Miracle-dz/UniFAR-FTUs huggingface dataset:
Fast mixing for Latent Dirichlet allocation

Markov chain Monte Carlo (MCMC) algorithms are ubiquitous in probability theory in general and in machine learning in particular. A Markov chain is devised so that its stationary distribution is some probability distribution of interest. Then one samples from the given distribution by running the Markov chain for a "long time" until it appears to be stationary and then collects the sample. However these chains are often very complex and there are no theoretical guarantees that stationarity is actually reached. In this paper we study the Gibbs sampler of the posterior distribution of a very simple case of Latent Dirichlet Allocation, an attractive Bayesian unsupervised learning model for text generation and text classification. It turns out that in some situations, the mixing time of the Gibbs sampler is exponential in the length of documents and so it is practically impossible to properly sample from the posterior when documents are sufficiently long.
Bioacoustical Periodic Pulse Train Signal Detection and Classification using Spectrogram Intensity Binarization and Energy Projection

The following work outlines an approach for automatic detection and recognition of periodic pulse train signals using a multi-stage process based on spectrogram edge detection, energy projection and classification. The method has been implemented to automatically detect and recognize pulse train songs of minke whales. While the long term goal of this work is to properly identify and detect minke songs from large multi-year datasets, this effort was developed using sounds off the coast of Massachusetts, in the Stellwagen Bank National Marine Sanctuary. The detection methodology is presented and evaluated on 232 continuous hours of acoustic recordings and a qualitative analysis of machine learning classifiers and their performance is described. The trained automatic detection and classification system is applied to 120 continuous hours, comprised of various challenges such as broadband and narrowband noises, low SNR, and other pulse train signatures. This automatic system achieves a TPR of 63% for FPR of 0.6% (or 0.87 FP/h), at a Precision (PPV) of 84% and an F1 score of 71%.
Bearing Fault Diagnosis Based on a Hybrid Classifier Ensemble Approach and the Improved Dempster-Shafer Theory

Bearing fault diagnosis of a rotating machine plays an important role in reliable operation. A novel intelligent fault diagnosis method for roller bearings has been developed based on a proposed hybrid classifier ensemble approach and the improved Dempster-Shafer theory. The improved Dempster-Shafer theory well considered the combination of unreliable evidence sources, the uncertainty information of basic probability assignment, and the relative credibility of the evidence on the weights in the process of decision making under the framework of fuzzy preference relations, which can effectively deal with conflicts of the evidences and then well improve the diagnostic accuracy for the hybrid classifier ensemble. The effectiveness of the improved Dempster-Shafer theory has been verified via a numerical example. In addition, deep neural networks, a support vector machine, and extreme learning machine techniques have been utilized in the single-stage classification based on singular spectrum entropy, power spectrum entropy, time-frequency entropy, and wavelet packet energy spectrum entropy in this work. Performances of the proposed hybrid ensemble classifier has been demonstrated on a bearing test-rig, compared with the original Dempster-Shafer theory. It can be found that the overall error rate can be greatly reduced with the hybrid ensemble classifier and the improved Dempster-Shafer theory.
Paternally Acting Canonical RNA-Directed DNA Methylation Pathway Genes Sensitize Arabidopsis Endosperm to Paternal Genome Dosage[OPEN]

