Miracle-dz/UniFAR-FTUs huggingface dataset:
Electroaddressing Functionalized Polysaccharides as Model Biofilms for Interrogating Cell Signaling

Bacteria often reside at surfaces as complex biofilms in which an exopolysaccharide matrix entraps the population while allowing access to its chemical environment. There is a growing awareness that the biofilm structure and activity are integral to a wide array of properties important to health (the microbiome), disease (drug resistance) and technology (fouling). Despite the importance of bacterial biofilms, few experimental platforms and systems are available to assemble complex populations and monitor their activities. Here, a functionalized alginate composite material for creating in vitro model biofilms suitable for cell‐cell signaling studies by entrapping bacterial cells in situ is reported. Biofilm assembly is achieved using device‐imposed electrical signals to electrodeposit the stimuli‐responsive polysaccharide alginate. This electrodeposition mechanism is versatile in that it allows control of the bacterial population density and distribution. For instance, it is demonstrated that a mixed population can be homogeneously distributed throughout the biofilm or can be assembled as spatially segregated populations within a stratified biofilm. The “electroaddressable” biofilms are visualized using both a planar 2D chip with patterned electrodes and a microfluidic bioMEMS device with sidewall electrodes. Specifically, it is observed that bacteria entrapped within the model biofilm recognize and respond to chemical stimuli imposed from the fluidic environment. Finally, reporter cells are used to demonstrate that bacteria entrapped within this model biofilm engage in intercellular quorum sensing. This work demonstrates the functionality of the stimuli‐responsive polysaccharide by biofabricating pseudo‐3D cell‐gel biocomposites, mimicking the formation of biofilms, for interrogating phenotypes of E. coli bacterial populations. In addition to controlling assembly, the microfluidic device allows the biofilm to be monitored through the fluorescence methods commonly used in biological research. This platform technology should be able to be exploited for monitoring biofilm development, as well as for extending the understanding of the interactions between various bacterial species arranged in controlled patterns.
Orbital Angular Momentum With Index Modulation

Orbital angular momentum (OAM)-based mode division multiplexing (MDM) is an emerging physical layer solution for short-distance line-of-sight wireless communications by providing high spectral efficiency with a considerably low detection complexity. Similarly, index modulation (IM) schemes have been extensively studied over the past few years due to their attractive features, such as improved error performance, low complexity, and high energy efficiency. In this paper, we propose the scheme of orbital angular momentum with index modulation (OAM-IM) by using the activated OAM modes themselves to carry additional information through the principle of IM. A general guideline is presented for the construction of optimal OAM-IM schemes along with the formulation of a low-complexity maximum likelihood detector. It is shown via computer simulations as well as theoretical bit error probability calculations that the proposed OAM-IM schemes can achieve considerably better error performance than the reference OAM-MDM schemes, while having the same level of detection complexity.
Toward the Commercialization of Organic Photovoltaic Cells

Photovoltaic technologies based on organic semiconductors are introduced, and the major issues for their successful commercialization are discussed. The concept of conjugated organic compounds are first described to elucidate how organic materials, commonly regarded as insulators, can function as semiconductors or conductors. Then, the working principle of organic photovoltaic (OPV) cells is presented in detail with emphasis on the concepts of donor‐acceptor heterojunctions, excitons, charge transfer, and carrier transport. Important figures of merit, which need to be maximized to achieve highly efficient OPV cells, are discussed. In the second half of the paper, the challenges toward commercially viable OPV technologies are discussed, and the efforts being made to overcome such challenges, along with examples that include new material development, interface engineering, innovative device architecture involving optical/nanostructures, and extension of their applications into flexible and/or see‐ through solar cells, are introduced.
Detection of transformed malwares using permission flow graphs

