bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated analysis of long non-coding RNAs and mRNAs reveals the regulatory network of maize seedling root responding to salt stress
Authors: Liu Peng , Zhang Yinchao , Zou Chaoying , Yang Cong , Pan Guangtang , Ma Langlang , Shen Yaou 
Published: January 2022

Abstract
Background
Long non-coding RNAs (lncRNAs) play important roles in response to abiotic stresses in plants, by acting as cis- or trans-acting regulators of protein-coding genes. As a widely cultivated crop worldwide, maize is sensitive to salt stress particularly at the seedling stage. However, it is unclear how the expressions of protein-coding genes are affected by non-coding RNAs in maize responding to salt tolerance.

Results
The whole transcriptome sequencing was employed to investigate the differential lncRNAs and target transcripts responding to salt stress between two maize inbred lines with contrasting salt tolerance. We developed a flexible, user-friendly, and modular RNA analysis workflow, which facilitated the identification of lncRNAs and novel mRNAs from whole transcriptome data. Using the workflow, 12,817 lncRNAs and 8,320 novel mRNAs in maize seedling roots were identified and characterized. A total of 742 lncRNAs and 7,835 mRNAs were identified as salt stress-responsive transcripts. Moreover, we obtained 41 cis- and 81 trans-target mRNA for 88 of the lncRNAs. Among these target transcripts, 11 belonged to 7 transcription factor (TF) families including bHLH, C2H2, Hap3/NF-YB, HAS, MYB, WD40, and WRKY. The above 8,577 salt stress-responsive transcripts were further classified into 28 modules by weighted gene co-expression network analysis. In the salt-tolerant module, we constructed an interaction network containing 79 nodes and 3081 edges, which included 5 lncRNAs, 18 TFs and 56 functional transcripts (FTs). As a trans-acting regulator, the lncRNA MSTRG.8888.1 affected the expressions of some salt tolerance-relative FTs, including protein-serine/threonine phosphatase 2C and galactinol synthase 1, by regulating the expression of the bHLH TF.

Conclusions
The contrasting genetic backgrounds of the two inbred lines generated considerable variations in the expression abundance of lncRNAs and protein-coding transcripts. In the co-expression networks responding to salt stress, some TFs were targeted by the lncRNAs, which further regulated the salt tolerance-related functional transcripts. We constructed a regulatory pathway of maize seedlings to salt stress, which was mediated by the hub lncRNA MSTRG.8888.1 and participated by the bHLH TF and its downstream target transcripts. Future work will be focused on the functional revelation of the regulatory pathway.
The antimicrobial activity of zinc against group B Streptococcus is strain-dependent across diverse sequence types, capsular serotypes, and invasive versus colonizing isolates
Authors: Francis Jamisha D. , Guevara Miriam A. , Lu Jacky , Madhi Shabir A. , Kwatra Gaurav , Aronoff David M. , Manning Shannon D. , Gaddy Jennifer A. 
Published: January 2022

Abstract
Background
Streptococcus agalactiae or Group B Streptococcus (GBS) is an encapsulated gram-positive bacterial pathobiont that commonly colonizes the lower gastrointestinal tract and reproductive tract of human hosts. This bacterium can infect the gravid reproductive tract and cause invasive infections of pregnant patients and neonates. Upon colonizing the reproductive tract, the bacterial cell is presented with numerous nutritional challenges imposed by the host. One strategy employed by the host innate immune system is intoxication of bacterial invaders with certain transition metals such as zinc.

Methodology
Previous work has demonstrated that GBS must employ elegant strategies to circumnavigate zinc stress in order to survive in the vertebrate host. We assessed 30 strains of GBS from diverse isolation sources, capsular serotypes, and sequence types for susceptibility or resistance to zinc intoxication.

