Miracle-dz/UniFAR-FTUs huggingface dataset:
A Naturalistic Comparison of Group Transdiagnostic Behaviour Therapy (TBT) and Disorder-Specific Cognitive Behavioural Therapy Groups for the Affective Disorders

Background: Transdiagnostic psychotherapies are designed to apply the same underlying treatment principles across a set of psychiatric disorders, without significant tailoring to specific diagnoses. Several transdiagnostic psychotherapy protocols have been developed recently, each of which has its own strengths and weaknesses. One promising treatment is Transdiagnostic Behaviour Therapy (TBT), in that it is one of the few transdiagnostic treatments to date shown to be effective in patients with depressive and anxiety disorders. However, TBT has only been investigated via individual psychotherapy. Aims: The present study investigated the effectiveness of a group protocol for TBT, compared with disorder-specific group psychotherapies, in a naturalistic setting. Method: 109 participants with various diagnoses of affective disorders completed either group TBT (n = 37) or a disorder-specific group psychotherapy (n = 72). Measures included assessments of psychiatric symptomatology and transdiagnostic impairment at baseline and post-treatment. Results: Overall, participants in the TBT group demonstrated significant improvements across all measures. When compared with disorder-specific groups, no statistical differences were observed between groups across symptoms; however, participants in the TBT group demonstrated roughly twice the treatment effect sizes in transdiagnostic impairment compared with participants in the disorder-specific groups. In addition, when participants from the most well-represented diagnosis and disorder-specific treatment (social anxiety disorder) were investigated separately, participants in the TBT group demonstrated significantly larger improvements in comorbid depressive symptoms than participants in the disorder-specific treatment. Conclusions: Pending replication and additional comparison studies, group TBT may provide an effective group treatment option for patients with affective disorders.
Comparative genomic analysis of Myroides odoratimimus isolates

Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related. Various prophages were identified in the four clinical isolate genomes, which possibly contributed to the genome evolution among the Myroides strains. CRISPR elements were only detected in the two clinical (PR63039 and CCUG10230) isolates and two environmental (CCUG12700 and H1bi) strains. With more stringent cutoff parameters in CARD analysis, the four clinical M. odoratimimus contained roughly equal antibiotic resistance genes, indicating their similar antibiotic resistance profiles. The three clinical (CCUG10230, CCUG12901, CIP101113) and three environmental (CCUG12700, L41, H1bi) M. odoratimimus strains were speculated to carry the indistinguishable virulent factors (VFs), which may involve in the similar pathogenesis mechanism. Moreover, some VFs might confer to the high capacity of dissemination, attacking tissue cells and induction of autoimmune complications. Our results facilitate the research of antibiotic resistance and the development of therapeutic regimens for the M. odoratimimus infections.
Working Memory-Related Effective Connectivity in Huntington’s Disease Patients

Huntington’s disease (HD) is a genetically caused neurodegenerative disorder characterized by heterogeneous motor, psychiatric, and cognitive symptoms. Although motor symptoms may be the most prominent presentation, cognitive symptoms such as memory deficits and executive dysfunction typically co-occur. We used functional magnetic resonance imaging (fMRI) and task fMRI-based dynamic causal modeling (DCM) to evaluate HD-related changes in the neural network underlying working memory (WM). Sixty-four pre-symptomatic HD mutation carriers (preHD), 20 patients with early manifest HD symptoms (earlyHD), and 83 healthy control subjects performed an n-back fMRI task with two levels of WM load. Effective connectivity was assessed in five predefined regions of interest, comprising bilateral inferior parietal cortex, left anterior cingulate cortex, and bilateral dorsolateral prefrontal cortex. HD mutation carriers performed less accurately and more slowly at high WM load compared with the control group. While between-group comparisons of brain activation did not reveal differential recruitment of the cortical WM network in mutation carriers, comparisons of brain connectivity as identified with DCM revealed a number of group differences across the whole WM network. Most strikingly, we observed decreasing connectivity from several regions toward right dorsolateral prefrontal cortex (rDLPFC) in preHD and even more so in earlyHD. The deterioration in rDLPFC connectivity complements results from previous studies and might mirror beginning cortical neural decline at premanifest and early manifest stages of HD. We were able to characterize effective connectivity in a WM network of HD mutation carriers yielding further insight into patterns of cognitive decline and accompanying neural deterioration.
Evaluation of DEFB1 polymorphisms in individuals with chronic periodontitis and diabetes mellitus type 2 in a population of northeastern Brazil.