With growing popularity of Android, it's attack surface has also increased. Prevalence of third party android marketplaces gives attackers an opportunity to plant their malicious apps in the mobile eco-system. To evade signature based detection, attackers often transform their malware, for instance, by introducing code level changes. In this paper we propose a lightweight static Permission Flow Graph (PFG) based approach to detect malware even when they have been transformed (obfuscated). A number of techniques based on behavioral analysis have also been proposed in the past; how-ever our interest lies in leveraging the permission framework alone to detect malware variants and transformations without considering behavioral aspects of a malware. Our proposed approach constructs Permission Flow Graph (PFG) for an Android App. Transformations performed at code level, often result in changing control flow, however, most of the time, the permission flow remains invariant. As a consequences, PFGs of transformed malware and non-transformed malware remain structurally similar as shown in this paper using state-of-the-art graph similarity algorithm. Furthermore, we propose graph based similarity metrics at both edge level and vertex level in order to bring forth the structural similarity of the two PFGs being compared. We validate our proposed methodology through machine learning algorithms. Results prove that our approach is successfully able to group together Android malware and its variants (transformations) together in the same cluster. Further, we demonstrate that our proposed approach is able to detect transformed malware with a detection accuracy of 98.26%, thereby ensuring that malicious Apps can be detected even after transformations.
Cognitive dimensions questionnaire applied to exploratory algorithm design

In software engineering, the stage between problem realization and implementation of a solution is not well supported by technology. It is common to see work being carried out on paper or whiteboards. This paper documents a pilot study to identify some reasons as to why paper and whiteboards are useful tools in early exploratory design and exposes some questions about where technology may fit in augmenting this stage of software engineering. The cognitive dimensions questionnaire was used to investigate notations and devices used in exploratory algorithm design.
Microneme Protein 5 Regulates the Activity of Toxoplasma Subtilisin 1 by Mimicking a Subtilisin Prodomain*

Background: TgSUB1 is a subtilisin protease that trims invasion proteins on the surface of Toxoplasma gondii. Results: TgMIC5 suppresses TgSUB1 activity and structurally mimics a subtilisin prodomain, suggesting a mechanism for inhibition. Conclusion: The C-terminal region of TgMIC5 is responsible for inhibition of TgSUB1. Significance: We identify a novel subtilisin propeptide mimic. Toxoplasma gondii is the model parasite of the phylum Apicomplexa, which contains obligate intracellular parasites of medical and veterinary importance. Apicomplexans invade host cells by a multistep process involving the secretion of adhesive microneme protein (MIC) complexes. The subtilisin protease TgSUB1 trims several MICs on the parasite surface to activate gliding motility and host invasion. Although a previous study showed that expression of the secretory protein TgMIC5 suppresses TgSUB1 activity, the mechanism was unknown. Here, we solve the three-dimensional structure of TgMIC5 by nuclear magnetic resonance (NMR), revealing that it mimics a subtilisin prodomain including a flexible C-terminal peptide that may insert into the subtilisin active site. We show that TgMIC5 is an almost 50-fold more potent inhibitor of TgSUB1 activity than the small molecule inhibitor N-[N-(N-acetyl-l-leucyl)-l-leucyl]-l-norleucine (ALLN). Moreover, we demonstrate that TgMIC5 is retained on the parasite plasma membrane via its physical interaction with the membrane-anchored TgSUB1.
Role of Chronobiology as a Transdisciplinary Field of Research: Its Applications in Treating Mood Disorders

