Miracle-dz/UniFAR-FTUs huggingface dataset:
Intrathecal dose intensification by CNS status at diagnosis in the treatment of children with acute lymphoblastic leukemia

ABSTRACT Objectives: Acute lymphoblastic leukemia (ALL) with CNS2 status predicts inferior outcome and a high rate of CNS relapse, similar to overt CNS leukemia (CNS3). The purpose of this study was to determine if intrathecal (IT) dose intensification during induction would improve outcomes and reduce CNS relapse for CNS2 disease. Methods: From January 2001 to December 2014, children (1–14 years) with newly diagnosed ALL were treated at the Princess Noorah Oncology Centre (PNOC) following modifications of the Children’s Oncology Group (COG) protocols. We intensified IT methotrexate (ITM) during induction for patients with CNS2 disease. Patients were evaluated for overall survival (OS), disease-free survival (DFS), and cumulative incidence of relapse (CIR). Results: 449 children with T-cell (14.3%) or B-cell (85.7%) ALL were treated using PNOC-SR or PNOC-HR regimens (Jan 2001- Dec 2007) or CALL08 regimens (Arm A [SR], Arm B [IR], and Arm C [HR]) (Jan 2008 - Dec 2014). The 5-year OS, DFS, and CIR were 87.2 ± 1.6%, 81.7 ± 1.9%, and 13.0 ± 1.7%, respectively. The OS and DFS of patients with CNS2 were significantly superior to that of patients with CNS3 (P = 0.025 and P = 0.019, respectively). Patients with CNS2 had similar OS and DFS to those with CNS1. None of the patients with CNS2 at initial diagnosis experienced CNS relapse. Conclusions: ITM intensification during induction was associated with elimination of CNS recurrence in patients with CNS2 disease and childhood ALL. Controlled studies are needed to confirm this observation.
Adaptation and Phenotypic Diversification in Arabidopsis through Loss-of-Function Mutations in Protein-Coding Genes[OPEN]

A large-scale study exploring how gene loss contributes to evolutionary change reveals that loss-of-function mutations contribute to the adaptation and phenotypic diversification of plants. According to the less-is-more hypothesis, gene loss is an engine for evolutionary change. Loss-of-function (LoF) mutations resulting in the natural knockout of protein-coding genes not only provide information about gene function but also play important roles in adaptation and phenotypic diversification. Although the less-is-more hypothesis was proposed two decades ago, it remains to be explored on a large scale. In this study, we identified 60,819 LoF variants in 1071 Arabidopsis (Arabidopsis thaliana) genomes and found that 34% of Arabidopsis protein-coding genes annotated in the Columbia-0 genome do not have any LoF variants. We found that nucleotide diversity, transposable element density, and gene family size are strongly correlated with the presence of LoF variants. Intriguingly, 0.9% of LoF variants with minor allele frequency larger than 0.5% are associated with climate change. In addition, in the Yangtze River basin population, 1% of genes with LoF mutations were under positive selection, providing important insights into the contribution of LoF mutations to adaptation. In particular, our results demonstrate that LoF mutations shape diverse phenotypic traits. Overall, our results highlight the importance of the LoF variants for the adaptation and phenotypic diversification of plants.
Calibration of Linear Time-Varying Frequency Errors for Distributed ISAR Imaging Based on the Entropy Minimization Principle

The inevitable frequency errors owing to the frequency mismatch of a transmitter and receiver oscillators could seriously deteriorate the imaging performance in distributed inverse synthetic aperture radar (ISAR) system. In this paper, for this issue, a novel method is proposed to calibrate the linear time-varying frequency errors (LTFE) between the transmitting node and the receiving node. The cost function is constructed based on the entropy minimization principle and the problem of LTFE calibration is transformed into cost function optimization. The frequency error coefficient, which minimizes the image entropy, is obtained by searching optimum solution in the solution space of cost function. Then, the original signal is calibrated by the frequency error coefficient. Finally, the effectiveness of the proposed method is demonstrated by simulation and real-data experiments.
Autonomous Language Learning: Bangladeshi Undergraduates' Attitudes and Perceptions

