julilili42/papers huggingface dataset:
Electric stimulation of neurons and neural networks in retinal prostheses
2013-11-01

A computational model is presented that can be used as a tool in experimental research in retinal implants. In this model a target volume (i.e., a probe cylinder approximating a bipolar cell) in the retina is chosen, and the passive Heaviside cable equation is solved inside the target volume to calculate the depolarization of the cell membrane. The depolarization as a function of time indicates that shorter signals stimulate better, as long as the current does not change sign during stimulation of the retina. The model is equally applicable to epiretinal, subretinal, and suprachoroidal vision implants.
Heat kernel asymptotics for magnetic Schrödinger operators
2013-11-01

We explicitly construct parametrices for magnetic Schrödinger operators on \\documentclass[12pt]{minimal}\\begin{document} \\end{document}Rd and prove that they provide a complete small-t expansion for the corresponding heat kernel, both on and off the diagonal.
PW02-041 - Canakinumab treatment regimens in CAPS-patients
2013-11-01

Canakinumab is a recombinant monoclonal fully human antibody against Interleukin-1β and currently the only drug approved for the treatment of CAPS in Europe. Current dose recommendations are 150mg (body weight >40kg) respectively 2mg/kg bodyweight (15 to 40kg) every 8 weeks but yield insufficient response in some individuals, especially in children and patients with severe phenotypes [1].
Story Link Detection in Turkish Corpus
2013-11-01

Story Link Detection (SLD) is known as a sub-task of Topic Detection and Tracking (TDT). SLD aims to specify whether two randomly selected stories discuss the same topic or not. This sub-task drew special attention within the TDT research community as many tasks in TDT are thought to be solved automatically once SLD performs as expected. In this study, performance tests were carried out on the BilCol-2005 Turkish news corpus composed of approximately 209,000 news items using vector space model (VSM) and relevance model (RM) methods with respect to varied index term counts. Accordingly, best results obtained were as follows: the VSM method performed best with 30 terms (F-measure=0.2970) while RM method did with 4 terms (F-measure=0.1910). Furthermore, the combination of two methods using the AND and OR functions increased the precision ratio by 7.9% and recall ratio by 1.2%, respectively, indicating that retrieval performance of SLD algorithms can be increased to some extent by employing both VSM and RM models.
When the United States Invaded Russia: Woodrow Wilson's Siberian Disaster
2013-11-01

When President Woodrow Wilson called on Congress to declare war on Germany in April 1917, the tsarist government in Russia had just been overthrown in a quasi-democratic revolution. Wilson led the United States in a war of democracies against authoritarian states. In the fall of 1917 the Russian Bolsheviks staged a coup d'état and arrested the members of the Provisional Government and in 1918 concluded a separate peace treaty with imperial Germany. Against that backdrop, Great Britain and the United States sent expeditionary armies to Russia in 1918. The United States dispatched 5,500 troops to Archangel in northern Russia and 8,500 soldiers to Siberia. Wilson's decision to intervene in Russia has received scholarly attention, and most facts appear to be beyond dispute. But questions remain regarding Wilson's intentions: Did he give in to British demands to reestablish an eastern front? Did he view the Siberian intervention as a humanitarian gesture to aid a few thousand Czech troops who had fought on the Allied side on the eastern front and who were now desperate to leave the country after Russia had signed the Treaty of Brest-Litovsk with Germany? What was Wilson's position in the Russian civil war of 1917–1921? Did he seek to overthrow the Bolsheviks?
The contrasting magnetic fields of superconducting pulsars and magnetars
2013-11-02

We study equilibrium magnetic field configurations in a neutron star (NS)\\nwhose core has type-II superconducting protons. Unlike the equations for normal\\nmatter, which feature no special field strength, those for superconductors\\ncontain the lower critical field, of order G. We find that the ratio\\nof this critical field to the smooth-averaged stellar field at the crust-core\\nboundary is the key feature dictating the field geometry. Our results suggest\\nthat pulsar and magnetar-strength fields have notably different configurations.\\nField decay for NSs with G could thus result in\\nsubstantial internal rearrangements, pushing the toroidal field component out\\nof the core; this may be related to observed magnetar activity. In addition, we\\ncalculate the magnetically-induced ellipticities of our models.\\n
Molecular determinants of PI3Kγ-mediated activation downstream of G-protein–coupled receptors (GPCRs)
2013-11-04

