bluuebunny/crossref_metadata_2025 huggingface dataset:
The personal presence of Jesus in the writings of Paul
Authors: Bockmuehl Markus
Published: February 2017

For Paul, where is Jesus now? The Apostle's Christ-mysticism provides one important clue to his sense of continued personal presence, but this coexists with an important eschatological dialectic that involves absence as much as presence. Moreoever, straightforward sublimation in terms of the Holy Spirit in no way exhausts the register of Jesus’ personal presence for Paul, which also finds specific application in repeated visionary experiences, as well as in the church gathered for worship, baptism, and eucharist. The dialectic of absence and presence appears on the one hand personally attuned in the assurance of Paul's Jesus that ‘My grace is sufficient for you’ (2 Cor 12:7), but it is also eschatologically and spatially articulated in the promise that ‘the Lord is near’ (Phil 4:5).
Legal Aspects of Research with Human Embryonic Stem Cells
Authors: Taupitz Jochen
Published: February 2017

Research with human embryonic stem cells (HESC) is very much disputed from an ethical point of view as it requires the destruction of the embryo to derive the stem cells. The legal situation in Europe is heterogeneous. This article gives an overview of the current debate on this topic by outlining the international regulations and the national legislation in the European Union. It is shown that the different legal positions are like an in vivo experiment for contrasting solutions. Furthermore, the legal situation in Germany is examined in more detail and with it the effectiveness and the constitutionality of the requirements.
Configural and Featural Face Processing Influences on Emotion Recognition in Schizophrenia and Bipolar Disorder
Authors: Van Rheenen Tamsyn E. , Joshua Nicole , Castle David J , Rossell Susan L.
Published: February 2017

Objectives: Emotion recognition impairments have been demonstrated in schizophrenia (Sz), but are less consistent and lesser in magnitude in bipolar disorder (BD). This may be related to the extent to which different face processing strategies are engaged during emotion recognition in each of these disorders. We recently showed that Sz patients had impairments in the use of both featural and configural face processing strategies, whereas BD patients were impaired only in the use of the latter. Here we examine the influence that these impairments have on facial emotion recognition in these cohorts. Methods: Twenty-eight individuals with Sz, 28 individuals with BD, and 28 healthy controls completed a facial emotion labeling task with two conditions designed to separate the use of featural and configural face processing strategies; part-based and whole-face emotion recognition. Results: Sz patients performed worse than controls on both conditions, and worse than BD patients on the whole-face condition. BD patients performed worse than controls on the whole-face condition only. Conclusions: Configural processing deficits appear to influence the recognition of facial emotions in BD, whereas both configural and featural processing abnormalities impair emotion recognition in Sz. This may explain discrepancies in the profiles of emotion recognition between the disorders. (JINS, 2017, 23, 287–291)
The ‘Best Available Science’ and the Paris Agreement on Climate Change
Authors: Hanekamp Jaap C. , Bergkamp Lucas
Published: February 2017

Recognising the importance of science to climate policies, the Paris Agreement on Climate Change (the ‘Paris Agreement’ or ‘Agreement’) stipulates that ‘an effective and progressive response to the urgent threat of climate change’ should be based on ‘the best available scientific knowledge.’ The terms ‘best available scientific knowledge’ or ‘best available science’ are used in several places throughout the agreement.
Repurposing doxycycline for synucleinopathies: remodelling of α-synuclein oligomers towards non-toxic parallel beta-sheet structured species
Authors: González-Lizárraga Florencia , Socías Sergio B. , Ávila César L. , Torres-Bugeau Clarisa M. , Barbosa Leandro R. S. , Binolfi Andres , Sepúlveda-Díaz Julia E. , Del-Bel Elaine , Fernandez Claudio O. , Papy-Garcia Dulce , Itri Rosangela , Raisman-Vozari Rita , Chehín Rosana N.
Published: February 2017

Synucleinophaties are progressive neurodegenerative disorders with no cure to date. An attractive strategy to tackle this problem is repurposing already tested safe drugs against novel targets. In this way, doxycycline prevents neurodegeneration in Parkinson models by modulating neuroinflammation. However, anti-inflammatory therapy per se is insufficient to account for neuroprotection. Herein we characterise novel targets of doxycycline describing the structural background supporting its effectiveness as a neuroprotector at subantibiotic doses. Our results show that doxycycline reshapes α-synuclein oligomers into off-pathway, high-molecular-weight species that do not evolve into fibrils. Off-pathway species present less hydrophobic surface than on-pathway oligomers and display different β-sheet structural arrangement. These structural changes affect the α-synuclein ability to destabilize biological membranes, cell viability, and formation of additional toxic species. Altogether, these mechanisms could act synergically giving novel targets for repurposing this drug.
The citrus flavanone naringenin impairs dengue virus replication in human cells
Authors: Frabasile Sandra , Koishi Andrea Cristine , Kuczera Diogo , Silveira Guilherme Ferreira , Verri Waldiceu Aparecido , Duarte dos Santos Claudia Nunes , Bordignon Juliano
Published: February 2017

