Miracle-dz/UniFAR-FTUs huggingface dataset:
The S-Layer Homology Domain-Containing Protein SlhA from Paenibacillus alvei CCM 2051T Is Important for Swarming and Biofilm Formation

Background Swarming and biofilm formation have been studied for a variety of bacteria. While this is well investigated for Gram-negative bacteria, less is known about Gram-positive bacteria, including Paenibacillus alvei, a secondary invader of diseased honeybee colonies infected with Melissococcus pluton , the causative agent of European foulbrood (EFB). Methodology Paenibacillus alvei CCM 2051T is a Gram-positive bacterium which was recently shown to employ S-layer homology (SLH) domains as cell wall targeting modules to display proteins on its cell surface. This study deals with the newly identified 1335-amino acid protein SlhA from P. alvei which carries at the C‑terminus three consecutive SLH-motifs containing the predicted binding sequences SRGE, VRQD, and LRGD instead of the common TRAE motif. Based on the proof of cell surface location of SlhA by fluorescence microscopy using a SlhA-GFP chimera, the binding mechanism was investigated in an in vitro assay. To unravel a putative function of the SlhA protein, a knockout mutant was constructed. Experimental data indicated that one SLH domain is sufficient for anchoring of SlhA to the cell surface, and the SLH domains of SlhA recognize both the peptidoglycan and the secondary cell wall polymer in vitro. This is in agreement with previous data from the S-layer protein SpaA, pinpointing a wider utilization of that mechanism for cell surface display of proteins in P. alvei. Compared to the wild-type bacterium ΔslhA revealed changed colony morphology, loss of swarming motility and impaired biofilm formation. The phenotype was similar to that of the flagella knockout Δhag, possibly due to reduced EPS production influencing the functionality of the flagella of ΔslhA. Conclusion This study demonstrates the involvement of the SLH domain-containing protein SlhA in swarming and biofilm formation of P. alvei CCM 2051T.
Introduction. Editorial on ‘Signal processing in vital rhythms and signs’

Signal processing has become a core technology in medical devices today, as it is crucial in a wide range of applications. It is used to automate the measurement of various signal characteristics, which previously was done manually and, as a result, subjectivity is reduced and reliability is increased. Another purpose is to filter out undesired signal components of technical or physiological origin so that the signalto-noise ratio is improved and subsequent analysis facilitated. Signal processing is also of key importance when uncovering components with low amplitude and/or subtle variations in frequency, which are very difficult, if not impossible, to observe by the naked eye. For example, signal processing plays a crucial role for the detection of the alternans phenomenon occurring during cardiac repolarization. Information about alternans has turned out to be the most useful for risk stratification of certain cardiac patients. The analysis of heart rate variability represents another application where signal processing is essential for the characterization of tiny oscillations in rhythm; the resulting measurements convey unique information about the autonomic nervous system. Considering that today’s recording equipment and computers are quite powerful and available at affordable prices, limitations related to implementation are rather procedural than computational. The role of signal processing can therefore be expected to further increase in the future as novel techniques are developed and used to uncover and characterize hidden activity which may be present in a signal. Traditionally, biomedical signal processing has been largely synonymous to ‘unimodal’ analysis in which only one type of signal has been subjected to analysis at a time. Countless approaches have been developed to unimodal analysis of the most common bioelectrical signals, i.e. the electrocardiogram (ECG), the electroencephalogram (EEG) and the electromyogram (EMG). However, multimodal signal modelling and processing are currently receiving considerable attention as it is highly desirable to account for the interdependence that exists between different
Morphologically Distinct Escherichia coli Bacteriophages Differ in Their Efficacy and Ability to Stimulate Cytokine Release In Vitro

