bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and biological heterogeneities in triple-negative breast cancer reveals a non-negligible role of HER2-low
Authors: Hu Xi′e , Yang Ping , Chen Songhao , Wei Gang , Yuan Lijuan , Yang Zhenyu , Gong Li , He Li , Yang Lin , Peng Shujia , Dong Yanming , He Xianli , Bao Guoqiang 
Published: March 2023

Abstract
Background
HER2-low could be found in some patients with triple-negative breast cancer (TNBC). However, its potential impacts on clinical features and tumor biological characteristics in TNBC remain unclear.

Methods
We enrolled 251 consecutive TNBC patients retrospectively, including 157 HER2-low (HER2low) and 94 HER2-negtive (HER2neg) patients to investigate the clinical and prognostic features. Then, we performed single-cell RNA sequencing (scRNA-seq) with another seven TNBC samples (HER2negvs. HER2low, 4 vs. 3) prospectively to further explore the differences of tumor biological properties between the two TNBC phenotypes. The underlying molecular distinctions were also explored and then verified in the additional TNBC samples.

Results
Compared with HER2neg TNBC, HER2low TNBC patients exhibited malignant clinical features with larger tumor size (P = 0.04), more lymph nodes involvement (P = 0.02), higher histological grade of lesions (P < 0.001), higher Ki67 status (P < 0.01), and a worse prognosis (P < 0.001; HR [CI 95%] = 3.44 [2.10–5.62]). Cox proportional hazards analysis showed that neoadjuvant systemic therapy, lymph nodes involvement and Ki67 levels were prognostic factors in HER2low TNBC but not in HER2neg TNBC patients. ScRNA-seq revealed that HER2low TNBC which showed more metabolically active and aggressive hallmarks, while HER2neg TNBC exhibited signatures more involved in immune activities with higher expressions of immunoglobulin-related genes (IGHG1, IGHG4, IGKC, IGLC2); this was further confirmed by immunofluorescence in clinical TNBC samples. Furthermore, HER2low and HER2neg TNBC exhibited distinct tumor evolutionary characteristics. Moreover, HER2neg TNBC revealed a potentially more active immune microenvironment than HER2low TNBC, as evidenced by positively active regulation of macrophage polarization, abundant CD8+ effector T cells, enriched diversity of T-cell receptors and higher levels of immunotherapy-targeted markers, which contributed to achieve immunotherapeutic response.

Conclusions
This study suggests that HER2low TNBC patients harbor more malignant clinical behavior and aggressive tumor biological properties than the HER2neg phenotype. The heterogeneity of HER2 may be a non-negligible factor in the clinical management of TNBC patients. Our data provide new insights into the development of a more refined classification and tailored therapeutic strategies for TNBC patients.
Microbiome differences in sugarcane and metabolically engineered oilcane accessions and their implications for bioenergy production
Authors: Yang Jihoon , Sooksa-nguan Thanwalee , Kannan Baskaran , Cano-Alfanar Sofia , Liu Hui , Kent Angela , Shanklin John , Altpeter Fredy , Howe Adina 
Published: March 2023

AbstractOilcane is a metabolically engineered sugarcane (Saccharum spp. hybrid) that hyper-accumulates lipids in its vegetable biomass to provide an advanced feedstock for biodiesel production. The potential impact of hyper-accumulation of lipids in vegetable biomass on microbiomes and the consequences of altered microbiomes on plant growth and lipid accumulation have not been explored so far. Here, we explore differences in the microbiome structure of different oilcane accessions and non-modified sugarcane. 16S SSU rRNA and ITS rRNA amplicon sequencing were performed to compare the characteristics of the microbiome structure from different plant compartments (leaf, stem, root, rhizosphere, and bulk soil) of four greenhouse-grown oilcane accessions and non-modified sugarcane. Significant differences were only observed in the bacterial microbiomes. In leaf and stem microbiomes, more than 90% of the entire microbiome of non-modified sugarcane and oilcane was dominated by similar core taxa. Taxa associated with Proteobacteria led to differences in the non-modified sugarcane and oilcane microbiome structure. While differences were observed between multiple accessions, accession 1566 was notable in that it was consistently observed to differ in its microbial membership than other accessions and had the lowest abundance of taxa associated with plant-growth-promoting bacteria. Accession 1566 is also unique among oilcane accessions in that it has the highest constitutive expression of the WRI1 transgene. The WRI1 transcription factor is known to contribute to significant changes in the global gene expression profile, impacting plant fatty acid biosynthesis and photomorphogenesis. This study reveals for the first time that genetically modified oilcanes associate with distinct microbiomes. Our findings suggest potential relationships between core taxa, biomass yield, and TAG in oilcane accessions and support further research on the relationship between plant genotypes and their microbiomes.
Global prevalence and species diversity of tick-borne pathogens in buffaloes worldwide: a systematic review and meta-analysis
Authors: El-Alfy El-Sayed , Abbas Ibrahim , Elseadawy Rana , Saleh Somaya , Elmishmishy Bassem , El-Sayed Shimaa Abd El-Salam , Rizk Mohamed Abdo 
Published: March 2023

