bluuebunny/crossref_metadata_2025 huggingface dataset:
Biomedical X-ray imaging enabled by carbon nanotube X-ray sources
Authors: Cao Guohua
Published: September 2018

Although discovered more than 100 years ago, X-ray source technology has evolved rather slowly. The recent invention of the carbon nanotube (CNT) X-ray source technology holds great promise to revolutionize the field of biomedical X-ray imaging. CNT X-ray sources have been successfully adapted to several biomedical imaging applications including dynamic micro-CT of small animals and stationary breast tomosynthesis of breast cancers. Yet their more important biomedical imaging applications still lie ahead in the future, with the development of stationary multi-source CT as a noteworthy example.
Ultraviolet photodissociation dynamics of m-bromofluorobenzene at around 240 nm
Authors: Chen Min , Liang Hao , He Chao , Zhao Dong-feng , Chen Yang
Published: September 2018

The photodissociation dynamics of m-bromofluorobenzene has been experimentally investigated at around 240 nm using the DC-slice velocity map imaging technique. The kinetic energy release spectra and the recoiling angular distributions of fragmented Br(2P3/2) and Br(2P1/2) atoms from photodissociation of m-bromofluorobenzene have been measured at different photolysis wavelengths around 240 nm. The experimental results indicate that two dissociation pathways via (pre-)dissociation of the two low-lying 1ππ* excited states dominate the production process of the ground state Br(2P3/2) atoms. Because of the weak spin-orbit coupling effect among the low-lying triplet and singlet states, the spin-orbit excited Br(2P1/2) atoms are mainly produced via singlet-triplet state coupling in the dissociation step. The similarity between the present results and that recently reported for o-bromofluorobenzene indicates that the substitution position of the fluorine atom does not significantly affect the UV photodissociation dynamics of bromofluorobenzenes.
Photoinduced decomposition of formaldehyde on rutile TiO2(100)-(1×1)
Authors: Chen Xiao , Li Fang-liang , Guo Qing , Dai Dong-xu , Yang Xue-ming
Published: September 2018

We have investigated the photoinduced decomposition of formaldehyde (CH2O) on a rutile TiO2(100)-(1×1) surface at 355 nm using temperature-programmed desorption. Products, formate (HCOO−), methyl radical (CH3·), ethylene (C2H4), and methanol (CH3OH) have been detected. The initial step in the decomposition of CH2O on the rutile TiO2(100)-(1×1) surface is the formation of a dioxymethylene intermediate in which the carbonyl O atom of CH2O is bound to a Ti atom at the five-fold-coordinated Ti4+ (Ti5c) site and its carbonyl C atom bound to a nearby bridge-bonded oxygen (Ob) atom, respectively. During 355 nm irradiation, the dioxymethylene intermediate can transfer an H atom to the Ob atom, thus forming HCOO− directly, which is considered as the main reaction channel. In addition, the dioxymethylene intermediate can also transfer methylene to the Ob row and break the C−O bond, thus leaving the original carbonyl O atom at the Ti5c site. After the transfer of methylene, several pathways to products are available. Thus, we have found that Ob atoms are intimately involved in the photoinduced decomposition of CH2O on the rutile TiO2(100)-(1×1) surface.
Exact generator and its high order expansions in time-convolutionless generalized master equation: Applications to spin-boson model and excitation energy transfer
Authors: Liu Yan-ying , Yan Ya-ming , Xu Meng , Song Kai , Shi Qiang
Published: September 2018

The time-convolutionless (TCL) quantum master equation provides a powerful tool to simulate reduced dynamics of a quantum system coupled to a bath. The key quantity in the TCL master equation is the so-called kernel or generator, which describes effects of the bath degrees of freedom. Since the exact TCL generators are usually hard to calculate analytically, most applications of the TCL generalized master equation have relied on approximate generators using second and fourth order perturbative expansions. By using the hierarchical equation of motion (HEOM) and extended HEOM methods, we present a new approach to calculating the exact TCL generator and its high order perturbative expansions. The new approach is applied to the spin-boson model with different sets of parameters, to investigate the convergence of the high order expansions of the TCL generator. We also discuss circumstances where the exact TCL generator becomes singular for the spin-boson model, and a model of excitation energy transfer in the Fenna-Matthews-Olson complex.
Clustering algorithms to analyze molecular dynamics simulation trajectories for complex chemical and biological systems
Authors: Peng Jun-hui , Wang Wei , Yu Ye-qing , Gu Han-lin , Huang Xuhui
Published: September 2018