Dengue is one of the most significant health problems in tropical and sub-tropical regions throughout the world. Nearly 390 million cases are reported each year. Although a vaccine was recently approved in certain countries, an anti-dengue virus drug is still needed. Fruits and vegetables may be sources of compounds with medicinal properties, such as flavonoids. This study demonstrates the anti-dengue virus activity of the citrus flavanone naringenin, a class of flavonoid. Naringenin prevented infection with four dengue virus serotypes in Huh7.5 cells. Additionally, experiments employing subgenomic RepDV-1 and RepDV-3 replicon systems confirmed the ability of naringenin to inhibit dengue virus replication. Antiviral activity was observed even when naringenin was used to treat Huh7.5 cells 24 h after dengue virus exposure. Finally, naringenin anti-dengue virus activity was demonstrated in primary human monocytes infected with dengue virus sertoype-4, supporting the potential use of naringenin to control dengue virus replication. In conclusion, naringenin is a suitable candidate molecule for the development of specific dengue virus treatments.
Longitudinal in vivo bioimaging of hepatocyte transcription factor activity following cholestatic liver injury in mice
Authors: Delhove Juliette M. K. M. , Buckley Suzanne M. K. , Perocheau Dany P. , Karda Rajvinder , Arbuthnot Patrick , Henderson Neil C. , Waddington Simon N. , McKay Tristan R.
Published: February 2017

Molecular mechanisms regulating liver repair following cholestatic injury remain largely unknown. We have combined a mouse model of acute cholestatic liver injury, partial bile duct ligation (pBDL), with a novel longitudinal bioimaging methodology to quantify transcription factor activity during hepatic injury and repair. We administered lentiviral transcription factor activated luciferase/eGFP reporter (TFAR) cassettes to neonatal mice enabling longitudinal TFAR profiling by continued bioimaging throughout the lives of the animals and following pBDL in adulthood. Neonatal intravascular injection of VSV-G pseudotyped lentivirus resulted in almost exclusive transduction of hepatocytes allowing analysis of hepatocyte-specific transcription factor activity. We recorded acute but transient responses with NF-κB and Smad2/3 TFAR whilst our Notch reporter was repressed over the 40 days of evaluation post-pBDL. The bipotent hepatic progenitor cell line, HepaRG, can be directed to differentiate into hepatocytes and biliary epithelia. We found that forced expression of the Notch inhibitor NUMB in HepaRG resulted in enhanced hepatocyte differentiation and proliferation whereas over-expressing the Notch agonist JAG1 resulted in biliary epithelial differentiation. In conclusion, our data demonstrates that hepatocytes rapidly upregulate NF-κB and Smad2/3 activity, whilst repressing Notch signalling. This transcriptional response to cholestatic liver injury likely promotes partial de-differentiation to allow pro-regenerative proliferation of hepatocytes.
Generation of cycloalkynes through deprotonation of cyclic enol triflates with magnesium bisamides
Authors: Hioki Yuto , Okano Kentaro , Mori Atsunori
Published: February 2017

Magnesium bis(2,2,6,6-tetramethylpiperidide)-mediated deprotonation of readily available cyclic enol triflates allows direct access to cyclohexynes, cycloheptynes, and cyclooctynes.
CN bond formation via palladium-catalyzed carbene insertion into NN bonds: inhibiting the general 1,2-migration process of ylide intermediates
Authors: Zhu Chuanle , Chen Pengquan , Zhu Rui , Lin Zhiming , Wu Wanqing , Jiang Huanfeng
Published: February 2017

Inhibiting the general 1,2-migration process of ylide intermediates, a new palladium-catalyzed carbene insertion into NN bonds affords various N,N-disubstituted hydrazones.
Tuning the ambipolar charge transport properties of tricyanovinyl-substituted carbazole-based materials
Authors: Reig Marta , Bagdziunas Gintautas , Volyniuk Dmytro , Grazulevicius Juozas V. , Velasco Dolores
Published: February 2017

The ambipolar charge transport properties of a series of push–pull carbazole-based semiconductors are here evaluated. The ambipolar characteristics depend on the supramolecular organization. Experimental results were confirmed and justified through the X-ray analysis of single crystals and by theoretical calculations.
Vinyltriethoxysilane as an electrolyte additive to improve the safety of lithium-ion batteries
Authors: Chen Renjie , Zhao Yuanyuan , Li Yuejiao , Ye Yusheng , Li Yajing , Wu Feng , Chen Shi
Published: February 2017

Vinyltriethoxysilane (VTES) is a promising environmentally-friendly additive for electrolytes to improve the safety of LIBs.
An in situ photoelectroreduction approach to fabricate Bi/BiOCl heterostructure photocathodes: understanding the role of Bi metal for solar water splitting
Authors: Fan Weiqiang , Li Chunfa , Bai Hongye , Zhao Yanyan , Luo Bifu , Li Yongjun , Ge Yilin , Shi Weidong , Li Hongping
Published: February 2017

This paper presents for the first time a novel method of in situ depositing plasmonic Bi nanoparticles on BiOCl nanosheets (Bi/BiOCl) for PEC water splitting.
Tailor-made synthesis of fully alkylated/arylated nicotinates by FeCl3-mediated condensation of enamino esters with enones
Authors: Hirai Sho , Horikawa Yurie , Asahara Haruyasu , Nishiwaki Nagatoshi
Published: February 2017

