bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oral anticoagulants increased 30-day survival in sepsis patients complicated with atrial fibrillation: a retrospective analysis from MIMIC-IV database
Authors: Ge Gaoyuan , Bo Dan , Jiang Rongli , Zhao Wei , Lu Yao 
Published: January 2024

BackgroundThe severity of sepsis is associated with systemic clotting activation. Atrial fibrillation (AF) is the most commonly observed arrhythmia in patients with sepsis and can lead to a poor prognosis. The aim of this study is to elucidate the association between oral anticoagulants and survival from septic patients complicated with AF.MethodsThe data of 8,828 septic patients, including 2,955 AF and 5,873 without AF, were all originated from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. Patients with sepsis and AF are divided into OAC- group (n = 1,774) and OAC+ group (n = 1,181) based on OAC therapy. Septic patients with no AF were considered as the control group (n = 5,873, sepsis and no AF group). The main outcome endpoint was the survival rate of 30 day. The secondary outcome endpoint was the length of stay (LOS) from intensive care unit and hospital. Propensity score matching (PSM) was used to adjust the influence of superfluous factors, and a restricted mean survival time (RMST) analysis was used for calculating the benefit of survival time and survival rate. Analysis including univariate and multivariate logistic regression analysis was conducted to find prognosis-related predictors.ResultsAfter PSM, the OAC+group had a higher 30-day survival rate compared to the OAC- group (81.59% vs. 58.10%; P &lt; 0.001) in the ICU. Despite the higher survival, the hospital LOS (14.65 days vs. 16.66 days; P = 0.15) and ICU LOS (6.93 days vs. 5.92 days; P = 0.02) were prolonged at OAC+ group than OAC- group. No difference was found in survival rate of 30 day between the sepsis patients using warfarin and patients using NOAC (85.60% vs. 79.84%, P = 0.12). The sepsis patients using warfarin had a prolonged LOS in ICU and hospital compared with the sepsis patients using NOAC. In the vasopressor subgroup, patients who received NOAC therapy were associated with a reduced 30-day survival rate (73.57% vs. 84.03%; P = 0.04) and reduced LOS in ICU and hospital than those on warfarin therapy.ConclusionThis study demonstrated that oral anticoagulants may increase the 30-day survival rate of patients with sepsis and AF.
Research on hot water chemical flooding technology in Bohai heavy oil field
Authors: Jian Zhang , Dan Liang , Wensheng Zhou , Qichen Zhang , Liqi Wang , Zhijie Wei 
Published: January 2024

Introduction: The hot water chemical flooding technology effectively improves the fluidity ratio and enhances the horizontal and vertical oil displacement efficiency of the reservoir through the synergistic effect of thermal energy and chemicals, which can further enhance the recovery rate on the basis of throughput thermal recovery.Methods: Based on the geological reservoir parameters of Bohai B oilfield, an oil recovery system evaluation experiment and scheme design study were carried out. Injection parameters such as hot water temperature, chemical agent concentration, and chemical agent dosage that affect the oil recovery effect of hot water chemical flooding were optimized and designed. The development characteristics and effects of two thermal recovery technologies, namely multi thermal fluid throughput and hot water chemical flooding, were compared and analyzed.Results: The results show that with the increase of temperature, the effect of chemical agents on improving the water-oil mobility ratio and reducing the viscosity of crude oil is weakened, and the thermal energy plays a leading role in enhancing oil recovery, but when the temperature is higher than 115°C, the improvement of oil recovery is slowed down, and the comprehensive economic indicators decline rapidly. As the concentration of chemical agent increases, the enhanced oil recovery increases monotonously. When the concentration is 1500 mg/L, the comprehensive economic indicators reach the peak and then decline, indicating that the efficiency of chemical agent decreases. The total amount of chemical agent shall be controlled within 0.25 ~ 0.30 PV. The case calculation shows that hot water chemical flooding can expand the effective radius from 80 m to 400 m, more effectively use the reserves between injection and production wells, increase the oil recovery by 4.8 percentage points, and increase the oil yield by 31.7 m3/t per ton of agent.Discussion: It is suggested that Bohai B Oilfield can adopt hot water chemical flooding after the multiple thermal fluid huff and puff to continuously guarantee the oilfield production.
Historical evolution of cancer genomics research in Latin America: a comprehensive visual and bibliometric analysis until 2023
Authors: Lozada-Martinez Ivan David , Lozada-Martinez Luz Miryam , Cabarcas-Martinez Andrés , Ruiz-Gutierrez Franklin Kevin , Aristizabal Vanegas Jose Gabriel , Amorocho Lozada Katherine Julieth , López-Álvarez Lina María , Fiorillo Moreno Ornella , Navarro Quiroz Elkin 
Published: January 2024

