bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of topology-based pathway enrichment analysis methods
Authors: Ma Jing , Shojaie Ali , Michailidis George 
Published: November 2019

AbstractBackgroundPathway enrichment extensively used in the analysis of Omics data for gaining biological insights into the functional roles of pre-defined subsets of genes, proteins and metabolites. A large number of methods have been proposed in the literature for this task. The vast majority of these methods use as input expression levels of the biomolecules under study together with their membership in pathways of interest. The latest generation of pathway enrichment methods also leverages information on the topology of the underlying pathways, which as evidence from their evaluation reveals, lead to improved sensitivity and specificity. Nevertheless, a systematic empirical comparison of such methods is still lacking, making selection of the most suitable method for a specific experimental setting challenging. This comparative study of nine network-based methods for pathway enrichment analysis aims to provide a systematic evaluation of their performance based on three real data sets with different number of features (genes/metabolites) and number of samples.ResultsThe findings highlight both methodological and empirical differences across the nine methods. In particular, certain methods assess pathway enrichment due to differences both across expression levels and in the strength of the interconnectedness of the members of the pathway, while others only leverage differential expression levels. In the more challenging setting involving a metabolomics data set, the results show that methods that utilize both pieces of information (with NetGSA being a prototypical one) exhibit superior statistical power in detecting pathway enrichment.ConclusionThe analysis reveals that a number of methods perform equally well when testing large size pathways, which is the case with genomic data. On the other hand, NetGSA that takes into consideration both differential expression of the biomolecules in the pathway, as well as changes in the topology exhibits a superior performance when testing small size pathways, which is usually the case for metabolomics data.
Trusting the hand that feeds: microbes evolve to anticipate a serial transfer protocol as individuals or collectives
Authors: van Dijk Bram , Meijer Jeroen , Cuypers Thomas D. , Hogeweg Paulien 
Published: November 2019

AbstractBackgroundExperimental evolution of microbes often involves a serial transfer protocol, where microbes are repeatedly diluted by transfer to a fresh medium, starting a new growth cycle. This has revealed that evolution can be remarkably reproducible, where microbes show parallel adaptations both on the level of the phenotype as well as the genotype. However, these studies also reveal a strong potential for divergent evolution, leading to diversity both between and within replicate populations. We here study how in silico evolved Virtual Microbe “wild types” (WTs) adapt to a serial transfer protocol to investigate generic evolutionary adaptations, and how these adaptations can be manifested by a variety of different mechanisms.ResultsWe show that all WTs evolve to anticipate the regularity of the serial transfer protocol by adopting a fine-tuned balance of growth and survival. This anticipation is done by evolving either a high yield mode, or a high growth rate mode. We find that both modes of anticipation can be achieved by individual lineages and by collectives of microbes. Moreover, these different outcomes can be achieved with or without regulation, although the individual-based anticipation without regulation is less well adapted in the high growth rate mode.ConclusionsAll our in silico WTs evolve to trust the hand that feeds by evolving to anticipate the periodicity of a serial transfer protocol, but can do so by evolving two distinct growth strategies. Furthermore, both these growth strategies can be accomplished by gene regulation, a variety of different polymorphisms, and combinations thereof. Our work reveals that, even under controlled conditions like those in the lab, it may not be possible to predict individual evolutionary trajectories, but repeated experiments may well result in only a limited number of possible outcomes.
Nutritional value of Sesamum indicum L. was improved by Azospirillum and Azotobacter under low input of NP fertilizers
Authors: Nosheen Asia , Bano Asghari , Naz Rabia , Yasmin Humaira , Hussain Ishtiaq , Ullah Faizan , Keyani Rumana , Hassan Muhammad Nadeem , Tahir Ayesha T. 
Published: November 2019

