bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study
Authors: Chapman Jonathan A. , Wroot Emily , Brown Toby , Beck Lauren C. , Embleton Nicholas D. , Berrington Janet E. , Stewart Christopher J. 
Published: December 2024

Abstract
Background
Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.

Results
Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.

Conclusions
Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.
Safflower CtFT genes orchestrating flowering time and flavonoid biosynthesis
Authors: Li Zhiling , Yu Lili , Umar Abdul Wakeel , Wang Jiaruo , Zhang Jian , Wang Nan , Zhang Min , Yao Na , Ahmad Naveed , Liu Xiuming 
Published: December 2024

Abstract
Background
Safflower thrives in dry environments but faces difficulties with flowering in wet and rainy summers. Flavonoids play a role in flower development and can potentially alleviate these challenges. Furthermore, the FLOWERING LOCUS T (FT) family of phosphatidylethanolamine-binding protein (PEBP) genes play a crucial role in the photoperiodic flowering pathway. However, their direct impact on flowering and flavonoid biosynthesis under different light duration is elusive.

Results
Utilizing the genome sequencing of Safflower (Jihong NO.1), the current study identifies three specific genes (CtFT1, CtFT2, and CtFT3) that exhibit upregulation in response to long-day conditions. The overexpression of CtFT2, displayed an early, whereas CtFT1 and CtFT3 late flowering phenotype in Arabidopsis thaliana. Interestingly, the transient overexpression of CtFT1 in safflower leaves caused early flowering, while overexpressing CtFT2 and CtFT3 led to late flowering. Additionally, overexpressing CtFT3 in Arabidopsis and CtFT1, CtFT2, and CtFT3 in safflower leaves, significantly increased flavonoid synthesis.

Conclusions
These findings showed that overexpression of CtFT genes could affect the flowering time and significantly increase the flavonoid content of safflower. The function of CtFT gene is different in safflower and Arabidopsis. This study provides valuable insights into the role of CtFT genes in flower formation and flavonoid synthesis in safflower, which may help in improving safflower breeding quality and its adaptability to diverse environmental conditions.
Genome-wide analysis of the cotton COBRA-like gene family and functional characterization of GhCOBL22 in relation to drought tolerance
Authors: Fu Wan-wan , Wang Zi-Yu , Liusui Yun-Hao , Zhang Xin , Han Ai-Xia , Zhong Xing-Yue , Zhang Jing-Bo , Guo Yan-Jun 
Published: December 2024

Abstract
Background
The COBRA-like (COBL) gene family is a crucial glycosylphosphatidylinositol (GPI)-anchored proteins that participate in various biological processes in plants by regulating the arrangement of cell wall microfibrils. While the functions of COBL genes have been analyzed in several plant species, their roles in cotton’s response to abiotic stress remain unexplored.

Results
This study identified and characterized the COBL gene family in Gossypium hirsutum, revealing a total of 39 COBL family members classified into five subgroups. Transcriptome analysis indicated that the transcription levels of several GhCOBL genes were upregulated following PEG treatment, with GhCOBL22 being significantly induced. Further silencing of the GhCOBL22 gene through virus-induced gene silencing (VIGS) technology demonstrated that this gene’s silencing reduced cotton’s drought stress tolerance. Under drought stress conditions, the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) enzymes, along with proline (PRO) content, were lower in GhCOBL22-silenced plants compared to control plants, while the accumulation of malondialdehyde (MDA) was significantly higher. Moreover, silencing the GhCOBL22 gene also led to reductions in the levels of cellulose, hemicellulose, and lignin content in cotton leaves.

Conclusion
A systematic survey of gene structure, motif composition, and evolutionary relationships of the COBL gene family was conducted in Gossypium hirsutum. Subsequent expression and functional studies indicated that GhCOBL22 plays a significant role in cotton’s drought tolerance. These findings enhance our understanding of the biological functions of the COBL family and highlight the critical role of the GhCOBL22 gene in cotton’s response to drought stress.
Trans-bronchial forceps biopsy for COVID-19 related diffuse parenchymal lung abnormalities
Authors: Kleymann Janina , Brückmann Sascha , Langner Simona , Koschel Dirk , Kolditz Martin 
Published: December 2024

Abstract
Purpose
The role of lung biopsy for evaluation of persistent chest radiographic abnormalities including secondary organizing pneumonia (OP) in COVID-19 remains uncertain. This study aimed to evaluate the diagnostic value of trans-bronchial forceps biopsy (TBFB) in patients with persistent lung abnormalities on thoracic computed tomography (CT) scan following SARS-CoV-2 infection with particular focus on cases with OP and immunocompromised (IC) patients.

