Miracle-dz/UniFAR-FTUs huggingface dataset:
Disordered Microbial Communities in Asthmatic Airways

Background A rich microbial environment in infancy protects against asthma [1], [2] and infections precipitate asthma exacerbations [3]. We compared the airway microbiota at three levels in adult patients with asthma, the related condition of COPD, and controls. We also studied bronchial lavage from asthmatic children and controls. Principal Findings We identified 5,054 16S rRNA bacterial sequences from 43 subjects, detecting >70% of species present. The bronchial tree was not sterile, and contained a mean of 2,000 bacterial genomes per cm2 surface sampled. Pathogenic Proteobacteria, particularly Haemophilus spp. , were much more frequent in bronchi of adult asthmatics or patients with COPD than controls. We found similar highly significant increases in Proteobacteria in asthmatic children. Conversely, Bacteroidetes, particularly Prevotella spp. , were more frequent in controls than adult or child asthmatics or COPD patients. Significance The results show the bronchial tree to contain a characteristic microbiota, and suggest that this microbiota is disturbed in asthmatic airways.
Addressing social and gender norms to improve uptake of maternal health services in Mali: a descriptive study of CARE’s Project Hope for Mothers and Newborns (PEMN)

Abstract This study examines the design and implementation of a maternal mortality prevention intervention in central Mali. It uses Project Hope for Mothers and Newborns (PEMN) as a case study to examine the context around implementation, with special emphasis on the role of social, gender and power norms in meeting programme objectives. Interventions to strengthen the health system and workforce were coupled with a social norms change approach to catalyse the personal transformation of staff, community-level health workers and communities via critical reflection and dialogue on gender and social power norms related to maternal health. Processes of reflection among staff, health workers and the community, coupled with activities that challenged restrictive norms, provided a platform for critical thinking, communication and motivation for change. Rigorous and comprehensive monitoring and evaluation is needed to identify and understand unique pathways to transformative change.
CRF tagging for head recognition based on Stanford parser

Chinese parsing has received more and more attention, and in this paper, we use toolkit to perform parsing on the data of Tsinghua Chinese Treebank (TCT) used in CIPS, and we use Conditional Random Fields (CRFs) to train specific model for the head recognition. At last, we compare different results on different POS results
Optical coherence tomography to guide percutaneous treatment of coronary bifurcation disease

ABSTRACT Introduction: Cardiovascular disease remains the most common cause of death worldwide. Enormous progress in the technology and applicability of percutaneous techniques to treat obstructive coronary heart disease has been made, and the number of percutaneous coronary interventions (PCI) is increasing. Coronary bifurcations are involved in a substantial number of PCIs and despite recent advances, bifurcation PCI remains a challenge in terms of immediate success and long-term outcome. Angiography has a limited capacity for showing important features of the 3 dimensional coronary vessel anatomy, position of stent struts and exact wire positions and is therefore suboptimal for guiding bifurcation PCI. Intracoronary optical coherence tomography (OCT) provides high resolution and the information gained during PCI is unprecedented compared with angiography guidance and intravascular ultrasound. Areas covered: This review will provide an overview of the use of OCT to guide bifurcation-PCI. Expert commentary: OCT is a promising guide for bifurcation-PCI at each individual step: from planning the strategy (provisional versus two-stent strategy), to guidance during PCI, and finally checking the interventional result. Until dedicated randomized trails are complete, we recommend OCT guidance for interventions in complex coronary bifurcation disease and for imaging when unexpected procedural events occur.
Elevated PIM2 gene expression is associated with poor survival of patients with acute myeloid leukemia

Abstract The PIM2 gene encodes the serine/threonine kinase involved in cell survival and apoptosis. The aim of the study was to evaluate the expression of the PIM2 gene in acute myeloid leukemia (AML) and to examine its role in apoptosis of the blastic cells. We analyzed the PIM2 expression in 148 patients: 91 with AML, 57 with acute lymphoblastic leukemia and 24 healthy controls by Real-Time PCR and Western blot. Inhibition of the PIM2 gene in human leukemic HL60 cell line was performed with RNAi and apoptosis rate was analyzed. Our results indicate that overexpression of PIM2 in AML is associated with low complete remission rate, high-risk cytogenetics, shorter leukemia-free survival, and event-free survival. Cytometric analysis of HL60/PAC-GFP and HL60/PAC-GFP-shPIM2 cells revealed an increase in the number of apoptotic cells after inhibition of PIM2 gene. In summary, the elevated expression of PIM2 in blastic cells is associated with poor prognosis of AML patients and their resistance to induction therapy.
How Prevalent Is Object-Based Attention?

