Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Diffusional Kurtosis Imaging and Dynamic Contrast-Enhanced MR Imaging to Predict Posttraumatic Epilepsy in Rabbits

BACKGROUND AND PURPOSE: Finding a reliable biomarker to thoroughly assess the brain structure changes in posttraumatic epilepsy is of great importance. Our aim was to explore the value of diffusional kurtosis imaging combined with dynamic contrast-enhanced MR imaging in the evaluation of posttraumatic epilepsy. MATERIALS AND METHODS: A modified weight-drop device was used to induce traumatic brain injury. Rabbits were exposed to traumatic brain injury or sham injury. Diffusional kurtosis imaging and dynamic contrast-enhanced MR imaging were performed 1 day after injury. Posttraumatic epilepsy was investigated 3 months after injury. The traumatic brain injury group was further divided into 2 groups: the posttraumatic epilepsy and the non-posttraumatic epilepsy groups. Mean kurtosis and volume transfer coefficient values in the cortex, hippocampus, and thalamus were analyzed. After follow-up, the experimental animals were sacrificed for Nissl staining. RESULTS: The posttraumatic epilepsy group comprised 8 rabbits. In the ipsilateral cortex, the volume transfer coefficient in the traumatic brain injury group was higher than that in the sham group; the volume transfer coefficient in the posttraumatic epilepsy group was higher than that in the non-posttraumatic epilepsy group. In the ipsilateral hippocampus, the volume transfer coefficient in the posttraumatic epilepsy group was higher than that in the non-posttraumatic epilepsy and sham groups. No difference was observed between the non-posttraumatic epilepsy and sham groups. In the ipsilateral cortex, mean kurtosis in the traumatic brain injury group was lower than that in the sham group, and mean kurtosis in the posttraumatic epilepsy group was lower than that in the non-posttraumatic epilepsy group. In the ipsilateral thalamus and hippocampus, mean kurtosis in the traumatic brain injury group was lower than that in the sham group, and mean kurtosis in the posttraumatic epilepsy group was lower than that in the non-posttraumatic epilepsy group. In the contralateral thalamus, mean kurtosis in the traumatic brain injury group was lower than that in the sham group; however, no difference was observed between the posttraumatic epilepsy and non-posttraumatic epilepsy groups. CONCLUSIONS: Diffusional kurtosis imaging and dynamic contrast-enhanced MR imaging could be used to predict the occurrence of posttraumatic epilepsy in rabbits exposed to experimental traumatic brain injury.
HITS-CLIP reveals sex-differential RNA binding and alterative splicing regulation of SRm160 in Drosophila

Serine/arginine (SR)-rich proteins are critical for the regulation of alternative splicing (AS), which generates multiple mRNA isoforms from one gene and provides protein diversity for cell differentiation and tissue development. Genetic evidence suggests that Drosophila genital-specific overexpression of SR-related nuclear matrix protein of 160 kDa (SRm160), an SR protein with a PWI RNA-binding motif, causes defective development only in male flies and results in abnormal male genital structures and abnormal testis. However, the molecular characterization of SRm160 is limited. Using the high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) method in two sex-specific embryonic cell lines, S2 from the male and Kc from the female, we first identified the genome-wide RNA-binding characteristics of SRm160, which preferred binding to the exonic tri-nucleotide repeats GCA and AAC. We then validated this binding through both in vitro gel-shift assay and in vivo splicing of minigenes and found that SRm160 level affects AS of many transcripts. Furthermore, we identified 492 differential binding sites (DBS) of SRm160 varying between the two sex-specific cell lines. Among these DBS-containing genes, splicing factors were highly enriched, including transformer, a key regulator in the sex determination cascade. Analyses of fly mutants demonstrated that the SRm160 level affects AS isoforms of transformer. These findings shed crucial light on SRm160's RNA-binding specificity and regulation of AS in Drosophila sex determination and development.
REVIEW OF THE TIMING AND CAUSES OF THE AMAZON-FAN MASS TRANSPORT AND AVULSION DEPOSITS DURING THE LATEST PLEISTOCENE

