Miracle-dz/UniFAR-FTUs huggingface dataset:
In situ identification of Gram-negative bacteria in human lungs using a topical fluorescent peptide targeting lipid A

A topically administered fluorescently labeled peptide targeting lipid A permits rapid, real-time visualization of bacteria in the distal human lung. Lung infection in real time Lung infections are frequent causes of complications in mechanically ventilated and immunosuppressed patients. However, the diagnosis is challenging, requires risky procedures, and is time consuming. Now, Akram et al. have developed an imaging method that is able to detect Gram-negative bacteria in real time in the distal part of the human lung. Using a fluorescent probe binding to lipid A, a molecule expressed on Gram-negative bacterial membranes, in combination with an optical endomicroscope, the researchers rapidly detected Gram-negative infections in distal airways in hospitalized individuals. The results suggest that the approach could accelerate the diagnosis of bacterial lung infection and facilitate the evaluation of antibiotic treatment efficacy. Respiratory infections in mechanically ventilated patients caused by Gram-negative bacteria are a major cause of morbidity. Rapid and unequivocal determination of the presence, localization, and abundance of bacteria is critical for positive resolution of the infections and could be used for patient stratification and for monitoring treatment efficacy. Here, we developed an in situ approach to visualize Gram-negative bacterial species and cellular infiltrates in distal human lungs in real time. We used optical endomicroscopy to visualize a water-soluble optical imaging probe based on the antimicrobial peptide polymyxin conjugated to an environmentally sensitive fluorophore. The probe was chemically stable and nontoxic and, after in-human intrapulmonary microdosing, enabled the specific detection of Gram-negative bacteria in distal human airways and alveoli within minutes. The results suggest that pulmonary molecular imaging using a topically administered fluorescent probe targeting bacterial lipid A is safe and practical, enabling rapid in situ identification of Gram-negative bacteria in humans.
The Effects of Zika Virus Risk Coverage on Familiarity, Knowledge and Behavior in the U.S. – A Time Series Analysis Combining Content Analysis and a Nationally Representative Survey

ABSTRACT This study assessed the effects of the February through September 2016 American news media’s coverage of Zika Virus (ZIKV) risk on the U.S. public’s familiarity, knowledge and behavior in the form of interpersonal discussions. A content analysis (N = 2,782 pieces) revealed that the Rio Olympic Games elicited a spike in coverage of Zika. We also found that newsworthy and easy- to- depict aspects of the disease, specifically its transmission by mosquitoes and its relation to microcephaly were covered more extensively than its sexual transmission and transmissibility from an infected person who is asymptomatic. Nevertheless, survey data over the same period of time (N = 37,180 respondents) revealed that the general amount of coverage, rather than the specifics about Zika transmission and its consequences, influenced the public’s familiarity, knowledge, and behavior.
Culturally Relevant Meanings of the Protestant Work Ethic and Attitudes towards Poor Persons

Abstract The Protestant work ethic (PWE), or the belief that hard work leads to success, is a popular belief across cultures. Much work indicates that PWE contributes to negative evaluations of disadvantaged groups presumably through the notion that they deserve their disadvantage for not working hard enough (“PWE-Justifier”). But there is another dimension of PWE that expresses the belief that everyone could succeed through hard work (“PWE-Equalizer”). We propose that the PWE-Justifier is meaningful in cultures that emphasize individualism and personal responsibility, but not in others. In a cross-cultural study, we compare how PWE-Justifier relates to evaluations of poor persons in the USA (individualist culture) and the Philippines (low individualist culture). In the USA sample, regression analysis indicated that internal attributions of poverty mediated the relationships of PWE-Justifier with negative stereotypes (R2 = .32) and with negative attitudes towards poor persons (R2 = .13). Bootstrapping analysis indicated that both indirect effects of PWE-Justifier were significant: Negative stereotypes, B = . 17, SE = . 03, p < . 0001, 95% CI [. 11, . 24]; negative attitudes, B = 2.52, SE = 1.11, p = . 014, 95% CI [0.49, 4.84]. The results were not found in the Philippine sample, where instead, PWE-Equalizer negatively predicted negative attitudes (R2 = .05) and positively predicted empathy (R2 = .05) for poor persons. The results are discussed in terms of how the negative consequences of PWE may derive from the cultural syndrome of individualism that emphasizes personal control and responsibility.
Neurophysiological Responses to Different Product Experiences

