Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative genomic analysis provides insight into the phylogeny and virulence of atypical enteropathogenic Escherichia coli strains from Brazil

Background Atypical enteropathogenic Escherichia coli (aEPEC) are one of the most frequent intestinal E. coli pathotypes isolated from diarrheal patients in Brazil. Isolates of aEPEC contain the locus of enterocyte effacement, but lack the genes of the bundle-forming pilus of typical EPEC, and the Shiga toxin of enterohemorrhagic E. coli (EHEC). The objective of this study was to evaluate the phylogeny and the gene content of Brazilian aEPEC genomes compared to a global aEPEC collection. Methodology Single nucleotide polymorphism (SNP)-based phylogenomic analysis was used to compare 106 sequenced Brazilian aEPEC with 221 aEPEC obtained from other geographic origins. Additionally, Large-Scale BLAST Score Ratio was used to determine the shared versus unique gene content of the aEPEC studied. Principal Findings Phylogenomic analysis demonstrated the 106 Brazilian aEPEC were present in phylogroups B1 (47.2%, 50/106), B2 (23.6%, 25/106), A (22.6%, 24/106), and E (6.6%, 7/106). Identification of EPEC and EHEC phylogenomic lineages demonstrated that 42.5% (45/106) of the Brazilian aEPEC were in four of the previously defined lineages: EPEC10 (17.9%, 19/106), EPEC9 (10.4%, 11/106), EHEC2 (7.5%, 8/106) and EPEC7 (6.6%, 7/106). Interestingly, an additional 28.3% (30/106) of the Brazilian aEPEC were identified in five novel lineages: EPEC11 (14.2%, 15/106), EPEC12 (4.7%, 5/106), EPEC13 (1.9%, 2/106), EPEC14 (5.7%, 6/106) and EPEC15 (1.9%, 2/106). We identified 246 genes that were more frequent among the aEPEC isolates from Brazil compared to the global aEPEC collection, including espG2, espT and espC (P<0.001). Moreover, the nleF gene was more frequently identified among Brazilian aEPEC isolates obtained from diarrheagenic patients when compared to healthy subjects (69.7% vs 41.2%, P<0.05). Conclusion The current study demonstrates significant genomic diversity among aEPEC from Brazil, with the identification of Brazilian aEPEC isolates to five novel EPEC lineages. The greater prevalence of some virulence genes among Brazilian aEPEC genomes could be important to the specific virulence strategies used by aEPEC in Brazil to cause diarrheal disease.
A palynological study of the genus Pedicularis (Orobanchaceae) in Iran

Abstract Saeidi Mehrvarz S. , Parsa Panah S. & Beygom Faghir M. : A palynological study of the genus Pedicularis (Orobanchaceae) in Iran. — Willdenowia 43: 279–285. December 2013. — ISSN 0511-9618; © 2013 BGBM Berlin-Dahlem. Stable URL: http://dx.doi. org/10.3372/wi.43. 43207 Pollen morphological features of nine Iranian species of the genus Pedicularis were examined using light microscopy (LM) and scanning electron microscopy (SEM). We studied the pollen morphology of P. cabulica, P. caucasica, P. condensata, P. pycnantha, P. rechingeri, P. rhinanthoides, P. sibthorpii, P. straussii and P. wilhelmsiana, among which all except P. condensata, P. rhinanthoides and P. sibthorpii are palynologically described here for the first time. We observed two main types of pollen aperture (trisyncolpate and bisyncolpate) and four of exine sculpturing (microscabrate-reticulate, microfoveolate-microscabrate, retipilate and microscabrate). The results reveal the taxonomic significance of palynological characters in the genus, and the taxonomic implications are discussed here.
The genetic architecture of plant defense tradeoffs in a common monkeyflower.

Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a QTL mapping experiment involving a cross between two populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in one or two PPGs. This result indicates that chemical defense arsenals can be finely-adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.
Drug-specific and dosage effects of statins and the risk of cancer: a population-based cohort study in South Korea.