Previous research suggests that visual attention can be allocated to locations in space (space-based attention) and to objects (object-based attention). The cueing effects associated with space-based attention tend to be large and are found consistently across experiments. Object-based attention effects, however, are small and found less consistently across experiments. In three experiments we address the possibility that variability in object-based attention effects across studies reflects low incidence of such effects at the level of individual subjects. Experiment 1 measured space-based and object-based cueing effects for horizontal and vertical rectangles in 60 subjects comparing commonly used target detection and discrimination tasks. In Experiment 2 we ran another 120 subjects in a target discrimination task in which rectangle orientation varied between subjects. Using parametric statistical methods, we found object-based effects only for horizontal rectangles. Bootstrapping methods were used to measure effects in individual subjects. Significant space-based cueing effects were found in nearly all subjects in both experiments, across tasks and rectangle orientations. However, only a small number of subjects exhibited significant object-based cueing effects. Experiment 3 measured only object-based attention effects using another common paradigm and again, using bootstrapping, we found only a small number of subjects that exhibited significant object-based cueing effects. Our results show that object-based effects are more prevalent for horizontal rectangles, which is in accordance with the theory that attention may be allocated more easily along the horizontal meridian. The fact that so few individuals exhibit a significant object-based cueing effect presumably is why previous studies of this effect might have yielded inconsistent results. The results from the current study highlight the importance of considering individual subject data in addition to commonly used statistical methods.
Cost-Effectiveness of a Health System-Based Smoking Cessation Program

Introduction Project CLIQ (Community Link to Quit) was a proactive population-outreach strategy using an electronic health records-based smoker registry and interactive voice recognition technology to connect low- to moderate-income smokers with cessation counseling, medications, and social services. A randomized trial demonstrated that the program increased cessation. We evaluated the cost-effectiveness of CLIQ from a provider organization's perspective if implemented outside the trial framework. Methods We calculated the cost, cost per smoker, incremental cost per additional quit, and, secondarily, incremental cost per additional life year saved of the CLIQ system compared to usual care using data from a 2011-2013 randomized trial assessing the effectiveness of the CLIQ system. Sensitivity analyses considered economies of scale and initial versus ongoing costs. Results Over a 20-month period (the duration of the trial) the program cost US $283 027 (95% confidence interval [CI] $209 824-$389 072) more than usual care in a population of 8544 registry-identified smokers, 707 of whom participated in the program. The cost per smoker was $33 (95% CI 28-40), incremental cost per additional quit was $4137 (95% CI $2671-$8460), and incremental cost per additional life year saved was $7301 (95% CI $4545-$15 400). One-time costs constituted 28% of costs over 20 months. Ongoing costs were dominated by personnel costs (71% of ongoing costs). Sensitivity analyses showed sharp gains in cost-effectiveness as the number of identified smokers increased because of the large initial costs. Conclusions The CLIQ system has favorable cost-effectiveness compared to other smoking cessation interventions. Cost-effectiveness will be greatest for health systems with high numbers of smokers and with the high smoker participation rates. Implications Health information systems capable of establishing registries of patients who are smokers are becoming more prevalent. This economic analysis illustrates the cost implications for health care systems adopting a proactive tobacco treatment outreach strategy for low- and middle-income smokers. We find that under many circumstances, the CLIQ system has a favorable cost-per-quit compared to other population-based tobacco treatment strategies. The strategy could be widely disseminable if health systems leverage economies of scale.
The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome1[OPEN]

