bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct changes in morphometric networks in aging versus Alzheimer’s disease dementia
Authors: Binette Alexa Pichet , Gonneaud Julie , Vogel Jacob W. , La Joie Renaud , Rosa-Neto Pedro , Collins D. Louis , Poirier Judes , Breitner John C.S. , Villeneuve Sylvia , Vachon-Presseau Etienne ,   Alzheimer’s Disease Neuroimaging Initiative,   PREVENT-AD Research Group
Published: April 2019

AbstractBrain gray matter (GM) morphometric changes are prevalent in both aging and Alzheimers disease (AD), though disentangling these two processes has proved challenging. Using independent component analysis, we derived morphometric networks from a large, multi-cohort dataset, and investigated how GM volume within these networks differs in young adulthood, old adulthood, and AD. Aging and AD contributed additive effects on GM loss in nearly all networks, except frontal lobe networks, where GM reductions were more specific to aging. While no networks show GM loss highly specific to AD, a higher degree of variability in the whole-brain pattern of GM volume characterized AD only. Preservation of the whole-brain GM pattern in cognitively normal older adults was related to better cognition and lower risk of developing cognitive impairment. These results suggest both aging and AD involve widespread atrophy, but that cognitive impairment is uniquely associated with disruption of morphometric organization.
Homeostatic mechanisms may shape the type and duration of oscillatory modulation
Authors: Peterson Erik J. , Voytek Bradley 
Published: April 2019

Neural oscillations are observed ubiquitously in the mammalian brain, but their stability is known to be rather variable. Some oscillations are tonic and last for seconds or even minutes. Other oscillations appear as unstable bursts. Likewise, some oscillations rely on excitatory AMPAergic synapses, but others are GABAergic and inhibitory. Why this diversity exists is not clear. We hypothesized Ca 2+ -dependent homeostasis could be important in finding an explanation. We tested this hypothesis in a highly simplified model of hippocampal neurons. In this model homeostasis profoundly alters the modulatory effect of neural oscillations. Under homeostasis, tonic AMPAergic oscillations actually decrease excitability and desynchronize firing. Tonic oscillations that are synaptically GABAergic–like those in real hippocampus–don’t provoke a homeostatic response, however. If our simple model is correct, homeostasis can explain why the theta rhythm in the hippocampus is synaptically inhibitory: GABA has little to no intrinsic homeostatic response, and so can preserve the pyramidal cell’s natural dynamic range. Based on these results we can also speculate that homeostasis may explain why AMPAergic oscillations in cortex, and hippocampus, often appear as bursts. Bursts do not interact with the slow homeostatic time constant, and so retain their normal excitatory effect.New and NoteworthyThe intricate interplay of neuromodulators, like acetylcholine, with homeostasis is well known. The interplay between oscillatory modulation and homeostasis is not. We studied oscillatory modulation and homeostasis for the first time using a simplified model of hippocampus. We report a paradoxical result: Ca-mediated homeostasis causes AMPAergic oscillations to become effectively inhibitory. This result, along with other new observations, means homeostasis might be just as complex and important for oscillations as it is for other neuromodulators.
The histidine kinase PdtaS is a cyclic di-GMP binding metabolic sensor that controls mycobacterial adaptation to nutrient deprivation
Authors: Hariharan Vignesh Narayan , Thakur Chandrani , Singh Albel , Gopinathan Renu , Singh Devendra Pratap , Sankhe Gaurav , Chandra Nagasuma , Bhatt Apoorva , Saini Deepak Kumar 
Published: April 2019

