julilili42/papers huggingface dataset:
A septal chromosome segregator protein evolved into a conjugative DNA-translocator protein
2011-09-01

Streptomycetes, Gram-positive soil bacteria well known for the production of antibiotics feature a unique conjugative DNA transfer system. In contrast to classical conjugation which is characterized by the secretion of a pilot protein covalently linked to a single-stranded DNA molecule, in Streptomyces a double-stranded DNA molecule is translocated during conjugative transfer. This transfer involves a single plasmid encoded protein, TraB. A detailed biochemical and biophysical characterization of TraB, revealed a close relationship to FtsK, mediating chromosome segregation during bacterial cell division. TraB translocates plasmid DNA by recognizing 8-bp direct repeats located in a specific plasmid region clt. Similar sequences accidentally also occur on chromosomes and have been shown to be bound by TraB. We suggest that TraB mobilizes chromosomal genes by the interaction with these chromosomal clt-like sequences not relying on the integration of the conjugative plasmid into the chromosome.
Visual mapping with uncertainty for correspondence-free localization using Gaussian process regression
2011-09-01

We present a framework that allows for localization based on very low resolution omnidirectional image data using regression techniques. Previous related methods are constrained to image data labeled with exact position information acquired in the training phase. We relax this constraint and propose to learn local heteroscedastic Gaussian processes by accumulating odometry data which can easily be acquired. The processes are used as a probabilistic map to predict recording positions of newly acquired images by a fusion of the uncertain training data. In contrast to many feature-based approaches, our framework does not rely on any explicit correspondences over images as well as over positions and only imposes very weak assumptions on the type and quality of the image representations.
Characterization of feline hereditary retinal dystrophies using clinical, functional, structural and molecular genetic studies
2011-09-01

Abstract Only in recent years have specific mutations been elucidated for feline hereditary retinal dystrophies. Molecular genetic characterization of feline diseases has so far been a slow process but with a full genome sequence for the cat recently completed and the development of a feline single nucleotide polymorphism chip, the characterization of feline monogenic disorders will be significantly simplified. This review summarizes current knowledge with regard to specific hereditary retinal dystrophies in cats and gives an overview of how cats can be used as models in translational research.
EEG Alpha Spindles as Indicators for Prolonged Brake Reaction Time During Auditory Secondary Tasks in a Real Road Driving Study
2011-09-01

Driver distraction accounts for a substantial number of traffic accidents. Therefore, the impact of auditory secondary tasks on driving performance was examined. In addition to performance measures, i.e. reaction time on emergency brakings of a leading vehicle, mental driver states were described by electroencephalographic (EEG: alpha spindles, alpha band power) as well as cardiac activity (ECG: heart rate variability). Results show that brake reaction time (RT) increased with time-on-task during all conditions (p<.001), and was significantly higher while performing the secondary task (p<.001). Physiological measures showed similar effects. Alpha spindle rate, alpha band power as well as heart rate variability (HRV) increased with time-on-task and were significantly different during the secondary task, indicating inhibited visual information processing and reduced concentration ability. This study shows that reduced driving performance measured by means of prolonged brake reactions during increased cognitive load elicited by auditory secondary tasks is indicated by EEG measures as well as cardiac activity, enabling the direct quantification of driver distraction in experiments during real road driving.
Predicate inversion and Englishthere-sentences
2011-09-01

This squib argues against the predicate inversion analysis of English existential there-sentences. The main problem of this analysis is caused by wh-extraction data. Wh-extraction is possible of and from the noun phrase in there-BE (there-sentences with the copula), but not in there-V sentences (there-sentences with other verbs). This is not predicted by the predicate inversion analysis. It is shown that the predicate inversion analysis is adequate (with some modifications) for there-V sentences and locative inversion. Existential there-sentences, however, need to be analysed differently. They are derived from a predication configuration in which there is the subject of predication and the sentence states about this location that it contains the kind and amount/number of individuals given in the noun phrase. The existential reading arises from the interaction of this predication configuration and existential closure of an empty D-layer of the noun phrase.
Barrett's esophagus: treatments of adenocarcinomas I
2011-09-01

The following on the treatments of adenocarcinomas in Barrett's esophagus contains commentaries on endo mucosal resection; choice between other ablative therapies; the remaining genetic abnormalities following stepwise endoscopic mucosal resection and possible recurrences; the Fotelo–Fotesi PDT; the CT TNM classification of early stages of Barrett's carcinoma; the indications of lymphadenectomy in intramucosal cancer; the differences in lymph node yield in transthoracic versus transhiatal dissection; video‐assisted lymphadenectomy; and the importance of the length of proximal esophageal resectipon; and indications of sentinel node dissection.
The new requirements of endoscopy
2011-09-01

