bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cefazolin and imipenem enhance AmpC expression and resistance in NagZ-dependent manner in Enterobacter cloacae complex
Authors: Yang Xianggui , Wang Zhenguo , Liu Mingquan , Yu Xuejing , Zhong Yuanxiu , Wang Fuying , Xu Ying 
Published: November 2022

Abstract
Background
Enterobacter cloacae complex (ECC) is a common opportunistic pathogen and is responsible for causing various infections in humans. Owing to its inducible chromosomal AmpC β-lactamase (AmpC), ECC is inherently resistant to the 1st- and 2nd- generation cephalosporins. However, whether β-lactams antibiotics enhance ECC resistance remains unclear.

Results
In this study, we found that subinhibitory concentrations (SICs) of cefazolin (CFZ) and imipenem (IMP) can advance the expression of AmpC and enhance its resistance towards β-lactams through NagZ in Enterobacter cloacae (EC). Further, AmpC manifested a substantial upregulation in EC in response to SICs of CFZ and IMP. In nagZ knockout EC (ΔnagZ), the resistance to β-lactam antibiotics was rather weakened and the effect of CFZ and IMP on AmpC induction was completely abrogated. NagZ ectopic expression can rescue the induction effects of CFZ and IMP on AmpC and increase ΔnagZ resistance. More importantly, CFZ and IMP have the potential to induce the expression of AmpR's target genes in a NagZ-dependent manner.

Conclusions
Our findings suggest that NagZ is a critical determinant for CFZ and IMP to promote AmpC expression and resistance and that CFZ and IMP should be used with caution since they may aggravate ECC resistance. At the same time, this study further improves our understanding of resistance mechanisms in ECC.
Increased neutrophil-to-lymphocyte ratio is associated with unfavorable functional outcomes in acute pontine infarction
Authors: Zhai Mingfeng , Cao Shugang , Wang Xinlin , Liu Yingli , Tu Feng , Xia Mingwu , Li Zongyou 
Published: November 2022

Background
The neutrophil-to-lymphocyte ratio (NLR) is positively associated with unfavorable outcomes in patients with cerebral infarction. This study aimed to investigate the relationship between the NLR and the short-term clinical outcome of acute pontine infarction.

Methods
Patients with acute pontine infarction were consecutively included. Clinical and laboratory data were collected. All patients were followed up at 3 months using modified Rankin Scale (mRS) scores. An unfavorable outcome was defined as an mRS score ≥ 3. Receiver operating characteristic (ROC) curve analysis was used to calculate the optimal cutoff values for patients with acute pontine infarction. risk factors can be predictive factors for an unfavorable outcome after acute pontine infarction.

Results
Two hundred fifty-six patients with acute pontine infarction were included in this study. The NLR was significantly higher in the unfavorable outcome group than in the favorable outcome group (P < 0.05). Additionally, the infarct size was significantly higher in the high NLR tertile group than in the low NLR tertile group (P < 0.05). Multivariate logistic regression analysis revealed that the baseline National Institutes of Health Stroke Scale (NIHSS) score, NLR, platelet count, and fasting blood glucose (FBG) level were significantly associated with unfavorable outcomes 3 months after acute pontine infarction. The optimal cutoff value of the NLR for predicting the 3-month outcome of acute pontine infarction was 3.055. The negative and positive predictive values of NLR were 85.7% and 61.3%, respectively, and the sensitivity and specificity of NLR were 69.2% and 80.9%.

Conclusions
We found that the NLR may be an independent predictive factor for the outcome of acute pontine infarction.
Prognostic ability of lung immune prognostic index in limited-stage small cell lung cancer
Authors: Sun Bochen , Hou Qing , Liang Yu , Xue Shuqin , Yao Ningning , Wei Lijuan , Cao Xin , Li Hongwei , Si Hongwei , Cao Jianzhong 
Published: November 2022

Abstract
Background
Lung immune prognostic index (LIPI) is a prognostic marker of extensive-stage small cell lung cancer (ES-SCLC) patients received immunotherapy or chemotherapy. However, its ability in limited-stage SCLC (LS-SCLC) should be evaluated extensively.

