bluuebunny/crossref_metadata_2025 huggingface dataset:
Associations between declining antimicrobial use in primary care in Scotland and patient satisfaction and hospitalisation due to infection: a longitudinal study of greater than five million patients
Authors: Guthrie Isobel , Marwick Charis
Published: March 2020

Background. Scottish antimicrobial prescribing in the community has fallen since 2012, but this could have unintended consequences. The aim was to examine associations between changes in antibiotic prescribing in primary care and hospital admissions and patient satisfaction.

Methods. Data for 877 Scottish general practices with 5.1 million patients were provided by NHS National Services Scotland. Practices were classified into four equal groups (quartiles) in terms of change in total antibiotic prescribing (rate/1000 registered patients in each quarter) 2012-2018. Changes in hospital admission with infection were examined comparing the four groups. Multivariate regression examined associations between change in antibiotic prescribing and patient satisfaction with the practice using national survey data.

Results. Across Scotland, primary care antibiotic prescribing decreased by 15% from 194.1 (95%CI 193.8-194.4) in Q1 2012 to 165.3 (95%CI 165.0-165.6 ) in Q2 2012, with considerable variation between practices (non-significant increase of 0.22 prescriptions/1000/quarter [p=0.49] for the quartile of practices with least reduction in antibiotic prescribing, vs reduction of -2.95 prescriptions/1000/quarter [p<0.001] for quartile with the largest reduction). Rates of hospital admissions with infection increased over the time period but there were no significant association with changes in antibiotic prescribing. Patient satisfaction decreased over the period, but change in antibiotic prescribing was not associated with patient satisfaction.

Conclusion. There have been clinically significant reductions in Scottish primary care antibiotic use since 2012, varying considerably between practices. Longitudinal analysis of Scotland-wide practice level data found no associations between practice-level reductions in primary care antibiotic prescribing and hospital admissions or patient satisfaction.
Knowledge of nursing staff and healthcare assistants on the diagnosis of urinary tract infections in patients with urinary catheters
Authors: Mekonnen Ellen , Khanna Priya , Rao Gopal
Published: March 2020

Background

Asymptomatic bacteriuria is common in patients with urinary catheters. Current clinicalguidelines advise against dipstick testing or treating urine culture results in asymptomatic catheterised patients which can promote the development of antimicrobial resistance and present an unnecessary risk to patients. This study aimed to assess the knowledge of nurses and healthcare assistants (HCAs) on the diagnosis of urinary tract infections (UTIs) in patients with urinary catheters.

Methods

This study employed a cross sectional survey of opportunistically sampled nursing staff and healthcare assistants working at Northwick Park Hospital in May 2018. Results were analysed descriptively.

Results

134 participants were included in the final analysis of whom 90% (N=120) were nurses and 10% (N=14) were HCAs. The majority of staff (38.6%, N=51) worked in a medical speciality and had over 15 years of work experience (45.3%, N=58). 79 participants (66%) believed that a positive dipstick result was diagnostic of a catheter associated urinary tract infection (CAUTI). A positive dipstick result was the most frequently selected indication (91% of respondents, N=108) for sending urine for culture in a catheterised patient, and was also the most frequently selected reason for sending urine for culture across staff of all years of experience and all specialities.

Conclusion

There is a need to improve the level of knowledge of nursing and HCA staff on the diagnosis of CAUTIs including misconceptions on the diagnostic value of dipstick testing in catheterised patients. The findings of this research will inform a quality improvement project to address these gaps in knowledge.
Enough is enough – is it time for the Scottish Antimicrobial Prescribing Group (SAPG) to develop the third age of antimicrobial stewardship in primary care in Scotland?
Authors: Malcolm William , Baxter Linsey , McNicol Megan , Sneddon Jacqueline
Published: March 2020

Background

From 2008 the SAPG focused on ‘what to prescribe’ to tackle Clostridium difficile infection and from 2013 on ‘whether to prescribe’ to tackle unnecessary prescribing for self-limiting infections. Following these successes SAPG is now moving to the age of ‘how much to prescribe’ to ensure correct duration of therapy. We aimed to compare current prescribing practice with guidance from Public Health England (PHE)/NICE which recommends five days’ treatment for most common community respiratory infections (RTI).

Methods

The durations of antibiotic courses for treatment of respiratory tract infections was derived from data on dispensed prescriptions in 2018 from the Prescribing Information System, a national database of all NHS prescriptions dispensed in Scotland. Observed course durations were compared to course lengths recommended by PHE/NICE and modelling was undertaken on the impact on antibiotic use if durations were in line with guidance.

Results

For antibiotics recommended for RTI, the most common length of treatment used was seven days. For amoxicillin the proportion of five day prescriptions varied across health boards from 1.8% to 68.7%. Modelling estimated if 75% of seven day prescriptions for antibiotics recommended for RTI were changed to five days this would deliver a 4.1% reduction in antibiotic use.

