Miracle-dz/UniFAR-FTUs huggingface dataset:
Stochastic Bounds For Some Stochastic Optimisation Problems

We consider the path length optimisation for an acyclic graph model with discrete random delays attributed to the edges. This problem has been largely studied in the literature and the application of the stochastic ordering is not new. We aim here to give a comprehensible presentation of some kinds of bounds with a particular attention to their numerical analysis. We propose to bound the output distribution in order to overcome the distribution size explosion. The proposed methodology can be applied for other stochastic optimisation problems such as maximum flow, and more generally for the analysis of stochastic discrete event systems whose evolutions are defined by non decreasing operations.
SPRINTER: A Fast n-ary Join Query Processing Method for Complex OLAP Queries

The concept of OLAP query processing is now being widely adopted in various applications. The number of complex queries containing the joins between non-unique keys (called FK-FK joins) increases in those applications. However, the existing in-memory OLAP systems tend not to handle such complex queries efficiently since they generate a large amount of intermediate results or incur a huge amount of probe cost. In this paper, we propose an effective query planning method for complex OLAP queries. It generates a query plan containing n-ary join operators based on a cost model. The plan does not generate intermediate results for processing FK-FK joins and significantly reduces the probe cost. We also propose an efficient processing method for n-ary join operators. We implement the prototype system SPRINTER by integrating our proposed methods into an open-source in-memory OLAP system. Through experiments using the TPC-DS benchmark, we have shown that SPRINTER outperforms the state-of-the-art OLAP systems for complex queries.
Designing a Chatbot as a Mediator for Promoting Deep Self-Disclosure to a Real Mental Health Professional

Chatbots are becoming increasingly popular. One promising application for chatbots is to elicit people's self-disclosure of their personal experiences, thoughts, and feelings. As receiving one's deep self-disclosure is critical for mental health professionals to understand people's mental status, chatbots show great potential in the mental health domain. However, there is a lack of research addressing if and how people self-disclose sensitive topics to a real mental health professional (MHP) through a chatbot. In this work, we designed, implemented and evaluated a chatbot that offered three chatting styles; we also conducted a study with 47 participants who were randomly assigned into three groups where each group experienced the chatbot's self-disclosure at varying levels respectively. After using the chatbot for a few weeks, participants were introduced to a MHP and were asked if they would like to share their self-disclosed content with the MHP. If they chose to share, the participants had the option of changing (adding, deleting, and editing) the content they self-disclosed to the chatbot. Comparing participants' self-disclosure data the week before and the week after sharing with the MHP, our results showed that, within each group, the depth of participants' self-disclosure to the chatbot remained after sharing with the MHP; participants exhibited deeper self-disclosure to the MHP through a more self-disclosing chatbot; further, through conversation log analysis, we found that some participants made different edits on their self-disclosed content before sharing it with the MHP. Participants' interview and survey feedback suggested an interaction between participants' trust in the chatbot and their trust in the MHP, which further explained participants' self-disclosure behavior.
T-Cell Hyperactivation and Paralysis in Severe COVID-19 Infection Revealed by Single-Cell Analysis

Severe COVID-19 patients can show respiratory failure, T-cell reduction, and cytokine release syndrome (CRS), which can be fatal in both young and aged patients and is a major concern of the pandemic. However, the pathogenetic mechanisms of CRS in COVID-19 are poorly understood. Here we show single cell-level mechanisms for T-cell dysregulation in severe SARS-CoV-2 infection, and thereby demonstrate the mechanisms underlying T-cell hyperactivation and paralysis in severe COVID-19 patients. By in silico sorting CD4+ T-cells from a single cell RNA-seq dataset, we found that CD4+ T-cells were highly activated and showed unique differentiation pathways in the lung of severe COVID-19 patients. Notably, those T-cells in severe COVID-19 patients highly expressed immunoregulatory receptors and CD25, whilst repressing the expression of the transcription factor FOXP3 and interestingly, both the differentiation of regulatory T-cells (Treg) and Th17 was inhibited. Meanwhile, highly activated CD4+ T-cells express PD-1 alongside macrophages that express PD-1 ligands in severe patients, suggesting that PD-1-mediated immunoregulation was partially operating. Furthermore, we show that CD25+ hyperactivated T-cells differentiate into multiple helper T-cell lineages, showing multifaceted effector T-cells with Th1 and Th2 characteristics. Lastly, we show that CD4+ T-cells, particularly CD25-expressing hyperactivated T-cells, produce the protease Furin, which facilitates the viral entry of SARS-CoV-2. Collectively, CD4+ T-cells from severe COVID-19 patients are hyperactivated and FOXP3-mediated negative feedback mechanisms are impaired in the lung, while activated CD4+ T-cells continue to promote further viral infection through the production of Furin. Therefore, our study proposes a new model of T-cell hyperactivation and paralysis that drives pulmonary damage, systemic CRS and organ failure in severe COVID-19 patients.
A comparative study of isothermal nucleic acid amplification methods for SARS-CoV-2 detection at point of care

