Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas chlororaphis Produces Two Distinct R-Tailocins That Contribute to Bacterial Competition in Biofilms and on Roots

ABSTRACT R-type tailocins are high-molecular-weight bacteriocins that resemble bacteriophage tails and are encoded within the genomes of many Pseudomonas species. In this study, analysis of the P. chlororaphis 30-84 R-tailocin gene cluster revealed that it contains the structural components to produce two R-tailocins of different ancestral origins. Two distinct R-tailocin populations differing in length were observed in UV-induced lysates of P. chlororaphis 30-84 via transmission electron microscopy. Mutants defective in the production of one or both R-tailocins demonstrated that the killing spectrum of each tailocin is limited to Pseudomonas species. The spectra of pseudomonads killed by the two R-tailocins differed, although a few Pseudomonas species were either killed by or insusceptible to both tailocins. Tailocin release was disrupted by deletion of the holin gene within the tailocin gene cluster, demonstrating that the lysis cassette is required for the release of both R-tailocins. The loss of functional tailocin production reduced the ability of P. chlororaphis 30-84 to compete with an R-tailocin-sensitive strain within biofilms and rhizosphere communities. Our study demonstrates that Pseudomonas species can produce more than one functional R-tailocin particle sharing the same lysis cassette but differing in their killing spectra. This study provides evidence for the role of R-tailocins as determinants of bacterial competition among plant-associated Pseudomonas in biofilms and the rhizosphere. IMPORTANCE Recent studies have identified R-tailocin gene clusters potentially encoding more than one R-tailocin within the genomes of plant-associated Pseudomonas but have not demonstrated that more than one particle is produced or the ecological significance of the production of multiple R-tailocins. This study demonstrates for the first time that Pseudomonas strains can produce two distinct R-tailocins with different killing spectra, both of which contribute to bacterial competition between rhizosphere-associated bacteria. These results provide new insight into the previously uncharacterized role of R-tailocin production by plant-associated Pseudomonas species in bacterial population dynamics within surface-attached biofilms and on roots.
A randomized, controlled trial of two strategies of offering the home‐based HPV self‐sampling test to non‐ participants in the Flemish cervical cancer screening program

We conducted a randomized, controlled trial to evaluate different strategies of offering an HPV‐self sampling program, and compared this with two control groups. All total of 35,354 women who did not participate in the Flemish cancer screening program were included in the study: 9,118 received a HPV self‐collection brush (RIATOL qPCR HPV genotyping test (qPCR [E6/E7]); 9,098 were offered the opportunity to order an HPV‐selfsampling brush, 8,830 received the recall letter; 8,849 received no intervention. Within 12 months after the mailing, 18.7% of the women who had received the brush, participated by returning a self‐sample sample, while 10.6% women allocated to the opt‐ in group did so. 10.5% women who received the standard recall letter, had a PAP smear taken within a period of 12 months; while 8% women did so without receiving an intervention at all. Participation in postmenopausal women was higher than in women younger than 50 in both self‐sampling arms. Screening by means of the self‐sample kit increased by age, contradictory when screening is performed by a PAP smear. Of those testing hrHPV positive (9.5%), 88.9% attended for follow up cytology. The mean DNA concentration, found in the self‐sampler, decreased by age, causing a higher number of inconclusive results. Our results support the efficacy of a self‐sampling strategy to increase participation in the Flemish screening program. Self‐sampling seems particularly acceptable to postmenopausal non‐responders. Future research should focus on the performance of different self‐sampling devices in post‐menopausal women as low DNA concentrations exponentially increased over age.
Adapting Behavioral Interventions for Social Media Delivery

Patients are increasingly using online social networks (ie, social media) to connect with other patients and health care professionals—a trend called peer-to-peer health care. Because online social networks provide a means for health care professionals to communicate with patients, and for patients to communicate with each other, an opportunity exists to use social media as a modality to deliver behavioral interventions. Social media-delivered behavioral interventions have the potential to reduce the expense of behavioral interventions by eliminating visits, as well as increase our access to patients by becoming embedded in their social media feeds. Trials of online social network-delivered behavioral interventions have shown promise, but much is unknown about intervention development and methodology. In this paper, we discuss the process by which investigators can translate behavioral interventions for social media delivery. We present a model that describes the steps and decision points in this process, including the necessary training and reporting requirements. We also discuss issues pertinent to social media-delivered interventions, including cost, scalability, and privacy. Finally, we identify areas of research that are needed to optimize this emerging behavioral intervention modality.
Ceramics and Orthodontics

