Miracle-dz/UniFAR-FTUs huggingface dataset:
To label or not to label: Applications of quantitative proteomics in neuroscience research

Proteomics has provided researchers with a sophisticated toolbox of labeling‐based and label‐free quantitative methods. These are now being applied in neuroscience research where they have already contributed to the elucidation of fundamental mechanisms and the discovery of candidate biomarkers. In this review, we evaluate and compare labeling‐based and label‐free quantitative proteomic techniques for applications in neuroscience research. We discuss the considerations required for the analysis of brain and central nervous system specimens, the experimental design of quantitative proteomic workflows as well as the feasibility, advantages, and disadvantages of the available techniques for neuroscience‐oriented questions. Furthermore, we assess the use of labeled standards as internal controls for comparative studies in humans and review applications of labeling‐based and label‐free mass spectrometry approaches in relevant model organisms and human subjects. Providing a comprehensive guide of feasible and meaningful quantitative proteomic methodologies for neuroscience research is crucial not only for overcoming current limitations but also for gaining useful insights into brain function and translating proteomics from bench to bedside.
Considerations on a Cost Model for High-Field Dipole Arc Magnets for FCC

In the frame of the European circular collider, a conceptual design study for a post-Large Hadron Collider research infrastructure based on an energy-frontier 100 TeV circular hadron collider, a cost model for the dipole arc magnets is being developed. This paper presents an analysis of the different cost drivers for these magnets, in particular for what concerns magnet aperture, the nature and extent of grading, margin and operating temperature.
On social semantics in information retrieval

In this thesis we analyze the performance of social semantics in textual information retrieval. By means of collaboratively constructed knowledge derived from web-based social networks, inducing both common-sense and domain-specific knowledge as constructed by a multitude of users, we will establish an improvement in performance of selected tasks within different areas of information retrieval. This work connects the concepts and the methods of social networks and the semantic web to support the analysis of a social semantic web that combines human intelligence with machine learning and natural language processing. In this context, social networks, as instances of the social web, are capable in delivering social network data and document collections on a tremendous scale, inducing thematic dynamics that cannot be achieved by traditional expert resources. The question of an automatic conversion, annotation and processing, however, is central to the debate of the benefits of the social semantic web. Which kind of technologies and methods are available, adequate and contribute to the processing of this rapidly rising flood of information and at the same time being capable of using the wealth of information in this large, but more importantly decentralized internet. The present work researches the performance of social semantic-induced categorization by means of different document models. We will shed light on the question, to which level social networks and social ontologies contribute to selected areas within the information retrieval area, such as automatically determining term and text associations, identifying topics, text and web genre categorization, and also the domain of sentiment analysis. We will show in extensive evaluations, comparing the classical apparatus of text categorization  Vector Space Model, Latent Semantic Analysis and Support Vector Maschine  that significant improvements can be obtained by considering the collaborative knowledge derived from the social web.
Self-perceived stress and the risk of peptic ulcer disease. A longitudinal study of US adults.

BACKGROUND Although many physicians and laypersons believe that stress plays a role in the occurrence of peptic ulcer disease, the importance of stress in the pathogenesis of peptic ulcers remains controversial. METHODS To investigate the relationship between perceived stress and peptic ulcer disease we used data from the National Health and Nutrition Examination Survey Epidemiologic Follow-up Study--a nationally representative cohort study of US adults. This analysis included 4511 persons who had not previously been diagnosed with peptic ulcer disease. RESULTS At baseline, 68% of the cohort perceived themselves as stressed. During 13 years of follow-up, 208 persons developed ulcers; the cumulative incidence of ulcers was 7.2% for persons who were stressed and 4.0% for persons who were not. After we adjusted for age, sex, education, smoking status, and regular aspirin use, persons who perceived themselves as stressed were 1.8 times more likely to develop ulcers than those who did not (95% confidence interval, 1.3 to 2.5). We also found a graded relationship between the perceived amount of stress and the incidence of peptic ulcers; relative to nonstressed persons, the relative risk of developing an ulcer was 1.4, 1.9, 2.3, 2.4, and 2.9 at five increasing levels of stress. CONCLUSIONS These findings suggest that persons who perceive their lives as stressful may be at increased risk for the development of peptic ulcer disease.
A Modified Aeration Process for Promoting Nutrient Removal Using Water Hyacinth to Treat Sewage

