Miracle-dz/UniFAR-FTUs huggingface dataset:
West Nile Virus Challenge Alters the Transcription Profiles of Innate Immune Genes in Rabbit Peripheral Blood Mononuclear Cells

The peripheral innate immune response to West Nile virus (WNV) is crucial for control of virus spread to the central nervous system. Therefore, transcriptomes encoding the innate immune response proteins against WNV were investigated in peripheral blood mononuclear cells (PBMCs) of New Zealand White rabbits, a recently established novel rabbit model for WNV pathogenesis studies. PBMCs were challenged with an Australian WNV strain, WNVNSW2011, in vitro, and mRNA expression of selected immune response genes were quantified at 2-, 6-, 12-, and 24-h post-infection (pi) using qRT-PCR. Compared to mock-inoculated PBMCs, WNV-stimulated PBMCs expressed high levels of interferon (IFN) alpha (IFNA), gamma (IFNG), IL6, IL12, IL22, CXCL10, and pentraxin 3 (PTX3) mRNA. Likewise, TLR1, 2, 3, 4, 6, and 10 mRNA became up-regulated with the highest expression seen for TLR3, 4, and 6. TLRs-signaling downstream genes (MyD88, STAT1, TRAF3, IRF7, and IRF9) subsequently became up-regulated. The high expression of IFNs, TLR3, TLR4, TRAF3, STAT1, IRF7, and IRF9 are in accordance with antiviral activities, while expression of TNFA, HO1, iNOS, caspase 3, and caspase 9 transcripts suggests the involvement of oxidative stress and apoptosis in WNV-stimulated rabbit PBMCs, respectively. The level of WNVNSW2011 RNA increased at 24-h pi in PBMCs challenged with virus in vitro compared to input virus. The expression dynamics of selected genes were validated in PBMCs from rabbits experimentally infected with WNV in vivo. Higher expression of IFNA, IFN beta (IFNB), IFNG, TNFA, IL6, IL22, PTX3, TLR3 and TLR4, IRF7, IRF9, STST1, TRAF3, caspase 3, and caspase 9 were seen in PBMCs from WNV-infected rabbits on day 3 post-intradermal virus inoculation compared to PBMCs from uninfected control rabbits. This study highlights the array of cytokines and TLRs involved in the host innate immune response to WNV in the rabbit leukocytes and suggests that these cells may be a useful in vitro model for WNV infection study.
Uncoating of vaccinia virus

Input vaccinia virus deoxyribonucleoproteids with buoyant densities (in CsCl) very similar (if not identical) to those of viral cores have been found in large cytoplasmic structures in which viral DNA replication takes place. The deoxyribonucleoproteids consist of at least five major and two minor core proteins and viral DNA which is protected against DNase digestion. It is suggested that viral core-like deoxyribonucleoproteids rather than released DNA are used in vaccinia-infected cells both for delayed-early gene transcription and viral DNA replication.
Multi-Strategy Approaches to Active Learning for Statistical Machine Translation

This paper investigates active learning to improve statistical machine translation (SMT) for low-resource language pairs, i.e., when there is very little pre-existing parallel text. Since generating additional parallel text to train SMT may be costly, active sampling selects the sentences from a monolingual corpus which if translated would have maximal positive impact in training SMT models. We investigate different strategies such as density and diversity preferences as well as multistrategy methods such as modified version of DUAL and our new ensemble approach GraDUAL. These result in significant BLEU-score improvements over strong baselines when parallel training data is scarce.
Small-Area Estimation of County-Level Forest Attributes Using Ground Data and Remote Sensed Auxiliary Information

Small-area estimation (SAE) is a concept that has considerable potential for precise estimation of forest ecosystem attributes in partitioned forest populations. In this study, several estimators were compared as SAE techniques for 12 counties in the northern Oregon Coast range. The estimators that were compared consisted of three indirect estimators, multiple linear regression (MLR), gradient nearest neighbor imputation (GNN), and most similar neighbor imputation (MSN), and five composite estimators based on MLR, MSN, and GNN with county-level direct estimates. Forest attributes of interest were density (trees/ha), basal area (m 2 /ha), cubic volume (m 3 /ha), quadratic mean diameter (cm), and average height of 100 largest trees per ha. The sample consisted of 680 annual Forest Inventory Analysis plots, a spatially balanced sample across all conditions and ownerships. The auxiliary data consisted of 16 Landsat variables, a land cover classification, tree cover, and elevation. Overall, the composite estimators were superior when both precision and bias of estimation were considered. FOR . S CI. 59(5):536-548.
Depression in headaches: chronification.

