Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeting of microvillus protein Eps8 by the NleH effector kinases from enteropathogenic E. coli

Significance Enteropathogenic Escherichia coli (EPEC) is a significant cause of diarrhea among children in lower income countries. A defining feature of EPEC infection is the formation of attaching and effacing lesions on enterocytes that are characterized by the localized destruction of intestinal microvilli, intimate attachment of the bacteria to the host cell surface, and focusing of filamentous actin beneath the adherent bacteria. Here, we report that the EPEC effector kinases NleH1 and NleH2 specifically phosphorylate a novel residue, Ser775, in the microvillus protein Eps8. Eps8 is an actin bundling protein located at the tips of microvilli that determines microvillus structure and growth. Our biochemical and structural studies showed that NleH1 and NleH2 target the bundling activity of Eps8 during infection.
Diplomarbeit PT-symmetric systems in the quantum regime

The phenomenon of PT -symmetric breaking in classical systems with balanced loss and gain is associated with a sharp transition from a purely real to complex eigenvalue spectrum of the underlying dynamical matrix. Over the past years this phenomenon has been extensively studied, for example, using coupled optical modes, where however, the system is always in a large amplitude classical state. In this thesis we study for the first time the effect of PT -symmetry breaking in the quantum regime where the effects of non-linearities and intrinsic quantum noise become important. In the first part we analyze the stationary states of two coupled harmonic oscillators with engineered loss and gain. By applying different numerical techniques to solve the corresponding master equation for this system we observe an unconventional transition from a high-noise symmetric state to a parity-broken lasing state with strongly reduced fluctuations. Moreover, we show that the transition point strongly depends on the quantumness of the system. In the second part we develop numerical techniques for the simulation of extended PT -symmetric spin chains, which we use to demonstrate a crossover from a symmetric to a symmetry broken phase also for finite dimensional quantum systems.
VItamin K In PEritonial DIAlysis (VIKIPEDIA): Rationale and study protocol for a randomized controlled trial

Vascular calcification (VC) is an active process, resulting from the disturbance of balance between inhibitors and promoters of calcification, in favor of the latter. Matrix Gla Protein, a powerful inhibitor of VC, needs vitamin K to become active. In vitamin K depletion, plasma levels of the inactive form of MGP, dephosphorylated, uncarboxylated MGP (dp-ucMGP) are increased and associated with VC and cardiovascular (CV) outcomes. End Stage Renal Disease (ESRD) patients have increased circulating dp-ucMGP levels and accelerated VC. VItamin K In PEritoneal DIAlysis (VIKIPEDIA) is a prospective, randomized, open label, placebo-controlled trial, evaluating the effect of vitamin K2 supplementation on arterial stiffness and CV events in ESRD patients undergoing peritoneal dialysis (PD). Forty-four PD patients will be included in the study. At baseline, dp-ucMGP and pulse-wave velocity (PWV) will be assessed and then patients will be randomized (1:1 ratio) to vitamin K (1000 μg MK-7/day) or placebo for 1.5 years. The primary endpoint of this trial is the change in PWV in the placebo group as compared to the treatment group. Secondary endpoints are the occurrence of CV events, mortality, changes in PD adequacy, change in 24-hour ambulatory blood pressure indexes and aortic systolic blood pressure and changes in calcium/phosphorus/parathormone metabolism. VIKIPEDIA is a new superiority randomized, open label, placebo-controlled trial aiming to determine the effect of vitamin K2 supplementation on VC, CV disease and calcium/phosphorus metabolism, in PD patients. Trial registration: The protocol of this study is registered at ClinicalTrials.gov with identification number NCT04900610 (25 May 2021).
What about diversity? The effect of organizational economic inequality on the perceived presence of women and ethnic minority groups

Economic inequality shapes the degree to which people and different social groups are perceived in stereotypical ways. Our research sought to investigate the impact of the perception of economic inequality in an organizational setting on expectations of social diversity in the organization’s workforce, across the dimensions of gender and ethnicity. Combining data from previous experiments, we first explored in one set of studies (Studies 1a and 1b; N = 378) whether the degree of economic inequality in a fictitious organization affected participants’ expectations of the representation of minority vs. majority group employees. We found that when we presented an organization with unequal (vs. equal) distribution of economic wealth amongst its employees to study participants, they expected the presence of men and White majority individuals to be larger than the presence of women and ethnic minorities. Second, we tested our hypotheses and replicated these initial effects in a pre-registered study (Study 2: N = 449). Moreover, we explored the potential mediating role of perceived diversity climate, that is, the perception that the organization promotes and deals well with demographic diversity. Findings revealed that an organizational setting that distributed resources unequally (vs. equally) was associated with a more adverse diversity climate, which, in turn, correlated with expectations of a lower presence of minority group employees in the organization. We concluded that economic inequality creates a context that modulates perceptions of a climate of social exclusion which likely affects the possibilities for members of disadvantaged groups to participate and develop in organizations.
Marriage survival in new married couples: A competing risks survival analysis

