Miracle-dz/UniFAR-FTUs huggingface dataset:
From Whole to Part: Reference-Based Representation for Clustering Categorical Data

Dissimilarity measures play a crucial role in clustering and, are directly related to the performance of clustering algorithms. However, effectively measuring the dissimilarity is not easy, especially for categorical data. The main difficulty of the dissimilarity measurement for categorical data is that its representation lacks a clear space structure. Therefore, the space structure-based representation has been proposed to provide the categorical data with a clear linear representation space. This representation improves the clustering performance obviously but only applies to small data sets because its dimensionality increases rapidly with the size of the data set. In this paper, we investigate the possibility of reducing the dimensionality of the space structure-based representation while maintaining the same representation ability. A lightweight representation scheme is proposed by taking a set of representative objects as the reference system (called the reference set) to position other objects in the Euclidean space. Moreover, a preclustering-based strategy is designed to select an appropriate reference set quickly. Finally, the representation scheme together with the $k$ -means algorithm provides an efficient method to cluster the categorical data. The theoretical and the experimental analysis shows that the proposed method outperforms state-of-the-art methods in terms of both accuracy and efficiency.
'Non-self' Mutation: Double-stranded RNA elicits antiviral pathogenic response in a Drosophila model of expanded CAG repeat neurodegenerative diseases.

Inflammation is activated prior to symptoms in neurodegenerative diseases, providing a plausible pathogenic mechanism. Indeed genetic and pharmacological ablation studies in animal models of several neurodegenerative diseases demonstrate that inflammation is required for pathology. However, while there is growing evidence that inflammation-mediated pathology may be the common mechanism underlying neurodegenerative diseases, including those due to dominantly inherited expanded repeats, the proximal causal agent is unknown. Expanded CAG.CUG repeat double stranded RNA causes inflammation-mediated pathology when expressed in Drosophila. Repeat dsRNA is recognized by Dicer2 as a foreign or 'non-self' molecule triggering both antiviral RNA and RNAi pathways. Neither of the RNAi pathway cofactors R2D2 nor loquacious are necessary, indicating antiviral RNA activation. RNA modification enables avoidance of recognition as 'non-self' by the innate inflammatory surveillance system. Human ADAR1 edits RNA conferring 'self' status and when co-expressed with expanded CAG.CUG dsRNA in Drosophila the pathology is lost. Cricket Paralysis Virus protein CrPV-1A is a known antagonist of Argonaute2 in Drosophila antiviral defense. CrPV-1A co-expression also rescues pathogenesis, confirming anti-viral-RNA response. Repeat expansion mutation therefore confers 'non-self' recognition of endogenous RNA, thereby providing a proximal, autoinflammatory trigger for expanded repeat neurodegenerative diseases.
Non-crossing partitions, non-nesting partitions and Coxeter sortable elements in types A and B

First, we investigate a generalization of the area statistic on Dyck paths for all crystallographic reflection groups. In particular, we explore Dyck paths of type B together with an area statistic and a major index. Then, we construct bijections between non-nesting and reverse non-crossing partitions for types A and B. These bijections simultaneously send the area statistic and the major index on non-nesting partitions to the length function and to the sum of the major index and the inverse major index on reverse non-crossing partitions. Finally, we construct bijections between non-nesting partitions and Coxeter sortable elements for types A and B having exactly the same properties.
Selective Autophagy Eats Up Invading Viruses

Autophagy is a cellular process by which cellular components are engulfed inside distinct double-membrane structures (autophagosomes) and shuttled to the lysosomes for degradation. In addition to non-selective, bulk degradation of cytoplasmic contents, autophagosomes can selectively recycle unwanted organelles, remove protein aggregates, and eliminate invading viruses [1-4]. In recent years, the subject of the pathophysiological function of selective autophagy has received increasing attention.
Semantic Proto-Role Labeling

