Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of MKNK2 alternative splicing by splice-switching oligonucleotides as a novel approach for glioblastoma treatment

Abstract The gene encoding the kinase Mnk2 (MKNK2) is alternatively spliced to produce two isoforms—Mnk2a and Mnk2b. We previously showed that Mnk2a is downregulated in several types of cancer and acts as a tumor suppressor by activation of the p38–MAPK stress pathway, inducing apoptosis. Moreover, Mnk2a overexpression suppressed Ras-induced transformation in culture and in vivo. In contrast, the Mnk2b isoform acts as a pro-oncogenic factor. In this study, we designed modified-RNA antisense oligonucleotides and screened for those that specifically induce a strong switch in alternative splicing of the MKNK2 gene (splice switching oligonucleotides or SSOs), elevating the tumor suppressive isoform Mnk2a at the expense of the pro-oncogenic isoform Mnk2b. Induction of Mnk2a by SSOs in glioblastoma cells activated the p38–MAPK pathway, inhibited the oncogenic properties of the cells, re-sensitized the cells to chemotherapy and inhibited glioblastoma development in vivo. Moreover, inhibition of p38–MAPK partially rescued glioblastoma cells suggesting that most of the anti-oncogenic activity of the SSO is mediated by activation of this pathway. These results suggest that manipulation of MKNK2 alternative splicing by SSOs is a novel approach to inhibit glioblastoma tumorigenesis.
The Heart : Pressure-Propulsion Pump or Organ of Impedance ?

From the Department of Anesthesiology, Albany Medical College, Albany, NY. Address reprint requests to Branko Furst, MD, Department of Anesthesiology, Albany Medical College, 47 New Scotland Avenue, MC-131, Albany, NY 12208. E-mail: furstb@mail.amc. edu © 2015 The Authors. Published by Elsevier Inc. All rights reserved. 1053-0770/2601-0001$36.00/0 http://dx.doi. org/10.1053/j.jvca. 2015.02. 022
Low-complexity estimation of signal parameters via rotational invariance techniques algorithm for mixed far-field and near-field cyclostationary sources localisation

In this study, the authors propose an efficient third-order cyclic moment-based estimation of signal parameters via rotational invariance techniques algorithm to cope with the mixed far-field and near-field cyclostationary sources localisation problem. The key point is that the auto-pairing parameters of near-field bearing and range is realised by estimating the unique non-singular matrix between the signal subspace and the matrix of direction vectors. This algorithm firstly constructs two special third-order cyclic moment matrices, in which the rotational factor is the function of the direction-of-arrival (DOA) and range of mixed far-field and near-field sources. By implementing the singular value decomposition and the high-resolution multiple signal classification spectral search, the authors estimate the azimuth DOAs for all the incoming sources. Then, the authors perform the estimation of the unique non-singular matrix between the signal subspace and the matrix of direction vectors. Finally, the range of near-field sources is determined from the obtained rotational factor. The proposed algorithm is computationally more efficient than the previous works, and it avoids pairing parameters. Computer simulations are carried out to demonstrate the performance of the proposed algorithm.
Variations of Alkaloid Accumulation and Gene Transcription in Nicotiana tabacum

To increase the understanding of alkaloid biosynthesis in Nicotiana tabacum during whole plant growth periods, variations of the contents of alkaloids and the transcription of key biosynthetic genes in fresh leaves were investigated in three varieties at five developmental stages. Six alkaloids were analyzed by gas chromatograph–mass spectrometry (GC–MS) and the most abundant alkaloid was observed during the upper leaves maturing stage in the varieties, among which the alkaloid content of K326 was the highest. Considering the genetic effect, variance analysis indicated that the developmental stage played a predominant role in alkaloid accumulation. Moreover, the levels of biosynthetic gene transcripts in the leaves at the vigorous growing stage might contribute to the contents of alkaloids in the leaves during the maturing stages. To further illuminate the metabolism of alkaloid biosynthesis, a correlation among alkaloids was also documented.
Loss of histone methyltransferase Ezh2 stimulates an osteogenic transcriptional program in chondrocytes but does not affect cartilage development

