julilili42/papers huggingface dataset:
Probing the Recognition of Post-Translational Modifications by Combining Sortase-Mediated Ligation and Phage-Assisted Selection
2013-05-30

Reversible post-translational modifications (PTMs) are key regulators of protein function and modulate a multitude of protein-protein interactions in signal transduction networks. Here, we describe a strategy for determining the modification preferences of PTM-binding proteins with only minimal protein amounts that can be obtained by immunoprecipitation from mammalian cell lysates. This method bases on the combination of sortase-mediated ligation and phage-assisted selection strategies. This method can be used to analyze the type of modification that mediates the interaction as well as the influence of the amino acids flanking the modification sites. We have demonstrated the applicability of this method by probing the interaction of phosphorylated tyrosine and serine residues with their respective binding domains.
Benzene Dynamics and Biodegradation in Alluvial Aquifers Affected by River Fluctuations
2013-05-30

Abstract The spatial distribution and temporal dynamics of a benzene plume in an alluvial aquifer strongly affected by river fluctuations was studied. Benzene concentrations, aquifer geochemistry datasets, past river morphology, and benzene degradation rates estimated in situ using stable carbon isotope enrichment were analyzed in concert with aquifer heterogeneity and river fluctuations. Geochemistry data demonstrated that benzene biodegradation was on‐going under sulfate reducing conditions. Long‐term monitoring of hydraulic heads and characterization of the alluvial aquifer formed the basis of a detailed modeled image of aquifer heterogeneity. Hydraulic conductivity was found to strongly correlate with benzene degradation, indicating that low hydraulic conductivity areas are capable of sustaining benzene anaerobic biodegradation provided the electron acceptor ( SO 4 2– ) does not become rate limiting. Modeling results demonstrated that the groundwater flux direction is reversed on annual basis when the river level rises up to 2 m, thereby forcing the infiltration of oxygenated surface water into the aquifer. The mobilization state of metal trace elements such as Zn, Cd, and As present in the aquifer predominantly depended on the strong potential gradient within the plume. However, infiltration of oxygenated water was found to trigger a change from strongly reducing to oxic conditions near the river, causing mobilization of previously immobile metal species and vice versa. MNA appears to be an appropriate remediation strategy in this type of dynamic environment provided that aquifer characterization and targeted monitoring of redox conditions are adequate and electron acceptors remain available until concentrations of toxic compounds reduce to acceptable levels.
Phosphoglycerate kinase 1 as a promoter of metastasis in colon cancer
2013-05-31

Oxidative stress due to intratumoral hypoxia in solid cancer has been shown to be associated with increased mortality. Phosphoglycerate kinase 1 (PGK1) is an enzyme of the glycolytic pathway, which is regulated by hypoxia-inducible factor-1α (HIF-1α) and has been described for its role in tumor progression and metastasis in several malignancies. We investigated whether the expression of PGK1 varies between metastatic and non-metastatic colon cancer. We compared PGK1 expression in colon cancer patients either with or without metastasis via polymerase chain reaction (PCR) and immunohistochemistry. Microarray analysis was performed to test altered gene expression after PGK1 silencing, using isolates from HCT116 cell lines. PCR results showed an increased expression of PGK1 in colon cancer tissue from metastatic patients in comparison to patients with no metastasis (fold change 2.6, p<0.001). Immunohistochemical staining of PGK1 showed stronger staining in metastatic tissue in comparison to non-metastatic cancer tissue according to a semi-quantitative evaluation. Microarray and subsequent pathway analysis provided 4 genes of interest (CYR61, FOS, JUN and EGR1) used for pathway proposal. The results indicate that increased expression of PGK1 in colon cancer tissue is associated with metastasis. Furthermore, we propose several genes induced by PGK1 that could account for cell migration, mainly EGR1 and CYR61 together with the transcription factors FOS and JUN.
Differential Effects on Fast and Slow Spindle Activity, and the Sleep Slow Oscillation in Humans with Carbamazepine and Flunarizine to Antagonize Voltage-Dependent Na+ and Ca2+ Channel Activity
2013-05-31