RNA-directed DNA methylation pathway genes act paternally to sensitize endosperm to excess paternal genomes, challenging previous models of dosage sensitivity in endosperm. Seed development is sensitive to parental dosage, with excess maternal or paternal genomes creating reciprocal phenotypes. Paternal genomic excess frequently results in extensive endosperm proliferation without cellularization and seed abortion. We previously showed that loss of the RNA polymerase IV gene NUCLEAR RNA POLYMERASE D1 (NRPD1) in tetraploid fathers represses seed abortion in paternal excess crosses. Here, we show genetically that RNA-directed DNA methylation (RdDM) pathway activity in the paternal parent is sufficient to determine the viability of paternal excess Arabidopsis (Arabidopsis thaliana) seeds. We compared transcriptomes, DNA methylation, and small RNAs from the endosperm of seeds from balanced crosses (diploid × diploid) and lethal (diploid × tetraploid) and viable paternal excess crosses (diploid × tetraploid nrpd1). Endosperms from both lethal and viable paternal excess seeds share widespread transcriptional and DNA methylation changes at genes and transposable elements. Interploidy seed abortion is thus unlikely to be caused by transposable elements or imprinted gene misregulation, and its repression by the loss of paternal RdDM is associated with only modest gene expression changes. Finally, using allele-specific transcription data, we present evidence for a transcriptional buffering system that increases the expression of maternal alleles and represses paternal alleles in response to excess paternal genomic dosage. These findings prompt reconsideration of models for dosage sensitivity in endosperm.
A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations

The psychrophilic and mesophilic endonucleases A (EndA) from Aliivibrio salmonicida (VsEndA) and Vibrio cholera (VcEndA) have been studied experimentally in terms of the biophysical properties related to thermal adaptation. The analyses of their static X-ray structures was no sufficient to rationalize the determinants of their adaptive traits at the molecular level. Thus, we used Molecular Dynamics (MD) simulations to compare the two proteins and unveil their structural and dynamical differences. Our simulations did not show a substantial increase in flexibility in the cold-adapted variant on the nanosecond time scale. The only exception is a more rigid C-terminal region in VcEndA, which is ascribable to a cluster of electrostatic interactions and hydrogen bonds, as also supported by MD simulations of the VsEndA mutant variant where the cluster of interactions was introduced. Moreover, we identified three additional amino acidic substitutions through multiple sequence alignment and the analyses of MD-based protein structure networks. In particular, T120V occurs in the proximity of the catalytic residue H80 and alters the interaction with the residue Y43, which belongs to the second coordination sphere of the Mg2+ ion. This makes T120V an amenable candidate for future experimental mutagenesis.
Walking speed as a predictor of community mobility and quality of life after stroke

ABSTRACT Background: Community mobility (CM) is considered a part of community reintegration that enhances Quality of Life (QoL). Achieving an appropriate gait speed is essential in attaining an independent outdoor ambulation and satisfactory CM. Objective: The aim of this study was to identify whether gait speed is a predictor of CM and QoL in patients with stroke following a multimodal rehabilitation program (MRP). Methods: This was a baseline control trial with 6-months follow-up in an outpatient rehabilitation setting at a university hospital. Twenty-six stroke survivors completed the MRP (24 sessions, 2 days/wk, 1 hr/session). The MRP consisted of aerobic exercise, task-oriented exercises, balance exercises and stretching. Participants also performed an ambulation program at home. Outcome variables were: walking speed (10-m walking test) and QoL (physical and psychosocial domains of Euroquol and Sickness Impact Profile). Results: At the end of the intervention, comfortable and fast walking speed increased by an average of 0.16 (SD 0.21) (*p < .05) and 0.40 (SD 0.51) (**p < .001) m/s, respectively. After the intervention, all participants achieved independent outdoor ambulation with an increase of 34.14 of walking minutes/day in the community and a decrease of sitting time of 95.45 minutes/day. Regarding QoL there were increased mean scores on the physical and psychosocial dimensions of Euroquol and the Sickness Impact Profile, respectively (**p < .001). Conclusions: The results suggest that improved walking speed after the MRP is associated with CM and higher scores in QoL. These findings support the need to implement rehabilitation programs to promote increased speed.
Specific Versus Diverse Computing in Media Cloud

