julilili42/papers huggingface dataset:
New Role of the Disulfide Stress Effector YjbH in β-Lactam Susceptibility of Staphylococcus aureus
2011-09-27

ABSTRACT Staphylococcus aureus is exposed to multiple antimicrobial compounds, including oxidative burst products and antibiotics. The various mechanisms and regulatory pathways governing susceptibility or resistance are complex and only superficially understood. Bacillus subtilis recently has been shown to control disulfide stress responses by the thioredoxin-related YjbH protein, which binds to the transcriptional regulator Spx and controls its degradation via the proteasome-like ClpXP protease. We show that the S. aureus YjbH homolog has a role in susceptibility to the disulfide stress-inducing agent diamide that is similar to that in B. subtilis , and we demonstrate that the four cysteine residues in YjbH are required for this activity. In addition, the inactivation of YjbH led to moderate resistance to oxacillin and other β-lactam antibiotics, and this phenotypic change was associated with higher penicillin-binding protein 4 levels and increased peptidoglycan cross-linking. Of note, the impact of YjbH on β-lactam susceptibility still was observed when the four cysteines of YjbH were mutated, indicating that the roles of YjbH in disulfide stress and β-lactam resistance rely on different types of interactions. These data suggest that the ClpXP adaptor YjbH has more target proteins than previously thought, and that oxidative burst and β-lactam resistance mechanisms of S. aureus are closely linked.
Two Pathways for Pyrrole Formation in Coumermycin A1 Biosynthesis: The Central Pyrrole Moiety Is Formed From L‐Threonine
2011-09-27

Abstract Coumermycin A 1 is an aminocoumarin antibiotic produced by Streptomyces rishiriensis . It contains three pyrrole rings, that is, two terminal 5‐methyl‐pyrrole‐2‐carboxyl moieties and a central 3‐methylpyrrole‐2,4‐dicarboxylic acid moiety. The biosynthesis of the terminal pyrrole moieties has been elucidated previously. However, the biosynthetic precursors of the central pyrrole moiety have remained unknown, and none of the genes or enzymes involved in its formation has been identified. We now show that five genes, contained in a contiguous 4.7 kb region within the coumermycin biosynthetic gene cluster, are required for the biosynthesis of this central pyrrole moiety. Each of these genes was deleted individually, resulting in a strong reduction or an abolishment of coumermycin production. External feeding of the central pyrrole moiety restored coumermycin production. One of these genes shows similarity to L ‐threonine kinase genes. Feeding of [U‐ 13 C, 15 N] L ‐threonine and 13 C NMR analysis of the resulting compound unequivocally proved that threonine was incorporated intact into the central pyrrole (19 % enrichment) to provide the heterocyclic nitrogen as well as four of the seven carbons of this moiety. Therefore, this pyrrole is formed via a new, hitherto unknown biosynthetic pathway. A hypothesis for the reaction sequence leading to the central pyrrole moiety of coumermycin A 1 is presented.
Copeptin—A Novel Marker in Acute Myocardial Infarction
2011-09-27

To the Editor: We read with great interest the recent report on copeptin by Karakas et al. (1), because it appears to contradict several previous larger studies. The authors conclude that copeptin does not add diagnostic information to high-sensitivity cardiac troponin T (hs-cTnT)1 in patients with acute chest pain. On closer scrutiny, however, the conclusions appear to be based on methodological inconsistencies and on inadequate timing of blood sampling. First, copeptin is not considered a rule-out marker of acute coronary syndromes, but rather a rule-out marker of acute myocardial infarction (AMI) (2, 3). Second, the present study draws conclusions from only 8 patients with AMI. The reason might be that patients had to consent to enrollment in a study of coronary computed tomography angiography, adding bias to the selection of patients. Third, the timing of blood sampling is essential for reaching a correct rule-out of AMI with copeptin. ...
Is the world unfinished? On interactions between science and theology in the concepts of nature, time and the future
2011-09-27

This paper is the text of Professor Moltmann’s 2011 Boyle lecture. In it he explores interactions between theology and the sciences. It proceeds from the Cappadocian insight that the world is ‘readable’ both in ‘the Book of Books’ and in the ‘book of nature’. The empirical concept of nature corresponds to the theological concept of creation, between which there is no contradiction. This leads to a reflection on the nature of time, and in particular the differences between times ‘past’ and ‘future’, the former fixed, the latter open. The lecture concludes by reflecting that, in eschatological perspective, nature presents itself as a being with a history open to the future.
Orbital Parameters and Spectroscopy of the Transient X-Ray Pulsar 4U 0115+63
2011-09-27

