bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data
Authors: Koehorst Jasper J. , van Dam Jesse C. J. , van Heck Ruben G. A. , Saccenti Edoardo , dos Santos Vitor A. P. Martins , Suarez-Diez Maria , Schaap Peter J. 
Published: December 2016

AbstractPseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.
IP3 accumulation and/or inositol depletion: two downstream lithium’s effects that may mediate its behavioral and cellular changes
Authors: Sade Y , Toker L , Kara N Z , Einat H , Rapoport S , Moechars D , Berry G T , Bersudsky Y , Agam G 
Published: December 2016

AbstractLithium is the prototype mood stabilizer but its mechanism is still unresolved. Two hypotheses dominate—the consequences of lithium’s inhibition of inositol monophosphatase at therapeutically relevant concentrations (the ‘inositol depletion’ hypothesis), and of glycogen-synthase kinase-3. To further elaborate the inositol depletion hypothesis that did not decisively determine whether inositol depletion per se, or phosphoinositols accumulation induces the beneficial effects, we utilized knockout mice of either of two inositol metabolism-related genes—IMPA1 or SMIT1, both mimic several lithium’s behavioral and biochemical effects. We assessed in vivo, under non-agonist-stimulated conditions, 3H-inositol incorporation into brain phosphoinositols and phosphoinositides in wild-type, lithium-treated, IMPA1 and SMIT1 knockout mice. Lithium treatment increased frontal cortex and hippocampal phosphoinositols labeling by several fold, but decreased phosphoinositides labeling in the frontal cortex of the wild-type mice of the IMPA1 colony strain by ~50%. Inositol metabolites were differently affected by IMPA1 and SMIT1 knockout. Inositoltrisphosphate administered intracerebroventricularly affected bipolar-related behaviors and autophagy markers in a lithium-like manner. Namely, IP3 but not IP1 reduced the immobility time of wild-type mice in the forced swim test model of antidepressant action by 30%, an effect that was reversed by an antagonist of all three IP3 receptors; amphetamine-induced hyperlocomotion of wild-type mice (distance traveled) was 35% reduced by IP3 administration; IP3 administration increased hippocampal messenger RNA levels of Beclin-1 (required for autophagy execution) and hippocampal and frontal cortex protein levels ratio of Beclin-1/p62 by about threefold (p62 is degraded by autophagy). To conclude, lithium affects the phosphatidylinositol signaling system in two ways: depleting inositol, consequently decreasing phosphoinositides; elevating inositol monophosphate levels followed by phosphoinositols accumulation. Each or both may mediate lithium-induced behavior.
Increased plasma levels of circulating cell-free mitochondrial DNA in suicide attempters: associations with HPA-axis hyperactivity
Authors: Lindqvist D , Fernström J , Grudet C , Ljunggren L , Träskman-Bendz L , Ohlsson L , Westrin Å 
Published: December 2016

AbstractPreclinical data suggest that chronic stress may cause cellular damage and mitochondrial dysfunction, potentially leading to the release of mitochondrial DNA (mtDNA) into the bloodstream. Major depressive disorder has been associated with an increased amount of mtDNA in leukocytes from saliva samples and blood; however, no previous studies have measured plasma levels of free-circulating mtDNA in a clinical psychiatric sample. In this study, free circulating mtDNA was quantified in plasma samples from 37 suicide attempters, who had undergone a dexamethasone suppression test (DST), and 37 healthy controls. We hypothesized that free circulating mtDNA would be elevated in the suicide attempters and would be associated with hypothalamic–pituitary–adrenal (HPA)-axis hyperactivity. Suicide attempters had significantly higher plasma levels of free-circulating mtDNA compared with healthy controls at different time points (pre- and post-DST; allP-values<2.98E−12, Cohen’sdranging from 2.55 to 4.01). Pre-DST plasma levels of mtDNA were positively correlated with post-DST cortisol levels (rho=0.49,P<0.003). Suicide attempters may have elevated plasma levels of free-circulating mtDNA, which are related to impaired HPA-axis negative feedback. This peripheral index is consistent with an increased cellular or mitochondrial damage. The specific cells and tissues contributing to plasma levels of free-circulating mtDNA are not known, as is the specificity of this finding for suicide attempters. Future studies are needed in order to better understand the relevance of increased free-circulating mtDNA in relation to the pathophysiology underlying suicidal behavior and depression.
The gendered construction of reparations: an exploration of women’s exclusion from the Niger Delta reintegration processes
Authors: Michael Folami Olakunle 
Published: December 2016

