julilili42/papers huggingface dataset:
mzML—a Community Standard for Mass Spectrometry Data
2010-08-17

Mass spectrometry is a fundamental tool for discovery and analysis in the life sciences. With the rapid advances in mass spectrometry technology and methods, it has become imperative to provide a standard output format for mass spectrometry data that will facilitate data sharing and analysis. Initially, the efforts to develop a standard format for mass spectrometry data resulted in multiple formats, each designed with a different underlying philosophy. To resolve the issues associated with having multiple formats, vendors, researchers, and software developers convened under the banner of the HUPO PSI to develop a single standard. The new data format incorporated many of the desirable technical attributes from the previous data formats, while adding a number of improvements, including features such as a controlled vocabulary with validation tools to ensure consistent usage of the format, improved support for selected reaction monitoring data, and immediately available implementations to facilitate rapid adoption by the community. The resulting standard data format, mzML, is a well tested open-source format for mass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.
Comparative Evaluation of Left and Right Ventricular Endomyocardial Biopsy
2010-08-17

Background— Endomyocardial biopsy (EMB) represents the gold standard for diagnosing myocarditis and nonischemic cardiomyopathies. This study focuses on the risk of complications and the respective diagnostic performance of left ventricular (LV), right ventricular (RV), or biventricular EMB in patients with suspected myocarditis and/or cardiomyopathy of unknown origin. Methods and Results— In this 2-center study, 755 patients with clinically suspected myocarditis (n=481) and/or cardiomyopathy of nonischemic origin including those with infiltrative or connective tissue disease (n=274) underwent either selective LV-EMB (n=265; 35.1%), selective RV-EMB (n=133; 17.6%), or biventricular EMB (n=357; 47.3%) after coronary angiography and exclusion of significant coronary artery disease. Cardiovascular magnetic resonance, including late gadolinium enhancement, imaging was performed in 540 patients (71.5%). The major complication rate for LV-EMB was 0.64% and for RV-EMB, 0.82%. Considering postprocedural pericardial effusion that occurred after biventricular EMB, the minor complication rate for LV-EMB varied between 0.64% to 2.89% and for RV-EMB, between 2.24% and 5.10%. Diagnostic EMB results were achieved significantly more often in those patients who underwent biventricular EMBs (79.3%) compared to those who underwent either selective LV-EMB or selective RV-EMB (67.3%; P &lt;0.001). In patients with biventricular EMB, myocarditis was diagnosed in LV-EMB samples in 18.7% and in RV-EMB samples in 7.9% ( P =0.002) , and it was diagnosed in both ventricles in 73.4%. There were no differences in the number of positive LV-EMB, RV-EMB, or LV- and RV-EMB findings when related to the site of cardiovascular magnetic resonance–based late gadolinium enhancement. Conclusions— Both LV-EMB and RV-EMB are safe procedures if performed by experienced interventionalists. The diagnostic yield of EMB may be optimized when samples from both ventricles are available. Preferential biopsy in regions showing late gadolinium enhancement on cardiovascular magnetic resonance does not increase the number of positive diagnoses of myocarditis.
Structural basis for the regulation of NtcA-dependent transcription by proteins PipX and PII
2010-08-17

PII, an ancient and widespread signaling protein, transduces nitrogen/carbon/energy abundance signals through interactions with target proteins. We clarify structurally how PII regulates gene expression mediated by the transcription factor NtcA, the global nitrogen regulator of cyanobacteria, shedding light on NtcA structure and function and on how NtcA is activated by 2-oxoglutarate (2OG) and coactivated by the nonenzymatic PII target, protein PipX. We determine for the cyanobacteria Synechococcus elongatus the crystal structures of the PII–PipX and PipX–NtcA complexes and of NtcA in active and inactive conformations (respective resolutions, 3.2, 2.25, 2.3, and 3.05 Å). The structures and the conclusions derived from them are consistent with the results of present and prior site-directed mutagenesis and functional studies. A tudor-like domain (TLD) makes up most of the PipX structure and mediates virtually all the contacts of PipX with PII and NtcA. In the PII–PipX complex, one PII trimer sequesters the TLDs of three PipX molecules between its body and its extended T loops, preventing PipX activation of NtcA. Changes in T loop conformation triggered by 2OG explain PII–PipX dissociation when 2OG is bound. The structure of active dimeric NtcA closely resembles that of the active cAMP receptor protein (CRP). This strongly suggests that with these proteins DNA binding, transcription activation, and allosteric regulation occur by common mechanisms, although the effectors are different. The PipX–NtcA complex consists of one active NtcA dimer and two PipX monomers. PipX coactivates NtcA by stabilizing its active conformation and by possibly helping recruit RNA polymerase but not by providing extra DNA contacts.
Follow-up Whole-Body Assessment of Adipose Tissue Compartments during a Lifestyle Intervention in a Large Cohort at Increased Risk for Type 2 Diabetes
2010-08-17

