Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Network Analysis by Quasi-Bayesian Method

Genetic network analysis provides an important statistical strategy for the study of gene-gene interactions. Although existing methods work well in practice, several opportunities for improvement remain. For example, the regulation coefficients of some of the existing methods are not easy to solve, nor are the solutions they provide unique. Also, as genetic network analysis are typically applied to small datasets with large number of parameters, having prior knowledge about the parameters is valuable and should be incorporated into the analysis. The uniqueness of the parameter estimate and computational simplicity are also desirable in practice. To address these problems, we considered a quasi-Bayesian method for the analysis of gene regulatory networks by a multivariate linear model in which the data distribution is a quasi-likelihood, and the inference is Bayesian. This method incorporates prior information on the regulatory relationships; the set of regulation coefficients has a unique closed-form solution, and is very simple to compute. The model is evaluated by simulation and illustrated using a real dataset. This method is simple to use, permits information updating, is flexible to incorporate desired features, and has closed-form solution. Simulation studies show that the model fits the data quite well.
Confessus pro iudicato

Il faut considerer ensemble l'aveu civil et l'aveu penal, qui forment antithese. Le regime de l'un s'eclaire par contraste avec le regime de l'autre. En procedure civile, l'aveu procede d'un accord sur une composition pecuniaire. N'est pro iudicato que le defendeur qui reconnait sa dette, accepte de monnayer sa faute ou d'estimer en argent la prestation qu'il doit. En procedure penale, l'aveu n'a aucune efficacite juridique, puisque le contrat ne s'y substitue pas au jugement. La seule confessio possible est la priere de grâce, procede exorbitant du droit commun, parce qu'est rompue l'egalite du rapport judiciaire. Entre ces deux poles opposes du civil et du penal, un rapprochement s'opere chez les rheteurs et les juristes de l'Empire. Sur le double registre de la dette et de la faute, le confessus apparait se condamner lui-meme ! Coaction interne de l'aveu spontane, qui pour le citoyen prepare a la violence externe de l'aveu arrache.
Consistent Estimation of the Filtering and Marginal Smoothing Distributions in Nonparametric Hidden Markov Models

In this paper, we consider the filtering and smoothing recursions in nonparametric finite state space hidden Markov models (HMMs) when the parameters of the model are unknown and replaced by estimators. We provide an explicit and time uniform control of the filtering and smoothing errors in total variation norm as a function of the parameter estimation errors. We prove that the risk for the filtering and smoothing errors may be uniformly upper bounded by the <inline-formula> <tex-math notation="LaTeX">$\mathrm {L}^{1}$ </tex-math></inline-formula>-risk of the estimators. It has been proved very recently that statistical inference for finite state space nonparametric HMMs is possible. We study how the recent spectral methods developed in the parametric setting may be extended to the nonparametric framework and we give explicit upper bounds for the <inline-formula> <tex-math notation="LaTeX">$\mathrm {L}^{2}$ </tex-math></inline-formula>-risk of the nonparametric spectral estimators. In the case where the observation space is compact, this provides explicit rates for the filtering and smoothing errors in total variation norm. The performance of the spectral method is assessed with simulated data for both the estimation of the (nonparametric) conditional distribution of the observations and the estimation of the marginal smoothing distributions.
No Association Between Telomere Length and Survival Among the Elderly and Oldest Old

