Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance Enhancement Strategies for Sparse Matrix-Vector Multiplication (SpMV) and Iterative Linear Solvers

Iterative solutions of sparse linear systems and sparse eigenvalue problems have a fundamental role in vital fields of scientific research and engineering. The crucial computing kernel for such iterative solutions is the multiplication of a sparse matrix by a dense vector. Efficient implementation of sparse matrix-vector multiplication (SpMV) and linear solvers are therefore essential and has been subjected to extensive research across a variety of computing architectures and accelerators such as central processing units (CPUs), graphical processing units (GPUs), many integrated cores (MICs), and field programmable gate arrays (FPGAs). Unleashing the full potential of an architecture/accelerator requires determining the factors that affect an efficient implementation of SpMV. This article presents the first of its kind, in-depth survey covering over two hundred state-of-the-art optimization schemes for solving sparse iterative linear systems with a focus on computing SpMV. A new taxonomy for iterative solutions and SpMV techniques common to all architectures is proposed. This article includes reviews of SpMV techniques for all architectures to consolidate a single taxonomy to encourage cross-architectural and heterogeneous-architecture developments. However, the primary focus is on GPUs. The major contributions as well as the primary, secondary, and tertiary contributions of the SpMV techniques are first highlighted utilizing the taxonomy and then qualitatively compared. A summary of the current state of the research for each architecture is discussed separately. Finally, several open problems and key challenges for future research directions are outlined.
Evaluating Weakly Supervised Object Localization Methods Right? A Study on Heatmap-Based Xai and Neural Backed Decision Tree

Choe et al have investigated several aspects of Weakly Supervised Object Localization (WSOL) with only image label. They addressed the ill-posed nature of the problem and showed that WSOL has not significantly improved beyond the baseline method class activation mapping (CAM). We report the results of similar experiments on ResNet50 with some crucial differences: (1) we perform WSOL using heatmap-based eXplanaible AI (XAI) methods (2) we consider the XAI aspect of WSOL in which localization is used as the explanation of a class prediction task. Under similar protocol, we find that XAI methods perform WSOL with very sub-standard MaxBoxAcc scores. The experiment is then repeated for the same model trained with Neural Backed Decision Tree (NBDT) and we found that vanilla CAM yields significantly better WSOL performance after NBDT training.
SEX DIFFERENCES IN MATHEMATICS ACHIEVEMENT–A LONGITUDINAL STUDY

With the objective of investigating sex-typed interests as possible causes of difference in mathematics achieve ment between the sexes, this study made use of longitudinal data from the Growth Study, begun at Educational Testing Service (ETS) in 1961. Growth in mathematics achievement as measured by STEP Math and SCAT-Q was compared with changing interest patterns as reflected in certain biographical questionnaire responses. At grade 5 there were no differences in achievement but thereafter the boys pulled ahead, while parallel differences emerged in the percentage perceiving mathematics as interesting and as likely to be helpful in earning a living. MANY PREVIOUS studies have examined sex differences in ability and achievement in mathe matics. Tyler (18:240ff), Anastasi (3:497), and Maccoby (15:26-28) surveyed the field of sex dif ferences in aptitude and achievement and report that girls usually do better in verbal and linguistic studies, while boys generally do better in nu merical and spatial aptitudes and in tests of arithmetical reasoning. Maccoby points out that during grade school years, some studies show boys beginning to forge ahead on tests of i(arithmetical reasoning," although a number of studies reveal no sex differences on this dimension at this time. Fairly consistently, however, boys excel at arithmetical reason ing in high school, and the differences are substantially in favor of men among college students and adults (15:26).
The Band Structure of Silver and Optical Interband Transitions

The band structure of silver has been calculated using the relativistic augmented plane wave method. Relativistic effects must be included if a quantitative interpretation of optical experiments is made. The L′2 → L1 gap is 1 eV smaller in the relativistic calculation than it is in a non-relativistic band structure obtained from the same potential. This reduction of the L-gap is in the present case sufficient to lead to an extra interband edge below the main edge at 3.98 eV. The optical function e2(ω) and the energy distributions of photoemitted electrons have been calculated.
Antibiotic Tolerance and Treatment Outcomes in Cystic Fibrosis Methicillin-Resistant Staphylococcus aureus Infections

