bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decline of gastric cancer mortality in common variable immunodeficiency in the years 2018-2022
Authors: Milito Cinzia , Pulvirenti Federica , Garzi Giulia , Sculco Eleonora , Cinetto Francesco , Firinu Davide , Lagnese Gianluca , Punziano Alessandra , Discardi Claudia , Costanzo Giulia , Felice Carla , Spadaro Giuseppe , Ferrari Simona , Quinti Isabella 
Published: October 2023

IntroductionIn patients with Common Variable Immunodeficiency, malignancy has been reported as the leading cause of death in adults, with a high risk of B-cell lymphomas and gastric cancer.MethodsWe conducted a five-year prospective study aiming to update the incidence and mortality of gastric cancer and the incidence of gastric precancerous lesions in 512 CVID patients who underwent a total of 400 upper gastrointestinal endoscopies.ResultsIn the pre-pandemic period, 0.58 endoscopies were performed per patient/year and in the COVID-19 period, 0.39 endoscopies were performed per patient/year. Histology revealed areas with precancerous lesions in about a third of patients. Patients who had more than one gastroscopy during the study period were more likely to have precancerous lesions. Two patients received a diagnosis of gastric cancer in the absence of Helicobacter pylori infection. The overall prevalence of Helicobacter pylori infection in biopsy specimens was 19.8% and related only to active gastritis. Among patients who had repeated gastroscopies, about 20% progressed to precancerous lesions, mostly independent of Helicobacter pylori.DiscussionWhile gastric cancer accounted for one in five deaths from CVID in our previous survey, no gastric cancer deaths were recorded in the past five years, likely consistent with the decline in stomach cancer mortality observed in the general population. However, during the COVID-19 pandemic, cancer screening has been delayed. Whether such a delay or true decline could be the reason for the lack of gastric cancer detection seen in CVID may become clear in the coming years. Due to the high incidence of precancerous lesions, we cannot rely on observed and predicted trends in gastric cancer mortality and strongly recommend tailored surveillance programs.
Survival after radiofrequency ablation and/or chemotherapy for lung cancer and pulmonary metastases: a systematic review and meta-analysis
Authors: Yang Ziyi , Lyu Xia , Yang Huilin , Wang Bingbing , Xu Dan , Huo Lingyi , Zhang Runzi , Huang Yingjun , Diao Benshu 
Published: October 2023

BackgroundRadiofrequency ablation (RFA) and chemotherapy are used to treat lung cancer or pulmonary metastases, but no direct comparison of overall survival (OS) has been published. The present study aimed to assess the OS of RFA and/or chemotherapy in patients with lung cancer or pulmonary metastases who were not candidates for surgical resection.MethodsTo identify relevant studies, the following databases were electronically searched from their inception to 31 March 2023: PubMed, Embase, Web of Science, Cochrane Library, Scopus, Ovid, ScienceDirect, SinoMed, China National Knowledge Infrastructure Database, Chongqing VIP Chinese Science and Technology Periodical Database, Wanfang Database, LILACS, ClinicalTrials.gov, and Chictr.org. Manual retrieval was also conducted. We used published hazard ratios (HRs) if available or estimates from other survival data.ResultsA total of 1,387 participants from 14 trials were included in the final analysis. Patients treated with RFA combined with chemotherapy significantly improved OS compared with those treated with chemotherapy alone [HR 0.50, 95% confidence interval (CI) 0.41–0.61; p &lt; 0.00001], with an absolute difference at 12 months of 29.6% (95% CI 23.7–35.5), at 24 months of 19.2% (95% CI 10.1–28.2), and at 36 months of 22.9% (95% CI 12.0–33.7). No statistically significant difference was observed in the subgroups of case type, cancer type, chemotherapy drugs, and tumor size. The HR for OS with RFA plus chemotherapy vs. RFA alone was 0.53 (95% CI 0.41–0.70; p &lt; 0.00001), corresponding to a 27.1% (95% CI 18.3–35.8), 31.0% (95% CI 19.9–41.9), and 24.9% (95% CI 15.0–34.7) absolute difference in survival at 12 months, 24 months, and 36 months, respectively. Subgroup analysis by geographic region and TNM stage showed that RFA combined with chemotherapy still significantly improved OS compared to RFA. The HR of RFA vs. chemotherapy was 0.98 (95% CI 0.60–1.60; p = 0.94), with an absolute difference at 12 months of 1.4% (95% CI -19.2 to 22.1), at 24 months of 7.8% (95% CI -11.3 to 26.8), and at 36 months of 0.3% (95% CI -13.2 to 13.8). The overall indirect comparison of OS for RFA vs. chemotherapy was 0.95 (95% CI 0.72–1.26; p = 0.74). Data on progression-free survival were not sufficiently reported.ConclusionRFA combined with chemotherapy might be a better treatment option for patients with lung cancer or pulmonary metastases than chemotherapy alone or RFA alone. The comparison between RFA and/or chemotherapy remains to be specifically tested.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=335032, identifier CRD42022335032.
The prognostic value of the tertiary lymphoid structure in gastrointestinal cancers
Authors: Yu Aoyang , Cao Menghan , Zhang Kaile , Yang Yule , Ma Luyao , Zhang Xinran , Zhao Yang , Ma Xiao , Fan Zhixiang , Han Zhengxiang , Wang Hongmei 
Published: October 2023

