Miracle-dz/UniFAR-FTUs huggingface dataset:
Single-Error Detection and Correction for Duplication and Substitution Channels

Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula>, and at most a single substitution occurring at any time during the mutation process.
Unrelated partially matched lymphocyte infusions in a patient with complete DiGeorge/CHARGE syndrome

Abstract: We present an infant with cDGS overlapping with CHARGE syndrome, who suffered from T‐cell deficiency treated with screened healthy DLI from an unrelated donor (8/10 match). The first dose of DLI (1.1 × 106 CD3+/kg) was administered at the age of six months, the second one (0.9 × 106 CD3+/kg) 36 days later. No conditioning was employed, GvHD prophylaxis consisting of CsA was used only during the second infusion. Since day+10 after the first DLI, split chimerism showing T‐cell engraftment has been documented. Proliferative response to PHA was detected on day+145. The treatment was complicated by severe acute GvHD (grade II‐III) after the first DLI and prolonged chronic liver cholestatic GvHD developing after the second DLI. Vigorous EBV proliferation four wk after the second DLI was accompanied by peripheral expansion of CD8+ donor cells. The patient, 26‐months old, is clinically well and has slowly started to gain his developmental milestones. We believe that infusions of small doses of DLI from an unrelated donor represent a potentially helpful therapeutic option in patients with cDGS/CHARGE phenotype.
Contrôle santé des structures composites : approche expérimentale et statistique

L'industrie aeronautique utilise des materiaux toujours plus performants pour ses avions et systemes spatiaux. Ainsi, pour realiser les communications, les avionneurs souhaiteraient aller vers une reelle integration des structures antennaires a la structure de l'avion et donc de passer de la structure antennaire vue comme equipement embarque a la structure antennaire devenue equipement integre. Notre travail de these se situe dans le cadre du projet MSIE (Materiaux et Structures Intelligentes pour l'Electromagnetisme). L'objectif de ce projet est de repondre aux demandes du secteur aeronautique, en evaluant le concept de nouveaux materiaux susceptibles de permettre la realisation de structures antennaires conformees, compactes et reconfigurables. Cette adaptabilite suppose que ces structures soient reconfigurables et donc capables, une fois munies de capteurs/actionneurs, de realiser un controle actif de la directivite, du rendement et du gain des structures antennaires. Il est alors apparu necessaire d'adjoindre a ces futures structures, une fonction de Controle sante ou Structural Health Monitoring "SHM", de maniere a pouvoir detecter d'eventuels endommagements (impact, delaminage entre le reseau d'antennes et la structure composite, rupture des fibres, etc.) susceptibles de se produire au cours du vol ou au cours du vieillissement de la structure. C'est dans le developpement de la fonction SHM que s'inscrit ce travail de these. A cet effet, nous avons realise des dispositifs experimentaux en tenant compte des demandes de l'industriel. Ces dispositifs comportent des structures composites antennaires munies de capteurs et d'actionneurs piezoelectriques. A travers les informations transmises par les capteurs, nous avons developpe deux methodes de detection de l'endommagement a base d'Analyse en Composantes Principales (ACP) et d'Analyse en Composantes Independantes (ACI). Ces deux methodes sont des approches statistiques qui ne necessitent pas la connaissance du modele mecanique de la structure a surveiller. Il s'agit de methodes traitant des observations vectorielles (multivariees) transmises par les capteurs piezoelectriques, afin d'en extraire des caracteristiques de fonctionnement de la structure a l'etat sain et de la structure dans un etat inconnu. La comparaison entre ces caracteristiques nous a permis de calculer pour chacune des deux methodes, un residu indicateur d'endommagement. Nous avons complete ce residu par une robustification de la prise de decision et cela par le calcul d'une borne, au-dela de laquelle l'endommagement est detecte.
Final devoicing and voicing assimilation in Dutch derivation and cliticization