Development in learner centered approaches in education has brought with it the significant notion of ̳learner autonomy‘ which refers to the readiness of learners to be responsible for their own learning. However, this is an issue which is not independent of educational culture and context as context and culture construct the site within which the whole learning process takes place. Since autonomy depends on learners‘ readiness to take charge of their own learning, it is dependent, to a large extent, on learners‘ attitudes and perceptions of autonomy. These attitudes and perceptions, in turn, are shaped by the context and culture where learners live. Therefore, in any given context, it is necessary to assess the level of learners‘ autonomy to predict the success or failure of a learner centered approach. This paper investigated tertiary level Bangladeshi learners‘ attitudes and perceptions towards autonomous or independent learning. Data were collected from eighty undergraduates of the Department of English, University of Dhaka, using a survey questionnaire and focus-group interviews. The findings of the study revealed that learners share a highly teacher-dependent attitude and they perceive autonomous learning helpful only when there is a teacher to assist and guide them.
PRX9 and PRX40 Are Extensin Peroxidases Essential for Maintaining Tapetum and Microspore Cell Wall Integrity during Arabidopsis Anther Development

PRX9 and PRX40 are essential class III peroxidases that act redundantly to cross-link extensins in tapetal cell walls, which prevents tapetum swelling and enables pollen development. Pollen and microspore development are essential steps in the life cycle of all land plants that generate male gametes. Within flowering plants, pollen development occurs inside of the anther. Here, we report the identification of two class III peroxidase-encoding genes, PEROXIDASE9 (PRX9) and PRX40, that are genetically redundant and essential for proper anther and pollen development in Arabidopsis (Arabidopsis thaliana). Arabidopsis double mutants devoid of functional PRX9 and PRX40 are male sterile. The mutant anthers display swollen, hypertrophic tapetal cells and pollen grains, suggesting disrupted cell wall integrity. These phenotypes lead to nearly 100%-penetrant pollen degeneration upon anther maturation. Using immunochemical and biochemical approaches, we show that PRX9 and PRX40 likely cross-link extensins to contribute to tapetal cell wall integrity during anther development. This work suggests that PRX9 and PRX40 encode Arabidopsis extensin peroxidases and highlights the importance of extensin cross-linking during pollen development.
Caregivers navigating rehabilitative care for people with aphasia after stroke: a multi-lens perspective.

BACKGROUND Up to 40% of stroke survivors acquire aphasia and require long-term caregiver assistance after discharge from the hospital. Caregivers assume multiple roles as they help people with aphasia to access outpatient rehabilitative care in an increasingly person-centred model of care. Examining caregiver roles and how different stakeholders in the rehabilitative journey perceive these roles may be the first step in providing more tailored support to caregivers and improving outcomes for both caregivers and people with aphasia. AIMS To characterize the roles caregivers assume while navigating outpatient rehabilitative care for people with aphasia after stroke from the perspective of different stakeholders in the rehabilitative process. METHODS & PROCEDURES Thirty-six people participated in the study, including seven caregivers, 22 stroke survivors with aphasia and seven healthcare providers. Focus groups were conducted, and an iterative thematic analysis was used to identify themes. OUTCOMES & RESULTS Results indicate that caregivers are perceived differently by varying stakeholders, and that caregivers adopt diverse roles as advocates, therapists, motivators and guardians. They assume these roles in order to fill gaps in services or otherwise to facilitate the recovery journey for the person with aphasia. CONCLUSIONS & IMPLICATIONS This study provides a valuable glimpse into how varying stakeholders view the role of the caregiver during rehabilitation for people with aphasia after stroke. Providing caregivers with the training and support they need throughout the recovery journey by treating them as partners in the process may mitigate the perception of caregivers as feeling compelled to adopt multiple roles.
Reflections on the Concept of Open Data

Though “open data” is much discussed as a practice, it is much less discussed as a concept. There is consensus that open data is an emerging global social movement — an Open Data Movement — that encourages a shift in behaviour about performing data-centric tasks, such as governing or researching, to make them more connected and collaborative and thereby improve transparency, accountability, research discovery, knowledge access and knowledge co-production. But just what do we mean by the qualifying word “open”? Open data is understood to mean data resources that are: (1) free for people to access; (2) free from most legal constraints on reuse; and (3) put into formats that maximise interoperability and linkage. This definition, however, fails to fully address all the conceptual and policy issues at play in the Open Data Movement. In this analysis piece, I offer some critical reflections on the Open Data Movement and unpack the meaning of “open” data so as to offer a richer understanding of the concept.
Depression in Emergency Department Patients and Association With Health Care Utilization.

