bluuebunny/crossref_metadata_2025 huggingface dataset:
Host‐targeted RAD‐Seq reveals genetic changes in the coral Oculina patagonica associated with range expansion along the Spanish Mediterranean coast
Authors: Leydet Karine Posbic , Grupstra Carsten G. B. , Coma Rafel , Ribes Marta , Hellberg Michael E.
Published: April 2018

Many organisms are expanding their ranges in response to changing environmental conditions. Understanding the patterns of genetic diversity and adaptation along an expansion front is crucial to assessing a species’ long‐term success. While next‐generation sequencing techniques can reveal these changes in fine detail, ascribing them to a particular species can be difficult for organisms that live in close association with symbionts. Using a novel modified restriction site‐associated DNA sequencing (RAD‐Seq) protocol to target coral DNA, we collected 595 coral‐specific single nucleotide polymorphisms from 189 colonies of the invasive coral Oculina patagonica from the Spanish Mediterranean coast, including established core populations and two expansion fronts. Surprisingly, populations from the recent northern expansion are genetically distinct from the westward expansion and core populations and also harbour greater genetic diversity. We found that temperature may have driven adaptation along the northern expansion, as genome scans for selection found three candidate loci associated with temperature in the north but none in the west. We found no genomic signature of selection associated with artificial substrate, which has been proposed for explaining the rapid spread of O. patagonica. This suggests that this coral is simply an opportunistic colonizer of free space made available by coastal habitat modifications. Our results suggest that unique genetic variation, possibly due to limited dispersal across the Ibiza Channel, an influx of individuals from different depths and/or adaptation to cooler temperatures along the northern expansion front may have facilitated the northward range expansion of O. patagonica in the western Mediterranean.
Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence‐related genes
Authors: Pritchard Victoria L. , Mäkinen Hannu , Vähä Juha‐Pekka , Erkinaro Jaakko , Orell Panu , Primmer Craig R.
Published: April 2018

Elucidating the genetic basis of adaptation to the local environment can improve our understanding of how the diversity of life has evolved. In this study, we used a dense SNP array to identify candidate loci potentially underlying fine‐scale local adaptation within a large Atlantic salmon (Salmo salar) population. By combining outlier, gene–environment association and haplotype homozygosity analyses, we identified multiple regions of the genome with strong evidence for diversifying selection. Several of these candidate regions had previously been identified in other studies, demonstrating that the same loci could be adaptively important in Atlantic salmon at subdrainage, regional and continental scales. Notably, we identified signals consistent with local selection around genes associated with variation in sexual maturation, energy homeostasis and immune defence. These included the large‐effect age‐at‐maturity gene vgll3, the known obesity gene mc4r, and major histocompatibility complex II. Most strikingly, we confirmed a genomic region on Ssa09 that was extremely differentiated among subpopulations and that is also a candidate for local selection over the global range of Atlantic salmon. This region colocalized with a haplotype strongly associated with spawning ecotype in sockeye salmon (Oncorhynchus nerka), with circumstantial evidence that the same gene (six6) may be the selective target in both cases. The phenotypic effect of this region in Atlantic salmon remains cryptic, although allelic variation is related to upstream catchment area and covaries with timing of the return spawning migration. Our results further inform management of Atlantic salmon and open multiple avenues for future research.
How to prophylax against invasive fungal infections in adult ALL? An unmet need
Authors: Cornely Oliver A. , Kontoyiannis Dimitrios P.
Published: April 2018

Although the benefit for any type of antifungal prophylaxis in patients with acute myelogenous leukaemia is well accepted, less is known about the risk for invasive fungal infections (IFIs) and the optimal prophylaxis strategies in patients with acute lymphocytic leukaemia (ALL). Based on recent studies, ALL is a disease that appears to be associated with significant risk for IFIs. The pharmacokinetic interactions between azoles and vincristine, an antineoplastic agent that is part of modern combination chemotherapies in ALL, results in clinically significant neurotoxicity that makes the use of azoles problematic. However, a number of questions regarding azole‐vincristine interactions remain unanswered. In this viewpoint, we call for a renewed interest in antifungal prophylaxis studies in ALL in view of the availability of several non‐azole novel antifungal agents that are under preclinical and/or clinical development. This is clearly a major unmet need in modern clinical mycology.
Circadian rhythms, refractive development, and myopia
Authors: Chakraborty Ranjay , Ostrin Lisa A. , Nickla Debora L. , Iuvone P. Michael , Pardue Machelle T. , Stone Richard A.
Published: April 2018

Purpose

Despite extensive research, mechanisms regulating postnatal eye growth and those responsible for ametropias are poorly understood. With the marked recent increases in myopia prevalence, robust and biologically‐based clinical therapies to normalize refractive development in childhood are needed. Here, we review classic and contemporary literature about how circadian biology might provide clues to develop a framework to improve the understanding of myopia etiology, and possibly lead to rational approaches to ameliorate refractive errors developing in children.

