bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic analysis revealed genetic divergence between Bifidobacterium catenulatum subspecies present in infant versus adult guts
Authors: Liu Jiaqi , Li Weicheng , Yao Caiqing , Yu Jie , Zhang Heping 
Published: June 2022

Abstract
Background
The two subspecies of Bifidobacterium catenulatum, B. catenulatum subsp. kashiwanohense and B. catenulatum subsp. catenulatum, are usually from the infant and adult gut, respectively. However, the genomic analysis of their functional difference and genetic divergence has been rare. Here, 16 B. catenulatum strains, including 2 newly sequenced strains, were analysed through comparative genomics.

Results
A phylogenetic tree based on 785 core genes indicated that the two subspecies of B. catenulatum were significantly separated. The comparison of genomic characteristics revealed that the two subspecies had significantly different genomic sizes (p < 0.05) but similar GC contents. The functional comparison revealed the most significant difference in genes of carbohydrate utilisation. Carbohydrate-active enzymes (CAZyme) present two clustering patterns in B. catenulatum. The B. catenulatum subsp. kashiwanohense specially including the glycoside hydrolases 95 (GH95) and carbohydrate-binding modules 51 (CBM51) families involved in the metabolism of human milk oligosaccharides (HMO) common in infants, also, the corresponding fucosylated HMO gene clusters were detected. Meanwhile, B. catenulatum subsp. catenulatum rich in GH3 may metabolise more plant-derived glycan in the adult intestine.

Conclusions
These findings provide genomic evidence of carbohydrate utilisation bias, which may be a key cause of the genetic divergence of two B. catenulatum subspecies.
Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat
Authors: Rabieyan Ehsan , Bihamta Mohammad Reza , Moghaddam Mohsen Esmaeilzadeh , Mohammadi Valiollah , Alipour Hadi 
Published: June 2022

Abstract
Background
Pre-harvest sprouting (PHS) refers to a phenomenon, in which the physiologically mature seeds are germinated on the spike before or during the harvesting practice owing to high humidity or prolonged period of rainfall. Pre-harvest sprouting (PHS) remarkably decreases seed quality and yield in wheat; hence it is imperative to uncover genomic regions responsible for PHS tolerance to be used in wheat breeding. A genome-wide association study (GWAS) was carried out using 298 bread wheat landraces and varieties from Iran to dissect the genomic regions of PHS tolerance in a well-irrigated environment. Three different approaches (RRBLUP, GBLUP and BRR) were followed to estimate prediction accuracies in wheat genomic selection.

Results
Genomes B, A, and D harbored the largest number of significant marker pairs (MPs) in both landraces (427,017, 328,006, 92,702 MPs) and varieties (370,359, 266,708, 63,924 MPs), respectively. However, the LD levels were found the opposite, i.e., genomes D, A, and B have the highest LD, respectively. Association mapping by using GLM and MLM models resulted in 572 and 598 marker-trait associations (MTAs) for imputed SNPs (− log10 P > 3), respectively. Gene ontology exhibited that the pleitropic MPs located on 1A control seed color, α-Amy activity, and PHS. RRBLUP model indicated genetic effects better than GBLUP and BRR, offering a favorable tool for wheat genomic selection.

Conclusions
Gene ontology exhibited that the pleitropic MPs located on 1A can control seed color, α-Amy activity, and PHS. The verified markers in the current work can provide an opportunity to clone the underlying QTLs/genes, fine mapping, and genome-assisted selection.Our observations uncovered key MTAs related to seed color, α-Amy activity, and PHS that can be exploited in the genome-mediated development of novel varieties in wheat.
Management practice and treatment outcomes of adult patients with Lupus Nephritis at the Renal Clinic of St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
Authors: Hailu Gebre-Mariam Tsegay , Hussen Shemsu Umer , Getachew Seifemichael , Berha Alemseged Beyene 
Published: June 2022

Abstract
Background
Lupus nephritis (LN) is the most common severe complication of systemic lupus erythematosus (SLE) which results in high morbidity and mortality. Up to 60% of adult patients with SLE develop the renal disease with different severity. Even with potent anti-inflammatory and immunosuppressive therapies, many LN patients still progress to chronic kidney disease or end-stage renal disease. Thus, this study aimed to assess the management practice, treatment outcomes and to identify the associated factors of poor renal outcome in adult LN patients at the renal clinic of St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia.

