bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matched control analysis suggests that R-CHOP followed by (R)-ICE may improve outcome in non-GCB DLBCL compared with R-CHOP
Authors: Bantilan Kurt S. , Smith Alexandra N. , Maurer Matthew J. , Teruya-Feldstein Julie , Matasar Matthew J. , Moskowitz Alison J. , Straus David J. , Noy Ariela , Palomba M. Lia , Horwitz Steven M. , Hamlin Paul A. , Portlock Carol S. , Cerhan James R. , Habermann Thomas M. , Salles Gilles A. , Nowakowski Grzegorz S. , Moskowitz Craig H. , Zelenetz Andrew D. 
Published: January 2024

Abstract
Rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) is considered the standard-of-care for patients with advanced-stage diffuse large B-cell lymphoma (DLBCL), despite findings that patients with nongerminal center B-cell like (non-GCB) have significantly worse outcome with this regimen. We evaluated the prognostic significance of baseline risk factors, including cell of origin (COO) classified by the Hans algorithm, within an alternative chemoimmunotherapy program. At Memorial Sloan Kettering Cancer Center (MSK), 151 patients with DLBCL received sequential R-CHOP induction and (R)-ICE (rituximab, ifosfamide, carboplatin, and etoposide) consolidation. Outcome analysis based on COO was validated with a propensity score–matched cohort treated with R-CHOP from the Mayo Clinic component of the Molecular Epidemiology Resource (MER). Among the patients with GCB (n = 69) and non-GCB (n = 69) at MSK, event-free survival (EFS) of non-GCB was superior to that of GCB (hazard ratio [HR], 0.53; 95% confidence interval [CI], 0.29-0.98). Overall survival (OS) demonstrated an association in the same direction but was not statistically significant (HR, 0.68; 95% CI, 0.33-1.42). Propensity score–matched patients from MSK (n = 108) demonstrated a small attenuation in the HRs for EFS (HR, 0.57; 95% CI, 0.27-1.18) and OS (HR, 0.76; 95% CI, 0.33-1.79) and were no longer statistically significant. In contrast, the matched MER cohort (n = 108) demonstrated an EFS association (HR, 1.17; 95% CI, 0.70-1.95) and OS association (HR, 1.13; 95% CI, 0.64-2.00) in the opposite direction, but were also not statistically significant. R-CHOP induction and (R)-ICE consolidation may overcome the negative prognostic impact of the non-GCB phenotype, per the Hans algorithm, and can be preferentially selected for this population. This trial was registered at www.ClinicalTrials.gov as #NCT00039195 and #NCT00712582.
Decoding the complete organelle genomic architecture of Stewartia gemmata: an early-diverging species in Theaceae
Authors: Liu Daliang , Zhang Zhihan , Hao Yanlin , Li Mengge , Yu Houlin , Zhang Xingruo , Mi Haoyang , Cheng Lin , Zhao Yiyong 
Published: January 2024

Abstract
Background
Theaceae, comprising 300 + species, holds significance in biodiversity, economics, and culture, notably including the globally consumed tea plant. Stewartia gemmata, a species of the earliest diverging tribe Stewartieae, is critical to offer insights into Theaceae's origin and evolutionary history.

Result
We sequenced the complete organelle genomes of Stewartia gemmata using short/long reads sequencing technologies. The chloroplast genome (158,406 bp) exhibited a quadripartite structure including the large single-copy region (LSC), a small single-copy region (SSC), and a pair of inverted repeat regions (IRs); 114 genes encoded 80 proteins, 30 tRNAs, and four rRNAs. The mitochondrial genome (681,203 bp) exhibited alternative conformations alongside a monocyclic structure: 61 genes encoding 38 proteins, 20 tRNAs, three rRNAs, and RNA editing-impacting genes, including ATP6, RPL16, COX2, NAD4L, NAD5, NAD7, and RPS1. Comparative analyses revealed frequent recombination events and apparent rRNA gene gains and losses in the mitochondrial genome of Theaceae. In organelle genomes, the protein-coding genes exhibited a strong A/U bias at codon endings; ENC-GC3 analysis implies selection-driven codon bias. Transposable elements might facilitate interorganelle sequence transfer. Phylogenetic analysis confirmed Stewartieae's early divergence within Theaceae, shedding light on organelle genome characteristics and evolution in Theaceae.

