Miracle-dz/UniFAR-FTUs huggingface dataset:
Glutamate Receptor Antagonists and Benzodiazepine Inhibit the Progression of Granule Cell Dispersion in a Mouse Model of Mesial Temporal Lobe Epilepsy

Summary: Purpose: Unilateral intrahippocampal injection of kainic acid (KA) in adult mice induces the progressive dispersion of dentate granule cells, one of the characteristic pathologic changes of mesial temporal lobe epilepsy. However, little is known about the mechanisms that trigger this dispersion. In this study, the possible involvement of glutamatergic and γ‐aminobutyric acid (GABA)ergic neurotransmissions in the development of granule cell dispersion (GCD) was examined in this model.
Pathogenesis of hemangioma.

Hemangioma is the most common tumor of any kind seen in infancy. It is also, perhaps, the least understood. This stems in part from a long history of confusing nomenclature for vascular anomalies that employed classification schemes based on superficial descriptions of the lesions. The first major step toward clarifying this nomenclatural morass was made by Mulliken and colleagues (1, 2), who employed a biological classification scheme based on the differing clinical courses and endothelial proliferative activity of hemangiomas versus malformations. Hemangiomas, often called infantile or juvenile hemangiomas for clarity, are benign tumors that exhibit an early and rapid proliferation phase during the first year of life characterized by endothelial and pericytic hyperplasia, followed by a slower but steady involution phase that may last for years. This basic scheme of histopathological classification has been refined by immunohistochemical characterization of hemangioma in each of the phases (3). Nonetheless, the pathogenesis of hemangioma is still not understood. Although growth factors and hormonal and mechanical influences have been postulated to affect the abnormal proliferation of endothelial cells in hemangioma, the primary, causative defect in hemangiogenesis remains unknown and no genetic alteration has been implicated.
Cytoplasmic membrane vesicles of Escherichia coli. A simple method for preparing the cytoplasmic and outer membranes.

A simple preparative method is described for isolation of the cytoplasmic and outer membranes from E. coli. The characteristics of both membrane fractions were studied chemically, biologically, and morphologically. Spheroplasts of E. coli K-12 strain W3092, prepared by treating cells with EDTA-lysozyme [EC 3.2. 1.17], were disrupted in a French press. The crude membrane fraction was washed with 3 mM EDTA-10% (w/v) sucrose, pH 7.2, and the cytoplasmic membranes and outer membranes were separated by sucrose isopycnic density gradient centrifugation. The crude membrane fraction contained approximately 10% of the protein of the whole cells, 0.3% of the DNA, 0.7% of the RNA, 0.3% of the peptidoglycan, and about 30% of the lipopolysaccharide. The cytoplasmic membrane fraction was rich in phospholipid, while the outer membrane fraction contained much lipopolysaccharide and carbohydrate; the relative contents of lipopolysaccharide and carbohydrate per mg protein in the cytoplasmic membrane fraction were 12 and 40%, respectively, of the contents in the outer membrane fraction. Cytochrome b1, NADH oxidase, D-lactate dehydrogenase [EC 1.1. 1.28], succinate dehydrogenase [EC 1.3. 99.1], ATPase [EC 3.5. 1.3], and activity for concentrative uptake of proline were found to be localized mainly in the cytoplasmic membranes; their specific activities in the outer membrane fraction were 1.5 to 3% of those in the cytoplasmic membrane fraction. In contrast, a phospholipase A appeared to be localized mainly in the outer membranes and its specific activity in the cytoplasmic membrane fraction was only 5% of that in the outer membrane fraction. The cytoplasmic and outer membrane fractions both appeared homogeneous in size and shape and show vesicular structures by electron microscopy. The advantages of this method for large scale preparation of the cytoplasmic and outer membrane fractions are discussed.
The effect of fire interval on post-fire understorey communities in Yellowstone National Park