AbstractThe Niger Delta is located in the South-south region of Nigeria. Oil exploration and exploitation by the multinational oil companies led to environmental degradation. The agitations among the inhabitants for environmental protection led to a protracted conflict between the Nigerian security forces and the militant groups in the region. Amnesty, disarmament, demobilization and reintegration (DDR) were adopted in the region to resolve the conflict by the government. The Niger Delta post-conflict DDR processes were gendered: exclusion of women from the peace processes was a major concern for peacebuilding actors and academics in the region. Men were significantly favoured in the DDR peacebuilding processes because they belonged to militant groups. The roles played by women in the conflict were not however recognised; these included roles in demonstrations, strikes, campaigns, lobbies, and as carers, nurses and cooks. Women have therefore sought redress in the peacebuilding processes. This study aims to identify roles played by men and women in the Niger Delta conflict. It examines methods of conflict resolution adopted in the region and also investigates the reason why women were largely excluded from the DDR processes. Recognition Theory is used in this study to examine the institutionalised norms that make gender inclusion in the Niger Delta peacebuilding processes problematic. Recognition theory considers equal treatment to be an important part of a just society, while distributive justice theorists believe that economic goods and wealth must be shared equally. This study was carried out in the Gbaramatu Kingdom, Niger Delta region, Nigeria, in three selected communities: Okerenkoko; Egwa; and Oporoza. A qualitative method involving in-depth interviews was used to collect data from 24 participants. I report that many men and women participated in the conflict but a small number of women (0.6%) were included in the DDR peacebuilding processes. I find that men and women demand that reparations should be considered in addition to the reintegration process that has been adopted in the Niger Delta. Furthermore, I find that apart from patriarchal culture, DDR operational norms only focus on security and not on human rights. I conclude that men’s and women’s rights could be recognized through the combination of DDR and reparations rights in the Niger Delta peacebuilding processes. This article is published as part of a collection on gender studies.
Exploring the effectiveness, efficiency and equity (3e’s) of research and research impact assessment
Authors: Hinrichs-Krapels Saba , Grant Jonathan 
Published: December 2016

AbstractThe allocation of research funding can benefit greatly from robust analysis of what has worked in research. In turn, these analyses can help advocacy initiatives and demonstrate accountability to taxpayers and donors. Capturing and mapping data on the inputs, processes, outputs, outcome and impact of research is crucial for these analyses. In this article we argue that the research community as a whole—including funders, researchers and administrators—is potentially in a position where it can assess or evaluate research not just according to academic outputs (production of knowledge), but also its outcomes and/or impact (effects on society). Using an exploratory framework that assesses effectiveness, efficiency and equity (3e’s) of research and research assessment both in terms of academic outputs and non-academic impact, we also argue that most assessments are primarily examining the effectiveness of research, as tools are not yet available to systematically assess research for its efficiency and equity. This article is published as part of a special issue on the future of research assessment.
Experimental evolution reveals hyperparasitic interactions among transposable elements
Authors: Robillard Émilie , Le Rouzic Arnaud , Zhang Zheng , Capy Pierre , Hua-Van Aurélie 
Published: December 2016

Significance
Transposable elements (TEs) are DNA sequences that colonize every genome and have a great impact on the genome evolution and structure. Here, we report experimental evolution results that confirm the intrinsic “selfish” properties of TEs in sexual populations. We also show how different kinds of copies from the same family strongly interfere: cheating nonautonomous copies parasitize autonomous ones, to the extent of endangering the survival of the whole TE family. These results nicely illustrate the “genome-ecology” analogy, according to which genome components are assimilated with interacting species in an ecosystem.
Covariation of axon initial segment location and dendritic tree normalizes the somatic action potential
Authors: Hamada Mustafa S. , Goethals Sarah , de Vries Sharon I. , Brette Romain , Kole Maarten H. P. 
Published: December 2016

