Miracle-dz/UniFAR-FTUs huggingface dataset:
A Direct Interaction between Leucine-rich Repeat Kinase 2 and Specific-Tubulin Isoforms Regulates Tubulin Acetylation Journal Item

Law, Bernard M. H. ; Spain, Victoria A. ; Leinster, Veronica H. L. ; Chia, Ruth; Beilina, Alexandra; Cho, Hyun J.; Taymans, Jean-Marc; Urban, Mary K. ; Sancho, Rosa M. ; Blanca Raḿırez, Marian; Biskup, Saskia; Baekelandt, Veerle; Cai, Huaibin; Cookson, Mark R. ; Berwick, Daniel C. and Harvey, Kirsten (2014). A Direct Interaction between Leucine-rich Repeat Kinase 2 and Specific -Tubulin Isoforms Regulates Tubulin Acetylation. Journal of Biological Chemistry, 289(2) pp. 895–908.
Sample size calculation for the augmented logrank test in randomized clinical trials

In randomized clinical trials, incorporating baseline covariates can improve the power in hypothesis testing for treatment effects. For survival endpoints, the Cox proportional hazards model with baseline covariates as explanatory variables can improve the standard logrank test in power. Although this has long been recognized, this adjustment is not commonly used as the primary analysis and instead the logrank test followed by the estimation of the hazard ratio between treatment groups is often used. By projecting the score function for the Cox proportional hazards model onto a space of covariates, the logrank test can be more powerful. We derive a power formula for this augmented logrank test under the same setting as the widely used power formula for the logrank test and propose a simple strategy for sizing randomized clinical trials utilizing historical data of the control treatment. Through numerical studies, the proposed procedure was found to have the potential to reduce the sample size substantially as compared to the standard logrank test. A concern to utilize historical data is that those might not reflect well the data structure of the study to design and then the sample size calculated might not be accurate. Since our power formula is applicable to datasets pooled across the treatment arms, the validity of the power calculation at the design stage can be checked in blind reviews.
A composite bilayer scaffold functionalized for osteochondral tissue regeneration in rat animal model

Osteochondral defects are defined most typically by damages to both cartilage and subchondral bone tissue. It is challenging to develop bilayered scaffolds that regenerate both of these lineages simultaneously. In the present study, an electrospun bilayer nanofibrous scaffold was designed to repair osteochondral lesions. A nanocomposite of hydroxyapatite, strontium, and reduced graphene oxide were combined with polycaprolactone polymer to fabricate the osteogenic differentiation layer. Additionally, the chondrogenic differentiation layer was also formed using polyethersulfone polymer and benzyl hyaluronan. The physical, mechanical, and chemical properties of the scaffolds were determined, and adipose‐derived mesenchymal stem cells were cultured on each layer to evaluate their biocompatibility and differentiation potential. Cell viability, mineralization, alkaline phosphatase enzyme (ALP) expression, and extracellular calcium deposition were measured using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyl tetrazolium bromide assay, alizarin red staining, ALP activity, and calcium deposition. Real‐time polymerase chain reaction (PCR) was used to assess the expression levels of osteogenic (Collagen I, Runx II, ALP, Osteocalcin) and chondrogenic (Sox9, Collagen II (Col II), Aggrecan) genes. Finally, the osteochondral scaffold was created by electrospinning these two layers for 2 days. The scaffold was grafted into the osteochondral defect of a Wistar rat's knee. 60 days after surgery, real‐time PCR, immunohistochemistry (IHC), and hematoxylin and eosin staining were performed. The expression of chondrogenic and osteogenic genes was increased compared to the control group, as confirmed by real‐time PCR. Furthermore, IHC revealed a rise in Col II and Collagen X expression. Finally, in vivo and in vitro studies have shown that the electrospun bilayer scaffold is biocompatible, which facilitates osteochondral healing.
Spatial variability of concentration and aggressiveness of precipitation in North-East of Algeria

Abstract In this study, the spatial variation of daily and monthly concentration precipitation index and its aggressiveness were used in 23 rainfall stations in the extreme north-east of Algeria over the period 1970–2010. The trend was analysed by the Mann–Kendall (MK) test. The results show that daily precipitation concentration index (CI) values are noticeably higher in places where the amount of total precipitation is low, the results of MK test show that areas of high precipitation concentration tend to increase. The seasonality and aggressiveness of precipitation are high in the eastern and western parts of the study region (eastern and central coastal of Constantine catchments), whereas a moderately seasonal distribution with low aggressiveness is found in the middle of the study area (plains and central Seybouse catchment). As a result, the modified Fournier index (MFI) has a significant correlation with annual precipitation, whereas the CI and monthly precipitation concentration index (PCI) show an opposite correlation in relation to annual precipitation.
Joint optimization of segmentation and appearance models Technical report

