bluuebunny/crossref_metadata_2025 huggingface dataset:
Glaucoma referral refinement in Ireland: managing the sensitivity‐specificity paradox in optometric practice
Authors: Barrett Catriona , O'Brien Colm , Loughman James
Published: March 2018

Purpose

Glaucoma referral refinement (GRR) has proven a successful demand management strategy for glaucoma suspect cases in the United Kingdom (UK). A GRR clinic was established in Dublin, Ireland to investigate the clinical viability of this pathway outside the UK's National Health Service (NHS) structures, and away from the influence of National Institute for Clinical Excellence (NICE) guidance.

Methods

Glaucoma suspect patients were recruited into the scheme following referral from community optometrists in the greater Dublin area. The GRR exam protocol was designed in consultation with the participating ophthalmology department. The refinement scheme optometrist, trained through apprenticeship style experience at a hospital outpatient clinic, made a tentative management decision after carrying out the GRR exam. The final management decision was made in a ‘virtual clinic’ by a glaucoma specialist consultant ophthalmologist.

Results

Two hundred and twenty‐five glaucoma suspect patients were seen in the scheme. After their first GRR visit, 28% were discharged back to their own optometrist, 42% were monitored in the GRR clinic, and 30% were referred to ophthalmology. After this monitoring cohort were further assessed, a total of 38% of the patients seen within the scheme required referral to ophthalmology. Sixteen percent of the total participant group (n = 225) were lost to follow up. Cohen's κ was used to determine the level of agreement between the scheme optometrist and ophthalmologist. There was substantial agreement, with κ = 0.63 for the first visit management decisions (n = 225). Agreement increased for subsequent monitoring visits with κ = 0.85 for second visits (n = 65), and κ = 0.69 for all management decisions within the scheme (n = 301). We received management outcomes for 44 of the 86 patients referred to ophthalmology. Of these 44, 57% received medical treatment for glaucoma, 34% were monitored without treatment, 2% were discharged, and 7% had comorbidities that were assessed and managed.

Conclusion

Of the patients seen within the scheme, 62% did not require referral onward to ophthalmology, thus releasing the significant majority of hospital clinic slots that would previously have been required to examine such patients. The high level of inter‐professional decision agreement likely reflects the benefits of pre‐scheme apprenticeship style training and ongoing hospital clinic participation by the scheme optometrist. The rate of loss to follow up compares favourably with ophthalmology led, hospital based, glaucoma clinics. Nevertheless, the losses indicate that patient education remains a key priority for future planning.
Use of topical therapies for pediatric psoriasis: A systematic review
Authors: Kravvas Georgios , Gholam Karolina
Published: March 2018

Psoriasis is one of the most common chronic skin diseases, affecting 1%‐3% of the general population. It can have a significant negative impact on a patient's quality of life, and in approximately 30% of patients first symptoms can be traced back to childhood. We have performed a comprehensive literature search using the MEDLINE database in order to ascertain the efficacy and adverse reactions of topical treatments in pediatric psoriasis. A total of 13 relevant articles were identified on the following topical agents: corticosteroids, calcineurin inhibitors, vitamin D analogs, and dithranol. Corticosteroids achieved clearance in 72.7% of patients. Calcitriol lead to a 57.2%‐100% mean improvement in severity, and calcipotriol to 52%‐64%. Combination of calcipotriol and corticosteroids achieved an improvement in mean severity ranging between 32.1% and 80%. Treatment with tacrolimus lead to an >50% improvement. Finally, short contact dithranol lead to a variable response in clearance between different studies, ranging between 3.7% and 81%. No serious adverse reactions were documented, the most common local reaction being irritation. Pediatric psoriasis is a common and challenging condition with no easy and definitive solution. Topical agents are safe, easy to use, readily available and cheap. However, they need to be applied repeatedly, may cause skin irritation, and can be messy. Based on the results presented above, we recommend utilizing all the available topical options before escalating to systemic treatments.
Presepsin as a predictor of early onset neonatal sepsis in the umbilical cord blood of premature infants with premature rupture of membranes
Authors: Seliem Wael , Sultan Amira M.
Published: March 2018

Background

The aim of this study was to investigate whether presepsin level in umbilical cord blood can be used as a predictor of early onset neonatal sepsis (EONS) in preterm labor with premature rupture of membranes (PROM), allowing rational use of antibiotics.

Methods

All preterm infants between 24 + 0 and 36 + 6 weeks of gestation born to pregnant women with PROM were enrolled in the study. Blood samples were obtained from clamped umbilical cords after delivery of the neonate and prior to the delivery of the placenta for C‐reactive protein and presepsin measurement. A diagnosis or suspicion of EONS was based on clinical symptoms or laboratory results in the absence of positive blood culture.

Results

A total of 288 women were included in the study and delivered at 31 + 4 weeks (range, 25–36 + 5 weeks). Microbial invasion of the amniotic cavity was identified in 62 women (81.6%) with EONS and in 31 (14.6%) without (P = 0.004). The prevalence of EONS was 26.4% (76/288). Median umbilical cord presepsin was significantly higher in neonates with EONS than in those without: 2,231 pg/mL (range, 1,442–3,988 pg/mL) versus 275 pg/mL (range, 116–326 pg/mL; P < 0.000). On logistic regression analysis the only independent predictor of EONS was umbilical cord blood presepsin (OR, 12.6; 95% CI: 2.5–28.1, P = 0.000).