Significance
Neurons generate highly reliable and temporally precise action potentials with a spatial onset in the axon initial segment. The axon initial segment location relative to the soma is, however, highly variable across neurons within the same cell class. Here, we experimentally and theoretically investigated the structure–function relationship of axon distances in neocortical pyramidal neurons. We discovered a scaling principle between the size of the dendritic tree and the axon distance supported by the cable properties and electrophysiological recordings. The work reveals that axons are not randomly positioned but covary with dendrites normalizing the somatic action potential in the face of diverse cellular morphologies.
UV-B photoreceptor-mediated protection of the photosynthetic machinery in
Chlamydomonas reinhardtii
Authors: Allorent Guillaume , Lefebvre-Legendre Linnka , Chappuis Richard , Kuntz Marcel , Truong Thuy B. , Niyogi Krishna K. , Ulm Roman , Goldschmidt-Clermont Michel 
Published: December 2016

Significance
Life on earth largely depends on the capture of light energy by plants through photosynthesis. Light is essential, but excess light is dangerous. Energy dissipation as heat is a major mechanism induced to protect the photosynthetic machinery. We report that UV-B perception by a specific photoreceptor in the nucleocytosolic compartment leads to protection of the photosynthetic machinery in the chloroplast of a green alga. The underlying mechanism is markedly different from the response to high light. UV-B photoreceptor-mediated signaling activates a safety valve, allowing the release of the excess energy as heat, helping the algae to cope with too much light energy.
The plant component of an Acheulian diet at Gesher Benot Ya‘aqov, Israel
Authors: Melamed Yoel , Kislev Mordechai E. , Geffen Eli , Lev-Yadun Simcha , Goren-Inbar Naama 
Published: December 2016

Significance
Our knowledge of the diet of early hominins derives mainly from animal skeletal remains found in archaeological sites, leading to a bias toward a protein-based diet. We report on the earliest known archive of food plants found in the superimposed Acheulian sites excavated at Gesher Benot Ya‘aqov, Israel. These remains, some 780,000 y old, comprise 55 taxa, including nuts, fruits, seeds, vegetables, and plants producing underground storage organs. They reflect a varied plant diet, staple plant foods, seasonality, and hominins’ environmental knowledge and use of fire in food processing. Our results change previous notions of paleo diet and shed light on hominin abilities to adjust to new environments and exploit different flora, facilitating population diffusion, survival, and colonization beyond Africa.
Reprogramming cell fate with a genome-scale library of artificial transcription factors
Authors: Eguchi Asuka , Wleklinski Matthew J. , Spurgat Mackenzie C. , Heiderscheit Evan A. , Kropornicka Anna S. , Vu Catherine K. , Bhimsaria Devesh , Swanson Scott A. , Stewart Ron , Ramanathan Parameswaran , Kamp Timothy J. , Slukvin Igor , Thomson James A. , Dutton James R. , Ansari Aseem Z. 
Published: December 2016

Significance
The ability to convert cells into desired cell types enables tissue engineering, disease modeling, and regenerative medicine; however, methods to generate desired cell types remain difficult, uncertain, and laborious. We developed a strategy to screen gene regulatory elements on a genome scale to discover paths that trigger cell fate changes. The proteins used in this study cooperatively bind DNA and activate genes in a synergistic manner. Subsequent identification of transcriptional networks does not depend on prior knowledge of specific regulators important in the biological system being tested. This powerful forward genetic approach enables direct cell state conversions as well as other challenging manipulations of cell fate.
Emergent oscillations assist obstacle negotiation during ant cooperative transport
Authors: Gelblum Aviram , Pinkoviezky Itai , Fonio Ehud , Gov Nir S. , Feinerman Ofer 
Published: December 2016

