Miracle-dz/UniFAR-FTUs huggingface dataset:
AAV2 vectors mediate efficient and sustained transduction of rat embryonic ventral mesencephalon

The success of transplantation of human embryonic mesencephalic tissue to treat parkinsonian patients is limited by the poor survival of the transplant. We show that an AAV2 vector mediates efficient expression of the egfp reporter gene in organotypic cultures of freshly explanted solid fragments of rat embryonic ventral mesencephalon (VM). We observed early and sustained transgene expression (4 days to ≥ 6 weeks). Furthermore, rAAV-infected rat embryonic VM transplanted in the adult striatum continued to express EGFP for ≥ 3 months. More than 95% of the transduced cells were neurons. Dopaminergic neurons were transduced at low frequency at earlier time points. This method of gene delivery could prove useful to achieve local, continuous secretion of neurotrophic factors at physiologically relevant doses to treat Parkinson's disease.
Visual and Auditory Temporal Processing, Cross-Modal Transfer, and Reading

The present study reexamined the relevance of auditory and visual cross-modal matching to reading ability, an issue first addressed in a seminal study by Birch and Belmont (1964). By presenting all patterns to be matched as temporal sequences of tones and lights, including intramodal as well as cross-modal conditions, and covarying memory, three problems with the Birch and Belmont design were corrected. Results showed that poor readers had difficulty in perceiving temporal patterns generally: They did worse than good readers not only on cross-modal conditions but also on intramodal ones. These results were replicated in two tasks. Nonetheless, hierarchical regressions provided some indication that cross-modal abilities themselves are relevant to reading. For one of the two tasks, cross-modal performance contributed to the prediction of reading ability over and above intramodal performance. Poor readers also showed slower response times—a factor that contributed marginally to the prediction of reading independent of temporal processing.
Structure‐activity relationship approaches and applications

New techniques and software have enabled ubiquitous use of structure‐activity relationships (SARs) in the pharmaceutical industry and toxicological sciences. We review the status of SAR technology by using examples to underscore the advances as well as the unique technical challenges. Applying SAR involves two steps: Characterization of the chemicals under investigation, and application of chemometric approaches to explore data patterns or to establish the relationships between structure and activity. We describe generally but not exhaustively the SAR methodologies popular use in toxicology, including representation of chemical structure, and chemometric techniques where models are both unsupervised and supervised. The utility of SAR technology is most evident when supervised methods are used to predict toxicity of untested chemicals based only on chemical structure. Such models can predict on both an ordinal scale (e.g., active vs inactive) or a continuous scale (e.g., median lethal dose [LD50] dose). The reader is also referred to a companion paper in this issue that discusses quantitative structure‐activity relationship (QSAR) methods that have advanced markedly over the past decade.
Tuning technique for active FSS arrays

A novel biasing technique is described for active frequency selective slot arrays. The bandpass response can be switched between transmitting and reflecting modes, or tuned over a predetermined frequency range using two different biasing circuit configurations based on the same technology. The biasing layer is separated from the slot layer by a very thin, flexible, substrate while pin and varactor diodes are employed for switching and tuning, respectively. One application is the time-dependent modification of the EM architecture of buildings, permitting access to frequency bands as desired.
Long-Run and Short-Run Dynamics among the Sectoral Stock Indices: Evidence from Turkey

This paper investigates the short-run and long-run dynamics among the major sectoral stock indices of the Istanbul Stock Exchange over the period 1997-2011. Long-run relationship among these indices is analyzed by using both conventional Engle and Granger (1987) and Johansen-Juselius (1990) cointegration tests, causal relationship through Vector Error Correction Model (VECM). Likewise, variance decomposition analysis is employed to partition the variance of the forecast error of one sector index into proportions attributable to shocks in each sector index in the system including its own. The findings suggest that all sectors show consistent and strong evidence of a long-run relationship, the short-term causal relationships between the sector indices are considerably limited and, where they exist, especially unidirectional. The variance decomposition analysis confirms that even though a high percentage of error variance is accounted for by the innovations in the same index, innovations in the variance of returns in the Banking sector are able to explain, on average, 63% innovations in the variance of the Chemistry, Petrol and Plastic, 57% of the Basic Metal and 79% of the Holding and Investment sector returns. These results indicate that the Banking sector is the most influential sector in the ISE.
Genetic analysis of phase change in Bordetella pertussis

