Miracle-dz/UniFAR-FTUs huggingface dataset:
Expression and Characterization of the Borna Disease Virus Polymerase

ABSTRACT Borna disease virus is the prototype of a new family,Bornaviridae, within the order Mononegavirales, that is characterized by nuclear transcription, splicing, low level replication, and neurotropism. The products of five open reading frames predicted from the genomic sequence have been confirmed; however, expression of the sixth, corresponding to the putative viral polymerase (L), has not been demonstrated. Here, we describe expression and characterization of a 190-kDa protein proposed to represent L. Expression of this protein from the third transcription unit of the viral genome is dependent on a splicing event that fuses a small upstream open reading frame in frame with the larger downstream continuous open reading frame. The protein is detected by serum antibodies from infected rats and is present in the nucleus, where it colocalizes with the phosphoprotein. L is also shown to be phosphorylated by cellular kinases and to interact with the viral phosphoprotein in coimmunoprecipitation studies. These findings are consistent with the identity of the 190-kDa protein as the viral polymerase and provide insights and describe reagents that will be useful for Bornavirus molecular biology and pathobiology.
From Sensor Data to Animal Behaviour: An Oystercatcher Example

Animal-borne sensors enable researchers to remotely track animals, their physiological state and body movements. Accelerometers, for example, have been used in several studies to measure body movement, posture, and energy expenditure, although predominantly in marine animals. In many studies, behaviour is often inferred from expert interpretation of sensor data and not validated with direct observations of the animal. The aim of this study was to derive models that could be used to classify oystercatcher (Haematopus ostralegus) behaviour based on sensor data. We measured the location, speed, and tri-axial acceleration of three oystercatchers using a flexible GPS tracking system and conducted simultaneous visual observations of the behaviour of these birds in their natural environment. We then used these data to develop three supervised classification trees of behaviour and finally applied one of the models to calculate time-activity budgets. The model based on accelerometer data developed to classify three behaviours (fly, terrestrial locomotion, and no movement) was much more accurate (cross-validation error = 0.14) than the model based on GPS-speed alone (cross-validation error = 0.35). The most parsimonious acceleration model designed to classify eight behaviours could distinguish five: fly, forage, body care, stand, and sit (cross-validation error = 0.28); other behaviours that were observed, such as aggression or handling of prey, could not be distinguished. Model limitations and potential improvements are discussed. The workflow design presented in this study can facilitate model development, be adapted to a wide range of species, and together with the appropriate measurements, can foster the study of behaviour and habitat use of free living animals throughout their annual routine.
A Hindi Question Answering system for E-learning documents

To empower the general mass through access to information and knowledge, organized efforts are being made to develop relevant content in local languages and provide local language capabilities to utility software. We have developed a question answering (QA) system for Hindi documents that would be relevant for masses using Hindi as the primary language of education. The user should be able to access information from e-learning documents in a user friendly way, that is by questioning the system in their native language Hindi and the system returns the intended answer (also in Hindi) by searching in context from the repository of Hindi documents. The language constructs, query structure, common words, etc. are completely different in Hindi as compared to English. A novel strategy, in addition to conventional search and NLP techniques, was used to construct the Hindi QA system. The focus is on context based retrieval of information. For this purpose we implemented a Hindi search engine that works on locality-based similarity heuristics to retrieve relevant passages from the collection. It also incorporates language analysis modules like stemmer and morphological analyzer as well as self constructed lexical database of synonyms. The experimental results over corpus of two important domains of agriculture and science show effectiveness of our approach
Defect Detection in SEM Images of Nanofibrous Materials