Conclusions

Umbilical cord blood presepsin is a predictor for EONS in preterm infants with PROM and may help to reduce the unnecessary use of antibiotics.
Modelling and automated calibration of a general multi‐projective camera
Authors: Khoramshahi Ehsan , Honkavaara Eija
Published: March 2018

Recently, multi‐projective cameras (MPCs), often based on frame‐mounted multiple cameras with a small baseline and arbitrary overlap, have found a remarkable place in geomatics and vision‐based applications. This paper outlines the geometric calibration of a general MPC by presenting a mathematical model that describes its unknown generic geometry. A modified bundle block adjustment is employed to calibrate an industrial‐level 360° non‐metric camera. The structure of any MPC can be retrieved as a calibration set of relative and interior orientation parameters (as well as the pose of the MPC shots) using a calibration room which has been accurately determined by close range photogrammetry. To demonstrate the efficiency and precision of the model, a Panono camera (an MPC with 36 individual cameras) was calibrated. After the adjustment, sub‐pixel image residuals and acceptable object‐space errors were observed.
Chili anthracnose: Colletotrichum taxonomy and pathogenicity
Authors: Mongkolporn O. , Taylor P. W. J.
Published: March 2018

Chili anthracnose is caused by Colletotrichum species mostly associated with the acutatum, truncatum and gloeosporioides complexes. Since 2009 the Colletotrichum taxonomy has been extensively revised based on multigene phylogenetics, which has had a large impact on the number of species known to cause anthracnose disease of chili. This review discusses (i) the taxonomy of Colletotrichum spp. infecting chili, and (ii) the impact of Colletotrichum pathotypes on breeding for resistance to anthracnose. To date, 24 Colletotrichum species have been identified as pathogens of chili anthracnose, with the three main pathogens being C. scovillei, C. truncatum and C. siamense. Identification of several pathotypes within these three Colletotrichum species, particularly pathotypes that can overcome resistance in the related Capsicum species, Ca. chinense and Ca. baccatum, will be of major concern to plant breeders as they develop resistant chili genotypes from the transfer of resistance genes from these Capsicum species into Ca. annuum. Accurate identification of the Colletotrichum species causing anthracnose and improved understanding of the biology of the Colletotrichum species and their interaction with the host will enable the application of improved integrated disease management techniques.
Anatomical and hormonal description of rootlet primordium development along white lupin cluster root
Authors: Gallardo Cécilia , Hufnagel Bárbara , Casset Célia , Alcon Carine , Garcia Fanny , Divol Fanchon , Marquès Laurence , Doumas Patrick , Péret Benjamin
Published: March 2018

Cluster root (CR) is one of the most spectacular plant developmental adaptations to hostile environment. It can be found in a few species from a dozen botanical families, including white lupin (Lupinus albus) in the Fabaceae family. These amazing structures are produced in phosphate‐deprived conditions and are made of hundreds of short roots also known as rootlets. White lupin is the only crop bearing CRs and is considered as the model species for CR studies. However, little information is available on CRs atypical development, including the molecular events that trigger their formation. To provide insights on CR formation, we performed an anatomical and cellular description of rootlet development in white lupin. Starting with a classic histological approach, we described rootlet primordium development and defined eight developmental stages from rootlet initiation to their emergence. Due to the major role of hormones in the developmental program of root system, we next focussed on auxin‐related mechanisms. We observed the establishment of an auxin maximum through rootlet development in transgenic roots expressing the DR5:GUS auxin reporter. Expression analysis of the main auxin‐related genes [TIR, Auxin Response Factor (ARF) and AUX/IAA] during a detailed time course revealed specific expression associated with the formation of the rootlet primordium. We showed that L. albus TRANSPORT INHIBITOR RESPONSE 1b is expressed during rootlet primordium formation and that L. albus AUXIN RESPONSE FACTOR 5 is expressed in the vasculature but absent in the primordium itself. Altogether, our results describe the very early cellular events leading to CR formation and reveal some of the auxin‐related mechanisms.
Surgery without papilla incision: tunneling flap procedures in plastic periodontal and implant surgery
Authors: Zuhr Otto , Rebele Stephan F. , Cheung Stefani L. , Hürzeler Markus B. ,   the Research Group on Oral Soft Tissue Biology and Wound Healing
Published: March 2018

Diverse clinical advancements, together with some relevant technical innovations, have led to an increase in popularity of tunneling flap procedures in plastic periodontal and implant surgery in the recent past. This trend is further promoted by the fact that these techniques have lately been introduced to a considerably expanded range of indications. While originally described for the treatment of gingival recession‐type defects, tunneling flap procedures may now be applied successfully in a variety of clinical situations in which augmentation of the soft tissues is indicated in the esthetic zone. Potential clinical scenarios include surgical thickening of thin buccal gingiva or peri‐implant mucosa, alveolar ridge/socket preservation and implant second‐stage surgery, as well as soft‐tissue ridge augmentation or pontic site development. In this way, tunneling flap procedures developed from a technique, originally merely intended for surgical root coverage, into a capacious surgical conception in plastic periodontal and implant surgery. The purpose of this article is to provide a comprehensive overview on tunneling flap procedures, to introduce the successive development of the approach along with underlying ideas on surgical wound healing and to present contemporary clinical scenarios in step‐by‐step photograph‐illustrated sequences, which aim to provide clinicians with guidance to help them integrate tunneling flap procedures into their daily clinical routine.
A novel HLA‐A*31 allele, A*31:126N, was identified by sequence‐based typing
Authors: Chi X.‐Y. , Liu L. , Hu B. , Jiao S.‐X.
Published: March 2018

A novel allele A*31:126N was identified in a Chinese individual by sequence‐based typing method.
Blood donation barriers and facilitators of Sub‐Saharan African migrants and minorities in Western high‐income countries: a systematic review of the literature
Authors: Klinkenberg E. F. , Huis In't Veld E. M. J. , de Wit P. D. , van Dongen A. , Daams J. G. , de Kort W. L. A. M. , Fransen M. P.
Published: March 2018

Objectives

The present study aimed to gain more insight into, and summarise, blood donation determinants among migrants or minorities of Sub‐Saharan heritage by systematically reviewing the current literature.