Background: Cancer genomics, as an interdisciplinary research area within the Global Cancer Research agenda, genomics and precision medicine, its important in research and clinical practice in Latin America. To date, there has been no study investigating evolution of this area in this region. The aim of this study was to evaluate for first time, the historical evolution of cancer genomics research in Latin America.Methods: Bibliometric cross-sectional study of documents on cancer genomics published by Latin American authors until 2023 in Scopus was performed. Statistical and visual analysis was performed with R programming language.Results: A total of 1534 documents were obtained. The first document of cancer genomics research was published in 1997, marking the inception of a 26-year evaluation period that extended until 2023. Among the documents, 74.3% (n = 1140) constituted original articles, followed by 22.7% (n = 349) classified as reviews. International collaboration was observed in 6.5% (n = 100) of the articles. Within the compilation of the ten most prolific authors in this region, 90% of them are from Brazil. This observed pattern extends to affiliations as well, wherein the Universidade de São Paulo emerges as the most active institution (n = 255 documents). This arrangement firmly establishes Brazil’s prominence as the preeminent country in the region concerning cancer genomics research, showcasing robust collaboration networks both regionally and intercontinentally. An important transition in the studied hot topics over the last 20 years was identified, from the exploration of the human genome and the characterization of genomic and proteomic cancer profiles (1997–2010) to an in-depth investigation of cancer stem cells and personalized medicine (2011–2023). Among the array of cancer types under study, predominant attention has been directed towards breast, lung, prostate, and leukemia.Conclusion: Over the course of the past 26 years, a favorable and notable evolution has characterized cancer genomics research within Latin America, with Brazil leading the way, which possess a robust network of regional and intercontinental collaboration. Furthermore, the lines of research and hot topics have change in harmony with the region’s objectives, strategies, and requisites.
Full-length transcriptome characterization of Platycladus orientalis based on the PacBio platform
Authors: Liao Ting , Zhang Linyi , Wang Ye , Guo Liqin , Cao Jun , Liu Guobin 
Published: January 2024

As a unique and native conifer in China, Platycladus orientalis is widely used in soil erosion control, garden landscapes, timber, and traditional Chinese medicine. However, due to the lack of reference genome and transcriptome, it is limited to the further molecular mechanism research and gene function mining. To develop a full-length reference transcriptome, tissues from five different parts of P. orientalis and four cone developmental stages were sequenced and analyzed by single-molecule real-time (SMRT) sequencing through the PacBio platform in this study. Overall, 37,111 isoforms were detected by PacBio with an N50 length of 2,317 nt, an average length of 1,999 bp, and the GC content of 41.81%. Meanwhile, 36,120 coding sequences, 5,645 simple sequence repeats (SSRs), 1,201 non-coding RNAs (lncRNAs), and 182 alternative splicing (AS) events with five types were identified using the results obtained from the PacBio transcript isoforms. Furthermore, 1,659 transcription factors (TFs) were detected and belonged to 51 TF families. A total of 35,689 transcripts (96.17%) were annotated through the NCBI nr, KOG, Swiss-Prot and KEGG databases, and 385 transcript isoforms related to 8 types of hormones were identified incorporated into plant hormone signal transduction pathways. The assembly and revelation of the full-length transcriptome of P. orientalis offer a pioneering insight for future investigations into gene function and genetic breeding within Platycladus species.
High monocytic MDSC signature predicts multi-drug resistance and cancer relapse in non-Hodgkin lymphoma patients treated with R-CHOP
Authors: Dhar Sukanya , Chakravarti Mohona , Ganguly Nilanjan , Saha Akata , Dasgupta Shayani , Bera Saurav , Sarkar Anirban , Roy Kamalika , Das Juhina , Bhuniya Avishek , Ghosh Sarbari , Sarkar Madhurima , Hajra Srabanti , Banerjee Saptak , Pal Chiranjib , Saha Bhaskar , Mukherjee Kalyan Kusum , Baral Rathindranath , Bose Anamika 
Published: January 2024

