Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Kidney Disease with iPS Cells

Induced pluripotent stem cells (iPSCs) are somatic cells that have been transcriptionally reprogrammed to an embryonic stem cell (ESC)-like state. iPSCs are a renewable source of diverse somatic cell types and tissues matching the original patient, including nephron-like kidney organoids. iPSCs have been derived representing several kidney disorders, such as ADPKD, ARPKD, Alport syndrome, and lupus nephritis, with the goals of generating replacement tissue and ‘disease in a dish’ laboratory models. Cellular defects in iPSCs and derived kidney organoids provide functional, personalized biomarkers, which can be correlated with genetic and clinical information. In proof of principle, disease-specific phenotypes have been described in iPSCs and ESCs with mutations linked to polycystic kidney disease or focal segmental glomerulosclerosis. In addition, these cells can be used to model nephrotoxic chemical injury. Recent advances in directed differentiation and CRISPR genome editing enable more specific iPSC models and present new possibilities for diagnostics, disease modeling, therapeutic screens, and tissue regeneration using human cells. This review outlines growth opportunities and design strategies for this rapidly expanding and evolving field.
A linear dynamic model for microgrid voltages in presence of distributed generation

We consider the scenario of a low voltage microgrid populated by a number of distributed microgenerators. We focus on the problem of obtaining a dynamic model that describes the input-output relation between complex power commands sent to the microgenerator inverters and the voltage measurements across the network. Such a model is intended as a necessary tool in the design of distributed and centralized control algorithms for the provision of ancillary services in the power distribution grid. Because this model is to be used for the design of such algorithms, we look for an analytical derivation instead of a simulative tool. The proposed model is linear and explicitly contains the network parameters and topology. Simulation shows how the proposed model approximates well the behavior of the original nonlinear system.
Preliminary application of CT perfusion source images for evaluating regional collateral circulation in unilateral Moyamoya disease.

Background Collateral flow is associated with clinical outcomes for patients with Moyamoya disease and served as a parameter for patient selection of therapeutic strategies. Therefore, we explored whether a noninvasive imaging modality, computed tomography perfusion (CTP) source images (CTP-Sis), could be used to identify the presence and intensity of collateral flow using digital subtraction angiography (DSA) as a gold standard for collateral flow. Methods CTP-Sis and DSA were performed for 24 patients with unilateral Moyamoya disease. A collateral grading system was developed based on arterial and venous phase CTP-Sis, imitating the DSA score system. Two neuroradiologists scored the DSA images using a collateral grading scale for the regions of interest corresponding to the Alberta Stroke Program Early computed tomography Score (ASPECTS) methodology. Another two neuroradiologists scored CTP-Sis in a similar manner. Agreement between the CTP-Sis and DSA consensus scores was determined, including kappa statistics. Results The agreement between the CTP-Sis and DSA consensus readings was moderate to strong, with a weighted kappa value of 0.768 [95% confidence interval (CI), 0.703-0.832], but there was a better agreement for readers of CTP-Sis, as compared with those of DSA. The sensitivity and specificity for identifying collaterals with CTP-Sis were 0.714 (95% CI, 0.578-0.851) and 0.995 (95% CI, 0.985-1.000), respectively. Conclusions CTP-Sis could help identify in a noninvasive manner the presence and intensity of collateral flow in patients with unilateral Moyamoya disease using DSA as a gold standard. Further study with a large number of cases is warranted. Further application of this method to other cerebrovascular diseases including acute ischemic stroke can also be warranted.
Empirical constraints on source properties and host galaxies of cosmological gamma-ray bursts

We discuss several constraints on the properties of gamma-ray bursts (GRB) at cosmological distances. First we use the requirement that burst sources must be optically thin to pair production by photon-photon collisions in order to produce the observed nonthermal spectra. We derive probability distributions for the minimum Lorentz expansion factor, the radiation energy, the maximum baryonic mass, and the maximum surrounding gas density in the events, based on 254 events from the second BATSE catalog. Secondly, the time variabilities of the bursts in the BATSE catalog are used to place an upper bound on the curvature radius of the emitting surface in the events. This is based on the requirement that the emitting region seen by the observer must be sufficiently small to produce the observed variability without violating causality. Finally, we discuss the association of cosmological GRB with galaxies. We consider eight bright and well-localized bursts detected by the Pioneer Venus Orbiter, whose positional error boxes contain no bright galaxies. Using the local luminosity function of galaxies, we calculate the probability for not seeing the GRB host galaxy. This probability tends to increase as the width of the GRB luminosity function increases. However, the allowed width of the GRB luminosity function is restricted by the number-count statistics of the bursts.
Isometric Stretch Alters Vascular Reactivity of Mouse Aortic Segments