AbstractBackgroundSesame (Sesame indicumL.) is well-known as a versatile industrial crop having various usages and contains 50–55% oil, 20% protein, 14–20% carbohydrate and 2–3% fiber. Several environmental factors are known to adversely affect yield and productivity of sesame. Our overall aim was to improve the growth, yield and quality of sesame cv. TS-3 using plant growth promoting rhizobacteria (PGPR) and saving the nitrogen and phosphate fertilizers (NP) by 50%. Field experiment (randomized complete block design) was conducted during the months of July to October of two consecutive years 2012–2013.Azospirillum(AL) andAzotobacter(AV) were applied as seed inoculation alone as well as along with half of the recommended dose of nitrogen (N) and phosphate (P) fertilizers (urea and diammonium phosphate) at the rate of 25 kg/ha and 30 kg/ha respectively.ResultsHere we report thatA. lipoferumalong with half dose of NP fertilizers (ALCF) were highly effective in increasing the agronomic and yield traits of sesame as compared to the control.A. vinelandiiplus NP fertilizers (AVCF) exhibited higher seed oil content. Minimum acid value, optimum specific gravity and modified fatty acid composition were observed in ALCF treatment. Increase in oleic acid by ALCF is directly linked with improved oil quality for health benefits as oleic acid is the fatty acid which creates a balance between saturation and unsaturation of oil and for the hypotensive (blood pressure reducing) effects.ConclusionIt is inferred that ALCF treatment improved plant growth, seed yield and oil quality of sesame pertaining to good quality edible oil production.
The effect of intraoperative lidocaine versus esmolol infusion on postoperative analgesia in laparoscopic cholecystectomy: a randomized clinical trial
Authors: Bajracharya Joshan Lal , Subedi Asish , Pokharel Krishna , Bhattarai Balkrishna 
Published: November 2019

Abstract

Background
As a part of multimodal analgesia for laparoscopic cholecystectomy, both intraoperative lidocaine and esmolol facilitate postoperative analgesia. Our objective was to compare these two emerging strategies that challenge the use of intraoperative opioids. We aimed to assess if intraoperative esmolol infusion is not inferior to lidocaine infusion for opioid consumption after laparoscopic cholecystectomy.

Methods
In this prospective, randomized, double-blind, non-inferiority clinical trial, 90 female patients scheduled for elective laparoscopic cholecystectomy received either intravenous (IV) lidocaine bolus 1.5 mg/kg at induction followed by an infusion (1.5 mg/ kg/h) or IV bolus of esmolol 0.5 mg/kg at induction followed by an infusion (5–15 μg/kg/min) till the end of surgery. Remaining aspect of anesthesia followed a standard protocol apart from no intraoperative opioid supplementation. Postoperatively, patients received either morphine or tramadol IV to maintain visual analogue scale (VAS) scores ≤3. The primary outcome was opioid consumption (in morphine equivalents) during the first 24 postoperative hours. Pain and sedation scores, time to first perception of pain and void, and occurrence of nausea/vomiting were secondary outcomes measured up to 24 h postoperatively.

Results
Two patients in each group were excluded from the analysis. The postoperative median (IQR) morphine equivalent consumption in patients receiving esmolol was 1 (0–1.5) mg compared to 1.5 (1–2) mg in lidocaine group (p = 0.27). The median pain scores at various time points were similar between the two groups (p > 0.05). More patients receiving lidocaine were sedated in the post-anesthesia care unit (PACU) than those receiving esmolol (p < 0.05); however, no difference was detected later.

Conclusion
Infusion of esmolol is not inferior to lidocaine in terms of opioid requirement and pain severity in the first 24 h after surgery. Patients receiving lidocaine were more sedated during their stay in PACU than those receiving esmolol.

Trial registration
ClinicalTrials.gov- NCT02327923. Date of registration: December 31, 2014.
Evaluation of tools to assess psychological distress: how to measure psychological stress reactions in citizen responders– a systematic review
Authors: Kragh Astrid Rolin , Folke Fredrik , Andelius Linn , Ries Emma Slebsager , Rasmussen Rasmus Vedby , Hansen Carolina Malta 
Published: November 2019