Avirulent-phase derivatives of Bordetella pertussis (those which have simultaneously lost the ability to synthesize several virulence-associated factors) and the genetic mechanism of the phase change were studied. Increased tolerance to erythromycin was shown to be an avirulent-phase marker. By the use of efficiency of plating on erythromycin, the proportion of avirulent-phase (Vir) variants in a virulent-phase (Vir+) population was determined to be between 10(-3) and 10(-6), depending on the strain. We showed that the phase shift is reversible and detected a complete Vir- to Vir+ to Vir- to cycle. In other experiments, hybridization studies with avirulent-phase mutants obtained by Tn5 mutagenesis suggested that a single region located at a unique site in the B. pertussis chromosome controls the phase change. One of the avirulent Tn5 mutants was used as a recipient in a conjugative cross with a virulent-phase donor. All recombinants which had reacquired the virulence-associated factors also lost Tn5, indicating the loss of Tn5 was required to restore the Vir+ phenotype. The Tn5 avirulent-phase mutants behave as if the insertion interrupted the function of a transacting gene product which is required for the expression of the other virulent-phase genes. A model of the molecular basis of the phase regulation is presented.
A Flexible B‐Spline Model for Multiple Longitudinal Biomarkers and Survival

Summary Often when jointly modeling longitudinal and survival data, we are interested in a multivariate longitudinal measure that may not fit well by linear models. To overcome this problem, we propose a joint longitudinal and survival model that has a nonparametric model for the longitudinal markers. We use cubic B‐splines to specify the longitudinal model and a proportional hazards model to link the longitudinal measures to the hazard. To fit the model, we use a Markov chain Monte Carlo algorithm. We select the number of knots for the cubic B‐spline model using the Conditional Predictive Ordinate (CPO) and the Deviance Information Criterion (DIC). The method and model selection approach are validated in a simulation. We apply this method to examine the link between viral load, CD4 count, and time to event in data from an AIDS clinical trial. The cubic B‐spline model provides a good fit to the longitudinal data that could not be obtained with simple parametric models.
Complications of Intrathecal Baclofen Pump Therapy in Pediatric Patients

Background The aim of this study was to investigate and evaluate complications of intrathecal baclofen (ITB) pump implantation and maintenance in children with cerebral palsy. Methods We reviewed our entire consecutive series of pediatric patients treated with ITB between 1997 and 2006 at our hospital. There were 174 patients with a diagnosis of cerebral palsy, 8 with mixed dystonia, 2 with athetosis, and 3 with pure dystonia. During follow-up, 8 deaths occurred with no evidence of pump or catheter malfunction in any way contributing to the cause of death. Acute infection within 60 days of the surgery and late infection rates were calculated on the basis of number of incidents and incidents/follow-up patient years, respectively. Independently, a blinded caregiver phone questionnaire was completed in 92 cases. Results There were 316 surgical procedures; 161 were initial ITB pump implants at our institution. The average age at initial implant was 12 years, with an average follow-up of 3 years, 2 months. There were 80 planned replacement procedures (46 battery expirations and 3 planned pump replacements during posterior spinal fusion, 26 catheter replacements for posterior spinal fusion, and 5 reinsertions). There were 78 procedures in 57 patients related to complications, and the acute infection rate was 4.0%. The probability of developing a late infection was 1.0% per year of follow-up. On the basis of the follow-up questionnaire, 81% of parents/caregivers were satisfied with the treatment, and 87% would recommend ITB therapy. Conclusions ITB therapy is a safe and effective treatment for severe spasticity in the pediatric population, but does have a 31% rate of complications requiring surgical management over a 3-year treatment period. Parents and caregivers have a high rate of satisfaction and most would recommend the treatment to others.
Teaching single-cell digital analysis using droplet-based microfluidics.