Significance
When ants that cooperatively carry large food items encounter obstacles, they switch their collective motion from radial, nest-bound movement to nearly deterministic, tangential oscillations that facilitate obstacle circumvention. This oscillatory motion cannot be explained by a “wisdom-of-the-crowds” model in which all ants are informed of the direction to the nest and the collective motion reflects an average effort. Rather, oscillations emerge due to two, often conflicting, forces: Some ants pull the load toward the nest whereas others align their pull with the momentary direction of motion. Interestingly, these two forces suffice to generate both nest-bound and oscillatory motion without any requirement that individual ants directly sense the obstacle. This is an example of emergent problem solving at the group-level scale.
Epithelial self-healing is recapitulated by a 3D biomimetic E-cadherin junction
Authors: Cohen Daniel J. , Gloerich Martijn , Nelson W. James 
Published: December 2016

Significance
Injured tissues can self-heal. The healing process requires that tissue first migrate into the injury site and, upon collision with other expanding tissue fronts, switch from migration to cell–cell adhesion to seal the injury mechanically. The minimum signal inducing this switch is unknown due to the complexity of natural healing interfaces. We made a 3D barrier that mimicked the edge of a tissue and induced healing tissues to collide with it. When we coated the barrier with E-cadherin, a key cell–cell adhesion protein, epithelial tissues behaved as if the barrier were a tissue and stably healed against the barrier. This work reveals a key role for E-cadherin in self-healing, and an alternate way to integrate objects into tissue.
Spop promotes skeletal development and homeostasis by positively regulating Ihh signaling
Authors: Cai Hongchen , Liu Aimin 
Published: December 2016

Significance
Skeletal diseases place a huge burden on patients and society, and yet their genetic basis remains poorly understood. In this article, we identify Speckle-type POZ protein (Spop) as a regulator of skeletal development, loss of which leads to shorter digit bones and lower bone density. We also show that, in striking contrast to the current dogma positing Spop as a negative regulator of Hedgehog (Hh) signaling, Spop regulates skeletal development by promoting Indian Hedgehog (Ihh) signaling. Therefore, our work represents an important conceptual advance in the understanding of Ihh signaling and skeletal development and provides a potential new target for the diagnosis and intervention of bone diseases such as osteoporosis.
Analysis of 138 pathogenic mutations in presenilin-1 on the in vitro production of Aβ42 and Aβ40 peptides by γ-secretase
Authors: Sun Linfeng , Zhou Rui , Yang Guanghui , Shi Yigong 
Published: December 2016

Significance
Alzheimer’s disease (AD) is the most common form of dementia, but the cause of AD remains poorly understood. Using highly purified recombinant γ-secretase, we examined the effect of 138 AD-derived presenilin-1 (PS1) mutations on the production of β-amyloid peptides (Aβ42 and Aβ40). These 138 mutations cover virtually all AD-targeted amino acids in PS1. Our results reveal no significant correlation between the Aβ42/Aβ40 ratio produced by a γ-secretase variant with a specific PS1 mutation and the mean age at onset of patients carrying this mutation. The comprehensive characterization of pathogenic PS1 mutations serves as a valuable resource for the analysis of γ-secretase activities and AD pathogenesis.
Vestibular schwannoma diagnosis
Authors: Di Giustino Fabio , Pecci Rudi , Vannucchi Paolo 
Published: December 2016

Objective:
Gadolinium-enhanced Magnetic Resonance Imaging (MRI) constitutes the gold standard technique in detecting vestibular schwannomas (VS). The investigation aimed to verify whether it is possible to reach high sensitivity in the early diagnosis of VS, combining Auditory Brainstem Responses (ABRs) with other bedside and electrophysiological neuro-otological tests.

Methods:
Fifty-five patients suffering from VS smaller than 2 cm in major diameter, detected by gadolinium-enhanced MRI, were submitted to: Pure Tone Audiometry, Speech Audiometry, Vestibular Examination, Caloric Test, Head Shaking Test (HST), Head Impulse Test (HIT), Hyperventilation Test (HT), Vibration Test (VT), ABRs, Cervical Vestibular Evoked Myogenic Potentials (cVEMPs).

Results:
HST showed pathological results in 34 cases (61.82% sensitivity), HIT in 29 (52.73% sensitivity), HT in 38 (69.09% sensitivity), VT in 27 (49.1% sensitivity), ABRs in 35 (in 12 cases this examination was not conducted because of the high pure tone hearing threshold level, 81.39% sensitivity), cVEMPs in 34 (61.82% sensitivity). If we consider only symptomatic patients (54 out of 55), in all cases we observed at least one pathological test (100% sensitivity).

