bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical impact of the accelerate PhenoTest® BC system on patients with gram-negative bacteremia and high risk of antimicrobial resistance: a prospective before-after implementation study
Authors: Brosh-Nissimov Tal , Tzur Anka , Grupel Daniel , Cahan Amos , Ma’aravi Nir , Heled-Akiva Maya , Jawamis Hasan , Leskes Hanna , Barenboim Erez , Sorek Nadav 
Published: July 2023

Abstract
Background
The Accelerate PhenoTest® BC system (AXDX) is a novel assay for rapid bacterial identification and antimicrobial susceptibility (AST). We report an evaluation of its impact on treatment of patients with Gram-negative bacteremia (GNB) with a high risk of antimicrobial resistance (AMR).

Methods
A prospective single-center evaluation before and after implementation of AXDX in addition to standard-of-care (SOC) microbiology and antimicrobial stewardship program (ASP). Patients with GNB reported during laboratory working hours and prespecified risk factors for AMR were included. The primary outcome was an ASP-oriented beneficial antimicrobial change, defined as either an escalation of an inappropriate empiric treatment or de-escalation of a broad-spectrum treatment of a susceptible organism. Main secondary outcomes were time to an appropriate treatment, antimicrobial treatment duration, length of stay (LOS) and mortality.

Results
Included were 46 and 57 patients in the pre- and post-intervention periods, respectively. The median time to an AST-oriented beneficial change was 29.2 h vs. 49.6 h, respectively (p < 0.0001). There were no significant differences in the time to appropriate treatment, LOS or mortality. Antimicrobial treatment duration was longer during the intervention period (10 vs. 8 days, p = 0.007). AXDX failed to correctly identify pathogens in all 6 cases of polymicrobial bacteremia. In two cases patient care was potentially compromised due to inappropriate de-escalation.

Conclusions
AXDX implementation resulted in a 20.4-hour shorter time to an ASP-oriented beneficial antimicrobial change. This should be weighed against the higher costs, the lack of other proven clinical benefits and the potential harm from mis-identification of polymicrobial bacteremias.
Reigniting hope in cancer treatment: the promise and pitfalls of IL-2 and IL-2R targeting strategies
Authors: Muhammad Shan , Fan Tao , Hai Yang , Gao Yibo , He Jie 
Published: July 2023

AbstractInterleukin-2 (IL-2) and its receptor (IL-2R) are essential in orchestrating immune responses. Their function and expression in the tumor microenvironment make them attractive targets for immunotherapy, leading to the development of IL-2/IL-2R-targeted therapeutic strategies. However, the dynamic interplay between IL-2/IL-2R and various immune cells and their dual roles in promoting immune activation and tolerance presents a complex landscape for clinical exploitation. This review discusses the pivotal roles of IL-2 and IL-2R in tumorigenesis, shedding light on their potential as diagnostic and prognostic markers and their therapeutic manipulation in cancer. It underlines the necessity to balance the anti-tumor activity with regulatory T-cell expansion and evaluates strategies such as dose optimization and selective targeting for enhanced therapeutic effectiveness. The article explores recent advancements in the field, including developing genetically engineered IL-2 variants, combining IL-2/IL-2R-targeted therapies with other cancer treatments, and the potential benefits of a multidimensional approach integrating molecular profiling, immunological analyses, and clinical data. The review concludes that a deeper understanding of IL-2/IL-2R interactions within the tumor microenvironment is crucial for realizing the full potential of IL-2-based therapies, heralding the promise of improved outcomes for cancer patients.
Systemic inflammatory proteins in offspring following maternal probiotic supplementation for atopic dermatitis prevention
Authors: Zakiudin Dinastry Pramadita , Rø Anne Dorthea Bjerkenes , Videm Vibeke , Øien Torbjørn , Simpson Melanie Rae 
Published: July 2023

Abstract
Background
Maternal probiotic supplementation has a promising effect on atopic dermatitis (AD) prevention in infancy. In the randomised controlled study, Probiotics in the Prevention of Allergy among Children in Trondheim (ProPACT), maternal probiotics reduced the cumulative incidence of AD in their offspring by 40% at 2 years of age. However, our understanding on how probiotics prevented AD is still limited, and the role of inflammatory proteins in infants following maternal probiotic supplementation is unclear. We hypothesised that maternal probiotics lowered pro-inflammatory proteins and increased anti-inflammatory proteins in their 2-year-old children as a mechanism of AD prevention. We aimed to explore this hypothesis and the association between these proteins and the presence of AD, severity of AD, and the degree of preventive effect of probiotics.

