Miracle-dz/UniFAR-FTUs huggingface dataset:
Trends and outcomes of percutaneous endoscopic gastrostomy in hospitalized patients with malignant and nonmalignant ascites: a nationwide population study

Background Patients with ascites resulting from chronic debilitating diseases often require non-oral enteral nutrition and undergo placement of a percutaneous endoscopic gastrostomy (PEG) tube. The aim of our study was to assess the nationwide trends and outcomes of PEG tube placement among patients with ascites. Methods Using the Nationwide Inpatient Sample (NIS), we conducted a retrospective analysis of adult patients (≥18 years) who underwent PEG tube placement (n=789,167) from 2010-2014. We divided these patients into 2 groups: with or without ascites. We compared demographics, complications, and in-hospital outcomes between the groups. STATA-13 was used for statistical analysis. Statistical significance was assigned at P<0.05. Results Patients with ascites who underwent PEG tube placement were found to have a significantly higher rate of complications, including peritonitis (7.52 vs. 0.72%; P<0.001), aspiration pneumonia (20.41 vs. 2.69%; P<0.001), hemoperitoneum (0.72 vs. 0.19%; P<0.001), procedure-related hemorrhage (1.69 vs. 0.9%; P<0.001) and esophageal perforation (0.51 vs. 0.47%; P<0.001). In addition, these patients also had higher in-hospital mortality (16.33% vs. 7.02%; P<0.001) despite having a relatively lower prevalence of comorbidities. Length of stay was longer in the ascites group (28.08 vs. 19.45 days; 0.001). Over the study period, however, we observed an increasing trend for PEG tube placement in hospitalized patients with ascites. Conclusion PEG tube placement in hospitalized patients with ascites is associated with significantly higher mortality, a longer stay, and more procedure-related complications.
Frequency of typhoon occurrence accounts for the Poisson distribution of human leptospirosis cases across the different geographic regions in the Philippines

Objective: To study the distribution of human leptospirosis cases across the different geographic regions in the Philippines in 2015-2017 and to determine the relationship between the frequency of typhoon occurrence and human leptospirosis cases. Methods: Information on the frequency of leptospirosis cases and typhoon occurrence across the different regions in the Philippines from 2015 to 2017 was retrieved from the databases of the Department of Health and the Philippine Atmospheric, Geophysical, and Astronomical Services Administration, respectively. Descriptive measures on the prevalent cases and occurrence of typhoons across the different regions were summarized. Linear regression analysis was employed to establish the functional relationship between leptospirosis cases and typhoon occurrence. The distribution of human leptospirosis cases was assessed using the Poisson distribution. Results: The frequency of typhoon occurrence accounted for the significant linear variation in the geographic distribution of human leptospirosis cases in the Philippines (P<0.001). Moreover, the human leptospirosis cases obeyed a Poisson distribution (λ=6.89, P<0.001). Conclusions: The Philippines has frequently experienced severe weather perturbations such as typhoons resulting in flooding and subsequently increasing the risk of transmitting bacterial infections including leptospirosis. Information obtained regarding the determinants and distribution of human leptospirosis will provide better understanding of the disease propagation for subsequent design of optimal disease prevention measures, appropriate resource allocation, effective control strategies, and necessary public health programs.
Effect of a Supervised Peridialytic Exercise Program on Serum Asymmetric Dimethylarginine in Maintenance Hemodialysis Patients

