Miracle-dz/UniFAR-FTUs huggingface dataset:
Gravity Optimizer: a Kinematic Approach on Optimization in Deep Learning

We introduce Gravity, another algorithm for gradient-based optimization. In this paper, we explain how our novel idea change parameters to reduce the deep learning model's loss. It has three intuitive hyper-parameters that the best values for them are proposed. Also, we propose an alternative to moving average. To compare the performance of the Gravity optimizer with two common optimizers, Adam and RMSProp, five standard datasets were trained on two VGGNet models with a batch size of 128 for 100 epochs. Gravity hyper-parameters did not need to be tuned for different models. As will be explained more in the paper, to investigate the direct impact of the optimizer itself on loss reduction no overfitting prevention technique was used. The obtained results show that the Gravity optimizer has more stable performance than Adam and RMSProp and gives greater values of validation accuracy for datasets with more output classes like CIFAR-100 (Fine).
SUTRA: An Approach to Modelling Pandemics with Asymptomatic Patients,and Applications to COVID-19

In this paper, we present a new mathematical model for pandemics that have asymptomatic patients, called SUTRA. The acronym stands for Susceptible, Undetected, Tested (positive), and Removed Approach. There are several novel features of our proposed model. First, whereas previous papers have divided the patient population into Asymptomatic and Infected, we have explicitly accounted for the fact that, due to contact tracing and other such protocols, some fraction of asymptomatic patients could also be detected; in addition, there would also be large numbers of undetected asymptomatic patients. Second, we have explicitly taken into account the spatial spread of a pandemic over time, through a parameter called “reach. ” Third, we present numerically stable methods for estimating the parameters in our model. We have applied our model to predict the progression of the COVID-19 pandemic in several countries. Where data on the number of recovered patients is available, we predict the number of active cases as a function of time. Where recovery data is not available, we predict the number of daily new cases. We present our predictions for three countries with quite distinct types of disease progression, namely: (i) India which has had a smooth rise followed by an equally smooth fall-off in the number of active cases, (ii) Italy, which has witnessed multiple peaks in the number of active cases, and has also witnessed multiple “phases” of the pandemic, and (iii) the USA which has erratic recovery data. In all cases, the predictions closely match the actually observed outcomes.
Efficient Near-Field Imaging Using Cylindrical MIMO Arrays

Multiple-input–multiple-output (MIMO) array-based millimeter-wave (MMW) imaging has a tangible prospect in applications of concealed weapons detection. A near-field imaging algorithm based on wavenumber domain processing is proposed for a cylindrical MIMO array scheme with uniformly spaced transmit and receive antennas over both the vertical and horizontal-arc directions. The spectrum aliasing associated with the proposed MIMO array is analyzed through a zero-filling discrete-time Fourier transform. The analysis shows that an undersampled array can be used in recovering the MMW image by a wavenumber domain algorithm. The requirements for the antenna interelement spacing of the MIMO array are delineated. Numerical simulations as well as comparisons with the backprojection algorithm are provided to demonstrate the effectiveness of the proposed method.
Fully Depleted Monolithic Active Microstrip Sensors: TCAD Simulation Study of an Innovative Design Concept

The paper presents the simulation studies of 10 μm pitch microstrips on a fully depleted monolithic active CMOS technology and describes their potential to provide a new and cost-effective solution for particle tracking and timing applications. The Fully Depleted Monolithic Active Microstrip Sensors (FD-MAMS) described in this work, which are developed within the framework of the ARCADIA project, are compliant with commercial CMOS fabrication processes. A set of Technology Computer-Aided Design (TCAD) parametric simulations was performed in the perspective of an upcoming engineering production run with the aim of designing FD-MAMS, studying their electrical characteristics, and optimizing the sensor layout for enhanced performance in terms of low capacitance, fast charge collection, and low-power operation. A fine pitch of 10 μm was chosen to provide high spatial resolution. This small pitch still allows readout electronics to be monolithically integrated in the inter-strip regions, enabling the segmentation of long strips and the implementation of distributed readout architectures. The effects of surface radiation damage expected for total ionizing doses of the order of 10 to 105 krad were also modeled in the simulations. The results of the simulations exhibit promising performance in terms of timing and low power consumption and motivate R&D efforts to further develop FD-MAMS; the results will be experimentally verified through measurements on the test structures that will be available from mid-2021.
Occlusion Handling in Generic Object Detection: A Review