Conclusion

SAPG has agreed to lead work to encourage the use of five day courses of antibiotics where indicated. Switching to five day courses would support reduction in total antibiotic use to achieve the ambitions of the UK AMR National Action Plan.
Coinfection Mechanisms ofCampylobacter andEscherichia coli in Human and Chicken Epithelial cells
Authors: Hanford Taylor , Wilkinson Thomas , Williams Lisa , Humphrey Thomas
Published: March 2020

Campylobacter jejuniis the world’s most common food-borne pathogen. Campylobacterpathogenesis involves translocation across the intestinal epithelial cell barrier in both humans and chickens and previous work has suggested that strains of E. coli (ExPEC / APEC) may facilitate this process. This study aims to determine the effect that this relationship may have upon the invasive and adhesive potential of the two microbes using our recently published human and avian in vitromodel.

Invasiveness of C. jejuni and E. coli strains were measured using human (Caco-2) and avian (8E-11) epithelial cell lines derived from the gastrointestinal tract and were characterised by epifluorescent and confocal microscopy. Adhesion and invasion assays were carried out to determine the pathogenicity of the different bacteria. Metabolic activity of Caco-2 and 8E-11 together with bacterial strains using alamar blue assay.

Confocal and epifluorescence microscopy determined the strong presence of cytokeratin in Caco-2 cells whilst weak to medium signals were detected in 8E-11 cells. Optimal doses and times for of gentamicin across all strains was 0.02mg/ml for 90 minutes which did not affect metabolic activity of epithelial cells. Significant diversity was found in the adhesive/invasive potential of bacteria when exposed to human and avian cell types. The metabolic rate of C. jejuni (11168) and E. coli (K12) was investigated with the presence of K12 having negative impacts upon the activity of 11168.

The model described here will provide opportunity to improve our understanding of Campylobacterinvasion mechanisms in human and chickens so that improved strategies to negate these consequences may be designed.
Culture-independent Multilocus Sequence Typing (MLST) screening for Haemophilus influenzae cross-infection in non-cystic fibrosis bronchiectasis (NCFB)
Authors: Wilson Catherine , Mitchelmore Philip , Brown Alan
Published: March 2020

Background

There is some evidence of Pseudomonas aeruginos across-infection between patients with non-cystic fibrosis bronchiectasis (NCFB), and clear evidence in Cystic Fibrosis. Haemophilus influenzae (H. influenzae) is the more common pathogen in NFCB patients, yet cross-infectionremains unexplored. We present the novel application of culture-independent Multilocus Sequence Typing (MLST) to screen for cross-infection of H. influenzae in NCFB in both culture-positive and -negative samples.

Methods

We interrogated DNA from 32 sputum samples (26 patients) in our NCFB biorepository, who were known to have H.influenzae in their sputum by preceding 16S rRNA sequencing. Fragments of 7 H. influenzae housekeeping genes were amplified and sequenced. Sequence types were allocated via the MLST scheme. For 5 patients, multiple sputum samples taken at least 4 months apart were assessed longitudinally.

Results

Culture-independent MLST identified 31 of 32 sputum samples as harboring H. influenzae. Of these, 26 were positive for H. influenzae using culture methods. 25 of the 26 culture-positive samples were MLST positive. All 6 culture-negative samples were MLST positive. A MLST sequence type (ST) was allocated to 27 of 32 sputum samples. Five patients had multiple sputum samples with matching STs, indicating strain stability and the consistency of MLST. Two patients who were known household contacts had matching STs and possibly transmitted H.influenzae in their household. The remaining 15 STs were unique, suggesting no evidence of cross-infection.

Conclusion

Culture-independent MLST identifies H. influenzae in culture-negative patients with NCFB and is a potential screening tool for cross-infection. This study did not reveal potential cross-infection events in this cohort.
Spontaneous Bacterial Peritonitis at University Hospitals of North Midlands NHS Trust: A Retrospective Study
Authors: Ziada Ahmed , Behzadnia Alireza , Khalid Junaid , Desai Seema
Published: March 2020

Background

Spontaneous bacterial peritonitis is an acute infection of ascitic fluid that is not related to an underlying intra-abdominal pathology.

Methods

This is a retrospective study of data on ascitic fluid samples taken during the period of January to December 2017 to assess the management of SBP patients and associated mortality. Kaplan-Meir method was used to estimate survival probability at 30 and 90 days. Cox proportional models were used to evaluate aetiology and causative organism in predicting mortality. Analyses were done using R: A language and environment for statistical computing.

Results

Total of 53 patients were identified as having SBP based on ascitic fluid cultures. Sixteen of these also fulfilled the national criteria of ascitic neutrophil count of more than 250 or total cell count of more than 500.

Thirty-three (62.8%) samples grew pathogenic organisms. The most common pathogenic organisms were E coli (30.3%) followed by Enterococcus (21.2%) – in which four were ESBL tagged – Klebsiella (6%) and Staph Aureus (6%). In majority of the patients, the underlying aetiology of ascites was secondary to ALD (68.9%), Malignancy (11.8%) and NASH cirrhosis (11.8%). In this cohort, the overall 30-day survival was 64.2% and 90-day survival was 43.4%. About half mortality occurred during the same admission to hospital.