Many interactive image segmentation approaches use an objective function which includes appearance models as an unknown variable. Since the resulting optimization problem is NP-hard the segmentation and appearance are typically optimized separately, in an EM-style fashion. One contribution of this paper is to express the objective function purely in terms of the unknown segmentation, using higher-order cliques. This formulation reveals an interesting bias of the model towards balanced segmentations. Furthermore, it enables us to develop a new dual decomposition optimization procedure, which provides additional ly a lower bound. Hence, we are able to improve on existing optimizers, and verify that for a considerable number of rea l world examples we even achieve global optimality. This is important since we are able, for the first time, to analyze the deficiencies of the model. Another contribution is to establish a property of a particular dual decomposition approach which involves convex functions depending on foreground area. As a consequence, we show that the optimal decomposition for our problem can be computed efficiently via a parametric maxflow algorithm.
Efficacy and safety of nanoparticle albumin-bound paclitaxel for treating metastatic breast cancer : a meta-analysis

Objective: Clinical trials have reported conflicting results about the efficacy and toxicity of nanoparticle albumin-bound paclitaxel (nab-paclitaxel) for treating metastatic breast cancer. This meta-analysis was performed to gain a clearer picture of the efficacy and safety of this drug. Methods: We systematically searched PubMed, Chinese National Knowledge Infrastructure (CNKI), Ovid, EMBASE and Cochrane literature databases for randomized controlled trials (RCTs) of nab-paclitaxel to treat metastatic breast cancer. Data on overall response rate (ORR), progression-free survival (PFS), overall survival (OS), and incidence of adverse effects were meta-analyzed to yield pooled odds ratios (ORs) or hazard ratios (HRs) with 95% confidence intervals (CI). Potential heterogeneity was calculated using the Q statistic and I2 value. Results: The meta-analysis included six RCTs involving 1614 patients. Nab-paclitaxel was associated with significantly higher ORR than were control drug treatments (OR 2.46, 95% CI 1.92 to 3.14, P < 0.00001). It was also associated with higher PFS than were control drug treatments (HR 0.83, 95% CI 0.73 to 0.94, P = 0.003). However, OS was similar for nab-paclitaxel and control treatments (HR 0.87, 95% CI 0.71 to 1.05, P = 0.14). Analysis of the six studies showed that nab-paclitaxel was associated with significantly higher risk of grade 3 sensory neuropathy than were control drug treatments (OR 1.82, 95% CI 1.21 to 2.74, P = 0.004). Conclusions: These findings suggest that nab-paclitaxel is associated with significantly higher ORR but also greater risk of toxicity than are other drug treatments for metastatic breast cancer.
Employment, Partnership and Childbearing Decisions of German Women and Men: A Simultaneous Hazards Approach

This paper investigates the interrelated dynamics of employment, cohabitation and fertility for German women and men. Using a simultaneous hazards approach due to Lillard (1993), I estimate a five-equation model with unobserved heterogeneity. One of the contributions of this paper is to include the current employment and nonemployment hazard rates and the union formation and union dissolution hazard rates as regressors. My results suggest that being employed or nonemployed only has small effects on other transitions, but that employed women with a high hazard of becoming nonemployed are less likely to have children, while nonemployed men having a low hazard of finding a job are more likely to have children. Children reduce the hazard of taking up a job for women and reduce the hazard of becoming nonemployed for women and men. Children also increase the stability of unions. Having a partner strongly increases the likelihood for having children. Interestingly, unions with a high risk of splitting up are more likely to have children. Economically, this can be interpreted as an attempt to invest in partner-specification capital in order to reduce the likelihood of splitting up.
Mechanism of Impact of Big Data Resources on Medical Collaborative Networks From the Perspective of Transaction Efficiency of Medical Services: Survey Study

Background The application of big data resources and the development of medical collaborative networks (MCNs) boost each other. However, MCNs are often assumed to be exogenous. How big data resources affect the emergence, development, and evolution of endogenous MCNs has not been well explained. Objective This study aimed to explore and understand the influence of the mechanism of a wide range of shared and private big data resources on the transaction efficiency of medical services to reveal the impact of big data resources on the emergence and development of endogenous MCNs. Methods This study was conducted by administering a survey questionnaire to information technology staff and medical staff from 132 medical institutions in China. Data from information technology staff and medical staff were integrated. Structural equation modeling was used to test the direct impact of big data resources on transaction efficiency of medical services. For those big data resources that had no direct impact, we analyzed their indirect impact. Results Sharing of diagnosis and treatment data (β=.222; P=.03) and sharing of medical research data (β=.289; P=.04) at the network level (as big data itself) positively directly affected the transaction efficiency of medical services. Network protection of the external link systems (β=.271; P=.008) at the level of medical institutions (as big data technology) positively directly affected the transaction efficiency of medical services. Encryption security of web-based data (as big data technology) at the level of medical institutions, medical service capacity available for external use, real-time data of diagnosis and treatment services (as big data itself) at the level of medical institutions, and policies and regulations at the network level indirectly affected the transaction efficiency through network protection of the external link systems at the level of medical institutions. Conclusions This study found that big data technology, big data itself, and policy at the network and organizational levels interact with, and influence, each other to form the transaction efficiency of medical services. On the basis of the theory of neoclassical economics, the study highlighted the implications of big data resources for the emergence and development of endogenous MCNs.
Robust and accurate terahertz time-domain spectroscopic ellipsometry

