Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnosing Necrotizing Fasciitis Using Procalcitonin and a Laboratory Risk Indicator: Brief Overview

Necrotizing fasciitis is a progressive inflammatory disease that requires an early diagnosis to avoid limb salvage and other deadly manifestations. The current protocol is the microbiological and histopathological sampling of the tissue. Once the diagnosis is made, it should be managed with antimicrobial therapy, debridement, and surgical interventions. Such interventions can be invasive and increase the time to treat, which may increase morbidity. Our article discusses procalcitonin, C-reactive protein, and other markers, such as "pain out of proportion,” lactate, creatinine, and creatine kinase, to make a quicker diagnosis before proceeding with invasive procedures. We discussed a similar non-invasive approach called the "Laboratory Risk Indicator for Necrotizing Fasciitis" scoring system that can aid in the early diagnosis of necrotizing fasciitis, which can prompt rapid empiric therapy, reducing the chances of morbidity. This scoring system comprises C-reactive protein, white blood cell count, hemoglobin level, creatinine, sodium, and glucose. Such non-invasive, bedside, and quick tests can help in reducing the time required to make the diagnosis and can affect the course of the disease, hence, improving patient outcomes.
Effect of sleep deprivation on emotional working memory

The emotional dysregulation and impaired working memory found after sleep loss can have severe implications for our daily functioning. Considering the intertwined relationship between emotion and cognition in stimuli processing, there could be further implications of sleep deprivation in high‐complex emotional situations. Although studied separately, this interaction between emotion and cognitive processes has been neglected in sleep research. The aim of the present study was to investigate the effect of 1 night of sleep deprivation on emotional working memory. Sixty‐one healthy participants (mean age: 23.4 years) were either sleep deprived for 1 night (n = 30) or had a normal night’s sleep (n = 31). They performed an N‐back task with two levels of working memory load (1‐back and 3‐back) using positive, neutral and negative picture scenes. Sleep deprivation, compared with full night sleep, impaired emotional working memory accuracy, but not reaction times. The sleep‐deprived participants, but not the controls, responded faster to positive than to negative and neutral pictures. The effect of sleep deprivation was similar for both high and low working memory loads. The results showed that although detrimental in terms of accuracy, sleep deprivation did not impair working memory speed. In fact, our findings indicate that positive stimuli may facilitate working memory processing speed after sleep deprivation.
Serological evidence of duck Tembusu virus infection in free‐grazing ducks, Thailand

Duck Tembusu virus (DTMUV) has been reported in ducks raised in farming system since its emergence in 2010. No information is available on DTMUV infection in free-grazing ducks, which are commonly raised and widespread in several Asian countries. To determine the presence of DTMUV infection in free-grazing ducks in Thailand, retrospective serum samples collected from 1,000 free-grazing ducks during 2008-2015 were tested for DTMUV infection. Our result showed that 91 (9.10%) were positive for DTMUV neutralizing antibodies and DTMUV seropositive ducks have been detected in Thailand since 2008. To further investigate the seroprevalence and geographic distribution of DTMUV infection in free-grazing ducks in Thailand, a cross-sectional serological survey of DTMUV was conducted in 2016. Of 1,200 free-grazing ducks in the 60 flocks from 20 provinces located in the major free-grazing duck raising areas of Thailand, 365 (30.42%) were positive for DTMUV neutralizing antibodies and 56 flocks (93.33%) had at least one DTMUV seropositive duck. Additionally, DTMUV seropositive ducks were observed in all provinces tested. In conclusion, our data demonstrated the presence of DTMUV infection in free-grazing ducks since 2008 and widespread DTMUV infection in free-grazing ducks in Thailand with a relatively high seroprevalence. These findings suggest the potential role of free-grazing ducks in the dissemination of DTMUV and highlight the necessity of systemic DTMUV surveillance in free-grazing ducks in addition to farm ducks for early detection, prevention, and control of this emerging disease.
Authorship Attribution with Neural Networks and Multiple Features: Notebook for PAN at CLEF 2018

