Miracle-dz/UniFAR-FTUs huggingface dataset:
Piracetam and vinpocetine ameliorate rotenone-induced Parkinsonism in rats

Objective: To evaluate the neuroprotective effect of the nootropic drugs, piracetam (PIR) and vinpocetine (VIN), in rotenone-induced Parkinsonism in rats. Materials and Methods: Sixty male rats were divided into 6 groups of 10 rats each. The groups were administered vehicle, control (rotenone, 1.5 mg/kg/48 h/6 doses, s.c.), PIR (100 and 200 mg/kg/day, p.o.) and VIN (3 and 6 mg/kg/day, p.o.). The motor performance of the rats was evaluated by the open field and pole test. Striatal dopamine level, malondialdehyde (MDA), reduced glutathione (GSH) and tumor necrosis factor-α (TNF-α) were assayed. Histopathological study of the substantia nigra was also done. Results: Results showed that rotenone-treated rats exhibited bradykinesia and motor impairment in the open-field test. In addition, GSH level was decreased whereas MDA and TNF-α increased in striata of rotenone-treated rats as compared to vehicle-treated rats. Marked degeneration of the substantia nigra pars compacta (SNpc) neurons and depletion of striatal dopamine was also observed in the rotenone-treated rats. Treatment with PIR or VIN significantly reversed the locomotor deficits and increased striatal dopamine level. Treatment with VIN significantly (P < 0.05) reduced the striatal level of MDA and GSH in comparison to rotenone group whereas TNF-α production was found to be significantly decreased in PIR group (P < 0.05). Conclusion: VIN and PIR exhibit neuroprotective activity in rotenone-induced Parkinsonism. Hence, these nootropic agents may be considered as possible candidates in the treatment of Parkinson's disease.
Integrated silicon-PDMS process for microrobot mechanisms

The first MEMS process integrating soft elastomers in a standard silicon-on-insulator (SOI) wafer without assembly has been demonstrated for use in microrobotic mechanisms. This process allows silicon and poly(dimethylsiloxane) (PDMS) features to be defined in-plane with feature sizes down to 2 µm. Test structures have been used to characterize the Young's modulus of the resulting PDMS at 1.4 MPa along with adhesion to silicon structures. In addition, compliant flexures have been designed, fabricated and characterized for eventual use in microrobot legs. Test structures have been mechanically folded 180° out of plane over 60 times without failure.
Induction of Fas Ligand Expression by HIV Involves the Interaction of Nef with the T Cell Receptor ζ Chain

During HIV/SIV infection, there is widespread programmed cell death in infected and, perhaps more importantly, uninfected cells. Much of this apoptosis is mediated by Fas–Fas ligand (FasL) interactions. Previously we demonstrated in macaques that induction of FasL expression and apoptotic cell death of both CD4+ and CD8+ T cells by SIV is dependent on a functional nef gene. However, the molecular mechanism whereby HIV-1 induces the expression of FasL remained poorly understood. Here we report a direct association of HIV-1 Nef with the ζ chain of the T cell receptor (TCR) complex and the requirement of both proteins for HIV-mediated upregulation of FasL. Expression of FasL through Nef depended upon the integrity of the immunoreceptor tyrosine-based activation motifs (ITAMs) of the TCR ζ chain. Conformation for the importance of ζ for Nef-mediated signaling in T cells came from an independent finding. A single ITAM motif of ζ but not CD3ε was both required and sufficient to promote activation and binding of the Nef-associated kinase (NAK/p62). Our data imply that Nef can form a signaling complex with the TCR, which bypasses the requirement of antigen to initiate T cell activation and subsequently upregulation of FasL expression. Thus, our study may provide critical insights into the molecular mechanism whereby the HIV-1 accessory protein Nef contributes to the pathogenesis of HIV.
Integration of Ligand‐ and Target‐Based Virtual Screening for the Discovery of Cruzain Inhibitors