End-stage renal disease (ESRD) patients treated with maintenance haemodialysis (MHD) have alarmingly high atherosclerotic cardiovascular disease morbidity and mortality. Nitric oxide (NO) is the principal endogenous antiatherosclerotic molecule. Increased asymmetric dimethylarginine (ADMA), an endogenous NO synthase inhibitor, was strongly implicated in endothelial dysfunction, premature atherosclerosis, vascular events, and mortality. Regular physical exercise effectively decreased serum ADMA in several patient cohorts, but this potential benefit has not been specifically explored among MHD patients. Forty-four middle-aged ESRD patients treated with thrice-weekly MHD for ≥6 months completed a 6-months regimen of peridialytic lower limb exercise comprising predialytic 10–12 stretching cycles and 20–30 minutes of intradialytic pedaling cycles. Before and after the study, predialytic haemoglobin, serum ADMA, urea, creatinine, calcium, phosphorus, and C-reactive protein (CRP) were measured. Dialysis adequacy was assessed by single-pool Kt/V. The average total physical activity (PA) level was assessed by the International Physical Activity Questionnaire (IPAQ). P values <0.05 denoted a statistical significance. The overall level of PA, on both categorical and continuous scales, has significantly increased after application of the exercise program. However, S. ADMA increased from a median of 2375 to 3000 ng/mL (P=0.016). Thirty-one patients sustained an increase in S. ADMA (ADMA_Inc), whereas 13 patients had a declining or stable S. ADMA (ADMA_Dec). Compared with ADMA_Inc, ADMA_Dec patients had significantly higher Kt/V (P=0.02), higher grade of the basal general PA level (P=0.017), and significantly fewer intradialytic hypotension episodes (IDHs) (P=0.019). The increase in the S. ADMA and the poststudy S. ADMA level had statistically significant positive correlations with the number of IDHs (r = 0.401, P=0.007 and r = 0.305, P=0.044, respectively). A 6-month program of combined aerobic and resistance peridialytic exercise failed to reduce S. ADMA in most MHD patients studied. A modest S. ADMA decline, however, occurred in patients with higher basal PA levels, higher Kt/V, and less IDHs. A potential exercise benefit may be promoted by a multidisciplinary approach targeting increased PA, improved dialysis efficiency, and prevention of IDHs.
Deep transfer learning of brain shape morphometry predicts Body Mass Index (BMI) in the UK Biobank

Prior studies show that obesity is associated with accelerated brain aging and specific patterns of brain atrophy. Finerscale mapping of the effects of obesity on the brain would help to understand how it promotes or interacts with disease effects, but so far, the influence of the obesity on finer-scale maps of anatomy remains unclear. In this study, we propose a deep transfer learning network based on Optimal Mass Transport (OMTNet) to classify individuals with normal versus overweight/obese body mass index (BMI) using vertex-wise brain shape metrics extracted from structural MRI scans from the UK Biobank study. First, an area-preserving mapping was used to project 3D brain surface meshes onto 2D planar meshes. Vertex-wise maps of brain metrics such as cortical thickness were mapped into 2D planar images for each brain surface extracted from each person’s MRI scan. Second, several popular networks pretrained on the ImageNet database, i.e., VGG19, ResNet152 and DenseNet201, were used for transfer learning of brain shape metrics. We combined all shape metrics and generated a metric ensemble classification, and then combined all three networks and generated a network ensemble classification. The results reveal that transfer learning always outperforms direct learning, and we obtained accuracies of 65.6±0.7% and 62.7±0.7% for transfer and direct learning in the network ensemble classification, respectively. Moreover, surface area and cortical thickness, especially in the left hemisphere, consistently achieved the highest classification accuracies, together with subcortical shape metrics. The findings suggest a significant and classifiable influence of obesity on brain shape. Our proposed OMTNet method may offer a powerful transfer learning framework that can be extended to other vertex-wise brain structural and functional imaging measures.
Numerical Modeling of Tsunami-Induced Scouring around a Square Column: Performance Assessment of FLOW-3D and Delft3D

ABSTRACT April Le Quéré, P.; Nistor, I. , and Mohammadian, A. , 2020. Numerical modeling of tsunami-induced scouring around a square column: Performance assessment of FLOW-3D and Delft3D. Journal of Coastal Research, 36(6), 1278–1291. Coconut Creek (Florida), ISSN 0749-0208. In recent years, tsunamis have caused considerable damage to coastal infrastructures and inflicted numerous casualties in coastal communities in the impacted regions. The information, which the design requirements for tsunami-resistant infrastructures is based on, is still in its preliminary stages. The focus of the study was to investigate, by means of a numerical model, the scouring occurring around a single, square column subjected to tsunami floods. A three-dimensional (3D) hydrostatic numerical model (Delft3D) and a 3D nonhydrostatic model (FLOW-3D) were used to replicate a series of physical tests conducted at the University of Ottawa, which consisted of a dam-break wave impacting onto a single square column installed over a movable sediment bed. These experimental tests were conducted in the Dambreak Flume at the University of Ottawa. Four different turbulence models and two different sediment-transport models were tested to find the most appropriate combination, which could model the complex flow characteristics associated with a dam-break–type bore. An extensive review of the hydrodynamic and scouring performance of various numerical models was also included in this study.
MetaDigit: Towards A Practical Digits Input System with Few User Effort