Abstract
Background
Buffaloes are important contributors to the livestock economy in many countries, particularly in Asia, and tick-borne pathogens (TBPs) commonly infect buffaloes, giving rise to serious pathologies other than their zoonotic potential.

Methods
The present investigation focuses on the prevalence of TBPs infecting buffaloes worldwide. All published global data on TBPs in buffaloes were collected from different databases (e.g., PubMed, Scopus, ScienceDirect, and Google Scholar) and subjected to various meta-analyses using OpenMeta[Analyst] software, and all analyses were conducted based on a 95% confidence interval.

Results
Over 100 articles discussing the prevalence and species diversity of TBPs in buffaloes were retrieved. Most of these reports focused on water buffaloes (Bubalus bubalis), whereas a few reports on TBPs in African buffaloes (Syncerus caffer) had been published. The pooled global prevalence of the apicomplexan parasites Babesia and Theileria, as well as the bacterial pathogens Anaplasma, Coxiella burnetii, Borrelia, Bartonella, and Ehrlichia in addition to Crimean-Congo hemorrhagic fever virus, were all evaluated based on the detection methods and 95% confidence intervals. Interestingly, no Rickettsia spp. were detected in buffaloes with scarce data. TBPs of buffaloes displayed a fairly high species diversity, which underlines the high infection risk to other animals, especially cattle. Babesia bovis, B. bigemina, B. orientalis, B. occultans and B. naoakii, Theileria annulata, T. orientalis complex (orientalis/sergenti/buffeli), T. parva, T. mutans, T. sinensis, T. velifera, T. lestoquardi-like, T. taurotragi, T. sp. (buffalo) and T. ovis, and Anaplasma marginale, A. centrale, A. platys, A. platys-like and “Candidatus Anaplasma boleense” were all were identified from naturally infected buffaloes.

Conclusions
Several important aspects were highlighted for the status of TBPs, which have serious economic implications for the buffalo as well as cattle industries, particularly in Asian and African countries, which should aid in the development and implementation of prevention and control methods for veterinary care practitioners, and animal owners.

Graphical Abstract
Pay more for me, I’m from the mountains! The role of the EU Mountain Product term and other credence attributes in consumers’ valuation of lamb meat
Authors: Cei Leonardo , Defrancesco Edi , Gatto Paola , Pagliacci Francesco 
Published: March 2023

AbstractOn-farm product differentiation represents a valuable opportunity for mountain agriculture. Consumers appreciate mountain products’ characteristics, but when signalling instruments are lacking, consumers might not be able to recognize (and pay for) them. Through a choice experiment, this paper considers consumers’ willingness to pay for three attributes (mountain origin through the EU Mountain Product term; local endangered landrace; agroecosystems stewardship through rotational grazing). It considers lamb meat production and North-Eastern Italian consumers, also exploring attitudes towards food and differences across groups of consumers. The highest willingness to pay is associated with the EU Mountain Product term, but communication strategies and public information provision are needed to enhance consumers’ overall knowledge.
Gut commensal Enterocloster species host inoviruses that are secreted in vitro and in vivo
Authors: Burckhardt Juan C. , Chong Derrick H. Y. , Pett Nicola , Tropini Carolina 
Published: March 2023

Abstract
Background
Bacteriophages in the family Inoviridae, or inoviruses, are under-characterized phages previously implicated in bacterial pathogenesis by contributing to biofilm formation, immune evasion, and toxin secretion. Unlike most bacteriophages, inoviruses do not lyse their host cells to release new progeny virions; rather, they encode a secretion system that actively pumps them out of the bacterial cell. To date, no inovirus associated with the human gut microbiome has been isolated or characterized.

