bluuebunny/crossref_metadata_2025 huggingface dataset:
Public Interest Litigation
Authors: Divan Shyam
Published: February 2017

This chapter examines public interest litigation (PIL) and its place in Indian constitutional law. The chapter begins with an overview of PIL as an instrument for dealing with public grievances such as flagrant human rights violations by the State, or for vindicating the public policies embodied in statutes or constitutional provisions. It then discusses the evolution of PIL in India and four distinct factors that contributed to its growth. It also explores how courts efficiently deploy judicial resources and decide genuine disputes of a legal character by recognising only those persons with locus standi, or legal standing. Finally, it describes a range of procedural innovations that distinguish PIL from conventional litigation and explains how the growth of PIL affected traditional notions of justiciability. It shows how the phenomenon of PIL has shaped both the nature of rights-based claims within Indian constitutional law as well as the role of the Supreme Court within Indian democracy.
The Constitutionalisation of Indian Private Law
Authors: Balganesh Shyamkrishna
Published: February 2017

This chapter examines the relationship between private law and constitutional law in India, with particular emphasis on tort law. It considers the Indian Supreme Court’s expansion of its fundamental rights jurisprudence over the past thirty years, as well as its effort to transcend the public law/private law divide. It also explains how the Court’s fusion of constitutional law and tort law has affected the independent efficacy, normativity, and analytical basis of equivalent private law claims in India. It argues that the Court’s efforts have only undermined the overall legitimacy of private law mechanisms in the country, and that this phenomenon is evident not only with respect to tort law, but also to a lesser degree in other areas of private law, such as contract law and property law.
Assembly and Association
Authors: Guruswamy Menaka
Published: February 2017

This chapter examines the relevant provisions of the Indian Constitution with respect to freedom of assembly and freedom of association. It begins with a historical background on the restrictions to the freedom to assemble peaceably in colonial India, as well as restrictions under the Criminal Procedure Code covering public meetings and the right of government employees to participate in demonstrations. It then considers the power of the State to curtail the freedom to assemble, the constitutionality of Section 144 of the Criminal Procedure Code, the right to strike, and what constitutes unlawful association. It also discusses the jurisprudence of the Indian Supreme Court with regard to the freedom of association.
Too small to succeed: the difficulty of sustaining star formation in low-mass haloes
Authors: Cashmore Claire R. , Wilkinson Mark I. , Power Chris , Bourne Martin
Published: February 2017

We present high-resolution simulations of an isolated dwarf spheroidal (dSph) galaxy between redshifts z ∼ 10 and z ∼ 4, the epoch when several Milky Way dSph satellites experienced extended star formation, in order to understand in detail the physical processes which affect a low-mass halo's ability to retain gas. It is well established that supernova feedback is very effective at expelling gas from a 3 × 107 M⊙ halo, the mass of a typical redshift 10 progenitor of a redshift 0 halo with mass ∼109 M⊙. We investigate the conditions under which such a halo is able to retain sufficient high-density gas to support extended star formation. In particular, we explore the effects of: an increased relative concentration of the gas compared to the dark matter; a higher concentration dark matter halo; significantly lower supernova rates; enhanced metal cooling due to enrichment from earlier supernovae. We show that disc-like gas distributions retain more gas than spherical ones, primarily due to the shorter gas cooling times in the disc. However, a significant reduction in the number of supernovae compared to that expected for a standard initial mass function is still needed to allow the retention of high-density gas. We conclude that the progenitors of the observed dSphs would only have retained the gas required to sustain star formation if their mass, concentration and gas morphology were already unusual for those of a dSph-mass halo progenitor by a redshift of 10.
Early science with the Large Millimeter Telescope: molecules in the extreme outflow of a protoplanetary nebula
Authors: Gómez-Ruiz A. I. , Guzman-Ramirez L. , Serrano E. O. , Sánchez-Argüelles D. , Luna A. , Schloerb F. P. , Narayanan G. , Yun M. S. , Sahai R. , Zijlstra A. A. , Chavez-Dagostino M. , Montaña A. , Hughes D. H. , Rodríguez M.
Published: February 2017

Extremely high velocity emission, likely related to jets, is known to occur in some protoplanetary nebulae. However, the molecular complexity of this kinematic component is largely unknown. We observed the known extreme outflow from the protoplanetary nebula IRAS 16342−3814, a prototype water fountain, over the full frequency range from 73–111 GHz with the Redshift Search Receiver (RSR) on the Large Millimetre Telescope. We detected the molecules SiO, HCN, SO and 13CO. All molecular transitions, with the exception of the latter, are detected for the first time in this source and all present emission with velocities up to a few hundred km s−1. IRAS 16342−3814 is therefore the only source of this kind presenting extreme outflow activity in all these molecules simultaneously, with SO and SiO emission showing the highest velocities found for these species in protoplanetary nebulae. A tentative weak SO component with a full width at half-maximum of ∼700 km s−1 remains to be confirmed. The extreme outflow gas consists of dense gas ($n_{\rm H_2} > 10^{4.8}$–105.7 cm−3) with a mass larger than ∼ 0.02–0.15 M⊙. The relatively high abundances of SiO and SO may be an indication of oxygen-rich extremely high velocity gas.
Revealing strong bias in common measures of galaxy properties using new inclination-independent structures
Authors: Devour Brian M. , Bell Eric F.
Published: February 2017