Methods
We retrospectively enrolled 497 patients diagnosed as LS-SCLC between 2015 and 2018, and clinical data included pretreatment lactate dehydrogenase (LDH), white blood cell count, and absolute neutrophil count levels were collected. According to the LIPI scores, the patients were stratified into low-risk (0 points) and high-risk (1–2 points). The correlations between LIPI and overall survival (OS) or progression-free survival (PFS) were analyzed by the Cox regression. Additionally, the propensity score matching (PSM) and inverse probability of treatment weight (IPTW) methods were used to reduce the selection and confounding bias. A nomogram was constructed using on multivariable Cox model.

Results
Two hundred fifty and 247 patients were in the LIPI high-risk group and low-risk group, and their median OS was 14.67 months (95% CI: 12.30–16.85) and 20.53 months (95% CI: 17.67–23.39), respectively. In the statistical analysis, High-risk LIPI was significantly against worse OS (HR = 1.377, 95%CI:1.114–1.702) and poor PFS (HR = 1.338, 95%CI:1.1–1.626), and the result was similar after matching and compensating with the PSM or IPTW method. A novel nomogram based on LIPI has a decent level of predictive power.

Conclusion
LIPI stratification was a significant factor against OS or PFS of LS-SCLC patients.
Clinical and genetic analysis in Chinese children with Alagille syndrome
Authors: Chen Ying , Sun Mei , Teng Xu 
Published: November 2022

Abstract
Background
Alagille syndrome (ALGS) is a multisystem disorder with variable clinical penetrance. The genes responsible for this disease are JAGGED1 (JAG1) and NOTCH2. Clinical data of this disease are limited in China. The purpose of this study was to enrich the present data of Chinese children with Alagille syndrome by summarizing the clinical characteristics and genetic variations of these cases.

Case summary
From January 2011 to February 2022, 10 children were diagnosed with ALGS. The organs involved in ALGS were as follows: liver (10, 100%); heart (7, 70%); characteristic facial features (7, 70%); skeleton (4, 40%); brain (1,10%) and kidney (3, 30%). Four patients (40%) were small for gestational age. The main clinical manifestations were cholestasis, heart disease, and facial features. The median total bilirubin, direct bilirubin, and total bile acid levels were 138.75 μmol/L (normal, 3.4–20.5 μmol/L), 107.25 μmol/L (normal, 0–8.6 μmol/L), and 110.65 μmol/L (normal, 0.5–10.0 μmol/L), respectively. The median value of gamma-glutamyltranspeptidase was 223 U/L (normal, 9–64 U/L). Six (60%) children had hypercholesteremia. Eight different JAG1 gene variations and one NOTCH2 gene pathogenic variant in the 10 Chinese ALGS patients were identified.

Conclusion
Cholestasis was the most common initial presenting symptom in Chinese ALGS pediatric patients. Pathogenic variants in JAG1 and NOTCH2 are the primary mutations in Chinese children with ALGS, but we had our own unique variant spectrum. ALGS should be considered for cholestasis in infants and young children, especially those with multiorgan abnormalities.
Effectiveness of early warning systems in the detection of infectious diseases outbreaks: a systematic review
Authors: Meckawy Rehab , Stuckler David , Mehta Adityavarman , Al-Ahdal Tareq , Doebbeling Bradley N. 
Published: November 2022

Abstract
Background
Global pandemics have occurred with increasing frequency over the past decade reflecting the sub-optimum operationalization of surveillance systems handling human health data. Despite the wide array of current surveillance methods, their effectiveness varies with multiple factors. Here, we perform a systematic review of the effectiveness of alternative infectious diseases Early Warning Systems (EWSs) with a focus on the surveillance data collection methods, and taking into consideration feasibility in different settings.

Methods
We searched PubMed and Scopus databases on 21 October 2022. Articles were included if they covered the implementation of an early warning system and evaluated infectious diseases outbreaks that had potential to become pandemics. Of 1669 studies screened, 68 were included in the final sample. We performed quality assessment using an adapted CASP Checklist.

Results
Of the 68 articles included, 42 articles found EWSs successfully functioned independently as surveillance systems for pandemic-wide infectious diseases outbreaks, and 16 studies reported EWSs to have contributing surveillance features through complementary roles. Chief complaints from emergency departments’ data is an effective EWS but it requires standardized formats across hospitals. Centralized Public Health records-based EWSs facilitate information sharing; however, they rely on clinicians’ reporting of cases. Facilitated reporting by remote health settings and rapid alarm transmission are key advantages of Web-based EWSs. Pharmaceutical sales and laboratory results did not prove solo effectiveness. The EWS design combining surveillance data from both health records and staff was very successful. Also, daily surveillance data notification was the most successful and accepted enhancement strategy especially during mass gathering events. Eventually, in Low Middle Income Countries, working to improve and enhance existing systems was more critical than implementing new Syndromic Surveillance approaches.

