Miracle-dz/UniFAR-FTUs huggingface dataset:
Anti-biofilm Properties of the Fecal Probiotic Lactobacilli Against Vibrio spp.

Diarrheal disease caused by Vibrio cholerae is endemic in developing countries including India and is associated with high rate of mortality especially in children. V. cholerae is known to form biofilms on the gut epithelium, and the biofilms once formed are resistant to the action of antibiotics. Therefore agents that prevent the biofilm formation and disperse the preformed biofilms are associated with therapeutic benefits. The use of antibiotics for the treatment of cholera is associated with side effects such as gut dysbiosis due to depletion of gut microflora, and the increasing problem of antibiotic resistance. Thus search for safe alternative therapeutic agents is warranted. Herein, we screened the lactobacilli spp. isolated from the fecal samples of healthy children for their abilities to prevent biofilm formation and to disperse the preformed biofilms of V. cholerae and V. parahaemolyticus by using an in vitro assay. The results showed that the culture supernatant (CS) of all the seven isolates of Lactobacillus spp. used in the study inhibited the biofilm formation of V. cholerae by more than 90%. Neutralization of pH of CS completely abrogated their antimicrobial activities against V. cholera, but had negligible effects on their biofilm inhibitory potential. Further, CS of all the lactobacilli isolates caused the dispersion of preformed V. cholerae biofilms in the range 62–85%; however, pH neutralization of CS reduced the biofilm dispersal potential of the 4 out of 7 isolates by 19–57%. Furthermore, the studies showed that CS of none of the lactobacilii isolates had antimicrobial activity against V. parahaemolyticus, but 5 out of 7 isolates inhibited the formation of its biofilm in the range 62–82%. However, none of the CS dispersed the preformed biofilms of V. parahaemolyticus. The ability of CS to inhibit the adherence of Vibrio spp. to the epithelial cell line was also determined. Thus, we conclude that the biofilm dispersive action of CS of lactobacilli is strain-specific and pH-dependent. As Vibrio is known to form biofilms in the intestinal niche having physiological pH in the range 6–7, the probiotic strains that have dispersive action at high pH may have better therapeutic potential.
Jointly Localizing and Describing Events for Dense Video Captioning

Automatically describing a video with natural language is regarded as a fundamental challenge in computer vision. The problem nevertheless is not trivial especially when a video contains multiple events to be worthy of mention, which often happens in real videos. A valid question is how to temporally localize and then describe events, which is known as "dense video captioning. " In this paper, we present a novel framework for dense video captioning that unifies the localization of temporal event proposals and sentence generation of each proposal, by jointly training them in an end-to-end manner. To combine these two worlds, we integrate a new design, namely descriptiveness regression, into a single shot detection structure to infer the descriptive complexity of each detected proposal via sentence generation. This in turn adjusts the temporal locations of each event proposal. Our model differs from existing dense video captioning methods since we propose a joint and global optimization of detection and captioning, and the framework uniquely capitalizes on an attribute-augmented video captioning architecture. Extensive experiments are conducted on ActivityNet Captions dataset and our framework shows clear improvements when compared to the state-of-the-art techniques. More remarkably, we obtain a new record: METEOR of 12.96% on ActivityNet Captions official test set.
Material recognition based on thermal cues: Mechanisms and applications

ABSTRACT Some materials feel colder to the touch than others, and we can use this difference in perceived coldness for material recognition. This review focuses on the mechanisms underlying material recognition based on thermal cues. It provides an overview of the physical, perceptual, and cognitive processes involved in material recognition. It also describes engineering domains in which material recognition based on thermal cues have been applied. This includes haptic interfaces that seek to reproduce the sensations associated with contact in virtual environments and tactile sensors aim for automatic material recognition. The review concludes by considering the contributions of this line of research in both science and engineering.
Multivariate and Phylogenetic Analyses Assessing the Response of Bacterial Mat Communities from an Ancient Oligotrophic Aquatic Ecosystem to Different Scenarios of Long-Term Environmental Disturbance