IntroductionNon-Hodgkin Lymphoma (NHL) is a heterogeneous lymphoproliferative malignancy with B cell origin. Combinatorial treatment of rituximab, cyclophsphamide, hydroxydaunorubicin, oncovin, prednisone (R-CHOP) is the standard treatment regimen for NHL, yielding a complete remission (CR) rate of 40-50%. Unfortunately, considerable patients undergo relapse after CR or initial treatment, resulting in poor clinical implications. Patient’s response to chemotherapy varies widely from static disease to cancer recurrence and later is primarily associated with the development of multi-drug resistance (MDR). The immunosuppressive cells within the tumor microenvironment (TME) have become a crucial target for improving the therapy efficacy. However, a better understanding of their involvement is needed for distinctive response of NHL patients after receiving chemotherapy to design more effective front-line treatment algorithms based on reliable predictive biomarkers.MethodsPeripheral blood from 61 CD20+ NHL patients before and after chemotherapy was utilized for immunophenotyping by flow-cytometry at different phases of treatment. In-vivo and in-vitro doxorubicin (Dox) resistance models were developed with murine Dalton’s lymphoma and Jurkat/Raji cell-lines respectively and impact of responsible immune cells on generation of drug resistance was studied by RT-PCR, flow-cytometry and colorimetric assays. Gene silencing, ChIP and western blot were performed to explore the involved signaling pathways.ResultsWe observed a strong positive correlation between elevated level of CD33+CD11b+CD14+CD15- monocytic MDSCs (M-MDSC) and MDR in NHL relapse cohorts. We executed the role of M-MDSCs in fostering drug resistance phenomenon in doxorubicin-resistant cancer cells in both in-vitro, in-vivo models. Moreover, in-vitro supplementation of MDSCs in murine and human lymphoma culture augments early expression of MDR phenotypes than culture without MDSCs, correlated well with in-vitro drug efflux and tumor progression. We found that MDSC secreted cytokines IL-6, IL-10, IL-1β are the dominant factors elevating MDR expression in cancer cells, neutralization of MDSC secreted IL-6, IL-10, IL-1β reversed the MDR trait. Moreover, we identified MDSC secreted IL-6/IL-10/IL-1β induced STAT1/STAT3/NF-κβ signaling axis as a targeted cascade to promote early drug resistance in cancer cells.ConclusionOur data suggests that screening patients for high titre of M-MDSCs might be considered as a new potential biomarker and treatment modality in overcoming chemo-resistance in NHL patients.
Causal relationship between the gut microbiome and basal cell carcinoma, melanoma skin cancer, ease of skin tanning: evidence from three two-sample mendelian randomisation studies
Authors: Lou Jiaqi , Cui Shengyong , Li Jiliang , Jin Guoying , Fan Youfen , Huang Neng 
Published: January 2024