Chronic MRSA infections remain challenging to treat in patients with cystic fibrosis (CF). The ability of the bacterial population to survive high concentrations of bactericidal antibiotics, including vancomycin, despite lacking resistance is considered one of the main reasons for treatment failures. ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) is highly prevalent in U.S. cystic fibrosis (CF) patients and is associated with worse clinical outcomes in CF. These infections often become chronic despite repeated antibiotic therapy. Here, we assessed whether bacterial phenotypes, including antibiotic tolerance, can predict the clinical outcomes of MRSA infections. MRSA isolates (n = 90) collected at the incident (i.e., acute) and early infection states from 57 patients were characterized for growth rates, biofilm formation, hemolysis, pigmentation, and vancomycin tolerance. The resistance profiles were consistent with those in prior studies. Isolates from the early stage of infection were found to produce biofilms, and 70% of the isolates exhibited delta-hemolysis, an indicator of agr activity. Strong vancomycin tolerance was present in 24% of the isolates but was not associated with intermediate vancomycin susceptibility. There were no associations between these phenotypic measures, antibiotic tolerance, and MRSA clearance. Our research suggests that additional factors may be relevant for predicting the clearance of MRSA. IMPORTANCE Chronic MRSA infections remain challenging to treat in patients with cystic fibrosis (CF). The ability of the bacterial population to survive high concentrations of bactericidal antibiotics, including vancomycin, despite lacking resistance is considered one of the main reasons for treatment failures. The connection between antibiotic tolerance and treatment outcomes remains unexplored and can be crucial for prognosis and regimen design toward eradication. In this study, we measured the capacity of 90 MRSA isolates from CF patients to form vancomycin-tolerant persister cells and evaluated their correlation with the clinical outcomes. Additionally, various traits that could reflect the metabolism and/or virulence of those MRSA isolates were systematically phenotyped and included for their predictive power. Our research highlights that despite the importance of antibiotic tolerance, additional factors need to be considered for predicting the clearance of MRSA.
Perception and identification of tones in different timbres: Using pupil diameter to investigate absolute pitch ability

Absolute pitch (AP) is the ability to effortlessly identify or produce pitches without reference. However, behavioral research has shown that pitch perception and identification in certain timbres are more difficult for AP possessors. In this study, we investigate whether pitch identification and labeling in different timbres (piano and voice) would require different amounts of cognitive resource allocation. We measured accuracy, response time, and pupillary responses of 18 musicians with varying degrees of AP while performing a pitch identification test. We also examined whether behavioral and psychophysiological responses were related to aspects of musical experience, such as the age of onset of musical training, daily hours of practice, and years of musical training. Behavioral results revealed significantly longer response time for vocal tones compared to piano tones. However, there was no difference in accuracy when comparing pitch labeling in piano and vocal tones. On the psychophysiological level, pupillary responses were significantly different across timbre conditions, with larger pupil dilation for vocal tones than piano tones. We also observed an effect of key color (whether the tones corresponded to diatonic or chromatic tones in a C major scale) on pupil dilation, with greater dilation for pitches corresponding to black keys compared to white keys. These findings expand the current knowledge regarding how pitches in different timbres are processed by musicians with varying degrees of AP and open new avenues for the investigation of potentially different cognitive mechanisms involved in the processing of the human voice and musical timbres by AP possessors.
Low-grade inflammation in type 2 diabetes: a cross-sectional study from a Danish diabetes outpatient clinic

Objectives To investigate low-grade inflammation in type 2 diabetes and explore associations to clinical aspects as well as microvascular and macrovascular complications. Design Cross-sectional analysis. Setting The outpatient diabetes clinic at the Department of Endocrinology at Aalborg University Hospital, Denmark. Participants 100 participants with type 2 diabetes confirmed by a haemoglobin A1c (HbA1c)≥6.5% for a minimum of 1 year and 21 healthy controls. Outcome measures Serum levels of 27 inflammation-related biomarkers measured by immunoassay. Associations with microvascular and macrovascular complications, body weight, glycaemic control, medication and sex were investigated in the diabetes cohort. Results Serum levels of tumour necrosis factor (TNF)-α and eotaxin were elevated in type 2 diabetes (p<0.05), while interleukin (IL)-7 was decreased (p<0.001). IL-12/IL-23p40, IL-15, macrophage-derived chemokine (MDC) and C reactive protein (CRP) levels were increased with body weight (p<0.05), while eotaxin and TNF-α were increased with elevated HbA1c levels (p<0.04). Dipeptidyl peptidase-4 inhibitor therapy was associated with lower levels of induced protein-10, MDC and thymus and activation regulated chemokine (p<0.02), while females had higher levels of MDC (p=0.027). Individuals with ≥3 diabetic complications had elevated levels of IL-6, IL-10, IL-12/IL-23p40, IL-15 and CRP compared with those with ≤3 (p<0.05). Conclusion The level of low-grade inflammation in type 2 diabetes is associated with obesity, glycaemic regulation, therapeutical management, sex and complications. Our results underline the importance of addressing inflammatory issues in type 2 diabetes, as these may predispose for crippling comorbidities.
Hyperbolicity for symmetric periodic orbits in the isosceles three body problem

