Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular epidemiology of Campylobacter isolates from broiler slaughterhouses in Tripoli, North of Lebanon

ABSTRACT 1. The real burden of Campylobacter spp. in Lebanon is still unknown. The aims of this study were to unravel the epidemiology of Campylobacter spp. in broilers at slaughterhouses in Tripoli, North of Lebanon and to characterise their antibiotic resistance profiles. 2. From May to November 2015, sampling was performed through five repeated surveys from 15 slaughterhouses that sold chicken directly to Lebanese customers. Isolates were subjected to pulsed field gel electrophoresis (PFGE) and flaA-restriction fragment length polymorphism (flaA-RFLP). 3. All investigated slaughterhouses were found to be positive for Campylobacter spp. Campylobacter coli was the predominant species (38 isolates) followed by C. jejuni (eight isolates). A noticeable level of resistance was detected among isolates against ciprofloxacin (97% of C. coli and 87.5% of C. jejuni), amoxicillin (89% of C. coli and 75% of C. jejuni), gentamicin (79% of C. coli and 50% of C. jejuni), and co-amoxiclav (24% of C. coli and 25% of C. jejuni). Erythromycin and ertapenem resistance were observed only in C. coli with the following percentages 74% and 13% respectively, but not in C. jejuni. PFGE and flaA-RFLP using DdeI as restriction enzyme divided the strains into 27 and 25 types respectively. 4. The high observed genetic diversity of Campylobacter spp. revealed the complexity of the spread of this genus in broilers. This study highlighted the pressing need to monitor antibiotic resistance and to ensure food safety from ‘farm to fork’ in Lebanon.
Longitudinal Changes in CD4+, CD8+ T Cell Phenotype and Activation Marker Expression Following Antiretroviral Therapy Initiation among Patients with Cryptococcal Meningitis

Despite improvement in the prognosis of HIV/AIDS (human immunodeficiency virus/acquired immune deficiency syndrome) patients on antiretroviral therapy (ART), cryptococcal meningitis (CM) still causes 10–15% mortality among HIV-infected patients. The immunological impact of ART on the CD4+ and CD8+ T cell repertoire during cryptococcal co-infection is unclear. We determined longitudinal phenotypic changes in T cell subsets among patients with CM after they initiated ART. We hypothesized that ART alters the clonotypic phenotype and structural composition of CD4+ and CD8+ T cells during CM co-infection. For this substudy, peripheral blood mononuclear cells (PBMC) were isolated at four time points from CM patients following ART initiation during the parent study (ClinicalTrials.gov number, NCT01075152). Phenotypic characterization of CD4+ and CD8+ T cells was done using T cell surface marker monoclonal antibodies by flow cytometry. There was variation in the expression of immunophenotypic markers defining central memory (CD27+CD45R0+), effector memory (CD45R0+CD27–), immune activation (CD38+ and Human Leucocyte Antigen DR (HLA-DR+), and exhaustion (Programmed cell death protein one (PD-1) in the CD4+ T cell subset. In comparison to the CD4+ T cell population, the CD8+ central memory subset declined gradually with minimal increase in the effector memory subset. Both CD4+ and CD8+ T cell immune exhaustion and activation markers remained elevated over 12 weeks. The relative surge and decline in the expression of T cell surface markers outlines a variation in the differentiation of CD4+ T cells during ART treatment during CM co-infection.
Rapid Detection of Botulinum Neurotoxins—A Review

A toxin is a poisonous substance produced within living cells or organisms. One of the most potent groups of toxins currently known are the Botulinum Neurotoxins (BoNTs). These are so deadly that as little as 62 ng could kill an average human; to put this into context that is approximately 200,000 × less than the weight of a grain of sand. The extreme toxicity of BoNTs leads to the need for methods of determining their concentration at very low levels of sensitivity. Currently the mouse bioassay is the most widely used detection method monitoring the activity of the toxin; however, this assay is not only lengthy, it also has both cost and ethical issues due to the use of live animals. This review focuses on detection methods both existing and emerging that remove the need for the use of animals and will look at three areas; speed of detection, sensitivity of detection and finally cost. The assays will have wide reaching interest, ranging from the pharmaceutical/clinical industry for production quality management or as a point of care sensor in suspected cases of botulism, the food industry as a quality control measure, to the military, detecting BoNT that has been potentially used as a bio warfare agent.
Early treated HIV-infected children remain at risk of growth retardation during the first five years of life: Results from the ANRS-PEDIACAM cohort in Cameroon