Understanding the response of bacterial communities to environmental change is extremely important in predicting the effect of biogeochemical modifications in ecosystem functioning. The Cuatro Cienegas Basin is an ancient oasis in the Mexican Chihuahuan desert that hosts a wide diversity of microbial mats and stromatolites that have survived in extremely oligotrophic pools with nearly constant conditions. However, thus far, the response of these unique microbial communities to long-term environmental disturbances remains unexplored. We therefore studied the compositional stability of these bacterial mat communities by using a replicated (3x) mesocosm experiment: a) Control; b) Fluct: fluctuating temperature; c) 40C: increase to 40 ºC; d) UVplus: artificial increase in UV radiation; and f) UVmin: UV radiation protection. In order to observe the changes in biodiversity, we obtained 16S rRNA gene clone libraries from microbial mats at the end of the experiment (eight months) and analyzed them using multivariate and phylogenetic tools. Sequences were assigned to 13 major lineages, among which Cyanobacteria (38.8%) and Alphaproteobacteria (25.5%) were the most abundant. The less extreme treatments (Control and UVmin) had a more similar composition and distribution of the phylogenetic groups with the natural pools than the most extreme treatments (Fluct, 40C, and UVplus), which showed drastic changes in the community composition and structure, indicating a different community response to each environmental disturbance. An increase in bacterial diversity was found in the UVmin treatment, suggesting that protected environments promote the establishment of complex bacterial communities, while stressful environments reduce diversity and increase the dominance of a few Cyanobacterial OTUs (mainly Leptolyngbya sp) through environmental filtering. Mesocosm experiments using complex bacterial communities, along with multivariate and phylogenetic analyses of molecular data, can assist in addressing questions about bacterial responses to long-term environmental stress.
A Study on the Fatigue Behavior of Hot Dip Galvanized Steel Connections

The effect of a galvanizing coating on the fatigue strength of S355 structural steel is analyzed in detail showing that the decrease of the fatigue life is very limited if compared with that of uncoated joints and the results are in good agreement with Eurocode detail category, without substantial reductions. The procedure for the preparation of the specimens is systematically described in this note providing a useful tool for engineers involved in similar practical applications. The results are compared with previous data from notched galvanized specimens weakened by a central hole and not treated specimens characterized by the same geometry.
Circular RNA participates in the carcinogenesis and the malignant behavior of cancer

Abstract Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear pre-mRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the “microRNA sponge” function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.
Annals of the New York Academy of Sciences Neuroscience of Aesthetics

Aesthetic evaluations are appraisals that influence choices in important domains of human activity, including mate selection, consumer behavior, art appreciation, and possibly even moral judgment. The nascent field of neuroaesthetics is advancing our understanding of the role of aesthetic evaluations by examining their biological bases. Here, we conduct a selective review of the literature on neuroaesthetics to demonstrate that aesthetic experiences likely emerge from the interaction between emotion–valuation, sensory–motor, and meaning–knowledge neural systems. This tripartite model can in turn be evoked to explain phenomena central to aesthetics, such as context effects on preferences. Indeed, context-dependent appraisals that focus on objects rather than on outcomes could be an important factor distinguishing aesthetic experiences from other kinds of evaluations.
Impact of Bias-Correction Methods on Effectiveness of Assimilating SMAP Soil Moisture Data into NCEP Global Forecast System Using the Ensemble Kalman Filter

Improving numerical weather prediction was one of the main justifications for National Aeronautics and Space Administration’s Soil Moisture Active/Passive (SMAP) Mission. The ensemble Kalman filter (EnKF) has been extensively applied to assimilate the SM observations into numerical weather predication models. Implementation of EnKF requires the observations and model simulations to be Gaussian distributed and not biased from each other. In this letter, we tested the impacts of three bias-correction methods on effectiveness of assimilating SMAP retrievals into the National Oceanic and Atmospheric Administration—National Centers for Environmental Prediction Global Forecast System (GFS). They are: 1) global cumulative distribution function (CDF) matching with only one CDF for all grids and time series; 2) monthly CDF matching with one CDF for each grid; 3) the linear transformation technique that matches monthly mean and standard deviation of the SMAP retrievals and model simulations for each grid; and 4) assimilating SMAP SM data into GFS without any bias-correction procedure. With respect to the global land data assimilation (DA) system precipitation product, the results demonstrate that the effectiveness of assimilating SMAP retrievals into GFS is significantly impacted by the bias-correction methods. Relative to other DA cases, the monthly CDF matching produces the best precipitation forecast performance. Improvements of the three-hourly GFS precipitation prediction with SMAP assimilation using the monthly CDF matching can reach to 8% and 10% in sparsely and densely vegetated areas, respectively, and marginally positive in medium vegetation areas. Based on these results, assimilating SMAP retrievals into the GFS with the EnKF algorithm using the monthly CDF matching method is suggested for enhancing accuracy of the precipitation forecasts.
Assessment of SRM, MRM3, and DIA for the targeted analysis of phosphorylation dynamics in non‐small cell lung cancer

