bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CHIP Score: A Valuable Method for Determining Risk of Surgical Intervention for Hemangioma Patients
Authors: Shah Pearl , Royek Amanda , Kumar Anand R. 
Published: March 2024

Background: Infantile hemangiomas (IHs) are the most common benign tumor of infancy. These tumors may have wide-ranging effects on functional and cosmetic outcomes for patients. With variations in recommendations for surgery among providers, it can be difficult to counsel patients and their families on potential surgical treatment. Through the development of the Case Western Hemangioma Intervention Predictor (CHIP) score, this study aims to improve the consistency of counseling regarding surgery and timing of surgical referral. Methods: This was a retrospective review of all patients (179) treated for IHs at a single tertiary care center over 17 years. Patients were divided equally into 2 cohorts. Descriptive statistics and correlation plots were performed on the first cohort to evaluate which disease factors (including size, location, and complications) and patient factors significantly correlated with the decision to pursue surgical treatment (surgical risk). These factors were used to form a CHIP score, which was then validated through logistic regression with length of medical management as a covariate against the second cohort of patients. Results: After controlling for length of medical management to treat IH, lack of medical management, functional impairment, and ulceration were found to be significantly correlated with the risk of surgical intervention ( P < .05). When validated against the second half of our cohort, a CHIP score of 3 (of a maximum score of 3) was found to have a specificity of 92% and a sensitivity of 81% in predicting risk of surgical intervention. Conclusion: IHs can have clinical characteristics that may be predictors of complexity and surgical intervention. The CHIP score can assist in educating patients and families on surgery as a treatment option and guiding appropriate referrals.
Transformation, leaching and plant uptake simulations of 6:2 and 8:2 polyfluoroalkyl phosphate diesters (diPAPs) and related transformation products under near-natural conditions
Authors: Weidemann Eva , Lämmer René , Göckener Bernd , Bücking Mark , Gassmann Matthias 
Published: March 2024

AbstractIn response to the growing concern over PFAS contamination, employing models to simulate PFAS behavior in the environment becomes necessary. This facilitates evaluating risks tied to leaching into groundwater, adsorption in soil, plant uptake, entry into the food chain, and the conversion of precursors into persistent PFAS. We utilized the MACRO model to simulate the behavior of the precursors 6:2 diPAP and 8:2 diPAP using data from a 2-year lysimeter experiment, key compound parameters were optimized via the caRamel evolutionary algorithm. We assumed that the transformation of both diPAP precursors into stable PFAAs is influenced by temperature and soil moisture, similar to pesticide degradation by microorganisms. Results reveal that the model accurately represents transformation, leaching, soil retention, and plant uptake of diPAP and transformation products. A comparison with a lab-based soil column study supports the slower natural degradation of precursors, affirming our modeling approach. Temperature and soil moisture could indicate that a worst-case scenario for transformation product leaching into groundwater could occur during a mild summer with moderate evapotranspiration and heavy rainfall. Plant uptake involves multiple elements: PFAS availability in the root zone depends on prior degradation or presence. Increased moisture in the root zone favors PFAS uptake combined with temperatures high enough for prior biotransformation. The calculation of temperature and moisture-based conversion rates was adopted directly from MACRO. It is recommended to further investigate these effects to validate and possibly modify them.
A common regulatory haplotype doubles lactoferrin concentration in milk
Authors: Lopdell Thomas J. , Trevarton Alexander J. , Moody Janelle , Prowse-Wilkins Claire , Knowles Sarah , Tiplady Kathryn , Chamberlain Amanda J. , Goddard Michael E. , Spelman Richard J. , Lehnert Klaus , Snell Russell G. , Davis Stephen R. , Littlejohn Mathew D. 
Published: March 2024

Abstract
Background
Bovine lactoferrin (Lf) is an iron absorbing whey protein with antibacterial, antiviral, and antifungal activity. Lactoferrin is economically valuable and has an extremely variable concentration in milk, partly driven by environmental influences such as milking frequency, involution, or mastitis. A significant genetic influence has also been previously observed to regulate lactoferrin content in milk. Here, we conducted genetic mapping of lactoferrin protein concentration in conjunction with RNA-seq, ChIP-seq, and ATAC-seq data to pinpoint candidate causative variants that regulate lactoferrin concentrations in milk.