PURPOSE OF REVIEW Recent evidence supports the suggestion that migraine is a chronic disorder with episodic attacks that increase in frequency in a subgroup of patients, transforming migraine into a refractory chronic condition with poor outcome and severe impact. Among the risk factors for migraine chronification depression figures notably. Early diagnosis and management of risk factors in migraineurs prevent migraine chronification and its consequences. The scope of this article is to review depression as a potential cofactor for migraine chronification. RECENT FINDINGS Population-based studies revealed that migraineurs often have symptoms of depression, with strongest associations for migraine with aura. Patients with depression also have an increased risk for migraine, migraine with aura in particular. Twin studies showed similar findings. This bidirectional relationship suggests that migraine and depression may share common causative factors, possibly genetically determined, that might control migraine chronification. Migraine patients may develop depression as a result of the demoralizing experience of recurrent and disabling headaches and depressed patients may develop migraine because of increased pain sensitivity, in the basis of a common genetic background. SUMMARY We suggest that clinicians consider depression as part of migraine management in order to optimize treatment and avoid migraine progression.
The Influence of Huntingtin Protein Size on Nuclear Localization and Cellular Toxicity

Huntington disease is an autosomal dominant neurodegenerative disorder caused by the pathological expansion of a polyglutamine tract. In this study we directly assess the influence of protein size on the formation and subcellular localization of huntingtin aggregates. We have created numerous deletion constructs expressing successively smaller fragments of huntingtin and show that these smaller proteins containing 128 glutamines form both intranuclear and perinuclear aggregates. In contrast, larger NH2-terminal fragments of huntingtin proteins with 128 glutamines form exclusively perinuclear aggregates. These aggregates can form in the absence of endogenous huntingtin. Furthermore, expression of mutant huntingtin results in increased susceptibility to apoptotic stress that is greater with decreasing protein length and increasing polyglutamine size. As both intranuclear and perinuclear aggregates are clearly associated with increased cellular toxicity, this supports an important role for toxic polyglutamine-containing fragments forming aggregates and playing a key role in the pathogenesis of Huntington disease.
Animation of Natural Virtual Characters

Virtual characters can be a powerful tool for a range of applications, from storytelling and games to tutoring, training, and general interfaces. Yet, human users’ keen observation skills means they will be aware of any errors in the virtual character’s performance and may easily read unintended messages into the communication if an agent’s performance is flawed. This special issue takes up these challenges in order to move the field closer to being able to reap the benefits of virtual characters.
Effects of a Diet Rich in N-3 Polyunsaturated Fatty Acids on Systemic Inflammation in Renal Transplant Recipients

Objective: n-3 Polyunsaturated fatty acids (PUFAs) supplementation reduces systemic inflammation and improves renal and cardiovascular prognosis in kidney transplant recipients. However, patient compliance is poor because bad-tasting fish oils are used as an n-3 PUFA source. Therefore, we explored whether the beneficial effects of n-3 can be obtained by administering a diet based on n-3-rich foods. Methods: Sixty kidney transplant recipients were assigned to 2 different groups: the CON group (n = 28), which continued with their usual diet, and the DIET group (n = 32), which followed an n-3-rich diet for 6 months. Twenty-six patients in the DIET group and 24 in the CON group completed the study. End points of the study were changes in n-3 PUFAs intake, n-6:n-3 PUFAs ratio, systemic inflammation markers, and renal function during the 6 months of the dietary treatment. Results: Three and 6 months after the beginning of the study, n-3 PUFA intake was significantly higher and the n-6:n-3 PUFA ratio was markedly lower than baseline in the DIET group. Plasma total cholesterol, triglycerides, C-reactive protein, and interleukin (IL)-6 decreased as well. IL-6 mRNA levels in peripheral blood mononuclear cells were also lower than at the beginning of the study. Proteinuria and microalbuminuria were reduced by 50% with respect to the baseline, whereas glomerular filtration rate (GFR) was unchanged. No change in the aforementioned parameters was observed in the CON group throughout the study. Conclusion: In long-term kidney transplant recipients a naturally n-3 PUFA-rich dietary plan causes an increase in n-3 PUFA intake, decreases systemic inflammation and proteinuria, and improves plasma lipid pattern.
Partial Meet Revision and Contraction in Logic Programs