Methods
Descriptive retrospective single center analysis of all TBFB performed for diffuse lung parenchymal changes after COVID-19 03–2020 to 06–2023.

Results
Twenty seven consecutive TBFB including 23 in IC patients resulted in 100% samples with alveolar tissue showing a high frequency of 12/27 (44%) histological pattern of OP. Steroids were used in 21/27 patients (78%) including 11/12 (92%) with OP. Clinical outcome at discharge was favorable in 89% (92% with OP).

Conclusion
TBFB contributes to the diagnosis of diffuse parenchymal lung abnormalities in the context of COVID-19 including a frequent OP pattern particularly in IC patients. Larger studies are necessary to confirm our data and elucidate on the optimal steroid treatment modality.

Trial registration
Clinical trial number: not applicable. The study was approved by the Ethics Committee of the University Medicine Carl Gustav Carus, TU Dresden (BO-EK-309072023). Waiver of informed consent was granted because of the retrospective nature of the study.
Functional characterization of the second feedback loop in the circadian clock of the Antarctic krill Euphausia superba
Authors: Stefanelli Chiara , Colaianni Davide , Mazzotta Gabriella M. , Sales Gabriele , Bertolucci Cristiano , Meyer Bettina , Biscontin Alberto , De Pittà Cristiano 
Published: December 2024

Abstract
Background
The Antarctic krill Euphausia superba is a keystone species in the Southern Ocean ecosystem. This crustacean has an ancestral clock whose main components have been identified and characterized in the past few years. However, the second feedback loop, modulating clock gene expression through two transcription factors, VRI and PDP1, has yet to be described. The presence of this second regulatory mechanism is suggested by the identification of its negative component, vrille, at the transcriptional level.

Results
Here, we describe the second feedback loop of krill by identifying the positive component, pdp1, and functionally characterizing both pdp1 and vrille. Starting from the online transcriptome database KrillDB2, we identified and cloned three putative pdp1 sequences which were subsequently analyzed for tissue expression and functional activity using luciferase assays, individually and in combination with two vrille isoforms. Among the pdp1 isoforms, Espdp1_3 displayed higher expression levels in relevant circadian districts than the other two. Furthermore, EsPDP1_3 and EsVRI_2 exhibited the expected positive and negative regulation of the V/P-box in our in vitro system. Finally, Espdp1_3 and Esvrille also showed rhythmic expression in light–dark cycles, supporting their involvement in the regulation of the main circadian clock of the Antarctic krill.

Conclusions
This study expands our knowledge about the molecular architecture of the Antarctic krill circadian clock by defining the components that take part in the modulation of clock expression, establishing a second feedback loop.
Partially substituting roughage with traditional Chinese herbal medicine residues in the diet of goats improved feed quality, growth performance, hematology, and rumen microbial profiles
Authors: Long Yong , Zhang Naifeng , Bi Yanliang , Ma Tao , Paengkoum Pramote , Xin Jiamin , Xiao Wen , Zhao Yanpin , Yuan Chao , Wang Defeng , Yang Yang , Su Chaozhi , Han Yong 
Published: December 2024

AbstractThis study aimed to reveal the effect of traditional Chinese herbal medicine residues (TCHMR) on growth performance, hematology, ruminal microbiota, and economic benefits of Guizhou black male goats through the fermented total mixed ration (FTMR) diet technique. A total of 22 Guizhou black male goats with an initial weight of 21.77 ± 0.85 kg were randomly divided into 2 groups (n = 11), with 11 goats in each group. The control group (CON) was fed a traditional total mixed ration (TMR) diet without the TCHMR. The TCHMR group was fed an FTMR diet containing 40%TCHMR. Compared with the CON group, the results showed that the incorporation of TCHMR into goat diets reduced feeding costs and Feed conversion ratio (FCR). On the contrary, it improved (P < 0.01) feed quality, apparent digestibility of Dry matter (DM), Crude Protein (CP), Neutral detergent fiber (NDF), average daily gain (ADG), and dry matter intake. Interestingly, TCHMR also reduced (P < 0.01) acetate levels in the rumen of goats. Supplementally, TCHMR significantly increased (P < 0.01) the levels of GH, IgM, IgA (p < 0.05), and IFN-γ (P < 0.05), while significantly reducing (P < 0.01) the levels of IL-6, ALT, and AST in serum. Notably, at the phylum level, TCHMR significantly reduced (P < 0.01) the abundance of Bacteroidota and increased (P < 0.01) the abundance of Firmicutes. Moreover. at the genus level, TCHMR significantly reduced (P < 0.01) the abundance of Prevotella, F082, and Bacteroidales_RF16_group, while Muribaculaceae, Proteus, Lachnospiraceae_ND3007_group, and Ruminococcus were increased (P < 0.01). In conclusion, our current findings indicated that 40% TCHMR improved feed quality and the apparent digestibility of nutrients. Additionally, 40% TCHMR improved the growth performance and immunity of Guizhou black male goats, while also reorganizing the composition of ruminal microbiota. So far, under the conditions of this experiment, we have not found any negative effects of 40% TCHMR on goats. This study will be a new idea for developing feed resources, which will reduce environmental pollution and the cost of animal husbandry.
Microbial enzymes as powerful natural anti-biofilm candidates
Authors: Al-Madboly Lamiaa A. , Aboulmagd Asmaa , El-Salam Mohamed Abd , Kushkevych Ivan , El-Morsi Rasha M. 
Published: December 2024

