julilili42/papers huggingface dataset:
HSV-2 sacral radiculitis (Elsberg syndrome)
2004-08-24

<h3>Abstract</h3> We recently presented a statistical comparison between two models of latent dynamics in macaque lateral intraparietal (LIP) area spike trains—a continuous ‘ramping’ (diffusion-to-bound) model, and a discrete ‘stepping’ model—and found that a substantial fraction of neurons (recorded in two different studies) were better supported by the stepping model (Latimer et al., 2015). Here, we respond to a recent challenge to the validity of these findings that focuses primarily on the possibility of a lower bound on LIP firing rates (Zylberberg &amp; Shadlen, 2016). The paper in question proposed alternate formulations of the ramping model, and argued (via indirect analyses) that half the neurons in the population were better explained by the new model; if correct, this would lead to an even split in the number of neurons better explained by each model. These analyses, while interesting, do not alter the conclusions of our original paper. Here, we review the criticisms raised by Zylberberg &amp; Shadlen and report several new analyses using models with lower bounds. First, we show that the stepping model continued to provide a better description of LIP spike trains when fit using only an early period of each trial. Second, we performed a direct model comparison between our stepping model and a ramping-with-baseline model proposed by Zylberberg &amp; Shadlen; we found that (in a pleasing moment of agreement) roughly half the neurons were better explained by each model. Interestingly, inspection of the cells that switched classifications revealed that many did not strictly exhibit the classical ramping PSTHs that motivated these analyses in the first place. We also examined two other issues raised in recent discussions of LIP: (1) We show that a non-integrating model is consistent with some core aspects of behavioral data previously offered as evidence for continuous integration; and (2) We examine analyses based on the response covariance (“CorCE”), and show that it does not reliably distinguish ramping and stepping dynamics for our dataset. Taken together, these discussions highlight the value of data-driven characterizations of both neural and behavioral dynamics with appropriate statistical tools.
Spectral function at high missing energies and momenta
2004-08-25

The nuclear spectral function at high missing energies and momenta has been\\ndetermined from a self-consistent calculation of the Green's function in\\nnuclear matter using realistic nucleon-nucleon interactions. The results are\\ncompared with recent experimental data derived from ( ) reactions on\\n . A rather good agreement is obtained if the Green's functions are\\ncalculated in a non-perturbative way.\\n
Effect of Age on the Pupillomotor Field
2004-08-25

To differentiate physiologic variation from visual field loss with pupillomotor perimetry, the effect of age on the normal pupillomotor field must be known. Given the absence of reported data, the authors aimed to analyze the effect of age on the pupillomotor field as measured with light stimuli of different properties. Subjects consisted of 23 healthy volunteers aged 20 to 28 years ("younger subjects") and 20 healthy volunteers aged 50 to 67 years ("older subjects"). Within a field of 20 degrees, a sequence of 25 focal light stimuli was performed repeatedly on a monitor. The pupil light reflex (PLR) was recorded to stimuli of different diameter and luminance under mesopic conditions. The mean amplitude of the PLR was calculated for each stimulus location and condition. Increasing stimulus luminance or size caused a larger PLR amplitude and a steeper decline of the PLR amplitude from the center to the periphery of the pupillomotor field. The older subjects had reduced mean PLR amplitude with a less pronounced decrease of PLR amplitude toward the field periphery. For the peripheral locations, the largest PLR amplitude was found in the temporal superior quadrants. There was considerable intra-individual test-retest variation in PLR amplitudes in younger and older subjects. The PLR is markedly reduced in older compared with younger subjects. Older subjects have a relatively less pronounced central peak of sensitivity. There are intra-individual test-retest variations in PLR amplitude and asymmetries in sensitivity within the normal pupillomotor field at any age. These findings must be considered in interpreting the results of pupillomotor perimetry.
Cover Picture: Ab Initio NMR Spectra for Molecular Systems with a Thousand and More Atoms: A Linear‐Scaling Method (Angew. Chem. Int. Ed. 34/2004)
2004-08-25

A missing link between theory and experiment for the difficult puzzle of assigning NMR spectra for molecules with more than a thousand atoms is provided by the calculation of ab initio NMR spectra, as symbolized in the cover picture. In their Communication on page 4485 ff., C. Ochsenfeld et al. describe how an approximate solution of the Schrödinger equation becomes possible by reducing the computational effort from cubic to linear.
Thoracic Spondylitis From a Mycotic (Streptococcus pneumoniae) Aortic Aneurysm
2004-08-26