Chronobiology is a field that studies the effects of time on biological systems. Periodicity is of particular interest. The master biological clock in the suprachiasmatic nucleus controls daily rhythms of core body temperature, rest-activity cycle, physiological and behavioral functions, psychomotor functions and mood in humans. The clock genes are involved in the generation of the circadian rhythms and the biological clock is synchronized to solar day by direct photic inputs. Various circadian rhythm abnormalities have been demonstrated in mood disorders such as unipolar depression, bipolar depression and seasonal affective disorder. Hypotheses involving circadian rhythm abnormalities related to the etiology of mood disorders have been raised. The resulting circadian rhythm changes can be measured and evaluated that these techniques can be used to identify subtypes of mood disorders associated with circadian rhythm changes. The data obtained from chronobiological studies reveal methods that manipulate circadian rhythms. The effects of light and melatonin on circadian rhythms are determined by these studies. Chronobiological research has been applied to the psychiatric clinic and light therapy has been used as a chronotherapeutic in the treatment of mood disorders. On the other hand, chronotherapeutic approaches with effects on circadian rhythms such as sleep deprivation therapy have been used in the treatment of mood disorders too. As a good example of translational psychiatry, chronobiological studies have been projected in the psychiatry clinic. It may be possible, the data obtained from the basic sciences are used in the diagnosis of mood disorders and in the treatment of psychiatric disorders as chronotherapeutic techniques. Developments in the field of chronobiology and data obtained from chronotherapeutics may enable the development of evidence-based diagnosis and treatment in psychiatry.
Secular trends in regional differences in nutritional biomarkers and self-reported dietary intakes among American adults: National Health and Nutrition Examination Survey (NHANES) 1988–1994 to 2009–2010

Abstract Objective To understand the contribution of regional differentials in dietary exposures to regional gradients in health, we examined 20-year trends in the association of US census region of residence with nutritional biomarkers and dietary intakes of American adults. Design Observational. Setting The biomarker and 24 h dietary recall data were from the National Health and Nutrition Examination Surveys (NHANES) conducted during 1988–1994 and 1999–2010. The US census region was operationalized as Northeast, Midwest, South and West. Nutritional biomarker outcomes were serum folate, vitamins B6, B12, C, D and E, and carotenoids; dietary outcomes were intakes of nutrients, food groups and eating patterns. Subjects US adults, n>8000–40 000 for biomarkers and >43 000 for dietary outcomes. Results The interactions of survey time period and region were not significant for the examined biomarker and dietary outcomes, indicating similar secular trends among regions. The main effect of region was significant for all nutritional biomarkers except serum vitamin B6, most dietary micronutrients, food groups and eating patterns (P<0·001). The mean serum folate, vitamins B12, C and E, and all carotenoid (except lycopene) biomarker levels, and intakes of dietary fibre, vitamins A, E, C and B6, folate, K, Ca, Mg and Fe, fruits, vegetables and whole grains, were higher in the West and Northeast regions, relative to the South and Midwest regions. Conclusions Overall, the regional gradients in dietary exposure, expressed objectively as biomarkers or as self-reported nutrient and food group intakes, paralleled trajectories reported for health outcomes and were remarkably persistent over time.
Evaluation of C‐reactive protein as an inflammatory marker of pemphigus foliaceus and superficial pyoderma in dogs

BACKGROUND C-reactive protein (CRP) is a major acute phase protein in dogs and may be an inflammatory marker of autoimmune diseases. HYPOTHESIS/OBJECTIVES To measure pre- and post-treatment CRP levels in dogs with superficial pyoderma (SP) and pemphigus foliaceus (PF) compared to normal dogs; to evaluate possible correlation between CRP values, indirect immunofluorescence (IIF), and pemphigus foliaceus extent and severity index (PEFESI) scores. ANIMALS Fifty nine dogs divided into three groups: Group I (control, n = 31), Group II (SP, n = 14) and Group III (PF, n = 14). METHODS CRP levels were measured in Group I dogs. Skin biopsies of Groups II and III dogs were obtained for histopathological examination. In Group II dogs, CRP levels were measured at days 0, 15, 30 and 60. In Group III dogs were evaluated by PEFESI, IIF and CRP levels at days 0, 15, 30, 60 and 90. RESULTS Group III showed a higher median CRP (37.4 mg/mL) compared to the other groups (Group I, CRP 2.9 mg/mL, P < 0.0001; Group II CRP 3.8 mg/mL, P = 0.008). There was no significant difference in CRP levels between groups I and II. IIF titres and CRP levels decreased in most cases of PF with clinical improvement. Dogs with CRP >10.6 μg/mL were 5.5 times more likely to have PF than SP. There was a strong positive correlation between CRP values and PEFESI and a weak positive correlation between CRP values and IIF titres. CONCLUSION AND CLINICAL IMPORTANCE CRP levels are increased in dogs with PF and exceed levels found in most dogs with SP.
A multicenter randomized phase III trial of vinorelbine/gemcitabine doublet versus capecitabine monotherapy in anthracycline- and taxane-pretreated women with metastatic breast cancer.