We study the isosceles three body problem with fixed symmetry line for arbitrary masses, as a subsystem of the N-body problem. Our goal is to construct minimizing noncollision periodic orbits using a symmetric variational method with a finite order symmetry group. The solution of this variational problem gives existence of noncollision periodic orbits which realize certain symbolic sequences of rotations and oscillations in the isosceles three body problem for any choice of the mass ratio. The Maslov index for these periodic orbits is used to prove the main result, Theorem 4.1, which states that the minimizing curves in the three dimensional reduced energy momentum surface can be extended to periodic curves which are generically hyperbolic. This reminds one of a theorem of Poincare [8], concerning minimizing periodic geodesics on orientable 2D surfaces. The results in this paper are novel in two directions: in addition to the higher dimensional setting, the minimization in the current problem is over a symmetry class, rather than a loop space.
Nonlinear dynamics of standing shear Alfvén waves

The nonlinear evolution of driven standing shear Alfven waves is investigated by virtue of a model which includes the interaction of the waves with density perturbations excited by the ponderomotive force. It is shown that the plasma density perturbations take the form of a slow magnetosonic wave which nonlinearly shifts the frequency of the shear Alfven wave and decouples it from the external source. This results in a complicated and sometimes chaotic temporal behavior of the amplitude of the excited waves which depends strongly on the plasma pressure, driver strength, and the frequency mismatch between the driver and shear Alfven eigenmode. The results are discussed in the context of ultra low frequency (ULF) field line resonances in the Earth’s magnetosphere and the excitation of waves in the Alfvenic wave resonator near to the polar ionosphere.
Three-dimensional linear stability analysis of incompressible viscous flows using the finite element method

The linear stability of incompressible flows is investigated on the basis of the finite element method. The two-dimensional base flows computed numerically over a range of Reynolds numbers are perturbed with three-dimensional disturbances. The three-dimensionality in the flow associated with the secondary instability is identified precisely. First, by using linear stability theory and normal mode analysis, the partial differential equations governing the evolution of perturbation are derived from the linearized Navier–Stokes equation with slight compressibility. In terms of the mixed finite element discretization, in which six-node quadratic Lagrange triangular elements with quadratic interpolation for velocities (P2) and three-node linear Lagrange triangular elements for pressure (P1) are employed, a non-singular generalized eigenproblem is formulated from these equations, whose solution gives the dispersion relation between complex growth rate and wave number. Then, the stabilities of two cases, i.e. the lid-driven cavity flow and flow past a circular cylinder, are examined. These studies determine accurately stability curves to identify the critical Reynolds number and the critical wavelength of the neutral mode by means of the Krylov subspace method and discuss the mechanism of instability. For the cavity flow, the estimated critical results are Rec=920.277±0.010 for the Reynolds number and kc=7.40±0.02 for the wave number. These results are in good agreement with the observation of Aidun et al. and are more accurate than those by the finite difference method. This instability in the cavity is associated with absolute instability [Huerre and Monkewitz, Annu. Rev. Fluid Mech. , 22, 473–537 (1990)]. The Taylor–Goertler-like vortices in the cavity are verified by means of the reconstruction of three-dimensional flows. As for the flow past a circular cylinder, the primary instability result shows that the flow has only two-dimensional characteristics at the onset of the von Karman vortex street, when Re<49. The estimated critical values of primary instability are Rec=46.389±0.010 and Stc=0.126 for the Strouhal number. These values are very close to the observation data [Williamson, J. Fluid Mech. , 206, 579–627 (1989)] and other stability results [Morzynski and Thiele, Z. Agnew. Math. Mech. , 71, T424–T428 (1991); Jackson, J. Fluid Mech. , 182, 23–45 (1987)]. This onset of vortex shedding is associated with the symmetry-breaking bifurcation at the Hopf point. Copyright © 1999 John Wiley & Sons, Ltd.
A comprehensive model of Drosophila epithelium reveals the role of embryo geometry and cell topology in mechanical responses

