Miracle-dz/UniFAR-FTUs huggingface dataset:
A Single N-Linked Glycosylation Site in the Japanese Encephalitis Virus prM Protein Is Critical for Cell Type-Specific prM Protein Biogenesis, Virus Particle Release, and Pathogenicity in Mice

ABSTRACT The prM protein of Japanese encephalitis virus (JEV) contains a single potential N-linked glycosylation site, N15-X16-T17, which is highly conserved among JEV strains and closely related flaviviruses. To investigate the role of this site in JEV replication and pathogenesis, we manipulated the RNA genome by using infectious JEV cDNA to generate three prM mutants (N15A, T17A, and N15A/T17A) with alanine substiting for N15 and/or T17 and one mutant with silent point mutations introduced into the nucleotide sequences corresponding to all three residues in the glycosylation site. An analysis of these mutants in the presence or absence of endoglycosidases confirmed the addition of oligosaccharides to this potential glycosylation site. The loss of prM N glycosylation, without significantly altering the intracellular levels of viral RNA and proteins, led to an ≈20-fold reduction in the production of extracellular virions, which had protein compositions and infectivities nearly identical to those of wild-type virions; this reduction occurred at the stage of virus release, rather than assembly. This release defect was correlated with small-plaque morphology and an N-glycosylation-dependent delay in viral growth. A more conservative mutation, N15Q, had the same effect as N15A. One of the four prM mutants, N15A/T17A, showed an additional defect in virus growth in mosquito C6/36 cells but not human neuroblastoma SH-SY5Y or hamster BHK-21 cells. This cell type dependence was attributed to abnormal N-glycosylation-independent biogenesis of prM. In mice, the elimination of prM N glycosylation resulted in a drastic decrease in virulence after peripheral inoculation. Overall, our findings indicate that this highly conserved N-glycosylation motif in prM is crucial for multiple stages of JEV biology: prM biogenesis, virus release, and pathogenesis.
Exercise-Induced Pulmonary Arterial Hypertension

Background— The clinical relevance of exercise-induced pulmonary arterial hypertension (PAH) is uncertain, and its existence has never been well studied by direct measurements of central hemodynamics. Using invasive cardiopulmonary exercise testing, we hypothesized that exercise-induced PAH represents a symptomatic stage of PAH, physiologically intermediate between resting pulmonary arterial hypertension and normal. Methods and Results— A total of 406 consecutive clinically indicated cardiopulmonary exercise tests with radial and pulmonary arterial catheters and radionuclide ventriculographic scanning were analyzed. The invasive hemodynamic phenotype of exercise-induced PAH (n=78) was compared with resting PAH (n=15) and normals (n=16). Log-log plots of mean pulmonary artery pressure versus oxygen uptake (&OV0312;o2) were obtained, and a “join-point” for a least residual sum of squares for 2 straight-line segments (slopes m1, m2) was determined; m2m1=“takeoff” pattern. At maximum exercise, &OV0312;o2 (55.8±20.3% versus 66.5±16.3% versus 91.7±13.7% predicted) was lowest in resting PAH, intermediate in exercise-induced PAH, and highest in normals, whereas mean pulmonary artery pressure (48.4±11.1 versus 36.6±5.7 versus 27.4+3.7 mm Hg) and pulmonary vascular resistance (294±158 versus 161±60 versus 62±20 dyne · s · cm−5, respectively; P<0.05) followed an opposite pattern. An exercise-induced PAH plateau (n=32) was associated with lower &OV0312;o2max (60.6±15.1% versus 72.0±16.1% predicted) and maximum cardiac output (78.2±17.1% versus 87.8±18.3% predicted) and a higher resting pulmonary vascular resistance (247±101 versus 199±56 dyne · s · cm−5; P<0.05) than takeoff (n=40). The plateau pattern was most common in resting PAH, and the takeoff pattern was present in nearly all normals. Conclusions— Exercise-induced PAH is an early, mild, and clinically relevant phase of the PAH spectrum.
Electromyography in the Study of Muscle Reactions to Vibration Treatment