Methods
A retrospective cross-sectional study design was used to collect the data using an abstraction tool from patients’ records. The Kidney Disease Improving Global Outcomes (KDIGO) criteria were used to diagnose LN among SLE patients. Logistic regression was used to determine crude and adjusted odds ratio and a p-value of < 0.05 was considered statistically significant. Ethical approval was obtained from the ethical review committee of the School of Pharmacy, Addis Ababa University and institutional review board of St. Paul’s Hospital Millennium Medical College.

Results
Out of 168 study participants enrolled from September 1, 2016 to October 30, 2020, a total of 114 adult LN patients were included for final analysis. The mean (± SD) age of the LN patients at onset was 29.10 ± 9.67 years and 99 (86.8%) of all the patients were females. More than three-fourths (78.9%) of the LN patients had a good prognosis. However, 24 (21.1%) of the patients who didn’t achieve complete or partial remission had a poor prognosis. A kidney biopsy was done for 71 patients at initial presentation with class IV and III as the commonest class. The commonly prescribed immunosuppressive medications were cyclophosphamide as induction therapy in 67 (58.7%) and mycophenolate mofetil (MMF) as maintenance therapy in 76 (66.7%). Gastrointestinal intolerances like abdominal pain, nausea, or diarrhea from MMF were the most common 27(31.2%) treatment-related adverse events reported. Acute kidney injury (AKI) at onset (AOR = 4.83, P = 0.026), high serum creatinine (SCr) at six months (AOR = 0.12, P = 0.003), no response at six months to attain complete remission (AOR = 0.05, P = 0.041) and presence of flare (AOR = 0.04, P = 0.004) were predictors poor treatment outcomes.

Conclusion
Despite good response with the present immunosuppressive regimens, relapse, treatment-related complications and adverse events are major problems that require close monitoring. The results and identified gaps of this study are used as an input to improve the management practice of LN in the study setting. Overall, this study is comparable with other findings and strengthen the present available literatures.
Intratumoral fibrosis and patterns of immune infiltration in clear cell renal cell carcinoma
Authors: Han Songchen , Yang Wenbo , Qin Caipeng , Du Yiqing , Ding Mengting , Yin Huaqi , Xu Tao 
Published: June 2022

AbstractBackgroundIntratumoral fibrosis was positively correlated with histological grade of renal clear cell carcinoma (ccRCC) and intratumoral inflammation. However, the association of intratumoral fibrosis with the immune infiltration of ccRCC was few evaluated.MethodsWe used the second harmonic generation (SHG)-based imaging technology and evaluated the intratumoral fibrosis in ccRCC, and then divided the patients into the high fibrosis group (HF) and the low fibrosis group (LF). Meanwhile, the Kaplan–Meier survival curve analysis was performed to analyze the relationship between intratumoral fibrosis and the disease-free survival rate. Antibody arrays were used for seeking difference in cytokines and immune infiltration between the HF group (N = 11) and LF group (N = 11). The selected immune infiltration marker was then verified by immunohistochemistry (IHC) staining in 45 ccRCC samples.ResultsOut of 640 cytokines and immune infiltration markers, we identified 115 proteins that were significantly different in quantity between ccRCC and adjacent normal tissues. In addition, the Venn diagram indicated that six proteins, including Cytotoxic T-Lymphocyte Associated Protein 4 (CTLA4), were significantly associated with intratumoral fibrosis (p < 0.05). The GO/KEGG enrichment analysis indicated that the proteins associated with intratumoral fibrosis were involved in the immunity and tumor-infiltrating lymphocytes. The expression of the CTLA4 was negatively correlated with collagen level, confirmed by IHC staining of CTLA4 (p < 0.05).ConclusionsThe study indicated that the intratumoral fibrosis level was negatively correlated with the expression of CTLA4 in the tumor immune microenvironment of the ccRCC, which posed the potential value of targeting the stroma of the tumor, a supplement to immunotherapy. However, the specific mechanism of this association is still unclear and needs further investigation.
Circulating tumour cell gene expression and chemosensitivity analyses: predictive accuracy for response to multidisciplinary treatment of patients with unresectable refractory recurrent rectal cancer or unresectable refractory colorectal cancer liver metastases
Authors: Guadagni Stefano , Masedu Francesco , Fiorentini Giammaria , Sarti Donatella , Fiorentini Caterina , Guadagni Veronica , Apostolou Panagiotis , Papasotiriou Ioannis , Parsonidis Panagiotis , Valenti Marco , Ricevuto Enrico , Bruera Gemma , Farina Antonietta R. , Mackay Andrew R. , Clementi Marco 
Published: June 2022

