bluuebunny/crossref_metadata_2025_split huggingface dataset:
Far-red light photoacclimation in a desert Chroococcidiopsis strain with a reduced FaRLiP gene cluster and expression of its chlorophyll f synthase in space-resistant isolates
Authors: di Stefano Giorgia , Battistuzzi Mariano , La Rocca Nicoletta , Selinger Vera M. , Nürnberg Dennis J. , Billi Daniela 
Published: September 2024

IntroductionSome cyanobacteria can use far-red light (FRL) to drive oxygenic photosynthesis, a phenomenon known as Far-Red Light Photoacclimation (FaRLiP). It can expand photosynthetically active radiation beyond the visible light (VL) range. Therefore, it holds promise for biotechnological applications and may prove useful for the future human exploration of outer space. Typically, FaRLiP relies on a cluster of ~20 genes, encoding paralogs of the standard photosynthetic machinery. One of them, a highly divergent D1 gene known as chlF (or psbA4), is the synthase responsible for the formation of the FRL-absorbing chlorophyll f (Chl f) that is essential for FaRLiP. The minimum gene set required for this phenotype is unclear. The desert cyanobacterium Chroococcidiopsis sp. CCMEE 010 is unusual in being capable of FaRLiP with a reduced gene cluster (15 genes), and it lacks most of the genes encoding FR-Photosystem I.MethodsHere we investigated whether the reduced gene cluster of Chroococcidiopsis sp. CCMEE 010 is transcriptionally regulated by FRL and characterized the spectral changes that occur during the FaRLiP response of Chroococcidiopsis sp. CCMEE 010. In addition, the heterologous expression of the Chl f synthase from CCMEE 010 was attempted in three closely related desert strains of Chroococcidiopsis.ResultsAll 15 genes of the FaRLiP cluster were preferentially expressed under FRL, accompanied by a progressive red-shift of the photosynthetic absorption spectrum. The Chl f synthase from CCMEE 010 was successfully expressed in two desert strains of Chroococcidiopsis and transformants could be selected in both VL and FRL.DiscussionIn Chroococcidiopsis sp. CCME 010, all the far-red genes of the unusually reduced FaRLiP cluster, are transcriptionally regulated by FRL and two closely related desert strains heterologously expressing the chlF010 gene could grow in FRL. Since the transformation hosts had been reported to survive outer space conditions, such an achievement lays the foundation toward novel cyanobacteria-based technologies to support human space exploration.
Whole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation
Authors: Ong Chian Teng , Blackall Patrick. J. , Boe-Hansen Gry B. , deWet Sharon , Hayes Ben J. , Indjein Lea , Korolik Victoria , Minchin Catherine , Nguyen Loan To , Nordin Yusralimuna , Siddle Hannah , Turni Conny , Venus Bronwyn , Westman Mark E. , Zhang Zhetao , Tabor Ala E. 
Published: September 2024

IntroductionBovine Genital Campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between C. fetus subsp. venerealis and C. fetus subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between C. fetus subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.Methods and resultsThis study reported the complete genomes of four C. fetus subsp. fetus and five C. fetus subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses (n = 25) were conducted, incorporating an additional 16 complete C. fetus genomes from the NCBI database, to investigate the genomic differences between these two closely related C. fetus subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two C. fetus subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the C. fetus subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG “Peptidoglycan Biosynthesis” pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of C. fetus subsp. venerealis and its biovar variant. Verification with 58 annotated C. fetus genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF (Campylobacter fetus subsp. fetus) or CFV/CFVi (Campylobacter fetus subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting C. fetus subspecies using a quantitative PCR assay.DiscussionOur results highlighted the high genetic stability of C. fetus subspecies. Nevertheless, Campylobacter fetus subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from C. fetus subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of C. fetus subspecies.
Antibiotic-induced dysbiosis in the SCIME™ recapitulates microbial community diversity and metabolites modulation of in vivo disease
Authors: Dalle Vedove Elena , Benvenga Alessia , Nicolai Gianluca , Massimini Marcella , Giordano Maria Veronica , Di Pierro Francesco , Bachetti Benedetta 
Published: September 2024