Recent findings

Increasing evidence implicates diurnal and circadian rhythms in eye growth and refractive error development. In both humans and animals, ocular length and other anatomical and physiological features of the eye undergo diurnal oscillations. Systemically, such rhythms are primarily generated by the ‘master clock’ in the surpachiasmatic nucleus, which receives input from the intrinsically photosensitive retinal ganglion cells (ipRGCs) through the activation of the photopigment melanopsin. The retina also has an endogenous circadian clock. In laboratory animals developing experimental myopia, oscillations of ocular parameters are perturbed. Retinal signaling is now believed to influence refractive development; dopamine, an important neurotransmitter found in the retina, not only entrains intrinsic retinal rhythms to the light:dark cycle, but it also modulates refractive development. Circadian clocks comprise a transcription/translation feedback control mechanism utilizing so‐called clock genes that have now been associated with experimental ametropias. Contemporary clinical research is also reviving ideas first proposed in the nineteenth century that light exposures might impact refraction in children. As a result, properties of ambient lighting are being investigated in refractive development. In other areas of medical science, circadian dysregulation is now thought to impact many non‐ocular disorders, likely because the patterns of modern artificial lighting exert adverse physiological effects on circadian pacemakers. How, or if, such modern light exposures and circadian dysregulation contribute to refractive development is not known.

The premise of this review is that circadian biology could be a productive area worthy of increased investigation, which might lead to the improved understanding of refractive development and improved therapeutic interventions.
Parental attitudes to myopia: a key agent of change for myopia control?
Authors: McCrann Saoirse , Flitcroft Ian , Lalor Kevin , Butler John , Bush Aaron , Loughman James
Published: April 2018

Purpose

With the increasing prevalence in myopia there is growing interest in active myopia prevention. This study aims to increase our understanding of parental attitudes to myopia development and control, as a means to inform future health planning and policy. It evaluates, for the first time, the attitude of parents to myopia and its associated risks, as well as assessing the exposure of Irish children to environmental factors that may influence their risk profile for myopia development.

Methods

Parents of 8–13 year old children in eight participating schools completed a questionnaire designed to assess their knowledge of and attitudes towards myopia and its risk factors. A structured diary was also used to capture daily activities of children in relation to myopia risk factors.

Results

Of 329 parents, just 46% considered that myopia presented a health risk to their children, while an identical number (46%) regarded it as an optical inconvenience. Myopia was also, but less frequently, considered an expense (31% of parents), a cosmetic inconvenience (14% of parents) and, by some, as a sign of intelligence (4% of parents) 76% of parents recognised the potential of digital technology to impact the eye, particularly as a cause of eyestrain and need for spectacles. Only 14% of parents expressed concern should their child be diagnosed with myopia. Compared to non myopic parents, myopic parents viewed myopia as more of an optical inconvenience (p < 0.001), an expense (p < 0.005) and a cosmetic inconvenience (p < 0.001). There was a trend for myopic parents to limit screen time use in their household more than non‐myopic parents (p = 0.05). Parents who considered myopia a health risk sought to limit screen time more than parents who did not regard myopia as a health risk to their child (p = 0.01). Children spent significantly longer performing indoor proximal tasks (255 min) compared to time spent outdoors (180 min;p < 0.0001) daily. Older (p = 0.001), urban (p = 0.0005) myopic (=0.04) children spent significantly more time at digital screens compared to younger non‐myopic children from a rural background.

Conclusion

Parental attitudes to myopia were typically nonchalant in relation to health risk. This is of particular concern given the impact parents have on children's behaviour and choices with respect to such risk factors, demonstrating an acute need for societal sensitisation to the public health importance of myopia.
Five‐year incidence and progression of myopic maculopathy in a rural Chinese adult population: the Handan Eye Study
Authors: Lin Caixia , Li Shi‐Ming , Ohno‐Matsui Kyoko , Wang Bing Song , Fang Yu Xin , Cao Kai , Gao Li Qin , Hao Jie , Zhang Ye , Wu Jian , Wang Ning Li ,   the Handan Eye Study Group
Published: April 2018

Purpose

To determine the cumulative five‐year incidence and progression of myopic maculopathy in a rural Chinese adult population.

Methods

The Handan Eye Study was a population‐based longitudinal study. In 2006, 6830 subjects aged 30+ years participated in this study (baseline). Five years later, 5394 subjects (follow‐up rate: 85.3%) took part in the follow‐up study. Participants had a detailed eye examination, including visual acuity, standardized refraction and fundus photography according to a similar protocol at both baseline and follow‐up. Myopic maculopathy was defined as any of the following signs: diffuse chorioretinal atrophy, patchy chorioretinal atrophy, macular atrophy, lacquer cracks and myopic choroidal neovascularization at the posterior pole. Parapapillary atrophy was assessed separately.

Results

Of 5394 participants, 5078 (10 021 eyes) had gradable fundus photographs. Over the five years, four participants (five eyes) developed new myopic maculopathy, with an eye‐specific incidence of 0.05% (95% CI, 0.02–0.10%). Among the 51 eyes with myopic maculopathy at baseline, the progression occurred in 18 eyes (35.3%), with new signs of patchy chorioretinal atrophy in 11 eyes (21.6%), diffuse chorioretinal atrophy in seven eyes (13.7%), lacquer cracks in three eyes (6.9%), macular atrophy in three eyes (6.9%) and myopic choroidal neovascularization in two eyes (3.9%). By multivariable analysis, female gender (OR, 9.14; p = 0.004) and higher educational level (OR, 8.24; p = 0.004) were associated with a higher risk of progression of myopic maculopathy, whereas lower myopia at baseline (OR, 0.79; p < 0.0001) and hypertension (OR, 0.21; p = 0.017) were associated with a reduced risk.