Most vaso-reactive studies in mouse aortic segments are performed in isometric conditions and at an optimal preload, which is the preload corresponding to a maximal contraction by non-receptor or receptor-mediated stimulation. In general, this optimal preload ranges from about 1.2 to 8.0 mN/mm, which according to Laplace's law roughly correlates with transmural pressures of 10–65 mmHg. For physiologic transmural pressures around 100 mmHg, preloads of 15.0 mN/mm should be implemented. The present study aimed to compare vascular reactivity of 2 mm mouse (C57Bl6) aortic segments preloaded at optimal (8.0 mN/mm) vs. (patho) physiological (10.0–32.5 mN/mm) preload. Voltage-dependent contractions of aortic segments, induced by increasing extracellular K+, and contractions by α1-adrenergic stimulation with phenylephrine (PE) were studied at these preloads in the absence and presence of L-NAME to inhibit basal release of NO from endothelial cells (EC). In the absence of basal NO release and with higher than optimal preload, contractions evoked by depolarization or PE were attenuated, whereas in the presence of basal release of NO PE-, but not depolarization-induced contractions were preload-independent. Phasic contractions by PE, as measured in the absence of external Ca2+, were decreased at higher than optimal preload suggestive for a lower contractile SR Ca2+ content at physiological preload. Further, in the presence of external Ca2+, contractions by Ca2+ influx via voltage-dependent Ca2+ channels were preload-independent, whereas non-selective cation channel-mediated contractions were increased. The latter contractions were very sensitive to the basal release of NO, which itself seemed to be preload-independent. Relaxation by endogenous NO (acetylcholine) of aortic segments pre-contracted with PE was preload-independent, whereas relaxation by exogenous NO (diethylamine NONOate) displayed higher sensitivity at high preload. Results indicated that stretching aortic segments to higher than optimal preload depolarizes the SMC and causes Ca2+ unloading of the contractile SR, making them extremely sensitive to small changes in the basal release of NO from EC as can occur in hypertension or arterial stiffening.
Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks

The cAMP receptor protein (CRP)/fumarate and nitrate reduction regulatory protein (FNR)-type transcription factors (TFs) are members of a well-characterized global TF family in bacteria and have two conserved domains: the N-terminal ligand-binding domain for small molecules (e.g., cAMP, NO, or O2) and the C-terminal DNA-binding domain. Although the CRP/FNR-type TFs recognize very similar consensus DNA target sequences, they can regulate different sets of genes in response to environmental signals. To clarify the evolution of the CRP/FNR-type TFs throughout the bacterial kingdom, we undertook a comprehensive computational analysis of a large number of annotated CRP/FNR-type TFs and the corresponding bacterial genomes. Based on the amino acid sequence similarities among 1,455 annotated CRP/FNR-type TFs, spectral clustering classified the TFs into 12 representative groups, and stepwise clustering allowed us to propose a possible process of protein evolution. Although each cluster mainly consists of functionally distinct members (e.g., CRP, NTC, FNR-like protein, and FixK), FNR-related TFs are found in several groups and are distributed in a wide range of bacterial phyla in the sequence similarity network. This result suggests that the CRP/FNR-type TFs originated from an ancestral FNR protein, involved in nitrogen fixation. Furthermore, a phylogenetic profiling analysis showed that combinations of TFs and their target genes have fluctuated dynamically during bacterial evolution. A genome-wide analysis of TF-binding sites also suggested that the diversity of the transcriptional regulatory system was derived by the stepwise adaptation of TF-binding sites to the evolution of TFs.
Control Law Design for Switched Repetitive Processes with a Metal Rolling Example

Discrete linear repetitive processes are a distinct class of 2D systems where the information propagates in two independent directions, one of which is limited to a finite and fixed duration or interval. Recently, applications areas have been uncovered where suitably developed system theory for repetitive processes whose dynamics switch in one or other of the two independent directions of information propagation has potentially much to contribute. In this paper, we continue previous work in this general area by developing an efficient and numerically reliable solution to the stabilization problem, i.e. the design of a control law to ensure stability for the case of more complicated switching schemes and, in particular, when more than two different models are the subject of switching. The results are in the form of sufficient conditions which can be implemented through the use of the linear matrix inequality (LMI) algorithms.
Development of MATLAB Kinect Skeletal Tracking System (MKSTS) for gait analysis

