Miracle-dz/UniFAR-FTUs huggingface dataset:
Intra- and intercellular fluctuations in Min-protein dynamics decrease with cell length

Self-organization of proteins in space and time is of crucial importance for the functioning of cellular processes. Often, this organization takes place in the presence of strong random fluctuations due to the small number of molecules involved. We report on stochastic switching of the Min-protein distributions between the two cell halves in short Escherichia coli cells. A computational model provides strong evidence that the macroscopic switching is rooted in microscopic noise on the molecular scale. In longer bacteria, the switching turns into regular oscillations that are required for positioning of the division plane. As the pattern becomes more regular, cell-to-cell variability also lessens, indicating cell length-dependent regulation of Min-protein activity.
Simultaneous Training for Children with Autism Spectrum Disorder and Their Parents with a Focus on Social Skills Enhancement

The objective of this study was to evaluate the effectiveness of simultaneous training for children with autism spectrum disorder (ASD) and their parents, with a focus on social skills enhancement (STSSE) by evaluating behavioral changes in children with ASD and changes in family functioning. STSSE was conducted on 17 children of elementary school age with ASD and their parents. Changes in scores on the social skills scale for education (SS-scale), the child behavior checklist, the Feetham Family Functioning Survey (FFFS), and the confidence degree questionnaire for families (CDQ) were used to assess the effectiveness of STSSE. Improvements were seen for “Communication Skills” on the children’s SS-scale (p = 0.029). Significant improvements were seen in the mothers’ FFFS scores for “The 4th factor: illness and worries” (p = 0.016) and in the median CDQ scores for one of 18 items after STSSE (p = 0.01). Although additional studies with larger sample sizes will be necessary before these findings are generalizable, the positive changes seen in both parents and children as a result of STSSE are promising.
Kaposi's Sarcoma-Associated Herpesvirus Hijacks RNA Polymerase II To Create a Viral Transcriptional Factory

ABSTRACT Locally concentrated nuclear factors ensure efficient binding to DNA templates, facilitating RNA polymerase II recruitment and frequent reutilization of stable preinitiation complexes. We have uncovered a mechanism for effective viral transcription by focal assembly of RNA polymerase II around Kaposi's sarcoma-associated herpesvirus (KSHV) genomes in the host cell nucleus. Using immunofluorescence labeling of latent nuclear antigen (LANA) protein, together with fluorescence in situ RNA hybridization (RNA-FISH) of the intron region of immediate early transcripts, we visualized active transcription of viral genomes in naturally infected cells. At the single-cell level, we found that not all episomes were uniformly transcribed following reactivation stimuli. However, those episomes that were being transcribed would spontaneously aggregate to form transcriptional “factories,” which recruited a significant fraction of cellular RNA polymerase II. Focal assembly of “viral transcriptional factories” decreased the pool of cellular RNA polymerase II available for cellular gene transcription, which consequently impaired cellular gene expression globally, with the exception of selected ones. The viral transcriptional factories localized with replicating viral genomic DNAs. The observed colocalization of viral transcriptional factories with replicating viral genomic DNA suggests that KSHV assembles an “all-in-one” factory for both gene transcription and DNA replication. We propose that the assembly of RNA polymerase II around viral episomes in the nucleus may be a previously unexplored aspect of KSHV gene regulation by confiscation of a limited supply of RNA polymerase II in infected cells. IMPORTANCE B cells infected with Kaposi's sarcoma-associated herpesvirus (KSHV) harbor multiple copies of the KSHV genome in the form of episomes. Three-dimensional imaging of viral gene expression in the nucleus allows us to study interactions and changes in the physical distribution of these episomes following stimulation. The results showed heterogeneity in the responses of individual KSHV episomes to stimuli within a single reactivating cell; those episomes that did respond to stimulation, aggregated within large domains that appear to function as viral transcription factories. A significant portion of cellular RNA polymerase II was trapped in these factories and served to transcribe viral genomes, which coincided with an overall decrease in cellular gene expression. Our findings uncover a strategy of KSHV gene regulation through focal assembly of KSHV episomes and a molecular mechanism of late gene expression.
Classifying Human Voices by Using Hybrid SFX Time-Series Preprocessing and Ensemble Feature Selection

