bluuebunny/crossref_metadata_2025 huggingface dataset:
A self-training interpretable cell type annotation framework using specific marker gene
Authors: Chen Hegang , Lu Yuyin , Rao Yanghui
Published: September 2024

Motivation

Recent advances in sequencing technology provide opportunities to study biological processes at a higher resolution. Cell type annotation is an important step in scRNA-seq analysis, which often relies on established marker genes. However, most of the previous methods divide the identification of cell types into two stages, clustering and assignment, whose performances are susceptible to the clustering algorithm, and the marker information cannot effectively guide the clustering process. Furthermore, their linear heuristic-based cell assignment process is often insufficient to capture potential dependencies between cells and types.

Results

Here, we present Interpretable Cell Type Annotation based on self-training (sICTA), a marker-based cell type annotation method that combines the self-training strategy with pseudo-labeling and the nonlinear association capturing capability of Transformer. In addition, we incorporate biological priori knowledge of genes and pathways into the classifier through an attention mechanism to enhance the transparency of the model. A benchmark analysis on 11 publicly available single-cell datasets demonstrates the superiority of sICTA compared to state-of-the-art methods. The robustness of our method is further validated by evaluating the prediction accuracy of the model on different cell types for each single-cell data. Moreover, ablation studies show that self-training and the ability to capture potential dependencies between cells and cell types, both of which are mutually reinforcing, work together to improve model performance. Finally, we apply sICTA to the pancreatic dataset, exemplifying the interpretable attention matrix captured by sICTA.

Availability and implementation

The source code of sICTA is available in public at https://github.com/nbnbhwyy/sICTA. The processed datasets can be found at https://drive.google.com/drive/folders/1jbqSxacL_IDIZ4uPjq220C9Kv024m9eL. The final version of the model will be permanently available at https://doi.org/10.5281/zenodo.13474010
How do hydroelectric dams affect non-migratory fish?: genomic evidence for Cichla temensis (Perciformes: Cichlidae) in the Uatumã River, Amazonas, Brazil
Authors: Escobar Maria D , Barroco Lorenzo , Martínez José G , Bertuol Fabricio , Pouilly Marc , Freitas Carlos E , Hrbek Tomas
Published: September 2024

The Balbina hydroelectric dam was built in the 1980s on the Uatumã River to supply electricity to Manaus, capital of the state of Amazonas, Brazil. Its construction caused a drastic change to the alluvial landscape, forming a large, lentic, artificial reservoir rather than a previously dynamic river system. The objective of our research was to evaluate the impact of the hydroelectric dam on the microevolutionary processes of fish, taking as a model Cichla temensis, an iconic non-migratory fish from the Amazon, abundant in this ecosystem. We collected double digest restriction site-associated DNA sequencing data and extracted single nucleotide polymorphisms, which we identified at neutral and adaptive loci, for subsequent analyses. The results showed that the connectivity of the population was affected historically by natural physical barriers, before the construction of the hydroelectric dam, recognizing two independent population units. We detected that the hydroelectric dam increased the differentiation between populations and affected the genetic diversity and effective population sizes, in addition to promoting a recent population expansion upstream of the dam, as a consequence of adaptation to the new environment. This study provides the first evidence that hydroelectric dams can promote local adaptation in some fish, such as non-migratory ones.
Short-term impact of cardiovascular screening by traditional risk assessment or coronary artery calcium score on health-related quality of life: the ROBINSCA trial
Authors: Moldovanu Dana , de Koning Harry J , Vonder Marleen , Gratama Jan Willem C , Adriaansen Henk J , Roeters van Lennep Jeanine E , Vliegenthart Rozemarijn , van der Harst Pim , Braam Richard L , van Dijkman Paul R M , Oudkerk Matthijs , van der Aalst Carlijn M
Published: September 2024

Aims

Evidence on the impact of screening for cardiovascular diseases (CVDs) on health-related quality of life (HRQoL) is important for policy decisions about screening implementation and to uncover teachable moments to motivate healthy lifestyle choices. It is unknown whether screening by cardiac computed tomography (CT) scan has a stronger impact on HRQoL than screening by traditional risk prediction models. The study aims to investigate differences in HRQoL across the screening process between participants who were randomized to CVD risk estimation by coronary artery calcium score or Systematic COronary Risk Evaluation.

Methods and results

A subset of 2687 ROBINSCA participants filled in questionnaires at (T0) randomization, (T1) invitation, (T2) 1–3 days before screening, (T3) 1–3 days after, and (T4) screening result. Generic HRQoL (SF-12; EQ-5D) and anxiety (STAI-6) were measured. We investigated the differences in changes in HRQoL across the screening process with linear mixed models. We found comparable levels of HRQoL at all screening moments for the two intervention groups. Mental health scores were worse at invitation and randomization than at the later time points, irrespective of screening group (all P < 0.001). A result indicating a heightened CVD risk was associated with increased anxiety in the CT screening group.

Conclusion

Computed tomography screening for CVD risk has no detrimental impact on HRQoL and anxiety levels compared to screening by traditional risk assessment. Receiving an invitation to screenning or a result implying increased CVD risk could function as teachable moments for high-risk individuals.

