Miracle-dz/UniFAR-FTUs huggingface dataset:
Robust support vector regression model in the presence of outliers and leverage points

Support vector regression is used to evaluate the linear and non-linear relationships among variables. Although it is non-parametric technique, it is still affected by outliers, because the possibility to select them as support vectors. In this article, we proposed a robust support vector regression for linear and nonlinear target functions. In order to carry out this goal, the support vector regression model with fixed parameters is used to detect and minimize the effects of abnormal points in the data set. The efficiency of the proposed method is investigated by using real and simulation examples.
Editorial: Highlights in psychology: cognitive bias

COPYRIGHT © 2023 Da Silva, Gupta and Monzani. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Editorial: Highlights in psychology: cognitive bias
Differential splicing choices made by neurons and astrocytes and their importance when investigating signal-dependent alternative splicing in neural cells

A variety of proteins can be encoded by a single gene via the differential splicing of exons. In neurons this form of alternative splicing can be controlled by activity-dependent calcium signaling, leading to the properties of proteins being altered, including ion channels, neurotransmitter receptors and synaptic cell adhesion molecules. The pre-synaptic cell adhesion molecule Neurexin 1 (Nrxn1) is alternatively spliced at splice-site 4 (SS4) which governs exon 22 inclusion (SS4+) and consequently postsynaptic NMDA receptor responses. Nrxn1 was reported to be subject to a delayed-onset shift in Nrxn1 SS4 splicing resulting in increased exon 22 inclusion, involving epigenetic mechanisms which, if disrupted, reduce memory stability. Exon inclusion at SS4 represented one of hundreds of exons reported to be subject to a genome-wide shift in fractional exon inclusion following membrane depolarization with high extracellular K+ that was delayed in onset. We report that high K+ does not increase the SS4+/SS4− ratio in cortical neurons, but does induce a delayed-onset NMDA receptor-dependent neuronal death. In mixed neuronal/astrocyte cultures this neuronal death results in an increase in the astrocyte: neuron ratio, and a misleading increase in SS4+/SS4− ratio attributable to astrocytes having a far higher SS4+/SS4− ratio than neurons, rather than any change in the neurons themselves. We reassessed the previously reported genome-wide delayed-onset shift in fractional exon inclusion after high K+ exposure. This revealed that the reported changes correlated strongly with differences in exon inclusion level between astrocytes and neurons, and was accompanied by a strong decrease in the ratio of neuron-specific: astrocyte-specific gene expression. As such, these changes can be explained by the neurotoxic nature of the stimulation paradigm, underlining the importance of NMDA receptor blockade when using high K+ depolarizing stimuli.
The use of nonnormalized surface EMG and feature inputs for LSTM-based powered ankle prosthesis control algorithm development

Advancements in instrumentation support improved powered ankle prostheses hardware development. However, control algorithms have limitations regarding number and type of sensors utilized and achieving autonomous adaptation, which is key to a natural ambulation. Surface electromyogram (sEMG) sensors are promising. With a minimized number of sEMG inputs an economic control algorithm can be developed, whereas limiting the use of lower leg muscles will provide a practical algorithm for both ankle disarticulation and transtibial amputation. To determine appropriate sensor combinations, a systematic assessment of the predictive success of variations of multiple sEMG inputs in estimating ankle position and moment has to conducted. More importantly, tackling the use of nonnormalized sEMG data in such algorithm development to overcome processing complexities in real-time is essential, but lacking. We used healthy population level walking data to (1) develop sagittal ankle position and moment predicting algorithms using nonnormalized sEMG, and (2) rank all muscle combinations based on success to determine economic and practical algorithms. Eight lower extremity muscles were studied as sEMG inputs to a long-short-term memory (LSTM) neural network architecture: tibialis anterior (TA), soleus (SO), medial gastrocnemius (MG), peroneus longus (PL), rectus femoris (RF), vastus medialis (VM), biceps femoris (BF) and gluteus maximus (GMax). Five features extracted from nonnormalized sEMG amplitudes were used: integrated EMG (IEMG), mean absolute value (MAV), Willison amplitude (WAMP), root mean square (RMS) and waveform length (WL). Muscle and feature combination variations were ranked using Pearson’s correlation coefficient (r > 0.90 indicates successful correlations), the root-mean-square error and one-dimensional statistical parametric mapping between the original data and LSTM response. The results showed that IEMG+WL yields the best feature combination performance. The best performing variation was MG + RF + VM (rposition = 0.9099 and rmoment = 0.9707) whereas, PL (rposition = 0.9001, rmoment = 0.9703) and GMax+VM (rposition = 0.9010, rmoment = 0.9718) were distinguished as the economic and practical variations, respectively. The study established for the first time the use of nonnormalized sEMG in control algorithm development for level walking.
Identification of miRNAs in extracellular vesicles as potential diagnostic markers for pediatric epilepsy and drug-resistant epilepsy via bioinformatics analysis