Visceral adipose tissue and hepatic lipids, as assessed with MR imaging and MR spectroscopy, can be significantly reduced during lifestyle intervention. Their baseline values emerged as predictive factors for an improvement of insulin sensitivity.
Functional mapping of harpin HrpZ of Pseudomonas syringae reveals the sites responsible for protein oligomerization, lipid interactions and plant defence induction
2010-08-17

SUMMARY Harpin HrpZ is one of the most abundant proteins secreted through the pathogenesis‐associated type III secretion system of the plant pathogen Pseudomonas syringae . HrpZ shows membrane‐binding and pore‐forming activities in vitro , suggesting that it could be targeted to the host cell plasma membrane. We studied the native molecular forms of HrpZ and found that it forms dimers and higher order oligomers. Lipid binding by HrpZ was tested with 15 different membrane lipids, with HrpZ interacting only with phosphatidic acid. Pore formation by HrpZ in artificial lipid vesicles was found to be dependent on the presence of phosphatidic acid. In addition, HrpZ was able to form pores in vesicles prepared from Arabidopsis thaliana plasma membrane, providing evidence for the suggested target of HrpZ in the host. To map the functions associated with HrpZ, we constructed a comprehensive series of deletions in the hrpZ gene derived from P. syringae pv. phaseolicola , and studied the mutant proteins. We found that oligomerization is mainly mediated by a region near the C‐terminus of the protein, and that the same region is also essential for membrane pore formation. Phosphatidic acid binding seems to be mediated by two regions separate in the primary structure. Tobacco, a nonhost plant, recognizes, as a defence elicitor, a 24‐amino‐acid HrpZ fragment which resides in the region indispensable for the oligomerization and pore formation functions of HrpZ.
Predictive Value of Platelet Activation for the Rate of Cognitive Decline in Alzheimer's Disease Patients
2010-08-18

Vascular risk factors contribute to the progression of dementia in Alzheimer's disease (AD) and influence platelet activation. However, the degree of platelet activation as a possible underlying mechanism of this progression has not been studied till now. Significantly higher baseline expression of both platelet activation biomarkers, activated glycoprotein IIb–IIIa complex and P-selectin, was observed in patients with AD with fast cognitive decline compared with AD patients with slow cognitive decline during a 1-year follow-up period. These results suggest that platelet activation could be a putative prognostic biomarker for the rate of cognitive decline and a potential new treatment target in AD patients.
Globalization and educational inequality during the 18thto 20thcenturies: Latin America in global comparison
2010-08-18

Abstract This paper explores the inequality of numeracy and education by studying school years and numeracy of the rich and poor, as well as of tall and short individuals. To estimate numeracy, the age-heaping method is used for the 18 th to early 20 th centuries. Testing the hypothesis that globalization might have increased the inequality of education, we find evidence that 19 th century globalization actually increased inequality in Latin America, but 20 th century globalization had positive effects by reducing educational inequality in a broader sample of developing countries. Moreover, we find strong evidence for Kuznets’s inverted U hypothesis, that is, rising educational inequality with GDP per capita in the period until 1913 and the opposite after 1945.
Hyperaldosteronism in Klotho-deficient mice
2010-08-19

