Miracle-dz/UniFAR-FTUs huggingface dataset:
Taking Possession: Biogenesis of the Salmonella‐Containing Vacuole

The Gram‐negative pathogen Salmonella enterica can survive and replicate within a variety of mammalian cells. Regardless of the cell type, internalized bacteria survive and replicate within the Salmonella‐containing vacuole, the biogenesis of which is dependent on bacterially encoded virulence factors. In particular, Type III secretion systems translocate bacterial effector proteins into the eukaryotic cell where they can specifically interact with a variety of targets. Salmonella has two distinct Type III secretion systems that are believed to have completely different functions. The SPI2 system is induced intracellularly and is required for intracellular survival in macrophages; it plays no role in invasion but is categorized as being required for Salmonella‐containing vacuole biogenesis. In contrast, the SPI1 Type III secretion system is induced extracellularly and is essential for invasion of nonphagocytic cells. Its role in post‐invasion processes has not been well studied. Recent studies indicate that Salmonella‐containing vacuole biogenesis may be more dependent on SPI1 than previously believed. Other non‐SPI2 virulence factors and the host cell itself may play critical roles in determining the intracellular environment of this facultative intracellular pathogen. In this review we discuss the recent advances in determining the mechanisms by which Salmonella regulate Salmonella‐containing vacuole biogenesis and the implications of these findings.
Stent thrombosis in randomized clinical trials of drug-eluting stents.

BACKGROUND Definitions of stent thrombosis that have been used in clinical trials of drug-eluting stents have been restrictive and have not been used in a uniform manner. METHODS We applied a hierarchical classification of stent thrombosis set by the Academic Research Consortium (ARC) across randomized trials involving 878 patients treated with sirolimus-eluting stents, 1400 treated with paclitaxel-eluting stents, and 2267 treated with bare-metal stents. We then pooled 4 years of follow-up data. All events were adjudicated by an independent clinical-events committee. RESULTS The cumulative incidence of stent thrombosis according to the original protocol definitions was 1.2% in the sirolimus-stent group versus 0.6% in the bare-metal-stent group (P=0.20; 95% confidence interval [CI], -0.4 to 1.5) and 1.3% in the paclitaxel-stent group versus 0.8% in the bare-metal-stent group (P=0.24; 95% CI, -0.3 to 1.4). The incidence of definite or probable stent thrombosis as defined by the ARC was 1.5% in the sirolimus-stent group versus 1.7% in the bare-metal-stent group (P=0.70; 95% CI, -1.5 to 1.0) and 1.8% in the paclitaxel-stent group versus 1.4% in the bare-metal-stent group (P=0.52; 95% CI, -0.7 to 1.4). The incidence of definite or probable events occurring 1 to 4 years after implantation was 0.9% in the sirolimus-stent group versus 0.4% in the bare-metal-stent group and 0.9% in the paclitaxel-stent group versus 0.6% in the bare-metal-stent group. CONCLUSIONS The incidence of stent thrombosis did not differ significantly between patients with drug-eluting stents and those with bare-metal stents in randomized clinical trials, although the power to detect small differences in rates was limited.
Evaluation of some physiological statements about seizure, using processing of epileptic EEG signals

Seizure genesis is usually attributed to imbalance of the excitation and inhibition activities of neurons. It is claimed that slow inhibition mechanism is responsible for controlling the variations of the excitation mechanism, and any deficiency in this function will lead to disturbance of their natural balance. Fast inhibition mechanism is also known to collaborate with slow inhibitory processes. Any proof about the excitation and inhibition mechanisms refers to the ex-vivo or in-vitro experiments, i.e. from the microscopic point of view. Up to now, there is not a straight road into evaluating these hypotheses from the macroscopic view. In this paper we try to interpret the excitation-inhibition sequences extracted from some depth-EEG signals through an identification-based procedure. The aim is to check out whether the statements gained from microscopic observations are re-established in population of neurons in the case of MTLE or not. Using Neyman-Pearson hypothesis test technique we try to answer these questions. We observe that even in population of neurons slow inhibition is responsible for compensating excitatory processes to balance inhibitory /excitatory ratio, such that when it is impaired causes seizures to arise; also the average fast inhibitory process of population of neurons follows its slow inhibition dynamics. Also, we check the differentiation of the excitation-inhibition ratio between normal and ictal states, as well as between normal and pre-ictal states. Ictal activity is properly a state of abnormal high excitation-inhibition ratio but before beginning of seizures there are not unique patterns.
Morphological and Mechanical Properties of Osteosarcoma Microenvironment Cells Explored by Atomic Force Microscopy