It is well known that the evaluation of a product from the shelf considers the simultaneous cerebral and emotional evaluation of the different qualities of the product such as its colour, the eventual images shown, and the envelope's texture (hereafter all included in the term “product experience”). However, the measurement of cerebral and emotional reactions during the interaction with food products has not been investigated in depth in specialized literature. The aim of this paper was to investigate such reactions by the EEG and the autonomic activities, as elicited by the cross-sensory interaction (sight and touch) across several different products. In addition, we investigated whether (i) the brand (Major Brand or Private Label), (ii) the familiarity (Foreign or Local Brand), and (iii) the hedonic value of products (Comfort Food or Daily Food) influenced the reaction of a group of volunteers during their interaction with the products. Results showed statistically significantly higher tendency of cerebral approach (as indexed by EEG frontal alpha asymmetry) in response to comfort food during the visual exploration and the visual and tactile exploration phases. Furthermore, for the same index, a higher tendency of approach has been found toward foreign food products in comparison with local food products during the visual and tactile exploration phase. Finally, the same comparison performed on a different index (EEG frontal theta) showed higher mental effort during the interaction with foreign products during the visual exploration and the visual and tactile exploration phases. Results from the present study could deepen the knowledge on the neurophysiological response to food products characterized by different nature in terms of hedonic value familiarity; moreover, they could have implications for food marketers and finally lead to further study on how people make food choices through the interactions with their commercial envelope.
Modulation of cerebral ketone metabolism following traumatic brain injury in humans

Adaptive metabolic response to injury includes the utilization of alternative energy substrates – such as ketone bodies (KB) – to protect the brain against further damage. Here, we examined cerebral ketone metabolism in patients with traumatic brain injury (TBI; n = 34 subjects) monitored with cerebral microdialysis to measure total brain interstitial tissue KB levels (acetoacetate and β-hydroxybutyrate). Nutrition – from fasting vs. stable nutrition state – was associated with a significant decrease of brain KB (34.7 [10th–90th percentiles 10.7–189] µmol/L vs. 13.1 [6.5–64.3] µmol/L, p < 0.001) and blood KB (668 [168.4–3824.9] vs. 129.4 [82.6–1033.8] µmol/L, p < 0.01). Blood KB correlated with brain KB (Spearman’s rho 0.56, p = 0.0013). Continuous feeding with medium-chain triglycerides-enriched enteral nutrition did not increase blood KB, and provided a modest increase in blood and brain free medium chain fatty acids. Higher brain KB at the acute TBI phase correlated with age and brain lactate, pyruvate and glutamate, but not brain glucose. These novel findings suggest that nutritional ketosis was the main determinant of cerebral KB metabolism following TBI. Age and cerebral metabolic distress contributed to brain KB supporting the hypothesis that ketones might act as alternative energy substrates to glucose. Further studies testing KB supplementation after TBI are warranted.
Automatic Generation of Safety-Critical Test Scenarios for Collision Avoidance of Road Vehicles

It is apparent that one cannot rely solely on physical test drives for ensuring the correct functionality of autonomous vehicles. Since physical test drives are costly and time consuming, it is advantageous to accompany them with computer simulations. However, since most traffic scenarios are not challenging, even simulations are often too time consuming. To address this issue, we present an approach that creates automatically critical driving situations, i.e., situations with a small solution space for avoiding a collision. Our approach combines reachability analysis for determining the size of the solution space with optimization techniques to shrink it. The solution space is reduced by shifting the initial states of traffic participants, demanding an immediate and correct action of the vehicle under test. We demonstrate our approach by automatically increasing the criticality of several initially uncritical situations recorded from real traffic.
Combinatorial Optimization with Graph Convolutional Networks and Guided Tree Search