Background

Sub‐Saharan Africans are under‐represented in the blood donor population in Western high‐income countries. This causes a lack of specific blood types for transfusions and prevention of alloimmunisation among Sub‐Saharan African patients.

Methods/materials

Medline, EMBASE, PsycINFO and BIOSIS were searched for relevant empirical studies that focused on barriers and facilitators of blood donation among Sub‐Saharan Africans in Western countries until 22 June 2017. Of the 679 articles screened by title and abstract, 152 were subsequently screened by full text. Paired reviewers independently assessed the studies based on predefined eligibility and quality criteria.

Results

Of the 31 included studies, 24 used quantitative and 7 used qualitative research methods. Target cohorts varied from Black African Americans and refugees from Sub‐Sahara Africa to specific Sub‐Saharan migrant groups such as Comorians or Ethiopians. Main recurring barriers for Sub‐Saharan Africans were haemoglobin deferral, fear of needles and pain, social exclusion, lack of awareness, negative attitudes and accessibility problems. Important recurring facilitators for Sub‐Saharan Africans were altruism, free health checks and specific recruitment and awareness‐raising campaigns.

Conclusion

The findings of this review can be used as a starting point to develop recruitment and retention strategies for Sub‐Saharan African persons. Further research is needed to gain more insight in the role of these determinants in specific contexts as socioeconomic features, personal histories and host country regulations may differ per country.
Molecular and serological infection marker screening in blood donors indicates high endemicity of hepatitis E virus in Poland
Authors: Grabarczyk Piotr , Sulkowska Ewa , Gdowska Jolanta , Kopacz Aneta , Liszewski Grzegorz , Kubicka‐Russel Dorota , Baylis Sally A. , Corman Victor M. , Noceń Ewa , Piotrowski Dariusz , Antoniewicz‐Papis Jolanta , Łętowska Magdalena
Published: March 2018

BACKGROUND

Until now, markers of hepatitis E virus (HEV) infection have not been studied in blood donors throughout Poland, and no acute case of HEV infection has been closely documented or confirmed by HEV RNA detection. The prevalence of HEV infection markers, including HEV RNA in Polish blood donors and virus genotypes was investigated.

STUDY DESIGN AND METHODS

In total, 12,664 individual donations from 22 Polish blood transfusion centers were tested for HEV RNA by transcription‐mediated amplification. In addition, 3079 first‐time donors sampled throughout Poland also were screened for antibodies to HEV. HEV RNA and immunoglobulin M‐positive donations were confirmed using real‐time reverse transcription‐polymerase chain reaction and Western blotting, respectively.

RESULTS

Ten donors were identified as RNA initial reactive (one of 1266 donors), and six (one of 2109) were identified as repeat reactive and confirmed by real‐time reverse transcription‐polymerase chain reaction or seroconversion. Sequence analysis identified HEV Genotype 3c in one donor and Genotype 3i in two others. On average, 43.5% of donors were immunoglobulin G‐positive. Immunoglobulin G seroprevalence ranged from 22.7% to 60.8% in group ages 18 to 27 years and 48 to 57 years, respectively and differed between administrative regions from 28.9% in Podlasie to 61.3% in Wielkopolska. Thirty‐nine of the donors were immunoglobulin M‐positive, and seven donors were IgM positive only (0.2%). Of 37 immunoglobulin M‐reactive samples tested by Western blot, 24 (64.9%) were confirmed.

CONCLUSIONS

The current results indicate a high level of HEV endemicity throughout Poland compared with other countries. There is an urgent need to consider the protection of recipients of blood components against transfusion‐transmitted HEV infection.
Multiple ocular developmental defects in four closely related alpacas
Authors: Knickelbein Kelly E. , Maggs David J. , Reilly Christopher M. , Good Kathryn L. , Gionfriddo Juliet R.
Published: March 2018

Objective

To describe the clinical, gross pathologic, and histopathologic findings for a visually impaired 5.8‐year‐old female alpaca with multiple ocular abnormalities, as well as the clinical findings for three closely related alpacas.

Animals studied

Four alpacas.

Procedures

Ophthalmic examination was performed on a 16‐month‐old female alpaca following observation of visual impairment while hospitalized for an unrelated illness. Following acute systemic decline and death 4.5 years later, the alpaca's brain, optic nerves, and eyes were examined grossly and histologically. Ophthalmic examination of three closely related alpacas was subsequently performed.

Results

The 16‐month‐old female alpaca (Alpaca 1) had ophthalmoscopic findings suggestive of a coloboma or hypoplasia of the retinal pigment epithelium (RPE) and choroid, and suspected optic nerve hypoplasia OU. Histopathology performed 4.5 years later revealed moderate to severe choroidal, RPE, and retinal hypoplasia with multifocal retinal detachments OU. However, the optic nerves were normal in size and histologic appearance when compared to an age‐matched control. Clinical evaluation of the 2‐year‐old son of Alpaca 1 revealed iris colobomata OU and choroidal dysplasia/hypoplasia OD in addition to nonpathologic variations in melanin density including heterochromia iridis and a subalbinotic fundus OU. Clinical evaluation of the 13‐year‐old mother of Alpaca 1 revealed heterochromia iridis, cataracts, and a subalbinotic fundus OU. A 2‐year‐old half‐brother of Alpaca 1 had an RPE and choroidal coloboma OS.

