Miracle-dz/UniFAR-FTUs huggingface dataset:
Galois coverings and simple connectedness of piecewise hereditary algebras

Let A a basic connected and finite dimensional piecewise hereditary algebra of type Q. We prove that A admits a universal Galois covering with group the fundamental group of Q. As a corollary, we deduce that A is simply connected if and only if Q is a tree, if and only if the Hocschild cohomology group HH^1(A) vanishes. As an application, we prove that if C->A is a Galois covering with group G, then C is piecewise hereditary of type a Galois covering with group G of Q.
Turnover in fish species composition is related to water colour of Amazonian rivers

Abstract Variation in water colour is a remarkable characteristic of Amazonian rivers and reflects their limnological properties and the geomorphology of sub-basins. We present here a literature-based study to examine the relationships between fish species turnover and abiotic properties of Amazonian rivers with contrasting water colours. We analysed fish records and water physicochemical properties (pH, colour, turbidity, dissolved oxygen, ammonia and suspended solids) of eight Amazonian rivers with white-, black- and clearwaters. Rivers with similar water colour shared more fish species than those that contrasted in colour. Increased differences in abiotic parameters imply an increased dissimilarity in fish species composition. Species composition is also related to distance among rivers with high dissimilarity observed in rivers distant to each other. The fish species turnover could be ultimately driven by the geological history of rivers which provides different opportunities to speciation and biotic interchange. Water types likely influence species turnover by selecting fishes with different limits of physiological tolerance and specialized use of different habitat types. Our findings suggest that river water colours are reliable proxies for historical and ecological mechanisms affected fish species distribution. Antropic disturbances of Amazonian rivers with distinct water colours could threaten unique fish assemblages.
High electron mobility AlGaN/AlN/GaN HEMT structure with a nano-scale AlN interlayer

Epitaxies of AlGaN/AlN/GaN high electron mobility transistor (HEMT) structures with different thickness of nano-scale AlN interlayers have been realized by metalorganic chemical vapor deposition (MOCVD) technology. After epitaxy, high resolution X-ray diffraction (HRXRD), temperature-dependent Hall Effect and atomic force microscopy (AFM) measurements were used to characterize the properties of these samples. First, it was found that the Al composition of AlGaN layer increases from 21.6 to 34.2% with increasing the thickness of AlN interlayer from 0 to 5 nm under the same AlGaN growth conditions. This result may due to the influences of compressive stress and Al incorporation induced by the AlN interlayer. Then, we also found that the room-temperature (RT) electron mobility stays higher than 1500 cm2/Vs in the samples within AlN interlayer thickness range of 1.5 nm, on the other hand, the low-temperature (80K) electron mobility drops dramatically from 8180 to 5720 cm2/Vs in the samples with AlN interlayer thickness increasing from 1 to 1.5 nm. Furthermore, it was found that the two-dimensional electron gas (2DEG) density increases from 1.15×1013 to 1.58×1013 cm-2 beyond the AlN interlayer thickness of 1 nm. It was also found that the temperature independent 2DEG densities are observed in the samples with AlN interlayer thickness of 0.5 and 1 nm. The degenerated characteristics of the samples with AlN thickness thicker than 1.5 nm show the degraded crystalline quality which matched the observation of surface defects and small cracks formations from their AFM images. Finally, the 2DEG mobilities of the proposed structures can be achieved as high as 1705 and 8180 cm2/Vs at RT and 80K, respectively.
A Multiple-Path Routing Model for Quality of Service in Software Defined Networking

The Internet of Things (IoT) has recently emerged as a new family of technologies that allow a great number of things to be connected over heterogeneous networks. Conventional networks, however, face a technological barrier in efficiently handling such a large number of devices. The approach based on software-defined networks (SDNs), with its speed and flexibility, has recently been introduced into IoT area to potentially achieve scalability and adaptability, resulting in the SDN-IoT, a unique IoT design. In this work, we describe a new multiple-path routing model for the SDN-IoT. This model consists of two components: 1) a congested source path discovery technique; 2) a multi-path selection method taking into account route similarity and priority. In this paper we first describe the SDN based Quality of Service and highlight the unique features of this routing technique, then report on the performance evaluation of such system, which achieves an approximate 17% decrease in packet loss ratio over the existing approaches.
Efficient template matching algorithm based on interval estimations on correlation

