Miracle-dz/UniFAR-FTUs huggingface dataset:
The Role of Information Processing Speed in Clinical and Social Support Variables of Patients with Multiple Sclerosis

Background and Purpose Information processing speed is one of the most impaired cognitive functions in multiple sclerosis (MS). There are two tests widely used for evaluating information processing speed: the Symbol Digit Modalities Test (SDMT) and the Paced Auditory Serial Addition Test (PASAT). To analyze the relationship between processing speed and the clinical and social support variables of patients with MS. Methods A group of 47 patients with relapsing-remitting MS was studied, 31 were women and 16, men. Age: 39.04±13.17, years of schooling: 13.00±3.87, Expanded Disability Status Scale (EDSS): 2.78±1.81, and disease evolution: 8.07±6.26. Instruments of measure; processing speed: SDMT, PASAT, clinical variables: EDSS, Fatigue Severity Scale (FSS), Beck's Depression Inventory II (BDI-II), and social support: Medical Outcomes Study Social Support Survey (MOS). Results Significant correlations were found between information processing speed and psychiatric, motor disability and social support variables. The SDMT correlated significantly and negatively with BDI-II, FSS, EDSS, and MOS (p<0.05), whereas the PASAT correlated negatively with FSS and positively with MOS (p<0.05). Information processing speed appeared as the performance predictor of these variables. The SDMT produced significant changes in EDSS (R2=0.343, p=0.000); FSS (R2=0.109, p=0.031); BDI-II (R2=0.124, p=0.018), and MOS (R2=between 0.212 and 0.379, p<0.05). Conclusions Information processing speed has influence on the clinical variables and the social support of patients with MS. These aspects are important to bear in mind for therapeutic approach.
Seizure evolution can be characterized as path through synaptic gain space of a neural mass model

Physiologically based models could facilitate better understanding of mechanisms underlying epileptic seizures. In this paper, we attempt to reveal the dynamic evolution of intracranial EEG activity during epileptic seizures based on synaptic gain identification procedure of a neural mass model. The distribution of average excitatory, slow and fast inhibitory synaptic gain in the parameter space and their temporal evolution, i.e., the path through the model parameter space, were analyzed in thirty seizures from ten temporal lobe epileptic patients. Results showed that the synaptic gain values located roughly on a plane before seizure onset, dispersed during seizure and returned to the plane when seizure terminated. Cluster analysis was performed on seizure paths and demonstrated consistency in synaptic gain evolution across different seizures from the individual patient. Furthermore, two patient groups were identified, each one corresponding to a specific synaptic gain evolution in the parameter space during a seizure. Results were validated by a bootstrapping approach based on comparison with random paths. The differences in the path revealed variations in EEG dynamics for patients despite showing identical seizure onset pattern. Our approach may have the potential to classify the epileptic patients into subgroups based on different mechanisms revealed by subtle changes in synaptic gains and further enable more robust decisions regarding treatment strategy.
Fenestrated ASD device “angioplasty”: How to adjust a “pop‐off” mechanism when needed

We report on three cases of atrial septal defect (ASD) closure where a handmade fenestration had to be modified after device implantation. Two patients suffered from left ventricular diastolic dysfunction and one had severe pulmonary arterial hypertension. Amplatzer ASD occluder fenestration was created in all patients. Devices were implanted using an “over‐the‐wire” implantation technique. Due to a sub‐optimal hemodynamic result, fenestration was upsized by using a new technique.
Comparison of inhibitory neuromuscular transmission in the Cynomolgus monkey IAS and rectum: special emphasis on differences in purinergic transmission

Inhibitory neuromuscular transmission (NMT) was compared in the internal anal sphincter (IAS) and rectum of the Cynomolgus monkey, an animal with high gene sequence identity to humans. Nitrergic NMT was present in both muscles while purinergic NMT was limited to the rectum and VIPergic NMT to the IAS. The profile for monkey IAS more closely resembles humans than rodents. In both muscles, SK3 channels were localized to PDGFRα+ cells that were closely associated with nNOS+/VIP+ nerves. Gene expression levels of P2RY subtypes were the same in IAS and rectum while KCNN expression levels were very similar. SK3 channel activation and inhibition caused faster/greater changes in contractile activity in rectum than IAS. P2Y1 receptor activation inhibited contraction in rectum while increasing contraction in IAS. The absence of purinergic NMT in the IAS may be due to poor coupling between P2Y1 receptors and SK3 channels on PDGFRα+ cells.
Local Music Event Recommendation with Long Tail Artists