BACKGROUND Depression is one of the most common illnesses in the United States, with increased prevalence among people with lower socioeconomic status and chronic mental illness who often seek care in the emergency department (ED). We sought to estimate the rate and severity of major depressive disorder (MDD) in a nonpsychiatric ED population and its association with subsequent ED visits and hospitalizations. METHODS This prospective cohort study enrolled a convenience sample of English-speaking adults presenting to an urban academic medical center ED without psychiatric complaints between January 1, 2015, and September 21, 2015. Patients completed a computerized adaptive depression diagnostic screen (CAD-MDD) and dimensional depression severity measurement test (CAT-DI) via tablet computer. Primary outcomes included number of ED visits and hospitalizations assessed from index visit until January 1, 2016. Negative binomial regression modeling was performed to assess associations between depression, depression severity, clinical covariates, and utilization outcomes. RESULTS Of 999 enrolled patients, 27% screened positive for MDD. The presence of MDD conveyed a 61% increase in the rate of ED visits (incidence rate ratio [IRR] = 1.61, 95% confidence interval [CI] = 1.27 to 2.03) and a 49% increase in the rate of hospitalizations (IRR = 1.49, 95% CI = 1.06-2.09). For each 10% increase in MDD severity, there was a 10% increase in the relative rate of subsequent ED visits (IRR = 1.10, 95% CI = 1.04 to 1.16) and hospitalizations (IRR = 1.10, 95% CI = 1.02 to 1.18). Across the range of the severity scale there was over a 2.5-fold increase in the rate of ED visits and hospitalization rates. CONCLUSIONS Rates of depression were high among a convenience sample of English-speaking adult ED patients presenting with nonpsychiatric complaints and independently associated with increased risk of subsequent ED utilization and hospitalization. Standardized assessment tools that provide rapid, accurate, and precise classification of MDD severity have the potential to play an important role in identifying ED patients in need of urgent psychiatric resource referral.
Development of interception capacity equations according to grate inlet types

Recently, natural disasters, which are hard to predict and prevent, are rapidly increasing due to climate change worldwide. Particularly the damage scale of urban areas is increasing because of local torrential rainfall. In urban areas, the rain water cannot flow to pipes well due to the high percentage of impervious areas by the indiscriminate development. As a result, the inundation damage is getting higher in urban areas. So we need to characterize the interception of the grate inlets to ensure good drainage in impervious areas. But Korean installation criteria of grate inlets does not reflect road and drainage sector characteristics so the grate inlets do not function properly in many areas. In this study, we suggest the interception capacity equations about grate inlets through hydraulic experiments in various conditions. Therefore, the interception capacity changes are analyzed according to bearing bar slopes of grate inlets, grate inlet sizes and shapes and connecting pipe numbers. Though this, we developed the interception capacity equations about domestic grate inlets.
Exceptional Solvent Tolerance in Yarrowia lipolytica Is Enhanced by Sterols