A synthetic method for fully alkylated/arylated nicotinates was achieved by FeCl3-mediated condensation of enamino esters and enones.
Pd/Cu cooperative catalysis: an efficient synthesis of (3-isoindazolyl)allenes via cross-coupling of 2-alkynyl azobenzenes and terminal alkynes
Authors: Zhu Chuan , Feng Chao , Yamane Motoki
Published: February 2017

We report a cooperative Pd/Cu-catalyzed synthesis of (3-isoindazolyl)allenes via cross-coupling of 2-alkynyl azobenzenes and terminal alkynes.
Single source bins detection‐based localisation scheme for multiple speech sources
Authors: Jia Maoshen , Sun Jundai , Deng Feng , Sun Junyue
Published: February 2017

A single source bins (SSBs) detection based multiple source localisation scheme is proposed. This scheme is based on detecting the SSBs in mixture signals that are only derived from one source. Specifically, after proposing a ‘DOA convergence’ assumption, K‐means clustering algorithm is used for SSBs detecting. Thus, the multiple source localisation is converted to a single source one among these SSBs. Moreover, the proposed SSBs detection is applicable to other localisation methods and not limited to specific microphone topology. Experimental results demonstrate the localisation accuracy of the proposed method outperforms the localisation approaches which are based on single source zone detection.
Enantioselective Synthesis of anti-β-Hydroxy-α-amino Esters via an Organocatalyzed Decarboxylative Aldol Reaction
Authors: Takemoto Yoshiji , March Taryn , Murata Akihiro , Kobayashi Yusuke
Published: February 2017

The first enantioselective decarboxylative aldol addition with α-amido-substituted malonic acid half oxyesters (MAHOs) is described. The combined use of a newly designed bifunctional sulfonamide catalyst with pentafluorobenzoic acid as an additive afforded the β-hydroxy-α-amino acid derivatives in moderate to high yields and with high enantioselectivities.
Thermal conductivity of vitreous silica from molecular dynamics simulations: The effects of force field, heat flux and system size
Authors: Tian Ye , Du Jincheng , Han Wei , Zu Xiaotao , Yuan Xiaodong , Zheng Wanguo
Published: February 2017

The thermal conductivity of vitreous silica is computed using the direct method in molecular dynamics simulations with three sets of empirical force fields, including the BKS, Teter, and ReaxFF, to investigate their performance in thermal characterization. Various heat flux and system sizes are used in the simulations to evaluate the statistical uncertainty and the finite-size effect. While all these potentials can reproduce realistic silica structures, the ReaxFF provides better agreement with experiments at 300 K than the BKS and Teter, which is due to its improved description of low-frequency vibrations. Increasing the heat flux and cross-sectional area tends to reduce the calculated standard deviation induced by thermal fluctuations, thus contributing to more accurate thermal conductivity predictions.
Gyromagnetic RF source for interdisciplinary research
Authors: Romanchenko I. V. , Rostov V. V. , Gunin A. V. , Konev V. Yu.
Published: February 2017

We demonstrate a source of high power nanosecond RF pulses based on gyromagnetic nonlinear transmission line. The source is designed to explore the exposure of different biological objects to strong RF fields in an air filled rectangular waveguide loaded onto ethanol RF load. The RF pulse amplitude can be varied by 52 dB, reaching a maximum value of nearly 40 kV/cm and decreasing to tens of V/cm. The RF pulse amplitude is controlled by decreasing the incident pulse amplitude from the high voltage driver. The duration of RF pulses lies in the range from 4 to 25 ns and the frequency from 0.6 to 1.0 GHz.
Communication: Band bending at the interface in polyethylene-MgO nanocomposite dielectric
Authors: Kubyshkina Elena , Unge Mikael , Jonsson B. L. G.
Published: February 2017

Polymer nanocomposite dielectrics are promising materials for electrical insulation in high voltage applications. However, the physics behind their performance is not yet fully understood. We use density functional theory to investigate the electronic properties of the interfacial area in magnesium oxide-polyethylene nanocomposite. Our results demonstrate polyethylene conduction band matching with conduction bands of different surfaces of magnesium oxide. Such band bending results in long range potential wells of up to 2.6 eV deep. Furthermore, the fundamental influence of silicon treatment on magnesium oxide surface properties is assessed. We report a reduction of the surface-induced states at the silicon-treated interface. The simulations provide information used to propose a new model for charge trapping in nanocomposite dielectrics.
Biopower and geopolitics as Russia's neighborhood strategies: reconnecting people or reaggregating lands?
Authors: Makarychev Andrey , Yatsyk Alexandra
Published: February 2017