Conclusions

The five‐year incidence of myopic maculopathy was 0.05% in rural Chinese adults aged 30+ years. The progression rate in participants with myopic maculopathy was 35.3%, indicating the importance of regular follow‐up for these patients.
Optical ‘dampening’ of the refractive error to axial length ratio: implications for outcome measures in myopia control studies
Authors: Cruickshank Fiona E. , Logan Nicola S.
Published: April 2018

Purpose

To gauge the extent to which differences in the refractive error axial length relationship predicted by geometrical optics are observed in actual refractive/biometric data.

Methods

This study is a retrospective analysis of existing data. Right eye refractive error [RX] and axial length [AXL] data were collected on 343 6‐to‐7‐year‐old children [mean 7.18 years (S.D. 0.35)], 294 12‐to‐13‐year‐old children [mean 13.12 years (S.D. 0.32)] and 123 young adults aged 18‐to‐25‐years [mean 20.56 years (S.D. 1.91)]. Distance RX was measured with the Shin‐Nippon NVision‐K 5001 infrared open‐field autorefractor. Child participants were cyclopleged prior to data collection (1% Cyclopentolate Hydrochloride). Myopia was defined as a mean spherical equivalent [MSE] ≤−0.50 D. Axial length was measured using the Zeiss IOLMaster 500. Optical modelling was based on ray tracing and manipulation of parameters of a Gullstrand reduced model eye.

Results

There was a myopic shift in mean MSE with age (6–7 years +0.87 D, 12–13 years −0.06 D and 18–25 years −1.41 D), associated with an increase in mean AXL (6–7 years 22.70 mm, 12–13 years 23.49 mm and 18–25 years 23.98 mm). There was a significant negative correlation between MSE and AXL for all age groups (all p < 0.005). RX: AXL ratios for participant data were compared with the ratio generated from Gullstrand model eyes. Both modelled and actual data showed non‐linearity and non‐constancy, and that as axial length is increased, the relationship between myopia and axial length differs, such that it becomes more negative.

Conclusions

Optical theory predicts that there will be a reduction in the RX: AXL ratio with longer eyes. The participant data although adhering to this theory show a reduced effect, with eyes with longer axial lengths having a lower refractive error to axial length ratio than predicted by model eye calculations. We propose that in myopia control intervention studies when comparing efficacy, consideration should be given to the dampening effect seen with a longer eye.
Expression of cutaneous immunity markers during infant skin maturation
Authors: Kirchner Frank , Capone Kimberly A. , Mack M. Catherine , Stamatas Georgios N.
Published: April 2018

Background/Objectives

Infant skin undergoes a maturation process during the early years of life. Little is known about the skin's innate immunity. We investigated the dynamics of innate immunity markers collected from the surface of infant skin during the first 36 months of life.

Methods

A total of 117 healthy infants aged 3‐36 months participated in the study. We extracted human beta defensin‐1 and interleukin 1 alpha and its receptor antagonist using transdermal analysis patches from the skin surface of the posterior lower leg area. The extracts were analyzed using a spot enzyme‐linked immunosorbent assay.

Results

Skin surface human beta defensin‐1 levels were higher early in life and decreased with infant age. The ratio of interleukin 1 alpha receptor antagonist to interleukin 1 alpha did not change significantly with age but showed a distinct difference between sexes, with female infants having higher values than male infants.

Conclusion

As is the case with skin structure and functional properties, cutaneous innate immunity also appears to undergo a maturation period during infancy, with innate immunity slowly declining as adaptive immunity takes over. Sex differences in immune markers may explain sex‐dependent susceptibilities to infection.
Gymnomonas nepalensis gen. et sp. nov. for the naked flagellate strain ‘Nepal’, formerly identified as Dunaliella lateralis (Volvocales, Chlorophyceae)
Authors: Watanabe Shin , Nakada Takashi
Published: April 2018

This study revisited the naked green flagellate strain ‘Nepal’, formerly identified as Dunaliella lateralis Pascher & Jahoda. This strain was concordant with the original description of motile cells, but different in features of the chloroplast morphology, eyespot position and asexual reproduction. Belonging to Oogamochlamydinia, this strain was distinguished from the walled species and another naked species Hapalochloris nozakii Nakada in cell size, ultrastructural features and phylogenetic positions. Based on these features, Gymnomonas nepalensis gen. et sp. nov. is proposed.
HLA‐C*15:29, an HLA‐C*15 variant, identified in a Taiwanese individual
Authors: Yang K. L. , Lin P. Y.
Published: April 2018

One nucleotide substitution at codon 116 of HLA‐C*15:02:01:01 results in a new allele, HLA‐C*15:29.
The relationship between social support, treatment interruption and treatment outcome in patients with multidrug‐resistant tuberculosis in China: a mixed‐methods study
Authors: Yin Jia , Wang Xiaomeng , Zhou Lin , Wei Xiaolin
Published: April 2018

Objective

Multidrug‐resistant tuberculosis (MDR‐TB) has been a major threat for successful TB control. We examined the relationship between social support and treatment outcomes in MDR‐TB patients and evaluated barriers to social support.