Background Long-term growth in HIV-infected infants treated early in resource-limited settings is poorly documented. Incidence of growth retardation, instantaneous risk of death related to malnutrition and growth parameters evolution during the first five years of life of uninfected and early treated HIV-infected children were compared and associated factors with growth retardation were identified. Methods Weight-for-age (WAZ), weight-for-length (WLZ), and length-for-age (LAZ) Z-scores were calculated. The ANRS-PEDIACAM cohort includes four groups of infants with three enrolled during the first week of life: HIV-infected (HI, n = 69), HIV-exposed uninfected (HEU, n = 205) and HIV-unexposed uninfected (HUU, n = 196). The last group included HIV-infected infants diagnosed before 7 months of age (HIL, n = 141). The multi-state Markov model was used to describe the incidence of growth retardation and identified associated factors. Results During the first 5 years, 27.5% of children experienced underweight (WAZ<-2), 60.4% stunting (LAZ<-2) and 41.1% wasting (WLZ<-2) at least once. The instantaneous risk of death observed from underweight state (35.3 [14.1–88.2], 84.0 [25.5–276.3], and 6.0 [1.5–24.1] per 1000 person-months for 0–6 months, 6–12 months, and 12–60 months respectively) was higher than from non-underweight state (9.6 [5.7–16.1], 20.1 [10.3–39.4] and 0.3 [0.1–0.9] per 1000 person-months). Compared to HEU, HIL and HI children were most at risk of wasting (adjusted HR (aHR) = 4.3 (95%CI: 1.9–9.8), P<0.001 and aHR = 3.3 (95%CI: 1.4–7.9), P = 0.01 respectively) and stunting for HIL (aHR = 8.4 (95%CI: 2.4–29.7). The risk of underweight was higher in HEU compared to HUU children (aHR = 5.0 (CI: 1.4–10.0), P = 0.001). Others associated factors to growth retardation were chronic pathologies, small size at birth, diarrhea and CD4< 25%. Conclusions HIV-infected children remained at high risk of wasting and stunting within the first 5 years period of follow-up. There is a need of identifying suitable nutritional support and best ways to integrate it with cART in pediatric HIV infection global care.
Exploration of pathomechanism using comprehensive analysis of serum cytokines in polymyositis/dermatomyositis-interstitial lung disease.

OBJECTIVES To elucidate the serum cytokine profile and address the pathomechanism of interstitial lung disease (ILD) complicated with PM/DM. METHODS Forty patients with PM/DM-ILD were enrolled, and principal components analysis and cluster analysis were performed to classify patients into subgroups. Additionally, we compared cytokine profiles between the survivors and dead patients and between anti-melanoma differentiation-associated gene 5 antibody- and anti-aminoacyl tRNA synthetase antibody-positive ILD patients. We also examined the association of various cytokines with disease activity indicators and prognosis of ILD. RESULTS The principal components analysis data allowed classification of the cytokine profile into three groups: group 1, neutrophilic and M1-macrophage-driven cytokines; group 2, type 1 Th cell-driven and M2-macrophage-induced cytokines; and group 3, M2-macrophage-driven cytokines. Cluster analysis showed the presence of PM/DM-ILD patient groups with high or low levels of total cytokines. Ninety percent of patients who died of ILD were included in clusters with high cytokine levels. Serum cytokine levels of all groups were significantly higher in the anti-melanoma differentiation-associated gene 5 antibody-positive patients than in the anti-aminoacyl tRNA synthetase antibody-positive patients. Groups 1 and 2 significantly correlated with known factors for poor prognosis, such as serum ferritin levels and alveolar-arterial oxygen difference. Serum cytokine levels of patients in group 1 were significantly higher initially and at 2 and 4 weeks in those who died. CONCLUSION These findings suggested that the activation of monocytes, macrophages and type 1 Th cells, and neutrophils play roles in the pathomechanism of PM/DM-ILD, and group 1 cytokines could be useful biomarkers for predicting prognosis of PM/DM-ILD.
Delayed death in the malaria parasite Plasmodium falciparum is caused by disruption of prenylation-dependent intracellular trafficking