Molecular dynamics (MD) simulation has become a powerful tool to investigate the structure-function relationship of proteins and other biological macromolecules at atomic resolution and biologically relevant timescales. MD simulations often produce massive datasets containing millions of snapshots describing proteins in motion. Therefore, clustering algorithms have been in high demand to be developed and applied to classify these MD snapshots and gain biological insights. There mainly exist two categories of clustering algorithms that aim to group protein conformations into clusters based on the similarity of their shape (geometric clustering) and kinetics (kinetic clustering). In this paper, we review a series of frequently used clustering algorithms applied in MD simulations, including divisive algorithms, agglomerative algorithms (single-linkage, complete-linkage, average-linkage, centroid-linkage and ward-linkage), center-based algorithms (K-Means, K-Medoids, K-Centers, and APM), density-based algorithms (neighbor-based, DBSCAN, density-peaks, and Robust-DB), and spectral-based algorithms (PCCA and PCCA+). In particular, differences between geometric and kinetic clustering metrics will be discussed along with the performances of different clustering algorithms. We note that there does not exist a one-size-fits-all algorithm in the classification of MD datasets. For a specific application, the right choice of clustering algorithm should be based on the purpose of clustering, and the intrinsic properties of the MD conformational ensembles. Therefore, a main focus of our review is to describe the merits and limitations of each clustering algorithm. We expect that this review would be helpful to guide researchers to choose appropriate clustering algorithms for their own MD datasets.
Mode-Coupling theory for glass transition of active-passive binary mixture
Authors: Feng Meng-kai , Hou Zhong-huai
Published: September 2018

Collective behaviours of active particle systems have gained great research attentions in recent years. Here we present a mode-coupling theory (MCT) framework to study the glass transition of a mixture system of active and passive Brownian particles. The starting point is an effective Smoluchowski equation, which governs the dynamics of the probability distribution function in the position phase space. With the assumption of the existence of a nonequilibrium steady state, we are able to obtain dynamic equations for the intermediate scattering functions (ISFs), wherein an irreducible memory function is introduced which in turn can be written as functions of the ISFs based on standard mode-coupling approximations. The effect of particle activity is included through an effective diffusion coefficient which can be obtained via short time simulations. By calculating the long-time limit of the ISF, the Debye-Waller (DW) factor, one can determine the critical packing fraction ηc of glass transition. We find that for active-passive (AP) mixtures with the same particle sizes, ηc increases as the partial fraction of active particle xA increases, which is in agreement with previous simulation works. For system with different active/passive particle sizes, we find an interesting reentrance behaviour of glass transition, i.e., ηc shows a non-monotonic dependence on xA. In addition, such a reentrance behaviour would disappear if the particle activity is large enough. Our results thus provide a useful theoretical scheme to study glass transition behaviour of active-passive mixture systems in a promising way.
Understanding the long-term impact of prescribed burning in mediterranean-climate biodiversity hotspots, with a focus on south-western Australia
Authors: Bradshaw S. D. , Dixon K. W. , Lambers H. , Cross A. T. , Bailey J. , Hopper S. D.
Published: September 2018

Wildfires are expected to increase worldwide both in frequency and intensity owing to global warming, but are likely to vary geographically. This is of particular concern in the five mediterranean regions of the world that are all biodiversity hotspots with extraordinary plant and animal diversity that may be impacted by deliberately imposed fire. Wildland managers attempt to reduce the impact and mitigate the outcomes of wildfires on human assets and biodiversity by the use of prescribed burning. The response that we must ‘fight fire with fire’ is understandable, perceived as reducing the flammability of wildlands in fire-prone regions and lessening the impact of wildfires. The long-term impact on biodiversity is, however, less clear. The practice of prescribed burning has been in place and monitored in south-western Australia for 50 years, longer and more intensively than in most other mediterranean ecosystems. The present target is for 200 000 ha burned each year in this biodiversity hotspot. Published studies on the impact of this burning on infrastructure protection and on biodiversity are here used to understand the protective capacity of the practice and to foreshadow its possible long-term ecological impact across all mediterranean ecosystems.
Generalized least squares can overcome the critical threshold in respondent-driven sampling
Authors: Roch Sebastien , Rohe Karl
Published: September 2018

Significance

Respondent-driven sampling (RDS) is a popular technique to sample marginalized or hard-to-reach populations, where participants can refer multiple contacts into the sample. Using the sampled participants, we wish to estimate properties of the population, often the proportion of individuals that are HIV+. Because contacts often share the same HIV status, adjacent samples are dependent. As a result, RDS can lead to highly variable estimates of HIV prevalence. This paper studies an estimation technique for HIV prevalence that is based upon the classical idea of generalized least squares.
Contrasting dynamics and trait controls in first-order root compared with leaf litter decomposition
Authors: Sun Tao , Hobbie Sarah E. , Berg Björn , Zhang Hongguang , Wang Qingkui , Wang Zhengwen , Hättenschwiler Stephan
Published: September 2018

Significance

Decomposition of plant roots and associated fungal mutualists is a dominant process in ecosystem carbon cycles, yet is woefully understudied compared with decomposition of leaf litter, particularly for the finest order roots that have the highest turnover. In a field experiment, we compared decomposition of the finest, most distal roots and leaf litter among 35 cooccurring temperate forest species over 6 years. We found that decomposition rates of root tips were considerably lower than those of leaf litter and were controlled by nonlignin carbon compounds in contrast to lignin:nitrogen ratio control over leaf litter decomposition. Our study suggests that models of terrestrial carbon cycling based on aboveground patterns are inadequate to describe decomposition of the finest plant roots.
Striatal dopamine 2 receptor upregulation during development predisposes to diet-induced obesity by reducing energy output in mice
Authors: Labouesse Marie A. , Sartori Andrea M. , Weinmann Oliver , Simpson Eleanor H. , Kellendonk Christoph , Weber-Stadlbauer Ulrike
Published: September 2018