Conclusion

E coli was the most commonly isolated organism. Alcoholic Liver Disease was the most common underlying aetiology in SBP patients. SBP is associated with a high 30-day and 90-day mortality. Isolation of pathogenic organisms was associated with a four-fold higher mortality than non-pathogenic organisms.
A case of the ‘unusual’ in the ‘usual’
Authors: Williams Caroline , Sahota Amandip , Pareek Manish
Published: March 2020

Background

Only five cases of Salmonella paratyphi infective endocarditis (IE) have been previously reported. Two were paediatric patients, one other had an underlying cardiac lesion, and all were living in endemic areas. Here we present the first case of salmonella paratyphi IE in a returning traveller.

Case

A 61 year old Indian born British national with no significant past medical history or recent dental procedures presented with a 4 week history of fever and weight loss following travel to India. Whilst abroad she had a self-limiting episode of diarrhoea with fever for 1 week with no antimicrobials. Three weeks after her return the fever returned (without diarrhoea) and she presented to hospital 4 weeks later.

Examinations findings were; haemodynamically stable, temperature 39.5°C, no splinter haemorrhages, no lymphadenopathy, soft systolic murmur best heard at parasternal edge.

Investigations revealed raised inflammatory markers (CRP 80) and blood cultures grew gram negative bacilli within 24 hours which cultured as Salmonella paratyphi A.

Trans-thoracic Echocardiogram showed echo-bright thickening of the non-coronary cusp of the aortic valve, which was confirmed as a small vegetation (0.5cm x0.2cm) on trans-oesophageal echocardiogram.

IV antibiotics were given for a total of 6 weeks and repeated TOE at 1 month showed a healing vegetation. Repeated imaging is awaited.

Conclusions

This interesting case in an otherwise healthy patient highlights the need to be vigilant for unusual organisms causing infective endocarditis – a relatively common condition - in returning travellers.
Impact of serum procalcitonin on antibiotic stewardship in surgical high-dependency unit and intensive care unit settings
Authors: Zorzoli Azul , Meney Laura , Shone John , Taylor Aaron , Hilton-Christie Sharon , Dorfmueller Helge , Parcell Benjamin
Published: March 2020

Background

Procalcitonin (PCT) testing is used as a biomarker for bacterial infection. We assessed the impact of using a PCT-guided algorithm in Ninewells hospital & Medical School (Dundee, Scotland, UK).

Methods

We conducted a retrospective analysis of the use of PCT-testing to evaluate the escalation or de-escalation of antibiotic therapy. For this, we analysed patients admitted to the intensive care unit (ICU) and surgical high dependency unit (SHDU) from November 2018 to April 2019.

Results

We analysed a dataset of 235 adult patients, 23% of which were at the hospital’s ICU and 77% at the SHDU. Within the ICU, 49% of admitted patients were already on antibacterial therapy, compared to 93% at SHDU. The PCT results influenced the prescription of antibiotics in 33% of total patients (89% and 16% of all ICU and SHDU patients, respectively). Escalation of the antimicrobial therapy was prescribed to 34% of ICU patients after PCT testing, compared to 20% of SHDU patients. Continuation of the previously-established antibacterial scheme was more pronounced in SHDU patients (43% against 23% ICU). In contrast, while discontinuation of the therapy was observed in similar levels on both units (27% SHDU, 28% ICU).

Conclusion

PCT has become a useful tool in antimicrobial stewardship. Its use aided the prescription of antibiotics in 33% of the overall total cases in ICU and SHDU. Further work should be carried out to assess its role in other clinical environments.
Nucleic acid amplification tests (NAATs) for diagnosing sexually transmitted infections (STIs): NHS Grampian (NHSG) experience
Authors: Gunasekera Chathuri , Sakka Noha El , Cook Isabel , Butt Ambreen
Published: March 2020

Background:

We present 2 studies conducted on Chlamydia trachomatis(CT) and Trichomonas vaginalis(TV) testing in NHSG, leading to streamlining of NAATs of Neisseria gonorrhoeae, CT and TV in triplex.

Methods:

Formerly, positive CT-NAATs needed confirmation by repeat testing on the same sample using same platform. According to SMI guidelines, when confirmatory testing results are consistently concordant following audit, confirmation may be unnecessary. CT testing over 3 years (2015-2017) was analysed to review outcomes of confirmatory testing.

A pilot study was conducted on TV-NAAT testing in comparison with TV-microscopy. In addition, TV testing data over 30months (29/07/2016-31/01/2019) was analysed.

Results:

A total of 88533 samples were tested for CT-NAAT over 3 years: 7059 were positive, 81321 negative. A total of 153 were equivocal (initially positive, negative on repeat) which were reanalysed with results on receival of repeat samples. Over the years, percentage of equivocal tests out of the total positives remained at 0.2%; rates for positive-repeats and tests-not-repeated fluctuated; negative-repeats increased from 18 to 38.