This second of two volumes on EMG (Electromyography) covers a wide range of clinical applications, as a complement to the methods discussed in volume 1. Topics range from gait and vibration analysis, through posture and falls prevention, to biofeedback in the treatment of neurologic swallowing impairment. The volume includes sections on back care, sports and performance medicine, gynecology/urology and orofacial function. Authors describe the procedures for their experimental studies with detailed and clear illustrations and references to the literature. The limitations of SEMG measures and methods for careful analysis are discussed. This broad compilation of articles discussing the use of EMG in both clinical and research applications demonstrates the utility of the method as a tool in a wide variety of disciplines and clinical fields.
De novo isolation of antibodies with pH-dependent binding properties

pH-dependent antibodies are engineered to release their target at a slightly acidic pH, a property making them suitable for clinical as well as biotechnological applications. Such antibodies were previously obtained by histidine scanning of pre-existing antibodies, a labor-intensive strategy resulting in antibodies that displayed residual binding to their target at pH 6.0. We report here the de novo isolation of pH-dependent antibodies selected by phage display from libraries enriched in histidines. Strongly pH-dependent clones with various affinity profiles against CXCL10 were isolated by this method. Our best candidate has nanomolar affinity for CXCL10 at pH 7.2, but no residual binding was detected at pH 6.0. We therefore propose that this new process is an efficient strategy to generate pH-dependent antibodies.
Indexing glomerular filtration rate for body surface area is useful in obese subjects.

We thank Rigalleau and colleagues for their interest in our work [1]. We completely agree with the fact that the Cockcroft formula is inaccurate when applied to obese patients. This inaccuracy was already described in the original article published by Cockcroft and Gault [2]. The MDRD formula has been elaborated from an American population which does not seem to be obese in the large majority, but without precision of the real percentage of obesity (defined as body mass index >30kg/m 2 ). In the MDRD study, the mean weight was 79.6 ± 16.8 kg. In our work, we have clearly shown that body surface area (BSA) correction has little influence on glomerular filtration rate (GFR) results in non-obese patients [1]. However, using this formula, developed and adapted for non-obese patients, re-correcting its results by BSA with obese parameters and asserting that the result represents non-corrected GFR is thus a nonsense. The fundamental question is to know if the simplified MDRD formula is accurate in its current presentation (with BSA correction integrated which, once again, has little impact on the results because it considers the population as non-obese), in a specific obese population. We have shown that 'true' GFR in obesity is closer to absolute, non-corrected GFR than to BSA-corrected GFR. This assertion is made in an absolute manner. Measured GFR (e.g. with [ 51 Cr]EDTA clearance) must be used to validate MDRD results (and not the inverse! ). Some authors, including Rigalleau et al., have studied the MDRD formula's accuracy in obese patients [3,4]. All authors used BSA-corrected GFR (which is misleading), but conclusions of these studies are divergent. Other studies are thus required. In this field of research, better methodology is necessary, i.e. with use of non-corrected GFR and of calibrated creatinine [1,5]. While we await such studies, we recommend continuing using [ 51 Cr]EDTA clearance in obese patients when precise, accurate GFR determination is needed (i.e. before proposing a slimming diet regimen or chemotherapy, for a living kidney donor, when proteinuria is detected, etc.).
The Balance Model of Dyslexia and Remedial Training

The aim of this study was to test the validity of Bakker's (1983, 1990) theory and treatment paradigm of dyslexia. Twenty-one children (mean age = 9.9 years) categorized as P-type dyslexics (showing accurate but slow and fragmented reading) and 19 children (mean age = 9.7 years) categorized as L-type dyslexics (fast but inaccurate readers) were presented with hemisphere-specific stimulation (HSS) and hemisphere-alluding stimulation (HAS). HSS was produced by presenting words to either the left or the right visual half-field, or to the left or right hand of the participant. HAS training was achieved through the presentation of either semantically /phonetically demanding or perceptually demanding text. Participants were given either a treatment program that was specifically designed for their particular dyslexia subtype, or a program that had been deliberately chosen to be inconsistent with their subtype. Contrary to predictions, participants made gains on all of the reading measures, regardless of the type of treatment given. On the basis of these findings it is suggested that treatment gains made are due to nonspecific training effects and not to the specific nature of Bakker's remedial strategies.
Ameliorating Spinal Cord Injury in an Animal Model With Mechanical Tissue Resuscitation.