Cell mechanical properties that depend on cytoskeleton architecture are critical to the mechanotransduction process, and have great potential for cancer diagnosis and therapy. In this study, the morphological and mechanical properties of typical osteosarcoma microenvironment cells, including mesenchymal stem cells (MSC), normal human osteoblast cells (NHOst) and osteosarcoma cells (MG-63), were compared using atomic force microscopy (AFM). The MG-63 cells were smaller and thicker than the MSC and NHOst cells. The membrane roughness of MG-63 cells was higher than that of MSC and NHOst cells. The MG-63 cells had lower stiffness than their normal counterparts due to their reduced organization of the cytoskeleton structure. The cell stiffness influenced the mechanotransduction. The MG-63 cells had a lower percentage of nuclear YAP/TAZ compared with the MSC and NHOst cells. The F-actin assembly was disrupted by the cytochalasin D (cyto D) treatment used to investigate its influence on mechanotransduction. Disruption of the cytoskeleton leaded to a decrease of the cell stiffness, and reduced the nuclear YAP/TAZ percentage, indicating its inhibition in the cell mechanotransduction process. This study would shed light on the development of a novel cancer diagnosis strategy and would contribute to reveal the relationship between the cytoskeleton structure and the cell mechanical properties.
Effectiveness of physical activity on cardiorespiratory fitness and health-related quality of life in young and middle-aged cancer patients shortly after chemotherapy.

PURPOSE To evaluate the effectiveness of a supervised home-based flexible training program on cardiorespiratory fitness (CRF), mental distress, and health-related quality of life (HRQOL) parameters in young and middle-aged cancer patients shortly after curative chemotherapy. PATIENTS AND METHODS One hundred eleven patients age 18 to 50 years who had received chemotherapy for lymphomas or breast, gynecologic, or testicular cancer completed the trial. These patients were randomly allocated to either an intervention group (n = 59), which underwent a 14-week training program, or a control group (n = 52) that received standard care. Primary outcome was change in CRF, as determined by Astrand-Rhyming indirect bicycle ergometer test (maximum oxygen uptake [VO(2max)]), between baseline (T0) and follow-up (T1). Secondary outcomes were mental distress, as assessed by the Hospital Anxiety and Depression Scale, and HRQOL, as assessed by the European Organisation for Research and Treatment of Cancer Core Quality of Life Questionnaire. Two-way analysis of covariance was used to analyze changes from T0 to T1. RESULTS VO(2max) increased by 6.4 mL/kg(-1)/min(-1) in patients in the intervention group and by 3.1 mL/kg(-1)/min(-1) in patients in the control group (P < .01). The fatigue score decreased by 17.0 points in the control group compared with only 5.8 points in the intervention group (P < .01). There were no intergroup differences in mental distress or HRQOL. CONCLUSION A supervised, home-based, flexible training program has significant effect on CRF in young and middle-aged cancer patients shortly after curative chemotherapy, but it has no favorable effect on patients' experience of fatigue, mental distress, or HRQOL.
Modeling HIV-1 integrase complexes based on their hydrodynamic properties.