Klotho is a membrane protein participating in the inhibitory effect of FGF23 on the formation of 1,25-dihydroxyvitamin-D 3 [1,25(OH) 2 D 3 ]. It participates in the regulation of renal tubular phosphate reabsorption and stimulates renal tubular Ca 2+ reabsorption. Klotho hypomorphic mice ( klotho hm ) suffer from severe growth deficit, rapid aging, and early death, events largely reversed by a vitamin D-deficient diet. The present study explored the role of Klotho deficiency in mineral and electrolyte metabolism. To this end, klotho hm mice and wild-type mice ( klotho +/+ ) were subjected to a normal (D + ) or vitamin D-deficient (D − ) diet or to a vitamin D-deficient diet for 4 wk and then to a normal diet (D −/+ ). At the age of 8 wk, body weight was significantly lower in klotho hm D + mice than in klotho +/+ D + mice, klotho hm D − mice, and klotho hm D −/+ mice. Plasma concentrations of 1,25(OH) 2 D 3, adrenocorticotropic hormone (ACTH), antidiuretic hormone (ADH), and aldosterone were significantly higher in klotho hm D + mice than in klotho +/+ D + mice. Plasma volume was significantly smaller in klotho hm D −/+ mice, and plasma urea, Ca 2+ , phosphate and Na + , but not K + concentrations were significantly higher in klotho hm D + mice than in klotho +/+ D + mice. The differences were partially abrogated by a vitamin D-deficient diet. Moreover, the hyperaldosteronism was partially reversed by Ca 2+ -deficient diet. Ussing chamber experiments revealed a marked increase in amiloride-sensitive current across the colonic epithelium, pointing to enhanced epithelial sodium channel (ENaC) activity. A salt-deficient diet tended to decrease and a salt-rich diet significantly increased the life span of klotho hm D + mice. In conclusion, the present observation disclose that the excessive formation of 1,25(OH) 2 D 3 in Klotho-deficient mice results in extracellular volume depletion, which significantly contributes to the shortening of life span.
Risk factors for severe Muckle‐Wells syndrome
2010-08-19

Abstract Objective Muckle‐Wells syndrome (MWS) is an inherited autoinflammatory disease resulting in excessive interleukin‐1 release. It is unknown whether demographic, clinical, or laboratory characteristics at the time of diagnosis may identify patients who are at high risk for severe disease activity. This study was undertaken to analyze clinical and laboratory features of MWS, compare genetically defined subcohorts, and identify risk factors for severe MWS. Methods A multicenter cohort study of consecutive MWS patients was performed. Parameters assessed included clinical features, MWS Disease Activity Score (MWS‐DAS), inflammation markers, and cytokine levels. E311K mutation–positive patients were compared with E311K mutation–negative patients. Putative risk factors for severe MWS (defined as an MWS‐DAS score of ≥10) were assessed in univariate analyses, and significant predictors were entered into a multivariate model. Results Thirty‐two patients (15 male and 17 female) were studied. The most frequent organ manifestations were musculoskeletal symptoms and eye and skin disorders. Renal disease and hearing loss were seen in &gt;50% of the patients. Genetically defined subcohorts had distinct phenotypes. Severe disease activity was documented in 19 patients (59%). Predictors of severe MWS identified at the time of diagnosis were female sex, hearing loss, musculoskeletal disease, increased erythrocyte sedimentation rate, and low hemoglobin level. Female sex and hearing loss remained significant after adjustment for age in a multivariate model (relative risk 1.8 and 2.6, respectively). Conclusion MWS patients at high risk for severe disease can be identified at the time of diagnosis. Female patients presenting with hearing loss have the highest likelihood of manifesting severe MWS and should be considered a high‐risk group.
Efficiency of porcine endothelial cell infection with human cytomegalovirus depends on both virus tropism and endothelial cell vascular origin
2010-08-19

Our data demonstrate that HCMV productively infects pEC, therefore finding strategies to render pEC resistant to HCMV infection will be of interest to reduce the potential risk carried by HCMV reactivation in xenotransplantation.
p38 MAP Kinase and MAPKAP Kinases MK2/3 Cooperatively Phosphorylate Epithelial Keratins*
2010-08-20