Conclusions
We studied the detailed characterization of organelle genomes, including genome structure, composition, and repeated sequences, along with the identification of lateral gene transfer (LGT) events and complexities. The discovery of a large number of repetitive sequences and simple sequence repeats (SSRs) has led to new insights into molecular phylogenetic markers. Decoding the Stewartia gemmata organellar genome provides valuable genomic resources for further studies in tea plant phylogenomics and evolutionary biology.
Intersectional race and gender disparities in kidney transplant access in the United States: a scoping review
Authors: Gompers Annika , Rossi Ana , Harding Jessica L 
Published: January 2024

Abstract
Background
Gender and racial disparities in kidney transplant access are well established, however how gender and race interact to shape access to kidney transplant is less clear. Therefore, we examined existing literature to assess what is known about the potential interaction of gender and race and the impact on access to kidney transplantation in the US.

Methods
Following PRISMA guidelines, we conducted a scoping review and included quantitative and qualitative studies published in English between 1990 and May 31, 2023 among adult end-stage kidney disease patients in the US. All studies reported on access to specific transplant steps or perceived barriers to transplant access in gender and race subgroups, and the intersection between the two. We narratively synthesized findings across studies.

Results
Fourteen studies met inclusion criteria and included outcomes of referral (n = 4, 29%), evaluation (n = 2, 14%), waitlisting (n = 4, 29%), transplantation (n = 5, 36%), provider perceptions of patient transplant candidacy (n = 3, 21%), and patient preferences and requests for a living donor (n = 5, 36%). Overall, we found that White men have the greatest access at all steps of the transplant process, from referral to eventual living or deceased donor transplantation. In contrast, women from racial or ethnic minorities tend to have the lowest access to kidney transplant, in particular living donor transplant, though this was not consistent across all studies.

Conclusions
Examining how racism and sexism interact to shape kidney transplant access should be investigated in future research, in order to ultimately shape policies and interventions to improve equity.
Screening, identifying, and treating chronic kidney disease: why, who, when, how, and what?
Authors: Farrell Douglas R. , Vassalotti Joseph A. 
Published: January 2024

Abstract1 in 7 American adults have chronic kidney disease (CKD); a disease that increases risk for CKD progression, cardiovascular events, and mortality. Currently, the US Preventative Services Task Force does not have a screening recommendation, though evidence suggests that screening can prevent progression and is cost-effective. Populations at risk for CKD, such as those with hypertension, diabetes, and age greater than 50 years should be targeted for screening. CKD is diagnosed and risk stratified with estimated glomerular filtration rate utilizing serum creatinine and measuring urine albumin-to-creatinine ratio. Once identified, CKD is staged according to C-G-A classification, and managed with lifestyle modification, interdisciplinary care and the recently expanding repertoire of pharmacotherapy which includes angiotensin converting enzyme inhibitors or angiotensin-II receptor blockers, sodium-glucose-cotransporter-2 inhibitors, and mineralocorticorticoid receptor antagonists. In this paper, we present the why, who, when, how, and what of CKD screening.
Colonoscopy screening for colorectal cancer in Egypt: a nationwide cross-sectional study
Authors: Allam Abdallah R. , Elsayed Mostafa A. , Daghash Ibrahim Tawfiq , Abdelaziz Ali M. , Mostafa Omnia M. , Sabra Hamdy Khaled , Eldaboush Ahmed Monib , Ahmed Noor Maged Badrawy , Elweza Rawan Tarek , Adwy Enas Sherif , Hammad Abdelrahman Elbendary , Kabbash Ibrahim Ali , Allam Ahmed Hafez , Bahbah Ammar Ayman , Ewis Marwa Ibrahim , Mohamed Shawqi Mohamed , Behery Mostafa B. , Mohamed El-Said Yara , Radwan Ahmed Eid , KhallafAllah Mahmoud T. , Aboshady Omar Ali , Gouda Mohamed A. 
Published: January 2024

Abstract
Background
Current guidelines advocate for colorectal cancer (CRC) screening in adults who are at risk by using direct visualization methods such as colonoscopy. However, in Egypt, there is a paucity of data regarding the current practice of colonoscopy screening. Moreover, more information is needed about the knowledge and attitudes of potential participants regarding the procedure and possible barriers that can limit their participation.

