Miracle-dz/UniFAR-FTUs huggingface dataset:
Endoscopic full-thickness resection in the colorectum: a single-center case series evaluating indication, efficacy and safety

Abstract Background and study aims Endoscopic full-thickness resection (eFTR) allows en-bloc and transmural resection of colorectal lesions for which other advanced endoscopic techniques are unsuitable. We present our experience with a novel “clip first, cut later” eFTR-device and evaluate its indications, efficacy and safety. Patients and methods From July 2015 through October 2017, 51 eFTR-procedures were performed in 48 patients. Technical success and R0-resection rates were prospectively recorded and retrospectively analyzed. Results Indications for eFTR were non-lifting adenoma (n = 19), primary resection of malignant lesion (n = 2), resection of scar tissue after incomplete endoscopic resection of low-risk T1 colorectal carcinoma (n = 26), adenoma involving a diverticulum (n = 2) and neuroendocrine tumor (n = 2). Two lesions were treated by combining endoscopic mucosal resection and eFTR. Technical success was achieved in 45 of 51 procedures (88 %). Histopathology confirmed full-thickness resection in 43 of 50 specimens (86 %) and radical resection (R0) in 40 procedures (80 %). eFTR-specimens, obtained for indeterminate previous T1 colorectal carcinoma resection, were free of residual carcinoma in 25 of 26 cases (96 %). In six patients (13 %) a total of eight adverse events occurred within 30 days after eFTR. One perforation occurred, which was corrected endoscopically. No emergency surgery was necessary. Conclusion In this study eFTR appears to be safe and effective for the resection of colorectal lesions. Technical success, R0-resection and major adverse events rate were reasonable and comparable with eFTR data reported elsewhere. Mean specimen diameter (23 mm) limits its use to relatively small lesions. A clinical algorithm for eFTR case selection is proposed. eFTR ensured local radical excision where other endoscopic techniques did not suffice and reduced the need for surgery in selected cases.
Prediction of cognitive dysfunction after resuscitation – a systematic review

Cardiac arrest (CA) due to cardiovascular disease is the leading cause of death in developed countries. It is estimated that over 350,000 people in Europe suffer from out-of-hospital cardiac arrest. According to the literature, the longer the episode of cardiac arrest, the greater the risk of cognitive impairment, especially short-term memory, as well as immediate and delayed recall. Other common dysfunctions include attention deficits and executive function disorders. The aim of this systematic review was to summarize current research on cognitive impairment in patients after sudden cardiac arrest. The electronic databases PubMed/MEDLINE, OVID, Web of Science, and EBSCO were searched using the following key words: ‘sudden cardiac arrest’, ‘out-of-hospital cardiac arrest’, ‘cognitive function’, ‘cognitive impairment’, ‘functional outcome’, ‘cardiopulmonary resuscitation’. The most recent studies from the last 7 years (2011–2018) were included. Cognitive disorders occurred in a broad range of cases: from 13% to even 100%. In one study, cognitive deficits did not occur at all. Amongst the reviewed articles only two studies were carried out on a large group of patients. The remaining studies were conducted on a small group of respondents; therefore there was no possibility to generalize the results to the entire population. The areas in which the most cognitive impairment occurred were memory, executive functions and visual–motor skills. One of the conclusions derived from the reviewed literature is the importance of continuous training of cognitive functions, especially for people with cardiovascular risk.
Streptococcus pyogenes Causing Skin and Soft Tissue Infections Are Enriched in the Recently Emerged emm89 Clade 3 and Are Not Associated With Abrogation of CovRS