BackgroundNumerous studies and research papers have provided evidence suggesting that tertiary lymphoid structures (TLS) play a crucial role in combating and suppressing tumor growth and progression. Despite the wealth of information on the significance of TLS in various types of cancer, their prognostic value in gastrointestinal (GI) cancers remains uncertain. Therefore, this meta-analysis investigated the prognostic value of TLS in GI cancers.MethodsWe searched Web of science, Pubmed, Embase and Cochrane Library for studies that met the requirements as of May 1, 2023, and the hazard ratio (HR) and the corresponding 95% confidence interval (CI) were included in the analysis. The bioinformatics analysis results based on the TCGA database are used to supplement our research.ResultsThe meta-analysis included 32 studies involving 5778 patients. The results of comprehensive analysis showed that TLS-High is associated with prolonged OS (HR=0.525,95%CI:0.447-0.616 (P &lt; 0.001), RFS (HR=0.546,95%CI:0.461-0.647, P &lt; 0.001), DFS (HR=0.519,95%CI:0.417-0.646, P &lt; 0.001) and PFS (HR=0.588,95%CI:0.406-0.852, P=0.005) in GI cancer. Among the patients who received immunotherapy, TLS-High is associated with significantly prolonged OS (HR=0.475, 95%CI:0.282-0.799, P=0.005) and PFS(HR=0.576, 95%CI:0.381-0.871, P=0.009). It is worth noting that subgroup analysis showed that there was no significant relationship between TLS and OS(HR=0.775, 95%CI:0.570-1.053,P=0.103) in CRC. And when Present is used as the cut-off criteria of TLS, there is no significant correlation between TLS and OS (HR=0.850, 95%CI:0.721-1.002, P=0.053)in HCC.ConclusionTLS is a significant predictor of the prognosis of GI cancers and has the potential to become a prognostic biomarker of immunotherapy-related patients.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/#recordDetails, identifier CRD42023443562.
Spatial distribution and composition of marine litter on sandy beaches along the Indian Ocean coastline in the south Java region, Indonesia
Authors: Yona Defri , Nooraini Pratiwi , Putri Sisylia Eka Narriyah , Sari Syarifah Hikmah Julinda , Lestariadi Riski Agung , Amirudin Akhmad 
Published: October 2023

Marine litter in coastal areas can bring economic, social, and environmental damage, especially the loss of aesthetic value of a tourist site. Therefore, research on the composition of marine litter to identify its sources is important for planning strategic action to minimize the problem. This study analyzed beach litter composition on five beaches (Kondangmerak, Balekambang, Ungapan, Ngudel, and Goa Cina) along the Indian Ocean coastline in the eastern part of the south Java region, Indonesia. All the beaches are known as the famous touristic beaches of Malang City, and receive many visitors, especially during the holiday season. Beach litter composition was obtained by collecting different types of litter in a 5 x 5 m square transect. Five square transects were placed along the beach strandline at each beach, and intervals of 20 m separated each transect. In each transect, the litter was collected and counted based on its category (plastic, paper, rubber, fabric, processed wood, metal, glass, ceramic, and hazardous items) and size (0.5–2.5cm, 2.5–5cm, 5–10 cm, and &gt; 10 cm). There was a statistically significant variation in the number of litters among the sizes (p&lt;0.05). However, the distribution of beach litter remained consistent across beaches regardless of its size. In general, beach litter with a size &gt; 10 cm was found least on all beaches (&lt; 15%), while the other three size categories were found in similar numbers (in the range of 20% to 50%). Plastic was the dominating type of litter on all beaches. Based on the Clean Coastal Index, all beaches were considered dirty to extremely dirty. All litter on the beaches was the product of tourism activities, and littering habits play a significant role as the source of marine litter in the study areas. Since this is the first study on the marine litter composition in the eastern part of south Java, the results of this study can be used as a baseline for future studies to prevent marine debris pollution and to develop management strategies for reducing the impact of marine debris on the environment.
Development and validation of an artificial intelligence-powered acne grading system incorporating lesion identification
Authors: Li Jiaqi , Du Dan , Zhang Jianwei , Liu Wenjie , Wang Junyou , Wei Xin , Xue Li , Li Xiaoxue , Diao Ping , Zhang Lei , Jiang Xian 
Published: October 2023