In derivational frameworks, final devoicing and voicing assimilation have always been regarded as evidence for rule ordering in Dutch (e.g., Berendsen 1983, Berendsen et al 1984, Zonneveld 1983). In more recent constraint-based approaches, lexical and postlexical levels have been assumed to account for some Dutch voicing phenomena (Booij 1996), and other linguists propose context-specific faithfulness constraints for a few cases of final devoicing and voicing assimilation (e.g. Lombardi 1995, 1996). A unified analysis of all phenomena related to final devoicing and/or voicing assimilation in Dutch has not been proposed yet. In this paper, we will first point out the various problems rule-based approaches encounter when all relevant facts are taken into consideration. We will then suggest an analysis that uses the Correspondence version of Optimality Theory (McCarthy & Prince 1995) and that does not assume different levels, nor Output-Output constraints (Benua 1995), nor a device such as "Sympathy" (McCarthy 1998). Our analysis is based on ideas presented by Booij (1995) and Selkirk (1995) who both suggest that suffixes may differ in their prosodic structure. Some suffixes do not form a Prosodic Word of their own, whereas others do. We argue that clitics in Dutch differ from suffixes in that they are directly adjoined to a Phonological Phrase. Because the prosodic structure is distinct, we expect to find differences regarding syllabification (and, hence, syllable-final devoicing) between the two kinds of suffixes and clitics. We will show that this is in fact the case. We will furthermore demonstrate that prosodic structure is also relevant to voicing assimilation. More specifically, it will be shown that it is more important to preserve the underlying voicing specification of a plosive in initial position of a Prosodic Word than to preserve voicing of a plosive that is not initial in a Prosodic Word. We will develop an analysis with (i) Alignment constraints which say that the edge of certain morphological categories should be aligned with the corresponding edge of a Prosodic Word and (ii) Identity constraints which say that the
Interactive Tool

Understanding driver behavior and response to traffic information is necessary in order to achieve the maximum benefit from Advanced Traveler Information Systems (ATIS). This paper describes the development of a travel simulator to collect information on driver route choice in response to traffic information. A main feature of the simulator is the realistic representation of multiple traffic information sources (currently VMS and radio messages). Furthermore, the simulator is one of the first Internet-based travel simulators, and the only one that accurately simulated the driving task. The simulator consists of collection of pre-trip information and default route information followed by multiple simulated trips with varying incidents and traffic information. The simulator is evaluated and measures well against established guidelines for travel simulator development. Results will be discussed in future papers as data collection using the simulator is ongoing as of August 2007.
UvA-DARE (Digital Academic Repository) How adhesive friction decreases with increasing surface roughness due to the suppression of capillary adhesion

Friction originates at the area of real contact which depends on the (changing) surface topography. Ob-serving and measuring the area of real contact at multi-asperity interfaces is difﬁcult, making it challenging to quantitatively study the interplay between the frictional force and surface topography. In this paper, we systematically manipulate surface topography and use a ﬂuorescence microscopy-based contact visualization technique to reveal this interplay. We demonstrate good agreement between elastoplastic boundary element method contact calculations and experimental visualization of the area of real contact. While the area of real contact and thus contact pressure could be varied by a factor of 4 through control of the surface topography, this had only a modest effect on the coefﬁcient of friction (CoF). We do ﬁnd a small but systematic increase in the proportionality constant between frictional force and normal force (CoF) with decreasing surface roughness. The observation that smoother surfaces have a greater CoF is due to capillary adhesion between the two surfaces. We quantitatively model this behavior using a simple capillary adhesion model without adjustable parameters. Our results provide quantitative insights into the interplay between contact mechanics, friction, and capillary adhesion. A predictive understanding of this interplay is essential to demanding applications such as precision positioning.
High-Infiltration of Tumor-Associated Macrophages Predicts Unfavorable Clinical Outcome for Node-Negative Breast Cancer

The tumor microenvironment is composed of tumor cells, fibroblasts, endothelial cells and infiltrating immune cells, which may inhibit or promote tumor growth and progression. The objectives of this retrospective study were to characterize the density of tumor-associated macrophages (TAMs) in breast cancer, and to correlate the density of TAMs with clinicopathological parameters. Paraffin-embedded specimens and clinicopathological data, including up to 5 years follow-up information, were obtained from 172 breast cancer patients. Immunohistochemical staining for CD68 (marker for macrophages) was performed and evaluated in a blinded fashion. We found that TAMs were significantly frequent in high histopathological grade breast cancer patients. Breast cancer patients with a high density of TAMs had significantly lower rates of disease-free survival and 5-year overall survival than patients with low density of TAMs. Furthermore, high-infiltration of TAMs indicated worse survival rate for patients with node-negative breast cancer. In conclusion, the number of TAMs in the tumor stroma is an independent predictor of survival time for breast cancer patients. High-infiltration of TAMs is a significant unfavorable prognostic factor for patients with invasive breast cancer and, as such, is a potentially useful prognostic marker for breast cancer.
Impact of mating systems on patterns of sequence polymorphism in flowering plants