Although skin and soft tissue infections (SSTI) are the most common focal infections associated with invasive disease caused by Streptococcus pyogenes (Lancefield Group A streptococci - GAS), there is scarce information on the characteristics of isolates recovered from SSTI in temperate-climate regions. In this study, 320 GAS isolated from SSTI in Portugal were characterized by multiple typing methods and tested for antimicrobial susceptibility and SpeB activity. The covRS and ropB genes of isolates with no detectable SpeB activity were sequenced. The antimicrobial susceptibility profile was similar to that of previously characterized isolates from invasive infections (iGAS), presenting a decreasing trend in macrolide resistance. However, the clonal composition of SSTI between 2005 and 2009 was significantly different from that of contemporary iGAS. Overall, iGAS were associated with emm1 and emm3, while SSTI were associated with emm89, the dominant emm type among SSTI (19%). Within emm89, SSTI were only significantly associated with isolates lacking the hasABC locus, suggesting that the recently emerged emm89 clade 3 may have an increased potential to cause SSTI. Reflecting these associations between emm type and disease presentation, there were also differences in the distribution of emm clusters, sequence types, and superantigen gene profiles between SSTI and iGAS. According to the predicted ability of each emm cluster to interact with host proteins, iGAS were associated with the ability to bind fibrinogen and albumin, whereas SSTI isolates were associated with the ability to bind C4BP, IgA, and IgG. SpeB activity was absent in 79 isolates (25%), in line with the proportion previously observed among iGAS. Null covS and ropB alleles (predicted to eliminate protein function) were detected in 10 (3%) and 12 (4%) isolates, corresponding to an underrepresentation of mutations impairing CovRS function in SSTI relative to iGAS. Overall, these results indicate that the isolates responsible for SSTI are genetically distinct from those recovered from normally sterile sites, supporting a role for mutations impairing CovRS activity specifically in invasive infection and suggesting that this role relies on a differential regulation of other virulence factors besides SpeB.
A Survey of Neighbourhood Construction Models for Categorizing Data Points

Finding neighbourhood structures is very useful in extracting valuable relationships among data samples. This paper presents a survey of recent neighbourhood construction algorithms for pattern clustering and classifying data points. Extracting neighbourhoods and connections among the points is extremely useful for clustering and classifying the data. Many applications such as detecting social network communities, bundling related edges, and solving location and routing problems all indicate the usefulness of this problem. Finding data point neighbourhood in data mining and pattern recognition should generally improve knowledge extraction from databases. Several algorithms of data point neighbourhood construction have been proposed to analyse the data in this sense. They will be described and discussed from different aspects in this paper. Finally, the future challenges concerning the title of the present paper will be outlined.
Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model

Clostridium difficile infection (CDI) is a major cause of infectious diarrhea among hospitalized patients. Probiotics could be instrumental in restoring the intestinal dysbiosis caused by CDI. Here, we examined the protective effect of Pediococcus pentosaceus LI05 in a mouse CDI model. C57BL/6 mice were administrated P. pentosaceus LI05 (LI05 group) or sterile anaerobic PBS (CDI group) everyday for 14 days. Mice were exposed to antibiotics cocktail for 5 days; then challenged with C. difficile strain VPI10463. Mice were monitored daily for survival and weight loss. Colonic tissue and serum samples were assessed for intestinal histopathology, intestinal barrier function and systemic inflammation. The oral administration of P. pentosaceus LI05 improved the survival rate and alleviated the histopathological impact of C. difficile. Compared to the CDI group, the levels of inflammatory mediators in the colon as well as inflammatory cytokines and chemokines in serum were substantially attenuated in the LI05 group. P. pentosaceus LI05 alleviated the CDI-induced of disruption of ZO-1, occludin and claudin-1. Additionally, fecal microbiome analysis showed an enrichment in the abundance of the Porphyromonadaceae and Rikenellaceae, while, the relative abundance of Enterobacteriaceae were decreased. Our results demonstrated that the preventive effect of P. pentosaceus LI05 against CDI was mediated via improving tight junction proteins and down-regulating the inflammatory response. Therefore, P. pentosaceus LI05 could be a promising probiotic in CDI.
Neural reactivation in parietal cortex enhances memory for episodically linked information