Registration

ROBINSCA trial registration number: NTR6471 in Dutch Trial Register (NTR).
Selection on the vascular-remodeling BMPER gene is associated with altitudinal adaptation in an insular lizard
Authors: Serén Nina , Pinho Catarina , Megía-Palma Rodrigo , Aguilar Prem , Žagar Anamarija , Andrade Pedro , Carretero Miguel A
Published: September 2024

High altitude imposes several extreme constraints on life, such as low oxygen pressure and high levels of ultraviolet radiation, which require specialized adaptations. Many studies have focused on how endothermic vertebrates respond to these challenging environments, but there is still uncertainty on how ectotherms adapt to these conditions. Here, we used whole-genome sequencing of low-altitude (100–600 m) and high-altitude (3,550 m) populations of the wide-ranging Tenerife lizard Gallotia galloti to uncover signatures of selection for altitudinal adaptation. The studied populations show reduced differentiation, sharing similar patterns of genetic variation. Selective sweep mapping suggests that signatures of adaptation to high altitude are not widespread across the genome, clustering in a relatively small number of genomic regions. One of these regions contains BMPER, a gene involved with vascular remodeling, and that has been associated with hypoxia-induced angiogenic response. By genotyping samples across 2 altitudinal transects, we show that allele frequency changes at this locus are not gradual, but rather show a well-defined shift above ca. 1,900 m. Transcript and protein structure analyses on this gene suggest that putative selection likely acts on noncoding variation. These results underline how low oxygen pressure generates the most consistent selective constraint in high-altitude environments, to which vertebrates with vastly contrasting physiological profiles need to adapt in the context of ongoing climate change.
Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculata from Asia reveals rapid expansion and adaptive evolution
Authors: Lu Yan , Luo Fang , Zhou An , Yi Cun , Chen Hao , Li Jian , Guo Yunhai , Xie Yuxiang , Zhang Wei , Lin Datao , Yang Yaming , Wu Zhongdao , Zhang Yi , Xu Shuhua , Hu Wei
Published: September 2024

Pomacea canaliculata, an invasive species native to South America, is recognized for its broad geographic distribution and adaptability to a variety of ecological conditions. The details concerning the evolution and adaptation of P. canaliculate remain unclear due to a lack of whole-genome resequencing data. We examined 173 P. canaliculata genomes representing 17 geographic populations in East and Southeast Asia. Interestingly, P. canaliculata showed a higher level of genetic diversity than other mollusks, and our analysis suggested that the dispersal of P. canaliculata could have been driven by climate changes and human activities. Notably, we identified a set of genes associated with low temperature adaptation, including Csde1, a cold shock protein coding gene. Further RNA sequencing analysis and reverse transcription quantitative polymerase chain reaction experiments demonstrated the gene’s dynamic pattern and biological functions during cold exposure. Moreover, both positive selection and balancing selection are likely to have contributed to the rapid environmental adaptation of P. canaliculata populations. In particular, genes associated with energy metabolism and stress response were undergoing positive selection, while a large number of immune-related genes showed strong signatures of balancing selection. Our study has advanced our understanding of the evolution of P. canaliculata and has provided a valuable resource concerning an invasive species.
The impact of laboratory data missingness on sepsis diagnosis timeliness
Authors: Lam Jonathan Y , Boussina Aaron , Shashikumar Supreeth P , Owens Robert L , Nemati Shamim , Josef Christopher S
Published: September 2024

Objective

To investigate the impact of missing laboratory measurements on sepsis diagnostic delays.

Materials and Methods

In adult patients admitted to 2 University of California San Diego (UCSD) hospitals from January 1, 2021 to June 30, 2024, we evaluated the relative time of organ failure (TOF) and time of clinical suspicion of sepsis (Tsuspicion) in patients with sepsis according to the Centers for Medicare & Medicaid Services (CMS) definition.

Results

Of the patients studied, 48.7% (n = 2017) in the emergency department (ED), 30.8% (n = 209) in the wards, and 14.4% (n = 167) in the intensive care unit (ICU) had TOF after Tsuspicion. Patients with TOF after Tsuspicion had significantly higher data missingness of 1 or more of the 5 laboratory components used to determine organ failure. The mean number of missing labs was 4.23 vs 2.83 in the ED, 4.04 vs 3.38 in the wards, and 3.98 vs 3.19 in the ICU.

Discussion

Our study identified many sepsis patients with missing laboratory results vital for the identification of organ failure and the diagnosis of sepsis at or before the time of clinical suspicion of sepsis. Addressing data missingness via more timely laboratory assessment could precipitate an earlier recognition of organ failure and potentially earlier diagnosis of and treatment initiation for sepsis.

Conclusions

More prompt laboratory assessment might improve the timeliness of sepsis recognition and treatment.
A case report of a colouterine fistula due to sigmoid diverticulitis
Authors: Chang Catherine L A , Unruh Kenley R , Cragle Chad E , Moonka Ravi
Published: September 2024

Colouterine fistulas are generally seen in post-menopausal patients and present with abdominal pain and non-physiologic vaginal drainage. A history of uterine pathology or diverticulitis is generally lacking. Visualization of the passage of contrast from the gastrointestinal tract to the uterus is not necessary to make the diagnosis. We present the case of a 44-year-old woman successfully treated for a colouterine fistula due to sigmoid diverticulitis. A variety of surgical approaches have been described to correct this fistula, and a minimally invasive colectomy without ileostomy or colostomy appears to be a safe approach.
Neglected finger ring entrapment: a case series illustrating lessons for clinical practice
Authors: Seidu Anwar Sadat , Tano Kouakou Emile , Botchway Anita Esi , Addo-Tham Jeffery , Hoyte-Williams Paa Ekow
Published: September 2024