A fundamental challenge in population genetics and molecular evolution is to understand the forces shaping the patterns of genetic diversity within and among species. Among them, mating systems are thought to have important influences on molecular diversity and genome evolution. Selfing is expected to reduce effective population size, Ne, and effective recombination rates, directly leading to reduced polymorphism and increased linkage disequilibrium compared with outcrossing. Increased isolation between populations also results directly from selfing or indirectly from evolutionary changes, such as small flowers and low pollen output, leading to greater differentiation of molecular markers than under outcrossing. The lower effective recombination rate increases the likelihood of hitch-hiking, further reducing within-deme diversity of selfers and thus increasing their genetic differentiation. There are also indirect effects on molecular evolutionary processes. Low Ne reduces the efficacy of selection; in selfers, selection should thus be less efficient in removing deleterious mutations. The rarity of heterozygous sites in selfers leads to infrequent action of biased conversion towards GC, which tends to increase sequences' GC content in the most highly recombining genome regions of outcrossers. To test these predictions in plants, we used a newly developed sequence polymorphism database to investigate the effects of mating system differences on sequence polymorphism and genome evolution in a wide set of plant species. We also took into account other life-history traits, including life form (whether annual or perennial herbs, and woody perennial) and the modes of pollination and seed dispersal, which are known to affect enzyme and DNA marker polymorphism. We show that among various life-history traits, mating systems have the greatest influence on patterns of polymorphism.
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction

MOTIVATION For biological pathways, it is common to measure a gene expression time series after various knockdowns of genes that are putatively involved in the process of interest. These interventional time-resolved data are most suitable for the elucidation of dynamic causal relationships in signaling networks. Even with this kind of data it is still a major and largely unsolved challenge to infer the topology and interaction logic of the underlying regulatory network. RESULTS In this work, we present a novel model-based approach involving Boolean networks to reconstruct small to medium-sized regulatory networks. In particular, we solve the problem of exact likelihood computation in Boolean networks with probabilistic exponential time delays. Simulations demonstrate the high accuracy of our approach. We apply our method to data of Ivanova et al. (2006), where RNA interference knockdown experiments were used to build a network of the key regulatory genes governing mouse stem cell maintenance and differentiation. In contrast to previous analyses of that data set, our method can identify feedback loops and provides new insights into the interplay of some master regulators in embryonic stem cell development. AVAILABILITY AND IMPLEMENTATION The algorithm is implemented in the statistical language R. Code and documentation are available at Bioinformatics online. CONTACT duemcke@mpipz.mpg. de or tresch@mpipz.mpg. de SUPPLEMENTARY INFORMATION Supplementary Materials are available at Bioinfomatics online.
A Behavioral Role for Feature Detection by Sensory Bursts

Brief episodes of high-frequency firing of sensory neurons, or bursts, occur in many systems, including mammalian auditory and visual systems, and are believed to signal the occurrence of particularly important stimulus features, i.e., to function as feature detectors. However, the behavioral relevance of sensory bursts has not been established in any system. Here, we show that bursts in an identified auditory interneuron of crickets reliably signal salient stimulus features and reliably predict behavioral responses. Our results thus demonstrate the close link between sensory bursts and behavior.
Topography on a subcellular scale modulates cellular adhesions and actin stress fiber dynamics in tumor associated fibroblasts

Cells can sense and adapt to mechanical properties of their environment. The local geometry of the extracellular matrix, such as its topography, has been shown to modulate cell morphology, migration, and proliferation. Here we investigate the effect of micro/nanotopography on the morphology and cytoskeletal dynamics of human pancreatic tumor-associated fibroblast cells (TAFs). We use arrays of parallel nanoridges with variable spacings on a subcellular scale to investigate the response of TAFs to the topography of their environment. We find that cell shape and stress fiber organization both align along the direction of the nanoridges. Our analysis reveals a strong bimodal relationship between the degree of alignment and the spacing of the nanoridges. Furthermore, focal adhesions align along ridges and form preferentially on top of the ridges. Tracking actin stress fiber movement reveals enhanced dynamics of stress fibers on topographically patterned surfaces. We find that components of the actin cytoskeleton move preferentially along the ridges with a significantly higher velocity along the ridges than on a flat surface. Our results suggest that a complex interplay between the actin cytoskeleton and focal adhesions coordinates the cellular response to micro/nanotopography.
ML Detection in Phase Noise Impaired SIMO Channels With Uplink Training

The problem of maximum likelihood (ML) detection in training-assisted single-input multiple-output (SIMO) systems with phase noise impairments is studied for two different scenarios, i.e., the case when the channel is deterministic and known (constant channel) and the case when the channel is stochastic and unknown (fading channel). Furthermore, two different operations with respect to the phase noise sources are considered, namely, the case of identical phase noise sources and the case of independent phase noise sources over the antennas. In all scenarios, the optimal detector is derived for a very general parameterization of the phase noise distribution. Furthermore, a high signal-to-noise-ratio (SNR) analysis is performed to show that symbol-error-rate (SER) floors appear in all cases. The SER floor in the case of identical phase noise sources (for both constant and fading channels) is independent of the number of antenna elements. In contrast, the SER floor in the case of independent phase noise sources is reduced when increasing the number of antenna elements (for both constant and fading channels). Finally, the system model is extended to multiple data channel uses and it is shown that the conclusion is valid for these setups, as well.
Automatic Generation of High-Level State Features for Generalized Planning

