Miracle-dz/UniFAR-FTUs huggingface dataset:
Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models

A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Previously, the motifs were explained by an overlap of the non-palindromic motif being present on one of the half-site of targeted sequences. Here, we applied multicomponent mixture models to integration site sequences of diverse retroviruses. We demonstrate that the weak palindromic motifs result from a combination of independent sub-motifs restricted to only a few positions proximal to the site of integration. The sub-motifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identified HIV-1-favored palindromic sequences in Alu repeats serving as hotspots for integration. Our work presents a novel statistical approach to the analysis of retroviral integration site sequences, which can form a valuable tool in the analysis of DNA motifs. The presented results shed new light on the selection of target site sequences for retroviral integration.
Structural role for DNA Ligase IV in promoting the fidelity of non-homologous end joining

Nonhomologous end joining (NHEJ) is the primary pathway of vertebrate DNA double-strand-break repair. NHEJ polymerases and nucleases can modify DNA ends to render them compatible for ligation, but these enzymes are usually deployed only when necessary for repair of damaged DNA ends, thereby minimizing mutagenesis. Using frog egg extracts, we reveal a structural role for the NHEJ-specific DNA Ligase IV (Lig4) in promoting NHEJ fidelity. Mutational analysis demonstrates that Lig4 must bind DNA ends to form the short-range synaptic complex, in which DNA ends are closely aligned prior to ligation. Furthermore, single-molecule experiments show that a single Lig4 binds both DNA ends at the instant of short-range synapsis. In this way, compatible ends can be rapidly ligated without polymerase or nuclease activity, which we previously showed is restricted to the short-range synaptic complex. Our results provide a molecular basis for the fidelity of NHEJ.
Novel estimators for family-based genome-wide association studies increase power and robustness

A goal of genome-wide association studies (GWASs) is to estimate the causal effects of alleles carried by an individual on that individual (‘direct genetic effects’). Typical GWAS designs, however, are susceptible to confounding due to gene-environment correlation and non-random mating (population stratification and assortative mating). Family-based GWAS, in contrast, is robust to such confounding since it uses random, within-family genetic variation. When both parents are genotyped, a regression controlling for parental genotype provides the most powerful approach. However, parental genotypes are often missing. We have previously shown that imputing the genotypes of missing parent(s) can increase power for estimation of direct genetic effects over using genetic differences between siblings. We extend the imputation method, which previously only applied to samples with at least one genotyped sibling or parent, to ‘singletons’ (individuals without any genotyped relatives). By including singletons, the effective sample size for estimation of direct effects can be increased by up to 50%. We apply this method to 408,254 ‘White British’ individuals from the UK Biobank, obtaining an effective sample size increase of between 25% and 43% (depending upon phenotype) by including 368,629 singletons. While this approach maximizes power, it can be biased when there is strong population structure. We therefore introduce an imputation based estimator that is robust to population structure and more powerful than other robust estimators. We implement our estimators in the software package snipar using an efficient linear-mixed model (LMM) specified by a sparse genetic relatedness matrix. We examine the bias and variance of different family-based and standard GWAS estimators theoretically and in simulations with differing levels of population structure, enabling researchers to choose the appropriate approach depending on their research goals.
An extensive photometric catalogue of CALIFA galaxies

We present an extensive compendium of photometrically-determined structural properties for all CALIFA galaxies in the Third Data Release (DR3). We exploit Sloan Digital Sky Survey (SDSS) images in order to extract one-dimensional (1D) $gri$ surface brightness profiles for all CALIFA DR3 galaxies. We also derive a variety of non-parametric quantities and parametric models fitted to 1D i-band profiles. The galaxy images are decomposed using the 2D bulge-disc decomposition programs IMFIT and GALFIT. The relative performance and merit of our 1D and 2D modelling approaches are assessed. Where possible, we compare and augment our photometry with existing measurements from the literature. Close agreement is generally found with the studies of Walcher et al. (2014) and M\'endez-Abreu et al. (2017), though some significant differences exist. Various structural metrics are also highlighted on account of their tight dispersion against an independent variable, such as the circular velocity.
What drives the Quasar Main Sequence