AIMS The role of genetic variations in genes related to innate response, as β-defensin-1 (DEFB1), in the context of chronic periodontitis (CP) and diabetes mellitus type 2 (DM2), is still not clear. The present study evaluates the distribution of DEFB1 single nucleotide polymorphisms (SNPs) 5'-untranslated (5'UTR) region and its relation with the CP in DM2 individuals in northeastern Brazilians. METHODS Two hundred and eighty individuals participated in the study, being 116 DM2+CP, 95 CP, and 69 healthy individuals. Three known DEFB1 functional SNPs [-52 G > A (rs1799946), -44 C > G (rs1800972), -20 G > A (rs11362)] were genotyped with allele-specific assays. RESULTS Association was found for the DEFB1 -20 G > A SNP. The G allele, the GA and GG genotypes were significantly (P < 0.05) more frequent in the DM2+CP (59.5%, 50%, and 34.5%, respectively) and CP (61%, 44.2%, and 38.9%, respectively) than in healthy individuals (26.8%, 36.2%, and 8.7%, respectively). The GCG and ACG combinations (-52, -44, -20) were significantly more frequent among DM2+CP and CP than in the healthy individuals. CONCLUSION The results indicate that genetic variations of DEFB1 gene (SNP-20: G allele and GA and GG genotypes) and the DEFB1 5'UTR haplotypes (GCG and ACG) may be associated with a susceptibility to CP in DM2 individuals as well as CP individuals without DM2.
Upper airway dynamic imaging during tidal breathing in awake and asleep subjects with obstructive sleep apnea and healthy controls

We used magnetic resonance imaging (MRI) to quantify change in upper airway dimension during tidal breathing in subjects with obstructive sleep apnea (OSA, N = 7) and BMI‐matched healthy controls (N = 7) during both wakefulness and natural sleep. Dynamic MR images of the upper airway were obtained on a 1.5 T MR scanner in contiguous 7.5 mm‐thick axial slices from the hard palate to the epiglottis along with synchronous MRI‐compatible electroencephalogram and nasal/oral flow measurements. The physiologic data were retrospectively scored to identify sleep state, and synchronized with dynamic MR images. For each image, the upper airway was characterized by its area, and linear dimensions (lateral and anterior–posterior). The dynamic behavior of the upper airway was assessed by the maximum change in these parameters over the tidal breath. Mean upper airway caliber was obtained by averaging data over the tidal breath. There was no major difference in the upper airway structure between OSA and controls except for a narrower airway at the low‐retropalatal/high‐retroglossal level in OSA than in controls. Changes in upper airway size over the tidal breath ((maximum − minimum)/mean) were significantly larger in the OSA than in the control group in the low retropalatal/high retroglossal region during both wakefulness and sleep. In the four OSA subjects who experienced obstructive apneas during MR imaging, the site of airway collapse during sleep corresponded to the region of the upper airway where changes in caliber during awake tidal breathing were the greatest. These observations suggest a potential role for dynamic OSA imaging during wakefulness.
Oleanolic Acid Ameliorates Aβ25-35 Injection-induced Memory Deficit in Alzheimer’s Disease Model Rats by Maintaining Synaptic Plasticity