In this article, we address geopolitics and biopower as two different yet mutually correlative discursive strategies of sovereign power in Russia. We challenge the dominant realist approaches to Russia's neighborhood policy by introducing the concept of biopolitics as its key element, which makes analysis of political relations in the post-Soviet area more nuanced and variegated. More specifically, we address an important distinction between geopolitical control over territories and management of population as two of Russia's strategies in its “near abroad.”
Outcome and Treatment of Nocardiosis After Solid Organ Transplantation: New Insights From a European Study
Authors: Lebeaux David , Freund Romain , van Delden Christian , Guillot Hélène , Marbus Sierk D. , Matignon Marie , Van Wijngaerden Eric , Douvry Benoit , De Greef Julien , Vuotto Fanny , Tricot Leïla , Fernández-Ruiz Mario , Dantal Jacques , Hirzel Cédric , Jais Jean-Philippe , Rodriguez-Nava Veronica , Jacobs Frédérique , Lortholary Olivier , Coussement Julien ,   for the European Study Group for Nocardia in Solid Organ Transplantation, Anstey James R. , Antoine Martine , Ausselet Nathalie , Belhaj Asmae , Boelens Jerina , de Beenhouwer Hans , Denis Catherine , Ho Erwin , Ieven Margareta , Jonckheere Stijn , Knoop Christiane , le Moine Alain , Rodriguez-Villalobos Hector , Racapé Judith , Roisin Sandrine , Vandercam Bernard , Vander Zwalmen Marie-Laure , Vanfraechem Gaëlle , Van Laecke Steven , Verhaegen Jan , Barrou Benoit , Battistella Pascal , Bergeron Emmanuelle , Bouvier Nicolas , Caillard Sophie , Caumes Eric , Chaussade Hélène , Chauvet Cécile , Crochette Romain , Epailly Eric , Essig Marie , Gallien Sébastien , Guillemain Romain , Herel Canan , Hoen Bruno , Kamar Nassim , le Gall Thierry , Levi Charlene , Lionet Arnaud , Longuet Hélène , Melica Giovanna , Miel Anaick , Morel Hélène , Ammar Salima Ould , Pattier Sabine , Peraldi Marie-Noelle , Sayegh Johnny , Scemla Anne , Senechal Agathe , Tourret Jérome , Boggian Katia , Egli Adrian , Garzoni Christian , Hoffman Matthias , Hirsch Hans H. , Khanna Nina , Manuel Oriol , Meylan Pascal , Mueller Nicolas J. , Posfay-Barbe Klara M. , Vu Diem-Lan , Weisser Maja , Vollaard Albert M. , Wunderink Herman F.
Published: February 2017

In our study of 117 organ transplant recipients with nocardiosis, a history of tumor, invasive fungal infection, donor age, and no acute rejection were independently associated with 1-year mortality. Short-course antibiotic treatment (≤120 days), used in 17 patients, appeared promising.
Should Human Immunodeficiency Virus Specialty Clinics Treat Patients With Hypertension or Refer to Primary Care? An Analysis of Treatment Outcomes
Authors: Appenheimer A. Ben , Bokhour Barbara , McInnes D. Keith , Richardson Kelly K. , Thurman Andrew L. , Beck Brice F. , Vaughan-Sarrazin Mary , Asch Steven M. , Midboe Amanda M. , Taylor Thom , Dvorin Kelly , Gifford Allen L. , Ohl Michael E.
Published: February 2017

Background

Care for people with human immunodeficiency virus (HIV) increasingly focuses on comorbidities, including hypertension. Evidence indicates that antiretroviral therapy and opportunistic infections are best managed by providers experienced in HIV medicine, but it is unclear how to structure comorbidity care. Approaches include providing comorbidity care in HIV clinics (“consolidated care”) or combining HIV care with comorbidity management in primary care clinics (“shared care”). We compared blood pressure (BP) control in HIV clinics practicing consolidated care versus shared care.

Methods

We created a national cohort of Veterans with HIV and hypertension receiving care in HIV clinics in Veterans Administration facilities and merged these data with a survey asking HIV providers how they delivered hypertension care (5794 Veterans in 73 clinics). We defined BP control as BP ≤140/90 mmHg on the most recent measure. We compared patients’ likelihood of experiencing BP control in clinics offering consolidated versus shared care, adjusting for patient and clinic characteristics.

Results

Forty-two of 73 clinics (57.5%) practiced consolidated care for hypertension. These clinics were larger and more likely to use multidisciplinary teams. The unadjusted frequency of BP control was 65.6% in consolidated care clinics vs 59.4% in shared care clinics (P < .01). The likelihood of BP control remained higher for patients in consolidated care clinics after adjusting for patient and clinic characteristics (odds ratio, 1.32; 95% confidence interval, 1.04–1.68).

Conclusions

Patients were more likely to experience BP control in clinics reporting consolidated care compared with clinics reporting shared care. For shared-care clinics, improving care coordination between HIV and primary care clinics may improve outcomes.
POINT PATTERN ANALYSIS OF THE SPATIAL PROXIMITY OF RESIDENCES PRIOR TO DIAGNOSIS OF PERSONS WITH HODGKIN'S DISEASE
Authors: ROSS ANDREW , DAVIS SCOTT
Published: February 2017

