Miracle-dz/UniFAR-FTUs huggingface dataset:
Class III Histidine Kinases: a Recently Accessorized Kinase Domain in Putative Modulators of Type IV Pilus-Based Motility

ABSTRACT Histidine kinases are key components of regulatory systems that enable bacteria to respond to environmental changes. Two major classes of histidine kinases are recognized on the basis of their modular design: classical (HKI) and chemotaxis specific (HKII). Recently, a new type of histidine kinase that appeared to have features of both HKIs and HKIIs was identified and termed HKIII; however, the details of HKIII's relationship to other two classes of histidine kinases, their function, and evolutionary history remain unknown. Here, we carried out genomic, phylogenetic, and protein sequence analyses that allowed us to reveal the unusual evolutionary history of this protein family, formalize its distinctive features, and propose its putative function. HKIIIs are characterized by the presence of sensory domains and the lack of a dimerization domain, which is typically present in all histidine kinases. In addition to a single-domain response regulator, HKIII signal transduction systems utilize CheX phosphatase and, in many instances, an unorthodox soluble chemoreceptor that are usual components of chemotaxis signal transduction systems. However, many HKIII genes are found in genomes completely lacking chemotaxis genes, thus decoupling their function from chemotaxis. By contrast, all HKIII-containing genomes also contain pilT, a marker gene for bacterial type IV pilus-based motility, whose regulation is proposed as a putative function for HKIII. These signal transduction systems have a narrow phyletic distribution but are present in many emerging and opportunistic pathogens, thus offering an attractive potential target for future antimicrobial drug design. IMPORTANCE Bacteria adapt to their environment and their hosts by detecting signals and regulating their cellular functions accordingly. Here, we describe a largely unexplored family of signal transduction histidine kinases, called HKIII, that have a unique modular design. While they are currently identified in a relatively short list of bacterial species, this list contains many emerging pathogens. We show that HKIIIs likely control bacterial motility across solid surfaces, which is a key virulence factor in many bacteria, including those causing severe infections. Full understanding of this putative function may help in designing effective drugs against pathogens that will not affect the majority of the beneficial human microbiome.
How to Empower Users for Co-Creation - Conceptualizing an Engagement Platform for Benefits Realization

Organizations invest huge portions of their budget in IT with the goal to realize benefits as improving work practice and establishing new processes. To achieve this goal, users are engaged throughout projects by various methods and approaches. Nevertheless, after the completion of a project, users lack power and opportunities to further realize benefits and thus assuring the overall success of a project. To close this gap, we present the concept of an engagement platform that empowers users collectively to induce change initiatives that enhances the realization of benefits in the post-project phase. By doing so, benefits management practices undergo a paradigm shift from recent top-down management towards bottom-up realization of benefits. This change in perspective also incorporates a service systems perspective as it focusses on the dynamic configuration of actors and resources to enable value creation in a
Involvement of Hospitalized Persons With Dementia in Everyday Decisions: A Dyadic Study

Background and Objectives To examine the involvement of persons with dementia (PWDs) in everyday decision making from the perspectives of hospitalized PWDs and their family caregivers, and to identify determinants thereof. Research Design and Methods Using multilevel modeling, we examined cross-sectional data collected prospectively from 42 family care dyads regarding the care values of the PWD. Results Both members of the dyad rated the PWD, on average, as being "somewhat involved". There was a significant amount of variability around the average perceptions of PWD involvement in decision making for both PWDs (χ2 = 351.02, p < .001) and family caregivers (χ2 = 327.01, p < .001). Both PWDs and family caregivers were significantly more likely to perceive greater PWD involvement in decision making when the family caregiver reported the PWD as valuing autonomy. Additionally, PWDs were significantly more likely to report greater involvement when they had greater cognitive function. Finally, family caregivers perceived significantly greater involvement of the patient in decision making when they reported less strain in the relationship. Together, autonomy, relationship strain, cognitive function, and care-related strain accounted for 38% and 46% of the variability in PWDs' and family caregivers' perceptions, respectively, of the PWD's decision-making involvement. Discussion and Implications Although research indicates that decision-making abilities decline with advancing dementia, these results imply that working with families to support PWDs in their value of autonomy and mitigate strain in the dyad's relationship may help prolong PWDs' decision-making involvement.
Exosomes serve as nanoparticles to suppress tumor growth and angiogenesis in gastric cancer by delivering hepatocyte growth factor siRNA