This study aimed to investigate whether the drug-specific and dosage effects of statin use were associated with a lower risk of cancer in adults in South Korea. We evaluated the adult population registered in the 2010 sample cohort database of South Korea. Subjects were divided into the statin group (those who had been prescribed continuous oral statin over 1 year) and the control group (those who had never been prescribed statin from 2010 to 2016). In total, 687 396 individuals were included in the analysis [statin group, 53 592 (7.8%); control group, 633 804 (92.2%)]. In a multivariable Cox model, the hazard of cancer in the statin group was 5% lower than that in the control group [hazard ratio, 0.95; 95% confidence interval (CI), 0.91-0.98; P = 0.004]. Additionally, the hazard of cancer in patients receiving moderate- and high-intensity daily dosages of statin were 5% (hazard ratio, 0.95; 95% CI, 0.91-0.98; P = 0.005) and 9% (hazard ratio, 0.91; 95% CI, 0.83-0.99; P = 0.042) lower than that of the control group, respectively. The hazard of cancer in patients receiving atorvastatin was 6% (hazard ratio, 0.94; 95% CI, 0.90-0.98; P = 0.005) lower than that in the control group, while other types of statins showed no significant associations (all P > 0.05). Statin use was associated with a lower risk of cancer in South Korea. This association was stronger in patients receiving moderate and high daily dosages of statin and in patients receiving atorvastatin.
Structure of Dark Triad Dirty Dozen Across Eight World Regions

The Dark Triad (i.e., narcissism, psychopathy, Machiavellianism) has garnered intense attention over the past 15 years. We examined the structure of these traits’ measure—the Dark Triad Dirty Dozen (DTDD)—in a sample of 11,488 participants from three W.E. I.R. D. (i.e., North America, Oceania, Western Europe) and five non-W.E. I.R. D. (i.e., Asia, Middle East, non-Western Europe, South America, sub-Saharan Africa) world regions. The results confirmed the measurement invariance of the DTDD across participants’ sex in all world regions, with men scoring higher than women on all traits (except for psychopathy in Asia, where the difference was not significant). We found evidence for metric (and partial scalar) measurement invariance within and between W.E. I.R. D. and non-W.E. I.R. D. world regions. The results generally support the structure of the DTDD.
A case report of Hodgkin lymphoma in a patient treated with ustekinumab for psoriasis

Abstract Rationale: Ustekinumab is a biological agent that inhibits interleukin 12 and 23 and has been approved for the treatment of moderate and severe plaque psoriasis. There have been case reports that raise concerns about its oncogenic potential. We are the first authors to report a case of Hodgkin lymphoma in a psoriatic patient receiving ustekinumab. Patient concerns: A 22-year-old asymptomatic female patient presented to our department to investigate an enlarged cervical lymph node. Her past history was unremarkable, except for psoriasis since age 13. Two months before presentation the decision to administer Ustekinumab was taken and the patient had already received 3 doses. Diagnoses: During workup a Stage IV Hodgkin lymphoma was discovered. Interventions: Ustekinumab administration was discontinued. The patient received treatment with the ABVD regimen. Outcomes: The patient's disease was refractory to the above-mentioned treatment. Therefore, a more aggressive regimen (BEACOPP escalated) was administered. Lessons: Growing postmarketing surveillance data and case reports indicate that further research is warranted in order to elucidate a potential association between Ustekinumab and malignancy.
Red meat consumption and its association with hypertension and hyperlipidaemia among adult Maasai pastoralists of Ngorongoro Conservation Area, Tanzania