We present a model structure of a candidate tetramer for HIV-1 integrase. The model was built in three steps using data from fluorescence anisotropy, structures of the individual integrase domains, cross-linking data, and other biochemical data. First, the structure of the full-length integrase monomer was modeled using the individual domain structures and the hydrodynamic properties of the full-length protein that were recently measured by fluorescence depolarization. We calculated the rotational correlation times for different arrangements of three integrase domains, revealing that only structures with close proximity among the domains satisfied the experimental data. The orientations of the domains were constrained by iterative tests against the data on cross-linking and footprinting in integrase-DNA complexes. Second, the structure of an integrase dimer was obtained by joining the model monomers in accordance with the available dimeric crystal structures of the catalytic core. The hydrodynamic properties of the dimer were in agreement with the experimental values. Third, the active sites of the two model dimers were placed in agreement with the spacing between the sites of integration on target DNA as well as the integrase-DNA cross-linking data, resulting in twofold symmetry of a tetrameric complex. The model is consistent with the experimental data indicating that the F185K substitution, which is found in the model at a tetramerization interface, selectively disrupts correct complex formation in vitro and HIV replication in vivo. Our model of the integrase tetramer bound to DNA may help to design anti-integrase inhibitors.
Seropathotypes, Phylogroups, Stx Subtypes, and Intimin Types of Wildlife-Carried, Shiga Toxin-Producing Escherichia coli Strains with the Same Characteristics as Human-Pathogenic Isolates

ABSTRACT The objectives of this study were to investigate the presence of Shiga toxin-producing Escherichia coli (STEC) strains in wildlife that have spread in Europe, living near human settlements; to analyze their epidemiological role in maintenance and transmission to domestic livestock; and to assess the potential health risk of wildlife-carried strains. STEC strains were recovered from 53% of roe deer, 8.4% of wild boars, and 1.9% of foxes sampled in the northwest of Spain (Galicia). Of the 40 serotypes identified, 21 were classified as seropathotypes associated with human disease, accounting for 81.5% of the wildlife-carried STEC strains, including the enterohemorrhagic serotypes O157:H7-D-eae-γ1, O26:[H11]-B1-eae-β1, O121:H19-B1-eae-ε1, and O145:[H28]-D-eae-γ1. None of the wildlife-carried strains belonged to the highly pathogenic serotype O104:H4-B1 from the recent Germany outbreak. Forty percent of wildlife-carried STEC strains shared serotypes, phylogroups, intimin types, and Stx profiles with isolates from human patients from the same geographic area. Furthermore, wildlife-carried strains belonging to serotypes O5:HNM-A, O26:[H11]-B1, O76:H19-B1, O145:[H28]-D, O146:H21-B1, and O157:H7-D showed pulsed-field gel electrophoresis (PFGE) profiles with >85% similarity to human-pathogenic STEC strains. We also found a high level of similarity among STEC strains of serotypes O5:HNM-A, O26:[H11]-B1, and O145:HNM-D of bovine (feces and beef) and wildlife origins. Interestingly, O146:H21-B1, the second most frequently detected serotype in this study, is commonly associated with human diarrhea and isolated from beef and vegetables sold in Galicia. Importantly, at least 3 STEC isolates from foxes (O5:HNM-A-eae-β1, O98:[H21]-B1-eae-ζ1, and O146:[H21]-B1) showed characteristics similar to those of human STEC strains. In conclusion, roe deer, wild boar, and fox in Galicia are confirmed to be carriers of STEC strains potentially pathogenic for humans and seem to play an important role in the maintenance of STEC.
Dissemination of transferable CTX‐M‐type extended‐spectrum β‐lactamase‐producing Escherichia coli in Korea

Aims: Among 365 Escherichia coli isolated in 2003, 31 cefotaxime‐resistant isolates were obtained from clinical specimens taken from adults hospitalized in Busan, Korea. Six extended‐spectrum β‐lactamase (ESBL)‐producing isolates were investigated further to determine the mechanism of resistance.
Hydrodynamic Chromatography of Silica Colloids on Small Spherical Nonporous Silica Particles

Hydrodynamic chromatography of silica colloids with 5 – 78 nm was investigated for spherical nonporous silica packed columns. Use of phosphate buffer as the eluent improved peak shape of silica colloids and allowed elution of the analytes at times relating to their sizes. The larger the diameter of the silica colloids, the faster the elution time was. Elution volumes of analytes were slightly increased with decreasing eluent flow rate, which may be due to more diffusion to narrower interstitial channels at lower flow rates. The separation column packed with 1.9-µm nonporous silica achieved slightly better resolution than that with 3.1-µm nonporous silica. Silica colloids were monitored based on turbidity using a UV detector, and larger signals were observed for larger silica colloids.
Satb2, modularity, and the evolvability of the vertebrate jaw

