bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplicity does not significantly affect outcomes in brain metastasis patients treated with surgery
Authors: Yang Kaiyun , Gutiérrez-Valencia Enrique , Landry Alexander P , Kalyvas Aristotelis , Millesi Matthias , Leite Matheuss , Jablonska Paola Anna , Weiss Jessica , Millar Barbara-Ann , Conrad Tatiana , Laperriere Normand , Bernstein Mark , Zadeh Gelareh , Shultz David , Kongkham Paul N 
Published: March 2022

Abstract

Background
Brain metastasis quantity may be a negative prognostic factor for patients requiring resection of at least one lesion.

Methods
We retrospectively reviewed patients who underwent surgical resection of brain metastases from July 2018 to June 2019 at our institution, and examined outcomes including overall survival (OS), progression free survival (PFS), and rates of local failure (LF). Patients were grouped according to the number of metastases at the time of surgery (single vs multiple).

Results
We identified 130 patients who underwent surgical resection as the initial treatment modality. At the time of surgery, 87 patients had only one lesion (control) and 43 had multiple (&gt;1). Two-year OS for the entire cohort was 46%, with equal rates in both the multiple metastases group and the control group (P = .335). 2-year PFS was 27%; 21% in the multiple metastases group and 31% in the control group (P = .766). The rate of LF at 2 years was 32%, with equal rates in both the multiple lesion group and control group (P = .889). On univariate analysis, multiplicity was not significantly correlated to OS (HR = 0.80, 95% CI: 0.51–1.26, P = .336), PFS (HR = 1.06, 95% CI: 0.71–1.59, P = .766) or LF (HR = 1.06, 95% CI: 0.57–1.97, P = .840). Multivariate analysis revealed preoperative tumor volume of the resected lesion to be the single correlate for OS (P = .0032) and PFS (P = .0081).

Conclusions
Having more than one metastasis does not negatively impact outcomes in patients treated with surgery. In carefully selected patients, especially those with large tumors, surgery should be considered regardless of the total number of lesions.
The Effect of Systemic Antibiotics for Suppurative Skin and Soft Tissue Infections on the Skin Microbiome
Authors: Chan Alfred A , Flores Evelyn A , Navarrete Marian , Phan Tran Donna , Lee Delphine J , Miller Loren G 
Published: March 2022

Abstract

Background
Skin and soft tissue infections (SSTIs) are very common bacterial infections. There are few data on the microbiome of persons with and without SSTIs and the effects of systemic antibiotic therapy.

Methods
We sampled the skin microbiome from 10 outpatients with acute suppurative SSTI before and after systemic antibiotic therapy and enrolled 10 matched controls. Samples were collected at 6 skin body sites (occipital scalp, axilla, interdigital hand web spaces, gluteal crease, inguinal creases, and popliteal fossa), 2 mucosal sites (throat, anterior nares), and the site of skin infection (for case subjects) at baseline and a week later after abscess incision, drainage, and oral antibiotics.

Result
Among 10 SSTI cases, mean age was 41.5 years and 3 had diabetes mellitus. The gluteal crease at baseline had higher α-diversity in controls vs cases (P = .039); β-diversity analysis showed significant differences in overall bacterial community composition (P = .046). However, at other body sites there were no significant differences by either α- or β-diversity. Systemic antibiotic use did not affect body site diversity indices except at the SSTI site (α-diversity increased, P = .001).

Conclusions
We surprisingly found no significant differences in microbiome comparing noninfected skin sites before and after systemic SSTI antibiotic therapy nor significant differences at noninfected skin sites between SSTI cases and uninfected controls. We also found minimal significant differences between microbiome diversity and bacterial signatures at noninfected skin sites between patients with acute skin infection and uninfected controls. Our findings challenge the dogma that systemic antibiotics impact the skin microbiome.
LONGL-Net: temporal correlation structure guided deep learning model to predict longitudinal age-related macular degeneration severity
Authors: Ganjdanesh Alireza , Zhang Jipeng , Chew Emily Y , Ding Ying , Huang Heng , Chen Wei 
Published: March 2022