Nanoproducts represent a potential growing sector and nanofibrous materials are widely requested in industrial, medical, and environmental applications. Unfortunately, the production processes at the nanoscale are difficult to control and nanoproducts often exhibit localized defects that impair their functional properties. Therefore, defect detection is a particularly important feature in smart-manufacturing systems to raise alerts as soon as defects exceed a given tolerance level and to design production processes that both optimize the physical properties and control the defectiveness of the produced materials. Here, we present a novel solution to detect defects in nanofibrous materials by analyzing scanning electron microscope images. We employ an algorithm that learns, during a training phase, a model yielding sparse representations of the structures that characterize correctly produced nanofiborus materials. Defects are then detected by analyzing each patch of an input image and extracting features that quantitatively assess whether the patch conforms or not to the learned model. The proposed solution has been successfully validated over 45 images acquired from samples produced by a prototype electrospinning machine. The low computational times indicate that the proposed solution can be effectively adopted in a monitoring system for industrial production.
Embedded hardware architecture based on microcontrollers for the action and perception of a transradial prosthesis

This paper presents the design of a flexible, embedded control architecture for the action and perception of an anthropomorphic 16 degree of freedom, 4 degree of actuation prosthetic hand for use by transradial amputees. The prosthetic hand is provided with 40 structurally integrated sensors useful both for automatic grasp control and for biofeedback delivery to the user through an appropriate interface (either neural or noninvasive). The paper briefly describes the mechatronic design of the prosthesis, the set of sensors embedded in the hand and finally focuses on the design of the control architecture that allows action and perception for such a sophisticated device.
A cross-media evolutionary timeline generation framework based on iterative recommendation

Summarization methods such as timelines have greatly helped people to understand all kinds of news events within limited time. However, there are few studies probing into cross-media summarization, for example, generating timelines which contain both texts and images that can reinforce each other. In this paper, we tackle this important and challenging problem by proposing a novel solution. Specifically, we first reveal three requisite characteristics of an ideal image-text timeline. With the idea of recommendation, all these requisites will be modeled respectively, and fused compactly in a unified cross-media framework. Finally, we put all sentences and images into either the schema of referrer or the schema of recommended candidate, and the former recommends the latter. After changing their roles iteratively, we can achieve the optimal timelines which will significantly improve user experience and satisfaction. Experiments on real-world datasets show that the timelines generated by our framework outperform several competitive baselines.
Association of ABCB1 polymorphisms with erlotinib pharmacokinetics and toxicity in Japanese patients with non-small-cell lung cancer.

AIMS We analyzed the association of ABCB1 polymorphisms with erlotinib-induced toxicity and the pharmacokinetics in patients with non-small-cell lung cancer. MATERIALS & METHODS After erlotinib 150 mg was administered to 50 patients, ABCB1 polymorphisms were analyzed via either TaqMan(®) assays or direct nucleotide sequencing. Plasma concentrations were measured by HPLC. RESULTS The trough concentration at steady state in patients with the ABCB1 1236TT-2677TT-3435TT genotype was higher compared with others groups (p = 0.021) and patients carrying this genotype had a higher risk of developing higher grade 2 toxicity (p = 0.012). CONCLUSION The present study suggested that the ABCB1 1236TT-2677TT-3435TT genotype was associated with higher plasma concentration and the risk of developing higher toxicity in patients treated with erlotinib.
Architectural knowledge discovery: why and how?

The need for a method for architectural knowledge discovery stems from the difficulty to find relevant architectural knowledge in the documentation that accompanies a software product. This difficulty arises in particular when the document set is very large, and has been expressed by auditors as a need for a "reading guide" during a case study we conducted at a company that performs software product audits. Based on the needs of these auditors, we identify the main characteristics an architectural knowledge discovery method should exhibit. This paper argues that Latent Semantic Analysis (LSA) is a promising technique for architectural knowledge discovery.
A taste for words and sounds: a case of lexical-gustatory and sound-gustatory synesthesia

