facial nerve preservation rate (HB1) was 92.5%. Hearing preservation rate (AAO-HNS A/B classes) was 68.2% (26 out of 36). Adopting a 0 to 3 scale, the mean surgeon satisfaction rate of usefulness of laser fiber was 2.7.
Conclusion The use of 2μ-thulium hand-held flexible laser fiber in AN microsurgery seems to be safe and subjectively facilitates tumor resection especially in “difficult” conditions (e.g., highly vascularized and hard tumors). In this limited retrospective trial, the good functional outcome following conventional microsurgery had not further improved, nor the surgical time reduced by laser. Focusing its use on “difficult” (large and vascularized) cases may lead to different results in future.
Low escape-rate genome safeguards with minimal molecular perturbation ofSaccharomyces cerevisiae
Authors: Agmon Neta , Tang Zuojian , Yang Kun , Sutter Ben , Ikushima Shigehito , Cai Yizhi , Caravelli Katrina , Martin James A. , Sun Xiaoji , Choi Woo Jin , Zhang Allen , Stracquadanio Giovanni , Hao Haiping , Tu Benjamin P. , Fenyo David , Bader Joel S. , Boeke Jef D. 
Published: February 2017

SignificanceAs the use of synthetic biology grows, there is an increasing need to ensure biocontainment both to protect engineered proprietary strains and to mitigate potential inadvertent or advertent release to the environment. Here, we screen for the best-performing construct for essential gene-dependent transcriptional safeguards (SGs) in yeast. We have engineered strains that have near-WT fitness and a low escape rate, and grow in the presence of a nanomolar concentration of essential supplement. We also improved our “safeguard” construct by promoter engineering, as well as by analyzing a series of potential “decoy molecules” that could be used to mask the existence of critical chemical ligands required to grow the SG strain.
State of the Scholarship in Classics on Ancient Roman Rhetoric
Authors: Kennerly Michele , Lamp Kathleen S. 
Published: February 2017

ABSTRACTLimiting ourselves to scholarly books published in English from 2009–2016, we survey classics scholarship about rhetoric in ancient Rome from the late republic through the early empire. We seek traditional threads and growing trends across those works that advance our understanding of rhetoric’s practical, theoretical, and material manifestations during that time of tumult and transition. We begin broadly, using companion books to delineate three structural pillars in the scholarship: rhetoric as a formal cultural system, the republic as subject to ruptures and reinventions, and Cicero as a foremost statesman of the late republic. Then we move into scholarship that draws upon nontraditional rhetorical objects, such as art, and that moves into increasingly vibrant areas of interest in rhetoric, such as the senses. Overall, we find that classicists writing about ancient Roman rhetorical culture share with their counterparts in rhetoric an urge to test old verities and to add historical depth to larger scholarly turns within the humanities.
Phyx: phylogenetic tools for unix
Authors: Brown Joseph W , Walker Joseph F , Smith Stephen A 
Published: February 2017

Abstract

Summary
The ease with which phylogenomic data can be generated has drastically escalated the computational burden for even routine phylogenetic investigations. To address this, we present phyx: a collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects (alignments, trees and MCMC logs). Modelled after Unix/GNU/Linux command line tools, individual programs perform a single task and operate on standard I/O streams that can be piped to quickly and easily form complex analytical pipelines. Because of the stream-centric paradigm, memory requirements are minimized (often only a single tree or sequence in memory at any instance), and hence phyx is capable of efficiently processing very large datasets.

Availability and Implementation
phyx runs on POSIX-compliant operating systems. Source code, installation instructions, documentation and example files are freely available under the GNU General Public License at https://github.com/FePhyFoFum/phyx

Supplementary information
Supplementary data are available at Bioinformatics online.
Morphometric analysis of Passiflora leaves: the relationship between landmarks of the vasculature and elliptical Fourier descriptors of the blade
Authors: Chitwood Daniel H. , Otoni Wagner C. 
Published: February 2017

Abstract
Background: Leaf shape among Passiflora species is spectacularly diverse. Underlying this diversity in leaf shape are profound changes in the patterning of the primary vasculature and laminar outgrowth. Each of these aspects of leaf morphology—vasculature and blade—provides different insights into leaf patterning.
Results: Here, we morphometrically analyze &gt;3300 leaves from 40 different Passiflora species collected sequentially across the vine. Each leaf is measured in two different ways: using 1) 15 homologous Procrustes-adjusted landmarks of the vasculature, sinuses, and lobes; and 2) Elliptical Fourier Descriptors (EFDs), which quantify the outline of the leaf. The ability of landmarks, EFDs, and both datasets together are compared to determine their relative ability to predict species and node position within the vine. Pairwise correlation of x and y landmark coordinates and EFD harmonic coefficients reveals close associations between traits and insights into the relationship between vasculature and blade patterning.
Conclusions: Landmarks, more reflective of the vasculature, and EFDs, more reflective of the blade contour, describe both similar and distinct features of leaf morphology. Landmarks and EFDs vary in ability to predict species identity and node position in the vine and exhibit a correlational structure (both within landmark or EFD traits and between the two data types) revealing constraints between vascular and blade patterning underlying natural variation in leaf morphology among Passiflora species.
Locating Indian Constitutionalism
Authors: Choudhry Sujit , Khosla Madhav , Bhanu Mehta Pratap 
Published: February 2017

