Miracle-dz/UniFAR-FTUs huggingface dataset:
To Err...

As noted science fiction author Robert Heinlein once said: "Man is not a rational animal, he is a rationalizing animal. " [3] As recent work in behavioral economics has made clear, our irrationality is not random; we are irrational in predictable ways [4]. Despite this, many "human-centered" systems do not leverage this predictable irrationality in a way that is potentially productive for users. Hypertext research has its roots in the field of human computer interaction. Some of the most influential early writers in hypertext (e.g., Bush [1] and Engelbart [2]) described hypertext systems as ones that would extend and augment human capabilities. This foundational perspective on hypertext is still well-evidenced in some of the most recent research. Bush focused largely on extending human memory; Engelbart on augmenting human intellect. For these two pioneers, as well as a host of other hypertext researchers, the key aspect of hyper-text that allows it to augment humans so well is its rich under-standing of structure and the computations in and around it. It is practically axiomatic within the field that this rich structure is somehow closer to "how humans think," though, as with most axioms, exactly why or how this is so is never fully and satisfactorily explained. Instead, the hypertext field relies on argument from example: non-linear traversals of information spaces (as opposed to an artificial linearity imposed by technologies such as writing) or emergent spatial organization of information (as opposed to prematurely formal organizations such as outlines). These examples (and others) work from generally "correct" forms of human thinking. Hypertext researchers, for example, do not claim that non-linear traversals of information spaces augment human intellect because some of the traversed links are faulty. On the contrary, linear representations are in some sense "defective" because they cannot represent the inherently non-linear thinking engaged in by humans, this "defectiveness" apparently attributable to a failure to capture useful associations that are (or could usefully be) present in the mind of the traverser. However, if fidelity of representation is the basis of the belief that hypertext can augment human thought, should we not also build into our understanding of structure the predictable biases we know are present? In this talk, we will explore the idea of accounting for the types of predictable irrationality discussed by behavioral economists in the understanding of hypertext structure. How can we model our biases? Does this bring us closer to accurate representations of human thought? Can we, in turn, find new applications for hypertext based not only on non-linear, emergent and rich structures, but ones that are flawed in a predictable way?
Unsupervised Dictionary Learning via a Spiking Locally Competitive Algorithm

A new class of neuromorphic processors promises to provide fast and power-efficient execution of spiking neural networks with on-chip synaptic plasticity. This efficiency derives in part from the fine-grained parallelism as well as event-driven communication mediated by spatially and temporally sparse spike messages. Another source of efficiency arises from the close spatial proximity between synapses and the sites where their weights are applied and updated. This proximity of compute and memory elements drastically reduces expensive data movements but imposes the constraint that only local operations can be efficiently performed, similar to constraints present in biological neural circuits. Efficient weight update operations should therefore only depend on information available locally at each synapse as non-local operations that involve copying, taking a transpose, or normalizing an entire weight matrix are not efficiently supported by present neuromorphic architectures. Moreover, spikes are typically non-negative events, which imposes additional constraints on how local weight update operations can be performed. The Locally Competitive Algorithm (LCA) is a dynamical sparse solver that uses only local computations between non-spiking leaky integrator neurons, allowing for massively parallel implementations on compatible neuromorphic architectures such as Intel's Loihi research chip. It has been previously demonstrated that non-spiking LCA can be used to learn dictionaries of convolutional kernels in an unsupervised manner from raw, unlabeled input, although only by employing non-local computation and signed non-spiking outputs. Here, we show how unsupervised dictionary learning with spiking LCA (S-LCA) can be implemented using only local computation and unsigned spike events, providing a promising strategy for constructing self-organizing neuromorphic chips.
The Presence of a CMV Immunodominant Allele in the Recipient Is Associated With Increased Survival in CMV Positive Patients Undergoing Haploidentical Hematopoietic Stem Cell Transplantation