Exosomes derived from cells have been found to mediate signal transduction between cells and to act as efficient carriers to deliver drugs and small RNA. Hepatocyte growth factor (HGF) is known to promote the growth of both cancer cells and vascular cells, and the HGF‐cMET pathway is a potential clinical target. Here, we characterized the inhibitory effect of HGF siRNA on tumor growth and angiogenesis in gastric cancer. In addition, we showed that HGF siRNA packed in exosomes can be transported into cancer cells, where it dramatically downregulates HGF expression. A cell co‐culture model was used to show that exosomes loaded with HGF siRNA suppress proliferation and migration of both cancer cells and vascular cells. Moreover, exosomes were able to transfer HGF siRNA in vivo, decreasing the growth rates of tumors and blood vessels. The results of our study demonstrate that exosomes have potential for use in targeted cancer therapy by delivering siRNA.
Comparing the effects of Essix and Hawley retainers on the acoustics of speech

Objective The aim of this study was to compare the effects of two retainer types (Essix and Hawley) on speech performance. Subjects and methods The speech articulation of 30 patients was evaluated prospectively. Five patients did not appear during the follow-up periods. The patients were randomly divided into retention groups by treatment allocation cards as Essix and Hawley. The Essix group included 13 participants with a mean age of 15.3±2.4 years; the Hawley group included 12 participants with a mean age of 16.3±2.56 years. Speech sound assessments were performed on the first day and 1 week, 4 weeks, and 3 months later. On the first day, the assessments were conducted prior to inserting the retainers, immediately after maxillary and mandibular retainer application, individually, and with both retainers applied. The acoustic analyses were obtained using spectral and temporal parameters. Results Statistical analyses were performed with IBM SPSS for Windows, version 20. A P value less than 0.05 was considered statistically significant. The most apparent changes were found in the [a] vowel in the Hawley group, the [e] vowel in the Essix group, and the [u] vowel in both groups (P < 0.05). While the number of affected consonant-vowel couples in the Essix group was low, alterations were common in the Hawley group. There was a statistically significant difference (P < 0.05) in voice onset time of the [d] sound between the groups. Limitations The trial had a small sample size and a short follow-up period. Conclusions The Hawley retainer affected articulatory movements in consonant-vowel combinations more prominently than the Essix retainer did. Voice onset time of the consonant [d] in the Hawley group was shorter than normal, indicating rapid articulatory movement in the alveolar region.
Real Time Face Recognition System based on KLT Algorithm and Wiener Filtering

Main objective of this paper is to represent an approach for biometric recognition of human faces based on KLT algorithm and Wiener filtering techniques. This approach involves registering a set of human faces to a face database, matching real time faces with already stored faces. Matlab based programs are implemented for this approach. KLT algorithm is used for create face database as well as face recognition purpose. Wiener filtering is implemented to separate the illusion-invariant features from face images. Keywords—KLT algorithm, Wiener filtering, Face detection, Face recognition
Inappropriate doses of direct oral anticoagulants in real-world clinical practice: prevalence and associated factors. A subanalysis of the FANTASIIA Registry