BACKGROUND Traumatic spinal cord injury (SCI) is a major worldwide cause of mortality and disability with limited treatment options. Previous research applying controlled negative pressure to traumatic brain injury in rat and swine models resulted in smaller injuries and more rapid recovery. OBJECTIVE To examine the effects of the application of a controlled vacuum (mechanical tissue resuscitation [MTR]) to SCI in a rat model under several magnitudes of vacuum. METHODS Controlled contusion SCIs were created in rats. Vacuums of -50 and -75 mm Hg were compared. Analysis included open-field locomotor performance, magnetic resonance imaging (in vivo T2, ex vivo diffusion tensor imaging and fiber tractography), and histological assessments. RESULTS MTR treatment significantly improved the locomotor recovery from a Basso, Beattie, and Bresnahan score of 7.8 ± 1.9 to 11.4 ± 1.2 and 10.7 ± 1.9 at -50- and -75-mm Hg pressures, respectively, 4 weeks after injury. Both pressures also reduced fluid accumulations > 10% by T2-imaging in SCI sites. The mean fiber number and mean fiber length were greater across injured sites after MTR treatment, especially with treatment with -50 mm Hg. Myelin volume was increased significantly by 60% in the group treated with -50 mm Hg. CONCLUSION MTR of SCI in a rat model is effective in reducing edema in the injured cord, preserving myelin survival, and improving the rate and quantity of functional recovery. ABBREVIATIONS BBB, Basso, Beattie, and BresnahanDTI, diffusion tensor imagingFA, fractional anisotropyMTR, mechanical tissue resuscitationMTR50, mechanical tissue resuscitation with 50-mm Hg subatmospheric pressureMTR75, mechanical tissue resuscitation with 75-mm Hg subatmospheric pressureROI, region of interestSCI, spinal cord injury.
Novel methods improve prediction of species' distributions from occurrence data

Prediction of species' distributions is central to diverse applications in ecology, evolution and conservation science. There is increasing electronic access to vast sets of occurrence records in museums and herbaria, yet little effective guidance on how best to use this information in the context of numerous approaches for modelling distributions. To meet this need, we compared 16 modelling methods over 226 species from 6 regions of the world, creating the most comprehensive set of model comparisons to date. We used presence-only data to fit models, and independent presence-absence data to evaluate the predictions. Along with well-established modelling methods such as generalised additive models and GARP and BIOCLIM, we explored methods that either have been developed recently or have rarely been applied to modelling species' distributions. These include machine-learning methods and community models, both of which have features that may make them particularly well suited to noisy or sparse information, as is typical of species' occurrence data. Presence-only data were effective for modelling species' distributions for many species and regions. The novel methods consistently outperformed more established methods. The results of our analysis are promising for the use of data from museums and herbaria, especially as methods suited to the noise inherent in such data improve.
Adaptive beamforming using improved decision tree model for BPSK communication system

In Multi-sensor data fusion technology, array processing is an area of signal processing. A sensor array captures spatially propagating signals arriving from a certain direction and processes them to obtain useful information. To this end, it is intended to linearly combine the signals from all the sensors with coefficients in a manner, so as to estimate transmitted data radiating from a specific direction. In beamforming, an array processor steers a beam to a certain direction by computing a properly weighted sum of the individual sensor signals just as an finite impulse response (FIR) filter generates an output (at a frequency of interest) that is the weighted sum of time samples. Current methods to calculate the weight coefficients are complex. Designed model is a simple and effective weight coefficient calculation method based on improved decision tree model where it combines the best features of neural network and decision trees. This technique is based on the optimum beamformer and makes it robust to an faulty estimate of the Direction Of Arrival (DOA) even when powerful interferences are within the uncertainty range of the desired source. The proposed algorithm is the product of an effort to provide more efficient procedure for real time implementation of array signal processing and is useful for wireless communication with Binary Phase Shift Keying signalling.
Comparison of risk scoring systems in congenital heart surgery.