In an attempt to upgrade some conventional aeration processes, a laboratory-scale system for promoting nitrogen and phosphorus removal was set up and studied through a series of experiments, in which water hyacinth was planted on the surface of the mixed liquor in aeration tanks. The main purpose of this study was to evaluate the effects of aeration, organic load (chemical oxygen demand) and residence time on the nutrient removal efficiency of a water hyacinth based system for the purification of raw and settled sewage wastewaters. The experiments indicated that the aeration with airflow intensity of 4 l min−1 can provide enough oxygen supply but no significant disturbance of water hyacinth growth. The water hyacinth grew better in a moderate organic strength of chemical oxygen demand (COD) = 18 - 80 mg l−1. In this study, it was observed that chlorosis of water hyacinth occurred under conditions of nutrient deficiency, and possibility that it was caused by iron (Fe) deficiency was analyzed. The increase of solids retention time (SRT) from 5 to 20 days was of benefit for organic and nutrient removals. The system demonstrated a high performance of nitrogen and phosphorus removals up to 86 % and 80 % respectively from the raw sewage, which are far better than that in floating aquatic macrophyte-based treatment systems (FAMS) and wetland systems. Dissimilation via nitrification and denitrification was considered as a major pathway of N removal, and assimilation via plant uptake was thought to be responsible for more than half of the P removal in the designed system.
Multi-index hashing for information retrieval

We describe a technique for building hash indices for a large dictionary of strings. This technique permits robust retrieval of strings from the dictionary even when the query pattern has a significant number of errors. This technique is closely related to the classical Turan problem for hypergraphs. We propose a general method of multi-index construction by generalizing certain Turan hypergraphs. We also develop an accompanying theory for analyzing such hashing schemes. The resulting algorithms have been implemented and can be applied to a wide variety of recognition and retrieval problems. <<ETX>>
Stimulating human accommodation without changes in focus

Purpose: Inspired by the finding in chickens that preferential stimulation of the ON retinal system suppresses myopia induced by negative spectacle lens wear and that stimulation of the OFF system suppresses the hyperopia induced by positive lens wear, we sought to determine whether stimulation of the ON‐OFF retinal systems could drive directional accommodation responses in humans. If emmetropisation and accommodation use similar image processing algorithms, more accommodation would be expected with OFF stimulation.
Scaling up all pairs similarity search pdf

Given a large collection of sparse vector data in a high dimensional space, we investigate the problem of finding all pairs of vectors whose similarity.ABSTRACT. Given a large collection of sparse vector data in a high dimensional space, we investigate the problem of finding all pairs of vectors whose similarity. Scaling up all pairs similarity search, Published by ACM. The problem of finding all pairs of vectors whose similarity score as determined by a function such as cosine distance is above a given threshold.This problem is also known as the similarity join. Scaling Up All-Pairs Similarity Search. Download from: http:www.bayardo. orgpswww2007.pdf. All pairs similarity search is used in many web search and.
A Historical Ecology of the Limpopo and Kruger National Parks and Lower Limpopo Valley

The paper uses new palaeo-ecological data and a selective review of archaeological and written sources to show how social and natural history over the last 1200 years have interacted to form the present day landscape of Limpopo National Park and Northern Kruger National Park. The long-term mosaic of different communities in this landscape, hunter and gatherers, pastoralists, farmers and traders has, over time, contributed to shape and reshape a heterogeneous landscape. While some features in this landscape, such as water scarcity, have remained stable over time, there have also been major transformations in both the physical landscape and social life. The natural mosaics have been utilised and enhanced over time and the combination of natural and cultural mosaics are reflected in the landscape through archaeological sites, the pollen record and in the present day landscape.
The Timing of Using Patent Information by University Scientists: A Lesson from the Biotechnology Sector in Taiwan

This paper investigates the timing of employment of patent information for conducting university patenting, as the latter is related to the success of university entrepreneurship. Particularly focus is put on the role of their working experiences related to university entrepreneurship. By surveying 111 university scientists working in biotechnology sectors in Taiwan, it showed that the timing of using patent information for university patenting is correlated with the source of patent information and working experience.
Online MDL-Markov analysis of a discussion process in CSCL

An online visualization system of a discussion process in computer-supported collaborative learning (CSCL) has been developed to assist learners by enabling them to monitor the actual states of their discussion and allowing them to improve their learning community. The unique features of this system are 1) the learners have to select the most suitable category that represents his/her message content from the choices presented in the developed BBS and 2) the proposed system estimates the structure of the Markov from the stored categories' data sequences and visualizes the structure online. We demonstrate the effectiveness of this system using actual data and provide some evaluations. The results show that the proposed system motivates the learners and improves their methods of discussion
Plasma membrane‐dependent activation of gelatinase A in human vascular endothelial cells