In this paper, we explore the task of local music event recommendation. Many local artists tend to be obscure long-tail artists with a small digital footprint. That is, it can be hard to find social tag and artist similarity information for many of the artists who are playing shows in the local music community. To address this problem, we explore using Latent Semantic Analysis (LSA) to embed artists and tags into a latent feature space and examine how well artists with small digital footprints are represented in this space. We find that only a relatively small digital footprint is needed to effectively model artist similarity. We also introduce the concept of a Music Event Graph as a data structure that makes it easy and efficient to recommend events based on user-selected genre tags and popular artists. Finally, we conduct a small user study to explore the feasibility of our proposed system for event recommendation.
Neural Field Theory of Corticothalamic Prediction With Control Systems Analysis

Neural field theory is used to model and analyze realistic corticothalamic responses to simple visual stimuli. This yields system transfer functions that embody key features in common with those of engineering control systems, which enables interpretation of brain dynamics in terms of data filters. In particular, these features assist in finding internal signals that represent input stimuli and their changes, which are exactly the types of quantities used in control systems to enable prediction of future input signals, and adjustment of gains which is argued to be the analog of attention in control theory. Corticothalamic dynamics are shown to be analogous to the classical proportional-integral-derivative (PID) filters that are widely used in engineering.
Using Sparse Semantic Embeddings Learned from Multimodal Text and Image Data to Model Human Conceptual Knowledge

Distributional models provide a convenient way to model semantics using dense embedding spaces derived from unsupervised learning algorithms. However, the dimensions of dense embedding spaces are not designed to resemble human semantic knowledge. Moreover, embeddings are often built from a single source of information (typically text data), even though neurocognitive research suggests that semantics is deeply linked to both language and perception. In this paper, we combine multimodal information from both text and image-based representations derived from state-of-the-art distributional models to produce sparse, interpretable vectors using Joint Non-Negative Sparse Embedding. Through in-depth analyses comparing these sparse models to human-derived behavioural and neuroimaging data, we demonstrate their ability to predict interpretable linguistic descriptions of human ground-truth semantic knowledge.
Annexin A12–26 Treatment Improves Skin Heterologous Transplantation by Modulating Inflammation and Angiogenesis Processes

Skin graft successful depends on reduction of local inflammation evoked by the surgical lesion and efficient neovascularization to nutrition the graft. It has been shown that N-terminal portion of the Annexin A1 protein (AnxA1) with its anti-inflammatory properties induces epithelial mucosa repair and presents potential therapeutic approaches. The role of AnxA1 on wound healing has not been explored and we investigated in this study the effect of the peptide Ac2–26 (N-terminal AnxA1 peptide Ac2–26; AnxA12–26) on heterologous skin scaffolds transplantation in BALB/c mice, focusing on inflammation and angiogenesis. Treatment with AnxA12–26, once a day, from day 3–60 after scaffold implantation improved the take of the implant, induced vessels formation, enhanced gene and protein levels of the vascular growth factor-A (VEGF-A) and fibroblast influx into allograft tissue. It also decreased pro- while increasing anti-inflammatory cytokines. The pro-angiogenic activity of AnxA12–26 was corroborated by topical application of AnxA12–26 on the subcutaneous tissue of mice. Moreover, treatment of human umbilical endothelial cells (HUVECs) with AnxA12–26 improved proliferation, shortened cycle, increased migration and actin polymerization similarly to those evoked by VEGF-A. The peptide treatment instead only potentiated the tube formation induced by VEGF-A. Collectively, our data showed that AnxA12–26 treatment favors the tissue regeneration after skin grafting by avoiding exacerbated inflammation and improving the angiogenesis process.
Decoupled maternal and zygotic genetic effects shape the evolution of development