Significance Recalling information is useful for more than just accessing memories; it is also a powerful way to enhance long-term memory. Using brain imaging, we discovered that, when trying to remember, people reactivate the specific information they are searching for, along with other information from the same event. The results demonstrate that memories of the past are organized in terms of integrated events and the act of recalling even a small part of an event engages brain networks that have powerful effects on the ability to retain information from the entire event. Remembering is a complex process that involves recalling specific details, such as who you were with when you celebrated your last birthday, as well as contextual information, such as the place where you celebrated. It is well established that the act of remembering enhances long-term retention of the retrieved information, but the neural and cognitive mechanisms that drive memory enhancement are not yet understood. One possibility is that the process of remembering results in reactivation of the broader episodic context. Consistent with this idea, in two experiments, we found that multiple retrieval attempts enhanced long-term retention of both the retrieved object and the nontarget object that shared scene context, compared with a restudy control. Using representational similarity analysis of fMRI data in experiment 2, we found that retrieval resulted in greater neural reactivation of both the target objects and contextually linked objects compared with restudy. Furthermore, this reactivation occurred in a network of medial and lateral parietal lobe regions that have been linked to episodic recollection. The results demonstrate that retrieving a memory can enhance retention of information that is linked in the broader event context and the hippocampus and a posterior medial network of parietal cortical areas (also known as the Default Network) play complementary roles in supporting the reactivation of episodically linked information during retrieval.
Group B Streptococcal Neonatal and Early Infancy Infections in Iceland, 1976-2015.

BACKGROUND Despite a risk-based peripartum chemoprophylaxis approach in Iceland since 1996, Streptococcus agalactiae [group B streptococci (GBS)] remains an important cause of early-onset [<7 days, early-onset disease (EOD)] and late-onset disease (LOD; 7 days to 3 months). METHODS We studied GBS invasive disease in children <1 year in Iceland in 1976-2015. Bacteria (n = 98) were characterized by susceptibility to a panel of antimicrobials, capsular serotyping, resistance genes, surface protein and pilus-locus profiling and multilocus sequence typing. RESULTS Both EOD and LOD increased during the early years, but while EOD subsequently decreased from 0.7/1000 live births in 1991-1995 to 0.2/1000 in 2011-2015, LOD showed a nonsignificant decrease from its peak value of 0.6/1000 in 2001-2005 to 0.4/1000 in 2006-2015. Serotype III was the most frequently found (n = 48), represented mostly by the hypervirulent lineage CC17/III/rib/PI-1+PI-2b (62%), but also by CC19/III/rib/PI-1+PI-2a (35%) frequently associated with colonization. Serotype Ia (n = 22) was represented by CC23/Ia/eps/PI-2a (68%) and CC7/Ia/bca/PI-1+PI-2b (23%) of possible zoonotic origin. Resistance to erythromycin and clindamycin was increasingly detected in the last years of the study (5 of the 9 cases were isolated after 2013), including representatives of a multiresistant CC17/III/rib/PI-2b sublineage described recently in other countries and expressing resistance to erythromycin, clindamycin and streptomycin. CONCLUSIONS The risk-based chemoprophylaxis adopted in Iceland possibly contributed to the decline of EOD but has had limited effect on LOD. GBS causing neonatal and early infancy invasive infections in Iceland are genetically diverse, and the recent emergence of antimicrobial resistant lineages may reduce the choices for prophylaxis and therapy of these infections.
Circadian variations in the onset of aortic dissection in northern China

ABSTRACT This study explored the periodic changes in the onset of aortic dissection in a single center in northern China, with the goal to improve predictability and prevention. We collected the clinical data of 1121 patients from Hebei Province treated for acute aortic dissection at Fuwai Hospital between January 2010 and December 2016. The patterns of aortic dissection during different periods of each day, each month, and each quarter of a year were analyzed. Variations in the number of cases were summarized for weekdays, weekends, and different periods of a day in each season. We compared the differences in gender, age, body mass index, Marfan syndrome, hypertension, and the type of aortic dissection during different time periods and different seasons. In the study, 774 patients (69.1%) with type A aortic dissection and 347 patients (30.9%) with type B aortic dissection were included. The average age of 1121 patients was 51.4 ± 12.0 years. Overall, the peak period for the onset of aortic dissection in a day was between 13:00 and 18:00. There was no statistically significant difference in the number of cases between weekdays and weekend (P = 0.94). Most cases occurred in winter (30.9%); the rate of onset was the lowest in summer (16.6%). No statistically significant difference was observed between male and female patients in terms of variations during different periods of a day (P = 0.45) and seasons (P = 0.12). In conclusion, aortic dissection displayed circadian and seasonal patterns in northern China. Onset of the disease peaked between 13:00 and 18:00 in a day. Winter was the peak season for the onset of acute aortic dissection, regardless of sex, type of dissection and age.
Levels of the Autophagy-Related 5 Protein Affect Progression and Metastasis of Pancreatic Tumors in Mice.