The late Pleistocene Amazon deep-sea fan provides a "modern" analogue to ancient fan systems containing sandy hydrocarbon reservoirs. Extensive deposits of sand-rich material are found in the Amazon Fan mass-transport deposits (MTDs) and the base-of-channel avulsed sand bodies which underlie the channel-levee systems. These deposits were drilled as part of ODP Leg 155, the results of which form the basis of this review. The hemipelagic sediment above the MTDs and avulsed sand bodies were dated using primarily AMS radiocarbon dating. The dating provides support for the interpretation that the MTDs and avulsed sand bodies were triggered by relatively small, millennial-scale changes in relative global sea level (+/- 5-20 m). Equally controversial has been the suggestion that changes in sea level also control the architecture of the channel-levee distributive systems within the Amazon Fan. For example, Maslin et al. (2006) proposed that prior to 22,000 calendar years BP a tripartite channel system existed while afterwards only one active channel-levee system existed. This switch may have been due to the fall in sea level below the shelf break, providing direct access between the canyon and the sediment supplied to and eroded from the shelf-edge delta front. This would have significantly increased the sediment supply to the Amazon Fan at 22 ka, contributing to channel entrenchment involving channel-floor erosion and the growth of levees within the canyon-channel transition area, promoting the development of a single deep, incised channel. If future work confirms that Amazon deep-sea Fan sedimentation is sensitive to relatively small changes in sea level, this will provide support for the central assumption of the theory of sequence stratigraphy, namely that changes in sea level control basin sedimentation and the emplacement of sand-rich, potential hydrocarbon-bearing, deposits. It is hoped that these controversial suggestions reviewed here will stimulate more investigations into the Amazon Fan and other deep-sea fans.
An empirical, 21st century evaluation of phrenology

Phrenology was a nineteenth century endeavour to link personality traits with scalp morphology. It has been both influential and fiercely criticised, not least because of the assumption that scalp morphology can be informative of the underlying brain function. Here we test this idea empirically, rather than dismissing it out of hand. Whereas nineteenth century phrenologists had access to coarse measurement tools (digital technology then referring to fingers), we were able to re-examine phrenology using 21st century methods and thousands of subjects drawn from the largest neuroimaging study to date. High-quality structural MRI was used to quantify local scalp curvature. The resulting measurements were compared against lifestyle measures acquired on the same cohort of subjects. We were careful to match a subset of lifestyle measures to phrenological ideas of brain organisation, in an effort to evoke the character of Victorian times. The results represent the most rigorous evaluation of phrenological claims to date.
Two distinct patterns of treatment resistance: clinical predictors of treatment resistance in first-episode schizophrenia spectrum psychoses

Background Clozapine remains the only evidence-based antipsychotic for treatment-resistant schizophrenia (TRS). The ability to predict which patients with their first onset of schizophrenia would subsequently meet criteria for treatment resistance (TR) could help to diminish the severe functional disability which may ensue if TR is not recognized and correctly treated. Method This is a 5-year longitudinal assessment of clinical outcomes in a cohort of 246 first-episode schizophrenia spectrum patients recruited as part of the NIHR Genetics and Psychosis (GAP) study conducted in South London from 2005 to 2010. We examined the relationship between baseline demographic and clinical measures and the emergence of TR. TR status was determined from a review of electronic case records. We assessed for associations with early-, and late-onset TR, and non-TR, and differences between those TR patients treated with clozapine and those who were not. Results Seventy per cent (n = 56) of TR patients, and 23% of the total study population (n = 246) were treatment resistant from illness onset. Those who met criteria for TR during the first 5 years of illness were more likely to have an early age of first contact for psychosis (<20 years) [odds ratio (OR) 2.49, 95% confidence interval (CI) 1.25–4.94] compared to those with non-TR. The relationship between an early age of first contact (<20 years) and TR was significant in patients of Black ethnicity (OR 3.71, 95% CI 1.44–9.56); and patients of male gender (OR 3.13 95% CI 1.35–7.23). Conclusions For the majority of the TR group, antipsychotic TR is present from illness onset, necessitating increased consideration for the earlier use of clozapine.
Redefining Relationships