We propose an efficient template matching algorithm for binary image search. When we use template matching techniques, the computation cost depends on size of images. If we have large size images, we spend a lot of time for searching similar objects in scene image to template image. We design a scanning-type upper limit estimation that can be useful for neglect correlation calculation. For calculating the scanning-type upper limits, template and scene images are divided into two regions: R-region and P-region. In R-region, an upper limit of correlation coefficients can be derived as an interval estimation based on mathematical analysis of correlations of the object image and a pivot image. In P-region, another upper limit is formalized based on the number of white and black pixels in a template and the object image. By use of these upper limits, the scanning-type upper limit estimation of correlation coefficients can be formalized for the efficient matching algorithm. This upper limits estimation isn't over true values of correlation, so the accuracy of search by conventional search is the same as one by conventional search. The experiments with document images show the effectiveness and efficiency of the proposed matching algorithm. In these experiments, computation time by the proposed algorithm is between 5 and 20% compare of the conventional search.
Conditional symmetric instability in sting‐jet storms

Sting jets are transient mesoscale jets of air that descend from the tip of the cloud head towards the top of the boundary layer in severe extratropical cyclones and can lead to damaging surface wind gusts. This recently identified jet is distinct from the well‐documented jets associated with the cold and warm conveyor belts. One mechanism proposed for their development is the release of conditional symmetric instability (CSI). Here the spatial distribution and temporal evolution of several CSI diagnostics in four severe storms are analysed. A sting jet has been identified in three of these storms; for comparison, we also analysed one storm that did not have a sting jet, even though it had many of the apparent features of sting‐jet storms. The sting‐jet storms are distinct from the non‐sting‐jet storms by having much greater and more extensive conditional instability (CI) and CSI. CSI is released by ascending air parcels in the cloud head in two of the sting‐jet storms and by descending air parcels in the other sting‐jet storm. By contrast, only weak CI to ascending air parcels is present at the cloud‐head tip in the non‐sting‐jet storm. CSI released by descending air parcels, as diagnosed by decaying downdraught slantwise convective available potential energy (DSCAPE), is collocated with the sting jets in all three sting‐jet storms and has a localised maximum in two of them. Consistent evolutions of saturated moist potential vorticity are found. We conclude that CSI release has a role in the generation of the sting jet, that the sting jet may be driven by the release of instability to both ascending and descending parcels, and that DSCAPE could be used as a discriminating diagnostic for the sting jet based on these four case‐studies. Copyright © 2011 Royal Meteorological Society and British Crown Copyright, the Met Office
Observation of neutral hydrogen in the globular cluster NGC 2808

The Parkes 64-m reflector of the Australia Telescope National Facility was used to observe globular clusters in the 21-cm line. In the direction of NGC 2808, H I emission was detected with the following characteristics: (1) the peak of the spatial distribution is located on the cluster's center; (2) the peak of the velocity distribution matches the cluster's published radial velocity of 98 km/s to within its quoted uncertainly of 4 km/s; and (3) the FWHM of the H I profile is consistent with the cluster's published stellar velocity dispersion and escape velocity. The characteristics of this emission are very suggestive of its being due, at least in part, to gas which is physically associated with the cluster. This is not beyond dispute, however, since there is known to be an extended region around the cluster exhibiting foreground 21-cm emission at about the cluster's radial velocity. If further observations confirm that the emitting gas is intrinsic to NGC 2808, this would constitute the first significant detection of H I within a globular cluster. 32 refs.
Identifying the Most Probable Mammal Reservoir Hosts for Monkeypox Virus Based on Ecological Niche Comparisons

Background Previous human cases or epidemics have suggested that Monkeypox virus (MPXV) can be transmitted through contacts with animals of African rainforests. Although MPXV has been identified in many mammal species, most are likely secondary hosts and the reservoir host has yet to be discovered. Methodology/Principal Findings In this study, we provide the full list of African mammal genera (and species) in which MPXV was previously detected and predict the geographic distributions of all species of these genera based on museum specimens and an ecological niche modelling (ENM) method. Then, we reconstruct the ecological niche of MPXV using georeferenced data on animal MPXV sequences and human index cases, and conduct overlap analyses with the ecological niches inferred for 99 mammal species in order to identify the most probable animal reservoir. Conclusions/Significance Our results show that the MPXV niche covers three African rainforests, the Congo Basin and Upper and Lower Guinean forests. The four mammal species showing the best niche overlap with MPXV are all arboreal rodents, including three squirrels, Funisciurus anerythrus, Funisciurus pyrropus, and Heliosciurus rufobrachium, and Graphiurus lorraineus. We conclude that the most probable MPXV reservoir is F. anerythrus based on two niche overlap metrics, the areas of higher probabilities of occurrence, and available data on MPXV detection. Summary Monkeypox (MPX) is an emerging zoonotic disease, endemic to rainforests of West and Central Africa, which manifests as a fever, swollen lymph nodes, and fatigue, followed by a rash with macular lesions progressing from papules to vesicles, pustules and scabs, usually on the face, hands, and feet for two to four weeks. The case fatality rate ranges from 1-3% in West Africa to 5-10% in Central Africa. The disease has been reported in 10 African countries between 1970 and today, with an increasing number of cases over the last decades and several exportations outside the continent, the last one in 2022 resulting in an epidemic involving mostly men who have sex with men, with more than 80,000 cases detected worldwide. Although MPX virus has been identified in many mammal species, most are likely secondary hosts and the reservoir host has yet to be discovered. In this study, we compare the predicted geographic distribution (ecological niche) of the MPX virus with that of 99 mammal species, and conclude that the most probable MPX reservoir is Thomas’s rope squirrel (Funisciurus anerythrus), followed by three other arboreal rodents, including two squirrels (Funisciurus pyrropus and Heliosciurus rufobrachium) and the Lorrain dormouse (Graphiurus lorraineus).
The impact of genetically controlled splicing on exon inclusion and protein structure