Significance Pathology of many diseases depends on signaling by phosphoinositide 3-kinase gamma (PI3Kγ), the lipid kinase that is exquisitely adapted to activation downstream of heterotrimeric G-protein–coupled receptors (GPCRs). Using hydrogen–deuterium exchange mass spectrometry, we demonstrate the mechanism by which the p110γ catalytic subunit and its p101 regulatory subunit interact with G-protein Gβγ heterodimers liberated upon GPCR activation. We identify residues in both p110γ and p101 interacting with Gβγ heterodimers on membranes. This enabled us to generate Gβγ-insensitive p110γ and p101 variants that eliminate activation of PI3Kγ by Gβγs without affecting the enzyme’s basal activity or its activation by the small G-protein Ras. Ablating the interaction of PI3Kγ with Gβγ heterodimers attenuates signaling, chemotaxis, and transformation driven by a GPCR agonist in cell lines.
From Genome-Wide Association Studies to Next-Generation Sequencing
2013-11-04

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Neurology HomeNew OnlineCurrent IssueFor Authors Podcast Publications JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2023 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Neurology journal
Multidimensional morphometric 3D MRI analyses for detecting brain abnormalities in children: Impact of control population
2013-11-04

Automated morphometric approaches are used to detect epileptogenic structural abnormalities in 3D MR images in adults, using the variance of a control population to obtain z-score maps in an individual patient. Due to the substantial changes the developing human brain undergoes, performing such analyses in children is challenging. This study investigated six features derived from high-resolution T1 datasets in four groups: normal children (1.5T or 3T data), normal clinical scans (3T data), and patients with structural brain lesions (3T data), with each n = 10. Normative control data were obtained from the NIH study on normal brain development (n = 401). We show that control group size substantially influences the captured variance, directly impacting the patient's z-scores. Interestingly, matching on gender does not seem to be beneficial, which was unexpected. Using data obtained at higher field scanners produces slightly different base rates of suprathreshold voxels, as does using clinically derived normal studies, suggesting a subtle but systematic effect of both factors. Two approaches for controlling suprathreshold voxels in a multidimensional approach (combining features and requiring a minimum cluster size) were shown to be substantial and effective in reducing this number. Finally, specific strengths and limitations of such an approach could be demonstrated in individual cases.
Comparison of gadobenate dimeglumine-enhanced breast MRI and gadopentetate dimeglumine-enhanced breast MRI with mammography and ultrasound for the detection of breast cancer
2013-11-04

Gadobenate dimeglumine-enhanced MRI significantly improves cancer detection compared to gadopentetate dimeglumine-enhanced MRI, mammography, and ultrasound in a selected group of patients undergoing breast MRI for preoperative staging or because of inconclusive findings at conventional imaging.
Teaching Neuro Images : Hypomyelinating leukodystrophy with hypodontia due to POLR3B
2013-11-04

An 18-year-old German woman presented with progressive cerebellar ataxia since early childhood, delayed cognitive development, and hypogonadotropic hypogonadism. MRI demonstrated diffuse cerebral hypomyelination, cerebellar atrophy, and thin corpus callosum; X-ray revealed persistent milk teeth and hypoplastic crowns and roots (figure), indicative of 4H syndrome (hypomyelination, hypodontia, hypogonadotropic hypogonadism). POLR3B sequencing(1) revealed 2 compound heterozygous mutations (C527R [C.1579T>C] and the common ancestral V523E [C.1568T>A](2)).
Automated Assessment of Cardiac Autonomic Function by Means of Deceleration Capacity from Noisy, Nonstationary ECG Signals: Validation Study
2013-11-05

