bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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

AbstractAimsCorona 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.MethodsA 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.ResultsThere 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.ConclusionsLymphopenia 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

AbstractInferring 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

AbstractSimple 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

AbstractSelf-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

ABSTRACTChromosome 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.
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

PurposeInformation-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/approachThe 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.FindingsThe 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 implicationsThe 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/valueThe 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

PurposeInvestigate 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/approachBy 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.FindingsThis 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 implicationsThe 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/valueBy 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.