Miracle-dz/UniFAR-FTUs huggingface dataset:
Mutations Affecting Transcriptional Termination in the P Gene End of Subacute Sclerosing Panencephalitis Viruses

ABSTRACT Numerous mutations are found in subacute sclerosing panencephalitis (SSPE) viruses, and the M gene is the gene most commonly affected. In some SSPE viruses, such as the MF, Osaka-1, Osaka-2, and Yamagata-1 strains, translation of the M protein is complicated by a transcriptional defect that leads to an almost exclusive synthesis of dicistronic P-M mRNA. To understand the molecular mechanisms of this defect, we sequenced the P gene at the P-M gene junction for several virus strains and probed the involvement of several mutations in the readthrough region via their expression in measles virus minigenomes containing different sequences of the P-M gene junction and flanking reporter genes. The deletion of a single U residue in the U tract of the Osaka-1 strain (3′-UAAUAUUUUU-5′) compared with the consensus sequence resulted in a marked reduction of the expression of the downstream reporter gene. In addition, the expression of the downstream gene was markedly decreased by (i) the substitution of a C residue in the U tract of the P gene end of the OSA-2/Fr/B strain of the Osaka-2 virus (3′-UGAUAUUCUU-5′ compared with the sequence 3′-UGAUAUUUUU-5′ from a sibling virus of the same strain, OSA-2/Fr/V), and (ii) the substitution of a G in the sequence of the P gene end of the Yamagata-1 strain at a variable site immediately upstream from the six-U tract (3′-UGAUGUUUUUU-5′ instead of 3′-UGAUUUUUUUU-5′). Mutations at the P gene end can account for the readthrough transcription variation at the P-M gene junction, which directly affects M protein expression.
Analysis of operation modes for a neighborhood electric vehicle with power sources hybridization

Electric vehicles will have a fundamental place in sustainable mobility due to its very high efficiency and local/global emissions levels. To accomplish this role, both high power and high energy sources are desirable. In spite of recent advances in battery technology, this was not yet achieved and power sources hybridization can be a way to accomplish it. This is particularly true in the case of urban electric vehicles with very frequent speed variations and where regenerative braking can play an important role. In this paper the operation modes for a neighborhood electric vehicle with power sources hybridization are analyzed to define the convenient control strategy for its DC-DC converters. A system simulation is performed and an energetic analysis of different energy sources mix is done considering different acceleration requests. This is used to obtain a maximum energetic efficiency equation that can be used to optimize the control of the DC-DC converters.
The Etiology of Muscle Fatigue Differs between Two Electrical Stimulation Protocols.

PURPOSE This study aimed at investigating the mechanisms involved in the force reduction induced by two electrical stimulation (ES) protocols that were designed to activate motor units differently. METHODS The triceps surae of 11 healthy subjects (8 men; age, ~28 yr) was activated using ES applied over the tibial nerve. Two ES protocols (conventional [CONV]: 20 Hz, 0.05 ms vs wide-pulse high-frequency [WPHF]: 80 Hz, 1 ms) were performed and involved 40 trains (6 s on-6 s off) delivered at an intensity (IES) evoking 20% of maximal voluntary contraction. To analyze the mechanical properties of the motor units activated at IES, force-frequency relation was evoked before and after each protocol. H-reflex and M-wave responses evoked by the last stimulation pulse were also assessed during each ES protocol. Electromyographic responses (∑EMG) were recorded after each train to analyze the behavior of the motor units activated at IES. Metabolic variables, including relative concentrations of phosphocreatine and inorganic phosphate as well as intracellular pH, were assessed using P-MR spectroscopy during each protocol. RESULTS Larger H-reflex amplitudes were observed during WPHF as compared with CONV, whereas opposite findings were observed for M-wave amplitudes. Despite this difference, both the force reduction (-26%) and metabolic changes were similar between the two protocols. The CONV protocol induced a rightward shift of the force-frequency relation, whereas a significant reduction of the ∑EMG evoked at IES was observed only for the WPHF. CONCLUSIONS These results suggest that a decreased number of active motor units mainly contributed to WPHF-induced force decrease, whereas intracellular processes were most likely involved in the force reduction occurring during CONV stimulation.
Cholesterol Synthesis and De Novo Lipogenesis in Premature Infants Determined by Mass Isotopomer Distribution Analysis