Background: The consistent findings of a negative correlation between telomere length and replicative potential of cultured cells, as well as a decreasing telomere length in a number of different tissues in humans with age, have led to the suggestion that telomeres play a role in cellular aging in vivo and ultimately even in organismal aging. Furthermore, one small longitudinal study of elderly individuals has suggested that longer telomeres are associated with better survival. Methods: Telomere length was measured as mean terminal restriction fragment length on blood cells from 812 persons, age 73 to 101 years, who participated in population-based surveys in 1997–1998. Among the participants were 652 twins. The participants were followed up through the Danish Civil Registration system until January 2005, at which time 412 (51%) were dead. Results: Univariate Cox regression analyses revealed that longer telomeres were associated with better survival (hazard ratios = 0.89 [95% confidence interval = 0.76–1.04] per 1 kb in males and 0.79 [0.72–0.88] per 1 kb in females, respectively). However, including age in the analyses changed the estimates to 0.97 (0.83–1.14) and 0.93 (0.85–1.03), respectively. Intrapair comparison showed that among 175 twin pairs in which at least one died during follow up, it was the twin with the shorter telomere length who died first in 97 (55%) of the pairs (95% confidence interval = 48–63%). We could not confirm the recently reported negative correlation between telomere length and obesity or between telomere length and smoking. Conclusion: This longitudinal study of the elderly and oldest old does not support the hypothesis that telomere length is a predictor for remaining lifespan once age is controlled for.
Serum Response Factor Regulates Hippocampal Lamination and Dendrite Development and Is Connected with Reelin Signaling

ABSTRACT During brain development, neurons and their nerve fibers are often segregated in specific layers. The hippocampus is a well-suited model system to study lamination in health and aberrant cell/fiber lamination associated with neurological disorders. SRF (serum response factor), a transcription factor, regulates synaptic-activity-induced immediate-early gene (IEG) induction and cytoskeleton-based neuronal motility. Using early postnatal conditional SRF ablation, we uncovered distorted hippocampal lamination, including malpositioning of granule cell neurons and disruption of layer-restricted termination of commissural-associational and mossy fiber axons. Besides axons, dendrite branching and spine morphogenesis in Srf mutants were impaired, offering a first morphological basis for SRF's reported role in learning and memory. Srf mutants resemble mice lacking components of the reelin signaling cascade, a fundamental signaling entity in brain lamination. Our data indicate that reelin signaling and SRF-mediated gene transcription might be connected: reelin induces IEG and cytoskeletal genes in an SRF-dependent manner. Further, reelin-induced neurite motility is blocked in Srf mutants and constitutively active SRF rescues impaired neurite extension in reeler mouse mutants in vitro. In sum, data provided in this report show that SRF contributes to hippocampal layer and nerve fiber organization and point at a link between Srf gene transcription and reelin signaling.
LJ2M dataset: Toward better understanding of music listening behavior and user mood

Recent years have witnessed a growing interest in modeling user behaviors in multimedia research, emphasizing the need to consider human factors such as preference, activity, and emotion in system development and evaluation. Following this research line, we present in this paper the LiveJournal two-million post (LJ2M) dataset to foster research on user-centered music information retrieval. The new dataset is characterized by the great diversity of real-life listening contexts where people and music interact. It contains blog articles from the social blogging website LiveJournal, along with tags self-reporting a user's emotional state while posting and the musical track that the user considered as the best match for the post. More importantly, the data are contributed by users spontaneously in their daily lives, instead of being collected in a controlled environment. Therefore, it offers new opportunities to understand the interrelationship among the personal, situational, and musical factors of music listening. As an example application, we present research investigating the interaction between the affective context of the listener and the affective content of music, using audio-based music emotion recognition techniques and a psycholinguistic tool. The study offers insights into the role of music in mood regulation and demonstrates how LJ2M can contribute to studies on real-world music listening behavior.
AUTOLOGOUS PLASMIN FOR PHARMACOLOGIC VITREOLYSIS PREPARED 1 HOUR BEFORE SURGERY

Purpose: To evaluate the safety and efficacy of intravitreal injection of autologous plasmin enzyme (APE) in inducing a posterior vitreous detachment (PVD). APE was obtained by a modified method 1 hour before surgery. Methods: APE was obtained by centrifugation of autologous whole blood from the patients 1 hour before surgery and by incubation with streptokinase. APE was injected in the vitreous cavity 20 minutes before surgery. This procedure was applied for 20 patients who underwent vitrectomy for macular pucker, macular hole, and macular edema due to vitreoretinal traction. The status of PVD was graded intraoperatively. The plasmin concentration obtained by this method and the plasminogen titer of the plasma from each patient were compared. Activated partial thromboplastin time was controlled before surgery and 1, 6, 12, and 24 hours after surgery to evaluate alteration of the coagulation due to systemic absorption of the plasmin. Results: Preparation of APE was easy and took on average 45 minutes for all patients. A PVD with an evident Weiss ring was observed during surgery in 17 eyes (85%). The average plasmin activity was 0.26 IU/0.2 mL activated plasma. The partial thromboplastin time did not show any alteration in any of the patients with respect to preoperative values. Conclusion: APE obtained by this method can lead to a PVD and facilitate the complete remotion of vitreous cortex. The intravitreal injection does not lead to alteration of systemic blood coagulation.
DEVELOPMENT OF ELISA TECHNIQUE FOR THE ANALYSIS OF ATRAZINE RESIDUES IN WATER