Microfluidics allows the manipulation of small quantities of reagents in a high-throughput manner and is therefore highly amenable to single cell characterization and more generally to digital analysis, with applications in fields as varied as genomics, diagnostics, directed evolution, and drug screening. The growing place of microfluidics in biology laboratories encouraged us to develop a teaching method where advanced undergraduate or first-year graduate-level students are taught to fabricate droplet-based microfluidic devices, characterize them, and finally use them to perform a digital analysis of bacterial samples based on a phenotypic marker.
Effect of Organic Potato Farming on Human and Environmental Health and Benefits from New Plant Breeding Techniques. Is It Only a Matter of Public Acceptance

Organic farming practices are commonly thought to reduce the environmental impact of agriculture and to preserve the naturalness of the products. Herein, we report the effect of crop management practices on nutritional and toxicological value of potato tubers. Comparative studies are often controversial and the results are dependent on genotype and methodological approach. Targeted analysis and “omics” strategies are discussed, pointing at the nutritional aspects and the corresponding biological and molecular processes involved. Organic farming supporters still do not accept the use of genetic modification to produce new varieties suited for organic agriculture and crop improvement by genetic engineering still sparks hot debate among various scientific and social factions whose major concern is the possible existence of unintended effects both on human and world health. In this context, the advent of “new plant breeding techniques” has reignited the discussion on genetic engineering and on the compatibility of the new technologies with an eco-friendly agriculture. Could cisgenic and genome-edited potatoes be new good options for organic agriculture? We discuss how these approaches can be used to address food security challenges and to overcome specific problems based on the biological characteristics of potato tubers, producing new varieties that can improve farmers’ profit with a lower impact on public opinion. However, political, ethical, and social fears will probably persist much longer, mainly in Italy, historically a fiercely anti-GM country with a European leadership in organic food production and export.
Geometrical and Visual Feature Quantization for 3D Face Recognition

In this paper, we present an efficient method for 3D face recognition based on vector quantization of both geometrical and visual proprieties of the face. The method starts by describing each 3D face using a set of orderless features, and use then the Bag-of-Features paradigm to construct the face signature. We analyze the performance of three well-known classifiers: the Naı̈ve Bayes, the Multilayer perceptron and the Random forests. The results reported on the FRGCv2 dataset show the effectiveness of our approach and prove that the method is robust to facial expression.
Iterative correction of intersymbol interference: Turbo-equalization

This paper presents a receiving scheme intended to combat the detrimental effects of intersymbol interference for digital transmissions protected by convolutional codes. The receiver performs two successive soft-output decisions, achieved by a symbol detector and a channel decoder, through an iterative process. At each iteration, extrinsic information is extracted from the detection and decoding steps and is then used at the next iteration as in turbo-decoding. From the implementation point of view, the receiver can be structured in a modular way and its performance, in bit error rate terms, is directly related to the number of modules used. Simulation results are presented for transmissions on Gauss and Rayleigh channels. The results obtained show that turbo-equalization manages to overcome multipath effects, totally on Gauss channels, and partially but still satisfactorily on Rayleigh channels.
PhD thesis proposal Simulation of random geometric structures

The complexity of geometric algorithms is often express in terms of the input size and sometimes of the output size, but the behavior of these algorithms may depend drastically on the geometric distribution of the input. The difference between the best-case and the worst-case can be important. An alternative is to analyze these algorithms under the hypothesis of a probabilistic distribution of the data. When the input is a point set, an easy probabilistic hypothesis is to consider that points are independently distributed under some law (Poisson distribution, uniform distribution. . . ), unfortunately this hypothesis of independance may be unsuitable for several applications. The use of non independent distribution is very difficult to analyze theoretically, thus having access to simulations of practical instances would be of tremendous help to guide the intuition and to lead to reasonable conjectures. Unfortunately, the generation of useful random instances is a difficult question in itself. We plan to attack three specific questions, as described below: simulation of geometric structures, of conditioned structures, and of dependent pointsets.
Elevated expression of TANK-binding kinase 1 enhances tamoxifen resistance in breast cancer