Background: Abnormal amyloid β (Aβ) accumulation and deposition in the hippocampus is an essential process in Alzheimer’s disease (AD). Objective: To investigate whether Oleanolic acid (OA) could improve memory deficit in AD model and its possible mechanism. Methods: Forty-five SD rats were randomly divided into sham operation group, model group, and OA group. AD models by injection of Aβ25-35 were built. Morris water maze (MWM) was applied to inves-tigate learning and memory, transmission electron microscope (TEM) to observe the ultrastructure of synapse, western blot to the proteins, electrophysiology for long-term potentiation (LTP), and Ca2+ con-centration in synapse was also measured. Results: The latency time in model group was significantly longer than that in sham operation group (P=0.0001); while it was significantly shorter in the OA group than that in model group (P=0.0001); compared with model group, the times of cross-platform in OA group significantly increased (P=0.0001). TEM results showed OA could alleviate neuron damage and synapses changes induced by Aβ25-35. The expressions of CaMKII, PKC, NMDAR2B, BDNF, TrkB, and CREB protein were signif-icantly improved by OA (P=0.0001, 0.036, 0.041, 0.0001, 0.0001, 0.026, respectively) compared with that in model group; the concentration of Ca2+ was significantly lower in OA group (1.11±0.42) than that in model group (1.68±0.18); and the slope rate (P=0.0001) and amplitude (P=0.0001) of f-EPSP significantly increased in OA group. Conclusion: The present results support that OA could ameliorate Aβ-induced memory loss of AD rats by maintaining synaptic plasticity of the hippocampus
Comparing two techniques for viscosity measurements in poultry feedstuffs: does it render similar conclusions?

ABSTRACT Viscosity of intestinal contents is known to affect digestion and absorption of nutrients. In most poultry studies, intestinal viscosity has been measured only after complete removal of solid particles by centrifugation. Centrifugation may however remove particles that contribute to viscosity, hence giving rise to an underestimation of viscosity. Two viscosity measurement techniques, one including a centrifugation step (Brookfield) and the other without (Haake), were compared in‐vitro to assess whether both techniques result in similar conclusions regarding viscosity in feedstuffs. Two sets of feedstuff preparations were used. The first set was prepared with different combinations of milled feedstuffs in order to have a wide range of viscosity: 100% corn, 25% corn + 75% wheat, 100% wheat, 90% wheat + 10% rye, all mixed with distilled water. In the second set, barley was incubated with different beta‐glucanases, and soybean and sunflower meal were incubated with different pectinases, again all mixed with distilled water. Viscosity was assessed using both techniques (Haake and Brookfield equipments) at six different time points. To evaluate the extent of agreement between the two methods, the Lin's concordance correlation coefficient (CCC) was assessed using the percentage of increase in viscosity within each method, based on pairwise feedstuffs comparison (first set), or relative to the feedstuff without enzyme (second set). The rate of the agreement between the two methods was substantial for the first set of feedstuffs (66%) and for the barley diets incubated with beta‐glucanases (69%), whereas the CCC score for the soybean meal diets was very poor (2%) and fair for the sunflower meal diets, incubated with pectinases (32%). The lack of agreement for the latter can be explained by the limited variation in viscosity in these low‐viscous mixtures. Although the two techniques are considerably different (e.g., with or without preceding particle removal), they seem to render similar conclusions when applied to poultry feedstuffs to identify distinct differences under the tested circumstances.
Secret Channel Training to Enhance Physical Layer Security With a Full-Duplex Receiver

This paper proposes a new channel training (CT) scheme for a full-duplex receiver to enhance physical layer security. Equipped with $N_{B}$ full-duplex antennas, the receiver simultaneously receives the information signal and transmits artificial noise (AN). In order to reduce the non-cancellable self-interference due to the transmitted AN, the receiver has to estimate the self-interference channel prior to the data communication phase. In the proposed CT scheme, the receiver transmits a limited number of pilot symbols that are known only to itself. Such a secret CT scheme prevents an eavesdropper from estimating the jamming channel from the receiver to the eavesdropper, hence effectively degrading the eavesdropping capability. We analytically examine the connection probability (i.e., the probability of the data being successfully decoded by the receiver) of the legitimate channel and the secrecy outage probability due to eavesdropping for the proposed secret CT scheme. Based on our analysis, the optimal power allocation between CT and data/AN transmission at the legitimate transmitter/receiver is determined. Our examination shows that the newly proposed secret CT scheme significantly outperforms the non-secret CT scheme that uses publicly known pilots when the number of antennas at the eavesdropper is larger than one.
Listeria monocytogenes InlP interacts with afadin and facilitates basement membrane crossing

