Miracle-dz/UniFAR-FTUs huggingface dataset:
A Wrapper Feature Subset Selection Method Based on Randomized Search and Multilayer Structure

The identification of discriminative features from information-rich data with the goal of clinical diagnosis is crucial in the field of biomedical science. In this context, many machine-learning techniques have been widely applied and achieved remarkable results. However, disease, especially cancer, is often caused by a group of features with complex interactions. Unlike traditional feature selection methods, which only focused on finding single discriminative features, a multilayer feature subset selection method (MLFSSM), which employs randomized search and multilayer structure to select a discriminative subset, is proposed herein. In each level of this method, many feature subsets are generated to assure the diversity of the combinations, and the weights of features are evaluated on the performances of the subsets. The weight of a feature would increase if the feature is selected into more subsets with better performances compared with other features on the current layer. In this manner, the values of feature weights are revised layer-by-layer; the precision of feature weights is constantly improved; and better subsets are repeatedly constructed by the features with higher weights. Finally, the topmost feature subset of the last layer is returned. The experimental results based on five public gene datasets showed that the subsets selected by MLFSSM were more discriminative than the results by traditional feature methods including LVW (a feature subset method used the Las Vegas method for randomized search strategy), GAANN (a feature subset selection method based genetic algorithm (GA)), and support vector machine recursive feature elimination (SVM-RFE). Furthermore, MLFSSM showed higher classification performance than some state-of-the-art methods which selected feature pairs or groups, including top scoring pair (TSP), k-top scoring pairs (K-TSP), and relative simplicity-based direct classifier (RS-DC).
Letters to the Editor

I write in regard to Dr. Peter Ngan's excellent Guest Editorial, "Dental Specialists and IADR" [J Dent Res 74(2):628-629, 19951. Indeed there is a dearth of clinicians contributing to the Journal, but I feel that it is a matter of the old question, "Which came first, the chicken or the egg? " Dr. Ngan is correct in asserting that the Journal of Dental Research is one of the most prestigious dental journals in the world. Likewise, it is true when he states that research in the various disciplines cannot be updated in a specialty meeting in which the majority of participants are clinicians. However, I would venture to suggest that this is because a significant number of students are placed under the tutelage of the academicians in the various dental school faculties. What appears to be missed is the fact that there are many clinical scholars on dental school faculties who are carrying out very meaningful clinical research. Unfortunately, when they come to select a journal to which their paper(s) might be submitted, the Journal of Dental Research presents a daunting barrier which strikes fear into the most selfconfident author. Speaking for myself, I have on numerous occasions picked up a copy of the Journal to read the "Instructions to Authors" and have been deterred by the fact that more or less every publication is pure basic science. As an example, rarely does one see a good solid paper on clinical drug trials or sedation techniques, and I am sure that this could be said of many other areas of clinical research. Dr. Ngan points out that "Many of the clinical presentations have small audiences". Perhaps this is because the academicians who constitute the majority of IADR have no interest in clinical matters. Ergo, the clinical researchers feel shut out. I agree that all dental specialists should take an active part in IADR. Perhaps one way to do this would be to set up a separate section of the Journal of Dental Research devoted to clinical research. This would, of course, require that clinical researchers be appointed to the Editorial Board. However, I am certain that the results would more than justify the effort.
Modeling and Optimization of Catalytic Performance of SAPO-34 Nanocatalysts Synthesized Sonochemically Using a new hybrid of Non-dominated Sorting Genetic Algorithm-II based Artificial Neural Networks (NSGA-II – ANN)

Effects of ultrasound-related variables on catalytic properties of sonochemically prepared SAPO-34 nanocatalyst in methanol to olefins (MTO) reactions were investigated. The different catalytic behaviors are observed which can be explained by the differences in the catalysts physicochemical properties affected by ultrasonic (US) power intensity, sonication temperature, irradiation time and sonotorode size. This result confirms that the activity of SAPO-34 catalysts improves with the rise in US power, time and temperature. In order to find a catalyst with maximum conversion of methanol, maximum light olefins content and maximum lifetime, the hybrid of non-dominated sorting genetic algorithm-II based artificial neural networks (NSGA-II – ANN) was used. The multilayer feed forward neural networks with backpropagation structures were implemented using different training rules in the neural networks approach to relate the ultrasound-related variables and the catalytic performance of SAPO-34 catalysts. A comparison between experimental and artificial neural network (ANN) values indicates that the ANN model with a 310-3 structure using the Bayesian regulation training rule has the best fit and can be used as a fitness evaluation inside the non-dominated sorting genetic algorithm-II (NSGA-II). Also, the multiple linear regressions (MLR) was used to predict these objective functions. The results indicate a poor fit for the objective functions with low coefficient of determination. This confirms the ANN technique is more effective than the traditional statistical-based prediction models. Finally, this ANN model was linked to the NSGA-II and Pareto-optimal solutions were determined by NSGA-II.
Analysis of Chromatographic Data using the Probabilistic PARAFAC2