Results
We identified a highly-significant lactoferrin protein quantitative trait locus (pQTL), as well as a cislactotransferrin (LTF) expression QTL (cis-eQTL) mapping to the LTF locus. Using ChIP-seq and ATAC-seq datasets representing lactating mammary tissue samples, we also report a number of regions where the openness of chromatin is under genetic influence. Several of these also show highly significant QTL with genetic signatures similar to those highlighted through pQTL and eQTL analysis. By performing correlation analysis between these QTL, we revealed an ATAC-seq peak in the putative promotor region of LTF, that highlights a set of 115 high-frequency variants that are potentially responsible for these effects. One of the 115 variants (rs110000337), which maps within the ATAC-seq peak, was predicted to alter binding sites of transcription factors known to be involved in lactation-related pathways.

Conclusions
Here, we report a regulatory haplotype of 115 variants with conspicuously large impacts on milk lactoferrin concentration. These findings could enable the selection of animals for high-producing specialist herds.
Mechanism of action of microRNA166 on nitric oxide in alfalfa (Medicago sativa L.) under drought stress
Authors: Wei Bochuang , Wang Yizhen , Ruan Qian , Zhu Xiaolin , Wang Xian , Wang Tianjie , Zhao Ying , Wei Xiaohong 
Published: March 2024

Abstract
Background
Alfalfa is a perennial forage crop of high importance, but its cultivation is often affected by drought stress. Currently, the investigation of drought-related small RNAs is a popular research topic to uncover plant drought resistance mechanisms. Among these small RNAs, microRNA166 (miR166) is associated with drought in numerous plant species. Initial small RNA sequencing studies have shown that miR166 is highly responsive to exogenous nitric oxide (NO) and drought. Therefore, analyzing the expression of Msa-miR166 under nitric oxide and drought treatment is significant.

Result
Bioinformatics analysis revealed that the miR166 family is widely distributed among plants, ranging from mosses to eudicots, with significant distribution differences between species. The evolutionary degree of Msa-miR166s is highly similar to that of Barrel medic (Medicago truncatula) and Soybean (Glycine max), but significantly different from the model plant Arabidopsis (Arabidopsis thaliana). It is suggested that there are no significant differences in miR166s within the species, and members of Msa-miR166s can form a typical stem-loop. The lowest level of exogenous nitric oxide was observed in Msa-miR166s under drought stress, followed by individual drought, and the highest level was observed after removing endogenous nitric oxide.

Conclusion
In response to short-term drought, Msa-miR166s down-regulate expression in alfalfa (Medicago sativa L.). Exogenous nitric oxide can reduce the expression of Msa-miR166s in response to short-term drought. These findings suggest that Msa-miR166e-5p is responsive to environmental changes. The expression levels of target genes showed an opposite trend to Msa-miR166s, verifying the accuracy of Degradome sequencing in the early stage. This suggests that alfalfa experiences drought stress when regulated by exogenous nitric oxide, targeting HD ZIP-III, FRI, and CoA ligase genes. Additionally, the expression of Msa-miR166s in response to drought stress varies between leaves and roots, indicating spatiotemporal specificity.
Transcriptome disclosure of hormones inducing stigma exsertion in Nicotiana tabacum by corolla shortening
Authors: Zhang Xiaoquan , Li Juxu , Xing Xuexia , Li Hongchen , Zhang Songtao , Chang Jianbo , Wei Fengjie , Zhang Yongfeng , Huang Jinhui , Zhang Xuelin , Wang Zhaojun 
Published: March 2024

Abstract
Background
Stigma exsertion is an essential agricultural trait that can promote cross-pollination to improve hybrid seed production efficiency. However, the molecular mechanism controlling stigma exsertion remains unknown.

