Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetically encodable bioluminescent system from fungi

Significance We present identification of the luciferase and enzymes of the biosynthesis of a eukaryotic luciferin from fungi. Fungi possess a simple bioluminescent system, with luciferin being only two enzymatic steps from well-known metabolic pathways. The expression of genes from the fungal bioluminescent pathway is not toxic to eukaryotic cells, and the luciferase can be easily co-opted to bioimaging applications. With the fungal system being a genetically encodable bioluminescent system from eukaryotes, it is now possible to create artificially bioluminescent eukaryotes by expression of three genes. The fungal bioluminescent system represents an example of molecular evolution of a complex ecological trait and with molecular details reported in the paper, will allow additional research into ecological significance of fungal bioluminescence. Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering.
Prevalence of Antibiotic Residues and Antibiotic Resistance in Isolates of Chicken Meat in Korea

Abstract The aim of study was to investigate the correlation between the level of 17 antibiotic residues and 6 antibiotic resistances of Escherichia coli isolates in chicken meats. A total of 58 chicken meats were collected from retail grocery stores in five provinces in Korea. The total detection rate of antibiotic residues was 45% (26 out of 58). Ten out of 17 antibiotics were detected in chicken meats. None of the antibiotics exceeded the maximum residue level (MRLs) in chicken established by the Ministry of Food and Drug Safety (MFDS). The most detected antibiotics were amoxicillin (15.5%), followed by enrofloxacin (12.1%) and sulfamethoxazole (10.3%). In a total of 58 chicken meats, 51 E. coli strains were isolated. E. coli isolates showed the highest resistance to ampicillin (75%), followed by tetracycline (69%), ciprofloxacin (65%), trimethoprim/ sulfamethoxazole (41%), ceftiofur (22%), and amoxicillin/clavulanic acid (12%). The results of study showed basic information on relationship between antibiotic residue and resistance for 6 compounds in 13 chicken samples. Further investigation on the antibiotic resistance patterns of various bacteria species is needed to improve food safety.
Ontology-Based Resolution of Cloud Data Lock-in Problem

Cloud computing is nowadays becoming a popular paradigm for the provision of computing infrastructure that enables organizations to achieve financial savings. On the other hand, there are some known obstacles, among which vendor lock-in stands out. Furthermore, due to missing standards and heterogeneities of cloud storage systems, the migration of data to alternative cloud providers is expensive and time-consuming. We propose an approach based on Semantic Web services and AI planning to tackle cloud vendor data lock-in problem. To complete the mentioned task, data structures and data type mapping rules between different types of cloud storage systems are defined. The migration of data among different providers of platform as a service is presented in order to prove the practical applicability of the proposed approach. Additionally, this concept was also applied to software as a service model of cloud computing to perform one-shot data migration from Zoho CRM to Salesforce CRM.
Hypertension Risk with Abacavir Use among HIV-Infected Individuals: A Nationwide Cohort Study

Purpose A high risk of cardiovascular disease (CVD) is reported for HIV-infected individuals. While a link between abacavir and CVD risk is suggested, an association between abacavir and hypertension remains unclear. This study evaluated hypertension risk with abacavir use in comparison to non-abacavir antiretroviral treatment (ART). Materials and Methods From a nationwide cohort of HIV-infected individuals on their initial ART, 6493 who were free of hypertension at baseline were analyzed. The use of ART was treated as a time-varying covariate measured as a daily unit. Incidence rate of hypertension was calculated, and Cox proportional hazard models were used to estimate adjusted hazard ratios (HRs) with 95% confidence interval (CI) of incident hypertension overall and among subgroups. Results From the 6493 participants, 24072 person-years (PY) of follow-up were contributed during 2008–2016. The incidence rates of hypertension were 4.6 and 3.6 per 100 PY for abacavir and non-abacavir ART users, respectively. The population attributable fraction of abacavir use on hypertension was 12%. Abacavir exposure did not elevate the risk of hypertension among overall study population [HR, 1.2 (95% CI, 1.0–1.4), p=0.061]. However, those with poor ART adherence, defined as a medication possession ratio <50% [HR, 1.9 (95% CI, 1.5–2.4), p<0.0001] or requiring prophylactic antibiotics [HR, 1.2 (95% CI, 1.0–1.3), p=0.023], were at risk of hypertension induced by abacavir, as were men, individuals aged ≥40 years, and patients visiting tertiary hospitals in urban areas. Conclusion When present, poor ART adherence, requiring prophylactic antibiotics, male sex, and older age may warrant additional concern for hypertension in patients treated with abacavir.
Détresse psychologique et stratégies de coping des étudiants en première année universitaire