The semantic function tags of Bonial, Stowe, and Palmer (2013) and the ordinal, multi-property annotations of Reisinger et al. (2015) draw inspiration from Ddowty's semantic proto-role theory. We approach proto-role labeling as a multi-label classification problem and establish strong results for the task by adapting a successful model of traditional semantic role labeling. We achieve a proto-role micro-averaged F1 of 81.7 using gold syntax and explore joint and conditional models of proto-roles and categorical roles. In comparing the effect of Bonial, Stowe, and Palmer's tags to PropBank ArgN-style role labels, we are surprised that neither annotations greatly improve proto-role prediction; however, we observe that ArgN models benefit much from observed syntax and from observed or modeled proto-roles while our models of the semantic function tags do not.
Reversible Dissolution of Microdomains in Detergent-Resistant Membranes at Physiological Temperature

The formation of lipid microdomains (“rafts”) is presumed to play an important role in various cellular functions, but their nature remains controversial. Here we report on microdomain formation in isolated, detergent-resistant membranes from MDA-MB-231 human breast cancer cells, studied by atomic force microscopy (AFM). Whereas microdomains were readily observed at room temperature, they shrunk in size and mostly disappeared at higher temperatures. This shrinking in microdomain size was accompanied by a gradual reduction of the height difference between the microdomains and the surrounding membrane, consistent with the behaviour expected for lipids that are laterally segregated in liquid ordered and liquid disordered domains. Immunolabeling experiments demonstrated that the microdomains contained flotillin-1, a protein associated with lipid rafts. The microdomains reversibly dissolved and reappeared, respectively, on heating to and cooling below temperatures around 37°C, which is indicative of radical changes in local membrane order close to physiological temperature.
Tolerogenic vaccine composited with islet-derived multipeptides and cyclosporin A induces pTreg and prevents Type 1 diabetes in murine model

ABSTRACT Regulatory T cells (Tregs) play a crucial role in the control of the initiation and progression of type 1 diabetes (T1D). Various immunological interventions including those to ex vivo expansion Tregs transfer, in vivo induction of peripherally derived Treg (pTreg) have been considered as promising approaches for T1D therapy. In this study, we developed a novel tolerogenic vaccine using four autoantigenic peptides of islet-derived with cyclosporine A (CsA) as the pTreg inducer, designated as GAD-IN+CsA. This vaccine immunized into prediabetic NOD mice subcutaneously could induce IL-10 and TGF-β expressing pTregs and lead to suppressing autoreactive T cells responses, resulting in the prevention of T1D in these animals. Furthermore, we demonstrated that CsA with autoantigenic peptides modulates dendritic cells (DCs) to become immature IL-10hiCD40lo DCs. Such modulated DCs could foster naïve CD4+CD25− T cell into Tregs when presenting antigen peptides in vitro. This novel approach offers an alternative strategy to induce pTregs to treat T1D.
On sum capacity of continuous-time overloaded CDMA systems

In this paper, the optimal design problem of overloaded code-division multiple-access (CDMA) systems is examined. Unlike previous results for chip or symbol synchronous systems, a continuous-time, band-limited, additive white Gaussian noise channel is considered for the multiple-access communications. First, non-information theoretic results are summarized, where the total transmit power is minimized, subject to lower bounds on the signal-to-interference-plus-noise ratio at the output of the linear minimum mean-squared error receivers. Second, the sum capacity is derived and shown to be the same as that of the optimal frequency-division multiple-access system, where each user's bandwidth is upper-bounded by the cycle frequency of the corresponding CDMA system. As the non-information theoretic results, the geometric procedure called multi-user constrained water-pouring leads to the optimal system that maximizes the sum rate. It is shown that orthogonal waveforms are assigned to oversized users and continuous-time equivalents of generalized Welch bound equality sequences are assigned to non-oversized users. A method to construct an optimal codebook is also proposed to be used in a CDMA signal modulator in each transmitter.
The Phylogeny and Evolutionary Timescale of Muscoidea (Diptera: Brachycera: Calyptratae) Inferred from Mitochondrial Genomes