The MAPK-activated protein kinases (MAPKAP kinases) MK2 and MK3 are directly activated via p38 MAPK phosphorylation, stabilize p38 by complex formation, and contribute to the stress response. The list of substrates of MK2/3 is increasing steadily. We applied a phosphoproteomics approach to compare protein phosphorylation in MK2/3-deficient cells rescued or not by ectopic expression of MK2. In addition to differences in phosphorylation of the known substrates of MK2, HSPB1 and Bag-2, we identified strong differences in phosphorylation of keratin 8 (K8). The phosphorylation of K8-Ser(73) is catalyzed directly by p38, which in turn shows MK2-dependent expression. Notably, analysis of small molecule p38 inhibitors on K8-Ser(73) phosphorylation also demonstrated reduced phosphorylations of keratins K18-Ser(52) and K20-Ser(13) but not of K8-Ser(431) or K18-Ser(33). Interestingly, K18-Ser(52) and K20-Ser(13) are not directly phosphorylated by p38 in vitro, but by MK2. Furthermore, anisomycin-stimulated phosphorylations of K20-Ser(13) and K18-Ser(52) are inhibited by small molecule inhibitors of both p38 and MK2. MK2 knockdown in HT29 cells leads to reduced K20-Ser(13) phosphorylation, which further supports the notion that MK2 is responsible for K20 phosphorylation in vivo. Physiologic relevance of these findings was confirmed by differences of K20-Ser(13) phosphorylation between the ileum of wild-type and MK2/3-deficient mice and by demonstrating p38- and MK2-dependent mucin secretion of HT29 cells. Therefore, MK2 and p38 MAPK function in concert to phosphorylate K8, K18, and K20 in intestinal epithelia.
Test of the Universality of Naive-time-reversal-odd Fragmentation Functions
2010-08-20

We investigate the ''spontaneous'' hyperon transverse polarization in annihilation and semi-inclusive deep inelastic scattering processes as a test of the universality of the naive-time-reversal-odd transverse momentum dependent fragmentation functions. We find that universality implies definite sign relations among various observables. This provides a unique opportunity to study initial/final state interaction effects in the fragmentation process and test the associated factorization.
Universality of protein reentrant condensation in solution induced by multivalent metal ions
2010-08-21

Abstract The effective interactions and phase behavior of protein solutions under strong electrostatic coupling conditions are difficult to understand due to the complex charge pattern and irregular geometry of protein surfaces. This distinguishes them from related systems such as DNA or conventional colloids. In this work, we discuss the question of universality of the reentrant condensation (RC) of proteins in solution induced by multivalent counterions, i.e., redissolution on adding further salts after phase separation, as recently discovered (Zhang et al ., Phys Rev Lett 2008; 101:148101). The discussion is based on a systematic investigation of five different proteins with different charge patterns and five different multivalent counterions. Zeta potential measurements confirm the effective charge inversion of proteins in the reentrant regime via binding of multivalent counterions, which is supported by Monte Carlo simulations. Charge inversion by trivalent cations requires an overall negative net charge of the protein. Statistical analysis of a representative set of protein sequences reveals that, in theory, this effect could be possible for about half of all proteins. Our results can be exploited for the control of the phase behavior of proteins, in particular facilitating protein crystallization. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Increased [11C]PIB-PET levels in inclusion body myositis are indicative of amyloid deposition
2010-08-22

Pittsburgh Compound B ([11C]PIB), a 11C-labelled substituted benzothiazole, is a positron emission tomography (PET) marker recently described to detect amyloid β in vivo in the brains of patients with Alzheimer's disease.1 As amyloid β is also accumulated and misfolded in sporadic inclusion body myositis (IBM), and PIB has been demonstrated to penetrate the cell membrane,2 it is assumed that [11C]PIB may have the potential to depict amyloid β in the skeletal muscles of IBM patients. Thirteen subjects with clinical symptoms suggestive of IBM underwent complete clinical workup, including electrophysiology, muscle biopsy and [11C]PIB-PET. Biopsy specimens underwent standard histopathological staining. Based on clinical, electrophysiological and standard histopathological criteria, seven subjects were diagnosed as having IBM, two as having polymyositis, two as having neurogenic muscle atrophy, one as having peripheral neuropathy and one as having myalgia of unclear aetiology. Demographic and clinical details as well as biopsy results can be provided by the authors on request. The analysis was approved by the ethics committee of the University of Tuebingen. All subjects gave written informed consent. Twenty minutes after intravenous bolus injection of 740MBq [11C]PIB, whole body distribution of radioactivity was measured with a Hi-Rez Biograph 16 (Siemens Medical Solutions, Knoxville, USA), consisting of a high resolution three dimensional LSO PET and a 16 row multi slice CT. PET acquisition time was 3 min per field of view. Patients were measured from the lower leg to the neck to enable interindividual comparison of [11C]PIB uptake. Whole body CT was performed with low radiation dose used for attenuation correction and anatomical ...
Promoting Adaptive Emotion Regulation and Coping in Adolescence
2010-08-23