Establishing the contextIntestinal dysbiosis is a significant concern among dog owners, and the gut health of pets is an emerging research field. In this context, the Simulator of the Canine Intestinal Microbial Ecosystem (SCIME™) was recently developed and validated with in vivo data.Stating the purpose/introducing the studyThe current study presents a further application of this model by using amoxicillin and clavulanic acid to induce dysbiosis, aiming to provoke changes in microbial community and metabolite production, which are well-known markers of the disease in vivo.Describing methodologyFollowing the induction of dysbiosis, prebiotic supplementation was tested to investigate the potential for microbiota recovery under different dietary conditions.Presenting the resultsThe results showed that antibiotic stimulation in the SCIME™ model can produce significant changes in microbial communities and metabolic activity, including a decrease in microbial richness, a reduction in propionic acid production, and alterations in microbial composition. Additionally, changes in ammonium and butyric acid levels induced by the tested diets were observed.Discussing the findingsThis alteration in microbial community and metabolites production mimicks in vivo canine dysbiosis patterns. A novel dynamic in vitro model simulating canine antibiotic-induced dysbiosis, capable of reproducing microbial and metabolic changes observed in vivo, has been developed and is suitable for testing the effects of nutritional changes.
Systematic review of photobiomodulation for multiple sclerosis
Authors: Oliveira de Andrade Filho Vander , Amarante Marina Oliveira Coura , Gonzalez-Lima Francisco , Gomes da Silva Sérgio , Cardoso Fabrízio dos Santos 
Published: September 2024

BackgroundMultiple sclerosis (MS) is an inflammatory chronic autoimmune and neurodegenerative disorder of the brain and spinal cord, resulting in loss of motor, sensorial, and cognitive function. Among the non-pharmacological interventions for several brain conditions, photobiomodulation (PBM) has gained attention in medical society for its neuroprotective effects. We systematically reviewed the effects of PBM on MS.MethodsWe conducted a systematic search on the bibliographic databases (PubMed and ScienceDirect) with the keywords based on MeSH terms: PBM, low-level laser therapy, multiple sclerosis, autoimmune encephalomyelitis, demyelination, and progressive multiple sclerosis. Data search was limited from 2012 to July 2024. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The initial systematic search identified 126 articles. Of these, 68 articles were removed by duplicity and 50 by screening. Thus, 8 studies satisfied the inclusion criteria.ResultsThe reviewed studies showed that PBM modulates brain markers linked to inflammation, oxidative stress, and apoptosis. Improvements in motor, sensorial, and cognitive functions in MS patients were also observed after PBM therapy. No study reported adverse effects of PBM.ConclusionThese findings suggest the potential of PBM as a promising non-pharmacological intervention for the management of MS, although further research is needed to standardize PBM protocols and assess its long-term effects.
Status quo and influencing factors of readiness for hospital discharge in patients with brain tumours after surgery
Authors: Qin Yue-Hong , Shi Xiao-Mei 
Published: September 2024

ObjectiveThis study aimed to investigate the status quo of readiness for hospital discharge in patients with brain tumours after surgery and to analyse its influencing factors.MethodA total of 300 patients with brain tumours who were admitted to the neurosurgery ward of our hospital between September 2020 and December 2022 were selected as the study participants using the convenient sampling method. The readiness for hospital discharge in patients with brain tumours after surgery was investigated using a general information questionnaire, the Readiness for Hospital Discharge Scale (RHDS), the Quality of Discharge Teaching Scale (QDTS), the University of Washington Quality of Life Questionnaire (UW-QOL), and the Social Support Rating Scale (SSRS), and its influencing factors were analysed.ResultsThe total RHDS score of patients with brain tumours was (155.02 ± 14.67), which was at a medium level. There was a positive correlation between readiness for hospital discharge in patients with brain tumours after surgery and the UW-QOL score (r = 0.459, p = 0.001), SSRS score (r = 0.322, p = 0.000), and QDTS score (r = 0.407, p = 0.001). The influencing factors of readiness for hospital discharge in patients with brain tumours included the content actually obtained by patients (health guidance) before discharge (p = 0.001), discharge teaching skills (p = 0.001), age (p = 0.006), swallowing status (p = 0.021), education level (p = 0.016), and objective support (p = 0.022).ConclusionThe readiness for hospital discharge in patients with brain tumours is at a medium level. Medical staff should give inpatients more targeted knowledge and implement personalised health education according to the patient’s age, education level, swallowing status, and objective support to improve the patient’s readiness for hospital discharge.
2-methoxyestradiol inhibits the malignant behavior of triple negative breast cancer cells by altering their miRNome
Authors: Subramani Ramadevi , Chatterjee Animesh , Pedroza Diego A. , Poudel Seeta , Rajkumar Preetha , Annabi Jeffrey , Penner Elizabeth , Lakshmanaswamy Rajkumar 
Published: September 2024