Abstract Questions: How does the time interval between subsequent stand-replacing fire events affect post-fire understorey cover and composition following the recent event? How important is fire interval relative to broad- or local-scale environmental variability in structuring post-fire understorey communities? Location: Subalpine plateaus of Yellowstone National Park (USA) that burned in 1988. Methods: In 2000, we sampled understorey cover and Pinus contorta density in pairs of 12-yr old stands at 25 locations. In each pair, the previous fire interval was either short (7–100 yr) or long (100–395 yr). We analysed variation in understorey species richness, total cover, and cover of functional groups both between site pairs (using paired t-tests) and across sites that experienced the short fire intervals (using regression and ordination). We regressed three principal components to assess the relative importance of disturbance and broad or local environmental variability on post-fire understorey cover and richness. Results: Between paired plots, annuals were less abundant and fire-intolerant species (mostly slow-growing shrubs) were more abundant following long intervals between prior fires. However, mean total cover and richness did not vary between paired interval classes. Across a gradient of fire intervals ranging from 7–100 yr, total cover, species richness, and the cover of annuals and nitrogen-fixing species all declined while the abundance of shrubs and fire-intolerant species increased. The few exotics showed no response to fire interval. Across all sites, broad-scale variability related to elevation influenced total cover and richness more than fire interval. Conclusions: Significant variation in fire intervals had only minor effects on post-fire understorey communities following the 1988 fires in Yellowstone National Park. Nomenclature: Dorn (1992). Abbreviations: YNP = Yellowstone National Park.
Barley ABI5 (Abscisic Acid INSENSITIVE 5) Is Involved in Abscisic Acid-Dependent Drought Response

ABA INSENSITIVE 5 (ABI5) is a basic leucine zipper (bZIP) transcription factor which acts in the abscisic acid (ABA) network and is activated in response to abiotic stresses. However, the precise role of barley (Hordeum vulgare) ABI5 in ABA signaling and its function under stress remains elusive. Here, we show that HvABI5 is involved in ABA-dependent regulation of barley response to drought stress. We identified barley TILLING mutants carrying different alleles in the HvABI5 gene and we studied in detail the physiological and molecular response to drought and ABA for one of them. The hvabi5.d mutant, carrying G1751A transition, was insensitive to ABA during seed germination, yet it showed the ability to store more water than its parent cv. “Sebastian” (WT) in response to drought stress. The drought-tolerant phenotype of hvabi5.d was associated with better membrane protection, higher flavonoid content, and faster stomatal closure in the mutant under stress compared to the WT. The microarray transcriptome analysis revealed up-regulation of genes associated with cell protection mechanisms in the mutant. Furthermore, HvABI5 target genes: HVA1 and HVA22 showed higher activity after drought, which may imply better adaptation of hvabi5.d to stress. On the other hand, chlorophyll content in hvabi5.d was lower than in WT, which was associated with decreased photosynthesis efficiency observed in the mutant after drought treatment. To verify that HvABI5 acts in the ABA-dependent manner we analyzed expression of selected genes related to ABA pathway in hvabi5.d and its WT parent after drought and ABA treatments. The expression of key genes involved in ABA metabolism and signaling differed in the mutant and the WT under stress. Drought-induced increase of expression of HvNCED1, HvBG8, HvSnRK2.1, and HvPP2C4 genes was 2–20 times higher in hvabi5.d compared to “Sebastian”. We also observed a faster stomatal closure in hvabi5.d and much higher induction of HvNCED1 and HvSnRK2.1 genes after ABA treatment. Together, these findings demonstrate that HvABI5 plays a role in regulation of drought response in barley and suggest that HvABI5 might be engaged in the fine tuning of ABA signaling by a feedback regulation between biosynthetic and signaling events. In addition, they point to different mechanisms of HvABI5 action in regulating drought response and seed germination in barley.
Assessment of silent embolism from carotid endarterectomy by use of diffusion-weighted imaging: work in progress.

