Miracle-dz/UniFAR-FTUs huggingface dataset:
Psychiatric comorbidities in patients with major depressive disorder

Background: Psychiatric comorbidities are common in major depressive disorder (MDD). They may worsen outcome and cause economic burden. The primary objective was to examine the prevalence of psychiatric comorbidities in MDD. The secondary objectives were to compare the presence of comorbidities between currently active and past MDD, and between patients with and without suicidal risk. Methods: This was a cross-sectional study. A total of 250 patients with lifetime MDD and age  18 years were enrolled. The Mini International Neuropsychiatric Interview (MINI), Thai version, was used to confirm MDD diagnosis and classify comorbidities. MDD diagnosis was confirmed in 190, and 60 patients were excluded due to diagnosis of bipolar disorder. Results: Of the 190 MDD patients, 25.8% had current MDD and 74.2% had past MDD. Eighty percent were women. The mean age at enrollment was 50 years, and at MDD onset was 41 years. Most patients were married (53.2%), employed (54.8%), and had  12 years of education (66.9%). There were 67 patients (35.3%) with one or more psychiatric comorbidities. Comorbidities included dysthymia (19.5%), any anxiety disorders (21.1%) (panic disorder [6.8%], agoraphobia [5.8%], social phobia [3.7%], obsessive–compulsive disorder [OCD] [4.7%], generalized anxiety disorder [5.3%], and post-traumatic stress disorder [4.2%]), alcohol dependence (0.5%), psychotic disorder (1.6%), antisocial personality (1.1%), and eating disorders (0%). Compared with past MDD, the current MDD group had significantly higher OCD ( P  0.001), psychotic disorder ( P = 0.048), past panic disorder ( P = 0.017), and suicidal risk ( P  0.001). Suicidal risk was found in 32.1% of patients. Patients with suicidal risk had more comorbid anxiety disorder of any type ( P = 0.019) and psychotic disorder ( P = 0.032). Conclusion: Several comorbidities were associated with MDD. Patients with active MDD had higher comorbid OCD, psychotic disorder, past panic disorder, and suicidal risk. Patients with suicide risk had higher comorbid
Whole genome analysis of Black Bengal goat from Savar Goat Farm, Bangladesh

Ziqrul Haq Chowdhury Bangladesh Agricultural Research Council Nazmul Hussain Bangladesh Agricultural University Saam Hasan North South University Ajran Kabir Bangladesh Agricultural University Muket Mahmud Bangladesh Agricultural University Mahdi Robbani North South University Tahmina Tabassum North South University Tamanna Afroze North South University Aura Rahman North South University Ra qul Islam Bangladesh Agricultural Research Council Maqsud Hossain (  muhammad.maqsud@northsouth.edu ) North South University https://orcid.org/0000-0001-9794-411X
A Triangulation Meta-Learning Framework for Imputing Missing Values in Weather Time Series

Machine learning and statistical methods can help model meteorological phenomena, especially in a context with many variables. However, it is not unusual that the measurement of those variables fails, generating data gaps and compromising data history analysis. The framework combines the predictions provided by three machine learning methods: decision trees, artificial neural networks and support vector machine, together with values calculated through five triangulation methods: arithmetic average, inverse distance weighted, optimized inverse distance weighted, optimized normal ratio and regional weight. Each machine learning algorithm generates eight regression models. One of the machine learning models makes predictions based only on the date. The remaining seven models make predictions based on one weather parameter (max. temperature, min. temperature, insolation, among others), in addition to the respective date. The triangulation methods use the climatic data from three neighboring cities to estimate the parameter of the target city. The generated dataset is, posteriorly, optimized by meta-learning algorithms. The results show that the additional information provided by the new machine learning models and the triangulation methods offered a significant increase in the accuracy of the imputed data. Moreover, the statistical analysis and coefficient of determination R² showed that the meta-learning model based on regression trees successfully combined the base-level outputs to generate outputs that best fill in the missing values of the time series studied in this paper.
COMPUTATIONAL IDENTIFICATION OF MICRORNA IN FIVE WOODY OIL TREE CROPS AND THEIR miRNA TARGET SEQUENCES