BackgroundTriple-negative breast cancer (TNBC) is a subtype of breast cancer with no effective targeted treatment currently available. Estrogen and its metabolites influence the growth of mammary cancer. Previously, we demonstrated the anti-cancer effects of 2-methoxyestradiol (2ME2) on mammary carcinogenesis.Materials and methodsIn the present study, we investigated the effects of 2ME2 on TNBC cells. TNBC (MDA-MB-231 and MDA-MB-468) and non-tumorigenic breast (MCF10A) cell lines were used to determine the effects of 2ME2 on cell proliferation (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium; MTS assay), cell cycle (flow cytometric assay), migration (transwell migration assay), invasion (matrigel invasion assay), apoptosis (annexin V/propidium iodide assay), colony formation (soft agar assay), and miRNome (human miRNA profiling array). The miRNome data were analyzed using the c-BioPortal and Xena platforms. Moreover, Kyoto Encyclopedia of Genes and Genomes, Gene Ontology, and reactome pathway analyses were performed.ResultsWe found that 2ME2 effectively inhibited cell proliferation and induced apoptosis. Furthermore, 2ME2 treatment arrested TNBC cells in the S-phase of the cell cycle. Treatment with 2ME2 also significantly decreased the aggressiveness of TNBC cells by inhibiting their migration and invasion. In addition, 2ME2 altered the miRNA expression in these cells. In silico analysis of the miRNome profile of 2ME2-treated MDA-MB-468 cells revealed that miRNAs altered the target genes involved in many different cancer hallmarks.Conclusion2ME2 inhibits triple negative breast cancer by impacting major cellular processes like proliferation, apoptosis, metastasis, etc. It further modifies gene expression by altering the miRNome of triple negative breast cancer cells. Overall, our findings suggest 2ME2 as a potent anti-cancer drug for the treatment of TNBC.
Effect of prehabilitation exercises on postoperative frailty in patients undergoing laparoscopic colorectal cancer surgery
Authors: Yang Fuyu , Yuan Ye , Liu Wenwen , Tang Chenglin , He Fan , Chen Defei , Xiong Junjie , Huang Guoquan , Qian Kun 
Published: September 2024

BackgroundTo improve perioperative frailty status in patients undergoing laparoscopic colorectal cancer surgery (LCCS), we explored a new intensive prehabilitation program that combines prehabilitation exercises with standard enhanced recovery after surgery (ERAS) and explored its impact.MethodsWe conducted a prospective randomized controlled trial. Between April 2021 to August 2021, patients undergoing elective LCCS were randomized into the standardized ERAS (S-ERAS) group or ERAS based on prehabilitation (group PR-ERAS). Patients in the PR-ERAS group undergoing prehabilitation exercises in the perioperative period in addition to standard enhanced recovery after surgery. We explored the effects of this prehabilitation protocol on frailty, short-term quality of recovery (QoR), psychological status, postoperative functional capacity, postoperative outcomes, and pain.ResultsIn total, 125 patients were evaluated, and 95 eligible patients were enrolled and randomly allocated to the S-ERAS (n = 45) and PR-ERAS (n = 50) groups. The Fried score was higher in the PR-ERAS group on postoperative day (7 (2(2,3) vs. 3(2,4), P = 0.012). The QoR-9 was higher in the PR-ERAS group than in the S-ERAS group on the 1st, 2nd, 3rd, and 7th postoperative days. The PR-ERAS group had an earlier time to first ambulation (P &lt; 0.050) and time to first flatus (P &lt; 0.050).ConclusionPrehabilitation exercises can improve postoperative frailty and accelerate recovery in patients undergoing LCCS but may not improve surgical safety. Therefore, better and more targeted prehabilitation recovery protocols should be explored.Clinical trial registrationwww.clinicaltrials.org, identifier NCT04964856.
Clinicopathological features, treatment patterns, and survival outcomes among Syrian patients with advanced breast cancer
Authors: Muhammad Muhammad , Alali Mousa , Saifo Maher 
Published: September 2024