PARAFAC2 is a widely applicable method often used for analyzing multi-way chromatographic data. We recently proposed a probabilistic framework for PARAFAC2[1]. The probabilistic formulations allow for a principled way of determining the number of latent components as well as modeling heteroscedastic noise. In this work we present a summary of the probabilistic PARAFAC2 models and their properties by revisiting the previous results of the analyzed data sets in a concise fashion.
Notch signaling governs the expression of glypican Dally to define the stem cell niche

ABSTRACT Extracellular glypicans play pivotal roles in organogenesis, stem cell maintenance and cancer development. However, the growth phenotypes associated with different levels of glypican are not consistent in development or tumorigenesis. This requires clarification on how the spatial patterns of glypican relate to the distribution of signaling molecules in different cellular contexts, and how glypican expression is regulated. We have previously reported that Dally, one of the glypican members in Drosophila, is required in the niche for the maintenance of germline stem cells (GSCs) via short-range BMP signaling in ovary. However, the regulatory mechanism of glypican pattern in the ovarian stem cell niche remains elusive. Our current data demonstrate that the Notch pathway is genetically upstream of Dally and its function to maintain GSCs relies on Dally expression. Combining yeast and fruit fly genetics, we illustrate that Dally is under the transcriptional control of Notch signaling via the transcription factor Su(H). Further, we assayed human glypicans and disease-associated variants in Drosophila ovary, which can serve as an effective system to evaluate the structure–function relationship of human homologs. Summary: Spatial regulation of a cell surface glycoprotein defines the territory of germline stem cells.
ARL3, a small GTPase with a functionally conserved role in primary cilia and immune synapses

ABSTRACT The primary cilium and the immunological synapse are both specialized functional plasma membrane domains that share several similarities. Signalling output of membrane domains is regulated, spatially and temporally, by segregating and focusing lipids and proteins. ARL3, a small GTPase, plays a major role in concentrating lipid-modified proteins in both the immunological synapse and the primary cilia. Here in this review we will introduce the role of ARL3 in health and disease and its role in polarizing signalling at the primary cilia and immunological synapses.
Perceived problems with academic achievement in school-aged children with recurrent pain – a longitudinal study

Aims: The overall aim was to explore the relationship between recurrent pain and perceived problems with academic achievement among boys and girls in middle and late elementary school. Methods: This 3-year follow-up study was based on data from the Study of Health in School-aged Children from Umeå (Sweden) and included children attending grade 6 in years 2003 and 2006, and a follow-up 3 years later in grade 9 (n = 1524, participation rate 90%). Results: Recurrent pain (head, stomach or back) at least doubled the odds of concurrent- and subsequent perceived problems with academic achievement. This applied for pain on a monthly and weekly basis, from single and multiple sites, and from each of the three studied pain sites. The odds increased with increasing pain frequency and number of pain sites. Problems with sleep, concentration or school absenteeism did not explain the association. Conclusions: Recurrent pain seems to be a potential predictor of perceived problems with academic achievement for school-aged children. This emphasises the importance of early identification and prevention of recurrent pain problems.
Multichannel correlation improves the noise tolerance of real-time hyperspectral microimage mosaicking

Abstract. Live-subject microscopies, including microendoscopy and other related technologies, offer promise for basic biology research as well as the optical biopsy of disease in the clinic. However, cellular resolution generally comes with the trade-off of a microscopic field-of-view. Microimage mosaicking enables stitching many small scenes together to aid visualization, quantitative interpretation, and mapping of microscale features, for example, to guide surgical intervention. The development of hyperspectral and multispectral systems for biomedical applications provides motivation for adapting mosaicking algorithms to process a number of simultaneous spectral channels. We present an algorithm that mosaics multichannel video by correlating channels of consecutive frames as a basis for efficiently calculating image alignments. We characterize the noise tolerance of the algorithm by using simulated video with known ground-truth alignments to quantify mosaicking accuracy and speed, showing that multiplexed molecular imaging enhances mosaic accuracy by leveraging observations of distinct molecular constituents to inform frame alignment. A simple mathematical model is introduced to characterize the noise suppression provided by a given group of spectral channels, thus predicting the performance of selected subsets of data channels in order to balance mosaic computation accuracy and speed. The characteristic noise tolerance of a given number of channels is shown to improve through selection of an optimal subset of channels that maximizes this model. We also demonstrate that the multichannel algorithm produces higher quality mosaics than the analogous single-channel methods in an empirical test case. To compensate for the increased data rate of hyperspectral video compared to single-channel systems, we employ parallel processing via GPUs to alleviate computational bottlenecks and to achieve real-time mosaicking even for video-rate multichannel systems anticipated in the future. This implementation paves the way for real-time multichannel mosaicking to accompany next-generation hyperspectral and multispectral video microscopy.
Luminance Potentiates Human Visuocortical Responses.