Eigenvector 1 (EV1) was found to be the dominant component behind the significant correlations for the measured parameters in quasar spectra (Boroson & Green, 1992). The parameter R$_{\mathrm{FeII}}$, which strongly correlates to the EV1, is the ${\mathrm{FeII}}$ strength, defined to be the ratio of the equivalent width of ${\mathrm{FeII}}$ to the equivalent width of ${\mathrm{H\beta}}$. This allows to construct a quasar main sequence analogous to the stellar properties driven HR diagram (Sulentic et al. 2001). We try to find the main driver behind the EV1 among the basic (theoretically motivated) parameters of an active nucleus (Eddington ratio, black hole mass, accretion rate, spin, and viewing angle). Based on theoretical modeling using the photoionization code CLOUDY (Ferland et al. 2013), we test the hypothesis that the physical driver of EV1 is the maximum of the accretion disk temperature ($\mathrm{T_{BBB}}$), reflected in the shape of the spectral energy distribution (SED). We have assumed that both H$\mathrm{\beta}$ and Fe${\mathrm{II}}$ emission come from the Broad Line Region represented as a constant density cloud in a plane-parallel geometry. We test the effect of changing Eddington ratio on the $\mathrm{R_{FeII} - T_{BBB}}$ trends with varying mean hydrogen densities. We also test the effect of adding microturbulence that affect the line intensities on the overall $\mathrm{R_{FeII} - T_{BBB}}$ picture.
Sensitization of colonic nociceptors by IL-13 is dependent on JAK and p38 MAPK activity

The effective management of visceral pain is a significant unmet clinical need for those affected by gastrointestinal diseases, such as inflammatory bowel disease (IBD). The rational design of novel analgesics requires a greater understanding of the mediators and mechanisms underpinning visceral pain. Interleukin-13 (IL-13) production by immune cells residing in the gut is elevated in IBD, and IL-13 appears to be important in the development of experimental colitis. What’s more, receptors for IL-13 are expressed by neurons innervating the colon, though it is not known whether IL-13 plays any role in visceral nociception per se. To resolve this, we employed Ca2+ imaging of cultured sensory neurons and ex vivo electrophysiological recording from the lumbar splanchnic nerve innervating the distal colon. Ca2+ imaging revealed the stimulation of small-diameter, capsaicin-sensitive sensory neurons by IL-13, indicating that IL-13 likely stimulates nociceptors. IL-13-evoked Ca2+ signals were attenuated by inhibition of Janus (JAK) and p38 kinases. In the lumbar splanchnic nerve, IL-13 did not elevate baseline firing, nor sensitise the response to capsaicin application, but did enhance the response to distention of the colon. In line with Ca2+ imaging experiments, IL-13-mediated sensitisation of the afferent response to colon distention was blocked by inhibition of either JAK or p38 kinase signalling. Together, these data highlight a potential role for IL-13 in visceral nociception and implicate JAK and p38 kinases in pro-nociceptive signalling downstream of IL-13. Key Points Summary The pro-inflammatory cytokine IL-13 is elevated in gastrointestinal (GI) diseases and known to sensitise sensory neurons. This study confirms a role for IL-13 in colonic afferent sensitisation and defines a role for downstream JAK and p38 MAPK signalling in colonic mechanosensitisation. IL-13-mediated increase in [Ca2+]i in capsaicin-sensitive sensory neurons is dependent on p38 MAPK and JAK signalling. IL-13-induced sensitisation of colonic afferents to noxious mechanical distension is abolished by inhibition of p38 MAPK and JAK. We have built on the current understanding of IL-13 and its neuronal interactions, highlighting the therapeutic potential of targeting p38 MAPK and JAK signalling pathways to treat visceral pain in GI disease.
Motivations of educators for participating in an authentic astronomy research experience professional development program

