Miracle-dz/UniFAR-FTUs huggingface dataset:
Zac1 Regulates the Differentiation and Migration of Neocortical Neurons via Pac1

Imprinted genes are dosage sensitive, and their dysregulated expression is linked to disorders of growth and proliferation, including fetal and postnatal growth restriction. Common sequelae of growth disorders include neurodevelopmental defects, some of which are indirectly related to placental insufficiency. However, several growth-associated imprinted genes are also expressed in the embryonic CNS, in which their aberrant expression may more directly affect neurodevelopment. To test whether growth-associated genes influence neural lineage progression, we focused on the maternally imprinted gene Zac1. In humans, either loss or gain of ZAC1 expression is associated with reduced growth rates and intellectual disability. To test whether increased Zac1 expression directly perturbs neurodevelopment, we misexpressed Zac1 in murine neocortical progenitors. The effects were striking: Zac1 delayed the transition of apical radial glial cells to basal intermediate neuronal progenitors and postponed their subsequent differentiation into neurons. Zac1 misexpression also blocked neuronal migration, with Zac1-overexpressing neurons pausing more frequently and forming fewer neurite branches during the period when locomoting neurons undergo dynamic morphological transitions. Similar, albeit less striking, neuronal migration and morphological defects were observed on Zac1 knockdown, indicating that Zac1 levels must be regulated precisely. Finally, Zac1 controlled neuronal migration by regulating Pac1 transcription, a receptor for the neuropeptide pituitary adenylate cyclase-activating polypeptide (PACAP). Pac1 and Zac1 loss- and gain-of-function presented as phenocopies, and overexpression of Pac1 rescued the Zac1 knockdown neuronal migration phenotype. Thus, dysregulated Zac1 expression has striking consequences on neocortical development, suggesting that misexpression of this transcription factor in the brain in certain growth disorders may contribute to neurocognitive deficits. SIGNIFICANCE STATEMENT Altered expression of imprinted genes is linked to cognitive dysfunction and neuropsychological disorders, such as Angelman and Prader–Willi syndromes, and autism spectrum disorder. Mouse models have also revealed the importance of imprinting for brain development, with chimeras generated with parthenogenetic (two maternal chromosomes) or androgenetic (two paternal chromosomes) cells displaying altered brain sizes and cellular defects. Despite these striking phenotypes, only a handful of imprinted genes are known or suspected to regulate brain development (e.g., Dlk1, Peg3, Ube3a, necdin, and Grb10). Herein we show that the maternally imprinted gene Zac1 is a critical regulator of neocortical development. Our studies are relevant because loss of 6q24 maternal imprinting in humans results in elevated ZAC1 expression, which has been associated with neurocognitive defects.
Denoising MEG sensor data using wavelets

Magnetoencephalography (MEG) is a noninvasive technology for analyzing cerebral neuronal activity. The noise level in the MEG data is large enough to affect the desired signal. This paper describes a denoising technique based on Wavelet Transform (WT). It compares denoising MEG data with different wavelet techniques like Discrete Wavelet Transform (DWT), Wavelet Packet Transform (WPT) and Stationary Wavelet Transform (SWT). Here WT is implemented using Multiresolution Analysis (MRA). Spectrogram of original MEG data and its denoised version are also compared.
Dynamic Simulation and Hemolysis Evaluation of the Regurgitant Flow over a Tilting-Disc Mechanical Heart Valve in Pulsatile Flow

Regurgitation in the heart diastolic phase represents a critical flow condition associated with many heart valve design considerations. The finite volume method, the Low-Reynolds-Number k-ω turbulent model and sliding mesh model are employed to solve and compare the complex flow field and the torque in each case. The end results expected from a cardiovascular CFD analysis are not limited only to the flowfield investigations. More importantly, it needs an evaluation criterion to judge if the design is acceptable as considered from a broader blood cell damage or activation perspective. In this study, blood cell damage index developed based on stress-time empirical rule and Lagrangian particle tracking is introduced to assess the viscous and turbulence-induced stresses effect to the blood cells.
SAR Image Reconstruction From Undersampled Raw Data Using Maximum A Posteriori Estimation