The COVID-19, caused by the novel coronavirus SARS-CoV-2, has broken out of control all over the globe and put the majority of the world under lockdown. There have been no specific antiviral medications for SARS-CoV-2 while vaccines are still under development. Thus, rapid diagnosis and necessary public health measures are currently key parts to contain the pandemic. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is the gold standard method for SARS-CoV-2 detection. However, this method is not suitable for point-of-care (POC) diagnosis because of the timeconsuming procedure, the requirements of biosafety conditions and expensive equipment. In this study, the colorimetric isothermal nucleic acid amplification tests (iNAATs) for SARS-CoV-2 based on loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and polymerase spiral reaction (PSR) were developed and compared. The three methods exhibited similar performance with the limit of detection (LOD) as low as just 1 copy per reaction when evaluated on the synthetic DNA fragments. The results can be read with naked eyes within 30 minutes without crossreactivity to closely related coronaviruses. When tested with SARS-CoV-2 extracted genomic-RNA, LAMP outperformed both CPA and PSR assays. Moreover, the direct detection of SARS-CoV-2 in simulated patient samples (oropharyngeal and nasopharyngeal swabs) by colorimetric iNAATs was also successful. Further preparation of the lyophilized reagents for LAMP reactions revealed that the freeze-dried, ready-to-use kit maintained the sensitivity and LOD value of the liquid assays. These results strongly indicate that the colorimetric lyophilized LAMP test kit developed herein is highly suitable for detecting SARS-CoV-2 at POC.
Locomotor activity rhythms in high arctic freshwater crustacean: Lepidurus arcticus (Branchiopoda; Notostraca)

All living organisms have “biological clocks” that regulate physiological and behavioural functions by means of rhythms similar to the geophysical rhythms of the earth; these rhythms have an evident adaptive value to enable organisms to anticipate and, hence, to prepare for predictable changes in their environment (King & Takahashi 2000). This occurs as interaction between the clocks and exogenous time cues (Zeitgebers), the most prominent of which is the 24-h light–dark (LD) cycle. However, in polar environments, the strength of this Zeitgebers is greatly reduced around the summer and winter solstices, when the sun never sets or never rises. The presence of circadian clocks is independent of the environmental conditions. There are recent evidences that when daily transitions of dusk and dawn are not present, reindeer and ptarmigan that live in the Arctic do not exhibit circadian rhythms in their behaviour and physiology. Free-ranging reindeer do not exhibit 24-h locomotor activity rhythms in summer and winter (continuous light and continuous darkness). Differently, during the equinoxes, animals express a circadian regulation of locomotor activity (van Oort et al. 2005, 2007). Seasonal absence of circadian rhythmicity has been recorded also in the daily activity of the Svalbard ptarmigan (Stokkan et al. 1986; Reierth & Stokkan 1998). New molecular and hormonal evidence suggest that reindeer living at high latitudes in the Arctic lack the underlying biological clock necessary for generating circadian rhythmicity (Stokkan et al. 2007; Lu et al. 2010). The diversity of behavioural responses, even within the limited number of species tested, is surprising and suggests that several factors may be involved in regulating circadian variability. It has been proposed that circadian clocks can be adaptively modified to enable species-specific time-keeping under polar conditions (Daan & Aschoff 1975; van Oort et al. 2007; Lu et al. 2010; Bloch et al. 2013). Thereby, clocks would be “fitted” to specific aspects of the ecology and behaviour of an organism. Animals everywhere are confronted by environments that demand specialized behavioural and metabolic responses; for those of us intent on understanding the adaptive significance of clocks and rhythms, arctic organisms represent an excellent model in chronobiological studies.
Perspectives and predictions on the microbial ecology of the hyporheic zone