Significance

The need to understand the early determinants for obesity has never been greater with currently over 700 million obese people worldwide. Several decades of research have suggested that dopamine 2 receptors (D2R) in the striatum might be particularly important for obesity etiology, but no study has thus far outlined an unambiguous causal relationship. Here we show that striatal D2R upregulation induces obesity in mice fed a high-fat diet and this is due to reduced energy expenditure rather than increased eating. Importantly, we show that elevated D2R during development is sufficient to persistently increase obesity susceptibility. This work identifies excess D2Rs early in life as a potential key predisposition factor toward obesity and therefore may help uncover strategies for early interventions.
Bottom-up saliency and top-down learning in the primary visual cortex of monkeys
Authors: Yan Yin , Zhaoping Li , Li Wu
Published: September 2018

Significance

A visual item in sharp contrast with its neighboring items in a simple feature, such as color or orientation, automatically captures attention. Although cortical area V1 signals such simple feature contrasts, it is unclear whether these signals are utilized for saliency effects in behavior and whether they are enhanced by training. By training monkeys to detect a short bar in various degrees of orientation contrast with uniformly oriented background bars, we show that the feature contrast signals in V1, which start from the beginning of neuronal responses, are correlated with the detection performance and are therefore perceptual saliency signals. Training makes the early saliency signals more behaviorally correlated, consistent with more reflexive and less effortful task performance after training.
The interaction of talin with the cell membrane is essential for integrin activation and focal adhesion formation
Authors: Chinthalapudi Krishna , Rangarajan Erumbi S. , Izard Tina
Published: September 2018

Significance

Vertebrate cell growth, division, locomotion, morphogenesis, and development rely on the dynamic interactions of cells with extracellular matrix components via cell surface complexes termed focal adhesions that are composed of heterodimeric αβ integrin receptors, associated signaling molecules, and the large cytoskeletal protein talin. While it is known that talin activation and binding to β-integrin requires interactions with lipids, little is known regarding the structure and function of inactive vs. activated talin, and what is known is often disputed. Here we report that talin binding to the cell membrane seems necessary for integrin activation and focal adhesion formation, a finding that significantly advances our understanding of integrin activation and might aid the development of novel integrin therapeutic agents.
The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation
Authors: Kotani Tetsuya , Kirisako Hiromi , Koizumi Michiko , Ohsumi Yoshinori , Nakatogawa Hitoshi
Published: September 2018

Significance

A central event during autophagy is the biogenesis of double-membrane vesicles called autophagosomes, which sequester various intracellular materials for degradation in lysosomes/vacuoles. Recent studies have suggested the involvement of the endoplasmic reticulum (ER) in autophagosome formation, and that pre-autophagosomal membranes contact with the ER. However, the mechanistic basis of these contacts has remained unknown. Here we describe two membrane-binding domains responsible for autophagosome formation in the autophagy-related protein Atg2, which localizes to the pre-autophagosomal membrane–ER contact sites in yeast cells. Our data suggest that the amphipathic helix in the C-terminal region of Atg2 targets the protein to pre-autophagosomal membranes, whereas the N-terminal region of the same molecule associates with the ER, tethering these membranes together to mediate membrane expansion during autophagosome formation.
ZFAND5/ZNF216 is an activator of the 26S proteasome that stimulates overall protein degradation
Authors: Lee Donghoon , Takayama Shinichi , Goldberg Alfred L.
Published: September 2018

Significance

ZFAND5/ZNF216, a member of the ubiquitous ZFAND protein family, contains two zinc finger domains. It is induced in skeletal muscle during atrophy and was shown to be essential for the resulting large loss of muscle mass. We show here that purified ZFAND5 stimulates the 26S proteasomes’ capacity to degrade peptides and ubiquitinated proteins. In cells, it promotes the degradation of endogenous cell proteins through its ubiquitin-binding zinc finger domain (A20). Unlike several ZFAND proteins, it is not induced in proteotoxic stresses. Unlike other proteasome activators, ZFAND5 actually stimulates overall protein breakdown by the ubiquitin proteasome pathway.
Structure of a PSI–LHCI–cyt b
6
f supercomplex in
Chlamydomonas reinhardtii
promoting cyclic electron flow under anaerobic conditions
Authors: Steinbeck Janina , Ross Ian L. , Rothnagel Rosalba , Gäbelein Philipp , Schulze Stefan , Giles Nichole , Ali Rubbiya , Drysdale Rohan , Sierecki Emma , Gambin Yann , Stahlberg Henning , Takahashi Yuichiro , Hippler Michael , Hankamer Ben
Published: September 2018

Significance

To optimize photosynthetic performance and minimize photooxidative damage, photosynthetic organisms evolved to efficiently balance light energy absorption and electron transport with cellular energy requirements under constantly changing light conditions. The regulation of linear electron flow (LEF) and cyclic electron flow (CEF) contributes to this fine-tuning. Here we present a model of the formation and structural molecular organization of a CEF-performing photosystem I (PSI)–light harvesting complex I (LHCI)–cytochrome (cyt) b
6
f supercomplex from the green alga
Chlamydomonas reinhardtii
. Such a structural arrangement could modulate the distinct operation of LEF and CEF to optimize light energy utilization, despite the same individual structural units contributing to these two different functional modes.
A single phosphorylation site of SIK3 regulates daily sleep amounts and sleep need in mice
Authors: Honda Takato , Fujiyama Tomoyuki , Miyoshi Chika , Ikkyu Aya , Hotta-Hirashima Noriko , Kanno Satomi , Mizuno Seiya , Sugiyama Fumihiro , Takahashi Satoru , Funato Hiromasa , Yanagisawa Masashi
Published: September 2018

