Miracle-dz/UniFAR-FTUs huggingface dataset:
Interpretation of the Precision Matrix and Its Application in Estimating Sparse Brain Connectivity during Sleep Spindles from Human Electrocorticography Recordings

The correlation method from brain imaging has been used to estimate functional connectivity in the human brain. However, brain regions might show very high correlation even when the two regions are not directly connected due to the strong interaction of the two regions with common input from a third region. One previously proposed solution to this problem is to use a sparse regularized inverse covariance matrix or precision matrix (SRPM) assuming that the connectivity structure is sparse. This method yields partial correlations to measure strong direct interactions between pairs of regions while simultaneously removing the influence of the rest of the regions, thus identifying regions that are conditionally independent. To test our methods, we first demonstrated conditions under which the SRPM method could indeed find the true physical connection between a pair of nodes for a spring-mass example and an RC circuit example. The recovery of the connectivity structure using the SRPM method can be explained by energy models using the Boltzmann distribution. We then demonstrated the application of the SRPM method for estimating brain connectivity during stage 2 sleep spindles from human electrocorticography (ECoG) recordings using an electrode array. The ECoG recordings that we analyzed were from a 32-year-old male patient with long-standing pharmaco-resistant left temporal lobe complex partial epilepsy. Sleep spindles were automatically detected using delay differential analysis and then analyzed with SRPM and the Louvain method for community detection. We found spatially localized brain networks within and between neighboring cortical areas during spindles, in contrast to the case when sleep spindles were not present.
What are the family needs when a parent has mental health problems? Evidence from a systematic literature review

PROBLEM Little evidence exists showing how a given high-risk group of children born to parents with poor mental health seek help and how care may be improved in order to better reach and support their families. METHODS A systematic literature review was undertaken to identify the needs and help-seeking behaviors of children and their parents. Through an analysis of both quantitative and qualitative studies, published in German- and English-speaking research literature, the needs of children and parents were identified and categorized. Findings concerning their help-seeking behavior and the influence of demographic variables on needs and help-seeking behaviors were also described. FINDINGS In the primary studies, the most identified parental needs were "the need for being a good parent"; "worries about the child's well-being"; and "the need for practical help. " For children, the categories identified included "the need for knowledge"; "worries about parent's well-being"; and "the need for normality. " However, information about help-seeking behaviors and influences of demographic factors was fairly limited in the literature. CONCLUSIONS In families with parental mental health problems, it seems especially important to take a family-focused approach. The individual needs of children (and their families) should shape the planning of treatment and nursing care.
A Comparative Evaluation of Approximate Probabilistic Simulation and Deep Neural Networks as Accounts of Human Physical Scene Understanding

Humans demonstrate remarkable abilities to predict physical events in complex scenes. Two classes of models for physical scene understanding have recently been proposed: "Intuitive Physics Engines", or IPEs, which posit that people make predictions by running approximate probabilistic simulations in causal mental models similar in nature to video-game physics engines, and memory-based models, which make judgments based on analogies to stored experiences of previously encountered scenes and physical outcomes. Versions of the latter have recently been instantiated in convolutional neural network (CNN) architectures. Here we report four experiments that, to our knowledge, are the first rigorous comparisons of simulation-based and CNN-based models, where both approaches are concretely instantiated in algorithms that can run on raw image inputs and produce as outputs physical judgments such as whether a stack of blocks will fall. Both approaches can achieve super-human accuracy levels and can quantitatively predict human judgments to a similar degree, but only the simulation-based models generalize to novel situations in ways that people do, and are qualitatively consistent with systematic perceptual illusions and judgment asymmetries that people show.
Intravascular fibrin molecular imaging improves the detection of unhealed stents assessed by optical coherence tomography in vivo