TV-NAAT was more sensitive/ specific compared to TV-microscopy (relative specificity was 99.6%, relative sensitivity was 92.8%), and was adopted for routine testing. A total of 44407 samples were tested for TV NAATs over 30 months. Of this, 433 were positive and 43796 negative. Further cross-sectional analyses were done.

Conclusions:

We concluded that positive CT-NAATs do not require repeat testing for confirmation. TV-NAAT testing proved more sensitive/specific than TV-microscopy and was useful to adopt as routine testing and help streamlining testing on one molecular platform.
Investigation into the presence of Hepatitis E Virus in commercially available venison charcuterie in Scotland
Authors: Maroulis Dimitrios
Published: March 2020

Hepatitis E Virus is an RNA virus of the Hepeviridae family that affects hepatocytes and seriously impacts the health of immunocompromised patients. Genotypes 3 and 4 have been circulating in animal populations such as swine and deer in developed countries, causing food borne infections associated with consumption of contaminated animal food products. While HEV has been circulating in European deer populations and causing food borne infections in Asia, its presence in Scottish venison food products has not been investigated. This study assesses 4 ready-to-eat venison charcuterie products for HEV by performing RNA extraction on duplicate samples with a Qiagen RNeasy Midi kit and using Mengovirus as a process control to determine virus recovery by RT-qPCR. This was followed by RT-PCR with previously described HEV primers, and ligation of the suspected positive fragments in a recombinant pGEMT Easy Vector system which was then cloned in competent E. coli cells for propagation. Recombinant plasmids were isolated and subjected to Sanger sequencing. An average RNA extraction efficiency of 5.02% was achieved across all samples, but large deviations between duplicates suggests that further optimisation is necessary in RNA extraction from food products with complex matrices. HEV-sized PCR fragments were detected in 3 out of 4 food products, but the sequencing data showed inefficient ligation of the fragments in the vector, possibly due to low RNA amount and excess of dimerised primers. The likelihood of HEV presence in Scottish venison needs to be investigated further for the detection of transmission routes and the implementation of improved surveillance policies.
Klebsiella variicola causing nosocomial transmission among neonates – an emerging pathogen?
Authors: Piepenbrock Ellen , Higgins Paul G. , Wille Julia , Xanthopoulou Kyriaki , Zweigner Janine , Jahn Peter , Reuter Stefan , Skov Robert , Eichhorn Joachim , Seifert Harald
Published: March 2020

Introduction. Transmission of Enterobacterales in neonatal intensive care units (NICU) can cause outbreaks of colonization and invasive infections among neonates. Two clusters of nosocomial transmission of

Klebsiella pneumoniae

identified by MALDI-ToF mass-spectrometry were suspected at two NICUs in July and August 2016.

Aim. To assess the potential transmission of

K. pneumoniae

among neonates.

Methodology. Whole-genome sequencing (WGS) was performed of

K. pneumoniae

isolates obtained through targeted surveillance of patients and environmental sampling.

Results. WGS data revealed that patient and environmental isolates represented two species,

K. pneumoniae

and

K. variicola

. Core-genome multi-locus sequence typing (cgMLST) of the isolates identified three separate transmission clusters, in Hospital A a cluster of

K. pneumoniae

isolates in 12 children and two environmental samples and a second cluster of

K. variicola

isolates in five children. In Hospital B a cluster of

K. pneumoniae

isolates from three children and five unrelated isolates of

K. pneumoniae

and two unrelated isolates of

K. variicola

were found.

Conclusion.

K. variicola

can cause hospital outbreaks of colonization and infection similar to other

Klebsiella

spp.

Preliminary results from this study were presented at the 27th European Congress of Clinical Microbiology and Infectious Diseases, April 22-25, 2018, Vienna, Austria.
Risk factors related to hepatic injury in patients with corona virus disease 2019
Authors: Li Lu , Li Shuang , Xu Manman , Yu Pengfei , Zheng Sujun , Duan Zhongping , Liu Jing , Chen Yu , Li Junfeng
Published: March 2020

Aims

Corona virus disease 2019 (COVID-19) has rapidly become the most severe public health issue all over the world. Despite respiratory symptoms, hepatic injury has also been observed in clinical settings. This study aimed to investigate the risk factors involved with hepatic injury in the patients with COVID-19.

Methods

A total of 85 hospitalized patients who were diagnosed with COVID-19 in Beijing You’an Hospital were retrospectively analyzed. According to liver function, they were divided into ALT normal group (n=52) and ALT elevation group (n=33). Clinical features and laboratory data were compared between the two groups. The independent risk factors for liver injury were analyzed.

Results

There were 33 patients with hepatic injury in our study, accounting for 38.8% (33/85). The patients in ALT elevation group were older than those in ALT normal group. The levels of lactic acid, CRP, myoglobin, and neutrophils were significantly higher in ALT elevation group. The lymphocytes and albumin were significantly lower in ALT elevation group. The proportion of severe and critical patients in ALT elevation group was significantly higher. Multivariate logistic regression analysis showed CRP ≥20 mg/L and lymphocyte count< 1.1×10^9/L were independently related to hepatic injury.

