Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Variation of the Amino-Terminal Glutamine-Rich Domain in Drosophila Argonaute2 Is Not Associated with Developmental Defects

The Drosophila argonaute2 (ago2) gene plays a major role in siRNA mediated RNA silencing pathways. Unlike mammalian Argonaute proteins, the Drosophila protein has an unusual amino-terminal domain made up largely of multiple copies of glutamine-rich repeats (GRRs). We report here that the ago2 locus produces an alternative transcript that encodes a putative short isoform without this amino-terminal domain. Several ago2 mutations previously reported to be null alleles only abolish expression of the long, GRR-containing isoform. Analysis of drop out (dop) mutations had previously suggested that variations in GRR copy number result in defects in RNAi and embryonic development. However, we find that dop mutations genetically complement transcript-null alleles of ago2 and that ago2 alleles with variant GRR copy numbers support normal development. In addition, we show that the assembly of the central RNAi machinery, the RISC (RNA induced silencing complex), is unimpaired in embryos when GRR copy number is altered. In fact, we find that GRR copy number is highly variable in natural D. melanogaster populations as well as in laboratory strains. Finally, while many other insects share an extensive, glutamine-rich Ago2 amino-terminal domain, its primary sequence varies drastically between species. Our data indicate that GRR variation does not modulate an essential function of Ago2 and that the amino-terminal domain of Ago2 is subject to rapid evolution.
Ants might use different view-matching strategies on and off the route

SUMMARY Individual foraging ants are known to rely on views of their surroundings for route learning and for pinpointing goals. Different strategies have been proposed to explain how ants might process visual information for navigation, but little is known about the actual development and nature of the view-based strategies used by ants in complex natural environments. Here, we constrained the knowledge of Melophorus bagoti ants to either the nest vicinity or a curved route (length 10 m) and analysed their initial direction when released at both novel and familiar locations. In parallel, we used 360 deg pictures of the scene as a basis for modelling different navigational strategies. We propose here a new hypothesis based on skyline height comparison to explain how ants home from novel locations. Interestingly, this strategy succeeded well at novel locations but failed on familiar terrain. By contrast, the use of a visual compass strategy failed at novel locations but could explain the results on familiar routes. We suggest that ants might switch between skyline height comparison and a visual compass strategy, depending on whether they are on familiar terrain or not. How ants could switch between strategies and how their memories develop are discussed in turn.
Sequential source localization on graphs: A case study of cholera outbreak

Identifying the source of network diffusion is an important task in different applications such as epidemics management and understanding the propagation of trends over social networks. Observing a timestamp of infection of each node carries a cost, hence, the goal is to identify the source with the smallest number of observed nodes. When nodes for observations are selected dynamically, the timestamps of previously observed nodes can be used to determine which node should subsequently be observed. We propose an algorithm for sequential source localization, based on sequential multiple hypothesis testing and apply a criterion for node selection motivated by adaptive submodularity. We validate our approach on a real dataset of a cholera outbreak in a South African province in 2000, with the algorithm successfully identifying the first infected community.
Protein multiple sequence alignment benchmarking through secondary structure prediction

Motivation: Multiple sequence alignment (MSA) is commonly used to analyze sets of homologous protein or DNA sequences. This has lead to the development of many methods and packages for MSA over the past 30 years. Being able to compare different methods has been problematic and has relied on gold standard benchmark datasets of ‘true’ alignments or on MSA simulations. A number of protein benchmark datasets have been produced which rely on a combination of manual alignment and/or automated superposition of protein structures. These are either restricted to very small MSAs with few sequences or require manual alignment which can be subjective. In both cases, it remains very difficult to properly test MSAs of more than a few dozen sequences. PREFAB and HomFam both rely on using a small subset of sequences of known structure and do not fairly test the quality of a full MSA. Results: In this paper we describe QuanTest, a fully automated and highly scalable test system for protein MSAs which is based on using secondary structure prediction accuracy (SSPA) to measure alignment quality. This is based on the assumption that better MSAs will give more accurate secondary structure predictions when we include sequences of known structure. SSPA measures the quality of an entire alignment however, not just the accuracy on a handful of selected sequences. It can be scaled to alignments of any size but here we demonstrate its use on alignments of either 200 or 1000 sequences. This allows the testing of slow accurate programs as well as faster, less accurate ones. We show that the scores from QuanTest are highly correlated with existing benchmark scores. We also validate the method by comparing a wide range of MSA alignment options and by including different levels of mis‐alignment into MSA, and examining the effects on the scores. Availability and Implementation: QuanTest is available from http://www.bioinf. ucd.ie/download/QuanTest.tgz Contact: quan.le@ucd.ie Supplementary information: Supplementary data are available at Bioinformatics online.
Censorship-resistant and privacy-preserving distributed web search

