Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward a quantitative basis for assessment and diagnosis of apraxia of speech.

PURPOSE We explored the reliability and validity of 2 quantitative approaches to document presence and severity of speech properties associated with apraxia of speech (AOS). METHOD A motor speech evaluation was administered to 39 individuals with aphasia. Audio-recordings of the evaluation were presented to 3 experienced clinicians to determine AOS diagnosis and to rate severity of 11 speech dimensions. Additionally, research assistants coded 11 operationalized metrics of articulation, fluency, and prosody in the same speech samples and in recordings from 20 neurologically healthy participants. RESULTS Agreement among the 3 clinicians was limited for both AOS diagnosis and perceptual scaling, but inter-observer reliability for the operationalized metrics was strong. The relationships between most operationalized metrics and mean severity ratings for corresponding perceptual dimensions were moderately strong and statistically significant. Both perceptual scaling and operationalized quantification approaches were sensitive to the presence or absence of AOS. CONCLUSIONS Perceptual scaling and operationalized metrics are promising quantification techniques that can help establish diagnostic transparency for AOS. However, because satisfactory reliability cannot be assumed for scaling techniques, effective training and calibration procedures should be implemented. Operationalized metrics show strong potential for enhancing diagnostic objectivity and sensitivity.
Putting the Spotlight Back on Plant Suspension Cultures

Plant cell suspension cultures have several advantages that make them suitable for the production of recombinant proteins. They can be cultivated under aseptic conditions using classical fermentation technology, they are easy to scale-up for manufacturing, and the regulatory requirements are similar to those established for well-characterized production systems based on microbial and mammalian cells. It is therefore no surprise that taliglucerase alfa (Elelyso®)—the first licensed recombinant pharmaceutical protein derived from plants—is produced in plant cell suspension cultures. But despite this breakthrough, plant cells are still largely neglected compared to transgenic plants and the more recent plant-based transient expression systems. Here, we revisit plant cell suspension cultures and highlight recent developments in the field that show how the rise of plant cells parallels that of Chinese hamster ovary cells, currently the most widespread and successful manufacturing platform for biologics. These developments include medium optimization, process engineering, statistical experimental designs, scale-up/scale-down models, and process analytical technologies. Significant yield increases for diverse target proteins will encourage a gold rush to adopt plant cells as a platform technology, and the first indications of this breakthrough are already on the horizon.
A single Hox3 gene with composite bicoid and zerknüllt expression characteristics in non-Cyclorrhaphan flies

The members of the evolutionarily conserved Hox-gene complex, termed Hox genes, are required for specifying segmental identity during embryogenesis in various animal phyla. The Hox3 genes of winged insects have lost this ancestral function and are required for the development of extraembryonic epithelia, which do not contribute to any larval structure. Higher flies (Cyclorrhapha) such as Drosophila melanogaster contain Hox3 genes of two types, the zerknüllt type and the bicoid type. The zerknüllt gene is expressed zygotically on the dorsal side of the embryo and is required for establishing extraembryonic tissue. Its sister gene bicoid is expressed maternally and the transcripts are localized at the anterior pole of the mature egg. BICOID protein, which emerges from this localized source during early development, is required for embryonic patterning. All known direct bicoid homologues are confined to Cyclorrhaphan flies. Here, we describe Hox3 genes of the non-Cyclorrhaphan flies Empis livida (Empididae), Haematopota pluvialis (Tabanidae), and Clogmia albipunctata (Psychodidae). The gene sequences are more similar to zerknüllt homologues than to bicoid homologues, but they share expression characteristics of both genes. We propose that an ancestral Hox3 gene had been duplicated in the stem lineage of Cyclorrhaphan flies. During evolution, one of the gene copies lost maternal expression and evolved as zerknüllt, whereas the second copy lost zygotic expression and evolved as bicoid. Our finding correlates well with a partial reduction of zerknüllt-dependent extraembryonic tissue during Dipteran evolution.
An optical brain