Apicomplexan parasites possess a plastid organelle called the apicoplast. Inhibitors that selectively target apicoplast housekeeping functions, including DNA replication and protein translation, are lethal for the parasite, and several (doxycycline, clindamycin, and azithromycin) are in clinical use as antimalarials. A major limitation of such drugs is that treated parasites only arrest one intraerythrocytic development cycle (approximately 48 hours) after treatment commences, a phenotype known as the ‘delayed death’ effect. The molecular basis of delayed death is a long-standing mystery in parasitology, and establishing the mechanism would aid rational clinical implementation of apicoplast-targeted drugs. Parasites undergoing delayed death transmit defective apicoplasts to their daughter cells and cannot produce the sole, blood-stage essential metabolic product of the apicoplast: the isoprenoid precursor isopentenyl-pyrophosphate. How the isoprenoid precursor depletion kills the parasite remains unknown. We investigated the requirements for the range of isoprenoids in the human malaria parasite Plasmodium falciparum and characterised the molecular and morphological phenotype of parasites experiencing delayed death. Metabolomic profiling reveals disruption of digestive vacuole function in the absence of apicoplast derived isoprenoids. Three-dimensional electron microscopy reveals digestive vacuole fragmentation and the accumulation of cytostomal invaginations, characteristics common in digestive vacuole disruption. We show that digestive vacuole disruption results from a defect in the trafficking of vesicles to the digestive vacuole. The loss of prenylation of vesicular trafficking proteins abrogates their membrane attachment and function and prevents the parasite from feeding. Our data show that the proximate cause of delayed death is an interruption of protein prenylation and consequent cellular trafficking defects.
Anti-biofilm potential of silver sulfadiazine loaded nanoparticle formulations: a study on the role of DNase-I in microbial biofilm and wound healing activity.

Biofilm resistance is one of the severe complication associated with chronic wound infections which impose the extreme microbial tolerance against antibiotic therapy. Interestingly, DNase-I has empirically proved efficacy to improve the antibiotics susceptibility against biofilm-associated infections. DNase-I hydrolyzes the extracellular DNA, a key component of the biofilm responsible for the cell adhesion and strength. Moreover, Silver sulfadiazine, a frontline therapy in burn wound infections, exhibit delayed wound healing due to fibroblast toxicity. In this study, solid lipid nanoparticles of silver sulfadiazine (SSD-SLNs) laden chitosan gel supplemented with DNase-I has been developed to reduce the fibroblast cytotoxicity and overcome the biofilm imposed resistance. The extensive optimization by using Box-Behnken Design (BBD) resulted in the formation of SSD-SLNs with smooth surface as confirmed by scanning electron microscopy and controlled release (83%) for up to 24h. The compatibility between the SSD and other formulation excipients was confirmed by FTIR, differential scanning calorimetry and powder X-ray diffraction studies. Developed SSD-SLNs demonstrated improved cell viability (90.3±3.8%) as compared to SSD alone (76.9±4.2%) and combination of SSD-SLNs with DNase-I, inhibited around 96.8% of biofilm of Pseudomonas aeruginosa as compared to SSD with DNase-I (82.9%). In line with our hypothesis, SSD-SLNs were found less toxic (cell viability 90.3±3.8% at 100 µg/mL) in comparison with SSD (Cell viability 76.9±4.2 %) against human dermal fibroblasts cell line. Eventually, the results of in-vivo wound healing study showed complete wound healing after 21 days' treatment with SSD-SLNs with DNase-I, whereas, marketed formulation, SSD and SSD-LSNs showed incomplete healing after 21 days. Data in hand suggest, SSD-SLNs with DNase-I as an effective treatment strategy against the biofilm-associated wound infections and to accelerate the wound healing.
Workplace Homicides in Northern Tunisia: A 15-Year Study (2003-2017).

BACKGROUND Death in workplaces remains a public health issue. However, data regarding workplace homicides are scarce in most of regions, especially in the Arab world. The aim of our study was to analyze the epidemiological features of workplace homicides in northern Tunisia. MATERIALS AND METHODS This is a descriptive study with retrospective data collection over a 15-year period (January 2003 to December 2017). RESULTS We recorded 50 workplace homicide cases. Sex ratio was 49:1 (male/female). The mean age was 41.6 ± 15.13 years. Occupations the most at risk were security guards (odds ratio, 8.25; 95% confidence interval, 4.28-15.91; P < 0.0001) and taxi drivers (odds ratio, 5.61; 95% confidence interval, 2.39-13.18; P < 0.00001). The motive of the aggression was either interpersonal conflict or robbery (47.9% and 43.8%, respectively). Victims working as security guards or taxi drivers were most frequently assaulted by an unknown perpetrator, the motive being robbery. Death was most frequently secondary to blunt trauma (n = 20) or stab wounds (n = 15). CONCLUSIONS Workplace homicides represent a substantial phenomenon in Tunisia. The application of prevention measures is required based on improving environmental measures targeting, in priority, security guards and taxi drivers.
Design, Synthesis, and Biological Evaluation of EdAP, a 4′-Ethynyl-2′-Deoxyadenosine 5′-Monophosphate Analog, as a Potent Influenza a Inhibitor