A highly sensitive enzyme immunoassay is described for the detection of atrazine residues in water. Atrazine derivative was conjugated to Bovine Serum Albumin (BSA) to obtain an immunizing antigen and to Horseradish Peroxidase enzyme (POD) to obtain a marker for immunoassay. The formation of these conjugations was confirmed by UV spectroscopy as well as by gel-electrophoresis. Polyclonal antibodies were raised in rabbits by immunization with an atrazine–BSA conjugate containing 29 atrazine residues per BSA molecule. An ELISA on microtitration plates was optimized with peroxidase–atrazine conjugate. The middle of the test (50% B/Bo) was found to be at 90 ng/l, which is well below the maximum concentration permitted by the EC guidelines for drinking water. Detection limits for atrazine of about 1 ng/l could be reached. The assay did not require concentration or cleanup steps for drinking or ground water samples. Validation experiments showed good accuracy and precision. No cross-reactivities were shown by other s-triazines like terbutryn, ametryn, terbuthylazine, des-isopropylatrazine, and de-ethylatrazine except hydroxyatrazine. The latter was present at very low levels that can be calibrated/standardized before analysis or it may be considered as leftover residues of atrazine. Based on these results, it is suggested that this test can be applied to obtain fairly accurate results for atrazine concentration in water samples from different sources.
Biodesalination: A Case Study for Applications of Photosynthetic Bacteria in Water Treatment1[C]

Current knowledge, methodologies, and public acceptance issues present challenges and opportunities for the use of cyanobacteria in water treatment. Shortage of freshwater is a serious problem in many regions worldwide, and is expected to become even more urgent over the next decades as a result of increased demand for food production and adverse effects of climate change. Vast water resources in the oceans can only be tapped into if sustainable, energy-efficient technologies for desalination are developed. Energization of desalination by sunlight through photosynthetic organisms offers a potential opportunity to exploit biological processes for this purpose. Cyanobacterial cultures in particular can generate a large biomass in brackish and seawater, thereby forming a low-salt reservoir within the saline water. The latter could be used as an ion exchanger through manipulation of transport proteins in the cell membrane. In this article, we use the example of biodesalination as a vehicle to review the availability of tools and methods for the exploitation of cyanobacteria in water biotechnology. Issues discussed relate to strain selection, environmental factors, genetic manipulation, ion transport, cell-water separation, process design, safety, and public acceptance.
Splicing Factor SRp30c Interaction with Y-box Protein-1 Confers Nuclear YB-1 Shuttling and Alternative Splice Site Selection*

The multifunctional DNA- and RNA-associated Y-box protein 1 (YB-1) specifically binds to splicing recognition motifs and regulates alternative splice site selection. Here, we identify the arginine/serine-rich SRp30c protein as an interacting protein of YB-1 by performing a two-hybrid screen against a human mesangial cell cDNA library. Co-immunoprecipitation studies confirm a direct interaction of tagged proteins YB-1 and SRp30c in the absence of RNA via two independent protein domains of YB-1. A high affinity interaction is conferred through the N-terminal region. We show that the subcellular YB-1 localization is dependent on the cellular SRp30c content. In proliferating cells, YB-1 localizes to the cytoplasm, whereas FLAG-SRp30c protein is detected in the nucleus. After overexpression of YB-1 and FLAG-SRp30c, both proteins are co-localized in the nucleus, and this requires the N-terminal region of YB-1. Heat shock treatment of cells, a condition under which SRp30c accumulates in stress-induced Sam68 nuclear bodies, abrogates the co-localization and YB-1 shuttles back to the cytoplasm. Finally, the functional relevance of the YB-1/SRp30c interaction for in vivo splicing is demonstrated in the E1A minigene model system. Here, changes in splice site selection are detected, that is, overexpression of YB-1 is accompanied by preferential 5′ splicing site selection and formation of the 12 S isoform.
The biological degradation of cellulose.