Significance

The neural substrate for “sleepiness,” as well as the molecular mechanisms determining daily sleep amounts, remain mysterious. Here, we found that a single amino acid, S551, of the protein kinase SIK3 has a crucial role in the regulation of sleep need and daily nonrapid-eye movement sleep amounts. Importantly, S551 in SIK3 is evolutionally conserved as a PKA phosphorylation site from nematodes and fruit flies to mice and humans. These findings implicate SIK3 in the molecular basis of homeostatic sleep/wake regulation.
Blood-derived plasminogen drives brain inflammation and plaque deposition in a mouse model of Alzheimer’s disease
Authors: Baker Sarah K. , Chen Zu-Lin , Norris Erin H. , Revenko Alexey S. , MacLeod A. Robert , Strickland Sidney
Published: September 2018

Significance

We demonstrate that depletion of blood plasminogen is sufficient to protect against both innate immune cell activation in the brain and Alzheimer’s disease (AD) pathology in a mouse model of AD. This work provides a molecular mechanism for initiation of AD-related brain inflammation and for regulation of β-amyloid deposition, and could lead to therapeutic strategies in human AD patients, including the targeting of systemic molecules.
Talin as a mechanosensitive signaling hub
Authors: Goult Benjamin T. , Yan Jie , Schwartz Martin A.
Published: September 2018

Cell adhesion to the extracellular matrix (ECM), mediated by transmembrane receptors of the integrin family, is exquisitely sensitive to biochemical, structural, and mechanical features of the ECM. Talin is a cytoplasmic protein consisting of a globular head domain and a series of α-helical bundles that form its long rod domain. Talin binds to the cytoplasmic domain of integrin β-subunits, activates integrins, couples them to the actin cytoskeleton, and regulates integrin signaling. Recent evidence suggests switch-like behavior of the helix bundles that make up the talin rod domains, where individual domains open at different tension levels, exerting positive or negative effects on different protein interactions. These results lead us to propose that talin functions as a mechanosensitive signaling hub that integrates multiple extracellular and intracellular inputs to define a major axis of adhesion signaling.
ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS–STING
Authors: Aden Konrad , Tran Florian , Ito Go , Sheibani-Tezerji Raheleh , Lipinski Simone , Kuiper Jan W. , Tschurtschenthaler Markus , Saveljeva Svetlana , Bhattacharyya Joya , Häsler Robert , Bartsch Kareen , Luzius Anne , Jentzsch Marlene , Falk-Paulsen Maren , Stengel Stephanie T. , Welz Lina , Schwarzer Robin , Rabe Björn , Barchet Winfried , Krautwald Stefan , Hartmann Gunther , Pasparakis Manolis , Blumberg Richard S. , Schreiber Stefan , Kaser Arthur , Rosenstiel Philip
Published: September 2018

A coding variant of the inflammatory bowel disease (IBD) risk gene ATG16L1 has been associated with defective autophagy and deregulation of endoplasmic reticulum (ER) function. IL-22 is a barrier protective cytokine by inducing regeneration and antimicrobial responses in the intestinal mucosa. We show that ATG16L1 critically orchestrates IL-22 signaling in the intestinal epithelium. IL-22 stimulation physiologically leads to transient ER stress and subsequent activation of STING-dependent type I interferon (IFN-I) signaling, which is augmented in Atg16l1ΔIEC intestinal organoids. IFN-I signals amplify epithelial TNF production downstream of IL-22 and contribute to necroptotic cell death. In vivo, IL-22 treatment in Atg16l1ΔIEC and Atg16l1ΔIEC/Xbp1ΔIEC mice potentiates endogenous ileal inflammation and causes widespread necroptotic epithelial cell death. Therapeutic blockade of IFN-I signaling ameliorates IL-22–induced ileal inflammation in Atg16l1ΔIEC mice. Our data demonstrate an unexpected role of ATG16L1 in coordinating the outcome of IL-22 signaling in the intestinal epithelium.
The Cross-sectional and Longitudinal Associations Between IL-6, IL-10, and TNFα and Cognitive Outcomes in the Mayo Clinic Study of Aging
Authors: Wennberg Alexandra M V , Hagen Clinton E , Machulda Mary M , Knopman David S , Petersen Ronald C , Mielke Michelle M
Published: September 2018

Background

Chronic inflammation has been linked with geriatric-related conditions, including dementia. Inflammatory cytokine levels, including interleukin (IL)-6, IL-10, and tumor necrosis factor (TNF) α, in the blood have been associated with cognitive impairment and decline. However, evidence has been mixed.