The significant power of deep learning networks has led to enormous development in object detection. Over the last few years, object detector frameworks have achieved tremendous success in both accuracy and efficiency. However, their ability is far from that of human beings due to several factors, occlusion being one of them. Since occlusion can happen in various locations, scale, and ratio, it is very difficult to handle. In this paper, we address the challenges in occlusion handling in generic object detection in both outdoor and indoor scenes, then we refer to the recent works that have been carried out to overcome these challenges. Finally, we discuss some possible future directions of research.
Adaptive Neighbourhoods for the Discovery of Adversarial Examples

Deep Neural Networks (DNNs) have often supplied state-of-the-art results in pattern recognition tasks. Despite their advances, however, the existence of adversarial examples have caught the attention of the community. Many existing works have proposed methods for searching for adversarial examples within fixed-sized regions around training points. Our work complements and improves these existing approaches by adapting the size of these regions based on the problem complexity and data sampling density. This makes such approaches more appropriate for other types of data and may further improve adversarial training methods by increasing the region sizes without creating incorrect labels.
Skew localizer and $\mathbb{Z}_2$-flows for real index pairings

Real index pairings of projections and unitaries on a separable Hilbert space with a real structure are defined when the projections and unitaries fulfill symmetry relations invoking the real structure, namely projections can be real, quaternionic, even or odd Lagrangian and unitaries can be real, quaternionic, symmetric or anti-symmetric. There are 64 such real index pairings of real K-theory with real K-homology. For 16 of them, the index of the Fredholm operator representing the pairing vanishes, but there is a secondary Z2-valued invariant. The first set of results provides index formulas expressing each of these 16 Z2-valued pairings as either an orientation flow or a half-spectral flow. The second and main set of results constructs the skew localizer for a pairing stemming from an unbounded Fredholm module and shows that the Z2-invariant can be computed as the sign of the Pfaffian of the skew localizer and in 8 of the cases as the sign of the determinant of the off-diagonal entry of the skew localizer. This is of relevance for the numerical computation of invariants of topological insulators. MSC: 19K56, 58J30, 46L80
Fourier Series-Based Approximation of Time-Varying Parameters Using the Ensemble Kalman Filter

In this work, we propose a Fourier series-based approximation method using ensemble Kalman filtering to estimate time-varying parameters in deterministic dynamical systems. We demonstrate the capability of this approach in estimating both sinusoidal and polynomial forcing parameters in a mass-spring system. Results emphasize the importance of the choice of frequencies in the approximation model terms on the corresponding time-varying parameter estimates.
Measurement of Absolute Single and Double Electron Capture Cross Sections for O6+ Ion Collisions with CO2, CH4, H2, and N2

The absolute electron capture cross sections for single and double charge exchanges (CEs) between the highly charged ion O6+ and CO2, CH4, H2, and N2, the dominant collision processes in the solar wind, have been measured in the energies from 7 keV · q (2.63 keV u−1) to 52 keV · q (19.5 keV u−1). These measurements were carried out in the new experimental instrument setup at Fudan University, and the errors of the cross sections for single and double CEs at the 1σ confidence level were about 11% and 16%, respectively. Limited agreement is achieved with single electron capture results calculated by the classical overbarrier model. These cross section data are useful for the simulation of ion–neutral processes in astrophysical environments and to improve the present theoretical model of fundamental atomic processes.
Awake Laser Ablation for Patients With Tumors in Eloquent Brain Areas: Operative Technique and Case Series

Background Magnetic resonance imaging (MRI)-guided laser interstitial thermal therapy (LITT) is a minimally invasive treatment modality that has been gaining traction in neuro-oncology. Laser ablation is a particularly appealing treatment option when eloquent neurologic function at the tumor location precludes conventional surgical excision. Although typically performed under general anesthesia, LITT in awake patients may help monitor and preserve critical neurologic functions. Objective To describe intraoperative workflow and clinical outcomes in patients undergoing awake laser ablation of brain tumors. Methods We present a cohort of six patients with tumors located in eloquent brain areas that were treated with awake LITT and report three different workflow paradigms involving diagnostic or intraoperative MRI. In all cases, we used NeuroBlate® (Monteris Medical, Plymouth, MN) fiberoptic laser probes for stereotactic laser ablation of tumors. The neurologic status of patients was intermittently assessed every few minutes during the ablation. Results The mean preoperative tumor volume that was targeted was 12.09 ± 3.20 cm3, and the estimated ablation volume was 12.06 ± 2.75 cm3. Performing the procedure in awake patients allowed us close monitoring of neurologic function intraoperatively. There were no surgical complications. The length of stay was one day for all patients except one. Three patients experienced acute or delayed worsening of pre-existing neurologic deficits that responded to corticosteroids. Conclusion We propose that awake LITT is a safe approach when tumors in eloquent brain areas are considered for laser ablation.
Dietary chromium effects on tissue chromium concentrations and chromium absorption in rats

