Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical Analysis of Pseudomonas aeruginosa Biofilm Development: Impact of Mutations in Genes Involved in Twitching Motility, Cell-to-Cell Signaling, and Stationary-Phase Sigma Factor Expression

ABSTRACT Four strains of Pseudomonas aeruginosa (wild type, ΔpilHIJK mutant, lasI mutant, and rpoS mutant) were genetically tagged with the green fluorescent protein, and the development of flow chamber-grown biofilms by each of them was investigated by confocal laser scanning microscopy. The structural developments of the biofilms were quantified by the computer program COMSTAT (A. Heydorn, A. T. Nielsen, M. Hentzer, C. Sternberg, M. Givskov, B. K. Ersbøll, and S. Molin, Microbiology 146:2395-2407, 2000). Two structural key variables, average thickness and roughness, formed the basis for an analysis of variance model comprising the four P. aeruginosa strains, five time points (55, 98, 146, 242, and 314 h), and three independent rounds of biofilm experiments. The results showed that the wild type, the ΔpilHIJK mutant, and the rpoS mutant display conspicuously different types of temporal biofilm development, whereas the lasI mutant was indistinguishable from the wild type at all time points. The wild type and the lasI mutant formed uniform, densely packed biofilms. The rpoS mutant formed densely packed biofilms that were significantly thicker than those of the wild type, whereas the ΔpilHIJK mutant formed distinct microcolonies that were regularly spaced and almost uniform in size. The results are discussed in relation to the current model of P. aeruginosa biofilm development.
Spatially Distributed Local Fields in the Hippocampus Encode Rat Position

Extracting Spatial Information The location of a rat can be deciphered from hippocampal activity by detecting the firing of individual place-selective neurons. In contrast, the local field potential (LFP), which arises from the coherent voltage fluctuations of large hippocampal cell populations, has been hard to decode. Agarwal et al. (p. 626) worked out how to recover positional information exclusively from multiple-site LFP measurements in the rat hippocampus. The information was as precise as that derived from spiking place cells. The approach might also be applicable more generally for deciphering information from coherent population activity anywhere in the brain. Electrical fields within the hippocampus can now be decoded to reveal a rat’s location. Although neuronal spikes can be readily detected from extracellular recordings, synaptic and subthreshold activity remains undifferentiated within the local field potential (LFP). In the hippocampus, neurons discharge selectively when the rat is at certain locations, while LFPs at single anatomical sites exhibit no such place-tuning. Nonetheless, because the representation of position is sparse and distributed, we hypothesized that spatial information can be recovered from multiple-site LFP recordings. Using high-density sampling of LFP and computational methods, we show that the spatiotemporal structure of the theta rhythm can encode position as robustly as neuronal spiking populations. Because our approach exploits the rhythmicity and sparse structure of neural activity, features found in many brain regions, it is useful as a general tool for discovering distributed LFP codes.
Uncertainty-Aware Reinforcement Learning for Collision Avoidance

Reinforcement learning can enable complex, adaptive behavior to be learned automatically for autonomous robotic platforms. However, practical deployment of reinforcement learning methods must contend with the fact that the training process itself can be unsafe for the robot. In this paper, we consider the specific case of a mobile robot learning to navigate an a priori unknown environment while avoiding collisions. In order to learn collision avoidance, the robot must experience collisions at training time. However, high-speed collisions, even at training time, could damage the robot. A successful learning method must therefore proceed cautiously, experiencing only low-speed collisions until it gains confidence. To this end, we present an uncertainty-aware model-based learning algorithm that estimates the probability of collision together with a statistical estimate of uncertainty. By formulating an uncertainty-dependent cost function, we show that the algorithm naturally chooses to proceed cautiously in unfamiliar environments, and increases the velocity of the robot in settings where it has high confidence. Our predictive model is based on bootstrapped neural networks using dropout, allowing it to process raw sensory inputs from high-bandwidth sensors such as cameras. Our experimental evaluation demonstrates that our method effectively minimizes dangerous collisions at training time in an obstacle avoidance task for a simulated and real-world quadrotor, and a real-world RC car. Videos of the experiments can be found at this https URL
Salmonella and Eggs: From Production to Plate

