Miracle-dz/UniFAR-FTUs huggingface dataset:
Low-rank Updates of Preconditioners for Sequences of Symmetric Linear Systems

The aim of this survey is to review some recent developements in devising efficient preconditioners for sequences of linear systems A x = b. Such a problem arise in many scientific applications, such as discretization of transient PDEs, solution of eigenvalue problems, (Inexact) Newton method applied to nonlinear systems, rational Krylov methods for computing a function of a matrix. Full purpose preconditioners such as the Incomplete Cholesky (IC) factorization or approximate inverses are aimed at clustering eigenvalues of the preconditioned matrices around one. In this paper we will analyze a number of techniques of updating a given IC preconditioner (which we denote as P0 in the sequel) by a low-rank matrix with the aim of further improving this clustering. The most popular low-rank strategies are aimed at removing the smallest eigenvalues (deflation) or at shifting them towards the middle of the spectrum. The low-rank correction is based on a (small) number of linearly independent vectors whose choice is crucial for the effectiveness of the approach. In many cases these vectors are approximations of eigenvectors corresponding to the smallest eigenvalues of the preconditioned matrix P0 A. We will also review some techniques to efficiently approximate these vectors when incorporated within a sequence of linear systems all possibly having constant (or slightly changing) coefficient matrices. Numerical results concerning sequences arising from discretization of linear/nonlinear PDEs and iterative solution of eigenvalue problems show that the performance of a given iterative solver can be very much enhanced by the use of low-rank updates.
Coverage Analysis and Visualization in Clinical Exome Sequencing

Motivation : The advent of clinical exome sequencing will require new tools to handle coverage data and making it relevant to clinicians. That means genes over targets, smart software over BED-ﬁles, and full stack, automated solutions from BAM-ﬁles to genetic test report. Fresh ideas can also provide new insights into the factors that cause certain regions of the exome to receive poor coverage. Results : A novel coverage analysis tool for analyzing clinical exome sequencing data has been developed. Named Chanjo , it’s capable of converting between different elements such as targets and exons, supports custom annotations, and provides powerful statistics and plotting options. A coverage investigation using Chanjo linked both extreme GC content and low sequence complexity to poor coverage. High bait density was shown to increase reliability of exome capture but not improve coverage of regions that had already proven tricky. To improve coverage of especially very G+C rich regions, developing new ways to amplify rather than enrich DNA will likely make the biggest difference. Availability : The source code for Chanjo is freely available at https://github.
The Psychometric Properties of the Session Rating Scale: A Narrative Review.

Background: The Session Rating Scale (SRS) is a measure used in psychotherapy practice. Given its application and frequent use in clinical practice settings, several studies including primary validation studies as well as outcome studies reporting psychometric properties have examined the validity and reliability of the SRS. Because the SRS is designed to be used in clinical practice, demonstration of reliability and validity is ideal with clinical populations instead of non-clinical populations. To our knowledge, there have been no reviews evaluating the psychometric properties of the SRS with clinical populations.Purpose: The aim of this study was to review and synthesize the psychometric properties of the SRS by examining all relevant outcome and validation studies.Methods: We completed an electronic literature search of several online databases in order to identify relevant articles. We identified 12 articles that met our inclusion and analyzed the reliability and validity evidence for the SRS with clinical populations.Results: Findings showed high internal consistency for the SRS and support evidence that the underlying dimension is a measure of therapeutic alliance. Test-retest reliability estimates were reported in 4 of the 12 studies included in this review (ranging from .54 to .70). The SRS had low to moderate concurrent validity with other longer measures of therapeutic alliance (.29 with ORS; .48 with HAQ II; .57-.65 with WAI). Discussion: Clinicians should be aware of the limitations in validity evidence for the SRS that may result from its brevity. However, clinicians should also consider the relative stability of the SRS as a pragmatic global measure of the construct of therapeutic alliance. Future research efforts should focus on validation of the SRS with larger, more diverse samples and specific clinical populations with a wider range of symptom severity.
“The Local Consultant Will Not Be Credible”: How Epistemic Injustice Is Experienced and Practised in Development Aid

ABSTRACT This paper uses the concept of epistemic injustice to shed light on the discriminatory treatment of experts in and by development aid. While the literature on epistemic justice is largely based on philosophical reasoning, I provide an empirical case study which substantiates theoretical claims with findings from social science research. Drawing on expert interviews conducted in South Africa and Tanzania, I reveal how epistemic injustice is experienced, practiced and institutionalised in a field which claims to work towards global justice. Focusing on aid-related advisory processes, the paper highlights how epistemic authority therein is tied to identity-based prejudice. The systematic credibility deficit policy experts from aid-receiving countries suffer is closely interrelated with the credibility excess so-called ‘international’ experts profit from. Their privilege is backed by an imaginary that maintains the idea of Northern epistemic superiority and sustained by prevailing employment and procurement practices of donor organisations. The paper suggests that the concurrence of testimonial and hermeneutical injustice prevents experts from the Global South from taking the lead in interpreting their own societies’ realities. This, I argue, is not only detrimental to the countries whose knowers are marginalised but also a root cause of persisting global inequality.
The fern genus Oreogrammitis (Grammitidoideae: Polypodiaceae) re-defined