Abstract
Background
Patients with unresectable recurrent rectal cancer (RRC) or colorectal cancer (CRC) with liver metastases, refractory to at least two lines of traditional systemic therapy, may receive third line intraarterial chemotherapy (IC) and targeted therapy (TT) using drugs selected by chemosensitivity and tumor gene expression analyses of liquid biopsy-derived circulating tumor cells (CTCs).

Methods
In this retrospective study, 36 patients with refractory unresectable RRC or refractory unresectable CRC liver metastases were submitted for IC and TT with agents selected by precision oncotherapy chemosensitivity assays performed on liquid biopsy-derived CTCs, transiently cultured in vitro, and by tumor gene expression in the same CTC population, as a ratio to tumor gene expression in peripheral mononuclear blood cells (PMBCs) from the same individual. The endpoint was to evaluate the predictive accuracy of a specific liquid biopsy precision oncotherapy CTC purification and in vitro culture methodology for a positive RECIST 1.1 response to the therapy selected.

Results
Our analyses resulted in evaluations of 94.12% (95% CI 0.71–0.99) for sensitivity, 5.26% (95% CI 0.01–0.26) for specificity, a predictive value of 47.06% (95% CI 0.29–0.65) for a positive response, a predictive value of 50% (95% CI 0.01–0.98) for a negative response, with an overall calculated predictive accuracy of 47.22% (95% CI 0.30–0.64).

Conclusions
This is the first reported estimation of predictive accuracy derived from combining chemosensitivity and tumor gene expression analyses on liquid biopsy-derived CTCs, transiently cultured in vitro which, despite limitations, represents a baseline and benchmark which we envisage will be improve upon by methodological and technological advances and future clinical trials.
Spatial analysis of vaccine coverage on the first year of life in the northeast of Brazil
Authors: Cunha Nairmara Soares Pimentel , Fahrat Sylvia Costa Lima , de Olinda Ricardo Alves , Braga Alfésio Luís Ferreira , Barbieri Carolina Luisa Alves , de Aguiar Pontes Pamplona Ysabely , Martins Lourdes Conceição 
Published: June 2022

Abstract
Background
Over time, vaccination has been consolidated as one of the most cost effective and successful public health interventions and a right of every human being. This study aimed to assess the spatial dynamics of the vaccine coverage (VC) rate of children aged < 1 year per municipality in the Brazilian Northeast at 2016 and 2017.

Methods
This is a mixed-type ecological study that use a Public domain data Health Information. Vaccine doses were obtained from the Information System of the Brazilian National Immunization Program, and live births from the Brazilian Information System of Live Births of the Brazilian Unified Health System. Descriptive analysis of the coverage of all the vaccines for each year of the study was conducted, and Mann–Whitney U test was used to compare VC between the study years. Chi-squared test was used to evaluate the association between the years and VC, which was stratified into four ranges, very low, low, adequate, and high. Spatial distribution was analyzed according to both each study year and vaccine and presented as thematic maps. Spatial autocorrelation was analyzed using Moran’s Global and Local statistics.

Results
Compared with 2017, 2016 showed better VC (p < 0.05), except for Bacillus Calmette–Guérin. In the spatial analysis of the studied vaccines, the Global Moran’s Index did not show any spatial autocorrelation (p > 0.05), but the Local Moran’s Index showed some municipalities, particularly the Sertão Paraibano region, with high VC, high similarity, and a positive influence on neighboring municipalities (p < 0.05). In contrast, most municipalities with low VC were concentrated in the Mata Paraibano region, negatively influencing their neighbors (p < 0.05).