Common variants affecting mRNA splicing are typically identified though splicing quantitative trait locus (sQTL) mapping and have been shown to be enriched for GWAS signals by a similar degree to eQTLs. However, the specific splicing changes induced by these variants have been difficult to characterize, making it more complicated to analyze the effect size and direction of sQTLs, and to determine downstream splicing effects on protein structure. In this study, we catalogue sQTLs using exon percent spliced in (PSI) scores as a quantitative phenotype. PSI is an interpretable metric for identifying exon skipping events and has some advantages over other methods for quantifying splicing from short read RNA sequencing. In our set of sQTL variants, we find evidence of selective effects based on splicing effect size and effect direction, as well as exon symmetry. Additionally, we utilize AlphaFold2 to predict changes in protein structure associated with sQTLs overlapping GWAS traits, highlighting a potential new use-case for this technology for interpreting genetic effects on traits and disorders.
Inductive biases of neural specialization in spatial navigation

The brain may have evolved a modular architecture for reward-based learning in daily tasks, with circuits featuring functionally specialized modules that match the task structure. We propose that this architecture enables better learning and generalization than architectures with less specialized modules. To test this hypothesis, we trained reinforcement learning agents with various neural architectures on a naturalistic navigation task. We found that the architecture that largely segregates computations of state representation, value, and action into specialized modules enables more efficient learning and better generalization. Behaviors of agents with this architecture also resemble macaque behaviors more closely. Investigating the latent state computations in these agents, we discovered that the learned state representation combines prediction and observation, weighted by their relative uncertainty, akin to a Kalman filter. These results shed light on the possible rationale for the brain’s modular specializations and suggest that artificial systems can use this insight from neuroscience to improve learning and generalization in natural tasks.
Pleiotropy of autism-associated chromatin regulators

Gene ontology analyses of high confidence autism spectrum disorder (hcASD) risk genes have historically highlighted chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated microtubule biology and identified disrupted cellular proliferation as a convergent ASD phenotype. As many chromatin regulators, including ASD risk genes ADNP and CHD3, are known to directly regulate both tubulins and histones, we studied the five chromatin regulators most strongly associated with ASD (ADNP, CHD8, CHD2, POGZ, and SUV420H1/KMT5B) specifically with respect to microtubule biology. We observe that all five localize to microtubules of the mitotic spindle in vitro and in vivo. Further in-depth investigation of CHD2 provides evidence that patient-derived mutations lead to a range of microtubule-related phenotypes, including disrupted localization of the protein at the mitotic spindle, spindle defects, cell cycle stalling, DNA damage, and cell death. Lastly, we observe that ASD genetic risk is significantly enriched among microtubule-associated proteins, suggesting broader relevance. Together, these results provide further evidence that the role of tubulin biology and cellular proliferation in ASD warrant further investigation and highlight the pitfalls of relying solely on annotated gene functions in the search for pathological mechanisms.
A PHOTOELECTRIC BVRI SEQUENCE IN THE FIELD OF THE GLOBULAR CLUSTER NGC 6205 (M 13).

Photoelectric BVRI observations of 20 stars in the field of the galactic globular cluster NGC 6205 (M13) are presented. These stars have been observed in the UBV system by Arp and Johnson (1955) and should be useful in the calibration of photometry obtained by other means.
Noncommutative Curves of Genus Zero: Related to Finite Dimensional Algebras

In these notes the author investigates noncommutative smooth projective curves of genus zero, also called exceptional curves. As a main result he shows that each such curve X admits, up to some weighting, a projective coordinate algebra which is a not necessarily commutative graded factorial domain R in the sense of Chatters and Jordan. Moreover, there is a natural bijection between the points of X and the homogeneous prime ideals of height one in R, and these prime ideals are principal in a strong sense.
Gremlin 1 is required for macrophage M2 polarization