Background Pediatric epilepsy (PE) is a common neurological disease. However, many challenges regarding the clinical diagnosis and treatment of PE and drug-resistant epilepsy (DRE) remain unsettled. Our study aimed to identify potential miRNA biomarkers in children with epilepsy and drug-resistant epilepsy by scrutinizing differential miRNA expression profiles. Methods In this study, miRNA expression profiles in plasma extracellular vesicles (EV) of normal controls, children with drug-effective epilepsy (DEE), and children with DRE were obtained. In addition, differential analysis, transcription factor (TF) enrichment analysis, Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, and target gene prediction were used to identify specifically expressed miRNAs and their potential mechanisms of action. Potential diagnostic markers for DRE were identified using machine learning algorithms, and their diagnostic efficiency was assessed by the receiver operating characteristic curve (ROC). Results The hsa-miR-1307-3p, hsa-miR-196a-5p, hsa-miR-199a-3p, and hsa-miR-21-5p were identified as diagnostic markers for PE, with values of area under curve (AUC) 0.780, 0.840, 0.832, and 0.816, respectively. In addition, the logistic regression model incorporating these four miRNAs had an AUC value of 0.940, and its target gene enrichment analysis highlighted that these miRNAs were primarily enriched in the PI3K-Akt, MAPK signaling pathways, and cell cycle. Furthermore, hsa-miR-99a-5p, hsa-miR-532-5p, hsa-miR-181d-5p, and hsa-miR-181a-5p showed good performance in differentiating children with DRE from those with DEE, with AUC values of 0.737 (0.534–0.940), 0.737 (0.523–0.952), 0.788 (0.592–0.985), and 0.788 (0.603–0.974), respectively. Conclusion This study characterized the expression profile of miRNAs in plasma EVs of children with epilepsy and identified miRNAs that can be used for the diagnosis of DRE.
Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry

Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4–67.6 megabases genomes in 178–204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.
Early selection for drought tolerance in popcorn based on gene effects estimated in seedlings

Low rainfall rates are becoming increasingly frequent because of climate change, causing droughts and threatening world food security. For popcorn, drought is the most limiting abiotic factor for plant’s growth and development. Thus, the water deficit directly impacts for crop productivity. Based on knowledge of the genetic basis of traits involved in stages of popcorn germination and seedling development under water stress, genotypes with potential for adaptation to adverse growing conditions can be selected early. Therefore, data on genetic effects and combining ability of 10 popcorn parents were compiled to propose breeding strategies for the development of cultivars with greater adaptation to water stress in the early stages. Forty-five diallel hybrids were evaluated under two different water regimes, that is, water stress and full irrigation. This corresponded to a water retention capacity of 25% and 70% of the germination paper. The plants were watered daily as needed for seven days. A range of factors were evaluated, that is, germination traits including the germination speed index and germination on the seventh day; shoot traits including length and dry weight; and root system including length, dry weight, root-to-shoot ratio, maximum root number, root network area, specific and root network length, and root volume. Breeding for drought adaption in the early stages of popcorn development can be successful when hybrids are used, because of the genetic effects of dominance (ϕs). These control the traits evaluated at the seedling stage. The combinations L61 x P2 and L71 x P3 were recommended, in view of the more successful performance estimated for traits related to the shoot and root system.
New treatment options in elderly patients with Diffuse Large B-cell Lymphoma

Most patients with Diffuse Large B-cell Lymphoma (DLBCL) are old (>65 years of age) and this population is expected to increase in the following years. A simplified geriatric assessment based on a careful evaluation of the fitness status and comorbidities is essential to choose the correct intensity of treatment. Fit older patients can benefit from a standard immunochemotherapy, while unfit/frail patients frequently need reduced doses or substitution of particular agents with less toxic ones. This review focuses on new therapies (e.g., polatuzumab vedotin, tafasitamab, bispecific antibodies) that have indicated promising results in relapsed/refractory patients, particularly in cases not eligible to transplant. Some of these new drugs have been tested as single agents or in combinations as first-line treatment, aiming to improve the outcome of the traditional chemotherapy. If preliminary efficacy and safety data are confirmed in future clinical trials, a chemo-free immunotherapic approach could become an alternative option to offer a curative treatment even in frail patients.
The role of mononuclear phagocyte system in IgA nephropathy: pathogenesis and prognosis