Aims Fibrin deposition and absent endothelium characterize unhealed stents that are at heightened risk of stent thrombosis. Optical coherence tomography (OCT) is increasingly used for assessing stent tissue coverage as a measure of healed stents, but cannot precisely identify whether overlying tissue represents physiological neointima. Here we assessed and compared fibrin deposition and persistence on bare metal stent (BMS) and drug-eluting stent (DES) using near-infrared fluorescence (NIRF) molecular imaging in vivo, in combination with simultaneous OCT stent coverage. Methods and results Rabbits underwent implantation of one BMS and one DES without overlap in the infrarenal aorta (N = 20 3.5 × 12 mm). At Days 7 and/or 28, intravascular NIRF-OCT was performed following the injection of fibrin-targeted NIRF molecular imaging agent FTP11-CyAm7. Intravascular NIRF-OCT enabled high-resolution imaging of fibrin overlying stent struts in vivo, as validated by histopathology. Compared with BMS, DES showed greater fibrin deposition and fibrin persistence at Days 7 and 28 (P < 0.01 vs. BMS). Notably, for edge stent struts identified as covered by OCT on Day 7, 92.8 ± 9.5% of DES and 55.8 ± 23.6% of BMS struts were NIRF fibrin positive (P < 0.001). At Day 28, 18.6 ± 10.6% (DES) and 5.1 ± 8.7% (BMS) of OCT-covered struts remained fibrin positive (P < 0.001). Conclusion Intravascular NIRF fibrin molecular imaging improves the detection of unhealed stents, using clinically translatable technology that complements OCT. A sizeable percentage of struts deemed covered by OCT are actually covered by fibrin, particularly in DES, and therefore such stents might remain prothrombotic. These findings have implications for the specificity of standalone clinical OCT assessments of stent healing.
Convergent Evolution of Human-Isolated H7N9 Avian Influenza A Viruses

Background Avian influenza A virus H7N9 has caused 5 epidemic waves of human infections in China since 2013. Avian influenza A viruses may face strong selection to adapt to novel conditions when establishing themselves in humans. In this study, we sought to determine whether adaptive evolution had occurred in human-isolated H7N9 viruses. Methods We evaluated all available genomes of H7N9 avian influenza A virus. Maximum likelihood trees were separately reconstructed for all 8 genes. Signals of positive selection and convergent evolution were then detected on branches that lead to changes in host tropism (from avian to human). Results We found that 3 genes had significant signals of positive selection (all of them P < .05). In addition, we detected 34 sites having significant signals for parallel evolution in 8 genes (all of them P < .05), including 7 well-known sites (Q591K, E627K, and D701N in PB2 gene; R156K, V202A, and L244Q in HA; and R289K in NA) that play roles in crossing species barriers for avian influenza A viruses. Conclusion Our study suggests that, during infection in humans, H7N9 viruses have undergone adaptive evolution to adapt to their new host environment and that the sites where parallel evolution occurred might play roles in crossing species barriers and respond to the new selection pressures arising from their new host environments.
Quality Assessment of DSMs Produced from UAV Flights Georeferenced with On-Board RTK Positioning

High-resolution Digital Surface Models (DSMs) from unmanned aerial vehicles (UAVs) imagery with accuracy better than 10 cm open new possibilities in geosciences and engineering. The accuracy of such DSMs depends on the number and distribution of ground control points (GCPs). Placing and measuring GCPs are often the most time-consuming on-site tasks in a UAV project. Safety or accessibility concerns may impede their proper placement, so either costlier techniques must be used, or a less accurate DSM is obtained. Photogrammetric blocks flown by drones with on-board receivers capable of RTK (real-time kinematic) positioning do not need GCPs, as camera stations at exposure time can be determined with cm-level accuracy, and used to georeference the block and control its deformations. This paper presents an experimental investigation on the repeatability of DSM generation from several blocks acquired with a RTK-enabled drone, where differential corrections were sent from a local master station or a network of Continuously Operating Reference Stations (CORS). Four different flights for each RTK mode were executed over a test field, according to the same flight plan. DSM generation was performed with three block control configurations: GCP only, camera stations only, and with camera stations and one GCP. The results show that irrespective of the RTK mode, the first and third configurations provide the best DSM inner consistency. The average range of the elevation discrepancies among the DSMs in such cases is about 6 cm (2.5 GSD, ground sampling density) for a 10-cm resolution DSM. Using camera stations only, the average range is almost twice as large (4.7 GSD). The average DSM accuracy, which was verified on checkpoints, turned out to be about 2.1 GSD with the first and third configurations, and 3.7 GSD with camera stations only.
Soma to germline inheritance of extrachromosomal genetic information via a LINE‐1 reverse transcriptase‐based mechanism