BackgroundAdvanced breast cancer (ABC) is a heterogeneous disease with varied prognoses, that is affected by many clinicopathological features. This study aimed to investigate the clinicopathological characteristics, first-line treatment (FLx), and prognostic impact of these features on survival among Syrian patients with ABC.Materials and methodsThis retrospective cohort study included patients with ABC. The association of clinicopathological factors with survival was assessed using Kaplan-Meier curves and the log-rank test, as well as the Cox proportional hazards regression model to calculate the hazard ratio (HaR).ResultsA total of 423 patients with ABC were included in the study, with a median age (range) of 47 years (23-82). 83% of metastases were metachronous. Most patients (91.8%) received chemotherapy as the FLx. The median progression-free survival (PFS) and overall survival (OS) of all the patients were 7 and 16 months, respectively. The median PFS was associated with four factors, which were time of metastasis (adjusted HaR=1.861, 95% CI 1.420-2.438, P&lt;0.0001), performance status (PS) (adjusted HaR=1.456, 95% CI 1.049-2.021, P=0.025), ovarian metastasis (adjusted HaR=7.907, 95% CI 1.049-59.576, P=0.045), and FLx (adjusted HaR=2.536, 95% CI 1.581-4.068, P&lt;0.0001). Similarly, the OS was associated with three factors, including hormone receptors (HRs) status (adjusted HaR=1.124, 95% CI 1.009-1.252, P=0.034), time of metastasis (adjusted HaR=2.099, 95% CI 1.588-2.775, P&lt;0.0001), and PS (adjusted HaR=1.787, 95% CI 1.429-2.233, P&lt;0.0001). In the HR-positive/human epidermal growth receptor 2 (HER2)-negative group, endocrine therapy was significantly associated with longer PFS compared with chemotherapy (15 vs 7 months, adjusted HaR=2.699, 95% CI 1.417-5.143, P=0.003). Furthermore, there was no difference in OS between the two treatment modalities (P=0.855).ConclusionsABC survival varies depending on the location of metastases. Good PS and synchronous stage 4 disease were independent prognostic factors for longer PFS and OS. In the HR-positive/HER2-negative group, PFS for endocrine therapy was significantly longer than chemotherapy, with no differences in OS. This study confirms that endocrine therapy is preferred as an FLx for ABC in the HR-positive/HER2-negative group.
Digital Spatial Profiling identifies distinct patterns of immuno-oncology-related gene expression within oropharyngeal tumours in relation to HPV and p16 status
Authors: Brooks Jill M. , Zheng Yuanning , Hunter Kelly , Willcox Benjamin E. , Dunn Janet , Nankivell Paul , Gevaert Olivier , Mehanna Hisham 
Published: September 2024