Thirty-six new combinations are provided in Oreogrammitis Copel. (Polypodiaceae: Polypodiopsida). The species have previously been included in Radiogrammitis Parris and Themelium (T.Moore) Parris. Lectotypes are chosen for Polypodium allocotum Alderw. , P. ctenoideum Brause, P. flagelliforme Brause, P. loherianum Christ, P. subpinnatifidum Blume and P. yoderi var. denudatum Alderw.
An Atlas of Immunofluorescence in Cultured Cells

and provides a useful summary of existing cell lines. Although several of the techniques described in this book still involve the use of live animals, most of them illustrate how pluripotent embryonic cell lines can be used to carry out basic research on embryonic differentiation of mammals. Most of these methods will soon become standard procedures in developmental biology. Since they also hold promise for investigations on embryotoxic rp.echanisms, they should also be adopted by reproductive toxicologists who are trying to establish in vitro systems for teratological testing. This volume is therefore an essential acquisition for up-to-date developmental biology and toxicology laboratories.
E2f1, E2f2, and E2f3 Control E2F Target Expression and Cellular Proliferation via a p53-Dependent Negative Feedback Loop

ABSTRACT E2F-mediated control of gene expression is believed to have an essential role in the control of cellular proliferation. Using a conditional gene-targeting approach, we show that the targeted disruption of the entire E2F activator subclass composed of E2f1, E2f2, and E2f3 in mouse embryonic fibroblasts leads to the activation of p53 and the induction of p53 target genes, including p21CIP1. Consequently, cyclin-dependent kinase activity and retinoblastoma (Rb) phosphorylation are dramatically inhibited, leading to Rb/E2F-mediated repression of E2F target gene expression and a severe block in cellular proliferation. Inactivation of p53 in E2f1-, E2f2-, and E2f3-deficient cells, either by spontaneous mutation or by conditional gene ablation, prevented the induction of p21CIP1 and many other p53 target genes. As a result, cyclin-dependent kinase activity, Rb phosphorylation, and E2F target gene expression were restored to nearly normal levels, rendering cells responsive to normal growth signals. These findings suggest that a critical function of the E2F1, E2F2, and E2F3 activators is in the control of a p53-dependent axis that indirectly regulates E2F-mediated transcriptional repression and cellular proliferation.
A Group-Based Energy-Efficient Dual Priority Scheduling for Real-Time Embedded Systems

As the limitation of energy consumption of real-time embedded systems becomes more and more strict, it has been difficult to ignore the time overhead and energy consumption of context switches for fixed-priority tasks with preemption scheduling (FPP) in multitasking environments. In addition, the scheduling for different types of tasks may disrupt each other and affect system reliability. A group-based energy-efficient dual priority scheduling (GEDP) is proposed in this paper. The GEDP isolates different types of tasks to avoid the disruption. Furthermore, it also reduces context switches effectively, thus decreasing system energy consumption. As many studies ignored the context switches’ overhead in the worst-case response time (WCRT) model, and it will affect the accuracy of WCRT, thereby affecting the system schedulability. Consequently, the WCRT model is improved based on considering context switches’ overhead. The GEDP is designed and implemented in Linux, and the time overhead and energy consumption of context switches is compared in different situations with GEDP and FPP. The experimental results show that GEDP can reduce context switches by about 1% and decrease energy consumption by about 0.6% for given tasks.
How to Measure Digital Literacy? A Case of Croatian Adult Learners