Methods

We examined the cross-sectional and longitudinal associations between baseline-measured IL-6, IL-10, and TNFα levels and the ratio of IL-6/IL-10 with cognitive test performance and mild cognitive impairment (MCI) among 1,602 community-dwelling older adults (median age = 72.8) enrolled in the Mayo Clinic Study of Aging. Approximately half (46.5%) of participants were female and 98.6% were white. At baseline and follow-up visits (occurring at 15-month intervals), participants completed neuropsychological testing, blood draws, and had a clinical consensus diagnosis.

Results

In multivariable cross-sectional analyses, we did not observe an association between inflammatory cytokine levels and global or domain-specific cognitive z scores; however, higher IL-6 and IL-10 levels were associated with greater odds of a MCI diagnosis. Longitudinally, we did not observe any association between inflammatory cytokine levels and cognitive test performance or risk of MCI. Sex, age, cognitive status, APOE ε4 genotype, diabetes, depression, and cerebral amyloid-beta deposition were not effect modifiers.

Conclusions

These results suggest that plasma inflammatory markers may not be useful to ascertain risk for cognitive decline and MCI in the general population.
Chronic Treatment With the ACE Inhibitor Enalapril Attenuates the Development of Frailty and Differentially Modifies Pro- and Anti-inflammatory Cytokines in Aging Male and Female C57BL/6 Mice
Authors: Keller Kaitlyn , Kane Alice , Heinze-Milne Stefan , Grandy Scott A , Howlett Susan E
Published: September 2018

Studies on interventions that can delay or treat frailty in humans are limited. There is evidence of beneficial effects of angiotensin converting enzyme (ACE) inhibitors on aspects related to frailty, such as physical function, even in those without cardiovascular disease. This study aimed to longitudinally investigate the effect of an ACE inhibitor on frailty in aging male and female mice. Frailty was assessed with a clinical frailty index (FI) which quantifies health-related deficits in middle-aged (9–13 months) and older (16–25 months) mice. Chronic treatment with enalapril (30 mg/kg/day in feed) attenuated frailty in middle-aged and older female mice, and older male mice, without a long-term effect on blood pressure. Enalapril treatment resulted in a reduction in the proinflammatory cytokines interleukin (IL)-1α, monocyte chemoattractant protein-1 and macrophage inflammatory protein-1a in older female mice, and an increase in the anti-inflammatory cytokine IL-10 in older male mice compared with control animals. These sex-specific effects on inflammation may contribute to the protective effects of enalapril against frailty. This is the first study to examine the longitudinal effect of an intervention on the FI in mice, and provides preclinical evidence that enalapril may delay the onset of frailty, even when started later in life.
Effects of Vitamin D3 Supplementation on Epigenetic Aging in Overweight and Obese African Americans With Suboptimal Vitamin D Status: A Randomized Clinical Trial
Authors: Chen Li , Dong Yanbin , Bhagatwala Jigar , Raed Anas , Huang Ying , Zhu Haidong
Published: September 2018

Background

We have previously shown that vitamin D supplementation increases telomerase activity, suggesting an anti-aging effect. In this study, we aim to test the hypothesis that vitamin D supplementation would slow down epigenetic aging, a new marker of biological aging.

Methods

A randomized clinical trial was previously conducted among 70 overweight/obese African Americans with serum 25-hydroxyvitamin D [25(OH)D] < 50 nmol/L, who were randomly assigned into four groups of 600 IU/d, 2,000 IU/d, 4,000 IU/d of vitamin D3 supplements or placebo followed by 16-week interventions. Whole genome-wide DNA methylation analysis was conducted in 51 participants. DNA methylation ages were calculated according to the Horvath and the Hannum methods. Methylation-based age acceleration index (∆Age) is defined as the difference between DNA methylation age and chronological age in years. Mixed-effects models were used to evaluate the treatment effects.

Results

Fifty-one participants (aged 26.1 ± 9.3 years, 16% are male) were included in the study. After the adjustment of multi-covariates, vitamin D3 supplementation of 4,000 IU/d was associated with 1.85 years decrease in Horvath epigenetic aging compared with placebo (p value = .046), and 2,000 IU/d was associated with 1.90 years decrease in Hannum epigenetic aging (p value = .044). Serum 25(OH)D concentrations were significantly associated with decreased Horvath ∆Age only (p values = .002), regardless of treatments.

Conclusions

Our results suggest that vitamin D supplementation may slow down Horvath epigenetic aging. But the effect on Hannum epigenetic aging is not conclusive. Large-scale and longer duration clinical trials are needed to replicate the findings.
The genome of common long-arm octopus Octopus minor
Authors: Kim Bo-Mi , Kang Seunghyun , Ahn Do-Hwan , Jung Seung-Hyun , Rhee Hwanseok , Yoo Jong Su , Lee Jong-Eun , Lee SeungJae , Han Yong-Hee , Ryu Kyoung-Bin , Cho Sung-Jin , Park Hyun , An Hye Suck
Published: September 2018

Background

The common long-arm octopus (Octopus minor) is found in mudflats of subtidal zones and faces numerous environmental challenges. The ability to adapt its morphology and behavioral repertoire to diverse environmental conditions makes the species a promising model for understanding genomic adaptation and evolution in cephalopods.