However neural networks are receiving more and more attention from different fields of computer-aided research, application of this approach to stylometry and authorship attribution is still relatively infrequent in comparison to other domains of natural language processing. In this paper we present our attempt to analyse frequencies of different types of linguistic data (Part-of-speech, most frequent words, n-grams and skip-grams) with the means of simple neural networks.
UMass at ImageCLEF Medical Visual Question Answering(Med-VQA) 2018 Task

This paper describes the participation of the University of Massachusetts Medical School in the ImageCLEF 2018 Med-VQA task. The goal is to build a system that is able to reason over medial images and questions and generate the corresponding answers. We explored and implemented a co-attention based deep learning framework where residual networks is used to extract visual features from image that interact with the long-short term memory(LSTM) based question representation providing fine-grained contextual information for answer derivation. To efficiently integrate visual features from the image and textual features from the question, we employed Multi-modal Factorized Bilinear(MFB) pooling as well as Multi-modal Factorized High-order(MFH) pooling. In addition, we exploited transfer learning on pre-trained ImageNet model where embedding based topic model(ETM) is applied on the question texts of the training data and the corresponding topic labels are attached to each image for transfer learning. We submitted 3 valid runs for this task, and we found the ETM based transfer learning outperformed other models, achieving the best WBSS score of 0.186, which ranked first among participating groups.
Dilating and fracturing side struts of open cell stents frequently used in pediatric cardiac interventions—An in vitro study

Background Open cell stents are frequently used in interventional therapy of congenital heart disease. Overstenting of vessel branches may necessitate strut dilation. Methods and Results The strut size achievable in Bard Valeo and Cook Formula stents, and the pressure necessary to fracture struts was assessed. In addition, a self expanding stent (Optimed SinusflexDS) was also tested. With the original balloon at nominal pressure, in Valeo stents side struts could be dilated to approximately 90% of the nominal stent diameter, in Formula stents to approximately 80%. With larger high pressure woven balloons, strut size increased to approximately 125% in Valeo stents, and to approximately 105% in the Formula. Strut fracture can connect two adjoining struts. Pressures were dependent on the balloon utilized. Sidestruts of the Sinusflex could lastingly overdilated with large balloons only. Conclusion Dilation and overdilation of side struts in open cell stents can be achieved. Dependent on the clinical context, the original balloon used to place the premounted stent can be used to achieve strut dilation, but woven high pressure balloons maybe safer for patients. Should a larger diameter be required, these high pressure woven balloons can achieve bigger diameters and even strut fracture.
Neuroimaging of Early Life Epilepsy

This study reveals the high yield of radiographic abnormalities in children presenting with epilepsy who are <3 years old regardless of multiple clinical factors. OBJECTIVES: We assessed the adherence to neuroimaging guidelines and the diagnostically relevant yield of neuroimaging in newly presenting early life epilepsy (ELE). METHODS: There were 775 children with a new diagnosis of epilepsy (<3 years old at onset) who were recruited through the ELE study at 17 US pediatric epilepsy centers (2012–2015) and managed prospectively for 1 year. The data were analyzed to assess the proportion of children who underwent neuroimaging, the type of neuroimaging, and abnormalities. RESULTS: Of 725 children (93.5%) with neuroimaging, 714 had an MRI (87% with seizure protocols) and 11 had computed tomography or ultrasound only. Etiologically relevant abnormalities were present in 290 individuals (40%) and included: an acquired injury in 97 (13.4%), malformations of cortical development in 56 (7.7%), and other diffuse disorders of brain development in 51 (7.0%). Neuroimaging was abnormal in 160 of 262 (61%) children with abnormal development at diagnosis versus 113 of 463 (24%) children with typical development. Neuroimaging abnormalities were most common in association with focal seizure semiology (40%), spasms (47%), or unclear semiology (42%). In children without spasms or focal semiology with typical development, 29 of 185 (16%) had imaging abnormalities. Pathogenic genetic variants were identified in 53 of 121 (44%) children with abnormal neuroimaging in whom genetic testing was performed. CONCLUSIONS: Structural abnormalities occur commonly in ELE, and adherence to neuroimaging guidelines is high at US pediatric epilepsy centers. These data support the universal adoption of imaging guidelines because the yield is substantially high, even in the lowest risk group.
Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan

Indigenous cattle in Sichuan Province, southwestern China, provide abundant genetic resources. However, their genetic diversity and population structure remain largely unknown, especially on the genome-wide scale. In the present study, we successfully employed the restriction site-associated DNA sequencing approach (RADseq) to explore genome-wide SNPs among six breeds of Sichuan cattle. A total of 238,725 high-confidence SNPs were finally obtained with a mean distance of 11,140 bp between two adjacent sites, and 43.4% were revealed to be novel in comparison with a public reference database of genetic variants. The mean nucleotide diversity and polymorphism information content (PIC) among all six breeds were 0.1878 and 0.1555, respectively. Pingwu and Ganzi cattle showed the highest and lowest genetic diversity, respectively. The inter-breed comparisons revealed that Ganzi and Ebian cattle were obviously separate from the others. Our reference set of genome-wide SNPs specific to indigenous cattle in Sichuan is the first of its kind. Moreover, our set can be used to investigate the genetic diversity and population structure and for genome-wide association studies.
Use of metformin and survival of patients with high‐grade glioma

High‐grade glioma (HGG) is associated with poor prognosis. Drug repurposing evolves as new modality to improve standard therapy. The antidiabetic drug metformin has been found to inhibit glioma cell growth in vitro and in vivo. The aim of the present retrospective cohort study was to evaluate the survival of patients with HGG with or without treatment with metformin, based on a large cohort of a cancer registry. The analysis included 1,093 patients with HGG diagnosed between 1998 and 2013 from the population‐based clinical cancer registry Regensburg (Germany), which covers 2.1 Mio inhabitants and 98% of all cancer diagnoses. We performed multivariable adjusted Cox‐regression analyses. Hazard Ratios (HRs) with 95% Confidence Intervals (CIs) for overall survival (OS) and progression‐free survival (PFS) of patients with HGG with or without treatment with metformin were obtained. Use of metformin was associated with a significantly better overall and progression‐free survival of patients with WHO grade III glioma (HR for OS = 0.30; 95% CI = 0.11–0.81, HR for PFS = 0.29; 95% CI = 0.11–0.78), while there were no significant relations with OS (HR = 0.83; 95% CI = 0.57–1.20) or PFS (HR = 0.85; 95% CI = 0.59–1.22) in patients with WHO grade IV glioma. In conclusion, use of metformin is associated with better overall and progression‐free survival of patients with WHO grade III. Possible underlying mechanisms include the higher prevalence of IDH mutations in WHO grade III glioma, which might sensitize to the metabolic drug metformin.
Relationship between digestive tract colonization and subsequent ventilator-associated pneumonia related to ESBL-producing Enterobacteriaceae

Background Ventilator-associated pneumonia (VAP) is the most common ICU-acquired infection. Recently, the incidence of extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBLE) has substantially increased in critically ill patients. Identifying patients at risk for VAP related to ESBLE could be helpful to improve the rate of appropriate initial antibiotic treatment, and to reduce unnecessary exposure to carbapenems. The primary objective was to identify risk factors for VAP related to ESBLE. Secondary objective was to determine the impact of ESBLE on outcome in VAP patients. Methods This retrospective study was conducted in a single mixed intensive care unit (ICU), during a 4-year period. All patients with confirmed VAP were included. VAP was defined using clinical, radiologic and quantitative microbiological data. VAP first episodes were prospectively identified using the continuous surveillance data. Exposure to different risk factors was taken into account until the diagnosis of ESBLE VAP or until ICU discharge, in patients with ESBLE VAP and VAP related to other bacteria, respectively. In all patients, routine screening for ESBLE (rectal swab) was performed at ICU admission and once a week. Patients with ESBLE VAP were compared with those with VAP related to other bacteria using univariate analysis. All significant factors were included in the multivariate logistic regression model. Results Among the 410 patients with VAP, 43 (10.5%) had ESBLE VAP, 76 (19%) patients had polymicrobial VAP and 189 (46%) had VAP related to multidrug resistant bacteria. Multivariate analysis identified prior ESBLE colonization of the digestive tract as the only independent risk factor for ESBLE VAP (OR [95% CI] = 23 [10–55], p < 0.001). Whilst the positive predictive value of ESBLE digestive colonization was low (43.6%), its negative predictive value was excellent (97.3%) in predicting ESBLE VAP. Duration of mechanical ventilation (median [IQR], 28 [18,42] vs 23 [15,42] d, p = 0.4), length of ICU stay (31 [19,53] vs 29 [18,46] d, p = 0.6), and mortality rates (55.8% vs 50%, p = 0.48) were similar in ESBLE VAP, compared with VAP related to other bacteria. Conclusion Digestive tract colonization related to ESBLE is independently associated with ESBLE VAP. Its excellent negative predictive value suggests that patients without ESBLE colonization should not receive carbapenems as part of their initial empirical treatment to cover ESBLE.
Making IVF more effective through the evolution of prediction models: is prognosis the missing piece of the puzzle?