During pregnancy, the placenta protects the fetus against the maternal immune response, as well as bacterial and viral pathogens. Bacterial pathogens that have evolved specific mechanisms of breaching this barrier, such as Listeria monocytogenes, present a unique opportunity for learning how the placenta carries out its protective function. We previously identified the L. monocytogenes protein Internalin P (InlP) as a secreted virulence factor critical for placental infection (1). Here, we show that InlP, but not the highly similar L. monocytogenes internalin Lmo2027, binds to human afadin (encoded by AF-6), a protein associated with cell-cell junctions. A crystal structure of InlP reveals several unique features, including an extended leucine-rich repeat (LRR) domain with a distinctive Ca2+-binding site. Despite afadin’s involvement in the formation of cell-cell junctions, MDCK epithelial cells expressing InlP displayed a decrease in the magnitude of the traction stresses they could exert on deformable substrates, similar to the decrease in traction exhibited by AF-6 knock-out MDCK cells. L. monocytogenes ∆inlP mutants were deficient in their ability to form actin-rich protrusions from the basal face of polarized epithelial monolayers, a necessary step in the crossing of such monolayers (transcytosis). A similar phenotype was observed for bacteria expressing an internal in-frame deletion in inlP (inlP ∆LRR5) that specifically disrupts its interaction with afadin. However, afadin deletion in the host cells did not rescue the transcytosis defect. We conclude that secreted InlP targets cytosolic afadin to specifically promote L. monocytogenes transcytosis across the basal face of epithelial monolayers, which may contribute to the crossing of the basement membrane during placental infection.
Isolation screening and identification of bile salt hydrolase producing bacteria from waste samples

January March 2018 104 JCPS Volume 11 Issue 1 Isolation screening and identification of bile salt hydrolase producing bacteria from waste samples Akhila B Rajan and Fathimathu Zuhara K* Department of Life Sciences, University of Calicut, Malappuram, Kerala673635, India. *Corresponding author: E-Mail: kfzuhra@gmail.com, Phone No: +91 9446252428 ABSTRACT Recently the significance of bile salt hydrolase (BSH, EC 3.1.24) enzyme has been increased since it is highly effective in reducing serum cholesterol levels in humans and animals. High cholesterol level is found as an important reason of atherosclerosis which results in cardiovascular diseases (CVD's). In this study, the search for novel BSH producing bacteria leads to their finding in soil from fish wasteyards. The soil bacteria with potent bile salt hydrolase production and bile tolerant activity was isolated through sequential screening methods and identified based on its phenotypic and genotypic characteristics as Staphylococcus saprophyiticus ZABR2. The media and culture conditions of this selected isolate were optimized for the maximum production of the significant enzyme. The optimum production of the enzyme was observed in sodium glutamate medium, with glucose as carbon source, peptone as nitrogen source, medium pH 5 and when incubated at 45oC, 160 rpm for 14 hours. A two fold increase in the production of enzyme was observed in the optimized media.
Toward Rigorous Parameterization of Underconstrained Neural Network Models Through Interactive Visualization and Steering of Connectivity Generation

Simulation models in many scientific fields can have non-unique solutions or unique solutions which can be difficult to find. Moreover, in evolving systems, unique final state solutions can be reached by multiple different trajectories. Neuroscience is no exception. Often, neural network models are subject to parameter fitting to obtain desirable output comparable to experimental data. Parameter fitting without sufficient constraints and a systematic exploration of the possible solution space can lead to conclusions valid only around local minima or around non-minima. To address this issue, we have developed an interactive tool for visualizing and steering parameters in neural network simulation models. In this work, we focus particularly on connectivity generation, since finding suitable connectivity configurations for neural network models constitutes a complex parameter search scenario. The development of the tool has been guided by several use cases—the tool allows researchers to steer the parameters of the connectivity generation during the simulation, thus quickly growing networks composed of multiple populations with a targeted mean activity. The flexibility of the software allows scientists to explore other connectivity and neuron variables apart from the ones presented as use cases. With this tool, we enable an interactive exploration of parameter spaces and a better understanding of neural network models and grapple with the crucial problem of non-unique network solutions and trajectories. In addition, we observe a reduction in turn around times for the assessment of these models, due to interactive visualization while the simulation is computed.
Astronomical metronome of geological consequence