BackgroundThe incidence of oropharyngeal cancer (OPC) is increasing, due mainly to a rise in Human Papilloma Virus (HPV)-mediated disease. HPV-mediated OPC has significantly better prognosis compared with HPV-negative OPC, stimulating interest in treatment de-intensification approaches to reduce long-term sequelae. Routine clinical testing frequently utilises immunohistochemistry to detect upregulation of p16 as a surrogate marker of HPV-mediation. However, this does not detect discordant p16-/HPV+ cases and incorrectly assigns p16+/HPV- cases, which, given their inferior prognosis compared to p16+/HPV+, may have important clinical implications. The biology underlying poorer prognosis of p16/HPV discordant OPC requires exploration.MethodsGeoMx digital spatial profiling was used to compare the expression patterns of selected immuno-oncology-related genes/gene families (n=73) within the tumour and stromal compartments of formalin-fixed, paraffin-embedded OPC tumour tissues (n=12) representing the three subgroups, p16+/HPV+, p16+/HPV- and p16-/HPV-.ResultsKeratin (multi KRT) and HIF1A, a key regulator of hypoxia adaptation, were upregulated in both p16+/HPV- and p16-/HPV- tumours relative to p16+/HPV+. Several genes associated with tumour cell proliferation and survival (CCND1, AKT1 and CD44) were more highly expressed in p16-/HPV- tumours relative to p16+/HPV+. Conversely, multiple genes with potential roles in anti-tumour immune responses (immune cell recruitment/trafficking, antigen processing and presentation), such as CXCL9, CXCL10, ITGB2, PSMB10, CD74, HLA-DRB and B2M, were more highly expressed in the tumour and stromal compartments of p16+/HPV+ OPC versus p16-/HPV- and p16+/HPV-. CXCL9 was the only gene showing significant differential expression between p16+/HPV- and p16-/HPV- tumours being upregulated within the stromal compartment of the former.ConclusionsIn terms of immune-oncology-related gene expression, discordant p16+/HPV- OPCs are much more closely aligned with p16-/HPV-OPCs and quite distinct from p16+/HPV+ tumours. This is consistent with previously described prognostic patterns (p16+/HPV+ &gt;&gt; p16+/HPV- &gt; p16-/HPV-) and underlines the need for dual p16 and HPV testing to guide clinical decision making.
Case report: Epilepsy during the use of recombinant human growth hormone: a report on two cases and a literature review
Authors: Zhou Yuan , Jia Ruofan , Xu Zhuangjian , Ma Yaping 
Published: September 2024

BackgroundEpilepsy during recombinant human growth hormone (rhGH) therapy is rare in children. The potential association between rhGH treatment and epilepsy remains unclear.MethodsWe retrospectively analyzed the clinical data of two Chinese boys who experienced epilepsy during the use of rhGH and reviewed the relevant literature.Results:Case 1, an 8-year and 2-month-old boy, was diagnosed with short stature, malnutrition, and congenital hypothyroidism. He was on levothyroxine sodium tablets for a long time. Recurrent febrile convulsions were present at 6–7 years. Electroencephalogram and magnetic resonance imaging (MRI) showed no abnormality, and no treatment was given. He was diagnosed with complex febrile convulsions. The boy started rhGH treatment (approximately 0.15 IU/kg/day, sc, qd) at 8 years and 4 months. Epilepsy occurred three times during the 6 months of rhGH treatment. Electroencephalography confirmed a definitive diagnosis of epilepsy. Then, he discontinued rhGH treatment at 8 years and 11 months and started taking levetiracetam (0.25 g, po, bid) for antiepileptic therapy. Epilepsy was well-controlled 4 months later. He continued rhGH treatment at 10 years and 3 months and has been on rhGH treatment until now, with no recurrence of epilepsy. He has been taking levetiracetam to date. Case 2, a 9-year and 1-month-old boy, was diagnosed with central precocious puberty, predicted short final height, and overweight. He started treatment with triptorelin (3.75 mg, im, q4w) and rhGH (approximately 0.15 IU/kg/day, sc, qd) at 9 years and 3 months. He tended to fall repeatedly when he was approximately 10 years old. Electroencephalography showed a few medium- to high-amplitude sharp waves and sporadic sharp slow waves in the left middle temporal region, sometimes involving the left posterior temporal region. He was diagnosed with epilepsy. Triptorelin discontinuance provided no symptom relief, which worsened further. Subsequently, he withdrew from rhGH treatment, and the symptoms occurred occasionally within a week and stopped after 15 days. The electroencephalogram returned to normal. No further seizures occurred during follow-up to date.ConclusionDuring the use of rhGH in short-stature children with complex febrile convulsions or underlying lesions related to neurological impairment or those being treated with antiepileptic drugs, epilepsy may be induced.