Miracle-dz/UniFAR-FTUs huggingface dataset:
A Clostridia-rich microbiota contributes to increased excretion of bile acids in diarrhea-predominant irritable bowel syndrome

Objective An excess of fecal bile acids (BAs) is thought to be one of the mechanisms for diarrhea-predominant irritable bowel syndrome (IBS-D). However, the factors causing excessive BA excretion remains unclear. Given the importance of gut microbiota in BA metabolism, we hypothesized that gut dysbiosis might contribute to excessive BA excretion in IBS-D. Design Metabolomic and metagenomic analyses were performed of specimens from 290 IBS-D patients and 89 healthy volunteers. By transplanting human microbiota and manipulating specific microbiome species in mice, the effects of microbiota on host BA metabolism were assessed at metabolic, genetic and protein levels. Effects of individual and mixed BAs on enterohepatic feedback pathways were also tested in vitro and in vivo. Results Total fecal BAs were excessively excreted in 24.5% of IBS-D patients. Their fecal metagenomes showed increased abundances of Clostridia and BA-transforming genes (hdhA and bais). The increases of Clostridia bacteria (e.g. C. scindens) were positively associated with the levels of fecal BAs and serum 7α-hydroxy-4-cholesten-3-one (C4), while being negatively correlated with serum fibroblast growth factor 19 (FGF19). Both Clostridia-rich human microbiota and C. scindens enhanced levels of serum C4 and hepatic conjugated BAs in mice recipients and reduced ileal FGF19 expression. Inhibition of Clostridium species by vancomycin yielded opposite findings. Clostridia-derived BAs (e.g. conjugated and free ursodeoxycholic acid) significantly suppressed intestinal FGF19 expression. Conclusion The Clostridia-rich microbiota contributes to excessive BA excretion in IBS-D patients. This study provided the basis for more precise clinical diagnosis and management for IBS-D.
G.718: A new embedded speech and audio coding standard with high resilience to error-prone transmission channels

This article is an overview of the standardization, architecture, and performance of the new ITU-T Recommendation G.718. G.718 is an embedded variable bit rate codec providing a scalable solution for compression of 8 and 16 kHz sampled speech and audio signals at rates between 8 kb/s and 32 kb/s. It comprises five layers where higher-layer bitstreams can be discarded without affecting the lower layersiquest decoding. The codec also has an optional core layer interoperable with ITU-T G.722. 2 (3GPP AMR-WB) at 12.65 kb/s. G.718 was designed to provide high speech quality at low bit rates and to be robust to significant rates of frame erasures or packet losses. It is also targeting good quality for generic audio at higher rates.
Semiparametric spectral modeling of the Drosophila connectome

We present semiparametric spectral modeling of the complete larval Drosophila mushroom body connectome. Motivated by a thorough exploratory data analysis of the network via Gaussian mixture modeling (GMM) in the adjacency spectral embedding (ASE) representation space, we introduce the latent structure model (LSM) for network modeling and inference. LSM is a generalization of the stochastic block model (SBM) and a special case of the random dot product graph (RDPG) latent position model, and is amenable to semiparametric GMM in the ASE representation space. The resulting connectome code derived via semiparametric GMM composed with ASE captures latent connectome structure and elucidates biologically relevant neuronal properties.
Análisis del fracaso durante el proceso de rendimiento deportivo : aplicación de un programa de ordenador inductor de fracaso