Methods

Retrospective cohort study with MDR‐TB patients enrolled in the Global Fund programme between 1 January 2009 and 30 June 2014 in Zhejiang, China. We reviewed all MDR‐TB patients’ diagnoses and treatment outcomes. In‐depth interviews were conducted with 10 community health workers and 10 patients. Pathway analysis was employed to examine the association between social support and treatment outcomes, and the mediating effect of medication adherence on their relationship.

Results

Of 218 participants, 144 (66%) were successfully treated and 59 (27%) had poor treatment adherence. Directly observed therapy (DOT) had an indirect positive effect on treatment success, mediating through medication adherence (β = 0.541, P = 0.008; β = 0.538, P < 0.001). Financial support had both a direct (β = 0.769, P < 0.001) and an indirect positive effect on treatment success, which was mediated by a self‐reported social support scale (β = 0.541, P = 0.008; β = 0.538, P < 0.001). The interviews indicated poor performance of DOT. Patients often suffered from substantial stigma, but were not provided with psychological support.

Conclusion

DOT and financial support were effective strategies for improving successful treatment outcomes in MDR‐TB patients, but they were delivered not considering patients’ perspectives. There is an urgent need for consistent and specific psychological support for MDR‐TB patients in their communities.
A simulation algorithm with uncertain random variables
Authors: Dalman Hasan
Published: April 2018

In many situations, uncertainty and randomness concurrently occur in a system. Thus this paper presents a new concept for uncertain random variable. Also, a simulation algorithm based on uncertain random variables is presented to approximate the chance distribution using  pessimistic value and  optimistic value. An example is also given to illustrate how to use the presented simulation algorithm.
Effects of language experience and task demands on talker recognition by children and adults
Authors: Fecher Natalie , Johnson Elizabeth K.
Published: April 2018

Talker recognition is a language-dependent process, with listeners recognizing talkers better when the talkers speak a familiar versus an unfamiliar language. This language familiarity effect (LFE) is firmly established in adults, but its developmental trajectory in children is not well understood. Some evidence suggests that the effect already exists in infancy, but little is known about how it unfolds in childhood. The present study explored whether the strength of the LFE increases in early childhood. Adults and children were tested in their native language and a foreign language using a “same-different” talker discrimination task and a “voice line-up” talker recognition task. Results showed that adults and 6-year-olds, but not 5-year-olds, exhibit a robust LFE, suggesting that the effect strengthens as children's language competence increases. For both adults and older children, the emergence of an LFE moreover appeared to be task-dependent. This study contributes to a better understanding of how children develop mature talker recognition abilities and when children's processing of indexical and linguistic information in speech approaches adult-like levels. Furthermore, the findings reported here contribute to the debates regarding the origins of the LFE—a hallmark of adult talker recognition.
Moving chairs in Starbucks: Observational studies find rice-wheat cultural differences in daily life in China
Authors: Talhelm Thomas , Zhang Xuemin , Oishi Shigehiro
Published: April 2018

More people in wheat-growing northern China were sitting alone and moved a chair blocking the aisle in cafes than people in the rice-farming south.
Translucent soft robots driven by frameless fluid electrode dielectric elastomer actuators
Authors: Christianson Caleb , Goldberg Nathaniel N. , Deheyn Dimitri D. , Cai Shengqiang , Tolley Michael T.
Published: April 2018

Translucent, undulating actuators are developed for submersible, swimming, soft robotic applications.
Westworld
and the uncanny valley
Authors: Murphy Robin R.
Published: April 2018

HBO’s
Westworld
is located to the right of the uncanny valley and left of government regulations.
Alloreactive fetal T cells promote uterine contractility in preterm labor via IFN-γ and TNF-α
Authors: Frascoli Michela , Coniglio Lacy , Witt Russell , Jeanty Cerine , Fleck-Derderian Shannon , Myers Dana E. , Lee Tzong-Hae , Keating Sheila , Busch Michael P. , Norris Philip J. , Tang Qizhi , Cruz Giovanna , Barcellos Lisa F. , Gomez-Lopez Nardhy , Romero Roberto , MacKenzie Tippi C.
Published: April 2018

Human fetal T cell activation against maternal antigens could promote uterine contractions in preterm labor.
PPARγ agonist pioglitazone reverses pulmonary hypertension and prevents right heart failure via fatty acid oxidation
Authors: Legchenko Ekaterina , Chouvarine Philippe , Borchert Paul , Fernandez-Gonzalez Angeles , Snay Erin , Meier Martin , Maegel Lavinia , Mitsialis S. Alex , Rog-Zielinska Eva A. , Kourembanas Stella , Jonigk Danny , Hansmann Georg
Published: April 2018

Oral pioglitazone reverses pulmonary hypertensive vascular disease and prevents right heart failure via epigenetic, transcriptional, and metabolic mechanisms.
Human fetal immune cells fight back
Authors: Chougnet Claire A.
Published: April 2018

Immune dysregulation begins in utero, influenced by inflammation, maternal micro-chimerism, and the activation of fetal immune responses (Frascoli
et al
., this issue).
A firsthand view of how secondhand smoke disrupts airway immunity
Authors: Langelier Chaz
Published: April 2018

Chronic tobacco smoke exposure exacerbates
Haemophilus influenzae
infection by disrupting innate and adaptive immune responses in mice.
Needles no more
Authors: Shen Keyue
Published: April 2018