Findings

The final genome assembly of O. minor is 5.09 Gb, with a contig N50 size of 197 kb and longest size of 3.027 Mb, from a total of 419 Gb raw reads generated using the Pacific Biosciences RS II platform. We identified 30,010 genes; 44.43% of the genome is composed of repeat elements. The genome-wide phylogenetic tree indicated the divergence time between O. minor and Octopus bimaculoides was estimated to be 43 million years ago based on single-copy orthologous genes. In total, 178 gene families are expanded in O. minor in the 14 bilaterian species.

Conclusions

We found that the O. minor genome was larger than that of closely related O. bimaculoides, and this difference could be explained by enlarged introns and recently diversified transposable elements. The high-quality O. minor genome assembly provides a valuable resource for understanding octopus genome evolution and the molecular basis of adaptations to mudflats.
Perceived Impact of Participation in a One-Time Expressive Arts Workshop
Authors: Morrison Penny , Nishimoto Patricia W , Kim John B , Medina-Dupaix Carolina , Bantum Erin O’Carroll
Published: September 2018

Introduction

This 2015 study examined the use of art to express the experience of the cancer journey of military cancer patients/cancer survivors, family and friends, caregivers, volunteers, and staff members through a one-time art-making workshop, administered by non-art therapists.

Using art to express a medical/cancer journey may give participants, who cannot express their feelings in words, the ability to articulate their experience through art that looks at the creative process rather than the end result – expressive art.

Materials and Methods

This mixed methods study examined the use of art to express the cancer journey of participants. Twenty-eight adults participated in a one-time expressive arts workshop conducted by non-professional art therapists at a military medical center. The five domains of the Emotion Thermometer were analyzed to determine if the pre-event and post-event assessment results would differ. The Silver Drawing Test and Draw-a-Story assessment tools were used to identify emotions and attitudinal stance on six separate five-point scales. A qualitative analysis was done using the phenomenological method of the post-interviews that facilitated open expression to identify themes.

Results

A significant difference was found between the pre-event and post-event analyses using the Emotion Thermometer, with post-assessment results revealing lower levels in the three domains of distress, anxiety, and depression. The Silver Drawing Test and Draw-a-Story were analyzed for six components using a five-point scale, with the highest scores being content/meaning, ability to combine, and creativity. A qualitative analysis was done using the phenomenological method; post-interviews provided information to categorize the experience into four key themes: environment, connection, emotions, and discoveries.

Conclusions

Using art to express one’s journey through cancer allows participants to articulate that journey “beyond language.” This mixed methods study was administered by five non-professional art therapists with three having no expressive arts background. This study established that an expressive arts workshop can effectively be conducted by non-professional art therapists. The team of non-professional art therapists, who facilitated this one-time art-making workshop, demonstrated that a military member’s stress can be decreased by giving them “a voice” through expressive art.
Real-World Effectiveness of Pharmaceutical Smoking Cessation Aids: Time-Varying Effects
Authors: Chaiton Michael , Diemert Lori M , Bondy Susan J , Cohen Joanna E , Fung Michael D , Zhang Bo R , Ferrence Roberta G
Published: September 2018

Background

There are a limited number of studies that have examined the real-world effectiveness of smoking cessation aids and relapse longitudinally in population-representative samples. This study examines the association between use of nicotine gum, patch, bupropion, and varenicline and time to relapse as well as any changes in the association with increased length of abstinence.

Methods

Data of 1821 current adult smokers (18+) making their first serious quit attempt were compiled from 4504 individuals enrolled in the Ontario Tobacco Survey, a representative telephone survey of Ontario adults, which followed smokers every 6 months for up to 3 years. Use of cessation aids at the time of initial report of a quit attempt was analyzed. A flexible parametric survival model was developed to model length of abstinence, controlling for potential confounders.

Results

The best fit model found knots at 3, 13, 43, and 212 days abstinent, suggesting different rates of relapse in the periods marked by those days. Use of the patch and varenicline was associated with lower rates of relapse, but no positive effect was found for bupropion or nicotine gum. The effectiveness of the patch reversed in effect after the first month of abstinence.

Conclusions

This study is one of few reports of long-term quitting in a population-representative sample and demonstrates that the effectiveness of some pharmacological cessation aids (the patch and varenicline can be seen in a population sample). Previous failures in real-world studies of the effectiveness of smoking cessation aids may reflect differences in the products individuals use and differences in the timing of self-reported cessation.

Implications

While a large number of randomized controlled trials have shown the efficacy of many pharmaceutical smoking cessation aids, evidence of their effectiveness in observational studies in the real world is ambiguous. This study uses a longitudinal cohort of a representative sample of smokers to show that the effectiveness of pharmaceutical cessation aids can be demonstrated in real-world use situations, but effectiveness varies by product type and has time-varying effects.
Social Work and Social Welfare in Europe
Authors: Jones David N. , Lima Ana
Published: September 2018