Specific major histocompatibility (MHC) class I alleles dominate anti-CMV responses in a hierarchal manner. These CMV immunodominant (IMD) alleles are associated with a higher magnitude and frequency of cytotoxic lymphocyte responses as compared to other human leukocyte antigen (HLA) alleles. CMV reactivation has been associated with an increased incidence of graft-vs.-host disease and non-relapse mortality, as well as protection from relapse in HLA-matched HSCT settings. Less is known about the impact of CMV reactivation on these major outcomes after haploidentical (HI) HSCT, an increasingly applied therapeutic option. In HI HSCT, the efficiency of the immune response is decreased due to the immune suppression required to cross the MHC barrier as well as MHC mismatch between presenting and responding cells. We hypothesized that the presence of a CMV IMD allele would increase the efficiency of CMV responses after HI HSCT potentially impacting CMV-related outcomes. In this retrospective, multivariable review of 216 HI HSCT patients, we found that CMV+ recipients possessing at least 1 of 5 identified CMV IMD alleles had a lower hazard of death (HR = 0.40, p = 0.003) compared to CMV+ recipients not possessing a CMV IMD allele, and an overall survival rate similar to their CMV– counterparts. The analysis delineated subgroups within the CMV+ population at greater risk for death due to CMV reactivation.
The T-cell Response to Epstein-Barr Virus–New Tricks From an Old Dog

Epstein-Barr virus (EBV) infects most people and establishes life-long infection controlled by the host's immune system. The genetic stability of the virus, deep understanding of the viral antigens and immune epitopes recognized by the host's T-cell system and the fact that recent infection can be identified by the development of symptomatic infectious mononucleosis makes EBV a powerful system in which to study human immunology. The association between EBV and multiple cancers also means that the lessons learned have strong translational potential. Increasing evidence of a role for resident memory T-cells and non-conventional γδ T-cells in controlling EBV infection suggests new opportunities for research and means the virus will continue to provide exciting new insights into human biology and immunology into the future.
A simple multi-armed nearest-neighbor bandit for interactive recommendation

The cyclic nature of the recommendation task is being increasingly taken into account in recommender systems research. In this line, framing interactive recommendation as a genuine reinforcement learning problem, multi-armed bandit approaches have been increasingly considered as a means to cope with the dual exploitation/exploration goal of recommendation. In this paper we develop a simple multi-armed bandit elaboration of neighbor-based collaborative filtering. The approach can be seen as a variant of the nearest-neighbors scheme, but endowed with a controlled stochastic exploration capability of the users' neighborhood, by a parameter-free application of Thompson sampling. Our approach is based on a formal development and a reasonably simple design, whereby it aims to be easy to reproduce and further elaborate upon. We report experiments using datasets from different domains showing that neighbor-based bandits indeed achieve recommendation accuracy enhancements in the mid to long run.
Effect of a Moderate-Intensity Aerobic Training on Joint Biomarkers and Functional Adaptations in Rats Subjected to Induced Knee Osteoarthritis

Background Knee osteoarthritis (kOA) is a common chronic disease that induces changes in redox status and inflammatory biomarkers, cell death, and motor impairment. Aerobic training can be a non-pharmacological alternative to prevent the progression of the disease. Objective To evaluate the effects of an 8 weeks moderate-intensity treadmill aerobic training program on redox status and inflammatory biomarkers and motor performance in kOA-like changes induced by monosodium iodoacetate (MIA) in rats. Methods Twenty-seven rats were randomly divided into three groups: SHAM; induced kOA (OA); and induced kOA + aerobic training (OAE). Motor performance was evaluated by the number of falls on rotarod test, the total time of displacement and the number of failures on a 100 cm footbridge. Data for cytokines and histology were investigated locally, whereas plasma was used for redox status biomarkers. Results The OA group, compared to the SHAM group, increased 1.13 times the total time of displacement, 6.05 times the number of failures, 2.40 times the number of falls. There was also an increase in cytokine and in thiobarbituric acid reactive substances (TBARS) (IL1β: 5.55-fold, TNF: 2.84-fold, IL10: 1.27-fold, IL6: 1.50-fold, TBARS: 1.14-fold), and a reduction of 6.83% in the total antioxidant capacity (FRAP), and of 35% in the number of chondrocytes. The aerobic training improved the motor performance in all joint function tests matching to SHAM scores. Also, it reduced inflammatory biomarkers and TBARS level at values close to those of the SHAM group, with no change in FRAP level. The number of falls was explained by IL1β and TNF (58%), and the number of failures and the total time of displacement were also explained by TNF (29 and 21%, respectively). Conclusion All findings indicate the efficacy of moderate-intensity aerobic training to regulate inflammatory biomarkers associated with improved motor performance in induced kOA-like changes, thus preventing the loss of chondrocytes.
Exposure in vivo Induced Changes in Neural Circuitry for Pain-Related Fear: A Longitudinal fMRI Study in Chronic Low Back Pain