1. Studies of hyporheic microbial ecology have suggested an important role for hyporheic microbial processes in stream ecosystem functioning. Using evidence from microbial communities in other aquatic habitats, some predictions are made concerning the diversity of microbial types and microbial processes likely to occur in the hyporheic zone, and the relative importance of these various types to the hyporheic ecosystem. 2. It is predicted that the biofilm growth form of interstitial micro-organisms will create a variety of microniches, allowing coexistence of a great diversity of microbial types, and promoting the activity of some otherwise poor competitors. It is further predicted that the confluence of reduced groundwaters and aerobic surface waters will favour chemolithotrophic processes in the hyporheic zone, but that these will contribute significantly to hyporheic production only if surface water is very low in dissolved organic carbon, or the groundwater is extremely reduced, such as by the influence of riparian wetlands. A variety of anaerobic respiratory pathways, such as nitrate, ferric ion, sulphate and even methanogenic respiration will be employed in the hyporheic zone, with biofilm dynamics permitting these to occur even in aerobic sediments. Anaerobic pathways may account for a significant proportion of total hyporheic organic matter mineralization. 3. The role of fungi in hyporheic dynamics is, as yet, almost completely unstudied. However, it is expected that they will be important in breaking down buried particulate organic matter (POM), which may account for a large proportion of total stream POM. 4. Physicochemical conditions in hyporheic sediments appear to be highly heterogeneous, and this heterogeneity may be very important in the cycling of certain nutrients, especially nitrogen, which involves a series of steps requiring different conditions. 5. Various new techniques are now available by which biofilm dynamics and in situ microbial processes may be measured. Studies are recommended of intact microbial communities both at the microscale of the biofilm and at the scale of the heterogeneities occurring in hyporheic sediments. Studies are needed that measure actual rates of microbial processes under in situ conditions.
The evolutionary loss of aerenchyma limits both realized and fundamental ecohydrological niches in the Cape reeds (Restionaceae)

The basic physiological mechanisms that determine the niche limits, and so the local ranges, of species are often poorly understood. Here, we assessed whether the presence of root aerenchyma can account for both the fundamental and realized ecohydrological niche in the Restionaceae. We documented the ability to make aerenchyma of almost 300 of the c. 350 South African Restionaceae species with the help of field observations, cultivation experiments and herbarium collections, and correlated this information with the ecohydrological niche of the species. We used a diversity of sampling approaches to account for variation in both aerenchyma and habitat at individual, population and species level. Tolerance of waterlogging in species with and without aerenchyma was investigated experimentally. To account for phylogenetic relatedness, the evolution of both aerenchyma and the ecohydrological niche was explored in the context of an almost complete species‐level phylogeny using both parsimony and maximum likelihood optimization methods. We showed that the presence of aerenchyma was correlated with the ecohydrological niche at population and at species level, and after phylogenetic correction. Most individuals of non‐aerenchymatous species died when waterlogged, whereas most species with aerenchyma were waterlogging tolerant. This indicates that waterlogging acts as an environmental filter that excludes non‐aerenchymatous species from these conditions. The absence, and to a certain degree also the presence, of aerenchyma predicts both the field‐observed realized and experimentally determined fundamental ecohydrological niche. Aerenchyma was ancestrally present as inferred by both parsimony and maximum likelihood reconstruction and showed a strong phylogenetic signal with frequent losses but few gains. The ecohydrological niche was evolutionary more labile, with niche changes in many evolutionary lineages. Changes from wetland to dry habitats were reconstructed in species with aerenchyma, whereas the reverse change was never inferred for species that had lost aerenchyma. Synthesis. Our study provides evidence that functional traits can effectively predict species niches, and evolution of these may constrain the habitats available to the clades. We underpin the importance of understanding the causal driver of the local distribution of species for making robust predictions of species range shifts under climate change.
Potencial genético da população de milho UFV 7 para o melhoramento em Minas Gerais

