bluuebunny/crossref_metadata_2025_split huggingface dataset:
Resilience &amp; Stability of the CF- Intestinal &amp; Respiratory Microbiome During Nutritional &amp; Exercise Intervention
Authors: Knoll Rebecca Luise , Jarquín-Díaz Víctor Hugo , Klopp Jonas , Kemper Alissa , Hilbert Katja , Hillen Barlo , Pfirrmann Daniel , Simon Perikles , Bähner Viola , Nitsche Oliver , Gehring Stephan , Markó Lajos , Forslund Sofia K. , Poplawska Krystyna 
Published: July 2022

Abstract
Background: Impaired respiratory and intestinal microbiome composition is linked to cystic fibrosis lung disease severity. In people with cystic fibrosis (pwCF), regular exercise is recommended to delay disease progression and preserve a stable lung function. An optimal nutritional status is vital for best clinical outcomes. Our study investigated whether regular and monitored exercise and nutritional support promotes CF microbiome health.Methods: A personalized nutrition and exercise program promoted nutritional intake and physical fitness in 18 pwCF for 12 months. Throughout the study, patients performed strength and endurance training monitored by a sports scientist via an internet platform. After three months, food supplementation with Lactobacillus rhamnosus LGG was introduced. Nutritional status and physical fitness were assessed before the study started, after three and nine months. Sputum and stool were collected, and microbial composition was analyzed by 16S rRNA gene sequencing.Results: Sputum and stool microbiome composition remained stable and highly specific to each patient during the study period. Disease-associated pathogens dominated sputum composition. Lung disease severity and recent antibiotic treatment had the highest impact on taxonomic composition in stool and sputum microbiome. Strikingly, the long-term antibiotic treatment burden had only a minor influence. Conclusion: Despite the exercise and nutritional intervention, respiratory and intestinal microbiomes proved to be resilient. Dominant pathogens drove the composition and functionality of the microbiome. Further studies are required to understand which therapy could destabilize the dominant disease-associated microbial composition of pwCF.
The complete chloroplast genome of Allium mongolicum: insights into comparative and phylogenetic analyses with genus Allium
Authors: Jin Yanan , Zhang Ting , Liu Binke , Zheng Chengzhong , Huo Hongyan , Zhang Jixing 
Published: July 2022

Abstract
Allium mongolicum Regel is a wild and sandy vegetable with unique flavours. In this study, a complete chloroplast (cp) genome of A. mongolicum was obtained (Genbank accession number: OM630416), and contained 153,609 base pairs with the GC ratio as 36.8%. 130 genes were annotated including 84 protein-coding genes, 38 tRNA, and 8 rRNA genes. The large single-copy (LSC) region was 82,644 bp, and a small single-copy (SSC) region was 18,049 bp, which were separated by two inverted repeats (IRs, including IRa and IRb) of 26,458 bp. Comparative genome analyses of 55 Allium species suggested that genomic structure of genus Allium was conserved, and LSC and SSC regions were outstanding with high variability. Among them, more divergent loci were in the SSC region covering ycf1-rrn4.5 and ndhF-ccsA. Phylogenetic analysis on cp genomes of 55 Allium determined that all members were clustered into 13 clades with strong section-specificity, and A. mongolicum had close relationship with A. senescens. Corresponding analyses of four protein-coding genes (ycf1, ndhF, rpl32, and ccsA) in aforementioned divergent loci confirmed that ycf1 was finally chosen as the candidate gene for species identification and evolutionary classification of genus Allium. These data provide valuable genetic resources for future research on Allium.
Non-invasive screening of breast cancer from fingertip smears - a proof of concept study
Authors: Russo Cristina , Wyld Lynda , Abreu Marjory Da Costa , Bury Charles , Heaton Cameron , Cole Laura Margaret , Francese Simona 
Published: July 2022