AbstractBackgroundDispatched citizen responders are increasingly involved in out-of-hospital cardiac arrest (OHCA) resuscitation which can lead to severe stress. It is unknown which psychological assessment tools are most appropriate to evaluate psychological distress in this population.The aim of this systematic review was to identify and evaluate existing assessment tools used to measure psychological distress with emphasis on citizen responders who attempted resuscitation.MethodsA systematic literature search conducted by two reviewers was carried out in March 2018 and revised in July 2018. Four databases were searched: PubMed, PsycInfo, Scopus, and The Social Sciences Citation Index. A total of 504 studies examining assessment tools to measure psychological distress reactions after acute traumatic events were identified, and 9 fulfilled the inclusion criteria for further analysis. The selected studies were assessed for methodological quality using the Scottish Intercollegiate Guidelines Network.ResultsThe Impact of Event Scale (IES) and The Impact of Event Scale-Revised (IES-R) were the preferred assessment tools, and were used on diverse populations exposed to various traumatic events. One study included lay rescuers performing bystander cardiopulmonary resuscitation and this study used the IES. The IES and the IES-R also have proven a high validity in various other populations. The Clinical administered PTSD scale (CAPS) was applied in two studies. Though the CAPS is comparable to both the IES-R and the IES, the CAPS assess PTSD symptoms in general and not in relation to a specific experienced event, which makes the scale less suitable when measuring stress due to a specific resuscitation attempt.ConclusionsThe IES and the IES-R seem to be solid measures for psychological distress among people experiencing an acute psychological traumatic event. However, only one study has assessed psychological distress among citizen responders in OHCA for which the IES-R scale was used, and therefore, further research on this topic is warranted.
Definition of a systematic review used in overviews of systematic reviews, meta-epidemiological studies and textbooks
Authors: Krnic Martinic Marina , Pieper Dawid , Glatt Angelina , Puljak Livia 
Published: November 2019

Abstract

Background
A standard or consensus definition of a systematic review does not exist. Therefore, if there is no definition about a systematic review in secondary studies that analyse them or the definition is too broad, inappropriate studies might be included in such evidence synthesis. The aim of this study was to analyse the definition of a systematic review (SR) in health care literature, elements of the definitions that are used and to propose a starting point for an explicit and non-ambiguous SR definition.

Methods
We included overviews of systematic reviews (OSRs), meta-epidemiological studies and epidemiology textbooks. We extracted the definitions of SRs, as well as the inclusion and exclusion criteria that could indicate which definition of a SR the authors used. We extracted individual elements of SR definitions, categorised and quantified them.

Results
Among the 535 analysed sources of information, 188 (35%) provided a definition of a SR. The most commonly used reference points for the definitions of SRs were Cochrane and the PRISMA statement. We found 188 different elements of SR definitions and divided them into 14 categories. The highest number of SR definition elements was found in categories related to searching (N = 51), analysis/synthesis (N = 23), overall methods (N = 22), quality/bias/appraisal/validity (N = 22) and aim/question (N = 13). The same five categories were also the most commonly used combination of categories in the SR definitions.

Conclusion
Currently used definitions of SRs are vague and ambiguous, often using terms such as clear, explicit and systematic, without further elaboration. In this manuscript we propose a more specific definition of a systematic review, with the ultimate aim of motivating the research community to establish a clear and unambiguous definition of this type of research.
Advanced glycation end products and their ratio to soluble receptor are associated with limitations in physical functioning only in women: results from the CARLA cohort
Authors: Ebert Helen , Lacruz Maria Elena , Kluttig Alexander , Simm Andreas , Greiser Karin Halina , Tiller Daniel , Kartschmit Nadja , Mikolajczyk Rafael 
Published: November 2019

Abstract

Background
Advanced glycation end products (AGEs), modifications of proteins or amino acids, are increasingly produced and accumulated with age-related diseases. Recent studies suggested that the ratio of AGEs and their soluble receptor (sRAGE) is a more accurate biomarker for age-related diseases than each separately. We aim to investigate whether this also applies for physical functioning in a broad age-spectrum.

Methods
AGE and sRAGE levels, and physical functioning (SF-12 questionnaire) of 967 men and 812 women (45–83 years) were measured in the CARLA study. We used ordinal logistic regression to examine associations between AGEs, sRAGE, and AGE/sRAGE ratio with physical functioning in sex- and age-stratified models.

Results
Higher levels of AGEs and AGE/sRAGE ratio were associated with lower physical functioning only in women, even after consideration of classical lifestyle and age-related factors (education, BMI, smoking, alcohol consumption, diet, creatinine clearance, diabetes mellitus, lipid lowering and antihypertensive drugs) (odds ratio (OR) =0.86, 95%confidence interval = 0.74–0.98 and OR = 0.86, 95%CI = 0.75–0.98 for AGEs and AGE/sRAGE ratio respectively). We could not demonstrate a significant difference across age.