AbstractCell signalling relies on second messengers to transduce signals from the sensory apparatus to downstream components of the signalling pathway. In bacteria, one of the most important and ubiquitous second messengers is the small molecule cyclic diguanosine monophosphate (c-di-GMP). While the biosynthesis, degradation and regulatory pathways controlled by c-di-GMP are well characterized, the mechanisms through which c-di-GMP controls these processes is not completely understood. Here we present the first report of a c-di-GMP regulated sensor histidine kinase previously named PdtaS (Rv3220c), which binds to c-di-GMP at sub-micromolar concentrations, subsequently perturbing signalling of the PdtaS-PdtaR (Rv1626) two component system. Aided by biochemical analysis, molecular docking and structural modelling, we have characterized the binding site of c-di-GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in M. smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. Perturbation of the c-di-GMP-PdtaS-PdtaR axis results in a cascade of cellular changes recorded by a multi-parametric systems approach of transcriptomics, unbiased metabolomics and lipid analyses.One-sentence summaryThe universal bacterial second messenger cyclic di-GMP controls the mycobacterial nutrient stress response
Microclimate and larval habitat density predict adult Aedes albopictus abundance in urban areas
Authors: Evans Michelle V. , Hintz Carl W. , Jones Lindsey , Shiau Justine , Solano Nicole , Drake John M. , Murdock Courtney C. 
Published: April 2019

ABSTRACTThe Asian tiger mosquito, Aedes albopictus, transmits several arboviruses of public health importance, including chikungunya and Zika. Since its introduction to the United States in 1985, the species has invaded over forty states, including temperate areas not previously at risk of Aedes-transmitted arboviruses. Mathematical models incorporate climatic variables in predictions of site-specific Ae. albopictus abundances to identify human populations at risk of disease. However, these models rely on coarse resolutions of environmental data that may not accurately represent the climatic profile experienced by mosquitoes in the field, particularly in climatically-heterogeneous urban areas. In this study, we pair field surveys of larval and adult Ae. albopictus mosquitoes with site-specific microclimate data across a range of land use types to investigate the relationships between microclimate, density of larval habitat, and adult mosquito abundance and determine whether these relationships change across an urban gradient. We find no evidence for a difference in larval habitat density or adult abundance between rural, suburban, and urban land classes. Adult abundance increases with increasing larval habitat density, which itself is dependent on microclimate. Adult abundance is strongly explained by microclimate variables, demonstrating that theoretically derived, lab-parameterized relationships in ectotherm physiology apply to the field. Our results provide support for the continued use of temperature-dependent models to predict Ae. albopictus abundance in urban areas.
A Cys2/His2 zinc finger protein acts as a repressor of gibberellins biosynthesis by regulating SD1/OsGA20ox2 in rice (Oryza sativa L.)
Authors: Duan Min , Ke Xiao-Juan , Lan Hong-Xia , Yuan Xi , Huang Peng , Xu En-Shun , Gao Xiu-Ying , Wang Ru-Qin , Tang Hai-Juan , Zhang Hong-Sheng , Huang Ji 
Published: April 2019

AbstractGibberellins (GAs) play important roles in the regulation of plant growth and development. The green evolution geneSD1encoding gibberellin 20-oxidase 2 (GA20ox2) has been widely used in modern rice breeding. However, the molecular mechanism of howSD1/OsGA20ox2expression is regulated remains unclear. Here we report a Cys2/His2 zinc finger protein ZFP207 acting as a transcriptional repressor ofOsGA20ox2.ZFP207was mainly accumulated in young tissues and more specifically in culm nodes.ZFP207-overexpression (ZFP207OE) plants displayed semi-dwarfism phenotype and small grains by modulating cell length. RNA interference ofZFP207caused higher plant and longer grains. The endogenous bioactive GA levels were significantly reduced inZFP207OEplants and application of exogenous GA3rescued the semi-dwarf phenotype. Thein vivoandin vitrostudies showed that ZFP207 repressed the expression ofOsGA20ox2via binding to its promoter region. Together, ZFP207 acts as a transcriptional repressor of gibberellins biosynthesis and it may play a critical role in plant growth and development through fine-tuning GA biosynthesis in rice.
Targeted transcript quantification in single disseminated cancer cells after whole transcriptome amplification
Authors: Durst Franziska C. , Grujovic Ana , Ganser Iris , Hoffmann Martin , Ugocsai Peter , Klein Christoph A. , Czyż Zbigniew T. 
Published: April 2019