Accurate measurement of galaxy structures is a prerequisite for quantitative investigation of galaxy properties or evolution. Yet, the impact of galaxy inclination and dust on commonly used metrics of galaxy structure is poorly quantified. We use infrared data sets to select inclination-independent samples of disc and flattened elliptical galaxies. These samples show strong variation in Sérsic index, concentration and half-light radii with inclination. We develop novel inclination-independent galaxy structures by collapsing the light distribution in the near-infrared on to the major axis, yielding inclination-independent ‘linear’ measures of size and concentration. With these new metrics we select a sample of Milky Way analogue galaxies with similar stellar masses, star formation rates, sizes and concentrations. Optical luminosities, light distributions and spectral properties are all found to vary strongly with inclination: When inclining to edge-on, r-band luminosities dim by >1 magnitude, sizes decrease by a factor of 2, ‘dust-corrected’ estimates of star formation rate drop threefold, metallicities decrease by 0.1 dex and edge-on galaxies are half as likely to be classified as star forming. These systematic effects should be accounted for in analyses of galaxy properties.
Can Intraneural Perineuriomas Occur Intradurally? An Anatomic Perspective
Authors: Prasad Nikhil K. , Tubbs R. Shane , Amrami Kimberly K. , Dyck P. James B. , Mauermann Michelle L. , Giannini Caterina , de Divitiis Oreste , Spinner Robert J.
Published: February 2017

BACKGROUND: Intraneural perineuriomas are rare, benign lesions produced by the neoplastic proliferation of perineurial cells. They typically present in adolescents and affect nerves of the limbs. In our experience, we have not encountered a single case of classic intraneural perineurioma at an intradural location.

OBJECTIVE: To determine whether intraneural perineuriomas could occur intradurally, given the prevalence of intradural nerve sheath tumors, and explain our findings with an anatomic perspective.

METHODS: We retrospectively reviewed the high-resolution magnetic resonance images of 56 patients from an institutional registry of patients with intraneural perineurioma. All cases were analyzed for signs of proximal extension toward spinal nerves, roots, and spinal cord. A literature review was performed. The clinical, radiological, and histopathological features of potential intradural lesions were critically appraised against strict criteria for a diagnosis of classic intraneural perineurioma.

RESULTS: Fifteen of 56 (27%) patients with intraneural perineurioma had a proximal localization in the lumbosacral or brachial plexus. Not a single case occurred proximal to the dorsal root ganglia (DRG). One case of trigeminal intraneural perineurioma occurred distal to the gasserian ganglion. A literature review did not reveal any convincing cases of classic intraneural perineuriomas occurring in an intraspinal intradural location and revealed only 1 possible case in an intracranial intradural location.

CONCLUSION: Based on our study, the occurrence of classic intraneural perineuriomas intradurally is exceedingly rare, if at all present. This may be related to the paucity of perineurial cells at the nerve root level and reciprocal interactions between neuroglial cells at the central-to-peripheral transition zones.
Multifocal Intradural Extramedullary Pilocytic Astrocytomas of the Spinal Cord: A Case Report and Review of the Literature
Authors: Basheer Azam , Rammo Richard , Kalkanis Steven , Felicella Michelle M. , Chedid Mokbel
Published: February 2017

BACKGROUND AND IMPORTANCE: Pilocytic astrocytoma (PA) is among the most common of the central nervous system gliomas in the pediatric population; however, it is uncommon in adults. PAs of the spinal cord in adults are even rarer, with only a few cases found in the literature. We report here the first case in the literature of multifocal intradural extramedullary spinal cord PAs in an adult.

CLINICAL PRESENTATION: Our patient is a 56-yr-old female who presented with loss of balance and an ataxic gait. Multiple extramedullary spinal cord tumors were identified intraoperatively, the lesions completely resected, and all diagnosed as PAs.

CONCLUSION: This case illustrates a unique instance of multifocal intradural extramedullary spinal cord PAs in an adult with no previous history of PA during childhood, no known familial syndromes, and no brain involvement.
Hepatitis A Cases Among Food Handlers: A Local Health Department Response—New York City, 2013
Authors: Ridpath Alison , Reddy Vasudha , Layton Marcelle , Misener Mark , Scaccia Allison , Starr David , Stavinsky Faina , Varma Jay K. , Waechter HaeNa , Zucker Jane R. , Balter Sharon
Published: February 2017