Ezh2 is a histone methyltransferase that suppresses osteoblast maturation and skeletal development. We evaluated the role of Ezh2 in chondrocyte lineage differentiation and endochondral ossification. Ezh2 was genetically inactivated in the mesenchymal, osteoblastic, and chondrocytic lineages in mice using the Prrx1-Cre, Osx1-Cre, and Col2a1-Cre drivers, respectively. WT and conditional knockout mice were phenotypically assessed by gross morphology, histology, and micro-CT imaging. Ezh2-deficient chondrocytes in micromass culture models were evaluated using RNA-Seq, histologic evaluation, and Western blotting. Aged mice with Ezh2 deficiency were also evaluated for premature development of osteoarthritis using radiographic analysis. Ezh2 deficiency in murine chondrocytes reduced bone density at 4 weeks of age but caused no other gross developmental effects. Knockdown of Ezh2 in chondrocyte micromass cultures resulted in a global reduction in trimethylation of histone 3 lysine 27 (H3K27me3) and altered differentiation in vitro. RNA-Seq analysis revealed enrichment of an osteogenic gene expression profile in Ezh2-deficient chondrocytes. Joint development proceeded normally in the absence of Ezh2 in chondrocytes without inducing excessive hypertrophy or premature osteoarthritis in vivo. In summary, loss of Ezh2 reduced H3K27me3 levels, increased the expression of osteogenic genes in chondrocytes, and resulted in a transient post-natal bone phenotype. Remarkably, Ezh2 activity is dispensable for normal chondrocyte maturation and endochondral ossification in vivo, even though it appears to have a critical role during early stages of mesenchymal lineage commitment.
The reliability and validity of the Turkish version of the oxford shoulder instability score

Abstract Background: The aim of this study was to adapt the Oxford Shoulder Instability Score to Turkish culture and test its reliability and validity. Methods: This study included 118 patients with shoulder instability. Confirmatory factor analyses, and correlation coefficient between Oxford Shoulder Instability Score and Short Form 36 were calculated in order to test construct validity. Internal consistency was tested using Cronbach’s alpha. Pearson correlation were calculated to test reliability. Differential item functioning analysis was performed to detect whether items exhibited differences according to gender. Results: Confirmatory factor analysis indicating the single structure of the Oxford Shoulder Instability Score was confirmed. Cronbach’s alpha was calculated as 0.87 for the whole scale. There were positive and strong correlations between the first and follow-up assessments (r = 0.86, p < 0.01). The Turkish version of OSIS showed moderate and significant correlations with domains of the SF-36 in general. Results also showed that there was no item exhibiting differential item functioning analysis in the Turkish version of Oxford Shoulder Instability Score. Conclusion: The Turkish version of the Oxford Shoulder Instability Score is a reliable, valid, reproducible and practical tool. It can be used for patients with shoulder disorders and is recommended for clinical use. Implications for Rehabilitation Oxford Shoulder Instability Score is a 12-item tool measuring health-related quality of life and shoulder functions. Since the Turkish version of the Oxford Shoulder Instability Score is confirm to be a reliable, valid, and reproducible tool, it can be used in clinics to assess the functional status in patient with shoulder instability. It can be recommended to identify improvements in patients with shoulder problems for research purposes as well.
Measurement properties of the upright motor control test in adults with subacute stroke