A myriad of methods are available for virtual screening of small organic compound databases. In this study we have successfully applied a quantitative model of consensus measurements, using a combination of 3D similarity searches (ROCS and EON), Hologram Quantitative Structure Activity Relationships (HQSAR) and docking (FRED, FlexX, Glide and AutoDock Vina), to retrieve cruzain inhibitors from collected databases. All methods were assessed individually and then combined in a Ligand‐Based Virtual Screening (LBVS) and Target‐Based Virtual Screening (TBVS) consensus scoring, using Receiving Operating Characteristic (ROC) curves to evaluate their performance. Three consensus strategies were used: scaled‐rank‐by‐number, rank‐by‐rank and rank‐by‐vote, with the most thriving the scaled‐rank‐by‐number strategy, considering that the stiff ROC curve appeared to be satisfactory in every way to indicate a higher enrichment power at early retrieval of active compounds from the database. The ligand‐based method provided access to a robust and predictive HQSAR model that was developed to show superior discrimination between active and inactive compounds, which was also better than ROCS and EON procedures. Overall, the integration of fast computational techniques based on ligand and target structures resulted in a more efficient retrieval of cruzain inhibitors with desired pharmacological profiles that may be useful to advance the discovery of new trypanocidal agents.
Hypersensitivity of Escherichia coli Δ(uvrB-bio) Mutants to 6-Hydroxylaminopurine and Other Base Analogs Is Due to a Defect in Molybdenum Cofactor Biosynthesis

ABSTRACT We have shown previously that Escherichia coli andSalmonella enterica serovar Typhimurium strains carrying a deletion of the uvrB-bio region are hypersensitive to the mutagenic and toxic action of 6-hydroxylaminopurine (HAP) and related base analogs. This sensitivity is not due to theuvrB excision repair defect associated with this deletion because a uvrB point mutation or a uvrAdeficiency does not cause hypersensitivity. In the present work, we have investigated which gene(s) within the deleted region may be responsible for this effect. Using independent approaches, we isolated both a point mutation and a transposon insertion in themoeA gene, which is located in the region covered by the deletion, that conferred HAP sensitivity equal to that conferred by theuvrB-bio deletion. The moeAB operon provides one of a large number of genes responsible for biosynthesis of the molybdenum cofactor. Defects in other genes in the same pathway, such as moa or mod, also lead to the same HAP-hypersensitive phenotype. We propose that the molybdenum cofactor is required as a cofactor for an as yet unidentified enzyme (or enzymes) that acts to inactivate HAP and other related compounds.
Transcription of the Stationary-Phase-AssociatedhspX Gene of Mycobacterium tuberculosis Is Inversely Related to Synthesis of the 16-Kilodalton Protein

ABSTRACT The 16-kDa protein, an α-crystallin homologue, is one of the most abundant proteins in stationary-phase Mycobacterium tuberculosis. Here, transcription and translation of thehspX gene, which encodes the 16-kDa protein, have been investigated by Northern blotting analysis, primer extension, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis with a microaerophilic stationary-phase model. Two transcripts of about 2.5 and 1.1 kb were demonstrated by Northern blot analysis and hybridized to the hspX gene probe. Primer extension analysis revealed that the transcription start site is located 33 nucleotides upstream of the hspX gene start codon. The cellular level of thehspX mRNA was maximum in log-phase bacilli and was markedly reduced after 20 days in unagitated culture, when the organisms had entered the stationary phase. A third transcript of 0.5 kb was detected 0.6 kb downstream of the hspX gene; this transcript has a transcriptional pattern completely different from that of the 1.1- and 2.5-kb products, suggesting that there may be another gene in this region. In contrast to the high level of hspX mRNA in log-phase bacilli, 16-kDa protein synthesis was low in log-phase bacteria and rose to its maximum after 20 days. In both log-phase and stationary-phase bacteria the mRNA was unstable, with a half-life of 2 min, which indicated that the transcript stability was growth rate independent and not a general means for controlling the gene expression. However, the cellular content of 16-kDa protein, while low in log-phase bacteria, rose to a maximum at 10 days and remained at this high level for up to 50 days, which indicates that this protein is a stable molecule with a low turnover rate. These data suggest that the regulation of hspX expression during entry into and maintenance of stationary phase involves translation initiation efficiency and protein stability as potential mechanisms.
A Snail Perspective on the Biogeography of Sulawesi, Indonesia: Origin and Intra-Island Dispersal of the Viviparous Freshwater Gastropod Tylomelania