Our findings indicate a differential pharmacologic response of the two types of sleep spindles and underscore a close linkage of the generating mechanisms underlying the sleep slow oscillation and the slow frontal sleep spindles for the signal transmission processes manipulated in the current study.
Altered Serum IgG Levels to α-Synuclein in Dementia with Lewy Bodies and Alzheimer’s Disease
2013-05-31

Natural self-reactive antibodies in the peripheral blood may play a considerable role in the control of potentially toxic proteins that may otherwise accumulate in the aging brain. The significance of serum antibodies reactive against α-synuclein is not well known. We explored serum IgG levels to monomeric α-synuclein in dementia with Lewy bodies (DLB) and Alzheimer's disease (AD) with a novel and validated highly sensitive ELISA assay. Antibody levels revealed stark differences in patients compared to healthy subjects and were dependent on diagnosis, disease duration and age. Anti-α-synuclein IgG levels were increased in both patient groups, but in early DLB to a much greater extent than in AD. Increased antibody levels were most evident in younger patients, while with advanced age relatively low levels were observed, similar to healthy individuals, exhibiting stable antibody levels independent of age. Our data show the presence of differentially altered IgG levels against α-synuclein in DLB and AD, which may relate to a disturbed α-synuclein homeostasis triggered by the disease process. These observations may foster the development of novel, possibly preclinical biomarkers and immunotherapeutic strategies that target α-synuclein in neurodegenerative disease.
When luminance increment thresholds depend on apparent lightness
2013-05-31

A fundamental question in visual perception research is whether the sensitivity to stimulus differences is limited by the sensory representation of the external stimulus, that is, the proximal stimulus, or by its perceptual representation, i.e., stimulus appearance. In the domain of lightness perception, the question translates into whether discrimination thresholds depend on the local luminance in the retinal image or on the apparent lightness of the corresponding image region. The majority of findings seem to indicate that sensitivity is limited by the sensory stimulus representation, which would imply different mechanisms for stimulus discrimination and appearance. We think this conclusion needs to be qualified. We report data suggesting that the relationship between discrimination and appearance judgments depends on how exactly they are being measured. We propose a theoretical account that provides a common mechanism for appearance and sensitivity. An interesting corollary of this model is that it also accounts for the perceptual phenomenon of assimilation.
Identification of C/EBPβ Target Genes in ALK+ Anaplastic Large Cell Lymphoma (ALCL) by Gene Expression Profiling and Chromatin Immunoprecipitation
2013-05-31

C/EBPβ (CCAAT enhancer binding protein) is a transcription factor that plays a crucial role in survival and transformation of ALK+ anaplastic large cell lymphoma (ALCL). The aim of this study was to identify the downstream targets of C/EBPβ responsible for ALK-mediated oncogenesis. C/EBPβ was knocked down in ALK+ ALCL cell lines with a C/EBPβ-shRNA, followed by gene expression profiling (GEP). GEP analysis revealed a reproducible signature of genes that were significantly regulated by C/EBPβ. Classification into biological categories revealed overrepresentation of genes involved in the immune response, apoptosis and cell proliferation. Transcriptional regulation by C/EBPβ was found in 6 of 11 (BCL2A1, G0S2, TRIB1, S100A9, DDX21 and DDIT4) genes investigated by chromatin immunoprecipitation. We demonstrated that BCL2A1, G0S2 and DDX21 play a crucial role in survival and proliferation of ALK+ ALCL cells. DDX21, a gene involved in rRNA biogenesis, was found differentially overexpressed in primary ALK+ ALCL cases. All three candidate genes were validated in primary ALCL cases by either immunohistochemistry or RT-qPCR. In conclusion, we identified and validated several key C/EBPβ-regulated genes with major impact on survival and cell growth in ALK+ ALCL, supporting the central role of C/EBPβ in ALK-mediated oncogenesis.
Effect of cephalograms on decisions for early orthodontic treatment
2013-05-31