El presente trabajo es un estudio piloto en el que se aplica por primera vez un procedimiento por ordenador, cuya peculiaridad es que induce fracaso de forma individualizada durante periodos de tiempo relativamente largos, en deporte. 20 estudiantes de Educacion Fisica fueron divididos segun su disposicion para el control de la ejecucion: “orientacion a la accion (HO)” vs. “orientacion a la situacion (LO)” y fueron sometidos a 50 min. de carrera en la cinta ergometrica durante los que tuvieron que solucionar una tarea de tipo figurativo controlada a traves de ordenador. Se partio de la suposicion de que en situaciones de fracaso continuo1 los deportistas HO tenderan a centrarse mas en la accion que estan realizando y obtendran mejores resultados, mientras que los LO percibiran las situaciones de fracaso como mas amenazadoras y mostraran conductas de evitacion. Los resultados mostraron que efectivamente los LO obtienen en situaciones de fracaso mantenido peores resultados en la tarea que los HO. Su rendimiento deportivo tambien es peor, pero esta diferencia no se debe a la condicion inducida de fracaso a traves del ordenador, sino a otro tipo de factores.
The Application of Quantile Regression in the Analysis of Influential Factors of Uric Acid

Because only one set of parameter estimates can be obtained using ordinary least squares regression, it is impossible to analyze the effect of different body mass index (BMI) values on uric acid in depth. Therefore, we can only analyze the effect of body mass index on average level of uric acid. In this study, we attempt to build a regression model using quantile regression theory and use the model to analyze the effect of BMI on uric acid. Based on the quantile regression simulation results using sample data of uric acid and BMI collected from adult in Tianjin, we found that different BMI values have different effects on uric acid. In addition, we also obtained uric acid values for people in different genders and people with different BMI values under various tau values using quantile regression.
Sequential eviction of crowded nucleoprotein complexes by the exonuclease RecBCD molecular motor

Significance Chromosomes are crowded places, and any nucleic acid motor proteins that act on DNA must function within these crowded environments. How crowded environments affect motor protein behaviors remains largely unexplored. Here, we use single-molecule fluorescence microscopy to visualize the ATP-dependent motor protein RecBCD as it travels along crowded DNA molecules bearing long tandem arrays of DNA binding proteins. Our findings show that RecBCD can push through highly crowded protein arrays while evicting the proteins from DNA. This behavior on crowded DNA is distinct from a previously described mechanism by which RecBCD disrupts single isolated nucleoprotein complexes. These findings may provide insights into how other types of motor proteins travel along crowded nucleic acids. In physiological settings, all nucleic acids motor proteins must travel along substrates that are crowded with other proteins. However, the physical basis for how motor proteins behave in these highly crowded environments remains unknown. Here, we use real-time single-molecule imaging to determine how the ATP-dependent translocase RecBCD travels along DNA occupied by tandem arrays of high-affinity DNA binding proteins. We show that RecBCD forces each protein into its nearest adjacent neighbor, causing rapid disruption of the protein–nucleic acid interaction. This mechanism is not the same way that RecBCD disrupts isolated nucleoprotein complexes on otherwise naked DNA. Instead, molecular crowding itself completely alters the mechanism by which RecBCD removes tightly bound protein obstacles from DNA.
An Agent Based Distributed Event System Framework

In the last years, event-based communication paradigm has been extensively studied and it is considered a promising approach to develop the communication infrastructure of distributed systems. In most of the event systems developed previously, events are defined as simple messages such as records, tuples or simple objects. Our work involves a new agent based distributed event system (Agvent System), in which events are represented by mobile and intelligent agents that are called agvents ( ag ent e vent ). In this paper, we present the framework of the Agvent System, and describe the communication protocol between system participants and the message/ agvent flow between system components.
Teenage girls’ experience of the determinants of physical activity promotion: A theory-based qualitative content analysis