Current gait analysis systems are expensive and require large space with well controlled environments, which limits the measurement to laboratory settings such as ViCON motion analysis system. An economical alternative method of gait analysis system is proposed, in which MATLAB Kinect Skeletal Tracking System (MKSTS) is developed using MATLAB programming software and Microsoft Kinect Sensor to accumulate the important gait parameters based on the pixel coordinates of the body joints which requires no markers. The validity of MKSTS as an alternative method in determining the gait parameters is investigated and compared to ViCON motion analysis system. A healthy participant walked along the Kistler force plate with her lower limb kinematics data are measured by ViCON motion analysis system and MKSTS concurrently. Gait parameters of right hip and right knee joint angles were extracted from both devices and compared graphically in a period of one complete gait cycle. The results indicated that the correlation coefficients of MKSTS were 0.996 for right hip angles and 0.987 for right knee angles compared to ViCON motion analysis system as reference measurement. Therefore, MKSTS is able to measure the gait parameters, though there was a substantial error in accuracy. As a conclusion, the result of the research suggests that MKSTS is valid to be used as an alternative method in determining the gait parameters, depending on the required accuracy level. MKSTS will then further developed to be implemented into telerehabilitation system.
The Emotional Climate Scale: Understanding Emotions, Context and Justice

The Emotional Climate Scale (ECS) was used to study the emotional responses of minority and majority elementary school students to different settings within their schools. The ECS applies a 7 point Likert scale to assess the emotions of anger, sadness, anxiety, loneliness, calmness, excitement, happiness, and hope in the school settings of the school bus, the playground, the principal office as well as the English, mathematics, social studies, and science classes. Minority children are significantly happier and lonelier on the bus and they are also more excited, angry and lonely in English classes than their white peers. In math classes minority children are more excited but lonelier. On the playground minority children are significantly sadder than majority children. In the principal’s office, minority children are significantly calmer than majority children. In science, minority children were significantly more excited and hopeful. In social studies minority children were also more excited. In the gym, there were no significant differences between majority and minority children. Excitement and happiness are the two positive emotions are preferred and appropriate for all classes. A key question raised by the ECS is the question “Is this school fair to minority children? ” The presence of loneliness, sadness, and anger are troubling indicators of something that is not right in this school.
A Magnetic Bead-Integrated Chip for the Large Scale Manufacture of Normalized esiRNAs

The chemically-synthesized siRNA duplex has become a powerful and widely used tool for RNAi loss-of-function studies, but suffers from a high off-target effect problem. Recently, endoribonulease-prepared siRNA (esiRNA) has been shown to be an attractive alternative due to its lower off-target effect and cost effectiveness. However, the current manufacturing method for esiRNA is complicated, mainly in regards to purification and normalization on a large-scale level. In this study, we present a magnetic bead-integrated chip that can immobilize amplification or transcription products on beads and accomplish transcription, digestion, normalization and purification in a robust and convenient manner. This chip is equipped to manufacture ready-to-use esiRNAs on a large-scale level. Silencing specificity and efficiency of these esiRNAs were validated at the transcriptional, translational and functional levels. Manufacture of several normalized esiRNAs in a single well, including those silencing PARP1 and BRCA1, was successfully achieved, and the esiRNAs were subsequently utilized to effectively investigate their synergistic effect on cell viability. A small esiRNA library targeting 68 tyrosine kinase genes was constructed for a loss-of-function study, and four genes were identified in regulating the migration capability of Hela cells. We believe that this approach provides a more robust and cost-effective choice for manufacturing esiRNAs than current approaches, and therefore these heterogeneous RNA strands may have utility in most intensive and extensive applications.
SURROUND SOUND FOR LARGE AUDIENCES: WHAT ARE THE PROBLEMS?

When replaying surround sound to large audiences it is inevitable that some people will not be in the ideal central listening position relative to the loudspeakers. As a result of this, their surround sound experience is degraded. The purpose of this paper is to outline how and why the listening experience is affected. This work is part of an ongoing study which aims to improve surround playback in large spaces both for listeners in central positions and off-centre positions.
Rethinking Risk : Aspiration as Pure Risk

There exists no satisfactory theory of risk in current normative decision theories. Notions based on utility curvature, loss aversion and probability weighting are derivative, cannot be applied to nonnumerical consequences, and are not psychologically intuitive. I develop Pure Risk theory which resolves these problems – it is consistent with existing normative theories, and both internalises and generalises the intuitive notion of risk being related to the probability of not achieving one’s aspirations. The theory shows that existing models are misspeci.ed. E¤ects hitherto modelled as loss aversion or utility curvature may be due instead to Pure Risk.
Terminology and the construction of ontology

This paper discusses a method for corpus-driven ontology design: extracting conceptual hierarchies from arbitrary domain-specific collections of texts. These hierarchies can form the basis for a concept-oriented (onomasiological) terminology collection, and hence may be used as the basis for developing knowledge-based systems using ontology editors. This reference to ontology is explored in the context of collections of terms. The method presented is a hybrid of statistical and linguistic techniques, employing statistical techniques initially to elicit a conceptual hierarchy, which is then augmented through linguistic analysis. The result of such an extraction may be useful in information retrieval, knowledge management, or in the discipline of terminology science itself.
Energy and Spectral Efficiencies Trade-off with Filter Optimization in Multiple Access Interference-Aware