Conclusions

Lymphopenia and CRP may serve as the risk factors related to hepatic injury in patients with COVID-19, which might be related to inflammatory cytokine storm in liver injury. Early detection and timely treatment of hepatic injury in patients with COVID-19 are necessary.
Causal Inference in Microbiomes Using Intervention Calculus
Authors: Sazal Musfiqur Rahman , Stebliankin Vitalii , Mathee Kalai , Narasimhan Giri
Published: March 2020

Inferring causal effects is critically important in biomedical research as it allows us to move from the typical paradigm of associational studies to causal inference, and can impact treatments and therapeutics. Association patterns can be coincidental and may lead to wrong inferences in complex systems. Microbiomes are highly complex, diverse, and dynamic environments. Microbes are key players in health and diseases. Hence knowledge of genuine causal relationships among the entities in a microbiome, and the impact of internal and external factors on microbial abundance and interactions are essential for understanding disease mechanisms and making treatment recommendations.

In this paper, we investigate fundamental causal inference techniques to measure the causal effects of various entities in a microbiome. In particular, we show how to use these techniques on microbiome datasets to study the rise and impact of antibiotic-resistance in microbiomes. Our main contributions include the following. We introduce a novel pipeline for microbiome studies, new ideas for experimental design under weaker assumptions, and data augmentation by context embedding. Our pipeline is robust, different from traditional approaches, and able to predict interventional effects without any controlled experiments. Our work shows the advantages of causal inference in identifying potential pathogenic, beneficial, and antibiotic-resistant bacteria. We validate our results using results that were previously published.
Relatively semi-conservative replication and a folded slippage model for simple sequence repeats
Authors: Zhang Hongxi , Li Douyue , Zhao Xiangyan , Pan Saichao , Wu Xiaolong , Peng Shan , Huang Hanrou , Shi Ruixue , Tan Zhongyang
Published: March 2020

Simple sequence repeats (SSRs) are found ubiquitously in almost all genome, and their formation mechanism is ambiguous yet. Here, the SSRs were analyzed in 55 randomly selected segments of genomes from a fairly wide range of species, with introducing more open standard for extensively mining repeats. A high percentage of repeats were discovered in these segments, which is inconsistent with the current theory suggested that repeats tend to disappear over long-term evolution. Therefore, a mechanism is most probably responsible for continually producing repeats during replication to balance continuous repeat disappearance, which may makes the replicating process relatively semi-conservative. To improve the current straight-line slippage model, we proposed a folded slippage model involving the geometric space of nucleotides and hydrogen bond stability to explain the high-percent SSR occurrence, which can describe SSR expansion and contraction more reasonably. And analysis of external forces in the folding template strands suggested that the microsatellites tend to expand than contract. Our research may provide implements for contributions of microsatellites to genome evolution and complement semi-conservative replication.
Bulk-surface coupling reconciles Min-protein pattern formationin vitroandin vivo
Authors: Brauns Fridtjof , Pawlik Grzegorz , Halatek Jacob , Kerssemakers Jacob , Frey Erwin , Dekker Cees
Published: March 2020

Self-organisation of Min proteins is responsible for the spatial control of cell division inEscherichia coli, and has been studied bothin vivoandin vitro. Intriguingly, the protein patterns observed in these settings differ qualitatively and quantitatively. This puzzling dichotomy has not been resolved to date. Using reconstituted proteins in laterally wide microchambers with a well-controlled height, we show that the Min protein dynamics on the membrane crucially depend on bulk gradients normal to the membrane. A theoretical analysis shows thatin vitropatterns at low bulk height are driven by the samelateraloscillation mode as pole-to-pole oscillationsin vivo. At larger bulk height, additionalverticaloscillation modes set in, marking the transition to a qualitatively differentin vitroregime. Our work qualitatively resolves the Min system’sin vivo/in vitroconundrum and provides important insights on the mechanisms underlying protein patterns in bulk-surface coupled systems.
Targeted high-resolution chromosome conformation capture at genome-wide scale
Authors: Downes Damien J. , Gosden Matthew E. , Telenius Jelena , Carpenter Stephanie J. , Nussbaum Lea , De Ornellas Sara , Sergeant Martin , Eijsbouts Chris Q. , Schwessinger Ron , Kerry Jon , Roberts Nigel , Shivalingam Arun , El-Sagheer Afaf , Oudelaar A. Marieke , Brown Tom , Buckle Veronica J. , Davies James O.J. , Hughes Jim R.
Published: March 2020

Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods provide either low-resolution interaction profiles across the entire genome, or high-resolution interaction profiles at up to several hundred loci. All 3C methods are affected to varying degrees by inefficiency, bias and noise. As such, generation of reproducible high-resolution interaction profiles has not been achieved at scale. To overcome this barrier, we systematically tested and improved upon current methods. We show that isolation of 3C libraries from intact nuclei, as well as shortening and titration of enrichment oligonucleotides used in high-resolution methods reduces noise and increases on-target sequencing. We combined these technical modifications into a new method Nuclear-Titrated (NuTi) Capture-C, which provides a >3-fold increase in informative sequencing content over current Capture-C protocols. Using NuTi Capture-C we target 8,061 promoters in triplicate, demonstrating that this method generates reproducible high-resolution genome-wide 3C interaction profiles at scale.
Multi-kingdom quantitation reveals distinct ecological drivers of predictable early-life microbiome assembly
Authors: Rao Chitong , Coyte Katharine Z. , Bainter Wayne , Geha Raif S. , Martin Camilia R. , Rakoff-Nahoum Seth
Published: March 2020