During 2013, the New York City Department of Health and Mental Hygiene (DOHMH) received reports of 6 hepatitis A cases among food handlers. We describe our decision-making process for public notification, type of postexposure prophylaxis (PEP) offered, and lessons learned. For 3 cases, public notification was issued and DOHMH offered only hepatitis A vaccine as PEP. Subsequent outbreaks resulted from 1 case for which no public notification was issued or PEP offered, and 1 for which public notification was issued and PEP was offered too late. DOHMH continues to use environmental assessments to guide public notification decisions and offer only hepatitis A vaccine as PEP after public notification but recognizes the need to evaluate each situation individually. The PEP strategy employed by DOHMH should be considered because hepatitis A vaccine is immunogenic in all age groups, can be obtained by local jurisdictions more quickly, and is logistically easier to administer in mass clinics than immunoglobulin.
Community Health Workers: Addressing Client Objectives Among Frequent Emergency Department Users
Authors: Kwan Bethany M. , Rockwood Amy , Bandle Brian , Fernald Douglas , Hamer Mika K. , Capp Roberta
Published: February 2017

Objectives:

To evaluate effectiveness of a community health worker (CHW) program designed to address client objectives among frequent emergency department (ED) users.

Design:

Program evaluation using secondary analysis of client objectives from program records. Client objectives were characterized according to the World Health Organization's social determinants of health framework. Hierarchical generalized linear modeling was used to assess factors associated with objective achievement.

Setting:

An ED and the surrounding community in an economically disadvantaged area of Buffalo, New York.

Participants:

A total of 1600 adults over age 18 eligible for Medicaid and/or Medicare and who had at least 2 ED visits in the prior year.

Intervention:

Clients worked with CHWs in the community to identify diverse needs and objectives. Community health workers provided individualized services to help achieve objectives.

Main Outcome Measure:

Achievement of client-focused objectives.

Results:

Most objectives pertained to linkage to community resources and health care navigation, emphasizing chronic medical conditions and connection to primary care. Clients and CHWs together achieved 43% of total objectives. Objective achievement was positively associated with greater client engagement in CHW services.

Conclusions:

Low objective achievement may stem from system- and policy-level barriers, such as lack of affordable housing and access to primary care. Strategies for improving client engagement in CHW services are needed. Community health workers and their clients were most successful in areas in which public health policies and systems made resources easy to access or where the program had formalized relationships with resources, such as primary care.
Multi-step excitation energy transfer engineered in genetic fusions of natural and synthetic light-harvesting proteins
Authors: Mancini Joshua A. , Kodali Goutham , Jiang Jianbing , Reddy Kanumuri Ramesh , Lindsey Jonathan S. , Bryant Donald A. , Dutton P. Leslie , Moser Christopher C.
Published: February 2017

Synthetic proteins designed and constructed from first principles with minimal reference to the sequence of any natural protein have proven robust and extraordinarily adaptable for engineering a range of functions. Here for the first time we describe the expression and genetic fusion of a natural photosynthetic light-harvesting subunit with a synthetic protein designed for light energy capture and multi-step transfer. We demonstrate excitation energy transfer from the bilin of the CpcA subunit (phycocyanin α subunit) of the cyanobacterial photosynthetic light-harvesting phycobilisome to synthetic four-helix-bundle proteins accommodating sites that specifically bind a variety of selected photoactive tetrapyrroles positioned to enhance energy transfer by relay. The examination of combinations of different bilin, chlorin and bacteriochlorin cofactors has led to identification of the preconditions for directing energy from the bilin light-harvesting antenna into synthetic protein–cofactor constructs that can be customized for light-activated chemistry in the cell.
Ninein is essential for apico-basal microtubule formation and CLIP-170 facilitates its redeployment to non-centrosomal microtubule organizing centres
Authors: Goldspink Deborah A. , Rookyard Chris , Tyrrell Benjamin J. , Gadsby Jonathan , Perkins James , Lund Elizabeth K. , Galjart Niels , Thomas Paul , Wileman Tom , Mogensen Mette M.
Published: February 2017

Differentiation of columnar epithelial cells involves a dramatic reorganization of the microtubules (MTs) and centrosomal components into an apico-basal array no longer anchored at the centrosome. Instead, the minus-ends of the MTs become anchored at apical non-centrosomal microtubule organizing centres (n-MTOCs). Formation of n-MTOCs is critical as they determine the spatial organization of MTs, which in turn influences cell shape and function. However, how they are formed is poorly understood. We have previously shown that the centrosomal anchoring protein ninein is released from the centrosome, moves in a microtubule-dependent manner and accumulates at n-MTOCs during epithelial differentiation. Here, we report using depletion and knockout (KO) approaches that ninein expression is essential for apico-basal array formation and epithelial elongation and that CLIP-170 is required for its redeployment to n-MTOCs. Functional inhibition also revealed that IQGAP1 and active Rac1 coordinate with CLIP-170 to facilitate microtubule plus-end cortical targeting and ninein redeployment. Intestinal tissue andin vitroorganoids from theClip1/Clip2double KO mouse with deletions in the genes encoding CLIP-170 and CLIP-115, respectively, confirmed requirement of CLIP-170 for ninein recruitment to n-MTOCs, with possible compensation by other anchoring factors such as p150Gluedand CAMSAP2 ensuring apico-basal microtubule formation despite loss of ninein at n-MTOCs.
A non-conventional discontinuous Lagrangian for viscous flow
Authors: Scholle M. , Marner F.
Published: February 2017