Our visual system is tasked with transforming variations in light within our environment into a coherent percept, typically described using properties such as luminance and contrast. Models of vision often downplay the importance of luminance in shaping cortical responses, instead prioritizing representations that do not co-vary with overall luminance (i.e., contrast), and yet visuocortical response properties that may reflect luminance encoding remain poorly understood. In this study, we examined whether well-established visuocortical response properties may also reflect luminance encoding, challenging the idea that luminance information itself plays no significant role in supporting visual perception. To do so, we measured functional activity in human visual cortex when presenting stimuli varying in contrast and mean luminance, and found that luminance response functions are strongly contrast dependent between 50 to 250 cd/m2, confirmed with a subsequent experiment. High contrast stimuli produced linearly increasing responses as luminance increased logarithmically for all early visual areas, whereas low contrast stimuli produced either flat (V1) or positive linear (V2 & V3) response profiles. These results reveal that the mean luminance information of a visual signal persists within visuocortical representations, potentially reflecting an inherent imbalance of excitatory and inhibitory components that can be either contrast-dependent (V1 & V2) or contrast-invariant (V3). The role of luminance should be considered when aiming to drive potent visually-evoked responses, and when comparing activity across studies. More broadly, overall luminance should be weighed heavily as a core feature of the visual system, and play a significant role in cortical models of vision.
Novel frameshift mutation in NYX gene in a Russian family with complete congenital stationary night blindness

ABSTRACT Background: The complete form of X-linked congenital stationary night blindness (CSNB1A) is a very rare genetic disease caused by mutation in the NYX gene. CSNB1A-associated several mutations in the NYX gene have been reported earlier. Methods: In this case report, we have clinically diagnosed and genetically confirmed a novel mutation associated with CSNB1A in four members of a Russian family. Two male siblings from a family of four siblings (two girls, two boys) with non-progressive stable night blindness since early childhood and high myopia underwent - visual acuity test, perimetry, biomicroscopy, OCT, ophthalmoscopy, electroretinography, color vision Hue test, NGS based whole exome analysis and Sanger sequencing for clinical characterization and genetic confirmation of CSNB. Results: The members are clinically diagnosed and genetically confirmed with CSNB1A. All the patients had a novel frameshift mutation in the NYX gene (c.283delC, p.His95fs, NM_022567.2) that is found to segregate in X-linked manner Conclusions: This is probably the first case report with a novel mutation from Russia associated with CSNB1A.
Effects of dechlorane plus on oxidative stress, inflammatory response, and cell apoptosis in Cyprinus carpio

Abstract The levels of the chlorinated organic compound Dechlorane Plus (DP) are increasing in aquatic ecosystems. To investigate the adverse effects of DP on aquatic animals, common carp (Cyprinus carpio) were subjected to three different DP concentrations (30 μg L−1, 60 μg L−1, and 120 μg L−1) for 1 d, 15 d, and 30 d. Histology and the hepatic and cerebral expression levels of several key antioxidant, detoxification, and apoptotic factors were then examined. Histopathological inspections showed that the liver and brain were severely damaged in carp exposed to 60 μg L−1 and 120 μg L−1 DP. Relative to the controls, the superoxide dismutase and glutathione activity levels and the malondialdehyde content were also changed in livers and brains exposed to DP. Besides, significant alterations in the expression levels of the inflammatory cytokines IL-1β, IL-6, and IL-10 were observed in the livers of carp subjected to DP. Relative to the control, the brains of DP-exposed carp presented with significantly upregulated IL-1β and IL-6 in carp treated with 120 μg L−1 DP for 30 d. The transcription levels of hepatic cyp2b4, cyp1b1, and cyp3a138 were all increased compared with the untreated at all DP exposure concentrations. The aforementioned results suggest that DP exposure perturbs fish metabolism and causes liver injury by inhibiting antioxidant enzyme activity, increasing lipid peroxidation, promoting inflammation, and inducing cell apoptosis. This information and the analytical methodology used to acquire it may form the basis for future ecological risk assessments on DP and related xenobiotics in aquatic animals.
Impaired hemostatic activity of healthy transfused platelets in inherited and acquired platelet disorders: Mechanisms and implications