The initiation of the angiogenic process requires a locally confined and time‐limited proteolysis of the basement membrane (BM) components at the site of new vessel sprout. Gelatinase A, a member of the matrix metalloproteinase family, degrades BM type IV collagen and is involved in the BM breakdown by migrating tumor cells and endothelial cells (EC). Gelatinase A is synthesized as latent proenzyme and must be activated in order to express its proteolytic activity. A plasma membrane‐dependent mechanism of activation has been described for several tumor and transformed cell lines. In the present study, we show that latent (72 kD) and mature (62‐59 kD) froms of gelatinase A are present in EC membrane fraction from Triton X‐114 extract while only latent form is found in the cytosolic fraction. The incubation of EC membrane fraction with exogenous latent gelatinase A resulted in a significant activation giving rise to 62–59 kD mature forms. 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA), a strong potentiator of angiogenesis in vitro and in vivo, increases the amount of both latent and activated forms of gelatinase A in EC membrane fraction as well as the ability of this latter fraction to activate exogenous latent gelatinase A. We show that the mRNA transcript coding for the membrane‐integrated MMP, the MT‐MMP, previously described as a potential gelatinase A activator in invasive tumor cells is also expressed in vascular EC and is regulated through a TPA sensitive process. This enzyme may be responsible for membrane‐dependent gelatinase A activation in normal vascular EC and may therefore be a determinant in the control of BM proteolysis during angiogenesis. © 1995 Wiley‐Liss Inc.
Role of network analysis in comparative ecosystem ecology of estuaries

Assessments of trophic structure through ecological network analysis (ENA) have been done in a wide variety of estuarine and coastal environments. For example, some have used it to compare trophic structures within ecosystems focusing on temporal conditions (Baird and Ulanowicz 1989; Baird et al. 1998) and among ecosystems focusing on spatial conditions (e.g. Baird and Ulanowicz 1993; Christensen 1995). These comparisons have used carbon or energy as the currency with which to trace the interactions of the food webs, although other key elements such as nitrogen and phosphorus have also been used in ENA (Baird et al. 1995; Ulanowicz and Baird 1999; Christian and Thomas 2003). One of the primary features of ENA is that the interactions are weighted. That is, they represent rates of flow of energy or matter and not simply their existence. Other kinds of comparisons have been attempted less frequently. Effects of currency used to track trophic dynamics has received little attention (Christian et al. 1996; Ulanowicz and Baird 1999), and comparisons of ENA with other modeling approaches are quite rare (Kremer 1989; Lin et al. 2001). There is a need to expand the applications of network analysis (NA) to address specific questions in food-web ecology, and to use it more frequently to explain and resolve specific management issues. The NA approach must be combined with other existing methods of identifying ecosystem performance to validate and improve our inferences on trophic structure and dynamics. Estuaries are excellent ecosystems to test the veracity of the inferences of ENA for three reasons. First, more NAs have been conducted on estuaries than on any other kind of ecosystem. Second, estuarine environments are often stressed by natural and anthropogenic forcing functions. This affords opportunities for evaluating controls on trophic structure. Third, sampling of estuaries has often been extensive, such that reasonable food webs can be constructed under different conditions of stress. Finally, other modeling approaches have been used in numerous estuarine ecosystems. Results of these alternate modeling approaches can be compared to those of ENA to test the coherence of inferences across perspectives of ecosystem structure and function. These conditions set the stage for an evaluation of the status of ENA as a tool for comparative ecosystem ecology. Comparative ecosystem ecology makes valuable contributions to both basic ecology and its application to environmental management. Given the critical position of estuaries as conduits for materials to the oceans and often as sites of intense human activities in close proximity to important natural resources, ENA has been used frequently for the assessment of the effects of environmental conditions within estuaries related to management. Early in the use of ENA in ecology, Finn and Leschine (1980) examined the link between fertilization of saltmarsh grasses and shellfish production.
Synthesis and Application of Peptide Dendrimers As Protein Mimetics

The use of peptides to mimic a portion of a protein structure is a challenging and powerful tool in the discovery of new drugs. In native proteins, discontinuous bioactive peptide surfaces are held together in a particular conformation by the structural rigidity of the protein. Approaches to mimicking a structural surface center on bringing the potential peptide sequences together by assembling the peptide chains on a template. These templates can be flexible dendrimeric or cyclic peptides as well as more rigid organic molecules. The Multiple Antigen Peptide (MAP) system represents a novel approach to preparing peptide immunogens. The MAP consists of an inner core matrix built up of a large layer of Lys residues and a surface of peptide chains attached to the core matrix. Because of its dendrimeric structure, MAP can be very useful as a template for assembling potential peptide surfaces. A variation of this procedure, the cyclic Multiple Antigen Peptide (cMAP) approach, is also presented here. Having branched multiple closed‐chain architectures, the cMAP system is often a superior approach for protein mimetics because the multiple constrained peptides can mimic bioactive conformations. Whether to select this approach over MAP depends on the properties of the peptides, but usually if the peptides are too small to adopt a stable conformation on their own, incorporation of a cyclic structure may be necessary. MAPs have been applied to areas of study such as inhibitors, artificial proteins, affinity purifications, and intracellular transport.
Classification and prediction in pharmacogenetics--context, construction and validation.