Methods
Plasma samples were collected from 2-year-old children (n = 202) during the ProPACT study, a randomised placebo-controlled trial of maternal probiotic supplementation. These samples were analysed for 92 inflammatory proteins using a multiplex proximity extension assay. Associations between inflammatory proteins and the presence and severity of AD, and the degree of preventive effect, was estimated individually using regression analysis and then collectively using unsupervised cluster analysis.

Results
Several proteins were observed to differ between the groups. The probiotic group had lower CCL11 and IL-17C, while children with AD had higher IL-17C, MCP-4, uPA, and CD6. Cytokine CCL20 and IL-18 had moderate correlation (r = 0.35 and r = 0.46) with the severity of AD. The cluster analysis revealed that children in the cluster of samples with the highest value of immune checkpoint receptors and inflammatory suppressor enzymes showed the greatest AD preventive effect from probiotics.

Conclusions
The proteins associated with both maternal probiotic supplementation and the presence and severity of AD warrant attention because of their potential biological relevance. Cluster analysis may provide a new insight when considering which subgroups benefit from probiotic supplementation. Larger studies are needed to confirm the results.
Trial registration number: The study was retrospectively registered at ClinicalTrials.gov (NCT00159523) on 12nd September 2005.
Non-disclosure of drug injection practices as a barrier to HCV testing: results from the PrebupIV community-based research study
Authors: Anwar Ilhame , Donadille Cécile , Protopopescu Camelia , Michels David , Herin Joris , Pladys Adélaïde , Bader Danièle , Carrieri Patrizia , Roux Perrine 
Published: July 2023

Abstract
Background
Hepatitis C virus (HCV) infection prevalence is particularly high in people who inject drugs (PWID), a population that faces many barriers to HCV testing and care. A better understanding of the determinants of access to HCV testing is needed to improve their engagement in the HCV care cascade. We used data from a cross-sectional survey of people who inject drugs, mainly opioids, to identify factors associated with recent HCV testing.

Methods
Self-reported data on HCV antibody testing were analyzed for 550 of the 557 PWID enrolled in PrebupIV, a French cross-sectional community-based survey which assessed PWID acceptability of injectable buprenorphine as a treatment. Factors associated with recent (i.e., in the previous six months) HCV antibody testing were identified performing multivariable logistic regression.

Results
Among the study sample, 79% were men and 31% reported recent HCV antibody testing. Multivariable analysis found that PWID who did not disclose their injection practices to anyone (aOR [95% CI] 0.31 [0.12,0.82], p = 0.018), older PWID (aOR [95% CI] 0.97 [0.95,1.00], p = 0.030) and employed respondents (aOR [95% CI] 0.58 [0.37,0.92], p = 0.019) were all less likely to report recent HCV testing. No association was found between opioid agonist therapy and HCV testing.

Conclusions
Our findings suggest that non-disclosure of injection practices, employment and age were all barriers to HCV antibody testing. Preventing stigma around injection practices, developing the HCV testing offer in primary care and addiction care services, and training healthcare providers in HCV care management could improve HCV testing and therefore, the HCV care cascade in PWID.
Population norms for the EQ-5D-3L and EQ-5D-5L in Romania
Authors: Olariu Elena , Caplescu Raluca , Vale Luke , Niculescu-Aron Ileana Gabriela , Oluboyede Yemi , Paveliu Marian Sorin 
Published: July 2023