Exposure in vivo (EXP) is a cognitive-behavioral treatment aimed at reducing pain-related fear in chronic pain, and has proven successful in reducing pain-related disability in patients with chronic low back pain (cLBP). The current longitudinal study aimed to reveal the neural correlates of changes in pain-related fear as a result of EXP. Twenty-three patients with cLBP were included in this study. Patients with cLBP underwent MRI scanning pre-treatment (pre-EXP), post-treatment (post-EXP), and 6 months after end of treatment (FU-EXP). Pain-free controls were scanned at two time points. In the scanner, participants were presented with pictures involving back-related movements, evoking pain-related fear in patients. Pre-treatment, functional MRI revealed increased activation in right posterior insula and increased deactivation in medial prefrontal cortex (mPFC) in patients compared to controls. Post-treatment, patients reported reduced fear and pre-EXP group differences were no longer present. Contrasting pre- to post- and FU-EXP in patients revealed that stimulus-evoked neural responses changed in sensorimotor as well as cognitive/affective brain regions. Lastly, exploratory analyses revealed a tendency toward an association between changes in neural activation and changes in fear ratings, including the hippocampus and temporal lobe (pre- to post-EXP changes), and mPFC and posterior cingulate cortex (pre- to FU-EXP changes). Taken together, we show evidence that neural circuitry for pain-related fear is modulated by EXP, and that changes are associated with self-reported decreases in pain-related fear.
Adaptive view and illumination planning for SVBRDF measurement of complicated three-dimensional objects

Abstract. Appearance attributes of a three-dimensional (3-D) object, including reflection and color, are modeled as a spatially varying bidirectional reflectance distribution function (SVBRDF). However, a considerable number of images of the object are required to accurately define an SVBRDF when it exhibits complicated geometric components, thereby leading to a considerable amount of time to acquire, store, and process them. We propose a method to considerably decrease the number of images for SVBRDF modeling while maintaining the quality of the model that is achieved with several images. We introduce an acquisition score and its corresponding objective function by considering the local geometry and reflectance properties to estimate the optimal view and illumination directions for the image acquisition in which an object is measured with a reduced number of images. The captured images are subsequently processed to obtain an SVBRDF of the object. The experimental results demonstrate that the proposed method measures the appearance of a 3-D object with complicated shapes by using a few hundred images and efficiently produces an SVBRDF of the object with complicated shapes. The results indicate that the proposed method photorealistically renders an object with fewer artifacts than existing methods when any arbitrary view and illumination directions are given.
Cellular functions and molecular mechanisms of non-lysine ubiquitination

Protein ubiquitination is of great cellular importance through its central role in processes such as degradation, DNA repair, endocytosis and inflammation. Canonical ubiquitination takes place on lysine residues, but in the past 15 years non-lysine ubiquitination on serine, threonine and cysteine has been firmly established. With the emerging importance of non-lysine ubiquitination, it is crucial to identify the responsible molecular machinery and understand the mechanistic basis for non-lysine ubiquitination. Here, we first provide an overview of the literature that has documented non-lysine ubiquitination. Informed by these examples, we then discuss the molecular mechanisms and cellular implications of non-lysine ubiquitination, and conclude by outlining open questions and future perspectives in the field.
Expression Level Dominance and Homeolog Expression Bias in Recurrent Origins of the Allopolyploid Fern Polypodium hesperium