Lower back pain might be a projected pain. Particularly in older patients or in the presence of comorbidities resulting in an immunocompromised status, an aggressive workup may be indicated. Radical resection of inflammatory tissues, sparse use of implant material, and prolonged administration of antibiotics proved a successful strategy in this patient.
Yeast copper thionein: solving a small but long-standing puzzle
2004-08-26

In these postgenomic days the Protein Data Bank is featuring protein structures of increasingly large size, thanks to the progress in the power of the X-ray sources and in the computer programs to solve X-ray structures.&#13;\\nYet, there are small proteins whose structures remain elusive. One of the most striking examples is a stable and well-folded protein whose existence has been known for nearly thirty years, whose central importance in eukaryotes metabolism is undisputed, whose size is ridiculously small (Mr 5655), but whose detailed structure is still unknown. Such protein is yeast copper thionein (Cu-MT) Besides the different structure of the metal cluster, the main differences lie in the cysteine topology and in the conformation of some portions of the backbone. The present structure suggests that Cu-MT, in addition to its role as a safe depository for copper ions in the cell, may play an active role in the delivery of copper to metal-free chaperones.
PEG200 improved crystallisation of a mycobacterial adenylyl cyclase regulatory domain
2004-08-26

The structures of three functionally uncharacterized YLBA homologs from Escherichia Coli, Enterococcus faecalis and Deinococcus radiodurans are described.The first structure was solved by SeMet MAD and refined to R(cryst) =0.232, R(free)=0.267at 2.6Å resolution.The second structure was solved by molecular replacement using first structure as the search model (~55% identity) and refined to R(cryst)=0.208, R(free)=0.220at 2.0Å resolution.The third structure (~28% identity with first two) was solved by Hg SAD and refined to R(cryst)=0.229, R(free)=0.278at 2.4Å resolution.All data were collected at NSLS beam line X9A.All three structures have a common fold and differ only in the placement of outer loops segments.The molecule is composed of two similar domains positioned face to face around a pseudo two-fold axis.Each domain contains two antiparallel beta-sheets forming a beta-sandwich.Details of the structures and functional predictions will be presented.
Incretin mimetics: type 2 diabetes therapy beyond glucose control
2004-08-27

Incretins are gut hormones that elicit insulin secretion after glucose ingestion. The incretin effect describes the enhanced insulin response from orally introduced glucose compared to intravenous glucose. It comprises between 20% and 60% of the postprandial insulin secretion but is diminished in type 2 diabetes (T2D). Glucagon-like peptide-1 (GLP-1) is an important incretin. In vitro and animal experiments demonstrated that GLP-1 increases β-cell mass by stimulating islet cell neogenesis. In vitro data also show the inhibition of apoptosis of islets by GLP-1. The improvement of β-cell function can be indirectly observed from the increased insulin secretory capacity of humans receiving GLP-1. Furthermore, GLP-1 inhibits glucagon secretion and the risk of hypoglycaemia is extremely rare. It may represent an attractive therapeutic method for T2D due to its multiple effects. However, only 20% of the GLP-1 administered intravenously is estimated to reach circulation biologically intact. Therefore, exenatide and long-acting GLP-1 analogues, both of which are resistant to degradation and classified as incretin mimetics, are under study, as well as a compound that inhibits incretin degradation.
Proceedings of the Workshop on eLearning for Computational Linguistics and Computational Linguistics for eLearning
2004-08-28

The idea of this workshop arose on the occasion of an international workshop on eLearning and Computational Linguistics, organized by the MiLCA project and held in Blaubeuren in November 2003 (in the MiLCA project - Medienintensive Lehrmodule in der Computerlinguistik-Ausbildung, cf. http://milca.sfs.unituebingen. de -, five German partners are developing core modules for a CL curriculum as web based trainings or virtual courses.). It, therefore, seemed fitting and timely to identify this topic as one of the leading themes of the workshop. The COLING 2004 conference appeared to the participants as a good opportunity for such an event. We are very grateful to the COLING organizers to have given us the opportunity to conduct a workshop with the title eLearning for Computational Linguistics and Computational Linguistics for eLearning. This title reflects the two main topics that the participants of the MiLCA workshop had identified as the two leading themes to be addressed.
Consolidation Treatment With Chimeric Anti-GD2-Antibody ch14.18 in Children Older Than 1 Year With Metastatic Neuroblastoma
2004-08-30