We present a learning-based approach to computing solutions for certain NP-hard problems. Our approach combines deep learning techniques with useful algorithmic elements from classic heuristics. The central component is a graph convolutional network that is trained to estimate the likelihood, for each vertex in a graph, of whether this vertex is part of the optimal solution. The network is designed and trained to synthesize a diverse set of solutions, which enables rapid exploration of the solution space via tree search. The presented approach is evaluated on four canonical NP-hard problems and five datasets, which include benchmark satisfiability problems and real social network graphs with up to a hundred thousand nodes. Experimental results demonstrate that the presented approach substantially outperforms recent deep learning work, and performs on par with highly optimized state-of-the-art heuristic solvers for some NP-hard problems. Experiments indicate that our approach generalizes across datasets, and scales to graphs that are orders of magnitude larger than those used during training.
Stray Dog Population in a City of Southern Mexico and Its Impact on the Contamination of Public Areas

To assess the risk of zoonotic pathogen transmission as function of stray dog presence and health status, a cross-sectional study was carried out in a large city of southern Mexico that lacks comprehensive strategies for the control of stray canine populations. The photographic capture-recapture method was used to estimate the density of dogs/km2. In the same way, dog feces from 14 public parks of the city were collected to determine the prevalence and intensity of infection with gastrointestinal parasites. The canine population was estimated between 65 and 80 thousand dogs, with a population density of 1,081 dogs/km2, mostly males (71.4%). A high proportion of dogs (72.3%) were found to be in good body condition score (BCS 3). The person:dog ratio was 2.3. The likelihood of being in the BCS 2 category was lower in areas with a higher density of dogs. All feces collected from the parks contained eggs of intestinal parasites, most of them with a medium (42.9%) to high (35.7%) infection intensity, notably Ancylostoma caninum. It was recorded that cases with a low-intensity of GI infection showed polyparasitism (35.7%) associated with A. caninum. There is a large population of stray dogs that roam freely in the streets of Campeche city with access to sources of food, which is reflected by their good BCS, and dogs do not have access to preventive medicine programs (de-worming) and thus contaminate public parks with feces with significant parasitic egg loads of zoonotic importance.
Hepatic hydatid cyst – diagnose and treatment algorithm

Introduction: the hydatic disease, caused by the larvae of Echinococcus granulosus, is a serious disease, potentially lethal, which can be found anywhere in the world, but especially in endemic areas such as the Mediterranean Basin, Australia, New Zealand, North Africa, Eastern Europe, the Balkans, Middle East and South America. The hydatic cyst is mainly found in the liver (75% of the cases), being asymptomatic in most cases and discovered accidentally on a routine abdominal ultrasound or an ultrasound performed for diagnosing other pathologies. The hepatic hydatid cyst therapy is multimodal, including medical, surgical, and, lately, minimally invasive techniques. Materials and methods: 88 patients were diagnosed with liver hydatid cyst at the General Surgery Clinic of the Colentina Hospital in Bucharest where they were admitted from January 2014 to July 2017. Data collection was realized by consulting the patients’ observation sheets, followed by organizing a database of clinical, paraclinical and treatment parameters. Age, gender, place of origin, year and duration of admission, symptoms and signs at admission, paraclinical serological tests relevant for liver function and E. granulosus infection, imaging investigations performed and their results, type of treatment received and post-treatment progress with the complications that occurred were taken in account. Results: some of the results of the study showed some differences comparing to the data from specialty literature, the possible causes being the small number of patients, the paraclinical examinations that were not sufficiently detailed to allow the study of a phenomenon in all its complexity, the lack of information from the patients’ first presentation to a doctor or from their previous admissions. Conclusions: patients with hepatic hydatid cyst form a heterogeneous group, semiology being poor and unspecific. Among the laboratory examinations, eosinophilia is a sign of concern but is present in less than half of the patients. Imaging findings are the basis for the diagnosis of hepatic hydatid cysts. Surgical treatment remains the “gold standard” in therapy, but minimally invasive methods with high applicability, less frequent complications and lower hospital requirements are starting to gain ground.
Taxonomic status of Corynebacterium diphtheriae biovar Belfanti and proposal of Corynebacterium belfantii sp. nov.

