Miracle-dz/UniFAR-FTUs huggingface dataset:
SEMI-CONVERGENCE OF THE PARAMETERIZED INEXACT UZAWA METHOD FOR SINGULAR SADDLE POINT PROBLEMS

Abstract. In this paper, we provide semi-convergence results of theparameterized inexact Uzawa method with singular preconditioners forsolving singular saddle point problems. We also provide numerical exper-iments to examine the eﬀectiveness of the parameterized inexact Uzawamethod with singular preconditioners. 1. IntroductionWe consider the singular saddle point problem of the form(1)A B−B T 0xy=f−g,where A ∈ R m×m is a symmetric positive deﬁnite matrix, B ∈ R m×n is arank-deﬁcient matrix of rank(B) = r < n with m ≥ n, f ∈ R m and g ∈ R n . The singular saddle point problem (1) is important and arises in many diﬀerentapplications of scientiﬁc computing and engineering, such as the mixed ﬁniteelement methods for Navier-Stokes equations, computational ﬂuid dynamics,constrained optimization, the weighted least squares problems, electronic net-works, linear elasticity, and so forth [1, 10, 14, 15]. When B is of full column rank, the linear system (1) is nonsingular. Forthis case, many relaxation iterative methods based on matrix splittings andtheir convergence properties have been proposed and analyzed, e.g., SOR-likemethod [11], GSOR (Generalized SOR) method [2], PIU (Parameterized Inex-act Uzawa) method [3], SSOR-like method [8, 20], GSSOR (Generalized SSOR)method [7, 18], several variants of Uzawa method [16, 17], and so on.
Dynamic brain responses to Russian word acquisition among Chinese adult learners: An event‐related potential study

Human learners are capable to acquire foreign language vocabulary at an impressive speed even in adulthood. Previous studies have examined the neural mechanisms underlying rapid acquisition of Latin‐alphabet vocabulary and revealed dynamic changes in several event‐related potential (ERP) components during novel word learning. However, scant attention has been paid to the acquisition of Russian words. The present study used ERP and examined dynamic brain responses to rapid Russian word acquisition in 53 native Chinese speakers with no prior knowledge of Russian language. Behavioral data showed robust individual differences in Russian word acquisition, with most participants being able to rapidly learn a subset of novel Russian words in a few exposures. ERP results revealed significant learning effects in the P200, N400, and P600 amplitudes. Moreover, P600 amplitude changes predicted participants' word acquisition after learning. These findings demonstrated dynamic brain responses to rapid Russian word learning and suggested that the P600 component may serve as a bio‐marker for individual learning ability in Russian word acquisition.
NON-REDUNDANT APERTURE MASKING INTERFEROMETRY WITH ADAPTIVE OPTICS: DEVELOPING HIGHER CONTRAST IMAGING TO TEST BROWN DWARF AND EXOPLANET EVOLUTION MODELS

Leadership Vision • Research Minded: Measurable record of scientific & technical development drives confidence. • Sciences Perspective: Physics trained; unification of technical disciplines drives innovation. • Scalable Technology: Day one ideation must be built to scale engineering to drive capacity. • Team Built:Inventive people resourced to do seemingly impossible tasks drives human capital. • Knowledge: Centralized knowledge scales org capital; individual autonomy drives org scale.
Effects of He–Ne laser on Daphnia magna Straus manifested in subsequent generations

The effects of He–Ne laser irradiation (including visible laser light 632.8 nm in wavelength and an attendant electromagnetic field from the laser apparatus) on the fertility, newborn quality and linear dimensions of the body of Cladocera Daphnia magna Straus were determined. It is shown that the attendant electromagnetic field generated by the laser apparatus can have significant impact on the results of low-intensity laser therapy. The laser light exposure of daphnia to a dose range of 1.7–1300 mJ cm−2 stimulates the integral functions of the daphnia’s body. At the same time, the attendant electromagnetic field (72 mA m−1 in the frequency range of 0.02–20 kHz and 400 mA m−1 in the frequency range of 3–4 MHz) causes the appearance of quickly dying and/or abnormal newborn (up to a small percent) that has never been observed in the control. Anomalies of daphnia mainly consisted of swimming antenna pathologies. Moreover, under the influence of the attendant electromagnetic field on parental daphnia only, these anomalies appear even in several subsequent generations of newborn. The negative impact on daphnia disappears completely after the suppression of the attendant electromagnetic field to laboratory background level. It is shown that laser light can partially compensate the negative impact of the attendant electromagnetic field on Daphnia.
Properly Colored Paths and Cycles in Complete Graphs