Abstract
Age-related macular degeneration (AMD) is the principal cause of blindness in developed countries, and its prevalence will increase to 288 million people in 2040. Therefore, automated grading and prediction methods can be highly beneficial for recognizing susceptible subjects to late-AMD and enabling clinicians to start preventive actions for them. Clinically, AMD severity is quantified by Color Fundus Photographs (CFP) of the retina, and many machine-learning-based methods are proposed for grading AMD severity. However, few models were developed to predict the longitudinal progression status, i.e. predicting future late-AMD risk based on the current CFP, which is more clinically interesting. In this paper, we propose a new deep-learning-based classification model (LONGL-Net) that can simultaneously grade the current CFP and predict the longitudinal outcome, i.e. whether the subject will be in late-AMD in the future time-point. We design a new temporal-correlation-structure-guided Generative Adversarial Network model that learns the interrelations of temporal changes in CFPs in consecutive time-points and provides interpretability for the classifier's decisions by forecasting AMD symptoms in the future CFPs. We used about 30,000 CFP images from 4,628 participants in the Age-Related Eye Disease Study. Our classifier showed average 0.905 (95% CI: 0.886–0.922) AUC and 0.762 (95% CI: 0.733–0.792) accuracy on the 3-class classification problem of simultaneously grading current time-point's AMD condition and predicting late AMD progression of subjects in the future time-point. We further validated our model on the UK Biobank dataset, where our model showed average 0.905 accuracy and 0.797 sensitivity in grading 300 CFP images.
Promoting organic food production through flagship regions
Authors: Mennig Philipp , Sauer Johannes 
Published: March 2022

AbstractMitigating the environmental impact of agriculture is a major issue in negotiations on the future of the European Union's Common Agricultural Policy. Organic farming is commonly put forward in these discussions as a promising way to reduce the negative environmental impact of agriculture. Consequently, different promotional strategies aiming at the adoption of organic farming practices have been developed. In 2013, the German federal state of Bavaria initiated an innovative programme that resulted in ‘organic flagship regions’ being appointed in the years that followed. These regions are allocated support with the main goal of motivating farmers to switch to organic production. By applying a difference-in-differences estimator, we evaluate whether the programme has achieved its aims, i.e. whether more farmers have adopted organic farming practices within the flagship regions as compared to farmers outside such regions. The Theory of Planned Behaviour provides the conceptual framework to identify the main factors influencing a farmer's decision to go organic. Our results suggest that the programme fails to motivate farmers to switch to organic production and that there is a need to more effectively target decision-influencing factors.
Microorganisms and Antibiotic Resistance of Bacterial Keratitis at a Rural County Hospital in Seville
Authors: Lorente Pascua José , García Bernal Ana , Garcia Sanchez Estefania , Almeida González Carmen V. 
Published: March 2022

Purpose:
To review the incidence, resistance patterns, and management of bacterial keratitis during the past 4 years.

Methods:
We retrospectively reviewed the clinical records of microbiological isolates from patients with a clinical diagnosis of bacterial keratitis.

Results:
A total of 159 patients were analyzed, and 102 microorganisms were isolated from 129 cultures. In these cultures, 23.7% of the microorganisms were gram positive, 60.8% were gram negative, and 15.5% were fungi. Pseudomonas aeruginosa was the most common bacteria (9.2%), followed by Serratia marcescens (4.4%) and Staphylococcus aureus (4%). Resistance to fluoroquinolones and aminoglycosides was found to be 23.1% and 53.1% in gram-positive and 2.8% and 13.9% in gram-negative bacteria, respectively. Resistance to ceftazidime against gram-negative bacteria was 13.9%. No resistance to vancomycin was observed.

Conclusions:
A high resistance rate to aminoglycosides and fluoroquinolones was observed in gram-positive bacteria. We concluded that fluoroquinolones or aminoglycosides may not be suitable for initial monotherapy in patients with severe bacterial keratitis.
The Role of Orthokeratology in Myopia Management
Authors: Lipson Michael J. 
Published: March 2022