Mature spermatozoa are permeable to foreign DNA and RNA molecules. Here I propose a model, whereby extrachromosomal genetic information, mostly encoded in the form of RNA in somatic cells, can cross the Weismann barrier and reach epididymal spermatozoa. LINE‐1 retrotransposon‐derived reverse transcriptase (RT) can play key roles in the process by expanding the RNA‐encoded information. Retrotransposon‐encoded RT is stored in mature gametes, is highly expressed in early embryos and undifferentiated cells, and becomes downregulated in differentiated cells. In turn, RT plays a role in developmental control, as its inhibition arrests developmental progression of early embryos with globally altered transcriptomic profiles. Thus, sperm cells act as recipients, and transgenerational vectors of somatically derived genetic information which they pass to the next generation with the potential to modify the fate of the developing embryos.
Large-Scale Spatial Distribution Patterns of Echinoderms in Nearshore Rocky Habitats

This study examined echinoderm assemblages from nearshore rocky habitats for large-scale distribution patterns with specific emphasis on identifying latitudinal trends and large regional hotspots. Echinoderms were sampled from 76 globally-distributed sites within 12 ecoregions, following the standardized sampling protocol of the Census of Marine Life NaGISA project (www.nagisa.coml.org). Sample-based species richness was overall low (<1–5 species per site), with a total of 32 asteroid, 18 echinoid, 21 ophiuroid, and 15 holothuroid species. Abundance and species richness in intertidal assemblages sampled with visual methods (organisms >2 cm in 1 m2 quadrats) was highest in the Caribbean ecoregions and echinoids dominated these assemblages with an average of 5 ind m−2. In contrast, intertidal echinoderm assemblages collected from clearings of 0.0625 m2 quadrats had the highest abundance and richness in the Northeast Pacific ecoregions where asteroids and holothurians dominated with an average of 14 ind 0.0625 m−2. Distinct latitudinal trends existed for abundance and richness in intertidal assemblages with declines from peaks at high northern latitudes. No latitudinal trends were found for subtidal echinoderm assemblages with either sampling technique. Latitudinal gradients appear to be superseded by regional diversity hotspots. In these hotspots echinoderm assemblages may be driven by local and regional processes, such as overall productivity and evolutionary history. We also tested a set of 14 environmental variables (six natural and eight anthropogenic) as potential drivers of echinoderm assemblages by ecoregions. The natural variables of salinity, sea-surface temperature, chlorophyll a, and primary productivity were strongly correlated with echinoderm assemblages; the anthropogenic variables of inorganic pollution and nutrient contamination also contributed to correlations. Our results indicate that nearshore echinoderm assemblages appear to be shaped by a network of environmental and ecological processes, and by the differing responses of various echinoderm taxa, making generalizations about the patterns of nearshore rocky habitat echinoderm assemblages difficult.
Minimal Peroxide Exposure of Neuronal Cells Induces Multifaceted Adaptive Responses