A needle-free graphene-based biosensor monitors blood glucose levels in real time.
Draft Genome Sequence of Multidrug-Resistant Escherichia coli NIVEDI-P44, Isolated from a Chicken Fecal Sample in Northeast India
Authors: Tewari Rituparna , Das Mitra Susweta , Das Sangita , Jadhao Sudhir , Mishra Gayatri , Ganaie Feroze , Shome Rajeswari , Rahman Habibur , Shome Bibek Ranjan
Published: April 2018

We report here the draft genome sequence of a multidrug-resistant
Escherichia coli
strain (NIVEDI-P44) isolated from a chicken fecal sample. The estimated genome size is 4.76 Mb, with a G+C content of 50.65%. The genome harbors multiple antibiotic resistance genes,
bla
DHA-1
,
mph
(A),
strA
,
strB
,
dfrA14
,
sul-2
,
tet
(A), and
qnrS1
.
Draft Genome Sequence of the Putative Marine Pathogen Aquimarina sp. Strain I32.4
Authors: Ranson Hilary J. , LaPorte Jason , Spinard Edward , Chistoserdov Andrei Y. , Gomez-Chiarri Marta , Nelson David R. , Rowley David C.
Published: April 2018

Aquimarina
sp. strain I32.4 (formerly
Aquimarina
sp. ‘
homaria
’) is a putative pathogen involved in epizootic shell disease in the American lobster (
Homarus americanus
). We report here the draft genome sequence for
Aquimarina
sp. strain I32.4 and describe virulence factors that may provide insight into its mechanism of pathogenicity.
Draft Genome Sequence of Bacillus sp. Strain M21, Isolated from the Arid Area of Matmata, Tunisia
Authors: Nasfi Zina , Poehlein Anja , Harms Henrik , Goralski Emilie , Fisch Katja M. , Daniel Rolf , König Gabriele M. , Schäberle Till F. , Bachoual Rafik
Published: April 2018

Bacillus
sp. strain M21 was isolated from an environmental sample. In antibacterial screenings, the strain inhibited growth of Gram-positive and Gram-negative test strains. The genome was assembled into 69 contigs with a total size of 5.178 Mb. The strain contains at least nine biosynthetic gene clusters for the production of specialized metabolites.
Draft Genome Sequence of Burkholderia cepacia ATCC 17759, a Polyhydroxybutyrate-Co-Valerate Copolymer-Producing Bacterium
Authors: Crooks Casey , Palmer Jonathan M. , Lindner Daniel L.
Published: April 2018

Burkholderia cepacia
ATCC 17759, isolated from forest soils in Trinidad, accumulates large amounts of polyhydroxyalkanoate copolymers when grown on xylose, mannose, arabinose, other carbohydrates, and organic acid cosubstrates. This 8.72-Mb draft genome sequence of
B. cepacia
ATCC 17759 will provide better insight into this organism's utility in lignocellulose bioconversion.
Draft Genome Sequence of the Thermophilic Acetogen
Moorella humiferrea
DSM 23265
Authors: Poehlein Anja , Keyl Alisa , Milsch Jan C. , Daniel Rolf
Published: April 2018

Moorella humiferrea
is an endospore-forming, anaerobic, and thermophilic bacterium which was isolated from a terrestrial hydrothermal spring.
M. humiferrea
is able to use humic acid or 10-anthraquinone-2,6-disulfonate as an electron-shuttling compound for growth and Fe(III) reduction. The genome has a size of 2.629 Mb and contains 2,668 predicted protein-coding genes.
Complete Genome Sequences of Two Bacillus pumilus Strains from Cuatrociénegas, Coahuila, Mexico
Authors: Zarza Eugenia , Alcaraz Luis D. , Aguilar-Salinas Bernardo , Islas Africa , Olmedo-Álvarez Gabriela
Published: April 2018

We assembled the complete genome sequences of
Bacillus pumilus
strains 145 and 150a from Cuatrociénegas, Mexico. We detected genes codifying for proteins potentially involved in antagonism (bacteriocins) and defense mechanisms (abortive infection bacteriophage proteins and 4-azaleucine resistance). Both strains harbored prophage sequences. Our results provide insights into understanding the establishment of microbial interactions.
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information
Authors: Janssen Stefan , McDonald Daniel , Gonzalez Antonio , Navas-Molina Jose A. , Jiang Lingjing , Xu Zhenjiang Zech , Winker Kevin , Kado Deborah M. , Orwoll Eric , Manary Mark , Mirarab Siavash , Knight Rob
Published: April 2018

The move from OTU-based to sOTU-based analysis, while providing additional resolution, also introduces computational challenges. We demonstrate that one popular method of dealing with sOTUs (building a
de novo
tree from the short sequences) can provide incorrect results in human gut metagenomic studies and show that phylogenetic placement of the new sequences with SEPP resolves this problem while also yielding other benefits over existing methods.
SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control
Authors: Al-Ghalith Gabriel A. , Hillmann Benjamin , Ang Kaiwei , Shields-Cutler Robin , Knights Dan
Published: April 2018