A method for synthetic aperture radar (SAR) imaging using maximum a posteriori (MAP) estimation based on multiplicative speckle model is presented. The new method uses the total variation (TV) minimization to regularize the solution. The reconstruction of SAR image is formulated as a biconvex optimization problem, which is solved by the alternate convex search (ACS) method. Experiments on Radarsat-1 raw data show that the proposed method can recover most of the structural and texture details of the imaged scene using only a half of raw data. Compared with regular regularization methods for SAR imaging with incomplete data, the proposed method performs much better on less sparse scenes.
Functional involvement of Rab1A in microtubule-dependent anterograde melanosome transport in melanocytes

Summary Melanosomes are transported to the cell periphery of melanocytes by coordination between bidirectional microtubule-dependent movements and unidirectional actin-dependent movement. Although both the mechanism of the actin-dependent melanosome transport and the mechanism of the microtubule-dependent retrograde melanosome transport in mammalian skin melanocytes have already been determined, almost nothing is known about the mechanism of the microtubule-dependent anterograde melanosome transport. Small GTPase Rab proteins are common regulators of membrane traffic in all eukaryotes, and in this study we performed genome-wide screening for Rab proteins that are involved in anterograde melanosome transport by expressing 60 different constitutive active (and negative) mutants, and succeeded in identifying Rab1A, originally described as a Golgi-resident Rab, as a prime candidate. Endogenous Rab1A protein was found to be localized to mature melanosomes in melanocytes, and its functional ablation either by siRNA-mediated knockdown or by overexpression of a cytosolic form of Rab1A-GTPase-activating protein/TBC1D20 induced perinuclear melanosome aggregation. The results of time-lapse imaging further revealed that long-range anterograde melanosome movements were specifically suppressed in Rab1A-deficient melanocytes, whereas retrograde melanosome transport occurred normally. Taken together, these findings indicate that Rab1A is the first crucial component of the anterograde melanosome transport machinery to be identified in mammalian skin melanocytes.
Improved Medium for Detection of Citrate-Fermenting Streptococcus lactis subsp. diacetylactis

A modified medium which distinguished between citrate-fermenting and non-citrate-fermenting species of lactic streptococci within 48 h was developed. In addition, the occurrence of citrate-negative variants in citrate-positive populations of Streptococcus lactis subsp. diacetylactis could be detected.
Auxin-Gibberellin Interaction in Rice Coleoptile Elongation.

\Vhile, oIn present evidence, it is generally agreed that both auxin and gibberellin contribute to the control of plant cell enlargement, the nature of their contributions is not known (1). Four hypotheses on their contributions, the first tlhree of which postulate that gibberellin's contribution is auxin-dependent while the fourth postulates independent contributions by auxin and gibberellin to cell enlargement, are as follows: 0 I. Galston (5, 6) suggested that gibberellin increased the concentration of a phenolic inhibitor (4) of the indoleacetic acid (IAA) oxidase system, thereby producing greater auxin concentrations in tissues.
Denoising by Singular Value Decomposition and Its Application to Electronic Nose Data Processing

This paper analyzes the role of singular value decomposition (SVD) in denoising sensor array data of electronic nose systems. It is argued that the SVD decomposition of raw data matrix distributes additive noise over orthogonal singular directions representing both the sensor and the odor variables. The noise removal is done by truncating the SVD matrices up to a few largest singular value components, and then reconstructing a denoised data matrix by using the remaining singular vectors. In electronic nose systems this method seems to be very effective in reducing noise components arising from both the odor sampling and delivery system and the sensors electronics. The feature extraction by principal component analysis based on the SVD denoised data matrix is seen to reduce separation between samples of the same class and increase separation between samples of different classes. This is beneficial for improving classification efficiency of electronic noses by reducing overlap between classes in feature space. The efficacy of SVD denoising method in electronic nose data analysis is demonstrated by analyzing five data sets available in public domain which are based on surface acoustic wave (SAW) sensors, conducting composite polymer sensors and the tin-oxide sensors arrays.
The Cytochrome c Maturation Components CcmF, CcmH, and CcmI Form a Membrane-integral Multisubunit Heme Ligation Complex*