Oxidative exposure of cells occurs naturally and may be associated with cellular damage and dysfunction. Protracted low level oxidative exposure can induce accumulated cell disruption, affecting multiple cellular functions. Accumulated oxidative exposure has also been proposed as one of the potential hallmarks of the physiological/pathophysiological aging process. We investigated the multifactorial effects of long-term minimal peroxide exposure upon SH-SY5Y neural cells to understand how they respond to the continued presence of oxidative stressors. We show that minimal protracted oxidative stresses induce complex molecular and physiological alterations in cell functionality. Upon chronic exposure to minimal doses of hydrogen peroxide, SH-SY5Y cells displayed a multifactorial response to the stressor. To fully appreciate the peroxide-mediated cellular effects, we assessed these adaptive effects at the genomic, proteomic and cellular signal processing level. Combined analyses of these multiple levels of investigation revealed a complex cellular adaptive response to the protracted peroxide exposure. This adaptive response involved changes in cytoskeletal structure, energy metabolic shifts towards glycolysis and selective alterations in transmembrane receptor activity. Our analyses of the global responses to chronic stressor exposure, at multiple biological levels, revealed a viable neural phenotype in-part reminiscent of aged or damaged neural tissue. Our paradigm indicates how cellular physiology can subtly change in different contexts and potentially aid the appreciation of stress response adaptations.
Obstructive Sleep Apnea is Associated With Early but Possibly Modifiable Alzheimer’s Disease Biomarkers Changes

Study Objectives Obstructive sleep apnea (OSA) is a common sleep disorder. The, literature lacks studies examining sleep, cognition, and Alzheimer's Disease (AD) cerebrospinal fluid (CSF) biomarkers in OSA patients. Therefore, we first studied cognitive performances, polysomnographic sleep, and CSF β-amyloid42, tau proteins, and lactate levels in patients affected by subjective cognitive impairment (SCI) divided in three groups: OSA patients (showing an Apnea-Hypopnea Index [AHI] ≥15/hr), controls (showing an AHI < 15/hr), and patients with OSA treated by continuous positive airway pressure (CPAP). Methods We compared results among 25 OSA, 10 OSA-CPAP, and 15 controls who underwent a protocol counting neuropsychological testing in the morning, 48-hr polysomnography followed by CSF analysis. Results OSA patients showed lower CSF Aβ42 concentrations, higher CSF lactate levels, and higher t-tau/Aβ42 ratio compared to controls and OSA-CPAP patients. OSA patients also showed reduced sleep quality and continuity and lower performances at memory, intelligence, and executive tests than controls and OSA-CPAP patients. We found significant relationships among higher CSF tau proteins levels, sleep impairment, and increased CSF lactate levels in the OSA group. Moreover, lower CSF Aβ42 levels correlate with memory impairment and nocturnal oxygen saturation parameters in OSA patients. Conclusions We hypothesize that OSA reducing sleep quality and producing intermittent hypoxia lowers CSF Aβ42 levels, increases CSF lactate levels, and alters cognitive performances in SCI patients, thus inducing early AD clinical and neuropathological biomarkers changes. Notably, controls as well as OSA-CPAP SCI patients did not show clinical and biochemical AD markers. Therefore, OSA may induce early but possibly CPAP-modifiable AD biomarkers changes.
Emotion-regulation ability, role stress and teachers' mental health.

Background Work-related stressors, including role ambiguity and role conflict, are related to psychological maladjustment and mental ill-health. However, to date, the role of personal resources such as emotion-regulation ability (ERA) in the prediction of mental health indicators has not been addressed. Aims To examine whether ERA would contribute to explaining teachers' depression, anxiety and stress symptoms beyond role ambiguity and role conflict. Methods We carried out a cross-sectional questionnaire survey. We used a correlation matrix and hierarchical regression models to analyse the data. Results Three hundred and thirty-six Spanish teachers (185 female) from several grade levels completed the surveys (40% response rate). Role ambiguity and role conflict were positively related to depression, anxiety and stress symptoms. ERA was negatively related to teachers' scores on depressive, anxious and stress symptoms, with predictive power above the main effects of role ambiguity and role conflict. An interaction between role ambiguity and ERA was also significant in predicting depression. Conclusions Our study provides preliminary evidence suggesting the development of integrative models considering work-related stressors along with personal resources such as ERA aiming to prevent teachers' mental ill-health. Future studies should examine the influence of ERA on psychological symptoms using longitudinal designs.
On optimal signaling over Gaussian MIMO channels under interference constraints