Results
In this study, the Nicotiana tabacum cv. K326 and its two homonuclear-heteroplasmic lines, MSK326 (male-sterile) and MSK326SE (male-sterile and stigma exserted), were used to investigate the mechanism of tobacco stigma exsertion. A comparison of the flowers between the three lines showed that the stigma exsertion of MSK326SE was mainly due to corolla shortening. Therefore, the corollas of the three lines were sampled and presented for RNA-seq analysis, which found 338 candidate genes that may cause corolla shortening. These genes were equally expressed in K326 and MSK326, but differentially expressed in MSK326SE. Among these 338 genes, 15 were involved in hormone synthesis or signal transduction pathways. Consistently, the content of auxin, dihydrozeatin, gibberellin, and jasmonic acid was significantly decreased in the MSK326SE corolla, whereas abscisic acid levels were significantly increased. Additionally, seven genes involved in cell division, cell cycle, or cell expansion were identified. Protein-protein interaction network analysis identified 45 nodes and 79 protein interactions, and the largest module contained 20 nodes and 52 protein interactions, mainly involved in the hormone signal transduction and pathogen defensive pathways. Furthermore, a putative hub gene coding a serine/threonine-protein kinase was identified for the network.

Conclusions
Our results suggest that hormones may play a key role in regulating tobacco stigma exsertion induced by corolla shortening.
Comparative genomic analysis of the Growth-Regulating Factors-Interacting Factors (GIFs) in six Salicaceae species and functional analysis of PeGIF3 reveals their regulatory role in Populus heteromorphic leaves
Authors: Yang Yuqi , Sun Jianhao , Qiu Chen , Jiao Peipei , Wang Houling , Wu Zhihua , Li Zhijun 
Published: March 2024

Abstract
Background
The growth-regulating factor-interacting factor (GIF) gene family plays a vital role in regulating plant growth and development, particularly in controlling leaf, seed, and root meristem homeostasis. However, the regulatory mechanism of heteromorphic leaves by GIF genes in Populus euphratica as an important adaptative trait of heteromorphic leaves in response to desert environment remains unknown.

Results
This study aimed to identify and characterize the GIF genes in P. euphratica and other five Salicaceae species to investigate their role in regulating heteromorphic leaf development. A total of 27 GIF genes were identified and characterized across six Salicaceae species (P. euphratica, Populus pruinose, Populus deltoides, Populus trichocarpa, Salix sinopurpurea, and Salix suchowensis) at the genome-wide level. Comparative genomic analysis among these species suggested that the expansion of GIFs may be derived from the specific Salicaceae whole-genome duplication event after their divergence from Arabidopsis thaliana. Furthermore, the expression data of PeGIFs in heteromorphic leaves, combined with functional information on GIF genes in Arabidopsis, indicated the role of PeGIFs in regulating the leaf development of P. euphratica, especially PeGIFs containing several cis-acting elements associated with plant growth and development. By heterologous expression of the PeGIF3 gene in wild-type plants (Col-0) and atgif1 mutant of A. thaliana, a significant difference in leaf expansion along the medial-lateral axis, and an increased number of leaf cells, were observed between the overexpressed plants and the wild type.

Conclusion
PeGIF3 enhances leaf cell proliferation, thereby resulting in the expansion of the central-lateral region of the leaf. The findings not only provide global insights into the evolutionary features of Salicaceae GIFs but also reveal the regulatory mechanism of PeGIF3 in heteromorphic leaves of P. euphratica.
Promiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy
Authors: Hourigan David , Stefanovic Ewelina , Hill Colin , Ross R. Paul 
Published: March 2024

AbstractVancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.
Bacillus subtilis SOM8 isolated from sesame oil meal for potential probiotic application in inhibiting human enteropathogens
Authors: Zhao Zhongtian , Li Wenrui , Tran The Thien , Loo Say Chye Joachim 
Published: March 2024

Abstract
Background
While particular strains within the Bacillus species, such as Bacillus subtilis, have been commercially utilised as probiotics, it is critical to implement screening assays and evaluate the safety to identify potential Bacillus probiotic strains before clinical trials. This is because some Bacillus species, including B. cereus and B. anthracis, can produce toxins that are harmful to humans.