Many animals develop indirectly via a larval stage that is morphologically and ecologically distinct from its adult form. Hundreds of lineages across animal phylogeny have secondarily lost larval forms, instead producing offspring that directly develop into adult form without a distinct larval ecological niche1–7. Indirect development in the sea is typically planktotrophic: females produce large numbers of small offspring that require exogenous planktonic food to develop before metamorphosing into benthic juveniles. Direct development is typically lecithotrophic: females produce a smaller number of larger eggs, each developing into a juvenile without the need for larval feeding, provisioned by yolk. Evolutionary theory suggests that these alternative developmental strategies represent stable alternative fitness peaks, while intermediate states are disfavored4,8–11. Transitions from planktotrophy to lecithotrophy thus require crossing a fitness valley and represent radical and coordinated transformations of life-history, fecundity, ecology, dispersal, and development7,12–16. Here we dissect this transition in Streblospio benedicti, the sole genetically tractable species that harbors both states as heritable variation17–19. We identify large-effect loci that act maternally to influence larval size and independent, unlinked large-effect loci that act zygotically to affect discrete aspects of larval morphology. Because lecithotrophs and planktotrophs differ in both size and morphology, the genetic basis of larval form exhibits strong maternal-by-zygotic epistasis for fitness20. The fitness of zygotic alleles depends on their maternal background, creating a positive frequency-dependence that may homogenize local populations. Developmental and population genetics interact to shape larval evolution.
MSMEG_6292, a Mycobacterium smegmatis RNA polymerase secondary channel-binding protein: purification, crystallization and X-ray diffraction analysis.

The transcriptional activity of RNA polymerase (RNAP) is controlled by a diverse set of regulatory factors. A subset of these regulators modulate the activity of RNAP through its secondary channel. Gre factors reactivate stalled elongation complexes by enhancing the intrinsic cleavage activity of RNAP. In the present study, the protein MSMEG_6292, a Gre-factor homologue from Mycobacterium smegmatis, was expressed heterologously in Escherichia coli and purified using standard chromatographic techniques. The hanging-drop vapour-diffusion crystallization method yielded diffraction-quality crystals. The crystals belonged to the trigonal space group P3121 (or its enantiomorph P3221), with unit-cell parameters a = b = 83.15, c = 107.07 Å, α = β = 90, γ = 120°. The crystals diffracted to better than 3.0 Å resolution. Molecular-replacement attempts did not yield any phasing models; hence, platinum derivatization was carried out with K2PtCl4 and derivative data were collected to 3.4 Å resolution.
A Mouse Model of Delayed Rotator Cuff Repair Results in Persistent Muscle Atrophy and Fatty Infiltration

Background: Rotator cuff (RC) tears are common tendon injuries seen in orthopaedic patients. Successful repair of large and massive RC tears remains a challenge due to our limited understanding of the pathophysiological features of this injury. Clinically relevant small animal models that can be used to study the pathophysiological response to repair are limited by the lack of chronic repair models. Purpose: To develop a highly clinically relevant mouse model of delayed RC repair. Study Design: Controlled laboratory study. Methods: Three-month-old C57BL/6J mice underwent unilateral supraspinatus (SS) and infraspinatus (IS) tendon tear with immediate, 2-week delayed, or 6-week delayed tendon repair. Animals with no repair or sham surgery served as controls. Gait analysis was conducted to measure shoulder function at 2 weeks and 6 weeks after surgery. Animals were sacrificed 6 weeks after the last surgery. Shoulder joint, SS, and IS muscles were harvested and analyzed histologically. Ex vivo mechanical testing of intact and repaired SS and IS tendons was conducted. Reverse-transcriptase polymerase chain reaction was performed on SS and IS muscles to quantify atrophy, fibrosis, and fatty infiltration–related gene expression. Results: Histological and tendon mechanical testing showed that torn tendons could be successfully repaired as late as 6 weeks after transection. However, significant atrophy and fatty infiltration of muscle, with impaired shoulder function, were persistent in the 6-week delayed repair group. Shoulder function correlated with the severity of RC muscle weight loss and fatty infiltration. Conclusion: We successfully developed a clinically relevant mouse model of delayed RC repair. Six-week delayed RC repair resulted in persistent muscle atrophy and fatty infiltration with inferior shoulder function compared with acute repair. Clinical Relevance: Our novel mouse model could serve as a powerful tool to understand the pathophysiological and cellular/molecular mechanisms of RC muscle and tendon degeneration, eventually improving our strategies for treating and repairing RC tears.
Calculation of Average Mutual Information (AMI) and False-Nearest Neighbors (FNN) for the Estimation of Embedding Parameters of Multidimensional Time Series in Matlab