Quality control of high-throughput DNA sequencing data is an important but sometimes laborious task requiring background knowledge of the sequencing protocol used (such as adaptor type, sequencing technology, insert size/stitchability, paired-endedness, etc.). Quality control protocols typically require applying this background knowledge to selecting and executing numerous quality control steps with the appropriate parameters, which is especially difficult when working with public data or data from collaborators who use different protocols. We have created a streamlined quality control pipeline intended to substantially simplify the process of DNA quality control from raw machine output files to actionable sequence data. In contrast to other methods, our proposed pipeline is easy to install and use and attempts to learn the necessary parameters from the data automatically with a single command.
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
Authors: Bauer Eugen , Thiele Ines
Published: April 2018

An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities.
Systematic development of a tennis injury prevention programme
Authors: Pas Haiko I M F L , Bodde Stefan , Kerkhoffs Gino M M J , Pluim Babette , Tiemessen Ivo J H , Tol Johannes L , Verhagen Evert , Gouttebarge Vincent
Published: April 2018

Introduction

Despite an injury incidence of up to 3.0/1000 hours of play, there are no published tennis injury prevention programmes. This article aims to describe the developmental process of TennisReady, an e-health tennis-specific injury programme for adult recreational tennis players.

Five-step approach

A bottom-up, five-step approach was used with the Knowledge Transfer Scheme as a guideline. During the first step, a problem statement among targeted users was carried out. 475 (partially) completed surveys and group interviews (n=8) revealed a preference for an app-based prevention intervention of 10–15 min. As a second step, a systematic review was performed to identify prevention strategies in tennis. None were found. In step 3, during two expert group meetings (n=18), the findings of the first two steps were discussed and goals were formulated. Relevant and potential exercises for the programme were discussed. A subgroup of a total of six physical therapists, physicians and trainers developed the content of the programme in step 4. Step 5 included an evaluation of the exercises in 33 recreational tennis players. Participants evaluated the exercises during training sessions with trainers involved in the programme’s development or their colleagues. Participants evaluated the programme through standardised surveys or group interviews. Based on this evaluation, the programme was adjusted by altering exercises and frequencies, and it was evaluated in a second target group (n=27). The second evaluation did not result in any major changes to the final prevention programme.

Conclusion

Through a five-step approach guided by the Knowledge Transfer Scheme, we developed an e-health tennis-specific prevention programme for adult tennis players. This 10 min intervention will require testing in a randomised controlled setting.
Human rights-based approach to unintentional injury prevention
Authors: MacKay J Morag , Ryan Mark Andrew
Published: April 2018

Unintentional injury remains an important global public health issue, and efforts to address it are often hampered by a lack of visibility, leadership, funding, infrastructure, capacity and evidence of effective solutions. The growing support for a socioecological model and a systems approach to prevention—along with the acknowledgement that injury prevention can be a byproduct of salutogenic design and activities—has increased opportunities to integrate unintentional injury prevention into other health promotion and disease prevention agendas. It has also helped to integrate it into the broader human development agenda through the Sustainable Development Goals. This growing support provides new opportunities to use a human rights-based approach to address the issue. The human rights-based approach is based on the idea that all members of society have social, economic and cultural rights and that governments are responsible and accountable for upholding those rights. It incorporates a systems approach, addresses inequity and places an emphasis on the most vulnerable corners of humanity. It also leverages legal statutes and provides organisations with the opportunity to build existing international goals and benchmarks into their monitoring efforts. This paper describes the approach and highlights how it can leverage attention and investment to address current challenges for unintentional injury.
KRASfluorescence in situ hybridisation testing for the detection and diagnosis of pancreatic adenocarcinoma
Authors: Shiroma Noriyuki , Arihiro Koji , Oda Miyo , Orita Makoto
Published: April 2018

Aims

The aim of our study was to analyse correlations betweenKRASmutation status, chromosomal changes that affectKRASstatus in cells from pancreatic tumours.

Methods

We collected 69 cases of surgically resected pancreatic ductal adenocarcinoma (PDA) and seven cases of chronic pancreatitis (CP). Chromosomal abnormalities ofKRASand CEP12 were detected using fluorescence in situ hybridisation (FISH).

Results

The number of CEP12 signals per cell ranged from 1.78 to 2.04 and 1.46 to 4.88 in CP and PDA samples, respectively, while the number ofKRASsignals per cell ranged from 1.94 to 2.06 and 1.88 to 8.18 in CP and PDA samples, respectively. The ‘chromosomal instability index’, which was defined as the percentage of cells with any chromosomal abnormality, was over 5.7 times greater in PDA than in CP. We performedKRASmutation analysis by direct sequencing and found that tumours withKRASmutations have a significantly higher meanKRASsignal per cell from PDA samples compared with tumours with wild-typeKRAS. KRASamplification was noted in 10% of cases. Although we found that lymph node metastasis and distal metastasis of PDA were more frequent in cases withKRASamplification, this was not correlated with overall survival. Using a threshold of 40%, we found that the chromosomal instability index robustly discriminated PDA cells from CP cells.

Conclusions

Based on these findings, we concluded that FISH testing ofKRASusing cytology samples may represent an accurate approach for the diagnosis of PDA.
Intermediate catheter placement distal to the cerebral aneurysm during flow diversion embolization with the Surpass device
Authors: Topcuoglu Osman Melih , Arat Anil , Peker Ahmet , Sarikaya Basar
Published: April 2018

Purpose

We present the preliminary angiographic and clinical results of the combined utilization of an AXS Catalyst 5 (Cat5) distal access catheter and a Surpass flow diverter (SFD) for the endovascular treatment of intracranial aneurysms.