ABSTRACT Background: Previous studies have distilled the Upright Motor Control Test Knee Extension and Knee Flexion subscales (UMCT-KE and UMCT-KF, respectively) from the original 6-item instrument and examined these as stand-alone rapid tests of voluntary movement control in the standing position. Systematic review evidence suggests that the UMCT-KE and UMCT-KF may have value in predicting walking ability after stroke. Objective: To examine the interrater and intrarater reliability, and concurrent validity of the UMCT-KE and UMCT-KF, and associations with walking ability in adults with subacute stroke. Methods: A prospective repeated assessments design was implemented in a rehabilitation department in a public teaching hospital. A consecutive sample of patients with subacute first-time stroke (N = 50; mean age = 51 ± 12 years; 20 females; mean time post-stroke = 68 ± 48 days) completed the study. Three physical therapists independently administered the UMCT-KE and UMCT-KF on two testing occasions 2 days apart (t1 and t2). On t2, a fourth rater administered the Leg subscale of the Motricity Index (MI-Leg) as criterion standard. Results: The UMCT-KE and UMCT-KF demonstrated substantial to almost perfect interrater and intrarater reliability (W = 0.77–0.95), with lower limits of 95% confidence intervals extending to no lower than the substantial level. Both the UMCT-KE and UMCT-KF showed high correlations with the MI-Leg (ρ = 0.747–0.775) and significant associations with walking ability. p Values for all tests were <0.001. Conclusions: The UMCT-KE and UMCT-KF are reliable and valid tests for rapidly estimating voluntary movement control of the lower limbs in adults with subacute stroke.
Influence of Orexinergic System on Survival in Septic Rats

Background: The orexinergic (OXergic) system contributes to the defense system. It has also been reported that the degeneration of OXergic neurons occurs during sepsis. Thus, the decline of OXergic activity may contribute to impairment of the defense system in sepsis. In this study, we determined whether: (i) lipopolysaccharide (LPS) reduces the brain orexin A (OXA) content and (ii) the OXergic system contributes to survival from sepsis in rats. Methods: With approval of our protocol by our University Animal Ethics Committee, OX neuron-ablated (OX/ataxin-3 transgenic [OX/AT3 TG]) and wild-type Sprague-Dawley rats, weighing 250–350 g, were used. LPS (10 mg/kg) was administered intraperitonally to the wild-type rats (group SD, n = 26) and OX/AT3 TG rats (group TG, n = 14). Another 7 SD rats were included as a saline control (group C). Survival analysis was then performed over a period of 3 days. All surviving rats were decapitated and the brain OXA contents (from the cerebrocortex, hippocampus, hypothalamus, and pons) were quantified using ELISA kits. Results: In group SD, 61.5% rats survived, while in group TG, only 21.4% survived (p < 0.05). LPS significantly reduced OXA content (pg/mg of tissue) in group SD (2.92 ± 0.38) compared to in group C (4.10 ± 1.21) in the pons (p < 0.05). OXA content in group TG was substantially lower than in group C and group SD in all brain regions. Conclusions: LPS significantly reduced OXA contents in the pons which contains the locus coeruleus to regulate sympathetic activity in the defense system.
Interference cancellation and alignment techniques for multiple-input and multiple-output cognitive relay networks

We consider a multiple-input and multiple-output (MIMO) cognitive radio (CR) network with a MIMO relay that opportunistically accesses the same frequency band as that of a MIMO primary network. In particular, both interference cancellation and interference alignment techniques have been investigated to enhance the achievable degrees of freedom (DoF) for the MIMO CR network. Based on the number of antennas at the primary network and the secondary network, the authors analytically quantify the maximum achievable DoF of the secondary network by using the proposed techniques. It is shown that the DoF obtained by the CR network in the presence of a MIMO relay is higher than that could be obtained without a relay. The analyses consider both sufficient and insufficient number of antennas at the relay in terms of the ability to separate and decode both the primary and secondary transmitted signals. The simulation results support the analytically quantified achievable DoF results.
Neural Relation Classification Using Selective Attention and Symmetrical Directional Instances

Relation classification (RC) is an important task in information extraction from unstructured text. Recently, several neural methods based on various network architectures have been adopted for the task of RC. Among them, convolution neural network (CNN)-based models stand out due to their simple structure, low model complexity and “good” performance. Nevertheless, there are still at least two limitations associated with existing CNN-based RC models. First, when handling samples with long distances between entities, they fail to extract effective features, even obtaining disturbing ones from the clauses, which results in decreased accuracy. Second, existing RC models tend to produce inconsistent results when fed with forward and backward instances of an identical sample. Therefore, we present a novel CNN-based sentence encoder with selective attention by leveraging the shortest dependency paths, and devise a classification framework using symmetrical directional—forward and backward—instances via information fusion. Comprehensive experiments verify the superior performance of the proposed RC model over mainstream competitors without additional artificial features.
Quality assessment for the putative intrinsic disorder in proteins