In many domains generalized plans can only be computed if certain high-level state features, i.e. features that capture key concepts to accurately distinguish between states and make good decisions, are available. In most applications of generalized planning such features are hand-coded by an expert. This paper presents a novel method to automatically generate high-level state features for solving a generalized planning problem. Our method extends a compilation of generalized planning into classical planning and integrates the computation of generalized plans with the computation of features, in the form of conjunctive queries. Experiments show that we generate features for diverse generalized planning problems and hence, compute generalized plans without providing a prior high-level representation of the states. We also bring a new landscape of challenging benchmarks to classical planning since our compilation naturally models classification tasks as classical planning problems.
A system for retrieving speech documents

An information retrieval model is presented for the retrieval of speech documents, i.e. audio recordings containing speech. The indexing vocabulary consists of indexing features that have the following characteristics. First, they are easy to recognize by speech recognition methods. Second, the number of different indexing features is small such that a reasonable amount of training data is sufficent to train the hidden Markov models that are used by the speech recognition process. Third, the retrieval method based on such indexing features achieves an acceptable retrieval effectiveness as shown by experiments on text collections. Fourth, these indexing features cannot only be identified in speech documents but also in text documents. From the last characteristic follows that speech documents and text documents can be retrieved simultaneously. Analogously, the queries may contain either speech or text. Thus, we have a simple multimedia retrieval model where two different medias are indexed coherently. We also describe a prototype retrieval system under development.
The Epstein-Barr Virus-encoded miR-BART22 targets MAP3K5 to promote host cell proliferative and invasive abilities in nasopharyngeal carcinoma

miR-BART22, a new discovered Epstein-Barr virus (EBV) miRNA, is abundant in Nasopharyngeal carcinoma (NPC). It has been reported that miR-BART22 promoted the tumor development by down-modulating EBV LMP2 expression to evade the host immune response. But its cell target genes have still been obscure. We have reported an inverse correlation between the BART-22 and MAP3K5 protein expression in NPC tissues and NPC cell lines. Meanwhile, MAP3K5 protein expression level was significantly decreased in primary NPC tissues compared with nasopharyngitis when MAP3K5 mRNA expression was consistent in two group tissues. According to our data and target prediction by miRnada, we assume MAP3K5 is an important target gene of NPC. MAP3K5, also named apoptosis signal-regulating kinase1 (ASK1), is an important early answer gene in P38MAPK pathway and an apoptosis-related gene. In present study, MAP3K5 was verified the target gene of miR-BART22 by luciferase assay. miRBART-22 decreased MAP3K5 protein level. Moreover, it also decreased MAP3K5 downstream gene MAP2K4 expression in P38MAPK pathway, and even their activated phosphorylation forms. Additionally, we found stable transfection of miR-BAT22 could improve tumor cells' proliferative and invasive abilities in NPC cell line 5-8F. The data highlight the role of the EBV miR-BART22 in regulating genes involving in apoptosis and some important pathways to promote cancer development. And it also raises the possibility that inhibitors of miR-BART22 can be as a therapeutic strategy for NPC and other EBV-infected tumors treatment.
Alcohol and the nervous system

Alcohol is an available, legal, and frequently used drug in our society. However, its misuse and toxic effects are estimated to cost the British National Health Service £160 million each year in treatment costs. It is estimated that 28 000 people die each year in the UK as a result of their alcohol consumption.1 Alcohol’s associated morbidity impacts greatly on the work of the neurologist. Approximately 25% of male medical admissions may be regarded as problem drinkers, with the group at highest risk being young male patients admitted to medical or orthopaedic wards.2 One of the key messages of this article must be to always ask patients about their alcohol use. This needs to be routinely documented in notes, perhaps most usefully with a full drug use history. People may minimise their alcohol use, so tact is necessary. Table 1 contains a list of questions that may be helpful; clearly it is important to get your own routine and to be guided by what the patient is able to tell you at that time. Relatives may also provide enlightening and not always corroborative histories. View this table: Table 1 The alcohol history Alcohol’s central nervous system (CNS) effects are mediated through actions on a variety of neurotransmitters. There is a complex interplay between excitatory and inhibitory systems (table 2). The numerous transmitters involved in alcohol’s action explain its diverse effects and the large number of drug interactions with both prescribed and illicit drugs. View this table: Table 2 Alcohol and neurotransmitters Many practitioners reading this article will be aware on both a personal and occupational level of the effects of acute intoxication. Blood alcohol concentrations reflect rate of intake, degree of tolerance, and the simultaneous effects of other drugs. Extreme intoxication (> 300 mg/100 ml) leads to increasing drowsiness and then coma, with depressed tendon reflexes, hypotension, hypothermia, …