Nowadays, smart devices have become increasingly essential in humans' life. However, traditional input methods may not work effectively due to the tiny screen of the devices. Moreover, most learning-based gesture input schemes only perform well in terms of certain metrics such as accuracy, without considering other aspects like response time and user training overhead which are essential for real-world usage scenarios. Without taking the trade-off between different metrics into account, existing learning-based gesture input systems suffer from severe performance degradation in practice. In this paper, we investigate the trade-off between evaluation metrics of mobile interaction systems and then report our attempt towards a more practical digits input system based on our previous work. We propose an acoustic-based device-free digits input system named MetaDigit which achieves over 85% accuracy of real-time digits recognition with even zero-shot from new users.
CML/RAGE Signal Bridges a Common Pathogenesis Between Atherosclerosis and Non-alcoholic Fatty Liver

Non-alcoholic fatty liver disease (NAFLD) has become a common chronic disease in the world. NAFLD is not only a simple intrahepatic lesion, but also affects the occurrence of a variety of extrahepatic complications. In particular, cardiovascular complications are particularly serious, which is the main cause of death in patients with NAFLD. To study the relationship between NAFLD and AS may be a new way to improve the quality of life in patients with NAFLD. As we all known, inflammatory response plays an important role in the occurrence and development of NAFLD and AS. In this study, we found that the accumulation of Nε-carboxymethyllysine (CML) in the liver leads to hepatic steatosis. CML can induce the expression of interleukin (IL-1β), interleukin (IL-6), tumor necrosis factor (TNF-α), C-reactionprotein (CRP) by binding with advanced glycosylation end-product receptor (RAGE) and accelerate the development of AS. After silencing RAGE expression, the expression of pro-inflammatory cytokines was inhibited and liver and aorta pathological changes were relieved. In conclusion, CML/RAGE signal promotes the progression of non-alcoholic fatty liver disease and atherosclerosis. We hope to provide new ideas for the study of liver vascular dialogue in multi organ communication.
Lapatinib Plus Local Radiation Therapy for Brain Metastases From HER-2 Positive Breast Cancer Patients and Role of Trastuzumab: A Systematic Review and Meta-Analysis

Background Intracranial activity of lapatinib has been demonstrated in several studies in patients with human epidermal growth factor receptor-2 positive breast cancers (HER-2+ BC). Stereotactic radiosurgery (SRS) has been increasingly used as the local therapy for brain metastases in breast cancer patients. Increased objective response rate was observed for lapatinib plus whole brain radiotherapy (WBRT) is such patients with high toxicity. Objective We seek to obtain clinical evidence of synergistic efficacy of lapatinib in combination with radiation therapy, in particular, SRS. Materials and methods We carried out a comprehensive research using the following databases: PubMed; Medline; EMBASE; Cochrane library. These databases were searched until 10 June 2020. PRISMA guidelines were followed step by step for carrying out this systematic review and meta-analysis. Review Manager v 5.4 software was used for statistical evaluation of data. Results Overall 6 studies with 843 HER-2 positive breast cancer patients (442 HER-2 amplified disease, 399 luminal B disease) were included in this systematic review and meta-analysis. A total 279 patients had received lapatinib in addition to HER-2 antibody (trastuzumab) plus/minus chemoradiotherapy, while 610 patients had received trastuzumab-based management or only chemoradiotherapy. Lapatinib-based management of BM was associated with significant increase in overall survival (HR 0.63 [0.52, 0.77], p < 0.00001). Combination of the two (trastuzumab plus lapatinib) was associated with increased survival advantage compared to each agent alone (0.55 [0.32, 0.92], p = 0.02). SRS in combination with lapatinib was associated with increased local control (HR 0.47 [0.33, 0.66], p = 0.0001). Ever use of lapatinib with SRS was associated an increased survival as reported in two studies (Shireen et al.: 27.3 vs. 19.5 months, p = 0.03; Kim et al.: 33.3 vs. 23.6 months, p = 0.009). Kim et al. also revealed significant increase in intracranial activity with concurrent lapatinib reporting 57% complete response compared to 38% (p < 0.001) and lower progressive disease rate of 11 vs. 19% (p < 0.001). Risk of radiation necrosis was decreased with lapatinib use. Conclusions Lapatinib has shown intracranial activity and yielded better survival for HER-2+ BC patients with BMs. SRS in combination with ever use of lapatinib had better local control and were associated with better survival. Radiation necrosis risk was reduced with the use of lapatinib.
Modelling plastics exposure for the marine biota: Risk maps for fin whales in the Pelagos Sanctuary (North-Western Mediterranean)