Ulrich Mansmann† & Bernhard R Winkelmann †Author for correspondence 1IMBI, University of Heidelberg, INF 305, 69120 Heidelberg, Germany Tel. : +49 6221 564128; Fax: +49 6221 564195; E-mail: mansmann@ imbi.uni-heidelberg.de 2Cooperation Unit Pharmacogenomics/Applied Genomics, Department of Internal Medicine VI (Clinical Pharmacology and Pharmacoepidemiology) and Coordination Centre for Clinical Trials, University of Heidelberg, Germany ‘Above all the aim of developing a classification rule is the prediction of outcome for patients, both optimizing future benefit and minimizing future adverse events. ’
In vitro characterization of the Mig1 repressor from Saccharomyces cerevisiae reveals evidence for monomeric and higher molecular weight forms

The Mig1 DNA‐binding protein of Saccharomyces cerevisiae was expressed and purified from yeast and the physical properties were characterized by several methods, including gel filtration, sucrose gradient sedimentation and native gel electrophoresis. Purified Mig1 exists as a monomer with a Stokes' radius of 48 Å and a sedimentation coefficient of 3.55 S. Mig1 has an elongated shape with a frictional coefficient of 1.83. The Kd of purified Mig1 for the SUC2 A site is 2.8 nM and for SUC2 B site 25.8 nM; these values were similar for Mig1 purified from repressed and derepressed cells. Full‐length Mig1 expressed in yeast binds more tightly to SUC2 B than bacterially expressed GST–Mig1. Sucrose gradient sedimentation resolved a larger molecular weight form of Mig1 in whole‐cell extracts that was not seen in purified samples and may represent a complex with another protein. This complex is found within the nucleus and is seen only in repressed cells. Mig1 exists in multiple phosphorylation states and only less phosphorylated forms of Mig1 are associated with this complex. Copyright © 2006 John Wiley & Sons, Ltd.
Describing the Relationships between Tourist Satisfaction and Destination Loyalty in a Segmented and Digitalized Market

As a result of advances in ICT services, transportation and local development, among others, more destinations are competing to attract both national and international visitors. Globalization requires destinations to increase their competitiveness or risk losing out on tourist revenues. While the research into destination competitiveness and tourist loyalty is well founded, recent progress in e-services has opened up new opportunities for informing and attracting visitors. This paper examines the potential effects of e-services in an inclusive model of destination loyalty to the city of Leipzig in Germany. The results of the path analysis indicate possibilities for e-services to increase both satisfaction and loyalty, especially with regard to various tourist subgroups.
Performance Analsis of Wireless Transmitters

Wi­Fi is a Wireless Local Area Network (WLAN) technology using 2.4 GHz and 5 GHz ISM bands (Industrial, Scientific and Medical) for allowing electronic equipment to be interconnected. [Rappaport96] tells us that wireless signal strength, measured in decibels (dB) experiences interference and multipath fading when transmitted over the channel. Several factors affect the signal strength. In this study, we select some commercially available adapters and antenna equipment to transmit a wireless signal and measure the received signal strength. We do statistical performance comparison using one­factor [Jain91] full factorial analysis and determine the best transmission combination equipment.
Unimolecular Photochemistry of 4-Thiouracils

Abstract Unimolecular phototautomeric reactions in 4-thiouracil, 1-methyl-4-thiouracil and 6-aza-4-thiouracil were studied using the matrix-isolation technique combined with infrared absorption spectroscopy. For monomers of these compounds, isolated in solid argon at 10 K, an intramolecular proton-transfer photoreaction was observed. Upon UV (λ > 345 nm) irradiation, the initial oxo–thione forms of 4-thiouracils were converted into the corresponding oxo–thiol tautomers. The photogenerated oxo–thiol isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-311++G(2d,p) level. Good agreement between the observed and predicted pattern of spectral bands allowed a reliable identification. This is the first report on experimental observation of isomeric forms of 4-thiouracils other than the canonical oxo–thione tautomers.
A Two-Stage Fuzzy Logic Approach for Wireless LAN Indoor Positioning

Alternatively to GNSS, in indoor environments WLAN according to the IEEE 802.11 standard can provide location information by using signal strength measurements to access points (AP) and hence offers a smart synthesis of communication and navigation functionality. Especially the approach of pattern recognition of signal strength fingerprints can obtain location accuracies of 1 to 5 m. The presented approach makes use of this approach but goes further and takes up the idea of fuzzy logic theory since various information of the signal strength measurements can be used to form linguistic variables according to an assessment made by humans. The accuracy of the location results of the fuzzy logic approach is compared to the results of commercial WLAN positioning software as well as to a simple approach of processing Euclidian distances. Although still without the necessary fine tuning of the algorithms, the preliminary results already show that the fuzzy logic approach is very suitable since it obtains significant accuracy improvements, especially in large rooms and on sites not being in the vicinity of a calibration site.