Methods
We conducted a nationwide cross-sectional study using an interview-based survey of patients aged 45 years or above who presented to outpatient clinics of nine university hospitals throughout Egypt. Participants were surveyed to assess their compliance with CRC colonoscopy screening guidelines, their knowledge of and attitude towards colonoscopy screening, and their perspective on potential barriers to colonoscopy screening.

Results
A total of 1,453 participants responded to our survey in the nine study centers. Only a minority of participants (2.3%) were referred for CRC screening. Referral rates were higher among those who knew someone with a history of CRC (5.3% vs 1.5%, p < 0.001) or had a discussion with their physician about CRC (25.8% vs 0.7%, p < 0.001). Few responders (3.2%) had good knowledge regarding CRC screening. After introducing the concept of CRC screening to all participants, most patients (66.7%) showed a positive attitude towards having the procedure. Financial burden and fear of results were the two most frequently cited barriers to undergoing CRC screening (81.1%; and 60.1%, respecteively).

Conclusions
Despite the positive attitude, there is insufficient knowledge about CRC screening among eligible participants in Egypt. This has probably contributed to low compliance with current CRC screening guidelines and needs to be addressed at the national level.
The evaluation of bariatric surgery effect on cardiac structure and function using transthoracic echocardiography: a cohort study
Authors: Abtahi Firoozeh , Atashbarg Malek , Rahmanian Mahdi , Moeinvaziri Nader , Bazrafshan Mehdi , Bazrafshan Hanieh , Moammer Farzaneh , Bazroodi Helia , Zolghadrasli Abdolali , Bazrafshan drissi Hamed 
Published: January 2024

Abstract
Background
Obesity is a pathology and a leading cause of death worldwide. Obesity can harm multiple organs, including the heart. In this study, we aim to investigate the effect of bariatric surgery and following weight loss on cardiac structure and functions using echocardiography parameters in patients with morbid obesity.

Methods
In this cohort study, 30 patients older than 18 with BMI > 40 or BMI > 35 and comorbidity between March 2020 to March 2021 were studied. The patients underwent transthoracic echocardiography before and after six months of the bariatric surgery.

Results
In total, 30 patients (28 women, 93.3%) with a mean age of 38.70 ± 9.19 were studied. Nine (30%) were diabetic, and 9 (30%) had hypertension. After six months of bariatric surgery, all physical measurements, including weight, Body mass index, and Body surface area, decreased significantly (p < 0.001). After bariatric surgery, all parameters regarding left ventricular morphology, including left ventricular mass, interventricular septal thickness, left ventricular posterior wall thickness, left ventricular end-systolic diameter, and left ventricular end-diastolic diameter, improved significantly (p < 0.001). Also, LVEF rose post-bariatric surgery (p < 0.001). TAPSE parameter indicating right ventricular function also improved (p < 0.001). Right ventricular diameter, left atrium volume, and mitral inflow E/e’ decreased significantly (p < 0.001).

Conclusion
Systolic and diastolic parameters refine significantly after bariatric surgery in patients with obesity. Bariatric surgery lead to significant cardiac structure and function improvement.
Characterization, modeling, and anticancer activity of L.arginase production from marine Bacillus licheniformis OF2
Authors: Selim Manal S. , Mounier Marwa M. , Abdelhamid Sayeda A. , Hamed Ahmed Abdelghani , Abo Elsoud Mostafa M. , Mohamed Sahar S. 
Published: January 2024

Abstract
Background
L-arginase, is a powerful anticancer that hydrolyzes L-arginine to L-ornithine and urea. This enzyme is widely distributed and expressed in organisms like plants, fungi, however very scarce from bacteria. Our study is based on isolating, purifying, and screening the marine bacteria that can produce arginase.

Results
The highest arginase producing bacteria will be identified by using microbiological and molecular biology methods as Bacillus licheniformis OF2. Characterization of arginase is the objective of this study. The activity of enzyme was screened, and estimated beside partial sequencing of arginase gene was analyzed. In silico homology modeling was applied to generate the protein's 3D structure, and COACH and COFACTOR were applied to determine the protein's binding sites and biological annotations based on the I-TASSER structure prediction. The purified enzyme was undergone an in vitro anticancer test.