The objective was to assess the genetic potential of maize population UFV 7 for breeding in Minas Gerais, Brazil. Three experiments were installed with the maize population UFV 7 in the three regions of Minas Gerais, in the harvest of 2006/2007. There was genotype x environment interaction for all characters. It was observed genetic variability for grain yield, plant height and ear height in maize population UFV 7, in the three regions. The Southeast region was where the maize population UFV 7 had the highest parameters. The population UFV 7 presented high grain yield, 9 112kg ha-1 in the Southeast, average grain yield, 6 510kg ha-1 in the West and low, 4 572kg ha-1 in the Central Region. Heritability estimate and CVg / CVe for grain yield were higher than 60% and 1.00, respectively. Grain yield had significant and positive genetic correlation with plant height and ear height, in Western and Central, and the prolificacy in Central and Southeast. For maize population UFV 7 it was conclude that it has potential for extraction of lines in the Central Region; it has the potential for immediate use in the Southeast and for new cycles selection in the Western Region of Minas Gerais. The selection for PG provides an indirect increase in plant height and ear height, in the West and Central.
The Perfect Storm: Gene Tree Estimation Error, Incomplete Lineage Sorting, and Ancient Gene Flow Explain the Most Recalcitrant Ancient Angiosperm Clade, Malpighiales

The genomic revolution offers renewed hope of resolving rapid radiations in the Tree of Life. The development of the multispecies coalescent (MSC) model and improved gene tree estimation methods can better accommodate gene tree heterogeneity caused by incomplete lineage sorting (ILS) and gene tree estimation error stemming from the short internal branches. However, the relative influence of these factors in species tree inference is not well understood. Using anchored hybrid enrichment, we generated a data set including 423 single-copy loci from 64 taxa representing 39 families to infer the species tree of the flowering plant order Malpighiales. This order alone includes nine of the top ten most unstable nodes in angiosperms, and the recalcitrant relationships along the backbone of the order have been hypothesized to arise from the rapid radiation during the Cretaceous. Here, we show that coalescent-based methods do not resolve the backbone of Malpighiales and concatenation methods yield inconsistent estimations, providing evidence that gene tree heterogeneity is high in this clade. Despite high levels of ILS and gene tree estimation error, our simulations demonstrate that these two factors alone are insufficient to explain the lack of resolution in this order. To explore this further, we examined triplet frequencies among empirical gene trees and discovered some of them deviated significantly from those attributed to ILS and estimation error, suggesting gene flow as an additional and previously unappreciated phenomenon promoting gene tree variation in Malpighiales. Finally, we applied a novel method to quantify the relative contribution of these three primary sources of gene tree heterogeneity and demonstrated that ILS, gene tree estimation error, and gene flow contributed to 15%, 52%, and 32% of the variation, respectively. Together, our results suggest that a perfect storm of factors likely influence this lack of resolution, and further indicate that recalcitrant phylogenetic relationships like the backbone of Malpighiales may be better represented as phylogenetic networks. Thus, reducing such groups solely to existing models that adhere strictly to bifurcating trees greatly oversimplifies reality, and obscures our ability to more clearly discern the process of evolution.
DNAE-GAN: Noise-free acoustic signal generator by integrating autoencoder and generative adversarial network

Linear predictive coding is an extremely effective voice generation method that operates through simple process. However, linear predictive coding–generated voices have limited variations and exhibit excessive noise. To resolve these problems, this article proposes an artificial intelligence model that combines a denoise autoencoder with generative adversarial networks. This model generates voices with similar semantics through the random input from the latent space of generator. The experimental results indicate that voices generated exclusively by generative adversarial networks exhibit excessive noise. To solve this problem, a denoise autoencoder was connected to the generator for denoising. The experimental results prove the feasibility of the proposed voice generation method. In the future, this method can be applied in robots and voice generation applications to increase the humanistic language expression ability of robots and enable robots to demonstrate more humanistic and natural speaking performance.
The 2004 Sumatra tsunami effect on the Itajaí-Açu estuary water level, Santa Catarina, Brazil