We report on an outburst of the high mass X-ray binary 4U 0115+63 with a pulse period of 3.6s in spring 2008 as observed with INTEGRAL and RXTE. By analyzing the lightcurves we derive an updated orbital- and pulse period ephemeris of the neutron star. We also study the pulse profile variations as a function of time and energy as well as the variability of the spectral parameters. We find clear evidence for at least three cyclotron line features. In agreement with previous observations of 4U 0115+63, we detect an anti-correlation between the luminosity and the fundamental cyclotron line energy.
Data-driven correction of function words in non-native English
2011-09-28

We extend the n-gram-based data-driven prediction approach (Elghafari, Meurers and Wunsch, 2010) to identify function word errors in non-native academic texts as part of the Helping Our Own (HOO) Shared Task. We focus on substitution errors for four categories: prepositions, determiners, conjunctions, and quantifiers. These error types make up 12 % of the errors annotated in the HOO training data. In our best submission in terms of the error detection score, we detected 67 % of preposition and determiner substitution errors, 40% of conjunction substitution errors, and 33% of quantifier substitution errors. For approximately half of the errors detected, we were also able to provide an appropriate correction. 1
Reproducibility of 3D 1H MR spectroscopic imaging of the prostate at 1.5T
2011-09-29

Abstract Purpose: To determine the reproducibility of 3D proton magnetic resonance spectroscopic imaging ( 1 H‐MRSI) of the human prostate in a multicenter setting at 1.5T. Materials and Methods: Fourteen subjects were measured twice with 3D point‐resolved spectroscopy (PRESS) 1 H‐MRSI using an endorectal coil. MRSI voxels were selected in the peripheral zone and combined central gland at the same location in the prostate in both measurements. Voxels with approved spectral quality were included to calculate Bland–Altman parameters for reproducibility from the choline plus creatine to citrate ratio (CC/C). The repeated spectroscopic data were also evaluated with a standardized clinical scoring system. Results: A total of 74 voxels were included for reproducibility analysis. The complete range of biologically interesting CC/C ratios was covered. The overall within‐voxel standard deviation (SD) of the CC/C ratio of the repeated measurements was 0.13. This value is equal to the between‐subject SD of noncancer prostate tissue. In &gt;90% of the voxels the standardized clinical score did not differ relevantly between the measurements. Conclusion: Repeated measurements of in vivo 3D 1 H‐MRSI of the complete prostate at 1.5T produce equal and quantitative results. The reproducibility of the technique is high enough to provide it as a reliable tool in assessing tumor presence in the prostate. J. Magn. Reson. Imaging 2012;35:166‐173. © 2011 Wiley Periodicals, Inc.
Intracellular monitoring of target protein production in Staphylococcus aureus by peptide tag‐induced reporter fluorescence
2011-09-29

Summary An intracellular approach for monitoring protein production in Staphylococcus aureus is described. mCherry, fused to the dodecapeptide Tip, was capable of inducing tetracycline repressor (TetR). Time‐ and concentration‐dependent production of mCherry could be correlated to TetR‐controlled GFPmut2 activity. This approach can potentially be extended to native S. aureus proteins.
Noble Gas Atoms as Electron Donors: Is the Stabilization of Strongly Electrophilic Borylnitrenes Feasible?
2011-09-29