Finger ring entrapment could compromise the neurovascular status of the finger if not treated promptly. We aimed to report two cases of neglected finger ring entrapment following minor blunt trauma to the hand and illustrate some lessons for clinical practice. Both patients were right-hand dominant, presented 3–4 weeks after the onset of symptoms, and had circumferential ulceration of the affected fingers. The removal of both rings was performed using a wire cutter and bender. Neglected finger ring entrapment could result in multiple sequelae of the affected finger. Timely invention in finger ring entrapment is crucial to forestall neurovascular sequelae. We recommend immediate removal of all jewellery on fingers following any form of hand trauma as a primary preventive measure. We also recommend that clinicians who intend to use a ring-cutting method assess the material used to forge the ring to aid proper selection of a cutting device.
Successful treatment of pan-drug resistant Acinetobacter baumannii meningitis/ventriculitis following craniotomy and external ventricular drainage: a case report
Authors: Gavrilovska Aleksandra Dimovska , Veljanovski Hristijan , Jovchevski Radomir
Published: September 2024

Healthcare-associated central nervous system infections are a significant complication for patients undergoing neurosurgical interventions. We present a case of a 6-year-old patient with an embryonal tumor of the central nervous system. Following a craniotomy for the resection of the tumor, an external ventricular drainage was placed. Several weeks after surgery, she developed signs of meningism. Cerebrospinal fluid cultures were positive for pan-drug resistant Acinetobacter baumannii. Several revisions with the insertion of new external valves were done. She was treated with intravenously meropenem and vancomycin combined with colistin administrated intraventricularly. Significant improvement was seen clinically with negative cultures after 2 weeks. The synergistic action of colistin administrated locally combined with systemic antibiotics may be a promising option for critically ill patients with pan-drug resistant A. baumannii central nervous system infection.
Improving Cancer Care for Women Seeking Services in the Veterans Health Administration Through the Breast and Gynecological Oncology System of Excellence
Authors: Shepherd-Banigan Megan , Zullig Leah L , Berkowitz Theodore S Z , Cummin Graham , Goldstein Karen M , Kelley Michael J , Chawla Neetu , Weidenbacher Hollis J , Hazra Aditi , Halwani Ahmad S , Patil Vikas , Rasmussen Kelli M , Pace Rachel , Colonna Sarah , Moss Haley
Published: September 2024

Women are the fastest growing population among Veterans and have substantial risk factors that increase their likelihood for developing cancer. To ensure that the Department of Veterans Affairs Veterans Health Administration (VHA) offers the best possible cancer care to women Veterans, it established the Breast and Gynecologic Oncology System of Excellence (BGSoE) in 2021. The BGSoE offers telehealth oncology services and a comprehensive cancer navigation program. Veterans are identified through physician referral or through the BGSoE dashboard which integrates ICD-10 codes and text mining from VA electronic health records to identify eligible Veterans with breast or gynecological cancers. Descriptive statistics, including Veteran demographics and geographical location, were derived from BGSoE dashboard data. From January 1, 2021 to March 15, 2024, the BGSoE identified a total of 7,187 incident cases of breast or gynecological cancer among living Veterans. Most cancers were breast (78%) versus gynecological cancers (22%) and 10% of Veterans with breast cancer were identified as male. The average age at diagnosis was 59 for Veterans with breast cancer and 56 for those Veterans with gynecological cancers. Among Veterans in the BGSoE, 28% identified as Black and 6% identified as Hispanic. As the prevalence of women Veterans requiring cancer-related care continues to rise, it will be essential for VHA to evaluate the equitable reach, quality, and acceptability of women-focused cancer health services. The BGSoE focuses on providing high-quality and coordinated clinical cancer care. Veterans Health Administration also established the Center for Oncology Outcomes Review and Gender (COURAGE) to evaluate the BGSoE and continue to strengthen cancer care services in VHA. Initial evaluation objectives include establishing an evidence base regarding Veterans with breast and gynecological cancers, including their experiences with cancer care in the VHA. Eventually, COURAGE will provide ongoing monitoring and evaluation to continue to grow and improve cancer care in the VHA.
Highly Heterogeneous Kaposi Sarcoma–Associated Herpesvirus Oral Shedding Kinetics Among People With and Without Kaposi Sarcoma and Human Immunodeficiency Virus Coinfection
Authors: Krantz Elizabeth M , Mutyaba Innocent , Nankoma Janet , Okuku Fred , Casper Corey , Orem Jackson , Swan David A , Phipps Warren , Schiffer Joshua T
Published: September 2024

Background

An improved understanding of oral Kaposi sarcoma–associated herpesvirus (KSHV) viral dynamics could provide insights into transmission risk and guide vaccine development.

Methods

We evaluated KSHV oral shedding dynamics in Ugandan adults stratified by Kaposi sarcoma (KS) and human immunodeficiency virus (HIV) status. Participants were followed for ≥4 weeks, with daily home oral swab collection to quantify KSHV using polymerase chain reaction. Shedding rates were defined by number of days with KSHV DNA detected divided by total days with swabs and compared by group using hurdle models.

Results

Two hundred ninety-five participants were enrolled; median age was 35 years (range, 18–71 years), and 134 (45%) were male. KSHV was detected more frequently among participants with KS (HIV positive [HIV+]/KS+, 56/76 [74%]; HIV negative [HIV−]/KS+, 9/18 [50%]) than those without KS (HIV+/KS−, 36/125 [29%]; HIV−/KS−, 16/76 [21%]); odds of shedding did not differ significantly by HIV status. Among participants with KSHV detected, shedding rates did not differ significantly by group. Median per-participant viral loads among positive samples were lowest in HIV+/KS+ (3.1 log10 copies/mL) and HIV−/KS+ (3.3 log10 copies/mL) participants relative to HIV+/KS− (3.8 log10 copies/mL) and HIV−/KS− (4.0 log10 copies/mL) participants. All groups had participants with low viral load intermittent shedding and participants with high viral load persistent shedding. Within each group, individual KSHV shedding rate positively correlated with median KSHV log10 copies/mL, and episode duration positively correlated with peak viral load.