The recent years have seen several proposals aimed at placing the revision of logic programs within the belief change frameworks established for classical logic. A crucial challenge of this task lies in the nonmonotonicity of standard logic programming semantics. Existing approaches have thus used the monotonic characterisation via SE-models to develop semantic revision operators, which however neglect any syntactic information, or reverted to a syntax-oriented belief base approach altogether. In this paper, we bridge the gap between semantic and syntactic techniques by adapting the idea of a partial meet construction from classical belief change. This type of construction allows us to define new model-based operators for revising as well as contracting logic programs that preserve the syntactic structure of the programs involved. We demonstrate the rationality of our operators by testing them against the classic AGM or alternative belief change postulates adapted to the logic programming setting. We further present an algorithm that reduces the partial meet revision or contraction of a logic program to performing revision or contraction only on the relevant subsets of that program.
Memory impairment in abstinent MDMA (“Ecstasy”) users: A longitudinal investigation

To examine the neurotoxic potential of continued MDMA (“Ecstasy”) use in humans and its functional consequences over the course of 1 year, 15 MDMA users participated in a longitudinal study in which they completed a brief neuropsychological test battery composed mainly of retrospective and prospective memory tasks. Subjects were abstinent for 2 weeks on initial and 1-year testing. Continued use of MDMA was associated with progressive decline in terms of immediate and delayed recall.
When does financial sector (in)stability induce financial reforms

The article studies whether financial sector (in)stability had an effect on reforms in the financial sector in a large cross-country panel from 1990 to 2005. We forward the theory that countries are more likely to liberalize their financial sectors in times of financial stability. We argue that politicians are less likely to undertake financial reforms if they face a strong lobby in the financial sector which is able to block reforms that are not in its interest. Our empirical results suggest that financial instability leads to regulations, while financial stability is found to induce liberalizations. We also find that weaker financial lobbies are unable to block financial reforms while strong lobbies can effectively stop reforms.
Proteomic analyses of different human tumour-derived chaperone-rich cell lysate (CRCL) anti-cancer vaccines reveal antigen content and strong similarities amongst the vaccines along with a basis for CRCL's unique structure: CRCL vaccine proteome leads to unique structure

Abstract Purpose: The aim of this paper was to compare protein content of chaperone-rich cell lysate (CRCL) anti-cancer vaccines prepared from human tumours of different histological origins to evaluate the uniformity of their protein content. Materials and methods: Clinical grade CRCL was prepared under Good Manufacturing Practice (GMP) conditions from surgically resected human tumours (colorectal cancer, glioblastoma, non-small cell lung cancer, ovarian cancer). Protein samples were separated by SDS-PAGE and slices cut from gels for protease digestion followed by mass spectrometry analysis. Proteins were identified, and the content assessed by gene ontogeny/networking programmatic computation. CRCL preparations were also analysed by nanoparticle tracking analysis (NTA) and transmission electron microscopy (TEM). Results: We identified between 200 and 550 proteins in the various CRCL preparations. Gene ontogeny analysis indicated that the vaccines showed clear relationships, despite different tumour origins. A total of 95 proteins were common to all the CRCLs. Networking analyses implicated heat shock proteins in antigen processing pathways, and showed connections to the cytoskeletal network. We found that CRCL vaccines showed a particulate structure by NTA, and TEM revealed an extended fence-like structural network in CRCL, with regions that were microns in size. Conclusions: We conclude that it is feasible to prepare and characterise CRCL from a variety of different tissue sources; a substantial portion of the protein content is identical among the different CRCLs, while the overall compositions also suggest high overlaps in functional categories. The protein content indicates the presence of antigens and implies a potential structure, which we believe may play a role in CRCL's ability to stimulate innate antigen presenting cell activation.
Classification method for faults diagnosis in reluctance motors using Hidden Markov Models