Abstract The possible interaction between an electrophilic borylnitrene, CatBN (Cat = Catecholato), with the noble gas atoms Rg (Rg = Kr, Xe) is probed by computational chemistry techniques including hybrid density functional (B3LYP), second‐order Møller–Plesset perturbation (MP2), and coupled‐cluster theory with singles, doubles, and a perturbative estimate of triple excitations [CCSD(T)] in conjunction with aug‐cc‐pVDZ and cc‐pVTZ and the corresponding small‐core pseudopotential correlation consistent basis sets for krypton and xenon. In the triplet manifold the interaction between CatBN and Rg is of the van der Waals type with a small N–Rg bond dissociation energy. In contrast, the singlet CatBNRg( 1 A′) has a short N–Rg distance (Kr: 1.962 Å; Xe: 2.029 Å) in agreement with a single bond character. The N–Xe bond dissociation energy is 17 kcal · mol –1 at the highest level of theory, while the N–Kr bond is significantly weaker. Experiments in xenon or xenon doped argon matrices do not give any indication for the formation of the CatBNXe( 1 A′) compound in spite of the strong N–Xe interaction predicted by theory. The experimental observation is explained by the existence of a crossing of singlet and triplet potential energy surfaces. At the geometry of triplet CatBNRg (large N–Rg distance) the singlet state is higher in energy whereas at the geometry of singlet CatBNRg (short N–Rg distance) the triplet is higher. Fast intersystem crossing to the lower lying triplet surface in the presence of Xe is assumed to preclude the formation of CatBNXe( 1 A′).
Fast and Slow Spindles during the Sleep Slow Oscillation: Disparate Coalescence and Engagement in Memory Processing
2011-09-30

The finding that fast and slow spindles occur at different times of the SO cycle points to disparate generating mechanisms for the 2 kinds of spindles. The reported temporal relationships during SO sequences suggest that fast spindles, driven by the SO up-state feed back to enhance the likelihood of succeeding SOs together with slow spindles. By enforcing such SO-spindle cycles, particularly after prior learning, fast spindles possibly play a key role in sleep-dependent memory processing.
The Role of NiO Doping in Reducing the Impact of Humidity on the Performance of SnO2‐Based Gas Sensors: Synthesis Strategies, and Phenomenological and Spectroscopic Studies
2011-09-30

Abstract The humidity dependence of the gas‐sensing characteristics in SnO 2 ‐based sensors, one of the greatest obstacles in gas‐sensor applications, is reduced to a negligible level by NiO doping. In a dry atmosphere, undoped hierarchical SnO 2 nanostructures prepared by the self‐assembly of crystalline nanosheets show a high CO response and a rapid response speed. However, the gas response, response/recovery speeds, and resistance in air are deteriorated or changed significantly in a humid atmosphere. When hierarchical SnO 2 nanostructures are doped with 0.64–1.27 wt% NiO, all of the gas‐sensing characteristics remain similar, even after changing the atmosphere from a dry to wet one. According to diffuse‐reflectance Fourier transform IR measurements, it is found that the most of the water‐driven species are predominantly absorbed not by the SnO 2 but by the NiO, and thus the electrochemical interaction between the humidity and the SnO 2 sensor surface is totally blocked. NiO‐doped hierarchical SnO 2 sensors exhibit an exceptionally fast response speed (1.6 s), a fast recovery speed (2.8 s) and a superior gas response ( R a / R g = 2.8 at 50 ppm CO ( R a : resistance in air, R g : resistance in gas)) even in a 25% r.h. atmosphere. The doping of hierarchical SnO 2 nanostructures with NiO is a very‐promising approach to reduce the dependence of the gas‐sensing characteristics on humidity without sacrificing the high gas response, the ultrafast response and the ultrafast recovery.
Dendritic cell tumor in a salivary gland lymph node: a rare differential diagnosis of salivary gland neoplasms
2011-09-30

Dendritic cell tumors are extremely rare neoplasms arising from antigen-presenting cells of the immune system. We report a case of a 69-year-old man with an unremarkable medical history who presented with a 2-months history of a gradually enlarging painless, firm, mobile, 2 × 2-cm swelling at the caudal pole of the left parotid gland without systemic symptoms. Histologically, the tumor consisted of a spindle cell proliferation in an intraparotideal lymph node. Based on the histopathologic, immunohistochemical and electron microscopic findings, a dendritic cell tumor, not otherwise specified (NOS) in an intraparotideal lymph node was diagnosed.The patient underwent complete tumor resection, and is currently free of disease, 2 years after surgery. These extremely rare tumors must be distinguished from other more common tumors in the salivary glands. Awareness that dendritic cell tumors may occur in this localization, careful histologic evaluation and ancillary immunohistochemical and electron microscopical analyses should allow for recognition of this entity.
Ptychography: a powerful phase retrieval technique for biomedical imaging
2011-09-30