Abstract
This chapter explores the historical commitment to the idea of constitutionalism and how the framers understood India’s constitutional project. It begins with an overview of the concept of ‘constitutional morality’ as it relates to the Indian Constitution, along with the cosmopolitan character of Indian constitutionalism. It then considers some of the tensions that have characterised constitutional law in India, with particular emphasis on some of the sources of these tensions, for instance the debate between centralisation and decentralisation. It also discusses the major axes around which the normative and institutional imagination of the Indian Constitution is articulated and concludes by analysing the character of constitutional development in India and paying attention to the forces that have shaped its evolution.
The Indian Founding
Authors: Lerner Hanna 
Published: February 2017

Abstract
This chapter examines the making of the Indian Constitution from a comparative perspective, with particular emphasis on some of the significant and innovative aspects of the drafting process. After discussing constitution drafting in the post-colonial/post-World War II period, it considers the debate in the Indian Constituent Assembly over what it means to be an Indian and how the Constitution should facilitate political unity in the face of immense cultural, religious, and national diversity. It then explores some of the innovative constitutional strategies developed by the Indian framers to reconcile the deep disagreements among the Indian public regarding the religious, national, and linguistic identity of the State with the principles of democracy. These strategies include constitutional incrementalism, the deferral of controversial decisions, ambiguity, and non-justiciability.
Constitutional Identity
Authors: Jacobsohn Gary Jeffrey 
Published: February 2017

Abstract
This chapter examines the concept of constitutional identity as it applies to the Indian Constitution. It first considers the problem of constitutional identity, with particular emphasis on the preservative function of the constitution. It then explains how the constitution acquires an identity that emerges dialogically and represents a combination of political aspirations and commitments reflective of a nation’s past. It also explores the static and dynamic perspectives on identity with regard to the transformational agenda of Indian constitutionalism, along with the underlying politics of constitutional identity and the judiciary’s articulation of the meaning of constitutional identity. The chapter concludes by reviewing two highly controversial cases that have important implications for India’s constitutional identity.
Elections
Authors: Sondhi Aditya 
Published: February 2017

Abstract
This chapter examines India’s constitutional framework and its mechanisms that govern and control the electoral process, especially those that go beyond the domain of election law and raise a host of constitutional issues. Before discussing these mechanisms, their operation, and the extent to which they are justifiable, the chapter provides an overview of the right to vote and how it is treated in the Indian Constitution as a fundamental right. It then considers the Election Commission and its duties and functions, and proceeds by outlining the three levels by which elections are regulated in India: the first relates to the preparation of the electoral roll; the second stage to the electoral process; and the third to the outcome and verdict. Finally, it looks at potential challenges to free and fair elections, such as those posed by the problem of campaign finance.
Legislature
Authors: Madhavan M. R. 
Published: February 2017

Abstract
This chapter discusses the composition of Parliament and the State legislatures in India. It examines the qualifications and disqualifications applicable for membership to the legislative branch of government. India is a federal state, with a parliamentary form of government comprised of legislatures at the Union and State levels. The Indian Parliament consists of two Houses: the Rajya Sabha (the Council of States) and the Lok Sabha (the House of the People). The Rajya Sabha is an indirectly elected House whose members represent various States and Union Territories, whereas members of the Lok Sabha are directly elected from territorial constituencies. This chapter first considers some of the issues relating to the composition of the Rajya Sabha and Lok Sabha before explaining the qualifications and disqualifications of members of both Houses. In doing so, it provides an account of Articles 79 to 104 (Parliament) and Articles 168 to 193 (State legislatures) of the Indian Constitution.
Tribunals
Authors: Thiruvengadam Arun 
Published: February 2017

Abstract
This chapter examines the constitutional status of tribunals in India and how the law and policy on tribunals have evolved since 1950. It presents a brief historical background on the evolution of tribunals in India, starting from the origin of tribunals and debates among law reform bodies from 1950 to 1975 to the Swaran Singh Committee report recommending the creation of tribunals to combat delays in the Indian legal system. It then reviews constitutional litigation over tribunals during the period 1985–2014, focusing on the Sampath Kumar and other cases after it, along with the National Company Law Tribunals. It also considers the debate over the ‘tribunalisation’ of the Indian legal system and the constitutional arguments that have been raised to challenge the validity of particular tribunals. Finally, it looks at recent criticism of the growth of tribunals by practicing lawyers and argues that calls for their abolition are impractical.
Review of Administrative Action
Authors: Jalan Prateek , Rai Ritin 
Published: February 2017

Abstract
This chapter examines the concept of administrative review in the context of the Indian Constitution, with particular emphasis on how administrative actions are reviewed under Article 14. It first considers whether administrative review is different from legislative review, and especially whether the grounds of judicial review under Article 14 apply to the same extent when it comes to the validity of legislation compared with administrative action. It then discusses the scope of the power of administrative review under the concept of ‘reasonableness’ and whether this concept has been applied on a consistent basis. It also comments on the inherently abstract and imprecise nature of the concept of ‘reasonableness’ and how this has contributed to the lack of a judicially manageable test or standard for analysing the various cases adjudicated by the Indian Supreme Court. Finally, the chapter discusses the nature of executive power and how it may influence an adjudication of reasonableness.