Conclusions
We showed a sex-specific association between physical functioning and AGEs and AGE/sRAGE, but no stronger associations of the latter with physical functioning. Further investigation is needed in the pathophysiology of this association.
Infective endocarditis caused by Capnocytophaga canimorsus; a case report
Authors: Sakai Jun , Imanaka Kazuhito , Kodana Masahiro , Ohgane Kana , Sekine Susumu , Yamamoto Kei , Nishida Yusuke , Kawamura Toru , Matsuoka Takahiro , Maesaki Shigefumi , Oka Hideaki , Ohno Hideaki 
Published: November 2019

Abstract

Background
Capnocytophaga canimorsus is a gram-negative bacterium and an oral commensal in dogs and cats, but occasionally causes serious infections in humans. Septicemia is one of the most fulminant forms, but diagnosis of C. canimorsus infection is often difficult mainly because of its very slow growth. C. canimorsus infective endocarditis (IE) is rare and is poorly understood. Since quite a few strains produce β-lactamase, antimicrobial susceptibility is pivotal information for adequate treatment. We herein report a case with C. canimorsus IE and the results of drug susceptibility test.

Case presentation
A 46-year-old man had a dog bite in his left hand 3 months previously. The patient was referred to our hospital for fever (body temperature > 38 °C), visual disturbance, and dyspnea. Echocardiography showed aortic valve regurgitation and vegetation on the leaflets. IE was diagnosed, and we initially administered cefazolin and gentamycin assuming frequently encountered microorganisms and the patient underwent aortic valve replacement. C. canimorsus was detected in the aortic valve lesion and blood cultures. It was also identified by 16S ribosome DNA sequencing. Ceftriaxone were started and continued because disk diffusion test revealed the isolate was negative for β-lactamase and this case had cerebral symptoms. The patient successfully completed antibiotic treatment following surgery.

Conclusions
We diagnosed C. canimorsus sepsis and IE by extended-period blood cultures and 16S ribosome DNA sequencing by polymerase chain reaction, and successfully identified its drug susceptibility.
Modification of both functional neurological symptoms and neuroimaging patterns with a good anatomoclinical concordance: a case report
Authors: Galli Silvio , Aybek Selma , Chokron Sylvie , Moulin Thierry , Magnin Eloi 
Published: November 2019

Abstract

Background
In the nineteenth century, Jean Martin Charcot explained functional neurological disorder (formerly called conversion disorder) as a “psychodynamic” lesion. Numerous advances in neuroimaging have permitted identification of the neural underpinnings of this disorder.

Case presentation
Herein we describe a case of functional neurological disorder (FND) with initial left sensorimotor deficit, in-coordinated limb movements, neglect, clouded consciousness, slurred speech and a semiology of visual impairment. A single photon emission computed tomography (SPECT) showed a right thalamic hypoperfusion, which is rather concordant with the initial semiology. Later, the semiology changed, presenting with a predominantly neurovisual complex presentation. The second SPECT showed no more thalamic abnormalities but an hypoperfusion in the right temporo-occipital junction, right inferior parietal lobe and left superior frontal lobe, which is also rather concordant with the changing semiology.

Conclusions
This case illustrates the evolving neuroimaging patterns of FND but also the concordance between semiology and neuroimaging findings in FND supporting Charcot's theory of “dynamic lesion”.
Parenchymal central nervous system involvement in aggressive B-cell lymphoma: retrospective analysis of clinical and MRI features in a Chinese population
Authors: Wu Yuchen , Wang Yaming , Sun Xuefei , Bai Xueyan , Qian Jun , Zhu Hong , Cui Qu , Xing Ruixian , Chen Yuedan , Liu Qing , Guo Jiayuan , Ji Nan , Sun Shengjun , Liu Yuanbo 
Published: November 2019

Abstract

Background
Secondary central nervous system lymphoma (SCNSL) is defined as secondary central nervous system (CNS) involvement in patients with systemic lymphoma. It is considered a profoundly adverse complication with inferior clinical outcome. Parenchymal involvement in the CNS in aggressive B-cell lymphoma is not frequently seen and remains a diagnostic dilemma.

Methods
In our study, we retrospectively analyzed the clinical and magnetic resonance imaging (MRI) features of 26 parenchymal SCNSL patients. In addition, we compared MRI features of SCNSL and primary CNS lymphoma (PCNSL) patients after 1:1 propensity score matching. Also we presented two SCNSL cases with atypical MRI appearance.