Results
In this study, we implemented a funnel-shaped approach to isolate and evaluate prospective probiotics from homogenised food waste – sesame oil meal (SOM). Of nine isolated strains with antipathogenic properties, B. subtilis SOM8 displayed the most promising activities against five listed human enteropathogens and was selected for further comprehensive assessment. B. subtilis SOM8 exhibited good tolerance when exposed to adverse stressors including acidity, bile salts, simulated gastric fluid (SGF), simulated intestinal fluid (SIF), and heat treatment. Additionally, B. subtilis SOM8 possesses host-associated benefits such as antioxidant and bile salt hydrolase (BSH) activity. Furthermore, B. subtilis SOM8 contains only haemolysin toxin genes but has been proved to display partial haemolysis in the test and low cytotoxicity in Caco-2 cell models for in vitro evaluation. Moreover, B. subtilis SOM8 intrinsically resists only streptomycin and lacks plasmids or other mobile genetic elements. Bioinformatic analyses also predicted B. subtilis SOM8 encodes various bioactives compound like fengycin and lichendicin that could enable further biomedical applications.

Conclusions
Our comprehensive evaluation revealed the substantial potential of B. subtilis SOM8 as a probiotic for targeting human enteropathogens, attributable to its exceptional performance across selection assays. Furthermore, our safety assessment, encompassing both phenotypic and genotypic analyses, showed B. subtilis SOM8 has a favourable preclinical safety profile, without significant threats to human health. Collectively, these findings highlight the promising prospects of B. subtilis SOM8 as a potent probiotic candidate for additional clinical development.
Self-protective behaviors of Thai village health volunteers in community engagement during a COVID-19 outbreak: interpretation using the health belief model
Authors: Wongrith Paleeratana , Buakate Phuwasin , Doylee Lateefah , Phonla Naseeyah , Dadras Omid , Frampton Geoff 
Published: March 2024

Abstract
Background
Village health volunteers (VHVs) engaging in community-based COVID-19 prevention and control measures played a key role in mitigating effects of the COVID-19 pandemic in Thailand. We conducted a cross-sectional questionnaire survey study to investigate factors affecting VHVs’ COVID-19 self-protective behaviors and social distancing in Songkhla Province during the first COVID-19 outbreak. Such information may help to understand how to support VHVs in future pandemics.

Methods
A total of 152 VHVs from 13 sub-districts participated in the study, completing a 54-item questionnaire based on the Health Belief Model (HBM). The questionnaire included items assessing susceptibility, severity, benefits, barriers, self-efficacy, social distancing, and self-protective behavior. Stepwise multiple regression analysis determined which aspects of the HBM could explain VHVs’ self-protective behavior.

Results
The VHV population sampled broadly reflected the main demographic characteristics of the local population, although VHVs were predominantly female. Self-protective behavior was significantly associated with VHVs’ role (higher perceived compliance for village leaders than non-leaders) but not with other demographic characteristics. Most VHVs reported high levels of self-efficacy (80.5%), adherence to social distancing measures (70.9%), and engagement in self-protective behavior (72.8%) against COVID-19. However, compliance with hand hygiene appeared to be suboptimal, suggesting room for improvement. Self-efficacy and perceived social distancing showed strong and moderate correlations with self-protective behavior against COVID-19 (r = 0.917, β = 0.819; and r = 0.561, β = 0.173 respectively; p < 0.001). The final HBM-based regression model accounted for 87.2% of the variance in VHVs’ self-protective behavior.