Hacettepe University Faculty of Medicine Department of Cardiovascular Surgery; data of 413 patients under 18 years old who had congenital heart surgery were evaluated between 01.01. 2011-30.10. 2012 and risk scorings were made by "RACHS-1 (Risk Adjustment in Congenital Heart Surgery)", "Aristotle Basic Complexity Score (ABS)" and "Aristotle Comprehensive Complexity Score (ACS)" systems used in evaluation of the risk of mortality and morbidity in (ACS)" systems used in evaluation of the risk of mortality and morbidity in congenital heart surgery. Data obtained were compared by Mann-Whitney U test and how effective these systems were in evaluating mortality and morbidity and their superiorities over each other were examined. Following the research, it was observed that all three systems were effective in evaluating mortality and morbidity; the most successful of them in foreseeing the event was the ACS system, ACS system was followed by RACHS-1 system and ABS system was the most incapable of these in foreseeing the event. It was seen that in detecting time related mortality, rating of these tests changed, RACHS-1 system detected the time related mortality best. It was also seen that with RACHS-1 system, a previously evaluated concept, it was possible to determine morbidity.
Atypical Protein Kinase C in Neurodegenerative Disease II: PKC&igr;/&lgr; in Tauopathies and &agr;-Synucleinopathies

To study the role of atypical protein kinase C (aPKC) in neurodegenerative disease, we investigated the distribution of PKC&igr;/&lgr;, an aPKC isoform, in a variety of tauopathies and &agr;-synucleinopathies. Immunohistochemical study revealed PKC&igr;/&lgr; within tau-positive neurofibrillary inclusions in Alzheimer disease (AD), progressive supranuclear palsy, corticobasal degeneration (CBD), and Pick disease (PiD), within &agr;-synuclein-positive Lewy bodies in idiopathic Parkinson disease and dementia with Lewy bodies, as well as within glial inclusions in multisystem atrophy. We also observed PKC&igr;/&lgr; label of actin-rich Hirano bodies in AD, PiD, and elderly individuals. Double immunolabeling and fluorescence resonance energy transfer demonstrated close physical association between PKC&igr;/&lgr; and phospho-tau or &agr;-synuclein in some neurofibrillary tangles and Lewy bodies. Furthermore, PKC&igr;/&lgr; colocalized with p62, a chaperone protein that binds to both aPKC and ubiquitin, in most of these inclusions. PKC&igr;/&lgr; also closely associated with the inactivated form of glycogen synthase kinase-3&bgr;, GSK-3&bgr;[ser9]. Together, these findings suggest that PKC&igr;/&lgr; may play a role in common mechanisms involving the pathogenesis of neurodegenerative disease.
Herbicide-resistant weeds in Europe: the wider implications.

Herbicide-resistance occurs in 55 weed species in 21 European countries. 91% of cases are associated with just four herbicide mode of action groups: ACCase and ALS inhibitors, and triazine and urea/amide photosynthetic inhibitors. There are also a few cases of resistance to bypiridiliums, dinitroanilnes and synthetic auxins. Resistance to ALS inhibitors tends to be less prevalent in Europe than elsewhere, but is likely to increase. A small scale survey showed that Alopecurus myosuroides is considered to be the most important herbicide-resistant weed in Europe at present. Lolium spp. , and to a lesser extent Papaver rhoeas and Avena spp. , were also highlighted as being of major importance in many countries. One consequence of the ongoing EC review of pesticides may be a reduction in the range of modes of action available to European farmers. This may reduce the opportunities for rotating different modes of action as a method of reducing resistance risk. Greater dependence on high resistance risk herbicides, such as ACCase and ALS inhibitors, because of lack of alternative modes of action, is likely to increase the incidence of resistance in grass-weeds.
Flexibility and packing in proteins