Aims To describe the prevalence and associated factors of inappropriate doses of direct oral anticoagulants (DOAC) in a national registry of patients of real clinical practice. Methods and results Five hundred and thirty outpatients with atrial fibrillation treated with DOAC were included in a prospective, national, multicentre study. The appropriateness of the doses of DOAC was defined according to the recommendations of the European Heart Rhythm Association. Mean age was 73 ± 9 years, with a 46% of women. Two hundred and sixty-seven patients were prescribed dabigatran, 190 rivaroxaban, and 73 apixaban. A total of 172 patients (32%) did not receive the appropriate dose: 93 patients received a lower dose (18%) and 79 patients a higher dose (15%). In the comparisons among the subgroups of inappropriately low, appropriate, and inappropriately high dose, we observed significant trends to older age (69 ± 8 years vs. 73 ± 10 years vs. 77 ± 6 years), more frequent female sex (37% vs. 46% vs. 59%), antiplatelet drugs (5% vs. 8% vs. 25%), rivaroxaban (14% vs. 38% vs. 53%), and apixaban use (5% vs. 15% vs. 19%), higher CHAD2DS2-VASc (3.00 ± 1.38 vs. 3.58 ± 1.67 vs. 4.59 ± 1.44) and HAS-BLED scores (1.83 ± 0.87 vs. 1.92 ± 1.07 vs. 2.47 ± 1.13), lower body mass index (30 ± 6 kg/m2 vs. 29 ± 4 kg/m2 vs. 28 ± 4 kg/m2) and glomerular filtration rate (74 ± 27 mL/min vs. 70 ± 22 mL/min vs. 63 ± 16 mL/min), and lower frequency of dabigatran use (81% vs. 47% vs. 28%) (all comparisons P ≤ 0.01). Conclusion In this real-life study, 32% of patients received an inappropriate dose of DOAC. Several clinical factors can identify patients at risk of this situation.
AllergoOncology – the impact of allergy in oncology: EAACI position paper

Th2 immunity and allergic immune surveillance play critical roles in host responses to pathogens, parasites and allergens. Numerous studies have reported significant links between Th2 responses and cancer, including insights into the functions of IgE antibodies and associated effector cells in both antitumour immune surveillance and therapy. The interdisciplinary field of AllergoOncology was given Task Force status by the European Academy of Allergy and Clinical Immunology in 2014. Affiliated expert groups focus on the interface between allergic responses and cancer, applied to immune surveillance, immunomodulation and the functions of IgE‐mediated immune responses against cancer, to derive novel insights into more effective treatments. Coincident with rapid expansion in clinical application of cancer immunotherapies, here we review the current state‐of‐the‐art and future translational opportunities, as well as challenges in this relatively new field. Recent developments include improved understanding of Th2 antibodies, intratumoral innate allergy effector cells and mediators, IgE‐mediated tumour antigen cross‐presentation by dendritic cells, as well as immunotherapeutic strategies such as vaccines and recombinant antibodies, and finally, the management of allergy in daily clinical oncology. Shedding light on the crosstalk between allergic response and cancer is paving the way for new avenues of treatment.
PLAAF score as a novel predictor of long-term outcome after second-generation cryoballoon pulmonary vein isolation.

Aims Predictors of atrial arrhythmia recurrence have not been described in a long-term follow-up study of patients undergoing pulmonary vein isolation (PVI) using the cryoballoon technique. We aimed to evaluate the efficacy of a second-generation cryoballoon and identify pre-procedural predictors of 3-year outcome after PVI. Methods and results For this observational cohort study, we enrolled 440 patients ablated at our institution with a second-generation cryoballoon. The endpoint was the first documented recurrence (>30 s) of atrial fibrillation (AF), atrial flutter, or atrial tachycardia after a 3-month blanking period. The impact of several pre-existing variables on clinical outcome was evaluated by univariate and multivariate analyses using the Cox proportional hazards regression model. The PLAAF (persistent AF, left atrial area, abnormal PV anatomy, AF history, female gender) score was defined to predict outcome. After a median follow-up of 36 months (interquartile range 25/75-27/42), the endpoint was achieved in 95 of 440 (21.6%) patients. Cox regression analysis showed that persistent AF, left atrial (LA) area, abnormal PV anatomy, AF history, and female gender independently predicted recurrence. The calculated optimal cut-offs for LA area and AF history were 21 cm2 and 3 years, respectively. Patients with a PLAAF score of 0 showed the best outcome, with an arrhythmia-free survival of 86.7%. Conclusion PVI using the cryoballoon technique shows acceptable long-term results depending on predictors described by the new PLAAF score, which may facilitate patient selection for PVI.
Synchronization, Attention and Transformation: Multidimensional Exploration of the Aesthetic Experience of Contemporary Dance Spectators