Background Red meat is an important dietary source of protein and other essential nutrients. Its high intake has been associated with an increased risk of cardiovascular morbidity and mortality, including hypertension (HTN) and hyperlipidaemia (HLP). Despite being physically active, the Maasai at Ngorongoro Conservation Area (NCA) depend heavily on animals' products as their staple food with fewer intakes of vegetables or fruits due to restriction from carrying out agricultural activities within the NCA. This study aimed at determining the prevalence of HTN and HLP and their association with red meat consumption among adult Maasai of NCA. Methods A community-based cross-sectional study was conducted in October 2018 using multistage sampling technique. Eight hundred and ninety-four (894) participants enrolled from seven villages in three wards within NCA Data were collected using a modified WHO NCDs-STEPS tool. Anthropometric measurements, blood pressure (BP) measurements, and blood samples for glucose and cholesterol tests were obtained from the study participants. Crude and adjusted prevalence ratio (PR) for factors associated with HTN and HLP were estimated using Ordinal and Bayesian logistic regression models, respectively. Results The prevalence of HLP was 23.7 percent. The levels were higher among males than were among the females (29.0% vs. 20.1%, p = 0.002). The prevalence of HTN and pre-HTN (elevated BP) were 9.8 and 37.0 percent, respectively. Both HTN and elevated BP were higher among males than were among females (hypertensive [10.9% vs. 9.0%]; elevated BP [44.0% vs. 32.1%], p<0.001). The prevalence of HLP was significantly associated with level II (PR = 1.56, 95%CrI: 1.10–2.09) and level III (PR = 1.64, 95%CrI: 1.08–2.41) of red meat consumption as opposed to level I. Conclusion The prevalence of hyperlipidaemia and elevated BP were high among NCA Maasai. We found a significant association between red meat consumption and hyperlipidaemia. Further follow-up studies are warranted to establish a temporal relationship between red meat consumption and both conditions.
Surgical approach and orthodontic treatment of mandibular condylar osteochondroma

Osteochondroma is a common benign tumor of bones, but it is rare in the mandibular condyle. With its outgrowth it manifests clinically as deviation of the mandible limitation of mouth opening, and facial asymmetry. After the tumor is diagnosed on the basis of clinical symptoms and radiographic examination including cone-beam computed tomography (CBCT) analysis, an appropriate surgery and treatment plan should be formulated. Herein, we present the case of a 44-year-old female patient who visited our dental hospital because her chin point had been deviating to the left side slowly but progressively over the last 3 years and she had difficulty masticating. Based on CBCT, she was diagnosed with skeletal Class III malocclusion accompanied by osteochondroma of the right mandibular condyle. Maxillary occlusal cant with the right side down was observed, but it was confirmed to be an extrusion of the molars associated with dental compensation. Therefore, after intrusion of the right molars with the use of temporary anchorage devices, sagittal split ramus osteotomy was used to remove the tumor and perform orthognathic surgery simultaneously. During 6 months after the surgery, continuous bone resorption and remodeling were observed in the condyle of the affected side, which led to a change in occlusion. During the postoperative orthodontic treatment, intrusive force and buccal torque were applied to the molars on the affected side, and a proper buccal overjet was created. After 18 months, CBCT revealed that the rate of bone absorption was continuously reduced, bone corticalization appeared, and good occlusion and a satisfying facial profile were achieved.
Use of Non-Pharmacological Supplementations in Children and Adolescents with Attention Deficit/Hyperactivity Disorder: A Critical Review

Attention deficit hyperactivity disorder (ADHD) is a common neurodevelopmental disorder in children and adolescents, with environmental and biological causal influences. Pharmacological medication is the first choice in ADHD treatment; recently, many studies have concentrated on dietary supplementation approaches to address nutritional deficiencies, to which part of non-responses to medications have been imputed. This review aims to evaluate the efficacy of non-pharmacological supplementations in children or adolescents with ADHD. We reviewed 42 randomized controlled trials comprised of the following supplementation categories: polyunsaturated fatty acids (PUFAs), peptides and amino acids derivatives, single micronutrients, micronutrients mix, plant extracts and herbal supplementations, and probiotics. The reviewed studies applied heterogeneous methodologies, thus making it arduous to depict a systematic overview. No clear effect on single cognitive, affective, or behavioral domain was found for any supplementation category. Studies on PUFAs and micronutrients found symptomatology improvements. Peptides and amino acids derivatives, plant extracts, herbal supplementation, and probiotics represent innovative research fields and preliminary results may be promising. In conclusion, such findings, if confirmed through future research, should represent evidence for the efficacy of dietary supplementation as a support to standard pharmacological and psychological therapies in children and adolescents with ADHD.
Practical Applications of Deep Learning To Impute Heterogeneous Drug Discovery Data