BACKGROUND The Breast Cancer Study Group of the Hellenic Oncology Research Group conducted a phase III trial of single-agent capecitabine versus the vinorelbine/gemcitabine doublet in patients with metastatic breast cancer (MBC) pretreated with anthracyclines and taxanes. The primary objective was to demonstrate superiority of combination treatment in terms of progression-free survival (PFS). PATIENTS AND METHODS Women with MBC were randomly assigned to receive either capecitabine (Cap arm: 1250 mg/m(2) twice daily, on days 1-14) or vinorelbine/gemcitabine doublet (VG arm: vinorelbine 25 mg/m(2); gemcitabine 1000 mg/m(2); both drugs on days 1 and 15). RESULTS Seventy-four women were treated on each arm and median PFS was 5.4 versus 5.2 months (P = 0.736), for VG and Cap, respectively. Median overall survival was 20.4 months for the VG arm and 22.4 months for the Cap arm (P = 0.319). Overall response rate was 28.4% in the VG arm and 24.3% in the Cap arm (P = 0.576). Both regimens were generally well tolerated. Neutropenia and fatigue were more common with VG arm and hand-foot syndrome with Cap arm. CONCLUSIONS This trial failed to demonstrate superiority of vinorelbine/gemcitabine doublet over single-agent capecitabine in terms of PFS. Given the favorable toxicity and convenience of oral administration, single-agent capecitabine is recommended for compliant patients.
Enhancing Land Cover Mapping through Integration of Pixel-Based and Object-Based Classifications from Remotely Sensed Imagery

Pixel-based and object-based classifications are two commonly used approaches in extracting land cover information from remote sensing images. However, they each have their own inherent merits and limitations. This study, therefore, proposes a new classification method through the integration of pixel-based and object-based classifications (IPOC). Firstly, it employs pixel-based soft classification to obtain the class proportions of pixels to characterize the land cover details from pixel-scale properties. Secondly, it adopts area-to-point kriging to explore the class spatial dependence between objects for each pixel from object-based soft classification results. Thirdly, the class proportions of pixels and the class spatial dependence of pixels are fused as the class occurrence of pixels. Last, a linear optimization model on objects is built to determine the optimal class label of pixels within each object. Two remote sensing images are used to evaluate the effectiveness of IPOC. The experimental results demonstrate that IPOC performs better than the traditional pixel-based hard classification and object-based hard classification methods. Specifically, the overall accuracy of IPOC is 7.64% higher than that of pixel-based hard classification and 4.64% greater than that of object-based hard classification in the first experiment, while the overall accuracy improvements in the second experiment are 3.59% and 3.42%, respectively. Meanwhile, IPOC produces less salt and pepper effect than the pixel-based hard classification method and generates more accurate land cover details and small patches than the object-based hard classification method.
Exploring the oncoproteomic response of human prostate cancer to therapeutic radiation using data‐independent acquisition (DIA) mass spectrometry

The development of radioresistance in prostate cancer (PCa) is an important clinical issue and is still largely uninformed by personalized molecular characteristics. The aim of this study was to establish a platform that describes the early oncoproteomic response of human prostate tissue to radiation therapy (RT) using a prospective human tissue cohort.
What Motivates Young Adults to Talk About Physical Activity on Social Network Sites?