Background Assessment of heart rate variability by means of deceleration capacity (DC) provides a noninvasive probe of cardiac autonomic activity. However, clinical use of DC is limited by the need of manual review of the ECG signals to eliminate artifacts, noise, and nonstationarities. Objective To validate a novel approach to fully automatically assess DC from noisy, nonstationary signals Methods We analyzed 100 randomly selected ECG tracings recorded for 10 minutes by routine monitor devices (GE DASH 4000, sample size 100 Hz) in a medical emergency department. We used a novel automated R‐peak detection algorithm, which is mainly based on a Shannon energy envelope estimator and a Hilbert transformation. We transformed the automatically generated RR interval time series by phase‐rectified signal averaging (PRSA) to assess DC of heart rate (DC auto ). DC auto was compared to DC manual , which was obtained from the same manually preprocessed ECG signals. Results DC auto and DC manual showed good correlation and agreement, particularly if a low‐pass filter was implemented into the PRSA algorithm. Correlation coefficient between DC auto and DC manual was 0.983 (P &lt; 0.0001). Average difference between DC auto and DC manual was ‒0.23±0.49 ms with limits of agreement ranging from ‒1.19 to 0.73 ms. Significantly lower correlations were observed when a different R‐peak detection algorithm or conventional heart rate variability (HRV) measures were tested. Conclusions DC can be fully automatically assessed from noisy, nonstationary ECG signals.
NovelAmycolatopsis balhimycinabiochemical abilities unveiled by proteomics
2013-11-05

Amycolatopsis balhimycina DSM5908 is an actinomycete producer of balhimycin, an analogue of vancomycin, the antibiotic of 'last resort' against multidrug-resistant Gram-positive pathogens. Most knowledge on glycopeptide biosynthetic pathways comes from studies on A. balhimycina as this strain, among glycopeptide producers, is genetically more amenable. The recent availability of its genome sequence allowed to perform differential proteomic analyses elucidating key metabolic pathways leading to antibiotic production in different growth conditions. To implement proteomic data on A. balhimycina derived from 2-DE approaches and to identify novel components, a combined approach based on protein extraction with different detergents, SDS-PAGE resolution of intact proteins and nanoLC-ESI-LIT-MS/MS analysis of their tryptic digests was carried out. With this procedure, 206 additional new proteins such as very basic, hydrophobic or large species were identified. This analysis revealed either components whose expression was previously only inferred by growth conditions, that is, those involved in glutamate metabolism or in resistance, or proteins that allow the strain to metabolize alkanes. These findings will give additional insight into metabolic pathways that could really contribute to A. balhimycina growth and antibiotic production and metabolic enzymes that could be manipulated to generate a model producing strain to use for synthetic biology.
Faculty Opinions recommendation of Structural insight into the biogenesis of β-barrel membrane proteins.
2013-11-05

β-barrel membrane proteins are essential for nutrient import, signalling, motility and survival. In Gram-negative bacteria, the β-barrel assembly machinery (BAM) complex is responsible for the biogenesis of β-barrel membrane proteins, with homologous complexes found in mitochondria and chloroplasts. Here we describe the structure of BamA, the central and essential component of the BAM complex, from two species of bacteria: Neisseria gonorrhoeae and Haemophilus ducreyi. BamA consists of a large periplasmic domain attached to a 16-strand transmembrane β-barrel domain. Three structural features shed light on the mechanism by which BamA catalyses β-barrel assembly. First, the interior cavity is accessible in one BamA structure and conformationally closed in the other. Second, an exterior rim of the β-barrel has a distinctly narrowed hydrophobic surface, locally destabilizing the outer membrane. And third, the β-barrel can undergo lateral opening, suggesting a route from the interior cavity in BamA into the outer membrane. PMID: 23995689 Funding information This work was supported by: NIGMS NIH HHS, United States Grant ID: RC2 GM093307 Intramural NIH HHS, United States Grant ID: Z99 DK999999 NIAID NIH HHS, United States Grant ID: K22 AI100927 NIAID NIH HHS, United States Grant ID: K22-AI100927 NIGMS NIH HHS, United States Grant ID: R01 GM067887 NIGMS NIH HHS, United States Grant ID: RC2GM093307 NIGMS NIH HHS, United States Grant ID: R01-GM67887 Intramural NIH HHS, United States Grant ID: ZIA DK036139-06 More Less keyboard_arrow_down
Organic Carbon and Reducing Conditions Lead to Cadmium Immobilization by Secondary Fe Mineral Formation in a pH-Neutral Soil
2013-11-06