Due to a global increase in the range and number of infections caused by multi-resistant bacteria, phage therapy is currently experiencing a resurgence of interest. However, there are a number of well-known concerns over the use of phages to treat bacterial infections. In order to address concerns over safety and the poorly understood pharmacokinetics of phages and their associated cocktails, immunological characterization is required. In the current investigation, the immunogenicity of four distinct phages (taken from the main families that comprise the Caudovirales order) and their interaction with donor derived peripheral blood mononuclear cells and immortalized cell lines (HT-29 and Caco-2 intestinal epithelial cells) were investigated using standard immunological techniques. When exposed to high phage concentrations (109 PFU/well), cytokine driven inflammatory responses were induced from all cell types. Although phages appeared to inhibit the growth of intestinal epithelial cell lines, they also appear to be non-cytotoxic. Despite co-incubation with different cell types, phages maintained a high killing efficiency, reducing extended-spectrum beta-lactamase-producing Escherichia coli numbers by 1–4 log10 compared to untreated controls. When provided with a suitable bacterial host, phages were also able to actively reproduce in the presence of human cells resulting in an approximately 2 log10 increase in phage titer compared to the initial inoculum. Through an increased understanding of the complex pharmacokinetics of phages, it may be possible to address some of the safety concerns surrounding phage preparations prior to creating new therapeutic strategies.
Comparing Bioretention Designs With and Without an Internal Water Storage Layer for Treating Highway Runoff

This study compares the performance of a field bioretention cell with and without an internal water storage (IWS) layer for treating highway runoff. Both synthetic and natural runoff tests were conducted. Hydraulic performances on peak discharge reduction and detention time extension were measured. Pollutant removal efficiencies were evaluated for total suspended solids (TSS), copper (Cu), lead (Pb), zinc (Zn), total nitrogen, nitrate, ammonia, total phosphorus, and orthophosphate phosphorus. Pollutants in soil media were measured. Results reveal that both IWS and non‐IWS designs reduced peak discharge and extended detention time, while the IWS design performed better. For water quality performance, the non‐IWS design removed TSS, Cu, Pb, Zn, and total phosphorus to varying degrees of efficiency, but total nitrogen removal was minimal. The IWS layer significantly improved removal efficiencies for TSS, Cu, Zn, nitrogen, and phosphorus. Soil media accumulated some metals over time.
Dynein Regulates Epithelial Polarity and the Apical Localization of stardust A mRNA

Intense investigation has identified an elaborate protein network controlling epithelial polarity. Although precise subcellular targeting of apical and basolateral determinants is required for epithelial architecture, little is known about how the individual determinant proteins become localized within the cell. Through a genetic screen for epithelial defects in the Drosophila follicle cells, we have found that the cytoplasmic Dynein motor is an essential regulator of apico–basal polarity. Our data suggest that Dynein acts through the cytoplasmic scaffolding protein Stardust (Sdt) to localize the transmembrane protein Crumbs, in part through the apical targeting of specific sdt mRNA isoforms. We have mapped the sdt mRNA localization signal to an alternatively spliced coding exon. Intriguingly, the presence or absence of this exon corresponds to a developmental switch in sdt mRNA localization in which apical transcripts are only found during early stages of epithelial development, while unlocalized transcripts predominate in mature epithelia. This work represents the first demonstration that Dynein is required for epithelial polarity and suggests that mRNA localization may have a functional role in the regulation of apico–basal organization. Moreover, we introduce a unique mechanism in which alternative splicing of a coding exon is used to control mRNA localization during development.
Identification and localization of integral membrane proteins of virulent Treponema pallidum subsp. pallidum by phase partitioning with the nonionic detergent triton X-114