There is some evidence to suggest that the etiology of Hodgkin's disease includes an infectious component One approach to investigating this possibility is a formal assessment of the geographic and temporal variation in the incidence of the disease. The present study was designed to better evaluate space-time patterns of residence prior to diagnosis of persons with Hodgkln's disease. Lifetime residential histories were obtained from 279 incident cases of Hodgkin's disease diagnosed between 1974 and 1982 in a defined population in northwestern Washington State, and a similar number of population controls matched to the cases by age, sex, and socioeconomic status. A method of point pattern analysis was modified for use in this context to compare the spatial proximity of case residences to that expected under the null assumption of no difference between the spatial pattern of case and control residences. Analyses were applied within temporal groupings of residences specified a priori assuming 1) no specified latency, 2) four different 5-year latent intervals, and 3) three age at exposure intervals. Assuming no latency, there is no evidence that case residences are more or less clustered than would be expected by chance. Assuming latent intervals of up to 15 years prior to diagnosis, case residences are less clustered than expected, particularly among those who developed Hodgkin's disease after the age of 40 years. In contrast, there is suggestive evidence that persons diagnosed with Hodgkin's disease after age 40 years lived closer together than expected as young children and teenagers. These results illustrate the need to focus such analyses on specific time intervals defined a priori to most likely represent periods of greatest etiologic relevance. To the extent that these findings are not the result of some unknown artifact of the method itself, they may serve to focus additional attention on childhood environment as a particularly important period in the etiology of this disease. Furthermore, the analytic method employed may be useful in identifying space-time clustering using population-based data in other etiologic settings
TOXIC TORT LITIGATION: MEDICAL AND SCIENTIFIC PRINCIPLES IN CAUSATION
Authors: HENDERSON THOMAS W.
Published: February 2017

A definition and an explanation of the legal standard for imposition of legal liability in a toxic tort case are set forth. The focus is on how expert witnesses utilize the applicable medical and scientific data in order to provide opinion evidence of the causal relation between exposure to a toxic substance and disease in an individual case. The author concludes that policy considerations are present in both the legal standard and the basis for establishing a cause and effect relation.
Pregnancy following discontinuation of a calcium channel blocker in the male partner
Authors: Hershlag Avner , Cooper George W. , Benoff Susan
Published: February 2017

The fertility potential of human sperm populations can be assessed by the presence of head-directed mannose ligand receptors (mannose-specific lectin) and the occurrence of spontaneous acrosome reactions after incubation under capacitating conditions in vitro. We have reported previously on the interaction between anti-hypertensive medications and their effects on these parameters of male fertility potential. In this report we document the effects of cessation of calcium ion channel blocker medication on male fertility. Motile spermatozoa from a 30 year old infertile patient on a calcium ion channel blocker as anti-hypertensive treatment had subnormal expression of mannose-specific lectin and did not exhibit spontaneous acrosome reactions. Three months following discontinuation of the medications, complete recovery of both the expression of head-directed mannose ligand receptors and the acrosome reaction was documented, though sperm motility and morphology remained unchanged. The couple had 2 years of infertility and previously failed to conceive through seven cycles of Pergonal/intra-uterine insemination. Conception occurred on the second Pergonal/intra-uterine insemination cycle after the husband discontinued calcium ion channel blocker medication. Calcium ion channel blockers may adversely affect sperm fertilizing potential. Discontinuation of such medications enhances the chances for conception.
Is Democracy the Right System? Collaborative Approaches to Building an Engaged RDM Community
Authors: Teperek Marta , Higman Rosie , Kingsley Danny
Published: January 2017

When developing new products, tools or services, one always need to think about the end users to ensure a wide-spread adoption. While this applies equally to services developed at higher education institutions, sometimes these services are driven by policies and not by needs of end users. This policy-driven approach can prove challenging for building effective community engagement. The initial development of Research Data Management support services at the University of Cambridge was policy-driven and subsequently failed in the first instance to engage the community of researchers for whom these services were created.

In this practice paper we will describe the initial approach undertaken at Cambridge when developing RDM services, the results of this approach and lessons learnt. We will then provide an overview of alternative, democratic strategies employed and their positive effects on community engagement. We will summarise by performing a cost-benefit analysis of the two approaches. This paper might be a useful case study for any institutions aiming to develop central support services for researchers, with conclusions applicable to the wide sector, and extending beyond Research Data Management services.
Deep Recurrent Neural Network for Protein Function Prediction from Sequence
Authors: Liu Xueliang Leon
Published: January 2017

