Miracle-dz/UniFAR-FTUs huggingface dataset:
Pixel-by-pixel deconvolution of bolus-tracking data: optimization and implementation

Quantification of haemodynamic parameters with a deconvolution analysis of bolus-tracking data is an ill-posed problem which requires regularization. In a previous study, simulated data without structural errors were used to validate two methods for a pixel-by-pixel analysis: standard-form Tikhonov regularization with either the L-curve criterion (LCC) or generalized cross validation (GCV) for selecting the regularization parameter. However, problems of image artefacts were reported when the methods were applied to patient data. The aim of this study was to investigate the nature of these problems in more detail and evaluate strategies of optimization for routine application in the clinic. In addition we investigated to which extent the calculation time of the algorithm can be minimized. In order to ensure that the conclusions are relevant for a larger range of clinical applications, we relied on patient data for evaluation of the algorithms. Simulated data were used to validate the conclusions in a more quantitative manner. We conclude that the reported problems with image quality can be removed by appropriate optimization of either LCC or GCV. In all examples this could be achieved with LCC without significant perturbation of the values in pixels where the regularization parameter was originally selected accurately. GCV could not be optimized for the renal data, and in the CT data only at the cost of image resolution. Using the implementations given, calculation times were sufficiently short for routine application in the clinic.
Trust and Mindfulness as a Means for Teacher Professional Development in Ukrainian Public Schools

The problem of the study was to examine the current state of the level of trust of Ukrainian public school teachers regarding other teachers, parents, students, the principal, and the practice of mindfulness as important conditions for public school transformation. The research objectives were to identify the current state of the perception of trust between teacher-to-teachers, teacher-to-principal, teacher-to-parents, and teacher-to-students to identify how mindful the Ukrainian public school teachers are, and to identify existing patterns for trust and mindfulness in the Ukrainian public schools. The review of literature helped to clarify the direction of the study. It includes articles and books on organizational culture, individual trust and mindfulness, organizational trust and mindfulness, professional learning communities, leadership, and collaborative culture. The study relies on the concepts of trust and mindfulness developed by Hoy et al., Langer, Weick et al. and Bryk and Schneider. The study adopted a quantitative research design with some elements of qualitative analysis. The participants were K-12 teachers of the Ukrainian public (rural and urban) schools. Nonprobability sampling was used; the teachers were approached through e-mails. A database of e-mails was formed through school websites. A 40-item survey instrument was used to collect the data. Two open-ended questions included in the instrument gathered additional perceptions of teachers regarding school culture presented in their schools. For refinement and validation, the instrument was piloted to 20 teachers; feedback received contributed to a final instrument design. The study data were analyzed by each item of the instrument with the help of descriptive statistics. Responses to the open-ended questions were read and common themes were distinguished and coded. Results of the qualitative analysis are presented in the form of tables. The researcher translated all data into English from Ukrainian, which was the language used during data collection. The study revealed a significant level of ambivalence regarding perceptions and practices of trust and mindfulness present in Ukrainian public schools. The current practice of trust and mindfulness among teacher-to-teacher, teacher-to-principal, teacher-to-student, and teacherto-parent needs improvements. Analysis of data shows that the following factors are the most important for a school culture of trust and mindfulness: trust and collaboration among stakeholders, role and approach of the principal, responsibility of stakeholders, partnership with parents, and teacher competence. Moreover, teachers consider levels of bureaucracy, lack of autonomy in finance, management, and teaching, and low teacher status as factors that restrict the practice of trust and mindfulness.
Distances and directions in multidimensional shape spaces: implications for morphometric applications.