The infant gut microbiota develops remarkably predictably1–7, with pioneer species colonizing after birth, followed by an ordered succession of other microbes. This predictable assembly is vital to health8,9, yet the forces underlying it remain unknown. The environment, host and microbe-microbe interactions are all likely to shape microbiota dynamics, but in such a complex ecosystem identifying the specific role of any individual factor has remained a major challenge10–14. Here we use multi-kingdom absolute abundance quantitation, ecological modelling, and experimental validation to overcome this challenge. We quantify the absolute bacterial, fungal, and archaeal dynamics in a longitudinal cohort of 178 preterm infants. We uncover with exquisite precision microbial blooms and extinctions, and reveal an inverse correlation between bacterial and fungal loads the infant gut. We infer computationally then demonstrate experimentallyin vitroandin vivothat predictable assembly dynamics are driven by directed, context-dependent interactions between microbes. Mirroring the dynamics of macroscopic ecosystems15–17, a late-arriving member,Klebsiella,exploits the pioneer,Staphylococcus,to gain a foothold within the gut. Remarkably, we find that interactions between kingdoms drive assembly, with a single fungal species,Candida albicans, inhibiting multiple dominant gut bacteria. Our work unveils the centrality of simple microbe-microbe interactions in shaping host-associated microbiota, a critical step towards targeted microbiota engineering.
Structural insights into the catalytic mechanism of Bacillus subtilis BacF
Authors: Deshmukh Ashish , Gopal Balasubramanian
Published: March 2020

The nonribosomal biosynthesis of the dipeptide antibiotic bacilysin is achieved by the concerted action of multiple enzymes in the Bacillus subtilis bac operon. BacF (YwfG), encoded by the bacF gene, is a fold type I pyridoxal 5-phosphate (PLP)-dependent stereospecific transaminase. Activity assays with L-phenylalanine and 4-hydroxyphenylpyruvic acid (4HPP), a chemical analogue of tetrahydrohydroxyphenylpyruvic acid (H4HPP), revealed stereospecific substrate preferences, a finding that was consistent with previous reports on the role of this enzyme in bacilysin synthesis. The crystal structure of this dimeric enzyme was determined in its apo form as well as in substrate-bound and product-bound conformations. Two ligand-bound structures were determined by soaking BacF crystals with substrates (L-phenylalanine and 4-hydroxyphenylpyruvate). These structures reveal multiple catalytic steps: the internal aldimine with PLP and two external aldimine conformations that show the rearrangement of the external aldimine to generate product (L-tyrosine). Together, these structural snapshots provide an insight into the catalytic mechanism of this transaminase.
Estimating local protein model quality: prospects for molecular replacement
Authors: Wallner Björn
Published: March 2020

Model quality assessment programs estimate the quality of protein models and can be used to estimate local error in protein models.ProQ3Dis the most recent and most accurate version of our software. Here, it is demonstrated that it is possible to use local error estimates to substantially increase the quality of the models for molecular replacement (MR). Adjusting theBfactors usingProQ3Dimproved the log-likelihood gain (LLG) score by over 50% on average, resulting in significantly more successful models in MR compared with not using error estimates. On a data set of 431 homology models to address difficult MR targets, models with error estimates fromProQ3Dreceived an LLG of >50 for almost half of the models 209/431 (48.5%), compared with 175/431 (40.6%) for the previous version,ProQ2, and only 74/431 (17.2%) for models with no error estimates, clearly demonstrating the added value of using error estimates to enable MR for more targets.ProQ3Dis available from http://proq3.bioinfo.se/ both as a server and as a standalone download.
Bis(N-adamantyl-N′-ethylimidazolium) tetrabromidomanganate(II)
Authors: Giltzau Niels Ole , Köckerling Martin
Published: March 2020

The title compound, (C15H23N2)2[MnBr4], comprises two N-adamantyl-N′-ethylimidazolium cations and one tetrahedral [MnBr4]2− anion. Next to Coulombic interactions, weak hydrogen bonds of the type C—H...Br consolidate the crystal packing, building up a three-dimensional network.
Time-dependent reliability analysis of harmonic drive based on transient FEA and accelerated life test
Authors: Zhang Xian , Jiang Gedong , Zhang Hao , Yun Xialun , Mei Xuesong
Published: March 2020

Purpose

The purpose of this paper is to analyze the time-dependent reliability of harmonic drive.