Conclusion

The developmental ocular abnormalities diagnosed in these closely related alpacas are likely hereditary.
Evaluation of tendinosis of the long head of the biceps tendon by strain and shear wave elastography
Authors: Sahan Mehmet Hamdi , Inal Mikail , Burulday Veysel , Kultur Turgut
Published: March 2018

Aim: To investigate strain (SE) and shear wave elastography (SWE) characteristics of the long head of the biceps tendon (LHBT) tendinosis in comparison with magnetic resonance imaging (MRI) findings.Material and methods: Twenty patients with a MRI diagnosis of tendinosis and twenty healthy subjects with normal LHBT in MRI were prospectively examined by SE and SWE. SE color mapping was divided into four types in accordance with elasticity designs: type I predominantly blue (hardest tissue), type II predominantly blue-green (hard tissue), type III predominantly green (intermediate tissue), type IV predominantly green-yellow-red (soft tissue). Quantitative measurements of LHBT hardness with SWE were analyzed in kilopascals (kPa).Results: In the tendinosis group SE types in transverse scan were I in 24% of tendons, II in 50%, III in 25%, and in longitudinal scan I in 15%, II in 75%, and III in 10%. In the control group SE types in transversescan were II in 10% of tendons, III in 55%, IV in 35%, and in longitudinal scan II in 10%, III in 55%, and IV in 35%. SWE values in transverse scan were 38.32±7.2 kPa in the tendinosis group and 18.6±3.1 kPa in the control groupand in longitudinal scan 39.42±7.4 kPa in the tendinosis group, and 20.62±4.6 in the control group. There was a statistically significant difference in terms of elasticity patterns between the tendinosis and control groups (p<0.001). The receiver operating characteristic curve analysis was perfect and a cut-off value of tranverse 25.8 kPa and longitudinal, 24.6 kPa shear values had very high sensitivity and specificity for tendinosis.Conclusion: SE and SWE may be useful diagnostic tools for LHBT tendinosis when considering usability, cost effectiveness, and patient preference compared to MRI.
The joint influence of vowel duration and creak on the perception of internal phrase boundaries
Authors: Crowhurst Megan J.
Published: March 2018

Lengthening and creaky voice are associated with prosodic finality in English. Listeners can use lengthening to identify both utterance-internal and final prosodic phrase boundaries and can use creak to locate utterance endings. Less is known about listeners' use of creak to locate internal prosodic boundaries and the relative importance assigned to duration and creak when both are present. Participants in two experiments segmented structurally ambiguous sentences in which duration and creak were manipulated to signal prosodic boundaries. When duration- and creak-based cues provided redundant information, their effects were additive. When these cues conflicted, the effect of creak was subtractive.
Can Building Design Impact Physical Activity? A Natural Experiment
Authors: Eyler Amy A. , Hipp Aaron , Valko Cheryl Ann , Ramadas Ramya , Zwald Marissa
Published: March 2018

Background: Workplace design can impact workday physical activity (PA) and sedentary time. The purpose of this study was to evaluate PA behavior among university employees before and after moving into a new building. Methods: A pre–post, experimental versus control group study design was used. PA data were collected using surveys and accelerometers from university faculty and staff. Accelerometry was used to compare those moving into the new building (MOVERS) and those remaining in existing buildings (NONMOVERS) and from a control group (CONTROLS). Results: Survey results showed increased self-reported PA for MOVERS and NONMOVERS. All 3 groups significantly increased in objectively collected daily energy expenditure and steps per day. The greatest steps per day increase was in CONTROLS (29.8%) compared with MOVERS (27.5%) and NONMOVERS (15.9%), but there were no significant differences between groups at pretest or posttest. Conclusions: Self-reported and objectively measured PA increased from pretest to posttest in all groups; thus, the increase cannot be attributed to the new building. Confounding factors may include contamination bias due to proximity of control site to experimental site and introduction of a university PA tracking contest during postdata collection. Methodology and results can inform future studies on best design practices for increasing PA.
Coral reef structural complexity provides important coastal protection from waves under rising sea levels
Authors: Harris Daniel L. , Rovere Alessio , Casella Elisa , Power Hannah , Canavesio Remy , Collin Antoine , Pomeroy Andrew , Webster Jody M. , Parravicini Valeriano
Published: March 2018

If coral reefs continue to degrade, waves on coastlines may substantially increase, leading to greater coastal erosion.
Lessons in resilience
Authors: Underwood Emily
Published: March 2018

In war zones and refugee camps, researchers are putting resilience interventions to the test.
Science of science
Authors: Fortunato Santo , Bergstrom Carl T. , Börner Katy , Evans James A. , Helbing Dirk , Milojević Staša , Petersen Alexander M. , Radicchi Filippo , Sinatra Roberta , Uzzi Brian , Vespignani Alessandro , Waltman Ludo , Wang Dashun , Barabási Albert-László
Published: March 2018

The whys and wherefores of SciSci

The science of science (SciSci) is based on a transdisciplinary approach that uses large data sets to study the mechanisms underlying the doing of science—from the choice of a research problem to career trajectories and progress within a field. In a Review, Fortunato
et al.
explain that the underlying rationale is that with a deeper understanding of the precursors of impactful science, it will be possible to develop systems and policies that improve each scientist's ability to succeed and enhance the prospects of science as a whole.