The complex geological history of the Indonesian island Sulawesi has shaped the origin and subsequent diversification of its taxa. For the endemic freshwater snail Tylomelania a vicariant origin from the Australian margin has been hypothesized. Divergence time estimates from a mtDNA phylogeny based on a comprehensive island-wide sampling of Tylomelania fit regional tectonic constraints and support the ‘out-of-Australia’ vicariance hypothesis. The Banggai-Sula region of the Sula Spur, the Australian promontory colliding with West Sulawesi during the Miocene, is identified as a possible source area for the colonization of Sulawesi by the ancestor of Tylomelania. The molecular phylogeny also shows a rapid diversification of Tylomelania into eight major lineages with very little overlap in their distribution on the island. Haplotype networks provide further evidence for a strong spatial structure of genetic diversity in Tylomelania. Distribution boundaries of the major lineages do at best partially coincide with previously identified contact zones for other endemic species groups on Sulawesi. This pattern has likely been influenced by the poor dispersal capabilities and altitudinal distribution limits of this strict freshwater inhabitant. We suggest that late Miocene and Pliocene orogeny in large parts of Sulawesi has been the vicariant event driving primary diversification in Tylomelania.
Adaptive Object Tracking Based on an Effective Appearance Filter

We propose a similarity measure based on a spatial-color mixture of Gaussians (SMOG) appearance model for particle filters. This improves on the popular similarity measure based on color histograms because it considers not only the colors in a region but also the spatial layout of the colors. Hence, the SMOG-based similarity measure is more discriminative. To efficiently compute the parameters for SMOG, we propose a new technique with which the computational time is greatly reduced. We also extend our method by integrating multiple cues to increase the reliability and robustness. Experiments show that our method can successfully track objects in many difficult situations.
The Bone-specific Expression of Runx2 Oscillates during the Cell Cycle to Support a G1-related Antiproliferative Function in Osteoblasts*

The Runx2 (CBFA1/AML3/PEBP2αA) transcription factor promotes skeletal cell differentiation, but it also has a novel cell growth regulatory activity in osteoblasts. We addressed here whether Runx2 activity is functionally linked to cell cycle-related mechanisms that control normal osteoblast proliferation and differentiation. We found that the levels of Runx2 gene transcription, mRNA and protein, are each up-regulated with cessation of cell growth (i.e. G0/G1 transition) in preconfluent MC3T3 osteoblastic cells that do not yet express mature bone phenotypic gene expression. Cell growth regulation of Runx2 is also observed in primary calvarial osteoblasts and other osteoblastic cells with relatively normal cell growth characteristics, but not in osteosarcoma cells (e.g. SAOS-2 and ROS17/2.8). Runx2 levels are cell cycle-regulated in MC3T3 cells with respect to the G1/S and M/G1 transitions: oscillates from maximal expression levels during early G1 to minimal levels during early S phase and mitosis. However, in normal or immortalized (e.g. ATDC5) chondrocytic cells, Runx2 expression is suppressed during quiescence, and Runx2 levels are not regulated during G1 and S phase in ATDC5 cells. Antisense or small interfering RNA-mediated reduction of the low physiological levels of Runx2 in proliferating MC3T3 cells does not accelerate cell cycle progression. However, forced expression of Runx2 suppresses proliferation of MC3T3 preosteoblasts or C2C12 mesenchymal cells which have osteogenic potential. Forced elevation of Runx2 in synchronized MC3T3 cells causes a delay in G1. We propose that Runx2 levels and function are biologically linked to a cell growth-related G1 transition in osteoblastic cells.
Differential gene expression in migrating cortical interneurons during mouse forebrain development

γ‐Aminobutyric acid (GABA)ergic interneurons play a vital role in modulating the activity of the cerebral cortex, and disruptions to their function have been linked to neurological disorders such as schizophrenia and epilepsy. These cells originate in the ganglionic eminences (GE) of the ventral telencephalon and undergo tangential migration to enter the cortex. Currently, little is known about the signaling mechanisms that regulate interneuron migration. We therefore performed a microarray analysis comparing the changes in gene expression between the GABAergic interneurons that are actively migrating into the cortex with those in the GE. We were able to isolate pure populations of GABAergic cells by fluorescence‐activated cell sorting of cortex and GE from embryonic brains of glutamate decarboxylase 67 (GAD67)‐green fluorescent protein (GFP) transgenic mice. Our microarray analysis identified a number of novel genes that were upregulated in migrating cortical interneurons at both E13.5 and E15.5. Many of these genes have previously been shown to play a role in cell migration of both neuronal and non‐neuronal cell types. In addition, several of the genes identified are involved in the regulation of migratory processes, such as neurite outgrowth, cell adhesion, and remodeling of the actin cytoskeleton and microtubule network. Moreover, quantitative polymerase chain reaction and in situ hybridization analyses confirmed that the expression of some of these genes is restricted to cortical interneurons. These data therefore provide a framework for future studies aimed at elucidating the complexities of interneuron migration and, in turn, may reveal important genes that are related to the development of specific neurological disorders. J. Comp. Neurol. 518:1232–1248, 2010. © 2009 Wiley‐Liss, Inc.
Shift from Systemic to Site-Specific Memory by Tumor-Targeted IL-21