AbstractBackgroundThe majority of patient reported outcome measures (PROMs) don’t have population norms in Romania. This is the case with the EQ-5D as well. Therefore, we aimed to estimate population norms for the Romanian versions of the EQ-5D-5L, EQ-5D-3L, their indexes, and the EQ-VAS.MethodsA cross-sectional survey was conducted in all regions of Romania from November 2018 to November 2019. A three-stage probability sampling procedure stratified by region and settlement size was used to select a representative sample. Interviews were computer-assisted and conducted in respondents’ homes by trained interviewers. Health status was assessed with the EQ-5D-5L, the EQ-5D-3L and the EQ VAS. Descriptive statistics were used to estimate population norms by age groups and sex for the EQ-5D-5L, the EQ-5D-3L, their indexes and the EQ VAS. Population norms were weighted using survey weights. Indexes for the EQ-5D questionnaires were estimated using the recently developed Romanian value sets.ResultsData from 1,649 interviews was analysed in the present study. Survey weights were used so that sex and place of residence ratios for the weighted sample matched the Romanian general population distribution. Participants’ mean age was 47.4 years (SE = 1.157) and 50.3% of them reported being in good health. The dimension for which people reported the highest number of problems for both questionnaires was the pain/discomfort dimension. Men aged 35 plus reported fewer problems with pain/discomfort than women for both the EQ-5D-5L and EQ-5D-3L. Health decreased with age as shown by the decrease from age group 18–24 to age group 75 plus in the indexes of both questionnaires: from 0.977 (SE = 0.005) to 0.765 (SE = 0.017) for EQ-5D-5L and from 0.981 (SE = 0.005) to 0.784 (SE = 0.019) for EQ-5D-3L. There was 29.9 points drop in the EQ VAS score between the youngest and oldest group.ConclusionsPopulation norms for the Romanian versions of the EQ-5D-5L, EQ-5D-3L, their indexes, and the EQ VAS are now available. These can now be used as reference values by healthcare professionals, researchers and decision-makers leading to a further development of health-related quality of life research in Romania.
Cross-cultural adaptation and validation of a self-reporting tool to assess health-related quality of life for Egyptians with extremity bone sarcomas in childhood or adolescence
Authors: Farid Nesma , Chun Sungsoo , Hassanain Omneya , Salama Mohamed , Esam Elham , Adel Fatima , Rashad Ismail , El Ghoneimy Ahmed Mohamed 
Published: July 2023

Abstract
Background
Validated self-reporting tools are required to evaluate the functional outcome and health-related quality of life (HRQOL) for those who had extremity bone sarcomas in their childhood or adolescence. Our study pursued cross-cultural adaptation and validation of the pediatric Toronto Extremity Salvage Score (pTESS) and Toronto Extremity Salvage Score (TESS) to assess the functional outcome for Egyptian children and adult survivors following surgeries of extremity bone sarcomas. In the modified versions of pTESS and TESS, mental domains were added to allow the evaluation of HRQOL using a specific instrument for childhood bone cancer.

Methods
The internal consistency and test–retest reliability of the studied forms were assessed with Cronbach’s alpha and Intra-class coefficients (ICC), respectively. For convergent validity, correlations between scores of the generic Pediatric Quality of Life Inventory (PedsQL 4.0) and pTESS /TESS scores were reported. Factor Analysis was feasible for pTESS-leg; due to the insufficient samples, only the average inter-item correlation coefficients were reported for the remaining versions.

Results
Out of 233 participants, 134 responded to pTESS-leg, 53 to TESS-leg, 36 to pTESS-arm, and only 10 to TESS-arm. All versions showed excellent internal consistency (Cronbach’s alpha >0.9), good test–retest reliability (ICC >0.8), moderate to strong correlations with PedsQL, and acceptable average inter-item correlation coefficients (≥0.3). Three factors were extracted for the pTESS-leg, in which all mental items were loaded on one separate factor with factor loadings exceeding 0.4. Active chemotherapy, less than one year from primary surgery, or tibial tumors were associated with significantly inferior pTESS/TESS scores in the lower extremity group.

Conclusion
The Egyptian pTESS and TESS are valid and reliable self-reporting tools for assessing the functional outcome following surgeries for extremity bone sarcomas. The modified pTESS and TESS versions, which include additional mental domains, enabled the assessment of the overall health status of our population. Future studies should include a larger sample size and evaluate the ability of pTESS/TESS to track progress over time.
Lymphedema self-care: economic cost savings and opportunities to improve adherence
Authors: Karaca-Mandic Pinar , Solid Craig A. , Armer Jane M. , Skoracki Roman , Campione Elizabeth , Rockson Stanley G. 
Published: July 2023

Abstract
Background
Breast cancer-related lymphedema (BCRL) imposes a significant economic burden on patients, providers, and society. There is no curative therapy for BCRL, but management through self-care can reduce symptoms and lower the risk of adverse events.

Main body
The economic burden of BCRL stems from related adverse events, reductions in productivity and employment, and the burden placed on non-medical caregivers. Self-care regimens often include manual lymphatic drainage, compression garments, and meticulous skin care, and may incorporate pneumatic compression devices. These regimens can be effective in managing BCRL, but patients cite inconvenience and interference with daily activities as potential barriers to self-care adherence. As a result, adherence is generally poor and often worsens with time. Because self-care is on-going, poor adherence reduces the effectiveness of regimens and leads to costly treatment of BCRL complications.