Science
, this issue p.
eaao0185
Bacterial Enzymes Catalyzing the Synthesis of 1,8-Dihydroxynaphthalene, a Key Precursor of Dihydroxynaphthalene Melanin, from Sorangium cellulosum
Authors: Sone Yusuke , Nakamura Shuto , Sasaki Makoto , Hasebe Fumihito , Kim Seung-Young , Funa Nobutaka
Published: March 2018

1,8-Dihydroxynaphthalene (1,8-DHN) is a key intermediate in the biosynthesis of DHN melanin, which is specific to fungi. In this study, we characterized the enzymatic properties of the gene products of an operon consisting of
soceCHS1
,
bdsA
, and
bdsB
from the Gram-negative bacterium
Sorangium cellulosum
. Heterologous expression of
soceCHS1
,
bdsA
, and
bdsB
in
Streptomyces coelicolor
caused secretion of a dark-brown pigment into the broth. High-performance liquid chromatography (HPLC) analysis of the broth revealed that the recombinant strain produced 1,8-DHN, indicating that the operon encoded a novel enzymatic system for the synthesis of 1,8-DHN. Simultaneous incubation of the recombinant SoceCHS1, BdsA, and BdsB with malonyl-coenzyme A (malonyl-CoA) and NADPH resulted in the synthesis of 1,8-DHN. SoceCHS1, a type III polyketide synthase (PKS), catalyzed the synthesis of 1,3,6,8-tetrahydroxynaphthalene (T
4
HN)
in vitro
. T
4
HN was in turn converted to 1,8-DHN by successive steps of reduction and dehydration, which were catalyzed by BdsA and BdsB. BdsA, which is a member of the aldo-keto reductase (AKR) superfamily, catalyzed the reduction of T
4
HN and 1,3,8-tetrahydroxynaphthalene (T
3
HN) to scytalone and vermelone, respectively. The stereoselectivity of T
4
HN reduction by BdsA occurred on the
si
-face to give (
R
)-scytalone with more than 99% optical purity. BdsB, a SnoaL2-like protein, catalyzed the dehydration of scytalone and vermelone to T
3
HN and 1,8-DHN, respectively. The fungal pathway for the synthesis of 1,8-DHN is composed of a type I PKS, naphthol reductases of the short-chain dehydrogenase/reductase (SDR) superfamily, and scytalone dehydratase (SD). These findings demonstrated 1,8-DHN synthesis by novel enzymes of bacterial origin.

IMPORTANCE
Although the DHN biosynthetic pathway was thought to be specific to fungi, we discovered novel DHN synthesis enzymes of bacterial origin. The biosynthesis of bacterial DHN utilized a type III PKS for polyketide synthesis, an AKR superfamily for reduction, and a SnoaL2-like NTF2 superfamily for dehydration, whereas the biosynthesis of fungal DHN utilized a type I PKS, SDR superfamily enzyme, and SD-like NTF2 superfamily. Surprisingly, the enzyme systems comprising the pathway were significantly different from each other, suggesting independent, parallel evolution leading to the same biosynthesis. DHN melanin plays roles in host invasion and adaptation to stress in pathogenic fungi and is therefore important to study. However, it is unclear whether DHN biosynthesis occurs in bacteria. Importantly, we did find that bacterial DHN biosynthetic enzymes were conserved among pathogenic bacteria.
A Gene Homologous to rRNA Methylase Genes Confers Erythromycin and Clindamycin Resistance in Bifidobacterium breve
Authors: Martínez Noelia , Luque Roberto , Milani Christian , Ventura Marco , Bañuelos Oscar , Margolles Abelardo
Published: March 2018

Bifidobacteria are mutualistic intestinal bacteria, and their presence in the human gut has been associated with health-promoting activities. The presence of antibiotic resistance genes in this genus is controversial, since, although bifidobacteria are nonpathogenic microorganisms, they could serve as reservoirs of resistance determinants for intestinal pathogens. However, until now, few antibiotic resistance determinants have been functionally characterized in this genus. In this work, we show thatBifidobacterium breveCECT7263 displays atypical resistance to erythromycin and clindamycin. In order to delimit the genomic region responsible for the observed resistance phenotype, a library of genomic DNA was constructed and a fragment of 5.8 kb containing a gene homologous to rRNA methylase genes was able to confer erythromycin resistance inEscherichia coli. This genomic region seems to be very uncommon, and homologs of the gene have been detected in only one strain ofBifidobacterium longumand two other strains ofB. breve. In this context, analysis of shotgun metagenomics data sets revealed that the gene is also uncommon in the microbiomes of adults and infants. The structural gene and its upstream region were cloned into aB. breve-sensitive strain, which became resistant after acquiring the genetic material.In vitroconjugation experiments did not allow us to detect gene transfer to other recipients. Nevertheless, prediction of genes potentially acquired through horizontal gene transfer events revealed that the gene is located in a putative genomic island.