Recently discovered miRNA (microribonucleic acids) are a kind of endogenous small RNA that have important regulatory roles during eukaryote development and stress responses by controlling mRNA degradation or inhibiting translation. However, little is known about miRNA from commercially important woody oil crops. Using a comparative genomics approach and following a series of stringent filtering criteria, we identified 36 woody oil crop miRNA belonging to 22 families using expressed sequence tags and genome survey sequence databases. The numbers of miRNA found in walnut (Juglans regia) , oil palm (Elaeis guineensis) , tea (Camellia sinensis) , tung oil tree (Vernicia fordii) and barbados nut (Jatropha curcas) were 17, 11, 3, 3 and 2, respectively. In addition, 275 potential target genes were predicted for 27 newly identified miRNA utilising mRNA databases of J. curcas, E. guineensis, C. sinensis, J. regia, V. fordii and Olea europaea plant species. Most of the target mRNA encoded transcription factors that regulated plant growth and development, together with a few target genes that were involved in metabolism or stress responses. Sequence alignments of 10 miRNA families from different species showed that miRNA sequences within the same family were variable. Furthermore, the authenticity of 11 novel miRNA candidates from oil palm was verified by semi-quantitative and quantitative reverse transcription-polymerase chain reaction (RT-PCR). A correlation analysis revealed a close correlation between the two PCR assay methods. The expression levels of miRNA transcripts significantly differed between the leaf and the fruit tissues of E. guineensis .
Culture-dependent and culture-independent methods for molecular analysis of the diversity of lactobacilli in Camembert de Normandie cheese

Comparaison de methodes culture-dependante et culture-independante pour l'analyse moleculaire de la diversite des lactobacilles dans le Camembert de Normandie. La contribution de deux approches culture-dependante et culture-independante a ete etudiee dans le but d'apprecier la biodiversite et l'evolution des populations de lactobacilles au cours de la transformation de lait cru en camembert AOC dans trois fromageries. Une analyse par electrophorese en gradient de temperature (TGGE) a ete effectuee comparativement sur l'ADN microbien total et sur l'ADN extrait a partir d'isolats. Les profils TGGE obtenus a partir de l'ADN total de laits et de fromages ont montre que Lactobacillus paracasei subsp. paracasei etait une espece dominante au sein des trois fromageries et que Lb. plantarum co-dominait dans l'un des trois ateliers. Apres etude des profils TGGE des isolats, ces deux especes demeurent majoritaires mais Lactobacillus delbrueckii susbp. lactis, Lb. acidophilus, Lb. delbrueckii susbp. bulgaricus et Lb. casei subsp. casei sont egalement mis en evidence. Les deux approches ont conduit a l'obtention d'informations complementaires.
Autofocus Tracking System Based on Digital Holographic Microscopy and Electrically Tunable Lens

We present an autofocus tracking system implemented by the digital refocusing of digital holographic microscopy (DHM) and the tunability of an electrically tunable lens (ETL). Once the defocusing distance of an image is calculated with the DHM, then the focal plane of the imaging system is optically tuned so that it always gives a well-focused image regardless of the object location. The accuracy of the focus is evaluated by calculating the contrast of refocused images. The DHM is performed in an off-axis holographic configuration, and the ETL performs the focal plane tuning. With this proposed system, we can easily track down the object drifting along the depth direction without using any physical scanning. In addition, the proposed system can simultaneously obtain the digital hologram and the optical image by using the RGB channels of a color camera. In our experiment, the digital hologram is obtained by using the red channel and the optical image is obtained by the blue channel of the same camera at the same time. This technique is expected to find a good application in the long-term imaging of various floating cells.
Evaluation of the relationship between left atrial volume and myocardial ischemia: a systematic review