MOTIVATION While putative intrinsic disorder is widely used, none of the predictors provides quality assessment (QA) scores. QA scores estimate the likelihood that predictions are correct at a residue level and have been applied in other bioinformatics areas. We recently reported that QA scores derived from putative disorder propensities perform relatively poorly for native disordered residues. Here we design and validate a general approach to construct QA predictors for disorder predictions. RESULTS The QUARTER (QUality Assessment for pRotein inTrinsic disordEr pRedictions) toolbox of methods accommodates a diverse set of ten disorder predictors. It builds upon several innovative design elements including use and scaling of selected physicochemical properties of the input sequence, post-processing of disorder propensity scores, and a feature selection that optimizes the predictive models to a specific disorder predictor. We empirically establish that each one of these elements contributes to the overall predictive performance of our tool and that QUARTER's outputs significantly outperform QA scores derived from the outputs generated the disorder predictors. The best performing QA scores for a single disorder predictor identify 13% of residues that are predicted with 98% precision. QA scores computed by combining results of the ten disorder predictors cover 40% of residues with 95% precision. Case studies are used to show how to interpret the QA scores. QA scores based on the high precision combined predictions are applied to analyze disorder in the human proteome. AVAILABILITY AND IMPLEMENTATION http://biomine.cs. vcu.edu/servers/QUARTER/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Alimentação e estilos de vida da porpulação portuguesa: metodologia e resultados preliminares

A influencia dos estilos de vida sobre a incidencia e prevalencia de doencas cronicas nao-transmissiveis justifica a importância de estudar estes factores e suas relacoes, de modo a delinear estrategias de promocaoda saude mais eficientes. A informacao sobre a ingestao alimentar dos portugueses e limitada a certos grupos populacionais, e nao existe um estudo de uma amostra representativa da populacao portuguesa que inclua tambem as regioes autonomas dos Acores e da Madeira. As alteracoes sociais, politicas e economicas dos ultimos anos justificam a actualizacao do conhecimento da populacao portuguesaa estes niveis.Nesta publicacao apresentam-se os aspectos metodologicos da 1a fase do estudo Alimentacao e Estilos de Vida da Populacao Portuguesa e os resultados preliminares que caracterizam a populacao adulta. Este estudo foi planeado e promovido pela Sociedade Portuguesa de Ciencias da Nutricao e Alimentacao com o apoio da Nestle, no âmbito de um protocolo de mecenato cientifico entre as duas instituicoes, e teve como objectivo geral avaliar o estado nutricional, ingestao alimentar, niveis de actividade fisica, outras dimensoes dos estilos de vida e variaveis relacionadas com o estado de saude da populacao portuguesa.
Material Design for Photocatalytic Water Splitting from a Theoretical Perspective

Currently, problems associated with energy and environment have become increasingly serious. Producing hydrogen, a clean and renewable resource, through photocatalytic water splitting using solar energy is a feasible and efficient route for resolving these problems, and great efforts have been devoted to improve the solar‐to‐hydrogen efficiency. Light harvesting and electron–hole separation are key in enhancing the efficiency of solar energy utilization, which stimulates the development of new photocatalytic materials. Here, recent advances in material design for photocatalytic water splitting are presented from a theoretical perspective. Specifically, aiming to enhance the photocatalytic performance, general strategies of materials design are discussed, including codoping and introducing a built‐in electric field to improve the light harvesting of materials, reducing the dimension of materials to shorten the migration pathway of carriers to inhibit electron–hole recombination, and constructing heterojunctions to enhance light harvesting and electron–hole separation. Future opportunities and challenges in the theoretical design of photocatalytic materials toward water splitting are also included.
A New Approach to the Study of Jobless Recoveries