IMPORTANCEBifidobacterium breveis a very common human intestinal bacterium. Often described as a pioneer microorganism in the establishment of early-life intestinal microbiota, its presence has been associated with several beneficial effects for the host, including immune stimulation and protection against infections. Therefore, some strains of this species are considered probiotics. In relation to this, because probiotic bacteria are used for human and animal consumption, one of the safety concerns over these bacteria is the presence of antibiotic resistance genes, since the human gut is a densely populated habitat that could favor the transfer of genetic material to potential pathogens. In this study, we analyzed the genetic basis responsible for the erythromycin and clindamycin resistance phenotype ofB. breveCECT7263. We were able to identify and characterize a novel gene homologous to rRNA methylase genes which confers erythromycin and clindamycin resistance. This gene seems to be very uncommon in other bifidobacteria and in the gut microbiomes of both adults and infants. Even though conjugation experiments showed the absence of transferability underin vitroconditions, it has been predicted to be located in a putative genomic island recently acquired by specific bifidobacterial strains.
Euphyllophyte Paleoviruses Illuminate Hidden Diversity and Macroevolutionary Mode of Caulimoviridae
Authors: Gong Zhen , Han Guan-Zhu
Published: March 2018

Endogenous viral elements (paleoviruses) provide “molecular fossils” for studying the deep history and macroevolution of viruses. Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms, but little is known about EPRVs in earlier-branching plants. Here we use a large-scale phylogenomic approach to investigate the diversity and macroevolution of plant pararetroviruses (formally known as
Caulimoviridae
). We uncover an unprecedented and unappreciated diversity of EPRVs within the genomes of gymnosperms and ferns. The known angiosperm viruses constitute only a minor part of the
Caulimoviridae
diversity. By characterizing the distribution of EPRVs, we show that no major euphyllophyte lineages escape the activity of
Caulimoviridae
, raising the possibility that many exogenous
Caulimoviridae
remain to be discovered in euphyllophytes. We find that the copy numbers of EPRVs are generally high, suggesting that EPRVs might define a unique group of repetitive elements and represent important components of euphyllophyte genomes. Evolutionary analyses suggest an ancient origin of
Caulimoviridae
and at least three independent origins of
Caulimoviridae
in angiosperms. Our findings reveal the remarkable diversity of
Caulimoviridae
and have important implications for understanding the origin and macroevolution of plant pararetroviruses.

IMPORTANCE
Few viruses have been documented in plants outside angiosperms. Viruses can occasionally integrate into host genomes, forming endogenous viral elements (EVEs). Endogenous plant pararetroviruses (EPRVs) are widespread in angiosperms. In this study, we performed comprehensive comparative and phylogenetic analyses of EPRVs and found that EPRVs are present in the genomes of gymnosperms and ferns. We identified numerous EPRVs in gymnosperm and fern genomes, revealing an unprecedented depth in the diversity of plant pararetroviruses. Plant pararetroviruses mainly underwent cross-species transmission, and angiosperm pararetroviruses arose at least three times. Our study provides novel insights into the diversity and macroevolution of plant pararetroviruses.
Appendicular muscle mass and fasting triglycerides predict serum liver aminotransferases in young female collegiate athletes
Authors: Minato Satomi , Kitaoka Kaori , Takeuchi Mika , Tsuboi Ayaka , Kurata Miki , Tanaka Shigehiro , Kazumi Tsutomu , Fukuo Keisuke
Published: March 2018

Objective

We test the hypothesis that aspartate aminotransferase (AST) may be associated inversely with serum triglycerides (TG) and positively with high density lipoprotein (HDL) cholesterol in young athletes because athletes have larger amounts of muscle mass.

Research design and methods

Pearson’s correlation coefficients were calculated between serum AST and alanine aminotransferase (ALT) and body composition identified by dual-energy X-ray absorptiometry, markers of insulin resistance, serum lipids, lipoproteins, apolipoproteins, adiponectin and leptin in 174 female collegiate athletes (18–22 years). Multivariate linear regression analyses were used to identify independent determinants of the aminotransferases.

Results

AST and ALT showed positive correlation with appendicular skeletal muscle mass (ASM) and height-adjusted ASM. In addition, ALT as well as AST showed inverse, not positive, association with fasting TG. Further, both AST and ALT showed positive associations with HDL cholesterol and apolipoprotein AI, a major apolipoprotein of HDL particles. Multivariate analysis revealed that height-adjusted ASM and TG (inverse) were independent determinants for AST and ALT. Further, fat mass index (inverse) and resting heart rate (inverse) predicted AST and apolipoprotein AI predicted ALT.

Conclusions

In young female collegiate athletes, both serum AST and ALT showed inverse association with fasting TG and positive association with apoAI, both of which may be mediated through positive association between the aminotransferases and ASM. The association between ALT and TG is opposite in direction in young athletes (inverse) and in the general population (positive).
Does antenatal micronutrient supplementation improve children’s cognitive function? Evidence from the follow-up of a double-blind randomised controlled trial in Nepal
Authors: Dulal Sophiya , Liégeois Frédérique , Osrin David , Kuczynski Adam , Manandhar Dharma S , Shrestha Bhim P , Sen Aman , Saville Naomi , Devakumar Delan , Prost Audrey
Published: March 2018

Introduction

Multiple Micronutrient (MMN) supplementation during pregnancy can decrease the proportion of infants born low birth weight and small for gestational age. Supplementation could also enhance children’s cognitive function by improving access to key nutrients during fetal brain development and increasing birth weight, especially in areas where undernutrition is common. We tested the hypothesis that children whose mothers received MMN supplementation during pregnancy would have higher intelligence in early adolescence compared with those receiving Iron and Folic Acid (IFA) only.

Methods

We followed up children in Nepal, whose mothers took part in a double-blind Randomised Controlled Trial (RCT) that compared the effects on birth weight and gestational duration of antenatal MMN versus IFA supplementation. We assessed children’s Full Scale Intelligence Quotient (FSIQ) using the Universal Non-verbal Intelligence Test (UNIT), and their executive function using the counting Stroop test. The parent trial was registered asISRCTN88625934.