Conclusions
This study highlights the importance of VHVs’ self-efficacy for achieving self-protective behavior during a COVID-19 outbreak, and suggests that self-efficacy may help to overcome barriers that might otherwise hinder behaviors to mitigate against COVID-19. Policies that support self-efficacy should be implemented in any future pandemic, and steps to support VHVs with hand hygiene compliance and empower non-leaders to increase their self-protective behavior may also be helpful. Whilst the HBM provided a useful framework for interpretation, the final model was driven mainly by self-efficacy.
Emergency department visits by nursing home residents. A retrospective Italian study of administrative databases from 2015 to 2019
Authors: Albanesi Beatrice , Conti Alessio , Politano Gianfranco , Dimonte Valerio , Gianino Maria Michela , Campagna Sara 
Published: March 2024

Abstract
Background
Visits to Emergency Departments (ED) can be traumatic for Nursing Home (NH) residents. In Italy, the rate of ED visits by NH residents was recently calculated as 3.3%. The reduction of inappropriate ED visits represents a priority for National Healthcare Systems worldwide. Nevertheless, research on factors associated with ED visits is still under-studied in the Italian setting. This study has two main aims: (i) to describe the baseline characteristics of NH residents visiting ED at regional level; (ii) to assess the characteristics, trends, and factors associated with these visits.

Methods
A retrospective study of administrative data for five years was performed in the Piedmont Region. Data from 24,208 NH residents were analysed. Data were obtained by merging two ministerial databases of residential care and ED use. Sociodemographic and clinical characteristics of the residents, trends, and rates of ED visits were collected. A Generalized Linear Model (GLM) regression was used to evaluate the factors associated with ED visits.

Results
In 5 years, 12,672 residents made 24,609 ED visits. Aspecific symptoms (45%), dyspnea (17%) and trauma (16%) were the most frequent problems reported at ED. 51% of these visits were coded as non-critical, and 58% were discharged to the NH. The regression analysis showed an increased risk of ED visits for men (OR = 1.61, 95% CI 1.51–1.70) and for residents with a stay in NH longer than 400 days (OR = 2.19, 95% CI 2.08–2.31).

Conclusions
Our study indicates that more than half of NH residents’ ED visits could potentially be prevented by treating residents in NH. Investments in the creation of a structured and effective network within primary care services, promoting the use of health technology and palliative care approaches, could reduce ED visits and help clinicians manage residents on-site and remotely.
COVID-19 outbreaks surveillance through text mining applied to electronic health records
Authors: Rocha Hermano Alexandre Lima , Solha Erik Zarko Macêdo , Furtado Vasco , Justino Francion Linhares , Barreto Lucas Arêa Leão , da Silva Ronaldo Guedes , de Oliveira Ítalo Martins , Bates David Westfall , de Góes Cavalcanti Luciano Pamplona , Lima Neto Antônio Silva , de Oliveira Erneson Alves 
Published: March 2024

Abstract
Background
The COVID-19 pandemic has caused significant disruptions to everyday life and has had social, political, and financial consequences that will persist for years. Several initiatives with intensive use of technology were quickly developed in this scenario. However, technologies that enhance epidemiological surveillance in contexts with low testing capacity and healthcare resources are scarce. Therefore, this study aims to address this gap by developing a data science model that uses routinely generated healthcare encounter records to detect possible new outbreaks early in real-time.

Methods
We defined an epidemiological indicator that is a proxy for suspected cases of COVID-19 using the health records of Emergency Care Unit (ECU) patients and text mining techniques. The open-field dataset comprises 2,760,862 medical records from nine ECUs, where each record has information about the patient’s age, reported symptoms, and the time and date of admission. We also used a dataset where 1,026,804 cases of COVID-19 were officially confirmed. The records range from January 2020 to May 2022. Sample cross-correlation between two finite stochastic time series was used to evaluate the models.

Results
For patients with age ≥18 years, we find time-lag ($$\tau_c$$

τ
c

) = 72 days and cross-correlation ($${\widehat p}_{ij}$$

p
^

ij

) ~0.82, $$\tau_c$$

τ
c

= 25 days and $${\widehat p}_{ij}$$

p
^

ij

~0.93, and $$\tau_c$$

τ
c

= 17 days and $${\widehat p}_{ij}$$

p
^

ij

~0.88 for the first, second, and third waves, respectively.

Conclusions
In conclusion, the developed model can aid in the early detection of signs of possible new COVID-19 outbreaks, weeks before traditional surveillance systems, thereby anticipating in initiating preventive and control actions in public health with a higher likelihood of success.