Hypothesis‐driven MS‐based targeted proteomics has gained great popularity in a relatively short timespan. Next to the widely established selected reaction monitoring (SRM) workflow, data‐independent acquisition (DIA), also referred to as sequential window acquisition of all theoretical spectra (SWATH) was introduced as a high‐throughput targeted proteomics method. DIA facilitates increased proteome coverage, however, does not yet reach the sensitivity obtained with SRM. Therefore, a well‐informed method selection is crucial for designing a successful targeted proteomics experiment. This is especially the case when targeting less conventional peptides such as those that contain PTMs, as these peptides do not always adhere to the optimal fragmentation considerations for targeted assays. Here, we provide insight into the performance of DIA, SRM, and MRM cubed (MRM3) in the analysis of phosphorylation dynamics throughout the phosphoinositide 3‐kinase mechanistic target of rapamycin (PI3K‐mTOR) and mitogen‐activated protein kinase (MAPK) signaling network. We observe indeed that DIA is less sensitive when compared to SRM, however demonstrates increased flexibility, by postanalysis selection of alternative phosphopeptide precursors. Additionally, we demonstrate the added benefit of MRM3, allowing the quantification of two poorly accessible phosphosites. In total, targeted proteomics enabled the quantification of 42 PI3K‐mTOR and MAPK phosphosites, gaining a so far unachieved in‐depth view mTOR signaling events linked to tyrosine kinase inhibitor resistance in non‐small cell lung cancer.
Using High Frequency Accelerometer and Mouse to Compensate for End-to-end Latency in Indirect Interaction

End-to-end latency corresponds to the temporal difference between a user input and the corresponding output from a system. It has been shown to degrade user performance in both direct and indirect interaction. If it can be reduced to some extend, latency can also be compensated through software compensation by trying to predict the future position of the cursor based on previous positions, velocities and accelerations. In this paper, we propose a hybrid hardware and software prediction technique specifically designed for partially compensating end-to-end latency in indirect pointing. We combine a computer mouse with a high frequency accelerometer to predict the future location of the pointer using Euler based equations. Our prediction method results in more accurate prediction than previously introduced prediction algorithms for direct touch. A controlled experiment also revealed that it can improve target acquisition time in pointing tasks.
Myostatin deficiency but not anti‐myostatin blockade induces marked proteomic changes in mouse skeletal muscle

Pharmacologic blockade of the myostatin (Mstn)/activin receptor pathway is being pursued as a potential therapy for several muscle wasting disorders. The functional benefits of blocking this pathway are under investigation, in particular given the findings that greater muscle hypertrophy results from Mstn deficiency arising from genetic ablation compared to post‐developmental Mstn blockade. Using high‐resolution MS coupled with SILAC mouse technology, we quantitated the relative proteomic changes in gastrocnemius muscle from Mstn knockout (Mstn−/−) and mice treated for 2‐weeks with REGN1033, an anti‐Mstn antibody. Relative to wild‐type animals, Mstn−/− mice had a two‐fold greater muscle mass and a >1.5‐fold change in expression of 12.0% of 1137 quantified muscle proteins. In contrast, mice treated with REGN1033 had minimal changes in muscle proteome (0.7% of 1510 proteins >1.5‐fold change, similar to biological difference 0.5% of 1310) even though the treatment induced significant 20% muscle mass increase. Functional annotation of the altered proteins in Mstn−/− mice corroborates the mutiple physiological changes including slow‐to‐fast fiber type switch. Thus, the proteome‐wide protein expression differs between Mstn−/− mice and mice subjected to specific Mstn blockade post‐developmentally, providing molecular‐level insights to inform mechanistic hypotheses to explain the observed functional differences.
Making Sense of Blockchain Applications: A Typology for HCI

Blockchain is an emerging infrastructural technology that is proposed to fundamentally transform the ways in which people transact, trust, collaborate, organize and identify themselves. In this paper, we construct a typology of emerging blockchain applications, consider the domains in which they are applied, and identify distinguishing features of this new technology. We argue that there is a unique role for the HCI community in linking the design and application of blockchain technology towards lived experience and the articulation of human values. In particular, we note how the accounting of transactions, a trust in immutable code and algorithms, and the leveraging of distributed crowds and publics around vast interoperable databases all relate to longstanding issues of importance for the field. We conclude by highlighting core conceptual and methodological challenges for HCI researchers beginning to work with blockchain and distributed ledger technologies.
Examining the Demand for Spam: Who Clicks?

Despite significant advances in automated spam detection, some spam content manages to evade detection and engage users. While the spam supply chain is well understood through previous research, there is little understanding of spam consumers. We focus on the demand side of the spam equation examining what drives users to click on spam via a large-scale analysis of de-identified, aggregated Facebook log data (n=600,000). We find (1) that the volume of spam and clicking norms in a users' network are significantly related to individual consumption behavior; (2) that more active users are less likely to click, suggesting that experience and internet skill (weakly correlated with activity level) may create more savvy consumers; and (3) we confirm previous findings about the gender effect in spam consumption, but find this effect largely corresponds to spam topics. Our findings provide practical insights to reduce demand for spam content, thereby affecting spam profitability.
Exercise Training Restores Cardiac MicroRNA-1 and MicroRNA-29c to Nonpathological Levels in Obese Rats