Integral membrane proteins of Treponema pallidum subsp. pallidum (T. pallidum) were identified by phase partitioning with the nonionic detergent Triton X-114; antigens with apparent molecular masses of 47, 38, 36, 34, 32, 17, and 15 kilodaltons (kDa) were identified in the detergent phase. Immunoblotting with murine monoclonal antibodies directed against pathogen-specific 47- and 34-kDa T. pallidum antigens confirmed their presence in the detergent phase. Endoflagellar proteins of T. pallidum were not detected in immunoblots of detergent-phase proteins when monospecific antisera directed against endoflagella of the nonpathogenic T. phagedenis biotype Reiter were used. At detergent concentrations (0.02 and 0.1%) which appeared to solubilize selectively the outer membranes of treponemes radiolabeled with 35S in vitro, limited amounts of detergent-phase proteins were immunoprecipitated. Greater amounts of detergent-phase proteins were extracted at higher detergent concentrations (0.5 and 2.0%) which resulted in both outer membrane solubilization and ultrastructural derangements of the residual cytoplasmic bodies. Furthermore, Triton X-114 extraction of both intact treponemes and organisms without outer membranes yielded detergent phases with similar protein profiles. The results of these experiments indicate that the hydrophobic proteins identified by Triton X-114 are not located exclusively in the T. pallidum outer membrane. The results are also consistent with the hypothesis that the T. pallidum outer membrane is a protein-deficient lipid bilayer.
Visualization in Audio-Based Music Information Retrieval

Pampalk, and George Tzanetakis *FX Palo Alto Laboratory 3400 Hillview Avenue, Building 4 Palo Alto, California 94304 USA {foote, cooper}@fxpal.com †Austrian Research Institute for Artificial Intelligence (OFAI) Freyung 6/6 A-1010 Vienna, Austria elias.pampalk@ofai.at ††Department of Computer Science (also Music) University of Victoria PO Box 3055, STN CSC Victoria, British Columbia V8W 3P6 Canada gtzan@cs.uvic. ca
Disambiguating authenticity: Interpretations of value and appeal

While shaping aesthetic judgment and choice, socially constructed authenticity takes on some very different meanings among observers, consumers, producers and critics. Using a theoretical framework positing four distinct meanings of socially constructed authenticity–type, moral, craft, and idiosyncratic–we aim to document empirically the unique appeal of each type. We develop predictions about the relationships between attributed authenticity and corresponding increases in the value ascribed to it through: (1) consumer value ratings, (2) willingness to pay, and (3) behavioral choice. We report empirical analyses from a research program of three multi-method studies using (1) archival data from voluntary consumer evaluations of restaurants in an online review system, (2) a university-based behavioral lab experiment, and (3) an online survey-based experiment. Evidence is consistent across the studies and suggests that perceptions of four distinct subtypes of socially constructed authenticity generate increased appeal and value even after controlling for option quality. Findings suggest additional directions for research on authenticity.
SoccerMan-reconstructing soccer games from video sequences

We present SoccerMan, a soccer game reconstruction system. SoccerMan is capable of generating a description of an animated 3D scene from a video sequence of a soccer game, enabling the user to examine the respective scene from any virtual viewpoint. Starting from a manually marked initial frame, key features (i.e. playground lines) are tracked automatically, using template matching. Camera calibration is done by a specialized linear approximation method, where only a few key features have to be visible in the input frames. Then the playground texture is extracted from the video sequence, and player shapes are detected and tracked automatically over time. Finally, playground texture and textured player shapes are used to model the virtual 3D scene.
Association between facial expression and PTSD symptoms among young children exposed to the Great East Japan Earthquake: a pilot study

“Emotional numbing” is a symptom of post-traumatic stress disorder (PTSD) characterized by a loss of interest in usually enjoyable activities, feeling detached from others, and an inability to express a full range of emotions. Emotional numbing is usually assessed through self-report, and is particularly difficult to ascertain among young children. We conducted a pilot study to explore the use of facial expression ratings in response to a comedy video clip to assess emotional reactivity among preschool children directly exposed to the Great East Japan Earthquake. This study included 23 child participants. Child PTSD symptoms were measured using a modified version of the Parent’s Report of the Child’s Reaction to Stress scale. Children were filmed while watching a 2-min video compilation of natural scenes (‘baseline video’) followed by a 2-min video clip from a television comedy (‘comedy video’). Children’s facial expressions were processed the using Noldus FaceReader software, which implements the Facial Action Coding System (FACS). We investigated the association between PTSD symptom scores and facial emotion reactivity using linear regression analysis. Children with higher PTSD symptom scores showed a significantly greater proportion of neutral facial expressions, controlling for sex, age, and baseline facial expression (p < 0.05). This pilot study suggests that facial emotion reactivity, measured using facial expression recognition software, has the potential to index emotional numbing in young children. This pilot study adds to the emerging literature on using experimental psychopathology methods to characterize children’s reactions to disasters.
Mining Face-to-Face Interaction Networks Using Sociometric Badges: Evidence Predicting Productivity in IT Configuration