AbstractGene expression analysis of rare or heterogeneous cell populations such as disseminated cancer cells (DCCs) requires a sensitive method allowing reliable analysis of single cells. Therefore, we developed and explored the feasibility of a quantitative PCR (qPCR) assay to analyze single-cell cDNA pre-amplified using a previously established whole transcriptome amplification (WTA) protocol. We carefully selected and optimized multiple steps of the protocol, e.g. re-amplification of WTA products, quantification of amplified cDNA yields and final qPCR quantification, to identify the most reliable and accurate workflow for quantitation of gene expression of the ERBB2 gene in DCCs. We found that absolute quantification outperforms relative quantification. We then validated the performance of our method on single cells of established breast cancer cell lines displaying distinct levels of HER2 protein. The different protein levels were faithfully reflected by transcript expression across the tested cell lines thereby proving the accuracy of our approach. Finally, we applied our method on patient-derived breast cancer DCCs. Here, we were able to measure ERBB2 expression levels in all HER2-positive DCCs. In addition, we could detect ERBB2 transcript expression even in HER2-negative DCCs, suggesting post-transcriptional mechanisms of HER2 loss in anti-HER2-treated DCCs. In summary, we developed a reliable single-cell qPCR assay applicable to measure distinct levels of ERBB2 in DCCs.
Environmental reporting practices and performance of timber firms in Ghana
Authors: Agyei Samuel Kwaku , Yankey Benjamin 
Published: April 2019

Purpose
The purpose of this paper is to assess the motivations of timber firms in Ghana to undertake environmental accounting and reporting (EAR) and the perceived benefits from it.

Design/methodology/approach
Survey method involving primary data from a census of 13 timber firms in Kumasi (Ghana) and descriptive statistics including Kendall’s coefficient were used to analyze the perceptions of practitioners on EAR.

Findings
The study offered support for the political economy, legitimacy and stakeholder theories generally applied to the study of EAR. Specifically, the study concluded that EAR is common to timber firms in Ghana. Pressure from government, media, shareholders’ influence and the existence of environmental committee or department in the company are perceived to influence timber firms’ level of environmental disclosure. Meanwhile, perceived benefits from EAR include fostering cordial relationship between timber firms and the society, preventing government fines and improving firm reputation.

Research limitations/implications
The presence of biases in the responses of survey method studies can be difficult to eliminate. However, given the benefits associated with getting practitioners views on EAR and the reliability/validity procedures that the instruments and respondents were subjected to, this weakness was reduced to its barest minimum.

Practical implications
The study recommends that governments should adopt green tax policy to encourage EAR while regulatory bodies make EAR mandatory.

Originality/value
This study contributes to the discussion on EAR from the perspective of practitioners in the timber industry of Ghana, which has been neglected in previous studies.
Supervisors’ experience of delivering individual clinical supervision to qualified therapists: a meta-ethnographic synthesis
Authors: Forshaw Gemma , Sabin-Farrell Rachel , Schröder Thomas 
Published: April 2019

Purpose
The purpose of this paper is to systematically identify, appraise and synthesise qualitative literature exploring the experience, both positive and negative, of clinical supervision from the supervisor’s perspective.

Design/methodology/approach
A systematic search of three databases, grey literature, reference lists and citations was conducted. Six articles met the inclusion criteria and their quality was critically appraised by using a modified version of the Critical Appraisal Skills Programme tool. Data extracted from the articles were synthesised using meta-ethnography.

Findings
Four key themes were identified: experiencing difficulties in clinical supervision, responsibility, similarities to therapy and capabilities as a supervisor. These demonstrated that the role of a supervisor has the potential to be both beneficial and harmful to personal and professional development.

Research limitations/implications
The quality of the studies was variable. Further research is required to explore how supervisors manage difficult experiences to ensure personal development and growth.

Practical implications
Clinical implications include the need for employers to consider the additional pressure associated with providing clinical supervision and to ensure that appropriate support is available. Results complement previous research on the bi-directionality of parallel process in clinical supervision.