This paper discusses ptychography, a coherent diffraction imaging technique. Advantages of ptychography with respect conventional imaging techniques for cell visualisation are highlighted and demonstrated using unstained healthy and tumorous mouse cells as the object under investigation. A novel procedure to automatically refocus a possible slightly out of focus ptychographic data set will be discussed, by which an improved quantitative analysis and discrimination is enabled.
Neurofeedback and Basic Learning Theory: Implications for Research and Practice
2011-10-01

Brain activity assessed by electroencephalography (EEG) has been demonstrated to respond to conditioning techniques. The concept of modulating this activity has been called EEG biofeedback, more recently neurofeedback, and is based on operant learning principles. Technological advancements have significantly enhanced the ease and affordability of recording and analyzing brain activity. Thus, properly trained practitioners can implement these conditioning strategies in their practice. Recent research indicating evidenced-based efficacy has made this technique a more viable option for clinical intervention. The objective of this article is to highlight the learning principles that have provided the fundamentals of this neuromodulatory approach. In addition, it is recommended that future applications in clinical work, research, and development adhere to these principles.
Brain-Computer Interface in Stroke: A Review of Progress
2011-10-01

Brain-computer interface (BCI) technology has been used for rehabilitation after stroke and there are a number of reports involving stroke patients in BCI-feedback training. Most publications have demonstrated the efficacy of BCI technology in post-stroke rehabilitation using output devices such as Functional Electrical Stimulation, robot, and orthosis. The aim of this review is to focus on the progress of BCI-based rehabilitation strategies and to underline future challenges. A brief history of clinical BCI-approaches is presented focusing on stroke motor rehabilitation. A context for three approaches of a BCI-based motor rehabilitation program is outlined: the substitutive strategy, classical conditioning and operant conditioning. Furthermore, we include an overview of a pilot study concerning a new neuro-forcefeedback strategy. This pilot study involved healthy participants. Finally we address some challenges for future BCI-based rehabilitation.
A Brain-Computer Interface as Input Channel for a Standard Assistive Technology Software
2011-10-01

Recently brain-computer interface (BCI) control was integrated into the commercial assistive technology product QualiWORLD (QualiLife Inc., Paradiso-Lugano, CH). Usability of the first prototype was evaluated in terms of effectiveness (accuracy), efficiency (information transfer rate and subjective workload/NASA Task Load Index) and user satisfaction (Quebec User Evaluation of Satisfaction with assistive Technology, QUEST 2.0) by four end-users with severe disabilities. Three assistive technology experts evaluated the device from a third person perspective. The results revealed high performance levels in communication and internet tasks. Users and assistive technology experts were quite satisfied with the device. However, none could imagine using the device in daily life without improvements. Main obstacles were the EEG-cap and low speed.
ERD-Based Online Brain–Machine Interfaces (BMI) in the Context of Neurorehabilitation: Optimizing BMI Learning and Performance
2011-10-01

Event-related desynchronization (ERD) of sensori-motor rhythms (SMR) can be used for online brain-machine interface (BMI) control, but yields challenges related to the stability of ERD and feedback strategy to optimize BMI learning.Here, we compared two approaches to this challenge in 20 right-handed healthy subjects (HS, five sessions each, S1-S5) and four stroke patients (SP, 15 sessions each, S1-S15). ERD was recorded from a 275-sensor MEG system. During daily training,motor imagery-induced ERD led to visual and proprioceptive feedback delivered through an orthotic device attached to the subjects' hand and fingers. Group A trained with a heterogeneous reference value (RV) for ERD detection with binary feedback and Group B with a homogenous RV and graded feedback (10 HS and 2 SP in each group). HS in Group B showed better BMI performance than Group A (p < 0.001) and improved BMI control from S1 to S5 (p = 0.012) while Group A did not. In spite of the small n, SP in Group B showed a trend for a higher BMI performance (p = 0.06) and learning was significantly better (p < 0.05). Using a homogeneous RV and graded feedback led to improved modulation of ipsilesional activity resulting in superior BMI learning relative to use of a heterogeneous RV and binary feedback.
Disturbed Methylation at Multiple Imprinted Loci: an Increasing Observation in Imprinting Disorders
2011-10-01