The co-presence of bodies in intersubjective situations can give rise to processes of kinesthetic empathy and physiological synchronization, especially in the context of dance: the body and attention of the spectators are oriented towards the dancers. In this study, we investigate the processes of “body-mind” resonance between a choreography and its spectators, and more specifically the lasting impact of this resonance post-performance. We then explore the relation between the observed effects and subjective measures of attention. The study focuses on the work of the French choreographer Myriam Gourfink, who develops a unique movement, based on the slower breathing of dancers: the breathing generates an extremely slow movement without rhythmic ruptures. Phenomenological studies of her work report changes in temporal perception and changes in bodily attentional states. We made use of two cognitive tasks in order to quantify this change in temporal perception: Spontaneous Motor Tempo (SMT) and Apparent Motion effect (AM) before and after a 40-min live performance. Subjective reports were collected at the end of the performance. Physiological data were recorded before and after the performance. We performed a control experiment with a choreography of a distinctly different quality of movement. Post-Gourfink performance, we observed a significant deceleration of SMT and a decrease in its variability, while AM was reported with longer temporal intervals. Neither of these effects was observed in the control condition. Furthermore, an increase in perception of AM was correlated with a slower breathing rate after the performance. Correlations with subjective reports suggest a link between changes in cognitive and physiological dynamics and the degree of absorption of the spectators in the performance. In addition, these changes were related to specific reported attentional dispositions that we interpret as a form of attentional resonance. The ensemble of the results suggests an expansion of the “specious present” that is related to the slowing of physiological rhythms, and an attentional resonance between spectators and the choreography. The intricate relation we observed between inter-personal resonance and temporal cognition, foregrounds the notion of shared present as a neurophenomenological construct.
Using deep learning for detecting gender in adult chest radiographs

In this paper, we present a method for automatically identifying the gender of an imaged person using their frontal chest x-ray images. Our work is motivated by the need to determine missing gender information in some datasets. The proposed method employs the technique of convolutional neural network (CNN) based deep learning and transfer learning to overcome the challenge of developing handcrafted features in limited data. Specifically, the method consists of four main steps: pre-processing, CNN feature extractor, feature selection, and classifier. The method is tested on a combined dataset obtained from several sources with varying acquisition quality resulting in different pre-processing steps that are applied for each. For feature extraction, we tested and compared four CNN architectures, viz., AlexNet, VggNet, GoogLeNet, and ResNet. We applied a feature selection technique, since the feature length is larger than the number of images. Two popular classifiers: SVM and Random Forest, are used and compared. We evaluated the classification performance by cross-validation and used seven performance measures. The best performer is the VggNet-16 feature extractor with the SVM classifier, with accuracy of 86.6% and ROC Area being 0.932 for 5-fold cross validation. We also discuss several misclassified cases and describe future work for performance improvement.
Reversible Electroporation–Mediated Liposomal Doxorubicin Delivery to Tumors Can Be Monitored With 89Zr-Labeled Reporter Nanoparticles

Reversible electroporation (RE) can facilitate nanoparticle delivery to tumors through direct transfection and from changes in vascular permeability. We investigated a radiolabeled liposomal nanoparticle (89Zr-NRep) for monitoring RE-mediated liposomal doxorubicin (DOX) delivery in mouse tumors. Intravenously delivered 89Zr-NRep allowed positron emission tomography imaging of electroporation-mediated nanoparticle uptake. The relative order of 89Zr-NRep injection and electroporation did not result in significantly different overall tumor uptake, suggesting direct transfection and vascular permeability can independently mediate deposition of 89Zr-NRep in tumors. 89Zr-NRep and DOX uptake correlated well in both electroporated and control tumors at all experimental time points. Electroporation accelerated 89Zr-NRep and DOX deposition into tumors and increased DOX dosing. Reversible electroporation–related vascular effects seem to play an important role in nanoparticle delivery to tumors and drug uptake can be quantified with 89Zr-NRep.
A Robust Optomotor Assay for Assessing the Efficacy of Optogenetic Tools for Vision Restoration