Influenza A viruses leading to infectious respiratory diseases cause seasonal epidemics and sometimes periodic global pandemics. Viral polymerase is an attractive target in inhibiting viral replication, and 4′-ethynyladenosine, which has been reported as a highly potent anti-human immunodeficiency virus (HIV) nucleoside derivative, can work as an anti-influenza agent. Herein, we designed and synthesized a 4′-ethynyl-2′-deoxyadenosine 5′-monophosphate analog called EdAP (5). EdAP exhibited potent inhibition against influenza virus multiplication in Madin–Darby canine kidney (MDCK) cells transfected with human α2-6-sialyltransferase (SIAT1) cDNA and did not show any toxicity toward the cells. Surprisingly, this DNA-type nucleic acid analog (5) inhibited the multiplication of influenza A virus, although influenza virus is an RNA virus that does not generate DNA.
Distal Balloon Angioplasty of Cerebral Vasospasm Decreases the Risk of Delayed Cerebral Infarction

A group of 392 patients was analyzed (160 before versus 232 after January 2015). Distal balloon angioplasty was associated with the following: higher rates of angioplasty (43% versus 27%) and intravenous milrinone (31% versus 9%); lower rates of postangioplasty delayed cerebral infarction (2.2% versus 7.5%) and new angioplasty (8% versus 19%) independent of the rate of patients treated by angioplasty and milrinone; and the same rates of stroke related to angioplasty (3.6% versus 3.1%), delayed cerebral infarction (7.7% versus 12.5%), mortality (10% versus 11%), and favorable outcome (79% versus 73%). The authors conclude that distal balloon angioplasty is safe and decreases the risk of delayed cerebral infarction and the recurrence of vasospasm compared with conventional angioplasty. It fails to show a clinical benefit possibly because of confounding changes in adjuvant therapies of vasospasm during the study period. BACKGROUND AND PURPOSE: Conventional angioplasty of cerebral vasospasm combines proximal balloon angioplasty (up to the first segment of cerebral arteries) with chemical angioplasty for distal arteries. Distal balloon angioplasty (up to the second segment of cerebral arteries) has been used in our center instead of chemical angioplasty since January 2015. We aimed to assess the effect of this new approach in patients with aneurysmal SAH. MATERIALS AND METHODS: The occurrence, date, territory, and cause of any cerebral infarction were retrospectively determined and correlated to angioplasty procedures. Delayed cerebral infarction, new angioplasty in the territory of a previous angioplasty, angioplasty complications, 1-month mortality, and 6- to 12-month modified Rankin Scale ≤ 2 were compared between 2 periods (before-versus-after January 2015, from 2012 to 2017) with adjustment for age, sex, World Federation of Neurosurgical Societies score, and the modified Fisher grade. RESULTS: Three-hundred-ninety-two patients were analyzed (160 before versus 232 after January 2015). Distal balloon angioplasty was associated with the following: higher rates of angioplasty (43% versus 27%, P < .001) and intravenous milrinone (31% versus 9%, P < .001); lower rates of postangioplasty delayed cerebral infarction (2.2% versus 7.5%, P = .01) and new angioplasty (8% versus 19%, P = .003) independent of the rate of patients treated by angioplasty and milrinone; and the same rates of stroke related to angioplasty (3.6% versus 3.1%, P = .78), delayed cerebral infarction (7.7% versus 12.5%, P = .12), mortality (10% versus 11%, P = .81), and favorable outcome (79% versus 73%, P = .21). CONCLUSIONS: Our study suggests that distal balloon angioplasty is safe and decreases the risk of delayed cerebral infarction and the recurrence of vasospasm compared with conventional angioplasty. It fails to show a clinical benefit possibly because of confounding changes in adjuvant therapies of vasospasm during the study period.
Endometrial biopsy and density of nerve fibers in eutopic endometrium. Looking for easier ways to diagnose endometriosis