Abstract
Breast cancer is a global health issue affecting 2.3 million women per year, causing death in over 600,000. Mammography (and biopsy) is the gold standard for screening and diagnosis. Whilst effective, this test exposes individuals to radiation, has limitations to its sensitivity and specificity and may cause moderate to severe discomfort. Some women may also find this test culturally unacceptable. This proof-of-concept study, combining bottom-up proteomics with Matrix Assisted Laser Desorption Ionisation Mass Spectrometry (MALDI MS) detection, explores the potential for a non-invasive technique for the early detection of breast cancer from fingertip smears. A cohort of 15 women with either benign breast disease (n = 5), early breast cancer (n = 5) or metastatic breast cancer (n = 5) were recruited from a single UK breast unit. Fingertips smears were taken from each patient and from each of the ten digits, either at the time of diagnosis or, for metastatic patients, during active treatment. A number of statistical analyses and machine learning approaches were investigated and applied to the resulting mass spectral dataset. The highest performing predictive method, a 3-class Multilayer Perceptron (MLP) neural network, yielded an accuracy score of 97.8% when categorising unseen MALDI MS spectra as either the benign, early or metastatic cancer classes. These findings support the need for further research into the use of sweat deposits (in the form of fingertip smears or fingerprints) for non-invasive screening of breast cancer.
WITHDRAWN: Quality Problems in Low İrradiance at Grid Connected PV Solar System
Authors: adak suleyman , Cangi Hasan 
Published: July 2022

Abstract
Solar Photovoltaic (PV) energy is one of the main topics that have attracted the attention of researchers in recent years. The use of solar energy is increasing rapidly in the world. Although PV energy has many advantages, it has some disadvantages. Among these disadvantages, power factor (PF) and Total Harmonic Distortion (THD) issues are discussed in this article. PF and THD are dependent on the radiation values. The solar inverter output voltage and current waveform should be in sinusoidal waveform. However, the sinusoidal waveform of current and voltage lose their sinusoidal characteristics due to non-linear loads on grid-connected solar system. Harmonic components often occur in grid-connected solar PV systems. In addition, at low irradiance the amplitude of harmonic components increases, whereas the power factor of the PV system decreases. Low power factor and high amplitude of harmonics cause the efficiency of the solar system to decrease. PF and THD values were measured in a particular cloudy day for analysis. The grid-connected PV system was modeled by using Matlab /simulation program and carried out the analysis of the solar PV system. Thus, the analytical expression of the PF and THDI dependent on irradiation were found with a new method by using statistical package for the social sciences (SPSS) program and curve fitting method.
Exploration on the application of CBL and humanistic literacy in diagnostics teaching under the background of new medicine
Authors: Liu Lihui , Deng Langmei 
Published: July 2022

Abstract
Background: In the new era, medical teaching is faced with the dual tasks of knowledge transmission and value guidance. In this study, we applied CBL combined with humanistic literacy to undergraduate medical students’ internal medicine diagnostics teaching, so as to promote medical students’ better acquisition of knowledge and improvement of literacy.Methods: Fifty-six five-year undergraduate medical students from Xiangya Medical College of Central South University were randomly divided into experimental group and control group, with 28 students in each group. In the experimental group, CBL combined with humanistic literacy teaching mode was adopted, while in the control group, traditional teaching methods were adopted. The two groups were compared to explore the effect of innovative teaching mode in the course of medical diagnostics. Result: The scores of multiple choice questions and comprehensive analysis questions of the experimental group were significantly higher than those of the control group. The teaching satisfaction survey of the two groups of students shows that the students in the experimental group are significantly higher than the control group. In addition, the comprehensive ability questionnaire survey showed that the experimental group of students compared to the control group of students, this group of students believed that the innovative teaching mode of CBL combined with humanistic literacy could significantly improve humanistic literacy, learning motivation, independent thinking, clinical thinking, teamwork, clinical communication and other abilities ( P＜0.05) .Conclusion: Under the background of new medicine, CBL combined with humanistic literacy teaching mode is obviously superior to the traditional teaching mode in improving the professional knowledge level and cultivating the comprehensive quality and ability of undergraduate medical students. This teaching mode can not only improve the teaching quality, but also improve students’ learning ability, exercise their learning enthusiasm, and improve students' happiness in learning.
Three-dimensional strain imaging of irradiated chromium using multi-reflection Bragg coherent diffraction
Authors: Jossou Ericmoore , Assefa Tadesse , Suzana Ana , Wu Longlong , Campbell Colleen , Harder Ross , Cha Wonsuk , Kisslinger Kim , Sun Cheng , Gan Jian , Ecker Lynne , Robinson Ian , Gill Simerjeet 
Published: July 2022