Background and aim Marriage is one of the most important phenomena in human life. The survival of the marriage and the impact of various competing factors on the survival is of high importance. This study aimed at utilizing competing risks survival analysis to investigate the marriage survival of new couples in Tabriz. Methods In this longitudinal study, a number of 386 individuals who were married and divorced from 1991 to 2017, were selected by random sampling. The registered information was attained from the general registry office of Tabriz. Data analysis was carried out using the Lunn-McNeil procedure and the results were presented using an adjusted hazard ratio (AHR). Results The average age of marriage was about 23.9 (SD 6.6) years. The results of multivariate Lunn-McNeil models indicated that for the competing cause of having a relationship with another person (AHRs range: 1.12 to 2.03), the traditional mode of being familiar (AHRs range: 1.55 to 3.39), family weak role in choosing a wife/spouse (AHRs range: 0.25 to 3.25) and the role of moral-religious commitment (AHRs range: 0.37 to 0.47), along with other causes severed the risk of marriage survival reduction. Conclusion According to the results of this study in assessing competing risks, we conclude that the decline in marriage survival is a multifactorial phenomenon. Examining the survival of marriage in order to better understand all the dimensions and factors affecting this phenomenon and providing information to counselors and officials can play an important role in increasing marriage survival.
Spin-orbit coupling effects in two-electron coupled quantum dots

In the last years, the electron spin in quantum dots has become a most promising candidate for the realization of qubits, the basic element for quantum computation. In quantum dot spin qubits the exchange interaction implements a fundamental two qubit gate, which originates in the Coulomb interaction and the Pauli principle. Compared to single qubit gates, the exchange based gates are much faster and easier to control locally, motivating the solely exchange energy based quantum computation. The control is based on the exponential sensitivity of the exchange energy on the interparticle distance. Manipulation then can proceed, for example, shifting the single particle states electrically or compressing them magnetically. The practical manipulation schemes require quantitative knowledge of the exchange energy. The spin-orbit interaction plays an important role in this nano-system. Indeed the usual exchange interaction changes its magnitude, while a new term, called anisotropic exchange, appears. In this thesis we propose an accurate effective spin Hamiltonian for modeling spin-orbit-induced spin dynamics in the presence of the magnetic field. We have also performed numerically exact calculations of the isotropic and anisotropic exchange coupling in realistic two-electron GaAs coupled quantum dots in the presence of both Dresselhaus and Bychkov-Rashba spin-orbit interactions. The numerics allow us to establish the goodness of our model and to see the limits of previous statements. Furthermore we find that in zero magnetic field the second-order spin-orbit effects are absent at all interdot couplings.
Characterization of Macrophage-Tropic HIV-1 Infection of Central Nervous System Cells and the Influence of Inflammation

The major feature of HIV-1 pathogenesis is the induction of an immunodeficient state in the face of an enhanced state of inflammation. However, for many of those infected, there can be an impact on the central nervous system (CNS) resulting in a wide range of neurocognitive defects. ABSTRACT HIV-1 infection within the central nervous system (CNS) includes evolution of the virus, damaging inflammatory cascades, and the involvement of multiple cell types; however, our understanding of how Env tropism and inflammation can influence CNS infectivity is incomplete. In this study, we utilize macrophage-tropic and T cell-tropic HIV-1 Env proteins to establish accurate infection profiles for multiple CNS cells under basal and interferon alpha (IFN-α) or lipopolysaccharide (LPS)-induced inflammatory states. We found that macrophage-tropic viruses confer entry advantages in primary myeloid cells, including monocyte-derived macrophage, microglia, and induced pluripotent stem cell (iPSC)-derived microglia. However, neither macrophage-tropic or T cell-tropic HIV-1 Env proteins could mediate infection of astrocytes or neurons, and infection was not potentiated by induction of an inflammatory state in these cells. Additionally, we found that IFN-α and LPS restricted replication in myeloid cells, and IFN-α treatment prior to infection with vesicular stomatitis virus G protein (VSV G) Envs resulted in a conserved antiviral response across all CNS cell types. Further, using RNA sequencing (RNA-seq), we found that only myeloid cells express HIV-1 entry receptor/coreceptor transcripts at a significant level and that these transcripts in select cell types responded only modestly to inflammatory signals. We profiled the transcriptional response of multiple CNS cells to inflammation and found 57 IFN-induced genes that were differentially expressed across all cell types. Taken together, these data focus attention on the cells in the CNS that are truly permissive to HIV-1, further highlight the role of HIV-1 Env evolution in mediating infection in the CNS, and point to limitations in using model cell types versus primary cells to explore features of virus-host interaction. IMPORTANCE The major feature of HIV-1 pathogenesis is the induction of an immunodeficient state in the face of an enhanced state of inflammation. However, for many of those infected, there can be an impact on the central nervous system (CNS) resulting in a wide range of neurocognitive defects. Here, we use a highly sensitive and quantitative assay for viral infectivity to explore primary and model cell types of the brain for their susceptibility to infection using viral entry proteins derived from the CNS. In addition, we examine the ability of an inflammatory state to alter infectivity of these cells. We find that myeloid cells are the only cell types in the CNS that can be infected and that induction of an inflammatory state negatively impacts viral infection across all cell types.
Paired serial limiting dilution assays