Although the “multiple hits” theory is a widely accepted pathogenesis in IgA nephropathy (IgAN), increasing evidence suggests that the mononuclear/macrophage system plays important roles in the progression of IgAN; however, the exact mechanism is unclear. In the present study, we explored 1,067 patients in 15 studies and found that the number of macrophages per glomerulus was positively related with the degree of hematuria, and the macrophages in the glomeruli were mainly related to mesangial proliferation (M) in renal biopsy. In the tubulointerstitium, macrophages were significantly paralleled to tubulointerstitial α-SMA and NF-kB expression, tubulointerstitial lesion, tubule atrophy/interstitial fibrosis (T), and segmental glomerulosclerosis (S). In the glomeruli and tubulointerstitium, M1 accounted for 85.41% in the M classification according to the Oxford MEST-C, while in the blood, M1 accounted for 100%, and the patients with low CD89+ monocyte mean fluorescence intensity displayed more severe pathological characteristics (S1 and T1-2) and clinical symptoms. M1 (CD80+) macrophages were associated with proinflammation in the acute phase; however, M2 (CD163+) macrophages participated in tissue repair and remodeling, which correlated with chronic inflammation. In the glomeruli, M2 macrophages activated glomerular matrix expansion by secreting cytokines such as IL-10 and tumor necrosis factor-β (TGF-β), and M0 (CD68+) macrophages stimulated glomerular hypercellularity. In the tubulointerstitium, M2 macrophages played pivotal roles in renal fibrosis and sclerosis. It is assumed that macrophages acted as antigen-presenting cells to activate T cells and released diverse cytokines to stimulate an inflammatory response. Macrophages infiltrating glomeruli destroy the integrity of podocytes through the mesangio-podocytic-tubular crosstalk as well as the injury of the tubule.
Comparing the effects of microgravity and amyotrophic lateral sclerosis on mouse dorsal root ganglia

Introduction: Microgravity (MG) exposure causes motor deficits and decreased neuronal activity, effects that resemble the ones observed in motor neuron diseases such as amyotrophic lateral sclerosis (ALS). Several recent studies have shown that exposure to MG and ALS also impacts the sensory systems. Yet, the role of sensory impairment in this degenerative process of exposure to MG and ALS remains unknown. In this study, we aimed at elucidating how the sensory system is affected by exposure to MG and ALS. Methods: To this end, we compared gene expression in the mouse lumbar dorsal root ganglia (DRG) of MG-exposed animals with that of control animals that remained under artificial gravity conditions. We then investigated the effects of the human superoxide dismutase 1 (SOD1) G93A mutation in a mouse model of ALS (SOD1G93A mice) on gene expression in the DRG. Results: The overlap of genes with negatively correlated expression was greater than those with positively correlated expression between the DRG of MG-exposed and SOD1G93A mice. Additionally, genes related to Imoonglia (characteristics of both immune and glial cells) and macrophage increased in response to MG exposure, while satellite glial cell genes were expressed in response to SOD1 mutation. Next, we examined genes related to sensory neuron subtypes in the DRG. We found altered gene expression in genes related to proprioceptive and mechanoreceptive neurons in the DRG of MG-exposed and SOD1G93A mice. Remarkably, the expression of Atf3 and genes related to nociceptive neurons in the DRG of SOD1G93A mice at postnatal day (P) 120 was considerably altered, whereas MG-exposed and SOD1G93A mice at P30 presented little changes. Discussion: These results indicate that exposure to MG and ALS affect gene expression in genes related to neurons and non-neuronal cells in the DRG, with significant differences between the effects of MG and the SOD1 mutation. Elucidation of the impact of exposure to MG and ALS pathogenesis in the DRG, including identification of the molecular pathways that regulate DRG dysfunction, will help better understand the differences in vulnerability and the triggering processes of impaired motor function associated with MG and ALS.
Integrated analysis of circRNA, lncRNA, miRNA and mRNA to reveal the ceRNA regulatory network of postnatal skeletal muscle development in Ningxiang pig