Conclusion
Novel self-care solutions that are more convenient and that interfere less with daily activities could increase self-care adherence and ultimately reduce complication-related costs of BCRL.
Randomized, double-blinded, placebo-controlled pilot study: efficacy of faecal microbiota transplantation on chronic fatigue syndrome
Authors: Salonen Tapani , Jokinen Elina , Satokari Reetta , Lahtinen Perttu 
Published: July 2023

Abstract
Background
Chronic fatigue syndrome (CFS) is a disabling illness of unknown aetiology. Disruption of gut microbiota may play a role in several neurological disorders. In this study, the effect of faecal microbiota transplantation (FMT) on fatigue severity and health-related quality of life (HRQOL) in patients with CFS was evaluated.

Methods
Randomized, placebo-controlled pilot trial. Patients and researchers were blinded to treatment assignment. 11 patients with CFS (10 female and 1 male, mean age 42.2 years and mean duration of CFS 6.3 years) were randomly assigned to receive either FMT from a universal donor (n = 5) or autologous FMT (n = 6) via colonoscopy. Patients’ HRQOL was assessed by using visual analog scale (VAS) and self-reporting questionnaires Modified Fatigue Impact Scale (MFIS), 15D and EQ-5D-3L. Patients’ HRQOL was evaluated at baseline, and 1 and 6 months after the FMT.

Results
The baseline VAS scores in the FMT and placebo groups were 62.4 and 76.0 (p = 0.29). 1-month scores were 60.0 and 73.7 and 6-months scores 72.8 and 69.5, respectively. Total MFIS scores in the FMT and placebo groups were 59.6 and 61.0 at the baseline (p = 0.80), 53.5 and 62.0 at 1 month and 58.6 and 56.2 at 6 months. Compared to the baseline scores, differences at 1 and 6 months were statistically insignificant both in VAS and in MFIS. The 15D and EQ-5D-3L profiles did not change after the FMT or placebo. FMT-related adverse events were not reported.

Conclusion
FMT was safe but did not relieve symptoms or improve the HRQOL of patients with CFS. Small number of study subjects limits the generalizability of these results.
Trial Registration ClinicalTrials.gov Identifier NCT04158427, https://register.clinicaltrials.gov, date of registration 08/08/2019.
Targeted ablation of signal transducer and activator of transduction 1 alleviates inflammation by microglia/macrophages and promotes long-term recovery after ischemic stroke
Authors: Han Wenxuan , Pu Hongjian , Li Sicheng , Liu Yaan , Zhao Yongfang , Xu Mingyue , Chen Caixia , Wu Yun , Yang Tuo , Ye Qing , Wang Hong , Stetler R. Anne , Chen Jun , Shi Yejie 
Published: July 2023

Abstract
Background
Brain microglia and macrophages (Mi/MΦ) can shift to a harmful or advantageous phenotype following an ischemic stroke. Identification of key molecules that regulate the transformation of resting Mi/MΦ could aid in the development of innovative therapies for ischemic stroke. The transcription factor signal transducer and activator of transduction 1 (STAT1) has been found to contribute to acute neuronal death (in the first 24 h) following ischemic stroke, but its effects on Mi/MΦ and influence on long-term stroke outcomes have yet to be determined.

Methods
We generated mice with tamoxifen-induced, Mi/MΦ-specific knockout (mKO) of STAT1 driven by Cx3cr1CreER. Expression of STAT1 was examined in the brain by flow cytometry and RNA sequencing after ischemic stroke induced by transient middle cerebral artery occlusion (MCAO). The impact of STAT1 mKO on neuronal cell death, Mi/MΦ phenotype, and brain inflammation profiles were examined 3–5 days after MCAO. Neurological deficits and the integrity of gray and white matter were assessed for 5 weeks after MCAO by various neurobehavioral tests and immunohistochemistry.

Results
STAT1 was activated in Mi/MΦ at the subacute stage (3 days) after MCAO. Selective deletion of STAT1 in Mi/MΦ did not alter neuronal cell death or infarct size at 24 h after MCAO, but attenuated Mi/MΦ release of high mobility group box 1 and increased arginase 1-producing Mi/MΦ 3d after MCAO, suggesting boosted inflammation-resolving responses of Mi/MΦ. As a result, STAT1 mKO mice had mitigated brain inflammation at the subacute stage after MCAO and less white matter injury in the long term. Importantly, STAT1 mKO was sufficient to improve functional recovery for at least 5 weeks after MCAO in both male and female mice.