Cytochrome c maturation (Ccm) is a post-translational and post-export protein modification process that involves ten (CcmABCDEFGHI and CcdA or DsbD) components in most Gram-negative bacteria. The absence of any of these components abolishes the ability of cells to form cytochrome c, leading in the case of Rhodobacter capsulatus to the loss of photosynthetic proficiency and respiratory cytochrome oxidase activity. Based on earlier molecular genetic studies, we inferred that R. capsulatus CcmF, CcmH, and CcmI interact with each other to perform heme-apocytochrome c ligation. Here, using functional epitope-tagged derivatives of these components coproduced in appropriate mutant strains, we determined protein-protein interactions between them in detergent-dispersed membranes. Reciprocal affinity purification as well as tandem size exclusion and affinity chromatography analyses provided the first biochemical evidence that CcmF, CcmH, and CcmI associate stably with each other, indicating that these Ccm components form a membrane-integral complex. Under the conditions used, the CcmFHI complex does not contain CcmG, suggesting that the latter thio-reduction component is not always associated with the heme ligation components. The findings are discussed with respect to defining the obligatory components of a minimalistic heme-apocytochrome c ligation complex in R. capsulatus.
Prediction of Inventory Levels and Capacity Utilization with Artificial Neural Networks

Coping with increasingly complex production processes requires a continuous advancement of production control techniques. In this context, artificial neural networks have proven their potential in optimization, prediction, classification, control and other production related areas. This paper presents an approach for the workstation-specific prediction of inventory levels and capacity utilization within a shop floor environment. This includes the selection of the appropriate network architecture, the determination of suitable input variables as well as the training and validation of the applied neural networks. Further, an evaluation of the proposed networks takes place by means of a generic shop floor model. Key-Words: Artificial intelligence, artificial neural networks, Elman networks, prediction, shop floor production, predictive control, inventory, capacity utilization
Techniques for noninvasive genetic monitoring of Alpine Ibex Capra ibex

Noninvasive sampling is of increasing importance for the molecular genetic monitoring of wild animal populations, although reduced quality and quantity of such samples’ DNA can affect genetic data and their subsequent interpretation. Consequently, we performed a pilot study to establish a feasible approach for the genetic investigation of free-ranging Alpine ibex Capra ibex Linnaeus, 1758 populations. Establishing an ibex-specific PCR-RFLP based on Cytochrome b gene differences allowed the discrimination of noninvasive ibex samples from those of other sympatric ungulates. In addition, we established a quantitative PCR for ibex samples. The quantification of 35 faecal samples clearly exhibited a strong variability of DNA contents among samples and individuals. Furthermore, we performed threefold genotyping experiments on six microsatellite loci to determine the extent of genotyping errors in reference to blood samples of the respective individuals. The analyses exhibited a strong dependence of erroneous microsatellite genotypes on the starting amount of template DNA. Variability in reliability was observed between individual loci, resulting in a mandatory high DNA concentration necessary for consistent genotyping. This study serves as basis for further ibex research and we propose the application of DNA quantification of faecal samples to focus genotyping efforts solely on suitable samples.
Assessment of angiogenic properties of biomaterials using the chicken embryo chorioallantoic membrane assay

The angiogenic potential of a biomaterial is a critical factor for successful graft intake in tissue engineering. We developed a modified, rapid and reproducible chicken embryo chorioallantoic membrane (CAM) assay to evaluate the ability of biomaterials in inducing blood vessel density. Five biomaterials including one-layer porcine small intestinal submucosa (SIS), two-layer SIS, four-layer vacuum pressed (VP) SIS, polyglycolic acid (PGA) and PGA modified with poly(lactic-co-glycolic acid) (PLGA) were analyzed. A circular section (1.2 mm diameter) of each biomaterial was placed near a group of blood vessels in the CAM. Blood vessels around the biomaterials were captured with black and white images at 96 h post implantation; and the images were subjected to densitometry evaluation. One-layer SIS induced a significant increase in blood vessel density as compared to the cellulose nitrate negative control, and had the greatest increase in blood vessel density as compared to four-layer VP SIS, PGA, or PLGA modified PGA. Although two-layer SIS has enhanced physical structure for surgical manipulation, its induction in blood vessel density was significantly lower than the one-layer SIS. Stripping the SIS proteins or incubating one-layer SIS with neutralizing antibodies against basic fibroblast growth factor (bFGF) or vascular endothelial growth factor (VEGF) resulted in decreased angiogenesis. Consistent with results obtained from bladder augmentation animal models, these results confirmed that angiogenic growth factors were present in SIS and affected the angiogenic potential of biomaterials. These data also demonstrated that the CAM assay can be used to ascertain methodically the angiogenic potential of biomaterials.
Temporal changes in N‐acylethanolamine content and metabolism throughout the peri‐adolescent period