Drawing an analogy with quantum mechanics, a new Lagrangian is proposed for a variational formulation of the Navier–Stokes equations which to-date has remained elusive. A key feature is that the resulting Lagrangian is discontinuous in nature, posing additional challenges apropos the mathematical treatment of the related variational problem, all of which are resolvable. In addition to extending Lagrange's formalism to problems involving discontinuous behaviour, it is demonstrated that the associated equations of motion can self-consistently be interpreted within the framework of thermodynamics beyond local equilibrium, with the limiting case recovering the classical Navier–Stokes equations. Perspectives for applying the new formalism to discontinuous physical phenomena such as phase and grain boundaries, shock waves and flame fronts are provided.
The positive side of a negative reference: the delay between linguistic processing and common ground
Authors: Kronmüller Edmundo , Noveck Ira , Rivera Natalia , Jaume-Guazzini Francisco , Barr Dale
Published: February 2017

Interlocutors converge on names to refer to entities. For example, a speaker might refer to a novel looking object as
the jellyfish
and, once identified, the listener will too. The hypothesized mechanism behind such
referential precedents
is a subject of debate. The common ground view claims that listeners register the object as well as the identity of the speaker who coined the label. The linguistic view claims that, once established, precedents are treated by listeners like any other linguistic unit, i.e. without needing to keep track of the speaker. To test predictions from each account, we used visual-world eyetracking, which allows observations in real time, during a standard referential communication task. Participants had to select objects based on instructions from two speakers. In the critical condition, listeners sought an object with a negative reference such as
not the jellyfish
. We aimed to determine the extent to which listeners rely on the linguistic input, common ground or both. We found that initial interpretations were based on linguistic processing only and that common ground considerations do emerge but only after 1000 ms. Our findings support the idea that—at least temporally—linguistic processing can be isolated from common ground.
Nonlinear information fusion algorithms for data-efficient multi-fidelity modelling
Authors: Perdikaris P. , Raissi M. , Damianou A. , Lawrence N. D. , Karniadakis G. E.
Published: February 2017

Multi-fidelity modelling enables accurate inference of quantities of interest by synergistically combining realizations of low-cost/low-fidelity models with a small set of high-fidelity observations. This is particularly effective when the low- and high-fidelity models exhibit strong correlations, and can lead to significant computational gains over approaches that solely rely on high-fidelity models. However, in many cases of practical interest, low-fidelity models can only be well correlated to their high-fidelity counterparts for a specific range of input parameters, and potentially return wrong trends and erroneous predictions if probed outside of their validity regime. Here we put forth a probabilistic framework based on Gaussian process regression and nonlinear autoregressive schemes that is capable of learning complex nonlinear and space-dependent cross-correlations between models of variable fidelity, and can effectively safeguard against low-fidelity models that provide wrong trends. This introduces a new class of multi-fidelity information fusion algorithms that provide a fundamental extension to the existing linear autoregressive methodologies, while still maintaining the same algorithmic complexity and overall computational cost. The performance of the proposed methods is tested in several benchmark problems involving both synthetic and real multi-fidelity datasets from computational fluid dynamics simulations.
When COI barcodes deceive: complete genomes reveal introgression in hairstreaks
Authors: Cong Qian , Shen Jinhui , Borek Dominika , Robbins Robert K. , Opler Paul A. , Otwinowski Zbyszek , Grishin Nick V.
Published: February 2017

Two species of hairstreak butterflies from the genusCalycopisare known in the United States:C. cecropsandC. isobeon. Analysis of mitochondrial COI barcodes ofCalycopisrevealedcecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central AmericanCalycopisspecies. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27Calycopisspecimens of four species:C. cecrops,C. isobeon,C. quintanaandC. bactra. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USACalycopiswith atypical barcodes grouped with Central American speciesC. quintanaby mitochondria, nuclear genome trees placed them within typical USAC. cecropsin agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially betweenC. cecropsandC. isobeon. About 2.3% of eachC. cecropsgenome has probably (p-value < 0.01, FDR < 0.1) introgressed fromC. isobeonand about 3.4% of eachC. isobeongenome may have come fromC. cecrops.The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.
Spatio-temporal interactions facilitate large carnivore sympatry across a resource gradient
Authors: Karanth K. Ullas , Srivathsa Arjun , Vasudev Divya , Puri Mahi , Parameshwaran Ravishankar , Kumar N. Samba
Published: February 2017