Specific computing (SC) and diverse computing (DC), as two main visual computation manners, have been widely utilized in Media Cloud. However, how to choose SC or DC in a practical scenario is still an open and challenging problem. Unfortunately, the traditional fluid-based analysis method cannot address this issue due to the uncertain relationship between the computing manner and service dynamics. In this paper, we analytically study the characteristics of SC and DC by designing a so-called collapsing approximation (CA) method to precisely approximate the distribution of the service dynamics. On the qualitative end, we derive an exact expression for the dynamics of CA, thus enabling the cloud designer to choose different computing manners according to the application requests and analyze its impact on the degrees of DC. On the technical end, we show that the evolution of the service dynamics process can be approximated by the unique solution to a collapsing model over a finite time period. The highlight of this paper lies in demonstrating that the optimal computing configuration should largely depend on SC, and a little on DC.
Use of the Immune System to Investigate the Toxicity Induced by Environmental Pollutants in Fish, Amphibian, and Mammalian Species

In recent years, there has been growing concern about the effect of environmental pollutants on the immune system. In the current study, we investigated the toxicity induced by certain environmental pollutants on the immune systems of fish, amphibians, and mice. Fish in the laboratory were tested for susceptibility to immunosuppression by treatment with 1,3-Bis (chloroethyl)-1-nitrosourea (BCNU). Immunotoxicity of the tilapian immune system was detectable using mitogen-induced proliferation assay and cell-mediated toxicity assay. Fish from various streams of the Roanoke River were tested for immunotoxicity and parasitic infection. Fish from the more polluted North Fork of the Roanoke River exhibited a stronger mitogenic response when compared to fish from the South Fork of the Roanoke River. The effect of perinatal exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), commonly referred to as dioxin, a highly toxic environmental pollutant, was tested in C57BL/6 mice. TCDD was administered on gestational day 14 and pup thymocytes were studied for apoptosis on postnatal days 2, 4, 7, 14, and 21. Perinatal exposure to TCDD decreased thymic cellularity and induced apoptosis in the thymocytes of the pups. Amphibians from polluted areas of Bermuda were similarly tested for immunotoxicity and compared with amphibians from less polluted areas. The lymphocyte responsiveness of toads from the more polluted Bermuda Biological Station of
Micellization Behavior of Long-Chain Substituted Alkylguanidinium Surfactants

Surface activity and micelle formation of alkylguanidinium chlorides containing 10, 12, 14 and 16 carbon atoms in the hydrophobic tail were studied by combining conductivity and surface tension measurements with isothermal titration calorimetry. The purity of the resulting surfactants, their temperatures of Cr→LC and LC→I transitions, as well as their propensity of forming birefringent phases, were assessed based on the results of 1H and 13C NMR, differential scanning calorimetry (DSC), and polarizing microscopy studies. Whenever possible, the resulting values of Krafft temperature (TK), critical micelle concentration (CMC), minimum surface tension above the CMC, chloride counter-ion binding to the micelle, and the standard enthalpy of micelle formation per mole of surfactant (ΔmicH°) were compared to those characterizing alkyltrimethylammonium chlorides or bromides with the same tail lengths. The value of TK ranged between 292 and 314 K and increased strongly with the increase in the chain length of the hydrophobic tail. Micellization was described as both entropy and enthalpy-driven. Based on the direct calorimetry measurements, the general trends in the CMC with the temperature, hydrophobic tail length, and NaCl addition were found to be similar to those of other types of cationic surfactants. The particularly exothermic character of micellization was ascribed to the hydrogen-binding capacity of the guanidinium head-group.
Tibialis anterior tendinous tissue plays a key role in energy absorption during human walking