BackgroundThe management of acne requires the consideration of its severity; however, a universally adopted evaluation system for clinical practice is lacking. Artificial intelligence (AI) evaluation systems hold the promise of enhancing the efficiency and reproducibility of assessments. Artificial intelligence (AI) evaluation systems offer the potential to enhance the efficiency and reproducibility of assessments in this domain. While the identification of skin lesions represents a crucial component of acne evaluation, existing AI systems often overlook lesion identification or fail to integrate it with severity assessment. This study aimed to develop an AI-powered acne grading system and compare its performance with physician image-based scoring.MethodsA total of 1,501 acne patients were included in the study, and standardized pictures were obtained using the VISIA system. The initial evaluation involved 40 stratified sampled frontal photos assessed by seven dermatologists. Subsequently, the three doctors with the highest inter-rater agreement annotated the remaining 1,461 images, which served as the dataset for the development of the AI system. The dataset was randomly divided into two groups: 276 images were allocated for training the acne lesion identification platform, and 1,185 images were used to assess the severity of acne.ResultsThe average precision of our model for skin lesion identification was 0.507 and the average recall was 0.775. The AI severity grading system achieved good agreement with the true label (linear weighted kappa = 0.652). After integrating the lesion identification results into the severity assessment with fixed weights and learnable weights, the kappa rose to 0.737 and 0.696, respectively, and the entire evaluation on a Linux workstation with a Tesla K40m GPU took less than 0.1s per picture.ConclusionThis study developed a system that detects various types of acne lesions and correlates them well with acne severity grading, and the good accuracy and efficiency make this approach potentially an effective clinical decision support tool.
Comparison of plasma mitochondrial DNA copy number in asymptomatic and symptomatic COVID-19 patients
Authors: Shoraka Shahrzad , Mohebbi Seyed Reza , Hosseini Seyed Masoud , Zali Mohammad Reza 
Published: October 2023

IntroductionSince the beginning of the COVID-19 pandemic, a wide clinical spectrum, from asymptomatic infection to mild or severe disease and death, have been reported in COVID-19 patients. Studies have suggested several possible factors, which may affect the clinical outcome of COVID-19. A pro-inflammatory state and impaired antiviral response have been suggested as major contributing factors in severe COVID-19. Considering that mitochondria have an important role in regulating the immune responses to pathogens, pro-inflammatory signaling, and cell death, it has received much attention in SARS-CoV-2 infection. Recent studies have demonstrated that high levels of cell-free mitochondrial DNA (cf-mtDNA) are associated with an increased risk of COVID-19 intensive care unit (ICU) admission and mortality. However, there have been few studies on cf-mtDNA in SARS-CoV-2 infection, mainly focusing on critically ill COVID-19 cases. In the present study, we investigated cf-mtDNA copy number in COVID-19 patients and compared between asymptomatic and symptomatic cases, and assessed the clinical values. We also determined the cf-nuclear DNA (cf-nDNA) copy number and mitochondrial transcription factor A (TFAM) mRNA level in the studied groups.Materials and methodsPlasma and buffy coat samples were collected from 37 COVID-19 patients and 33 controls. Briefly, after total DNA extraction, plasma cf-mtDNA, and cf-nDNA copy numbers were measured by absolute qPCR using a standard curve method. Furthermore, after total RNA extraction from buffy coat and cDNA synthesis, TFAM mRNA levels were evaluated by qPCR.ResultsThe results showed that cf-mtDNA levels in asymptomatic COVID-19 patients were statistically significantly higher than in symptomatic cases (p value = 0.01). However, cf-nDNA levels were higher in symptomatic patients than in asymptomatic cases (p value = 0.00). There was no significant difference between TFAM levels in the buffy coat of these two groups (p value &gt; 0.05). Also, cf-mtDNA levels showed good diagnostic potential in COVID-19 subgroups.Conclusioncf-mtDNA is probably important in the outcome of SARS-CoV-2 infection due to its role in inflammation and immune response. It can also be a promising candidate biomarker for the diagnosis of COVID-19 subgroups. Further investigation will help understanding the COVID-19 pathophysiology and effective diagnostic and therapeutic strategies.
Biological methane production and accumulation under sulfate-rich conditions at Cape Lookout Bight, NC
Authors: Coon Gage R. , Duesing Paul D. , Paul Raegan , Baily Jennifer A. , Lloyd Karen G. 
Published: October 2023