Conclusions
Mi/MΦ-targeted STAT1 KO does not provide immediate neuroprotection but augments inflammation-resolving actions of Mi/MΦ, thereby facilitating long-term functional recovery after stroke. STAT1 is, therefore, a promising therapeutic target to harness beneficial Mi/MΦ responses and improve long-term outcomes after ischemic stroke.
Intelligent identification on cotton verticillium wilt based on spectral and image feature fusion
Authors: Lu Zhihao , Huang Shihao , Zhang Xiaojun , shi Yuxuan , Yang Wanneng , Zhu Longfu , Huang Chenglong 
Published: July 2023

Abstract
Background
Verticillium wilt is the major disease of cotton, which would cause serious yield reduction and economic losses, and the identification of cotton verticillium wilt is of great significance to cotton research. However, the traditional method is still manual, which is subjective, inefficient, and labor-intensive, and therefore, this study has proposed a novel method for cotton verticillium wilt identification based on spectral and image feature fusion. The cotton hyper-spectral images have been collected, while the regions of interest (ROI) have been extracted as samples including 499 healthy leaves and 498 diseased leaves, and the average spectral information and RGB image of each sample were obtained. In spectral feature processing, the preprocessing methods including Savitzky-Golay smoothing (SG), multiplicative scatter correction (MSC), de-trending (DT) and mean normalization (MN) algorithms have been adopted, while the feature band extraction methods have adopted principal component analysis (PCA) and successive projections algorithm (SPA). In RGB image feature processing, the EfficientNet was applied to build classification model and 16 image features have been extracted from the last convolutional layer. And then, the obtained spectral and image features were fused, while the classification model was established by support vector machine (SVM) and back propagation neural network (BPNN). Additionally, the spectral full bands and feature bands were used as comparison for SVM and BPNN classification respectively.

Result
The results showed that the average accuracy of EfficientNet for cotton verticillium wilt identification was 93.00%. By spectral full bands, SG-MSC-BPNN model obtained the better performance with classification accuracy of 93.78%. By feature bands, SG-MN-SPA-BPNN model obtained the better performance with classification accuracy of 93.78%. By spectral and image fused features, SG-MN-SPA-FF-BPNN model obtained the best performance with classification accuracy of 98.99%.

Conclusions
The study demonstrated that it was feasible and effective to use fused spectral and image features based on hyper-spectral imaging to improve identification accuracy of cotton verticillium wilt. The study provided theoretical basis and methods for non-destructive and accurate identification of cotton verticillium wilt.
Mono-valent salt corrections for RNA secondary structures in the ViennaRNA package
Authors: Yao Hua-Ting , Lorenz Ronny , Hofacker Ivo L. , Stadler Peter F. 
Published: July 2023

Abstract
Background
RNA features a highly negatively charged phosphate backbone that attracts a cloud of counter-ions that reduce the electrostatic repulsion in a concentration dependent manner. Ion concentrations thus have a large influence on folding and stability of RNA structures. Despite their well-documented effects, salt effects are not handled consistently by currently available secondary structure prediction algorithms. Combining Debye-Hückel potentials for line charges and Manning’s counter-ion condensation theory, Einert et al. (Biophys J 100: 2745-2753, 2011) modeled the energetic contributions of monovalent cations on loops and helices.

Results
The model of Einert et al. is adapted to match the structure of the dynamic programming recursion of RNA secondary structure prediction algorithms. An empirical term describing the salt dependence of the duplex initiation energy is added to improve co-folding predictions for two or more RNA strands. The slightly modified model is implemented in the package in such way that only the energy parameters but not the algorithmic structure is affected. A comparison with data from the literature show that predicted free energies and melting temperatures are in reasonable agreement with experiments.

Conclusion
The new feature in the package makes it possible to study effects of salt concentrations on RNA folding in a systematic manner. Strictly speaking, the model pertains only to mono-valent cations, and thus covers the most important parameter, i.e., the NaCl concentration. It remains a question for future research to what extent unspecific effects of bi- and tri-valent cations can be approximated in a similar manner.

Availability
Corrections for the concentration of monovalent cations are available in the package starting from version 2.6.0.