Miracle-dz/UniFAR-FTUs huggingface dataset:
Localization of nicotinic acetylcholine receptor alpha-subunit transcripts during myogenesis and motor endplate development in the chick

In 15-d-old chick latissimi dorsi muscles, the nicotinic acetylcholine receptor (AChR) alpha-subunit mRNA is densely accumulated at the level of subsynaptic nuclei of the motor endplate (Fontaine et al., 1988). In this paper, using in situ hybridization with genomic probes, we further show that the expression of the AChR alpha-subunit gene in the embryo, revealed by the accumulation of mature mRNAs, starts in myotomal cells and persists during the first stages of muscle development in a majority of muscle nuclei. Subsequently, the distribution of AChR alpha- subunit mRNAs becomes restricted to the newly formed motor endplates as neuromuscular junctions develop. To assess the transcriptional activity of individual nuclei in developing muscles, a strictly intronic fragment of the AChR alpha-subunit gene was used to probe in situ the level of unspliced transcripts. AChR alpha-subunit unspliced transcripts accumulate around a large number of sarcoplasmic nuclei at embryonic day 11, but can no longer be detected at their level after embryonic day 16 in the embryo. A similar decrease in the accumulation of AChR alpha-subunit transcripts is observed between day 4 and day 6 in primary cultures of muscle cells. On the other hand, in vivo denervation and in vitro blocking of muscle electrical activity by the sodium channel blocker tetrodotoxin results in an increase in the labeling of muscle nuclei. Yet, only 6% of the muscle nuclei appear labeled by the strictly intronic probes after denervation. The possible significance of such heterogeneity of muscle nuclei during motor endplate formation in AChR gene expression is discussed.
Information Visualization for DNA Microarray Data Analysis: A Critical Review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work.
The Pseudomonas syringae HopPtoV Protein Is Secreted in Culture and Translocated into Plant Cells via the Type III Protein Secretion System in a Manner Dependent on the ShcV Type III Chaperone

ABSTRACT The bacterial plant pathogen Pseudomonas syringae depends on a type III protein secretion system and the effector proteins that it translocates into plant cells to cause disease and to elicit the defense-associated hypersensitive response on resistant plants. The availability of the P. syringae pv. tomato DC3000 genome sequence has resulted in the identification of many novel effectors. We identified the hopPtoV effector gene on the basis of its location next to a candidate type III chaperone (TTC) gene, shcV, and within a pathogenicity island in the DC3000 chromosome. A DC3000 mutant lacking ShcV was unable to secrete detectable amounts of HopPtoV into culture supernatants or translocate HopPtoV into plant cells, based on an assay that tested whether HopPtoV-AvrRpt2 fusions were delivered into plant cells. Coimmunoprecipitation and Saccharomyces cerevisiae two-hybrid experiments showed that ShcV and HopPtoV interact directly with each other. The ShcV binding site was delimited to an N-terminal region of HopPtoV between amino acids 76 and 125 of the 391-residue full-length protein. Our results demonstrate that ShcV is a TTC for the HopPtoV effector. DC3000 overexpressing ShcV and HopPtoV and DC3000 mutants lacking either HopPtoV or both ShcV and HopPtoV were not significantly impaired in disease symptoms or bacterial multiplication in planta, suggesting that HopPtoV plays a subtle role in pathogenesis or that other effectors effectively mask the contribution of HopPtoV in plant pathogenesis.
Antisense Oligonucleotides Modulating Activation of a Nonsense-Mediated RNA Decay Switch Exon in the ATM Gene

ATM (ataxia-telangiectasia, mutated) is an important cancer susceptibility gene that encodes a key apical kinase in the DNA damage response pathway. ATM mutations in the germ line result in ataxia-telangiectasia (A-T), a rare genetic syndrome associated with hypersensitivity to double-strand DNA breaks and predisposition to lymphoid malignancies. ATM expression is limited by a tightly regulated nonsense-mediated RNA decay (NMD) switch exon (termed NSE) located in intron 28. In this study, we identify antisense oligonucleotides that modulate NSE inclusion in mature transcripts by systematically targeting the entire 3.1-kb-long intron. Their identification was assisted by a segmental deletion analysis of transposed elements, revealing NSE repression upon removal of a distant antisense Alu and NSE activation upon elimination of a long terminal repeat transposon MER51A. Efficient NSE repression was achieved by delivering optimized splice-switching oligonucleotides to embryonic and lymphoblastoid cells using chitosan-based nanoparticles. Together, these results provide a basis for possible sequence-specific radiosensitization of cancer cells, highlight the power of intronic antisense oligonucleotides to modify gene expression, and demonstrate transposon-mediated regulation of NSEs.
An unsupervised center sentence-based clustering approach for rule-based question answering