Fatty acid amide hydrolase (FAAH) regulates tissue concentrations of N‐acylethanolamines (NAEs), including the endocannabinoid, N‐arachidonylethanolamide (anandamide, AEA). FAAH activity and NAEs are widely distributed throughout the brain and FAAH activity regulates an array of processes including emotion, cognition, inflammation, and feeding. However, there is relatively little research describing how this system develops throughout adolescence, particularly within limbic circuits regulating stress and reward processing. Thus, this study characterized temporal changes in NAE content (AEA, oleoylethanolamine [OEA], and palmitoylethanolamide [PEA]) and FAAH activity across the peri‐adolescent period, in four corticolimbic structures (amygdala, hippocampus, prefrontal cortex, and hypothalamus). Brain tissue of male Sprague–Dawley rats was collected on postnatal days (PND) 25, 35, 45, and 70, representing pre‐adolescence, early‐ to mid‐adolescence, late adolescence, and adulthood, respectively. Tissue was analyzed for AEA, OEA, and PEA content as well as FAAH activity at each time point. AEA, OEA, and PEA exhibited a similar temporal pattern in all four brain regions. NAE concentrations were lowest at PND 25 and highest at PND 35. NAE concentrations decreased between PNDs 35 and 45 and increased between PNDs 45 and 70. FAAH activity mirrored the pattern of NAE content in which it decreased between PNDs 25 and 35, increased between PNDs 35 and 45, and decreased between PNDs 45 and 70. These age‐dependent patterns of NAE content and FAAH activity demonstrate temporal specificity to the development of this system and could contribute to alterations in stress sensitivity, emotionality, and executive function which also fluctuate during this developmental period. Synapse, 2013. © 2012 Wiley Periodicals, Inc.
Sulphonamide resistance gene sul3 found in Escherichia coli isolates from human sources.

OBJECTIVES The aim of this study was to investigate the molecular basis of an observed increasing resistance to trimethoprim and sulphonamides despite a simultaneous decline in co-trimoxazole consumption. The distribution of sulphonamide resistance genes sul1, sul2 and the recently discovered sul3 was studied in a collection of clinical isolates of Enterobacteriaceae. METHODS PCR with primers specific for sul1, sul2 and sul3 was used to detect the three known sulphonamide resistance genes in the isolate collection. Sequence analysis was used for confirmation of results. Restriction endonuclease digestion and conjugational transfer assays were used for plasmid analysis. RESULTS In 64 sulphonamide-resistant isolates, 39 sul1 genes and 48 sul2 genes were detected. Twenty-five isolates carried both sul1 and sul2 and two were negative for both genes. With PCR and sequence analysis these two were shown to harbour the new sulphonamide resistance gene sul3, which was carried by different plasmids. CONCLUSIONS Sulphonamide resistance gene sul3, which is widespread among pigs in Switzerland, has now also been identified in two different clinical isolates of Escherichia coli, located in urinary tract infections in patients in Sweden.
Local expression of interleukin-27 ameliorates collagen-induced arthritis.