IntroductionAnaerobic oxidation of methane (AOM) is hypothesized to occur through reverse hydrogenotrophic methanogenesis in marine sediments because sulfate reducers pull hydrogen concentrations so low that reverse hydrogenotrophic methanogenesis is exergonic. If true, hydrogenotrophic methanogenesis can theoretically co-occur with sulfate reduction if the organic matter is so labile that fermenters produce more hydrogen than sulfate reducers can consume, causing hydrogen concentrations to rise. Finding accumulation of biologically-produced methane in sulfate-containing organic-rich sediments would therefore support the theory that AOM occurs through reverse hydrogenotrophic methanogenesis since it would signal the absence of net AOM in the presence of sulfate.Methods16S rRNA gene libraries were compared to geochemistry and incubations in high depth-resolution sediment cores collected from organic-rich Cape Lookout Bight, North Carolina.ResultsWe found that methane began to accumulate while sulfate is still abundant (6–8 mM). Methane-cycling archaea ANME-1, Methanosarciniales, and Methanomicrobiales also increased at these depths. Incubations showed that methane production in the upper 16 cm in sulfate-rich sediments was biotic since it could be inhibited by 2-bromoethanosulfonoic acid (BES).DiscussionWe conclude that methanogens mediate biological methane production in these organic-rich sediments at sulfate concentrations that inhibit methanogenesis in sediments with less labile organic matter, and that methane accumulation and growth of methanogens can occur under these conditions as well. Our data supports the theory that H2 concentrations, rather than the co-occurrence of sulfate and methane, control whether methanogenesis or AOM via reverse hydrogenotrophic methanogenesis occurs. We hypothesize that the high amount of labile organic matter at this site prevents AOM, allowing methane accumulation when sulfate is low but still present in mM concentrations.
Global genomic epidemiology of chromosomally mediated non-enzymatic carbapenem resistance in Acinetobacter baumannii: on the way to predict and modify resistance
Authors: Nageeb Wedad M. , AlHarbi Nada , Alrehaili Amani A. , Zakai Shadi A. , Elfadadny Ahmed , Hetta Helal F. 
Published: October 2023

IntroductionAlthough carbapenemases are frequently reported in resistant A. baumannii clinical isolates, other chromosomally mediated elements of resistance that are considered essential are frequently underestimated. Having a wide substrate range, multidrug efflux pumps frequently underlie antibiotic treatment failure. Recognizing and exploiting variations in multidrug efflux pumps and penicillin-binding proteins (PBPs) is an essential approach in new antibiotic drug discovery and engineering to meet the growing challenge of multidrug-resistant Gram-negative bacteria.MethodsA total of 980 whole genome sequences of A. baumannii were analyzed. Nucleotide sequences for the genes studied were queried against a custom database of FASTA sequences using the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) system. The correlation between different variants and carbapenem Minimum Inhibitory Concentrations (MICs) was studied. PROVEAN and I-Mutant predictor suites were used to predict the effect of the studied amino acid substitutions on protein function and protein stability. Both PsiPred and FUpred were used for domain and secondary structure prediction. Phylogenetic reconstruction was performed using SANS serif and then visualized using iTOL and Phandango.ResultsExhibiting the highest detection rate, AdeB codes for an important efflux-pump structural protein. T48V, T584I, and P660Q were important variants identified in the AdeB-predicted multidrug efflux transporter pore domains. These can act as probable targets for designing new efflux-pump inhibitors. Each of AdeC Q239L and AdeS D167N can also act as probable targets for restoring carbapenem susceptibility. Membrane proteins appear to have lower predictive potential than efflux pump-related changes. OprB and OprD changes show a greater effect than OmpA, OmpW, Omp33, and CarO changes on carbapenem susceptibility. Functional and statistical evidence make the variants T636A and S382N at PBP1a good markers for imipenem susceptibility and potential important drug targets that can modify imipenem resistance. In addition, PBP3_370, PBP1a_T636A, and PBP1a_S382N may act as potential drug targets that can be exploited to counteract imipenem resistance.ConclusionThe study presents a comprehensive epidemiologic and statistical analysis of potential membrane proteins and efflux-pump variants related to carbapenem susceptibility in A. baumannii, shedding light on their clinical utility as diagnostic markers and treatment modification targets for more focused studies of candidate elements.
Modeling and in vivo experimental validation of 1,064 nm laser interstitial thermal therapy on brain tissue
Authors: Cao Peng , Shi Dingsheng , Li Ding , Zhu Zhoule , Zhu Junming , Zhang Jianmin , Bai Ruiliang 
Published: October 2023