ABSTRACT The elastic tendinous tissues of distal lower limb muscles can improve the economy of walking and running, amplify the power generated by a muscle and absorb energy. This paper explores the behaviour of the tibialis anterior (TA) muscle and its tendinous tissue during gait, as it absorbs energy during contact and controls foot position during swing. Simultaneous measurements of ultrasound, surface electromyography and 3D motion capture with musculoskeletal modelling from 12 healthy participants were recorded as they walked at preferred and fast walking speeds. We quantified the length changes and velocities of the TA muscle–tendon unit (MTU) and its fascicles across the stride at each speed. Fascicle length changes and velocities were relatively consistent across speeds, although the magnitude of fascicle length change differed between the deep and superficial regions. At contact, when the TA is actively generating force, the fascicles remained relatively isometric as the MTU actively lengthened, presumably stretching the TA tendinous tissue and absorbing energy. This potentially protects the muscle fibres from damage during weight acceptance and allows energy to be returned to the system later in the stride. During early swing, the fascicles and MTU both actively shortened to dorsiflex the foot, clearing the toes from the ground; however, at the fast walking velocity, the majority of shortening occurred through tendinous tissue recoil, highlighting its role in accelerating ankle dorsiflexion to power rapid foot clearance in swing. Summary: The tendinous tissues of the tibialis anterior play a key role in absorbing mechanical energy as the foot contacts the ground, as well as helping to power rapid acceleration of the ankle into dorsiflexion to aid foot clearance during leg swing.
DNA-mediated electrostatic assembly of gold nanoparticles into linear arrays by a simple drop-coating procedure

The assembly of nanoparticles in topologically predefined superstructures is an important problem in the area of nanoscale architecture. In this letter, we demonstrate the electrostatic assembly of lysine-capped colloidal gold particles on drop-coated DNA films. Electrostatic interaction between the positive charges on the gold nanoparticles and the negative charges on the phosphate groups of the DNA template molecules leads to the assembly of the gold nanoparticles in linear superstructures. The use of DNA as templates for the assembly of nanoparticles shows promise for extension to more complex geometries through rational design of the DNA base sequences as well as in the realization of nanowires by stringing together metal nanoparticles.
Argatroban for Prevention and Treatment of Thromboembolism in Heparin-Induced Thrombocytopenia

OBJECTIVE: To review the pharmacology, pharmacokinetics, efficacy, adverse events, and cost of argatroban in the prevention and treatment of thromboembolism in patients with heparin-induced thrombocytopenia (HIT). DATA SOURCES: A MEDLINE search (1980 to August 2000) of English-language literature was conducted using the search term argatroban to identify pertinent case reports, clinical trials, abstracts, and review articles. Additional reports were identified from the reference lists compiled in the literature reviewed, as well as from the manufacturer. DATA SYNTHESIS: Argatroban is a synthetic direct thrombin inhibitor indicated for parenteral use in the prevention and treatment of thromboembolism in patients with HIT. Its elimination half-life is approximately 40–50 minutes, and it is primarily eliminated by hepatic metabolism and biliary secretion. Compared with historical controls, argatroban-treated patients with HIT or HIT with thrombosis (HITTS) experienced lower rates of the composite end point of death, amputation, and new thrombosis. Dosing is initiated at 2 μg/kg/min and adjusted to maintain the activated partial thromboplastin time at 1.5–3 × the patient's baseline. In Japan, argatroban is approved for use in acute ischemic stroke and chronic peripheral occlusive disease. It has also been used as an alternative to unfractionated heparin (UFH) in patients with a history of HIT or HITTS undergoing percutaneous coronary intervention and other procedures. Additionally, argatroban has been compared with UFH in patients with acute myocardial infarction who were receiving thrombolytic therapy. Hemorrhage is the primary adverse event associated with argatroban. Argatroban increases the prothrombin time, making assessment of the intensity of warfarin therapy during concurrent administration more complex. CONCLUSIONS: The use of argatroban in patients with HIT and HITTS is associated with improvement in clinical outcomes compared with historical controls. Argatroban offers several practical advantages over other available agents with respect to dosing, monitoring, reversibility of effect with discontinuation of the drug, and cost.
Plasma Filtration Versus Centrifugation in Pediatric Therapeutic Plasma Exchange: Should the Diagnosis Define the Method?†

