bluuebunny/crossref_metadata_2025_split huggingface dataset:
CMAPLE: Efficient Phylogenetic Inference in the Pandemic Era
Authors: Ly-Trong Nhan , Bielow Chris , De Maio Nicola , Minh Bui Quang 
Published: June 2024

Abstract
We have recently introduced MAPLE (MAximum Parsimonious Likelihood Estimation), a new pandemic-scale phylogenetic inference method exclusively designed for genomic epidemiology. In response to the need for enhancing MAPLE's performance and scalability, here we present two key components: (i) CMAPLE software, a highly optimized C++ reimplementation of MAPLE with many new features and advancements, and (ii) CMAPLE library, a suite of application programming interfaces to facilitate the integration of the CMAPLE algorithm into existing phylogenetic inference packages. Notably, we have successfully integrated CMAPLE into the widely used IQ-TREE 2 software, enabling its rapid adoption in the scientific community. These advancements serve as a vital step toward better preparedness for future pandemics, offering researchers powerful tools for large-scale pathogen genomic analysis.
Unraveling glioblastoma diversity: Insights into methylation subtypes and spatial relationships
Authors: Foltyn-Dumitru Martha , Alzaid Haidar , Rastogi Aditya , Neuberger Ulf , Sahm Felix , Kessler Tobias , Wick Wolfgang , Bendszus Martin , Vollmuth Philipp , Schell Marianne 
Published: June 2024

Abstract

Background
The purpose of this study was to elucidate the relationship between distinct brain regions and molecular subtypes in glioblastoma (GB), focusing on integrating modern statistical tools and molecular profiling to better understand the heterogeneity of Isocitrate Dehydrogenase wild-type (IDH-wt) gliomas.

Methods
This retrospective study comprised 441 patients diagnosed with new IDH-wt glioma between 2009 and 2020 at Heidelberg University Hospital. The diagnostic process included preoperative magnetic resonance imaging and molecular characterization, encompassing IDH-status determination and subclassification, through DNA-methylation profiling. To discern and map distinct brain regions associated with specific methylation subtypes, a support-vector regression-based lesion-symptom mapping (SVR-LSM) was employed. Lesion maps were adjusted to 2 mm³ resolution. Significance was assessed with beta maps, using a threshold of P &lt; .005, with 10 000 permutations and a cluster size minimum of 100 voxels.

Results
Of 441 initially screened glioma patients, 423 (95.9%) met the inclusion criteria. Following DNA-methylation profiling, patients were classified into RTK II (40.7%), MES (33.8%), RTK I (18%), and other methylation subclasses (7.6%). Between molecular subtypes, there was no difference in tumor volume. Using SVR-LSM, distinct brain regions correlated with each subclass were identified: MES subtypes were associated with left-hemispheric regions involving the superior temporal gyrus and insula cortex, RTK I with right frontal regions, and RTK II with 3 clusters in the left hemisphere.

Conclusions
This study linked molecular diversity and spatial features in glioblastomas using SVR-LSM. Future studies should validate these findings in larger, independent cohorts to confirm the observed patterns.
PICC Your Poison: Resident Beliefs and Attitudes Regarding Discharge Parenteral Antibiotics for Patients Who Inject Drugs
Authors: Fabricant Scott A , Abramson Erika L , Hutchings Kayla , Vien Alexis , Scherer Matthew , Kapadia Shashi N 
Published: June 2024

Abstract

Background
Serious injection-related infections (SIRIs) in people who inject drugs often lead to prolonged hospitalizations or premature discharges. This may be in part due to provider reluctance to place peripherally inserted central catheters (PICCs) for outpatient parenteral antibiotic therapy in this population. Because internal medicine (IM) residents are often frontline providers in academic centers, understanding their perspectives on SIRI care is important to improve outcomes.

Methods
We surveyed IM residents in a large urban multicenter hospital system about SIRI care with a novel case-based survey that elicited preferences, comfort, experience, and stigma. The survey was developed using expert review, cognitive interviewing, and pilot testing. Results are reported with descriptive statistics and linear regression.

Results
Of 116 respondents (response rate 34%), most (73%) were uncomfortable discharging a patient with active substance use home with a PICC, but comfortable (87%) with discharge to postacute facilities. Many (∼40%) endorsed high levels of concern for PICC misuse or secondary line infections, but larger numbers cited concerns about home environment (50%) or loss to follow-up (68%). While overall rates were low, higher stigma was associated with more concerns around PICC use (r = −0.3, P = .002). A majority (58%) believed hospital policies against PICC use in SIRI may act as a barrier to discharge, and 74% felt initiation of medications for opioid use disorder (MOUD) would increase their comfort discharging with a PICC.