Cadmium (Cd) is of environmental relevance as it enters soils via Cd-containing phosphate fertilizers and endangers human health when taken up by crops. Cd is known to associate with Fe(III) (oxyhydr)oxides in pH-neutral to slightly acidic soils, though it is not well understood how the interrelation of Fe and Cd changes under Fe(III)-reducing conditions. Therefore, we investigated how the mobility of Cd changes when a Cd-bearing soil is faced with organic carbon input and reducing conditions. Using fatty acid profiles and quantitative PCR, we found that both fermenting and Fe(III)-reducing bacteria were stimulated by organic carbon-rich conditions, leading to significant Fe(III) reduction. The reduction of Fe(III) minerals was accompanied by increasing soil pH, increasing dissolved inorganic carbon, and decreasing Cd mobility. SEM-EDX mapping of soil particles showed that a minor fraction of Cd was transferred to Ca- and S-bearing minerals, probably carbonates and sulfides. Most of the Cd, however, correlated with a secondary iron mineral phase that was formed during microbial Fe(III) mineral reduction and contained mostly Fe, suggesting an iron oxide mineral such as magnetite (Fe3O4). Our data thus provide evidence that secondary Fe(II) and Fe(II)/Fe(III) mixed minerals could be a sink for Cd in soils under reducing conditions, thus decreasing the mobility of Cd in the soil.
Genetics, Epigenetics, and Regulation of Drug-Metabolizing Cytochrome P450 Enzymes
2013-11-06

Of 57 functional human cytochrome P450 (CYP) isoforms, about a dozen liver-expressed, highly variable forms are responsible for the biotransformation of most drugs. Owing to numerous genetic and nongenetic sources of variation, each individual possesses his/her own, rather unique, CYP profile. Here, we explore the potential of new technologies and developments in genetics, epigenetics, and the regulation of gene expression to increase our understanding of the mechanisms that lead to the enormous inter- and intraindividual variability of these enzymes.
Idiopathic-generalized epilepsy shows profound white matter diffusion-tensor imaging alterations
2013-11-06

IGE and JME patients showed clear microstructural alterations in several large white matter tracts. Similar findings have been reported in rodent models of IGE. Previous, region-of-interest-based DTI studies may have under-estimated the spatial extent of structural loss associated with generalized epilepsy. The comparison of clinically defined JME and IGE groups revealed no significant DTI differences in our cohort.
Catabolite Control Protein E (CcpE) Is a LysR-type Transcriptional Regulator of Tricarboxylic Acid Cycle Activity in Staphylococcus aureus
2013-11-06

The tricarboxylic acid cycle (TCA cycle) is a central metabolic pathway that provides energy, reducing potential, and biosynthetic intermediates. In Staphylococcus aureus, TCA cycle activity is controlled by several regulators (e.g. CcpA, CodY, and RpiRc) in response to the availability of sugars, amino acids, and environmental stress. Developing a bioinformatic search for additional carbon catabolite-responsive regulators in S. aureus, we identified a LysR-type regulator, catabolite control protein E (CcpE), with homology to the Bacillus subtilis CcpC regulator. Inactivation of ccpE in S. aureus strain Newman revealed that CcpE is a positive transcriptional effector of the first two enzymes of the TCA cycle, aconitase (citB) and to a lesser extent citrate synthase (citZ). Consistent with the transcriptional data, aconitase activity dramatically decreased in the ccpE mutant relative to the wild-type strain. The effect of ccpE inactivation on citB transcription and the lesser effect on citZ transcription were also reflected in electrophoretic mobility shift assays where CcpE bound to the citB promoter but not the citZ promoter. Metabolomic studies showed that inactivation of ccpE resulted in increased intracellular concentrations of acetate, citrate, lactate, and alanine, consistent with a redirection of carbon away from the TCA cycle. Taken together, our data suggest that CcpE is a major direct positive regulator of the TCA cycle gene citB.
Screening of the Relaxivity of Gadolinium‐Loaded Periodic Mesoporous Silica Functionalized by Means of Soft Metalorganic Silylamide Grafting
2013-11-06