Salmonella contamination of eggs and egg shells has been identified as a public health concern worldwide. A recent shift in consumer preferences has impacted on the egg industry, with a push for cage-free egg production methods. There has also been an increased desire from consumers for raw and unprocessed foods, potentially increasing the risk of salmonellosis. In response to these changes, this review explores the current literature regarding Salmonella contamination of eggs during the production processing through to food handling protocols. The contamination of eggs with Salmonella during the production process is a complex issue, influenced by many variables including flock size, flock age, stress, feed, vaccination, and cleaning routines. Currently there is no consensus regarding the impact of caged, barn and free range egg production has on Salmonella contamination of eggs. The literature regarding the management and control strategies post-collection, during storage, transport and food handling is also reviewed. Pasteurisation and irradiation were identified as the only certain methods for controlling Salmonella and are essential for the protection of high risk groups, whereas control of temperature and pH were identified as potential control methods to minimise the risk for foods containing raw eggs; however, further research is required to provide more detailed control protocols and education programs to reduce the risk of salmonellosis from egg consumption.
High prevalence of BRAF mutation in a Brazilian cohort of patients with sporadic papillary thyroid carcinomas

Although several studies undoubtedly demonstrated that BRAF mutation is an important genetic event in the pathogenesis of papillary thyroid carcinoma (PTC), its prognostic significance and correlation with less differentiated states remains unclear. It has been suggested that the discrepancy may be at least partially due to the insufficient number of cases analyzed, epidemiologic factors, and a combination of different variants of PTC included in these studies.
Self‐Assembly Protein Nanogels for Safer Cancer Immunotherapy

Soluble antigen-based cancer vaccines have poor retention in tissues along with suboptimal antigen processing by dendritic cells. Multiple booster doses are often needed, leading to dose-limiting systemic toxicity. A versatile, immunomodulatory, self-assembly protein nanogel vaccine is reported that induces robust immune cell response at lower antigen doses than soluble antigens, an important step towards biomaterials-based safer immunotherapy approaches.
Oxidative Stress-Related Genetic Variants May Modify Associations of Phthalate Exposures with Asthma

Background: Phthalate exposure may increase the risk of asthma. Little is known about whether oxidative-stress related genes may alter this association. First, this motivated us to investigate whether genetic polymorphisms of the oxidative-stress related genes glutathione S-transferase Mu 1 (GSTM1), glutathione S-transferase pi 1 (GSTP1), superoxide dismutase 2 (SOD2), catalase (CAT), myeloperoxidase (MPO), and EPHX1 in children are associated with phthalate urine concentrations. Second, we addressed the question whether these genes may affect the influence of phthalates on asthma. Methods: In a case-control study composed of 126 asthmatic children and 327 controls, urine phthalate metabolites (monoethyl phthalate (MEP), monobutyl phthalate (MBP), monobenzyl phthalate (MBzP), and mono(2-ethyl-5-hydroxyhexyl)phthalate (MEHHP) were measured by UPLC-MS/MS at age 3. Genetic variants were analyzed by TaqMan assay. Information on asthma and environmental exposures was also collected. Analyses of variance and logistic regressions were performed. Results: Urine MEHHP levels were associated with asthma (adjusted OR 1.33, 95% CI (1.11–1.60). Children with the GSTP1 (rs1695) AA and SOD2 (rs5746136) TT genotypes had higher MEHHP levels as compared to GG and CC types, respectively. Since only SOD2 TT genotype was significantly associated with asthma (adjusted OR (95% CI): 2.78 (1.54–5.02)), we estimated whether SOD2 variants modify the association of MEHHP levels and asthma. As MEHHP concentrations were dependent on GSTP1 and SOD2, but the assessment of interaction requires independent variables, we estimated MEHHP residuals and assessed their interaction, showing that the OR for SOD2 TT was further elevated to 3.32 (1.75–6.32) when the residuals of MEHHP were high. Conclusions: Urine phthalate metabolite concentrations are associated with oxidative-stress related genetic variants. Genetic variants of SOD2, considered to be reflect oxidative stress metabolisms, might modify the association of phthalate exposure with asthma.
Prospective pharmacokinetic study of intravenous busulfan in hematopoietic stem cell transplantation in 25 children