Microbial biocatalysis in organic solvents such as ionic liquids (ILs) is attractive for making fuels and chemicals from complex substrates including lignocellulosic biomass. However, low IL concentrations of 0.5-1.0 % (v/v) can drastically inhibit microbial activity. In this study, we engineered an exceptionally robust oleaginous yeast Yarrowia lipolytica, YlCW001, by adaptive laboratory evolution (ALE). The mutant YlWC001 shows robust growth in up to 18% (v/v) 1-ethyl-3-methylimidazolium acetate ([EMIM][OAc]), which makes it the most IL-tolerant microorganism published to our knowledge. Remarkably, YlCW001 exhibits broad tolerance in most commonly used hydrophilic ILs beyond [EMIM][OAc]. Scanning electron microscopy revealed that ILs significantly damage cell wall and/or membrane of wildtype Y. lipolytica with observed cavities, dents, and wrinkles while YlCW001 maintains healthy morphology even in high concentrations of ILs up to 18% (v/v). By performing comprehensive metabolomics, lipidomics, and transcriptomics to elucidate this unique phenotype, we discovered that both wildtype Y. lipolytica and YlCW001 reconfigured membrane composition (e.g., glycerophospholipids and sterols) and cell wall structure (e.g., chitin) under IL-stressful environments. By probing the steroid pathway at transcriptomic, enzymatic, and metabolic levels, we validated that sterols (i.e., ergosterol) are a key component of the cell membrane that enables Y. lipolytica to resist IL-responsive membrane damage and hence tolerate high IL concentrations. This study provides a better understanding of exceptional robustness of Y. lipolytica that can be potentially harnessed as a microbial manufacturing platform for production of fuels and chemicals in organic solvents.
ECTV Abolishes the Ability of GM-BM Cells to Stimulate Allogeneic CD4 T Cells in a Mouse Strain-Independent Manner

ABSTRACT Ectromelia virus (ECTV) is the etiological agent of mousepox, an acute and systemic disease with high mortality rates in susceptible strains of mice. Resistance and susceptibility to mousepox are triggered by the dichotomous T-helper (Th) immune response generated in infected animals, with strong protective Th1 or nonprotective Th2 profile, respectively. Th1/Th2 balance is influenced by dendritic cells (DCs), which were shown to differ in their ability to polarize naïve CD4+ T cells in different mouse strains. Therefore, we have studied the inner-strain differences in the ability of conventional DCs (cDCs), generated from resistant (C57BL/6) and susceptible (BALB/c) mice, to stimulate proliferation and activation of Th cells upon ECTV infection. We found that ECTV infection of GM-CSF-derived bone marrow (GM-BM) cells, composed of cDCs and macrophages, affected initiation of allogeneic CD4+ T cells proliferation in a mouse strain-independent manner. Moreover, infected GM-BM cells from both mouse strains failed to induce and even inhibited the production of Th1 (IFN-γ and IL-2), Th2 (IL-4 and IL-10) and Th17 (IL-17A) cytokines by allogeneic CD4+ T cells. These results indicate that in in vitro conditions ECTV compromises the ability of cDCs to initiate/polarize adaptive antiviral immune response independently of the host strain resistance/susceptibility to lethal infection.
An Inconvenient Variable: Sex Hormones and Their Impact on T Cell Responses

Epidemiologic data demonstrate sex differences in autoimmune diseases, immune responses against infection, and antitumor immunity, and accumulating evidence suggests a major role for sex hormones in mediating these differences. In this study, we review recent advances in understanding how sex hormones regulate T cell responses to alter susceptibility to autoimmunity. Although sex hormones can directly alter gene transcriptional programs of T cells, we focus in this study on how sex hormones alter T cell development and function through their effects on thymic stromal cells and innate cell types. In addition to contributing to our understanding of sex differences, these findings also have implications for the therapeutic use of sex hormones and sex hormone modulators, which are now being prescribed to increasing numbers of patients for a wide variety of indications.
Super Field-of-View Lensless Camera by Coded Image Sensors †

A lensless camera is an ultra-thin computational-imaging system. Existing lensless cameras are based on the axial arrangement of an image sensor and a coding mask, and therefore, the back side of the image sensor cannot be captured. In this paper, we propose a lensless camera with a novel design that can capture the front and back sides simultaneously. The proposed camera is composed of multiple coded image sensors, which are complementary-metal-oxide-semiconductor (CMOS) image sensors in which air holes are randomly made at some pixels by drilling processing. When the sensors are placed facing each other, the object-side sensor works as a coding mask and the other works as a sparsified image sensor. The captured image is a sparse coded image, which can be decoded computationally by using compressive sensing-based image reconstruction. We verified the feasibility of the proposed lensless camera by simulations and experiments. The proposed thin lensless camera realized super-field-of-view imaging without lenses or coding masks and therefore can be used for rich information sensing in confined spaces. This work also suggests a new direction in the design of CMOS image sensors in the era of computational imaging.
Rating early child development outcome measurement tools for routine health programme use