Muscoidea is a significant dipteran clade that includes house flies (Family Muscidae), latrine flies (F. Fannidae), dung flies (F. Scathophagidae) and root maggot flies (F. Anthomyiidae). It is comprised of approximately 7000 described species. The monophyly of the Muscoidea and the precise relationships of muscoids to the closest superfamily the Oestroidea (blow flies, flesh flies etc) are both unresolved. Until now mitochondrial (mt) genomes were available for only two of the four muscoid families precluding a thorough test of phylogenetic relationships using this data source. Here we present the first two mt genomes for the families Fanniidae (Euryomma sp.) (family Fanniidae) and Anthomyiidae (Delia platura (Meigen, 1826)). We also conducted phylogenetic analyses containing of these newly sequenced mt genomes plus 15 other species representative of dipteran diversity to address the internal relationship of Muscoidea and its systematic position. Both maximum-likelihood and Bayesian analyses suggested that Muscoidea was not a monophyletic group with the relationship: (Fanniidae + Muscidae) + ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)), supported by the majority of analysed datasets. This also infers that Oestroidea was paraphyletic in the majority of analyses. Divergence time estimation suggested that the earliest split within the Calyptratae, separating (Tachinidae + Oestridae) from the remaining families, occurred in the Early Eocene. The main divergence within the paraphyletic muscoidea grade was between Fanniidae + Muscidae and the lineage ((Anthomyiidae + Scathophagidae) + (Calliphoridae + Sarcophagidae)) which occurred in the Late Eocene.
Sol-gel processing of nanostructured inorganic scintillating materials

The development of scintillating materials is believed to reach a new step by controlling their preparation on a nanometric level. Sol-Gel chemistry offers very unique tools for nanoscale mastering of the materials preparation. In particular, shaping of the materials as thin films or nanoparticles offers new application in medical imaging. The control of doping ions dispersion thanks to soft chemistry is also a great advantage of such synthetic routes. In this paper, we will review recent work devoted to the sol-gel preparation of inorganic scintillating materials. We will focus on the new possibilities and advantages offered by sol-gel chemistry for the preparation of new scintillators and improvement of existing ones.
Fat body–specific vitellogenin expression regulates host-seeking behaviour in the mosquito Aedes albopictus

The high vector competence of mosquitoes is intrinsically linked to their reproductive strategy because females need a vertebrate blood meal to develop large batches of eggs. However, the molecular mechanisms and pathways regulating mosquito host-seeking behaviour are largely unknown. Here, we test whether host-seeking behaviour may be linked to the female’s energy reserves, with low energy levels triggering the search for a nutrient-rich blood meal. Our results demonstrate that sugar feeding delays host-seeking behaviour in the invasive tiger mosquito Aedes albopictus, but the levels of energy reserves do not correlate with changes in host-seeking behaviour. Using tissue-specific gene expression analyses, we show for the first time, to our knowledge, that sugar feeding alone induces a transient up-regulation of several vitellogenesis-related genes in the female fat body, resembling the transcriptional response after a blood meal. Specifically, high expression levels of a vitellogenin gene (Vg-2) correlated with the lowest host-seeking activity of sugar-fed females. Knocking down the Vg-2 gene via RNA interference (RNAi) restored host-seeking behaviour in these females, firmly establishing that Vg-2 gene expression has a pivotal role in regulating host-seeking behaviour in young Ae. albopictus females. The identification of a molecular mechanism regulating host-seeking behaviour in mosquitoes could pave the way for novel vector control strategies aiming to reduce the biting activity of mosquitoes. From an evolutionary perspective, this is the first demonstration of vitellogenin genes controlling feeding-related behaviours in nonsocial insects, while vitellogenins are known to regulate caste-specific foraging and brood-care behaviours in eusocial insects. Hence, this work confirms the key role of vitellogenin in controlling feeding-related behaviours in distantly related insect orders, suggesting that this function could be more ubiquitous than previously thought.
Software Development in the Cloud: Exploring the Affordances of Platform-as-a-Service