Contemporary deep learning approaches still struggle to bring a useful improvement in the field of drug discovery due to the challenges of sparse, noisy and heterogeneous data that are typically encountered in this context. We use a state-of-the-art deep learning method, Alchemite™, to impute data from drug discovery projects, including multi-target biochemical activities, phenotypic activities in cell-based assays, and a variety of absorption, distribution, metabolism, and excretion (ADME) endpoints. The resulting model gives excellent predictions for activity and ADME endpoints, offering an average increase in R2 of 0.22 versus quantitative structure-activity relationship methods. The model accuracy is robust to combining data across uncorrelated endpoints and projects with different chemical spaces, enabling a single model to be trained for all compounds and endpoints. We demonstrate improvements in accuracy on the latest chemistry and data when updating models with new data as an ongoing medicinal chemistry project progresses.
Use of Physical Restraints in Critical Care Units: Nurses' Knowledge, Attitudes, and Practices.

BACKGROUND Various factors affect the use of physical restraints in the intensive care unit, with nurses' knowledge and attitudes being the strongest determinants. OBJECTIVE To determine Turkish intensive care unit nurses' knowledge, attitudes, and practices regarding physical restraints and factors influencing them. METHODS This cross-sectional, correlational study was conducted in the intensive care units of state and university hospitals. A total of 191 nurses provided information on their sociodemographic and professional characteristics and completed a questionnaire on their knowledge, attitudes, and practices regarding physical restraints. RESULTS Statistically significant differences were found between average knowledge scores according to type of intensive care unit, weekly working hours, work shift, and frequency of using physical restraints, with the highest scores found in nurses who worked in the surgical unit, worked 40 hours a week, worked only during the day, and used physical restraints every day. Significant differences were found between average attitude scores according to type of intensive care unit, with the highest scores found in nurses who worked in the cardiology unit. Significant differences were found between average practice scores according to level of education and use of physical restraints without a physician's order, with the highest scores found in nurses with undergraduate and postgraduate degrees and those who did not use physical restraints without a physician's order. CONCLUSIONS This study revealed inadequate knowledge about physical restraints and some unsafe practices among participants. Evidence-based guidelines and laws regarding physical restraints are needed, as well as regular training programs for involved personnel.
Patterns of GABABR1a,b Receptor Gene Expression in Monkey and Human Visual Cortex

R1a,b immunoreactive. The majority of intensely immuno-reactive neurons in layers II, III, V and VI were pyramidal cells.Numerous non-pyramidal cells were intensely immunoreactive inlayer IV of area 17 but layer IV cells were only lightly immunoreactivein area 18. Following 10 day periods of monocular deprivation,induced by intravitreal injections of tetrodotoxin, levels ofGABA
Single Y-shaped tracheal self-expandable metallic stent for emergent carinal stenosis combined with stenosis of the right main and intermediate bronchi

Abstract To explore the outcome of placing a single Y-shaped tracheal self-expandable metallic stent (SEMS) to treat emergent carinal stenosis combined with stenosis of the right main and intermediate bronchi. The clinical and imaging data of 10 patients (8 males, 2 females) with carinal stenosis combined with stenosis of the right main and intermediate bronchi were retrospectively analyzed. There were 4 patients with esophageal cancer and 6 patients with lung cancer. All patients underwent treatment with a single Y-shaped tracheal SEMS. The long branch was inserted into the right main and intermediate bronchi, while the short branch was inserted into the left main bronchus. A modified Borg scale score was used as the criterion for assessing dyspnea in patients before and after stenting. A total of 10 Y-shaped tracheal SEMSs were successfully placed in 10 patients without any procedure-related complications. Compared with the score before stent placement, the mean Borg score for dyspnea after stent placement decreased from 7.6 to 0.8 (P = .04). Chest computed tomography showed that the stenosis disappeared 3 to 5 days poststenting. During the follow-up period, the most common complications were tumor ingrowth (n = 5) and granulation tissue hyperplasia (n = 7). The mean survival time after tracheal stent placement was 103 ± 50 (23–172) days. The application of a single Y-shaped tracheal SEMS for emergent carinal stenosis combined with stenosis of the right main and intermediate bronchi can effectively relieve dyspnea through a simple operation.
Modelling the effects of ephaptic coupling on selectivity and response patterns during artificial stimulation of peripheral nerves