The vast majority of Internet users are relying on centralized search engine providers to conduct their web searches. However, search results can be censored and search queries can be recorded by these providers without the user's knowledge. Distributed web search engines based on peer-to-peer networks have been proposed to mitigate these threats. In this paper we analyze the three most popular real-world distributed web search engines: Faroo, Seeks and Yacy, with respect to their censorship resistance and privacy protection. We show that none of them provides an adequate level of protection against an adversary with modest resources. Recognizing these flaws, we identify security properties a censorship-resistant and privacy-preserving distributed web search engine should provide. We propose two novel defense mechanisms called node density protocol and webpage verification protocol to achieve censorship resistance and show their effectiveness and feasibility with simulations. Finally, we elaborate on how state-of-the-art defense mechanisms achieve privacy protection in distributed web search engines.
Lymphovascular invasion is a high risk factor for stage I/II colorectal cancer: a systematic review and meta-analysis

The prognostic value of lymphovascular invasion (LVI) in stage I/II colorectal cancer (CRC) does not reach a consensus. To systematically assess prognostic significance of LVI, databases of PubMed, Web of Science, and Embase were searched from inception up to 10 Dec 2016. The pooled hazard ratio (HR) and 95% confidence intervals (CI) were used to determine the prognostic effects. Nineteen relevant studies including 9881 total patients were enrolled. Our results showed that LVI is significantly associated with poor prognosis in overall survival (OS) (HR=2.15, 95 % CI=1.72–2.68, P < 0.01) and disease-free survival (DFS) (HR=1.73, 95% CI=1.50–1.99, P < 0.01), which is similar in stage II patients. Further subgroup analysis revealed that the significance of the association between LVI and worse prognosis in CRC patients is not affected by below factors, including geographic setting, LVI positive rate, treatment, tumor site, and quality of the study. The current meta-analysis suggests that LVI may be a poor prognostic factor for stage I/II CRC patients.
Exploring Cross-cultural Differences in Persuasive Robotics

One of the fundamental aspects of social interaction is persuasion. It is a useful feature for a social robot to incorporate in its social behavior. Persuasiveness in human-robot interaction can be influenced by a number of factors including robot»s appearance and behavior. In this study, the effect of robot gender was investigated. The experiment was conducted in the university with a humanoid robot NAO interacting with local Kazakhstani citizens and foreign participants from Asia, Europe and North America. Robot introduced him/herself, made a persuasive appeal and offered to make a donation. During the experiment, robot»s gender was varied by changing its synthesized voice and name. The findings imply that the gender of robot has influenced participants» preferences in making donation. Specifically, female robot received more donations from female and male participants in comparison to a male robot. In addition, foreigners donated more money than locals. The overall results suggest that HRI designers could consider manipulating the robot»s gender when designing robots for persuasive applications.
Sleep Duration, Snoring Prevalence, Obesity, and Behavioral Problems in a Large Cohort of Primary School Students in Japan

Study Objectives Poor or short sleep and the presence of snoring indicative of sleep-disordered breathing (SDB) have been associated with behavioral problems in school-aged children. We examined the relationship between SDB, sleep duration, obesity risk, and behavioral characteristics in Japanese elementary school students using a large-scale survey. Methods We conducted a cross-sectional study of children enrolled in all 46 public primary schools in Matsuyama city, Japan. The children's parents or guardians completed a questionnaire that covered sleep habits, presence of SDB risk, and behavioral characteristics. Results In total, 24 296 responses were received (90% response rate). After excluding incomplete responses, we analyzed complete datasets for 17 769 children. Mean sleep duration decreased with age, as did the prevalence of pediatric SDB. We found an increased risk for the presence of SDB and short sleep among overweight/obese children. With SDB or short sleep, we observed significantly increased odds of restless behaviors, fidgety behaviors, and poor concentration in school. Conclusions Shorter sleep duration was associated with increased risk of obesity, and in turn, obesity increased SDB risk. Both short sleep duration and SDB risk were significantly associated with behavioral problems in school.
An Improvement for the Stability of Large-Margin Metric Learning for Partial Labelling Partitioning Problems