Conclusions

Oral KSHV shedding is highly heterogeneous across Ugandan adults with and without KS and HIV. Persistent shedding is associated with higher median viral loads regardless of HIV and KS status.
The urinary and sexual outcomes of buccal mucosal graft urethroplasty versus end-to-end anastomosis: a systematic review with meta-analysis
Authors: Zhao Xingming , Guo Qiang , Zhang Xi , Xing Qi , Ren Sheng , Song Yuting , Li Chengyong , Hao Chuan , Wang Jingqi
Published: September 2024

Background

The urinary and sexual outcomes after urethroplasty may be a concern for patients, but there are still some controversies regarding the consequences of buccal mucosal graft urethroplasty (BMG) in terms of erectile dysfunction (ED).

Aim

This meta-analysis aimed to compare urinary and sexual outcomes of BMG and end-to-end urethroplasty (EE).

Methods

The PubMed, Web of Science, Cochrane, and Embase databases were searched until February 31, 2023. Data extraction and quality assessment were performed by 2 designated researchers. Dichotomous data were analyzed as odds ratios with 95% confidence intervals (CIs). Heterogeneity across studies was assessed by the I2 quantification, and publication bias using Begg’s and Egger’s tests. Meta-analysis was performed using RevMan software.

Outcomes

Outcomes included stricture recurrence, ED, penile complications, and voiding symptoms.

Results

Eighteen studies, including 1648 participants, were included in our meta-analysis. The meta-analysis revealed that there was no significant difference in stricture recurrence (OR = 0.74; 95% CI, 0.48–1.13; P = .17) and voiding symptoms (OR = 1.12; 95% CI, 0.32–3.88; P = .86) between the BMG group and the EE group. BMG was associated with lower risk of penile complications (OR = 0.40; 95% CI, 0.24–0.69; P = .001) and ED (OR = 0.53, 95% CI, 0.32–0.90, P = .02).

Clinical Implications

The study may help clinicians choose procedures that achieve better recovery of the urological and sexual function in the treatment of urethral stricture.

Strengths and Limitations

This meta-analysis is the first to evaluate the urinary and sexual outcomes of BMG vs EE. A limitation is that most of the included studies were retrospective cohort studies.

Conclusion

BMG is as effective as EE in the treatment of bulbar urethral stricture, but BMG has fewer complications and ED than EE.
Overexpression of DTX1 inhibits D-GalN/TNF-α-induced pyroptosis and inflammation in hepatocytes by regulating NLRP3 ubiquitination
Authors: Liu Mingshui , Gu Jing , Chen Li , Sun Wei , Huang Xiaoping , Gan Jianhe
Published: September 2024

Background

Acute liver injury (ALI) is characterized by massive hepatocyte death and has high mortality and poor prognosis. Hepatocyte pyroptosis plays a key role in the pathophysiology of ALI and is involved in the inflammatory response mediated by NOD-like receptor protein 3 (NLRP3) inflammasome activation. Deltex 1 (DTX1) is a single transmembrane protein with ubiquitin E3 ligase activity and is closely involved in cell growth, differentiation, and apoptosis, as well as intracellular signal transduction. However, little is known about the influence of DTX1 on ALI. This study aimed to investigate the role of DTX1 in pyroptosis and inflammation induced by D-galactosamine (D-GalN) and tumor necrosis factoralpha (TNF-α) in human hepatocytes (LO2 cells) in vitro.

Methods

Cell pyroptosis was measured by flow cytometry. The levels of DTX1, pyroptosis-associated proteins, and inflammatory cytokines were detected by quantitative real-time polymerase chain reaction, western blotting, and enzyme-linked immunosorbent assay. Immunofluorescence staining, co-immunoprecipitation, ubiquitination, and luciferase reporter and chromatin immunoprecipitation assays were performed to detect the regulation between DTX1 and NLRP3 or hepatocyte nuclear factor 4 alpha (HNF4α). Analysis of variance was performed to compare groups.

Results

We found that DTX1 was decreased in D-GalN/TNF-α-induced LO2 cells. DTX1 overexpression significantly inhibited D-GalN/TNF-α-induced cell pyroptosis and inflammation. DTX1 interacted with NLRP3 and induced NLRP3 ubiquitination and degradation. Furthermore, by targeting NLRP3, DTX1 knockdown significantly induced cell pyroptosis and inflammation. In addition, HNF4α promoted DTX1 transcription by binding with its promoter.

Conclusion

Our study revealed that DTX1 suppressed D-GalN/TNF-α-induced hepatocyte pyroptosis and inflammation by regulating NLRP3 ubiquitination.
Effective paclitaxel: β-Cyclodextrin-based formulation boosts in vitro anti-tumor potential and lowers toxicity in zebrafish
Authors: Show Sautan , Dutta Debanjan , Nongthomba Upendra , Prasad A J Mahadesh
Published: September 2024