[This paper is part of the Focused Collection on Astronomy Education Research. ] The NASA/IPAC Teacher Archive Research Program (NITARP) partners small groups of educators with a research astronomer for a year-long authentic research project. This program aligns well with the characteristics of high-quality professional development (PD) programs and has worked with a total of 103 educators since 2005. In this paper, surveys were explored that were obtained from 74 different educators, at up to four waypoints during the course of 13 months, incorporating data from the class of 2010 through the class of 2017. This paper investigates how participating teachers describe their motivations for participating in NITARP as evidenced in these feedback forms. Analysis of self-reported data allows a mapping onto a continuum ranging from more inward focused to more outward focused; there is a shift from more inward-focused responses to more outward-focused responses. This insight into teacher motivations has implications for how the educators might be supported during their year with the program. This work provides a new way of parametrizing why educators participate in PD programs that require a considerable investment of time. NITARP, since it has many qualities of successful PD, serves as a model for similar PD programs in other STEM subjects. Likewise, the analysis method might also be useful to similarly evaluate other PD programs.
Designing an Editorialization Environment for Repeatable Self-Correcting Exercises

 Abstract — In order to design a cooperative e-learning platform, we observed teams of Teacher [T], Computer Scientist [CS] and exerciser's programmer-designer [ED] cooperating for the conception of a self-correcting exercise, but without the use of such a device in order to catch the kind of interactions a useful platform might provide. To do so, we first run a task analysis on how T, CS and ED should be cooperating in order to achieve, at best, the task of creating and implementing self-directed, self-paced, repeatable self-correcting exercises (RSE) in the context of open educational resources. The formalization of the whole process was based on the “objectives, activities and evaluations” theory of educational task analysis. Second, using the resulting frame as a “how-to-do it” guide, we run a series of three contrasted Hackathon of RSE-production to collect data about the cooperative process that could be later used to design the collaborative e-learning platform. Third, we used two complementary methods to collect, to code and to analyze the adequate survey data: the directional flow of interaction among T-CS-ED experts holding a functional role, and the Means-End Problem Solving analysis. Fourth, we listed the set of derived recommendations useful for the design of the exerciser as a cooperative e-learning platform. Final recommendations underline the necessity of building (i) an ecosystem that allows to sustain teams of T-CS-ED experts, (ii) a data safety platform although offering accessibility and open discussion about the production of exercises with their resources and (iii) a good architecture allowing the inheritance of parts of the coding of any exercise already in the data base as well as fast implementation of new kinds of exercises along with their associated learning activities.
CELL INJURY, REPAIR, AGING, AND APOPTOSIS Vasoactive Intestinal Peptide Promotes Corneal Allograft Survival

Corneal transplantation is the most prevalent form of tissue transplantation. The success of corneal transplantation mainly relies on the integrity of corneal endothelial cells (CEnCs), which maintain graft transparency. CEnC density decreases signi ﬁ cantly after corneal transplantation even in the absence of graft rejection. To date, different strategies have been used to enhance CEnC survival. The neuropeptide vasoactive intestinal peptide (VIP) improves CEnC integrity during donor cornea tissue storage and protects CEnCs against oxidative stress e induced apoptosis. However, little is known about the effect of exogenous administration of VIP on corneal transplant outcomes. We found that VIP signi ﬁ cantly accelerates endothelial wound closure and suppresses interferon- g e and tumor necrosis factor- a e induced CEnC apoptosis in vitro in a dose-dependent manner. In addition, we found that intracameral administration of VIP to mice undergoing syngeneic corneal transplantation with endothelial injury increases
Precise limits on cosmological variability of the fine-structure constant with zinc and chromium quasar absorption lines