Cellulolytic microorganisms play an important role in the biosphere by recycling cellulose, the most abundant carbohydrate produced by plants. Cellulose is a simple polymer, but it forms insoluble, crystalline microfibrils, which are highly resistant to enzymatic hydrolysis. All organisms known to degrade cellulose efficiently produce a battery of enzymes with different specificities, which act together in synergism. The study of cellulolytic enzymes at the molecular level has revealed some of the features that contribute to their activity. In spite of a considerable diversity, sequence comparisons show that the catalytic cores of cellulases belong to a restricted number of families. Within each family, available data suggest that the various enzymes share a common folding pattern, the same catalytic residues, and the same reaction mechanism, i.e. either single substitution with inversion of configuration or double substitution resulting in retention of the beta-configuration at the anomeric carbon. An increasing number of three-dimensional structures is becoming available for cellulases and xylanases belonging to different families, which will provide paradigms for molecular modeling of related enzymes. In addition to catalytic domains, many cellulolytic enzymes contain domains not involved in catalysis, but participating in substrate binding, multi-enzyme complex formation, or possibly attachment to the cell surface. Presumably, these domains assist in the degradation of crystalline cellulose by preventing the enzymes from being washed off from the surface of the substrate, by focusing hydrolysis on restricted areas in which the substrate is synergistically destabilized by multiple cutting events, and by facilitating recovery of the soluble degradation products by the cellulolytic organism. In most cellulolytic organisms, cellulase synthesis is repressed in the presence of easily metabolized, soluble carbon sources and induced in the presence of cellulose. Induction of cellulases appears to be effected by soluble products generated from cellulose by cellulolytic enzymes synthesized constitutively at a low level. These products are presumably converted into true inducers by transglycosylation reactions. Several applications of cellulases or hemicellulases are being developed for textile, food, and paper pulp processing. These applications are based on the modification of cellulose and hemicellulose by partial hydrolysis. Total hydrolysis of cellulose into glucose, which could be fermented into ethanol, isopropanol or butanol, is not yet economically feasible. However, the need to reduce emissions of greenhouse gases provides an added incentive for the development of processes generating fuels from cellulose, a major renewable carbon source.
Investigation of the Lateral Light-induced Migration of Photosystem II Light-harvesting Proteins by Nano-high Performance Liquid Chromatography Electrospray Ionization Mass Spectrometry*

This study reports a detailed analysis of the light-induced lateral migration of the photosystem II (PSII) antennae between appressed and non-appressed thylakoid membranes. The relative PSII antennae that migrated to stroma lamellae were readily established on the basis of peak areas of the separated stroma proteins in the ultraviolet chromatograms. Phosphorylation was predicted by intact molecular mass measurements, and this was confirmed by immunoblotting. When thylakoid membrane and chloroplasts were illuminated at 100 μE m–2s–1, light-harvesting complex type II (Lhcb2) was the first PSII antenna to migrate, preferentially in phosphorylated form. However, the amount of Lhcb2 that migrated decreased after the first 20 min when the total amount of the three different Lhcb1 isoforms (1.1, 1.2, and 1.3) reached maximum. Lhcb1.1 was always found in the unphosphorylated form and migrated later than the other two isoforms, although the latter were also found to have low levels of phosphorylation. At the same time, major antennae on the grana were not found to be phosphorylated, whereas Lhcb4 showed a significant increase in molecular mass. At higher light intensity Lhcb2 migration was negligible, whereas migration of Lhcb1 isoforms was little changed, increasing in irradiated chloroplasts. Because there was no significant phosphorylation at high light intensity, and yet pigments were found to have significantly increased on the stroma lamellae, it may be that pigments play a role in migration and that, in fact, there is no direct correlation between phosphorylation and migration. We hypothesize that the Lhcb1 isoforms expressed by the multigene families play a role in plant adaptation.
AEROBIC AND ANAEROBIC CORRELATES OF MULTIPLE SPRINT CYCLING PERFORMANCE