In order to understand morphogenesis, it is necessary to know the material properties or forces shaping the living tissue. In spite of this need, very few in vivo measurements are currently available. Here, using the early Drosophila embryo as a model, we describe a novel cantilever-based technique which allows for the simultaneous quantification of applied force and tissue displacement in a living embryo. By analyzing data from a series of experiments in which embryonic epithelium is subjected to developmentally relevant perturbations, we conclude that the response to applied force is adiabatic and is dominated by elastic forces and geometric constraints, or system size effects. Crucially, computational modeling of the experimental data indicated that the apical surface of the epithelium must be softer than the basal surface, a result which we confirmed experimentally. Further, we used the combination of experimental data and comprehensive computational model to estimate the elastic modulus of the apical surface and set a lower bound on the elastic modulus of the basal surface. More generally, our investigations revealed important general features that we believe should be more widely addressed when quantitatively modeling tissue mechanics in any system. Specifically, different compartments of the same cell can have very different mechanical properties; when they do, they can contribute differently to different mechanical stimuli and cannot be merely averaged together. Additionally, tissue geometry can play a substantial role in mechanical response, and cannot be neglected.
MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localized multicopper oxidase family enzymes LACCASES (LACs) catalyze the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem diameter. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing (miR397OX) and STTM397 chickpea lines showed sensitivity and tolerance, respectively, to drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to dry root rot. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and dry root rot in an agriculturally important crop chickpea.
Impact of growth-promoting alternatives on weight gain and gut microbial diversity and activity in piglets

In swine husbandry, weaning is a critical event for piglets which causes environmental, nutritional, and psychological stresses, with consequences such as intestinal dysbiosis. To counteract this issue, producers resorted to the use of in-feed antimicrobials to prevent post-weaning diarrhea and to promote growth for increased animal performance. However, the use of antibiotic for growth promotion was banned in many countries. In-feed supplements have great potential as alternative strategies. This study evaluated the effect on gut microbial activity, microbiome, and animal performance of combinations of peri-weaning feeding strategies such as bovine colostrum, medium-chain fatty acids and yeast extract. We quantified weight gain, intestinal pH, volatile fatty acids, and characterized the gut microbiota on ileum, cecum, and colon digestates. Overall, the feed supplements had limited impact on weight gain and volatile fatty acids production. However, the combined treatments have demonstrated a modulatory effect on gut microbiota which supports a potential role as an alternative to growth-promoting antibiotic in the swine industry.
Canonical formalism of N = 1 supergravity with the real Ashtekar variables

The canonical formalism of N = 1 supergravity with the real Ashtekar variables are considered. This canonical formalism is derived from that of the usual N = 1 supergravity by performing the Barbero-type canonical transformation with a free parameter β. We also introduce new variables to simplify the Dirac brackets of the canonical variables and give the canonical constraints in terms of these variables. We examine the canonical structure of the theory.
Characterization of the mIF4G domains in the RNA surveillance protein Upf2

Thirty percent of all mutations causing human diseases generate mRNAs with premature termination codons (PTCs). Recognition and degradation of these PTC-containing mRNAs is carried out by the mechanism known as nonsense-mediated mRNA decay (NMD). Upf2 is a scaffold protein known to be a central component of the NMD surveillance pathway. It harbors three middle domain of eukaryotic initiation factor 4G (mIF4G) domains in its N-terminal potentially important in regulating the surveillance pathway. In this study, we defined regions within the mIF4G-1 and mIF4G-2 that are required for proper function of NMD and translation termination in Saccharomyces cerevisiae Upf2. In addition, we narrowed down the activity of these regions to an aspartic acid (D59) in mIF4G-1 which is important for NMD activity and translation termination accuracy. Taken together, these studies suggest that inherent charged residues within mIF4G-1 of Upf2 play a role in the regulation of the NMD surveillance mechanism in S. cerevisiae.
Neural computations in prosopagnosia

We aimed to identify neural computations underlying the loss of face identification ability by modelling the brain activity of brain-lesioned patient PS, a well-documented case of acquired pure prosopagnosia. We collected a large dataset of high-density electrophysiological (EEG) recordings from PS and neurotypicals while they completed a one-back task on a stream of face, object, animal and scene images. We found reduced neural decoding of face identity around the N170 window in PS, and conjointly revealed normal non-face identification in this patient. We used Representational Similarity Analysis (RSA) to correlate human EEG representations with those of deep neural network (DNN) models of vision and caption-level semantics, offering a window into the neural computations at play in patient PS’s deficits. Brain representational dissimilarity matrices (RDMs) were computed for each participant at 4 ms steps using cross-validated classifiers. PS’s brain RDMs showed significant reliability across sessions, indicating meaningful measurements of brain representations with RSA even in the presence of significant lesions. Crucially, computational analyses were able to reveal PS’s representational deficits in high-level visual and semantic brain computations. Such multi-modal data-driven characterisations of prosopagnosia highlight the complex nature of processes contributing to face recognition in the human brain. Highlights We assess the neural computations in the prosopagnosic patient PS using EEG, RSA, and deep neural networks Neural dynamics of brain-lesioned PS are reliably captured using RSA Neural decoding shows normal evidence for non-face individuation in PS Neural decoding shows abnormal neural evidence for face individuation in PS PS shows impaired high-level visual and semantic neural computations