Results
Among SCNSL patients, the median CNS relapse time was 3 months, and multiple lesions were found in 76.9% of the cases. In PCNSL, this percentage was 42.3% (p = 0.011). None of the SCNSL patients and 23.1% of the PCNSL patients had solitary infratentorial lesions (p = 0.003).

Conclusions
The majority of parenchymal involvement occurred within the first year of systemic lymphoma, in which mostly cases presenting with multiple and supratentorial locations, unlike what was found in PCNSL.
Determinants of extended door-to-needle time in acute ischemic stroke and its influence on in-hospital mortality: results of a nationwide Dutch clinical audit
Authors:   on behalf of the Dutch Acute Stroke Audit consortium, Kuhrij Laurien S. , Marang-van de Mheen Perla J. , van den Berg-Vos Renske M. , de Leeuw Frank-Erik , Nederkoorn Paul J. 
Published: November 2019

Abstract

Background
Intravenous thrombolysis (IVT) plays a prominent role in the treatment of acute ischemic stroke (AIS). The sooner IVT is administered, the higher the odds of a good outcome. Therefore, registering the in-hospital time to treatment with IVT, i.e. the door-to-needle time (DNT), is a powerful way to measure quality improvement. The aim of this study was to identify determinants that are associated with extended DNT.

Methods
Patients receiving IVT in 2015 and 2016 registered in the Dutch Acute Stroke Audit were included. DNT and onset-to-door time (ODT) were dichotomized using the median (i.e. extended DNT) and the 90th percentile (i.e. severely extended DNT). Logistic regression was performed to identify determinants associated with (severely) extended DNT/ODT and its effect on in-hospital mortality. A linear model with natural spline was used to investigate the association between ODT and DNT.

Results
Included were 9518 IVT treated patients from 75 hospitals. Median DNT was 26 min (IQR 20–37). Determinants associated with a higher likelihood of extended DNT were female sex (OR 1.17, 95% CI 1.05–1.31) and admission during off-hours (OR 1.12, 95% CI 1.01–1.25). Short ODT correlated with longer DNT, whereas longer ODT correlated with shorter DNT. Young age (OR 1.38, 95% CI 1.07–1.76) and admission to a comprehensive stroke center (OR 1.26, 1.10–1.45) were associated with severely extended DNT, which was associated with in-hospital mortality (OR 1.54, 95%CI 1.19–1.98).

Conclusions
Even though DNT in the Netherlands is short compared to other countries, lowering the DNT may be achievable by focusing on specific subgroups.
Angiographic features of drug-induced bilateral angle closure and transient myopia with Ciliochoroidal effusion
Authors: Kang Yong Koo , Son Byeong Jae , Park Dong Ho , Shin Jae Pil 
Published: November 2019

Abstract

Background
To report five cases of acute drug-induced angle closure and transient myopia with ciliochoroidal effusion and to analyze angiographic findings of these cases.

Methods
This study is an observational case series. Five patients with acute drug-induced angle closure and transient myopia with ciliochoroidal effusion were examined by fluorescein angiography, indocyanine green angiography (ICGA) and ultrasound biomicroscopy (UBM).

Results
Five patients presented with bilateral visual loss and ocular pain after intake of topiramate, methazolamide, phendimetrazine tartrate or mefenamic acid. All patients showed elevated intraocular pressure (IOP) with shallow anterior chamber and myopic shift from − 0.5 to − 17.0 diopters (D). UBM showed ciliochoroidal effusions with diffuse thickening of the ciliary body in all cases. Rapid normalization of IOP and decrease of myopic shift occurred in all patients after discontinuing the suspected drugs. We classified the ICGA findings into 2 major signs (hypofluorescent dark spots, hyperfluorescent pinpoints) and 3 minor signs (diffuse choroidal hyperfluorescence, early hyperfluorescence of choroidal stromal vessel, and leakage and dilated retinal vessels).

Conclusions
The pathogenesis of acute drug-induced angle closure and transient myopia with ciliochoroidal effusion may be idiosyncratic reaction of uveal tissue to systemic drugs. Accumulation of extravascular fluid in the ciliochoroidal layer had a major role in the pathogenesis. ICGA could be a useful method to examine the pathophysiology of this condition by imaging of the choroidal layer.