Let K_n~c denote a complete graph on n vertices whose edges are colored in an arbitrary way. LetΔ~(mon)(K_n~c) denote the maximum number of edges of the same color incident with a vertex of K_n~c.A properly colored cycle(path) in K_n~c is a cycle (path) in which adjacent edges have distinct colors.B. Bollobas and P.Erd(o|¨)s(1976) proposed the following conjecture:IfΔ(mon)(K_n~c)[n/2],then K_n~c contains a properly colored Hamiltonian cycle.This conjecture is still open.In this paper,we study properly colored paths and cycles under the condition mentioned in the above conjecture.
AlphaFold2 protein structure prediction based on computer vision

Studying protein structure is helpful to understand the role of proteins and how proteins perform their biological functions. Therefore, exploring the structure of proteins is of great significance for biology and pharmacology. Among a number of experimental and computational tools, AlphaFold2 has made outstanding achievements in the field of protein structure prediction and is widely used. This paper studied the particular work of AlphaFold2 and applied it to predict the human epidermal growth factor receptor 2 (HER2), an important target of breast cancer which is a key disease endangering women's health. We hope to explore the effect of AlphaFold2 in practical application through case study on HER2. We explored the specific work of ResNet, a classic model in the field of computer vision, and Raptor-X, which exploited such techniques in the protein field for the first time. Finally, we applied the method of computer vision to the field of protein prediction as well as protein structure visualization. More specifically, we evaluated the prediction accuracy of AlphaFold2 by aligning the structure of protein and located some key binding residues in HER2 to help analysis and further exploration. In conclusion, we give the specific results and discuss the performance of AlphaFold2, and also find that computer vision plays an important role in the field of protein prediction.
Intraspecific Variation of Transposable Elements Reveals Differences in the Evolutionary History of Fungal Phytopathogen Pathotypes

Transposable elements (TEs) contribute to intraspecific variation and play important roles in the evolution of fungal genomes. However, our understanding of the processes that shape TE landscapes is limited, as is our understanding of the relationship between TE content, population structure, and evolutionary history of fungal species. Fungal plant pathogens, which often have host-specific populations, are useful systems in which to study intraspecific TE content diversity. Here, we describe TE dynamics in five lineages of Magnaporthe oryzae, the fungus that causes blast disease of rice, wheat, and many other grasses. We identified differences in TE content across these lineages, and showed that recent lineage-specific expansions of certain TEs have contributed to overall greater TE content in rice-infecting and Setaria-infecting lineages. We reconstructed the evolutionary histories of LTR-retrotransposon expansions and found that in some cases they were caused by complex proliferation dynamics of one element, and in others by multiple elements from an older population of TEs multiplying in parallel. Additionally, we found evidence suggesting the recent transfer of a DNA transposon between rice and wheat-infecting M. oryzae lineages, and a region showing evidence of homologous recombination between those lineages, which could have facilitated such a transfer. By investigating intraspecific TE content variation, we uncovered key differences in the proliferation dynamics of TEs in various pathotypes of a fungal plant pathogen, giving us a better understanding of the evolutionary history of the pathogen itself.
No general effects of advancing male age on ejaculates: a meta-analysis across the animal kingdom

Senescence, the deterioration of organismal function with advancing age, is a puzzling biological phenomenon. While actuarial senescence (i.e., age-dependent increases in mortality rates) is well described across some taxa, reproductive senescence (i.e. age- dependent declines in reproduction) is less understood, especially in males, with mixed patterns reported across studies. To examine the evidence for male reproductive senescence, we investigated how advancing male age affects ejaculate traits across non-human animals via a meta-analysis yielding 1814 effect sizes from 379 studies. We found no evidence for a general pattern of reproductive senescence. Instead, we found high heterogeneity for how reproduction changes with male age across animals. Some of this heterogeneity (>10%) was associated with biological factors. For example, there were taxonomical differences for some ejaculate traits — sperm motility declined with male age in lab rodents and fish, whereas ejaculate size improved with male age in bulls, fish, and insects. Some methodological factors were also important in explaining this heterogeneity: studies sampling a larger proportion of a species’ lifespan were more likely to detect senescence in ejaculate traits, emphasising the need to examine the full life cycle of species to document senescence. Contrary to predictions, we reveal that the evidence for senescence in ejaculate traits is sporadic. Our findings will help generate novel hypotheses and identify more effective methodological approaches for studying male reproductive senescence.
Similar enzymatic functions in distinct bioluminescence systems: Evolutionary recruitment of sulfotransferases in ostracod light organs