Green algae use a light-activated ion channel to control phototaxis. Now, Edward Boyden, Feng Zhang, Karl Deisseroth (Stanford University, Stanford, CA), and colleagues have used the same channel to control the rapid spiking activity of neurons. Figure Light pulses give reproducible spikes in different cells. Experimental control of neural activity has become more and more sophisticated, with glutamate uncaging and multineuron patch clamping allowing the targeting of a specific neural area. But there is a catch. “You can't target cell types in that way,” says Deisseroth. Usually the individual cell types “are sparsely embedded in the networks. ” The obvious solution to this is genetics. Promoters to drive expression in specific cell types are available, as many of the interneuron types express unique neuropeptides or other markers. Initial attempts have met with partial success, but the complexity of the introduced signal cascades has meant that control has been on the order of seconds and minutes rather than milliseconds. The Stanford group used rapid optical switches plus the single component channelrhodopsin-2 from the green alga Chlamydomonas reinhardtii. After lentivirus infection of rat neurons with their gene construct, blue light resulted in rapid depolarizing currents. Repeated light pulses could elicit spike trains typical of active neurons, with patterns that were reproducible in either the same or different neurons. In the absence of light, the resting potential, response to injected current, and cell health were unaffected. Deisseroth is interested in how certain cell types connect with others, and what specific function each one provides. He plans to apply the new technique in the mouse or rat hippocampus to get at some of the more enigmatic functions—such as mood—controlled by this brain region. Experiments with brain sections may be followed by experiments in live animals using optical fibers and 2-photon excitation. Reference: Boyden, E.S. , et al. 2005. Nat. Neurosci. doi:. 10.1038/nn1525 [PubMed] [Cross Ref]
Edge Sequences, Ribbon Tableaux, and an Action of Affine Permutations

An overview is provided of some of the basic facts concerning rim hook lattices and ribbon tableaux, using a representation of partitions by their edge sequences. An action is defined for the affine Coxeter group of type Ar? 1on ther-rim hook lattice, and thereby on the sets of standard and semistandardr-ribbon tableaux, and this action is related to the concept of chains inr-ribbon tableaux.
Developing an XML schema of BWW ontologies for semantic Web

The higher-degree relation widely exits in the real world but is not being supported by the current semantic Web. It needs to be converted into multiple binary relationships in the semantic Web. However, the semantics of a higher-degree relation is not always the same as those of multiple binary relationships. Even if a higher-degree relation can be represented by multiple binary relations, the former often provides a more "natural" representation of the real world. Wand and Weber introduced the ontology defined by Bunge into information modeling that is referred to as BWW ontologies. By using a mutual attribute rather than multiple binary relations to represent a higher-degree relation directly, BWW ontologies avoid the problem of inappropriate presentation of higher-degree relations. This paper presents an XML schema for BWW ontologies to support the semantic Web.
Context-based Messaging for Ad Hoc Networks

Ad hoc networks are spontaneously formed networks of devices such as PDAs and mobile phones that are connected through unreliable and slow wireless links. As the adoption into social situations of such devices increases, it is becoming increasingly desirable to support distributed applications over such networks. When dealing with unstable networks it is preferable to improve robustness by having devices interact with one another without explicitly specifying addresses [4]. Since these networks are likely to cover significant geographical regions and comprise devices that are diverse in both capability and purpose, we propose that addressing devices by their contextual situation may be useful for a range of applications.
Saccharomyces cerevisiae Sen1 Helicase Domain Exhibits 5′- to 3′-Helicase Activity with a Preference for Translocation on DNA Rather than RNA*♦