This article sets social work in Europe in its historical, political, and social context and presents insights into the development of the education, training, practice, and organization of the profession in twenty European countries. The practice of social work has evolved differently in each country but shares common characteristics; in some countries there has been a parallel development of social pedagogy, with close links to social work theory and practice. The development of social work in the Soviet Union effectively ended after the revolution, and the same applied across the Soviet bloc after 1945. Following the political changes in the 1990s, social work was reestablished across central and eastern Europe; developments in those countries are reflected in some of the national publications. The delivery of social work across the Continent has been affected by the implementation of New Public Management approaches and the impact of the service user movement (sometimes called “consumerism”) and more recently by economic austerity policies following the 2008 financial crash. The main political and social structures of Europe—the Council of Europe and the European Union (EU)—have a significant influence on the development of national social policies through EU Directives (laws), the human rights principles of the Council of Europe, and convergent visions. The key instruments that impact social work policy and practice are identified. Literature from the twenty countries was recommended by the social work associations/unions in those countries and is largely in local languages; this is possibly the first attempt to recognize the diversity of social work literature across Europe and to challenge the over-reliance on literature and ideas expressed in English.
Julian of Norwich
Authors: Baker Denise
Published: September 2018

The first English woman identified as an author, Julian of Norwich composed two accounts of the divine revelations she received on 13 (or 8) May 1373, as she lay dying at the age of thirty. She probably wrote the Short Text soon after her visionary experience, and later, around 1393, completed its revision into the Long Text, which expands all the showings, but especially increases Revelation Fourteen from the first three chapters on prayer to include the culmination of her resolution to the problem of evil by explaining how “alle shalle be wele” with the parable of the lord and servant and the analogy of Jesus as mother. Julian’s revision of the Short into the Long Text reveals her transformation from a visionary into an erudite theologian. Little is known about this woman’s life. A scribal note introduces the only surviving copy of the Short Text (British Library Additional MS 37790) as “a vision shown by the goodness of God to a devout woman and her name is Julian, who is a recluse at Norwich and still alive, A.D. 1413.” She is probably called Julian after the church in whose anchorhold she was enclosed from at least 1393–1394. Bequests to “‘Julian’ anakorite” in several wills from the last decade of the 14th century to 1416 verify that a female recluse occupied the cell. Margery Kempe also reports that she consulted with “Dame Ielyan” early in the second decade of the 15th century, “for the anchoress was expert in such things and could give good advice.” Only two witnesses to Julian’s texts are pre-Reformation: the sole manuscript of the Short Text and the excerpts from the Long Text compiled in Westminster Cathedral Treasury MS 4 around 1500. Four later manuscripts were copied at religious houses on the Continent around 1650 or later: Bibliothèque nationale fonds anglais 40 (Paris), in a “modernized” dialect; British Library Sloane 2499 (1) and Sloane 3705 (2), in a dialect closer to Julian’s East Anglian; and excerpts from the twelfth and thirteenth revelations in St. Joseph’s College, Upholland (Lancashire, England). In the 20th century, Julian’s Revelations of Divine Love found wide readership thanks to Grace Warrack’s Modern English translation of the Sloane Long Text published in 1901. Poets such as T. S. Eliot and prose writers like Annie Dillard echoed her words. Today, Julian of Norwich is the best known and most beloved of the medieval mystics.
Who Wants to Switch? Gauging Patient Interest in Novel Antiretroviral Therapies
Authors: Derrick Caroline B , Ostermann Jan , Weissman Sharon B , Hobbie Amy , Alshareef Noor , Weinhold Andrew , Yelverton Valerie , Thielman Nathan M
Published: September 2018

Study participants were asked about their interest in switching to novel drug delivery systems that reduce the dosing frequency of antiretroviral regimens. Across a diverse, treatment-experienced cohort, we describe greatest interest in switching to an oral regimen taken once weekly, followed by injections taken every other month and twice-annual implants.
Frequencies and severity of injection-site lesions in muscles from rounds of cow carcasses
Authors: Pfeiffer Morgan M , Mafi Gretchen G , Ramanathan Ranjith , Neilson Taylor M , VanOverbeke Deborah L
Published: September 2018

The frequency and severity of injection-site lesions in the outside round muscles of both beef and dairy cattle were evaluated through a series of audits. Audits were conducted in 2017 on 1,300 rounds from dairy and beef cows from seven locations throughout the United States. Outside round muscles were butterfly cut into 1.25-cm slices and, if present, lesions were counted, measured, and categorized. Rounds from beef (7%) and dairy cattle (15%) had at least one injection-site lesion present. The most common location of injection-site lesions was quadrant 2 and 3, which contained both the biceps femoris and semitendinosus muscles. Injection-site lesions were more frequent (P < 0.05) in the biceps femoris for both beef and dairy rounds. Clear lesions accounted for 57% of injection-sites in both beef and dairy rounds, whereas metallic lesions made up 23% of the total in beef and 25% in dairy. Overall, there was a dramatic decline in the frequency (P < 0.05) of injection-site lesions since the 1998 (24 and 45 percentage units greater in beef and dairy rounds, respectively) and 2000 audits (13 and 20 percentage units greater in beef and dairy rounds, respectively). Educational programs, such as Beef Quality Assurance (BQA) and requirements for BQA training, have resulted in substantial improvements in beef management practices for both the beef and dairy industries.
Legume Nodules: Massive Infection in the Absence of Defense Induction
Authors: Berrabah Fathi , Ratet Pascal , Gourion Benjamin
Published: September 2018