AbstractBacterial biofilms pose significant challenges, from healthcare-associated infections to biofouling in industrial systems, resulting in significant health impacts and financial losses globally. Classic antimicrobial methods often fail to eradicate sessile microbial communities within biofilms, requiring innovative approaches. This review explores the structure, formation, and role of biofilms, highlighting the critical importance of exopolysaccharides in biofilm stability and resistance mechanisms. We emphasize the potential of microbial enzymatic approaches, particularly focusing on glycosidases, proteases, and deoxyribonucleases, which can disrupt biofilm matrices effectively. We also delve into the importance of enzymes such as cellobiose dehydrogenase, which disrupts biofilms by degrading polysaccharides. This enzyme is mainly sourced from Aspergillus niger and Sclerotium rolfsii, with optimized production strategies enhancing its efficacy. Additionally, we explore levan hydrolase, alginate lyase, α-amylase, protease, and lysostaphin as potent antibiofilm agents, discussing their microbial origins and production optimization strategies. These enzymes offer promising avenues for combating biofilm-related challenges in healthcare, environmental, and industrial settings. Ultimately, enzymatic strategies present environmentally friendly solutions with high potential for biofilm management and infection control.
Automated total nucleic acid extraction with magnetic beads for the detection of Plasmodium falciparum in large study cohorts
Authors: Inoue Juliana , Huber Nina , Fendel Rolf , Held Jana 
Published: December 2024

Abstract
Background
Molecular methods play an important role in clinical trials assessing anti-malarial drugs and vaccines, as well as in epidemiological studies aimed at detecting Plasmodium species, especially when dealing with large sample sizes. Molecular techniques are more sensitive and generally have a higher throughput compared to the gold standard microscopy. Further optimization can be achieved with automation of nucleic acid isolation, allowing for rapid and precise extraction. This study evaluated the isolation of total nucleic acids from Plasmodium falciparum mocked samples using an automated extraction method with a magnetic bead-based kit compared to a manual silica column-based kit. Additionally, two different RNA preservation solutions were compared.

Methods
Plasmodium falciparum Dd2 parasites were serially diluted and spiked into whole blood. The dilutions were stored in two different RNA preservation solutions and total nucleic acids extracted with an automated magnetic bead-based kit and a manual silica column-based kit. Subsequently, a reverse transcription (RT) qPCR for Plasmodium detection targeting Plasmodium 18S rRNA and DNA in a single reaction was performed and the quantification cycle (Cq) values across the different sample groups were compared.

Results
Comparable Cq values across the various sample preparations were obtained, suggesting minimal influence from RNA preservation solutions (p = 0.686) or extraction methods (p = 0.119) on RT-qPCR outcomes. Automated nucleic acids extraction allowed processing numerous samples in a shorter timeframe and showed similar efficiency in detecting Plasmodium in blood samples by RT-qPCR as manual extraction.

Conclusions
The automated method for nucleic acid isolation is a valuable tool for the detection of Plasmodium infections in large-scale studies. It is efficient, reliable, and cost-effective. Its potential applications extend to other molecular surveillance studies to support malaria control measures.
The role of guideline organizations in nationwide guideline implementation: a qualitative study
Authors: Thoonsen Andrea C. , Merten Hanneke , Broeders Toby T. , Gans Anika , van Beusekom Ilse , Delnoij Diana M. J. , de Bruijne Martine C. 
Published: December 2024

Abstract
Background
Research indicates suboptimal uptake and impact of clinical practice guidelines in Dutch healthcare. Dutch guideline organizations, i.e. guideline developers, governmental agencies, health insurers and other national organizations, develop, authorize and/or support the use of guidelines in Dutch clinical practice. These organizations influence the end users’ awareness, accessibility, understanding, acceptability and applicability of guidelines and, therefore, play a crucial role in guideline implementation. This study explores how they plan, execute, monitor and evaluate guideline dissemination and implementation.