Background The progress of technology in developed countries has changed lifestyles to sedentary and has increased non-communicable diseases. Identifying factors affecting patterns of physical activity among adolescents is valuable and it is important to change these pattern. Objective This study aimed to explore teenage girls’ experiences regarding the determinants of physical activity promotion based on Pender’s Health Promotion Model. Methods This qualitative study is a content analysis research on the girls of three high schools in Minoodasht city for six months from September 2015 until the end of February 2016. The data were obtained by focused group discussions and semi-structured in-depth interviews from 48 girls ranging from 15 to 18 years old and six teachers. Data analysis was done using theory-driven qualitative content analysis. Results Data analysis resulted in a total number of 53 primary codes which were classified in the six predetermined classifications of Pender’s Health Promotion Model (Perceived benefits, perceived barriers, perceived self-efficacy of physical activity behavior, feelings related to physical activity behavior, interpersonal and situational influencers). The results showed that two classifications (perceived barriers, and situational influencers) were considered more important than other classifications in reducing levels of physical activity in adolescent girls and also high self-efficacy for promoting physical activity in adolescents. Conclusion The results obtained from this study specified the determinants affecting the promotion of physical activity among adolescent girls and can help the planners to choose the most appropriate methods and strategies in order to promote physical activity among adolescent girls and to prevent chronic non-communicable diseases in this age group and gender.
Resolution-improved microwave tomography by means of hyperspectral analysis tools

In microwave tomography, the underlying scattering phenomenon is often linearized to retrieve the associated induced currents maps. These maps are then summed together to provide a good estimation of the target position. This qualitative reconstruction scheme is robust with noise but has a spatial limitation linked to the bandwidth of the radiation operator. We will show that the result of this inverse source problem can be considered in a different way by storing, incidence after incidence, the reconstructed induced current maps. As in hyperspectral imaging, this hypercube can be formalized as several views of the same scene. In hyperspectral imaging, the wavelength is the varying parameter. In harmonic microwave tomography, the incidence angle is the varying parameter. By applying image processing techniques such as principal component analysis, we will show that we can improve the spatial resolution of the qualitative maps. Synthetic results in an aspect-limited configuration will be presented.
Expression of progesterone receptors is significantly impaired in the endometrium of infertile women during the implantation window: a prospective observational study

Abstract Objective: To compare the expression of progesterone receptors (A + B) and type-B progesterone receptors in the epithelial and stromal cells of fertile and infertile women. Methods: Women were divided into two groups, the group of fertile controls (group 1) and the group of infertile women (group 2) and were set on regular ultrasound imaging in order to detect ovulation. An endometrial biopsy was obtained on the seventh or eighth post-ovulatory day. Immunohistochemistry was performed to measure percentage of positive nuclei, intensity of staining and h-score for progesterone receptors (PgR) (A + B) as well as type-B progesterone receptors in epithelial and stromal cells. Secondary outcomes included endometrial tissue dating, the rate of tissues being out-of-phase and endometrial thickness. Results: Endometrial issue was obtained from 15 fertile and 30 infertile women. Expression of PgR (A + B) and PgR type-B was significantly lower in the epithelial cells of infertile women. PgR (A + B) h-score was 220.0 ± 18.5 for fertile versus 147.3 ± 18.0 for infertile women (p = 0.02). PgR type-B h-score in epithelial cells was 166.8 ± 30.7 for fertile versus 90.8 ± 20.6 for infertile (p = 0.04). No significant difference was observed in stromal cells. Conclusions: Expression levels of PgR (A + B) as well as type-B receptors are significantly lower in the epithelial cells of infertile women during implantation window.
Frequent hypomethylation of PTGS 2 gene promoter in human term placenta

Background: Gene expression profiles of several tumor suppressor genes are regulated by the methylation and demethylation of their promoters. Here, we aim to identify and quantify the methylation status of four tumor suppressor genes from placentas at term and compare them with the maternal white-blood-cells. Methods: In order to achieve this objective, DNA enriched from twenty placentas at term and maternal white blood cells was bisulfite-converted and amplified using quantitative real-time methyl-light polymerase chain reaction for the four-genes studied (RASSF1A, APC, RAR-beta, and PTGS2). Results: Among the four genes examined, RASSF1A, APC and RAR-beta promoter regions were hypermethylated in all the placental samples compared with maternal WBCs. Strikingly, PTGS2 was found to be hypomethylated in the placentas compared to the maternal cells. Conclusion: Since placental DNA represents fetal methylation profile and it is an established fact that there is certain amount of cell free circulating DNA in human plasma/serum, these data strongly suggest that hypermethylation of RASSF1A, APC and RAR-beta can be used as gender independent biomarkers to distinctly identify placental DNA in maternal blood. Inaddition, this is the first report which demonstrates hypomethylation of PTGS2 locus which may have important clinical implications e.g. placental abnormalities.
Firing properties of axotomized central nervous system neurons recover after graft reinnervation