BACKGROUND AND AIMS Cells in pancreatic ductal adenocarcinoma (PDAC) undergo autophagy, but its effects vary with tumor stage and genetic factors. We investigated the consequences of varying levels of the autophagy related 5 (Atg5) protein on pancreatic tumor formation and progression. METHODS We generated mice that express oncogenic Kras in primary pancreatic cancer cells and have homozygous disruption of Atg5 (A5;Kras) or heterozygous disruption of Atg5 (A5+/-;Kras), and compared them with mice with only oncogenic Kras (controls). Pancreata were analyzed by histology and immunohistochemistry. Primary tumor cells were isolated and used to perform transcriptome, metabolome, intracellular calcium, extracellular cathepsin activity, and cell migration and invasion analyses. The cells were injected into wild-type littermates, and orthotopic tumor growth and metastasis were monitored. Atg5 was knocked down in pancreatic cancer cell lines using small hairpin RNAs; cell migration and invasion were measured, and cells were injected into wild-type littermates. PDAC samples were obtained from independent cohorts of patients and protein levels were measured on immunoblot and immunohistochemistry; we tested the correlation of protein levels with metastasis and patient survival times. RESULTS A5+/-;Kras mice, with reduced Atg5 levels, developed more tumors and metastases, than control mice, whereas A5;Kras mice did not develop any tumors. Cultured A5+/-;Kras primary tumor cells were resistant to induction and inhibition of autophagy, had altered mitochondrial morphology, compromised mitochondrial function, changes in intracellular Ca2+ oscillations, and increased activity of extracellular cathepsin L and D. The tumors that formed in A5+/-;Kras mice contained greater numbers of type 2 macrophages than control mice, and primary A5+/-;Kras tumor cells had up-regulated expression of cytokines that regulate macrophage chemoattraction and differentiation into M2 macrophage. Knockdown of Atg5 in pancreatic cancer cell lines increased their migratory and invasive capabilities, and formation of metastases following injection into mice. In human PDAC samples, lower levels of ATG5 associated with tumor metastasis and shorter survival time. CONCLUSIONS In mice that express oncogenic Kras in pancreatic cells, heterozygous disruption of Atg5 and reduced protein levels promotes tumor development, whereas homozygous disruption of Atg5 blocks tumorigenesis. Therapeutic strategies to alter autophagy in PDAC should consider the effects of ATG5 levels to avoid the expansion of resistant and highly aggressive cells.
Migrating Web Applications from Monolithic Structure to Microservices Architecture

In the traditional software development and deployment, the centralized monolithic is always adopted, as the modules are tightly coupled, which caused many inconvenience in software DevOps. The modules with bottlenecks in monolithic application cannot be extend separately as the application is an integral part, and different module cannot use different technology stack. To prolong the lifecycle of the monolithic applications, its need to migrated it to microservice architecture. Due to the complex logic and large number of third party framework libraries depended, get an accurate comprehensive of the application characteristics is challenging. The existing research mostly based on the static characteristics, lack of consideration of the runtime dynamic characteristics, and the completeness and accuracy of the static analysis is inadequate. To resolve above problems, we combined static and dynamic analysis to get static structure and runtime behavior characteristics of monolithic application. We employed the coupling among functions to evaluate the degree of dependence, and through function clustering to achieve the migration of legacy monolithic applications and its data to microservices architecture. Through the empirical study of migrate the typical legacy project to microservices, it is proved that we proposed method can offer precise guidance and assistance in the migration procedure. Experiments show that the method has high accuracy and low performance cost.
Profiling Developer Expertise across Software Communities with Heterogeneous Information Network Analysis