ObjectivesThe present study used publicly available genome-wide association study (GWAS) summary data to perform three two-sample Mendelian randomization (MR) studies, aiming to examine the causal links between gut microbiome and BCC, melanoma skin cancer, ease of skin tanning.MethodsSNPs associated with exposures to basal cell carcinoma, melanoma skin cancer and ease of skin tanning from the genome-wide association study data of UK Biobank and MRC-IEU (MRC Integrative Epidemiology Unit), and the meta-analysis data from Biobank and MRC-IEU were used as instrumental variables (IVs). The casual estimates were assessed with a two-sample Mendelian randomisation test using the inverse-variance-weighted (IVW) method, Wald ratio, MR-Egger method, maximum likelihood, weighted median, simple mode, and weighted mode.ResultsAfter the application of MR analysis, diffirent effects of multiple groups of gut microbiota was observed for BCC, melanoma skin cancer and ease of skin tanning. The relationships between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning were supported by a suite of sensitivity analyses, with no statistical evidence of instrument heterogeneity or horizontal pleiotropy. Further investigation is required to explore the relationship between between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning.ConclusionOur study initially identified potential causal roles between the gut microbiome and BCC, melanoma skin cancer, ease of skin tanning, and highlighted the role of gut microbiome in the progression of basal cell carcinoma, melanoma skin cancer, ease of skin tanning.
Brain FADE syndrome: the final common pathway of chronic inflammation in neurological disease
Authors: Hanafy Khalid A. , Jovin Tudor G. 
Published: January 2024

ImportanceWhile the understanding of inflammation in the pathogenesis of many neurological diseases is now accepted, this special commentary addresses the need to study chronic inflammation in the propagation of cognitive Fog, Asthenia, and Depression Related to Inflammation which we name Brain FADE syndrome. Patients with Brain FADE syndrome fall in the void between neurology and psychiatry because the depression, fatigue, and fog seen in these patients are not idiopathic, but instead due to organic, inflammation involved in neurological disease initiation.ObservationsA review of randomized clinical trials in stroke, multiple sclerosis, Parkinson’s disease, COVID, traumatic brain injury, and Alzheimer’s disease reveal a paucity of studies with any component of Brain FADE syndrome as a primary endpoint. Furthermore, despite the relatively well-accepted notion that inflammation is a critical driving factor in these disease pathologies, none have connected chronic inflammation to depression, fatigue, or fog despite over half of the patients suffering from them.Conclusions and relevanceBrain FADE Syndrome is important and prevalent in the neurological diseases we examined. Classical “psychiatric medications” are insufficient to address Brain FADE Syndrome and a novel approach that utilizes sequential targeting of innate and adaptive immune responses should be studied.
Elucidating the susceptibility to breast cancer: an in-depth proteomic and transcriptomic investigation into novel potential plasma protein biomarkers
Authors: Wang Yang , Yi Kexin , Chen Baoyue , Zhang Bailin , Jidong Gao 
Published: January 2024

Objectives: This study aimed to identify plasma proteins that are associated with and causative of breast cancer through Proteome and Transcriptome-wide association studies combining Mendelian Randomization.Methods: Utilizing high-throughput datasets, we designed a two-phase analytical framework aimed at identifying novel plasma proteins that are both associated with and causative of breast cancer. Initially, we conducted Proteome/Transcriptome-wide association studies (P/TWAS) to identify plasma proteins with significant associations. Subsequently, Mendelian Randomization was employed to ascertain the causation. The validity and robustness of our findings were further reinforced through external validation and various sensitivity analyses, including Bayesian colocalization, Steiger filtering, heterogeneity and pleiotropy. Additionally, we performed functional enrichment analysis of the identified proteins to better understand their roles in breast cancer and to assess their potential as druggable targets.Results: We identified 5 plasma proteins demonstrating strong associations and causative links with breast cancer. Specifically, PEX14 (OR = 1.201, p = 0.016) and CTSF (OR = 1.114, p &lt; 0.001) both displayed positive and causal association with breast cancer. In contrast, SNUPN (OR = 0.905, p &lt; 0.001), CSK (OR = 0.962, p = 0.038), and PARK7 (OR = 0.954, p &lt; 0.001) were negatively associated with the disease. For the ER-positive subtype, 3 plasma proteins were identified, with CSK and CTSF exhibiting consistent trends, while GDI2 (OR = 0.920, p &lt; 0.001) was distinct to this subtype. In ER-negative subtype, PEX14 (OR = 1.645, p &lt; 0.001) stood out as the sole protein, even showing a stronger causal effect compared to breast cancer. These associations were robustly supported by colocalization and sensitivity analyses.Conclusion: Integrating multiple data dimensions, our study successfully pinpointed plasma proteins significantly associated with and causative of breast cancer, offering valuable insights for future research and potential new biomarkers and therapeutic targets.
A task-driven cerebral angiographic imaging based on CT perfusion
Authors: Wang Cheng , Chen Siqi , Mi Donghua 
Published: January 2024