Artificial electrical stimulation of peripheral nerves for sensory feedback restoration can greatly benefit from computational models for simulation-based neural implant design in order to reduce the trial-and-error approach usually taken, thus potentially significantly reducing research and development costs and time. To this end, we built a computational model of a peripheral nerve trunk in which the interstitial space between the fibers and the tissues was modelled using a resistor network, thus enabling distance-dependent ephaptic coupling between myelinated axons and between fascicles as well. We used the model to simulate a) the stimulation of a nerve trunk model with a cuff electrode, and b) the propagation of action potentials along the axons. Results were used to investigate the effect of ephaptic interactions on recruitment and selectivity stemming from artificial (i.e., neural implant) stimulation and on the relative timing between action potentials during propagation. Ephaptic coupling was found to increase the number of fibers that are activated by artificial stimulation, thus reducing the artificial currents required for axonal recruitment, and it was found to reduce and shift the range of optimal stimulation amplitudes for maximum inter-fascicular selectivity. During propagation, while fibers of similar diameters tended to lock their action potentials and reduce their conduction velocities, as expected from previous knowledge on bundles of identical axons, the presence of many other fibers of different diameters was found to make their interactions weaker and unstable.
Agglutination of human erythrocytes by Eikenella corrodens

Attachment phenomena are usually considered a prerequisite for both colonization of mucosal pathogens and their subsequent stimulation of biological activity in inflammatory cells [1,2]. The adherence of certain bacteria to mucosal surfaces may involve lectin-like proteins on the bacterial surface which bind to specific sugar residues on mammalian cell surfaces [3-6]. Eikenella corrodens has been recovered as the sole infecting agent in cases of endocarditis [7], meningitis [7,8], osteomyelitis [9], pulmonary infection [10], soft-tissue abscess [7,8], and oral infection [l 1]. This microorganism has also caused periodontal disease in mono-infected rats with severe alveolar bone loss [12] and is mainly isolated from deep subgingival plaque in patients with aggressive or advanced periodontitis [13,14]. We have investigated the interaction of E. corrodens with several human cell types. The present investigation focuses on the mechanism by which E. corrodens cells adhere to human erythrocytes, resulting in hemagglutination.
A Clinical Audit on the Predictors for Visual Morbidity in Patients with Behçet’s Disease Attending Cairo University Hospitals

ABSTRACT Objectives To study the visual disability predictors in Behçet’s disease (BD). Methods A cross-sectional observational study including 54 patients. Sociodemographic and cumulative clinical characteristics were obtained. Ophthalmic examination focused on disease activity and degree of visual loss. Results Presenting features included oral ulcers, orogenital ulcers, uveitis, and vascular involvement. Ocular involvement was also present in a majority of the cases 74.1%. The age at onset had no significant effect on diagnostic time lag (P = .9), unlike rural residency (P = .02). Laterality, ocular activity, and interventions significantly affected final visual acuity (P˂0.001). A diagnostic time lag ≥ 9 months significantly affected final visual acuity (P = .039). Conclusion BD is associated with considerable vision loss at a young age. Panuveitis, bilaterality, ocular activity, and interventions are significant predictors. A diagnostic time lag ≥ 9 months is associated with poor visual outcomes and is significantly associated with rural residency.