Genes from ancient families are sometimes involved in the convergent evolutionary origins of similar traits, even across vast phylogenetic distances. Sulfotransferases are an ancient family of enzymes that transfer sulfate from a donor to a wide variety of substrates, including probable roles in some bioluminescence systems. Here we demonstrate multiple sulfotransferases, highly expressed in light organs of the bioluminescent ostracod Vargula tsujii, transfer sulfate in vivo to the luciferin substrate, vargulin. We find luciferin sulfotransferases of ostracods are not orthologous to known luciferin sulfotransferases of fireflies or sea pansies; animals with distinct and convergently evolved bioluminescence systems compared to ostracods. Therefore, distantly related sulfotransferases were independently recruited at least three times, leading to parallel evolution of luciferin metabolism in three highly diverged organisms. Re-use of homologous genes is surprising in these bioluminescence systems because the other components, including luciferins and luciferases, are completely distinct. Whether convergently evolved traits incorporate ancient genes with similar functions or instead use distinct, often newer, genes may be constrained by how many genetic solutions exist for a particular function. When fewer solutions exist, as in genetic sulfation of small molecules, evolution may be more constrained to use the same genes time and again.
“Antimicrobial Properties and Physical Characteristics of Essential Oil Extracted from Artemisia herba alba Collected in El Bayadh, Algeria”

Artemisia herba-alba is a white mugwort harvested in the Bougtobe region of the El-Bayad province. Essential oils were extracted from the plant using hydrodistillation. The antibacterial study of Artemisia herba-alba essential oils revealed a significant inhibitory action on the growth of tested microorganisms including Bacillus cereus, Staphylococcus aureus. These results demonstrated significant activity compared to the positive control penicillin, amoxicillin, and spiramycin. Overall, the results showed that the tested essential oil possesses interesting antimicrobial activities, and therefore, opens up new perspectives in the field of natural applications as a promising alternative to chemical products and for industrial exploitation.
Universal baleen whale microsatellite panel for individual identification and power to detect parentage

Highly polymorphic single tandem repeat loci (STR, also known as microsatellite loci) remain a familiar, cost efficient class of markers for genetic analyses in ecology, behavior and conservation. We characterize a new universal set of ten STR loci (from 28 potential candidate loci) in seven baleen whale species, which are optimized for PCR amplification in two multiplex reactions along with a Y chromosome marker for sex determination. The optimized, universal set of STR loci provides an ideal starting point for new studies in baleen whales aimed at individual-based and population genetic studies, and facilitates data sharing among research groups. Data from the new STR loci were combined with genotypes from other published STR loci to assess the power to assign parentage (paternity) using exclusion in four species: fin whales, humpback whales, blue whales and bowhead whales. We argue that parentage studies should present a power analysis to demonstrate that the specific data are sufficiently informative to assign parentage with statistical rigor.
During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, in concert with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death

C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA in Myxococcus xanthus binds c-di-GMP and DNA in a mutually exclusive manner in vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxical cdbA essentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped to cdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function of cdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, stabilized CdbS, thereby enabling its increased accumulation and toxicity. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induces the CdbA/CsdK1/CsdK2/CdbA system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death in bacteria. Author summary The nucleotide-based second messenger c-di-GMP in bacteria controls numerous processes in response to environmental or cellular cues. Typically, these processes are related to lifestyle transitions between motile and sessile behaviors. However, c-di-GMP also regulates other processes. In Myxococcus xanthus, CdbA is a DNA-binding and nucleoid-associated protein that helps to organize the large chromosome. CdbA binds c-di-GMP and DNA in a mutually exclusive manner. While other nucleoid-associated proteins are not essential, CdbA is essential. Here, we show that the crucial function of CdbA is to maintain the level of the c-di-GMP-binding PilZ-domain protein CdbS appropriately low. The CdbS level is not only increased upon depletion of CdbA but also in response to heat stress. Under both conditions, the increased CdbS level perturbs chromosome organization and ultimately causes cell death. The CdbA/CdbS system represents a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death.
Loss of the extracellular matrix protein Perlecan disrupts axonal and synaptic stability during Drosophila development