In response to dramatic increases in imprisonment, a burgeoning literature considers the consequences of incarceration for family life, almost always documenting negative outcomes. But effects of incarceration may be more complicated and nuanced. In this article, we consider the countervailing consequences of paternal incarceration for a host of family relationships, including fathers’ parenting, mothers’ parenting, and the relationship between parents. Using longitudinal data from the Fragile Families and Child Wellbeing Study, we find recent paternal incarceration sharply diminishes parenting behaviors among residential but not nonresidential fathers. Virtually all of the association between incarceration and parenting among residential fathers is explained by changes in fathers’ relationships with their children’s mothers. Consequences for mothers’ parenting, however, are weak and inconsistent. Furthermore, our findings show recent paternal incarceration sharply increases the probability a mother repartners, potentially offsetting some losses from the biological father’s lesser involvement while simultaneously leading to greater family complexity. Taken together, the collateral consequences of paternal incarceration for family life are complex and countervailing.
Fréchet regression for random objects with Euclidean predictors

Increasingly, statisticians are faced with the task of analyzing complex data that are non-Euclidean and specifically do not lie in a vector space. To address the need for statistical methods for such data, we introduce the concept of Frechet regression. This is a general approach to regression when responses are complex random objects in a metric space and predictors are in $\mathcal{R}^p$, achieved by extending the classical concept of a Frechet mean to the notion of a conditional Frechet mean. We develop generalized versions of both global least squares regression and local weighted least squares smoothing. The target quantities are appropriately defined population versions of global and local regression for response objects in a metric space. We derive asymptotic rates of convergence for the corresponding fitted regressions using observed data to the population targets under suitable regularity conditions by applying empirical process methods. For the special case of random objects that reside in a Hilbert space, such as regression models with vector predictors and functional data as responses, we obtain a limit distribution. The proposed methods have broad applicability. Illustrative examples include responses that consist of probability distributions and correlation matrices, and we demonstrate both global and local Frechet regression for demographic and brain imaging data. Local Frechet regression is also illustrated via a simulation with response data which lie on the sphere.
What Is the Role of Archaea in Plants? New Insights from the Vegetation of Alpine Bogs

Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress. ABSTRACT The Archaea represent a significant component of the plant microbiome, whereas their function is still unclear. Different plant species representing the natural vegetation of alpine bogs harbor a substantial archaeal community originating from five phyla, 60 genera, and 334 operational taxonomic units (OTUs). We identified a core archaeome for all bog plants and ecosystem-specific, so far unclassified Archaea. In the metagenomic data set, Archaea were found to have the potential to interact with plants by (i) possible plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic (especially oxidative and osmotic) stress. The unexpectedly high degree of plant specificity supports plant-archaeon interactions. Moreover, functional signatures of Archaea reveal genetic capacity for the interplay with fungi and an important role in the carbon and nitrogen cycle: e.g., CO2 and N2 fixation. These facts reveal an important, yet unobserved role of the Archaea for plants as well as for the bog ecosystem. IMPORTANCE Archaea are still an underdetected and little-studied part of the plant microbiome. We provide first and novel insights into Archaea as a functional component of the plant microbiome obtained by metagenomic analyses. Archaea were found to have the potential to interact with plants by (i) plant growth promotion through auxin biosynthesis, (ii) nutrient supply, and (iii) protection against abiotic stress.
The protective effects of Morus nigra L. leaves on the kidney function tests and kidney and liver histological structures in streptozotocin-induced diabetic rats