The Mediterranean basin is among the most impacted marine ecoregions globally, being at the same time semi-enclosed by densely populated countries and crossed by trafficked maritime routes. Such anthropogenic pressure threatens both the qual-ity of its waters and the high biodiversity living in them, making the role of Marine Protected Areas (MPAs) crucial for pre-serving species suitable habitats. Under the European Union Marine Strategy Framework Directive, marine litter has been recognized as one of the principal causes of marine pollution, and public awareness on its environmental and biological impacts is raising. Using a quantitative and data-driven modelling approach, here we assess the presence of plastic waste within the feeding grounds of the fin whale Balaenoptera physalus, an endangered cetacean for which there is increasing evidence of impacts due to microplastic ingestion. To this end, we analyze a decade (2000 - 2010) of advection patterns of marine plastic litter, modelled with a Lagrangian approach. Particles are released in the MPA Pelagos, the International Sanctuary for the Protection of Mediterranean Marine Mammals (North-Western Mediterranean, between France, Italy and Monaco), from different sources (i.e., untreated waste along coasts, plastic discharged from rivers and plastic pollution released along maritime shipping routes). Risk of exposure of fin whales to microplastic pollution is evaluated by interlacing plastic litter distribution maps obtained through modelling with maps of suitable habitats obtained from the elaboration of satellite chlorophyll-a data in species-specific visited areas. Our modelling results show that all the three main sources of plastic litter taken into account clearly contribute to impacting cetaceans in the Sanctuary, yet in a different manner. The procedure formalized here can be extended to assess the risk caused by plastic pollution in other MPAs as well as to evaluate possible impacts on other taxa, thus informing targeted actions to tackle the complex issue of marine litter.
Does Shiga Toxin-Producing Escherichia coli and Listeria monocytogenes Contribute Significantly to the Burden of Antimicrobial Resistance in Uruguay?

Shiga toxin-producing Escherichia coli (STEC) and Listeria monocytogenes are worldwide recognized zoonotic pathogens. Recent reports have emerged about the circulation of antimicrobial-resistant STEC and L. monocytogenes isolates. To assess the frequency of antimicrobial resistance and related genes in these pathogens, we studied 45 STEC and 50 L. monocytogenes isolates locally recovered from different sources. Antimicrobial susceptibility testing was performed by disk-diffusion method, and the genomic sequences of three selected STEC and from all 50 L. monocytogenes isolates were analyzed for antibiotic resistance genes. Four STEC and three L. monocytogenes isolates were phenotypically resistant to at least one of the antibiotics tested. Resistance genes aph(3″)-Ib, aph(3′)-Ia, aph(6)-Id, blaTEM−1B, sul2, mef (A), and tet(A) were found in a human STEC ampicillin-resistant isolate. All L. monocytogenes isolates harbored fosX, lin, mdrL, lde fepA, and norB. Overall resistance in L. monocytogenes and STEC was low or middle. However, the high load of resistance genes found, even in susceptible isolates, suggests that these pathogens could contribute to the burden of antimicrobial resistance.
Tethered homing gene drives: A new design for spatially restricted population replacement and suppression