Abstract Soft metalorganic grafting of periodic mesoporous silica (PMS) materials is introduced as a method for obtaining nanostructured Gd III ‐loaded silica particles with relatively high 1 H relaxivity. The silylamide complex Gd[N(SiHMe 2 ) 2 ] 3 (THF) 2 was grafted onto MCM‐41, SBA‐15, and SBA‐1, thereby providing PMSs of distinct symmetry as well as pore size and configuration. The materials were characterized by infrared spectroscopy, elemental analysis, powder X‐ray diffraction (PXRD), N 2 physisorption, and scanning as well as transmission electron microscopy (SEM/TEM). Relaxivities up to 15.8 m M –1 s –1 were determined at high magnetic field strength (400 MHz). The nuclear magnetic resonance dispersion (NMRD) data of a calcined Gd[N(SiHMe 2 ) 2 ] 3 (THF) 2 @SBA‐1 material had a shape typical for slow‐tumbling systems, with a maximum at approximately 50 MHz. Temperature‐dependence studies of the relaxivity ( r 1 ) indicated that the grafted materials were characterized by an efficient water exchange. To maintain a high relaxivity, a low (1 wt.‐%) Gd III loading and a hydrophilic surface had to be provided. Varying the topology of the silica support only resulted in small variations in r 1 of the hybrid materials.
New Calcium‐Selective Smart Contrast Agents for Magnetic Resonance Imaging
2013-11-07

Abstract Calcium plays a vital role in the human body and especially in the central nervous system. Precise maintenance of Ca 2+ levels is very crucial for normal cell physiology and health. The deregulation of calcium homeostasis can lead to neuronal cell death and brain damage. To study this functional role played by Ca 2+ in the brain noninvasively by using magnetic resonance imaging, we have synthesized a new set of Ca 2+ ‐sensitive smart contrast agents (CAs). The agents were found to be highly selective to Ca 2+ in the presence of other competitive anions and cations in buffer and in physiological fluids. The structure of CAs comprises Gd 3+ ‐DO3A (DO3A=1,4,7‐tris(carboxymethyl)‐1,4,7,10‐tetraazacyclododecane) coupled to a Ca 2+ chelator o ‐amino phenol‐ N , N , O ‐triacetate (APTRA). The agents are designed to sense Ca 2+ present in extracellular fluid of the brain where its concentration is relatively high, that is, 1.2–0.8 m M . The determined dissociation constant of the CAs to Ca 2+ falls in the range required to sense and report changes in extracellular Ca 2+ levels followed by an increase in neural activity. In buffer, with the addition of Ca 2+ the increase in relaxivity ranged from 100–157 %, the highest ever known for any T 1 ‐based Ca 2+ ‐sensitive smart CA. The CAs were analyzed extensively by the measurement of luminescence lifetime measurement on Tb 3+ analogues, nuclear magnetic relaxation dispersion (NMRD), and 17 O NMR transverse relaxation and shift experiments. The results obtained confirmed that the large relaxivity enhancement observed upon Ca 2+ addition is due to the increase of the hydration state of the complexes together with the slowing down of the molecular rotation and the retention of a significant contribution of the water molecules of the second sphere of hydration.
Structure formation in perfluoropentacene:diindenoperylene blends and its impact on transient effects in the optical properties studied in real-time during growth
2013-11-07

We discuss the result of the competing effects of favourable intermolecular interactions and steric incompatibilities due to the size mismatch of perfluoropentacene (PFP) and diindenoperylene (DIP) on the structure formation and associated optical properties in mixed films. Using real-time grazing incidence X-ray diffraction we investigate the size of coherently scattering islands ls as a function of film thickness and mixing ratio. We find that for PFP:DIP 1:2 blends ls is by a factor of ∼4 smaller than in pure DIP films, while ls of the PFP:DIP 2:1 blends is not significantly reduced compared with pure PFP. Yet, we observe an increase in ls with film thickness for all of the samples, independent on the mixing ratio. In parallel with the structural characterization we investigate the evolution of the absorption spectra in the visible spectral range and its dependence on ls in situ during film growth using differential reflectance spectroscopy. We observe a surprisingly strong effect of changes in the structural order on the shape of ε2, xy(E), evident by a pronounced evolution of characteristic peaks in the thickness range from 1.6 nm to 9.6 nm. The combined results of the real-time experiments allow to identify the thickness dependent crystal grain size as the origin of the observed transient effects in the absorption spectra.