Conclusions
Our study was able to evaluate the effectiveness of Early Warning Systems in different contexts and resource settings based on the EWSs’ method of data collection. There is consistent evidence that EWSs compiling pre-diagnosis data are more proactive to detect outbreaks. However, the fact that Syndromic Surveillance Systems (SSS) are more proactive than diagnostic disease surveillance should not be taken as an effective clue for outbreaks detection.
Lifestyles and health-related quality of life in Chinese people: a national family study
Authors: Zou Shiqian , Feng Guanrui , Li Danyang , Ge Pu , Wang Siyi , Liu Tinlun , Li Haijun , Lai Yongjie , Tan Zijian , Huang Yuling , Huang Jian , Zhang Casper , Wu Yibo , Ming Wai-kit 
Published: November 2022

Abstract
Background
There were few studies that investigated health-related quality of life (HRQoL) of the general population in China, and many of them reported limitations in sampling.

Objective
To investigate the relationship between lifestyles and HRQoL in the Chinese population in both individual and family levels.

Method
Online questionnaires were distributed across China to collect demographic information and participants’ HRQoL using EuroQoL 5 Dimension scales. The EuroQoL Group’s 5 Dimension scale (EQ-5D) index and EuroQoL Group’s visual analog scale (EQ VAS) score were calculated to evaluate the HRQoL.

Results
A total of 1305 valid questionnaires were included. Higher HRQoL was found in people with intend to lower oil intake, intend to lower salt intake, intend to lower sugar intake, balanced diet, moderate sports every week, a sport hobby and joining a fitness organization (all p<.05). HRQoL was higher among male (female as reference), healthy weight (unhealthy weight as reference) (both p<.05). Negative correlation was found between HRQoL and clinical medical history and drinking history. Small families (1-2 persons, 83.19 ± 20.14) had poorer HRQoL (EQ VAS score) than big families (≥3 persons, 85.00 ± 17.96, p <.05).

Conclusion
In China, people with healthy dietary habits, regular sports habits, healthy weight and male groups tended to have better HRQoL. Clinical medical history and drinking history were negatively related to HRQoL. Small families tend to have poorer HRQoL than big families. The finding implicated influence of the number of family members on people’s perception of health and provided scientific evidence for the current policies to encourage birth in China. For a better HRQoL, we suggest people live in big families and take measures to lower salt/sugar/oil intake and exercise regularly in daily life.
Electrocardiogram lead conversion from single-lead blindly-segmented signals
Authors: Beco Sofia C. , Pinto João Ribeiro , Cardoso Jaime S. 
Published: November 2022

Abstract
Background
The standard configuration’s set of twelve electrocardiogram (ECG) leads is optimal for the medical diagnosis of diverse cardiac conditions. However, it requires ten electrodes on the patient’s limbs and chest, which is uncomfortable and cumbersome. Interlead conversion methods can reconstruct missing leads and enable more comfortable acquisitions, including in wearable devices, while still allowing for adequate diagnoses. Currently, methodologies for interlead ECG conversion either require multiple reference (input) leads and/or require input signals to be temporally aligned considering the ECG landmarks.

Methods
Unlike the methods in the literature, this paper studies the possibility of converting ECG signals into all twelve standard configuration leads using signal segments from only one reference lead, without temporal alignment (blindly-segmented). The proposed methodology is based on a deep learning encoder-decoder U-Net architecture, which is compared with adaptations based on convolutional autoencoders and label refinement networks. Moreover, the method is explored for conversion with one single shared encoder or multiple individual encoders for each lead.

Results
Despite the more challenging settings, the proposed methodology was able to attain state-of-the-art level performance in multiple target leads, and both lead I and lead II seem especially suitable to convert certain sets of leads. In cross-database tests, the methodology offered promising results despite acquisition setup differences. Furthermore, results show that the presence of medical conditions does not have a considerable effect on the method’s performance.