Knowing developer expertise is critical for achieving effective task allocation. However, it is of great challenge to accurately profile the expertise of developers over the Internet as their activities often disperse across different online communities. In this regard, the existing works either merely concern a single community, or simply sum up the expertise in individual communities. The former suffers from low accuracy due to incomplete data, while the latter impractically assumes that developer expertise is completely independent and irrelavant across communities. To overcome those limitations, we propose a new approach to profile developer expertise across software communities through heterogeneous information network (HIN) analysis. A HIN is first built by analyzing the developer activities in various communities, where nodes represent objects like developers and skills, and edges represent the relations among objects. Second, as random walk with restart (RWR) is known for its ability to capture the global structure of the whole network, we adopt RWR over the HIN to estimate the proximity of developer nodes and skill nodes, which essentially reflects developer expertise. Based on the data of 72,645 common users of GitHub and Stack Overflow, we conducted an empirical study and evaluated developer expertise using proposed approach. To evaluate the effect of our approach, we use the obtained expertise to estimate the competency of developers in answering the questions posted in Stack Overflow. The experimental results demonstrate the superiority of our approach over existing methods.
Advanced therapeutics in focal and segmental glomerulosclerosis

Focal segmental glomerulosclerosis (FSGS) is a glomerulonephritis with podocyte injury. The renal prognosis of FSGS is relative poor. The overall remission rate of the FSGS patients with nephrotic syndrome to immunosuppressive treatments was reported as 47–66%, highlighting its therapeutic challenge—lacking in sufficient evidence‐based interventions. In first‐line treatment of nephrotic syndrome, daily oral prednisolone is a commonly used drug, whereas optimal treatment strategies, like indications and duration, remain controversial. Calcineurin inhibitor and cyclophosphamide are recommended in steroid‐dependent/steroid‐resistant patients. However, the high unmet need in effective immunosuppressive treatments calls for the development of new therapy methods. Rituximab, a monoclonal antibody targeting CD20 B‐cells, could increase the complete or partial remission rate, and decrease the relapse rate based on several previous studies on FSGS. In addition, the using of rituximab could potentially help the FSGS patients to stop the concomitant therapy include steroid and immunosuppressive agents. Other treatment options like adalimumab or abatacept also showed potential therapeutic effect, but still required larger Randomized Controlled Trial study to determine its efficiency and safety. Besides, expanding understanding of the genetic basis of FSGS is necessary to investigate new therapeutic agents. With the unsatisfied patients’ outcome under the current treatments, innovation should be encouraged on the treatment strategy based on Kidney Disease: Improving Global Outcomes guideline and international collaborations are required for the potential novel immunosuppressive or immunomodulatory therapies.
Reducing emergency hospital admissions: a population health complex intervention of an enhanced model of primary care and compassionate communities.

BACKGROUND Reducing emergency admissions to hospital has been a cornerstone of healthcare policy. Little evidence exists to show that systematic interventions across a population have achieved this aim. The authors report the impact of a complex intervention over a 44-month period in Frome, Somerset, on unplanned admissions to hospital. AIM To evaluate a population health complex intervention of an enhanced model of primary care and compassionate communities on population health improvement and reduction of emergency admissions to hospital. DESIGN AND SETTING A cohort retrospective study of a complex intervention on all emergency admissions in Frome Medical Practice, Somerset, compared with the remainder of Somerset, from April 2013 to December 2017. METHOD Patients were identified using broad criteria, including anyone giving cause for concern. Patient-centred goal setting and care planning combined with a compassionate community social approach was implemented broadly across the population of Frome. RESULTS There was a progressive reduction, by 7.9 cases per quarter (95% confidence interval [CI] = 2.8 to 13.1, P = 0.006), in unplanned hospital admissions across the whole population of Frome during the study period from April 2013 to December 2017, a decrease of 14.0%. At the same time, there was a 28.5% increase in admissions per quarter within Somerset, with a rise in the number of unplanned admissions of 236 per quarter (95% CI = 152 to 320, P<0.001). CONCLUSION The complex intervention in Frome was associated with highly significant reductions in unplanned admissions to hospital, with a decrease in healthcare costs across the whole population of Frome.