Originality/value
This review presents an original synthesis of the supervisor’s experience of delivering clinical supervision to qualified therapists. This is achieved by utilising a systematic methodology and appraising the quality of the studies included. The review highlights how the effects of clinical supervision are not limited to the supervisee, but also experienced by the supervisor. The competing demands and responsibilities associated with clinical supervision impact upon the supervisor’s experience, both positively and negatively. When beneficial, delivering clinical supervision can lead to personal and professional growth in addition to the acquisition of new skills.
“I have more support around me to be able to change”: a qualitative exploration of probationers’ and parolees’ experiences living in sober living houses
Authors: DeGuzman Rebecca , Korcha Rachael , Polcin Douglas 
Published: April 2019

Purpose
Persons in the USA who are incarcerated for drug offenses are increasingly being released into the community as a way to decrease prison and jail overcrowding. One challenge is finding housing that supports compliance with probation and parole requirements, which often includes abstinence from drugs and alcohol. Sober living houses (SLHs) are alcohol- and drug-free living environments that are increasingly being used as housing options for probationers and parolees. Although a few studies have reported favorable outcomes for residents of SLHs, little is known about resident experiences or the factors that are experienced as helpful or counterproductive. The paper aims to discuss this issue.

Design/methodology/approach
This study conducted qualitative interviews with 28 SLH residents on probation or parole to understand their experiences living in the houses, aspects of the houses that facilitated recovery, ways residence in an SLH affected compliance with probation and parole, and ways the houses addressed HIV risk, a widespread problem among this population. Interviews were audiotaped and coded for dominant themes.

Findings
Study participants identified housing as a critically important need after incarceration. For residents nearing the end of their stay in the SLHs, there was significant concern about where they might live after they left. Residents emphasized that shared experiences and goals, consistent enforcement of rules (especially the requirement of abstinence) and encouragement from probation and parole officers as particularly helpful. There was very little focus in HIV issues, even though risk behaviors were fairly common. For some residents, inconsistent enforcement of house rules was experienced as highly problematic. Research is needed to identify the organizational and operational procedures that enhance factors experienced as helpful.

Research limitations/implications
Data for this study are self-reported views and experiences. Therefore, the study may not tap into a variety of reasons for resident experiences. In addition, the data set was small (n=28) and limited to one city in the USA (Los Angeles), so generalization of results might be limited. However, SLHs represent an important housing option for criminal justice involved persons and knowledge about resident experiences can help guide organization and operation of houses and identify areas for further research.

Originality/value
This paper is the first to document the views and experiences of persons on probation or parole who reside in sober living recovery houses. These data can be used by SLH operators to develop houses that are responsive to factors experienced as helpful and counterproductive. The significance of this paper is evident in the trend toward decreasing incarceration in the USA of persons convicted of drug offenses and the need for alcohol- and drug-free alternative living environments.
A pilin chaperone required for the expression of electrically conductive Geobacter sulfurreducens pili
Authors: Liu Xing , Zhan Ji , Jing Xianyue , Zhou Shungui , Lovley Derek R. 
Published: April 2019

SummaryMechanisms controlling the expression of the electrically conductive pili (e‐pili) of Geobacter species are of interest because of the important role of e‐pili in diverse biogeochemical processes, anaerobic digestion and electromicrobiological applications. We investigated the function of the protein, designated Spc (short pilin chaperone), encoded by the gene immediately downstream from the gene for PilA, the monomer that assembles into e‐pili. Multiple lines of evidence suggest that Spc forms an oligomer that is associated with the inner membrane. Mutating the start codon of spc to prevent translation increased the transcript abundance of pilA but greatly diminished the abundance of PilA, and e‐pili could no longer be detected. Cross‐linking, protein capture and two‐hybrid studies demonstrated that Spc and PilA interacted. Two sites in PilA for electrostatic interaction with Spc were identified. The results demonstrate that Spc is required for PilA stability prior to incorporation into e‐pili, suggesting that Spc has a chaperone function that may be specific to the relatively short PilA monomers that assemble into e‐pili. These results are important for identifying microorganisms likely to express e‐pili from (meta)genomic data and for the construction of microbial strains expressing e‐pili.
Sequence capture across large phylogenetic scales by using pooled PCR‐generated baits: A case study of Lepidoptera
Authors: Zhang Yuan , Deng Shaohong , Liang Dan , Zhang Peng 
Published: April 2019