Voice biometrics is one kind of physiological characteristics whose voice is different for each individual person. Due to this uniqueness, voice classification has found useful applications in classifying speakers' gender, mother tongue or ethnicity (accent), emotion states, identity verification, verbal command control, and so forth. In this paper, we adopt a new preprocessing method named Statistical Feature Extraction (SFX) for extracting important features in training a classification model, based on piecewise transformation treating an audio waveform as a time-series. Using SFX we can faithfully remodel statistical characteristics of the time-series; together with spectral analysis, a substantial amount of features are extracted in combination. An ensemble is utilized in selecting only the influential features to be used in classification model induction. We focus on the comparison of effects of various popular data mining algorithms on multiple datasets. Our experiment consists of classification tests over four typical categories of human voice data, namely, Female and Male, Emotional Speech, Speaker Identification, and Language Recognition. The experiments yield encouraging results supporting the fact that heuristically choosing significant features from both time and frequency domains indeed produces better performance in voice classification than traditional signal processing techniques alone, like wavelets and LPC-to-CC.
Modelling of electrovortex and heat flows in dc arc furnaces with bottom electrode

The article is devoted to the investigation of interaction between electrovortex and heat flows of liquid metal in dc arc furnaces with a bottom electrode. A mathematical model of liquid steel flows in a dc arc furnace with a bottom electrode was developed, and an algorithm of a three-stage solution was produced based on standard software packages. The results of electromagnetic, heat transfer and hydrodynamic analysis in industrial dc arc furnaces are given. It is shown that the Lorentz force makes up ∼30% of the volumetric gravity force and makes the main contribution to vortex flow of liquid metal in a dc arc furnace. The convection flows with the maximum heat power of furnace make a significant contribution to the vortex flow of liquid metal, and the maximum value of the vortex flow velocity is ∼1·5 times more than the movement without convection. The verification of results has been carried out by comparing them with general electrovortex flows theory, experimental data and results of similar software packages.
Fast and Simple PCA via Convex Optimization

The problem of principle component analysis (PCA) is traditionally solved by spectral or algebraic methods. We show how computing the leading principal component could be reduced to solving a \textit{small} number of well-conditioned {\it convex} optimization problems. This gives rise to a new efficient method for PCA based on recent advances in stochastic methods for convex optimization. In particular we show that given a $d\times d$ matrix $\X = \frac{1}{n}\sum_{i=1}^n\x_i\x_i^{\top}$ with top eigenvector $\u$ and top eigenvalue $\lambda_1$ it is possible to: \begin{itemize} \item compute a unit vector $\w$ such that $(\w^{\top}\u)^2 \geq 1-\epsilon$ in $\tilde{O}\left({\frac{d}{\delta^2}+N}\right)$ time, where $\delta = \lambda_1 - \lambda_2$ and $N$ is the total number of non-zero entries in $\x_1,. ,\x_n$, \item compute a unit vector $\w$ such that $\w^{\top}\X\w \geq \lambda_1-\epsilon$ in $\tilde{O}(d/\epsilon^2)$ time. \end{itemize} To the best of our knowledge, these bounds are the fastest to date for a wide regime of parameters. These results could be further accelerated when $\delta$ (in the first case) and $\epsilon$ (in the second case) are smaller than $\sqrt{d/N}$.
Compensation of thermal errors in vision based measurement systems using a system identification approach

This article presents a method to compensate thermal influences on optical 3D measurement devices which are widely used as high-accurate localisation devices. Thermal expansion caused by ambient temperature changes or by self-heating of the measurement device itself leads to a changing device geometry which in turn can lead to significant positioning errors since an accurate knowledge of the device geometry is essential for triangulation based 3D reconstruction. The changing imaging geometry of the device results in changing camera parameters which can be determined during a calibration step. The dependency between temperature change and the change of the camera parameters can be modeled using system identification methods. The device temperature is considered as the input signal to a linear time invariant (LTI) system and the vector of camera parameters describing the imaging geometry as the corresponding output. Once the model is determined for a specific camera it can be used online to adjust the values of the camera parameters.
Simultaneous administration of measles-mumps-rubella vaccine with booster doses of diphtheria-tetanus-pertussis and poliovirus vaccines.