The Switched Reluctance Machine (SRM) is ideal for safety critical applications due to its superior fault-tolerance characteristics. The switched reluctance drive is known to be fault tolerant, but it is not fault free. Fault diagnosis of SRM in the critical applications is often a difficult and daunting task. Thus, finding efficient and reliable fault diagnostics methods especially for SR machines is extremely important. This paper focuses on the development, and application of modern statistical classifier method, namely Hidden Markov Model (HMM) associated with a smoothed ambiguity plane Time-Frequency Representation (RTF) for the diagnosis based classification of electrical faults in this particular machine. The RTF-HMM Technique is composed of two steps: the Feature Extraction step based on the smoothed ambiguity plane designed for maximizing the separability between classes using Fisher's discriminant ratio and Hidden Markov Model algorithm applied for the classification step. The algorithm of each step is well developed. Classifier development and training data is carried out by the HMM using a set of fault scenarios, between healthy, single and combined faults, in terms of torque at different load level in order to deduce the fault severity. Parameter training of Hidden Markov Models generally need huge a mounts of historical data. Experimental results proves that the use of RTF-HMM based approaches is a suitable strategy for the automatic classification of new sample independent from de type of fault signal.
Results from the Upper Limb International Spasticity Study-II (ULIS-II): a large, international, prospective cohort study investigating practice and goal attainment following treatment with botulinum toxin A in real-life clinical management

Objective To describe real-life practice and person-centred outcomes in the treatment of poststroke upper limb spasticity with botulinum toxin A (BoNT-A). Design Observational, prospective study. Setting 84 secondary care centres in 22 countries. Participants 456 adults (≥18 years) with poststroke upper limb spasticity treated with one cycle of BoNT-A. Methods/outcomes Muscle selection, BoNT-A preparation, injection technique and timing of follow-up were conducted according to routine practice for each centre. Primary outcome: achievement of the patient's primary goal for treatment using goal-attainment scaling (GAS). Measurements of spasticity, standardised outcome measures and global benefits were also recorded. Results The median number of injected muscles was 5 (range 1–15) and the most frequently injected muscles were the long finger flexors, followed by biceps and brachioradialis. The median (range) follow-up time was 14 (2.6 to 32.3) weeks. The common primary treatment goals were passive function (132 (28.9%)), active function (104 (22.8%)), pain (61 (13.4%)), impairment (105 (23%)), involuntary movement (41 (9%)) and mobility (10 (2.2%)). Overall, 363 (79.6%) (95% CI 75.6% to 83.2%) patients achieved (or overachieved) their primary goal and 355 (75.4%) (95% CI 71.2% to 79.2%) achieved their secondary goal. Mean (SD) change from baseline in GAS T-scores was 17.6 (11.0) (95% CI 16.4 to 18.8; p<0.001). GAS T-scores were strongly correlated with global benefit and other standard measures (correlations of 0.38 and 0.63, respectively; p<0.001). Conclusions BoNT-A demonstrated a clinically significant effect on goal attainment for the real-life management of upper-limb spasticity following stroke. The study confirms the feasibility of a common international data set to collect systematic prospective data, and of using GAS to capture person-centred outcomes relating to passive and active functions and to pain. Registration ClinicalTrials.gov identifier: NCT01020500
Treatment Decision Making Among Chinese Women with DCIS