Introduction: The development of skeletal muscle is regulated by regulatory factors of genes and non-coding RNAs (ncRNAs). Methods: The objective of this study was to understand the transformation of muscle fiber type in the longissimus dorsi muscle of male Ningxiang pigs at four different growth stages (30, 90, 150, and 210 days after birth, n = 3) by histological analysis and whole transcriptome sequencing. Additionally, the study investigated the expression patterns of various RNAs involved in muscle fiber transformation and constructed a regulatory network for competing endogenous RNA (ceRNA) that includes circular RNA (circRNA)/long non-coding RNA (lncRNA)-microRNA (miRNA)-messenger RNA (mRNA). Results: Histomorphology analysis showed that the diameter of muscle fiber reached its maximum at 150 days after birth. The slow muscle fiber transformation showed a pattern of initial decrease followed by an increase. 29,963 circRNAs, 2,683 lncRNAs, 986 miRNAs and 22,411 mRNAs with expression level ≥0 were identified by whole transcriptome sequencing. Furthermore, 642 differentially expressed circRNAs (DEc), 505 differentially expressed lncRNAs (DEl), 316 differentially expressed miRNAs (DEmi) and 6,090 differentially expressed mRNAs (DEm) were identified by differential expression analysis. Functions of differentially expressed mRNA were identified by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). GO enrichment analysis indicates that 40 known genes and 6 new genes are associated with skeletal muscle development. Additionally, KEGG analysis shows that these genes regulate skeletal muscle development via MAPK, FoxO, Hedgehog, PI3K-Akt, Notch, VEGF and other signaling pathways. Through protein-protein interaction (PPI) and transcription factor prediction (TFP), the action mode of skeletal muscle-related genes was explored. PPI analysis showed that there were stable interactions among 19 proteins, meanwhile, TFP analysis predicted 22 transcription factors such as HMG20B, MYF6, MYOD1 and MYOG, and 12 of the 19 interacting proteins were transcription factors. The regulatory network of ceRNA related to skeletal muscle development was constructed based on the correlation of various RNA expression levels and the targeted binding characteristics with miRNA. The regulatory network included 31 DEms, 59 miRNAs, 667 circRNAs and 224 lncRNAs. conclusion: Overall, the study revealed the role of ceRNA regulatory network in the transformation of skeletal muscle fiber types in Ningxiang pigs, which contributes to the understanding of ceRNA regulatory network in Ningxiang pigs during the skeletal muscle development period.
Ca2+-stimulated ADCY1 and ADCY8 regulate distinct aspects of synaptic and cognitive flexibility

The type 1 and 8 adenylyl cyclase (ADCY1 and ADCY8) exclusively account for Ca2+-stimulated cyclic AMP (cAMP) production and regulate activity-dependent synaptic modification. In this study, we examined distinct forms of synaptic plasticity in the hippocampus of Adcy1−/− and Adcy8−/− mice. We found that, at the Schaffer collateral-CA1 synapses, while the Adcy8−/− mice displayed normal long-term potentiation (LTP) following various induction protocols with high-frequency stimulation (HFS), the Adcy1−/− mice showed protocol-dependent deficits in LTP. We also found that long-term depression (LTD) requires ADCY1 but not ADCY8. Interestingly, both Adcy1−/− and Adcy8−/− mice showed defective synaptic depotentiation (i.e., activity-dependent reversal of LTP); the deficits in Adcy8−/− mice were dependent on the induction protocol. Examination of spatial memory found that ADCY1 is required for the formation of both initial and reversal memory. ADCY8 is only required for reversal memory formation. These data demonstrate that ADCY1 and ADCY8 play distinct roles in regulating synaptic and cognitive flexibility that involves bidirectional modification of synaptic function.
Sensitivity of Sudden Stratospheric Warmings to Previous Stratospheric Conditions

AbstractThe Whole Atmosphere Community Climate Model, version 4 (WACCM4), is used to investigate the influence of stratospheric conditions on the development of sudden stratospheric warmings (SSWs). To this end, targeted experiments are performed on selected modeled SSW events. Specifically, the model is reinitialized three weeks before a given SSW, relaxing the surface fluxes, winds, and temperature below 10 km to the corresponding fields from the free-running simulation. Hence, the tropospheric wave evolution is unaltered across the targeted experiments, but the stratosphere itself can evolve freely. The stratospheric zonal-mean state is then altered 21 days prior to the selected SSWs and rerun with an ensemble of different initial conditions. It is found that a given tropospheric evolution concomitant with the development of an SSW does not uniquely determine the occurrence of an event and that the stratospheric conditions are relevant to the subsequent evolution of the stratospheric flow toward an SSW.
The Moduli Space of Compact Fiber Bundle Structures on a Fibration

by Stacy L. Hoehn Suppose that p is a fibration with total space E over a connected, finite CW complex B whose fibers are homotopy equivalent to a finite CW complex F . Then there is a fibration associated to p whose fibers are all homotopy equivalent to A(F ), the algebraic K-theory space of F . Dwyer, Weiss, and Williams have constructed a section of this fibration, called the parametrized Euler characteristic of p, which has a lift to a parametrized excisive Euler characteristic if and only if p is fiber homotopy equivalent to a topological fiber bundle whose fibers are homeomorphic to a compact topological manifold, possibly with boundary. Assuming that p does admit at least one compact topological fiber bundle structure, we can also try to classify the space of all such structures on p. We show that this space of structures on p is homotopy equivalent to the product of the space of all lifts of the parametrized Euler characteristic of p to a parametrized excisive Euler characteristic with the space of stable Euclidean bundles over E.