This article is concerned with the measurement of jobless recoveries and the elements that may explain their emergence. We first introduce a measure that maps the various elements that define a jobless recovery into a single number that we label the jobless recovery depth. We then construct a database of 389 state-level observations and study the cross-sectional variations that emerge. We find that jobless recoveries in the United States are not a nation-wide phenomena, but a local event confined within a cluster of states that expands slowly between 1975 and 2015. We find the state-level evidence to be consistent with theories that link jobless recoveries to unusually long expansionary periods, less dynamic labor markets, and the advent of the great moderation. The evidence is not consistent with theories that link them to decreases in union power, increases in income inequality, or increases in health care costs.
From Agent-Based Models to Network Analysis (and Return): The Policy-Making Perspective

An important perspective use of Agent-based models (ABMs) is that of being employed as tools to support decision systems in policy-making, in the complex systems framework. Such models can be usefully employed at two different levels: to help in deciding (policy-maker level) and to empower the capabilities of people in evaluating the effectiveness of policies (citizen level). Consequently, the class of ABMs for policymaking needs to be both quite simple in its structure and highly sophisticated in its outcomes. The pursuing of simplicity and sophistication can be made more effective by applying network analysis to the emergent results. Actually, in today’s world the consequences of choices and decisions and their effects on society, and on its organization, are equally relevant. Considering the agent-based and network techniques together, we have a further important possibility. Since it is easier to have network data (i.e. social network data) than detailed behavioral individual information, we can try to understand the relationships between the dynamic changes of the networks emerging from agent-based models and the behavior of the agents. As we understand these connections, we can apply them to actual networks, to try to understand what the behavioral black boxes of real-world agents contain. We propose a simple basic structure where events, scheduled upon time, call upon agents to behave, to modify their context, and to create new structures of links among them. Events are organized as collections of small acts and steps. The metaphor is that of a recipe, i.e. a set of directions with a list of ingredients for making or preparing something, especially food (as defined in the American Heritage dictionary). Technically, recipes are sequences of numerical or alphanumerical codes, reported in vectors, and move from an agent to another determining the events and generating the edges of the emerging networks. A basic code will be shown, useful to manage possible applications in different fields: production, health-care scenarios, paper co-authorship, opinion spreading, etc.
Optimization for source localization and geoacoustic inversion in underwater acoustics

OPTIMIZATION FOR SOURCE LOCALIZATION AND GEOACOUSTIC INVERSION IN UNDERWATER ACOUSTICS by Urmi Ghosh-Dastidar Matched-field inversion techniques are widely used for source localization and geoacoustic parameter estimation. These inversion methods correlate the received data with modeled data and find the model parameters which provide the maximum correlation. However, when a large number of unknown parameters is involved, many modeled data need to be generated and correlated with the observed data and thus, matchedfield inversion can be computationally intensive. An optimization process applied to matched-field inversion is often required to accelerate the inversion process. In this work, tabu is applied to matched-field inversion for source localization and environmental parameter estimation. Tabu is a global optimization technique which proceeds by finding the best model in a local neighborhood, where a best model is defined as the set of parameter values that provides the maximum correlation in a given neighborhood. However, the search moves beyond local areas by maintaining records of past moves. Using historical information, the approach avoids certain paths. Thus, tabu limits the search space and redefines neighborhoods in each iteration. Tabu is evaluated through a comparison to fast simulated annealing. To improve efficiency, a tabu approach is also developed for parameter estimation in a rotated coordinate system. Rotation is achieved through the identification of combinations of parameters that affect acoustic field computations. OPTIMIZATION FOR SOURCE LOCALIZATION AND GEOACOUSTIC INVERSION IN UNDERWATER ACOUSTICS by Urmi Ghosh-Dastidar A Dissertation Submitted to the Faculty of New Jersey Institute of Technology and Rutgers, The State University of New Jersey — Newark in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy in Mathematical Sciences Department of Mathematical Sciences Department of Mathematics and Computer Science, Rutgers-Newark