Paclitaxel (PCTX) is one of the most prevalently used chemotherapeutic agents. However, its use is currently beset with a host of problems: solubility issue, microplastic leaching, and drug resistance. Since drug discovery is challenging, we decided to focus on repurposing the drug itself by remedying its drawbacks and making it more effective. In this study, we have harnessed the aqueous solubility of sugars, and the high affinity of cancer cells for them, to entrap the hydrophobic PCTX within the hydrophilic shell of the carbohydrate β-cyclodextrin. We have characterized this novel drug formulation by testing its various physical and chemical parameters. Importantly, in all our in vitro assays, the conjugate performed better than the drug alone. We find that the conjugate is internalized by the cancer cells (A549) via caveolin 1-mediated endocytosis. Thereafter, it triggers apoptosis by inducing the formation of reactive oxygen species. Based on experiments on zebrafish larvae, the formulation displays lower toxicity compared to PCTX alone. Thus, our “Trojan Horse” approach, relying on minimal components and relatively faster formulation, enhances the anti-tumor potential of PCTX, while simultaneously making it more innocuous toward non-cancerous cells. The findings of this study have implications in the quest for the most cost-effective chemotherapeutic molecule.
Self-Compassion for Healthcare Communities: Exploring the Effects of a Synchronous Online Continuing Medical Education Program on Physician Burnout
Authors: Gardiner Paula , Pérez-Aranda Adrián , Bell Natalie , Clark Dawn R. , Schuman-Olivier Zev , Lin Elizabeth H.
Published: September 2024

Introduction:

Physician burnout is a common problem for which self-compassion training has shown positive effects. In this program evaluation, we explore the effects of a synchronous online continuing medical education program (Self-Compassion for Healthcare Communities, SCHC) to improve physician burnout and related outcomes.

Methods:

The SCHC program was delivered online via Zoom and consisted of six 1-hour weekly sessions to enhance self-compassion and well-being. The primary outcome was the “burnout” subscale of the Professional Quality of Life scale; compassion satisfaction, secondary traumatic stress, self-compassion, resilience activation and decompression, and job satisfaction were evaluated, and qualitative data were also collected.

Results:

A total of 116 physicians attended at least one session of the program, 48 of whom completed both the preprogram and postprogram surveys. The results showed that physicians experienced a reduction in their burnout levels (P = .001) as well as improvements in compassion satisfaction (P = .027), secondary traumatic stress (P = .001), self-compassion (P < .001), resilience decompression (P = .012), and job satisfaction (P = .038). Qualitative data, obtained from a total of 91 participants who attended at least one session, indicated that participants were satisfied with the SCHC program: they found it useful for learning to be compassionate with themselves and they highly valued having the chance to connect with other colleagues who experience similar struggles.

Discussion:

The live online SCHC program showed benefits on physician burnout and related outcomes such as compassion satisfaction, secondary traumatic stress, self-compassion, resilience decompression, and job satisfaction. Nonetheless, in addition to individual-focused well-being programs, systemic changes in health care delivery were also deemed necessary to decrease burnout.
Impact of short-term proton pump inhibitors vs. histamine-2 receptor antagonists on gut microbiota in patients with acute coronary syndrome: A multicenter randomized trial
Authors: Chen Chen , Liang Huizhu , He Meibo , Duan Ruqiao , Guan Yu , Wang Fangfang , Duan Liping
Published: September 2024

Background:

Several randomized controlled studies have suggested that the prophylactic use of proton pump inhibitors (PPIs) in intensive care unit (ICU) patients could not reduce the incidence of gastrointestinal bleeding (GIB) and may increase adverse events such as intestinal infection and pneumonia. Gut microbiota may play a critical role in the process. PPIs has been widely prescribed for GIB prophylaxis in patients with acute coronary syndrome (ACS). This study aimed to determine the short-term effects of PPI and histamine-2 receptor antagonist (H2RA) treatment on gut microbiota of ACS patients.

Methods:

The study was designed as a single-blind, multicenter, three-parallel-arm, randomized controlled trial conducted at three centers in Beijing, China. We enrolled ACS patients at low-to-medium risk of GIB and randomized (2:2:1) them to either PPI (n = 40), H2RA (n = 31), or control group (n = 21). The primary outcomes were the alterations in gut microbiota after 7 days of acid suppressant therapy. Stool samples were collected at baseline and 7 days and analyzed by 16S rRNA gene sequencing.

Results:

There were no significant changes in the diversity of gut microbiota after the short-term use of acid suppressants, but the abundance of Fusobacterium significantly increased and that of Bifidobacterium significantly decreased, especially in PPI users. In addition, the abundance of some pathogenic bacteria, including Enterococcus and Desulfovibrio, was significantly elevated in the PPI users. The fecal microbiota of the PPI users included more arachidonic acid metabolism than that of control group.

Conclusions:

PPIs may increase the risk of infection by adversely altering gut microbiota and elevating arachidonic acid metabolism, which may produce multiple proinflammatory mediators. For ACS patients at low-to-medium risk of GIB, sufficient caution should be paid when acid-suppressant drugs are prescribed, especially PPIs.

Registration:

www.chictr.org.cn/ (ChiCTR2000029552).
Key technologies and challenges in online adaptive radiotherapy for lung cancer
Authors: Dong Baiqiang , Zheng Shuohan , Chen Kelly , Zhu Xuan , Huang Sijuan , Jiang Xiaobo , Diao Wenchao , Li Hua , Jia Lecheng , Chi Feng , Huang Xiaoyan , Li Qiwen , Chen Ming
Published: September 2024

Definitive treatment of lung cancer with radiotherapy is challenging, as respiratory motion and anatomical changes can increase the risk of severe off-target effects during radiotherapy. Online adaptive radiotherapy (ART) is an evolving approach that enables timely modification of a treatment plan during the interfraction of radiotherapy, in response to physiologic or anatomic variations, aiming to improve the dose distribution for precise targeting and delivery in lung cancer patients. The effectiveness of online ART depends on the seamless integration of multiple components: sufficient quality of linear accelerator-integrated imaging guidance, deformable image registration, automatic recontouring, and efficient quality assurance and workflow. This review summarizes the present status of online ART for lung cancer, including key technologies, as well as the challenges and areas of active research in this field.
Endoscopic Ultrasound-Guided Fine Needle Acquisition for Evaluation of Pancreatic Neuroendocrine Tumors
Authors: Ye Xiaohua , Hua Hongjun , Hu Chunxiao , Dai Jianying , Wu Chenjiao , Huai Jiaping , Shen Zhe
Published: September 2024

Aims:

The aim of this meta-analysis was to assess the diagnostic performance of EUS-FNA/B in patients with panNETs.