Results
Invasive strains, such as those isolated from early onset disease manifestations of GBS infection were significantly less susceptible to zinc toxicity than colonizing strains isolated from rectovaginal swabs of pregnant patients. Additionally, capsular type III (cpsIII) strains and the ST-17 and ST-19 strains exhibited the greatest resilience to zinc stress, whereas ST-1 and ST-12 strains as well as those possessing capsular type Ib (cpsIb) were more sensitive to zinc intoxication. Thus, this study demonstrates that the transition metal zinc possesses antimicrobial properties against a wide range of GBS strains, with isolation source, capsular serotype, and sequence type contributing to susceptibility or resistance to zinc stress.
RETRACTED ARTICLE: Antimicrobial and anti-biofilm potencies of dermcidin-derived peptide DCD-1L against Acinetobacter baumannii: an in vivo wound healing model
Authors: Farshadzadeh Zahra , Pourhajibagher Maryam , Taheri Behrouz , Ekrami Alireza , Modarressi Mohammad Hossein , Azimzadeh Masoud , Bahador Abbas 
Published: January 2022

Abstract
Background
The global emergence of Acinetobacter baumannii resistance to most conventional antibiotics presents a major therapeutic challenge and necessitates the discovery of new antibacterial agents. The purpose of this study was to investigate in vitro and in vivo anti-biofilm potency of dermcidin-1L (DCD-1L) against extensively drug-resistant (XDR)-, pandrug-resistant (PDR)-, and ATCC19606-A. baumannii.

Methods
After determination of minimum inhibitory concentration (MIC) of DCD-1L, in vitro anti-adhesive and anti-biofilm activities of DCD-1L were evaluated. Cytotoxicity, hemolytic activity, and the effect of DCD-1L treatment on the expression of various biofilm-associated genes were determined. The inhibitory effect of DCD-1L on biofilm formation in the model of catheter-associated infection, as well as, histopathological examination of the burn wound sites of mice treated with DCD-1L were assessed.

Results
The bacterial adhesion and biofilm formation in all A. baumannii isolates were inhibited at 2 × , 4 × , and 8 × MIC of DCD-1L, while only 8 × MIC of DCD-1L was able to destroy the pre-formed biofilm in vitro. Also, reduce the expression of genes involved in biofilm formation was observed following DCD-1L treatment. DCD-1L without cytotoxic and hemolytic activities significantly reduced the biofilm formation in the model of catheter-associated infection. In vivo results showed that the count of A. baumannii in infected wounds was significantly decreased and the promotion in wound healing by the acceleration of skin re-epithelialization in mice was observed following treatment with 8 × MIC of DCD-1L.

Conclusions
Results of this study demonstrated that DCD-1L can inhibit bacterial attachment and biofilm formation and prevent the onset of infection. Taking these properties together, DCD-1L appears as a promising candidate for antimicrobial and anti-biofilm drug development.
Spatiotemporal variations in exposure: Chagas disease in Colombia as a case study
Authors: Ledien Julia , Cucunubá Zulma M. , Parra-Henao Gabriel , Rodríguez-Monguí Eliana , Dobson Andrew P. , Basáñez María-Gloria , Nouvellet Pierre 
Published: January 2022

AbstractAge-stratified serosurvey data are often used to understand spatiotemporal trends in disease incidence and exposure through estimating the Force-of-Infection (FoI). Typically, median or mean FoI estimates are used as the response variable in predictive models, often overlooking the uncertainty in estimated FoI values when fitting models and evaluating their predictive ability. To assess how this uncertainty impact predictions, we compared three approaches with three levels of uncertainty integration. We propose a performance indicator to assess how predictions reflect initial uncertainty.In Colombia, 76 serosurveys (1980–2014) conducted at municipality level provided age-stratified Chagas disease prevalence data. The yearly FoI was estimated at the serosurvey level using a time-varying catalytic model. Environmental, demographic and entomological predictors were used to fit and predict the FoI at municipality level from 1980 to 2010 across Colombia.A stratified bootstrap method was used to fit the models without temporal autocorrelation at the serosurvey level. The predictive ability of each model was evaluated to select the best-fit models within urban, rural and (Amerindian) indigenous settings. Model averaging, with the 10 best-fit models identified, was used to generate predictions.Our analysis shows a risk of overconfidence in model predictions when median estimates of FoI alone are used to fit and evaluate models, failing to account for uncertainty in FoI estimates. Our proposed methodology fully propagates uncertainty in the estimated FoI onto the generated predictions, providing realistic assessments of both central tendency and current uncertainty surrounding exposure to Chagas disease.
A randomized crossover study of functional electrical stimulation during walking in spastic cerebral palsy: the FES on participation (FESPa) trial
Authors: Moll Irene , Marcellis Rik G. J. , Coenen Marcel L. P. , Fleuren Sabine M. , Willems Paul J. B. , Speth Lucianne A. W. M. , Witlox M. Adhiambo , Meijer Kenneth , Vermeulen R. Jeroen 
Published: January 2022