Heparan sulfate proteoglycans (HSPGs) form essential components of the extracellular matrix (ECM) and basement membrane (BM) and have both structural and signaling roles. Perlecan is a secreted ECM-localized HSPG that contributes to tissue integrity and cell-cell communication. Although a core component of the ECM, the role of Perlecan in neuronal structure and function is less understood. Here we identify a role for Drosophila Perlecan in the maintenance of larval motoneuron axonal and synaptic stability. Loss of Perlecan causes alterations in the axonal cytoskeleton, followed by axonal breakage and synaptic retraction of neuromuscular junctions. These phenotypes are not prevented by blocking Wallerian degeneration and are independent of Perlecan’s role in Wingless signaling. Expression of Perlecan solely in motoneurons cannot rescue synaptic retraction phenotypes. Similarly, removing Perlecan specifically from neurons, glia or muscle does not cause synaptic retraction, indicating the protein is secreted from multiple cell types and functions non-cell autonomously. Within the peripheral nervous system, Perlecan predominantly localizes to the neural lamella, a specialized ECM surrounding nerve bundles. Indeed, the neural lamella is disrupted in the absence of Perlecan, with axons occasionally exiting their usual boundary in the nerve bundle. In addition, entire nerve bundles degenerate in a temporally coordinated manner across individual hemi-segments throughout larval development. These observations indicate disruption of neural lamella ECM function triggers axonal destabilization and synaptic retraction of motoneurons, revealing a role for Perlecan in axonal and synaptic integrity during nervous system development.
Declining food availability and habitat shifts drive community responses to marine hypoxia

Worsening marine hypoxia has had severe negative consequences for fish communities across the globe. While individual and populationlevel impacts of deoxygenation have been identified, it is unknown how they interact to drive changes in food webs. To address this, we incorporated several major impacts of hypoxia, including declines in benthic re sources, habitat shifts, increasing mortality, and changes to rates of feeding, assimilation, and reproductive efficiency, into an existing size spectrum food web modeling framework. We used this structure to ask the following questions: which of these direct effects are most critical to capturing population and community dynamics in a representative hypoxic system, how do they interact to result in community responses to deoxygenation, and what are the potential consequences of these effects in the context of accelerating deoxygenation? We tested the effect of different combinations of oxygendependent processes, driven by observed oxygen levels, on the food web model’s ability to explain time series of observed somatic growth, diets, biomass, and fishery yields of commercially relevant species in the Baltic Sea. Model results suggest that food availability is most critical to capturing observed dynamics. There is also some evidence for oxygendependent habitat use and physological rates as drivers of observed dynamics. Deoxygenation results in declining growth both of benthic and benthopelagic fish species, as the latter are unable to compensate for the loss of benthic resources by consuming more pelagic fish and resources. Analysis of scenarios of ideal, declining, and degraded oxygen conditions show that deoxygenation results in a decline in somatic growth of predators, an altered habitat occupancy resulting in changing species interactions, and a shift in energy flow to benthopelagic predators from benthic to pelagic resources. This may have important implications for management as oxygen declines or improves.
The Relationship between Power and Level for Generic Unit Root Tests in Finite Samples

The author shows that the maximum power of a generic unit root test against any stationary alternative is equal to the true level of the test. He then uses Monte Carlo methods to investigate the implications for several such tests. He shows patterns of rejection probabilities over a variety of unit root and stationary processes. He discusses the implications of these results for some of the uses of unit root tests in applied work. Copyright 1992 by John Wiley & Sons, Ltd.
GluK2 is a target for gene therapy in drug-resistant Temporal Lobe Epilepsy

Objective Temporal lobe epilepsy (TLE) is characterized by recurrent seizures generated in the limbic system, particularly in the hippocampus. In TLE, recurrent mossy fiber sprouting from dentate gyrus granule cells (DGCs) creates an aberrant epileptogenic network between DGCs which operates via ectopically expressed GluK2/GluK5-containing kainate receptors (KARs). TLE patients are often resistant to anti-seizure medications and suffer significant comorbidities; hence there is an urgent need for novel therapies. Previously we have shown that GluK2 knockout mice are protected from seizures. This study aims at providing evidence that downregulating KARs in the hippocampus using gene therapy reduces chronic epileptic discharges in TLE. Methods We combined molecular biology and electrophysiology in rodent models of TLE and in hippocampal slices surgically resected from patients with drug-resistant TLE. Results Here we confirmed the translational potential of KAR suppression using a non-selective KAR antagonist that markedly attenuated Interictal-like Epileptiform Discharges (IEDs) in TLE patient-derived hippocampal slices. An adeno-associated virus (AAV) serotype-9 vector expressing anti-grik2 miRNA was designed to specifically downregulate GluK2 expression. Direct delivery of AAV9-anti grik2 miRNA into the hippocampus of TLE mice led to a marked reduction in seizure activity. Transduction of TLE patient hippocampal slices reduced levels of GluK2 protein and, most importantly, significantly reduced IEDs. Interpretation Our gene silencing strategy to knock down aberrant GluK2 expression demonstrates inhibition of chronic seizure in a mouse TLE model and IEDs in cultured slices derived from TLE patients. These results provide proof-of-concept for a gene therapy approach targeting GluK2 KARs for drug-resistant TLE patients.