Particularly in adolescence, fostering adaptive emotion regulation is an important aim in health promotion. Expressive writing in combination with psycho-education on emotion regulation seems especially appropriate to serve this aim. In this study, school classes were randomly assigned either to a prevention ( N = 208) or to a non-treatment control group ( N = 151). The prevention group showed significant improvements regarding negative affect, grades, and days absent compared to the control-group. A combination of expressive writing with elements of psycho-education of emotion regulation might be an effective preventive tool, as it seems to improve psychosocial adjustment by establishing functional emotion regulation strategies.
Effects on colour discrimination during long term exposure to high altitudes on Mt Everest
2010-08-23

Chronic hypoxia induced by high altitude exposure transiently affects colour discrimination, in particular tritan axis discrimination. Decreased tritan discrimination is partly reversible upon physiological adaptation to high altitude and completely normalised upon return to low altitude.
Constrained quantum systems as an adiabatic problem
2010-08-23

We derive the effective Hamiltonian for a quantum system constrained to a submanifold (the constraint manifold) of configuration space (the ambient space) in the asymptotic limit where the restoring forces tend to infinity. In contrast to earlier works we consider at the same time the effects of variations in the constraining potential and the effects of interior and exterior geometry which appear at different energy scales and thus provide, for the first time, a complete picture ranging over all interesting energy scales. We show that the leading order contribution to the effective Hamiltonian is the adiabatic potential given by an eigenvalue of the confining potential well-known in the context of adiabatic quantum wave guides. At next to leading order we see effects from the variation of the normal eigenfunctions in form of a Berry connection. We apply our results to quantum wave guides and provide an example for the occurrence of a topological phase due to the geometry of a quantum wave circuit, i.e. a closed quantum wave guide.
Exploring the Data-Driven Prediction of Prepositions in English
2010-08-23

Prepositions in English are a well-known challenge for language learners, and the computational analysis of preposition usage has attracted significant attention. Such research generally starts out by developing models of preposition usage for native English based on a range of features, from shallow surface evidence to deep linguistically-informed properties. While we agree that ultimately a combination of shallow and deep features is needed to balance the preciseness of exemplars with the usefulness of generalizations to avoid data sparsity, in this paper we explore the limits of a purely surfacebased prediction of prepositions. Using a web-as-corpus approach, we investigate the classification based solely on the relative number of occurrences for target n-grams varying in preposition usage. We show that such a surface-based approach is competitive with the published state-of-the-art results relying on complex feature sets. Where enough data is available, in a surprising number of cases it thus is possible to obtain sufficient information from the relatively narrow window of context provided by n-grams which are small enough to frequently occur but large enough to contain enough predictive information about preposition usage. 1
Long‐term effects of coordinative training in degenerative cerebellar disease
2010-08-24

Abstract Few clinical studies have evaluated physiotherapeutic interventions for patients with degenerative cerebellar disease. In particular, evidence for long‐term effects and transfer to activities of daily life is rare. We have recently shown that coordinative training leads to short‐term improvements in motor performance. To evaluate long‐term benefits and translation to real world function, we here assessed motor performance and achievements in activities of daily life 1 year after a 4 week intensive coordinative training, which was followed by a home training program. Effects were assessed by clinical rating scales, a goal attainment score and quantitative movement analysis. Despite gradual decline of motor performance and gradual increase of ataxia symptoms due to progression of disease after 1 year, improvements in motor performance and achievements in activities of daily life persisted. Thus, also in patients with degenerative cerebellar disease, continuous coordinative training leads to long‐term improvements, which translate to real world function. © 2010 Movement Disorder Society