Abstract
Background
Spastic cerebral palsy is the most common cause of motor disability in children. It often leads to foot drop or equinus, interfering with walking. Ankle-foot orthoses (AFOs) are commonly used in these cases. However, AFOs can be too restrictive for mildly impaired patients. Functional electrical stimulation (FES) of the ankle-dorsiflexors is an alternative treatment as it could function as a dynamic functional orthosis. Despite previous research, high level evidence on the effects of FES on activities and participation in daily life is missing. The primary aim of this study is to evaluate whether FES improves the activity and participation level in daily life according to patients, and the secondary aim is to provide evidence of the effect of FES at the level of body functions and activities. Furthermore, we aim to collect relevant information for decisions on its clinical implementation.

Methods
A randomized crossover trial will be performed on 25 children with unilateral spastic cerebral palsy. Patients aged between 4 and 18 years, with Gross Motor Functioning Classification System level I or II and unilateral foot drop of central origin, currently treated with AFO or adapted shoes, will be included. All participants will undergo twelve weeks of conventional treatment (AFO/adapted shoes) and 12 weeks of FES treatment, separated by a six-week washout-phase. FES treatment consists of wearing the WalkAide® device, with surface electrodes stimulating the peroneal nerve during swing phase of gait. For the primary objective, the Goal Attainment Scale is used to test whether FES improves activities and participation in daily life. The secondary objective is to prove whether FES is effective at the level of body functions and structures, and activities, including ankle kinematics and kinetics measured during 3D-gait analysis and questionnaire-based frequency of falling. The tertiary objective is to collect relevant information for clinical implementation, including acceptability using the device log file and side effect registration, cost-effectiveness based on quality adjusted life years (QALYs) and clinical characteristics for patient selection.

Discussion
We anticipate that the results of this study will allow evidence-based use of FES during walking in children with unilateral spastic cerebral palsy.

Trial registration
ClinicalTrials.gov: NCT03440632.
Daily uplifts during the COVID-19 pandemic: what is considered helpful in everyday life?
Authors: Eklund Rakel , Bondjers Kristina , Hensler Ida , Bragesjö Maria , Johannesson Kerstin Bergh , Arnberg Filip K , Sveen Josefin 
Published: January 2022

Abstract
Background
Knowledge of what is uplifting and helpful during pandemics could inform the design of sustainable pandemic recommendations in the future. We have explored individuals’ views on helpful and uplifting aspects of everyday life during the coronavirus disease 2019 (COVID-19) pandemic.

Methods
Participants answered a brief, daily survey via text messages during 14 consecutive days in July–August, 2020. The survey included the question: “During the past 24 hours, is there anything that has made you feel good or helped you in your life?” We used content analysis to compile responses from 693 participants, who provided 4,490 free-text answers, which resulted in 24 categories subsumed under 7 themes.

Results
Positive aspects during the COVID-19 pandemic primarily related to social interactions, in real life or digitally, with family, friends and others. Other important aspects concerning work, colleagues and maintaining everyday life routines. One theme concerning vacations, going on excursions and being in nature. Leisure and recreation activities, such as hobbies and physical exercise, also emerged as important, as did health-related factors. Bodily sensations, thoughts, feelings and activities that benefited well-being were mentioned frequently. Lastly, people commented on the government strategies for containing COVID-19, and whether to comply with restrictions.