Background and aim: Diabetes Mellitus (DM) is associated with increased oxidative stress and its related complications. The phenolic components of mulberry (Morus nigra L.) leave have antioxidant components that can modulate oxidative stress. In this study, the beneficial effects of mulberry leaves extract were assessed in diabetic nephropathy and liver cells damage. Materials and methods: Diabetes induced by high-fat diet and injection of 35 mg/kgBW Streptozotocin (STZ). Forty-four male wistar rats were divided into four groups: healthy control, non-treated, glibenclamide-treated, and extract-treated. The extract-treated group was treated with mulberry leaf extract for 4 weeks. At the end of treatment, kidney, liver and blood samples were collected to assay the biochemical analysis including fasting blood glucose level, albumin, creatinine, urea and uric acid concentrations, white blood cells, hemoglobin, hematocrit and histological evaluation. Results: Fasting blood glucose, creatinine, urea and uric acid were significantly in low levels in extract-treated group compared with the non-treated diabetic rats (p<0.001, p=0.03, p=0.009, and p=0.002; respectively). White blood cells level was low level (p<0.001) and hemoglobin and hematocrit levels were higher in extract treated group (p<0.001 and p=0.01; respectively). Serum albumin level in extract-treated rats was significantly higher than untreated group (p<0.001). Evaluating the histopathology of kidney showed that glycogen accumulation, fatty degeneration, and lymphocyte infiltration in extract-treated group were mild; while they were moderate in non-treated group; moreover, liver tissue evaluation showed that the fatty degeneration in extracttreated rats was mild and the cytoplasm of hepatocytes was distended by smaller amount of fatty droplets. Conclusion: The antioxidant properties of Mulberry leaves inhibited kidney and liver damage in diabetic rats. These results can be a base to evaluate the effects of mulberry (Morus nigra L.) leaves extract in the management of hyperuricemia, nephropathy, and fatty degeneration in liver cells in diabetic human patients.
The Myth of the Square Chart

Summary The first nautical charts used to navigate in the Atlantic, in the late Middle Ages and Renaissance, were identical to the portolan charts of the Mediterranean, only differ- ing in their geographic limits. With the introduction of astronomical navigation, and when a scale of latitudes was for the first time added to these charts, it quickly be- came obvious that their geometry had to be modified in accordance with the new navigational methods. The resulting hybrid model represented a major breakthrough in the nautical cartography of the Renaissance, marking the beginning of the evolu- tion form the "maps based on routes", to the Ptolemy's system of geographical co- ordinates. Using cartometric analysis, and taking into account the navigational methods used in the 16 th century, it will be shown that these charts were projection- less, in the sense that they were constructed plotting directly on the plane the ob- served latitudes, courses and distances, as if the Earth were flat.
Evidence for a Resting State Network Abnormality in Adults Who Stutter

Neural network-based investigations of stuttering have begun to provide a possible integrative account for the large number of brain-based anomalies associated with stuttering. Here we used resting-state EEG to investigate functional brain networks in adults who stutter (AWS). Participants were 19 AWS and 52 age-, and gender-matched normally fluent speakers. EEGs were recorded and connectivity matrices were generated by LORETA in the theta (4–8 Hz), alpha (8–12 Hz), beta1 (12–20 Hz), and beta2 (20–30 Hz) bands. Small-world propensity (SWP), shortest path, and clustering coefficients were computed for weighted graphs. Minimum spanning tree analysis was also performed and measures were compared by non-parametric permutation test. The results show that small-world topology was evident in the functional networks of all participants. Three graph indices (diameter, clustering coefficient, and shortest path) exhibited significant differences between groups in the theta band and one [maximum betweenness centrality (BC)] measure was significantly different between groups in the beta2 band. AWS show higher BC than control in right temporal and inferior frontal areas and lower BC in the right primary motor cortex. Abnormal functional networks during rest state suggest an anomaly of DMN activity in AWS. Furthermore, functional segregation/integration deficits in the theta network are evident in AWS. These deficits reinforce the hypothesis that there is a neural basis for abnormal executive function in AWS. Increased beta2 BC in the right speech–motor related areas confirms previous evidence that right audio–speech areas are over-activated in AWS. Decreased beta2 BC in the right primary motor cortex is discussed in relation to abnormal neural mechanisms associated with time perception in AWS.
Lemur species-specific metapopulation responses to habitat loss and fragmentation