Clinical isolates belonging to Corynebacterium diphtheriae biovar Belfanti were characterized by genomic sequencing and biochemical and chemotaxonomic analyses. Phylogenetic analyses indicated that biovar Belfanti represents a branch that is clearly demarcated from C. diphtheriae strains of biovars Mitis and Gravis. The average nucleotide identity of isolates of biovar Belfanti with C. diphtheriae type strain NCTC 11397T (biovar Gravis) was 94.85 %. The inability to reduce nitrate differentiated biovar Belfanti from other strains of C. diphtheriae. On the basis of these results, we propose the name Corynebacterium belfantii sp. nov. for the group of strains previously considered as C. diphtheriaebiovar Belfanti. The type strain of C. belfantii is FRC0043T (=CIP 111412T=DSM 105776T). Strains of C. belfantii were isolated mostly from human respiratory samples.
DiffGRN: differential gene regulatory network analysis

Identification of differential gene regulators with significant changes under disparate conditions is essential to understand complex biological mechanism in a disease. Differential Network Analysis (DiNA) examines different biological processes based on gene regulatory networks that represent regulatory interactions between genes with a graph model. While most studies in DiNA have considered correlation-based inference to construct gene regulatory networks from gene expression data due to its intuitive representation and simple implementation, the approach lacks in the representation of causal effects and multivariate effects between genes. In this paper, we propose an approach named Differential Gene Regulatory Network (DiffGRN) that infers differential gene regulation between two groups. We infer gene regulatory networks of two groups using Random LASSO, and then we identify differential gene regulations by the proposed significance test. The advantages of DiffGRN are to capture multivariate effects of genes that regulate a gene simultaneously, to identify causality of gene regulations, and to discover differential gene regulators between regression-based gene regulatory networks. We assessed DiffGRN by simulation experiments and showed its outstanding performance than the current state-of-the-art correlation-based method, DINGO. DiffGRN is applied to gene expression data in asthma. The DiNA with asthma data showed a number of gene regulations, such as ADAM12 and RELB, reported in biological literature.
Colon capsule endoscopy and its effectiveness in the diagnosis and management of colorectal neoplastic lesions

ABSTRACT Introduction: Colorectal cancer (CRC) represents a major cause of morbidity and mortality in Western countries. Though colonoscopy is the benchmark for CRC diagnosis and management, other alternatives have been proposed. Colon capsule endoscopy (CCE) was first introduced in 2006 as a non-invasive painless technology that utilizes an ingestible, wireless, and disposable capsule to explore the colon, without sedation or air insufflation. Areas covered: To date, the European Society of Gastrointestinal Endoscopy (ESGE) guidelines consider CCE as an option for average-risk colorectal cancer screening patients and in patients with contraindications or unwilling to undergo colonoscopy and/or with an incomplete colonoscopy. Furthermore, Japan’s Pharmaceuticals and Medical Devices Agency (JPMDA) and Food and Drug Administration (FDA) approved the use of CCE in patients unwilling or unable to undergo colonoscopy. Expert commentary: CCE accuracy is nearly comparable to conventional colonoscopy for CRC and significant polyps. Moreover, in the setting of incomplete colonoscopy, CCE was demonstrated to have a higher diagnostic yield for significant polyps and to be better tolerated than CTC. However, the use of CCE is still limited. The lesson coming out is that we should explore new populations that are suitable for colon capsules and for which the colon capsule can be an advantage.
Biomarkers in the diagnosis of pleural diseases: a 2018 update