Abstract. Allopolyploidization is a common mode of speciation in ferns with many taxa having formed recurrently from distinct hybridization events between the same parent species. Each hybridization event marks the union of divergent parental gene copies, or homeologs, and the formation of an independently derived lineage. Little is known about the effects of recurrent origins on the genomic composition and phenotypic variation of allopolyploid fern taxa. To begin to address this knowledge gap, we investigated gene expression patterns in two naturally formed, independently derived lineages of the allotetraploid fern Polypodium hesperium relative to its diploid progenitor species, Polypodium amorphum and Polypodium glycyrrhiza. Using RNA-sequencing to survey total gene expression levels for 19194 genes and homeolog-specific expression for 1073 genes, we found that, in general, gene expression in both lineages of P. hesperium was biased toward P. amorphum—both by mirroring expression levels of P. amorphum and preferentially expressing homeologs derived from P. amorphum. However, we recovered substantial expression variation between the two lineages at the level of individual genes and among individual specimens. Our results align with similar transcriptome profile studies of angiosperms, suggesting that expression in many allopolyploid plants reflects the dominance of a specific parental subgenome, but that recurrent origins impart substantial expression, or phenotypic, variation to allopolyploid taxa.
Humidity-dependent colour change in the green forester moth, Adscita statices

The colours of insects serve important visual functions in aiding mate recognition, camouflage and warning. The display of insects is usually static, as cuticle coloration does not (or hardly) change during the lifespan of a mature imago form. Here, we describe a case of humidity-dependent, brilliant coloration in the green forester moth, Adscita statices. We show, by employing spectroscopic and ultrastructural methods, that the moth's colour results from the interference of incident light with an unusual hydrophilic melanized-chitin multilayer present in the wing scales. Humidity changes in the environment affect the multilayer properties, causing a significant shift of the green-peaking reflectance in the dry state to a rusty colour when damp, resulting in the strong colour change between day and dusk or dawn.
The conundrum of species delimitation: a genomic perspective on a mitogenetically super-variable butterfly

The Palaearctic butterfly Melitaea didyma stands out as one of the most striking cases of intraspecific genetic differentiation detected in Lepidoptera: 11 partially sympatric mitochondrial lineages have been reported, displaying levels of divergence of up to 7.4%. To better understand the evolutionary processes underlying the diversity observed in mtDNA, we compared mtDNA and genome-wide SNP data using double-digest restriction site-associated DNA sequencing (ddRADseq) results from 93 specimens of M. didyma ranging from Morocco to eastern Kazakhstan. We found that, between ddRADseq and mtDNA results, there is a match only in populations that probably remained allopatric for long periods of time. Other mtDNA lineages may have resulted from introgression events and were probably affected by Wolbachia infection. The five main ddRADseq clades supported by STRUCTURE were parapatric or allopatric and showed high pairwise FST values, but some were also estimated to display various levels of gene flow. Melitaea didyma represents one of the first cases of deep mtDNA splits among European butterflies assessed by a genome-wide DNA analysis and reveals that the interpretation of patterns remains challenging even when a high amount of genomic data is available. These findings actualize the ongoing debate of species delimitation in allopatry, an issue probably of relevance to a significant proportion of global biodiversity.
De Ritis Ratio (Aspartate Transaminase/Alanine Transaminase) as a Significant Prognostic Factor in Patients Undergoing Radical Cystectomy with Bladder Urothelial Carcinoma: A Propensity Score-Matched Study