The strongest transitions of Zn and CrII are the most sensitive to relative variations in the fine-structure constant ($\Delta\alpha/\alpha$) among the transitions commonly observed in quasar absorption spectra. They also lie within just 40A of each other (rest frame), so they are resistant to the main systematic error affecting most previous measurements of $\Delta\alpha/\alpha$: long-range distortions of the wavelength calibration. While Zn and CrII absorption is normally very weak in quasar spectra, we obtained high signal-to-noise, high-resolution echelle spectra from the Keck and Very Large Telescopes of 9 rare systems where it is strong enough to constrain $\Delta\alpha/\alpha$ from these species alone. These provide 12 independent measurements (3 quasars were observed with both telescopes) at redshifts 1.0--2.4, 11 of which pass stringent reliability criteria. These 11 are all consistent with $\Delta\alpha/\alpha=0$ within their individual uncertainties of 3.5--13 parts per million (ppm), with a weighted mean $\Delta\alpha/\alpha = 1.2\pm1. 7_{\rm stat}\pm0. 9_{\rm sys}$ ppm (1$\sigma$ statistical and systematic uncertainties), indicating no significant cosmological variations in $\alpha$. This is the first statistical sample of absorbers that is resistant to long-range calibration distortions (at the $<$1 ppm level), with a precision comparable to previous large samples of $\sim$150 (distortion-affected) absorbers. Our systematic error budget is instead dominated by much shorter-range distortions repeated across echelle orders of individual spectra.
Measurement report: High Arctic aerosol hygroscopicity at sub- and supersaturated conditions during spring and summer

Abstract. Aerosol hygroscopic growth and cloud droplet formation influence the radiation transfer budget of the atmosphere and thereby the climate. In the Arctic, these aerosol properties may have a more pronounced effect on the climate compared to the midlatitudes. Hygroscopic growth and cloud condensation nuclei (CCN) concentrations of high Arctic aerosols were measured during two field studies in the spring and summer of 2016. The study site was the Villum Research Station (Villum) at Station Nord in the northeastern region of Greenland. Aerosol hygroscopic growth was measured with a hygroscopic tandem differential mobility analyzer (HTDMA) over a total of 23 d, and CCN concentrations were measured over a period of 95 d. Continuous particle number size distributions were recorded, facilitating calculations of aerosol CCN activation diameters and aerosol κ values. In spring, average CCN concentrations, at supersaturations (SSs) of 0.1 % to 0.3 %, ranged from 53.7 to 85.3 cm−3, with critical activation diameters ranging from 130.2 to 80.2 nm and κCCN ranging from 0.28–0.35. In summer, average CCN concentrations were 20.8 to 47.6 cm−3, while critical activation diameters and κCCN were from 137.1 to 76.7 nm and 0.23–0.35, respectively. Mean particle hygroscopic growth factors ranged from 1.60 to 1.75 at 90 % relative humidity in spring, while values between 1.47 and 1.67 were observed in summer depending on the initial dry size. Although the summer aerosol number size distributions were characterized by frequent new particle formation events, the CCN population at cloud-relevant supersaturations was determined by accumulation-mode aerosols.
NVLeak: Off-Chip Side-Channel Attacks via Non-Volatile Memory Systems

We study microarchitectural side-channel attacks and defenses on non-volatile RAM (NVRAM) DIMMs. In this study, we ﬁrst perform reverse-engineering of NVRAMs as implemented by the Intel Optane DIMM and reveal several of its previously undocumented microarchitectural details: on-DIMM cache structures (NVCache) and wear-leveling policies. Based on these ﬁndings, we ﬁrst develop cross-core and cross-VM covert channels to establish the channel capacity of these shared hardware resources. Then, we devise NVCache-based side channels under the umbrella of NVLeak. We apply NVLeak to a series of attack case studies, including compromising the privacy of databases and key-value storage backed by NVRAM and spying on the execution path of code pages when NVRAM is used as a volatile runtime memory. Our results show that side-channel attacks exploiting NVRAM are practical and defeat previously-proposed defense that only focuses on on-chip hardware resources. To ﬁll this gap in defense, we develop system-level mitigations based on cache partitioning to prevent side-channel leakage from NVCache.
NIST 2022 Language Recognition Evaluation Plan