The following on new requirements of endoscopy contains commentaries on the risk of infection in endoscopy, the need to eliminate contamination, and the use of a disposable system in transnasal endoscopy.
Accuracy of time measurements with a QUASAR-370G hybrid vacuum photodetector in Cherenkov detectors of extensive air showers
2011-09-01

The accuracy of time measurements in the Cherenkov detectors of extensive air showers, based on QUASAR-370G hybrid vacuum photodetectors with a large-area hemispherical photocathode, is estimated. The dependence of the time measurement error on the amplitude of the output pulses from the photodetector and the light background of the night sky is determined.
A Semi-Automatic, Iterative Method for Creating a Domain-Specific Treebank
2011-09-01

In this paper we present the development process of NLP-QT, a question treebank that will be used for data-driven parsing in the context of a domain-specific QA system for querying NLP resource metadata. We motivate the need to build NLP-QT as a resource in its own right, by comparing the Penn Treebank-style annotation scheme used for QuestionBank (Judge et al., 2006) with the modified NP annotation for the Penn Treebank introduced by Vadas and Curran (2007). We argue that this modified annotation scheme provides a better interface representation for semantic interpretation and show how it can be incorporated into the NLP-QT resource, without significant loss in parser performance. The parsing experiments reported in the paper confirm the feasibility of an iterative, semi-automatic construction of the NLP-QT resource similar to the approach taken for QuestionBank. At the same time, we propose to improve the iterative refinement technique used for QuestionBank by adopting Hwa (2001)’s heuristics for selecting additional material to be handcorrected and added to the data set at each iteration.
Barrett's esophagus: treatments of adenocarcinomas II
2011-09-01

The following topics are explored in this collection of commentaries on treatments of adenocarcinomas related to Barrett's esophagus: the importance of intraoperative frozen sections of the margins for the detection of high dysplasia; the preferable way for sentinel node dissection; the current role of robotic surgery and of video‐endoscopic approach; the value of the Siewert's classification of adenocarcinomas; the indications of two‐step esophagectomy; the evaluation of pathological complete response; the role of PET scan in staging and response assessment; the role of p53 in the selection of adenocarcinomas patients; chemotherapy regimens for adenocarcinomas; the use of monoclonal antibodies in the control of cell proliferation; he attempt to define a stage‐specific strategy, and the possible indications of selective therapy; and changes in mortality rates from esophageal cancer.
Eliciting Customer Wishes Using Example-Based Heuristics in E-Commerce Applications
2011-09-01

The ubiquitous access to information via the Web has changed our daily life and business practices. E-commerce applications allow for a wide variety of vendors to compete in a world-wide market. But with a growing number of vendors, also the amount of available offers is increasing, which in turn leads to an information flood that may severely hamper the user experience. Skyline algorithms as introduced by the information systems community, promise to winnow suboptimal offers from electronic marketplaces. For the amount of Web data and the typical interaction style, however, the result sets are still too large and hard to manage. Recently, first approaches to integrate human decision processes like com-promises or trade-offs have been designed. In this paper we will build on these approaches and introduce a novel heuristic into the sky lining paradigm that not only allows for convenient Web-style user interaction, but also focuses searches on semantic clusters of offers. Thus, the view on interesting clusters is refined, whereas less interesting clusters are strongly reduced in size and strictly focused on only the outstanding items.
Residents’ corner September 2011. CarpeDIEM – Birbeck granule in Langerhans cell histiocytosis
2011-09-01

ejd.2011.1540 Auteur(s) : Emmanuella Guenova emmanuella.guenova@gmail.com, Martin Schaller Department of Dermatology, University of Tuebingen, Liebermeisterstrasse 25, 72076 Tubingen, Germany Langerhans cell histiocytosis (LCH) is characterized by lesions rich in langerin+ (CD207+)/CD1a+/Birbeck granule+ cells, with a dendritic Langerhans cell (LC) phenotype. The clinical course of the disease may range broadly, from spontaneous remission sometimes to a fatal outcome. Histology and immunocytochemical [...]
Late-breaking abstract: Is primary tumour standardized uptake value (SUV) an independent prognostic factor for non small cell lung cancer (NSCLC)? A meta-analysis based on individual data
2011-09-01