The use of biomarkers on pleural fluid (PF) specimens may assist the decision-making process and enhance clinical diagnostic pathways. Three paradigmatic examples are heart failure, tuberculosis and, particularly, malignancy. An elevated PF concentration of the amino-terminal fragment of probrain natriuretic peptide (>1500 pg/ml) is a hallmark of acute decompensated heart failure. Adenosine deaminase, interferon-γ and interleukin-27 are three valuable biomarkers for diagnosing tuberculous pleurisy, yet only the first has been firmly established in clinical practice. Diagnostic PF biomarkers for malignancy can be classified as soluble-protein based, immunocytochemical and nucleic-acid based. Soluble markers (e.g. carcinoembryonic antigen (CEA), carbohydrate antigen 15–3, mesothelin) are only indicative of cancer, but not confirmatory. Immunocytochemical studies on PF cell blocks allow: (a) to distinguish mesothelioma from reactive mesothelial proliferations (e.g. loss of BAP1 nuclear expression, complemented by the demonstration of p16 deletion using fluorescence in situ hybridization, indicate mesothelioma); (b) to separate mesothelioma from adenocarcinoma (e.g. calretinin, CK 5/6, WT-1 and D2-40 are markers of mesothelioma, whereas CEA, EPCAM, TTF-1, napsin A, and claudin 4 are markers of carcinoma); and (c) to reveal tumor origin in pleural metastases of an unknown primary site (e.g. TTF-1 and napsin A for lung adenocarcinoma, p40 for squamous lung cancer, GATA3 and mammaglobin for breast cancer, or synaptophysin and chromogranin A for neuroendocrine tumors). Finally, PF may provide an adequate sample for analysis of molecular markers to guide patients with non-small cell lung cancer to appropriate targeted therapies. Molecular testing must include, at least, mutations of epidermal growth-factor receptor and BRAF V600E, translocations of rat osteosarcoma and anaplastic lymphoma kinase, and expression of programmed death ligand 1.
Assessment of Passive Stiffness of Medial and Lateral Heads of Gastrocnemius Muscle, Achilles Tendon, and Plantar Fascia at Different Ankle and Knee Positions Using the MyotonPRO

Background The aim of this study was to assess the passive stiffness of the medial and lateral gastrocnemius (MG and LG), Achilles tendon (AT), and plantar fascia (PF) at different ankle and knee positions. Material/Methods Stiffness was assessed using a portable hand-held device (MyotonPRO). In 30 healthy participants (15 males, 15 females) with the knee fully extended or flexed 90°, stiffness of the MG, LG, AT, and PF was measured at 50° plantar flexion, 0° (neutral position), and 25° dorsiflexion (not for AT) of the ankle joint by passive joint rotation. Results With the knee fully extended, passive dorsiflexion caused significant increase in muscle stiffness (P<0.001), whereas AT and PF stiffness increased with passive ankle dorsiflexion regardless of knee position (P<0.001). Increased stiffness was observed in MG compared to LG (P<0.001) and at the 3-cm site of AT compared to the 6-cm site (P<0.05). Stiffness was greater in LG compared to MG at −50° plantar flexion (P<0.001) and was greater in MG compared to LG at 25° dorsiflexion (P<0.05). Stiffness of AT increased in a distal-to-proximal pattern: 0 cm >3 cm >6 cm (P<0.001). Conclusions Stiffness assessed by use of the MyotonPRO was similar assessments using other techniques, suggesting that the MyotonPRO is capable of detecting the variations in stiffness of MG, LG, AT, and PF at different ankle and knee positions.
Assessment of the optimal timing for early laparoscopic cholecystectomy in acute cholecystitis: a prospective study of the Club Coelio

Abstract Background: The optimal timing for cholecystectomy in patients with acute cholecystitis remains controversial. The aim of this study is to assess prospectively the impact of the duration of symptoms on outcomes in early laparoscopic cholecystectomy (ELC) for acute cholecystitis. Methods: The series consisted of 276 consecutive patients who underwent ELC for acute cholecystitis in 2016. The patients were divided into three groups according to the timing of surgery: within the first 3 days (group 1), between 4 and 7 days (group 2) and beyond 7 days (group 3) from the onset of symptoms. Results: The percentage of surgical procedure rated as difficult was respectively: 12% in G1, 18% in G2 and 38% in G3 (p < .001). Accordingly, we observed an increased mean operative time within groups but no significant difference in the conversion rate. We noted a different overall postoperative complication rate within groups, respectively: 9% in G1, 14% in G2 and 24% in G3 (p < .04). The median hospital stay was also different within groups, respectively: 3 in G1, 4 in G2 and 6 days in G3 (p < .001). On univariate analysis, age ≥60, male gender, ASA 3, WBC ≥13.000/µL, CRP ≥100 mg/l and delay between onset of symptoms and surgery were factors statistically associated with increased morbidity rate. On multivariate analysis, the delay was the only independent predictive factor of postoperative morbidity (OR: 1,08, 95% CI: 1.01–1.61, p < .031). Conclusion: Our study confirms that it is ideal to perform ELC within 3 days of symptoms onset and reasonable between 4 to 7 days. We do not recommend performing ELC beyond 7 days because of more difficult procedure and significantly increased risk of post-operative complications.