Purpose Antibody treatment is considered tolerable and potentially effective in the therapy of neuroblastoma. We have analyzed stage 4 neuroblastoma patients older than 1 year who underwent consolidation treatment with the chimeric monoclonal anti-GD2-antibody ch14.18. Patients and Methods Stage 4 patients older than 1 year who completed initial treatment without event were eligible. ch14.18 was scheduled in a dose of 20 mg/m 2 /d during 5 days in six cycles every 2 months. Patients who did not receive ch14.18 served as controls. Results Of 334 assessable patients, 166 received ch14.18, 99 received a 12-month low-dose maintenance chemotherapy (MT) instead, and 69 had no additional treatment. During 695 ch14.18 cycles, fever (55% of cycles), abnormal C-reactive protein without infection (35%), cough (24%), rash (22%), and pain (16%) were the main side effects. Univariate analysis found similar event-free survival (EFS) for the three groups (3-year EFS, 46.5% ± 4.1%, 44.4% ± 4.9%, 37.1% ± 5.9% for patients treated with antibody ch14.18, MT, and no additional therapy, respectively; log-rank test, P = .314). For overall survival (OS), ch14.18 treatment (3-year OS, 68.5% ± 3.9%) was superior to MT (3-year OS, 56.6% ± 5.0%) or no additional therapy (3-year OS, 46.8% ± 6.2%; log-rank test, P = .018). Separate univariate analysis of patients with autologous stem-cell transplantation revealed no difference between patients with ch14.18 treatment and no additional consolidation. Multivariate analysis failed to demonstrate an advantage of antibody treatment for EFS and OS. Conclusion Consolidation treatment of stage 4 neuroblastoma with ch14.18 was associated with considerable but manageable side effects. Compared with oral maintenance chemotherapy and no consolidation treatment, ch14.18 had no clear impact on the outcome of patients.
Novel homozygous p.E64D mutation in DJ1 in early onset Parkinson disease (PARK7)
2004-08-30

Mutations in the parkin gene have been identified as a common cause of autosomal recessive inherited Parkinson disease (PD) associated with early disease manifestation. However, based on linkage data, mutations in other genes contribute to the genetic heterogeneity of early-onset PD (EOPD). Recently, two mutations in the DJ1 gene were described as a second cause of autosomal recessive EOPD (PARK7). Analyzing the PARK7/DJ1 gene in 104 EOPD patients, we identified a third mutation, c.192G>C (p.E64D), associated with EOPD in a patient of Turkish ancestry and characterized the functional significance of this amino acid substitution. In the patient, a substantial reduction of dopamine uptake transporter (DAT) binding was found in the striatum using [(18)F]FP-CIT and PET, indicating a serious loss of presynaptic dopaminergic afferents. His sister, homozygous for E64D, was clinically unaffected but showed reduced dopamine uptake when compared with a clinically unaffected brother, who is heterozygous for E64D. We demonstrate by crystallography that the E64D mutation does not alter the structure of the DJ1 protein, however we observe a tendency towards decreased levels of the mutant protein when overexpressed in HEK293 or COS7 cells. Using immunocytochemistry in contrast to the homogenous nuclear and cytoplasmic staining in HEK293 cells overexpressing wild-type DJ1, about 5% of the cells expressing E64D and up to 80% of the cells expressing the recently described L166P mutation displayed a predominant nuclear localization of the mutant DJ1 protein.
Cell volume and the regulation of apoptotic cell death
2004-08-31