Premature infants change from placental supply of mainly carbohydrates to an enteral supply of mainly lipids earlier in their development than term infants. The metabolic consequences hereof are not known but might have long-lasting health effects. In fact, knowledge of lipid metabolism in premature infants is very limited. We have quantified de novo lipogenesis and cholesterogenesis on d 3 of life in seven premature infants (birth weight, 1319 ± 417 g; gestational age, 30 ± 2 wk). For comparison, five healthy adult subjects were also studied. All subjects received a 12-h [1-13C] acetate infusion, followed by mass isotopomer distribution analysis (MIDA) on lipoprotein-palmitate and plasma unesterified cholesterol. The fraction of lipoprotein-palmitate synthesized at the end of the infusion period was 5.4 ± 3.9% in infants, which was in the same range as found in adult subjects on a normal diet, suggesting that hepatic de novo lipogenesis is not a major contributor to fat accumulation in these premature neonates. The fractional contribution of newly synthesized cholesterol to plasma unesterified cholesterol was 7.4 ± 1.3% after a 12-h infusion. The calculated rate of endogenous cholesterol synthesis was 31 ± 7 mg/kg/d, a value approximately three times higher than that found in adult subjects (10 ± 6 mg/kg/d). These results indicate that the cholesterol-synthesizing machinery is well developed in premature infants.
Somatotopic organization of thalamocortical projection fibers as assessed with MR tractography.

PURPOSE To prospectively evaluate the course of sensory fibers through the supratentorial brain with diffusion-tensor-based tractography. MATERIALS AND METHODS This study was approved by the institutional review board. Informed consent was obtained. Seven healthy volunteers (five men, two women; age range, 20-55 years) underwent 1.5-T magnetic resonance imaging. Diffusion-tensor images with isotropic voxels (2 x 2 x 2 mm) were obtained by using a single-shot echo-planar imaging technique, with a motion-probing gradient in 15 orientations, a b value of 1000 sec/mm(2), and nine signals acquired. The total imaging time was approximately 30 minutes. Fiber tracking of the sensorimotor pathways was performed with the fiber assignment by continuous tracking method. RESULTS All the pyramidal tracts rotated anteriorly as they traveled through the centrum semiovale. On the other hand, the sensory tracts rotated posteriorly as they coursed through the centrum semiovale toward the cortex. When the sensorimotor tracts were viewed as a unit, the tracts of the lower extremity formed the axis of rotation around which the other parts of the pyramidal and sensory homunculus rotated. CONCLUSION Sensorimotor fibers of the lower extremity form an axis of rotation, around which the pyramidal fibers rotate anteriorly and the sensory fibers rotate posteriorly.
Digital control of DC-DC boost converters with inductor current estimation

This paper investigates a digital control of DC-DC boost converter operating in continuous-conduction mode (CCM) sensing only the output voltage and possibly the input voltage. In order to improve the dynamic performance compared to voltage mode control, the inductor current is estimated and used for the implementation of an internal sensorless current loop. Different solutions, either based on the prediction of inductor current variations or on state observers, are discussed, showing that the sensorless current mode control gives some advantages only if input voltage feedforward is used. The digital control has been implemented in a field programmable gate array (FPGA) using a hardware description language (VHDL), providing flexibility and technology independence. Experimental results on a 100 W DC-DC boost converter confirm the properties and limitations of the proposed approach.
Deguelin Inhibits the Migration and Invasion of U-2 OS Human Osteosarcoma Cells via the Inhibition of Matrix Metalloproteinase-2/-9 in Vitro