Therapeutic plasma exchange (TPE) is used for a variety of illnesses in critically ill pediatric patients. Although both centrifugation and filtration are known to be effective methods, to our knowledge, clinical results for TPE by these methods are not compared in pediatric patient populations. One hundred patients who had TPE for a variety of diagnoses were included in the study. In 55 patients plasma exchange was implemented by centrifugation and in 45, by filtration. These two groups were further divided into subgroups according to admittance diagnoses. The demographic information, admittance Pediatric Risk of Mortality scores, Pediatric Logistic Organ Dysfunction (PELOD) scores before beginning of therapy and PELOD at the end of therapy, durations of ventilatory support, pediatric intensive care unit and hospital stay, and outcomes were compared. Although the survival was significantly better in filtration group, it included more patients with neurologic diagnoses. Filtration group standard mortality rate was 0.6. In both groups, the PELOD scores after the termination of TPE were significantly decreased compared to that before beginning of TPE. Within thrombotic microangiopathy and hemophagocytic lymphohistiocytosis subgroups, median PELOD scores before treatment were higher in centrifugation patients but survival was similar with both methods. Both methods of TPE are alike in decreasing PELOD scores. In the filtration group, survival benefit of TPE is evident. In thrombotic microangiopathy patients, despite higher PELOD scores in the centrifugation group, survival is similar for both methods. These findings should be retested in randomized studies and the underlying physiology awaits to be uncovered.
PgMYB2, a MeJA-Responsive Transcription Factor, Positively Regulates the Dammarenediol Synthase Gene Expression in Panax Ginseng

The MYB transcription factor family members have been reported to play different roles in plant growth regulation, defense response, and secondary metabolism. However, MYB gene expression has not been reported in Panax ginseng. In this study, we isolated a gene from ginseng adventitious root, PgMYB2, which encodes an R2R3-MYB protein. Subcellular localization revealed that PgMYB2 protein was exclusively detected in the nucleus of Allium cepa epidermis. The highest expression level of PgMYB2 was found in ginseng root and it was significantly induced by plant hormones methyl jasmonate (MeJA). Furthermore, the binding interaction between PgMYB2 protein and the promoter of dammarenediol synthase (DDS) was found in the yeast strain Y1H Gold. Moreover, the electrophoretic mobility shift assay (EMSA) identified the binding site of the interaction and the results of transiently overexpressing PgMYB2 in plants also illustrated that it may positively regulate the expression of PgDDS. Based on the key role of PgDDS gene in ginsenoside synthesis, it is reasonable to believe that this report will be helpful for the future studies on the MYB family in P. ginseng and ultimately improving the ginsenoside production through genetic and metabolic engineering.
The RNA-Binding Protein HuR Confers Oxaliplatin Resistance of Colorectal Cancer By Upregulating CDC6

Human antigen R (HuR) is an RNA-binding protein that posttranscriptionally regulates many cancer-trait genes. CDC6, a central regulator of DNA replication, is regulated by HuR. In this study, we investigated the role of HuR in colorectal cancer tumorigenesis and oxaliplatin (L-OHP) resistance, as well as the underlying mechanisms involving CDC6. We detected increased HuR and CDC6 expression, along with a positive correlation between the two in human colorectal cancer tissues. HuR overexpression increased colorectal cancer cell proliferation in vitro and xenograft tumor growth in vivo, and induced resistance to L-OHP. In contrast, HuR knockdown sensitized colorectal cancer cells to L-OHP. CDC6 overexpression increased while CDC6 knockdown decreased colorectal cancer cell malignant behaviors (growth, DNA synthesis, EMT, migration, and invasion) and L-OHP resistance in vitro. Moreover, L-OHP resistance induced by HuR overexpression was reversed by CDC6 knockdown. Mechanistically, the results from our luciferase reporter and ribonucleoprotein immunoprecipitation assays indicated that HuR upregulates CDC6 by binding to CDC6 3′-UTR. Taken together, our findings identified HuR's regulation of CDC6 as an essential mechanism driving colorectal cancer tumorigenesis and L-OHP resistance, and this mechanism may represent a potential target for overcoming drug resistance in colorectal cancer.