Determining what factors affect species occurrence is vital to the study of primate biogeography. We investigated the metapopulation dynamics of a lemur community consisting of eight species (Avahi occidentalis, Propithecus coquereli, Microcebus murinus, Microcebus ravelobensis, Lepilemur edwardsi, Cheirogaleus medius, Eulemur mongoz, and Eulemur fulvus) within fragmented tropical dry deciduous forest habitat in Ankarafantsika National Park, Madagascar. We measured fragment size and isolation of 42 fragments of forest ranging in size from 0.23 to 117.7 ha adjacent to continuous forest. Between June and November 2011, we conducted 1218 surveys and observed six of eight lemur species (M. murinus, M. ravelobensis, C. medius, E. fulvus, P. coquereli, and L. edwardsi) in the 42 fragments. We applied among patch incidence function models (IFMs) with various measures of dispersal and a mainland-island IFM to lemur species occurrence, with the aim of answering the following questions: 1) Do lemur species in dry deciduous forest fragments form metapopulations? 2) What are the separate effects of area (extinction risk) and connectivity/isolation (colonization potential) within a lemur metapopulation? 3) Within simulated metapopulations over time, how do area and connectivity/isolation affect occurrence? and 4) What are the conservation implications of our findings? We found that M. murinus formed either a mainland-island or an among patch metapopulation, M. ravelobensis formed a mainland-island metapopulation, C. medius and E. fulvus formed among patch metapopulations, and neither P. coquereli or L. edwardsi formed a metapopulation. Metapopulation dynamics and simulations suggest that area was a more consistent positive factor determining lemur species occurrence than fragment isolation and is crucial to the maintenance of lemur populations within this fragmented landscape. Using a metapopulation approach to lemur biogeography is critical for understanding how lemur species respond to forest loss and fragmentation.
WEIGHT OPTIMIZED DYNAMIC HYBRID FUZZY JORDAN ARTIFICIAL NEURAL NETWORK FOR INTRUSION DETECTION

A Dynamic Hybrid Fuzzy Jordan Artificial Neural Network finds the intrusion very efficiently in timely behaviour varied networks. The development of DHFJAN is to influence the behavior of dynamic systems to achieve the pre-determinate objectives. In DHFJAN, the number of hidden layer in neural and Jordan networks and number of nodes in each hidden layers are determined at runtime based on error obtained in the training stage. Generally neural network and Jordan network approaches are inherent nonlinear optimization problem, the quality of Hybrid network local solution is determined the weight initialization. Stability and weight convergence are important issues in the performance analysis of dynamic networks. The weight initialization and optimization of hybrid networks is not discussed in DHFJAN. This paper finds the optimal weight values of each layer by utilizing the optimization techniques to improve the performance and final representation of hybrid network. Many researches were focused on the weight optimization of neural network using various optimization algorithm the PSO is best among them. Since two networks available in hybrid network, applying PSO leads time consumption because the search space size of PSO. This paper proposes a modified PSO algorithm named as CCPSO with constrained search space and controlled convergence degree. The constrained search space is achieved by generating initial weight values based on power-law distribution and Zipf's law. Convergence degree of population in the PSO is controlled by analyzing mean and variance values of fitness in each iteration. The optimal weights are updated in hybrid dynamic network while neuron state changing. Thus the proposed approach improves the performance of dynamic hybrid fuzzy Jordan neural network and also reduces the error rate significantly. Experimental result shows that the proposed WDHFJANN is better than the DIHFJANN.