Modularity is a key mechanism bridging development and evolution and is fundamental to evolvability. Herein, we investigate modularity of the Vertebrate jaw with the aim of understanding mechanisms of its morphological evolution. Conservation of the basic structural bauplan of Vertebrate jaws led to a Hinge and Caps model, in which polarity in the patterning system of developing jaws predicts modularity. We have tested the hypothesis that the Satb2+ cell population delineates a developmental module within the mandibular jaw. Satb2 is expressed in the mesenchyme of the jaw primordia that gives rise to distal elements of both the upper and lower jaws. Loss of Satb2 specifically affects structural elements of the distal (incisor) domain, reflecting the integration of these elements as well as their independence from other mandibular domains. Reducing Satb2 dosage leads to an increase in variation in mandibular length, providing insight into the developmental potential to generate variation. Inter‐taxa comparisons reveal that the Satb2 domain is conserved within gnathostomes. We complement previous loss of function studies in mice with gene knock‐down experiments in Xenopus, providing evidence for functional conservation of Satb2 in regulating size. Finally, we present evidence that the relative size of the amniote mandibular Satb2+ domain varies in relation to epithelial Fgf8 expression, suggesting a mechanism for evolutionary change in this domain. Taken together, our data support the Hinge and Caps model and provide evidence that Satb2 regulates coordinated distal jaw modules that are subject to evolutionary modification by signals emanating from the Hinge.
Effects of channel estimation errors on ultra-dense small cell networks

In this paper, we investigate the effect of channel estimation (CE) error on the performances for the ultra-dense small cell networks. Specifically, we examine its effect on the distribution of signal to interference and noise ratio (SINR) and trend of spectral efficiency (SE), and outage probability. From these, we found out that the SINR degradation due to the CE errors becomes larger, as the density ratio of small base station (BS) to UE increases. We derived the theoretical lower bound of the outage probability, which is the function of CE correlation coefficient. Finally, numerical results demonstrate that the CE errors diminish the increasing scaling of SE, as the small BS density increases.
Prevalence of occult HBV among hemodialysis patients in two districts in the northern part of the West Bank, Palestine

Occult hepatitis B infection is the case with undetectable HBsAg, but positive for HBV DNA in liver tissue and/or serum. Occult hepatitis B infection among hemodialysis patients in Palestine has been understudied. In this study, 148 hemodialysis patients from 2 northern districts in Palestine, Jenin (89) and Tulkarem (59), were investigated for occult hepatitis B, HBV, HCV infections with related risk factors. ELISA and PCR were used for the detection of anti‐HBc and viral DNA, respectively. The overall prevalence of occult hepatitis B infection among the study group was 12.5% (16/128). Occult hepatitis B infection is more prevalent among males with most cases (15/16) from Jenin District. About one‐third (42/132) of the hemodialysis patients were anti‐HBc positive. Approximately 27% of the hemodialysis patients were infected with HCV. Around 20% (28/140) were positive for HBV DNA, but only 8.2% (12/146) of the hemodialysis patients were positive for HBsAg. The comparison between hemodialysis patients with occult hepatitis B infection and those without occult hepatitis B infection for selected risk factors and parameters as liver Enzyme, age, sex, HCV infection, blood transfusion, kidney transplant, anti‐HBc, and vaccination showed no statistical significance between both categories. Duration of hemodialysis significantly affected the rate of HCV infection. HCV is significantly higher in hemodialysis patients with both Diabetes mellitus and hypertension. The prevalence of occult hepatitis B infection among hemodialysis patients is high; requiring stringent control policies. HBsAg assay is insufficient test for accurate diagnosis of HBV infection among hemodialysis patients. J. Med. Virol. 86: 1694–1699, 2014. © 2014 Wiley Periodicals, Inc.
Neuropsychological functioning during the year following severe traumatic brain injury