Results
In this study, we utilized in silico, in vitro, and in vivo methods to detect inoviruses in bacterial members of the gut microbiota. By screening a representative genome library of gut commensals, we detected inovirus prophages in Enterocloster spp. (formerly Clostridium spp.). We confirmed the secretion of inovirus particles in in vitro cultures of these organisms using imaging and qPCR. To assess how the gut abiotic environment, bacterial physiology, and inovirus secretion may be linked, we deployed a tripartite in vitro assay that progressively evaluated bacterial growth dynamics, biofilm formation, and inovirus secretion in the presence of changing osmotic environments. Counter to other inovirus-producing bacteria, inovirus production was not correlated with biofilm formation in Enterocloster spp. Instead, the Enterocloster strains had heterogeneous responses to changing osmolality levels relevant to gut physiology. Notably, increasing osmolality induced inovirus secretion in a strain-dependent manner. We confirmed inovirus secretion in a gnotobiotic mouse model inoculated with individual Enterocloster strains in vivo in unperturbed conditions. Furthermore, consistent with our in vitro observations, inovirus secretion was regulated by a changed osmotic environment in the gut due to osmotic laxatives.

Conclusion
In this study, we report on the detection and characterization of novel inoviruses from gut commensals in the Enterocloster genus. Together, our results demonstrate that human gut-associated bacteria can secrete inoviruses and begin to elucidate the environmental niche filled by inoviruses in commensal bacteria.
In silico prioritisation of microRNA-associated common variants in multiple sclerosis
Authors: Fashina Ifeolutembi A. , McCoy Claire E. , Furney Simon J. 
Published: March 2023

Abstract
Background
Genome-wide association studies (GWAS) have highlighted over 200 autosomal variants associated with multiple sclerosis (MS). However, variants in non-coding regions such as those encoding microRNAs have not been explored thoroughly, despite strong evidence of microRNA dysregulation in MS patients and model organisms. This study explores the effect of microRNA-associated variants in MS, through the largest publicly available GWAS, which involved 47,429 MS cases and 68,374 controls.

Methods
We identified SNPs within the coordinates of microRNAs, ± 5-kb microRNA flanking regions and predicted 3′UTR target-binding sites using miRBase v22, TargetScan 7.0 RNA22 v2.0 and dbSNP v151. We established the subset of microRNA-associated SNPs which were tested in the summary statistics of the largest MS GWAS by intersecting these datasets. Next, we prioritised those microRNA-associated SNPs which are among known MS susceptibility SNPs, are in strong linkage disequilibrium with the former or meet a microRNA-specific Bonferroni-corrected threshold. Finally, we predicted the effects of those prioritised SNPs on their microRNAs and 3′UTR target-binding sites using TargetScan v7.0, miRVaS and ADmiRE.

Results
We have identified 30 candidate microRNA-associated variants which meet at least one of our prioritisation criteria. Among these, we highlighted one microRNA variant rs1414273 (MIR548AC) and four 3′UTR microRNA-binding site variants within SLC2A4RG (rs6742), CD27 (rs1059501), MMEL1 (rs881640) and BCL2L13 (rs2587100). We determined changes to the predicted microRNA stability and binding site recognition of these microRNA and target sites.

Conclusions
We have systematically examined the functional, structural and regulatory effects of candidate MS variants among microRNAs and 3′UTR targets. This analysis allowed us to identify candidate microRNA-associated MS SNPs and highlights the value of prioritising non-coding RNA variation in GWAS. These candidate SNPs could influence microRNA regulation in MS patients. Our study is the first thorough investigation of both microRNA and 3′UTR target-binding site variation in multiple sclerosis using GWAS summary statistics.
Collateral consequences of COVID-19 for people on probation and parole
Authors: LeMasters Katherine , Benson Angela , Corsi Christopher , Krajewski Taylor , Seide Kapriskie , Brinkley-Rubinstein Lauren , Nowotny Kathryn 
Published: March 2023

Abstract
Background
While the severe detrimental impact of COVID-19 on incarcerated people is well known, little is known about the experience of COVID-19 on those on community supervision. Our objective was to better understand the experience of the COVID-19 pandemic and its collateral consequences for those on community supervision (e.g., probation, parole). Beginning in December 2020, we conducted 185 phone surveys about COVID-19 with participants in The Southern Pre-Exposure Prophylaxis (PrEP) Study across its three sites - Florida, Kentucky, and North Carolina. We conducted rapid assessment interviews with both closed- and open-ended questions. We calculated descriptive statistics for close-ended questions and conducted a content analysis for open-ended questions.