The aim of this study was to prospectively evaluate the PK and safety of ivBU in 25 Japanese children (median age six yr; range, five months–17 yr) as one of a combination of drugs in a pretransplant regimen. The patients had acute leukemia (n = 14), CML (2), JMML (5), solid tumors (2), chronic granulomatous disease (1), or metachromatic leukodystrophy (1). Five different dose schedules were used according to the patient's ABW: <9 kg (1.0 mg/kg), 9 to <16 (1.2 mg/kg), 16–23 (1.1 mg/kg), >23–34 (0.95 mg/kg), and >34 kg of BW (0.8 mg/kg). Each dose was given over two h, and sample blood was drawn at nine or 11 separate points for analysis by gas chromatography–mass spectrometry. The AUC varied from 796 to 1905 μmol min/L, and 19 of the 25 patients (76%) remained within the target range without dose adjustment. Two were diagnosed with engraftment failure. Hepatic VOD developed in four, and only one of these showed high AUC (>1500 μmol min/L). Toxicities did not correlate with the BU level. Our data showed very similar PK to those in previous studies, and these dose schedules are applicable to Japanese children.
Morphology and Molecular Phylogeny of Two New Ciliates, Holostichides heterotypicus n. sp. and Holosticha muuiensis n. sp. (Ciliophora: Urostylida)

Two new urostylid species, Holostichides heterotypicus n. sp. and Holosticha muuiensis n. sp. , were discovered in South Korea. Morphological and phylogenetic analyses were carried out to confirm that these species are new to science. Holostichides heterotypicus is mainly characterized by the following combination of features: 110–205 μm long in vivo; 5–10 frontoterminal cirri; 6–8 midventral pairs with 2–3 midventral cirral rows; cortical granules present; four bipolar dorsal kineties; and 6–9 caudal cirri. Ontogenetic features of H. heterotypicus are similar to those of H. typicus. Phylogenetic analyses revealed that H. heterotypicus was distantly separated from bakuellid genera Apobakuella, Bakuella, Metaurostylopsis, and Neobakuella. This result is supported by the following features: transverse cirri (present in the other four bakuellids vs. absent in Holostichides) and caudal cirri (absent in the other four bakuellids vs. present in Holostichides). Holosticha muuiensis n. sp. is mainly distinguished from its congeners by the following combination of features: 100–185 long in vivo; shortened undulating membrane; cortical granules lacking; contractile vacuole absent; 51–66 adoral zone of membranelles; 42–60 macronuclear nodules; and five bipolar dorsal kineties. In the phylogenetic tree, Holosticha muuiensis n. sp. clustered with a Holosticha group (containing Holosticha diademata, Holosticha foissneri, and Holosticha heterofoissneri).
Effects of Cathodal Trans-Spinal Direct Current Stimulation on Mouse Spinal Network and Complex Multijoint Movements

Cathodal trans-spinal direct current (c-tsDC) stimulation is a powerful technique to modulate spinal excitability. However, the manner in which c-tsDC stimulation modulates cortically evoked simple single-joint and complex multijoint movements is unknown. To address this issue, anesthetized mice were suspended with the hindlimb allowed to move freely in space. Simple and complex multijoint movements were elicited with short and prolonged trains of electrical stimulation, respectively, delivered to the area of primary motor cortex representing the hindlimb. In addition, spinal cord burst generators are known to be involved in a variety of motor activities, including locomotion, postural control, and voluntary movements. Therefore, to shed light into the mechanisms underlying movements modulated by c-tsDC stimulation, spinal circuit activity was induced using GABA and glycine receptor blockers, which produced three rates of spinal bursting activity: fast, intermediate, and slow. Characteristics of bursting activity were assessed during c-tsDC stimulation. During c-tsDC stimulation, significant increases were observed in (1) ankle dorsiflexion amplitude and speed; (2) ankle plantarflexion amplitude, speed, and duration; and (3) complex multijoint movement amplitude, speed, and duration. However, complex multijoint movement tracing showed that c-tsDC did not change the form of movements. In addition, spinal bursting activity was significantly modulated during c-tsDC stimulation: (1) fast bursting activity showed increased rate, amplitude, and duration; (2) intermediate bursting activity showed increased rate and duration, but decreased amplitude; and (3) slow bursting activity showed increased rate, but decreased duration and amplitude. These results suggest that c-tsDC stimulation amplifies cortically evoked movements through spinal mechanisms.
Transcriptional Regulation of Steroidogenic Genes: STARD1, CYP11A1 and HSD3B