ABSTRACT Objective: To assess the extent to which cephalograms modify therapeutic decisions related to early orthodontic treatment. Materials and Methods: Diagnostic records of six patients requiring early treatment were digitized for this purpose. A total of 234 orthodontists were then asked to select therapeutic measures on a treatment-planning sheet at two different times (T1 and T2). Three groups of orthodontists were formed and were provided with case-specific records either including or not including cephalograms and the appended tracing values. Forty-seven orthodontists completed all phases of the questions. Results: Statistical analysis revealed only two statistically significant differences between the first (T1) and second (T2) treatment plans, both concerning options of transverse treatment. None of the other results showed any significant changes from T1 to T2 treatment planning. Conclusion: It follows that cephalograms did not influence therapeutic decisions for early orthodontic treatment and should not be routinely used in very young patients.
SPATIAL THINKING FOR INNOVATION: THE LEONARDO-MAXWELL-EINSTEIN METHOD, REVIVED
2013-05-31

Free-running spatial intuition is like analog computation: it is indispensable for scientific progress despite its intrinsic inaccuracy. Do return to the first beginnings of a gold vein, was Maxwell’s advice. Returning to the gold vein of Einstein’s “happiest thought” leads to three other shiny results. Many accepted findings crumble as the barefoot method shows its mettle. A new cosmology is implicit and so is a new source of energy.
The Receptor-Like Protein ReMAX of Arabidopsis Detects the Microbe-Associated Molecular Pattern eMax from Xanthomonas
2013-06-01

Abstract As part of their immune system, plants have pattern recognition receptors (PRRs) that can detect a broad range of microbe-associated molecular patterns (MAMPs). Here, we identified a PRR of Arabidopsis thaliana with specificity for the bacterial MAMP eMax from xanthomonads. Response to eMax seems to be restricted to the Brassicaceae family and also varied among different accessions of Arabidopsis. In crosses between sensitive accessions and the insensitive accession Shakhdara, eMax perception mapped to RECEPTOR-LIKE PROTEIN1 (RLP1). Functional complementation of rlp1 mutants required gene constructs that code for a longer version of RLP1 that we termed ReMAX (for receptor of eMax). ReMAX/RLP1 is a typical RLP with structural similarity to the tomato (Solanum lycopersicum) RLP Eix2, which detects fungal xylanase as a MAMP. Attempts to demonstrate receptor function by interfamily transfer of ReMAX to Nicotiana benthamiana were successful after using hybrid receptors with the C-terminal part of ReMAX replaced by that of Eix2. These results show that ReMAX determines specificity for eMax. They also demonstrate hybrid receptor technology as a promising tool to overcome problems that impede interfamily transfer of PRRs to enhance pathogen detection in crop plants.
The Deubiquitinating Enzyme AMSH1 and the ESCRT-III Subunit VPS2.1 Are Required for Autophagic Degradation inArabidopsis
2013-06-01

Abstract In eukaryotes, posttranslational modification by ubiquitin regulates the activity and stability of many proteins and thus influences a variety of developmental processes as well as environmental responses. Ubiquitination also plays a critical role in intracellular trafficking by serving as a signal for endocytosis. We have previously shown that the Arabidopsis thaliana ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM3 (AMSH3) is a deubiquitinating enzyme (DUB) that interacts with ENDOSOMAL COMPLEX REQUIRED FOR TRANSPORT-III (ESCRT-III) and is essential for intracellular transport and vacuole biogenesis. However, physiological functions of AMSH3 in the context of its ESCRT-III interaction are not well understood due to the severe seedling lethal phenotype of its null mutant. In this article, we show that Arabidopsis AMSH1, an AMSH3-related DUB, interacts with the ESCRT-III subunit VACUOLAR PROTEIN SORTING2.1 (VPS2.1) and that impairment of both AMSH1 and VPS2.1 causes early senescence and hypersensitivity to artificial carbon starvation in the dark similar to previously reported autophagy mutants. Consistent with this, both mutants accumulate autophagosome markers and accumulate less autophagic bodies in the vacuole. Taken together, our results demonstrate that AMSH1 and the ESCRT-III-subunit VPS2.1 are important for autophagic degradation and autophagy-mediated physiological processes.
MTV1 and MTV4 Encode Plant-Specific ENTH and ARF GAP Proteins That Mediate Clathrin-Dependent Trafficking of Vacuolar Cargo from the Trans-Golgi Network
2013-06-01