Introduction: The pathophysiology of ischemia involves the cellular effect of myocardial ischemia, reactive oxygen species, and reactive inflammatory enzymes. Left atrial (LA) ischemia has been shown to have several mechanisms through which it can lead to abnormalities in left ventricular filling in early diastole and thus reduces LA passive functional reserve. In this review, we evaluated the physiological mechanisms of LA during myocardial ischemia, as previously demonstrated in experimental and clinical studies.Methods: Several databases were searched in order to find related articles. The outcome of interest included LA function measurements (measurement of LA volume) during ischemia. By applying a standardized protocol, reviewers independently extracted and assessed the studies.Results: The literature review indicated 50 publications, among which 15 studies were eligible for analysis. Assessment of LA dimension and function is essential for clinical evaluation and prognostic purposes. Conclusion: The present article revealed that LA passive emptying volume and LA emptying volume significantly increased in myocardial ischemia. Further researches could provide a better understanding of pathophysiological mechanisms behind LA enlargement and help to predict clinical outcomes in many cardiovascular disorders.
Tumor necrosis factor-alpha ( TNF-alpha ) enhances functional thermal and chemical responses of TRP cation channels in human synoviocytes

Background: We have shown functional expression of several TRP channels on human synovial cells, proposing significance in known calcium dependent proliferative and secretory responses in joint inflammation. The present study further characterizes synoviocyte TRP expression and activation responses to thermal and osmotic stimuli after pre-treatment with proinflammatory mediator tumor necrosis factor alpha (TNF-α, EC50 1.3221 × 10-10g/L). Results: Fluorescent imaging of Fura-2 loaded human SW982 synoviocytes reveals immediate and delayed cytosolic calcium oscillations elicited by (1) TRPV1 agonists capsaicin and resiniferatoxin (20 – 40% of cells), (2) moderate and noxious temperature change, and (3) osmotic stress TRPV4 activation (11.5% of cells). TNF-alpha pre-treatment (1 ng/ml, 8 – 16 hr) significantly increases (doubles) capsaicin responsive cell numbers and [Ca2+]i spike frequency, as well as enhances average amplitude of temperature induced [Ca]i responses. With TNF-alpha pre-treatment for 8, 12, and 16 hr, activation with 36 or 45 degree bath solution induces bimodal [Ca]i increase (temperature controlled chamber). Initial temperature induced rapid transient spikes and subsequent slower rise reflect TRPV1 and TRPV4 channel activation, respectively. Only after prolonged TNF-alpha exposure (12 and 16 hr) is recruitment of synoviocytes observed with sensitized TRPV4 responses to hypoosmolarity (3–4 fold increase). TNF-alpha increases TRPV1 (8 hr peak) and TRPV4 (12 hr peak) immunostaining, mRNA and protein expression, with a TRPV1 shift to membrane fractions. Conclusion: TNF-α provides differentially enhanced synoviocyte TRPV1 and TRPV4 expression and [Ca]i response dependent on the TRP stimulus and time after exposure. Augmented relevance of TRPV1 and TRPV4 as inflammatory conditions persist would provide calcium mediated cell signaling required for pathophysiological responses of synoviocytes in inflammatory pain states. Published: 20 August 2009 Molecular Pain 2009, 5:49 doi:10.1186/1744-8069-5-49 Received: 10 March 2009 Accepted: 20 August 2009 This article is available from: http://www.molecularpain. com/content/5/1/49 © 2009 Kochukov et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Molecular Pain 2009, 5:49 http://www.molecularpain. com/content/5/1/49
Social distancing to slow the US COVID-19 epidemic: Longitudinal pretest–posttest comparison group study