Conclusion
Uneven geographic regions and clusters of low VC for children aged < 1 year in the State of Paraíba were spatially visualized. Health policy makers and planners need to urgently devise and coordinate an action plan directed at each state’s regions to fulfill the vaccination calendar, thereby reversing the vulnerability of this age group, which is at a higher risk of diseases preventable by vaccination.
Effect of alendronate sodium plus vitamin D3 tablets on knee joint structure and osteoarthritis pain: a multi-center, randomized, double-blind, placebo-controlled study protocol
Authors: Peng Hui-ming , Weng Xi-sheng , Li Ye , Feng Bin , Qian Wenwei , Cai Dao-zhang , Zhao Chang , Yao Zhen-jun , Yang Yi , Zhang Chi , Wan Shengcheng 
Published: June 2022

Abstract
Background
Osteoarthritis (OA) is a major cause of pain and disability worldwide. Despite the relatively high burden of the disease, the currently available non-surgical treatment options are directed towards symptomatic relief. Therefore, we propose the use of alendronate as a disease modifying agent to help slow and prevent OA. In addition, this study will utilize Whole-Organ Magnetic Resonance Imaging Score (WORMS) to evaluate the structural integrity of cartilage in the study population. High-quality evidence, limited to a few well-conducted randomized trials, highlights contradictory results on the effect of bisphosphonates on knee function and progression of OA. Therefore, a placebo-controlled, randomized trial is needed to evaluate the combined effect of alendronate and vit D on the structure of cartilage utilizing the WORMS score and its ability to treat knee pain in OA patients.

Methods
This multicenter, randomized, double-blinded, placebo-controlled study will evaluate the efficacy and safety of alendronate in early OA. Patients will undergo a 1:1 double-blinded randomization to receive a one-year course of either alendronate sodium vitamin D3 or placebo. The primary outcome is to compare WORMS score of knee joint at 6 and 12 months between both groups. Secondary endpoints will include WORMS score at 24 months, knee pain, radiographic progression of OA, severity of OA, quality of life, and serum inflammatory biomarkers at different assessment timepoints. To detect a 2.2% difference in cartilage loss between both groups with power of 80%, a sample size of 60 (30 per group) is proposed.

Discussion
This trial will give helpful and high-quality evidence regarding the potential therapeutic role of alendronate sodium vitamin D3, as compared to placebo, in the management of patients with knee OA regarding its role on cartilage loss, radiographic progression of OA, severity of OA, knee pain, quality of life, and inflammatory biomarkers. If proven effective, this intervention would be a great option for providing beneficial outcomes with a reduced cost in this patient population.

Trial registration
This trial was registered on clinicaltrials.gov (registration number: NCT04739592).
Hidden blood loss of total knee arthroplasty in hemophilia arthritis: an analysis of influencing factors
Authors: Shen Shao Ning , Wu Dong Xiao , Lv Shuai Jie , Tong Pei Jian 
Published: June 2022

Abstract
Background
Total knee arthroplasty is the leading way to treat hemophilia arthritis. At present, there is a lack of research on the influencing factors of blood loss in total knee arthroplasty for hemophilia arthritis. This study comprehensively explores the definite factors affecting the hidden blood loss in total knee arthroplasty for hemophilia patients.

Materials and methods
Ninety-two hemophilia A patients who underwent total knee arthroplasty in our center were included. Demographics, laboratory data, surgical data, and complications were collected. The Gross equation and Sehat equation were used to calculate the estimated value of hidden blood loss. Multivariate linear regression analysis was used to determine the influencing factors of hidden blood loss.

Result
The hidden blood loss of hemophilia A patients undergoing total knee arthroplasty was 1069.51 ± 341.99 mL, and the age was positively correlated with the hidden blood loss (P < 0.001), while tranexamic acid, FVIII prophylaxis, and incremental invivo recovery were negatively correlated with the hidden blood loss (P < 0.001, P = 0.008, P = 0.017).