IntroductionLaser interstitial thermal therapy (LITT) at 1064 nm is widely used to treat epilepsy and brain tumors; however, no numerical model exists that can predict the ablation region with careful in vivo validation.MethodsIn this study, we proposed a model with a system of finite element methods simulating heat transfer inside the brain tissue, radiative transfer from the applicator into the brain tissue, and a model for tissue damage.ResultsTo speed up the computation for practical applications, we also validated P1-approximation as an efficient and fast method for calculating radiative transfer by comparing it with Monte Carlo simulation. Finally, we validated the proposed numerical model in vivo on six healthy canines and eight human patients with epilepsy and found strong agreement between the predicted temperature profile and ablation area and the magnetic resonance imaging-measured results.DiscussionOur results demonstrate the feasibility and reliability of the model in predicting the ablation area of 1,064 nm LITT, which is important for presurgical planning when using LITT.
Treatment of stroke in aged male and female rats with Vepoloxamer and tPA reduces neurovascular damage
Authors: Zhang Li , Luo Hao , Li Chao , Teng Hua , Powell Brianna , Lu Mei , Chopp Michael , Zhang Zheng Gang 
Published: October 2023

Stroke is a leading cause of death and disability worldwide, mainly affecting the elderly. Unfortunately, current treatments for acute ischemic stroke warrant improvement. To date, tissue plasminogen activator (tPA) is of limited use in stroke patients mainly due to its narrow therapeutic window and potential for hemorrhagic complication. The adjuvant treatment with Vepoloxamer, a purified amphipathic polymer has been shown to enhance the thrombolytic efficacy of tPA treatment in young adult male rats after embolic stroke. However, most stroke patients are aged; therefore, the current study investigated the therapeutic effect of the combined tPA and Vepoloxamer treatment in aged male and female rats subjected to embolic stroke.MethodsMale and female Wistar rats at 18 months of age were subjected to embolic middle cerebral artery occlusion and treated either with monotherapy of tPA or Vepoloxamer, a combination of these two agents, or saline at 4 h after stroke onset. Neurological outcomes were evaluated with a battery of behavioral tests including adhesive removal, foot-fault, and modified neurological severity score tests at 1 and 7 days after stroke onset, followed by histopathological analysis of infarct volume. Residual clot size and vascular patency and integrity were analyzed.ResultsThe combination treatment with Vepoloxamer and tPA significantly reduced infarct volume and neurological deficits in male and female rats compared to rats treated with saline and the monotherapies of tPA and Vepoloxamer. While Vepoloxamer monotherapy moderately reduced neurological deficits, monotherapies with tPA and Vepoloxamer failed to reduce infarct volume compared to saline treatment. Furthermore, the combination treatment with tPA and Vepoloxamer accelerated thrombolysis, reduced ischemia and tPA-potentiated microvascular disruption, and concomitantly improved cerebrovascular integrity and perfusion in the male ischemic rats.ConclusionCombination treatment with tPA and Vepoloxamer at 4 h after stroke onset effectively reduces ischemic neurovascular damage by accelerating thrombolysis and reducing ischemia and tPA potentiated side effects in the aged rats. This funding suggests that the combination treatment with tPA and Vepoloxamer represents a promising strategy to potentially apply to the general population of stroke patients.