As high-throughput biological sequencing becomes faster and cheaper, the need to extract useful information from sequencing becomes ever more paramount, often limited by low-throughput experimental characterizations. For proteins, accurate prediction of their functions directly from their primary amino-acid sequences has been a long standing challenge. Here, machine learning using artificial recurrent neural networks (RNN) was applied towards classification of protein function directly from primary sequence without sequence alignment, heuristic scoring or feature engineering. The RNN models containing long-short-term-memory (LSTM) units trained on public, annotated datasets from UniProt achieved high performance for in-class prediction of four important protein functions tested, particularly compared to other machine learning algorithms using sequence-derived protein features. RNN models were used also for out-of-class predictions of phylogenetically distinct protein families with similar functions, including proteins of the CRISPR-associated nuclease, ferritin-like iron storage and cytochrome P450 families. Applying the trained RNN models on the partially unannotated UniRef100 database predicted not only candidates validated by existing annotations but also currently unannotated sequences. Some RNN predictions for the ferritin-like iron sequestering function were experimentally validated, even though their sequences differ significantly from known, characterized proteins and from each other and cannot be easily predicted using popular bioinformatics methods. As sequencing and experimental characterization data increases rapidly, the machine-learning approach based on RNN could be useful for discovery and prediction of homologues for a wide range of protein functions.
Epidemic establishment and cryptic transmission of Zika virus in Brazil and the Americas
Authors: Faria N. R. , Quick J. , Morales I. , Thézé J. , Jesus J.G. , Giovanetti M. , Kraemer M. U. G. , Hill S. C. , Black A. , da Costa A. C. , Franco L.C. , Silva S. P. , Wu C.-H. , Raghwani J. , Cauchemez S. , du Plessis L. , Verotti M. P. , de Oliveira W. K. , Carmo E. H. , Coelho G. E. , Santelli A. C. F. S. , Vinhal L. C. , Henriques C. M. , Simpson J. T. , Loose M. , Andersen K. G. , Grubaugh N. D. , Somasekar S. , Chiu C. Y. , Muñoz-Medina J. E. , Gonzalez-Bonilla C. R. , Arias C. F. , Lewis-Ximenez L. L. , Baylis S.A. , Chieppe A. O. , Aguiar S. F. , Fernandes C. A. , Lemos P. S. , Nascimento B. L. S. , Monteiro H. A. O. , Siqueira I. C. , de Queiroz M. G. , de Souza T. R. , Bezerra J. F. , Lemos M. R. , Pereira G. F. , Loudal D. , Moura L. C. , Dhalia R. , França R. F. , Magalhães T. , Marques E. T. , Jaenisch T. , Wallau G. L. , de Lima M. C. , Nascimento V. , de Cerqueira E. M. , de Lima M. M. , Mascarenhas D. L. , Moura Neto J. P. , Levin A. S. , Tozetto-Mendoza T. R. , Fonseca S. N. , Mendes-Correa M. C. , Milagres F.P. , Segurado A. , Holmes E. C. , Rambaut A. , Bedford T. , Nunes M. R. T. , Sabino E. C. , Alcantara L. C. J. , Loman N. , Pybus O. G.
Published: February 2017

Zika virus (ZIKV) transmission in the Americas was first confirmed in May 2015 in Northeast Brazil1. Brazil has the highest number of reported ZIKV cases worldwide (>200,000 by 24 Dec 20162) as well as the greatest number of cases associated with microcephaly and other birth defects (2,366 confirmed cases by 31 Dec 20162). Following the initial detection of ZIKV in Brazil, 47 countries and territories in the Americas have reported local ZIKV transmission, with 24 of these reporting ZIKV-associated severe disease3. Yet the origin and epidemic history of ZIKV in Brazil and the Americas remain poorly understood, despite the value of such information for interpreting past and future trends in reported microcephaly. To address this we generated 54 complete or partial ZIKV genomes, mostly from Brazil, and report data generated by the ZiBRA project – a mobile genomics lab that travelled across Northeast (NE) Brazil in 2016. One sequence represents the earliest confirmed ZIKV infection in Brazil. Joint analyses of viral genomes with ecological and epidemiological data estimate that ZIKV epidemic was present in NE Brazil by March 2014 and likely disseminated from there, both nationally and internationally, before the first detection of ZIKV in the Americas. Estimated dates of the international spread of ZIKV from Brazil indicate the duration of pre-detection cryptic transmission in recipient regions. NE Brazil’s role in the establishment of ZIKV in the Americas is further supported by geographic analysis of ZIKV transmission potential and by estimates of the virus’ basic reproduction number.

One Sentence Summary

Virus genomes reveal the establishment of Zika virus in Brazil and the Americas, and provide an appropriate timeframe for baseline (pre-Zika) microcephaly in different regions.
Integrative analysis reveals genomic and epigenomic signatures of super-enhancers and its constituents
Authors: Khan Aziz , Zhang Xuegong
Published: February 2017

Background

Super-enhancers are clusters of transcriptional enhancers densely occupied by the Mediators, transcription factors and chromatin regulators. They control the expression of cell identity genes and disease associated genes. Current studies demonstrated the possibility of multiple factors with important roles in super-enhancer formation; however, a systematic analysis to assess the relative importance of chromatin and sequence signatures of super-enhancers and their constituents remain unclear.

Results

Here, we integrated diverse types of genomic and epigenomic datasets to identify key signatures of super-enhancers and their constituents and to investigate their relative importance. Through computational modelling, we found that Cdk8, Cdk9 and Smad3 as new key features of super-enhancers along with many known features such as H3K27ac. Comprehensive analysis of these features in embryonic stem cells and pro-B cells revealed their role in the super-enhancer formation and cellular identity. We also observed that super-enhancers are significantly GC-rich in contrast with typical enhancers. Further, we observed significant correlation among many cofactors at the constituents of super-enhancers.