Le but de notre etude est d'evaluer les effets d'une insertion universitaire difficile et d'une gestion du travail peu adaptee en fonction du stress percu, des strategies de coping (processus dynamiques qui permettent de reduire ou de supprimer les consequences defavorables des contraintes et des changements) mobilisees, et de la difference de genre sur la detresse psychologique des etudiant(e)s d'une universite de l'Est de la France. La population interrogee, d'âge moyen de 20 ans, se compose de 927 etudiants de premiere annee. Un questionnaire comportant differentes echelles a ete administre ; ces echelles evaluent : l'insertion et l'isolement ; la gestion du travail universitaire ; le stress percu (Cohen) ; les strategies de coping face a une nouvelle situation (Brief COPE, Carver) ; la detresse psychologique (GHQ-12). Resultats : en ce qui concerne la detresse psychologique (GHQ-12, cotation ordinale), le score moyen des etudiantes (13,45 ± 5,50) est significativement superieur a celui des etudiants (11,78 ± 5,08) (t = 4,59, p <0,001). De plus, selon la cotation binaire et la note seuil de 4 au GHQ-12, il y a un pourcentage significativement plus eleve de filles (40,0 %) qui presentent une detresse psychologique severe que de garcons (26,5 %), (Χ 2 = 17,27; p < 0,001). A la question "Avez-vous pense a la possibilite de vous supprimer? ", 16,6 % des etudiants et 13,9 % des etudiantes ont repondu de facon affirmative. Une insertion difficile, un sentiment d'isolement, des difficultes dans la gestion du travail universitaire, des strategies de coping d'evitement et de blâme de soi-meme sont autant de facteurs associes a une adaptation peu fonctionnelle a l'universite contribuant a un risque eleve de souffrance.
Altered Topological Properties of Gray Matter Structural Covariance Networks in Minimal Hepatic Encephalopathy

Background and Aims: Liver cirrhosis commonly induces brain structural impairments that are associated with neurological complications (e.g., minimal hepatic encephalopathy (MHE)), but the topological characteristics of the brain structural network are still less well understood in cirrhotic patients with MHE. This study aimed to conduct the first investigation on the topological alterations of brain structural covariance networks in MHE. Methods: This study included 22 healthy controls (HCs) and 22 cirrhotic patients with MHE. We calculated the gray matter volume of 90 brain regions using an automated anatomical labeling (AAL) template, followed by construction of gray matter structural covariance networks by thresholding interregional structural correlation matrices as well as graph theoretical analysis. Results: MHE patients showed abnormal small-world properties of the brain structural covariance network, i.e., decreased clustering coefficient and characteristic path length and lower small-worldness parameters, which indicated a tendency toward more random architecture. In addition, MHE patients lost hubs in the prefrontal and parietal regions, although they had new hubs in the temporal and occipital regions. Compared to HC, MHE patients had decreased regional degree/betweenness involving several regions, primarily the prefrontal and parietal lobes, motor region, insula and thalamus. In addition, the MHE group also showed increased degree/betweenness in the occipital lobe and hippocampus. Conclusion: These results suggest that MHE leads to altered coordination patterns of gray matter morphology and provide structural evidence supporting the idea that MHE is a neurological complication related to disrupted neural networks.
Brain-Derived Neurotrophic Factor (BDNF) Role in Cannabinoid-Mediated Neurogenesis