Abstract
Radiation-induced materials degradation is a key concern in limiting the performance of nuclear materials. The formation of nanoscale void and gas bubble superlattices in metals and alloys under radiation environments can effectively mitigate radiation-induced damage, such as swelling and aid the development of next generation radiation tolerant materials. To effectively manage radiation-induced damage via superlattice formation, it is critical to understand the microstructural changes and strain induced by such superlattices. In our approach, we utilize multi-reflection Bragg coherent diffraction imaging (BCDI) to quantify the full strain tensor induced by void superlattices in iron (Fe) irradiated chromium substrate, a model metallic system. Multi-reflection BCDI is a powerful method for detailed investigation of the strain and microstructural changes caused by radiation-induced defects during Fe ion implantation, a key fundamental understanding that is inaccessible via current conventional techniques. Our approach provides a quantitative estimation of radiation-induced three dimensional (3D) strain generated at the microscopic level and predicts the number density of defects with a high degree of sensitivity in bulk metallic substrates. Such quantitative evaluation of 3D strain in nuclear materials can have a major impact on predicting materials performance and degradation in radiation environments and can revolutionize design of radiation tolerant materials.
Legacy effects of a range-expanding shrub influence soil fungal communities and reduce conspecific seedling performance
Authors: Collins Courtney Grace , Diez Jeffrey , Spasojevic Marko , Pombubpa Nuttapon 
Published: July 2022

Abstract
Aims
Soil legacy effects can have long-term impacts on soil microbial communities with implications for plant growth and community structure. These effects are well studied for invasive plants, particularly after removal of invasive species, however very little work has considered the soil legacy effects of native range expanding species.
Methods
We used a controlled greenhouse experiment with a range-expanding sagebrush species (Artemisia rothrockii (Asteraceae)) to determine how sagebrush seedling performance was influenced by soil legacy effects of sagebrush in both the native and expansion range and over time since removal. We then used ITS2 sequencing to determine what soil microbial mechanisms drove these feedbacks.
Results
Conspecific sagebrush seedlings responded negatively to sagebrush soil legacy effects overall, with more negative plant-soil feedbacks, reduced height, and higher root:shoot ratios in shrub removal inoculum than in shrub and herbaceous soil inoculum. Seedlings with shrub removal inoculum had increased fungal diversity, pathogen, and saprotroph richness, and altered fungal community composition. Legacy effects on soil fungal diversity and functional group richness were present in seedlings with 1-year shrub removal inoculum, while effects on fungal community composition were found in 1 and 5-year shrub removal inoculated seedlings. Similarly, negative plant-soil feedbacks occurred for seedlings growing in both 1-year and in 5-year shrub removal inoculum.
Conclusions
This work provides novel insight into how soil legacy effects of native range expanding species may limit rather than promote the recruitment of conspecifics, with important implications for management as global change continues to shift the geographic ranges of woody plants.
New trends in the management of cytomegalovirus infection after allogeneic hematopoietic cell transplantation: a survey of the Infectious Diseases Working Party of EBMT
Authors: Cesaro Simone , Ljungman Per , Tridello Gloria , Mikulska Malgorzata , Wendel Lotus , Styczynski Jan , Averbuch Dina , LLanzá Rafael De la Cámara 
Published: July 2022