Design/methodology/approach

The transient finite element analysis (FEA) of harmonic drive is established to calculate the stress under different loads. Combined with the residual strength model and random variables, the time-dependent reliability model of harmonic drive is deduced by the stochastic perturbation method and Edgeworth series. Based on accelerated life tests, the degradation parameters are estimated by maximizing likelihood function. Under variable load, the key stress from transient FEA is transformed into probability density function by kernel density estimation, and the residual strength model is modified by adding adjustment factors to deal with strength degradation under different loads.

Findings

The critical position of stress concentration from transient FEA is consistent with the fatigue fracture position at the accelerated life test sample. Compared with the time-dependent reliability method with equivalent circular-shell static stress or empirical degradation parameters, the proposed method has the smallest prediction error of failure life. Under variable load, the state function should be expanded to second-order series for avoiding error items relevant to variance. The failure life expectation under random variable load is smaller than that under constant load.

Originality/value

The time-dependent reliability method of harmonic drive is firstly proposed under constant and variable load. The transient FEA of harmonic drive is established to calculate the stress for strength analysis. The accelerated life test of harmonic drive is conducted for degradation parameters estimation. The adjustment factor is added to the residual strength model for strength degradation under different loads.
Academic video lectures over named data networking
Authors: Kanellopoulos Dimitris
Published: March 2020

Purpose

Information-centric networking (ICN) is an innovative paradigm for the future internet architecture. This paper aims to provide a view on how academic video lectures can exploit the ICN paradigm. It discusses the design of academic video lectures over named data networking (NDN) (an ICN architecture) and speculates their future development. To the best of author’s knowledge, a similar study has not been presented.

Design/methodology/approach

The paper is a visionary essay that introduces the background, elaborates the basic concepts and presents the author’s views and insights into academic video lectures that exploit the latest development of NDN approach and its applications.

Findings

The ICN paradigm is closely related to the levels of automation and large-scale uptake of multimedia applications that provide video lectures. Academic video lectures over NDN have: improved efficiency, better scalability with respect to information/bandwidth demand and better robustness in challenging communication scenarios. A framework of academic video lectures over NDN must take into account various key issues such as naming (name resolution), optimized routing, resource control, congestion control, security and privacy. The size of the network in which academic video lectures are distributed, the content location dynamics and the popularity of the stored video lectures will determine which routing scheme must be selected. If semantic information is included into academic video lectures, the network dynamically may assist video (streaming) lecture service by permitting the network to locate the proper version of the requested video lecture that can be better delivered to e-learners and/or select the appropriate network paths.

Practical implications

The paper helps researchers already working on video lectures in finding a direction for designing and deploying platforms that will provide content-centric academic video lectures.

Originality/value

The paper pioneers the investigation of academic video lecture distribution in ICN and presents an in-depth view to its potentials and research trends.
Lean meeting buyer's expectations, enhanced supplier productivity and compliance capabilities in garment industry
Authors: Hoque Imranul , Hasle Peter , Maalouf Miguel Malek
Published: March 2020

Purpose

Investigate the potential of using “lean” in garment supplier factories to enhance productivity and compliance capability, so as to fulfill a buyer's expectation of lower price, shorter lead time, and higher occupational health and safety (OHS) standards.

Design/methodology/approach

By means of an intervention, lean tools integrated with OHS elements were introduced in four Bangladeshi key garment suppliers of a Danish buyer. By employing a qualitative approach, both quantitative and qualitative techniques were used to collect data on productivity, OHS, and buyer–supplier efforts.

Findings

This study demonstrates that lean tools, integrated with OHS elements, can be used to improve the productivity and compliance capabilities of supplier firms, which meet a buyers' changing demands for lower prices, shorter lead times, and higher compliance standards. This study suggests that the improvement of productivity and OHS in supplier firms through lean implementation could be a better choice for buyers than switching to new suppliers with uncertainties in productivity and delivery, as well as OHS compliance problems.

Practical implications

The findings of this study suggest that garment suppliers can benefit from implementing lean, thereby improving their capacity to meet buyers' expectations. Therefore, both suppliers and buyers have a mutual interest in the application of lean in suppliers' production facilities.

Originality/value

By considering both buyer and supplier perspectives, this research is a unique attempt to investigate the possibilities of lean implementation at the shop-floor level to meet the market challenges in the context of a developing country.
Detection and analysis of occurrences of spoofing in the Brazilian capital market
Authors: Mendonça Luisa , De Genaro Alan
Published: March 2020

Purpose

The purpose of this paper is to analyze a data set from a brokerage firm to find possible spoofing cases in ten stocks from the Ibovespa index. The studies proposed concerned the parameters used in the search for the practice, the frequency of occurrences during the negotiation period, the impact on the price caused by the size of the spoofing order and the correlation between the stock's liquidity and the number of occurrences.

Design/methodology/approach

By using intraday orders flows, the authors are able to reassemble the order book and perform an analysis of potential market manipulation.

Findings

The authors found six possible cases, all of them happened in the beginning or end of the negotiation period, confirming that there is a window of opportunity for the practice when there is greater uncertainty related to the stock's price. Moreover, they found that in the less liquid stocks, it was necessary to place greater spoofing orders aiming to narrow the wider spread.