Abstract:
Intervention to slow axial elongation and progressing degree of myopia has become an important public health issue. Although orthokeratology (OrthoK) has been prescribed to temporarily reduce or eliminate refractive error, myopic children undergoing OrthoK have shown significant slowing of axial elongation and myopic progression. This review presents data on the efficacy, benefits, and risks of the use of OrthoK to slow axial elongation in myopic children. It also discusses how OrthoK fits into an overall strategy of myopia management in practice compared with alternative prescribed interventions to slow myopic progression. Other factors discussed are patient candidacy, impact on vision-related quality of life, and use of OrthoK in combination with pharmaceutical agents. With precise fitting, careful follow-up, and patient compliance with recommended lens cleaning and disinfection, OrthoK is a safe and effective method to slow axial elongation in children.
Predictors of Dual E-Cigarette and Cigarette Use
Authors: Nagel Casey , Hugueley Brandon , Cui Yan , Nunez Denise M. , Kuo Tony , Kuo Alice A. 
Published: March 2022

Objective:
To compare prevalence of e-cigarette and cigarette use and to determine predictors of dual use.

Design, Setting, and Participants:
Using a countywide random digit dial telephone health survey conducted during January 2018 to March 2019, we analyzed data from a random sample of 6966 adults. Bivariate analyses described vaping, cigarette use, and sociodemographics. A multivariable logistic regression model examined dual use.

Results:
Young adults 18 to 24 years of age had the highest prevalence of e-cigarette-only use (11.5%), the second-highest prevalence of dual use (3.9%), and the lowest prevalence of cigarette-only use (5.8%). Males were more likely than females to use e-cigarettes (5.1% vs 2.7%), traditional cigarettes (11.1% vs 6.9%), or be dual users (3.6% vs 1.1%). Of those who used e-cigarettes or both, approximately half had also used marijuana in the past 30 days.

Conclusions:
E-cigarette use among young adults is concerning because it could lead to eventual dual use of e-cigarettes and traditional cigarettes.
Utility of Poison Control Center Data for Automated Opioid Overdose Surveillance
Authors: Radloff Christina L. , Bennett Heather , Staes Catherine J. 
Published: March 2022

Context:
Overdosing on opioids is a national epidemic and the number one cause of death from unintentional injury in the United States. Poison control centers (PCCs) may be a source of timely data that can track opioid exposure cases, identify clusters of opioid exposure cases by geographic region, and capture opioid exposure cases that may not seek medical attention from health care facilities.

Objective:
The objectives were to (a) identify data requirements for opioid overdose case ascertainment and classification and visualization in a dashboard, and (b) assess the availability and quality of the relevant PCC data for state-based opioid overdose surveillance.

Design:
We identified types of opioid exposure, demographic characteristics, and other features that may be relevant for public health officials to monitor and respond to opioid overdose events in the community. We operationalized case definitions for an opioid overdose event based on the Centers for Disease Control and Prevention case classification definitions. We assessed the PCC database for concepts and metrics needed to operationalize case definitions for opioid overdose events to determine the feasibility of using the PCC for automated surveillance.

Main Outcome Measure:
Quality and availability of required concepts to operationalize metrics and case definitions using PCC data.

Results:
A subset of the probable case definition may be used for automated surveillance with available structured PCC data. In contrast, logic for confirmed, suspected, and part of the probable case definitions requires additional structured data or analysis of narrative text, which may not contain needed concepts. For example, the confirmed case definition currently requires evidence from narrative text of laboratory confirmation of an opioid in a clinical specimen or diagnosis of opioid overdose in a health care record.

Conclusion:
PCC data are a timely and potentially useful source for automated surveillance of a subset of opioid overdose events, but additional structured and/or coded data are required.
Evaluating the use of a thermoplastic socket in Kenya: A pilot study
Authors: Barbareschi Giulia , Teerlink Wesley , Njuguna Josepg Gakunga , Musungu Purity , Kirino Mary Dama , Holloway Catherine 
Published: March 2022

Background:
Many people with amputations who live in low-resourced settings struggle to access the workshops where qualified prosthetists provide appropriate care. Novel technologies such as the thermoplastic Confidence Socket are emerging, which could help facilitate easier access to prosthetic services.

Objectives:
The objective of this study was to evaluate the satisfaction and the performance of transtibial prosthesis featuring the Confidence Socket.

Study design:
This is a longitudinal repeated-measures design study.