IL-2 has been approved for treatment of patients with cancer. Moreover, it has been used as a component of vaccines against cancer. In this regard, we have recently demonstrated that dendritic cell-based peptide vaccination in mice required IL-2 to mount an effective immune response against established melanoma metastases. In this study, we confirm this observation by use of tumor-targeted IL-2. However, the development of a protective systemic memory was substantially impaired by this measure, i.e., mice, which successfully rejected s.c. tumors of B16 melanoma after vaccination with dendritic cells pulsed with tyrosinase-related protein 2-derived peptides plus a boost with targeted IL-2, failed to reject a rechallenge with experimental pulmonary metastases. Detailed analysis revealed a change in the distribution of the tumor-reactive T cell population: although targeted IL-2 expanded the local effector population, tyrosinase-related protein 2-reactive T cells were almost completely depleted from lymphatic tissues.
Using Cognitive Modeling to Study Behavior Moderators: Pre-Task Appraisal and Anxiety

We present a cognitive model of a repeated serial subtraction arithmetic task in the ACT-R cognitive architecture (Anderson & Lebiere, 1998) that is modified to demonstrate how the influence of biobehavioral effects on cognition (sometimes called behavioral moderators) can be studied through a combination of cognitive modeling experimental psychology, and physiological psychology techniques.
Response of Atmospheric Convection to Vertical Wind Shear: Cloud-System-Resolving Simulations with Parameterized Large-Scale Circulation. Part II: Effect of Interactive Radiation

AbstractThe authors investigate the effects of cloud–radiation interaction and vertical wind shear on convective ensembles interacting with large-scale dynamics in cloud-resolving model simulations, with the large-scale circulation parameterized using the weak temperature gradient approximation. Numerical experiments with interactive radiation are conducted with imposed surface heat fluxes constant in space and time, an idealized lower boundary condition that prevents wind–evaporation feedback. Each simulation with interactive radiation is compared to a simulation in which the radiative heating profile is held constant in the horizontal and in time and is equal to the horizontal-mean profile from the interactive-radiation simulation with the same vertical shear profile and surface fluxes. Interactive radiation is found to reduce mean precipitation in all cases. The magnitude of the reduction is nearly independent of the vertical wind shear but increases with surface fluxes. Deep shear also reduces precipi.
T-Ag Transgenic Mice Binary Tetracycline-Regulated Polyomavirus Autoimmunity to DNA and Nucleosomes in

The mechanism(s) responsible for autoimmunity to DNA and nucleosomes in SLE is largely unknown. We have demonstrated that nucleosome-polyomavirus T-Ag complexes, formed in context of productive polyomavirus infection, activate dsDNA-speciﬁc B cells and nucleosome-speciﬁc CD4 (cid:1) T cells. To investigate whether de novo expressed T-Ag is able to terminate nucleosome-speciﬁc T cell tolerance and to maintain anti-dsDNA Ab production in nonautoimmune mice, we developed two binary transgenic mouse variants in which expression of SV40 large T-Ag is controlled by tetracycline, MUP tTA/T-Ag ( tet -off), and CMV rtTA/ T-Ag ( tet -on) mice. Data demonstrate that MUP tTA/T-Ag mice, but not CMV rtTA/T-Ag mice, are tightly controlling T-Ag expression. In MUP tTA/T-Ag transgenic mice, postnatal T-Ag expression activated CD8 (cid:1) T cells but not DNA-speciﬁc B cells, while immunization with T-Ag and nucleosome-T-Ag-complexes before T-Ag expression resulted in elevated and remarkably stable titers of anti-T-Ag and anti-dsDNA Abs and activation of T-Ag-speciﬁc CD4 (cid:1) T cells. Immunization of nonexpressing MUP tTA/T-Ag mice resulted in transient anti-T-Ag and anti-dsDNA Abs. This system reveals that a de novo expressed DNA-binding quasi-autoantigen maintain anti-dsDNA Abs and CD4 (cid:1) T cell activation once initiated by immunization, demonstrating direct impact of a single in vivo expressed molecule on sustained autoimmunity to DNA and nucleosomes. The Journal of Immunology,
Improved Efficiency and Pace of Generating Induced Pluripotent Stem Cells from Human Adult and Fetal Fibroblasts