Abstract The purpose of study was to evaluate if there is any difference between nerve fibers density in eutopic endometrium in women with and without endometriosis. The prospective case – control study conducted between October 2013 and December 2015. The study included 60 reproductive age women undergoing laparoscopy for suspected endometriosis, pelvic pain, or infertility and not currently receiving hormonal treatment for at least 3 months prior to laparoscopy. Immunohistochemical nerve fiber detection in endometrial curetting using anti-gene product 9.5 was compared with surgical diagnosis. The nerve fibers were detected in eutopic endometrium in women with and without endometriosis. PGP9.5 positive nerve fibers were found in 26 (43%) cases: 16 (50%) in women with endometriosis and 10 (36%) in women without endometriosis. The mean nerve fiber density was higher in the group with endometriosis (0.53 per mm2 ± 0.68) than without endometriosis (0.48 per mm2 ± 0.89), but no statistically significant difference was observed (p > .05). Test specificity was 64.3%, sensitivity 50%, positive predictive value – 61.5%, negative predictive value – 52.9%, and overall accuracy 56.7%. The detection of PGP9.5 positive nerve fibers in eutopic endometrium cannot be used as a reliable diagnostic test of diagnosing endometriosis.
Assessing a Spanish Translation of the End-User Computing Satisfaction Instrument

This study assesses the psychometric properties of a Spanish translation of Doll and Torkzadeh’s EndUser Computing Satisfaction (EUCS) survey instrument. The results show that the EUCS Spanish version is a valid and reliable measure of computing satisfaction among computer users in Mexico and adds support to the usefulness of the instrument in countries other than the United States and in languages other than English.
Measuring Speech Recognition With a Matrix Test Using Synthetic Speech

Speech audiometry is an essential part of audiological diagnostics and clinical measurements. Development times of speech recognition tests are rather long, depending on the size of speech corpus and optimization necessity. The aim of this study was to examine whether this development effort could be reduced by using synthetic speech in speech audiometry, especially in a matrix test for speech recognition. For this purpose, the speech material of the German matrix test was replicated using a preselected commercial system to generate the synthetic speech files. In contrast to the conventional matrix test, no level adjustments or optimization tests were performed while producing the synthetic speech material. Evaluation measurements were conducted by presenting both versions of the German matrix test (with natural or synthetic speech), alternately and at three different signal-to-noise ratios, to 48 young, normal-hearing participants. Psychometric functions were fitted to the empirical data. Speech recognition thresholds were 0.5 dB signal-to-noise ratio higher (worse) for the synthetic speech, while slopes were equal for both speech types. Nevertheless, speech recognition scores were comparable with the literature and the threshold difference lay within the same range as recordings of two different natural speakers. Although no optimization was applied, the synthetic-speech signals led to equivalent recognition of the different test lists and word categories. The outcomes of this study indicate that the application of synthetic speech in speech recognition tests could considerably reduce the development costs and evaluation time. This offers the opportunity to increase the speech corpus for speech recognition tests with acceptable effort.
The Autoimmune Regulator (Aire) transactivates HLA‐G gene expression in thymic epithelial cells

The Autoimmune Regulator (Aire) protein coordinates the negative selection of developing thymocytes by inducing the expression of hundreds of tissue‐specific antigens within the thymic medulla, which is also a primary site of the expression of the immune checkpoint HLA‐G molecule. Considering the immunomodulatory properties of Aire and HLA‐G, and considering that the role of the constitutive thymus expression of HLA‐G has not been elucidated, we studied the effect of AIRE cDNA transfection on HLA‐G expression in 4D6 thymic cells and in the HLA‐G‐positive JEG‐3 choriocarcinoma cells. Aire promoted the transactivation of HLA‐G gene by increasing the overall transcription, inducing the transcription of at least G1 and G2/G4 isoforms, and incrementing the occurrence and distribution of intracellular HLA‐G protein solely in 4D6 thymic cells. Luciferase‐based assays and chromatin immunoprecipitation experiments performed in 4D6 cells revealed that Aire targeted at least two regions within the 5′‐untranslated regulatory region (5′‐URR) extending 1·4 kb from the first ATG initiation codon. The interaction occurs independently of three putative Aire‐binding sites. These results indicate that the Aire‐induced upregulation of HLA‐G in thymic cells is likely to act through the interaction of Aire with specific HLA‐G 5′‐URR DNA‐binding factors. Such a multimeric transcriptional complex might operate in the thymus during the process of promiscuous gene expression.