Conclusions
To summarize, daily uplifts and helpful aspects of everyday life centered around social relationships. To comply with recommendations on physical distancing, people found creative ways to maintain social connections both digitally and face-to-face. Social interaction, maintenance of everyday life routines, hobbies and physical activity appeared to be important for well-being.
Healthcare professionals’ perceptions on barriers and facilitators to DMARD use in rheumatoid arthritis
Authors: Voshaar M. J. H. , van den Bemt B. J. F. , van de Laar M. A. F. J. , van Dulmen A. M. , Vriezekolk J. E. 
Published: January 2022

Abstract
Background
Disease-modifying anti-rheumatic drugs (DMARDs) are the cornerstone of rheumatoid arthritis (RA) treatment. However, the full benefits of DMARDs are often not realized because many patients are sub-optimally adherent to their medication. In order to optimize adherence, it is essential that healthcare professionals (HCPs) understand patients’ barriers and facilitators for medication use. Insight in these barriers and facilitators may foster the dialogue about adequate medication use between HCPs and patients. What HCPs perceive as barriers and facilitators has, so far, scarcely been investigated. This study aimed to identify the perceptions of HCPs on patients’ barriers and facilitators that might influence their adherence.

Methods
This qualitative study was performed using semi structured in-depth interviews with HCPs. An interview guide was used, based on an adjusted version of the Theoretical Domains Framework (TDF). Thematic analysis was conducted to identify factors that influence barriers and facilitators to DMARD use according to HCPs.

Results
Fifteen HCPs (5 rheumatologists, 5 nurses and 5 pharmacists) were interviewed. They mentioned a variety of factors that, according to their perceptions, influence DMARD adherence in patients with RA. Besides therapy-related factors, such as (onset of) medication effectiveness and side-effects, most variation was found within patient-related factors and reflected patients’ beliefs, ways of coping, and (self-management) skills toward medication and their condition. In addition, factors related to the condition (e.g., level of disease activity), healthcare team and system (e.g., trust in HCP), and social and economic context (e.g. support, work shifts) were reported.

Conclusions
This study provided insights in HCPs’ perceptions of the barriers and facilitators to DMARD use patients with RA. Most factors that were mentioned were patient-related and potentially modifiable. When physicians understand patients’ perceptions on medication use, adherence to DMARDs can probably be optimized in patients with RA leading to more effectiveness of treatment outcomes.
Sex-specific contribution of lipid accumulation product and cardiometabolic index in the identification of nonalcoholic fatty liver disease among Chinese adults
Authors: Liu Yiting , Wang Wei 
Published: January 2022

Abstract
Background
Lipid accumulation product (LAP) and cardiometabolic index (CMI) are two novel obesity-related indexes associated with enhancing metabolic disease (MD) risk. Current evidences suggest that the differences in sex hormones and regional fat distribution in both sexes are directly correlated with MD and nonalcoholic fatty liver disease (NAFLD) risk. Hence, NAFLD incidences reflect sex differences. Herein, we examined the accuracy of LAP and CMI in diagnosing NAFLD in both sexes.

Methods
Overall, 14,407 subjects, who underwent health check-up in the northeastern China, were enrolled in this study, and their corresponding LAP and CMI were calculated. Abdominal ultrasonography was employed for NAFLD diagnosis. Multivariate analyses were analyzed potential correlations between LAP and/or CMI and NAFLD. Odds ratios (ORs) and 95% confidence intervals (CIs) were evaluated. Receiver operating characteristic curve analyses was executed for the exploration of the diagnostic accuracies. Areas under the curves (AUCs) with 95%CIs were calculated.

Results
NAFLD prevalence increased with elevated quartiles of LAP and CMI in both sexes. In multivariate logistic regression analyses, LAP and CM expressed as continuous variables or quartiles, significantly correlated with NAFLD. The ORs for the top versus bottom quartile of LAP and CMI for NAFLD were 13.183 (95%CI = 8.512–20.417) and 8.662 (95%CI = 6.371–11.778) in women and 7.544 (95%CI = 5.748–9.902) and 5.400 (95%CI = 4.297–6.786) in men. LAP and CMI exhibited larger AUCs, compared to other obesity-related indexes in terms of discriminating NAFLD. The AUCs of LAP and CMI were 0.860 (95%CI = 0.852–0.867) and 0.833 (95%CI = 0.825–0.842) in women and 0.816 (95%CI = 0.806–0.825) and 0.779 (95%CI = 0.769–0.789) in men.