This work analyzes the optimized deployment of two resources scarcely available in mobile multiple access systems, i.e., spectrum and energy, as well as the impact of filter optimization in the system performance. Taking in perspective the two conflicting metrics, throughput maximization and power consumption minimization, the distributed energy efficiency (EE) cost function is formulated. Furthermore, the best energy-spectral efficiencies (EE-SE) trade-off is achieved when each node allocates exactly the power necessary to attain the best SINR response, which guarantees the maximal EE. To demonstrate the validity of our analysis, two low-complexity energy-spectral efficient algorithms, based on distributed instantaneous SINR level are developed, and the impact of single and multiuser detection filters on the EE-SE trade-off is analyzed.
Low Density Lipoproteins Promote Unstable Calcium Handling Accompanied by Reduced SERCA2 and Connexin-40 Expression in Cardiomyocytes

The damaging effects of high plasma levels of cholesterol in the cardiovascular system are widely known, but little attention has been paid to direct effects on cardiomyocyte function. We therefore aimed at testing the hypothesis that Low Density Lipoprotein (LDL) cholesterol affects calcium dynamics and signal propagation in cultured atrial myocytes. For this purpose, mRNA and protein expression levels were determined by real time PCR and western blot analysis, respectively, and intracellular calcium was visualized in fluo-4 loaded atrial HL-1 myocyte cultures subjected to field stimulation. At low stimulation frequencies all cultures had uniform calcium transients at all tested LDL concentrations. However, 500 µg LDL/mL maximally reduced the calcium transient amplitude by 43% from 0.30±0.04 to 0.17±0.02 (p<0.05). Moreover, LDL-cholesterol dose-dependently increased the fraction of alternating and irregular beat-to-beat responses observed when the stimulation interval was shortened. This effect was linked to a concurrent reduction in SERCA2, RyR2, IP3RI and IP3RII mRNA levels. SERCA2 protein levels were also reduced by 43% at 200 µg LDL/mL (p<0.05) and SR calcium loading was reduced by 38±6% (p<0.001). By contrast, HDL-cholesterol had no significant effect on SERCA expression or SR calcium loading. LDL-cholesterol also slowed the conduction velocity of the calcium signal from 3.2+0.2 mm/s without LDL to 1.7±0.1 mm/s with 500 µg LDL/mL (p<0.05). This coincided with a reduction in Cx40 expression (by 44±3%; p<0.05 for mRNA and by 79±2%; p<0.05 for Cx40 protein at 200 µg/ml LDL) whereas the Cx-43 expression did not significantly change. In conclusion, LDL-cholesterol destabilizes calcium handling in cultured atrial myocytes subjected to rapid pacing by reducing SERCA2 and Cx40 expression and by slowing the conduction velocity of the calcium signal.
Combating social isolation for people with severe chronic aphasia through community aphasia groups: consumer views on getting it right and wrong

ABSTRACT Background: Group participation has been demonstrated to have a range of benefits for people with chronic aphasia yet the strength of empirical findings is limited by the under-representation of people with severe aphasia. Little is known about what people with severe aphasia want, need and receive through participation in aphasia groups. Understanding the barriers and facilitators experienced by this population may assist the development of long-term strategies to manage significant communication disability. Aims: This study explored community aphasia group participation from the perspectives of people with severe aphasia. Method & Procedures: An interpretative phenomenological approach was employed to examine the reflections and experiences of seven people with severe, chronic aphasia. Reflections stemmed from people with aphasia who had withdrawn from groups as well as people who remained. Semi-structured interviews were conducted using techniques for enabling the participants to participate as fully as possible in the interviews. Field notes and journal entries also constituted data. Thematic analysis was used with all data sources. Outcomes & Results: Analysis revealed three core themes associated with community aphasia group participation experiences. Participants with severe aphasia can initially perceive the community aphasia group to be high risk. As a consequence, the group participation proposition can be met with substantial apprehension. Compared to participants with mild and moderate aphasia, the participants with severe aphasia demonstrated a need for increased structure and use of physical materials to support them to successfully interact and integrate in the group. Despite the need for increased structure, participants with severe aphasia valued group environments that offered authentic interaction opportunities and that provided a platform for them to demonstrate and reveal their individual strengths, most notably as active listeners. Conclusions: Participation in community aphasia groups presents additional challenges for people with severe aphasia. They risk becoming overwhelmed and excluded if the group is not adequately structured and resourced to support their interaction. People with severe aphasia value the explicit use of physical materials and group activities that support them to engage in group-based interactions. People with severe aphasia also seek to participate in authentic and meaningful activity that enables them to demonstrate identity and competency. In a community aphasia group that has a supportive communication environment, people with severe aphasia can experience fulfilling interactions and view themselves as valued group contributors.