Background Social distancing measures to address the US coronavirus disease 2019 (COVID-19) epidemic may have notable health and social impacts. Methods and findings We conducted a longitudinal pretest–posttest comparison group study to estimate the change in COVID-19 case growth before versus after implementation of statewide social distancing measures in the US. The primary exposure was time before (14 days prior to, and through 3 days after) versus after (beginning 4 days after, to up to 21 days after) implementation of the first statewide social distancing measures. Statewide restrictions on internal movement were examined as a secondary exposure. The primary outcome was the COVID-19 case growth rate. The secondary outcome was the COVID-19-attributed mortality growth rate. All states initiated social distancing measures between March 10 and March 25, 2020. The mean daily COVID-19 case growth rate decreased beginning 4 days after implementation of the first statewide social distancing measures, by 0.9% per day (95% CI −1.4% to −0.4%; P < 0.001). We did not observe a statistically significant difference in the mean daily case growth rate before versus after implementation of statewide restrictions on internal movement (0.1% per day; 95% CI −0.04% to 0.3%; P = 0.14), but there is substantial difficulty in disentangling the unique associations with statewide restrictions on internal movement from the unique associations with the first social distancing measures. Beginning 7 days after social distancing, the COVID-19-attributed mortality growth rate decreased by 2.0% per day (95% CI −3.0% to −0.9%; P < 0.001). Our analysis is susceptible to potential bias resulting from the aggregate nature of the ecological data, potential confounding by contemporaneous changes (e.g., increases in testing), and potential underestimation of social distancing due to spillover effects from neighboring states. Conclusions Statewide social distancing measures were associated with a decrease in the COVID-19 case growth rate that was statistically significant. Statewide social distancing measures were also associated with a decrease in the COVID-19-attributed mortality growth rate beginning 7 days after implementation, although this decrease was no longer statistically significant by 10 days.
Living donor nephrectomy: University of Miami technique and current results.

OBJECTIVES Living-donor nephrectomy has significantly expanded the pool of renal transplant donors, allowing for a marked increase in transplantation. Improvements in antirejection medications and refinement of donor selection criteria have allowed for extremely favorable rates of graft survival. More recently, laparoscopic donor nephrectomy (LDN) has significantly reduced the morbidity of renal transplantation in the donor population. The University of Miami/Jackson Memorial Hospital Transplant Center performs a large number of living-donor nephrectomies, with increasing use of LDN and here we report our cumulative experience. METHODS A retrospective review was performed of all live donor nephrectomies performed over the last 10 years, including LDN. Surgical complications, both minor and major, were ascertained. Conversion from LDN to open was similarly noted. Follow up, including creatinine one year post-transplant was recorded in open donor nephrectomy (ODN) and LDN groups. RESULTS Over 10 years, 413 live donor nephrectomies were performed. Of these, 257 were LDN, and 156 were ODN. In two cases, LDN was converted to ODN. Three patients needed reoperation after donor nephrectomy. There were no perioperative mortalities or deep venous thrombosis. Minor complications, including hernia, fever, and C. difficile diarrhea were very rare, the most common being testicular pain in eight patients. CONCLUSION Our extensive experience with living donor nephrectomy, with 413 cases spanning ten years, has been very favorable. The risk of major complications was extremely low, with six reported in the series. Minor complications were similarly rare. Living donor nephrectomy is a safe and feasible method of increasing the number of renal transplantation donors with minimal morbidity.
Analytical Mechanics: Solutions to Problems in Classical Physics

Fundamentals of Analytical Mechanics Constraints Classification Criteria for Constraints The Fundamental Dynamical Problem for a Constrained Particle System of Particles Subject to Constraints Lagrange Equations of the First Kind Elementary Displacements Generalities Real, Possible and Virtual Displacements Virtual Work and Connected Principles Principle of Virtual Work Principle of Virtual Velocities Torricelli's Principle Principles of Analytical Mechanics D'alembert's Principle Configuration Space Generalized Forces Hamilton's Principle The Simple Pendulum Problem Classical (Newtonian) Formalism Lagrange Equations of the first Kind Approach Lagrange Equations of the Second Kind Approach Hamilton's Canonical Equations Approach Hamilton-Jacobi Method Action-Angle Variables Formalism Problems Solved by Means of the Principle of Virtual Work Problems of Variational Calculus Elements of Variational Calculus Functionals. Functional Derivative Extrema of Functionals Problems whose solutions demand elements of variational calculus Brachistochrone problem Catenary problem Isoperimetric problem Surface of revolution of minimum area Geodesics of a Riemannian manifold Problems Solved by Means of the Lagrangian Formalism Atwood machine Double Atwood Machine Pendulum with Horizontally Oscillating Point of Suspension Problem of Two Identical Coupled Pendulums Problem of Two Different Coupled Pendulums Problem of Three Identical Coupled Pendulums Problem of Double Gravitational Pendulum Problems of Equilibrium and Small Oscillations Problems Solved By Means of the Hamiltonian Formalism Problems of Continuous Systems A. Problems of Classical Electrodynamics B. Problems of Fluid Mechanics C. Problems of Magnetofluid Dynamics and Quantum Mechanics APPENDICES REFERENCES
Socio-economic inequalities in access to maternal and child healthcare in Nigeria: changes over time and decomposition analysis