Purpose To develop an animal behavioral assay for the quantitative assessment of the functional efficacy of optogenetic therapies. Methods A triple-knockout (TKO) mouse line, Gnat1−/−Cnga3−/−Opn4−/−, and a double-knockout mouse line, Gnat1−/−Cnga3−/−, were employed. The expression of channelrhodopsin-2 (ChR2) and its three more light-sensitive mutants, ChR2-L132C, ChR2-L132C/T159C, and ChR2-132C/T159S, in inner retinal neurons was achieved using rAAV2 vectors via intravitreal delivery. Pupillary constriction was assessed by measuring the pupil diameter. The optomotor response (OMR) was examined using a homemade optomotor system equipped with light-emitting diodes as light stimulation. Results A robust OMR was restored in the ChR2-mutant-expressing TKO mice; however, significant pupillary constriction was observed only for the ChR2-L132C/T159S mutant. The ability to evoke an OMR was dependent on both the light intensity and grating frequency. The most light-sensitive frequency for the three ChR2 mutants was approximately 0.042 cycles per degree. Among the three ChR2 mutants, ChR2-L132C/T159S was the most light sensitive, followed by ChR2-L132C/T159C and ChR2-L132C. Melanopsin-mediated pupillary constriction resulted in a substantial reduction in the light sensitivity of the ChR2-mediated OMR. Conclusions The OMR assay using TKO mice enabled the quantitative assessment of the efficacy of different optogenetic tools and the properties of optogenetically restored vision. Thus, the assay can serve as a valuable tool for developing effective optogenetic therapies.
eHealth patient-provider communication in the United States: interest, inequalities, and predictors

Objective: Health-related Internet use and eHealth technologies, including online patient-provider communication (PPC), are continually being integrated into health care environments. This study aimed to describe sociodemographic and health- and Internet-related correlates that influence adult patients’ interest in and electronic exchange of medical information with health care providers in the United States. Methods: Nationally representative cross-sectional data from the 2014 Health Information National Trends Survey (N = 3677) were analyzed. Descriptive statistics and multivariable regression analyses were performed to examine associations between patient-level characteristics and online PPC behavior and interests. Results: Most respondents were Internet users (82.8%), and 61.5% of information seekers designated the Internet as their first source for health information. Younger respondents (<50 years), Hispanics, those from higher-income households, and those perceiving access to personal health information as important were more likely to be interested in online PPC. Despite varying levels of patient interest, 68.5% had no online PPC in the last year. However, Internet users (odds ratio, OR = 2.87, 95% CI, 1.35-6.08), college graduates (OR = 2.92, 95% CI, 1.42-5.99), and those with frequent provider visits (OR = 1.94, 95% CI, 1.02-3.71) had a higher likelihood of online PPC via email or fax, while Hispanics and those from higher-income households were 2–3 times more likely to communicate via text messaging or phone/mobile apps. Conclusion: Patients’ interest in and display of online PPC-related behaviors vary by age, race/ethnicity, education, income, Internet access/behaviors, and information type. These findings can inform efforts aimed at improving the use and adoption of eHealth technologies, which may contribute to a reduction in communication inequalities and health care disparities.
Quality Control for the Illumina HumanExome BeadChip

The Illumina HumanExome BeadChip and other exome‐based genotyping arrays offer inexpensive genotyping of some 240,000 mostly nonsynonymous coding variants across the human genome. The HumanExome chip, with its highly non‐uniform distribution of markers and emphasis on rare coding variants, presents some unique challenges for quality control (QC) and data cleaning. Here, we describe QC procedures for HumanExome data, with examples of challenges specific to exome arrays from our experience cleaning a data set of ∼7,500 samples from the NEIGHBORHOOD Consortium. We focus on standard procedures for QC of genome‐wide array data including genotype calling, sex verification, sample identity verification, relationship checking, and population structure that are complicated by the HumanExome panel's enrichment in rare, exonic variation. © 2016 by John Wiley & Sons, Inc.