Background: Yeast Sen1 helicase and its human ortholog senataxin promote accurate transcription termination. Results: Sen1 helicase domain exhibits 5′- to 3′-helicase activity on DNA and RNA and binds endogenous RNA. Conclusion: Biochemical activities of purified Sen1 helicase domain are consistent with its proposed function in resolving cotranscriptional R-loops. Significance: Mutations in senataxin and its paralog IGHMBP2 cause crippling neurodegenerative diseases. In the yeast Saccharomyces cerevisiae, the essential nuclear helicase Sen1 is required for efficient termination of transcription of short noncoding RNA genes by RNA polymerase II. However, the mechanism by which Sen1 promotes transcription termination is not known. Prior biochemical studies on the Sen1 homolog from Schizosaccharomyces pombe showed that it can bind and unwind both DNA and RNA, but the S. pombe protein is not essential and has not been demonstrated to function in transcription. Furthermore, Sen1 from either yeast has not previously been expressed as a recombinant protein, due to its large molecular mass (252 kDa in S. cerevisiae). Here, we report the purification and characterization of the 89-kDa S. cerevisiae Sen1 helicase domain (Sen1-HD) produced in Escherichia coli. Sen1-HD binds single-stranded RNA and DNA with similar affinity in the absence of ATP, but it binds RNA more stably than DNA in the presence of ATP, apparently due to a slower translocation rate on RNA. Translocation occurs in the 5′ to 3′ direction, as for the S. pombe protein. When purified from E. coli at a moderate salt concentration, Sen1-HD was associated with short RNAs that are enriched for the trinucleotide repeat (CAN)4. We propose that Sen1 binds to RNAs and prevents their stable pairing with DNA, consistent with in vivo studies by others showing increased R-loop (RNA/DNA hybrid) formation when Sen1 activity is impaired by mutations. Our results are consistent with a model in which Sen1 promotes transcription termination by resolving R-loops.
Analysis of navigational habituation

This paper presents a model of navigational habituation for human passengers riding an autonomous robotic wheelchair. We present an example on how robot technology is utilized to understand human behavior which is useful to build human-like navigation models. The work consists of three parts, data collection from manual driving participants, habituation modeling and autonomous navigation experimentation. Manual driving data collection consisted of recording human driving control behavior using a robotic wheelchair in a complex labyrinth-like environment, while measuring physiological activity and emotional state via subjective reports (questionnaires). The purpose of this first part was to collect a sufficient representation of the evolution of human driving behavior in a complex environment (23 participants), such that a numerical model could be found to approximate the trend in velocity usage; velocity usage characterizes navigational habituation. The complex environment habituation model was tested and evaluated, on a different set of 16 participants, in a fully autonomous navigation setting where the robotic wheelchair followed a pre-recorded path. Self-reports and physiological measures confirmed that the proposed habitation velocity regulation model provides a more comfortable ride compared to slow and fast pre-defined static velocity profiles.
An explorative analysis of user evaluation studies in information visualisation

This paper presents an analysis of user studies from a review of papers describing new visualisation applications and uses these to highlight various issues related to the evaluation of visualisations. We first consider some of the reasons why the process of evaluating visualisations is so difficult. We then dissect the problem by discussing the importance of recognising the nature of experimental design, datasets and participants as well as the statistical analysis of results. We propose explorative evaluation as a method of discovering new things about visualisation techniques, which may give us a better understanding of the mechanisms of visualisations. Finally we give some practical guidance on how to do evaluation correctly.
Human anti-murine immunoglobulin responses in patients receiving monoclonal antibody therapy.

Human anti-murine immunoglobulin responses were assessed in serum from three groups of patients receiving murine monoclonal antibody therapy. Each of the three patient groups responded differently. Chronic lymphocytic leukemia patients demonstrated little or no preexisting murine immunoglobulin G-reactive antiglobulin prior to treatment, while the cutaneous T-cell lymphoma and melanoma patients demonstrated preexisting antiglobulin levels in the same range as those demonstrated in healthy controls. None of 11 chronic lymphocytic leukemia patients receiving the T101 monoclonal antibody demonstrated an antiglobulin response, whereas all four of the cutaneous T-cell lymphoma patients receiving the same antibody developed increased levels of antiglobulins. Three of nine malignant melanoma patients receiving the 9.2. 27 monoclonal antibody showed an increase in antiglobulin titers. In patients developing antiglobulin responses, the response was rapid, typically being detectable within 2 weeks. The antiglobulins were primarily immunoglobulin G and, with the exception of a single melanoma patient in whom the response appeared to have a substantial 9.2. 27-specific component (i.e., antiidiotype), were cross-reactive with most murine immunoglobulin G preparations tested. This pattern of results suggested that the antiglobulin was a secondary immune reaction with elevation of the levels of preexisting antiglobulin which was cross-reactive with the mouse antibody administered. While the presence of serum antiglobulin would be expected to present major complications to monoclonal antibody therapy, no clinical toxicity related to antiglobulin responses was observed in these patients, and no inhibition of antibody localization on tumor cells was seen.
A Performance Debugging Framework for Unnecessary Lock Contentions with Record/Replay Techniques