Structural flexibility is an essential attribute, without which few proteins could carry out their biological functions. Much information about protein flexibility has come from x-ray crystallography, in the form of atomic mean-square displacements (AMSDs) or B factors. Profiles showing the AMSD variation along the polypeptide chain are usually interpreted in dynamical terms but are ultimately governed by the local features of a highly complex energy landscape. Here, we bypass this complexity by showing that the AMSD profile is essentially determined by spatial variations in local packing density. On the basis of elementary statistical mechanics and generic features of atomic distributions in proteins, we predict a direct inverse proportionality between the AMSD and the contact density, i.e., the number of noncovalent neighbor atoms within a local region of ∼1.5 nm3 volume. Testing this local density model against a set of high-quality crystal structures of 38 nonhomologous proteins, we find that it accurately and consistently reproduces the prominent peaks in the AMSD profile and even captures minor features, such as the periodic AMSD variation within α helices. The predicted rigidifying effect of crystal contacts also agrees with experimental data. With regard to accuracy and computational efficiency, the model is clearly superior to its predecessors. The quantitative link between flexibility and packing density found here implies that AMSDs provide little independent information beyond that contained in the mean atomic coordinates.
yellow-in-the-dark Mutants of Chlamydomonas Lack the CHLL Subunit of Light-Independent Protochlorophyllide Reductase

Light-independent protochlorophyllide reduction leading to chlorophyll formation in the dark requires both chloroplast and nuclear gene expression in Chlamydomonas reinhardtii. Mutations in any one of the plastid (chlL, chlN, and chlB) or nuclear (y-1 to y-10) genes required for this process result in the phenotype of the yellow-in-the-dark or y mutants. Analysis of the chlL, chlN, and chlB transcript levels in both light- and dark-grown wild-type and y mutant cells showed that the y mutations have no effect on the transcription of these plastid genes. Protein gel blot analysis showed that the CHLN and CHLB proteins are present in similar amounts in light- and dark-grown wild-type cells, whereas CHLL is present only in wild-type cells grown in the dark or at light intensities ≤15 μmol m–2 sec–1. Analysis of chlL transcript distribution on polysome profiles and rates of protein turnover in chloramphenicol-treated cells suggested that CHLL formation is most probably blocked at translation initiation or elongation. Furthermore, treatment of cells with metabolic inhibitors and uncouplers of photosynthetic electron transport showed that regulation of CHLL formation is linked to the physiologic status of the chloroplast. Similar to wild-type cells, y mutants contain nearly identical amounts of CHLN and CHLB when grown in either light or darkness. However, no CHLL is present in any of the y mutants except y-7, which contains an immunoreactive CHLL smaller than the expected size. Our findings indicate that CHLL translation is negatively photoregulated by the energy state or redox potential within the chloroplast in wild-type cells and that nuclear y genes are required for synthesis or accumulation of the CHLL protein.
Energy saving of TV by face detection

A major part of electric power is supplied by thermal power stations, which emit carbon dioxide (CO2) while generating electricity. Today, since we consume a lot of electricity, we are threatened by environmental problems including global warming. One of the key points for solving these problems is developing energy-saving appliances. Televisions, which are widely used in the home, can achieve energy savings by reducing the brightness of the screen. However, unless a user adjusts it, the TV maintains the same brightness. Furthermore, we tend to watch TV while doing other activities such as using a computer or reading a book. This means that when we do something else, we often do not look at the TV. In this article, an energy-saving TV system based on the recognition of users' faces is proposed. This system recognizes the face direction of the TV user and when the user is not looking at the TV, the system will reduce the brightness automatically. On the other hand, when the system detects users' attention to the TV, the brightness will increase. To develop the prototype of this system, the face detection program OpenCV is used. A hand-made signal transmitter and signal receiver were also used to change the brightness of the TV. As a result of an experiment with the prototype system, we could confirm a 30% reduction of the TV's watt-hours.
Integration and visualization of multimodality brain data for language mapping

A goal of the University of Washington Brain Project is to develop software tools for processing, integrating and visualizing multimodality language data obtained at the time of neurosurgery, both for surgical planning and for the study of language organization in the brain. Data from a single patient consist of four magnetic resonance-based image volumes, showing anatomy, veins, arteries and functional activation (fMRI). The data also include the location, on the exposed cortical surface, of sites that were electrically stimulated for the presence of language. These five sources are mapped to a common MR-based neuroanatomical model, then visualized to gain a qualitative appreciation of their relationships, prior to quantitative analysis. These procedures are described and illustrated, with emphasis on the visualization of fMRI activation, which may be deep in the brain, with respect to surface-based stimulation sites.