Conclusions
Most IM residents endorsed high levels of concern about PICC use for SIRI, related to patient outcomes and perceived institutional barriers, but identified MOUD as a mitigating factor.
Conservative treatment of sexual dysfunction among men undergoing prostate cancer treatment: a systematic review
Authors: da Fonseca Pedroso Isadora Martins , Siqueira Maria Luíza Souza , de Sousa Santos Thaísy Andressa Bastos Primo , de Paula Barbosa Keyla , de Lima Elio Armando Nunes , Sampaio Andréia Cristina Ribeiro Izidro , da Costa Cunha Katiane , da Silva Marianne Lucena , Alves Aline Teixeira 
Published: June 2024

Abstract

Introduction
One of the changes caused by pelvic cancers is the decrease in patients’ sexual function, which influences their quality of life (QoL) during and after treatment. Sexual dysfunction (SD) is associated with severe ejaculatory dysfunction, sexual dissatisfaction, reduced libido and sexual desire, decreased intensity of orgasm, difficulty in erection, and lower sexual frequency.

Objectives
This systematic review investigated the effectiveness of conservative treatments (nonsurgical and nonpharmacologic) for SD in males with pelvic cancer.

Methods
Systematic searches were performed in the Cochrane Library, PubMed, CINAHL, PEDro, Embase, and VHL databases in September 2023 by using MeSH terms related to population, study design, intervention, and outcome.

Results
Only prostate cancer studies were included due to a lack of studies in other treatments. Studies used pelvic floor muscle training (8 studies); biofeedback (1 study); a penile vibrator (1 study); electrostimulation (2 studies); shock wave therapy (2 studies); aerobic, resistance, and flexibility exercises (2 studies); and a vacuum erection device (1 study). All articles assessed sexual function and reported improvements in the intervention group, including 5 with no differences between the groups. Articles involving shock wave therapy described improvements in SD but were not clinically relevant. Studies evaluating QoL reported benefits in the experimental groups. Adverse effects of a vacuum erection device and penile vibrator were reported.

Conclusion
Conservative treatments are more effective than others in treating SD in men with prostate cancer. Further studies are needed to assess the unwanted effects of these treatments. In this study, we found evidence that this type of therapy improves sexual function and QoL in this population.
Integration of physiological, miRNA‐mRNA interaction and functional analysis reveals the molecular mechanism underlying hypoxia stress tolerance in crucian carp (Carassius auratus)
Authors: Li Yongjuan , Wu Shenji , Huang Jinqiang , Zhao Lu 
Published: June 2024

AbstractHypoxia has become one of the most critical factors limiting the development of aquaculture. Crucian carp (Carassius auratus) is widely consumed fish in China, with excellent tolerance to hypoxic environment. However, the molecular mechanisms underlying hypoxia adaptation and tolerance in crucian carp remain unclear. Compared with the control, increased T‐SOD, CAT, GSH‐Px, T‐AOC, ALT, and AST activities and MDA, TCHO, and TG contents, and decreased TP and ATP contents were observed after hypoxia stress. Based on RNA‐seq, 2479 differentially expressed (DE) mRNAs and 60 DE miRNAs were identified, and numerous DE mRNAs involved in HIF signaling pathway (hif‐1α, epo, vegfa, and ho), anaerobic metabolism (hk1/hk2, pfk, gapdh, pk, and ldh) and immune response (nlrp12, cxcr1, cxcr4, ccr9, and cxcl12) were significantly upregulated after hypoxia exposure. Integrated analysis found that ho, igfbp1, hsp70, and hk2 were predicted to be regulated by novel_867, dre‐miR‐125c‐3p/novel_173, dre‐miR‐181b‐5p, and dre‐miR‐338‐5p/dre‐miR‐17a‐3p, respectively, and targets of DE miRNAs were significantly enriched in MAPK signaling pathway, FoxO signaling pathway, and glycolysis/gluconeogenesis. Expression analysis showed that the mRNA levels of vegfa, epo, ho, hsp70, hsp90aa.1, igfbp1, ldh, hk1, pfk, pk, and gapdh exhibited a remarkable increase, whereas sdh and mdh were downregulated in the H3h, H12h, and H24h groups compared with the control. Furthermore, research found that hk2 is a target of dre‐miR‐17a‐3p, overexpression of dre‐miR‐17a‐3p significantly decreased the expression level of hk2, while the opposite results were obtained after dre‐miR‐17a‐3p silencing. These results contribute to our understanding of the molecular mechanisms of hypoxia tolerance in crucian carp.
TAT‐beclin1 treatment accelerates the development of atherosclerotic lesions in ApoE‐deficient mice
Authors: Liu Lianbo , Wang Qingjie , Li Yawen , Cai Jiali , Wang Yexing , Li Yun , Wang Ruxing , Sun Ling , Zheng Xiaowei , Yin Anwen 
Published: June 2024