Materials and methods

Interventional neuroradiology case records were evaluated retrospectively to identify patients treated with an SFD in combination with Cat5. Demographic data, technical success, location of the catheter tip, aneurysm occlusion rate, and procedure-related morbidity and mortality were noted.

Results

The analysis yielded 24 patients with 25 aneurysms with a mean age of 52.3±19.7 years. The mean aneurysm diameter was 15.7±8.8 mm. Twenty-one were anterior circulation (seven supraclinoid, one middle cerebral, one anterior choroidal and 12 petrocavernous) and four were posterior circulation (three basilar tip, one posterior inferior cerebellar) aneurysms. Only two of these aneurysms were re-treatments for recurrences. For SFD deployment, the distal tip of Cat5 was placed intradurally and at, or distal to, M1 segment in 88% and 48% of patients, respectively. Aneurysms were bypassed with Cat5 in 80% of the procedures. In one patient, flow diversion was abandoned totally due to arterial tortuosity. With the exclusion of this patient, the technical success rate was 91.7%. There was no permanent procedure-related morbidity or mortality. Of the 22 aneurysms treated successfully with the Surpass device, 20 had imaging follow-up at 6.3±3.8 months and 95% were totally occluded.

Conclusion

The Cat5 catheter, which was manufactured for the navigation of large-bore stent-like devices, is a useful adjunct to the Surpass device and allowed us to deploy the device safely.
Does medical students’ gender affect their clinical learning of gynaecological examination? A retrospective cohort study
Authors: Wallbridge Thomas , Holden Angela , Picton Aled , Gupta Janesh
Published: April 2018

Introduction

Medical graduates should be competent in gynaecological examination as well as associated skills including speculum use and swabbing. Male and female medical students may have different opportunities to practise these skills in clinical environments, potentially impacting on confidence and competence. This study explores this further via reviewing students’ learning experience in genitourinary medicine (GUM) and obstetrics and gynaecology (O&G) clinics.

Methods

Cross-sectional study of 759 year 4 and year 5 University of Birmingham medical students via an online questionnaire. This explored degree of participation, impact of gender and self-reported confidence.

Results

Overall response rate was 31% (233/759). Students of either gender who observed an examination being performed by a clinician were more likely to perform the same examination. Female students reported more opportunities to practise gynaecological examination and associated skills. Female students were more likely to be granted consent to perform speculum examinations, vaginal swabbing and vaginal bimanual examinations. Sixty-five per cent of male students felt that their gender affected their learning experience with female patients. Despite this, there was no significant difference in self-reported confidence level in performing gynaecological examinations between genders at the end of placement.

Conclusion

The majority of male students perceived that their gender impacted their clinical experience in O&G and GUM. Self-reported confidence levels were unaffected, which could reflect varying approaches to competence between genders. The link between observing examinations and subsequent opportunities to practise is key. This could demonstrate students developing rapport and trust with patients, and clinicians’ roles as gatekeepers.
Case series: periocular habronemiasis in five horses in the Netherlands
Authors: Verhaar Nicole , Hermans Hanneke , van Rooij Eugene , van Oldruitenborgh‐Oosterbaan Marianne Sloet , Ensink Jos
Published: April 2018

In tropical and subtropical climates, infection of periocular tissue by Habronema larvae is a recognised cause of conjunctivitis or blepharitis. To the authors’ knowledge, only a few cases of habronemiasis have been described in Western Europe, and it has not been documented previously in the Netherlands. The objective of this report is to describe the occurrence of five cases of (peri)ocular habronemiasis in the Netherlands, of which four date from the past few years. The diagnosis was based on the history, clinical signs and histopathologic examination of biopsy specimens. A granulomatous conjunctivitis/dermatitis and sulphur‐like granules were present in all cases. Histopathology showed an eosinophilic granulomatous inflammation, and three out of five (60 per cent) samples revealed one or more nematodes on section. Treatment combinations with surgical excision, local corticosteroid and/or anthelmintic drugs were used. Furthermore, all horses received ivermectin or moxidectin. Treatment resulted in healing of the lesions in four horses. One case, which was refractory to treatment, resolved spontaneously after the onset of colder weather. This case series suggests an increased prevalence of (peri)ocular habronemiasis in the Netherlands. This diagnosis should therefore be considered when being presented with a horse with granulomatous conjunctivitis/dermatitis in Western Europe, especially during the summer months.
Genomic investigation of porcine periweaning failure to thrive syndrome (PFTS)
Authors: Bertolini Francesca , Yang Tianfu , Huang Yanyun , Harding John C S , Plastow Graham S , Rothschild Max F
Published: April 2018

Porcine periweaning failure to thrive syndrome (PFTS) can be defined by anorexia, lethargy, progressive debilitation and compulsive behaviours that occur in seemingly healthy pigs within two to threeweeks of weaning in the absence of any known infectious, nutritional, management or environmental factors. A genetic component has been hypothesised for this syndrome. In the present study, 119 commercial pigs (80 cases and 39 controls) were genotyped with the porcine 80K single nucleotide polymorphism‐chip and were analysed with logistic regression and two Fixation Index‐based approaches. The analyses revealed several regions on chromosomes 1, 3, 6 and 11 with moderate divergence between cases and controls, particularly three haplotypes on SSC3 and 11. The gene‐based analyses of the candidate regions revealed the presence of genes that have been reported to be associated with phenotypes like PFST including depression (PDE10A) and intestinal villous atrophy (CUL4A). It is important to increase the effort of collecting more samples to improve the power of these analyses.
Time-dependent behaviour of sand with different fine contents under oedometric loading
Authors: Levin Friedrich , Vogt Stefan , Cudmani Roberto
Published: April 2018