This study aims to present the rationale, the instrument and the main findings of the assessment of digital literacy of adult learners in Croatia, as a part of the project Implementation of EU Agenda for Adult Learning 2017-2019, by Ministry of Science and Education. The concept of digital literacy is at the heart of EU development policies and encompasses skills, competences, and dispositions for using a wide range of technologies, from personal computers to smartphones, vending machines, and ATMs. The digital technologies are also being used for different purposes (work, leisure, communication, health, news, etc.) and differently by social groups (by age, gender socioeconomic status, etc.). Thus, testing digital literacy in the population is of great importance given the pervasiveness of digital technologies and the apparent inadequacy of self-reported measures of digital literacy. An original test was developed, testing the usage of Windows, Word, Excel, PowerPoint, internet browser and Google Maps. The test was implemented through the LimeSurvey software with the additional files available on the participant’s computer desktop. The questions were devised in a way that a participant had to solve a specific problem using the specific software, thus including the cognitive component of digital literacy. The difficulty level of the questions is approximate of those of the levels "Below Level 1" and "Level 1" of PSTRE PIAAC research. Additionally, the participants answered the question about their socio-economic status, the frequency of technology usage, and their self-perception of digital skills. The test was administered to 92 attendees of the specialization and qualification programs in seven adult learning facilities throughout Croatia (Knin, Karlovac, Zagreb, Split, Čakovec, Koprivnica, and Virovitica). The results indicate relatively low levels of digital literacy of the tested sample and the different patterns of technology usage by different socio-economic groups. Also, the questionnaire’s metric characteristics show that it can be successfully used for testing digital literacy outside the laboratory setting. Conclusion: The low levels of digital literacy among the adult attendees of the specialization and qualification programs implicate the need to include the digital literacy curriculum in their learning programs, according to individual needs and experiences. Also, this research is one of the very few that did not assess only the self-perceptions of the skills or test the skills in the research facility setting, but rather in the learning facilities of adult education. Since the questionnaire performed well under these circumstances, it can be modified to be implemented in multiple environments.
A comparison of animal color measurements using a commercially available digital color sensor and photograph analysis

Abstract An animal’s pelage, feather, or skin color can serve a variety of functions, so it is important to have multiple standardized methods for measuring color. One of the most common and reliable methods for measuring animal coloration is the use of standardized digital photographs of animals. New technology in the form of a commercially available handheld digital color sensor could provide an alternative to photography-based animal color measurements. To determine whether a digital color sensor could be used to measure animal coloration, we tested the ability of a digital color sensor to measure coloration of mammalian, avian, and lepidopteran museums specimens. We compared results from the sensor to measurements taken using traditional photography methods. Our study yielded significant differences between photography-based and digital color sensor measurements of brightness (light to dark) and colors along the green to red spectrum. There was no difference between photographs and the digital color sensor measurements for colors along the blue to yellow spectrum. The average difference in recorded color (ΔE) by the 2 methods was above the threshold at which humans can perceive a difference. There were significant correlations between the sensor and photographs for all measurements indicating that the sensor is an effective animal coloration measuring tool. However, the sensor’s small aperture and narrow light spectrum range designed for human-vision limit its value for ecological research. We discuss the conditions in which a digital color sensor can be an effective tool for measuring animal coloration in both laboratory settings and in the field.
Protective effect of green tea extract against cadmium-induced testicular damage in rats in respect of oxidant/antioxidant equilibrium and androgen production

Objective: Investigating the effect of green tea extract (GTE) on the testicular damage induced by cadmium chloride CdCl2 in male rats. Design: Randomized controlled study. Animals: 40 male Wistar rats. Procedures: Rats were randomly divided into four groups: A) control group (each rat daily received pellet diet); B) GTE group each rat daily received pellet diet as well as 3 ml of 1.5 % w/v GTE, C) CdCl2 group each rat was I/P injected a single dose of 1 mg/kg CdCl2, then daily received pellet diet, and D) CdCl2+GTE group each rat was I/P injected a single dose of 1 mg/kg CdCl2 then daily received pellet diet as well as 3 ml of 1.5 % w/v GTE. After 30 days, blood samples were collected for hormonal assays (testosterone, FSH, and LH). In addition, both testes were collected; one of them was used for quantification of 17-beta hydroxysteroid dehydrogenase III (17β-HSDIII) gene expression using a real-time PCR. The other testis was used for determination of catalase and reduced glutathione; GSH, Nitric oxide (NO) and malondialdehyde (MDA) levels. Results: CdCl2 decreased serum testosterone levels and its synthesis pathway (17β-HSDIII testicular gene expression). While antioxidants catalase and GSH were reduced, oxidants MDA were enriched in the testes of CdCl2-poisoned rats. This CdCl2-promoted testicular dysfunction was corrected via the administration of GTE to male rats. Conclusion and clinical relevance: GTE could be used as a remedy for protecting against CdCl2-induced testicular damage in male rats.
Damage‐sensitive impedance sensor placement on multi‐strand anchorage based on local stress variation analysis