AbstractThe importance of autophagy in atherosclerosis has garnered significant attention regarding the potential applications of autophagy inducers. However, the impact of TAT‐Beclin1, a peptide inducer of autophagy, on the development of atherosclerotic plaques remains unclear. Single‐cell omics analysis indicates a notable reduction in GAPR1 levels within fibroblasts, stromal cells, and macrophages during atherosclerosis. Tat‐beclin1 (T‐B), an autophagy‐inducing peptide derived from Beclin1, could selectively bind to GAPR1, relieving its inhibition on Beclin1 and thereby augmenting autophagosome formation. To investigate its impact on atherosclerosic plaque progression, we established the ApoE−/− mouse model of carotid atherosclerotic plaques. Surprisingly, intravenous administration of Tat‐beclin1 dramatically accelerated the development of carotid artery plaques. Immunofluorescence analysis suggested that macrophage aggregation and autophagosome formation within atherosclerotic plaques were significantly increased upon T‐B treatment. However, immunofluorescence and transmission electron microscopy (TEM) analysis revealed a reduction in autophagy flux through lysosomes. In vitro, the interaction between T‐B and GAPR1 was confirmed in RAW264.7 cells, resulting in the increased accumulation of p62/SQSTM1 and LC3‐II in the presence of ox‐LDL. Additionally, T‐B treatment elevated the protein levels of p62/SQSTM1, LC3‐II, and cleaved caspase 1, along with the secretion of IL‐1β in response to ox‐LDL exposure. In summary, our study underscores that T‐B treatment amplifies abnormal autophagy and inflammation, consequently exacerbating atherosclerotic plaque development in ApoE−/− mice.
Outcomes of Ponseti Method for the Treatment of Clubfeet in Children With Spina Bifida
Authors: Schaibley Claire , Torres-izquierdo Beltran , Meyer Zachary , Hosseinzadeh Pooya 
Published: June 2024

Introduction:
While the Ponseti method is the primary treatment for idiopathic clubfoot, its application in treating myelodysplastic clubfeet is less certain. Myelodysplastic clubfoot tends to be more severe and difficult to treat. Although the Ponseti method can initially correct these cases, there is conflicting evidence about recurrence rates and the need for additional treatment. This study aims to assess the effectiveness of the Ponseti method in treating myelodysplastic clubfeet compared with idiopathic clubfeet over a 20-year period.

Methods:
The study conducted a retrospective review of medical records from patients treated for clubfoot at a single institution (2002 to 2021), comparing children with myelodysplastic and idiopathic clubfoot. Included patients were under 18, initially treated with Ponseti-casting, and had a minimum 2-year follow-up. Data on demographics, treatment details, recurrence, and Patient-reported Outcomes Measurement Information System (PROMIS) scores were analyzed.

Results:
Forty-nine myelodysplastic and 512 idiopathic clubfeet in 366 patients met the inclusion criteria. Myelodysplastic cases had a median age of 5 months at presentation versus 2 months for idiopathic cases (P=0.002). Initial correction was achieved in 95% of idiopathic and 87.8% of myelodysplastic feet (P=0.185). Recurrence rates were higher in the myelodysplastic cohort, 65.3% versus 44.1% (P=0.005). Surgery was necessary to treat recurrence in 59.2% of myelodysplastic and 37.7% of idiopathic cases, P=0.003. Follow-up was 3.9±1.8 years for myelodysplastic and 3.3±1.5 years for idiopathic feet, P=0.030. Myelodysplastic feet had lower PROMIS mobility scores; 31.94±7.56 versus 49.21±8.64, P<0.001.