Introduction: An orthodontist has two clinical situations in which he is confronted with ceramics: 1. Use of ceramic brackets 2. Applying brackets on teeth with ceramic restorations. Aim: The present study wishes to emphasize the advantages and the disadvantages that the use of ceramics has brought to the orthodontic profession. Material And Method: 75 consecutive adult orthodontic patients after being presented with their treatment plan were administered a questioner to motivate their choice in the type of braces and the cases with aesthetic braces or which had ceramic restorations prior to orthodontics received a special follow-up threw-out their treatment. Results: Ceramic braces are chosen for aesthetic reasons but sometimes they create other type of problems during treatment. Adhesion between braces and ceramic restorations rests problematic. Conclusions: The use of ceramics in orthodontics was indispensable but dental materials still need to be perfected.
The Development and Growth of the Intervertebral Disc

I should, in the first instance, like to express my deep appreciation ? f the honour the Royal College of Surgeons has conferred on me ln my election to the appointment of Struthers Lecturer. The distlnguished list of anatomists who have held this Lectureship makes mY task no easy one and the standard of academic scholarship that has become the established custom in the lectures is beyond that ^hich I can hope to emulate.
Approximate Compressor for Efficient Multiplication in Image Processing Applications

Approximate computing is a promising candidate for minimizing the energy consumption of various image processing Algorithms, which also have error tolerable characteristics. The image processing algorithm intensively consists of matrix multiplications where the approximate multiplier (positive compressor, Negative compressor) replaces the exact multipliers for energy reduction. This paper discusses the design and analysis of the two approximate multiplier by using the two approximate 4–2 compressors with reduced delay, area, power, and comparable accuracy with the existing multipliers. The NC based 8×8 multiplier (NM) consumes 30.17% and 3.85% less power than exact 8×8 and PC 8×8 multiplier(PM) respectively. Similarly the LUT utilization of NC based 8×8 multiplier is 5.4% lesser than exact 8×8 and 2.7% less than the PC based 8×8 multiplier. The proposed approximated multiplier is used in the Sobel edge detection algorithm by replacing complex normal multiplier operations. The core part of the edge detection algorithm with approximate multiplier is implemented using the Verilog HDL program and the MATLAB is used to give the input image to the Verilog code based approximate multiplier and then the edge detected output is again fed to MATLAB and finally the edge detected output is displayed using MATLAB too.
Carbonic anhydrase 2 inhibits epithelial–mesenchymal transition and metastasis in hepatocellular carcinoma

Carbonic anhydrase 2 (CA2) plays vital role in the regulation of ion transport and pH balance and is involved in many biological processes; however, its role in cancer remains obscure. In this study, we identified a novel function of CA2 in facilitating hepatocellular carcinoma (HCC) metastasis. CA2 expression was elevated in Na+-K+-ATPase α1 (ATP1A1)-downregulated HCC cells and was inversely correlated with that of ATP1A1 in HCC. ATP1A1 acted as an oncoprotein whereas CA2 overexpression inhibited cell migration and invasion by reversing epithelial-mesenchymal transition (EMT) in HCC. CA2 downregulation promoted HCC metastasis and invasion whereas ATP1A1 downregulation inhibited HCC metastasis. Because of the opposing effects of CA2 and ATP1A1 in HCC, we examined the role of their correlation in HCC metastasis. CA2 attenuated ATP1A1-triggered tumor growth in vivo and ATP1A1-induced metastasis in vitro. Taken together, the present results suggest that CA2 serves as a suppressor of HCC metastasis and EMT and is correlated with favorable overall survival (OS) in HCC patients.
Document Layout Analysis Using Multigaussian Fitting