Osteosarcoma is the most common malignant primary bone tumor in children and young adults and lung metastasis is the main cause of death in those patients. Deguelin, a naturally occurring rotenoid, is known to be an Akt inhibitor and to exhibit cytotoxic effects, including antiproliferative and anticarcinogenic activities, in several cancers. In the present study, we determined if deguelin would inhibit migration and invasion in U-2 OS human osteosarcoma cells. Deguelin significantly inhibited migration and invasion of U-2 OS human osteosarcoma cells which was associated with a reduction of activities of matrix metalloproteinases-2 (MMP-2) and matrix metalloproteinases-9 (MMP-9). Furthermore, results from western blotting indicated that deguelin decreased the cell proliferation and cell growth-associated protein levels, such as SOS1, PKC, Ras, PI3K, p-AKT(Ser473), IRE-1α, MEKK3, iNOS, COX2, p-ERK1/2, p-JNK1/2, p-p38; the cell motility and focal adhesion-associated protein levels, such as Rho A, FAK, ROCK-1; the invasion-associated protein levels, such as TIMP1, uPA, MMP-2. MMP-9, MMP-13, MMP-1 and VEGF in U-2 OS cells. Confocal microscopy revealed that deguelin reduced NF-κB p65, Rho A and ROCK-1 protein levels in cytosol. MMP-7, MMP-9 and Rho A mRNA levels were suppressed by deguelin. These in vitro results provide evidence that deguelin may have potential as a novel anti-cancer agent for the treatment of osteosarcoma and provides the rationale for in vivo studies in animal models.
Fluorescence Resonance Energy Transfer-based Structural Analysis of the Dihydropyridine Receptor α1S Subunit Reveals Conformational Differences Induced by Binding of the β1a Subunit*

The skeletal muscle dihydropyridine receptor α1S subunit plays a key role in skeletal muscle excitation-contraction coupling by sensing membrane voltage changes and then triggering intracellular calcium release. The cytoplasmic loops connecting four homologous α1S structural domains have diverse functions, but their structural arrangement is poorly understood. Here, we used a novel FRET-based method to characterize the relative proximity of these intracellular loops in α1S subunits expressed in intact cells. In dysgenic myotubes, energy transfer was observed from an N-terminal-fused YFP to a FRET acceptor, ReAsH (resorufin arsenical hairpin binder), targeted to each α1S intracellular loop, with the highest FRET efficiencies measured to the α1S II-III loop and C-terminal tail. However, in HEK-293T cells, FRET efficiencies from the α1S N terminus to the II-III and III-IV loops and the C-terminal tail were significantly lower, thus suggesting that these loop structures are influenced by the cellular microenvironment. The addition of the β1a dihydropyridine receptor subunit enhanced FRET to the II-III loop, thus indicating that β1a binding directly affects II-III loop conformation. This specific structural change required the C-terminal 36 amino acids of β1a, which are essential to support EC coupling. Direct FRET measurements between α1S and β1a confirmed that both wild type and truncated β1a bind similarly to α1S. These results provide new insights into the role of muscle-specific proteins on the structural arrangement of α1S intracellular loops and point to a new conformational effect of the β1a subunit in supporting skeletal muscle excitation-contraction coupling.
Comparative Incorporation of P32 into Lung Phosphatidyl Choline in Mammals with Different Metabolic and Pulmonary Morphologic Characteristics

Summary In the present study the incorporation of P32 into lung PC (cpm/mg DNA) was lowest in the sloth, was progressively higher in the cat, rabbit, and rat, and was highest in the mouse. It was 25 times greater in the adult mouse than in the sloth when expressed per gram fresh weight of lung tissue; it was 15 times greater when expressed as per mg DNA; and it was 11 times greater when expressed as specific activity. Lung PC specific activity from this study correlates well with alveolar surface area per unit lung volume, alveolar diameter, and oxygen consumption.
Prediction of survival in patients suspected of disseminated intravascular coagulation

Although antithrombin (AT), protein C (PC), and antiplasmin (AP) are consumed during disseminated intravascular coagulation (DIC), their association with mortality in patients initially suspected of acute DIC is unknown. We examined how these proteins associate with mortality in consecutive patients initially suspected of DIC, fulfilling or not fulfilling overt DIC criteria.
Reciprocal Cdc25A and p27 Expression in B-Cell Non-Hodgkin Lymphomas