Conclusions

Our analysis and ranking of super-enhancer signatures can serve as a resource to further characterize and understand the formation of super-enhancers. Our observations are consistent with a cooperative or synergistic model underlying the interaction of super-enhancers and their constituents with numerous factors.
Demographic variability and heterogeneity among individuals within and among clonal bacteria strains
Authors: Jouvet Lionel , Rodríguez-Rojas Alexandro , Steiner Ulrich K.
Published: February 2017

Identifying what drives individual heterogeneity has been of long interest to ecologists, evolutionary biologists and biodemographers, because only such identification provides deeper understanding of ecological and evolutionary population dynamics. In natural populations one is challenged to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction is dominating at about 82-88%, over the 12-18% genetically (adaptive fixed) driven differences. The genetic differences among the clonal strains still lead to substantial variability in population growth rates (fitness), but, as well understood based on foundational work in population genetics, the within strain neutral variability slows adaptive change, by enhancing genetic drift, and lowering overall population growth. We also revealed a surprising diversity in senescence patterns among the clonal strains, which indicates diverse underlying cell-intrinsic processes that shape these demographic patterns. Such diversity is surprising since all cells belong to the same bacteria species, E. coli, and still exhibit patterns such as classical senescence, non-senescence, or negative senescence. We end by discussing whether similar levels of non-genetic variability might be detected in other systems and close by stating the open questions how such heterogeneity is maintained, how it has evolved, and whether it is adaptive.

Data deposition

The processed image analysis data, R code, as well as the Leslie matrices will be archived at Dryad.org.
Dynamic species classification of microorganisms across time, abiotic and biotic environments — a sliding window approach
Authors: Pennekamp Frank , Griffiths Jason I. , Fronhofer Emanuel A. , Garnier Aurélie , Seymour Mathew , Altermatt Florian , Petchey Owen L.
Published: February 2017

1. Technological advances have greatly simplified to take and analyze digital images and videos, and ecologists increasingly use these techniques for trait, behavioral and taxonomic analyses. The development of techniques to automate biological measurements from the environment opens up new possibilities to infer species numbers, observe presence/absence patterns and recognize individuals based on audio-visual information.

2. Streams of quantitative data, such as temporal species abundances, are processed by machine learning (ML) algorithms into meaningful information. Machine learning approaches learn to distinguish classes (e.g., species) from observed quantitative features (phenotypes), and in-turn predict the distinguished classes in subsequent observations. However, in biological systems, the environment changes, often driving phenotypic changes in behaviour and morphology.

3. Here we describe a framework for classifying species under dynamic biotic and abiotic conditions using a novel sliding window approach. We train a random forest classifier on subsets of the data, covering restricted temporal, biotic and abiotic ranges (i.e. windows). We test our approach by applying the classification framework to experimental microbial communities where results were validated against manual classification. Individuals from one to six ciliate species were monitored over hundreds of generations in dozens of different species combinations and over a temperature gradient. We describe the steps of our classification pipeline and systematically explore the effects of the abiotic and biotic environments as well as temporal effects on classification success.

4. Differences in biotic and abiotic conditions caused simplistic classification approaches to be unsuccessful. In contrast, the sliding window approach allowed classification to be highly successful, because phenotypic differences driven by environmental change could be captured in the learning algorithm. Importantly, automatic classification showed comparable success compared to manual identifications.

5. Our framework allows for reliable classification even in dynamic environmental contexts, and may help to improve long-term monitoring of species from environmental samples. It therefore has application in disciplines with automatic enumeration and phenotyping of organisms such as eco-toxicology, ecology and evolutionary ecology, and broad-scale environmental monitoring.
Sex chromosome evolution, heterochiasmy and physiological QTL in the salmonid Brook CharrSalvelinus fontinalis
Authors: Sutherland Ben J. G. , Rico Ciro , Audet Céline , Bernatchez Louis
Published: February 2017

Whole genome duplication can have large impacts on genome evolution, and much remains unknown about these impacts. This includes the mechanisms of coping with a duplicated sex determination system and whether this has an impact on increasing the diversity of sex determination mechanisms. Other impacts include sexual conflict, where alleles having different optimums in each sex can result in sequestration of genes into non-recombining sex chromosomes. Sex chromosome development itself may involve sex-specific recombination rate (i.e. heterochiasmy), which is also poorly understood. Family Salmonidae is a model system for these phenomena, having undergone autotetraploidization and subsequent rediploidization in most of the genome at the base of the lineage. The salmonid master sex determining gene is known, and many species have non-homologous sex chromosomes, putatively due to transposition of this gene. In this study, we identify the sex chromosome of Brook CharrSalvelinus fontinalisand compare sex chromosome identities across the lineage (eight species, four genera). Although non-homology is frequent, homologous sex chromosomes and other consistencies are present in distantly related species, indicating probable convergence on specific sex and neo-sex chromosomes. We also characterize strong heterochiasmy with 2.7-fold more crossovers in maternal than paternal haplotypes with paternal crossovers biased to chromosome ends. When considering only rediploidized chromosomes, the overall heterochiasmy trend remains, although with only 1.9-fold more recombination in the female than the male. Y chromosome crossovers are restricted to a single end of the chromosome, and this chromosome contains a large interspecific inversion, although its status between males and females remains unknown. Finally, we identify QTL for 21 unique growth, reproductive and stress-related phenotypes to improve knowledge of the genetic architecture of these traits important to aquaculture and evolution.
Informing service responses to co-occurring complex needs
Authors: Stathopoulos Mary , Jenkinson Rebecca
Published: February 2017

Purpose

The sexual assault and alcohol and other drug (AOD) sectors have much in common in the context of clients presenting with histories of abuse and trauma. The Establishing the Connection project aimed to improve understanding of the complex intersections between sexual victimisation and AOD use, and to build the capacity of the sexual assault and AOD sectors in Victoria, Australia, to respond more effectively to the needs of affected individuals. The paper aims to discuss these issues.