Gustatory forms of synesthesia involve the automatic and consistent experience of tastes that are triggered by non-taste related inducers. We present a case of lexical-gustatory and sound-gustatory synesthesia within one individual, SC. Most words and a subset of non-linguistic sounds induce the experience of taste, smell and physical sensations for SC. SC's lexical-gustatory associations were significantly more consistent than those of a group of controls. We tested for effects of presentation modality (visual vs. auditory), taste-related congruency, and synesthetic inducer-concurrent direction using a priming task. SC's performance did not differ significantly from a trained control group. We used functional magnetic resonance imaging to investigate the neural correlates of SC's synesthetic experiences by comparing her brain activation to the literature on brain networks related to language, music, and sound processing, in addition to synesthesia. Words that induced a strong taste were contrasted to words that induced weak-to-no tastes (“tasty” vs. “tasteless” words). Brain activation was also measured during passive listening to music and environmental sounds. Brain activation patterns showed evidence that two regions are implicated in SC's synesthetic experience of taste and smell: the left anterior insula and left superior parietal lobe. Anterior insula activation may reflect the synesthetic taste experience. The superior parietal lobe is proposed to be involved in binding sensory information across sub-types of synesthetes. We conclude that SC's synesthesia is genuine and reflected in her brain activation. The type of inducer (visual-lexical, auditory-lexical, and non-lexical auditory stimuli) could be differentiated based on patterns of brain activity.
Mutations in ftsZ that confer resistance to SulA affect the interaction of FtsZ with GTP

Mutations in the essential cell division gene ftsZ confer resistance to SulA, a cell division inhibitor that is induced as part of the SOS response. In this study we have purified and characterized the gene products of six of these mutant ftsZ alleles, ftsZ1, ftsZ2, ftsZ3, ftsZ9, ftsZ100, and ftsZ114, and compared their properties to those of the wild-type gene product. The binding of GTP was differentially affected by these mutations. FtsZ3 exhibited no detectable GTP binding, and FtsZ9 and FtsZ100 exhibited markedly reduced GTP binding. In contrast, FtsZ1 and FtsZ2 bound GTP almost as well as the wild type, and FtsZ114 displayed increased GTP binding. Furthermore, we observed that all mutant FtsZ proteins exhibited markedly reduced intrinsic GTPase activity. It is likely that mutations in ftsZ that confer sulA resistance alter the conformation of the protein such that it assumes the active form.
Saturation Density of Skin Fibroblasts as a Quantitative Screen for Human Cancer Susceptibility

Genomic analysis of human cancers reveals a large number of genetic changes per cell that presumably underlie development of the disease. The complexity of these changes that differ from one type of cancer to the other and from patient to patient with the same type of cancer raises questions about the feasibility of genomic analysis as an indicator of susceptibility to cancer. However, skin fibroblasts (SF) from individuals in families with heritable forms of cancer, and from cancer-bearing individuals, show correlation with a significant increase in saturation density (SD), as well as other neoplasia-related properties. Procedures are described for amplifying and quantifying differences in SD on the basis of studies of spontaneous transformation in the NIH 3T3 line of mouse fibroblasts. It is proposed that such procedures be evaluated as quantitative screens for susceptibility to cancer in the general population. (Cancer Epidemiol Biomarkers Prev 2009;18(9):2366–72)
Adult weight change and risk of postmenopausal breast cancer.

CONTEXT Endogenous hormones are a primary cause of breast cancer. Adiposity affects circulating hormones, particularly in postmenopausal women, and may be a modifiable risk factor for breast cancer. OBJECTIVE To assess the associations of adult weight change since age 18 years and since menopause with the risk of breast cancer among postmenopausal women. DESIGN, SETTING, AND PARTICIPANTS Prospective cohort study within the Nurses' Health Study. A total of 87,143 postmenopausal women, aged 30 to 55 years and free of cancer, were followed up for up to 26 years (1976-2002) to assess weight change since age 18 years. Weight change since menopause was assessed among 49,514 women who were followed up for up to 24 years. MAIN OUTCOME MEASURE Incidence of invasive breast cancer. RESULTS Overall, 4393 cases of invasive breast cancer were documented. Compared with those who maintained weight, women who gained 25.0 kg or more since age 18 years were at an increased risk of breast cancer (relative risk [RR], 1.45; 95% confidence interval [CI], 1.27-1.66; P<.001 for trend), with a stronger association among women who have never taken postmenopausal hormones (RR,1.98; 95% CI, 1.55-2.53). Compared with weight maintenance, women who gained 10.0 kg or more since menopause were at an increased risk of breast cancer (RR, 1.18; 95% CI, 1.03-1.35; P = .002 for trend). Women who had never used postmenopausal hormones, lost 10.0 kg or more since menopause, and kept the weight off were at a lower risk than those who maintained weight (RR, 0.43; 95% CI, 0.21-0.86; P = .01 for weight loss trend). Overall, 15.0% (95% CI, 12.8%-17.4%) of breast cancer cases in this population may be attributable to weight gain of 2.0 kg or more since age 18 years and 4.4% (95% CI, 3.6%-5.5%) attributable to weight gain of 2.0 kg or more since menopause. Among those who did not use postmenopausal hormones, the population attributable risks are 24.2% (95% CI, 19.8%-29.1%) for a weight gain since age 18 years and 7.6% (95% CI, 5.9%-9.7%) for weight gain since menopause. CONCLUSIONS These data suggest that weight gain during adult life, specifically since menopause, increases the risk of breast cancer among postmenopausal women, whereas weight loss after menopause is associated with a decreased risk of breast cancer. Thus, in addition to other known benefits of healthy weight, our results provide another reason for women approaching menopause to maintain or lose weight, as appropriate.
An approach to speed up RRT