This paper proposes a novel technique for layout analysis of documents with complex Manhattan layouts. The technique is designed for Indic script newspapers and works on many types of documents not necessarily with Indic scripts with Manhattan layout. The main idea behind the algorithm is to categorise the physical elements of a document into noise, text, titles and graphics based on their heights. A histogram of heights is computed from the bounding boxes of connected components and a multigaussian fit is used to discover optimal split points between the categories. The gaussian with the highest peak is assumed to correspond to running text. Running text regions are grouped into blocks using nearest neighbour analysis. These initial regions are further refined using a second-level classification of the other elements into graphics, light-coloured text on a dark background, and graphical separators. The resulting layouts show accuracies comparable to some of the best and most popular algorithms such as MHS (winner of ICDAR-RDCL2015 competition) and PRImA's Aletheia (tool developed by PRImA Research Lab). Results of testing on many Indic script newspapers and other documents, and comparison with Aletheia and MHS on ICDAR dataset show its performance. Our initial results on an Indic document dataset show high performance in identifying running text (> 98%) with an accuracy of 82% on identifying the other elements. Ground truth data for the Indic script newspaper documents is being generated for a more extensive quantitative testing. The strength of our algorithm is that it requires only one parameter - the number of gaussians to fit the height histogram data and is therefore easy to automate and adapt to many documents.
A Rapid Method for Quantifying Viable Mycobacterium avium subsp. paratuberculosis in Cellular Infection Assays

ABSTRACT Determining the viability of bacteria is a key outcome of in vitro cellular infection assays. Currently, this is done by culture, which is problematic for fastidious slow-growing bacteria such as Mycobacterium avium subsp. paratuberculosis, where it can take up to 4 months to confirm growth. This study aimed to identify an assay that can rapidly quantify the number of viable M. avium subsp. paratuberculosis cells in a cellular sample. Three commercially available bacterial viability assays along with a modified liquid culture method coupled with high-throughput quantitative PCR growth detection were assessed. Criteria for assessment included the ability of each assay to differentiate live and dead M. avium subsp. paratuberculosis organisms and their accuracy at low bacterial concentrations. Using the culture-based method, M. avium subsp. paratuberculosis growth was reliably detected and quantified within 2 weeks. There was a strong linear association between the 2-week growth rate and the initial inoculum concentration. The number of viable M. avium subsp. paratuberculosis cells in an unknown sample was quantified based on the growth rate, by using growth standards. In contrast, none of the commercially available viability assays were suitable for use with samples from in vitro cellular infection assays. IMPORTANCE Rapid quantification of the viability of Mycobacterium avium subsp. paratuberculosis in samples from in vitro cellular infection assays is important, as it allows these assays to be carried out on a large scale. In vitro cellular infection assays can function as a preliminary screening tool, for vaccine development or antimicrobial screening, and also to extend findings derived from experimental animal trials. Currently, by using culture, it takes up to 4 months to obtain quantifiable results regarding M. avium subsp. paratuberculosis viability after an in vitro infection assay; however, with the quantitative PCR and liquid culture method developed, reliable results can be obtained at 2 weeks. This method will be important for vaccine and antimicrobial screening work, as it will allow a greater number of candidates to be screened in the same amount of time, which will increase the likelihood that a favorable candidate will be found to be subjected to further testing.
Demonstration of Inherent Electromagnetic Energy Emanating from Isolated Human Hairs.

The presence of hair is widely prevalent in mammals. The human hair structurally consists of a follicle (under the skin) and a shaft protruding from the epidermis. The follicle (commonly known as the root) is described to be a mammalian skin organ, with different functions. One of the primary functions is hair growth and replacement; other role is acting as sensory mechanisms. It is stated that the hair senses changes in position by activating the nerve endings anchored in the follicle. This manuscript introduces for the first time the detection and documentation of inherent electromagnetic forces emanating from human hairs. That was accomplished by preparing a solution containing nano-sized iron nanoparticles (mean diameter 2000 nanometer, nm) and Prussian Blue Stain (PBS Fe 2000). The intact hair plucked from the forearm was mounted on a glass slide and covered with the PBS Fe 2000, then covered with a second slide. Electromagnetic forces express themselves as magnetic lines of force containing the aggregating iron particles circulating around the follicle. In addition, intermittent flashes of light emanating from the follicles were transformed into trails of aggregating iron particles. Journal of Nature and Science, 1(3):e55, 2015.
Leptomeningeal gadolinium enhancement across the spectrum of chronic neuroinflammatory diseases