We previously reported that aerobic exercise training (AET) consisted of 10 weeks of 60-min swimming sessions, and 5 days/week AET counteracts CH in obesity. Here, we evaluated the role of microRNAs and their target genes that are involved in heart collagen deposition and calcium signaling, as well as the cardiac remodeling induced by AET in obese Zucker rats. Among the four experimental Zucker groups: control lean rats (LZR), control obese rats (OZR), trained lean rats (LZR + TR), and trained obese rats (OZR + TR), heart weight was greater in the OZR than in the LZR group due to increased cardiac intramuscular fat and collagen. AET seems to exert a protective role in normalizing the heart weight in the OZR + TR group. Cardiac microRNA-29c expression was decreased in OZR compared with the LZR group, paralleled by an increase in the collagen volumetric fraction (CVF). MicroRNA-1 expression was upregulated while the expression of its target gene NCX1 was decreased in OZR compared with the LZR group. Interestingly, AET restored cardiac microRNA-1 to nonpathological levels in the OZR-TR group. Our findings suggest that AET could be used as a nonpharmacological therapy for the reversal of pathological cardiac remodeling and cardiac dysfunction in obesity.
Overexpressing CYP71Z2 Enhances Resistance to Bacterial Blight by Suppressing Auxin Biosynthesis in Rice

Background The hormone auxin plays an important role not only in the growth and development of rice, but also in its defense responses. We’ve previously shown that the P450 gene CYP71Z2 enhances disease resistance to pathogens through regulation of phytoalexin biosynthesis in rice, though it remains unclear if auxin is involved in this process or not. Methodology and Principal Findings The expression of CYP71Z2 was induced by Xanthomonas oryzae pv. oryzae (Xoo) inoculation was analyzed by qRT-PCR, with GUS histochemical staining showing that CYP71Z2 expression was limited to roots, blades and nodes. Overexpression of CYP71Z2 in rice durably and stably increased resistance to Xoo, though no significant difference in disease resistance was detected between CYP71Z2-RNA interference (RNAi) rice and wild-type. Moreover, IAA concentration was determined using the HPLC/electrospray ionization/tandem mass spectrometry system. The accumulation of IAA was significantly reduced in CYP71Z2-overexpressing rice regardless of whether plants were inoculated or not, whereas it was unaffected in CYP71Z2-RNAi rice. Furthermore, the expression of genes related to IAA, expansin and SA/JA signaling pathways was suppressed in CYP71Z2-overexpressing rice with or without inoculation. Conclusions and Significance These results suggest that CYP71Z2-mediated resistance to Xoo may be via suppression of IAA signaling in rice. Our studies also provide comprehensive insight into molecular mechanism of resistance to Xoo mediated by IAA in rice. Moreover, an available approach for understanding the P450 gene functions in interaction between rice and pathogens has been provided.
Turning frequency in adult bedridden patients to prevent hospital‐acquired pressure ulcer: A scoping review

The aim of this study was to identify current research on turning frequencies of adult bed‐bound patients and inform future turning practices for hospitals based on evidence‐based practice. We undertook a scoping review framework that provided a transparent and systematic methodology using 8 electronic databases (CINAHL, PubMed, Cochrane Library, ScienceDirect, PsycINFO, Scopus, ProQuest, and Web of Science) to identify articles published from 2000 to 2016. Articles were included if they focused on the prevention of hospital‐acquired pressure ulcers related to the frequency of turning or repositioning of bed‐bound patients. Literature search and data extraction were performed independently by 3 authors. The study followed the PRISMA guidelines. In total, 911 articles were identified, of which 10 were eligible. Of the eligible articles, 8 studies could not reach a conclusion on the effective frequency of turning and duration for repositioning patients to prevent the development of pressure ulcers. Only 2 studies found significant differences among the intervention and control groups. Results regarding turning and repositioning schedules are inconclusive; however, the topic needs further exploration to improve the outdated guidelines surrounding pressure ulcer prevention. This may, in turn, make the work of nurses more efficient and make treatment cost‐effective for both the patients and the hospitals.
Population Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.

Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were collected from 7 different tree species located throughout the District of Columbia, consisting of 101 samples of symptomatic and asymptomatic foliage from 84 different trees. Five strains of the bacteria were identified. Consistent with prior data, these strains were host specific, with only one strain associated with members of the red oak family, one strain associated with American elm, one strain associated with American sycamore, and two strains associated with mulberry. Strains found for asymptomatic foliage were the same as strains from the symptomatic foliage on individual trees. Cross transmission of the strains was not observed at sites with multiple species of infected trees within an approx. 25 m radius of one another. X. fastidiosa strain specificity observed for each genus of tree suggests a highly specialized host-pathogen relationship.