We present an improved algorithm to RRT* in this paper. Our algorithm tries to increase the efficiency by replacing the Initialtree() of RRT*with a RRT tree only contains one solution to speed up finding a feasible solution, and then applying a RRT*_S algorithm to optimize the current solution. This RRT*_S is similar with RRT* in principle, but it does not insert extra nodes into the current tree and optimizes just in fixed nodes instead of all the nearby nodes. We demonstrate the performance of this improved algorithm on two benchmark scenarios to show the effectiveness compared with RRT* and RRT.
Event Models for Historical Perspectives: Determining Relations between High and Low Level Events in Text, Based on the Classification of Time, Location and Participants.

In this paper, we report on a study that was performed within the Semantics of History project on how descriptions of historical events are realized in different types of text and what the implications are for modeling the event information. We believe that different historical perspectives of writers correspond in some degree with genre distinction and correlate with variation in language use. To capture differences between event representations in diverse text types and thus to identify relations between historical events, we defined an event model. We observed clear relations between particular parts of event descriptions - actors, time and location modifiers. Texts, written shortly after an event happened, use more specific and uniquely occurring event descriptions than texts describing the same events but written from a longer time perspective. We carried out some statistical corpus research to confirm this hypothesis. The ability to automatically determine relations between historical events and their sub-events over textual data, based on the relations between event participants, time markers and locations, will have important repercussions for the design of historical information retrieval systems.
Chronic dialysis and death among survivors of acute kidney injury requiring dialysis.

CONTEXT Severe acute kidney injury among hospitalized patients often necessitates initiation of short-term dialysis. Little is known about the long-term outcome of those who survive to hospital discharge. OBJECTIVE To assess the risk of chronic dialysis and all-cause mortality in individuals who experience an episode of acute kidney injury requiring dialysis. DESIGN, SETTING, AND PARTICIPANTS We conducted a population-based cohort study of all adult patients in Ontario, Canada, with acute kidney injury who required in-hospital dialysis and survived free of dialysis for at least 30 days after discharge between July 1, 1996, and December 31, 2006. These individuals were matched with patients without acute kidney injury or dialysis during their index hospitalization. Matching was by age plus or minus 5 years, sex, history of chronic kidney disease, receipt of mechanical ventilation during the index hospitalization, and a propensity score for developing acute kidney injury requiring dialysis. Patients were followed up until March 31, 2007. MAIN OUTCOME MEASURES The primary end point was the need for chronic dialysis and the secondary outcome was all-cause mortality. RESULTS We identified 3769 adults with acute kidney injury requiring in-hospital dialysis and 13 598 matched controls. The mean age was 62 years and median follow-up was 3 years. The incidence rate of chronic dialysis was 2.63 per 100 person-years among individuals with acute kidney injury requiring dialysis, and 0.91 per 100 person-years among control participants (adjusted hazard ratio, 3.23; 95% confidence interval, 2.70-3.86). All-cause mortality rates were 10.10 and 10.85 per 100 person-years, respectively (adjusted hazard ratio, 0.95; 95% confidence interval, 0.89-1.02). CONCLUSIONS Acute kidney injury necessitating in-hospital dialysis was associated with an increased risk of chronic dialysis but not all-cause mortality.
Increased satiety after intake of a chocolate milk drink compared with a carbonated beverage, but no difference in subsequent ad libitum lunch intake