Many soluble proteins transit through the trans-Golgi network (TGN) and the prevacuolar compartment (PVC) en route to the vacuole, but our mechanistic understanding of this vectorial trafficking step in plants is limited. In particular, it is unknown whether clathrin-coated vesicles (CCVs) participate in this transport step. Through a screen for modified transport to the vacuole (mtv) mutants that secrete the vacuolar protein VAC2, we identified MTV1, which encodes an epsin N-terminal homology protein, and MTV4, which encodes the ADP ribosylation factor GTPase-activating protein nevershed/AGD5. MTV1 and NEV/AGD5 have overlapping expression patterns and interact genetically to transport vacuolar cargo and promote plant growth, but they have no apparent roles in protein secretion or endocytosis. MTV1 and NEV/AGD5 colocalize with clathrin at the TGN and are incorporated into CCVs. Importantly, mtv1 nev/agd5 double mutants show altered subcellular distribution of CCV cargo exported from the TGN. Moreover, MTV1 binds clathrin in vitro, and NEV/AGD5 associates in vivo with clathrin, directly linking these proteins to CCV formation. These results indicate that MTV1 and NEV/AGD5 are key effectors for CCV-mediated trafficking of vacuolar proteins from the TGN to the PVC in plants.
HLA-DR15-derived self-peptides are involved in increased autologous T cell proliferation in multiple sclerosis
2013-06-01

The HLA-DR15 haplotype confers the largest part of the genetic risk to develop multiple sclerosis, a prototypic CD4+ T cell-mediated autoimmune disease. The mechanisms how certain HLA-class II molecules functionally contribute to autoimmune diseases are still poorly understood, but probably involve shaping an autoimmune-prone T cell repertoire during central tolerance in the thymus and subsequently maintaining or even expanding it in the peripheral immune system. Self-peptides that are presented by disease-associated HLA-class II molecules most likely play important roles during both processes. Here, we examined the functional involvement of the HLA-DR15 haplotype in autologous proliferation in multiple sclerosis and the contribution of HLA-DR15 haplotype-derived self-peptides in an in vitro system. We observe increased autologous T cell proliferation in patients with multiple sclerosis in relation to the multiple sclerosis risk-associated HLA-DR15 haplotype. Assuming that the spectrum of self-peptides that is presented by the two HLA-DR15 allelic products is important for sustaining autologous proliferation we performed peptide elution and identification experiments from the multiple sclerosis-associated DR15 molecules and a systematic analysis of a DR15 haplotype-derived self-peptide library. We identify HLA-derived self-peptides as potential mediators of altered autologous proliferation. Our data provide novel insights about perturbed T cell repertoire dynamics and the functional involvement of the major genetic risk factor, the HLA-DR15 haplotype, in multiple sclerosis.
Wound Fluid in Diabetic Foot Ulceration
2013-06-01

Valid and reproducible sampling techniques as well as processing protocols are required for the assessment of biomarkers and mediators contained in wound exudate. Moreover, the ideal technique should be easy to use even in daily clinical routine. This is challenging since wound fluid represents an inhomogeneous mixture of different exogenous and endogenous sources. Analyzing wound fluid, however, may facilitate clinical decision making. Many techniques for obtaining wound fluid have been described. There is very little validation data, and the array of different techniques appears confusing. Structuring and new standards are needed to avoid wound fluid sampling yielding an “undefined soup.” A lot of wound fluid parameters have been analyzed, although none of them have made its way into clinical practice. Nevertheless, basic principles of wound healing have been established from wound fluid analysis. With adequate techniques suitable for daily practice, basic research might foster our clinical understanding of wound healing with implications for new therapies. So far, research has mainly concentrated on analyzing available sample material with respect to either a wide variety of analytes or comparing acute with chronic wound exudate. Clinical endpoints such as healing or wound infection as well as longitudinal data may indeed be more valuable for clinical practice, enabling the discovery of meaningful biomarkers using a suitable technique.
CoMeT: Integrating different levels of linguistic modeling for meaning assessment
2013-06-01

This paper describes the CoMeT system, our contribution to the SemEval 2013 Task 7 challenge, focusing on the task of automatically assessing student answers to factual questions. CoMeT is based on a meta-classifier that uses the outputs of the sub-systems we developed: CoMiC, CoSeC, and three shallower bag approaches. We sketch the functionality of all sub-systems and evaluate their performance against the official test set of the challenge. CoMeT obtained the best result (73.1 % accuracy) for the 3-way unseen answers in Beetle among all challenge participants. We also discuss possible improvements and directions for future research.
Advanced driver assistance system for optimized recuperation under consideration of parameter uncertainties
2013-06-01