Conclusions
This study shows the feasibility of converting ECG signals using single-lead blindly-segmented inputs. Although the results are promising, further efforts should be devoted towards the improvement of the methodologies, especially the robustness to diverse acquisition setups, in order to be applicable to cardiac health monitoring in wearable devices and less obtrusive clinical scenarios.
Gene Coverage Count and Classification (GC3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum
Authors: Stabler Thomas C. , Dwivedi Ankit , Shrestha Biraj , Joshi Sudhaunshu , Schindler Tobias , Ouattara Amed , García Guillermo A. , Daubenberger Claudia , Silva Joana C. 
Published: November 2022

Abstract
Background
The ability of malaria rapid diagnostic tests (RDTs) to effectively detect active infections is being compromised by the presence of malaria strains with genomic deletions at the hrp2 and hrp3 loci, encoding the antigens most commonly targeted in diagnostics for Plasmodium falciparum detection. The presence of such deletions can be determined in publically available P. falciparum whole genome sequencing (WGS) datasets. A computational approach was developed and validated, termed Gene Coverage Count and Classification (GC3), to analyse genome-wide sequence coverage data and provide informative outputs to assess presence and coverage profile of a target locus in WGS data. GC3 was applied to detect deletions at hrp2 and hrp3 (hrp2/3) and flanking genes in different geographic regions and across time points.

Methods
GC3 uses Python and R scripts to extract locus read coverage metrics from mapped WGS data according to user-defined parameters and generates relevant tables and figures. GC3 was tested using WGS data for laboratory reference strains with known hrp2/3 genotypes, and its results compared to those of a hrp2/3-specific qPCR assay. Samples with at least 25% of coding region positions with zero coverage were classified as having a deletion. Publicly available sequence data was analysed and compared with published deletion frequency estimates.

Results
GC3 results matched the expected coverage of known laboratory reference strains. Agreement between GC3 and a hrp2/3-specific qPCR assay reported for 19/19 (100%) hrp2 deletions and 18/19 (94.7%) hrp3 deletions. Among Cambodian (n = 127) and Brazilian (n = 20) WGS datasets, which had not been previously analysed for hrp2/3 deletions, GC3 identified hrp2 deletions in three and four samples, and hrp3 deletions in 10 and 15 samples, respectively. Plots of hrp2/3 coding regions, grouped by year of sample collection, showed a decrease in median standardized coverage among Malawian samples (n = 150) suggesting the importance of a careful, properly controlled follow up to determine if an increase in frequency of deletions has occurred between 2007–2008 and 2014–2015. Among Malian (n = 90) samples, median standardized coverage was lower in 2002 than 2010, indicating widespread deletions present at the gene locus in 2002.

Conclusions
The GC3 tool accurately classified hrp2/3 deletions and provided informative tables and figures to analyse targeted gene coverage. GC3 is an appropriate tool when performing preliminary and exploratory assessment of locus coverage data.
An R3-MYB repressor, BnCPC forms a feedback regulation with MBW complex to modulate anthocyanin biosynthesis in Brassica napus
Authors: Xie Tao , Zan Xiongyun , Chen Xin , Zhu Haotian , Rong Hao , Wang Youping , Jiang Jinjin 
Published: November 2022

Abstract
Background
Anthocyanins are metabolites of phenylpropanoid pathway, and involves in diverse processes of plant development and adaptation, which are regulated by the MYB-bHLH-WD40 (MBW) protein complexes. Many R2R3-MYB activators have been well characterized, but the MYB repressors in anthocyanin biosynthesis were recognized recently, which are also important in modulating phenylpropanoid metabolism in plants. The regulatory mechanism of anthocyanin biosynthesis in oil crop Brassica napus remains to be revealed.

Results
In this study, we identified an anthocyanin repressor BnCPC in B. napus. BnCPC encoded a typical R3-MYB protein containing a conserved [D/E]Lx2[R/K]x3Lx6Lx3R motif for interaction with bHLH proteins. Overexpression of BnCPC in B. napus inhibited anthocyanin accumulation, especially under anthocyanin inducible conditions. Protein–protein interaction and dual-luciferase assays confirmed that BnCPC could compete with BnPAP1 to interact with bHLHs (BnTT8 and BnEGL3), and repress the expression of anthocyanin biosynthetic genes (e.g., BnDFR) that activated by MBW complexes. Moreover, we found BnCPC inhibited the MBW complex-induced BnCPC activity.