Cell cycle regulation is often altered in cancer and deregulation of the cell cycle checkpoints is common in human neoplasia. The dual-specificity phosphatase Cdc25A and the cell cycle inhibitor p27 both play an important role in the regulation of the G1-S transition. We evaluated Cdc25A mRNA expression by in situ hybridization and p27 protein expression by immunohistochemistry in 42 histologically indolent B-cell non-Hodgkin lymphoma (NHLand 51 histologically aggressive B-cell NHL. Overexpression of Cdc25A (>50% tumor cells positive) was detected in 5 of 42 cases (12%) of histologically indolent B-cell NHL and in 29 of 51 (57%) of histologically aggressive B-cell NHL (P < 0.001). In contrast, high p27 protein expression (>50% tumor cells positive) was observed in 29 (69%) cases of indolent but in only one case (2%) of aggressive B-cell NHL (P < 0.0001). Thus, overexpression of Cdc25A and concomitant loss of p27 expression are associated with high grade B-cell NHL and may contribute to their aggressive biologic behavior.
Purification and Characterization of the Coniferyl Aldehyde Dehydrogenase from Pseudomonas sp. Strain HR199 and Molecular Characterization of the Gene

ABSTRACT The coniferyl aldehyde dehydrogenase (CALDH) ofPseudomonas sp. strain HR199 (DSM7063), which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid and which is induced during growth with eugenol as the carbon source, was purified and characterized. The native protein exhibited an apparent molecular mass of 86,000 ± 5,000 Da, and the subunit mass was 49.5 ± 2.5 kDa, indicating an α2 structure of the native enzyme. The optimal oxidation of coniferyl aldehyde to ferulic acid was obtained at a pH of 8.8 and a temperature of 26°C. The Km values for coniferyl aldehyde and NAD+ were about 7 to 12 μM and 334 μM, respectively. The enzyme also accepted other aromatic aldehydes as substrates, whereas aliphatic aldehydes were not accepted. The NH2-terminal amino acid sequence of CALDH was determined in order to clone the encoding gene (calB). The corresponding nucleotide sequence was localized on a 9.4-kbp EcoRI fragment (E94), which was subcloned from a Pseudomonas sp. strain HR199 genomic library in the cosmid pVK100. The partial sequencing of this fragment revealed an open reading frame of 1,446 bp encoding a protein with a relative molecular weight of 51,822. The deduced amino acid sequence, which is reported for the first time for a structural gene of a CALDH, exhibited up to 38.5% amino acid identity (60% similarity) to NAD+-dependent aldehyde dehydrogenases from different sources.
Cloning and Tissue-Specific Expression of a Chitin Deacetylase Gene from Helicoverpa armigera (Lepidoptera: Noctuidae) and Its Response to Bacillus thuringiensis

Chitin deacetylases (CDAs) convert chitin into chitosan, the N-deacetylated form of chitin, which influences the mechanical and permeability properties of structures such as the cuticle and peritrophic matrices. In this article, a new CDA encoding gene, Hacda2, was cloned by reverse transcription-polymerase chain reaction method in Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae), with an open reading frame of 1,611 bp. The deduced protein composed of 536 amino acid residues with a signal peptide, a chitin-binding domain, a low-density lipoprotein receptor class A domain, and a polysaccharide deacetylase-like catalytic domain. The highest expression level of Hacda2 was detected in fat body among tissues tested in the fifth-instar larvae using real-time quantitative polymerase chain reaction method. Feeding of Bacillus thuringiensis (Bt) (Bacillales: Bacillaceae) diet changed the expression level of Hacda1, Hacda2, Hacda5a, and Hacda5b significantly and differentially in the third-instar larvae. Hacda5a and Hacda5b expression were initially down-regulated and then up-regulated, whereas, the expression level of Hacda1 and Hacda2 was suppressed constantly postfeeding on Bt diet. These results suggested that HaCDAs may be involved in the response of H. armigera larvae to Bt and may be helpful to elucidate the roles of HaCDAs in the action of Bt cry toxin. The potential of HaCDAs to be used as synergists of Bt insecticidal protein needs to be further tested.
HAWAIIAN SKIRT: An F-Box Gene That Regulates Organ Fusion and Growth in Arabidopsis1[C][W][OA]