BACKGROUND AND PURPOSE Transcranial Doppler studies have suggested that microemboli are released into the arterial circulation during the majority of carotid endarterectomy (CEA) procedures. This, together with the observation that neuropsychological performance may decline postoperatively, has led to concern that cerebral infarction may occur unrecognized during CEA. Our objective was to examine this risk with diffusion-weighted imaging, a technique that is highly sensitive to acute cerebral infarction. METHODS Eighteen participants (median age, 68 years; age range, 56-87 years) were assessed with diffusion-weighted imaging and the National Institutes of Health Stroke Scale before and after CEA. Imaging was performed using single-shot echo-planar imaging with a maximum diffusion sensitivity of b = 1000 s/mm(2) applied to three orthogonal planes. Preoperative imaging was performed a median of 2.5 hours before surgery (range, 0.5-12.5 hours) and 15 hours after surgery (range, 1.5-58.5 hours). Two neuroradiologists independently interpreted the diffusion-weighted images, blinded to operative status and clinical findings. RESULTS There was no diffusion-weighted imaging evidence of silent embolism in this series of 18 participants (95% confidence interval limits, 0 to 10%). Clinical complications were confined to one case of confusion occurring after CEA; the diffusion-weighted imaging results were normal in this case. CONCLUSION There is no evidence from our series that silent cerebral infarction is a common occurrence during CEA. These data provide further support for the safety of CEA.
A New Lower Bound for the Football Pool Problem for Six Matches

In the football pool problem one wants to minimize the cardinality of a ternary code, C? F3n, with covering radius one, and the size of a minimum code is denoted by ? n. The smallest unsettled case is 63? 6? 73. The lower bound is here improved to 65 in a coordinate-by-coordinate backtrack search using the LLL algorithm and complete equivalence checking of subcodes.
Phylogeography, population genetics and conservation of the European red deer Cervus elaphus

1 During the Last Glacial Maximum, European red deer Cervus elaphus occurred in refugia in Iberia/southern France, Italy, the Balkans and the Carpathians. Most of Europe, including large parts of the east and north-east, is now inhabited by red deer from the western lineage. The eastern lineage is largely confined to south-eastern Europe; a third lineage comprises Sardo-Corsican and Barbary red deer. 2 Sardo-Corsican, Barbary and Mesola red deer are genetically unique units. They exhibit low levels of genetic diversity and deserve particular protection, since conservation strategies should target genetic information. 3 Hybridization between sika Cervus nippon and red deer occurs rarely, but may lead to extensive introgression, particularly in parts of the British Isles. Further expansion of both species may lead to increased hybridization in continental Europe. 4 Although hunting has an impact on red deer gene pools, the main threat today is habitat fragmentation in human-dominated landscapes. The resulting increase in genetic drift and inbreeding reduces variability in isolated populations and may lead to inbreeding depression. To support vital meta-populations, migration corridors should be established.
Any novelty in hippocampal formation and memory?

Purpose of reviewNovel events tend to attract attention and become more effectively encoded in memory than predictable events. The hippocampus and medial-temporal cortical regions, along with regions of the prefrontal cortex, have been associated with enhanced memory for novel events. This review provides an update on recent studies of hippocampal novelty responses in relation to memory. Recent findingsSeveral different types of novelty have been studied. Stimulus novelty effects have been observed as reduced neural activity in the medial-temporal and prefrontal regions when the same stimulus is repeatedly presented. Contextual novelty effects, the detection of a stimulus or event in an unexpected context, is impaired in patients with hippocampal damage. Single-trial analyses of brain activity show that the hippocampus rapidly habituates to contextually novel situations. Associative novelty, the detection of new arrangements of familiar stimuli, has also been related to the medial-temporal regions. A division of labour among the medial-temporal regions has been proposed such that associative novelty selectively engages the hippocampus, whereas stimulus novelty is mediated by the perirhinal cortex. However, a simple account of when the hippocampus versus other medial-temporal cortical regions is recruited awaits further studies. Increased dopaminergic and cholinergic neurotransmission may account for enhanced memory encoding of novel events, and relate to structural neuronal changes. SummaryInterindividual variability in the responsiveness of the hippocampal-novelty system may be genetically mediated, and personality factors can also play a role. A better understanding of such variability can have implications for interventions aimed at supporting memory and for the treatment of drug abuse.
Stem–loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly

The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Sharma et al. report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice, and a component of the U2 snRNP complex, which assembles across the intron at the 3′ splice site. U1-SL4 interacts with the SF3A1 protein of the U2 snRNP, and this interaction occurs within prespliceosomal complexes assembled on the pre-mRNA.
On small‐sample inference in group randomized trials with binary outcomes and cluster‐level covariates

Group randomized trials (GRTs) randomize groups, or clusters, of people to intervention or control arms. To test for the effectiveness of the intervention when subject‐level outcomes are binary, and while fitting a marginal model that adjusts for cluster‐level covariates and utilizes a logistic link, we develop a pseudo‐Wald statistic to improve inference. Alternative Wald statistics could employ bias‐corrected empirical sandwich standard error estimates, which have received limited attention in the GRT literature despite their broad utility and applicability in our settings of interest. The test could also be carried out using popular approaches based upon cluster‐level summary outcomes. A simulation study covering a variety of realistic GRT settings is used to compare the accuracy of these methods in terms of producing nominal test sizes. Tests based upon the pseudo‐Wald statistic and a cluster‐level summary approach utilizing the natural log of observed cluster‐level odds worked best. Due to weighting, some popular cluster‐level summary approaches were found to lead to invalid inference in many settings. Finally, although use of bias‐corrected empirical sandwich standard error estimates did not consistently result in nominal sizes, they did work well, thus supporting the applicability of marginal models in GRT settings.
Ethical issues of clinical trials in children: a European perspective

Children should not be harmed by their participation in clinical trials, therefore should no clinical trials be performed? This is a view that needs to be balanced as clinical trials provide the evidence we need to allow children safe and effective prescribing of medicines. Therefore, is it unethical not to involve this population in research? This review looks at new ethical guidance released to support the recently introduced European legislation for the licensing of medicines.
Constitutively Active Parathyroid Hormone Receptor Signaling in Cells in Osteoblastic Lineage Suppresses Mechanical Unloading-induced Bone Resorption*

Multiple signaling pathways participate in the regulation of bone remodeling, and pathological negative balance in the regulation results in osteoporosis. However, interactions of signaling pathways that act comprehensively in concert to maintain bone mass are not fully understood. We investigated roles of parathyroid hormone receptor (PTH/PTHrP receptor) signaling in osteoblasts in unloading-induced bone loss using transgenic mice. Hind limb unloading by tail suspension reduced bone mass in wild-type mice. In contrast, signaling by constitutively active PTH/PTHrP receptor (caPPR), whose expression was regulated by the osteoblast-specific Col1a1 promoter (Col1a1-caPPR), suppressed unloading-induced reduction in bone mass in these transgenic mice. In Col1a1-caPPR transgenic (Tg) mice, hind limb unloading suppressed bone formation parameters in vivo and mineralized nodule formation in vitro similarly to those observed in wild-type mice. In addition, serum osteocalcin levels and mRNA expression levels of type I collagen, Runx2 and Osterix in bone were suppressed by unloading in both wild-type mice and Tg mice. However, in contrast to unloading-induced enhancement of bone resorption parameters in wild-type mice, Col1a1-caPPR signaling suppressed, rather than enhanced, osteoclast number and osteoclast surface as well as urinary deoxypyridinoline excretion upon unloading. Col1a1-caPPR signaling also suppressed mRNA expression levels of RANK and c-fms in bone upon unloading. Although the M-CSF and monocyte chemoattractant protein 1 (MCP-1) mRNA levels were enhanced in control Tg mice, these levels were suppressed in unloaded Tg mice. These results indicated that constitutive activation of PTH/PTHrP receptor signaling in osteoblastic cells suppresses unloading-induced bone loss specifically through the regulation of osteoclastic activity.
Measuring the Performance of Islamic Banks by Adapting Conventional Ratios