Results

We identified 813 (76%) of the 1069 children whose mothers took part in the parent trial. We found no differences in FSIQ at 12 years between MMN and IFA groups (absolute difference in means (diff): 1.25, 95% CI −0.57 to 3.06). Similarly, there were no differences in mean UNIT memory (diff: 1.41, 95% CI −0.48 to 3.30), reasoning (diff: 1.17, 95% CI −0.72 to 3.06), symbolic (diff: 0.97, 95% CI −0.67 to 2.60) or non-symbolic quotients (diff: 1.39, 95% CI −0.60 to 3.38).

Conclusion

Our follow-up of a double-blind RCT in Nepal found no evidence of benefit from antenatal MMN compared with IFA for children’s overall intelligence and executive function at 12 years.
Is Textbook Outcome a valuable composite measure for short-term outcomes of gastrointestinal treatments in the Netherlands using hospital information system data?A retrospective cohort study
Authors: Salet Nèwel , Bremmer Rolf H , Verhagen Marc A M T , Ekkelenkamp Vivian E , Hansen Bettina E , de Jonge Pieter J F , de Man Rob A
Published: March 2018

Objective

To develop a feasible model for monitoring short-term outcome of clinical care trajectories for hospitals in the Netherlands using data obtained from hospital information systems for identifying hospital variation.

Study design

Retrospective analysis of collected data from hospital information systems combined with clinical indicator definitions to define and compare short-term outcomes for three gastrointestinal pathways using the concept of Textbook Outcome.

Setting

62 Dutch hospitals.

Participants

45 848 unique gastrointestinal patients discharged in 2015.

Main outcome measure

A broad range of clinical outcomes including length of stay, reintervention, readmission and doctor–patient counselling.

Results

Patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) for gallstone disease (n=4369), colonoscopy for inflammatory bowel disease (IBD; n=19 330) and colonoscopy for colorectal cancer screening (n=22 149) were submitted to five suitable clinical indicators per treatment. The percentage of all patients who met all five criteria was 54%±9% (SD) for ERCP treatment. For IBD this was 47%±7% of the patients, and for colon cancer screening this number was 85%±14%.

Conclusion

This study shows that reusing data obtained from hospital information systems combined with clinical indicator definitions can be used to express short-term outcomes using the concept of Textbook Outcome without any excess registration. This information can provide meaningful insight into the clinical care trajectory on the level of individual patient care. Furthermore, this concept can be applied to many clinical trajectories within gastroenterology and beyond for monitoring and improving the clinical pathway and outcome for patients.
Audit of HIV counselling and testing services among primary healthcare facilities in Cameroon: a protocol for a multicentre national cross-sectional study
Authors: Tianyi Frank-Leonel , Tochie Joel Noutakdie , Agbor Valirie Ndip , Kadia Benjamin Momo
Published: March 2018

Introduction

HIV testing is an invaluable entry point to prevention, care and treatment services for people living with HIV and AIDS. Poor adherence to recommended protocols and guidelines reduces the performance of rapid diagnostic tests, leading to misdiagnosis and poor estimation of HIV seroprevalence. This study seeks to evaluate the adherence of primary healthcare facilities in Cameroon to recommended HIV counselling and testing (HCT) procedures and the impact this may have on the reliability of HIV test results.

Methods and analysis

This will be an analytical cross-sectional study involving primary healthcare facilities from all the 10 regions of Cameroon, selected by a multistaged random sampling of primary care facilities in each region. The study will last for 9 months. A structured questionnaire will be used to collect general information concerning the health facility, laboratory and other departments involved in the HCT process. The investigators will directly observe at least 10 HIV testing processes in each facility and fill out the checklist accordingly.

Ethics and dissemination

Clearance has been obtained from the National Ethical Committee to carry out the study. Informed consent will be sought from the patients to observe the HIV testing process. The final study will be published in a peer-reviewed journal and the findings presented to health policy-makers and the general public.
Visualisation of facet joint recesses of the cadaveric spine: a micro-CT and sheet plastination study
Authors: Thorpe Lowis Casper G , Xu Zhaoyang , Zhang Ming
Published: March 2018

Objectives

The size and shape of a joint cavity are the key determinates for the mobility of the joint. The anatomy and configuration of the facet joint (FJ) recesses at different levels of the spine remain unclear and controversial. The aim of this study was to identify the configuration of the FJ recesses in the cervical, thoracic and lumbar spine using a combination of micro-CT and sheet plastination techniques.

Methods

Of 19 cadavers (9 males, 10 females, age range of 54–89 years), the FJ cavities of 3 spines were injected with contrast filling and scanned with micro-CT, and 16 plastinated spines were prepared as the series of sagittal (9 sets), transverse (5 sets) or coronal (2 sets) sections with a thickness of 2.5 mm and examined under a stereoscopic microscope.

Results

This study characterised the FJ spaces and recesses of the spine and found that (1) the configuration and extent of the FJ recesses varied along the spine. The optimal needle approach to the FJ cavity was via an anterolateral or posterolateral recess at the cervical level, along the tip of the inferior articular process at the thoracic level and via the posteromedial recess at the lumbar level. (2) The FJ cavity did not communicate with the retrodural space.