The adult mammalian brain can produce new neurons in a process called adult neurogenesis, which occurs mainly in the subventricular zone (SVZ) and in the hippocampal dentate gyrus (DG). Brain-derived neurotrophic factor (BDNF) signaling and cannabinoid type 1 and 2 receptors (CB1R and CB2R) have been shown to independently modulate neurogenesis, but how they may interact is unknown. We now used SVZ and DG neurosphere cultures from early (P1-3) postnatal rats to study the CB1R and CB2R crosstalk with BDNF in modulating neurogenesis. BDNF promoted an increase in SVZ and DG stemness and cell proliferation, an effect blocked by a CB2R selective antagonist. CB2R selective activation promoted an increase in DG multipotency, which was inhibited by the presence of a BDNF scavenger. CB1R activation induced an increase in SVZ and DG cell proliferation, being both effects dependent on BDNF. Furthermore, SVZ and DG neuronal differentiation was facilitated by CB1R and/or CB2R activation and this effect was blocked by sequestering endogenous BDNF. Conversely, BDNF promoted neuronal differentiation, an effect abrogated in SVZ cells by CB1R or CB2R blockade while in DG cells was inhibited by CB2R blockade. We conclude that endogenous BDNF is crucial for the cannabinoid-mediated effects on SVZ and DG neurogenesis. On the other hand, cannabinoid receptor signaling is also determinant for BDNF actions upon neurogenesis. These findings provide support for an interaction between BDNF and endocannabinoid signaling to control neurogenesis at distinct levels, further contributing to highlight novel mechanisms in the emerging field of brain repair.
Green Platinum Nanoparticles Interaction With HEK293 Cells: Cellular Toxicity, Apoptosis, and Genetic Damage

Metal nanoparticles are widely used in industry, agriculture, textiles, drugs, and so on. The adverse effect of green platinum nanoparticles on human embryonic kidney (HEK293) cells is not well established. In the current study, green platinum nanoparticles were synthesized using leaf extract of Azadirachta indica L. Green platinum nanoparticles were characterized by dynamic light scattering and transmission electron microscope. The cytotoxicity of green platinum nanoparticle was observed in HEK293 cells by applying 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) and Neutral red uptake (NRU) assays. Cell viability of the cells was decreased in a concentration and duration-dependent manner. Generation of reactive oxygen species (ROS) in HEK293 cells due to green platinum nanoparticles was examined using fluorescent dye 2,7-dichlorofluorescein diacetate (DCFDA), and ROS was increased according to exposure pattern. The cytotoxicity of HEK293 cells was correlated with increased caspase 3, depolarization of mitochondrial membrane potential, and DNA fragmentation. The abovementioned finding confirmed that mitochondria play an important role in genotoxicity and cytotoxicity induced by nanoparticles in HEK293 cells. Further, we determined other oxidative stress biomarkers, lipid peroxide (LPO) and glutathione (GSH); LPO was increased and GSH was decreased in HEK293 cells. It is also important to indicate that HEK293 cells appear to be more susceptible to green platinum nanoparticles exposure after 24 hours. This result provides a dose- and time-dependent apoptosis and genotoxicity of green nanoparticles on HEK293 cells.
Association of Transcatheter Mitral Valve Repair With Quality of Life Outcomes at 30 Days and 1 Year: Analysis of the Transcatheter Valve Therapy Registry