It was reported recently that human fibroblasts can be reprogrammed into a pluripotent state that resembles that of human embryonic stem (hES) cells. This was achieved by ectopic expression of four genes followed by culture on mouse embryonic fibroblast (MEF) feeders under a condition favoring hES cell growth. However, the efficiency of generating human induced pluripotent stem (iPS) cells is low, especially for postnatal human fibroblasts. We started supplementing with an additional gene or bioactive molecules to increase the efficiency of generating iPS cells from human adult as well as fetal fibroblasts. We report here that adding SV40 large T antigen (T) to either set of the four reprogramming genes previously used enhanced the efficiency by 23–70‐fold from both human adult and fetal fibroblasts. Discernible hES‐like colonies also emerged 1–2 weeks earlier if T was added. With the improved efficiency, we succeeded in replacing MEFs with immortalized human feeder cells that we previously established for optimal hES cell growth. We further characterized individually picked hES‐like colonies after expansion (up to 24 passages). The majority of them expressed various undifferentiated hES markers. Some but not all the hES‐like clones can be induced to differentiate into the derivatives of the three embryonic germ layers in both teratoma formation and embryoid body (EB) formation assays. These pluripotent clones also differentiated into trophoblasts after EB formation or bone morphogenetic protein 4 induction as classic hES cells. Using this improved approach, we also generated hES‐like cells from homozygous fibroblasts containing the sickle cell anemia mutation Hemoglobin Sickle.
Overlapping Toxoplasma gondii Genotypes Circulating in Domestic Animals and Humans in Southeastern Brazil

Although several Toxoplasma gondii genotyping studies have been performed in Brazil, studies of isolates from animals in the state of Minas Gerais are rare. The objective of this study was to conduct a genotypic characterization of T. gondii isolates obtained from dogs, free-range chickens, and humans in Minas Gerais and to verify whether the T. gondii genotypes circulating in domestic animals correspond to the genotypes detected in humans. Genetic variability was assessed by restricted fragment length polymorphism at 11 loci (SAG1, 5′+3′SAG2, SAG2 alt, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico). Twelve different genotypes were identified among the 24 isolates studied, including 8 previously identified genotypes and 4 new genotypes. The genetic relationship of the 24 T. gondii isolates, together with the genotypes previously described from 24 human newborns with congenital toxoplasmosis, revealed a high degree of similarity among the genotypes circulating in humans and animals in Minas Gerais. The most common genotypes among these species were BrII, BrIII, ToxoDB #108, and ToxoDB #206. Restricted fragment length polymorphism at the CS3 locus of these 48 isolates showed that the majority of isolates presented alleles I (50%) or II (27%). Isolates harboring allele III at the CS3 locus presented low virulence for mice, whereas those harboring alleles I or II presented higher virulence. These results confirm the utility of marker CS3 for predicting the virulence of Brazilian isolates of T. gondii in mice. No association was found between the allele type and clinical manifestations of human congenital toxoplasmosis. This is the first report of T. gondii genotyping that verifies the overlapping genotypes of T. gondii from humans and animals in the same geographic region of Brazil. Our results suggest that there is a common source of infection to the species studied, most likely oocysts contaminating the environment.
On the Design of Perceptual MPEG-Video Encryption Algorithms

In this paper, some existing perceptual encryption algorithms of MPEG videos are reviewed and some problems, especially security defects of two recently proposed MPEG-video perceptual encryption schemes, are pointed out. Then, a simpler and more effective design is suggested, which selectively encrypts fixed-length codewords in MPEG-video bit streams under the control of three perceptibility factors. The proposed design is actually an encryption configuration that can work with any stream cipher or block cipher. Compared with the previously-proposed schemes, the new design provides more useful features, such as strict size-preservation, on-the-fly encryption and multiple perceptibility, which make it possible to support more applications with different requirements. In addition, four different measures are suggested to provide better security against known/chosen-plaintext attacks