OBJECTIVE To determine the mechanism of action of interleukin-27 (IL-27) against rheumatoid arthritis (RA). METHODS Adenovirus containing IL-27 transcript was constructed and was locally delivered into the ankles of mice with collagen-induced arthritis (CIA). Progression of arthritis was determined in treated and untreated mice by measuring ankle circumference and through histologic analysis. IL-17 and its downstream targets as well as cytokines promoting Th17 cell differentiation were quantified by enzyme-linked immunosorbent assay in CIA mouse ankles locally expressing adenoviral IL-27 as well as in control-treated mouse ankles. Ankles from both treatment groups were immunostained for neutrophil and monocyte migration (macrophages in the tissue). Finally, vascularization was quantified by histology and by determining ankle hemoglobin levels. RESULTS Ectopic expression of IL-27 in CIA mice ameliorated inflammation, lining hypertrophy, and bone erosion as compared with control-treated CIA mice. Serum and joint levels of IL-17 were significantly reduced in the IL-27-treated group compared with the control-treated group. Two of the main cytokines that induce Th17 cell differentiation and IL-17 downstream target molecules were greatly down-regulated in CIA mouse ankles receiving forced expression of IL-27. The control mice had higher levels of vascularization and monocyte trafficking than did mice ectopically expressing IL-27. CONCLUSION Our results suggest that increased levels of IL-27 relieve arthritis in CIA mouse ankles. This amelioration of arthritis involves a reduction in CIA mouse serum and joint levels of IL-17 and results in decreased IL-17-mediated monocyte recruitment and angiogenesis. Hence, the use of IL-27 may be a strategy for treatment of patients with RA.
Size and Surface Charge Effect of 5-Aminolevulinic Acid-Containing Liposomes on Photodynamic Therapy for Cultivated Cancer Cells

5-Aminolevulinic acid (ALA)-containing liposomes having various average diameters and/or positive surface charges were prepared, and their photodynamic therapy (PDT) efficacy for murine thymic lymphoma cells, EL-4 cells, cultivated in vitro was investigated. The PDT efficacy for EL-4 cells and the accumulation of ALA-induced protoporphyrin IX (PpIX) in the cells increased with a decrease in the average diameter of liposomes. In particular, the ALA-containing liposomes smaller than 63.5 nm in diameter promoted the PDT efficacy in comparison with that of ALA alone. We also found no significant changes in PDT efficacy and PpIX accumulation with increasing positive surface charges of liposomes.
Ecstasy (MDMA) exposure and neuropsychological functioning: A polydrug perspective

Ecstasy (MDMA) is a popular drug that can act as a selective serotonin neurotoxin in several species. The goal of the present study was to examine the relationship between ecstasy exposure and cognitive functioning after controlling for other drug use and demographic variables. Furthermore, we assessed whether gender was a moderator of the relationship between cognitive functioning and ecstasy use. Data were collected from 31 men and 34 women with a wide range of ecstasy use (17 marijuana users with no ecstasy use and 48 ecstasy users ranging from low to heavy use). Participants were interviewed and administered a battery of neuropsychological tests. The primary finding was that ecstasy exposure was significantly related to poorer verbal learning and memory ability in a dose-dependent manner, while no such relationship was observed between ecstasy exposure and executive functioning or attentional ability. Gender was found to significantly moderate the relationship between ecstasy consumption and design fluency. These results suggest primary memory dysfunction among abstinent recreational ecstasy users. This finding is consistent with reports of hippocampal vulnerability, particularly among heavy users. (JINS, 2005, 11, 753–765.)
Unsupervised acquisition of entailment relations from the Web

Abstract Entailment recognition is a primary generic task in natural language inference, whose focus is to detect whether the meaning of one expression can be inferred from the meaning of the other. Accordingly, many NLP applications would benefit from high coverage knowledgebases of paraphrases and entailment rules. To this end, learning such knowledgebases from the Web is especially appealing due to its huge size as well as its highly heterogeneous content, allowing for a more scalable rule extraction of various domains. However, the scalability of state-of-the-art entailment rule acquisition approaches from the Web is still limited. We present a fully unsupervised learning algorithm for Web-based extraction of entailment relations. We focus on increased scalability and generality with respect to prior work, with the potential of a large-scale Web-based knowledgebase. Our algorithm takes as its input a lexical–syntactic template and searches the Web for syntactic templates that participate in an entailment relation with the input template. Experiments show promising results, achieving performance similar to a state-of-the-art unsupervised algorithm, operating over an offline corpus, but with the benefit of learning rules for different domains with no additional effort.