Optimism regarding potential epidemiological and conservation applications of modern gene drives is tempered by concern about the potential unintended spread of engineered organisms beyond the target population. In response, several novel gene drive approaches have been proposed that can, under certain conditions, locally alter characteristics of a population. One challenge for these gene drives is the difficulty of achieving high levels of localized population suppression without very large releases in face of gene flow. We present a new gene drive system, Tethered Homing (TH), with improved capacity for localized population alteration, especially for population suppression. The TH drive is based on driving a payload gene using a homing construct that is anchored to a spatially restricted gene drive. We use a proof of principle mathematical model to show the dynamics of a TH drive that uses engineered underdominance as an anchor. This system is composed of a split homing drive and a two-locus engineered underdominance drive linked to one part of the split drive (the Cas endonuclease). In addition to improved localization, the TH system offers the ability to gradually adjust the genetic load in a population after the initial alteration, with minimal additional release effort.
Experimental Evolution of Campylobacter jejuni Leads to Loss of Motility, rpoN (σ54) Deletion and Genome Reduction

Evolution experiments in the laboratory have focused heavily on model organisms, often to the exclusion of clinically relevant pathogens. The foodborne bacterial pathogen Campylobacter jejuni belongs to a genus whose genomes are small compared to those of its closest genomic relative, the free-living genus Sulfurospirillum, suggesting genome reduction during the course of evolution to host association. In an in vitro experiment, C. jejuni serially passaged in rich medium in the laboratory exhibited loss of flagellar motility–an essential function for host colonization. At early time points the motility defect was often reversible, but after 35 days of serial culture, motility was irreversibly lost in most cells in 5 independently evolved populations. Population re-sequencing revealed disruptive mutations to genes in the flagellar transcriptional cascade, rpoN (σ54)—therefore disrupting the expression of the genes σ54 regulates—coupled with deletion of rpoN in all evolved lines. Additional mutations were detected in virulence-related loci. In separate in vivo experiments, we demonstrate that a phase variable (reversible) motility mutant carrying an adenine deletion within a homopolymeric tract resulting in truncation of the flagellar biosynthesis gene fliR was deficient for colonization in a C57BL/6 IL-10–/– mouse disease model. Re-insertion of an adenine residue partially restored motility and ability to colonize mice. Thus, a pathogenic C. jejuni strain was rapidly attenuated by experimental laboratory evolution and demonstrated genomic instability during this evolutionary process. The changes observed suggest C. jejuni is able to evolve in a novel environment through genome reduction as well as transition, transversion, and slip-strand mutations.
Trauma-Related Guillain–Barré Syndrome: Systematic Review of an Emerging Concept

Guillain–Barré syndrome (GBS) is mainly associated with preceding exposure to an infectious agent, although the precise pathogenic mechanisms and causes remain unknown. Increasing evidence indicates an association between trauma-related factors and GBS. Here, we performed a systematic review, summarized the current scientific literature related to the onset of GBS associated with trauma, and explored the possible pathogenesis. A literature search of various electronic databases was performed up to May 2020 to identify studies reporting diverse trauma-related triggers of GBS. Data were extracted, summarized descriptively, and evaluated with respect to possible mechanisms. In total, 100 publications, including 136 cases and 6 case series involving GBS triggered by injury, surgery, intracranial hemorrhage, and heatstroke, met our eligibility criteria. The median age of the patients was 53 [interquartile range (IQR) 45–63] years, and 72.1% of the patients were male. The median number of days between the trigger to onset of GBS symptoms was 9 (IQR 6.5–13). Overall, 121 patients (89.0%) developed post-injury/surgical GBS, whereas 13 (9.6%) and 2 (1.5%) patients had preexisting spontaneous intracranial hemorrhage and heatstroke, respectively. The main locations of injury or surgeries preceding GBS were the spine and brain. Based on available evidence, we highlight possible mechanisms of GBS induced by these triggers. Moreover, we propose the concept of “trauma-related GBS” as a new research direction, which may help uncover more pathogenic mechanisms than previously considered for typical GBS triggered by infection or vaccination.