This document proposes a new strategy for decelerating a battery electric vehicle from an initial velocity to a final velocity with optimized recuperation of kinetic excess energy. Thereby, we demonstrate a possibility to increase the efficiency - and hence range - without altering the powertrain. The algorithm is implemented in an advanced driver assistance system to guide the driver and - given he accepts the hints - leads to an energy-optimized deceleration trajectory. A situation-adaptive online estimation of influencing parameters, which are not measurable during the drive, is presented. The knowledge of these parameters allows an accurate operation of the proposed functionality. Simulations show an increased energy regeneration of up to 34% for an exemplary vehicle and typical road segments.
Combining Shallow and Linguistically Motivated Features in Native Language Identification
2013-06-01

We explore a range of features and ensembles for the task of Native Language Identification as part of the NLI Shared Task (Tetreault et al., 2013). Starting with recurring word-based n-grams (Bykh and Meurers, 2012), we tested different linguistic abstractions such as partof-speech, dependencies, and syntactic trees as features for NLI. We also experimented with features encoding morphological properties, the nature of the realizations of particular lemmas, and several measures of complexity developed for proficiency and readability classification (Vajjala and Meurers, 2012). Employing an ensemble classifier incorporating all of our features we achieved an accuracy of 82.2 % (rank 5) in the closed task and 83.5 % (rank 1) in the open-2 task. In the open-1 task, the word-based recurring n-grams outperformed the ensemble, yielding 38.5 % (rank 2). Overall, across all three tasks, our best accuracy of 83.5 % for the standard TOEFL11 test set came in second place. 1
Intuitive visualization of vehicle distance, velocity and risk potential in rear-view camera applications
2013-06-01

Many serious collisions on highways happen while changing lanes. One of the main causes for these accidents is the driver's incorrect assessment of the current rear traffic situation. To support the driver, we propose a framework to intuitively visualize distance, speed and risk potential of approaching vehicles in a rear-view camera application. The proposed visualization techniques are based on color coding, artificial motion blur and depth-of-field rendering, which are motivated by sensory effects of the human eye and interpreted intuitively by the human visual system. The impact on the human assessment of the moving speed of an object rendered with artificial motion enhancement is evaluated in a user study. The required distance and motion estimation of the vehicles are extracted out of monocular video images, by combining lane recognition, vehicle detection and segmentation machine vision algorithms.
The 1 : 1 Adduct of 1,3-Diisopropyl-4,5-dimethyl-2,3-dihydroimidazol-2- ylidene and Nitrous Oxide
2013-06-01

Abstract The nucleophilic carbene 1,3-diisopropyl-4,5-dimethyl-2,3-dihydroimidazol-2-ylidene (7) captures nitrous oxide under formation of both syn- (8) and anti-1,3-diisopropyl-4,5-imidazolium diazotate (9). The syn-isomer is the thermodynamically more stable form. As shown by X-ray crystallography, the two isomers are statistically distributed in the crystalline state
Relevance estimation of cooperative awareness messages in VANETs
2013-06-01

In Vehicular Ad-Hoc Networks (VANETs) a vehicle receives multiple Cooperative Awareness Messages (CAMs) from neighboring nodes which inform it about their status. As the rate of received CAMs may be high, their processing may be a challenge especially in series vehicles because their resources are constrained for economic reasons. In this work, we assume that only a fraction of the received CAMs can be handled. We suggest that most relevant messages should be preferably processed. This requires a simple function that calculates with little effort an estimate of the relevance of CAMs based on information such as location and speed of the sender that is contained in any CAM. We propose a function that - roughly speaking - calculates the relevance of a CAM for its receiver. That value increases with the potential of collision with the sender of the CAM. The function has only a few parameters. Another contribution of the paper is the receiver-centric analysis of the chosen relevance function. It illustrates the effect of the function's parameters on the relevance of CAMs originating from vehicles in different positions and movements relative to the receiver.