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Limnological study of a lake formed in limestone quarry [Krakow, Poland]. I. Zooplankton community

The zooplankton of a meromictic lake, in a former limestone quarry situated in southern Poland, was studied monthly in the years 2000-2001. A low density and diversity of zooplankton assemblage was noted. Individuals of the dominant species Daphnia longispina represented all body size classes and were present during the whole study period; the maximum number of Daphnia females carrying the eggs was noted in May. The normal dial vertical migration of Daphnia, studied in June, was observed.
A Compilation of the Full PDDL+ Language into SMT

Planning in hybrid systems is important for dealing with real-world applications. PDDL+ supports this representation of domains with mixed discrete and continuous dynamics, and supports events and processes modelling exogenous change. Motivated by numerous SAT-based planning approaches, we propose an approach to PDDL+ planning through SMT, describing an SMT encoding that captures all the features of the PDDL+ problem as published by Fox and Long. The encoding can be applied on domains with nonlinear continuous change. We apply this encoding in a simple planning algorithm, demonstrating excellent results on a set of benchmark problems.
Habitat suitability – density relationship in an endangered woodland species: the case of the Blue Chaffinch ([i]Fringilla polatzeki[i])

Methods. We studied the Gran Canaria blue chaffinch (Fringilla polatzeki), a habitat specialist endemic of the Canary Islands restricted to the pine forest of Inagua, the only area where the species has been naturally present as a regular breeder in the last 25 years. A suitability distribution model using occurrences with demographic relevance (i.e., nest locations of successful breeding attempts analysed using boosted classification trees) was built considering orographic, climatic and habitat structure predictors. By means of a standardized survey program we monitored the yearly abundance of the species in 100 sectors since the declaration of Inagua as a Strict Nature Reserve in 1994.
Probing navigation strategies of honey-bees - landmark experiments and simulations

In this study we probed the content of the spatial memory of honeybees in two landmark manipulation experiments accompanied by computer modelling. While the results of the first experiments are in line with an image-like representation of places, the findings of the second experiment suggest that bees also memorize the depth structure of a scene, most probably inferred from optic flow. This is supported by the fact that bees actively control their visual input.
The effectiveness of varenicline versus nicotine replacement therapy on long-term smoking cessation in primary care: a prospective cohort study of electronic medical records

Abstract Background There is limited evidence about the effectiveness of varenicline and nicotine replacement therapy (NRT) for long-term smoking cessation in primary care, or whether the treatment effectiveness differs by socioeconomic position (SEP). Therefore, we estimated the long-term effectiveness of varenicline versus NRT (> 2 years) on smoking cessation, and investigated whether effectiveness differs by SEP. Methods This is a prospective cohort study of electronic medical records from 654 general practices in England, within the Clinical Practice Research Datalink, using three different analytical methods: multivariable logistic regression, propensity score matching and instrumental variable analyses. Exposure was prescription of varenicline versus NRT, and the primary outcome was smoking cessation at 2 years’ follow-up; outcome was also assessed at 3, 6, and 9 months, and at 1 and 4 years after exposure. SEP was defined using the Index of Multiple Deprivation. Results At 2 years, 28.8% (N = 20 362/70 610) of participants prescribed varenicline and 24.3% (N = 36 268/149 526) of those prescribed NRT quit; adjusted odds ratio was 1.26 [95% confidence interval (CI): 1.23 to 1.29], P < 0.0001. The association persisted for up to 4 years and was consistent across all analyses. We found little evidence that the effectiveness of varenicline differed greatly by SEP. However, patients from areas of higher deprivation were less likely to be prescribed varenicline; adjusted odds ratio was 0.91 (95% CI: 0.90 to 0.92), P < 0.0001. Conclusions Patients prescribed varenicline were more likely to be abstinent up to 4 years after first prescription than those prescribed NRT. In combination with other evidence, the results from this study may be used to update clinical guidelines on the use of varenicline for smoking cessation.