To characterize the effects of creep, strain rate, and relaxation in granular soils, different sands have been studied under oedometric loading. The tests were analysed in the framework of the isotache concept. The results show increasing creep rates with increasing vertical stresses and a strong reduction of the creep rate upon unloading. A lower void ratio leads to less creep. Evaluation of the ratio Cα/Cc, where Cα is the creep coefficient and Cc is the compression index, demonstrates considerable deviation from a constant soil-specific value for the sands. With increasing fine content, however, a constant soil-specific ratio has been found for a silty sand. In strain rate–controlled tests, a sand with low and a sand with significant content of nonplastic fines were compared. Constant rate of strain tests displayed practically no strain rate dependency for the sand with little fines and a well visible strain rate dependency for the very silty sand. Tests with stepwise change of strain rate showed non-isotache behaviour for the sand with little fines and isotache behaviour for the other. Stress-relaxation tests displayed an isochronous behaviour. The analysis of the three viscous effects in sands showed they cannot altogether be mathematically described in the framework of the isotache concept. A new compression model for the creep behaviour of sands is presented.
Experimental setup influences the cardiovascular responses of decapod crustaceans to environmental change
Authors: McGaw I.J. , Nancollas S.J.
Published: April 2018

The effects of different holding methods on heart rate (HR) changes in the green crab, Carcinus maenas (Linnaeus, 1758), were investigated. Green crabs were held in perforated plastic boxes (with or without a layer of sand) suspended above the bottom of the tank or strapped to a weighted plastic grate. The HR of green crabs classified as unrestrained (plastic box with or without sand) dropped more rapidly compared with restrained (hanging from band, strapped to grate) green crabs. Within 1 h, unrestrained green crabs exhibited periods of cardiac pausing accounting for between 8% and 14% of the hourly time. In contrast, restrained green crabs rarely exhibited cardiac pausing. When the green crabs were subjected to a temperature increase (10–30 °C), the HR of unrestrained green crabs reached higher levels than that of the restrained animals. The four restraining methods were also used to investigate cardiac responses to hypoxia. During progressive hypoxia (100%–20% oxygen), the HR of unrestrained green crabs declined to lower levels than that of the restrained animals. The restraining methods appeared to be more stressful for the green crabs that maintained elevated HRs and were less able to respond to environmental change compared with green crabs that could move freely within a small chamber. This suggests that even subtle changes in experimental design may alter physiological responses.
Optical properties of uniaxially strained graphene on transition metal dichalcogenide substrate
Authors: Goswami Partha
Published: April 2018

The uniaxially strained graphene monolayer on transition metal dichalcogenide (GrTMD) substrate, constituting a van der Waals heterostructure (vdWH), is found to possess unusual intra-band plasmon dispersion ([Formula: see text]) with stronger incarceration compared to that of a standalone, doped graphene for finite doping in the long wavelength limit. The intra-band absorbance of GrTMD is found to be an increasing (decreasing) function of the strain field (frequency) at a given frequency (strain field). It is also observed that whereas the strain field is responsible for the valley polarization, a Rashba coupling-dependent pseudo Zeeman term arising due to the interplay of substrate-induced interactions is found to bring about the spin degeneracy lifting and the gate voltage tunable spin polarization. The latter turns out to be inversely proportional to the square root of the carrier concentration.
Image Captioning with Deep Bidirectional LSTMs and Multi-Task Learning
Authors: Wang Cheng , Yang Haojin , Meinel Christoph
Published: April 2018

Generating a novel and descriptive caption of an image is drawing increasing interests in computer vision, natural language processing, and multimedia communities. In this work, we propose an end-to-end trainable deep bidirectional LSTM (Bi-LSTM (Long Short-Term Memory)) model to address the problem. By combining a deep convolutional neural network (CNN) and two separate LSTM networks, our model is capable of learning long-term visual-language interactions by making use of history and future context information at high-level semantic space. We also explore deep multimodal bidirectional models, in which we increase the depth of nonlinearity transition in different ways to learn hierarchical visual-language embeddings. Data augmentation techniques such as multi-crop, multi-scale, and vertical mirror are proposed to prevent overfitting in training deep models. To understand how our models “translate” image to sentence, we visualize and qualitatively analyze the evolution of Bi-LSTM internal states over time. The effectiveness and generality of proposed models are evaluated on four benchmark datasets: Flickr8K, Flickr30K, MSCOCO, and Pascal1K datasets. We demonstrate that Bi-LSTM models achieve highly competitive performance on both caption generation and image-sentence retrieval even without integrating an additional mechanism (e.g., object detection, attention model). Our experiments also prove that multi-task learning is beneficial to increase model generality and gain performance. We also demonstrate the performance of transfer learning of the Bi-LSTM model significantly outperforms previous methods on the Pascal1K dataset.