Software development teams increasingly adopt platform-as-a-service (PaaS), i.e., cloud services that make software development infrastructure available over the internet. Yet, empirical evidence of whether and how software development work changes with the use of PaaS is difficult to find. We performed a grounded-theory study to explore the affordances of PaaS for software development teams. We find that PaaS enables software development teams to enforce uniformity, to exploit knowledge embedded in technology, to enhance agility, and to enrich jobs. These affordances do not arise in a vacuum. Their emergence is closely interwoven with changes in methodologies, roles, and norms that give rise to self-organizing, loosely coupled teams. Our study provides rich descriptions of PaaS-based software development and an emerging theory of affordances of PaaS for software development teams.
Too Much of a Good Thing? Causes and Consequences of Increases in Sugar Content of California Wine Grapes*

Abstract The sugar content of California wine grapes has increased significantly over the past 10–20 years, and this implies a corresponding increase in the alcohol content of wine made with those grapes. In this paper we develop a simple model of winegrape production and quality, including sugar content and other characteristics as choice variables along with yield. Using this model we derive hypotheses about alternative theoretical explanations for the phenomenon of rising sugar content of grapes, including effects of changes in climate and producer responses to changes in consumer demand. We analyze detailed data on changes in the sugar content of California wine grapes at crush to obtain insight into the relative importance of the different influences. We buttress this analysis of sugar content of wine grapes with data on the alcohol content of wine. (JEL Classification: Q54, Q19, D12, D22)
Early and Mid‐Term Outcomes of Patients Undergoing Coronary Artery Bypass Grafting in Ischemic Cardiomyopathy

Background Many observational studies and trials have shown that coronary artery bypass grafting improves the survival in patients with ischemic cardiomyopathy. However, these results are based on data generated from developed countries. Poor socioeconomic statuses, lack of uniformity in healthcare delivery, differences in risk profile, and affordability to access optimal health care are some factors that make the conclusions from these studies irrelevant to patients from India. Methods and Results One‐hundred and sixty‐two patients with severe left ventricular dysfunction (ejection fraction ≤35%) who underwent coronary artery bypass grafting from 2009 to 2017 were enrolled for this study. Mean age of the study population was 58.67±9.70 years. Operative mortality was 11.62%. Thirty day/in‐house composite outcome of stroke and perioperative myocardial infarction were 5.8%. The percentage of survival for 1 year was 86.6%, and 5‐year survival was 79.9%. Five‐year event‐free survival was 49.3%. The mean ejection fraction improved from 30.7±4.08% (range 18–35) to 39.9±8.3% (range 24–60). Lack of improvement of left ventricular function was a strong predictor of late mortality (hazard ratio, 21.41; CI 4.33–105.95). Even though there was a trend towards better early outcome in off‐pump CABG, the 5‐year survival rates were similar in off‐pump and on‐pump group (73.4% and 78.9%, respectively; P value 0.356). Conclusions We showed that coronary artery bypass grafting in ischemic cardiomyopathy was associated with high early composite outcomes. However, the 5‐year survival rates were good. Lack of improvement of left ventricular function was a strong predictor of late mortality.
A chart of failure risk for noninvasive ventilation in patients with COPD exacerbation

Knowing the likelihood of failure of noninvasive positive pressure ventilation (NPPV) in patients with exacerbation of chronic obstructive pulmonary disease (COPD) could indicate the best choice between NPPV and endotracheal intubation instituted earlier. For this purpose, two risk charts were designed (at admission and after 2 h of NPPV) that included all relevant measurable clinical prognostic indicators derived from a population representing the patients seen routinely in clinical practice. Risk stratification of NPPV failure was assessed in 1,033 consecutive patients admitted to experienced hospital units, including two intensive care units, six respiratory intermediate care units, and five general wards. NPPV was successful in 797 patients. Patients with a Glasgow Coma Score <11, acute physiology and chronic health evaluation (APACHE) II ≥29, respiratory rate ≥30 breaths·min−1 and pH at admission <7.25 have a predicted risk of failure >70%. A pH <7.25 after 2 h greatly increases the risk (>90%). The risk charts were validated on an independent group of 145 consecutive COPD patients treated with NPPV due to an acute ventilatory failure episode. To identify patients with a probability of failure >50%, the sensitivity and specificity were 33% and 96.7% on admission and 52.9% and 94.1% after 2 h of NPPV, respectively. The prediction chart, based on data from the current study, can function as a simple tool to predict the risk of failure of noninvasive positive pressure ventilation and thus improve clinical management of patients tailoring medical intervention.
What VR developers can learn from 20 years of UIMS