Locks have been widely used as an effective synchronization mechanism among processes and threads. However, we observe that, a large number of false inter-thread dependencies (i.e., unnecessary lock contentions) exist during the program execution on multicore processors, incurring significant performance overhead. This paper presents a performance debugging framework, PERFPLAY, to facilitate the identification of unnecessary lock contentions and to guide programmers to improve the program performance by eliminating the unnecessary lock contentions. Since the performance debugging of unnecessary lock contentions is input-sensitive, we first identify the representative inputs for performance debugging. Next, PERFPLAY quantifies the performance impact of unnecessary lock contention code regions for each candidate input. Taking into account conflicting attribute of performance impact and input coverage in the real world, we finally make the tradeoff between performance impact and input coverage to recommend the optimal unnecessary lock contention code regions. Our final results on five real-world programs and PARSEC benchmarks demonstrate the significant performance overhead of unnecessary lock contentions, and the effectiveness of PERFPLAY in troubleshooting the target unnecessary lock contention code regions with the consideration of both performance impact and input coverage.
Complete Genome Sequence of a New Megavirus Family Member Isolated from an Inland Water Lake for the First Time in India

ABSTRACT We report here the isolation and complete genome sequencing of a large double-stranded DNA virus, Powai Lake megavirus, for the first time from India. The isolation of a large DNA virus with genome size >1 Mb from India further attests to the prevalence of Giant viruses in different environmental niches.
A Real-Time System for Pedestrian Detection Based on GMM and HOG

The detection of pedestrian which has been widely used in digital surveillance systems is a popular topic in computer vision. This paper mainly discusses a system of pedestrian detection in video sequences captured from a stationary camera hanging in a public scene. We describe an efficient system combining background subtraction based on Gaussian Mixture Model (GMM) and object classification based on Histograms of Oriented Gradients (HOG). We first process moving objects segmentation using GMM. Then a HOG detector is used to classify the moving objects into person and none-person. Experimental results on video sequences have demonstrated that the real-time tracking system can process 15 to 30 frames per second robustly with a high accuracy.
The risk and outcome of cerebral oedema developing during diabetic ketoacidosis

BACKGROUND Cerebral oedema is a major cause of morbidity and mortality in children with insulin dependent diabetes. AIMS To determine the risk and outcome of cerebral oedema complicating diabetic ketoacidosis (DKA). METHODS All cases of cerebral oedema in England, Scotland, and Wales were reported through the British Paediatric Surveillance Unit between October 1995 and September 1998. All episodes of DKA were reported by 225 paediatricians identified as involved in the care of children with diabetes through a separate reporting system between March 1996 and February 1998. Further information about presentation, management, and outcome was requested about the cases of cerebral oedema. The risk of cerebral oedema was investigated in relation to age, sex, seasonality, and whether diabetes was newly or previously diagnosed. RESULTS A total of 34 cases of cerebral oedema and 2940 episodes of DKA were identified. The calculated risk of developing cerebral oedema was 6.8 per 1000 episodes of DKA. This was higher in new (11.9 per 1000 episodes) as opposed to established (3.8 per 1000) diabetes. There was no sex or age difference. Cerebral oedema was associated with a significant mortality (24%) and morbidity (35% of survivors). CONCLUSIONS This first large population based study of cerebral oedema complicating DKA has produced risk estimates which are more reliable and less susceptible to bias than those from previous studies. Our study indicates that cerebral oedema remains an important complication of DKA during childhood and is associated with significant morbidity and mortality. Little is known of the aetiology of cerebral oedema in this condition and we are currently undertaking a case control study to address this issue.
Helmets for Skiers and Snowboarders: An Injury Prevention Program