In PNAS, Kent et al. (1) describe a remarkable geochronologic correlation arising between the continental Triassic–Jurassic Newark Basin strata of eastern North America and the time-equivalent Chinle Formation of western North America that has far-reaching consequences for geology and astronomy, as follows. In geology, a reliable “metronome” in the geologic record with a sufficiently short repeat time would greatly enhance the resolving power of the geologic timescale. Astronomers recognized the potential importance of a dominant 405-ky cycle in Earth’s orbital eccentricity variation for supplying such a metronome (2, 3), leading geologists to turn to the stratigraphic record of astronomically forced paleoclimate change to search for this cycle. In fact, one of the first geological studies to describe 405-ky scale stratigraphic cycling was on the Triassic–Jurassic Newark Basin lacustrine strata (4, 5) recovered in the National Science Foundation-funded Newark Basin Coring Project, in which each of the prominent 60-m-thick McLaughlin cycles in the cored sequence was assigned a 412.885-ky periodicity based on a now-legacy analytical astronomical solution, BRE74/BER78 (6, 7). Since the 1990s, there have been dozens of reports for strong 405-ky scale cycles in stratigraphic sequences from around the world that appear to bear out this astronomical calculation (8). However, not one of these reports has presented incontrovertible support from independent geochronology that links specific 405-ky cycles, identified by their order of appearance relative to the present day, to those in the astronomical solution. Until now, this has included the Newark Basin, which, besides the flood basalts at the top of the core series, suffers from a lack of datable materials—for example, volcanic ashes—that could help establish a numerical timescale for the core series. In astronomy, the 405-ky cycle in Earth’s orbital eccentricity variation is due to a periodic interaction between the orbital motions of Venus (planet … [↵][1]1Email: lhinnov{at}gmu.edu. [1]: #xref-corresp-1-1
Ultrafast user-steered image segmentation paradigm: live-wire-on-the-fly

In the past, we have presented three user-steered image segmentation paradigms: live wire, live lane, and the 3D extension of the live-wire method. In this paper, we introduce an ultra-fast live-wire method, referred to as live-wire-on-the-fly, for further reducing user's time compared to live wire. For both approaches, given a slice and a 2D boundary of interest in this slice, we translate the problem of finding the best boundary segment between any two points specified by the user on this boundary to the problem of finding the minimum-cost path between two vertices in a weighted and directed graph. The entire 2D boundary is identified as a set of consecutive boundary segments, each specified and detected in this fashion. A drawback in live wire is that the speed for optimal path computation depends on image size, compromising the overall segmentation efficiency. In this work, we solve this problem by exploiting some properties of graph theory to avoid unnecessary minimum-cost path computation during segmentation. Based on 164 segmentation experiments from an actual medical application, we demonstrate that live-wire- on-the-fly is about 1.5 to 33 times faster than live wire for actual segmentation, although the pure computational part alone is found to be over a hundred times faster.
Quantum-Inspired Complex Word Embedding

A challenging task for word embeddings is to capture the emergent meaning or polarity of a combination of individual words. For example, existing approaches in word embeddings will assign high probabilities to the words “Penguin” and “Fly” if they frequently co-occur, but it fails to capture the fact that they occur in an opposite sense - Penguins do not fly. We hypothesize that humans do not associate a single polarity or sentiment to each word. The word contributes to the overall polarity of a combination of words depending upon which other words it is combined with. This is analogous to the behavior of microscopic particles which exist in all possible states at the same time and interfere with each other to give rise to new states depending upon their relative phases. We make use of the Hilbert Space representation of such particles in Quantum Mechanics where we subscribe a relative phase to each word, which is a complex number, and investigate two such quantum inspired models to derive the meaning of a combination of words. The proposed models achieve better performances than state-of-the-art non-quantum models on binary sentence classification tasks.