Plants of the legume family host massive intracellular bacterial populations in the tissues of specialized organs, the nodules. In these organs, the bacteria, named rhizobia, can fix atmospheric nitrogen and transfer it to the plant. This special metabolic skill provides to the legumes an advantage when they grow on nitrogen-scarce substrates. While packed with rhizobia, the nodule cells remain alive, metabolically active, and do not develop defense reactions. Here, we review our knowledge on the control of plant immunity during the rhizobia-legume symbiosis. We present the results of an evolutionary process that selected both divergence of microbial-associated molecular motifs and active suppressors of immunity on the rhizobial side and, on the legume side, active mechanisms that contribute to suppression of immunity.
Genotyping of Phytophthora infestans in Eastern Africa Reveals a Dominating Invasive European Lineage
Authors: Njoroge Anne W. , Andersson Björn , Lees Alison K. , Mutai Collins , Forbes Gregory A. , Yuen Jonathan E. , Pelle Roger
Published: September 2018

Strains of Phytophthora infestans, the pathogen causing late blight of potato and tomato, are thought to be moved around the world through infected planting material. Since its first appearance in 1941, late blight has caused important losses to potato production in the eastern-Africa region (EAR). In the current study, the genetic structure of the population in Kenya, Uganda, Tanzania, Burundi, and Rwanda was characterized using 12-plex microsatellite markers with the aim of testing the hypothesis that a strain originating from Europe, 2_A1, has recently dominated the population in EAR. Analyses of 1,093 potato and 165 tomato samples collected between 2013 and 2016 revealed the dominance on potato in all countries of the 2_A1 clonal lineage. On tomato, a host-specialized form of the US-1 lineage appears to persist in Rwanda, Uganda, and Tanzania whereas, in Kenya, most samples from tomato (72.5%) were 2_A1. The US-1 lineage in Tanzania had two private alleles at the Pi02 marker, suggesting a possible independent introduction into the region. US-1 had higher genetic variability than 2_A1, consistent with the earlier establishment of the former. Continuous tracking of P. infestans population changes should help identify new virulent and aggressive strains, which would inform strategic disease management options.
Inheritance of Resistance to Colletotrichum gloeosporioides and C. acutatum in Strawberry
Authors: Jacobs Raymond L. , Adhikari Tika B. , Pattison Jeremy , Yencho G. Craig , Fernandez Gina E. , Louws Frank J.
Published: September 2018

Information on the inheritance of resistance to Colletotrichum gloeosporioides and C. acutatum hemibiotrophic infections (HBI) in strawberry leaf tissue and the genetic control of anthracnose crown rot (ACR) in crown tissue are relatively unknown. Six parental genotypes were crossed in a half-diallel mating design to generate 15 full-sib families. HBI and ACR experiments were conducted concurrently. Both seedlings and parental clones were inoculated with 1 × 106 conidia/ml of C. gloeosporioides or C. acutatum. Percent sporulating leaf area, wilt symptoms, and relative area under the disease progress curve were calculated to characterize resistance among genotypes and full-sib families. Low dominance/additive variance ratios for C. acutatum HBI (0.13) and C. gloeosporioides ACR (0.20) were observed, indicating additive genetic control of resistance to these traits. Heritability estimates were low for C. acutatum HBI (0.25) and C. gloeosporioides HBI (0.16) but moderate for C. gloeosporioides ACR (0.61). A high genetic correlation (rA = 0.98) between resistance to C. acutatum HBI and C. gloeosporioides HBI was observed, suggesting that resistance to these two Colletotrichum spp. may be controlled by common genes in strawberry leaf tissue. In contrast, negative genetic correlations between ACR and both HBI traits (rA = −0.85 and −0.61) suggest that resistance in crown tissue is inherited independently of resistance in leaf tissue in the populations tested. Overall, these findings provide valuable insight into the genetic basis of resistance, and the evaluation and deployment of resistance to HBIs and ACR in strawberry breeding programs.
Schistosomiasis in a Scottish school group after freshwater swimming in Uganda: the need to raise awareness
Authors: Currie Sandra L. , Denvir Lucy , Mooka Busi , Perrow Kali , Alexander Claire L.
Published: September 2018

Introduction. Schistosomiasis, a travel-related trematode infection, can cause a range of symptoms with potentially life-threatening complications. In this report, we describe an outbreak of schistosomiasis in a Scottish school group that had travelled to Uganda. We discuss the requirement for robust and accurate pre-travel advice, and the importance of raising awareness in travellers, particularly due to the asymptomatic nature of the disease. In addition, we highlight the need to submit a serum sample for laboratory testing on return from endemic regions where freshwater exposure has occurred.

Case presentation. A Scottish school group consisting of 19 individuals visited Uganda during July 2016 with one positive symptomatic case identified on return to the UK. As three of the individuals were not Scottish residents, their data were excluded from this report. Freshwater exposure was noted from taking part in activities which included swimming in the Nile. The Scottish Parasite Diagnostic and Reference Laboratory performed serology testing using sera from 16 Scottish residents to detect IgG towards Schistosoma egg antigens. Thirteen were positive despite only one case being symptomatic.

Conclusion. The high positivity rate raised several issues. These included the lack of a robust risk assessment by the travel company organizing the trip, the lack of awareness of schistosomiasis by some individuals, the lack of appropriate and accurate pre-travel advice, and the asymptomatic nature of the infection. This report provides supportive evidence to strengthen the need for improvements to prevent largely asymptomatic cases being missed in future.