Conclusions
LAP and CMI are convenient indexes for the screening and quantification of NAFLD within a Chinese adult population. Their associations with NAFLD are substantially greater in women than men.
Time-to-antibiotics and clinical outcomes in patients with sepsis and septic shock: a prospective nationwide multicenter cohort study
Authors: Im Yunjoo , Kang Danbee , Ko Ryoung-Eun , Lee Yeon Joo , Lim Sung Yoon , Park Sunghoon , Na Soo Jin , Chung Chi Ryang , Park Mi Hyeon , Oh Dong Kyu , Lim Chae-Man , Suh Gee Young ,   the Korean Sepsis Alliance (KSA) investigators, Lim Chae-Man , Hong Sang-Bum , Oh Dong Kyu , Suh Gee Young , Jeon Kyeongman , Ko Ryoung-Eun , Cho Young-Jae , Lee Yeon Joo , Lim Sung Yoon , Park Sunghoon , Heo Jeongwon , Lee Jae-myeong , Kim Kyung Chan , Lee Yeon Joo , Chang Youjin , Jeon Kyeongman , Lee Sang-Min , Lim Chae-Man , Hong Suk-Kyung , Cho Woo Hyun , Kwak Sang Hyun , Lee Heung Bum , Ahn Jong-Joon , Seong Gil Myeong , Lee Song-I. , Park Sunghoon , Park Tai Sun , Lee Su Hwan , Choi Eun Young , Moon Jae Young 
Published: January 2022

Abstract
Background
Timely administration of antibiotics is one of the most important interventions in reducing mortality in sepsis. However, administering antibiotics within a strict time threshold in all patients suspected with sepsis will require huge amount of effort and resources and may increase the risk of unintentional exposure to broad-spectrum antibiotics in patients without infection with its consequences. Thus, controversy still exists on whether clinicians should target different time-to-antibiotics thresholds for patients with sepsis versus septic shock.

Methods
This study analyzed prospectively collected data from an ongoing multicenter cohort of patients with sepsis identified in the emergency department. Adjusted odds ratios (ORs) were compared for in-hospital mortality of patients who had received antibiotics within 1 h to that of those who did not. Spline regression models were used to assess the association of time-to-antibiotics as continuous variables and increasing risk of in-hospital mortality. The differences in the association between time-to-antibiotics and in-hospital mortality were assessed according to the presence of septic shock.

Results
Overall, 3035 patients were included in the analysis. Among them, 601 (19.8%) presented with septic shock, and 774 (25.5%) died. The adjusted OR for in-hospital mortality of patients whose time-to-antibiotics was within 1 h was 0.78 (95% confidence interval [CI] 0.61–0.99; p = 0.046). The adjusted OR for in-hospital mortality was 0.66 (95% CI 0.44–0.99; p = 0.049) and statistically significant in patients with septic shock, whereas it was 0.85 (95% CI 0.64–1.15; p = 0.300) in patients with sepsis but without shock. Among patients who received antibiotics within 3 h, those with septic shock showed 35% (p = 0.042) increased risk of mortality for every 1-h delay in antibiotics, but no such trend was observed in patients without shock.

Conclusion
Timely administration of antibiotics improved outcomes in patients with septic shock; however, the association between early antibiotic administration and outcome was not as clear in patients with sepsis without shock.
Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries
Authors: Liang Yanyu , Pividori Milton , Manichaikul Ani , Palmer Abraham A. , Cox Nancy J. , Wheeler Heather E. , Im Hae Kyung 
Published: January 2022

Abstract
Background
Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry.

Results
We introduce the polygenic transcriptome risk score (PTRS), which is based on predicted transcript levels (rather than SNPs), and explore the portability of PTRS across populations using UK Biobank data.

Conclusions
We show that PTRS has a significantly higher portability (Wilcoxon p=0.013) in the African-descent samples where the loss of performance is most acute with better performance than PRS when used in combination.