Design/methodology/approach

Establishing the Connection involved a detailed literature review; face-to-face semi-structured interviews and an online quantitative survey with key stakeholders from the AOD and sexual assault sectors; and a cross-sector forum to bring together the practice knowledge and needs of both sectors.

Findings

Most practitioners and clinicians were aware of the interrelationship between sexual victimisation and AOD use, but many lacked access to resources, formal referral processes and pathways, or information about how the other sector worked – all tools which would assist them to respond to clients with complex co-occurring issues. Participants expressed enthusiasm for greater cross-sector communication and collaboration, but emphasised the need for sophisticated governance and resourcing responses from peak bodies and government departments.

Originality/value

The new knowledge generated by this research resulted in the development of shared practice guidelines to guide practice towards the identification, assessment, response and referral of clients with co-occurring sexual victimisation and AOD use issues. The authors hope that the momentum and goodwill built between the two sectors will be harnessed by policy to drive further collaborative partnerships into the future.
The LMRDA. Another labor law that benefits firms?
Authors: Abraham Steven E.
Published: February 2017

Purpose

This paper aims to examine the impact of the Labor Management Reporting and Disclosure Act (LMRDA). It is expected that returns would have increased in response to the law’s passage, as it imposed a number of restrictions on unionsvis-à-vismanagement and instituted many rules regulating unions’ internal affairs.

Design/methodology/approach

This paper uses event study methodology, which examines the impact of the law’s passage on the shareholder returns to the firms likely to have been affected by the law. Three different samples are used. Shareholder returns are examined on critical dates associated with the passage of the law to assess whether it benefited the firms in the samples.

Findings

Shareholder returns to firms expected to have been affected by the LMRDA fell in comparison to their competitors’ returns, indicating that the law was viewed by investors as being beneficial for firms. Presumably, the restrictions the law placed on unions were judged to be more important by investors than the improvement in unions’ image that might have resulted from the law, indicating that the law benefitted firms.

Originality/value

This is the first paper that has examined the impact of the LMRDA empirically to assess its impact on firms.
Developing high performance work system for Indian insurance industry
Authors: Garg Naval , Punia Bijender Kumar
Published: February 2017

Purpose

Modern age witnessed an exponential growth of high performance work practices (HPWPs) at workplace. This phenomenal increase in quest of performance excellence has fascinated both researchers and practitioners. The purpose of this paper is to develop a conceptual model of HPWPs for insurance companies of India.

Design/methodology/approach

A structured questionnaire comprising of 35 HPWPs with a five-point rating scale has been used. Model is based on two important paradigm of HR practices – employees’ awareness and perception for HPWPs. Factor analysis is followed by confirmatory factor analysis to build a model of HPWPs for insurance industry in India.

Findings

Of the 35 practices 17 get reduced to most applicable practices constituting high performance work system (HPWS) for insurance industry. The paper arrives at appropriate model of HPWPs.

Research limitations/implications

Paper has successfully developed model for insurance companies. Taking clue from findings, insurance practitioners could deal with various HR related challenges in their respective companies.

Originality/value

The paper uses primary data collected using structured questionnaire to develop HPWS.
Unethically keeping the change while demeaning the act
Authors: Yang Lifeng , Vitell Scott , Bush Victoria D.
Published: February 2017

Purpose

In this research, the authors aim to identify a situation when a consumer’s judgment of unethical behavior is not consistent with their intention to act ethically.

Design/methodology/approach

Across two studies, participants were asked to evaluate how ethical an actor’s behavior was when the actor knowingly kept surplus change from a distracted cashier. The identity of the actor was manipulated to be of either high or low similarity to the participants. The business where the distracted cashier worked for was described as either locally owned or a chain. Participant’s intended action in similar situation was assessed after their evaluation of how ethical/unethical the actor’s behavior was.

Findings

While participants generally find the actor’s behavior to be unethical, identity overlap between the participant and the actor is found to moderate how likely one is to emulate the actor’s behavior in a similar situation. Identity overlap is found to positively predict one’s likelihood to act like the actor in the scenarios. Whether the business was locally owned or a chain was not found to affect one’s ethical judgment or ethical intention.

Research limitations/implications

Identity overlap is found to positively predict one’s likelihood to act like the actor in the scenarios.

Practical implications

Whether the business was locally owned or a chain was not found to affect one’s ethical judgment nor ethical intention. While participants in general do show that they judge the actor’s behavior as unethical, identity overlap between the participant and the actor moderates how likely one is to act like the actor if put in the same scenario.

Social implications

The research suggests that consumers are more likely to act unethically when they identify with “similar” others, regardless of how unethical they consider that behavior to be.

Originality/value

This research suggests that even when consumers acknowledge that certain behavior against a business is unethical, their intention to engage in the unethical behavior may not be predicted by their judgment of how unethical the behavior is. Instead, consumers are likely to emulate unethical behavior of those whom they consider similar to themselves, regardless of how unethical they judge that behavior to be.