Significance We investigated the possible role of TANK-binding kinase 1 (TBK1) protein in tamoxifen resistance and found that phosphorylation by TBK1 at the Ser-305 site stabilized estrogen receptor α (ERα) and modulated its transcriptional activity. Ectopic expression of TBK1 rendered breast cancer cells resistant to tamoxifen. TBK1 inhibition sensitized breast cancer cells to tamoxifen-induced cell death. The expression of TBK1 was increased in subjects with breast cancer and was positively correlated with ERα, ERα Ser-305, and cyclin D1 expression. Subjects with tumors that highly expressed TBK1 had poor responsiveness to tamoxifen treatment. Therefore, TBK1 is potentially a unique predictive marker of tamoxifen resistance and a potential therapeutic target for breast cancer. Resistance to antiestrogens is one of the major challenges in breast cancer treatment. Although phosphorylation of estrogen receptor α (ERα) is an important factor in endocrine resistance, the contributions of specific kinases in endocrine resistance are still not fully understood. Here, we report that an important innate immune response kinase, the IκB kinase-related TANK-binding kinase 1 (TBK1), is a crucial determinant of resistance to tamoxifen therapies. We show that TBK1 increases ERα transcriptional activity through phosphorylation modification of ERα at the Ser-305 site. Ectopic TBK1 expression impairs the responsiveness of breast cancer cells to tamoxifen. By studying the specimens from patients with breast cancer, we find a strong positive correlation of TBK1 with ERα, ERα Ser-305, and cyclin D1. Notably, patients with tumors highly expressing TBK1 respond poorly to tamoxifen treatment and show high potential for relapse. Therefore, our findings suggest that TBK1 contributes to tamoxifen resistance in breast cancer via phosphorylation modification of ERα.
ABO‐blood type incompatible living donor liver transplantation in a patient with Budd‐Chiari Syndrome secondary to essential thrombocythemia

Budd‐Chiari syndrome (BCS) results from diverse causative factors. Myeloproliferative disorders (MPDs) including essential thrombocythemia (ET) account for a minority of BCS cases in Japan. ABO‐blood‐type incompatible living donor liver transplantation (LDLT) in adults has become an acceptable procedure owing to the development of new strategies for preventing antibody‐mediated rejection. This report presents a rare case of BCS secondary to ET, which was cured by an ABO‐incompatible (AB to A) LDLT. In this case, prostaglandin E1 and gabexate mesilate were administered into portal vein and rituximab prophylaxis was applied. No splenectomy was performed as it is in most ABO‐incompatible cases, since a flow cytometry showed no anti‐B antibodies in the splenocytes collected by a wedge biopsy during the LDLT. The postoperative course was uneventful. Anti‐coagulation therapy was initiated with aspirin and warfarin instead of hydroxyurea. This report describes an ABO‐incompatible LDLT without a splenectomy for BCS secondary to ET.
Transthoracic echocardiography in models of cardiac disease in the mouse.