Conclusion
Elderly patients have a greater risk of blood loss, and additional preventive measures can be appropriately added. Intraoperative intra-articular injection of tranexamic acid is recommended to reduce hidden blood loss, FVIII prophylaxis is recommended for every patient. We recommend that all HA patients measure the incremental invivo recovery and develop a personalized infusion regimen of coagulation factor.
Hypoxia-inducible factor expression is related to apoptosis and cartilage degradation in temporomandibular joint osteoarthritis
Authors: Zhang Jun , Hu Yu , Wang Zihan , Wu Xuelian , Yang Chun , Yang Hefeng 
Published: June 2022

Abstract
Background
It remains unclear etiology of cartilaginous tissues in osteoarthritis (OA) lesions. In this study, we hypothesized the accumulation of hypoxia-inducible factor (HIF) and activated apoptosis relate to condylar cartilage degeneration in vivo.

Methods
Malocclusion stress was applied for 2 weeks, 4 weeks and 8 weeks to induce an OA-like lesion animal model in rats. Histological analysis was performed by H&E staining and Safranin O/fast green staining. The expression levels of protein in condylar cartilage were examined by immunostaining to evaluate cartilage degeneration.

Results
We found apparent histological phenotypes associated with degeneration in the occlusion disorder (OD) stress group. The OD group at 4 weeks and 8 weeks had obviously reduced expression of Aggrecan (Acan) and type II collagen (Col II) in cartilage. In contrast, the OD groups had higher levels of ADAM metallopeptidase with thrombospondin type 5 (ADAMTS5) and matrix metallopeptidase 13 (MMP13) in the condylar cartilage than the control group. Moreover, the OD group cartilage had prominent degenerative changes with reduced levels of hypoxia inducible factor 1 alpha (HIF1α) and increased levels of hypoxia inducible factor 2 alpha (HIF2α) and the apoptosis factor Caspase3 in condylar cartilage at 8 weeks.

Conclusion
Thus, abnormal hypoxic conditions inducing Occlusion disorder stress results in cartilage degeneration. opposite expression patterns of HIF1α and HIF2α could be involved in the pathogenesis of condylar cartilage degeneration and chondrocyte apoptosis. HIF2α may provide a potential negative feedback mechanism for HIF1α during cartilage damage.
Development of an efficient veterinary rabies vaccine production process in the avian suspension cell line AGE1.CR.pIX
Authors: Trabelsi Khaled , Zakour Meriem Ben , Jordan Ingo , Sandig Volker , Rourou Samia , Kallel Hela 
Published: June 2022

Abstract
Background
Mass vaccination of dogs as important rabies reservoir is proposed to most effectively reduce and eliminate rabies also in humans. However, a minimum coverage of 70% needs to be achieved for control of the disease in zoonotic regions. In numerous developing countries, dog vaccination rate is still dangerously low because of economic constraints and due to a high turnover in dog populations. Improved vaccine production processes may help to alleviate cost and supply limitations. In this work, we studied and optimized the replication and vaccine potency of PV rabies virus strain in the muscovy-duck derived AGE1.CR and AGE1.CR.pIX suspension cell lines.

Results
The BHK-21-adapted PV rabies virus strain replicated efficiently in the avian cell lines without requirement for prior passaging. CR.pIX was previously shown to augment heat shock responses and supported slightly higher infectious titers compared to the parental CR cell line. Both cell lines allowed replication of rabies virus also in absence of recombinant IGF, the only complex component of the chemically defined medium that was developed for the two cell lines. After scale-up from optimization experiments in shake flask to production in 7-l bioreactors peak virus titers of 2.4 × 108 FFU/ml were obtained. The potency of inactivated rabies virus harvest according to the NIH test was 3.5 IU/ml. Perfusion with the chemically defined medium during the virus replication phase improved the potency of the vaccine twofold, and increased the number of doses 9.6 fold.

Conclusion
This study demonstrates that a rabies vaccine for animal vaccination can be produced efficiently in the AGE1.CR.pIX suspension cell line in a scalable process in chemically defined medium.