Objective: To assess the prevalence and the specificity of leptomeningeal enhancement (LME) on postcontrast T2–fluid-attenuated inversion recovery (FLAIR) MRI in multiple sclerosis (MS) compared to a variety of inflammatory and noninflammatory neurologic conditions assessed in 2 academic research hospitals. Methods: On 3T postcontrast T2-FLAIR images, the presence of focal gadolinium enhancement was evaluated in the leptomeningeal compartment in 254 people with non-MS neurologic conditions or neurotropic viral infections. Based on their clinical diagnosis, patients were grouped as follows: (1) other-than-MS inflammatory neurologic diseases; (2) noninflammatory neurologic diseases; (3) human T-lymphotropic virus (HTLV)–infected; (4) HIV-infected; (5) healthy volunteers. Results: LME was detected in 56/254 non-MS cases (22%) vs 74/299 (25%) of MS cases. LME was nearly 4-fold more frequent in non-MS inflammatory neurologic conditions (18/51 cases, 35%) than in noninflammatory neurologic conditions (3/38, 8%) and healthy volunteers (5/66, 8%). The highest prevalence of LME was detected in HTLV infection (17/38 cases, 45%), particularly in the setting of HTLV-associated myelopathy (14/25 cases, 56%). LME also frequently occurred in HIV infection (13/61 cases, 21%). Unlike in MS, LME is not associated with lower brain and cortical volumes in non-MS inflammatory neurologic conditions, including HTLV and HIV infection. Conclusions: Despite its relevance to MS pathogenesis and cortical pathology, LME is not specific to MS, occurring frequently in non-MS inflammatory neurologic conditions and especially in those patients with HTLV-associated myelopathy. Overall, this strengthens the notion that LME localizes inflammation-related focal disruption of the blood–meninges barrier and associated scarring.
Hormone and receptor interplay in the regulation of mosquito lipid metabolism

Significance Mosquitoes require a blood meal to reproduce and by blood feeding transmit some of the most dangerous human diseases. Female mosquitoes have extremely high metabolism, and the elucidation of regulatory pathways coordinating reproductive and metabolic events is essential. RNAi of the juvenile hormone receptor Methoprene-tolerant (Met) promoted triacylglycerol (TAG) catabolism and β-oxidation and diminished TAG levels, whereas ecdysone receptor (EcR) RNAi had an opposite effect. Hepatocyte nuclear factor 4 (HNF4) directly regulated TAG catabolism and β-oxidation genes, and its RNAi silencing phenocopied EcR RNAi. The expression of the HNF4 gene was downregulated by Met and activated by EcR and Target of rapamycin. Thus, HNF4 mediates hormonal and nutritional signaling of lipid metabolism regulation in reproducing female Aedes aegypti mosquitoes. Mosquitoes transmit devastating human diseases because they need vertebrate blood for egg development. Metabolism in female mosquitoes is tightly coupled with blood meal-mediated reproduction, which requires an extremely high level of energy consumption. Functional analysis has shown that major genes encoding for enzymes involved in lipid metabolism (LM) in the mosquito fat bodies are down-regulated at the end of the juvenile hormone (JH)-controlled posteclosion (PE) phase but exhibit significant elevation in their transcript levels during the post-blood meal phase (PBM), which is regulated mainly by 20-hydroxyecdysone (20E). Reductions in the transcript levels of genes encoding triacylglycerol (TAG) catabolism and β-oxidation enzymes were observed to correlate with a dramatic accumulation of lipids in the PE phase; in contrast, these transcripts were elevated significantly and lipid stores were diminished during the PBM phase. The RNAi depletion of Methoprene-tolerant (Met) and ecdysone receptor (EcR), receptors for JH and 20E, respectively, reversed the LM gene expression and the levels of lipid stores and metabolites, demonstrating the critical roles of these hormones in LM regulation. Hepatocyte nuclear factor 4 (HNF4) RNAi-silenced mosquitoes exhibited down-regulation of the gene transcripts encoding TAG catabolism and β-oxidation enzymes and an inability to use lipids effectively, as manifested by TAG accumulation. The luciferase reporter assay showed direct regulation of LM-related genes by HNF4. Moreover, HNF4 gene expression was down-regulated by Met and activated by EcR and Target of rapamycin, providing a link between nutritional and hormonal regulation of LM in female mosquitoes.
JPR: Exploring Joint Partitioning and Replication for Traffic Minimization in Online Social Networks