Gaussian MIMO channel under total transmit and interference power constraints (TPC and IPC) is considered. A closed-form solution for the optimal transmit covariance matrix is obtained using the KKT-based approach. While closed-from solutions for optimal dual variables are possible in special cases, an iterative bisection algorithm (IBA) is proposed to find the optimal dual variables in the general case and its convergence is proved. Numerical experiments illustrate its efficient performance. Bounds for the optimal dual variables are given, which facilitate numerical solutions. An interplay between the TPC and IPC is studied, including the transition from power-limited to interference-limited regimes as the total transmit power increases.
On Constellation Rotation of NOMA With SIC Receiver

In this letter, we exploit constellation rotation to enhance the performance of uplink non-orthogonal multiple access (NOMA) with a successive interference cancellation receiver. We characterize the received signal with a Gaussian mixture model (GMM), where optimal rotation angle is obtained by maximizing the entropy of GMM. Then, we efficiently solve the entropy maximization problem by deriving an optimal closed-form approximate problem via variational approximation. Performance analysis and simulation results show that the proposed scheme achieves larger capacity and lower bit error rate compared with conventional NOMA. The performance gain is more significant with fewer receiving antennas or with smaller channel gain difference between multiplexed users.
Genetic background influences cardiac phenotype in murine chronic kidney disease

Background Levels of fibroblast growth factor 23 (FGF23) increase early in chronic kidney disease (CKD) and are independently associated with left ventricular hypertrophy (LVH), heart failure and death. Experimental models of CKD with elevated FGF23 and LVH are needed. We hypothesized that slow rates of CKD progression in the Col4a3 knockout (Col4a3KO) mouse model of CKD would promote development of LVH by prolonging exposure to elevated FGF23. Methods We studied congenic Col4a3KO and wild-type (WT) mice with either 75% 129X1/SvJ (129Sv) or 94% C57Bl6/J (B6) genomes. Results B6-Col4a3KO lived longer than 129Sv-Col4a3KO mice (21.4 ± 0.6 versus 11.4 ± 0.4 weeks; P < 0.05). 10-week-old 129Sv-Col4a3KO mice showed impaired renal function (blood urea nitrogen 191 ± 39 versus 34 ± 4 mg/dL), hyperphosphatemia (14.1 ± 1.4 versus 6.8 ± 0.3 mg/dL) and 33-fold higher serum FGF23 levels (P < 0.05 versus WT for each). Consistent with their slower CKD progression, 10 week-old B6-Col4a3KO mice showed milder impairment of renal function than 129Sv-Col4a3KO mice and modest FGF23 elevation without other alterations of mineral metabolism. At 20 weeks, further declines in renal function in B6-Col4a3KO mice was accompanied by hyperphosphatemia and 8-fold higher FGF23 levels (P < 0.05 versus WT for each). Only the 20-week-old B6-Col4a3KO mice developed LVH (LV mass 125 ± 3 versus 98 ± 6 mg; P < 0.05 versus WT) in association with significantly increased cardiac expression of FGF receptor 4 (FGFR4) messenger RNA and protein and markers of LVH (Atrial natriuretic peptide (ANP), B-type natriuretic peptide (BNP), beta-myosin heavy chain (β-MHC); P < 0.05 versus WT for each). Conclusions In conclusion, B6-Col4a3KO mice manifest slower CKD progression and longer survival than 129Sv-Col4a3KO mice and can serve as a novel model of cardiorenal disease.
Principles of ecological immunology

Defending self against nonself is a major problem in a world in which individuals are under constant pressure from parasites that gain fitness benefits at a cost to their host. Defences that have evolved are diverse, and range from behavioural adaptations to physiochemical barriers. The immune defence is a final line of protection and is therefore of great importance. Given this importance, variability in immune defence would seem counterintuitive, yet that is what is observed. Ecological immunology attempts to explain this variation by invoking costs and trade‐offs, and in turn proposing that the optimal immune defence will vary over environments. Studies in this field have been highly successful in establishing an evolutionary ecology framework around immunology. However, in order enrich our understanding of this area, it is perhaps time to broaden the focus to include parasites as more than simply elicitors of immune responses. In essence, to view immunity as produced by the host, the environment, and the active involvement of parasites.