Conclusions:
To the best of our knowledge, we report the largest series of myelodysplastic clubfeet treated by Ponseti casting and the first to assess PROMIS data. Overall, the Ponseti method is as effective in obtaining initial correction in myelodysplastic clubfoot as it is in idiopathic clubfoot. However, myelodysplastic clubfeet has a higher risk of relapse and increased need for surgical interventions. Children with spina bifida may need closer follow-ups and more stringent adherence to bracing.

Level of Evidence:
Level III—therapeutic studies—investigating the results of treatment
Rituximab as a Therapeutic Strategy in Hemophagocytic Lymphohistiocytosis: Efficacy, Outcomes, and Survival—Insights From a Systematic Review
Authors: Qureshi Zaheer , Altaf Faryal , Jamil Abdur , Siddique Rimsha 
Published: June 2024

Background:
Hemophagocytic lymphohistiocytosis (HLH) is a severe immunologic disorder that can be fatal if left untreated. The condition is characterized by excessive immune system activation and is often triggered by infections such as Epstein-Barr virus (EBV). Rituximab, an anti-CD20 monoclonal antibody, has been suggested as a treatment, particularly for EBV-associated HLH.

Methods:
A systematic review was conducted using PRISMA guidelines, with a literature search spanning PubMed, Scopus, Web of Science, and the Cochrane Library. The inclusion criteria focused on studies that assessed rituximab’s efficacy in treating HLH. Quality assessment was performed using the Joanna Briggs Institute Critical Appraisal Checklist for Case Reports.

Results:
Of 783 identified records, 24 studies were included in the final analysis. Rituximab was typically administered at 375 mg/m2, with varying doses and treatment frequency. Clinical response, often seen within 1 month, was assessed by improvements in clinical symptoms and laboratory findings. Survival rates posttreatment displayed a wide range, with instances of complete remission and disease-free periods, as well as reports of relapse and mortality.

Conclusions:
Rituximab demonstrates the potential for significant clinical benefit in treating HLH, particularly when associated with EBV, showing promise in reducing disease activity and contributing to remission. These findings encourage further research and clinical trials to refine the therapeutic protocols and better understand the long-term effects of rituximab in HLH management.
Penile microbiome: decoding its impact on HIV risk
Authors: Nelson Sydney G. , Liu Cindy M. 
Published: June 2024

Purpose of review
The penile microbiome has been linked to local inflammation and increased risk for sexually transmitted infections, including HIV. This review explores recent studies of this emerging area of HIV research

Recent findings
The male urogenital tract supports multiple distinct niches, where their associated microbiome are shaped by abiotic (e.g., oxygen, moisture) and biotic (e.g., host immunity) environmental factors and host behaviors, particularly sexual activity. In addition, male circumcision is a significant drivers of male genital microbiome in both children and adults. Recent sexual partner studies provide new insight into the exchange of genital bacteria and concurrent local immune changes that may impact HIV risk.

Summary
The male genital microbiome is shaped by the local microenvironment and host behaviors including sexual activity. Improving our understanding of the connection between the male genital microbiome, local inflammation, and HIV susceptibility, as well as how pro-inflammatory genital bacteria are transmitted between sexual partners may inform new strategies to prevent HIV transmission.
Human papillomavirus infection among adolescents living with HIV: a focus on prevention
Authors: Jongen Vita W. , van Dongen Nicola , Sohn Annette H. 
Published: June 2024

Purpose of review
To highlight recent data on HPV infection and cervical precancerous lesions in adolescents with HIV, and priorities for primary and secondary HPV prevention.

Recent findings
Incident and persistent high-risk HPV infections and cervical abnormalities are higher among young women with perinatally acquired HIV compared to their HIV-negative peers; data on HPV among males with perinatally acquired HIV are scarce. HPV vaccination is highly effective in preventing HPV-related disease, but antibody titers may decline in people with HIV. It remains unclear if emerging recommendations to reduce vaccine schedules from three doses to two or one dose are appropriate for children and adolescents with perinatally acquired HIV. Due to higher risks of HPV-related cancers, screening guidelines for cervical cancer differ in their frequency and age at initiation for women with HIV, but there are no recommendations for women with perinatally acquired HIV; nor for anal cancer screening for men with perinatally acquired HIV.