AbstractSequence capture across large phylogenetic scales is not easy because hybridization capture is only effective when the genetic distance between the bait and target is small. Here, we propose a simple but effective strategy to tackle this issue: pooling DNA from a number of selected representative species of different clades to prepare PCR‐generated baits to minimize the genetic distance between the bait and target. To demonstrate the utility of this strategy, we newly developed a set of universal nuclear markers (including 94 nuclear protein‐coding genes) for Lepidoptera, a superdiverse insect group. We used a DNA pool from six lepidopteran species (representing six superfamilies) to prepare PCR baits for the 94 markers. These homemade PCR baits were used to capture sequence data from 43 species of 17 lepidopteran families, and 94% of the target loci were recovered. We constructed two data sets from the obtained data (one containing ~90 kb target coding sequences and the other containing ~120 kb target + flanking coding sequences). Both data sets yielded highly similar and well‐resolved trees with 90% of nodes having >95% bootstrap support. Our capture experiment indicated that using DNA mixtures pooled from different clade‐representative species of Lepidoptera to prepare PCR baits can reliably capture a large number of targeted nuclear markers across different Lepidoptera lineages. We hope that this newly developed nuclear marker set will serve as a new phylogenetic tool for Lepidoptera phylogenetics, and the PCR bait preparation strategy can facilitate the application of sequence capture techniques by researchers to accelerate data collection.
Vegetation, land, and wood use at the sites of Bat and Al‐Khashbah in Oman (fourth–third millennium BC)
Authors: Deckers Katleen , Döpper Stephanie , Schmidt Conrad 
Published: April 2019

AbstractAbout 4200 charcoal fragments have been identified from the fourth‐ to third‐millennium BC archaeological sites of Bat and Al‐Khashbah in order to gain an understanding of plant resources available at the sites. Acacia sp., Ziziphus sp., and Tamarix sp. were the main taxa identified at both sites and indicate a similar vegetation composition as today. Phoenix sp. (date palm) charcoal also has been found at both sites. Whereas the cultivation of date palm for the 2700–2300 BC layers from Bat was likely, given other circumstantial evidence (i.e. local cereal cultivation and floodwater irrigation), it is unclear whether date palm was cultivated at Al‐Khashbah. Especially for the older periods (3300–2700 BC) it is possible that nomadic pastoralists were exploiting and/or managing wild date palms. The find of Avicennia marina at Al‐Khashbah indicates long‐distance contacts with the coast.
Incidence of chronic pain 6 y after major trauma
Authors: Kolstadbraaten Knut Magne , Spreng Ulrich Johannes , Wisloeff‐Aase Kristin , Gaarder Christine , Naess Paal Aksel , Raeder Johan 
Published: April 2019

BackgroundLife saving measures is the main focus in the initial treatment of major trauma. In surviving patients, chronic pain may be a serious problem, but the long term incidence and potential risk factors are not very well studied.MethodsAll adult trauma patients included in the institutional trauma registry in 2007 were assessed for eligibility. Among exclusion criteria were: Injury Severity Score < 9, endotracheal intubation before or during admission, spinal cord lesion, known chronic drug or substance abuse, major surgery within 3 h after admission. A patient questionnaire was sent out 6 y after injury focusing on frequency and intensity of pain. A subgroup analysis was done in patients with thoracic injuries, comparing patients with epidural analgesia (EDA) and patients without.ResultsSixty‐eight patients were included in the study. Sixty‐nine percent reported pain 6 y after injury and 24% had severe pain. The severity of the injury was a risk factor for development of chronic pain, whereas pain during initial hospital stay was not. In patients with thoracic injuries there was no correlation between initial treatment with EDA and decreased incidence of chronic pain, however patient numbers were small. Opioids were the main analgesics used initially; no patients received non‐steroidal anti‐inflammatory drugs or peripheral nerve blocks during the first 24 h.ConclusionTwo thirds of the trauma patients had chronic pain 6 y after injury and one out of four had severe pain. The initial pain treatment was focused on opioids.