ABSTRACT One result of the widespread screening mammography is a 200% increase in the rates of breast ductal carcinoma in situ (DCIS). Treatment decision making among Chinese women diagnosed with DCIS remains understudied. This study examined Chinese-Canadian women's experiences (N = 26): (1) with treatment decision making (mastectomy or breast conserving surgery) and (2) their reflections on the decision-making process. Interviews in Cantonese, Mandarin, or English were transcribed and translated, and a content analysis conducted. Women's treatment decisions reflected a lack of understanding of DCIS, the desire to rid themselves of breast cancer “forever,” and the influence of significant others. English as a second language and use of medical jargon impeded their ability to make informed treatment decisions. Women's reflections on the decision-making process provided insights into how to improve information and support treatment decision making in ways that are accessible to them.
Exploration and treatment of carotid stenoses in 1996.

Every year in France, ~12000 cerebrovascular acci- 65, the prevalence of carotid stenoses with a grade dents (CVA) can be blamed on atherosclerotic stenosis significantly higher than 50% is of the order of 5‐10%. of the extracranial carotid artery, which represents This steadily increases with age, and most high-grade 10‐15% of all first-occurrence CVA recorded. The stenoses 80% are found in elderly subjects above age human and socio-economic consequences of these 75 [6,7]. Smoking is a predominant factor; the relative strokes can be qualified as tragic because, 6 months stenotic risk increases with age and duration of smokafter the CVA, roughly one-third of patients have died ing, from 1.36 in a 40-year-old subject who smoked and another third retain sequelae, half of which are for 10 years, to 37 in a 70-year-old subject who smoked invaliding. In addition to the localized risk of ipsilateral for 50 years [8]. A number of studies have revealed an stroke, carotid stenoses, either symptomatic or asymp- increased incidence of carotid stenosis in patients who tomatic, carry a general risk of myocardial infarction presented with atherosclerotic disease complications. and vascular death of 4 and 6% per annum, respectively Thus, the prevalence of high-grade stenoses or carotid [1‐3]. This dually local and general risk of carotid occlusions is 8% in patients with coronary arterial stenoses raises the issue of estimating the cost‐eVec
Cross-regulation of Ngn1 and Math1 coordinates the production of neurons and sensory hair cells during inner ear development

Temporal and spatial coordination of multiple cell fate decisions is essential for proper organogenesis. Here, we define gene interactions that transform the neurogenic epithelium of the developing inner ear into specialized mechanosensory receptors. By Cre-loxP fate mapping, we show that vestibular sensory hair cells derive from a previously neurogenic region of the inner ear. The related bHLH genes Ngn1 (Neurog1) and Math1 (Atoh1) are required, respectively, for neural and sensory epithelial development in this system. Our analysis of mouse mutants indicates that a mutual antagonism between Ngn1 and Math1 regulates the transition from neurogenesis to sensory cell production during ear development. Furthermore, we provide evidence that the transition to sensory cell production involves distinct autoregulatory behaviors of Ngn1 (negative) and Math1 (positive). We propose that Ngn1, as well as promoting neurogenesis, maintains an uncommitted progenitor cell population through Notch-mediated lateral inhibition, and Math1 irreversibly commits these progenitors to a hair-cell fate.
Automatic sulcal basins segmentation using hill climbing based on cortical surface principal curvature

The human cortical surface is a highly folded structure composed of sulci and gyri. Sulci, the spaces between the folds, define location on the cortex and provide a parcellation into anatomically distinct areas. Automatic parcellation of the cortical surface into sulcal regions or sulcal basins is very important in structural and functional mapping of the human brain. In this paper, we propose a novel method for automatic cortical sulcal parcellation based on the maximum principal curvatures of the cortical surface. This method is composed of three major steps: 1) smoothing the original estimated maximum principal curvatures, 2) employing the graph-cut algorithm on the maximum principal curvatures of the cortical surface for sulcal region segmentation, and 3) using a maximum principal curvature hill climbing method on the cortical surface for sulcal basins segmentation. This method has been successfully applied to the inner cortical surfaces of several healthy human brain MR images. The segmentation results have demonstrated the validity and efficiency of the proposed method.