Serial limiting dilution (SLD) assays are a widely used tool in many areas of public health research to measure the concentration of target entities. This concentration can be estimated via maximum likelihood. Asymptotic as well as exact inference methods have been proposed for hypothesis testing and confidence interval construction in this one‐sample problem. However, in many scientific applications, it may be of interest to compare the concentration of target entities between a pair of samples and construct valid confidence intervals for the difference in concentrations. In this paper, an exact, computationally efficient inferential procedure is proposed for hypothesis testing and confidence interval construction in the two‐sample SLD assay problem. The proposed exact method is compared to an approach based on asymptotic approximations in simulation studies. The methods are illustrated using data from the University of North Carolina HIV Cure Center.
Chromosome-level Genome Assembly of the High-altitude Leopard (Panthera pardus) Sheds Light on Its Environmental Adaptation

Abstract The leopard (Panthera pardus) has the largest natural distribution from low- to high-altitude areas of any wild felid species, but recent studies have revealed that leopards have disappeared from large areas, probably owing to poaching, a decline of prey species, and habitat degradation. Here, we reported the chromosome-scale genome assembly of the high-altitude leopard (HL) based on nanopore sequencing and high-throughput chromatin conformation capture (Hi-C) technology. Panthera genomes revealed similar repeat composition, and there was an appreciably conserved synteny between HL and the other two Panthera genomes. Divergence time analysis based on the whole genomes revealed that the HL and the low-altitude leopard differentiate from a common ancestor ∼2.2 Ma. Through comparative genomics analyses, we found molecular genetic signatures that may reflect high-altitude adaptation of the HL. Three HL-specific missense mutations were detected in two positively selected genes, that is, ITGA7 (Ala112Gly, Asp113Val, and Gln115Pro) and NOTCH2 (Ala2398Ser), which are likely to be associated with hypoxia adaptation. The chromosome-level genome of the HL provides valuable resources for the investigation of high-altitude adaptation and protection management of the vulnerable leopard.
Exploring health and social services in Denmark, Norway, Spain and the United Kingdom for the development of Parkinson's care pathways. A document analysis

Abstract People with Parkinson's disease (PD) may find it difficult to identify and access the wide number of services they need and are entitled to along their complex PD journey. As part of the project OPTIM‐PARK – Optimisation of community resources and systems of support to enhance the process of living with Parkinson's Disease, document analysis was developed to create overviews of existing resources and systems of support in Denmark, Norway, Spain and the United Kingdom. Documents on community resources, policies, guidelines and professional recommendations were the main sources of information. They were sought systematically at official websites of the public sector (national and regional levels) and websites of non‐governmental organisations and scientific societies; searches were performed in October 2020 and updated in September 2021. A higher‐level cross‐national content analysis integrated all the country‐specific information. Data‐ and concept‐driven coding frames were developed; trial coding and peer review strengthened face validity and reliability. The analysis led to overviews of: (1) Key aims at patient and societal levels. (2) Key elements in form of professional approaches. (3) Community resources. (4) Legally anchored services. In general, clear descriptions of how to implement care pathways and tools to facilitate delivery were missing in the included documents, and pathways and guidelines did not include referral to general social support, social security support or labour and employment support. The results shed light on the complex support systems and resources and can inspire the planning of more comprehensive care pathways for people with PD and other long‐term conditions.
Seamless Capacitive Body Channel Wireless Power Transmission Toward Freely Moving Multiple Animals in an Animal Cage