December, 2004 off the coast of Sumatra, in the Indian Ocean, was generated by a megathrust earthquake of magnitude 9.3 on the Richter scale, and felt worldwide (Fig. 1A; TITOV et al., 2005). It was the longest-lasting ever recorded in history, of around 600 seconds, giving rise to a 1,500 km long failure in the seabed (NIO, 2011). The earthquake produced the largest trans-oceanic tsunami in over 40 years, and killed more people than any other tsunami in recorded history (NOAA, 2010), in Indonesia, Sri Lanka, India, Thailand, Myanmar and Somalia. According to Titov et al. (2005), the recorded worldwide effects revealed the unprecedented, truly global reach of the waves generated on 26
High pre- and postoperative symptom burden in non-responders to total knee arthroplasty

Objectives One in five patients does not improve in pain with walking (non-responders) 12 months after total knee arthroplasty (TKA). This longitudinal study investigated a broad range of symptoms before and after TKA and evaluated possible differences in symptom distress between responders and non-responders with regards to pain with walking after TKA. Methods Prior to TKA surgery, 182 patients completed a demographic questionnaire and the Memorial Symptom Assessment Scale—Short Form (MSAS-SF). The MSAS-SF was repeated 12 months following TKA. Clinical data were extracted from medical records. Patients were categorized as responders or non-responders based on their trajectories of pain with walking assessed prior to surgery, on postoperative day 4, at 6 weeks, and at 3 and 12 months. Results Overall, the most distressful preoperative symptoms were pain, lack of energy, difficulty sleeping, feeling drowsy, worrying, feeling bloated, and problems with sexual interest or activity. However, compared with patients classified as responders to TKA, non-responders had higher total symptom distress scores both preoperatively and 12 months postoperatively. Preoperatively, non-responders scored higher than responders on five of the seven most distressing symptoms (i.e., all except difficulty sleeping and feeling bloated), and 12 months postoperatively, non-responders scored higher than responders on six of the seven most distressing symptoms (i.e., all but feeling bloated). In a multivariate analysis, higher preoperative distress scores for pain and problems with sexual interest or activity were significant predictors of non-response to TKA, controlling for other relevant factors. Conclusions Patients’ preoperative symptom burden may be a useful indicator of their risk for non-improvement following TKA surgery. Future studies need to evaluate the effect of reducing patients’ preoperative symptom burden on TKA outcomes.
Fumigant Toxicity of Citruspeel Oils against Adult and Immature Stages of Storage Insect Pests

The biological action of citruspeel oils was shown to depend on a strong fumigant action. Bioassays conducted in air-tight glass chambers showed that all the six citrus oils tested had vapour toxicity towards adults of Callosobruchus maculatus F. , Sitophilus zeamais Motsch. and Dermestes maculatus Deg. The 24-h LC50 value of limepeel oil (a typical citrus oil) vapour against C. Maculatus was 7·99 μl litre−1 which made it 1·5 and 1·6 times less toxic against the smaller S. zeamais and the larger D. maculatus adult insects. When immature stages were fumigated, limepeel oil vapour had 24-h LC50 values of 7·8 and 21·5 μl litre−1 against eggs of C. maculatus and D. maculatus respectively, and 9·1, 17·8 and 23·1, 23·9 μl litre−1 against early larvae, pupae of C. maculatus and late larvae, pupae of D. maculatus respectively. X-ray studies showed that fumigated C. maculatus larvae within cowpea grains died immediately without further development. The bioactivities of five other citruspeel oils were similar to that of limepeel oil. Bioassays showed that sorption of citruspeel oil fumes occurred in the presence of grains or strips of dried fish, and that this tended to reduce the amount available for fumigant action outside the materials. The problems presented by sorption may hinder the development of citrus oils into practical fumigants for large-scale treatments of stored commodities.