In select platelet disorders, dysfunctional endogenous platelets affect the hemostatic activity of transfused platelets by multiple mechanisms. Strength in numbers (of platelets) Platelet transfusions are effective at restoring hemostasis in patients with low platelet counts, but this tactic does not necessarily work in patients who have normal numbers of platelets but impaired platelet function resulting from genetic or drug-induced defects. Using mouse models and platelets from human patients, Lee et al. demonstrated that dysfunctional platelets can interfere with the formation and/or consolidation of a platelet plug at the site of injury, but this impairment can be overcome by providing wild-type platelets at a sufficiently high ratio. Platelet transfusions can fail to prevent bleeding in patients with inherited platelet function disorders (IPDs), such as Glanzmann’s thrombasthenia (GT; integrin αIIbβ3 dysfunction), Bernard-Soulier syndrome [BSS; glycoprotein (GP) Ib/V/IX dysfunction], and the more recently identified nonsyndromic RASGRP2 variants. Here, we used IPD mouse models and real-time imaging of hemostatic plug formation to investigate whether dysfunctional platelets impair the hemostatic function of healthy donor [wild-type (WT)] platelets. In Rasgrp2−/− mice or mice with platelet-specific deficiency in the integrin adaptor protein TALIN1 (“GT-like”), WT platelet transfusion was ineffective unless the ratio between mutant and WT platelets was ~2:1. In contrast, thrombocytopenic mice or mice lacking the extracellular domain of GPIbα (“BSS-like”) required very few transfused WT platelets to normalize hemostasis. Both Rasgrp2−/− and GT-like, but not BSS-like, platelets effectively localized to the injury site. Mechanistic studies identified at least two mechanisms of interference by dysfunctional platelets in IPDs: (i) delayed adhesion of WT donor platelets due to reduced access to GPIbα ligands exposed at sites of vascular injury and (ii) impaired consolidation of the hemostatic plug. We also investigated the hemostatic activity of transfused platelets in the setting of dual antiplatelet therapy (DAPT), an acquired platelet function disorder (APD). “DAPT” platelets did not prolong the time to initial hemostasis, but plugs were unstable and frequent rebleeding was observed. Thus, we propose that the endogenous platelet count and the ratio of transfused versus endogenous platelets should be considered when treating select IPD and APD patients with platelet transfusions.
Reconfigurable graphene antenna for THz applications: a mode conversion approach

A reconfigurable graphene antenna is designed and numerically analyzed. The antenna structure contains a radiating graphene patch and non-radiating graphene ring. The operating frequency of the antenna can be tuned by applying the gate voltage on the graphene patch. This proximity coupled antenna structure operates with the T M 22 mode. In this configuration, the field is distributed in the form of horizontal magnetic dipole. The application of gate voltage at the periphery of graphene ring converts the field configuration to the form of the vertical electric dipole. Thus, the mode of operation of the antenna is changed to T M 01 . Consequently, the radiation pattern of the antenna can be steered in different directions as per the location of the applied gate voltage at the periphery of the graphene ring.
Histidine‐containing dipeptides reduce central obesity and improve glycaemic outcomes: A systematic review and meta‐analysis of randomized controlled trials

Supplementation with histidine‐containing dipeptides has been shown to improve obesity and glycaemic outcomes in animal and human studies. We conducted a systematic review and meta‐analysis of randomized controlled trials to examine these effects. Electronic databases were searched investigating the effects of histidine‐containing dipeptides supplementation on anthropometric and glycaemic outcomes. Meta‐analyses were performed using random‐effects models to calculate the weighted mean difference and 95% confidence interval. There were 30 studies for the systematic review and 23 studies pooled for meta‐analysis. Histidine‐containing dipeptide groups had a lower waist circumference (WMD [95% CI] = −3.53 cm [−5.65, −1.41], p = 0.001) and HbA1c level (WMD [95% CI] = −0.76% (8.5 mmol/mol) [−1.29% (14.3 mmol/mol), −0.24% (2.8 mmol/mol)], p = 0.004) at follow‐up compared with controls. In sensitivity analyses of studies with low risk of bias, waist circumference, HbA1c, and fasting glucose levels (WMD [95% CI] = −0.63 mmol/L [−1.09, −0.18], p = 0.006) were significantly lower in intervention groups versus controls. There was also a trend toward lower fat mass (p = 0.09), insulin resistance (p = 0.07), and higher insulin secretion (p = 0.06) in intervention versus control groups. Supplementation with histidine‐containing dipeptides may reduce central obesity and improve glycaemic outcomes. Further studies exploring histidine‐containing dipeptide use in obesity and diabetes prevention and treatment are warranted.