Background Identification of children at risk of developmental delay and/or impairment requires valid measurement of early child development (ECD). We systematically assess ECD measurement tools for accuracy and feasibility for use in routine services in low-income and middle-income countries (LMIC). Methods Building on World Bank and peer-reviewed literature reviews, we identified available ECD measurement tools for children aged 0–3 years used in ≥1 LMIC and matrixed these according to when (child age) and what (ECD domains) they measure at population or individual level. Tools measuring <2 years and covering ≥3 developmental domains, including cognition, were rated for accuracy and feasibility criteria using a rating approach derived from Grading of Recommendations, Assessment, Development and Evaluations. Results 61 tools were initially identified, 8% (n=5) population-level and 92% (n=56) individual-level screening or ability tests. Of these, 27 tools covering ≥3 domains beginning <2 years of age were selected for rating accuracy and feasibility. Recently developed population-level tools (n=2) rated highly overall, particularly in reliability, cultural adaptability, administration time and geographical uptake. Individual-level tool (n=25) ratings were variable, generally highest for reliability and lowest for accessibility, training, clinical relevance and geographical uptake. Conclusions and implications Although multiple measurement tools exist, few are designed for multidomain ECD measurement in young children, especially in LMIC. No available tools rated strongly across all accuracy and feasibility criteria with accessibility, training requirements, clinical relevance and geographical uptake being poor for most tools. Further research is recommended to explore this gap in fit-for-purpose tools to monitor ECD in routine LMIC health services.
Primary Cilium in Cancer Hallmarks

The primary cilium is a solitary, nonmotile and transitory appendage that is present in virtually all mammalian cells. Our knowledge of its ultrastructure and function is the result of more than fifty years of research that has dramatically changed our perspectives on the primary cilium. The mutual regulation between ciliogenesis and the cell cycle is now well-recognized, as well as the function of the primary cilium as a cellular “antenna” for perceiving external stimuli, such as light, odorants, and fluids. By displaying receptors and signaling molecules, the primary cilium is also a key coordinator of signaling pathways that converts extracellular cues into cellular responses. Given its critical tasks, any defects in primary cilium formation or function lead to a wide spectrum of diseases collectively called “ciliopathies”. An emerging role of primary cilium is in the regulation of cancer development. In this review, we seek to describe the current knowledge about the influence of the primary cilium in cancer progression, with a focus on some of the events that cancers need to face to sustain survival and growth in hypoxic microenvironment: the cancer hallmarks.
Background Risk Factors Associated with Shunt Intervention for Possible Idiopathic Normal Pressure Hydrocephalus: A Nationwide Hospital-Based Survey in Japan

Background: Patients with idiopathic normal-pressure hydrocephalus (iNPH) are typically older adults with multiple comorbidities that are associated with a reduction in the efficacy of iNPH treatment via cerebrospinal fluid (CSF) shunt placement. Objective: The present study aimed to investigate the effectiveness of CSF shunt for iNPH using data from a nationwide epidemiological survey in Japan. Methods: We examined 1,423 patients (581 women) aged ≥60 years (median age [25%–75%]: 77 [73–80] years) who were diagnosed with iNPH following a hospital visit in 2012. Patients who experienced an improvement of at least one modified Rankin Scale (mRS) grade after the CSF shunt were classified as “improvement” while the remaining patients were classified as “non-improvement. ” The efficacy of the shunt intervention (n = 842) was analyzed using a binomial logistic regression analysis. Results: An analysis of risk factors associated with shunt placement in patients with mRS grade 2 revealed an association between comorbid chronic ischemic lesions (odds ratio [OR], 2.28; 95% confidence interval [CI], 1.11–4.67; p = 0.025) and cervical spondylosis (OR, 3.62; 95% CI, 1.15–11.34; p = 0.027). Patients with mRS grade 3 at study entry had an association with comorbid Alzheimer’s disease (OR, 3.02; 95% CI, 1.44–6.31; p = 0.003). Conclusions: The results presented here showed that any age-related risk is minimal and should not be cause for rejection of surgical treatment options. Clinical decisions regarding CSF shunt should be individualized to each patient, with adequate consideration of the relative risks and benefits, including maximizing a healthy life expectancy.