Species within a guild vary their use of time, space and resources, thereby enabling sympatry. As intra-guild competition intensifies, such behavioural adaptations may become prominent. We assessed mechanisms of facilitating sympatry among dhole (
Cuon alpinus
), leopard (
Panthera pardus
) and tiger (
Panthera tigris
) in tropical forests of India using camera-trap surveys. We examined population-level temporal, spatial and spatio-temporal segregation among them across four reserves representing a gradient of carnivore and prey densities. Temporal and spatial overlaps were higher at lower prey densities. Combined spatio-temporal overlap was minimal, possibly due to chance. We found fine-scale avoidance behaviours at one high-density reserve. Our results suggest that: (i) patterns of spatial, temporal and spatio-temporal segregation in sympatric carnivores do not necessarily mirror each other; (ii) carnivores are likely to adopt temporal, spatial, and spatio-temporal segregation as alternative mechanisms to facilitate sympatry; and (iii) carnivores show adaptability across a gradient of resource availability, a driver of inter-species competition. We discuss behavioural mechanisms that permit carnivores to co-occupy rather than dominate functional niches, and adaptations to varying intensities of competition that are likely to shape structure and dynamics of carnivore guilds.
Historical amphibian declines and extinctions in Brazil linked to chytridiomycosis
Authors: Carvalho Tamilie , Becker C. Guilherme , Toledo Luís Felipe
Published: February 2017

The recent increase in emerging fungal diseases is causing unprecedented threats to biodiversity. The origin of spread of the frog-killing fungus
Batrachochytrium dendrobatidis
(
Bd
) is a matter of continued debate. To date, the historical amphibian declines in Brazil could not be attributed to chytridiomycosis; the high diversity of hosts coupled with the presence of several
Bd
lineages predating the reported declines raised the hypothesis that a hypervirulent
Bd
genotype spread from Brazil to other continents causing the recent global amphibian crisis. We tested for a spatio-temporal overlap between
Bd
and areas of historical amphibian population declines and extinctions in Brazil. A spatio-temporal convergence between
Bd
and declines would support the hypothesis that Brazilian amphibians were not adapted to
Bd
prior to the reported declines, thus weakening the hypothesis that Brazil was the global origin of
Bd
emergence. Alternatively, a lack of spatio-temporal association between
Bd
and frog declines would indicate an evolution of host resistance in Brazilian frogs predating
Bd
's global emergence
,
further supporting Brazil as the potential origin of the
Bd
panzootic. Here, we
Bd
-screened over 30 000 museum-preserved tadpoles collected in Brazil between 1930 and 2015 and overlaid spatio-temporal
Bd
data with areas of historical amphibian declines. We detected an increase in the proportion of
Bd
-infected tadpoles during the peak of amphibian declines (1979–1987). We also found that clusters of
Bd
-positive samples spatio-temporally overlapped with most records of amphibian declines in Brazil's Atlantic Forest. Our findings indicate that Brazil is post epizootic for chytridiomycosis and provide another piece to the puzzle to explain the origin of
Bd
globally.
Computational biomechanics changes our view on insect head evolution
Authors: Blanke Alexander , Watson Peter J. , Holbrey Richard , Fagan Michael J.
Published: February 2017

Despite large-scale molecular attempts, the relationships of the basal winged insect lineages dragonflies, mayflies and neopterans, are still unresolved. Other data sources, such as morphology, suffer from unclear functional dependencies of the structures considered, which might mislead phylogenetic inference. Here, we assess this problem by combining for the first time biomechanics with phylogenetics using two advanced engineering techniques, multibody dynamics analysis and finite-element analysis, toobjectivelyidentify functional linkages in insect head structures which have been used traditionally to argue basal winged insect relationships. With a biomechanical model of unprecedented detail, we are able to investigate the mechanics of morphological characters under biologically realistic load, i.e. biting. We show that a range of head characters, mainly ridges, endoskeletal elements and joints, are indeed mechanically linked to each other. An analysis of character state correlation in a morphological data matrix focused on head characters shows highly significant correlation of these mechanically linked structures. Phylogenetic tree reconstruction under different data exclusion schemes based on the correlation analysis unambiguously supports a sistergroup relationship of dragonflies and mayflies. The combination of biomechanics and phylogenetics as it is proposed here could be a promising approach to assess functional dependencies in many organisms to increase our understanding of phenotypic evolution.
Low-frequency hearing preceded the evolution of giant body size and filter feeding in baleen whales
Authors: Park Travis , Evans Alistair R. , Gallagher Stephen J. , Fitzgerald Erich M. G.
Published: February 2017

Living baleen whales (mysticetes) produce and hear the lowest-frequency (infrasonic) sounds among mammals. There is currently debate over whether the ancestor of crown cetaceans (Neoceti) was able to detect low frequencies. However, the lack of information on the most archaic fossil mysticetes has prevented us from determining the earliest evolution of their extreme acoustic biology. Here, we report the first anatomical analyses and frequency range estimation of the inner ear in Oligocene (34–23 Ma) fossils of archaic toothed mysticetes from Australia and the USA. The cochlear anatomy of these small fossil mysticetes resembles basilosaurid archaeocetes, but is also similar to that of today's baleen whales, indicating that even the earliest mysticetes detected low-frequency sounds, and lacked ultrasonic hearing and echolocation. This suggests that, in contrast to recent research, the plesiomorphic hearing condition for Neoceti was low frequency, which was retained by toothed mysticetes, and the high-frequency hearing of odontocetes is derived. Therefore, the low-frequency hearing of baleen whales has remained relatively unchanged over the last approximately 34 Myr, being present before the evolution of other signature mysticete traits, including filter feeding, baleen and giant body size.
Landscape context alters cost of living in honeybee metabolism and feeding
Authors: Tomlinson Sean , Dixon Kingsley W. , Didham Raphael K. , Bradshaw S. Donald
Published: February 2017