In this work, we show how fiber-based terahertz systems can be robustly configured for accurate terahertz ellipsometry. To this end, we explain how our algorithms can be successfully applied to achieve accurate spectroscopic ellipsometry with a high tolerance on the imperfect polarizer extinction ratio and pulse shift errors. Highly accurate characterization of transparent, absorptive, and conductive samples comprehensively demonstrates the versatility of our algorithms. The improved accuracy we achieve is a fundamental breakthrough for reflection-based measurements and overcomes the hurdle of phase uncertainty.
An Emphasis on Brilliance Fosters Masculinity-Contest Cultures

Women are underrepresented in fields in which success is believed to require brilliance, but the reasons for this pattern are poorly understood. We investigated perceptions of a “masculinity-contest culture,” an organizational environment of ruthless competition, as a key mechanism whereby a perceived emphasis on brilliance discourages female participation. Across three preregistered correlational and experimental studies involving adult lay participants online (N = 870) and academics from more than 30 disciplines (N = 1,347), we found a positive association between the perception that a field or an organization values brilliance and the perception that this field or organization is characterized by a masculinity-contest culture. This association was particularly strong among women. In turn, perceiving a masculinity-contest culture predicted lower interest and sense of belonging as well as stronger impostor feelings. Experimentally reducing the perception of a masculinity-contest culture eliminated gender gaps in interest and belonging in a brilliance-oriented organization, suggesting possible avenues for intervention.
Assessing the experience of person‐centred coordinated care of people with chronic conditions in the Netherlands: Validation of the Dutch P3CEQ

Countries are adapting their health and social care systems to better meet the needs of growing populations with (multiple) chronic conditions. To guide this process, assessment of the ‘patient experience’ is becoming increasingly important. For this purpose, the Person‐Centred Coordinated Care Experience Questionnaire (P3CEQ) was developed in the United Kingdom, and translated into several languages.
On structurally constrained H/sub 2/ performance bounds for stable MIMO plant models

This paper discusses optimal control problems in which the controller must satisfy sparsity structure constraints. Conditions are derived under which the optimal controller associated to an unconstrained quadratic performance index is naturally structured and, as a consequence, the sparsity constraint imposed on the controller has no impact on the optimal loop performance. The results are then applied to study the control of triangular plants that have to be controlled by triangular controllers. We derive explicit characterisations of the Youla parameter that defines an optimal triangular controller and of the performance loss associated to the structural restriction imposed on the controller.
Pandemic influenza A (H1N1) virus causes abortive infection of primary human T cells

ABSTRACT Influenza A virus still represents a noticeable epidemic risk to international public health at present, despite the extensive use of vaccines and anti-viral drugs. In the fight against pathogens, the immune defence lines consisting of diverse lymphocytes are indispensable for humans. However, the role of virus infection of lymphocytes and subsequent abnormal immune cell death remains to be explored. Different T cell subpopulations have distinct characterizations and functions, and we reveal the high heterogeneity of susceptibility to viral infection and biological responses such as apoptosis in various CD4+ T and CD8+ T cell subsets through single-cell transcriptome analyses. Effector memory CD8+ T cells (CD8+ TEM) that mediate protective memory are identified as the most susceptible subset to pandemic influenza A virus infection among primary human T cells. Non-productive infection is established in CD8+ TEM and naïve CD8+ T cells, which indicate the mechanism of intracellular antiviral activities for inhibition of virus replication such as abnormal viral splicing efficiency, incomplete life cycles and up-regulation of interferon-stimulated genes in human T cells. These findings provide insights into understanding lymphopenia and the infectious mechanisms of pandemic influenza A virus and broad immune host–pathogen interactional atlas in primary human T cells.
Multi-scale analysis of neural activity in humans : implications for microscale electrocorticography