ABSTRACT Assisted reproductive technology has evolved tremendously since the emergence of in vitro fertilization (IVF). In the course of the recent decade, there have been significant efforts in order to minimize multiple gestations, while improving percentages of singleton pregnancies and offering individualized services in IVF, in line with the trend of personalized medicine. Patients as well as clinicians and the entire IVF team benefit majorly from ‘knowing what to expect’ from an IVF cycle. Hereby, the question that has emerged is to what extent prognosis could facilitate toward the achievement of the above goal. In the current review, we present prediction models based on patients’ characteristics and IVF data, as well as models based on embryo morphology and biomarkers during culture shaping a complication free and cost-effective personalized treatment. The starting point for the implementation of prediction models was initiated by the aspiration of moving toward optimal practice. Thus, prediction models could serve as useful tools that could safely set the expectations involved during this journey guiding and making IVF treatment more effective. The aim and scope of this review is to thoroughly present the evolution and contribution of prediction models toward an efficient IVF treatment. Abbreviations: IVF: In vitro fertilization; ART: assisted reproduction techniques; BMI: body mass index; OHSS: ovarian hyperstimulation syndrome; eSET: elective single embryo transfer; ESHRE: European Society of Human Reproduction and Embryology; mtDNA: mitochondrial DNA; nDNA: nuclear DNA; ICSI: intracytoplasmic sperm injection; MBR: multiple birth rates; LBR: live birth rates; SART: Society for Assisted Reproductive Technology Clinic Outcome Reporting System; AFC: antral follicle count; GnRH: gonadotrophin releasing hormone; FSH: follicle stimulating hormone; LH: luteinizing hormone; AMH: anti-Müllerian hormone; DHEA: dehydroepiandrosterone; PCOS: polycystic ovarian syndrome; NPCOS: non-polycystic ovarian syndrome; CE: cost-effectiveness; CC: clomiphene citrate; ORT: ovarian reserve test; EU: embryo–uterus; DET: double embryo transfer; CES: Cumulative Embryo Score; GES: Graduated Embryo Score; CSS: Combined Scoring System; MSEQ: Mean Score of Embryo Quality; IMC: integrated morphology cleavage; EFNB2: ephrin-B2; CAMK1D: calcium/calmodulin-dependent protein kinase 1D; GSTA4: glutathione S-transferase alpha 4; GSR: glutathione reductase; PGR: progesterone receptor; AMHR2: anti-Müllerian hormone receptor 2; LIF: leukemia inhibitory factor; sHLA-G: soluble human leukocyte antigen G.
Validation of Calculated Globulin (CG) as a Screening Test for Antibody Deficiency in an Italian University Hospital.

BACKGROUND Morbidity and mortality of primary and secondary antibody deficiencies (AD) are frequently associated with diagnostic delays. These could be avoided by a combination of factors including a widespread and effective development in screening tests. METHODS Calculated globulin (CG), derived from the difference between serum total protein and albumin levels, reflects immunoglobulin serum levels and has shown to have a predictive value in the early diagnosis of antibody deficiencies. This study investigated the possibility to use low levels of CG to detect antibody deficiency in an Italian University Hospital. RESULTS First, we conducted an analysis of anonymized adult samples collected at our biochemistry laboratory with a range of calculated globulin levels from 15 to 22 g/l. A CG cut-off of 19 g/l detected subjects with IgG lower than 600 mg/dl with a sensitivity of 70% and a specificity of 75%. To further verify the clinical usefulness of CG, we retrospectively evaluated the relationship between CG values and serum IgG levels in 38 patients diagnosed with CVID at our Institution. Using a CG cut-off of 19 g/l, we detected antibody deficiency in 97.3% (37/38) of the subjects present in our cohort. CONCLUSION Finally, we chose a CG value of 19 g/l as the cut-off for a prospective AD screening program. The results of this study show that a screening CG test can be used as a tool to reduce diagnostic delays, improve long-term prognosis and reduce the healthcare costs of antibody deficiency.
The Role of Fault‐Zone Architectural Elements on Pore Pressure Propagation and Induced Seismicity