Conclusions
Overall, this research demonstrated that BnCPC repressed anthocyanin biosynthesis by affecting the formation of MBW complex, and formed a feedback loop to regulate anthocyanin accumulation in B. napus.
What evidence exists regarding the effects of photovoltaic panels on biodiversity? A critical systematic map protocol
Authors: Lafitte Alix , Sordello Romain , de Crespin de Billy Véronique , Froidevaux Jérémy , Gourdain Philippe , Kerbiriou Christian , Langridge Joseph , Marx Geoffroy , Schatz Bertrand , Thierry Chloé , Reyjol Yorick 
Published: November 2022

Abstract
Background
Climate change and the current phase-out of fossil fuel-fired power generation are currently expanding the market of renewable energy and more especially photovoltaic (PV) panels. Contrary to other types of renewable energies, such as wind and hydroelectricity, evidence on the effects of PV panels on biodiversity has been building up only fairly recently. PV panels have been linked to substantial impacts on species and ecosystems, the first and most obvious one being the degradation of natural habitats but they may also lead to mortality of individuals and displacements of populations. Hence, we propose a systematic map aiming to draw a comprehensive panorama of the available knowledge on the effects of photovoltaic and solar thermal (PVST) installations, whatever their scales (i.e. cells, panels, arrays, utility-scale facilities), on terrestrial and semi-aquatic species and natural/semi-natural habitats and ecosystems. This work aims at providing decision-makers with a better understanding of the effects of PVST installations and, therefore, help them further protect biodiversity while also mitigating anthropogenic climate change.

Methods
We will follow the collaboration for environmental evidence guidelines and search for relevant peer-reviewed and grey literature in English or French. The search string will combine population (all wild terrestrial and semi-aquatic species—e.g. animals, plants, fungi, microorganisms—as well as natural/semi-natural terrestrial habitats and ecosystems) and exposure/intervention (all technologies of PVST panels at all scales of installations and therefore excluding concentrated solar power) terms. A pre-built test list of relevant articles will be used to assess the comprehensiveness of the search string. Extracted citations will be screened at title and full-text stages thanks to pre-defined inclusion/exclusion criteria. Accepted citations will then be split into studies and observations, from which relevant metadata (e.g. taxon, exposure/intervention, outcome) will be extracted and their internal validity assessed through a critical appraisal. The database will be accessible alongside a map report which will draw a landscape of eligible studies. By describing studied populations, exposures/interventions, outcomes and internal study validity results, the report will identify potential knowledge clusters and gaps regarding the effects of PVST installations on biodiversity and ecosystems.
Spatial distribution and developmental trajectories of crime versus crime severity: do not abandon the count-based model just yet
Authors: Harinam Vincent , Bavcevic Zeljko , Ariel Barak 
Published: November 2022

Abstract
Purpose/background
A new body of research that focuses on crime harm scores rather than counts of crime incidents has emerged. Specifically in the context of spatial analysis of crime, focusing on crime harm suggests that harm is more concentrated than counts, at the level of crime hot spots. It remains presently unclear what drives the concentration distributions, and whether the count-based model should be abandoned.

Methods
Cross-sectional and longitudinal analysis of 6 year of spatiotemporal crime data in Toronto, Canada, to compare patterns and concentration of crime harm (measured in terms of the Crime Severity Index (CSI) against crime counts. Conditional probabilities, trajectory analyses, power few concentrations, and spatial Global Moran’s I are used to infer generalised trends from the data.

Findings
Overall CSI and crime counts tend to exhibit similar concentrations at the spatial micro levels, except against-the-body crimes such as violence which seems to drive nearly all the variations between the two measurement types. Violence harm spots tend to be more dispersed citywide and often do not remain constant year-to-year, whereas overall crime hotspots are more stable over time. Nevertheless, variations in disproportionally high crime hot spots are associated with total variations in crime, with as little as 1% increase in crime levels in these hot spots translating into substantial overall gains in recorded crime citywide.

Conclusions
Abandoning count-based models in spatial analysis of crime can lead to an incomplete picture of crime concentrations. Both models are needed not just for understanding spatial crime distributions but also for cost-effective allocation of policing resources.