IntroductionCurrent clinical computed tomography arteriography (cCTA) and clinical computed tomography venography (cCTV) images often display restricted cerebrovascular profiles, incomplete brain tissue segmentation, and incomplete artery-vein segmentation. Especially for vessels associated with diseases, capturing their complete profiles proves challenging.MethodsIn this work, we developed a Task-driven Cerebral Angiographic Imaging (TDCAI) technique using computed tomography perfusion (CTP) images of stroke patients. A evaluation on intracranial hemorrhagic stroke (IHS) and acute ischemic stroke (AIS) cases was performed with CT perfusion imaging. The TDCAI technique processed the CTP images, resulting in supplementary diagnostic images, including CTA, CTV, centerline images of the vessels-of-interest [internal carotid artery (ICA) for AIS patients, Labbé vein for IHS patients], and straightened images of the vessels-of-interest.ResultsWe conducted a comparison between the obtained CTA/CTV images and the cCTA/cCTV images in terms of overall image quality and visibility of the vessels-of-interest. By constructing a virtual vascular phantom, we extracted its centerline and compared it with the actual centerline to calculate maximum and average deviations. This allowed us to evaluate both the accuracy of the centerline extraction algorithm and its capability to resist the influence of side branches. We assessed whether vascular stenosis and dilatation could be expressed in straightened vessel images, conducting statistical analyses to establish the superiority of TDCAI technique.DiscussionThis study proposes a TDCAI technique to eliminate bone and soft tissue interference, effectively segregate the comprehensive cerebral venous and arterial systems, and extract centerlines and straighten the vessels-of-interest, which would aid doctors in assessing the outflow profiles of vessels after a stroke and seeking imaging biomarkers correlated with clinical outcomes.
Increasing striatal dopamine release through repeated bouts of theta burst transcranial magnetic stimulation of the left dorsolateral prefrontal cortex. A 18F-desmethoxyfallypride positron emission tomography study
Authors: Shaikh Usman Jawed , Pellicano Antonello , Schüppen Andre , Heinzel Alexander , Winz Oliver H. , Herzog Hans , Mottaghy Felix M. , Binkofski Ferdinand 
Published: January 2024

IntroductionTranscranial Magnetic Stimulation (TMS) can modulate fronto-striatal connectivity in the human brain. Here Positron Emission Tomography (PET) and neuro-navigated TMS were combined to investigate the dynamics of the fronto-striatal connectivity in the human brain. Employing 18F-DesmethoxyFallypride (DMFP) – a Dopamine receptor-antagonist – the release of endogenous dopamine in the striatum in response to time-spaced repeated bouts of excitatory, intermittent theta burst stimulation (iTBS) of the Left-Dorsolateral Prefrontal Cortex (L-DLPFC) was measured.Methods23 healthy participants underwent two PET sessions, each one with four blocks of iTBS separated by 30 minutes: sham (control) and verum (90% of individual resting motor threshold). Receptor Binding Ratios were collected for sham and verum sessions across 37 time frames (about 130 minutes) in striatal sub-regions (Caudate nucleus and Putamen).ResultsVerum iTBS increased the dopamine release in striatal sub-regions, relative to sham iTBS. Dopamine levels in the verum session increased progressively across the time frames until frame number 28 (approximately 85 minutes after the start of the session and after three iTBS bouts) and then essentially remained unchanged until the end of the session.ConclusionResults suggest that the short-timed iTBS protocol performed in time-spaced blocks can effectively induce a dynamic dose dependent increase in dopaminergic fronto-striatal connectivity. This scheme could provide an alternative to unpleasant and distressing, long stimulation protocols in experimental and therapeutic settings. Specifically, it was demonstrated that three repeated bouts of iTBS, spaced by short intervals, achieve larger effects than one single stimulation. This finding has implications for the planning of therapeutic interventions, for example, treatment of major depression.