A scalable storage system becomes more important today for online social networks (OSNs) as the volume of user data increases rapidly. Key-value store uses consistent hashing to save data in a distributed manner. As a defacto standard, it has been widely used in production environments of many OSNs. However, the random nature of hashing always leads to high inter-server traffic. Recently, partitioning and replication are respectively proposed in many existing works where the former aims to minimize the inter-server read traffic and the latter aims to optimize the inter-server write traffic. Nevertheless, the separated manners of optimization cannot efficiently reduce the traffic. Because the inter-server read traffic is changed during replication. In this paper, we suggest that performing partitioning and replication simultaneously could provide probability to further optimize traffic. Then we formulate the problem as a revised graph partitioning with overlaps, since overlaps partitioning naturally corresponds to replication. To solve the problem, we propose a Joint Partitioning and Replication (JPR) scheme. Through extensive experiments with a real world Facebook trace, we evaluate that JPR significantly reduces inter-server traffic with slightly sacrificing storage cost compared to hashing, and preserves a good load balancing across servers as well.
Improving stability of prediction models based on correlated omics data by using network approaches

Building prediction models based on complex omics datasets such as transcriptomics, proteomics, metabolomics remains a challenge in bioinformatics and biostatistics. Regularized regression techniques are typically used to deal with the high dimensionality of these datasets. However, due to the presence of correlation in the datasets, it is difficult to select the best model and application of these methods yields unstable results. We propose a novel strategy for model selection where the obtained models also perform well in terms of overall predictability. Several three step approaches are considered, where the steps are 1) network construction, 2) clustering to empirically derive modules or pathways, and 3) building a prediction model incorporating the information on the modules. For the first step, we use weighted correlation networks and Gaussian graphical modelling. Identification of groups of features is performed by hierarchical clustering. The grouping information is included in the prediction model by using group-based variable selection or group-specific penalization. We compare the performance of our new approaches with standard regularized regression via simulations. Based on these results we provide recommendations for selecting a strategy for building a prediction model given the specific goal of the analysis and the sizes of the datasets. Finally we illustrate the advantages of our approach by application of the methodology to two problems, namely prediction of body mass index in the DIetary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome study (DILGOM) and prediction of response of each breast cancer cell line to treatment with specific drugs using a breast cancer cell lines pharmacogenomics dataset.
Dysregulation of RNA Binding Protein Aggregation in Neurodegenerative Disorders

The unique biology of RNA binding proteins is altering our view of the genesis of protein misfolding diseases. These proteins use aggregation of low complexity domains (LCDs) as a means to regulate the localization and utilization of RNA by forming RNA granules, such as stress granules, transport granules and P-bodies. The reliance on reversible aggregation as a mechanism for biological regulation renders this family of proteins highly vulnerable to promoting diseases of protein misfolding. Mutations in RNA binding proteins are associated with many neurodegenerative disorders, such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar dementia (FTLD). The biology of RNA binding proteins also extends to microtubule associated protein tau. Tau is normally an axonal protein, but in stress it translocates to the somatodendritic arbor where it takes on a new function promoting formation of stress granules. The interaction of tau with stress granules also promotes tau aggregation, accelerating formation of the tau pathology that we associate with diseases such as Alzheimer's disease (AD).