Field metabolic rate (FMR) links the energy budget of an animal with the constraints of its ecosystem, but is particularly difficult to measure for small organisms. Landscape degradation exacerbates environmental adversity and reduces resource availability, imposing higher costs of living for many organisms. Here, we report a significant effect of landscape degradation on the FMR of free-flyingApis mellifera, estimated using86Rb radio-isotopic turnover. We validated the relationship between86Rbkband metabolic rate for worker bees in the laboratory using flow-through respirometry. We then released radioisotopically enriched individuals into a natural woodland and a heavily degraded and deforested plantation. FMRs of worker bees in natural woodland vegetation were significantly higher than in a deforested landscape. Nectar consumption, estimated using22Na radio-isotopic turnover, also differed significantly between natural and degraded landscapes. In the deforested landscape, we infer that the costs of foraging exceeded energetic availability, and honeybees instead foraged less and depended more on stored resources in the hive. If this is generally the case with increasing landscape degradation, this will have important implications for the provision of pollination services and the effectiveness and resilience of ecological restoration practice.
Determining the impact of putative loss-of-function variants in protein-coding genes
Authors: Balasubramanian Suganthi , Fu Yao , Pawashe Mayur , McGillivray Patrick , Jin Mike , Liu Jeremy , Karczewski Konrad J. , MacArthur Daniel G. , Gerstein Mark
Published: February 2017

Variants predicted to result in the loss of function (LoF) of human genes have attracted interest because of their clinical impact and surprising prevalence in healthy individuals. Here, we present ALoFT (Annotation of Loss-of-Function Transcripts), a method to annotate and predict the disease-causing potential of LoF variants. Using data from Mendelian disease-gene discovery projects, we show that ALoFT can distinguish between LoF variants deleterious as heterozygotes and those causing disease only in the homozygous state. Investigation of variants discovered in healthy populations suggests that each individual carries at least two heterozygous premature stop alleles that could potentially lead to disease if present as homozygotes. When applied tode novopLoF variants in autism-affected families, ALoFT distinguishes between deleterious variants in patients and benign variants in unaffected siblings. Finally, analysis of somatic variants in > 6,500 cancer exomes shows that pLoF variants predicted to be deleterious by ALoFT are enriched in known driver genes.
COBRAme: A Computational Framework for Genome-Scale Models of Metabolism and Gene Expression
Authors: Lloyd Colton J. , Ebrahim Ali , Yang Laurence , King Zachary , Catoiu Edward , O’Brien Edward J. , Liu Joanne K. , Palsson Bernhard O.
Published: February 2017

Genome-scale models of metabolism and macromolecular expression (ME-models) explicitly compute the optimal proteome composition of a growing cell. ME-models expand upon the well-established genome-scale models of metabolism (M-models), and they enable new and exciting insights that are fundamental to understanding the basis of cellular growth. ME-models have increased predictive capabilities and accuracy due to their inclusion of the biosynthetic costs for the machinery of life, but they come with a significant increase in model size and complexity. This challenge results in models which are both difficult to compute and challenging to understand conceptually. As a result, ME-models exist for only two organisms (Escherichia coli and Thermotoga maritima) and are still used by relatively few researchers. To address these challenges, we have developed a new software framework called COBRAme for building and simulating ME-models. It is coded in Python and built on COBRApy, a popular platform for using M-models. COBRAme streamlines computation and analysis of ME-models. It provides tools to simplify constructing and editing ME-models to enable ME-model reconstructions for new organisms. We used COBRAme to reconstruct a condensed E. coli ME-model called iJL1678b-ME. This reformulated model gives virtually identical solutions to previous E. coli ME-models while using ¼ the number of free variables and solving in less than 10 minutes, a marked improvement over the 6 hour solve time of previous ME-model formulations. This manuscript outlines the architecture of COBRAme and demonstrates how ME-models can be reconstructed and edited most efficiently using the software.
Neotrygon vali, a new species of the blue-spotted maskray complex (Myliobatoidei: Dasyatidae)
Authors: Borsa Philippe
Published: February 2017