Conclusions
L-arginase demonstrated more strong anti-cancer cells with an IC50 of 21.4 ug/ml in a dose-dependent manner. L-arginase underwent another investigation for its impact on the caspase 7 and BCL2 family of proteins (BCL2, Bax, and Bax/Bcl2). Through cell arrest in the G1/S phase, L-arginase signals the apoptotic cascade, which is supported by a flow cytometry analysis of cell cycle phases.
Alterations and correlations in dental plaque microbial communities and metabolome characteristics in patients with caries, periodontitis, and comorbid diseases
Authors: Wang Ying , Yang Fei , Wang Yuan , Deng Shuli , Zhu Rui 
Published: January 2024

Abstract
Backgrounds
The pathogenic microorganisms and clinical manifestations of caries and periodontitis are different, caries and periodontitis are usually discussed separately, and the relationship between them is ignored. Clinically, patients prone to dental caries generally have a healthier periodontal status, whereas patients with periodontitis generally have a lower incidence of dental caries. The relationship between dental caries and periodontitis remains unclear.

Objectives
This study aimed to explain the clinical phenomenon of antagonism between dental caries and periodontitis by exploring the ecological chain and bacterial interactions in dental caries, periodontitis, and other comorbid diseases.

Methods
The dental plaque microbiomes of 30 patients with oral diseases (10 each with caries, periodontitis, and comorbid diseases) were sequenced and analysed using 16 S rRNA gene sequencing. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) database was used for a differential functional analysis of dental plaque microbial communities in caries, periodontitis, and comorbid diseases.

Results
The coinfection group had the greatest bacterial richness in dental plaque. The principal coordinate analysis showed that caries and periodontitis were separate from each other, and comorbid diseases were located at the overlap of caries and periodontitis, with most of them being periodontitis. Simultaneously, we compared the microbiomes with significant differences among the three groups and the correlations between the microbiome samples. In addition, KEGG pathway analysis revealed significant differences in functional changes among the three groups.

Conclusions
This study revealed the composition of the dental plaque microbial communities in caries, periodontitis, and comorbidities and the differences among the three. Additionally, we identified a possible antagonism between periodontitis and caries. We identified a new treatment strategy for the prediction and diagnosis of caries and periodontitis.
Recurrent stroke in a reproductive age women with patent foramen ovale
Authors: Ye Jing , Yang Yujia , Tang Li , He Li , Zhou Muke 
Published: January 2024

Abstract
Background
Patent foramen ovale (PFO) is a known cause of ischemic stroke in young adults and combined oral contraceptives (COCs) are widely used by women of reproductive age. If young women with PFO are taking COCs, they may be subjected to a synergistic increase in the occurrence of stroke, though reports of ischemic stroke in this population are rare. We report a woman of reproductive age who was taking COC suffered repetitive ischemic strokes before a patent foramen ovale (PFO) was detected and closed, which may raise concerns in this field.

Case presentation
A 31-year-old woman presented to the emergency department with sudden-onset right upper- and lower-limb weakness and dysarthria for 1 hour, whose only risk factor of stroke was oral contraceptive use. On admission, she was alert with left gaze deviation, dysarthria, and right-sided hemiplegia. Her symptoms improved after receiving the revascularization therapy. About 24 hours later, her left eye experienced sudden painless vision loss. Then the PFO with a substantial right-to-left shunt was detected and then she received a trans-catheter closure of the defect. Over 3 months of follow-up, there were no signs of stroke, but visual loss persisted.

Conclusion
This case of disabling stroke raises concerns regarding optimal management in primary and secondary prevention of stroke in young women on COCs with additional risk factors of stroke.
Creating allies: qualitative exploration of young women’s preferences for PrEP methods and parents’ role in PrEP uptake and user support in urban and rural Zambia
Authors: Wong Christina Misa , Munthali Tendai , Mangunje Featherstone G. , Katoka Mercy L. , Burke Holly M. , Musonda Bupe , Musonda Musonda , Todd Catherine S. 
Published: January 2024

Abstract
Background
Zambian adolescent girls and young women (AGYW) have high HIV incidence and face barriers to the use of pre-exposure prophylaxis (PrEP). Parental support improves PrEP use and adherence in some settings, but negative parental attitudes toward HIV prevention may inhibit engagement with AGYW. We explored perceptions of future PrEP methods among AGYW and parents and parent-youth engagement on HIV prevention and PrEP use.