Background: 18 F-fluoro-2-deoxy-D-glucose positron emission tomography has an important role in staging lung cancer. In addition, its prognostic value has been studied in numerous studies as well as in two literature based meta-analyses. To assess further its independent value, we carried out a meta-analysis based on individual data. Methods: Following literature search, we contacted the authors of identified studies and tried to identify some unpublished data with a written protocol for the meta-analysis. Primary outcome was overall survival (OS) and data analysis used Cox regression models stratified for study. SUV was used as a binary covariate (cut-off: median value for each study). Results: Data were collected for 1462 patients (out of 2596 identified patients) from 10 publications and 1 unpublished series (median age: 64 years, gender: 61% male, 35% squamous cell, 45% adenocarcinoma, stage I: 49%, II: 8%, III: 32%, IV: 12%). Lower SUV was significantly associated with female gender, smaller tumour size, earlier stage and adenocarcinoma. Analyzing OS, univariate hazard ratio for SUV was 1.44 (95% CI: 1.23-1.68) without important heterogeneity in subgroups except for stage IV. When adjusted for stage, histology, age, tumour size and gender, HR estimate for SUV effect was 1.62, statistically significant (95% CI: 1.28-2.04, p Conclusions: This meta-analysis based on individual patients data shows that SUV is an independent prognostic factor for OS, at least in non metastatic stage. Selection bias and methodological differences are however present and further prospective studies are needed.
Aripiprazole use during pregnancy and lactation
2011-09-01

Introduction: Data on treatment with second generation antipsychotics during pregnancy and breast feeding are rare. Considering aripiprazole, published observations are confined to two single subjects. In one case exposure during pregnancy revealed no indication of teratogenicity. In the other case a low milk/plasma ratio was reported during breast feeding. Materials and Methods: We report a 34 year old patient with a diagnosis of schizophrenia paranoid type who suffered from two psychotic episodes since 2004. She remitted with 15 mg aripiprazole per day, while on treatment, she conceived. Medication was continued during pregnancy and lactation. After initiation of breast feeding we analysed 3 specimen of breast milk on day 27 after the infant's birth using high performance liquid chromatography (HPLC). Results: Apart from a perinatal group b streptococcal infection the newborn infant showed no morphological or developmental abnormality. No aripiprazole was detected in all obtained breast milk samples, whereas the detection limit was 10 ng/ml. Taking into account plasma aripiprazole concentration of 207 ng/ml and dehydroaripiprazole 42 ng/ml respectively, milk/plasma ratio was smaller than 0.04. No untoward side effect occurred during lactation in a 3 month follow up period. Conclusion: This case report gives evidence that aripiprazole use during pregnancy and lactation is relatively save, nevertheless no final conclusion can be drawn which antipsychotic agent should be preferred if treatment is required in the perinatal phase.
Neural correlates of Cognitive Behavioural Therapy effects on positive symptoms in patients with schizophrenic disorders
2011-09-01

The topic neural correlates of Cognitive Behavioural Therapy (CBT) effects in treatment of psychotic disorders has only been investigated for very small sample sizes. Thus the multicentre fMRI study evaluated a large sample of psychotic patients (n = 98) and controls (n = 89) from the POSITIVE clinical trial for the neural correlates of normal and pathological cognitive processes implicated in delusional thought, the potential modulations of components of the neural circuit by CBT and its differences to effects of Supportive Therapy (ST).‏ Patients were examined and re-examined before and after nine months of therapy (either with CBT or ST). Differences in brain activation relating to phenomena of premature reasoning (JTC-task) and biased attribution (AB-task) were analyzed. The fMRI measurements before psychotherapy showed activations in key areas for decision making for the JTC-task and evaluative processes for the AB-task. The comparison of patients with schizophrenia and healthy controls revealed significant decreased activations in these regions in patients. After nine months of psychotherapy the preliminary data analysis of the still blinded treatment arms showed significantly increased activations in the mentioned brain areas. These findings suggest neuroplastic changes due to relearning strategies in patients with chronified psychosis. This is an encouraging result, hopefully leading to a more widespread application of psychotherapy in treatment of schizophrenia.
NMP22 as a urine-based tumour marker for bladder cancer screening in a prospective cohort of chemical workers formerly exposed to aromatic amines: results of the UroScreen study
2011-09-01

&lt;sec&gt;&lt;st&gt;Objectives&lt;/st&gt; Cancer of the urinary bladder ranks among the four leading cancers among men in Germany. Because bladder cancer can be successfully treated, patients will benefit from early detection. Due to a lack of clinical signs besides haematuria, urine-based tumour markers have been proposed for early detection. One aim of the prospective UroScreen cohort is to evaluate the cancer predictive values of nuclear matrix protein NMP22 in bladder cancer screening. &lt;/sec&gt; &lt;sec&gt;&lt;st&gt;Methods&lt;/st&gt; Between 2003 and 2010 active or retired workers of two chemical plants took part in an annual voluntary bladder cancer screening program. All men were formerly exposed to aromatic amines. A total of 7092 urine samples from 1609 workers were collected for determination of urine status, cytology, and NMP22. Reference pathology was performed. &lt;/sec&gt; &lt;sec&gt;&lt;st&gt;Results&lt;/st&gt; During the study 20 bladder tumours occurred in nineteen workers, including two papilloma, 12 incident, and five recurrent bladder tumours. We observed a total of 224 positive NMP22 tests (cut point: 10 U/ml). NMP22 sensitivity was about 97% for all tumour types, NMP22 specificity ranged between 25% for high-grade and 40% for low-grade tumours. A similar pattern was observed for the predictive values (PVs). Negative PV was higher than 99%, and the positive PV ranged between 4% and 12%. &lt;/sec&gt; &lt;sec&gt;&lt;st&gt;Conclusions&lt;/st&gt; NMP22 cannot be recommended for bladder cancer screening in a symptom-free population due to the low incidence of bladder cancer and the high false-positive rate. However, the high specificity for low-grade tumours renders this marker suitable for the follow-up of patients on recurrent bladder cancer. &lt;/sec&gt;
f-Mode Instability in Relativistic Neutron Stars
2011-09-02