Pro-proliferative, M2-like polarization of macrophages is a critical step in the development of fibrosis and remodeling in chronic lung diseases such as pulmonary fibrosis and pulmonary hypertension. Macrophages in healthy and diseased lungs express gremlin 1 (Grem1), a secreted glycoprotein that acts in both paracrine and autocrine manners to modulate cellular function. Increased Grem1 expression plays a central role in pulmonary fibrosis and remodelling, however, the role of Grem1 in M2-like polarization of macrophages has not previously been explored. The results reported here show that recombinant Grem1 potentiated M2-like polarization of mouse macrophages and bone marrow derived macrophages (BMDM) in response to the Th2 cytokines IL4 and IL13. Genetic depletion of Grem1 in BMDMs inhibited M2 polarization while exogenous gremlin 1 could partially rescue this effect. Taken together, these findings reveal that gremlin 1 is required for M2-like polarization of macrophages.
Monopogen: single nucleotide variant calling from single cell sequencing

Distinguishing how genetics impact cellular processes can improve our understanding of variable risk for diseases. Although single-cell omics have provided molecular characterization of cell types and states on diverse tissue samples, their genetic ancestry and effects on cellular molecular traits are largely understudied. Here, we developed Monopogen, a computational tool enabling researchers to detect single nucleotide variants (SNVs) from a variety of single cell transcriptomic and epigenomic sequencing data. It leverages linkage disequilibrium from external reference panels to identify germline SNVs from sparse sequencing data and uses Monovar to identify novel SNVs at cluster (or cell type) levels. Monopogen can identify 100K~3M germline SNVs from various single cell sequencing platforms (scRNA-seq, snRNA-seq, snATAC-seq etc), with genotyping accuracy higher than 95%, when compared against matched whole genome sequencing data. We applied Monopogen on human retina, normal breast and Asian immune diversity atlases, showing that that derived genotypes enable accurate global and local ancestry inference and identification of admixed samples from ancestrally diverse donors. In addition, we applied Monopogen on ~4M cells from 65 human heart left ventricle single cell samples and identified novel variants associated with cardiomyocyte metabolic levels and epigenomic programs. In summary, Monopogen provides a novel computational framework that brings together population genetics and single cell omics to uncover genetic determinants of cellular quantitative traits.
Integral methods for quadratic programming: Theory and implementation

The contributions of this thesis are twofold. We show two theoretical results that are both related to quadratic programming. The first one concerns the abstract optimization framework of violator spaces and the randomized procedure called Clarkson’s algorithm, which is associated with solving violator spaces. Historically, Clarkson’s algorithm was developed to solve linear programs, and provided the earliest practical linear-time algorithm for linear programs. The underlying concept of the problems solvable by this algorithm was later expanded to LP-type problems, and finally to violator spaces. Quadratic programming is also an LP-type problem. In a nutshell, the algorithm randomly samples from a set of constraints, computes an optimal solution subject to these constraints, and then checks whether the ignored constraints agree with the solution. If not, some form of re-sampling occurs, until an optimal solution is found that satisfies all constraints. Originally, to make the analysis go through, there used to be a preliminary test whether the random sample is good in some sense. We show that this test is not necessary and we give evidence that the modified version of Clarkson’s approach is the easiest version that can still be analyzed successfully. The second contribution concerns quadratic programming more directly. It is well-known that a simplex like procedure can be applied to
Low Complexity GF(2m) Multiplier Based on Iterative Karatsuba Algorithm

The complexity is one important index for Galois Field multiplier. This paper presents one low complexity GF(2m) multiplier based on iterative Karatsuba algorithm. The multiplication is replaced iteratively by three ones of half-length operands which are performed in parallel. The operands are divided into different width such as 64-bit, 32-bit, 16-bit and so on. For the 2m*2m multiplier, we take 128 bit-widthGF(2128) multipliers as an example. We implement them on FPGA and count the number of the used LUTs and the used registers. Through analyzing the statistic, we find that, when the width of the two multiplication operands is divided to 8 bit, the multiplier consumes the least resources. Compared with the FPGA implementation of the other previous multiplier, this optimum multiplier can save 50% resources in LUTs and the registers.
Analysis of Longitudinal Data of Repeated Observations Using Generalized Estimating Equations Methodology

Data collected from longitudinal designs often have correlated observations arising from repeated measurements on the same subject. Conventional statistical methods (e.g., ordinary least squares linear regression, univariate analysis of variance with repeated measures) that assume independence of observations can be inadequate in providing test statistics. Liang and Zeger (1986) proposed a class of generalized estimating equations (GEE) to account for dependence among observations. The article provides a descriptive introduction to GEE and an example illustrating its use in continuous response data with a multivariate normal distribution. A discussion on the utility of the GEE procedure in longitudinal data analysis is provided.