Unstable wireless power transmission toward multiple living animals in an animal cage is one of the significant barriers to performing long-term and real-time neural monitoring in preclinical research. Here, seamless capacitive body channel (SCB) wireless power transmission (WPT) along with power management integrated circuit (PMIC) is designed using a standard 65 nm CMOS process. The SCB WPT enables stable wireless power transmission toward multiple 35 mm×20 mm×2 mm sized receivers (RXs) attached to freely moving animals in a 600 mm×600 mm×120 mm sized animal cage. By utilizing fringe-field capacitance and a body channel for wireless power link between the cage and RXs, the maximum difference in all measured power efficiencies in diverse scenarios is only 6.66<inline-formula><tex-math notation="LaTeX">$\% $</tex-math></inline-formula> with a 20 mW load. Even with a 90<inline-formula><tex-math notation="LaTeX">$^\circ$</tex-math></inline-formula> RX rotation against the cage, power efficiency marks 17.76<inline-formula><tex-math notation="LaTeX">$\%$</tex-math></inline-formula>. Furthermore, an <italic>in-vivo</italic> experiment conducted with three untethered rats demonstrates the capability of continuous long-term power delivery in practical situations.
comparative of chimeric viruses in Sphagnum-dominated peatlands.

A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identiﬁed by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intra-gene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the ‘Cruciviridae’ group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary ﬁrst step in progressing toward an accurate quantiﬁcation and host range identiﬁcation of these new viruses. Reps corresponding Geminiviridae several are endonuclease significantly than that of other CRESS-DNA viruses possess RC-Rep homologs. The detection of several chimeric RC-Reps is consistent with previous observations (Krupovic et al. 2015) and indicates that RC-Rep domain shuffling is relatively widespread within the ‘Cruciviridae’. Our results indicate a high diversity of cruciviruses even within a single sample. When considered alongside the multiple types of RC-Rep genes found associated with the CP genes in the cruciviral genomes (Roux et al. 2013), such sequence-and genome-level diversity might indicate that shortly after the emergence of chimeric the ‘Cruciviridae’ group has experienced an evolutionary which led to the emergence of contemporary diversity viruses. fen
Scalability analysis on the smart grid fast automated demand response aggregation Web services for widely distributed building facilities

In this paper, we modeled an aggregation communication server of the Fast Automated Demand Response (FastADR) system using an M/M/1 queuing system. Assuming that a very large number of FastADR participating BEMS gateways are widely distributed, scalability of aggregation communication performance was estimated by the M/M/1 transient analysis. Validity of our analysis model was confirmed by realistic wide‐area communication emulation system in the laboratory. Our scalability analysis has shown that at least parallel 25 aggregation systems will be necessary to realize expected communication time of approximately 30 s for an example of FastADR aggregation of 100 MW reduced demand.
Comparison of Inhaled Long-Acting (cid:1) -Agonist and Anticholinergic Effectiveness in Older Patients With Chronic Obstructive Pulmonary Disease A Cohort Study

Background: Chronic obstructive pulmonary disease (COPD), a largely preventable and manageable respiratory condition, affects an estimated 12% to 20% of adults. Long-acting inhaled (cid:1) -agonists and anticholinergics have both been shown to improve COPD outcomes and are recommended for moderate to severe disease; however, little is known about their comparative effectiveness. primary Overall a long-acting -agonist did not contain information about lung function. Conclusion: Older adults initially prescribed long-acting inhaled (cid:1) -agonists for the management of moderate COPD seem to have lower mortality than those initially prescribed long-acting anticholinergics. Further research is needed to confirm these findings in younger patients and in a randomized, controlled trial.
Identiﬁcation of Target Genes for the Ewing’s Sarcoma EWS/FLI Fusion Protein by Representational Difference Analysis

The EWS/FLI-1 fusion gene results from the 11;22 chromosomal translocation in Ewing’s sarcoma. The product of the gene is one of a growing number of structurally altered transcription factors implicated in oncogenesis. We have employed a subtractive cloning strategy of representational difference analysis in conjunction with a model transformation system to identify genes transcribed in response to EWS/FLI. We have characterized eight transcripts that are dependent on EWS/FLI for expression and two transcripts that are repressed in response to EWS/FLI. Three of the former were identiﬁed by sequence analysis as stromelysin 1, a murine homolog of cytochrome P-450 F1 and cytokeratin 15. Stromelysin 1 is induced rapidly after expression of EWS/FLI, suggesting that the stromelysin 1 gene may be a direct target gene of EWS/FLI. These results demonstrate that expression of EWS/FLI leads to signiﬁcant changes in the transcription of speciﬁc genes and that these effects are at least partially distinct from those caused by expression of germ line FLI-1. The representational difference analysis technique can potentially be applied to investigate transformation pathways activated by a broad array of genes in different tumor systems.