Chromium (Cr) absorption is low (<1%) and there is a need to find Cr compounds that are absorbed better than inorganic Cr salts. Therefore, the incorporation of nine different chromium (Cr) compounds on tissue Cr concentration of 6-week male Wistar rats was investigated. Chromium compounds tested were Cr chloride (Cr chloride), Cr acetate (Cr acetate), Cr potassium sulfate (CrAlum), Cr trihistidine (Cr histidine), Cr triglycine (Cr glycine), Cr trinicotinic acid (CrNA), Cr dinicotinic acid dihistidine (CrNA-HIS), Cr tripicolinic acid (Cr picolinate), and Cr dinicotinic acid diglycine cysteine glutamic acid (CrNA-AA). Complexes were fed to weanling rats for 3 weeks at 5,000 ng of Cr/g of diet. Basal control diet was a cornstarch-based diet containing 30 ng Cr/g. Chromium incorporation into the kidney was greatest for CrNA-AA complex (850 ng/g dry wt) followed by CrAlum (407 ng/g), Cr acetate (397), CrNA-HIS (394), Cr picolinate (368), Cr glycine (343), Cr nicotinate (166), Cr chloride (74), CrHIS (49), and control (23 ng/g). Chromium concentration of the liver was greatest for the Cr picolinate compound (50 ng/g) followed by CrNA-AA and Cr acetate. Liver Cr concentrations of remaining complexes were not significantly different from those of the control animals that received no added Cr. Chromium concentrations were significantly greater in the kidney than those for the liver, spleen, heart, lungs, and gastrocnemius muscle. Supplemental Cr did not affect tissue zinc and copper but did alter tissue iron concentrations. Absorption of radioactive forms of Cr did not explain the differences in tissue Cr concentrations. Chromium absorption after 4 hours and retention after 24 hours were not significantly different for the forms of Cr tested. These data demonstrate that Cr concentrations are greatest in the kidney and that the form of dietary Cr significantly affects tissue Cr concentrations. Absorption of Cr does not correlate with tissue Cr concentrations and blood Cr is not in equilibrium with tissue Cr stores. © 1996 Wiley-Liss, Inc. This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism

Abstract Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host–parasite adaptation.
The role of eutherian‐specific RTL1 in the nervous system and its implications for the Kagami‐Ogata and Temple syndromes

RTL1 (also termed paternal expressed 11 (PEG11)) is considered the major imprinted gene responsible for the placental and fetal/neonatal muscle defects that occur in the Kagami–Ogata and Temple syndromes (KOS14 and TS14, respectively). However, it remains elusive whether RTL1 is also involved in their neurological symptoms, such as behavioral and developmental delay/intellectual disability, feeding difficulties, motor delay, and delayed speech. Here, we demonstrate that the mouse RTL1 protein is widely expressed in the central nervous system (CNS), including the limbic system. Importantly, two disease model mice with over‐ and under‐expression of Rtl1 exhibited reduced locomotor activity, increased anxiety, and impaired amygdala‐dependent cued fear, demonstrating that Rtl1 also plays an important role in the CNS. These results indicate that the KOS14 and TS14 are neuromuscular as well as neuropsychiatric diseases caused by irregular CNS RTL1 expression, presumably leading to impaired innervation of motor neurons to skeletal muscles as well as malfunction of the hippocampus‐amygdala complex. It is of considerable interest that eutherian‐specific RTL1 is expressed in mammalian‐ and eutherian‐specific brain structures, that is, the corticospinal tract and corpus callosum, respectively, suggesting that RTL1 might have contributed to the acquisition of both these structures themselves and fine motor skill in eutherian brain evolution.
All you need is air—Alternating activated sludge system BIOCOS without electromechanical equipment

Exclusively air‐driven operation is an essential feature of the cyclic activated sludge process BIOCOS. Switching the air‐flow between diffusers, agitation, and recycle air‐lift keeps operation and maintenance simple and leads to significant energy savings used for mechanical devices. The overall energy demand for the whole biological system with settling was found to be below 20 kWh/PE.a. This hybrid technology shows a constant water level characteristic for continuous flow systems and time‐based control. Modular rectangular tank configuration and high solids operation targets a compact footprint. Process wise, the settling sludge blanket in the two alternating settling tanks was found to contribute considerably to post‐denitrification and enhances phosphorus removal. During the last years, approximately 200 BIOCOS plants have been implemented mainly in Germany, Austria, Spain, and China, some of the operational results are presented in this paper.
Fresh cheese from camel milk coagulated with Camifloc