Introduction Information workers now account for more than 70% of the U.S. labor force and 60% of the total value added in the U.S. economy (Apte & Nath 2004). As the information content of work increases, the role of information has become central to understanding the performance of workers and organizations. Previous research links the structure of individuals’ and groups’ networks to performance (Burt 1992) and information worker productivity (e.g. Aral, Brynjolfsson & Van Alstyne 2006; Aral & Van Alstyne 2006). By analyzing email communication networks, message content and employee performance Aral, Brynjolfsson and Van Alstyne (2006, 2007) find that network structure predicts productivity and shapes the types of information employees access. But while electronic communication has become ubiquitous, face-to-face (F2F) interactions also remain a powerful conduit for information exchange, especially for complex or tacit information. While previous research has shown that email social networks predict worker productivity and the ability to access novel information, it is unclear what effect F2F networks have on productivity. As F2F communication allows richer and deeper information exchange, understanding what types of F2F network structures enhance information access and productivity is important. We address this question by examining the physical interactions and F2F communications of 37 employees at an IT configuration firm. Specifically, we investigate how F2F communications impact productivity and performance, and if the impact is different from electronic communications.
Temporal trends in antihypertensive drug prescriptions in Canada before and after introduction of the Canadian Hypertension Education Program

Objective Poor control of hypertension is a world-wide health issue. In 1999, the Canadian Hypertension Education Program (CHEP) was launched to annually develop and implement evidence-based hypertension guidelines in an effort to improve hypertension control rates. This study was designed to examine temporal trends in antihypertensive drug prescribing and to explore whether drug prescriptions changed after initiation of the new CHEP guideline process. Design and methods We used longitudinal Canadian dispensing data (from the IMS CompuScript database; IMS Health, Pointe-Claire, Quebec) to examine antihypertensive prescriptions in the 3 years prior to and the 3 years following introduction of the new CHEP process. To control for temporal changes in the incidence of other cardiovascular conditions for which antihypertensive agents may be prescribed for their non-blood pressure-lowering effects (for example, angiotensin-converting enzyme (ACE) inhibitors for heart failure or coronary artery disease), prescription rates for digoxin, loop diuretics, and nitrates were also examined. Results Prescriptions for all antihypertensive agents increased significantly between 1996 and 2001 [11% for thiazides, 45% for beta-blockers, 68% for ACE inhibitors, 19% for calcium channel blockers, and 4332% for angiotensin receptor blockers (ARBs)]. Loop diuretic prescriptions increased 27%, but prescriptions for digoxin (−19%) and nitrates (−8%) declined over this time frame. Time series analyses demonstrated increases in the prescription growth rate for all four antihypertensive drug classes recommended in CHEP for the period 1999–2001 compared with 1996–1998, which were statistically significantly and of substantial magnitude (absolute annual increase in prescription growth rate of 4.6% (95% confidence interval 3.5–5.9%) for thiazides, 3.0% (1.8–4.2%) for beta-blockers, 8.2% (6.7–9.7%) for ACE inhibitors, and 6.1% (4.4–7.8%) for calcium channel blockers). The growth rate in nitrate prescriptions did not significantly change [1.1% (−0.6 to +3.0%)] and, although the changes in growth rate for loop diuretics [4.7% (3.2–6.3%)] and digoxin [2.1% (0.6–3.5%)] were statistically significant, they were of smaller magnitude than the changes in the four recommended antihypertensive agents. Similar results were observed when analysis was restricted to new prescriptions only. Conclusions Prescriptions for all antihypertensive drugs increased substantially in Canada between 1996 and 2001; the rate of increase was significantly greater after 1999 for all four drugs recommended as first-line therapy in the annual CHEP guidelines. This preliminary data is encouraging, but a national survey of blood pressure control is needed to fully evaluate the impact of the new Canadian guideline process.
Using Linguistic Analysis to Translate Arabic Natural Language Queries to SPARQL