The rising rate of obesity has been blamed on increased consumption of sugar-sweetened soft drinks, such as carbonated sodas, which fail to satisfy hunger. The objective of the present study was to compare the effect on appetite and energy intake of a sugar-sweetened beverage (cola) and a chocolate milk drink, matched for energy content and volume. It was hypothesised that chocolate milk may be more satiating because of its protein content. Twenty-two healthy young men (age 23 (sd 1·8) years) of normal weight (BMI 22·2 (sd 1·5) kg/m2) were recruited to the randomised cross-over study. Visual analogue scales were used to record subjective appetite ratings every 30 min on each of two test days. A drink of 500 ml cola or chocolate milk (900 kJ) was ingested 30 min before an ad libitum lunch. Satiety and fullness were significantly greater (P = 0·0007, P = 0·0004, respectively) 30 min after chocolate milk than after cola. Ratings of prospective consumption and hunger were significantly greater after cola than after chocolate milk, both immediately after preload intake (P = 0·008, P = 0·01, respectively) and 30 min afterwards (P = 0·004, P = 0·01, respectively). There was no significant difference (P = 0·42) in ad libitum lunch intake after ingestion of chocolate milk (3145 (sd 1268) kJ) compared with cola (3286 (sd 1346) kJ). The results support the hypothesis that sweetened soft drinks are different from milk products in their impact on short-term hunger and satiety, although differences in subjective appetite scores were not translated into differences in energy intake.
Role of Sigma Receptors in Methamphetamine-Induced Neurotoxicity

Methamphetamine (METH) is a widely abused substance world over. Currently, there is no effective pharmacotherapy to treat its effects. This necessitates identification of potential novel therapeutic targets. METH interacts with sigma (σ) receptors at physiologically relevant micromolar concentrations. In addition, σ receptors are present in organs like the brain, heart, and lungs at which METH acts. Additionally, σ receptors have been implicated in various acute and subchronic effects like locomotor stimulation, development of sensitization and neurotoxicity, where σ receptor antagonists attenuate these effects. σ Receptors may also have a role in METH-induced psychiatric complications such as depression, psychosis, cognitive and motor deficits. The neurotoxic effects of METH, which are cause for concern, can be prevented by σ receptor antagonists in mice. Mechanistically, METH-induced neurotoxicity involves factors like dopamine release, oxidative stress, endoplasmic reticulum stress, activation of mitochondrial death cascades, glutamate release, apoptosis, microglial activation, and hyperthermia. This review compiles studies from the literature that suggests an important role for σ receptors in many of the mechanisms of METH-induced neurotoxicity.
Murine fetal natural killer cells are functionally and structurally distinct from adult natural killer cells

Natural killer (NK) cell phenotype and activity was studied by analyzing uncultured and short‐time‐cultured murine NK cells from fetal day 17 spleen and thymus. In contrast to NK cells from adult mice, freshly sorted fetal NK cells did not contain NK receptor transcripts for Ly‐49A, B, C/I, D, F, G2, or H. The only NK receptor transcripts that could be detected were Ly‐49E and CD94. It is important that Ly‐49E was present at a 10‐ to 30‐fold higher level compared with uncultured NK cells from adult mice. After short‐time interleukin‐2 culture, the level of Ly‐49E mRNA was comparable between fetal and adult NK cells. Functionally, fetal NK cells only killed MHC class I‐negative tumor cells when activating NK receptors were cross‐linked with antibody. We show that fetal NK cells are mature but are different from NK cells in adult mice regarding their NK cell receptor repertoire and function. J. Leukoc. Biol. 66: 625–633 1999.