Abstract Apoptosis is a physiological mechanism allowing for the removal of abundant or potentially harmful cells. The hallmarks of apoptosis include degradation of cellular DNA, exposure of phosphatidylserine at the outer leaflet of the cell membrane and cell shrinkage. Phosphatidylserine exposure favours adhesion to macrophages with subsequent phagocytosis of the shrunken apoptotic particles. The interaction of cell volume regulatory mechanisms and apoptosis is illustrated in two different model systems, i.e. (a) lymphocyte apoptosis following stimulation of CD95 receptor and (b) erythrocyte apoptosis upon cell shrinkage. (a) Triggering of CD95 in Jurkat T lymphocytes is paralleled by activation of cell volume regulatory Cl − channels, inhibition of the Na + /H + exchanger and osmolyte release. The latter coincides with cell shrinkage, DNA fragmentation and phosphatidylserine exposure. CD95 stimulation leads to early inhibition of the voltage gated K + channel Kv1.3, which may contribute to the inhibition of the Ca 2+ release activated Ca 2+ channel I CRAC . (b) Osmotic shock of erythrocytes activates a cell volume regulatory cation conductance allowing the entry not only of Na + but of Ca 2+ as well. Increased cytosolic Ca 2+ stimulates a scramblase which disrupts the phosphatidylserine asymmetry of the cell membrane, leading to phosphatidylserine exposure. The cation conductance is further activated by oxidative stress and energy depletion and inhibited by Cl − . Shrinkage of erythrocytes stimulates in addition a sphingomyelinase with subsequent formation of ceramide which potentiates the effect of cytosolic Ca 2+ on phosphatidylserine. In conclusion, cell volume‐sensitive mechanisms participate in the triggering of apoptosis following receptor stimulation or cell injury. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Downregulation and/or Release of NKG2D Ligands as Immune Evasion Strategy of Human Neuroblastoma
2004-09-01

Neuroblastoma (NB) is a pediatric extracranial tumor characterized by downregulation of human leukocyte antigen class I and defects of the antigen processing machinery, two features that make it an appropriate target for natural killer (NK)-mediated lysis. NKG2D is an activating immunoreceptor expressed by cytotoxic T lymphocytes and NK cells. The ligands for NKG2D are the major histocompatibility complex class I-related chain (MIC)A and MICB glycoproteins, and the UL-16-binding proteins (ULBPs). Here, the expression of NKG2D ligands was investigated in human primary NB tumors and cell lines because scanty information is available on this issue. MICA, MICB, and ULBP transcripts were found in most tumors and cell lines. MICA protein was detected in some NB cell lines but not in primary tumors. A soluble form of MICA (sMICA) was identified in most patient sera and in some cell line supernatants. sMICA downregulated surface NKG2D in normal peripheral blood CD8(+) cells and decreased NK-mediated killing of MICA(+) NB cells. MICB was detected exclusively in the cytosol of primary tumors and cell lines. Approximately 50% of primary tumors expressed ULBP-2, but not ULBP-1 or -3. ULBP-3 was expressed in 5 of 9 cell lines, ULBP-2 in 2 of 9, whereas ULBP-1 was never detected. These studies delineate novel potential pathways of tumor escape and immunodeficiency in NB.
The Architecture of the Murein (Peptidoglycan) in Gram-Negative Bacteria: Vertical Scaffold or Horizontal Layer(s)?
2004-09-01

The murein (peptidoglycan) sacculus is the essential exoskeleton of all eubacteria (except Mycoplasma species and a few other species) that is needed to withstand the internal cytoplasmic turgor (osmotic) pressure ([60][1], [78][2]). Murein consists of oligo(GlcNAc-MurNAc) glycan strands that are
No Evidence for Increased Skin Cancer Risk in Psoriasis Patients Treated with Broadband or Narrowband UVB Phototherapy: A First Retrospective Study
2004-09-01

Phototherapy of skin diseases such as psoriasis is an effective and safe treatment modality. However, increasing the risk of skin cancer by phototherapy is a serious concern. An increased skin cancer risk occurs after prolonged photochemotherapy (PUVA). In contrast, the role of broadband UVB or narrowband UVB therapy in skin carcinogenesis of humans with psoriasis is less clear. Therefore, we investigated the incidence of skin tumours in a total of 195 psoriasis patients, receiving broadband (n=69) or narrowband (n=126) UVB from 1994 to 2000 with follow-up until 2003. Data were raised from the regional interdisciplinary cancer centre of the University of Tuebingen, Germany and compared with the tumour incidences given for the German population. In this study, with 80% statistical power to detect a 6-7-fold increase in skin cancer with broadband UVB and 83% power to detect a 5-6-fold increase with narrow band UVB at p=0.05, only one patient developed skin cancer - an in situ melanoma. The tumour occurred within the same year that phototherapy was initiated. Thus, the present study does not provide evidence for an increased skin cancer risk for patients treated with either broadband or narrowband UVB phototherapy
Hemozoin (Malarial Pigment) Inhibits Differentiation and Maturation of Human Monocyte-Derived Dendritic Cells: A Peroxisome Proliferator-Activated Receptor-γ-Mediated Effect
2004-09-01