Axotomy produces changes in the electrical properties of neurons and in their synaptic inputs, leading to alterations in firing pattern. We have considered the possibility that these changes occur as a result of the target deprivation induced by the lesion. Thus, we have provided a novel target to axotomized central neurons by grafting embryonic tissue at the lesion site to study the target dependence of discharge characteristics. The extracellular single‐unit electrical activity of abducens internuclear neurons was recorded in the alert behaving cat in control, after axotomy, and after axotomy plus the implantation of cerebellar primordium. As recently characterized (de la Cruz et al. [2000] J. Comp. Neurol. 427:391–404), firing alterations induced by axotomy included an overall decrease in firing rate and a loss of eye‐related signals, i.e., eye position and velocity neuronal sensitivities, that do not resume to normality with time. The grafting of a novel target to the injured abducens internuclear neurons restored the normal firing and sensitivities as recorded in the majority of units. To study the reinnervation of the implant, we performed anterograde labeling with biocytin combined with electron microscopy visualization. Axons of abducens internuclear neurons grew into the transplant sprouting into granule cell and molecular layers, as characterized by the immunostaining for γ‐aminobutyric acid and calbindin D‐28k. Ultrastructural examination of labeled axons and boutons revealed the establishment of synaptic contacts, mainly axodendritic, with different cell types of the grafted cerebellar cortex. Therefore, these data indicate that axotomized central neurons resume to normal firing after the reinnervation of a novel target. J. Comp. Neurol. 444:324–344, 2002. © 2002 Wiley‐Liss, Inc.
Interactive haptic display based on soft actuator and soft sensor

This paper demonstrates a new haptic display based on soft actuator and soft sensor. The device consists of an array rigid coupling actuator and an array tactile sensor which configured sensor located on the top of actuator. The actuator includes a frame with rigid coupling made by silicone and a dielectric elastomer actuator(DEA). The movement of the DEA is transferred to touch pad via rigid coupling. Thus, it provides a soft, comport touch feeling and eliminates the danger of applying high voltage to the human skin. The actuator can work at a wide range frequency of 0–150 Hz and produce sufficient force of 50 mN over the human hand threshold. The tactile sensor can measure the pressure, locate the objects and send the feedback signals to control the actuator. In this work, a 8×12 haptic tactile display is made with high resolution. In addition, the high voltage signal processing also developed to generate variable 0–3.5 kV, and can control individual cell by using the dynamic scanning actuation algorithm. Then, it can display any shape such as a circle, a smile/sad face, a star, etc. In the future, we will build the “emotion touch pad” system which can transfer a person's emotion to another one via internet.
Hybrid and Cooperative Strategies Using Harmony Search and Artificial Immune Systems for Solving the Nurse Rostering Problem

The nurse rostering problem is an important search problem that features many constraints. In a nurse rostering problem, these constraints are defined by processes such as maintaining work regulations, assigning nurse shifts, and considering nurse preferences. A number of approaches to address these constraints, such as penalty function methods, have been investigated in the literature. We propose two types of hybrid metaheuristic approaches for solving the nurse rostering problem, which are based on combining harmony search techniques and artificial immune systems to balance local and global searches and prevent slow convergence speeds and prematurity. The proposed algorithms are evaluated against a benchmarking dataset of nurse rostering problems; the results show that they identify better or best known solutions compared to those identified in other studies for most instances. The results also show that the combination of harmony search and artificial immune systems is better suited than using single metaheuristic or other hybridization methods for finding upper-bound solutions for nurse rostering problems and discrete optimization problems.
Clinical significance of putative cancer stem cell marker CD44 in different histological subtypes of lung cancer.