Question answering (QA) systems have widely employed clustering methods to improve efficiency. However, QA systems with unsupervised automatic statistical processing do not seem to achieve higher accuracies than other approaches. Therefore, with the motivation of obtaining optimal accuracy of retrieved answers under unsupervised automatic processing of sentences, we introduce a syntactic sequence clustering method for answer matching in rule-based QA. Our clustering method called CEnter SEntence-baseD (CESED) Clustering is able to achieve accuracies as high as 84.62% for WHERE-type questions.
Iowa State University From the SelectedWorks of Elena Cotos 2008 Automatic identification of discourse moves in scientific article introductions

This paper reports on the first stage of building an educational tool for international graduate students to improve their academic writing skills. Taking a text-categorization approach, we experimented with several models to automatically classify sentences in research article introductions into one of three rhetorical moves. The paper begins by situating the project within the larger framework of intelligent computer-assisted language learning. It then presents the details of the study with very encouraging results. The paper then concludes by commenting on how the system may be improved and how the project is intended to be pursued and evaluated.
Heat transfer from nanoparticles: A corresponding state analysis

In this contribution, we study situations in which nanoparticles in a fluid are strongly heated, generating high heat fluxes. This situation is relevant to experiments in which a fluid is locally heated by using selective absorption of radiation by solid particles. We first study this situation for different types of molecular interactions, using models for gold particles suspended in octane and in water. As already reported in experiments, very high heat fluxes and temperature elevations (leading eventually to particle destruction) can be observed in such situations. We show that a very simple modeling based on Lennard–Jones (LJ) interactions captures the essential features of such experiments and that the results for various liquids can be mapped onto the LJ case, provided a physically justified (corresponding state) choice of parameters is made. Physically, the possibility of sustaining very high heat fluxes is related to the strong curvature of the interface that inhibits the formation of an insulating vapor film.
Ngram-Based Statistical Machine Translation Enhanced with Multiple Weighted Reordering Hypotheses

This paper describes the 2007 Ngram-based statistical machine translation system developed at the TALP Research Center of the UPC (Universitat Politecnica de Catalunya) in Barcelona. Emphasis is put on improvements and extensions of the previous years system, being highlyghted and empirically compared. Mainly, these include a novel word ordering strategy based on: (1) statistically monotonizing the training source corpus and (2) a novel reordering approach based on weighted reordering graphs. In addition, this system introduces a target language model based on statistical classes, a feature for out-of-domain units and an improved optimization procedure. The paper provides details of this system participation in the ACL 2007 SECOND WORKSHOP ON STATISTICAL MACHINE TRANSLATION. Results on three pairs of languages are reported, namely from Spanish, French and German into English (and the other way round) for both the in-domain and out-of-domain tasks.
Ion Wind Generator Utilizing Bipolar Discharge in Parallel Pin Geometry

We present a simple and efficient airflow generator utilizing the effect of ion wind by generating simultaneously both the positive and negative ions from two sharp electrodes mounted parallel to each other. The unique bipolar geometrical setup eliminates the effect of space charge by the high recombination rate of oppositely charged ions. The two-electrode arrangement is symmetrical, where the electrode creating charged ions of one polarity also serves as the reference electrode to establish the electric field required for ion creation by the opposite electrode, and vice versa. Unlike the conventional setup, with a single electrode generating ion wind with movement toward the reference electrode, in this configuration the air movement is parallel to the electrodes, and is directed away from the device. The airflow behavior is studied by both experiments and numerical simulation. The ion wind speed has a linear relationship with the square root of the discharge current, U ∝ √I, and its measured values agree well with simulation. The characterization of the discharge current-voltage relationship was derived from mathematical processing in the general form I = b(V - Vo)n. The ion wind speed and the current-voltage characteristics depend on the interspace between the electrodes and the electrode geometry. An ion wind speed on the order of ms-1 is created with a microampere discharge current, resulting in a total net charge of only several femtoampere. The proposed configuration is beneficial in minimizing the power consumption of the system, and in enabling air recirculation for airflow control applications, cooling applications, propulsion technology, and micropump design, especially for the applications where neutralized ion wind flow is required.
Natural Product Research in the Australian Marine Invertebrate Dicathais orbita

The predatory marine gastropod Dicathais orbita has been the subject of a significant amount of biological and chemical research over the past five decades. Natural products research on D. orbita includes the isolation and identification of brominated indoles and choline esters as precursors of Tyrian purple, as well as the synthesis of structural analogues, bioactivity testing, biodistributional and biosynthetic studies. Here I also report on how well these compounds conform to Lipinski’s rule of five for druglikeness and their predicted receptor binding and enzyme inhibitor activity. The composition of mycosporine-like amino acids, fatty acids and sterols has also been described in the egg masses of D. orbita. The combination of bioactive compounds produced by D. orbita is of interest for further studies in chemical ecology, as well as for future nutraceutical development. Biological insights into the life history of this species, as well as ongoing research on the gene expression, microbial symbionts and biosynthetic capabilities, should facilitate sustainable production of the bioactive compounds. Knowledge of the phylogeny of D. orbita provides an excellent platform for novel research into the evolution of brominated secondary metabolites in marine molluscs. The range of polarities in the brominated indoles produced by D. orbita has also provided an effective model system used to develop a new method for biodistributional studies. The well characterized suite of chemical reactions that generate Tyrian purple, coupled with an in depth knowledge of the ecology, anatomy and genetics of D. orbita provide a good foundation for ongoing natural products research.
Maternal Care and Individual Differences in Defensive Responses