Methods
Utilizing a qualitative design, we conducted semi-structured interviews with 35 participants from 24 guideline organizations. We conducted framework analysis, using theories on guideline implementation planning, the ‘taxonomy of strategies for achieving guideline implementation and compliance’ and the principles of logic models to analyse the data.

Results
Most guideline organizations made limited use of implementation planning approaches that are known to enhance guideline uptake and impact. These approaches include pre-identifying implementation barriers, engaging stakeholders and applying implementation theories, models and frameworks to select and tailor implementation strategies. Instead, they primarily relied on a standard set of predominantly dissemination and occasional implementation strategies known to be practical in terms of ease, cost and time. Commonly used implementation strategies included distributing, advertising and presenting guideline materials, along with providing additional implementation supporting materials. Regarding monitoring and evaluation methods, few organizations assessed the process, outcome or impact of guideline implementation. Those that did primarily relied on clinical peer review and benchmark information for their assessments.

Conclusions
While Dutch guideline organizations recognized and endorsed the importance of implementation, this did not consistently translate into tailored implementation actions. Most guideline organizations did not have an integrated, structural and well-thought-out plan for implementation. The lack of regular, structured monitoring and evaluation raised uncertainties about the effectiveness of implementation in supporting end users and improving patient outcomes. Suggested follow-up research and practice enhancements could strengthen central-level implementation efforts, fostering more effective local implementation and, ultimately, improving health outcomes.
The efficacy of using continuous glucose monitoring as a behaviour change tool in populations with and without diabetes: a systematic review and meta-analysis of randomised controlled trials
Authors: Richardson Kelli M. , Jospe Michelle R. , Bohlen Lauren C. , Crawshaw Jacob , Saleh Ahlam A. , Schembre Susan M. 
Published: December 2024

Abstract
Background
Continuous glucose monitoring (CGM) holds potential as a precision public health intervention, offering personalised insights into how diet and physical activity affect glucose levels. Nevertheless, the efficacy of using CGM in populations with and without diabetes to support behaviour change and behaviour-driven outcomes remains unclear. This systematic review and meta-analysis examines whether using CGM-based feedback to support behaviour change affects glycaemic, anthropometric, and behavioural outcomes in adults with and without diabetes.

Methods
Ovid MEDLINE, Cochrane Central Register of Controlled Trials, Elsevier Embase, EBSCOhost PsycINFO, and ProQuest Dissertations & Theses Global were searched through January 2024. Eligible studies were randomised controlled trials in adults that implemented CGM-based feedback in at least one study arm compared to a control without CGM feedback. Dual screening, data extraction, and bias assessment were conducted independently. Mean differences in outcomes between intervention and comparison groups were analysed using generic inverse variance models and random effects. Robustness of pooled estimates from random-effects models was considered with sensitivity and subgroup analyses.

Results
Twenty-five clinical trials with 2996 participants were included. Most studies were conducted in adults with type 2 diabetes (n = 17/25; 68%), followed by type 1 diabetes (n = 3/25, 12%), gestational diabetes (n = 3/25, 12%), and obesity (n = 3/25, 12%). Eleven (44%) studies reported CGM-affiliated conflicts of interest. Interventions incorporating CGM-based feedback reduced HbA1c by 0.28% (95% CI 0.15, 0.42, p < 0.001; I2 = 88%), and increased time in range by 7.4% (95% CI 2.0, 12.8, p < 0.008; I2 = 80.5%) compared to arms without CGM, with non-significant effects on time above range, BMI, and weight. Sensitivity analyses showed consistent mean differences in HbA1c across different conditions, and differences between subgroups were non-significant. Only 4/25 studies evaluated the effect of CGM on dietary changes; 5/25 evaluated physical activity.

Conclusions
This evidence synthesis found favourable, though modest, effects of CGM-based feedback on glycaemic control in adults with and without diabetes. Further research is needed to establish the behaviours and behavioural mechanisms driving the observed effects across diverse populations.

Trial registration
CRD42024514135.