Importance Improvements in symptoms, functional capacity, and quality of life are among the key goals of edge-to-edge transcatheter mitral valve repair (TMVR) for mitral regurgitation. Objective To examine health status outcomes among patients undergoing TMVR in clinical practice and the factors associated with improvement. Design, Setting, and Participants This cohort study used the Society of Thoracic Surgeons/American College of Cardiology Transcatheter Valve Therapy Registry, which contains data on patients with severe mitral regurgitation treated with TMVR from 2013 through 2017 in 217 US hospitals. Main Outcomes and Measures Change in disease-specific health status (Kansas City Cardiomyopathy Questionnaire–Overall Summary score [KCCQ-OS]; range 0-100 points, with higher scores indicating better health status) at 30 days and 1 year after TMVR. We also examined factors associated with health status at 30 days after TMVR, by means of multivariable linear regression using a generalized estimating equations approach to account for clustering of patients within sites. Results The KCCQ data were available in 81.2% at baseline, 69.3% of survivors at 30 days, and 47.4% of survivors at 1 year. Among 4226 patients who underwent TMVR, survived 30 days, and completed the KCCQ at baseline and follow-up, the KCCQ-OS increased from 41.9 before TMVR to 66.7 at 30 days (mean change 24.8 [95% CI, 24.0-25.6] points; P < .001), representing a large clinical improvement. The KCCQ scores remained stable from 30 days to 1 year after TMVR, with no further significant increase or decline. On multivariable analysis, atrial fibrillation (−2.2 [95% CI, −3.7 to −0.6] points; P = .01), permanent pacemaker (−2.1 [95% CI, −3.7 to −0.4] points; P = .01), severe lung disease (−3.9 [95% CI, −6.2 to −1.5] points; P = .001), home oxygen (−2.7 [95% CI, −4.9 to −0.4] points; P = .02), and lower KCCQ scores at baseline (3.9 points for each 10-point increase [95% CI, 3.6-4.2]; P < .001) were independently associated with lower 30-day KCCQ-OS scores. In-hospital renal failure was uncommon but was also associated with significant reductions in 30-day KCCQ-OS scores (−7.3 [95% CI −13.3 to −1.2] points). In estimates calculated with inverse probability weighting, after 1 year after TMVR, 54.2% (95% CI 52.2%-56.1%) of patients were alive and well; 23.0% had died, 21.9% had persistently poor health status (KCCQ-OS <60 points), 5.5% had a health status decline from baseline, and 4.6% had both poor health status and health status decline. Conclusions and Relevance In a national cohort of US patients undergoing edge-to-edge TMVR in clinical practice, health status was impaired prior to the procedure, improved within 30 days, and remained stable through 1 year among surviving patients with available data. While long-term mortality remains high, most surviving patients demonstrate improvements in symptoms, functional status, and quality of life, with only modest differences by patient-level factors.
A Sensory-Motor Theory of Rhythm, Time Perception and Beat Induction

In this paper, we develop further a sensory-motor theory of rhythm, time perception and beat induction. We account for these phenomena by the interaction of sensory systems, which represent temporal information in terms of the power spectrum of the sensory image, and the motor system, which has certain natural frequencies. The central assumption is that beat induction is not a passive process but, rather, a form of sensory-guided action involving all the sensory and motor components that that entails, i.e., major portions of the nervous system and the musculoskeletal system which it controls. Even if the musculoskeletal system (‘the plant’, to use the terminology of control theory) is not activated, i.e., there is no motor output, the higher supraspinal levels of the system (‘the controller’) are. To be more specific, the principal agent mediating beat induction is the internal representation of the musculoskeletal system and its dynamic properties which the ‘controller’ requires as a ‘feedforward’ model.
Learning View Priors for Single-View 3D Reconstruction

There is some ambiguity in the 3D shape of an object when the number of observed views is small. Because of this ambiguity, although a 3D object reconstructor can be trained using a single view or a few views per object, reconstructed shapes only fit the observed views and appear incorrect from the unobserved viewpoints. To reconstruct shapes that look reasonable from any viewpoint, we propose to train a discriminator that learns prior knowledge regarding possible views. The discriminator is trained to distinguish the reconstructed views of the observed viewpoints from those of the unobserved viewpoints. The reconstructor is trained to correct unobserved views by fooling the discriminator. Our method outperforms current state-of-the-art methods on both synthetic and natural image datasets; this validates the effectiveness of our method.
Treatment goals in psoriasis from a patient perspective: a qualitative study