BACKGROUND According to the cancer stem cell theory, tumors originate from a subset of cells known as cancer stem cells (CSCs) that are responsible for tumor initiation, resistance and relapse. CD44 is a cell adhesion molecule that can aid in the identification of CSCs in various malignancies. OBJECTIVE The purpose of the current study is to evaluate the expression level and clinical significance of CD44 in lung cancer samples. METHODS One hundred and ninety-five lung tumor samples including 74 (38%) squamous cell carcinomas (SCC), 61 (31%) adenocarcinomas (ADC), 23 (12%) large cell carcinoma (LCC) in non-small cell lung cancer (NSCLC) group and 37 (19%) small cell lung cancer (SCLC) samples were examined for the expression of CD44 using immunohistochemistry method. The correlation of CD44 expression with clinicopathological parameters as well as Ki-67 status was also assessed. RESULTS Univariate analysis demonstrated that CD44 expression was significantly higher in NSCLC compared to SCLC (P < 0.001). Among NSCLC, higher level of CD44 expression was found in SCC compared to ADC (P< 0.001) and LCC (P=0.046). Increased expression of CD44 was significantly correlated with higher grade tumors which correspond to poor prognosis in SCC (P=0.012) and the lower level of CD44 expression was more often found in well differentiated ADC tumors (P=0.03). In addition, high expression of CD44 was significantly associated with decreased level of proliferative marker Ki-67 (P=0.04). CONCLUSIONS CD44 could be a valuable tool for the study of lung CSCs and provide a novel therapeutic target for treatment of the patients with lung cancer in combination with conventional therapy.
Use of an Isolated Joint Model to Detect Early Changes Induced by Intra-Articular Injection of Paclitaxel-Impregnated Polymeric Microspheres

Paclitaxel is a chemotherapeutic agent that suppresses cellular proliferation and angiogenesis and has been effective in suppressing proliferative synovitis in animal models. Local joint delivery ofpaclitaxel is being pursued as a treatment for rheumatoid arthritis in humans, to avoid systematic toxicity of the drug. We used an extracorporeal, isolated metacarpophalangeal joint preparation that uniquely permitted the simultaneous evaluation of codependent hemodynamic, microvascular, and transsynovial flow responses of a joint. Specifically in this study, the isolated joint preparation provided quantitative assessment of vascular flow, transsynovial flow, and morphologic changes in response to intraarticular injection of paclitaxel (50 ng) in poly-(DL)-lactide co-glycolide 50:50 microspheres (50 microm diameter) to assess initial intra-articular biocompatibility. Control joints were isolated but not injected. Serial hemodynamic measurements, transsynovial fluid forces, synovial fluid analysis, synovial and capillary permeability, and oxygen metabolism were measured every 30 min during a subsequent 3-h isolation period. At termination, synovium and cartilage were harvested from bilateral metacarpophalangeal joints for histopathologic assessment. Intra-articular injection of this formulation of paclitaxel did not significantly affect hemodynamic parameters in the joint during this short-term study, and early joint inflammatory reaction was minimal. However, transsynovial fluid forces were significantly greater in treated joints as evidenced by greater synovial fluid flow, intra-articular pressure, transitional microvascular pressure, and permeability to fluid transport. Gross and histologic morphology of synovium and articular cartilage were normal in all isolated joints. In conclusion, this extracorporeal in vivo isolated joint model permitted investigation of the early changes in joint physiology induced by this microsphere formulation and dose ofpaclitaxel in joints and could provide a more physiologic and dynamic model for study of the pharmacokinetics of drug absorption following intra-articular administration. Due to the minimal inflammation and lack of evidence of gross or histologic change in the joint, this formulation of paclitaxel should be adequately biocompatible for use in an in vivo animal model for further study of its feasibility for human use.