Expression of the genes that mediate the first steps in steroidogenesis, the steroidogenic acute regulatory protein (STARD1), the cholesterol side-chain cleavage enzyme, cytochrome P450scc (CYP11A1) and 3β-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase (HSD3B), is tightly controlled by a battery of transcription factors in the adrenal cortex, the gonads and the placenta. These genes generally respond to the same hormones that stimulate steroid production through common pathways such as cAMP signaling and common actions on their promoters by proteins such as NR5A and GATA family members. However, there are distinct temporal, tissue and species-specific differences in expression between the genes that are defined by combinatorial regulation and unique promoter elements. This review will provide an overview of the hormonal and transcriptional regulation of the STARD1, CYP11A1 and specific steroidogenic HSD3B genes in the adrenal, testis, ovary and placenta and discuss the current knowledge regarding the key transcriptional factors involved.
The Transcription Factor, T-bet, Primes Intestine Transplantation Rejection and Is Associated With Disrupted Mucosal Homeostasis

Background The transcription factor, t-bet, promotes inflammatory polarization and intestinal homing of many inflammatory cells. In previous studies, the t-bet and granulysin genes were upregulated in peripheral blood before and after intestine transplantation (ITx) rejection, but not during rejection, possibly because of sequestration in allograft mucosa. Mucosal sequestration of t-bet and granulysin may also explain the presence of inflammatory CD14+ monocyte-derived macrophages (MDM) and immunoglobulin G+ B-cell lineage cells, and loss of mature non-inflammatory CD138+ plasma cells in allograft mucosa during ITx rejection in these previous studies. Methodology T-bet–stained and granulysin-stained cells, MDM and CD138+ plasma cells were evaluated with immunohistochemistry in serial biopsies from 17 children, in whom changes in MDM and CD138+ plasma cells were observed previously. Results T-bet–positive mucosal cells were significantly higher in postperfusion (P = 0.035) and early posttransplant biopsies (P = 0.016) among rejectors, compared with nonrejectors. T-bet–positive cell counts per high-power field (hpf) were (a) positively correlated with MDM counts/hpf in postperfusion (Spearman r = 0.73; P = 0.01) and early posttransplant biopsies (r = 0.54, r = 0.046), and (b) negatively correlated with CD138+B-/pre-plasma cells in early posttransplant biopsies (r = 0.63, P = 0.038). T-bet expression in CD14+ monocytes, CD19+B cells, and several other leukocyte subsets was higher in random blood samples from two rejectors, compared with those from five normal human subjects and three nonrejectors. Scant granulysin-stained mucosal cells precluded additional evaluation of this cytotoxin and its role in ITx rejection. Significance The transcription factor, t-bet, primes ITx rejection, and associates with disrupted homeostatic relationships between innate and adaptive immune cells in the allograft mucosa during rejection.
A direct amygdala‐motor pathway for emotional displays to influence action: A diffusion tensor imaging study

An important evolutionary function of emotions is to prime individuals for action. Although functional neuroimaging has provided evidence for such a relationship, little is known about the anatomical substrates allowing the limbic system to influence cortical motor‐related areas. Using diffusion‐weighted magnetic resonance imaging and probabilistic tractography on a cohort of 40 participants, we provide evidence of a structural connection between the amygdala and motor‐related areas (lateral and medial precentral, motor cingulate and primary motor cortices, and postcentral gyrus) in humans. We then compare this connection with the connections of the amygdala with emotion‐related brain areas (superior temporal sulcus, fusiform gyrus, orbitofrontal cortex, and lateral inferior frontal gyrus) and determine which amygdala nuclei are at the origin of these projections. Beyond the well‐known subcortical influences over automatic and stereotypical emotional behaviors, a direct amygdala‐motor pathway might provide a mechanism by which the amygdala can influence more complex motor behaviors. Hum Brain Mapp 35:5974–5983, 2014. © 2014 Wiley Periodicals, Inc.
Association of HTRA1 mutations and familial ischemic cerebral small-vessel disease.