Familial transmission of mental illness is common. Recent studies in behavioral neuroscience and biological psychiatry reveal the importance of epigenetic mechanisms of transmission that center on the developmental consequences of variations in parental care. Studies with rats suggest that environmental adversity results in patterns of parent–offspring interactions that increase stress reactivity through sustained effects on gene expression in brain regions known to regulate behavioral, endocrine, and autonomic responses to stress. While such effects might be adaptive, the associated cost involves an increased risk for stress-related illness.
Estimating endogenous changes in task performance from EEG

Brain wave activity is known to correlate with decrements in behavioral performance as individuals enter states of fatigue, boredom, or low alertness.Many BCI technologies are adversely affected by these changes in user state, limiting their application and constraining their use to relatively short temporal epochs where behavioral performance is likely to be stable. Incorporating a passive BCI that detects when the user is performing poorly at a primary task, and adapts accordingly may prove to increase overall user performance. Here, we explore the potential for extending an established method to generate continuous estimates of behavioral performance from ongoing neural activity; evaluating the extended method by applying it to the original task domain, simulated driving; and generalizing the method by applying it to a BCI-relevant perceptual discrimination task. Specifically, we used EEG log power spectra and sequential forward floating selection (SFFS) to estimate endogenous changes in behavior in both a simulated driving task and a perceptual discrimination task. For the driving task the average correlation coefficient between the actual and estimated lane deviation was 0.37 ± 0.22 (μ ± σ). For the perceptual discrimination task we generated estimates of accuracy, reaction time, and button press duration for each participant. The correlation coefficients between the actual and estimated behavior were similar for these three metrics (accuracy = 0.25 ± 0.37, reaction time = 0.33 ± 0.23, button press duration = 0.36 ± 0.30). These findings illustrate the potential for modeling time-on-task decrements in performance from concurrent measures of neural activity.
Modeling the behavior of flooding on target location discovery in mobile ad hoc networks

In this paper, we model the behavior of packet forwarding via a multihop path in mobile ad hoc networks. In our analysis, we consider a densely populated network and assume a flooding protocol for packet forwarding. We find that the behavior of packet forwarding in such an environment can be regarded as dropping a stone into a lake, and then counting the number of ripples moving out from the source (i.e., the center) to the destination. What makes the problem complicated is the node mobility during the packet forwarding. As a result, we cannot solely count the number of ripples in between as the number of hops in the path on which the packet traverses. We then derive the probability distribution function of hop counts for packet forwarding, accounting for node movements. Based on the analytical model, we then evaluate several different types of flooding mechanisms commonly adopted for target searching in ad hoc networks. Compared with existing work, which assumes a snapshot of the network and all nodes are static in the analysis, our analytical framework provides more insights for the study of efficient flooding in mobile ad hoc networks.
Patupilone (Epothilone B) for Recurrent Glioblastoma: Clinical Outcome and Translational Analysis of a Single-Institution Phase I/II Trial

Background: Patients with glioblastoma (GBM) inevitably develop recurrent or progressive disease after initial multimodal treatment and have a median survival of 6–9 months from time of progression. To date, there is no accepted standard treatment for GBM relapse or progression. Patupilone (EPO906) is a novel natural microtubule-stabilizing cytotoxic agent that crosses the blood-brain barrier and has been found to have preclinical activity in glioma models. Methods: This is a single-institution, early-phase I/II trial of GBM patients with tumor progression who qualified for second surgery with the goal of evaluating efficacy and safety of the single-agent patupilone (10 mg/m2, every 3 weeks). Patients received patupilone 1 week prior to second surgery and every 3 weeks thereafter until tumor progression or toxicity. Primary end points were progression-free survival (PFS) and overall survival (OS) at 6 months as well as patupilone concentration in tumor tissue. Secondary end points were toxicity, patupilone concentration in plasma and translational analyses for predictive biomarkers. Results: Nine patients with a mean age of 54.6 ± 8.6 years were recruited between June 2008 and April 2010. Median survival and 1-year OS after second surgery were 11 months (95% CI, 5–17 months) and 45% (95% CI, 14–76), respectively. Median PFS was 1.5 months (95% CI, 1.3–1.7 months) and PFS6 was 22% (95% CI, 0–46), with 2 patients remaining recurrence-free at 9.75 and 22 months. At the time of surgery, the concentration of patupilone in tumor tissue was 30 times higher than in the plasma. Tumor response was not predictable by the tested biomarkers. Treatment was generally well tolerated with no hematological, but cumulative, though reversible sensory neuropathy grade ≤3 was seen in 2 patients (22%) at 8 months and grade 4 diarrhea in the 2nd patient (11%). Non-patupilone-related peri-operative complications occurred in 2 patients resulting in discontinuation of patupilone therapy. There were no neurocognitive changes 3 months after surgery compared to baseline. Conclusions: In recurrent GBM, patupilone can be given safely pre- and postoperatively. The drug accumulates in the tumor tissue. The treatment results in long-term PFS in some patients. Patupilone represents a valuable novel compound which deserves further evaluation in combination with radiation therapy in patients with GBM.
Stability of the Kalman filtering with two periodically switching sensors over lossy networks