Camel milk was processed into cheese using Camifloc and calcium chloride. Two types of cheeses were produced from camel milk, using Camifloc (CF cheese) and CaC 12 in addition to Camifloc (CFCC cheese). The study revealed the usefulness of Camifloc in coagulation of camel milk. The time of coagulation was found to be about 2-3 h, and the yield of CFCC cheese was found to be higher than the CF cheese, while a shelf life of 4 days was obtained for both cheeses. Both cheeses showed nonsignificant variations in compositional content except for the percentages of protein and ash, which showed significant differences at P < 0.007 and P < 0.05. Sensory evaluation by taste panellists was conducted to determine the acceptability of cheeses during the storage periods. Differences were found between the CF cheese and the CFCC cheese in saltiness and overall acceptability, and higher mean scores were recorded for the CF cheese than the CFCC cheese. The study recommends the use of Camifloc in making cheese from camel milk; and fCaCl 2 is added, it can improve the cheese yield. However, we suggest that the rate of salting should be reduced, and further drying and storage of the cheese should be done.
Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii

Citrobacter species often occur in sewage, food, soil, wastewater, and in the intestinal tract of animals and humans. Citrobacter spp. cause urinary tract infections (UTIs) and infantile meningitis in humans. Due to the presence of plasmid-encoded resistance genes, Citrobacter spp. are often resistant to many antibiotics. In this study, Citrobacter virus HCF1, a novel virulent bacteriophage capable of killing Citrobacter amalonaticus and Citrobacter freundii, was isolated from the sewage water. The isolated bacteriophage was characterized with respect to transmission electron microscopy, one-step growth curve, host range, in vitro efficacy, storage stability, and environmental stress tolerance. The one-step growth curve analysis revealed that the latent period of HCF1 was 30 min and the estimated burst size was 121 plaque-forming units (PFU) per bacterial cell. Host range testing indicated that the HCF1 was specific to the Citrobacter genus. In vitro efficacy assay in the effluent of an anaerobic biodigester showed that the HCF1 completely eliminated the host within 4 and 5 h at MOI:100 and MOI:10, respectively, thereby indicating its potential for combating C. amalonaticus infections. The isolated bacteriophage is considerably stable and tolerant to environmental stress. Furthermore, the complete genome of HCF1 was sequenced using Oxford Nanopore sequencing and the data were subjected to detailed bioinformatic analyses. NCBI-BLASTn analysis revealed that the HCF1 genome had a query coverage of 15–21% and a maximum similarity of 77.27–78.49% with 11 bacteriophages of the Drexlerviridae family. Detailed bioinformatic analysis of the genome profile suggests that HCF1 is a novel T1svirus belonging to the Tempevirinae subfamily of the Drexlerviridae family.
Insights Into the Role and Potential of Schwann Cells for Peripheral Nerve Repair From Studies of Development and Injury

Peripheral nerve injuries arising from trauma or disease can lead to sensory and motor deficits and neuropathic pain. Despite the purported ability of the peripheral nerve to self-repair, lifelong disability is common. New molecular and cellular insights have begun to reveal why the peripheral nerve has limited repair capacity. The peripheral nerve is primarily comprised of axons and Schwann cells, the supporting glial cells that produce myelin to facilitate the rapid conduction of electrical impulses. Schwann cells are required for successful nerve regeneration; they partially “de-differentiate” in response to injury, re-initiating the expression of developmental genes that support nerve repair. However, Schwann cell dysfunction, which occurs in chronic nerve injury, disease, and aging, limits their capacity to support endogenous repair, worsening patient outcomes. Cell replacement-based therapeutic approaches using exogenous Schwann cells could be curative, but not all Schwann cells have a “repair” phenotype, defined as the ability to promote axonal growth, maintain a proliferative phenotype, and remyelinate axons. Two cell replacement strategies are being championed for peripheral nerve repair: prospective isolation of “repair” Schwann cells for autologous cell transplants, which is hampered by supply challenges, and directed differentiation of pluripotent stem cells or lineage conversion of accessible somatic cells to induced Schwann cells, with the potential of “unlimited” supply. All approaches require a solid understanding of the molecular mechanisms guiding Schwann cell development and the repair phenotype, which we review herein. Together these studies provide essential context for current efforts to design glial cell-based therapies for peripheral nerve regeneration.