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An intelligent approach for optimizing Energy consumption and Schedule length of Embedded multiprocessors

In contemporary and future embedded as well as high-performance microprocessors, power consumption is one of the most important design considerations. Because in current technologies, the dynamic power consumption dominates the static power consumption, voltage scaling is an effective technique to reduce the power consumption. In multiprocessor systems, an efficient scheduling of sequential and parallel tasks onto the processors is known to be NP- Hard problem. In this paper, the problem of minimizing schedule length with energy consumption constraint and the problem of minimizing energy consumption with schedule length constraint on homogeneous and heterogeneous multiprocessor computers through inde- pendent sequential and parallel tasks are proposed. These problems emphasize the tradeoff between power and performance and are defined such that the power-performance product is optimized by fixing one factor and minimizing the other and vice versa. The performances of the proposed algorithm with optimal solutions are validated using Discrete Particle Swarm Optimization (DPSO). The proposed algorithms achieve 47.5% of power savings and 45.5% of energy saving with 23.5% increased schedule length when the processors operate its maximum frequency.
The Latency-Associated Nuclear Antigen of Rhesus Monkey Rhadinovirus Inhibits Viral Replication through Repression of Orf50/Rta Transcriptional Activation

ABSTRACT Rhesus monkey rhadinovirus (RRV) is a gamma-2-herpesvirus that is closely related to Kaposi's sarcoma-associated herpesvirus/human herpesvirus-8. We have previously reported that the transcript for RRV latency-associated nuclear antigen (R-LANA) is expressed during lytic replication in rhesus fibroblasts. In this article, we report the development of a latent culture system for RRV and show that mRNA specific for R-LANA is expressed during latency as well. We have characterized the R-LANA protein and demonstrate that it exhibits a nuclear speckled localization and possesses the ability to homodimerize. When expressed in rhesus fibroblasts, R-LANA can inhibit RRV lytic replication in vitro. We have investigated the mechanism behind this inhibition and find that, while R-LANA itself has very little effect on lytic promoters, it can dramatically decrease the transactivation function of RRV Orf50 (Rta), which is the major viral transcription factor. We further show that the mechanism for this repression involves the recruitment of histone deacetylase complexes (HDACs), because R-LANA's ability to repress Orf50 transactivation is completely reversed by the addition of the HDAC inhibitor trichostatin A (TSA). We also report that TSA alone can significantly reactivate RRV from latently infected cells. We propose that the repressive effects of R-LANA on RRV Orf50 transactivation serve to downregulate the transcription of early genes at late times during the lytic cycle and also help to maintain viral latency by preventing viral reactivation.
Adjuvant Immunotherapy of Experimental Autoimmune Encephalomyelitis: Immature Myeloid Cells Expressing CXCL10 and CXCL16 Attract CXCR3+CXCR6+ and Myelin-Specific T Cells to the Draining Lymph Nodes Rather Than the Central Nervous System

CFA is a strong adjuvant capable of stimulating cellular immune responses. Paradoxically, adjuvant immunotherapy by prior exposure to CFA or live mycobacteria suppresses the severity of experimental autoimmune encephalomyelitis (EAE) and spontaneous diabetes in rodents. In this study, we investigated immune responses during adjuvant immunotherapy of EAE. Induction of EAE in CFA-pretreated mice resulted in a rapid influx into the draining lymph nodes (dLNs) of large numbers of CD11b+Gr-1+ myeloid cells, consisting of immature cells with ring-shaped nuclei, macrophages, and neutrophils. Concurrently, a population of mycobacteria-specific IFN-γ–producing T cells appeared in the dLNs. Immature myeloid cells in dLNs expressed the chemokines CXCL10 and CXCL16 in an IFN-γ–dependent manner. Subsequently, CD4+ T cells coexpressing the cognate chemokine receptors CXCR3 and CXCR6 and myelin oligodendrocyte glycoprotein (MOG)-specific CD4+ T cells accumulated within the chemokine-expressing dLNs, rather than within the CNS. Migration of CD4+ T cells toward dLN cells was abolished by depleting the CD11b+ cells and was also mediated by the CD11b+ cells alone. In addition to altering the distribution of MOG-specific T cells, adjuvant treatment suppressed development of MOG-specific IL-17. Thus, adjuvant immunotherapy of EAE requires IFN-γ, which suppresses development of the Th17 response, and diverts autoreactive T cells away from the CNS toward immature myeloid cells expressing CXCL10 and CXCL16 in the lymph nodes.
Characterization of the Interaction between Tumor Necrosis Factor-stimulated Gene-6 and Heparin