Methods
We conducted a qualitative descriptive study among AGYW and parents of AGYW in five provinces in Zambia in September–October 2021. We conducted 10 focus group discussions (FGDs) and four in-depth interviews (IDIs) with AGYW participants (n = 87) and seven FGDs and four IDIs among parents of AGYW (n = 62). All FGDs and IDIs were audio-recorded, transcribed verbatim, and analyzed to identify qualitative themes.

Results
Most AGYW participants preferred the discreet nature and longer duration of injectable PrEP compared to the PrEP ring and oral PrEP. Many AGYWs reported inability to disclose PrEP use to their parents due to lack of parental support based on cultural taboos against premarital sex. Nevertheless, AGYW participants said they would like to talk to their parents about PrEP so their parents could support their use. Many parents also described difficulties discussing PrEP with their daughters because of cultural and religious beliefs about abstinence from sex before marriage. However, parents acknowledged that the threat of HIV is real and said they need PrEP knowledge and guidance on speaking with their children about HIV prevention and PrEP.

Conclusions
Although many parents are currently not playing a role in daughters’ decisions about PrEP use, both parents and AGYW are willing to engage with each other on HIV prevention issues. To foster parent-child engagement, HIV prevention programs should not only provide information about PrEP but also address social norms that impede discussion of HIV prevention and equip both parents and AGYW with skills and support for such conversations. Community sensitization is also needed as new PrEP products are introduced, to create an enabling environment for parent-child engagement by increasing awareness, countering misconceptions, and reducing stigma.
Involvement of TNFα, IL-1β, COX-2 and NO in the anti-inflammatory activity of Tamarix aphylla in Wistar albino rats: an in-vivo and in-vitro study
Authors: Fayez Nada , Khalil Waleed , Abdel-Sattar Essam , Abdel-Fattah Abdel-Fattah Mohamed 
Published: January 2024

Abstract
Background
With the emergence of many side effects from synthetic drugs, there is an urgent need to find a natural alternative to these products. Therefore, our primary aim was to evaluate the anti-inflammatory activity of Tamarix aphylla (TA) and investigate the potential mechanism underlying this action.

Methods
Initially, to ensure the safety of the extract and for dose selection, we performed an acute oral toxicity Assay through the oral administration of graded doses up to 4 g\kg in Wistar rats. then, we used the carrageenan-induced edema model to elucidate the anti-inflammatory activity. Using specific ELISA kits, we measured the levels of TNF-α, IL-1β, COX-2 and NO inside the inflamed paw tissue. Finally, for the in-vitro anti-inflammatory experiment, we used the erythrocyte membrane stability test.

Results
Based on the acute oral toxicity assay, T. aphylla was considered generally safe and three different doses of 100, 200, and 400 mg/kg were chosen for further experiments. Additionally, TA expressed a significant (P < 0.05) anti-inflammatory activity, showing the maximum inhibition percentage at the fifth hour of measurement at 53.47% and 70.06%, at doses of 200 and 400 mg/kg respectively, compared to 63.81% for the standard drug. Similarly, we found that TA effectively reduced the levels of TNF-α and IL-1β at all tested doses (100-200-400 mg/kg) to a greater extent than the standard drug. Moreover, at 400 mg/kg, TA was able to significantly lower the levels of COX-2 and NO inside the inflamed tissue to a level comparable (P < 0.05) with that measured inside the paw tissue of normal rats. Finally, Tamarix aphylla at 100, 200 and 400 mg/kg doses significantly (P < 0.05) inhibited the heat-induced hemolysis of RBCs membrane by 67.78, 74.82 and 82.08%, respectively, compared to 83.89% produced by Aspirin.

Conclusion
T. aphylla produced a significant (P < 0.05) anti-inflammatory activity compared to the standard drugs either through the reduction of pro-inflammatory mediators or the protection of the lysosomal membrane.