Background Electronic word-of-mouth on social network sites has been used successfully in marketing. In social marketing, electronic word-of-mouth about products as health behaviors has the potential to be more effective and reach more young adults than health education through traditional mass media. However, little is known about what motivates people to actively initiate electronic word-of-mouth about health behaviors on their personal pages or profiles on social network sites, thus potentially reaching all their contacts on those sites. Objective This study filled the gap by applying a marketing theoretical model to explore the factors associated with electronic word-of-mouth on social network sites about leisure-time physical activity. Methods A Web survey link was sent to undergraduate students at one of the Midwestern universities and 439 of them completed the survey. Results The average age of the 439 participants was 19 years (SD=1 year, range: 18-24). Results suggested that emotional engagement with leisure-time physical activity (ie, affective involvement in leisure-time physical activity) predicted providing relevant opinions or information on social network sites. Social network site users who perceived stronger ties with all their contacts were more likely to provide and seek leisure-time physical activity opinions and information. People who provided leisure-time physical activity opinions and information were more likely to seek opinions and information, and people who forwarded information about leisure-time physical activity were more likely to chat about it. Conclusions This study shed light on the application of the electronic word-of-mouth theoretical framework in promoting health behaviors. The findings can also guide the development of future social marketing interventions using social network sites to promote leisure-time physical activity.
Post-concussive symptoms after a mild traumatic brain injury during childhood and adolescence

ABSTRACT Objective: Mild traumatic brain injury (mTBI) is common injury during childhood and adolescence but the long-term outcomes are poorly understood. This study examined post-concussive symptoms and behavioural outcomes in children and adolescents up to 24 months post-mTBI. Method: Parents of children aged 8–15 years with mTBI completed the BASC-2 and Rivermead Post-Concussion Symptoms Questionnaire at baseline, 1-, 6-, 12- and 24 months post-injury. An age-matched traumatic brain injury-free cohort was recruited and assessed at 12- and 24 months. Results: PCSs decreased significantly over the first 12 months post-injury. At 12- and 24 months post-injury, the mTBI group reported more PCSs and behavioural symptoms compared to controls. Parents of children with mTBI were more likely to report ≥4 problematic PCS symptoms (28% at both time points) compared to controls (7.7% and 1.7% at 12 and 24 months, respectively). The mTBI group was 4.63 times more likely to have four or more ongoing PCS symptoms at 12 months post-injury compared to controls. Headache was the most common acute post-injury symptom (55%), while the most commonly reported persistent symptoms were irritability, frustration, forgetfulness and fatigue. Conclusions: PCSs are common 2 years post-mTBI in childhood or adolescence. Given this, additional intervention and support is needed for families post-injury.
Single image density map estimation based on multi-column CNN and boosting

In this paper, we explore the task to estimate the density map of objects from single image with unknown perspective map. We follow the recent progress in object counting through density map estimation. Object density map estimation is usually suffered from scale variance of objects caused by unknown perspective. In addition, the background and irrelevant objects in the image lead to artifacts in the resulting density maps, which build up the error when heat maps are needed by aggregating density maps. We propose a multi-CNN network with gradient boosting (MCNN-boost) to address these two problems at once. The receptive fields with different sizes in each column of CNNs make the model adaptive to variance in sizes caused by perspective, and the gradient boosting strategy will effectively remove the artifacts caused by the background and irrelevant objects. Thanks to the simple architecture of the network, MCNN-boost is efficient to train and highly adaptive to different data sets with different scenes. We run experiments on one shopping mall data sets with heavy perspective distortion and complex background to show the effectiveness of the proposed algorithm.
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins

Summary: ArachnoServer is a manually curated database that consolidates information on the sequence, structure, function and pharmacology of spider‐venom toxins. Although spider venoms are complex chemical arsenals, the primary constituents are small disulfide‐bridged peptides that target neuronal ion channels and receptors. Due to their high potency and selectivity, these peptides have been developed as pharmacological tools, bioinsecticides and drug leads. A new version of ArachnoServer (v3.0) has been developed that includes a bioinformatics pipeline for automated detection and analysis of peptide toxin transcripts in assembled venom‐gland transcriptomes. ArachnoServer v3.0 was updated with the latest sequence, structure and functional data, the search‐by‐mass feature has been enhanced, and toxin cards provide additional information about each mature toxin. Availability and implementation: http://arachnoserver.org Contact: support@arachnoserver.org Supplementary information: Supplementary data are available at Bioinformatics online.