TSG-6, the secreted product of tumor necrosis factor-stimulated gene-6, is not constitutively expressed but is up-regulated in various cell-types during inflammatory and inflammation-like processes. The mature protein is comprised largely of contiguous Link and CUB modules, the former binding several matrix components such as hyaluronan (HA) and aggrecan. Here we show that this domain can also associate with the glycosaminoglycan heparin/heparan sulfate. Docking predictions and site-directed mutagenesis demonstrate that this occurs at a site distinct from the HA binding surface and is likely to involve extensive electrostatic contacts. Despite these glycosaminoglycans binding to non-overlapping sites on the Link module, the interaction of heparin can inhibit subsequent binding to HA, and it is possible that this occurs via an allosteric mechanism. We also show that heparin can modify another property of the Link module, i.e. its potentiation of the anti-plasmin activity of inter-α-inhibitor (IαI). Experiments using the purified components of IαI indicate that TSG-6 only binds to the bikunin chain and that this is at a site on the Link module that overlaps the HA binding surface. The association of heparin with the Link module significantly increases the anti-plasmin activity of the TSG-6·IαI complex. Changes in plasmin activity have been observed previously at sites of TSG-6 expression, and the results presented here suggest that TSG-6 is likely to contribute to matrix remodeling, at least in part, through down-regulation of the protease network, especially in locations containing heparin/heparan sulfate proteoglycans. The differential effects of HA and heparin on TSG-6 function provide a mechanism for its regulation and functional partitioning in particular tissue microenvironments.
Age-related changes in intracranial pressure in rabbits with uncorrected familial coronal suture synostosis.

OBJECTIVE Chronic, elevated intracranial pressure (ICP) in craniosynostotic infants may result in ocular and neurocapsular problems; however, not all infants exhibit elevated ICP. Clinical ICP studies are further confounded by small and heterogeneic samples, multiple-suture involvement, and varying surgical management protocols. The present study was designed to describe longitudinal changes in ICP in a large, homogenous sample of rabbits with uncorrected familial, nonsyndromic coronal suture synostosis. METHODS Ninety-one rabbits were divided into four groups: (1) normal rabbits (n = 28), (2) rabbits with delayed-onset coronal suture synostosis (DOCS; n = 25), (3) rabbits with unilateral coronal suture synostosis (UCS; n = 12), and (4) rabbits with bilateral coronal suture synostosis (BCS; n = 26). ICP was measured at 24 and 42 days of age using a Codman epidural microtransducer. RESULTS Rabbits with BCS had a significantly (p < .05) higher mean ICP at 25 days of age than rabbits in the other three groups by approximately 146%. However, by 42 days of age, mean ICP in normal control rabbits and rabbits with DOCS was significantly (p < .01) increased compared with their mean ICP values seen at 25 days of age, while mean ICP in BCS rabbits significantly (p < .01) decreased (by 32%) over the same time period. ICP in rabbits with UCS was between that seen in normal control rabbits and rabbits with BCS and did not significantly (p > .05) change over time. CONCLUSIONS These findings suggest that the degree of suture involvement may be related to early increases in ICP. Possible multifactorial explanations for intracranial decompression and compensation in the craniosynostotic rabbit model are discussed.
Quantitative Phosphoproteomics Reveals Widespread Full Phosphorylation Site Occupancy During Mitosis

Protein phosphorylation during the cell cycle may be an all-or-none process in many instances. All-or-None Phosphorylation Phosphorylation is a key regulatory event that drives many cellular processes, including cell division. Olsen et al. undertook a phosphoproteomic analysis of HeLa cells at various stages in the cell cycle, which linked new phosphorylation sites and kinase substrates to specific stages. Furthermore, they established a method to calculate the fractional occupancy of particular phosphorylation sites (phosphorylation stoichiometry) on a global level and found that, contrary to expectations, many sites on functionally related proteins appeared to be nearly completely phosphorylated at particular stages of the cell cycle. They observed an inverse relationship in the phosphorylation occupancy of some sites in cells undergoing mitosis compared to those in S phase. The authors speculate that a high stoichiometry of phosphorylation may be necessary to inactivate an entire protein population to effectively block activity, whereas function may only require a low stoichiometry of phosphorylation, because only a small fraction of the protein population may be required for full activity. Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry–based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or ATR or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells.
A framework for systematic accumulation, sharing and reuse of task implementation knowledge