The widely accepted association between aberrant methylation at specific imprinted loci and distinct imprinting disorders has recently been brought into question by the identification of methylation defects at multiple loci (multilocus methylation defect [MLMD]). Strikingly, in different imprinting disorders, the same MLMD patterns can be observed. The cause for this ambiguous epigenotype-phenotype correlation is currently unknown. Future strategies to solve this enigma have to include all levels of imprinting regulation, ranging from DNA methylation to chromatin organization, as any disturbance of the balanced interaction between the different players in imprinting regulation might cause disturbed expression of imprinted factors. The molecular analysis of MLMD will help in discovering these interactions and contribute to the understanding of genomic imprinting and its disturbances.
Attenuation correction in MR-BrainPET with segmented T1-weighted MR images of the patient's head &#x2014; A comparative study with CT
2011-10-01

Our method for attenuation correction (AC) in MR-BrainPET with segmented T1-weighted MR images of the pa-tient's head was applied to data from different MR-BrainPET scanners (Jülich, Tübingen) and compared to CT-based results.
Spatial and Temporal Data Path Remapping for Fault-Tolerant Coarse-Grained Reconfigurable Architectures
2011-10-01

In this contribution we apply a novel strategy for partial remapping to significantly enhance the reliability of coarse-grained reconfigurable architectures. If a component of the architecture is affected by a permanent error, it will be deactivated and the architecture is reconfigured to relinquish the concerned resource. This is achieved by spatially moving operations from defective to unused components. If no unused component is available, operations are additionally moved within time domain to free the required resources. In our experiments, we regard the failure of each single component in an array of processing elements. Depending on the resource usage of the application, between 70% and 100% of the defects can be tolerated. In average, the repair of one failure takes 36 seconds, and the clock frequency has to be reduced by just 0.8% to enable the execution of the changed application mapping.
Aspekt, Temporalität und Argumentstruktur bei attributiven Partizipien des Deutschen
2011-10-01

Abstract German has two participles, both of which occur in prenominal position. Traditionally, both participles are considered to be associated with particular semantic and syntactic features. The present participle ( malend ‘painting’) is subject-oriented; it has imperfective aspect and indicates simultaneity of the participle event and the matrix clause event. The past participle ( gemalt ‘painted’) is object-oriented; it has perfective aspect and indicates that the participle event precedes the event of the matrix clause. In this paper, we will first argue that aspect is indeed an inherent – hence invariant – feature of the participle morphology: The present participle always presents an event as ongoing, whereas the past participle presents it as completed. Secondly, we will show that participles – as non-finite verb forms – lack tense. Hence, their temporal properties vary according to lexical, syntactic and pragmatic factors. It will be demonstrated that the unmarked temporal readings of the participles are due to the maxim of relation. Finally, we will argue that the argument selection properties of both participles are grammatically determined; however, these properties can be altered if certain conditions are met.
iHAT: Interactive hierarchical aggregation table
2011-10-01

In the search for single-nucleotide polymorphisms (SNPs), genome wide association studies have become an important technique for the identification of associations between genotype and phenotype of a diverse set of sequence-based data. In this work, we present a methodology for the visual assessment of SNPs using interactive hierarchical aggregation techniques combined with methods known from traditional sequence browsers and cluster heatmaps. Our prototype tool iHAT supports the visualization of multiple sequence alignments, associated metadata, and hierarchical clusterings. Moreover, data-type dependent colormaps and aggregation strategies as well as different filtering options support the user in finding correlations between sequences and metadata. Similar to other visualizations such as parallel coordinates or heatmaps, iHAT is aimed at exploiting the human pattern-recognition ability for spotting patterns that might indicate correlation or anticorrelation. Together with its interactive features and a database backend for fast data retrieval, we consider iHAT as a prototype for a visual analytics system for genome-wide association studies.
Learning ankle-tilt and foot-placement control for flat-footed bipedal balancing and walking
2011-10-01

We learn a controller for a flat-footed bipedal robot to optimally respond to both (1) external disturbances caused by, for example, stepping on objects or being pushed, and (2) rapid acceleration, such as reversal of demanded walk direction. The reinforcement learning method employed learns an optimal policy by actuating the ankle joints to assert pressure at different points along the support foot, and to determine the next swing foot placement. The controller is learnt in simulation using an inverted pendulum model and the control policy transferred and tested on two small physical humanoid robots.