Objective: Electrocorticography grids have been used to study and diagnose neural pathophysiology for over 50 years, and recently have been used for various neural prosthetic applications. Here we provide evidence that micro-scale electrodes are better suited for studying cortical pathology and function, and for implementing neural prostheses. Methods: This work compares dynamics in space, time, and frequency of cortical field potentials recorded by three types of electrodes: electrocorticographic (ECoG) electrodes, non-penetrating micro-ECoG (μECoG) electrodes that use microelectrodes and have tighter interelectrode spacing; and penetrating microelectrodes (MEA) that penetrate the cortex to record singleor multiunit activity (SUA or MUA) and local field potentials (LFP). Results: While the finest spatial scales are found in LFPs recorded intracortically, we found that LFP recorded from μECoG electrodes demonstrate scales of linear similarity (i.e., correlation, coherence, and phase) closer to the intracortical electrodes than the clinical ECoG electrodes. Conclusions: We conclude that LFPs can be recorded intracortically and epicortically at finer scales than clinical ECoG electrodes are capable of capturing. Significance: Recorded with appropriately scaled electrodes and grids, field potentials expose a more detailed representation of cortical network activity, enabling advanced analyses of cortical pathology and demanding applications such as brain-computer interfaces.
Investigating determinants of agricultural income diversification: an exploratory case study in Tuscany

This paper investigates on-farm income diversification determinants, using data from the Italian 2010 census. The determinants are investigated by simulating farmers’ behaviors as a two-step process through the application of the Heckman sample selection model. Model results are quite consistent with previous literature findings and confirm the relevance of risk exposure reduction as on-farm diversification strategy determinants. Results stress also that, besides farm characteristics and structures, spatial location and distances play a prominentrole in explaining the diversification process. Our results seem contrary to the demand-driven effects of diversification but stress that diversification could be considered a broader process driven by territorial potentiality and quality.
Hedging Rainbow Options in Discrete Time

A quadratic hedging strategy based on minimizing the hedging costs at each predetermined rebalancing time is used to hedge rainbow options. The corresponding hedging positions are simply obtained by solving a linear system, which is convenient for practical implementation. Quadratic hedging and the widely used delta hedging are compared to investigate their hedging performance for rainbow options in discrete time. By employing the Value-at-Risk (VaR) as the risk measure for comparing the hedging performance, simulation results indicate that the quadratic hedging performs better than the delta method in both static and dynamic scenarios.
‘We’ve come a very, very, long way’ Overcoming stigma of autism: An interpretative phenomenological analysis within the UK Jewish community

Autistic people contend with high levels of stigma in many cultures worldwide. There is a scarcity of literature on stigma in relation to autism in faith communities and virtually no research focussing on this topic in Jewish communities. In this study, we aimed to explore experiences of stigma towards autism and sought views on what steps have and can be taken to reduce such stigma. Using an interpretative phenomenological analysis approach, we conducted semi-structured interviews with 10 participants within the UK Jewish community, in both mainstream and specialist autistic schools. Interviews were conducted over 2 months in 2020. During analysis, 5 superordinate (central) themes and 13 subordinate themes were abstracted. Superordinate themes included ‘Stigma not specific to the Jewish community’; ‘Considerable strides made’; ‘More a lack of knowledge or denial than stigma’; ‘Fear of stigma is a real concern but not widely prevalent’; and ‘Potent factors that reduce stigma in the Jewish community’. We recommend workshops for greater awareness and training for teachers and parents on autism and autistic children’s experiences. We also recommend the formation of specialist autism schools in other communities and promotion of positive narratives concerning autistic people, as this successfully reduced stigma within the Jewish community. Lay abstract Autistic people contend with high levels of stigma in a wide array of cultures worldwide. There is a scarcity of literature on stigma in relation to autism in faith communities, with some limited research on this issue in Christian, Muslim and Hindu populations. There is virtually no research focussing on this topic in Jewish communities and to our knowledge, none at all within UK Jewish contexts. In this study, we aimed to explore experiences of stigma towards autism and sought views on what steps have and can be taken to reduce such stigma. Using an interpretative phenomenological analysis approach, we conducted semi-structured interviews with 10 participants within the UK Jewish community, including parents, rabbis, SENDCos, teachers, and headmasters of autistic children in both mainstream and specialist autistic schools. Interviews were conducted over 2 months in 2020. During analysis, 5 superordinate (central) themes and 13 subordinate themes were abstracted from the data. Superordinate themes included ‘Stigma not specific to the Jewish community’; ‘Considerable strides made’; ‘More a lack of knowledge or denial than stigma’; ‘Fear of stigma is a real concern but not widely prevalent’; and ‘Potent factors that reduce stigma in the Jewish community’. We recommend workshops for greater awareness and training for teachers and parents on autism and autistic children’s experiences. We also recommend the formation of specialist autism schools in other communities and promotion of positive narratives concerning autistic people, as this successfully reduced stigma within the Jewish community.