Using the method or time-delayed embedding, a signal can be embedded into higher-dimensional space in order to study its dynamics. This requires knowledge of two parameters: The delay parameter τ, and the embedding dimension parameter D. Two standard methods to estimate these parameters in one-dimensional time series involve the inspection of the Average Mutual Information (AMI) function and the False Nearest Neighbor (FNN) function. In some contexts, however, such as phase-space reconstruction for Multidimensional Recurrence Quantification Analysis (MdRQA), the empirical time series that need to be embedded already possess a dimensionality higher than one. In the current article, we present extensions of the AMI and FNN functions for higher dimensional time series and their application to data from the Lorenz system coded in Matlab.
Mobility-Aware Resource Allocation in VLC Networks Using T-Step Look-Ahead Policy

Visible light communication (VLC) uses huge license-free spectral bandwidth of visible light for high-speed wireless communication. Since each VLC access point covers a small area, handovers of mobile users are inevitable. In order to deal with these handovers, developing fast and effective resource allocation algorithms is a challenge. This paper introduces the problem of mobility-aware optimization of resources in VLC networks using the T-step look-ahead policy and employing the notion of handover efficiency. It is shown that the handover efficiency can correlate the overall performance of the network with future actions based on the mobility of users. Due to the stationary nature of indoor optical wireless channels, future channel state information (CSI) can be predicted by anticipating the future locations of users. A resource allocation algorithm is thus proposed, which uses CSI to dynamically allocate network resources to users. To solve this mathematically intractable problem, a novel relaxation method is proposed, which proves to be a useful tool to develop efficient algorithms for network optimization problems with a proportional fairness utility function. The resulting algorithm is extremely faster than the previous method and awareness of mobility enhances the overall performance of the network in terms of rate and fairness utility function.
Timing of palliative care access and outcomes of advanced cancer patients referred to an inpatient palliative care consultation team in Brazil

Abstract Objective Little is known about the outcomes of cancer patients referred to palliative care (PC) teams in developing countries. Our aim was to examine the timing of PC access and outcomes of patients with advanced cancer referred to an inpatient PC consultation team in Brazil. Method Retrospective study of consecutive patients with advanced cancer admitted to a tertiary care general hospital (April 2015–December 2016) and referred for the first time to an inpatient PC consultation team. Patients’ demographics, clinical features, time from first consult to death or discharge, and outcomes on medication use, clinical interventions, and end-of-life preferences were retrieved. An analysis was performed before and after PC. Result One hundred eleven patients were included. Median age was 68; 72% had an Eastern Cooperative Oncology Group performance status ≥3. The median timing of PC access was 9 days (first interquartile = 3, third interquartile = 19). The use of analgesics (from 75% to 85%, p = 0.001) and opioids (from 50% to 73%, p < .001) increased. A lower proportion was receiving antibiotics (68% vs 48%, p < 0.001), thromboprophylaxis (44% vs 26%, p < 0.001), antihypertensives (28% vs 15%, p = 0.001), and antiemetic agents (64% vs 54%, p = 0.027). Chemotherapy use was lower (39–25%, p < 0.001). More patients had an end-of-life preference (39% to 25%, p < 0.001) and were not willing to receive intubation (32% vs 60%, p < 0.001), intensive care treatment (30% vs 55%, p < 0.001), cardiopulmonary resuscitation (35% vs 62%, p < 0.001), and artificial nutrition (22% vs 34%, p < 0.001). Significance of results Although PC referrals occurred exceedingly late during the cancer disease trajectory, positive changes were observed in medication profiles, clinical interventions use, and end-of-life preferences of patients with advanced cancer referred to a specialized inpatient PC consultation team in Brazil. Further efforts are needed to improve early palliative cancer care in developing countries.
Prognostic implications of trunk muscle mass in liver cirrhosis