The aims of this study were to examine (a) the relationship between maximal oxygen uptake (&OV0312;O2max) and several performance indices of multiple sprint cycling; (b) the relationship between maximal accumulated oxygen deficit (MAOD) and those same performance indices; and (c) the influence of recovery duration on the magnitude of those relationships. Twenty-five physically active men completed a &OV0312;O2max test, a MAOD test, and 2 maximal intermittent (20 × 5 seconds) sprint cycling tests with contrasting recovery periods (10 seconds or 30 seconds). Mean ± SD for age, height, and body mass were 20.6 ± 1.5 years, 177.2 ± 5.4 cm, and 78.2 ± 8.2 kg, respectively. All tests were conducted on a friction-braked cycle ergometer with subsequent data normalized for body mass. Moderate (0.3 ≤ r < 0.5) positive correlations were observed between power output data and MAOD (range, 0.31–0.46; 95% confidence limits, −0.10 to 0.72). Moderate to large positive correlations also were observed between power output data and &OV0312;O2max, the magnitude of which increased as values were averaged across all sprints (range, 0.45–0.67; 95% confidence limits 0.07–0.84). Correlations between fatigue and &OV0312;O2max were greater in the intermittent protocol with 30-second recovery periods (r = −0.34; 95% confidence limits, 0.06 to −0.65). The results of this study reflect the complex energetics associated with multiple sprint work. Though the findings add support to the idea that multiple sprint sports demand a combination of speed and endurance, further longitudinal research is required to confirm the relative importance of these parameters.
Pharmacological characterization of a new antimuscarinic agent, solifenacin succinate, in comparison with other antimuscarinic agents.

Solifenacin succinate [YM905; (3R)-1-azabicyclo[2.2. 2]oct-3-yl(1S)-1-phenyl-3,4-dihydroisoquinoline-2(1H)-carboxylate monosuccinate] is a new muscarinic receptor antagonist developed for the treatment of overactive bladder. The aim of the present study was to evaluate the antimuscarinic properties of solifenacin and to compare the results with those obtained for tolterodine, oxybutynin, darifenacin, propiverine and atropine. In radioligand receptor binding assay, Ki values of solifenacin for human muscarinic M1, M2, M3, M4 and M5 receptors were 26, 170, 12, 110 and 31 nM, respectively. In isolated rat urinary bladder, solifenacin competitively antagonized carbachol-induced contractions, with a pA2 value of 7.44+/-0.09. In these in vitro studies, the antimuscarinic action of solifenacin was more potent than that of propiverine and less potent than those of tolterodine, oxybutynin, darifenacin and atropine. In anesthetized rats, solifenacin and oxybutynin increased the maximum bladder capacity in a dose-dependent manner and also decreased the maximum intravesical pressure. The dosages required to produce a 30% increase in maximum bladder capacity (ED30 values) of solifenacin and oxybutynin were 0.35 and 0.30 mg/kg i.v. , respectively, indicating approximately equal efficacies. These results support the fact that solifenacin, similarly to currently used antimuscarinic agents, is an effective agent in the treatment of overactive bladder symptoms such as urinary frequency and urge incontinence.
Mutations in the aph(2")-Ic Gene Are Responsible for Increased Levels of Aminoglycoside Resistance

ABSTRACT Random PCR mutagenesis of the enterococcal aph(2")-Ic gene followed by selection for mutant enzymes that confer enhanced levels of aminoglycoside resistance resulted in mutants of APH(2")-Ic with His-258-Leu and Phe-108-Leu substitutions, all of which conferred rises in the MICs of several aminoglycosides. The mutated residues are located outside conserved regions of aminoglycoside phosphotransferases.