One consequence of the current financial crisis is that many countries began to reevaluate their financial systems and recognize its flaws and drawbacks. They also began the search for alternative systems for their economies; one of the proposed systems is the current Islamic financial model. This model is still in its infancy and many modifications and additions are required. It also lacks the necessary financial performance measurement tools similar to those used by conventional banks for managers and investors alike. This paper evaluates this lack of performance measures. It then adapts a currently applied ROE Analysis Tool used in conventional banks, to the currently established model of Islamic Banks and tests its applicability and evaluates its usefulness. The findings suggest that such an adapted model would be quite successful for use in Islamic banks and would offer much better analysis and basis of comparison within the Islamic financial system. It also suggests that much of the previously measured performance of Islamic Banks is unsound and should be revised for accuracy and reliability because of the flawed methods used for measurement in the first place.
Shared and Specific Independent Components Analysis for Between-Group Comparison

Independent component analysis (ICA) has been extensively used in individual and within-group data sets in real-world applications, but how can it be employed in a between-groups or conditions design? Here, we propose a new method to embed group membership information into the FastICA algorithm so as to extract components that are either shared between groups or specific to one or a subset of groups. The proposed algorithm is designed to automatically extract the pattern of differences between different experimental groups or conditions. A new constraint is added to the FastICA algorithm to simultaneously deal with the data of multiple groups in a single ICA run. This cost function restricts the specific components of one group to be orthogonal to the subspace spanned by the data of the other groups. As a result of performing a single ICA on the aggregate data of several experimental groups, the entire variability of data sets is used to extract the shared components. The results of simulations show that the proposed algorithm performs better than the regular method in both the reconstruction of the source signals and classification of shared and specific components. Also, the sensitivity to detect variations in the amplitude of shared components across groups is enhanced. A rigorous proof of convergence is provided for the proposed iterative algorithm. Thus, this algorithm is guaranteed to extract and classify shared and specific independent components across different experimental groups and conditions in a systematic way.
The influence of exposure history on arsenic accumulation and toxicity in the killifish, Fundulus heteroclitus

Exposure to arsenic is known to cause adverse effects in aquatic biota and wildlife and is of major concern to human health. Although numerous studies have investigated the toxicity of arsenic, little is known about the effects of acquired tolerance on arsenic accumulation and toxicity outside of cell culture models. Accordingly, studies were conducted on the estuarine fish, Fundulus heteroclitus, that were preexposed to nontoxic concentrations of arsenic (as sodium arsenite; 0.7 and 106 μmol As/L) for 96 h or naïve to elevated arsenic to determine the effects of acclimation on arsenic toxicity and accumulation. Tolerance to arsenic was rapidly (96 h) acquired in killifish that were preexposed. In toxicity tests with arsenic‐acclimated killifish, preexposure to 106 μmol As/L resulted in a reduction in toxicity when compared to näive animals. Toxicity in arsenic‐acclimated fish also was distinguished by a delayed onset of mortality that manifested in dose‐dependent fashion and was significant even for the lower acclimation concentration (0.7 μmol As/L). The increase tolerance acquired following preexposure to 106 μmol As/L for 96 h was associated with lower concentrations of arsenic in all monitored tissues (e.g., gill, liver, kidney) and the whole body when fish were exposed to 240 μmol As/L for an additional 96 h. In accordance with these observations, expression of the multidrug resistance‐associated protein (MRP)‐2 gene, which is responsible for transporting arsenic conjugated to glutathione out of cells, was increased in the liver of arsenic‐acclimated fish.
Antimicrobial activity associated with extracellular matrices.

Materials derived from extracellular matrices (ECMs) are being evaluated as scaffolds for surgical reconstruction of damaged or missing tissues. It is important to understand the susceptibility of these biological materials to bacterial infections. ECMs derived from porcine small intestinal submucosa (SIS) and urinary bladder submucosa (UBS) were found to possess antimicrobial activity. ECM extracts, obtained by digesting these acellular matrices in acetic acid, demonstrated antibacterial activity against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus. Antimicrobial activity was determined using a minimal inhibitory concentration assay. Bacteriostatic activity was detected at protein concentrations of ECM extracts equivalent to 0.77-1.60 mg/mL. ECM extracts were found to inhibit bacterial growth for up to at least 13 h. The resulting extracts consisted of water-soluble peptides and proteins with molecular weights ranging from <4 to >100 kDa and lower molecular weight compounds, as determined by size exclusion liquid chromatography.