Abstract Background: Psoriasis is a chronic inflammatory skin disorder with marked impact on quality of life. In view of the well-recognized need to integrate the patient perspective in psoriasis care, treatment goals which originate entirely from the experiences of the patients are of utmost importance. Objective: To explore treatment goals in patients with psoriasis that originate entirely from the patient perspective. Methods: Data was generated using face-to-face in-depth interviews with 15 Dutch psoriasis patients, which were analyzed using template analysis resulting in 2 first-level, 10 second-level, and 14 third-level themes. Results: A wide variety of treatment goals was reported. Almost all patients reported their ‘ultimate’ treatment goal would be achieving total skin clearance. Barriers in achieving treatment goals included the fact that psoriasis is a chronic disease with no cure available, lack of effectiveness of current treatment options and side effects of treatments of which the treatment effect does not compensate. Conclusion: There is a great variety and inter-individual difference in treatment goals. Therefore, we recommend to define individualized patient-defined treatment goals, as every patient with psoriasis requires a tailor-made treatment program.
Data Leakage and Loss in Biodiversity Informatics

Abstract The field of biodiversity informatics is in a massive, “grow-out” phase of creating and enabling large-scale biodiversity data resources. Because perhaps 90% of existing biodiversity data nonetheless remains unavailable for science and policy applications, the question arises as to how these existing and available data records can be mobilized most efficiently and effectively. This situation led to our analysis of several large-scale biodiversity datasets regarding birds and plants, detecting information gaps and documenting data “leakage” or attrition, in terms of data on taxon, time, and place, in each data record. We documented significant data leakage in each data dimension in each dataset. That is, significant numbers of data records are lacking crucial information in terms of taxon, time, and/or place; information on place was consistently the least complete, such that geographic referencing presently represents the most significant factor in degradation of usability of information from biodiversity information resources. Although the full process of digital capture, quality control, and enrichment is important to developing a complete digital record of existing biodiversity information, payoffs in terms of immediate data usability will be greatest with attention paid to the georeferencing challenge.
Predictors of Cardiac Sparing in Deep Inspiration Breath-Hold for Patients With Left Sided Breast Cancer

Purpose: The purpose of this study was to evaluate patient-related non-dosimetric predictors of cardiac sparing with the use of deep inspiration breath-hold (DIBH) in patients with left-sided breast cancer undergoing irradiation (RT). Materials and Methods: We retrospectively reviewed charts and treatment plans of one-hundred and three patients with left-sided breast cancer. All patients had both free-breathing (FB) and DIBH (with body surface tracking) plans available. (MHD) and V4 (heart volume receiving at least 4 Gy) were extracted from dose volume histograms. Fisher's exact and Chi-square tests were used to identify predictors of reductions in MHD and V4 after DIBH. Results: One-hundred and three patients were identified and most underwent mastectomy. MHD and V4 decreased significantly in DIBH plans (0.74 ± 0.25 Gy vs. 1.72 ± 0.98 Gy, p < 0.0001 for MHD; 4 ± 4.98 cc vs. 20.79 ± 18.2 cc, p < 0.0001 for V4). Body mass index (BMI), smoking and timing of CT simulation (spring/winter vs. summer/fall) were significant predictors of reduction in MHD whereas BMI, field size, chemotherapy, axillary dissection, and timing of CT simulation predicted reduction in V4. On multivariate analysis, BMI, and timing of CT simulation remained significant predictors of the heart-sparing effect of DIBH. Conclusions: In the setting of limited resources, identifying patients who will benefit the most from DIBH is extremely important. Prior studies have identified multiple dosimetric predictors of cardiac sparing and hereby we identified new non-dosimetric factors such as BMI and timing of treatments.