Abstract
The management of cytomegalovirus (CMV) infection was assessed with a survey performed in 2020 by the Infectious Diseases Working Party of European Society for Blood and Marrow Transplantation (EBMT). One-hundred-eighty of the 579 EBMT centres (31%) responded. CMV monitoring with quantitative PCR for CMV-DNAemia was used by 97% of centres while the duration of monitoring was variable according to the patient immune recovery and the ongoing immunosuppressive therapy. CMV prophylaxis for high-risk patients was used in 56% (101) of centres: letermovir in 62 centres (61%), aciclovir/valaciclovir in 19 centres (19%), ganciclovir/valganciclovir in 17 centres (17%), foscarnet in 3 (3%). The most used trigger for pre-emptive therapy was a threshold of > 103 copies/ml or > 103 IU/ml, Ganciclovir/valganciclovir confirmed the preferred first line treatment both for pre-emptive and CMV disease therapy. CMV-cytotoxic T-cells were used mainly in the setting of relapsing/refractory CMV disease. Forty-eight centres reported CMV refractory/resistant infection due to mutated CMV strain. This survey showed that letermovir prophylaxis is adopted by more than half of centres using a prophylaxis approach for CMV infection. How letermovir prophylaxis will modify other important pillars of daily CMV management, such as frequency of CMV-DNAemia monitoring and preemptive therapy, remain a matter of investigation.
The burden of BRCA1 and BRCA2 gene mutations among Vietnamese women and their associated factors: A protocol for a systematic review and meta-analysis
Authors: Tran Phuc , Tran Duc , Vu Chi , Phan Quang , Nguyen Anh 
Published: July 2022

Abstract

Background: BReast CAncer gene (BRCA)1 and BRCA2 (also known as BRCA) mutation carriers are now frequently provided genetic counselling. A precise estimation of the prevalence of BRCA gene mutations is essential for the counsellor to provide an appropriate risk prediction. However, the data in Vietnam is ambiguous and unreliable risk factors from individual studies. Hence, the objective of this systematic review with meta-analysis protocol is to provide a method used to synthesize evidence pertaining to the proportion of BRCA mutations among Vietnamese women and their risk factors for cancers.Methods: Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P), a set of criteria for conducting systematic reviews, was followed in developing and reporting this protocol. From the databases' inception till June 2023, a comprehensive search will be undertaken in electronic PubMed and Scopus databases. In two stages, title/abstract screening and full-text screening, two independent authors will assess all retrieved articles for inclusion. This review includes papers providing the relevant results reflecting the prevalence of BRCA gene mutations in Vietnamese women who are at least 18 years old with or without cancer. Predefined selection criteria will be used to establish each publication's eligibility. Using the Newcastle-Ottawa Scale and Cochrane Risk of Bias tools, the quality of included studies will be assessed, and overall evidence quality will be appraised using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Initially, all pertinent data from the included articles will be entered into an online MS Excel spreadsheet for meta-analysis, which will thenbe imported into Rstudio. Meta-analyses using random effects will be used to obtain the pooled percentages. The chi-squared test and I2 parameter will be used to evaluate heterogeneity. Publication bias will be investigated visually using funnel plots for asymmetry and Egger's statistical tests.Conclusions:Based on the prevalence of BRCA muations and its comprehensive and specific risk factors for Vietnamese women, we hope our findings will be able to provide a reference for a future strategy to build an effective treatment plan and manage the risk of subsequent cancer development.Registration: PROSPERO (CRD42022340152; 30 June 2022).
Consistent responses to moisture stress within diverse mountain fynbos communities revealed by multi-year in situ physiological measurements
Authors: Skelton Robert Paul , West Adam Gerrard , Buttner Daniel , Dawson Todd 
Published: July 2022