For the introduction of robots to a variety of workplaces, accumulation, sharing and reuse of task implementation knowledge including complex motions of robots, tool and device usage for tasks are important. Further this knowledge need to be quickly accessed and utilized through the process of introducing a robot for a task, updating existing systems to more efficient ones, and implementing similar tasks. This paper proposes a framework to store data related to tasks and enable task implementation using search, customization and combination of the stored data. The stored data include motion patterns of robots, various meta-data including texts, images, 3D models and other documents. They are managed based on task models. The meta-data are used by humans to figure out the tasks and reusability of the associated motion patterns. The primary goal of this framework is to assist the process of thinking and implementation by humans. This paper presents an analysis of typical use-cases and system design of the framework, and implementation on Choreonoid. Then an experiment is presented, where a sequence of assembling a complex mechanical unit is described using the proposed framework. We also discuss issues on the current framework specifications and possible cooperation with automation technologies and external data sources.
Using a computer database to monitor compliance with pharmacotherapeutic guidelines for schizophrenia.

OBJECTIVE The study examined whether prescription data from a computerized database could be used to measure conformance with treatment recommendations of the Schizophrenia Patient Outcomes Research Team (PORT). METHODS Records of an academically affiliated Veterans Affairs medical center were reviewed to identify patients who were hospitalized for schizophrenia and later seen for at least two outpatient visits in the six months after discharge (N=353). RESULTS Conformance with only three of the 18 PORT pharmacotherapeutic recommendations could be measured with the available data. In regard to the recommendation to use antipsychotics other than clozapine as first-line treatments in acute episodes, 77 percent of the sample filled a prescription for an antipsychotic during the acute episode. Of these, only 6 percent received an antipsychotic regimen that included clozapine. In regard to the PORT recommendation on dosage during acute symptom episodes, 42 percent of the patients on conventional antipsychotics received dosages below the recommended range, 5 percent were above the range, and 53 percent were within it. In contrast, of the 53 patients who received clozapine or risperidone, 87 percent received prescriptions within the recommended dosage range. As for the recommendation to offer a trial of clozapine to patients who do not respond to adequate trials of two different classes of conventional drugs, 10 percent of patients who were switched from conventional regimens to clozapine were receiving dosages of conventional medications below the recommended range. CONCLUSIONS Patient prescription data can provide preliminary measures to cost-effectively assess conformance with treatment. However, the approach has several limitations, and complementary analyses would enhance its usefulness.
The development of insomnia within the first year: a focus on worry.

OBJECTIVES The aim of this investigation was to study the relationships between sleep-related worry and subjective sleep perception as a function of stage of chronicity. DESIGN A cross-sectional study consisting of 136 individuals with a short history of insomnia was used. METHODS The 136 participants were grouped to form two different levels of chronicity based on their duration of insomnia: short (3-7 months; n=69) and long (>7-12 months; n=67). Two domains of sleep-related worry (sleeplessness and health) were used as predictors of subjective sleep perception (sleep onset latency, time awake after sleep onset, and total sleep time). RESULTS The association between worry for sleeplessness and subjective sleep perception was significantly different across the stages of chronicity. In the group with a short duration of insomnia, worry for sleeplessness was not related to subjective sleep perception. Worry for sleeplessness was however a significant predictor of subjective sleep perception in the group with a long duration of insomnia (unique variance: 33% on sleep onset latency, 19% on time awake after sleep onset, and 13% on total sleep time). Even if marked differences were observed between the two groups, worry for health was not significantly different across stages of chronicity on subjective sleep perception. CONCLUSIONS This suggests that the role of sleep-related worry to subjective sleep perception may increase over time. Given that worry was a mechanism with an increasingly stronger impact over time, this supports the idea that worry is a potential mechanism related to the development of insomnia.