The safety and efficacy of simultaneous administration of measles-mumps-rubella (MMR), diphtheria-tetanus-pertussis (DTP), and trivalent oral poliovirus (OPV) vaccines in a test group of 405 children were compared with the safety and efficacy of sequential administration of the same vaccines in a control group of 410 children given MMR followed by booster doses of DTP and OPV 2 months later. The study was double blind and placebo controlled with respect to DTP and OPV. Seroconversion rates to measles, mumps, and rubella exceeded 96% in both groups. Geometric mean titers to measles (P = .05) and rubella (P = .004) were higher in the test group, and titers of antibodies to the other seven antigens were similar in both groups. Clinical reaction data were analyzed in 248 of 405 test children and 249 of 410 control children. The rates of serious vaccine-associated reactions were low and similar in the two groups. Some minor side effects were reported more frequently in the test group, but these differences were judged to be related to study design rather than to differences in the safety of the two vaccine schedules. The results indicate that the safety and serologic efficacy of administering MMR simultaneously with reinforcing doses of DTP and OPV in the second year of life is equivalent to the safety and efficacy observed after administering these antigens separately.
Aluminum foam core density and geometry influences on the deformation mechanisms and energy absorption capacity of foam filled braided tubular structures in axial and transverse loading

v DEDICATION. vi ACKNOWLEDGEMENTS. vii LIST OF TABLES. xi LIST OF FIGURES . xii LIST OF APPENDICES.xv LIST OF ABBREVIATIONS. xvi NOMENCLATURE . xvii
Thermal acclimation and subspecies-specific effects on heart and brain mitochondrial performance in a eurythermal teleost (Fundulus heteroclitus)

ABSTRACT Mitochondrial performance may play a role in setting whole-animal thermal tolerance limits and their plasticity, but the relative roles of adjustments in mitochondrial performance across different highly aerobic tissues remain poorly understood. We compared heart and brain mitochondrial responses to acute thermal challenges and to thermal acclimation using high-resolution respirometry in two locally adapted subspecies of Atlantic killifish (Fundulus heteroclitus). We predicted that 5°C acclimation would result in compensatory increases in mitochondrial performance, while 33°C acclimation would cause suppression of mitochondrial function to minimize the effects of high temperature on mitochondrial metabolism. In contrast, acclimation to both 33 and 5°C decreased mitochondrial performance compared with fish acclimated to 15°C. These adjustments could represent an energetic cost-saving mechanism at temperature extremes. Acclimation responses were similar in both heart and brain; however, this effect was smaller in the heart, which might indicate its importance in maintaining whole-animal thermal performance. Alternatively, larger acclimation effects in the brain might indicate greater thermal sensitivity compared with the heart. We detected only modest differences between subspecies that were dependent on the tissue assayed. These data demonstrate extensive plasticity in mitochondrial performance following thermal acclimation in killifish, and indicate that the extent of these responses differs between tissues, highlighting the importance and complexity of mitochondrial regulation in thermal acclimation in eurytherms. Summary: Heart and brain mitochondrial performance declines following acclimation to thermal extremes in killifish, which suggests that organismal performance at thermal extremes is, at least in part, constrained by mitochondrial performance.
A placebo-controlled trial of acotiamide for meal-related symptoms of functional dyspepsia