Practical implications

A methodology for spoofing detection that can be replicated by brokerage firms and other researchers was developed.

Social implications

The study contributes to the literature of capital market regulation by suggesting best practices for regulators and self-regulatory entities to avoid a predatory market practice.

Originality/value

The authors present an algorithm and parameters for detecting spoofing; other papers are not practical orientated.
Causal attribution and coping with classmates’ isolation and humiliation in young adults with mild intellectual disability
Authors: Kurtek Paweł
Published: March 2020

Purpose

The purpose of this study is to consider the role of causal attribution of isolation and humiliation from classmates in the coping of young people with mild intellectual disability.

Design/methodology/approach

The R-PI test (Kurtek, 2018) was administered to a sample of 151 transition-age students (age 18-22 years) in Poland. It consists of vignettes that describe stressful situations in which classmates might engage in isolating or humiliating behavior directed at the respondents. The respondents’ coping responses were interpreted according to a coding system based on a multi-axis approach by Hobfoll (1998) and Kelley’s attribution theory (1973).

Findings

The results have revealed that a majority of attributions are of defensive character. However, it was found that the justifying attributions were significantly associated with prosocial coping and the accusing attributions were related to antisocial coping.

Research limitations/implications

Because a vignette study is not based on actual interactions, the results refer to cognitive rather than behavioral performance.

Practical implications

The implications for supporting coping skills through attribution training, especially for youth with aggressive and passive behaviors, are discussed.

Social implications

Promoting positive and situational attributions to stressful interactions with classmates increases the likelihood of prosocial coping.

Originality/value

Applied cognitive approaches emphasize each respondent’s subjective perspective in attempting to explain humiliating and isolating incidents from classmates and the various coping strategies they personally considered effective in these situations. The present study contributes to the relatively small current literature available in this area.
Managing operations by a logistics company for sustainable service quality: Indian perspective
Authors: Gupta Anchal , Singh Rajesh Kumar
Published: March 2020

Purpose

The purpose of this paper is to understand how logistics service providers manage their operations for sustainable service quality and operational excellence. This study is also trying to propose a framework for measuring service quality index along with some research propositions for analyzing service quality and operational excellence.

Design/methodology/approach

The detailed case analysis on sustainable practices of Indian logistics service providers (LSPs) has been done on the basis of case study approach suggested by Eisenhardt (1989). After this case analysis, service quality index is evaluated for the given company based on Cleveland et al. (1989) framework. The SWOT and performance analysis of the case organization has been also done, which is further followed by development of framework and propositions for analyzing service quality and operational excellence for LSPs.

Findings

It can be observed from in-depth case analysis that LSPs are making use of green practices to conserve resources for long-term sustainability. LSPs optimize their resources and use sustainable practices in the form of use of reusable and recyclable packaging materials, rain water harvesting, use of solar panels, innovations such as trucking cube, safety concern toward goods and contribution toward environment and society.

Practical implications

Resources optimization and green management practices are essential for LSPs for benchmarking environmental performance and for improving service quality and operational excellence.

Originality/value

This study has tried to analyze green logistics practices for sustainable service quality and proposed a framework for quantifying sustainability.
International actors of democracy assistance in Egypt post 2011: German political foundations
Authors: Kubbara Ola Ashraf
Published: March 2020

Purpose

This paper aims at a qualitative investigation and analysis of the complicated situation of the four German Political Foundations (GPFs) – Friedrich Ebert Foundation, Konrad Adenauer Foundation, Friedrich Naumann Foundation and Hanns Seidel Foundation – as actors of democracy assistance in Egypt post 25 January 2011 revolution. It explores the relation between the restrictive political circumstances and the weakness and potential failure of the GPFs while considering their internal structural and operative misconducts as intervening variables.

Design/methodology/approach

The researcher uses the qualitative research method and its interpretive practices of data collection. The backbone of this study are the field visits and extensive interviews with the resident representatives of the GPFs in Egypt, and the representatives of the international departments of their headquarters in Germany. These interviews were complemented by further interviews with members of related organizations in Germany, as well as Egyptian professors, diplomats and experts on Egypt and the broader Middle East. The interviewing method is semi-structured in nature and audio-recorded. In Germany, interviews and information were gathered throughout a four-month field-research stay in Germany.

Findings

The paper concludes that the restrictive regime and political limitations were determining variables undermining the success of the GPFs in the area of democracy assistance in Egypt post 2011 revolution, while the GPFs’ own operative malfunctions and lack of adaptation to the political reality post 2011 were contributing factors in the process.

Research limitations/implications

Owing to security concerns and trust issues, many interviewees were reluctant to give information openly and freely; also requesting complete anonymity in the study. Some information and documents were denied to the researcher out of security concerns.

Originality/value

The added value of this paper lies in the qualitative research, investigations and personalized views on the functions and situation of the GPFs as international actors of democracy assistance in Egypt post 25 January 2011 revolution, considering the restrictive political landscape in which they exist. The study can assist scholars and researchers who explore the processes of democratization during transitional periods and the harsh grip of restrictive regime.