The neuropsychological functioning of a group of 65 adults with severe traumatic brain injury was assessed at 6 months and 1 year post-injury. The cognitive domains assessed were pre-morbid intellectual level, current level of general intellectual functioning, simple and complex attention, verbal memory, executive functioning, and perceptual functioning. At least 40%, and up to 74%, of the TBI patients displayed some degree of impairment on tests administered at 6 months. Improvement was found to occur in all areas of cognitive functioning over the first year following injury. Despite this improvement at least 31%, and up to 63%, of TBI patients displayed some degree of impairment on tests administered at 1 year post-injury. The various types of neuropsychological functioning were affected to different degrees, indicating that different aspects of cognition are more susceptible to injury, and that recovery takes place at a differential rate across functions. The implications of these findings for the appropriate planning and allocation of treatment and rehabilitation resources, and the development of effective rehabilitation interventions are outlined.
Fetal movement detection: comparison of the Toitu actograph with ultrasound from 20 weeks gestation.

OBJECTIVE This study evaluates the validity of Doppler-detected fetal movement by a commercially available monitor and investigates whether characteristics of maternal body habitus and the intrauterine environment affect its performance. METHODS Fetal movement was evaluated in normal pregnancies using both ultrasound visualization and a fetal actocardiograph (Toitu MT320; Tofa Medical Inc., Malvern, PA). Data were collected for 32 min on 34 fetuses stratified by gestational age (20-25 weeks; 28-32 weeks; 35-39 weeks). Fetal and maternal characteristics were recorded. Comparisons between ultrasound-detected trunk and limb movements and actograph records were conducted based both on 10-s time intervals and on detection of individual movements. RESULTS Time-based comparisons indicated agreement between ultrasound and actograph 94.7% of the time; this association rose to 98% when movements of less than 1 s duration were excluded. Individual movements observed on ultrasound were detected by the actograph 91% of the time, and 97% of the time when brief, isolated movements were excluded. The overall kappa value for agreement was 0.88. The actograph was reliable in detecting periods of quiescence as well as activity. These findings did not vary by gestational age. The number of movements detected by the actograph, but not the single-transducer ultrasound, significantly increased over gestation. Maternal age, parity, weight, height, or body mass index were not consistently associated with actograph validity. Characteristics of the uterine environment, including placenta location, fetal presentation, and amniotic fluid volume also did not affect results. CONCLUSIONS The Toitu actograph accurately detects fetal movement and quiescence from as early as 20 weeks gestation and has utility in both clinical and research settings. Actographs are most useful for providing objective and quantifiable measures of fetal activity level, including number and duration of movements, while visualization through ultrasound is necessary for studies of movement quality, source, or mechanics.
Sustained swimming increases the mineral content and osteocyte density of salmon vertebral bone

This study addresses the effects of increased mechanical load on the vertebral bone of post‐smolt Atlantic salmon by forcing them to swim at controlled speeds. The fish swam continuously in four circular tanks for 9 weeks, two groups at 0.47 body lengths (bl) × s−1 (non‐exercised group) and two groups at 2 bl × s−1 (exercised group), which is just below the limit for maximum sustained swimming speed in this species. Qualitative data concerning the vertebral structure were obtained from histology and electron microscopy, and quantitative data were based on histomorphometry, high‐resolution X‐ray micro‐computed tomography images and analysis of bone mineral content, while the mechanical properties were tested by compression. Our key findings are that the bone matrix secreted during sustained swimming had significantly higher mineral content and mechanical strength, while no effect was detected on bone in vivo architecture. mRNA levels for two mineralization‐related genes bgp and alp were significantly upregulated in the exercised fish, indicating promotion of mineralization. The osteocyte density of the lamellar bone of the amphicoel was also significantly higher in the exercised than non‐exercised fish, while the osteocyte density in the cancellous bone was similar in the two groups. The vertebral osteocytes did not form a functional syncytium, which shows that salmon vertebral bone responds to mechanical loading in the absence of an extensive connecting syncytial network of osteocytic cell processes as found in mammals, indicating the existence of a different mechanosensing mechanism. The adaptive response to increased load is thus probably mediated by osteoblasts or bone lining cells, a system in which signal detection and response may be co‐located. This study offers new insight into the teleost bone biology, and may have implications for maintaining acceptable welfare for farmed salmon.