We present the first calculation of the basic properties of the f-mode instability in rapidly rotating relativistic neutron stars, adopting the Cowling approximation. By accounting for dissipation in neutron star matter, i.e., shear or bulk viscosity and superfluid mutual friction, we calculate the associated instability window. For our specific stellar model, a relativistic polytrope, we obtain a minimum gravitational growth time scale (for the dominant l=m=4 mode) of the order of 10(3)-10(4) s near the Kepler frequency Ω(K) while the instability is active above ∼0.92 Ω(K) and for temperatures ∼(10(9)-2×10(10)) K, characteristic of newborn neutron stars.
Role of MbtH-like Proteins in the Adenylation of Tyrosine during Aminocoumarin and Vancomycin Biosynthesis
2011-09-03

MbtH-like proteins consist of ∼70 amino acids and are encoded in the biosynthetic gene clusters of non-ribosomally formed peptides and other secondary metabolites derived from amino acids. Recently, several MbtH-like proteins have been shown to be required for the adenylation of amino acid in non-ribosomal peptide synthesis. We now investigated the role of MbtH-like proteins in the biosynthesis of the aminocoumarin antibiotics novobiocin, clorobiocin, and simocyclinone D8 and of the glycopeptide antibiotic vancomycin. The tyrosine-adenylating enzymes CloH, SimH, and Pcza361.18, involved in the biosynthesis of clorobiocin, simocyclinone D8, and vancomycin, respectively, required the presence of MbtH-like proteins in a 1:1 molar ratio, forming heterotetrameric complexes. In contrast, NovH, involved in novobiocin biosynthesis, showed activity in the absence of MbtH-like proteins. Comparison of the active centers of CloH and NovH showed only one amino acid to be different, i.e. Leu-383 versus Met-383. Mutation of this amino acid in CloH (L383M) indeed led to MbtH-independent adenylating activity. All investigated tyrosine-adenylating enzymes exhibited remarkable promiscuity for MbtH-like proteins from different pathways and organisms. YbdZ, the MbtH-like protein from the expression host Escherichia coli, was found to bind to adenylating enzymes during expression and to influence their biochemical properties markedly. Therefore, the use of ybdZ-deficient expression hosts is important in biochemical studies of adenylating enzymes.
Genetic Analysis of SCO2997 , Encoding a TagF Homologue, Indicates a Role for Wall Teichoic Acids in Sporulation of Streptomyces coelicolor A3(2)
2011-09-03

ABSTRACT Streptomyces coelicolor contains two gene clusters putatively involved in wall teichoic acid biosynthesis. Inactivation of the tagF homologue SCO2997 or SCO2584 , a component of the Streptomyces spore wall synthesizing complex, affected sporulation. The mutant phenotypes resembled those of mre mutants, suggesting a function of wall teichoic acids in the differentiation of Streptomyces .
Researchers’ opinions about ethically sound dissemination of BCI research to the public media
2011-09-03

BCI research and (future) applications raise ethical questions. A websurvey among 144 BCI researchers identified disseminating BCI research to the public media as a central topic. Most researchers felt that BCI scientists must responsibly communicate with the media and that general ethical guidelines on BCI research and application are needed within the next 5 years. We recommend further debate on ethical aspects related to BCI and the development of guidelines.
A uniform analysis for concessive at least and optative at least
2011-09-03

This paper discusses a particular type of optative constructions (which are constructions that express a wish without containing an overt lexical item that means wish): If-clauses in which optativity is apparently licensed by 'at least'. I propose that the connection between 'at least' and optativity is indirect and can be explained as follows. On the one hand, if-clauses generally have an optative reading; on the other hand, optative 'at least' is an instance of concessive 'at least', which conveys desirability and thus supports ('cues') an optative reading. I propose that, as a consequence, the licensing of optativity by 'at least' is a semantic conspiracy: I argue that there is a pragmatic preference for using optativity cues, which blocks optative readings in cue-less utterances.
Geometric Numerical Integration
2011-09-04

The subject of this workshop was numerical methods that preserve geometric properties of the flow of an ordinary or partial differential equation. This was complemented by the question as to how structure preservation affects the long-time behaviour of numerical methods.