The blue-spotted maskray from Guadalcanal Island (Solomon archipelago) is distinct by its colour patterns fromNeotrygon kuhliiwith which it was previously confused, and belongs to a genetic lineage clearly separate from all other known species in the genusNeotrygon. It is here described as a new species,Neotrygon valisp. nov., on the basis of its nucleotide sequence at thecytochrome oxidase 1(CO1) gene locus. It is diagnosed from all other known species in the genusNeotrygonby the possession of nucleotide T at nucleotide site 420 and nucleotide G at nucleotide site 522 of theCO1gene.
A single transcription factor is sufficient to induce and maintain secretory cell architecture
Authors: Lo Hei-Yong G. , Jin Ramon U. , Sibbel Greg , Liu Dengqun , Karki Anju , Joens Matthew S. , Madison Blair B. , Zhang Bo , Blanc Valerie , Fitzpatrick James A.J. , Davidson Nicholas O. , Konieczny Stephen F. , Mills Jason C.
Published: February 2017

We hypothesized that basic helix–loop–helix (bHLH) MIST1 (BHLHA15) is a “scaling factor” that universally establishes secretory morphology in cells that perform regulated secretion. Here, we show that targeted deletion of MIST1 caused dismantling of the secretory apparatus of diverse exocrine cells. Parietal cells (PCs), whose function is to pump acid into the stomach, normally lack MIST1 and do not perform regulated secretion. Forced expression of MIST1 in PCs caused them to expand their apical cytoplasm, rearrange mitochondrial/lysosome trafficking, and generate large secretory granules. Mist1 induced a cohort of genes regulated by MIST1 in multiple organs but did not affect PC function. MIST1 bound CATATG/CAGCTG E boxes in the first intron of genes that regulate autophagosome/lysosomal degradation, mitochondrial trafficking, and amino acid metabolism. Similar alterations in cell architecture and gene expression were also caused by ectopically inducing MIST1 in vivo in hepatocytes. Thus, MIST1 is a scaling factor necessary and sufficient by itself to induce and maintain secretory cell architecture. Our results indicate that, whereas mature cell types in each organ may have unique developmental origins, cells performing similar physiological functions throughout the body share similar transcription factor-mediated architectural “blueprints.”
The ambient hydration of the aluminophosphate JDF-2 to AlPO-53(A): insights from NMR crystallography
Authors: Dawson Daniel M. , Walton Richard I. , Wimperis Stephen , Ashbrook Sharon E.
Published: February 2017

The aluminophosphate (AlPO) JDF-2 is prepared hydrothermally with methylammonium hydroxide (MAH+·HO−, MAH+= CH3NH3+), giving rise to a microporous AEN-type framework with occluded MAH+cations and extra-framework (Al-bound) HO−anions. Despite the presence of these species within its pores, JDF-2 can hydrate upon exposure to atmospheric moisture to give AlPO-53(A), an isostructural material whose crystal structure contains one molecule of H2O per formula unit. This hydration can be reversed by mild heating (such as the frictional heating from magic angle spinning). Previous work has shown good agreement between the NMR parameters obtained experimentally and those calculated from the (optimized) crystal structure of JDF-2. However, several discrepancies are apparent between the experimental NMR parameters for AlPO-53(A) and those calculated from the (optimized) crystal structure (e.g.four13C resonances are observed, rather than the expected two). The unexpected resonances appear and disappear reversibly with the respective addition and removal of H2O, so clearly arise from AlPO-53(A). We investigate the ambient hydration of JDF-2 using quantitative31P MAS NMR to follow the transformation over the course of ∼3 months. The structures of JDF-2 and AlPO-53(A) are also investigated using a combination of multinuclear solid-state NMR spectroscopy to characterize the samples, and first-principles density functional theory (DFT) calculations to evaluate a range of possible structural models in terms of calculated NMR parameters and energetics. The published structure of JDF-2 is shown to be a good representation of the dehydrated material, but modification of the published structure of AlPO-53(A) is required to provide calculated NMR parameters that are in better agreement with experiment. This modification includes reorientation of all the MAH+cations and partial occupancy of the H2O sites.
Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters
Authors: Mali Gregor
Published: February 2017

Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS2, exhibiting a modified rocksalt structure, in which S2− anions were replaced by S2
2− dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, 25Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined 25Mg NMR parameters of magnesium sulfide species.
Single-crystal X-ray diffraction and NMR crystallography of a 1:1 cocrystal of dithianon and pyrimethanil
Authors: Pöppler Ann-Christin , Corlett Emily K. , Pearce Harriet , Seymour Mark P. , Reid Matthew , Montgomery Mark G. , Brown Steven P.
Published: February 2017