Abstract Acute and chronic Plasmodium falciparum malaria are accompanied by severe immunodepression possibly related to subversion of dendritic cells (DC) functionality. Phagocytosed hemozoin (malarial pigment) was shown to inhibit monocyte functions related to immunity. Hemozoin-loaded monocytes, frequently found in circulation and adherent to endothelia in malaria, may interfere with DC development and play a role in immunodepression. Hemozoin-loaded and unloaded human monocytes were differentiated in vitro to immature DC (iDC) by treatment with GM-CSF and IL-4, and to mature DC (mDC) by LPS challenge. In a second setting, hemozoin was fed to iDC further cultured to give mDC. In both settings, cells ingested large amounts of hemozoin undegraded during DC maturation. Hemozoin-fed monocytes did not apoptose but their differentiation and maturation to DC was severely impaired as shown by blunted expression of MHC class II and costimulatory molecules CD83, CD80, CD54, CD40, CD1a, and lower levels of CD83-specific mRNA in hemozoin-loaded iDC and mDC compared with unfed or latex-loaded DC. Further studies indicated activation of peroxisome proliferator-activated receptor-γ (PPAR-γ) in hemozoin-loaded iDC and mDC, associated with increased expression of PPAR-γ mRNA, without apparent involvement of NF-κB. Moreover, expression of PPAR-γ was induced and up-regulation of CD83 was inhibited by supplementing iDC and mDC with plausible concentrations of 15(S)-hydroxyeicosatetraenoic acid, a PPAR-γ ligand abundantly produced by hemozoin via heme-catalyzed lipoperoxidation.
Evaluation of Combined Transmission and Emission Tomography for Classification of Skeletal Lesions
2004-09-01

TET improves the accuracy of bone scintigraphy by correctly classifying equivocal lesions, especially by identifying benign abnormalities in the axial skeleton and thus increasing the specificity of positive findings.
Dermcidin is constitutively produced by eccrine sweat glands and is not induced in epidermal cells under inflammatory skin conditions
2004-09-01

These results indicate that, unlike human cathelicidins and beta-defensins which are inducible peptides that primarily function in response to injury and inflammation, DCD is exclusively part of the constitutive innate defence of human skin. By modulating surface colonization, DCD may help to prevent local and systemic invasion of pathogens.
Acute Stress Impairs Recognition for Positive Words—Association with Stress-induced Cortisol Secretion
2004-09-01

Some studies suggest that stress-induced effects of cortisol on memory are modulated by the valence of the stimuli to be learned and retrieved. The present study investigated the effect of acute stress-induced cortisol secretion on acquisition and retrieval of pleasant, unpleasant and neutral words. Sixty healthy men were randomly assigned to one of the three experimental groups. Participants were either exposed to a standardized laboratory stressor (the Trier Social Stress Test) before learning a wordlist, or before retrieval, or were not stressed. Free recall and recognition were tested 24 h later. Free recall was not affected by stress exposure. For recognition, there was no main effect of the stressor, but a main effect of valence and a valence by group interaction emerged: recognition for positive words was significantly impaired when subjects were stressed before retrieval. In addition, a positive correlation between the cortisol response and errors of commission was found. The results suggest that acute stress impairs memory for positive stimuli and that stress-induced cortisol secretion interferes with accuracy of memory retrieval, i.e. the ability to discriminate true memories from false ones.
Larger Interregional Synchrony is Associated with Greater Behavioral Success in a Complex Sensory Integration Task in Humans
2004-09-01

Successful behavior depends on effective communication between distant brain regions. Moreover, disturbance of effective communication can cause neurological symptoms like apraxia, dyslexia or object agnosia. Interregional communication can be assessed by coherence analysis of synchronized neuronal oscillations, and has been referred to as synchrony or "binding". The concept of synchrony as a means of information coding is attractive, but its functional relevance has been challenged. We hypothesized that if synchrony is functionally relevant in humans, then more synchrony should determine better behavioral performance. Here, we show in a visuotactile integration task that the amount of low-frequency (7-13Hz), long-range electroencephalographic coherence between visual and sensorimotor cortex is significantly correlated with the level of performance. Trials with highest coherences were the most successful ones and vice versa in the absence of differences in regional activation measured as task-related spectral power. In summary, quantitatively linking the amount of long-range synchrony with the degree of behavioral success in humans, the present data suggest that the ability to generate topographically specific synchrony of high amplitude is functionally relevant for behavioral success. They also raise the possibility that the magnitude of regional activation is less representative of the efficacy of brain functioning than interregional synchrony.