Conclusion:
In patients suffering from unilateral or asymmetrical sensorineural hearing loss, we suggest the use of bedside and electrophysiological tests in order to reduce the use of imaging to high suspicion cases of retrocochlear disease, lowering costs and waiting lists.
Measuring the impact of illness perception on NHS audiology service usage in presbycusis patients – a feasibility study
Authors: Wolber Lisa E. , Pryce Helen 
Published: December 2016

Objective:
Coping behaviour in adult hearing loss is still not well understood. Despite the high prevalence of hearing loss in those over 65, many people do not seek help for hearing loss. The common sense model of illness perceptions suggests that illness perceptions are a strong predictor of adapted coping behaviours, including help-seeking and take-up of treatments.
This study aimed to determine the feasibility of using the brief illness perceptions questionnaire (bIPQ) to measure the impact of illness perception in predicting usage of NHS audiology services.

Study design:
Twenty-four volunteers were recruited from a standard NHS audiology outpatient clinic and illness perception was measured using the bIPQ. Two different recruitment strategies were explored and compared in terms of recruitment and retention rates. Comprehensibility of the questionnaire was assessed by Think Aloud Analysis in a subset of participants, while possible risks and burdens were monitored in structured telephone interviews.

Results:
The questionnaire is a comprehensive and quick tool to measure individual illness perception at minimal cost. We suggested minor adaptations of three questionnaire items to increase comprehension. Participants preferred to complete the questionnaire after their appointment at the clinic facilities rather than at home prior to their hearing assessment appointment. There were no identified risks or burdens to participants in this study.

Conclusions:
This approach met our criteria for feasibility. Understanding the impact of illness perception on patients’ coping behaviour in presbycusis could improve treatment outcomes and increase patient satisfaction, while promoting a more efficient and individualized audiology service.
3D impurity inspection of cylindrical transparent containers
Authors: Kragh Mikkel , Bjerge Kim , Ahrendt Peter 
Published: December 2016

Abstract
This paper presents a method for automatically detecting and three-dimensionally positioning particles based on sequences of 2D images of rotating cylindrical transparent containers. The method can be used in the manufacturing industry by distinguishing between particles residing inside or outside a closed container. A foreign particle on the inside is a cause of rejection, whereas a particle on the outside might represent harmless dirt. The proposed method detects, tracks and positions particles and classifies containers accordingly as either rejected or accepted. Experimental results have shown an accuracy of 85% on a test set of 20 containers and an average execution time per container of 1 s.
Co-pyrolysis of rice straw and polypropylene using fixed-bed pyrolyzer
Authors: Izzatie N I , Basha M H , Uemura Y , Mazlan M A , Hashim M S M , Amin N A M , Hamid M F 
Published: December 2016

Abstract
The present work encompasses the impact of temperature (450, 500, 550, 600 °C) on the properties of pyrolysis oil and on other product yield for the co-pyrolysis of Polypropylene (PP) plastics and rice straw. Co-pyrolysis of PP plastic and rice straw were conducted in a fixed-bed drop type pyrolyzer under an inert condition to attain maximum oil yield. Physically, the pyrolysis oil is dark-brown in colour with free flowing and has a strong acrid smell. Copyrolysis between these typically obtained in maximum pyrolysis oil yields up to 69% by ratio 1:1 at a maximum temperature of 550 °C. From the maximum yield of pyrolysis oil, characterization of pyrolysis product and effect of biomass type of the composition were evaluated. Pyrolysis oil contains a high water content of 66.137 wt.%. Furfural, 2- methylnaphthalene, tetrahydrofuran (THF), toluene and acetaldehyde were the major organic compounds found in pyrolysis oil of rice straw mixed with PP. Bio-char collected from co-pyrolysis of rice straw mixed with PP plastic has high calorific value of 21.190 kJ/g and also carbon content with 59.02 wt.% and could contribute to high heating value. The non-condensable gases consist of hydrogen, carbon monoxide, and methane as the major gas components.