There is an assumption that VR development has not reached its maturity, in comparison to development of WIMP based applications. This essay studies some important results related to WIMP and VR development during the last 20 years, in particular in the fields of User Interface Management Systems (UIMS) and VR Frameworks, which could be an inspiration and also a guide for new research. In particular, we propose a change in the way we pursue research in this field, in order to allow the community to easily build on top of previous results.
Effects of Qili Qiangxin Capsule on AQP2, V2R, and AT1R in Rats with Chronic Heart Failure

Qili qiangxin capsule (QL), a traditional Chinese herbal compound, has been proved to be effective and safe for the treatment of chronic heart failure (CHF). Upregulation of aquaporin-2 (AQP2) accounts for the water retention in CHF. The aim of the present study was to evaluate the effects of QL on the expression of AQP2 in rats with CHF induced by acute myocardial infarction and to investigate the underlying mechanisms. The urine output of all rats was quantified and collected every day at the first week and the 4th week after administration of QL or Valsartan. The expression of AQP2, vasopressin type 2 receptor (V2R), and angiotensin II type 1 receptor (AT1R) were examined after treatment for 4 weeks. Urinary output increased significantly after administration of QL. Importantly, the protein expression of AQP2 and AQP2 phosphorylated at serine 256 (pS256-AQP2) was downregulated after administration of QL and Valsartan to CHF rats. Furthermore, QL reduced plasma arginine vasopressin (AVP) and angiotensin II (AngII) level and downregulated V2R and AT1R protein expression. Thus, QL exerts its diuretic effect and improves cardiac function in CHF rats by reversing the increases in both AQP2 and pS256-AQP2 expression. The possible mechanisms may involve inhibition of V2R and AT1R.
Reconfigurable processor for public-key cryptography

This paper proposes a novel processor architecture that provides a reconfigurable computing platform for modular exponentiation used in RSA and Diffle-Hellman public-key cryptography. The processor can operate autonomously to perform all operations required for modular exponentiation. A parallel-processing pipeline offers the versatility to perform any large-integer arithmetic. The processor can perform modular exponentiation using classical exponentiation, Montgomery multiplication and Barrett reduction. Hardware exponent receding is used to improve the efficiency of square-and-multiply algorithms by 15%. The performance of the processor is competitive in comparison to fixed functionality hardware implementations and is significantly faster than general purpose public-key cryptographic processors previously reported in the literature.
Unsupervised Learning of Reflexive and Action-Based Affordances to Model Adaptive Navigational Behavior

Here we introduce a cognitive model capable to model a variety of behavioral domains and apply it to a navigational task. We used place cells as sensory representation, such that the cells’ place fields divided the environment into discrete states. The robot learns knowledge of the environment by memorizing the sensory outcome of its motor actions. This is composed of a central process, learning the probability of state-to-state transitions by motor actions and a distal processing routine, learning the extent to which these state-to-state transitions are caused by sensory-driven reflex behavior (obstacle avoidance). Navigational decision making integrates central and distal learned environmental knowledge to select an action that leads to a goal state. Differentiating distal and central processing increases the behavioral accuracy of the selected actions and the ability of behavioral adaptation to a changed environment. We propose that the system can canonically be expanded to model other behaviors, using alternative definitions of states and actions. The emphasis of this paper is to test this general cognitive model on a robot in a real-world environment.