We used hydrogeologic models to assess how fault‐zone properties promote or inhibit the downward propagation of fluid overpressures from a basal reservoir injection well (150 m from fault zone, Q = 5000 m3/day) into the underlying crystalline basement rocks. We varied the permeability of the fault‐zone architectural components and a crystalline basement weathered layer as part of a numerical sensitivity study. Realistic conduit‐barrier style fault zones effectively transmit elevated pore pressures associated with 4 years of continuous injection to depths of approximately 2.5 km within the crystalline basement while compartmentalizing fluid flow within the injection reservoir. The presence of a laterally continuous, relatively low‐permeability altered/weathered basement horizon (kaltered layer = 0.1 × kbasement) can limit the penetration depth of the pressure front to approximately 500 m. On the other hand, the presence of a discontinuous altered/weathered horizon that partially confines the injection reservoir without blocking the fault fluid conduit promotes downward propagation of pressures. Permeability enhancement via hydromechanical failure was found to increase the depth of early‐time pressure front migration by a factor of 1.3 to 1.85. Dynamic permeability models may help explain seismicity at depths of greater than 10 km such as is observed within the Permian Basin, NM.
Deoxynivalenol in wheat from the Northwestern region in China

ABSTRACT Because of global warming and changes in farming systems, Fusarium head blight has gradually spread towards high-latitude regions such as Northwestern China. A survey was conducted to assess the prevalence and concentration of deoxynivalenol (DON) in wheat harvested during 2013 from the Shaanxi, Ningxia, Gansu, and Xinjiang provinces in China. DON concentration in 181 wheat samples was analysed by high-performance liquid chromatography combined with ultraviolet detection. Of the wheat samples, 82.9% were contaminated with DON, with a mean DON concentration of 500 μg/kg. According to the Chinese standard limits for DON, 10% of the positive samples were above the maximum limit of 1000 μg/kg. Regions with higher humidity showed higher levels of DON in the wheat samples. These results show the necessity of raising awareness of DON contamination in people from Northwestern China to protect their health from the risk of exposure to DON.
LIA@CLEF 2018: Mining Events Opinion Argumentation from Raw Unlabeled Twitter Data using Convolutional Neural Network

Social networks on the Internet are becoming increasingly important in our society. In recent years, this type of media, through communication platforms such as Twitter, has brought new research issues due to the massive size of data exchanged and the important number of ever-increasing users. In this context, the CLEF 2018 Mining opinion argumentation task aims to retrieve, for a specific event (festival name or topic), the most diverse argumentative microblogs from a large collection of tweets about festivals in different languages. In this paper, we propose a four-step approach for extracting argumentative microblogs related to a specific query (or event) while no reference data is provided.
Overview of ImageCLEF 2018 Medical Domain Visual Question Answering Task

This paper presents an overview of the inaugural edition of the ImageCLEF 2018 Medical Domain Visual Question Answering (VQA-Med) task. Inspired by the recent success of visual question answering in the general domain, a pilot task was proposed this year to focus on visual question answering in the medical domain. Given medical images accompanied with clinically relevant questions, participating systems were tasked with answering the questions based on the visual image content. A dataset of 6,413 question-answer pairs accompanied with 2,866 medical images extracted from PubMed Central articles was provided; from which, 5,413 question-answer pairs with 2,278 medical images were used for training, 500 question-answer pairs with 324 medical images were used for validation, and 500 questions with 264 medical images were used for testing. Among 28 registered participants, 5 groups submitted a total of 17 runs, indicating a considerable interest in the VQA-Med task.