A fast neutron-mutagenized population of Arabidopsis (Arabidopsis thaliana) Columbia-0 wild-type plants was screened for floral phenotypes and a novel mutant, termed hawaiian skirt (hws), was identified that failed to shed its reproductive organs. The mutation is the consequence of a 28 bp deletion that introduces a premature amber termination codon into the open reading frame of a putative F-box protein (At3g61590). The most striking anatomical characteristic of hws plants is seen in flowers where individual sepals are fused along the lower part of their margins. Crossing of the abscission marker, ProPGAZAT:β-glucuronidase, into the mutant reveals that while floral organs are retained it is not the consequence of a failure of abscission zone cells to differentiate. Anatomical analysis indicates that the fusion of sepal margins precludes shedding even though abscission, albeit delayed, does occur. Spatial and temporal characterization, using ProHWS:β-glucuronidase or ProHWS:green fluorescent protein fusions, has identified HWS expression to be restricted to the stele and lateral root cap, cotyledonary margins, tip of the stigma, pollen, abscission zones, and developing seeds. Comparative phenotypic analyses performed on the hws mutant, Columbia-0 wild type, and Pro35S:HWS ectopically expressing lines has revealed that loss of HWS results in greater growth of both aerial and below-ground organs while overexpressing the gene brings about a converse effect. These observations are consistent with HWS playing an important role in regulating plant growth and development.
Surface Normal Reconstruction from Specular Information in Light Field Data

Specular highlights provide information about the shape of an object. Its characteristics are mostly unwanted in computer vision due to violation of the Lambertian assumption, which most algorithms require. Instead of neglecting this ubiquitous phenomenon we harvest it to extract surface normals with very high accuracy. Compared to photometric stereo our method works with multiple views and a fixed light source. We only require a low number of observation from a small part of the specular lobe to reconstruct the normal and reflection parameters. ,,,,,,This is achieved by jointly optimizing the normal and the light transport of surfaces points. This work is a proof of concept to demonstrate the feasibility of acquiring highly accurate surface normals from specular reflection, which can be combined with conventional methods. The model is tested and evaluated on synthetic as well as real world data acquired by a cross light field setup.
TD-60 is required for interphase cell cycle progression

We previously identified TD-60 (RCC2) as a mitotic centromere-associated protein that is necessary for proper completion of mitosis. We now report that TD-60 is an essential regulator of cell cycle progression during interphase. siRNA suppression blocks progression of mammalian G₁/S phase cells and progression of G₂ cells into mitosis. Prolonged arrest occurs both in non-transformed cells and in transformed cells lacking functional p53. TD-60 associates with Rac1 and Arf6 and has recently been demonstrated to be an element of α5β1 integrin and cortactin interactomes. These associations with known elements of cell cycle control, together with our data, suggest that TD-60 is an essential component of one or more signaling pathways that drive cell cycle progression. During mitosis, TD-60 is required for correct assembly of the mitotic spindle and activation of key mitotic proteins. In contrast, in interphase TD-60 promotes cell cycle progression through what must be distinct mechanisms. TD-60 thus appears to be one of the growing categories of proteins that “moonlight,” or have more than one distinct cellular function.
Genotyping Escherichia coli O157:H7 for Its Ability to Cause Disease in Humans

Escherichia coli are ubiquitous in the world, and for the most part are non‐pathogenic and part of the normal lower gastrointestinal tract in mammals. However, some pathogenic isolates can cause severe disease that range from meningitis to hemorrhagic colitis (HC). In recent years, Shiga toxin‐containing E. coli (STEC) have been a major cause of food borne and environmental cases of HC and hemolytic uremic syndrome. One STEC serotype, O157:H7, has been responsible for numerous food‐associated outbreaks and recalls worldwide. The protocols in this unit will allow the reader to use real‐time polymerase chain reaction genotyping to identify isolates that are more likely to cause disease in humans. The genotyping assay targets a single‐nucleotide polymorphism (SNP) in the tir gene. The tir gene is located in a virulence operon called the locus for enterocyte effacement and functions as a receptor for the tight adherence of E. coli O157:H7 to epithelial cells. As more genomes are sequenced, informative SNPs that associate with phenotypes will be identified. Identifying isolates not only by their genus and species, but also by using other informative genomic traits will increase the general knowledge about their genetic diversity. Curr. Protoc. Microbiol. 14:5A.3. 1‐5A.3. 10. © 2009 by John Wiley & Sons, Inc.