Summary
Data on the effectiveness of reduced HPV vaccine schedules in children and adolescents with HIV are needed. Implementation research to guide strategies for vaccination, screening, and treatment should include children, adolescents, and young adults with perinatally acquired HIV to ensure they are not left behind.
The vaginal microbiome and HIV transmission dynamics
Authors: Cherenack Emily M. , Broedlow Courtney A. , Klatt Nichole R. 
Published: June 2024

Purpose of review
Among women, having a nonoptimal, highly diverse vaginal microbiome dominated by bacteria other than optimal Lactobacillus species such as L. crispatus or L. jensenii predicts HIV transmission. Reducing HIV acquisition among women requires a better understanding of the mechanisms through which the vaginal microbiome impacts HIV transmission dynamics and how to more effectively treat and intervene. Technological advancements are improving the ability of researchers to fully characterize interacting host-bacteria mechanisms. Consequently, the purpose of this review was to summarize the most innovative research on the vaginal microbiome and its role in HIV transmission in the past year.

Recent findings
Studies combining multiomics, experimental, and translational approaches highlight the associations of a nonoptimal microbiome with maladaptive alterations in immune cell functioning, vaginal metabolites, host cell transcription, mucosal immunity, and epithelial barrier integrity. While there are multiple mechanisms proposed to increase HIV acquisition risk, there are virtually zero acceptable and effective treatments to improve the vaginal microbiome and immunity.

Summary
Women-centered solutions to modify the vaginal microbiome and bacterial metabolites should continue to be explored as a mechanism to reduce HIV acquisition.
Untangling the role of the microbiome across the stages of HIV disease
Authors: Ortiz Alexandra M. , Brenchley Jason M. 
Published: June 2024

Purpose of review
The primate microbiome consists of bacteria, eukaryotes, and viruses that dynamically shape and respond to host health and disease. Understanding how the symbiotic relationship between the host and microbiome responds to HIV has implications for therapeutic design.

Recent findings
Advances in microbiome identification technologies have expanded our ability to identify constituents of the microbiome and to infer their functional capacity. The dual use of these technologies and animal models has allowed interrogation into the role of the microbiome in lentiviral acquisition, vaccine efficacy, and the response to antiretrovirals. Lessons learned from such studies are now being harnessed to design microbiome-based interventions.

Summary
Previous studies considering the role of the microbiome in people living with HIV largely described viral acquisition as an intrusion on the host:microbiome interface. Re-framing this view to consider HIV as a novel, albeit unwelcome, component of the microbiome may better inform the research and development of pre and postexposure prophylaxes.
Coexistence of Hashimoto’s thyroiditis, rheumatoid arthritis, Sjogren’s syndrome, and ulcerative colitis
Authors: Kudsi Maysoun , Khalayli Naram , Haj Ali Diaa , Al-Darwish Lama 
Published: June 2024

Introduction and importance:
The coexistence of Hashimoto’s thyroiditis and ulcerative colitis has been previously mentioned, as these diseases are autoimmune diseases. Limited data about the coexistence of rheumatoid arthritis in patients with Hashimoto’s thyroiditis have been published till now. Meanwhile, the coexistence of Sjogren’s syndrome during the course of rheumatoid arthritis is well known. The coexistence of Hashimoto’s thyroiditis, Sjogren’s syndrome, and ulcerative colitis has also been reported in rare cases.

Case presentation:
A 32-year-old female, with a 10-year history of Hashimoto’s thyroiditis, 4 years of rheumatoid arthritis, and 2 years of secondary Sjogren’s syndrome, presented to our Rheumatology Department, complaining of fatigue, weight loss, intermittent abdominal pain, and bloody diarrhea for the last 6 weeks. Her colonoscopy findings were compatible with a diagnosis of ulcerative colitis.

Clinical discussion:
Multiple autoimmune syndromes are defined as the presence of three or more autoimmune diseases in the same patient. They have an increased frequency in patients with a previous history of another autoimmune disease, and a higher correlation with females. The prevalence is rare and was documented only by two systematic reviews, with the rest being separate case reports. Autoimmune thyroid disease and Sjögren’s syndrome were the most frequent diseases encountered, followed by rheumatoid arthritis, and systemic lupus erythematosus. The presence of these autoimmune diseases together suggests that they share a common pathological and physiological genesis.

Conclusion:
This is the first case report, to our knowledge, that describes the coexistence of Hashimoto’s thyroiditis, rheumatoid arthritis, Sjogren’s syndrome, and ulcerative colitis within 10 years, without a positive family history or psychological stress. Therefore, further studies and long-term surveys are needed to identify other factors that can contribute to the coexistence of these rare diseases.