Objective To determine the efficacy of acotiamide, an acetylcholinesterase inhibitor, in patients with functional dyspepsia (FD) in a 4-week trial Methods A multicentre, randomised, placebo-controlled, parallel-group, phase III trial was carried out, in which patients with FD received 100 mg of acotiamide or placebo three times a day for 4 weeks, with 4 weeks post-treatment follow-up. The primary efficacy end points were global assessment of overall treatment efficacy (OTE) and elimination rate of all three meal-related symptoms (postprandial fullness, upper abdominal bloating and early satiation), as derived from daily diaries. Secondary efficacy end points were individual symptom scores and quality of life. Adverse events were monitored. Results 52.2% of those receiving acotiamide and 34.8% in the placebo group (p<0.001) were classified as responders according to a global assessment of OTE. Over 4 weeks, the elimination rate for all three meal-related symptoms was 15.3% among patients receiving acotiamide compared with 9.0% in the placebo group (p=0.004). The significant benefit of acotiamide over placebo in OTE and elimination rate was maintained during the 4 week post-treatment follow-up. All other secondary efficacy end points, including quality of life, were significantly improved with 100 mg of acotiamide as compared with placebo. The number needed to treat was 6 for OTE and 16 for symptom elimination rate. The incidence of adverse events was similar between the acotiamide group and placebo group and no significant cardiovascular effects due to treatment were seen. Conclusions Over 4 weeks, acotiamide significantly improved symptom severity and eliminated meal-related symptoms in patients with FD. Trial registration number http://ClinicalTrials.gov number, NCT00761358.
Citrus Fruit Intake Substantially Reduces the Risk of Esophageal Cancer

AbstractMany epidemiologic studies indicate a potential association between fruit and vegetable intake and various cancers. The purpose of this meta-analysis is to investigate the association between citrus fruit intake and esophageal cancer risk. The authors conducted a comprehensive search on PubMed, EMBASE, and the Cochrane Library from inception until July 2014. Studies presenting information about citrus intake and esophageal cancer were analyzed. The authors extracted the categories of citrus intake, study-specific odds ratio or relative risk, and the P value and associated 95% confidence intervals for the highest versus lowest dietary intake of citrus fruit level. The association was quantified using meta-analysis of standard errors with a random-effects model. Thirteen case–control studies and 6 cohort studies were eligible for inclusion. Citrus intake may significantly reduce risk of esophageal cancer (summary odds ratio = 0.63; 95% confidence interval = 0.52–0.75; P = 0), without notable publication bias (intercept = −0.79, P = 0.288) and with significant heterogeneity across studies (I2 = 52%). The results from epidemiologic studies suggest an inverse association between citrus fruit intake and esophageal cancer risk. The significant effect is consistent between case–control and cohort studies. Larger prospective studies with rigorous methodology should be considered to validate the association between citrus fruits and esophageal cancer.
Gene Expression Analyses Support Fallopian Tube Epithelium as the Cell of Origin of Epithelial Ovarian Cancer

Folate receptor alpha (FOLR1/FRA) is reported to be overexpressed in epithelial ovarian cancers (EOC), especially the serous histotype. Further, while dysregulation of the folate-dependent 1-carbon cycle has been implicated in tumorogenesis, little is known relative to the potential mechanism of action of FOLR1 expression in these processes. We therefore investigated the expression of FOLR1, other folate receptors, and genes within the 1-carbon cycle in samples of EOC, normal ovary and fallopian tube on a custom TaqMan Low Density Array. Also included on this array were known markers of EOC such as MSLN, MUC16 and HE4. While few differences were observed in the expression profiles of genes in the 1-carbon cycle, genes previously considered to be overexpressed in EOC (e.g., FOLR1, MSLN, MUC16 and HE4) showed significantly increased expression when comparing EOC to normal ovary. However, when the comparator was changed to normal fallopian tube, these differences were abolished, supporting the hypothesis that EOC derives from fallopian fimbriae and, further, that markers previously considered to be upregulated or overexpressed in EOC are most likely not of ovarian origin, but fallopian in derivation. Our findings therefore support the hypothesis that the cell of origin of EOC is tubal epithelium.
Distinct fitness costs associated with the knockdown of RNAi pathway genes in western corn rootworm adults