BACKGROUND The genetic cause of cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy (CARASIL), which is characterized by ischemic, nonhypertensive, cerebral small-vessel disease with associated alopecia and spondylosis, is unclear. METHODS In five families with CARASIL, we carried out linkage analysis, fine mapping of the region implicated in the disease, and sequence analysis of a candidate gene. We also conducted functional analysis of wild-type and mutant gene products and measured the signaling by members of the transforming growth factor beta (TGF-beta) family and gene and protein expression in the small arteries in the cerebrum of two patients with CARASIL. RESULTS We found linkage of the disease to the 2.4-Mb region on chromosome 10q, which contains the HtrA serine protease 1 (HTRA1) gene. HTRA1 is a serine protease that represses signaling by TGF-beta family members. Sequence analysis revealed two nonsense mutations and two missense mutations in HTRA1. The missense mutations and one of the nonsense mutations resulted in protein products that had comparatively low levels of protease activity and did not repress signaling by the TGF-beta family. The other nonsense mutation resulted in the loss of HTRA1 protein by nonsense-mediated decay of messenger RNA. Immunohistochemical analysis of the cerebral small arteries in affected persons showed increased expression of the extra domain-A region of fibronectin and versican in the thickened tunica intima and of TGF-beta1 in the tunica media. CONCLUSIONS CARASIL is associated with mutations in the HTRA1 gene. Our findings indicate a link between repressed inhibition of signaling by the TGF-beta family and ischemic cerebral small-vessel disease, alopecia, and spondylosis.
PartSS: An Efficient Partition-based Filtering for Edit Distance Constraints

This paper introduces PartSS, a new partition-based filtering for tasks performing string comparisons under edit distance constraints. PartSS offers improvements over the state-of-the-art method NGPP with the implementation of a new partitioning scheme and also improves filtering abilities by exploiting theoretical results on shifting and scaling ranges, thus accelerating the rate of calculating edit distance between strings. PartSS filtering has been implemented within two major tasks of data integration: similarity join and approximate membership extraction under edit distance constraints. The evaluation on an extensive range of real-world datasets demonstrates major gain in efficiency over NGPP and QGrams approaches.
Remote Sensor for Spatial Measurements by Using Optical Scanning

In this paper, we propose a low-cost contact-free measurement system for both 3-D data acquisition and fast surface parameter registration by digitized points. Despite the fact that during the last decade several approaches for both contact-free measurement techniques aimed at carrying out object surface recognition and 3-D object recognition have been proposed, they often still require complex and expensive equipment. Therefore, alternative low cost solutions are in great demand. Here, two low-cost solutions to the above-mentioned problem are presented. These are two examples of practical applications of the novel passive optical scanning system presented in this paper.
Comments on deriving the equilibrium height of the stable boundary layer

Recently, the equilibrium height of the stable boundary layer received much attention in a series of papers by Zilitinkevich and co‐workers. In these studies the stable boundary‐layer height is derived in terms of inverse interpolation of different boundary‐layer height scales, each representing a prototype boundary layer. As an alternative we propose an inverse interpolation of the eddy diffusivities for each prototype before applying the definition of the Ekman layer depth. The new equation for the stable boundary‐layer height improves performance in a comparison against four observational datasets. Copyright © 2007 Royal Meteorological Society
Innate and acquired bacteriophage-mediated immunity

We recently described a novel, non-host-derived, phage-mediated immunity active at mucosal surfaces, the main site of pathogen entry in metazoans. In that work, we showed that phage T4 adheres to mucus glycoproteins via immunoglobulin-like domains displayed on its capsid. This adherence positions the phage in mucus surfaces where they are more likely to encounter and kill bacteria, thereby benefiting both the phage and its metazoan host. We presented this phage-metazoan symbiosis based on an exclusively lytic model of phage infection. Here we extend our bacteriophage adherence to mucus (BAM) model to consider the undoubtedly more complex dynamics in vivo. We hypothesize how mucus-adherent phages, both lytic and temperate, might impact the commensal microbiota as well as protect the metazoan epithelium from bacterial invasion. We suggest that BAM may provide both an innate and an acquired antimicrobial immunity.