The 2022 NIST language recognition evaluation (LRE22) is the 9th cycle in an on-going language recognition evaluation series that began in 1996. The objectives of the evaluation series are (1) to advance technologies in language recognition with innovative ideas, (2) to facilitate the development of language recognition technology incorporating these ideas, and (3) to measure the performance of the current stateof-the-art technology. Targeting researchers working on the general problem of text-independent, speakerindependent language recognition, the evaluation is designed to focus on core technology issues and to be simple and accessible to those wishing to participate. LRE22 will be organized in a similar manner to LRE17 [1], focusing on conversational telephone speech (CTS) and broadcast narrow band speech (BNBS) data. As in LRE17, fixed and open training conditions will be offered to allow cross-system comparisons and to understand the effect of additional and unconstrained amounts of training data on system performance. A new focus in LRE22 is an emphasis on language recognition of African languages, including lowresource languages. An additional new feature for LRE22 is expanded test segment durations. In prior LREs, test segments from CTS and BNBS were extracted from longer recordings to create smaller chunks containing approximately 3s, 10s, or 30s of speech. The LRE22 evaluation data will consist of segments that contain between 3s and 30s of speech that have been randomly sampled and extracted from longer recordings. NIST will distribute a small development set representative of the test set to participants. Participants will be asked to provide score vectors with the log-likelihood scores, rather than the log-likelihood ratios. Participation in LRE22 is open to all who find the evaluation of interest and are able to comply with the evaluation rules set forth in this plan. There is no cost to participate, but participating teams must be represented at the LRE virtual workshop planned for January 2023. Information about evaluation registration can be found on the LRE22 website1.
Barriers to the Use of Factoring Accounts Receivables: The Ghanaian Contractor’s Perception

— Factoring accounts receivable is widely accepted as an alternative financing source and utilized in almost every industry that sells business-to-business or business-to-government. However, its patronage in the construction industry is very limited as some barriers hinder its application in the construction industry. This study aims at assessing the barriers to the use of factoring accounts receivables in the Ghanaian construction industry. The study adopted the sequential exploratory research method where structured and unstructured questionnaires were conveniently distributed to D1K1 and D2K2 construction firms in Ghana. Using the one-sample t-test and Kendall’s Coefficient of concordance data were analyzed. The most severe challenge concluded is the high cost of factoring patronage. Other critical challenges identified were low knowledge on factoring processes, inadequate access to information on factoring, and high risks involved in factoring. Hence, it is recommended that contractors should be made aware of the prospects of factoring of accounts receivables in the construction industry. This study serves as basis for further rigorous research into factoring of accounts receivables in the industry.
Developmental Characteristics of Working Memory in Hard of Hearing Children: Analysis by Language Ability and Task Variables

Abstract:The study's purpose was to clarify the developmental characteristics of working memory in hard of hearing children on the basis of language ability and task variables. Eighty-three congenitally severely hard of hearing children in grades 3–9 attending Japanese elementary and junior high school were aggregated on the basis of grade and language ability into six groups and received verbal and nonverbal tasks to measure their working memory capacity. The results suggest that hard of hearing children's nonverbal working memory is less affected by language ability and develops slowly as the school year progresses, showing a developmental trend similar to that of hearing children. Verbal working memory showed differences between groups by language ability in all grades due to the influence of language ability underlying processing in the phonological loop, but the results suggest that significant improvement occurs during elementary school regardless of language ability.
Numerical renormalization group for impurity quantum phase transitions: structure of critical fixed points

The numerical renormalization group method is used to investigate zero-temperature phase transitions in quantum impurity systems, in particular in the particle–hole symmetric soft-gap Anderson model. The model displays two stable phases whose fixed points can be built up of non-interacting single-particle states. In contrast, the quantum phase transitions turn out to be described by interacting fixed points, and their excitations cannot be described in terms of free particles. We show that the structure of the many-body spectrum of these critical fixed points can be understood using renormalized perturbation theory close to certain values of the bath exponents which play the role of critical dimensions. Contact is made with perturbative renormalization group calculations for the soft-gap Anderson and Kondo models. A complete description of the quantum critical many-particle spectra is achieved using suitable marginal operators; technically this can be understood as epsilon-expansion for full many-body spectra.