Methods:
A convenience sample of 26 participants who underwent transtibial amputation were fitted with the Confidence Socket. The performance of the socket was evaluated after a follow-up period between 1 month and 6 months using the L test of functional mobility and the amputee mobility predictor. Satisfaction with the prosthesis was measured using the Trinity Amputation and Prosthetic Experience Scales and purposefully designed 7-point Likert scales.

Results:
Ten of the 26 participants returned for follow-up. Perceived activity restriction and L test times improved significantly at follow-up, but the self-reported satisfaction with the Confidence Socket was lower at follow-up compared with that after fitting.

Conclusions:
The Amparo Confidence Socket represents a potentially viable alternative to improve access to appropriate prosthesis in Kenya, but some aspects of users’ self-reported satisfaction should be further investigated.
Firing patterns of ventral hippocampal neurons predict the exploration of anxiogenic locations
Authors: Malagon-Vina Hugo , Ciocchi Stéphane , Klausberger Thomas 
Published: March 2022

SummaryThe ventral hippocampus (vH) plays a crucial role in anxiety-related behaviour and vH neurons increase their firing when animals explore anxiogenic environments. However, if and how such neuronal activity induces or restricts the exploration of an anxiogenic location remains unexplained. Here, we developed a novel behavioural paradigm to motivate rats to explore an anxiogenic area. Rats ran along an elevated linear maze with protective sidewalls, which were subsequently removed in parts of the track to introduce an anxiogenic location. We recorded neuronal action potentials during task performance and found that vH neurons exhibited remapping of activity, overrepresenting anxiogenic locations. Direction-dependent firing was homogenised by the anxiogenic experience. We further showed that the activity of vH neurons predicted the extent of exploration of the anxiogenic location. Our data suggest that anxiety-related firing does not solely depend on the exploration of anxiogenic environments, but also on intentions to explore them.
Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?
Authors: Wichmann Stefan , Ardern Zachary 
Published: March 2022

AbstractThe standard genetic code has been shown to have multiple interesting properties which impact on molecular biology and the evolutionary process. One facet of molecular biology where code structure is particularly important is the origin and evolution of overlapping genes. We have previously reported that the structure of the standard genetic code ensures that synonymous mutations in a protein coding gene will lead to a remarkably similar average “collateral” mutation effect size in at least four out of the five alternative reading frames. Here we show that only 0.26% of alternative codes with the block structure of the standard genetic code perform at least as well as the standard code in this property. Considering this finding within a code optimality framework suggests that this consistent effect size across the different frames may be adaptive. Here we give context for this finding and present a simple model where a trade-off between evolvability and robustness leads to an average mutation effect size which maximises population fitness. This supports the intuition that similar mutation effects across the different alternative reading frames may be an adaptive property of the standard genetic code which facilitates evolvability through the use of alternative reading frames.
Fusarium solanispecies complex genomes reveal bases of compartmentalisation and animal pathogenesis
Authors: Hoh Daphne Z. , Lee Hsin-Han , Wada Naohisa , Liu Wei-An , Lu Min R. , Lai Cheng-Kuo , Ke Huei-Mien , Sun Pei-Feng , Tang Sen-Lin , Chung Wen-Hsin , Chen Ying-Lien , Chung Chia-Lin , Tsai Isheng Jason 
Published: March 2022

AbstractTheFusarium solanispecies complex (FSSC) comprises fungal pathogens responsible for mortality in a diverse range of animals and plants, but their genome diversity and transcriptome responses in animal pathogenicity remain to be elucidated. We sequenced and compared six chromosome-level FSSC clade 3 genomes of aquatic animal and plant host origins and revealed a spectrum of conservation patterns in chromosomes categorised into three compartments: core, fast-core (FC), and lineage-specific (LS). Each chromosome type varied in structural architectures, with FC and LS chromosomes containing significantly higher proportions of repetitive elements and methylation levels than core chromosomes, with genes exhibiting higherdN/dS and enriched in functions related to pathogenicity and niche expansion. Mesosynteny were detected between FC chromosomes ofFusariumgenomes, indicating that these chromosomes were present in a common ancestor that predated FSSC species. These findings provide evidence that genome compartmentalisation was the outcome of multi-speed evolution amongst FSSC chromosomes. We further demonstrated thatF. falciformeandF. keratoplasticumare opportunistic pathogens by inoculatingPelodiscus sinensiseggs and identified differentially expressed genes also associated with plant pathogenicity. These included the most upregulated genes encoding the CFEM (Common in Fungal Extracellular Membrane) domain. The study establishes genomic resources and an animal model for fungal pathogens of trans-kingdom hosts.
Development of a Model for Differentiating PDAC from Benign Pancreatic Conditions: A Prospective Case-control Study
Authors: Zardab Mohamed , Balarajah Vickna , Banerjee Abhirup , Stasinos Konstantinos , Saad Amina , Imrali Ahmet , Hughes Christine , Roberts Rhiannon , Vajrala Ajith , Chelala Claude , Kocher Hemant M , Dayem Ullah Abu Z M 
Published: March 2022