Results
The COVID-19 pandemic affected those on community supervision through their experiences in the community and while incarcerated with over one-quarter of participants being reincarcerated during this time. In addition to many (128/185) experiencing COVID-19 symptoms, about half (85/185) of participants reported a diagnosis in their network with 16 of those participants losing loved ones to the pandemic. Participants experienced disruptions to their social network, healthcare, and livelihoods. Though many maintained their support systems, others felt isolated and depressed. Experiences during COVID-19 exacerbated difficulties already faced by those with criminal involvement.

Conclusions
The public health community must recognize those experiencing probation and parole, not only those housed in carceral facilities, as disproportionately impacted by the COVID-19 pandemic. We must tailor programs and services to meet their needs.
A biomechanical comparison between robotic and conventional total knee arthroplasty (TKA) in resection accuracy: a meta‐analysis on cadaveric specimens
Authors: Sequeira Sean B. , Duvall Grant T. , Boucher Henry 
Published: March 2023

AbstractPurposeRobotic total knee arthroplasty (TKA) has seen a rapid increase in utilization with recent literature suggesting that implant accuracy and resection are better optimized than in conventional TKA. The purpose of this study was to evaluate the biomechanical properties of robotic‐assisted versus conventional TKA in minimizing biplanar femoral and tibial resection error in cadaveric specimens.MethodsA systematic review and meta‐analysis was performed by searching through PubMed, Cochrane library, and Embase to identify studies that analyzed the biomechanical properties of robotic assisted and conventional TKA, according to standard PRISMA guidelines. Evaluated outcomes included femoral coronal resection error (deg), femoral sagittal resection error (deg), tibial coronal resection error (deg), and tibial sagittal resection error (deg).ResultsSeven studies met inclusion criteria, including a total of 140 cadaveric specimens (robotic: 70, conventional: 70), for resection accuracy between robotic and conventional TKA. Pooled analysis from seven studies revealed a significant difference in femoral coronal and sagittal resection error in favor of robotic systems compared to conventional systems (p < 0.001 & p < 0.001, respectively). The pooled analysis from seven studies revealed a significant difference in tibial sagittal resection error in favor of robotic systems compared to conventional systems following TKA (p = 0.012). Posthoc power analysis revealed a power of 87.2%.ConclusionThe use of robotic TKA is associated with lower femoral coronal, lower femoral sagittal and tibial sagittal resection error compared to conventional TKA. It should be noted that these findings are purely biomechanical – surgeons should interpret these findings along with clinical differences between conventional and robotic systems to determine which system is best for each patient.
Successful conversion surgery following chemotherapy with an immune checkpoint inhibitor in an older adult patient with stage IVB esophageal squamous cell carcinoma: a case report
Authors: Kawazoe Tetsuro , Ito Shuhei , Ohgaki Kippei , Fujinaka Yoshihiko , Funakoshi Hiroki , Otake Akihiko , Wang Huanlin , Morita Kazutoyo , Fushimi Fumiyoshi , Ikeda Yoichi 
Published: March 2023

Abstract
Background
Chemotherapy and chemoradiotherapy are common treatments for esophageal squamous cell carcinoma with distant metastasis; however, the prognosis remains poor, and complete remission is difficult to achieve. Here, we report a case of an older adult patient with esophageal squamous cell carcinoma who underwent surgery following combined treatment of immunotherapy and chemotherapy and achieved pathological complete response.