Corresponding author : Won Kim Division of Gastroenterology and Hepatology, Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul National University College of Medicine, 20 Boramae-ro 5-gil, Dongjak-gu, Seoul 07061, Korea Tel: +82-2-870-2233, Fax: +82-2-831-2826 E-mail: drwon1@snu.ac. kr https://orcid.org/0000-0002-2926-1007 Abbreviations: CT, computed tomography; PMTH, psoas muscle thickness per height; SMI, skeletal muscle index
Decoding Brain States for Planning Functional Grasps of Tools: A Functional Magnetic Resonance Imaging Multivoxel Pattern Analysis Study

Abstract Objectives: We used multivoxel pattern analysis (MVPA) to investigate neural selectivity for grasp planning within the left-lateralized temporo-parieto-frontal network of areas (praxis representation network, PRN) typically associated with tool-related actions, as studied with traditional neuroimaging contrasts. Methods: We used data from 20 participants whose task was to plan functional grasps of tools, with either right or left hands. Region of interest and whole-brain searchlight analyses were performed to show task-related neural patterns. Results: MVPA revealed significant contributions to functional grasp planning from the anterior intraparietal sulcus (aIPS) and its immediate vicinities, supplemented by inputs from posterior subdivisions of IPS, and the ventral lateral occipital complex (vLOC). Moreover, greater local selectivity was demonstrated in areas near the superior parieto-occipital cortex and dorsal premotor cortex, putatively forming the dorso-dorsal stream. Conclusions: A contribution from aIPS, consistent with its role in prospective grasp formation and/or encoding of relevant tool properties (e.g., potential graspable parts), is likely to accompany the retrieval of manipulation and/or mechanical knowledge subserved by the supramarginal gyrus for achieving action goals. An involvement of vLOC indicates that MVPA is particularly sensitive to coding of object properties, their identities and even functions, for a support of grip formation. Finally, the engagement of the superior parieto-frontal regions as revealed by MVPA is consistent with their selectivity for transient features of tools (i.e., variable affordances) for anticipatory hand postures. These outcomes support the notion that, compared to traditional approaches, MVPA can reveal more fine-grained patterns of neural activity. (JINS, 2018, 24, 1013–1025)
Infinite Curriculum Learning for Efficiently Detecting Gastric Ulcers in WCE Images

The Wireless Capsule Endoscopy (WCE) is becoming a popular way of screening gastrointestinal system diseases and cancer. However, the time-consuming process in inspecting WCE data limits its applications and increases the cost of examinations. This paper considers WCE-based gastric ulcer detection, in which the major challenge is to detect the lesions in a local region. We propose an approach named infinite curriculum learning, which generalizes curriculum learning to an infinite sampling space by approximately measuring the difficulty of each patch by its scale. This allows us to adapt our model from local patches to global images gradually, leading to a consistent accuracy gain. Experiments are performed on a large dataset with more than 3 million WCE images. Our approach achieves a binary classification accuracy of 87%, and is able to detect some lesions mis-annotated by the physicians. In a real-world application, our approach can reduce the workload of a physician by 90%-98% in gastric ulcer screening.
Cell-aware Stacked LSTMs for Modeling Sentences

We propose a method of stacking multiple long short-term memory (LSTM) layers for modeling sentences. In contrast to the conventional stacked LSTMs where only hidden states are fed as input to the next layer, the suggested architecture accepts both hidden and memory cell states of the preceding layer and fuses information from the left and the lower context using the soft gating mechanism of LSTMs. Thus the architecture modulates the amount of information to be delivered not only in horizontal recurrence but also in vertical connections, from which useful features extracted from lower layers are effectively conveyed to upper layers. We dub this architecture Cell-aware Stacked LSTM (CAS-LSTM) and show from experiments that our models bring significant performance gain over the standard LSTMs on benchmark datasets for natural language inference, paraphrase detection, sentiment classification, and machine translation. We also conduct extensive qualitative analysis to understand the internal behavior of the suggested approach.