AbstractBackground & aimsPancreatic ductal adenocarcinoma (PDAC) continues to be a devastating disease with late diagnosis and poor overall survival, complicated by clinical presentations similar to benign pancreatic diseases. We aimed to analyse clinical parameters with the goal of developing a prediction model for differentiating suspected PDAC from benign pancreatic conditions.Methods and resultsWe used a prospectively recruited cohort of patients with pancreatic disease (n=762) enrolled at the Barts Pancreas Tissue Bank between January 1, 2008 and September 21, 2021 to perform a case-control study examining the association of PDAC (n=340) with predictor variables including demographics, comorbidities, lifestyle factors, presenting symptoms and commonly performed blood tests. Using a machine learning approach, candidate PDAC risk-prediction algorithms were trained on 75% of the cohort, using a subset of the predictor variables identified from a preliminary observational association study. Models were assessed on the remaining 25%. Multiple imputed datasets were used for both training and validation to accommodate for unknown data.Age (over 55), weight loss in hypertensive patients, recent symptom of jaundice, high serum bilirubin, low serum creatinine, high serum alkaline phosphatase, low lymphocyte count and low serum sodium were the most important features when separating putative PDAC cases from less severe pancreatic conditions. A simple logistic regression model had the best performance with an area under the curve (AUC) of 0.88. Setting a probability threshold of 0.17 guided by the maximum F2 score, a sensitivity of 95.6% was reached in the full cohort which could lead to early detection of around 84% of the PDAC patients.ConclusionThe resultant prediction model significantly outperformed the current UK guidelines for suspected pancreatic cancer referral and could improve detection rates of PDAC in the community. After further work this approach could lead to an easy to understand, utilisable risk score to be applied in the primary and secondary care setting for referring patients to specialist hepato-pancreatico-biliary services.
Risk factors for SARS-CoV-2 transmission in student residences: a case-ascertained study in Leuven, Belgium from October 2020 until May 2021
Authors: Vanbesien Marte , Molenberghs Geert , Geenen Caspar , Thibaut Jonathan , Gorissen Sarah , André Emmanuel , Raymenants Joren 
Published: March 2022

ABSTRACTBackgroundStudent residences are at high risk for rapid COVID-transmission due to crowding and frequent close contact.AimWe aimed to investigate the overall secondary attack rates (SAR) in student residences and to discern risk factors for higher transmission in order to improve the evidence base for screening efforts and preventive measures.MethodsIn this retrospective case-ascertained study, we analysed data from student residences screened in Leuven, Belgium between October 2020 and May 2021, following detection of a COVID-19 case in the residence. We investigated the impact on the SAR in the living units screened of delay-time until follow-up, shared use of kitchen or sanitary facilities, presence of an external infection source and occurrence of social gatherings attended by the index case.ResultsWe included 200 residence units, representing 2326 screened residents, of which 68 units showed secondary transmission. The overall SAR was estimated at 0.0813 (95%CI 0.0705-0.0936). Both sharing sanitary facilities (p=0.04) and social gatherings attended by the index case (p=0.033) significantly impacted SAR, which increased from 3% to 13% when both risk factors were present compared to absent.ConclusionsWe identify risk factors which should be considered when selecting students for screening during an outbreak of COVID-19 in student residences to improve comprehensiveness and proportionality of testing. The identified risk factors improve the evidence base for preventive measures aimed at limiting social gatherings and improving ventilation of shared spaces in outbreak-prone settings. Lastly, they should be considered when designing student accommodation and other shared households.