Case presentation
An 80-year-old woman presenting with difficulty swallowing was referred to our hospital. She was diagnosed with esophageal squamous cell carcinoma with distant metastasis of the lymph node at the dorsal side of the IVC and the left supraclavicular lymph node. She was treated with pembrolizumab, cisplatin, and 5-fluorouracil. After four pharmacotherapy courses, primary tumor and metastatic lymph node shrinkage was observed. The patient underwent thoracoscopic subtotal esophagectomy and regional lymph node dissection. The lymph node at the dorsal side of the IVC was not resected, and the left supraclavicular lymph node was removed. Histological examination revealed complete response with no residual tumor or lymph node metastasis. The patient had no recurrence 10 months postoperatively without adjuvant chemotherapy.

Conclusions
Conversion surgery following preoperative therapy, including immunotherapy, may be an effective treatment strategy for improving survival in patients with esophageal squamous cell carcinoma even among older adult patients.
Culturally adapted family intervention for people with schizophrenia in Indonesia (FUSION): a development and feasibility study protocol
Authors: Renwick Laoise , Susanti Herni , Brooks Helen , Keliat Budi-anna , Bradshaw Tim , Bee Penny , Lovell Karina 
Published: March 2023

Abstract
Background
Mental illnesses comprise the single largest source of health-related economic burden globally, and low- and middle-income countries are disproportionately affected. The majority of people with schizophrenia who need treatment do not receive it and are often wholly reliant on family caregivers for daily care and support. Family interventions have an exceptionally robust evidence base for their efficacy in high-resource settings, but it is unknown whether they can produce equivalent effects in some low-resource settings where cultural beliefs, explanatory models of illness and contextual socio-economic issues differ.

Methods
This protocol describes the methods for a randomised controlled trial to determine the feasibility of testing culturally adapt and refine an evidence-based, family intervention for relatives and caregivers of people with schizophrenia in Indonesia. The feasibility and acceptability of implementing our adapted, co-produced intervention via task shifting in primary care settings will be evaluated using the Medical Research Council framework for complex interventions. We will recruit 60 carer-service-user dyads and randomise them in a 1:1 ratio either to receive our manualised intervention or continue to receive treatment as usual. Healthcare workers in primary care settings will be trained to deliver family interventions using our manualised intervention by a family intervention specialist. Participants will complete the ECI, IEQ, KAST and GHQ. Service-user symptom level and relapse status will be measured using the PANSS at baseline, post-intervention and 3 months later by trained researchers. Fidelity to the intervention model will be measured using the FIPAS. Qualitative evaluation will further assist with refining the intervention, evaluating trial processes and evaluating acceptability.

Discussion
National healthcare policy in Indonesia supports the delivery of mental health services in a complex network of primary care centres. This study will provide important information on the feasibility of delivering family interventions for people with schizophrenia via task shifting in primary care settings in Indonesia and allow further refinement of the intervention and trial processes.
Investigation of the effects of physical activity level on functionality level and quality of life in the postpartum period
Authors: Bulguroglu Halil I. , Bulguroglu Merve , Gevrek P. T. Cansu 
Published: March 2023

Abstract
Background
Physical activity, known to have positive effects in every period of life, may decrease due to anatomical and physiological changes and increased responsibilities in the postpartum period. This study aimed to understand how women's physical activity levels, functional levels, and quality of life are affected in the postpartum period and to emphasize the importance of physical activity levels in the postpartum period.

Methods
The population of our study was planned as a cross-sectional study of postpartum women who applied to a private center. The sample consists of 101 volunteer postpartum women participating in the study. Physical activity levels; with the International Physical Activity Questionnaire (IPAQ), postpartum functional levels; with the Inventory of Functional Status After Childbirth (IFSAC), postpartum quality of life level; with Maternal Postpartum Quality of Life (MAPP-QOL) were evaluated.

Results
It was determined that the amount of physical activity of postpartum women was 928.347 ± 281.27 MET-min/week, which means low physical activity level, and 35.64% were not physically active. The mean total score of IFSAC was 2.13 ± 0.79, and the mean total score of MAPP-QOL was 16.93 ± 6.87. It was determined that there was a positive and significant correlation (p < 0.05) between IPAQ and IFSAC (r = 0.034) and MAPP-QOL (r = 0.214). A significant difference was found when the IFSAC and MAPP-QOL scores were compared between the three groups with different physical activity levels (p < 0.05).

Conclusions
As a result, it was observed that the physical activity levels of women in the postpartum period were low, negatively affecting their functionality and quality of life.