Methods:

We conducted a computerized search of the MEDLINE and Embase databases to identify relevant articles. The primary outcomes involved grading concordance rate, diagnostic rate, and correlation coefficient (Cohen’s κ) for FNA/B samples compared with surgical specimens. Secondary outcomes included sample adequacy, mean number of passes, and adverse events.

Results:

Forty-five studies involving 2978 patients were finally included. The pooled concordance rate between EUS-FNA/B and surgical grading was 0.77 (95% CI: 0.73-0.80; I

2
=48.2%). A significantly higher level of concordance was observed in G1 subgroup (0.88, 95% CI: 0.84-0.91), whereas the G2 subgroup revealed the lowest level of agreement (0.59, 95% CI: 0.52-0.65; P < 0.001). Pooled diagnostic rate for FNA/B sampling was 0.83 (95% CI: 0.79-0.86; I

2
=63.3%). In addition, FNB outperformed FNA in terms of sample adequacy (0.93 for FNB vs. 0.81 for FNA; P=0.007) and number of needle passes required (2.53 for FNB vs. 3.32 for FNA; P=0.013). Moreover, the overall level of agreement for grading was moderate (κ=0.59, 95% CI: 0.49-0.68; I

2
=84.5%). There were a limited number of adverse events that had minor influence on patient outcomes (0.03, 95% CI: 0.02-0.05; I

2
=19.2%).

Conclusions:

EUS-FNA/B is a reliable approach for the diagnosis and preoperative grading of panNET, with FNB demonstrating superior performance compared with FNA.
Comparative Analysis of ERCP and PTBD for Biliary Interventions for Readmission Rates and Patient Outcomes
Authors: Wang Daniel Huai-En , Chang Patrick , Tintara Supisara , Chang Frederick , Phan Jennifer
Published: September 2024

Background:

Endoscopic retrograde cholangiopancreatography (ERCP) and percutaneous transhepatic biliary drainage (PTBD) are interventions used to relieve biliary obstruction. The utility of ERCP compared with PTBD is not fully understood from a utilization outcome standpoint. Our study compares readmission rates and hospitalization outcomes in ERCP and PTBD.

Methods:

Using the National Readmission Database (NRD) 2016 to 2020, we identified all patients with an ERCP or PTBD completed during admission. The study cohort was first analyzed by 3 weighted study arms including those admitted with cholangitis, biliary/pancreatic malignancy, and choledocholithiasis. Second, we analyzed the cohort by a 1:1, unweighted propensity match. The primary outcome was 30 day, 90 day, and 6 month readmission. Secondary outcomes were readmission/overall mortality, cost, and length of stay. Outcomes were analyzed using multivariate analysis.

Results:

A total of 621,735 admissions were identified associated with 589,796 ERCP and 31,939 PTBD. In the propensity matched cohort, PTBD had a higher readmission rate at 30 days (20.38% vs. 13.71% P<0.0001), 90 days (14.63% vs. 13.14%, P<0.0001) but lower rate at 6 months (8.50% vs. 9.67%, P=0.0003). Secondary outcomes included increased PTBD-associated hospital length of stay (9.01 d vs. 6.74 d, P<0.0001), hospitalization cost ($106,947.97 vs. $97,602.25, P<0.0001), and overall mortality (6.86% vs. 4.35%, P<0.0001). No major differences were found for mortality among readmissions at 30 days (7.19% vs. 6.88%, P=0.5382), 90 day (6.82% vs. 6.51%, P=0.5612), and 6 months (5.08% vs. 5.91%, P=0.1744).

Conclusions:

ERCP demonstrated superior results compared with PTBD for readmission rates, length of stay and overall mortality. For failed ERCP cases, emerging data for Endoscopic ultrasound guided-biliary drainage (EUS-BD) offers potential over PTBD and may provide additional options for the future in tertiary referral centers with experience.
Comparative Effectiveness of ERCP and EUS-Guided Techniques for “Primary Biliary Drainage” in Malignant Distal Biliary Obstruction
Authors: Nabi Zaheer , Samanta Jayanta , Dhar Jahnvi , Aggarwal Mona , Basha Jahangeer , Gahra Amrit , Golchha Aman , Crinò Stefano Francesco , Facciorusso Antonio , Lakhtakia Sundeep , Reddy D.Nageshwar
Published: September 2024

Background and Objectives:

Endoscopic ultrasound-guided biliary drainage (EUS-BD) is a viable alternative in cases with failed ERCP transpapillary drainage (ERCP-TPD). This systematic review and meta-analysis aimed to compare the efficacy and safety of EUS-BD and ERCP-TPD for primary biliary drainage in patients with distal malignant biliary obstruction (DMBO).

Methods:

We searched Embase, PubMed, and Medline databases for studies comparing EUS-BD and ERCP-TPD in DMBO, from inception until September 2023. The primary endpoint was clinical success and secondary endpoints included technical success, procedure duration, and adverse events.