The logic-based machine-understandable framework of the Semantic Web often challenges naive users when they try to query ontology-based knowledge bases. Existing research efforts have approached this problem by introducing Natural Language (NL) interfaces to ontologies. These NL interfaces have the ability to construct SPARQL queries based on NL user queries. However, most efforts were restricted to queries expressed in English, and they often benefited from the advancement of English NLP tools. However, little research has been done to support querying the Arabic content on the Semantic Web by using NL queries. This paper presents a domain-independent approach to translate Arabic NL queries to SPARQL by leveraging linguistic analysis. Based on a special consideration on Noun Phrases (NPs), our approach uses a language parser to extract NPs and the relations from Arabic parse trees and match them to the underlying ontology. It then utilizes knowledge in the ontology to group NPs into triple-based representations. A SPARQL query is finally generated by extracting targets and modifiers, and interpreting them into SPARQL. The interpretation of advanced semantic features including negation, conjunctive and disjunctive modifiers is also supported. The approach was evaluated by using two datasets consisting of OWL test data and queries, and the obtained results have confirmed its feasibility to translate Arabic NL queries to SPARQL.
Probabilistic natural mapping of gene‐level tests for genome‐wide association studies

&NA; Genome‐wide association studies (GWASs) generally focus on a single marker, which limits the elucidation of the genetic architecture of complex traits. Herein, we present a new computational framework, termed probabilistic natural mapping (PALM), for performing gene‐level association tests. PALM robustly reveals the inherent genomic structures of genes and generates feature representations that can be seamlessly incorporated into conventional statistic tests. Our approach substantially improves the effectiveness of uncovering associations derived from a subgroup of variants with weak effects, which represents a known challenge associated with existing methods. We applied PALM in a gastric cancer GWAS and identified two additional gastric cancer‐associated susceptibility genes, NOC3L and RUNDC2A. The robust susceptibility discoveries of PALM are widely supported by existing studies from other biological perspectives. PALM will be useful for further GWAS analytical strategies that use gene‐level analyses.
Edge Guided Reconstruction for Compressive Imaging

We propose EdgeCS---an edge guided compressive sensing reconstruction approach---to recover images of higher quality from fewer measurements than the current methods. Edges are important image features that are used in various ways in image recovery, analysis, and understanding. In compressive sensing, the sparsity of image edges has been successfully utilized to recover images. However, edge detectors have not been used on compressive sensing measurements to improve the edge recovery and subsequently the image recovery. This motivates us to propose EdgeCS, which alternatively performs edge detection and image reconstruction in a mutually beneficial way. The edge detector of EdgeCS is designed to faithfully return partial edges from intermediate image reconstructions even though these reconstructions may still have noise and artifacts. For complex-valued images, it incorporates joint sparsity between the real and imaginary components. EdgeCS has been implemented with both isotropic and anisotropic discret.
Parkinsonism

PARKINSONISM, described in its entirety over one hundred and fifty years ago,’ rarely presents itself as a diagnostic problem. In consequence, little scrutiny has been directed to the marked variability of this frequently encountered neurological syndrome and to the progression of the disease in large groups of patients. As with most chronic neurological disorders, marked diversity can be expected to exist in age and mode of onset, relative prominence of the cardinal signs and symptoms, rate of progression, and resultant degree of functional impairment. Controversy over the effectiveness of therapeutic measures for parkinsonism is due partially to this wide variability and to the paucity of clinical information about the natural history of the syndrome. It is also re-