This paper considers the stability of Kalman filtering of a discrete-time stochastic system using two periodically switching sensors over a network subject to random packet losses, which is modeled by an independent and identically distributed Bernoulli process. It is proved that this problem can be converted into the stability of Kalman filtering using two sensors at each time instant, where the measurements of each sensor are transmitted via an independent lossy channel. Some necessary and sufficient conditions for stability of the estimation error covariance matrices are respectively established, and the effect of the periodic switching on the stability is revealed. Their implications and relationships with related results in the literature are discussed.
Selective Disruption of Phosphatidylcholine Metabolism of the Intracellular Parasite Toxoplasma gondii Arrests Its Growth*

Toxoplasma gondii is an intracellular protozoan parasite capable of causing devastating infections in immunocompromised and immunologically immature individuals. In this report, we demonstrate the relative independence of T. gondii from its host cell for aminoglycerophospholipid synthesis. The parasite can acquire the lipid precursors serine, ethanolamine, and choline from its environment and use them for the synthesis of its major lipids, phosphatidylserine (PtdSer), phosphatidylethanolamine (PtdEtn), and phosphatidylcholine (PtdCho), respectively. Dimethylethanolamine (Etn(Me)2), a choline analog, dramatically interfered with the PtdCho metabolism of T. gondii and caused a marked inhibition of its growth within human foreskin fibroblasts. In tissue culture medium supplemented with 2 mm Etn(Me)2, the parasite-induced lysis of the host cells was dramatically attenuated, and the production of parasites was inhibited by more than 99%. The disruption of parasite growth was paralleled by structural abnormalities in its membranes. In contrast, no negative effect on host cell growth and morphology was observed. The data also reveal that the Etn(Me)2-supplemented parasite had a time-dependent decrease in its PtdCho content and an equivalent increase in phosphatidyldimethylethanolamine, whereas other major lipids, PtdSer, PtdEtn, and PtdIns, remained largely unchanged. Relative to host cells, the parasites incorporated more than 7 times as much Etn(Me)2 into their phospholipid. These findings reveal that Etn(Me)2 selectively alters parasite lipid metabolism and demonstrate how selective inhibition of PtdCho synthesis is a powerful approach to arresting parasite growth.
Profile of Atherosclerotic Risk Factors and Management in Patients of Peripheral Arterial Disease at a Tertiary Care Teaching Hospital of North India

Peripheral arterial disease, being a manifestation of systemic atherosclerosis, carries a high risk of adverse cardiovascular events. Secondary medical prevention therapies of same magnitude as that for coronary artery disease are recommended for peripheral arterial disease patients also. Available evidence indicates that this condition commonly remains underdiagnosed and undertreated. There is lack of any report about management of these patients in India. The objectives of the present study were to characterize the atherosclerotic risk factor profile and pattern of drug prescription for patients of peripheral arterial disease at a tertiary care teaching hospital and to compare this management with standard guidelines. Data were collected from prescriptions of patients attending cardiothoracic and vascular surgery outpatient department with diagnosis of atherosclerotic peripheral arterial disease from July 2012 to Jun 2013. One hundred twenty prescriptions were analysed. The mean age (±SD) of patients was 53±7.18 years and 23.3% were females. History of smoking, either past or present, was present in 91.6% patients. History of ischemic heart disease was present in 25%, while 26.7% patients were diabetic. Mean number of cardiovascular risk factors was 2.6. The percentage of eligible patients who were receiving a particular drug was 100% for aspirin and statins, 48.3% for angiotensin converting enzyme inhibitors, 46.7% for beta blockers and 66.7% for cilostazol. The vascular surgeons of this centre are using antiplatelet agents and statins adequately for peripheral arterial disease. The prescription of angiotensin converting enzyme inhibitors, beta blockers and cilostazol is low. Exercise therapy and smoking cessation need more attention.