Results:

Eight studies (815 patients, 56.1% male) were included in this analysis. Indications for biliary drainage were pancreatic carcinoma (75.1%), followed by cholangiocarcinoma (10.1%). Clinical success was comparable between EUS-BD and ERCP-TPD groups (OR 1.34; 95% CI, 0.75-2.40; P=0.32). Technical success was similar between the 2 groups (OR 2.09; 95% CI, 0.83-5.25; P=0.12). There was a trend toward fewer adverse events in the EUS-BD group (OR 0.65; 95% CI, 0.40-1.07; P=0.09), with significantly lower odds of post-procedure pancreatitis (OR 0.17; 95% CI, 0.06-0.50; P=0.001).

Conclusion:

EUS-BD is comparable to ERCP for primary biliary drainage in DMBO patients with shorter procedural time and a significantly reduced risk of post-procedure pancreatitis.
miR-200c targeting GLI3 inhibits cell proliferation and promotes apoptosis in non-small cell lung cancer cells
Authors: Yi Xiangjun , Chen Xuan , Li Zhenbin
Published: September 2024

Lung cancer is a common malignant tumor with low cure rate. It has an easy recurrence and metastasis. This study explored whether miR-200c could regulate the biological behavior of non-small cell lung cancer cells through targeting GLI3. Luciferase reporter gene analysis was used to verify the interaction between miR-200c-3p and GLI3. miR-200c-3p and GLI3 were transiently overexpressed into A549 cells. The cell viability rate was detected by cell counting kit-8, cell invasion ability was detected with Transwell, cell apoptosis and cell cycle was determined by flow cytometry, and the expression of GLI3 was detected using quantitative polymerase chain reaction and Western blot, to verify the effect of the interaction between miR-200c-3p and GLI3 on the cell activities. miR-200c-3p overexpression could inhibit cell viability and invasion, promote apoptosis, induce G0/G1 arrest, and inhibit cell division. GLI3 overexpression could reverse the miR-200c-3p inhibition on cell cycle, reduce the number of cells in the G0/G1 phase and increase the number of cells in the S phase. miR-200c-3p overexpression in A549 cells could inhibit cell viability and invasion, and promote apoptosis. miR-200c-3p could target GLI3 to regulate cell cycle and inhibit cell proliferation.
Effects of different traditional Chinese exercise for knee osteoarthritis patients: A network meta-analysis of randomized controlled trials
Authors: Tao Tao , Shi Ming-Peng , Zhang Xian-Shuai , Tan Bo-Yang , Xiao Ya-Nan , Sun Feng-Ling , Li Shao-Jun , Li Zhen-Hua
Published: September 2024

Background:

The most popular traditional Chinese exercise (TCE) techniques include Tai Chi, Yijinjing, Baduanjin, Wuqinxi, and Qigong. Exercise is advised as a primary treatment for knee osteoarthritis (KOA) according to clinical standards. According to several studies, TCE may be an effective way to help people with KOA manage their pain, stiffness, and physical function. Which TCE therapy is the most effective and whose particular usefulness is still debatable. The network meta-analysis (NMA) method is used in this study to evaluate and compare the effects of various TCE therapies on KOA patients.

Methods:

We will search PubMed, Embase, Scopus, Cochrane Library, Web of Science, the China National Knowledge Infrastructure, Wanfang, the Chinese Scientific Journal Database (VIP), and the China Biology Medical Literature Database (CBM) for randomized controlled trials reporting TCE therapy for KOA patients published before October 25, 2023. The Stata 16.0 program will compare the effectiveness of various TCE therapies on KOA patients using conventional pairwise and NMA.

Results:

The final 29 studies included 15 articles on Tai Chi, 7 articles on Baduanjin, 4 articles on Wuqinxi, and 3 articles on Yijinjing. Tai Chi was first for the effect sizes of VAS scores, WOMAC pain scores, and WOMAC available scores, while Baduanjin was ranked top for WOMAC stiffness scores. Research should continue to be conducted on the effect of Qigong on KOA intervention.

Conclusions:

This NMA will help determine the best TCE treatment for KOA and offer evidence-based bias for clinical decision-making.
Investigation of traditional Chinese medicine constitution in individuals afflicted by dry eye disease: A retrospective study
Authors: Yu Jing , Guo Yihan , Tian Lei , Qiu Lixin , Chen Xiaoniao , Cao Kai , Zhu Lei , Jie Ying
Published: September 2024

The aim of this study is to explore the traditional Chinese medicine (TCM) constitution among individuals suffering from dry eye disease. Following the diagnostic criteria outlined in TFO DEWS II, a total of 114 patients with dry eye were included in this study. Based on the classification criteria for dry eye, the patients were categorized into 3 distinct dry eye subtypes. Each participant underwent a thorough clinical assessment for dry eye, and their TCM pattern manifestations were assessed using the “Traditional Chinese Medicine Questionnaire for Dry Eye.” The Nine Constitutions Assessment Method was utilized for TCM pattern differentiation and classification. Spearman’s correlation analysis was employed to investigate the associations between TCM constitution and dry eye subtypes, clinical indicators, and the relationships between TCM syndromes and dry eye subtypes. Among the 114 patients, the Qi-Stagnation constitution was the most common, with variations in constitution distribution among different dry eye subtypes. Significant correlations were observed between the Blood-Stasis, Yin-Deficiency, Qi-Deficiency, and Yang-Deficiency constitutions and 2, 4, 1, and 4 dry eye indicators, respectively. Spearman’s analysis revealed that 5 out of 50 TCM syndromes were associated with mixed dry eye, 5 with evaporative dry eye, and 3 with aqueous tear deficiency dry eye. Further analysis, using lasso regression and binary unconditional logistic regression identified dizziness, lumbago, and weakness as influencing factors for both mixed-type and evaporative-type dry eye. In this study, we extensively examined the TCM constitution in individuals with dry eye, offering valuable insights and guiding future TCM-related research in the context of dry eye. Additionally, we established correlations between TCM syndrome patterns and dry eye indicators.
Acupuncture for the treatment of anxiety and depression in patients with spinal cord injury: A study protocol for systematic review and meta analysis
Authors: Liu Ke , Gao Xiaoyong , Ou Liang , Tang Zuyu , Zhao Haoming , Hua Sheng , Xiong Yixiao , Zhang Le , Kuang Jianjun
Published: September 2024

Background:

Spinal cord injury patients frequently suffer from anxiety and depression, which can seriously affect their quality of life and recovery. Acupuncture, as a traditional Chinese therapy, has been used to treat anxiety and depression for more than 2000 years. The aim is to evaluate the clinical efficacy of acupuncture in the treatment of anxiety and depression in spinal cord injury patients.