In this paper, a new framework for unsupervised partitioning problems are proposed in order to stabilize the performance of the Large-Margin Metric Learning method developed by Lajugie [lajugie et al. 2014] when the fraction of the given labels is low. The Large-Margin method could be used to deal with a wide range of partitioning problems such as clustering, image segmentation, video segmentation and change-detection problems but does not show robustness when applied to large set of data with a small number of labels. Hence, we combine the algorithm with the relevant component analysis algorithm [Bar-Hillel et al.2006] when the fraction of the labels is low and adhere to the original Large-Margin Method when the fraction is high. We also provide experiments to show that by implementing the new frame work, we can achieve more stable partitioning performance in synthetic examples.
Aging alters the expression of genes for neuroprotection and synaptic function following acute estradiol treatment

This study used microarray analysis to examine age‐related changes in gene expression 6 and 12 h following a single estradiol injection in ovariectomized mice. Estradiol‐responsive gene expression at the 6 h time point was reduced in aged (18 months) animals compared with young (4 months) and middle‐aged (MA, 12months) mice. Examination of gene clustering within biological and functional pathways indicated that young and MA mice exhibited increased expression of genes for cellular components of the synapse and decreased expression of genes related to oxidative phosphorylation and mitochondrial dysfunction. At the 12 h time point, estradiol‐responsive gene expression increased in aged animals and decreased in young and MA mice compared with the 6 h time point. Gene clustering analysis indicated that aged mice exhibited increased expression of genes for signaling pathways that are rapidly influenced by estradiol. The age differences in gene expression for rapid signaling pathways may relate to disparity in basal pathway activity and estradiol mediated activation of rapid signaling cascades. © 2009 Wiley‐Liss, Inc.
Resveratrol as a Growth Substrate for Bacteria from the Rhizosphere

ABSTRACT Resveratrol is among the best-known secondary plant metabolites because of its antioxidant, anti-inflammatory, and anticancer properties. It also is an important allelopathic chemical widely credited with the protection of plants from pathogens. The ecological role of resveratrol in natural habitats is difficult to establish rigorously, because it does not seem to accumulate outside plant tissue. It is likely that bacterial degradation plays a key role in determining the persistence, and thus the ecological role, of resveratrol in soil. Here, we report the isolation of an Acinetobacter species that can use resveratrol as a sole carbon source from the rhizosphere of peanut plants. Both molecular and biochemical techniques indicate that the pathway starts with the conversion of resveratrol to 3,5-dihydroxybenzaldehyde and 4-hydroxybenzaldehyde. The aldehydes are oxidized to substituted benzoates that subsequently enter central metabolism. The gene that encodes the enzyme responsible for the oxidative cleavage of resveratrol was cloned and expressed in Escherichia coli to establish its function. Its physiological role in the resveratrol catabolic pathway was established by knockouts and by the reverse transcription-quantitative PCR (RT-qPCR) demonstration of expression during growth on resveratrol. The results establish the presence and capabilities of resveratrol-degrading bacteria in the rhizosphere of the peanut plants and set the stage for studies to evaluate the role of the bacteria in plant allelopathy. IMPORTANCE In addition to its antioxidant properties, resveratrol is representative of a broad array of allelopathic chemicals produced by plants to inhibit competitors, herbivores, and pathogens. The bacterial degradation of such chemicals in the rhizosphere would reduce the effects of the chemicals. Therefore, it is important to understand the activity and ecological role of bacteria that biodegrade resveratrol near the plants that produce it. This study describes the isolation from the peanut rhizosphere of bacteria that can grow on resveratrol. The characterization of the initial steps in the biodegradation process sets the stage for the investigation of the evolution of the catabolic pathways responsible for the biodegradation of resveratrol and its homologs.
Speech Enhancement Based on Non-stationary Noise-driven Geometric Spectral Subtraction and Phase Spectrum Compensation

In this paper, a speech enhancement method based on noise compensation performed on short time magnitude as well phase spectra is presented. Unlike the conventional geometric approach (GA) to spectral subtraction (SS), here the noise estimate to be subtracted from the noisy speech spectrum is proposed to be determined by exploiting the low frequency regions of current frame of noisy speech rather than depending only on the initial silence frames. This approach gives the capability of tracking non-stationary noise thus resulting in a non-stationary noise-driven geometric approach of spectral subtraction for speech enhancement. The noise compensated magnitude spectrum from the GA step is then recombined with unchanged phase of noisy speech spectrum and used in phase compensation to obtain an enhanced complex spectrum, which is used to produce an enhanced speech frame. Extensive simulations are carried out using speech files available in the NOIZEUS database shows that the proposed method consistently outperforms some of the recent methods of speech enhancement when employed on the noisy speeches corrupted by street or babble noise at different levels of SNR in terms of objective measures, spectrogram analysis and formal subjective listening tests.
Novel hybrid design for microgrid control