Conclusion

The anatomical features of the FJ recesses at different levels of the spine confirm no direct communication between the FJ cavity and retrodural space.
Association between glucocorticoid therapy and incidence of diabetes mellitus in polymyalgia rheumatica and giant cell arteritis: a systematic review and meta-analysis
Authors: Lai Lana Yin Hui , Harris Emma , West Robert M , Mackie Sarah Louise
Published: March 2018

Background

Polymyalgia rheumatica (PMR) and giant cell arteritis (GCA) are almost always treated with glucocorticoids (GCs), but long-term GC use is associated with diabetes mellitus (DM). The absolute incidence of this complication in this patient group remains unclear.

Objective

To quantify the absolute risk of GC-induced DM in PMR and GCA from published literature.

Methods

We identified literature from inception to February 2017 reporting diabetes following exposure to oral GC in patients with PMR and/or GCA without pre-existing diabetes. A random-effects meta-analysis was performed to summarise the findings.

Results

25 eligible publications were identified. In studies of patients with GCA, mean cumulative GC dose was almost 1.5 times higher than in studies of PMR (8.2 g vs 5.6 g), with slightly longer treatment duration and longer duration of follow-up (6.4 years vs 4.4 years). The incidence proportion (cumulative incidence) of patients who developed new-onset DM was 6% (95% CI 3% to 9%) for PMR and 13% (95% CI 9% to 17%) for GCA. Based on UK data on incidence rate of DM in the general population, the expected background incidence rate of DM over 4.4 years in patients with PMR and 6.4 years in patients with GCA (follow-up duration) would be 4.8% and 7.0%, respectively. Heterogeneity between studies was high (I2=79.1%), as there were differences in study designs, patient population, geographical locations and treatment. Little information on predictors of DM was found.

Conclusion

Our meta-analysis produced plausible estimates of DM incidence in patients with PMR and GCA, but there is insufficient published data to allow precise quantification of DM risk.
American lobster: persistence in the face of high, size-selective, fishing mortality — a perspective from the southern Gulf of St. Lawrence
Authors: Comeau Michel , Hanson J. Mark
Published: March 2018

The American lobster (Homarus americanus) population in southern Gulf of St. Lawrence has long been subjected to high exploitation, and yet its population is currently at a high and increasing abundance level. The lobster fishery management is based on effort-control, with a short season, mandatory release of egg-bearing females, and strict enforcement of regulations. Another important factor is the high survival of lobster returned to the water. The combination of a minimum legal size limit and either an upper size limit for females or an effective size limit due to entrance-ring size on the traps has resulted in a slot fishery after which the larger, most fecund animals have low vulnerability to the fishery. These efforts to protect large individuals have had a positive effect on lobster larval production, which may lead to even higher adult population numbers. Comparisons with the management of snow crab (Chionoecetes opilio) and Atlantic cod (Gadus morhua) quota-based fisheries were made to try to explain the different trajectories that these three species’ populations have taken since the 1960s.
Mg65Ni20Y15–XAgX (X = 1, 2, 3, 5) alloys prepared via atmosphere controlled induction system
Authors: Kursun Celal , Gogebakan Musa , Azakli Yunus , Cengiz Sezgin , Eskalen Hasan , Tarakci Mehmet , Gencer Yucel
Published: March 2018

In this work, Mg65Ni20Y15–XAgX (X = 1, 2, 3, 5) alloys were manufactured by atmosphere controlled induction system. The effect of Ag ratio on the microstructural properties, micro-hardness, density, and homogeneity of the Mg–Ni–Y alloys were investigated. These alloys were characterized by X-ray diffraction (XRD), optical microscopy, scanning electron microscopy with energy dispersive X-ray (SEM-EDX) and Vickers micro-hardness measurement. According to XRD results, Ni3Y and Mg6Ni phases were observed as well as AgY and Ag17Mg54 phases, which were obtained in alloys. The quantitative results of EDX analysis confirm that the chemical composition of the obtained phases is very close and their homogeneities are so high. The average micro-hardness values of the ingot alloys were measured between 208 and 266 HV for matrix. The elastic modulus and densities of the Mg65Ni20Y15–XAgX (X = 1, 2, 3, 5) alloys increased by increasing Ag in the alloys and they were determined in the range of 58.18–68.12 GPa and 3.14–3.53 g/cm3, respectively.
Comparison of binding properties of a novel non-steroidal anti-inflammatory agent and ibuprofen to cyclooxygenase-1 and cyclooxygenase-2 enzymes by saturation transfer difference nuclear magnetic resonance
Authors: Binbay Nil E. , Ziyadanogullari Berrin
Published: March 2018

Saturation transfer difference nuclear magnetic resonance is a ligand-based screening technique that focuses directly on the physical interaction of a macromolecule (protein, enzyme, etc.) and a small ligand. It is a powerful tool in pharmaceutical research. Here, a comparison is reported of the binding characteristics of ibuprofen and a novel anti-inflammatory agent to cyclooxygenase-1 and cyclooxygenase-2 enzymes as an application of saturation transfer difference nuclear magnetic resonance. It has been shown that this novel agent is capable of binding to both isoforms of the cyclooxygenase enzymes. It has also been reported that novel agent binds better to cyclooxygenase-2.
CP violation in the lepton sector and implications for leptogenesis
Authors: Hagedorn C. , Mohapatra R. N. , Molinaro E. , Nishi C. C. , Petcov S. T.
Published: March 2018

We review the current status of the data on neutrino masses and lepton mixing and the prospects for measuring the CP-violating phases in the lepton sector. The possible connection between low energy CP violation encoded in the Dirac and Majorana phases of the Pontecorvo–Maki–Nakagawa–Sakata mixing matrix and successful leptogenesis is emphasized in the context of seesaw extensions of the Standard Model with a flavor symmetry [Formula: see text] (and CP symmetry).