Methods:

The literature on acupuncture treating anxiety and depression in patients with spinal cord injury in PubMed, Embase, Cochrane Library, Chinese Biomedical Literature Database, China National Knowledge Infrastructure, Chinese Scientific Journal Data, and Wanfang data were searched through computers from the establishment of the database to May 2024. In the study, the Cochrane tool for assessing the risk of bias was used and the meta-analyses were carried out using the software package Review Manager 5.4.

Results:

Ten trials were included in this systematic review, with 361 cases in the experimental group and 355 cases in the control group. Meta-analysis showed that compared with conventional treatment, acupuncture combined with conventional treatment was beneficial in improving the total clinical efficacy (odds ratio = 3.55 [95% confidence interval {CI}: 1.34–9.37], P < .001). We found acupuncture-assisted therapy could be beneficial in improving the Modified Barthel Index (MD = 10.48 [95% CI: 4.78–16.19], P < .001) and reducing anxiety or depression scores (such as the Self-Rating Anxiety Scale [MD = −6.08 {95% CI: −6.85 to −5.30}, P < .001]; reducing the Self-Rating Depression Scale [MD = −6.01 {95% CI: −6.95 to −5.07}, P < .001]). In addition, the study showed that the application of acupuncture treatment could improve 5-hydroxytryptamine compared to control group (MD = 44.99 [95% CI: 40.04–49.95], P < .001) and reduce TNF-α compared to control group (MD = −7.78 [95% CI: −8.73 to −6.83], P < .001).

Conclusion:

Acupuncture could be used as a complementary therapy to reduce anxiety and depression in spinal cord injury patients. Further original and high-quality research is needed to verify the conclusions of this study.
Mendelian study on air pollution and membranous nephropathy outcomes associations
Authors: Zhu Xiaoxiao , Zhou Hanjing , Xu Wanxian
Published: September 2024

Membranous nephropathy (MN) is an autoimmune disease of the kidney glomerulus, which mainly leads to nephrotic syndrome. This study investigates the associations between air pollution and MN risk and from an epigenomic perspective. In this study, we examine the associations between genetically predicted deoxyribonucleic acid methylation related to air pollution and MN risk. The data of air pollution included particulate matter (PM) with a diameter of 2.5 µm or less (PM2.5), PM with a diameter between 2.5 and 10 µm (PM2.5–10), PM with a diameter of 10 µm or less (PM10), nitrogen dioxide, and nitrogen oxides. Inverse variance weighted method was used as the main analysis method, and weighted median model and Mendelian randomization-Egger methods were selected for quality control. To assess the reliability of the results of the analyses, heterogeneity test, horizontal pleiotropy test, and the leave-one-out method were applied. There was a causal relationship between nitrogen oxides and MN risk (P = .010). Other types of air pollution were found no statistical association with MN disease (PM2.5: P = .378; PM2.5–10: P = .111; PM10: P = .035; nitrogen dioxide: P = .094). There was no heterogeneity or pleiotropy in the results. Our study suggests the association between nitrogen oxides and membrane nephropathy (MN) risk from the genetic perspective. This provides a theoretical basis for the prevention of MN disease.
Association between the systemic immune-inflammation index and hearing loss: A cross-sectional study of NHANES 2005 to 2018
Authors: Zhao Limei , Zhang Xi , Chen Lu
Published: September 2024

The relationship between systemic inflammation and hearing loss (HL) remains unclear. To investigate the association between the systemic immune-inflammation index (SII) and objective HL, this study was performed. Participants from the National Health and Nutrition Examination Survey (NHANES) spanning from 2005 to 2018 were analyzed. Two types of hearing loss were investigated: speech-frequency hearing loss (SFHL) and high-frequency hearing loss (HFHL). The SII score was constructed using the levels of peripheral neutrophil (N), lymphocyte (L), and platelet (P), and was defined as P multiplied by N/L (in units of 109/L). Weighted multivariable logistic regression and subgroup analysis were used to examine the relationship between HL and high-SII group (≥330 × 109/L). A total of 6428 participants were included in the study. This study found that the high-SII group was positively associated with a higher risk of HL (OR: 1.29, 95% CI: 1.05–1.57, P < .05) and HFHL (OR: 1.24, 95% CI: 1.05–1.46, P < .05), but not significant for SFHL (OR: 1.13, 95% CI: 0.94–1.37, P > .05). Subgroup analysis showed that this association was similar in different age groups. Finally, sensitivity analysis confirmed the robustness of the association. In the full model, increasing SII index per SD was associated with HL (OR: 1.17, 95% CI: 1.09–1.26, P < .001) and HFHL (OR: 1.13, 95% CI: 1.06–1.21, P < .001). The significance of SFHL was not detected with the increasing SII index (OR: 1.13, 95% CI: 0.94–1.37, P > .05). SII score was associated with HL and HFHL in the general adult population of the United States, but was not significantly correlated with SFHL.