The authors' Level I trauma center has advocated the use of ski helmets for several years and in 1998, undertook a social-marketing campaign and a helmet loaner program to increase helmet use among skiers and snowboarders. The loaner program's effect on helmet acceptance was measured by comparing helmet acceptance in participating rental stores with acceptance in nonparticipating stores during 3 years. For the 1998-1999 season, 13.8% of renters in the participating stores accepted a helmet compared to 1.38% in the nonparticipating stores (p < .01); for 2000-2001, 33.5% to 3.93% (p < .01); and for 2001-2002, 30.3% to 4.48% (p < .01). The authors believe that efforts to increase helmet use—by increasing education and public awareness and decreasing barriers, such as through helmet loaner programs or routinely including helmets in rental packages—have significant potential to decrease the incidence and severity of brain injuries from skiing and/or snowboarding accidents in Colorado.
Beyond the 3′ end: experimental validation of extended transcript isoforms

High throughput EST and full-length cDNA sequencing have revealed extensive variations at the 3′ ends of mammalian transcripts. Whether all of these changes are biologically meaningful has been the subject of controversy, as such, results may reflect in part transcription or polyadenylation leakage. We selected here a set of tandem poly(A) sites predicted from EST/cDNA sequence analysis that (i) are conserved between human and mouse, (ii) produce alternative 3′ isoforms with unusual size features and (iii) are not documented in current genome databases, and we submitted these sites to experimental validation in mouse tissues. Out of 86 tested poly(A) sites from 44 genes, 84 were individually confirmed using a specially devised RT-PCR strategy. We then focused on validating the exon structure between distant tandem poly(A) sites separated by over 3 kb, and between stop codons and alternative poly(A) sites located at 4.5 kb or more, using a long-distance RT-PCR strategy. In most cases, long transcripts spanning the whole poly(A)–poly(A) or stop-poly(A) distance were detected, confirming that tandem sites were part of the same transcription unit. Given the apparent conservation of these long alternative 3′ ends, different regulatory functions can be foreseen, depending on the location where transcription starts.
Decision making via semi-supervised machine learning techniques

Semi-supervised learning (SSL) is a class of supervised learning tasks and techniques that also exploits the unlabeled data for training. SSL significantly reduces labeling related costs and is able to handle large data sets. The primary objective is the extraction of robust inference rules. Decision support systems (DSSs) who utilize SSL have significant advantages. Only a small amount of labelled data is required for the initialization. Then, new (unlabeled) data can be utilized and improve system's performance. Thus, the DSS is continuously adopted to new conditions, with minimum effort. Techniques which are cost effective and easily adopted to dynamic systems, can be beneficial for many practical applications. Such applications fields are: (a) industrial assembly lines monitoring, (b) sea border surveillance, (c) elders' falls detection, (d) transportation tunnels inspection, (e) concrete foundation piles defect recognition, (f) commercial sector companies financial assessment and (g) image advanced filtering for cultural heritage applications.
An Intelligent Accessing Control System Based on Human Intention Analysis

An innovative automatic door control system is proposed in this paper to overcome the drawback of frequent false actions among the present devices while increasing their added values for security applications. Through human detection and trajectory tracking techniques, the proposed system can precisely identify those people with intention of entering or leaving the door, and then control opening and closing of this door as a response. The experimental results indicate that the proposed system has the advantages such as high precision, high reliability, and controllability in response to demands. In addition, the product prototype also has the economic benefits of low costs, high added-value, and other efficient properties.