Abstract
● Understanding climate change impacts on the Cape Floristic Region requires improved knowledge of plant physiological responses to the environment. Prior studies examining physiological responses of fynbos species have consisted of campaign-based measurements, capturing snapshots in time of plant water relations and photosynthesis. We examine conclusions drawn from these studies by tracking in situ physiological responses of three species, representing three dominant growth forms (proteoid, ericoid, restioid), over two years using miniature continuous sap flow technology, in combination with long-term observations of xylem water potentials, gas exchange and assessments of xylem vulnerability to embolism. ● We observed considerable inter-specific variation in the timing and extent of dehydration-induced declines in productivity. Erica monsoniana (a shallow-rooted ericoid) exhibited steep within-season declines in sap flow and water potentials, and pronounced inter-annual variability in total daily sap flux (Js). Protea repens showed steady reductions in Js across both years, despite maintaining less negative water potentials. Cannomois congesta - a shallow-rooted restioid - was least negatively impacted. Following rehydrating rain at the end of summer we compared gas exchange recovery in the representative dry year with the normal year, finding significant seasonal, but not species, effects. Loss of function in the drier year was partially accounted for by loss of stem xylem transport capacity, but only in E. monsoniana and C. congesta. ● Hitherto unseen water-use patterns, including inter-annual variability of gas exchange that were driven by contrasting water uptake properties, reveal that mountain fynbos species use different mechanisms to cope with summer dry periods.
Bayesian and evolutionary temperature dependent genome-scale models display alternative optima due to insufficient constraints
Authors: Pettersen Jakob Peder , Almaas Eivind 
Published: July 2022

Abstract
The metabolism of all living organisms is dependent on temperature, and therefore, having a good method to predict temperature effects at a systems level is of importance. Here, we investigate the properties and robustness of a recently developed computational framework for enzyme and temperature constrained genome-scale models (etcGEM). The approach predicts the temperature dependence of an organism's metabolic network from thermodynamic properties of the metabolic enzymes, markedly expanding the scope and applicability of constraint-based metabolic modelling. We show that the existing Bayesian algorithm for fitting an etcGEM converges under a range of different priors and random seeds, yet the solutions differ both in parameter space and on a phenotypic level. We quantified the phenotypic consequences by studying the impact of different solutions on six metabolic network signature reactions. While two of these reactions showed little phenotype variation between the solutions, the remainder displayed huge variation in flux-carrying capacity. Furthermore, we made software improvements to reduce the running time of the compute-intensive Bayesian algorithm by a factor of 8.5. In addition, we develop an evolutionary algorithm as an alternative to the Bayesian parameter fitting algorithm. Our analysis shows that it also gives decent convergence, but it yields solutions with lower variability.
Clinical Evaluation of Single Posterior Long-segment Fixation for Severe Thoracolumbar Fracture (AO type B)
Authors: Chen Yuanyuan , Lian Xiaofeng , Zhang Tao , Cai Bin , Xu Jianguang 
Published: July 2022

Abstract
Background Acute thoracolumbar fracture is a common spine injury in clinical practice, and AO type B injury is a severe fracture based on the morphology of distraction. Controversy remains in approach selection and few studies focused on this type alone. We evaluated the radiologic and clinical results of 56 cases from our university hospital data bases, and aim to provide some ideas during the surgical planning for this patient cohort.Methods From January 2015 to December 2019, fifty-six patients with AO type B thoracolumbar fractures were treated in spine unit of this tertiary hospital. Patient demographics, surgical details, and follow-up data were reviewed. Clinical outcome were analyzed using the Oswestry Disability Index (ODI), Patient Health Questionnaire-9 (PHQ-9), and Visual Analogue Scale (VAS) system. Results All patients received a single posterior approach and an average of 5.7±2.6 segments was instrumented. 41 patients received consecutive, long-segment pedicle screw fixation, while 15 patients were treated by satellite rod due to pedicle fractures. Average preoperative focal kyphotic angle was 26.2±5.6 degrees, which improved significantly to 13.8±7.2 degrees after the procedure (p<0.05). Similar improvements were found in anterior vertebral height (AVH). At the final follow up, no significant loss of correction angle and AVH was detected compared to postoperation. Pain scores had improved over the postoperative months as well as ODI and PHQ-9 scores. No proximal junction kyphotic change was noted, and none of the patients had any implant failure at the final follow-up.Conclusion AO type B thoracolumbar fractures are severely unstable and associated with complicated injuries. Single posterior consecutive, long-segment instrumentation for AO type B thoracolumbar fracture achieved and maintained satisfactory outcome. For patients with broken pedicles at the fractured level, satellite rod enhancement may be a feasible choice of a supplementary procedure.