Introduction To investigate the correlation between preoperative De Ritis ratio (aspartate transaminase (AST)/alanine transaminase (ALT)) and postoperative outcome in patients with urothelial cell carcinoma (UC) treated with radical cystectomy. Materials and Methods We analyzed the clinical and pathological data of 771 patients who underwent radical cystectomy for bladder UC. Patients were divided into two groups according to the optimal value of AST/ALT ratio. The effect of the AST/ALT ratio was analyzed using the Kaplan–Meier method and Cox regression hazard models for patients' cancer-specific survival (CSS), overall survival (OS), and recurrence-free survival (RFS). In addition, propensity score matching of 1 : 1 was performed between the two groups. Results Median follow-up was 84.0 (36–275) months. Mean age was 64.8 ± 10.0 years. According to the receiver operating characteristic (ROC) analysis, the optimal threshold of the AST/ALT ratio was 1.1. In Kaplan–Meier analyses, the high AST/ALT group showed worse outcomes in CSS and OS (all P < 0.001). Also, RFS (P = 0.001) in the Cox regression models of clinical and pathological parameters was used to predict CSS, OS, and AST/ALT ratio (HR 2.15, 95% CI 1.23-3.73, P = 0.007) and pathological T stage (HR 4.80, 95% CI 1.19-19.28, P = 0.003). To predict OS and AST/ALT ratio (HR 2.05, 95% CI 1.65–2.56, P < 0.001), pathological T stage (HR 2.96, 95% CI 0.57–17.09, P = 0.037) and positive lymph node (HR 1.71, 95% CI 1.50–1.91, P = 0.021) were determined as independent prognostic factors. Conclusion Preoperative AST/ALT ratio could be an independent prognostic factor in patients with UC treated with radical cystectomy.
Antiobesity, Regulation of Lipid Metabolism, and Attenuation of Liver Oxidative Stress Effects of Hydroxy-α-sanshool Isolated from Zanthoxylum bungeanum on High-Fat Diet-Induced Hyperlipidemic Rats

Zanthoxylum bungeanum is a traditional Chinese medicine (TCM) used to relieve pain, dispel dampness, stop diarrhea, and prevent itching. The aim of this study was to investigate the antiobesity and hypolipidemic effects of hydroxy-α-sanshool (HAS) isolated from Z. bungeanum on hyperlipidemic rats. Wistar rats (n = 48) were randomly divided into six groups: (1) normal diet rats (ND), (2) high-fat diet- (HFD-) treated rats, (3) HFD+fenofibrate-treated rats (HFD+FNB), (4) HFD+low dose of HAS-treated rats (HFD+LD, 9 mg/kg), (5) HFD+middle dose of HAS-treated rats (HFD+MD, 18 mg/kg), and (6) HFD+high dose of HAS-treated rats (HFD+HD, 36 mg/kg). The body weight and food intake of the rats were recorded during the treatment period. After 4 weeks of HAS treatment, abdominal adipose tissues were observed and total cholesterol (T-CHO), triglycerides (TG), high-density lipoprotein (HDL) cholesterol (HDL-C), and low-density lipoprotein (LDL) cholesterol (LDL-C) of serum and liver tissues were determined. Furthermore, histochemical examinations using oil red O and hematoxylin-eosin staining (H&E) were carried out and levels of malondialdehyde (MDA) and glutathione (GSH) and activities of superoxide dismutase (SOD) in the liver were determined. After HFD feeding, the body weight gain and food efficiency ratio of HFD rats were significantly enhanced (p < 0.05vs. ND rats) and HAS treatment (18 and 36 mg/kg) significantly decreased the body weight gain and food efficiency ratio (p < 0.05vs. HFD rats). In addition, HAS treatment could decrease the abdominal adipose tissues and liver adipocytes. Furthermore, HAS treatment significantly decreased the T-CHO, TG, and LDL-C, whereas it increased HDL-C (p < 0.05vs. HFD rats) in serum and the liver. HAS treatment increased the GSH level and SOD activity in the liver (p < 0.05vs. HFD rats), whereas it decreased the levels of MDA (p < 0.05vs. HFD rats). mRNA analyses suggested that HAS treatment increases the expression of Pparg (proliferator-activated receptor γ) and Apoe (peroxisome apolipoprotein E). Immunohistochemistry and Western blotting indicated that HAS stimulation increased the levels of PPARγ and APOE in the liver, as a stress response of the body defense system. These results revealed that HAS exerts antiobesity and hypolipidemic activities in HFD rats by reducing liver oxidative stress and thus could be considered as a potential candidate drug to cure or prevent obesity and hyperlipidemia.