RNA interference (RNAi) based approaches can potentially be used to control insect pests. These approaches may depend on the usage of microRNA (miRNA) or double stranded RNA (dsRNA) mediated gene knockdown, which likely involves proteins that regulate these pathways, such as Argonaute 1 (Ago1), Argonaute 2 (Ago2), Dicer 1 (Dcr1), Dicer 2 (Dcr2), and Drosha in insects. We previously performed functional characterization of Ago2 and Dcr2 of western corn rootworm (WCR), Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae) and observed that knockdown of Ago2 and Dcr2 ameliorated the lethal effect induced by the dsRNA-mediated knockdown of an essential gene in WCR, thereby confirming the involvement of Ago2 and Dcr2 in the dsRNA pathway. In the current study, we identified and characterized additional members of the Argonaute and Dicer gene families, namely Ago1, Ago3, Aubergine, and Dcr1, in a previously developed WCR transcriptome. We also identified a Drosha homolog in the same transcriptome. We evaluated the impacts on WCR adult fitness associated with the dsRNA-mediated knockdown of Ago1, Ago2, Dcr1, Dcr2, and Drosha genes. Among these putative RNAi pathway genes, only the knockdown of Ago1 incurred significant fitness costs such as reduced survival and oviposition rate, as well as decreased egg viability. The present study, to our knowledge, represents the first report showing that Ago1 is critical to the survival of insect adults. Our findings suggest that Ago1 plays an essential role in broader life stages of an insect than previously thought. Importantly, since fitness costs were not observed, downregulation or loss of function of RNAi pathway genes such as Ago2 or Dcr2 may confer resistance to pest control measures that rely on the normal functions of these genes. However, the precise roles of these genes under field conditions (i.e., in the presence of possible viral pathogens) requires further investigation.
Physiology of conduction block in multifocal motor neuropathy and other demyelinating neuropathies

Conduction block is an important functional consequence of demyelination whereby nervous transmission is abolished. Its mechanism has been discussed with respect to the loss of insulation due to disruption of myelin. Recent development of threshold tracking techniques, which enabled noninvasive assessment of axonal membrane potentials and ion channels, has provided evidence that axonal excitability changes significantly and contributes to conduction failure. This view, based upon axo‐glial interaction, clarifies the mechanism of muscle fatigue and fasciculation associated with peripheral demyelination and possibly explains selective motor involvement in multifocal motor neuropathy. Muscle Nerve 27: 285–296, 2003
Comparative analysis of proteins induced by heat shock, salinity, and osmotic stress in the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31

Heat, salinity, or osmotic stress influenced protein synthesis in nitrogen-fixing Anabaena sp. strain L-31. Salinity and osmotic stresses were identical and specifically induced 15 polypeptides. Four polypeptides were unique to heat shock, and four other polypeptides were induced under every stress. The results demonstrate a commonality and a stress specificity of protein synthesis regulation.
How Plantar Exteroceptive Efficiency Modulates Postural and Oculomotor Control: Inter-Individual Variability

In a previous experiment, we showed that among young and healthy subjects, thin plantar inserts improve postural control and modify vergence amplitudes. In this experiment, however, significant inter-individual variability was observed. We hypothesize that its origin could be attributed to a different reliance upon feet cutaneous afferents. In order to test this hypothesis, we re-analyzed the data relative to 31 young (age 25.7 ± 3.8) and healthy subjects who participated in the first experiment after having classified them into two groups depending on their Plantar Quotient (PQ = Surface area of CoPfoam/Surface area of CoPfirm ground × 100). Foam decreases the information arising from the feet, normally resulting in a PQ > 100. Hence, the PQ provides information on the weight of plantar cutaneous afferents used in postural control. Twelve people were Plantar-Independent Subjects, as indicated by a PQ < 100. These individuals did not behave like the Normal Plantar Quotient Subjects: they were almost insensitive to the plantar stimulations in terms of postural control and totally insensitive in terms of oculomotor control. We conclude that the inter-individual variability observed in our first experiment is explained by the subjects' degree of plantar reliance. We propose that plantar independence is a dysfunctional situation revealing inefficiency in plantar cutaneous afferents. The latter could be due to a latent somatosensory dysfunction generating a noise which prevents the CNS from correctly processing and using feet somatosensory afferents both for balance and vergence control: Plantar Irritating Stimulus. Considering the non-noxious nature and prevalence of this phenomenon, these results can be of great interest to researchers and clinicians who attempt to trigger postural or oculomotor responses through mechanical stimulation of the foot sole.