BACKGROUND Transthoracic echocardiography (M-mode and Doppler) offers a noninvasive approach for in vivo evaluation of the mouse heart. The present study examines its usefulness for assessing the morphological/functional phenotype of the left ventricle (LV) in several transgenic and surgical murine models of cardiac disease. METHODS AND RESULTS Observations were made in 83 intact, anesthetized mice. In mice with a surgical arteriovenous fistula, volume overload and LV dilation were detected. In normal mice, echocardiographic indexes of increased contractility (dobutamine) were confirmed by LV dP/dtmax. In transgenic mice with overexpression of the beta 2-adrenergic receptor, heart rate and mean velocity of circumferential fiber shortening were increased, indicating enhanced contractility. In colony screening of transgenic mice overexpressing the H-ras gene, 45% had increased LV wall thickness (> 0.9 mm), and those showing a striking increase were selected for breeding. In mice with LV hypertrophy (aortic constriction) and normal mice, the actual LV mass determined by echocardiography correlated well (r = .93), and 95% confidence limits were determined. The maximum intraobserver and interobserver coefficients of variation for M-mode data were 0.03 +/- 0.29 mm (+/- 2 SD), < 10% for LV internal dimensions but 27% to 30% for wall thickness. CONCLUSIONS These studies provide the first application of transthoracic echocardiography for morphological/functional characterization of the cardiac phenotype in transgenic and surgical murine models, including (1) high reliability for detecting LV chamber dilation and function; (2) reliability (and its limits) for determining abnormal LV wall thickness and LV mass; (3) identification of marked, sometimes asymmetrical, hypertrophy in a transgenic model of hypertrophic cardiomyopathy; and (4) usefulness for transgenic colony screening to identify markedly abnormal phenotypes.
Compact Asymmetric-Slit Microstrip Antennas for Circular Polarization

Four compact asymmetric-slit microstrip antennas are proposed and studied for circular polarization. By cutting asymmetrical slits in diagonal directions onto the square microstrip patches, the single coaxial-feed microstrip patch antennas are realized for circularly polarized radiation with compact antenna size. The performances of the proposed antennas with several asymmetric-slit shapes onto the patch radiators are compared. The measured 10-dB return loss and 3-dB axial-ratio bandwidths of the antenna prototype are around 2.5% and 0.5%, respectively. The proposed asymmetric-slit configurations are useful for compact circularly polarized microstrip patch antennas and array design.
Block Analysis of Bilingual Corpus for Chinese-English Statistical Machine Translation

In this paper, we describe a bilingual corpus processing strategy, block analysis, from a new point of view. By this analysis strategy, we want to extract more information from bilingual corpus for future statistical machine translation. At first, we define some block types and give some statistical data from a Chinese-English bilingual corpus under this framework. Then a block-based alignment algorithm is presented, by which we can extract and align the corresponding bilingual blocks automatically. Some experimental results show that block analysis is practical and more informative than any other word-based approach.
Sustained drug use changes following hepatitis C screening and counseling among recently infected persons who inject drugs : a longitudinal study

Bruneau, J 1,2 , Zang, G 1 , Abrahamowicz, M 3 , Jutras-Aswad, D 1,4 , Daniel, M 5 , Roy, E 6,7 . 1 Research Center, Centre hospitalier de l’Université de Montréal (CRCHUM), Montréal, Québec, Canada. 2 Department of Family Medicine, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada. 3 Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Québec, Canada; 4 Department of Psychiatry, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada. 5 School of Population Health, University of South Australia, Adelaide, South Australia, Australia 6 Addiction Research and Study Program, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Longueuil, Québec, Canada. 7 Montreal Public Health Department, Agence de la santé et des services sociaux de Montréal, Montréal, Québec, Canada.
Finding a practical method to increase engagement of residents on a dementia care unit

Previous research has shown that it is possible to increase the engagement of residents with dementia in daily activities by making changes in institutional care practices. However, these changes often require expensive and cumbersome staff training programs that longterm care facilities may be unlikely to adopt and maintain. This study evaluates a simple, inexpensive recording and feedback procedure to increase resident engagement in a way that may be more amenable to adoption by long-term care facilities. Nursing assistants working in a locked dementia care unit were asked to complete a daily activity record on which they recorded the amount and quality of resident engagement. The facility's activity director was asked to read these activity records each day and give immediate, positive feedback to the nursing assistants. This procedure was evaluated by using a control series design. Results revealed baseline engagement observations with a mean of 11 percent, which increased to a mean of 44 percent during observations under treatment conditions. This study suggests that simple, inexpensive changes in institutional practices can make meaningful improvements in the level of engagement of residents with dementia.