This paper proposes a new hybrid control system for an AC microgrid. The system uses both centralised and decentralised strategies to optimize the microgrid energy control while addressing the challenges introduced by current technologies and applied systems in real microgrid infrastructures. The well-known 3-level control (tertiary, secondary, primary) is employed with an enhanced hierarchical design using intelligent agent-based components in order to improve efficiency, diversity, modularity, and scalability. The main contribution of this paper is dual. During normal operation, the microgrid central controller (MGCC) is designed to undertake the management of the microgrid, while providing the local agents with the appropriate constraints for optimal power flow. During MGCC fault, a peer-to-peer communication is enabled between neighbouring agents in order to make their optimal decision locally. The initial design of the control structure and the detailed analysis of the different operating scenarios along with their requirements have shown the applicability of the new system in real microgrid environments.
Functional Performance, Pain and Strength in Patients with Knee Osteoarthritis after Photobiomodulation on Femoral Quadriceps Muscles. Study Protocol

Background: Osteoarthritis (OA) is the most prevalent rheumatic diseases in the elderly and is associated with pain, stiffness, deformity and progressive loss of function. Physical therapy through kinesiotherapy, proprioceptive exercises and physical agents can improve symptoms related to OA. Objective: The objective of the present clinical trial was to assess the functional performance, pain and muscular strength in patients with knee OA after phototherapy in the quadriceps femoral muscle. Design: The study was a two-armed controlled randomized clinical trial. Setting: The setting for this trial will be a physiotherapy clinic. Participants: The study participants will be those who seek physiotherapy care unit spontaneously after receiving a diagnosis of knee osteoarthritis by a medical specialist. Intervention: Participants performed a rehabilitation protocol that consisted of sensorimotor training and muscle strengthening and stretching exercises, for 60 min, three times a week for 12 weeks. In addition to intervention with exercises, the Phototherapy group will receive phototherapeutic applications on the quadriceps femoral muscle while the placebo group will receive sham phototherapy application. Measurements: All patients will be assessed pre-and post-treatment with SF-36 (Short Form 36), WOMAC (Western Ontario and McMaster Universities Osteoarthritis Index), the Berg balance scale, VAS (Visual Analogue Scale), ROM (range of motion) and muscle strength assessment. Conclusion: If phototherapy is beneficial, the results of the study will help in the discussion of treatment guidelines for patients with knee OA focused on functional performance and analgesia combined to exercises and phototherapy. It may also help therapists to make clinical decisions based on high-quality studies.
A Comparative Proteomic Analysis Reveals a New Bi-Lobe Protein Required for Bi-Lobe Duplication and Cell Division in Trypanosoma brucei

A Golgi-associated bi-lobed structure was previously found to be important for Golgi duplication and cell division in Trypanosoma brucei. To further understand its functions, comparative proteomics was performed on extracted flagellar complexes (including the flagellum and flagellum-associated structures such as the basal bodies and the bi-lobe) and purified flagella to identify new bi-lobe proteins. A leucine-rich repeats containing protein, TbLRRP1, was characterized as a new bi-lobe component. The anterior part of the TbLRRP1-labeled bi-lobe is adjacent to the single Golgi apparatus, and the posterior side is tightly associated with the flagellar pocket collar marked by TbBILBO1. Inducible depletion of TbLRRP1 by RNA interference inhibited duplication of the bi-lobe as well as the adjacent Golgi apparatus and flagellar pocket collar. Formation of a new flagellum attachment zone and subsequent cell division were also inhibited, suggesting a central role of bi-lobe in Golgi, flagellar pocket collar and flagellum attachment zone biogenesis.
REAL TIME EVENT LOCATION DETECTION BASED MOBILITY PATTERN MODELLING FOR SOCIAL MEDIA USER MOBILITY ANALYSIS

Detection of important events in a region through social media has been a recent development with scope for multiple applications. One of the applications is the analysis of the mobility of the users in the region to adapt the energy and resources as per their movement. For this purpose, the travel or movement behaviour of the social media users is analysed through their posts and related messages. An efficient method of mobility pattern modelling named as Event Location based Mobility Pattern Modelling WebClickviz (ELMPM-WebClickviz) is proposed in this paper based on the event location detection. Initially the social media data are collected and preprocessed. Then the geographical as well as temporal information are extracted along with the time and distance parameters. Then the pattern modelling is initiated using Sequential Hierarchical pattern clustering which detects the continuous events from the user data along with the location of occurrence. Based on these results, the mobility behaviour can be modelled with higher accuracy. The evaluation results prove that the proposed model provides efficient mobility patter modelling to be utilized for the organizations and official concerns in fulfilling the resources and needs of the users of that location.