An important issue in impedance‐based damage monitoring is to deploy sensors in proper positions in which damage‐sensitive impedance responses can be captured effectively. In this study, a full‐scale multi‐strand anchorage is analyzed to determine optimal locations of piezoelectric sensors for impedance‐based monitoring of locally damaged strands. First, stress variations of the multi‐strand anchorage are experimentally measured to estimate the anchorage behavior under the effect of locally damaged strands. Strain signals are examined for axial, circumferential, and radial stress components under the variation of prestress forces. Second, a finite element analysis is made on the multi‐strand anchorage to back up the experimental findings. Third, a damage‐sensitive structural model is interpreted for the local strand breakage. Finally, impedance responses sensitive to local strand breakage are experimentally examined for a few scenarios simulated in the anchorage system. PZT (lead zirconate titanate) sensors deployed on the anchor head and the bearing plate are evaluated to comparatively determine ideal regions of interest for impedance monitoring. The results show that the greater stress variation yields the greater variations in impedance responses and the near‐top and near‐anchor heads are ideal regions of interest for damage‐sensitive impedance monitoring.
There are 4 introns in the gene coding the DNA-binding protein HCc of Crypthecodinium cohnii (Dinophyceae)

HCc is a major basic nuclear protein of Crypthecodinium cohnii (Dinophyceae). In order to eluci date the gene organization of HCcl gene, it was amplified by PCR methods using the total DNA as a template and the nucleotide sequences of HCcl gene and its flanking regions were established. The results were as follows: [1] HCcl gene was composed of multiple copies and arranged in tandem; [2] it contained 4 introns lacking the GT-AG consensus sequences, which are conserved in other eukaryotic introns; and [3] eukaryotic promoter consensus sequences such as TATA box or CAAT box were not observed in the flanking regions of HCcl gene. An interesting point is whether such atypical-eukaryotic features of the HCcl gene organization are common in dinoflagellates or not.
Seasonal dietary niche contraction in coexisting Neotropical frugivorous bats (Stenodermatinae)

Tropical dry forests are characterized by punctuated seasonal precipitation patterns that drive primary production and the availability of fruits, seeds, flowers, and insects throughout the year. In environments in which the quantity and quality of food resources varies seasonally, consumers should adjust their foraging behavior to maximize energy intake while minimizing overlap with competitors during periods of low food availability. Here, we investigated how the diets of frugivorous bats in tropical dry forests of NW Mexico varied in response to seasonal availability and how this affected dietary overlap of morphologically similar species. We performed stable isotope analyses to understand temporal and interspecific patterns of overall isotopic niche breadth, trophic position, and niche overlap in the diet of six frugivorous species of closely related New World leaf‐nosed bats (family Phyllostomidae, subfamily Stenodermatinae). We estimated seasonal changes in resource abundance in two complementary ways: (a) vegetative phenology based on long‐term remote sensing data and (b) observational data on food availability from previously published insect and plant fruiting surveys. In all species, there was a consistent pattern of reduced isotopic niche breadth during periods of low food availability. However, patterns of niche overlap varied between morphologically similar species. Overall, results from our study and others suggest that seasonal food availability likely determines overall dietary niche breadth in Phyllostomidae and that despite morphological specialization, it is likely that other mechanisms, such as opportunistic foraging and spatiotemporal niche segregation, may play a role in maintaining coexistence rather than simply dietary displacement.
Durability of composite materials in deployable structures for space applications

Advanced composite materials are an excellent option for flexible deployable space structures, such as deployable antennas and booms. However, the harsh environment in space can degrade the performance of composite materials, thus limiting their wider application. In low Earth orbit (LEO), atomic oxygen (AO) resistance is a key limitation to service longevity. In this work, the AO resistance is examined for three commercial composite materials, which undergo exposure in a ground-based facility which simulates the AO environment of space. The degradation of the performance of the materials is determined by measuring selected properties (e.g. surface chemistry, and flexural stiffness) before and after exposure. The results indicated that the resin on the surface of all laminates has almost been entirely eroded and suffered significant degradation after exposure. The results presented in this work can act as a benchmark for the development of new composite systems or protection technologies which can provide an extended service life for flexible deployable structures in LEO.
Dispersion of Defects in TiO2 Semiconductor: Oxygen Vacancies in the Bulk and Surface of Rutile and Anatase

Oxygen deficiency (O-vacancy) contributes to the photoefficiency of TiO2 semiconductors by generating electron rich active sites. In this paper, the dispersion of O-vacancies in both bulk and surface of anatase and rutile phases was computationally investigated. The results showed that the O-vacancies dispersed in single- and double-cluster forms in the anatase and rutile phases, respectively, in both bulk and surface. The distribution of the O-vacancies was (roughly) homogeneous in anatase, and heterogenous in rutile bulk. The O-vacancy formation energy, width of defect band, and charge distribution indicated the overlap of the defect states in the rutile phase and thus eased the formation of clusters. Removal of the first and the second oxygen atoms from the rutile surface took less energy than the anatase one, which resulted in a higher deficiency concentration on the rutile surface. However, these deficiencies formed one active site per unit cell of rutile. On the other hand, the first O-vacancy formed on the surface and the second one formed in the subsurface of anatase (per unit cell). Supported by previous studies, we argue that this distribution of O-vacancies in anatase (surface and subsurface) could potentially create more active sites on its surface.