A single-crystal X-ray diffraction structure of a 1:1 cocrystal of two fungicides, namely dithianon (DI) and pyrimethanil (PM), is reported [systematic name: 5,10-dioxo-5H,10H-naphtho[2,3-b][1,4]dithiine-2,3-dicarbonitrile–4,6-dimethyl-N-phenylpyrimidin-2-amine (1/1), C14H4N2O2S2·C12H13N2]. Following an NMR crystallography approach, experimental solid-state magic angle spinning (MAS) NMR spectra are presented together with GIPAW (gauge-including projector augmented wave) calculations of NMR chemical shieldings. Specifically, experimental1H and13C chemical shifts are determined from two-dimensional1H–13C MAS NMR correlation spectra recorded with short and longer contact times so as to probe one-bond C—H connectivities and longer-range C...H proximities, whereas H...H proximities are identified in a1H double-quantum (DQ) MAS NMR spectrum. The performing of separate GIPAW calculations for the full periodic crystal structure and for isolated molecules allows the determination of the change in chemical shift upon going from an isolated molecule to the full crystal structure. For the1H NMR chemical shifts, changes of 3.6 and 2.0 ppm correspond to intermolecular N—H...O and C—H...O hydrogen bonding, while changes of −2.7 and −1.5 ppm are due to ring current effects associated with C—H...π interactions. Even though there is a close intermolecular S...O distance of 3.10 Å, it is of note that the molecule-to-crystal chemical shifts for the involved sulfur or oxygen nuclei are small.
Crystal structure of guanidinium hexafluoridovanadate(III), (CN3H6)3[VF6]: an unusual hybrid compound related to perovskite
Authors: Black Cameron , Lightfoot Philip
Published: February 2017

Vanadium fluorides with novel crystal–chemical features and interesting physical properties can be prepared by solvothermal synthetic routes. The title compound, guanidinium hexafluoridovanadate(III), has a cubic structure (space group Pa\overline{3}), exhibiting isolated regular VF6 octahedral units, which are hydrogen bonded to protonated guanidinium moieties. Although the VF6 octahedral units are not linked directly together, there are structural similarities between this crystal structure and those of the wider family of perovskite materials, in particular, hybrid perovskites based on extended ligands such as cyanide. In this context, the octahedral tilt system of the present compound is of interest and demonstrates that unusual tilt systems can be mediated via `molecular' linkers which allow only supramolecular rather than covalent interactions.
An examination of the factors contributing to participation in online social platforms
Authors: Bronstein Jenny , Gazit Tali , Perez Oren , Bar-Ilan Judit , Aharony Noa , Amichai-Hamburger Yair
Published: February 2017

Purpose

The purpose of this paper is to examine participation in online social platforms consisting of information exchange, social network interactions, and political deliberation. Despite the proven benefits of online participation, the majority of internet users read social media data but do not directly contribute, a phenomenon called lurking.

Design/methodology/approach

A survey was administered electronically to 507 participants and consisted of ten sections in a questionnaire to gather data on the relationship between online participation and the following variables: anonymity, social value orientation, motivations, and participation in offline activities, as well as the internet’s political influence and personality traits.

Findings

Findings show that users with high levels of participation also identify themselves, report higher levels of extroversion, openness, and activity outside the internet, the motivations being an intermediary variable in the relationship between the variables value.

Originality/value

The study shows that participation in online social platforms is not only related to personality traits, but they are impacted by the nature of the motivations that drive them to participate in the particular social platform, as well as by the interest toward the specific topic, or the type or nature of the social group with whom they are communicating.
Examining the occupancy–density relationship for a low‐density carnivore
Authors: Linden Daniel W. , Fuller Angela K. , Royle J. Andrew , Hare Matthew P.
Published: February 2017

The challenges associated with monitoring low‐density carnivores across large landscapes have limited the ability to implement and evaluate conservation and management strategies for such species. Non‐invasive sampling techniques and advanced statistical approaches have alleviated some of these challenges and can even allow for spatially explicit estimates of density, one of the most valuable wildlife monitoring tools.

For some species, individual identification comes at no cost when unique attributes (e.g. pelage patterns) can be discerned with remote cameras, while other species require viable genetic material and expensive laboratory processing for individual assignment. Prohibitive costs may still force monitoring efforts to use species distribution or occupancy as a surrogate for density, which may not be appropriate under many conditions.

Here, we used a large‐scale monitoring study of fisher Pekania pennanti to evaluate the effectiveness of occupancy as an approximation to density, particularly for informing harvest management decisions. We combined remote cameras with baited hair snares during 2013–2015 to sample across a 70 096‐km2 region of western New York, USA. We fit occupancy and Royle–Nichols models to species detection–non‐detection data collected by cameras, and spatial capture–recapture (SCR) models to individual encounter data obtained by genotyped hair samples. Variation in the state variables within 15‐km2 grid cells was modelled as a function of landscape attributes known to influence fisher distribution.

We found a close relationship between grid cell estimates of fisher state variables from the models using detection–non‐detection data and those from the SCR model, likely due to informative spatial covariates across a large landscape extent and a grid cell resolution that worked well with the movement ecology of the species. Fisher occupancy and density were both positively associated with the proportion of coniferous‐mixed forest and negatively associated with road density. As a result, spatially explicit management recommendations for fisher were similar across models, though relative variation was dampened for the detection–non‐detection data.

Synthesis and applications. Our work provides empirical evidence that models using detection–non‐detection data can make similar inferences regarding relative spatial variation of the focal population to models using more expensive individual encounters when the selected spatial grain approximates or is marginally smaller than home range size. When occupancy alone is chosen as a cost‐effective state variable for monitoring, simulation and sensitivity analyses should be used to understand how inferences from detection–non‐detection data will be affected by aspects of study design and species ecology.