The soybean genome encodes over 6,000 long intergenic noncoding RNAs implicated in many biological processes, including transcription, development, and possibly influencing agronomic traits. Long intergenic noncoding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean (Glycine max) is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities. Soybean cultivars have photoperiod requirements restricting its use and productivity. Molecular regulators of these legume-specific developmental processes remain enigmatic. Long noncoding RNAs may play important regulatory roles in soybean growth and development. In this study, over one billion RNA-seq read pairs from 37 samples representing nine tissues were used to discover 6,018 lincRNA loci. The lincRNAs were shorter than protein-coding transcripts and had lower expression levels and more sample specific expression. Few of the loci were found to be conserved in two other legume species (chickpea [Cicer arietinum] and Medicago truncatula), but almost 200 homeologous lincRNAs in the soybean genome were detected. Protein-coding gene-lincRNA coexpression analysis suggested an involvement of lincRNAs in stress response, signal transduction, and developmental processes. Positional analysis of lincRNA loci implicated involvement in transcriptional regulation. lincRNA expression from centromeric regions was observed especially in actively dividing tissues, suggesting possible roles in cell division. Integration of publicly available genome-wide association data with the lincRNA map of the soybean genome uncovered 23 lincRNAs potentially associated with agronomic traits.
Locating Defense Positions for Thwarting the Propagation of Topological Worms

A common view for the preferable positions of thwarting worm propagation is at the highly connected nodes. However, in certain conditions, such as when some popular users (highly connected nodes in the network) have more vigilance on the malicious codes, this may not always be the truth. In this letter, we propose a measure of betweenness and closeness to locate the most suitable positions for slowing down the worm propagation. This work provides practical values to the defense of topological worms.
Changes in Beliefs About Category Homogeneity and Variability Across Childhood.

Effective category-based induction requires understanding that categories include both fundamental similarities between members and important variation. This article explores 4- to 11-year-olds' (n = 207) and adults' (n = 49) intuitions about this balance between within-category homogeneity and variability using a novel induction task in which participants predict the distribution of a property among members of a novel category. Across childhood, children learned to recognize variability within categories-showing increasing sensitivity to the role of property type and domain in constraining inferences. Children below the age of 6 showed evidence for a domain-general assumption that categories are homogeneous-generalizing properties broadly to 100% of category members. These studies support important developmental changes in category representations that may influence category-based induction.
A method to gather/arrange particles based on thermal convection

We propose a novel method to gather or arrange multiple micro particles by using the thermal convection effect in the water. We fabricate the fiber tip to be a nonadiabatic-tapered shape and then plate a gold film on the fiber tip. The gold film coated on the fiber tip absorbs the light output from the fiber and then generate lots of heat in the water, which causes the thermal convection. The convection forces bring the micro particles moving towards the fiber tip where the temperature is much higher. By using this thermal convection effect, we can realize the multiple micro particles gathering or arranging quickly, easily and simply.
Viewpoint Invariant Person Re-Identification for Global Multi-Object Tracking with Non-Overlapping Cameras

Person re-identification is to match pedestrians observed from non-overlapping camera views. It has important applications in video surveillance such as person retrieval, person tracking, and activity analysis. However, it is a very challenging problem due to illumination, pose and viewpoint variations between non-overlapping camera views. In this work, we propose a viewpoint invariant method for matching pedestrian images using orientation of pedestrian. First, the proposed method divides a pedestrian image into patches and assigns angle to a patch using the orientation of the pedestrian under the assumption that a person body has the cylindrical shape. The difference between angles are then used to compute the similarity between patches. We applied the proposed method to real-time global multi-object tracking across multiple disjoint cameras with non-overlapping field of views. Re-identification algorithm makes global trajectories by connecting local trajectories obtained by different local trackers. The effectiveness of the viewpoint invariant method for person re-identification was validated on the VIPeR dataset. In addition, we demonstrated the effectiveness of the proposed approach for the inter-camera multiple object tracking on the MCT dataset with ground truth data for local tracking.
Association Between Inhaled Corticosteroid Use and Bone Fracture in Children With Asthma

Importance Daily use of inhaled corticosteroids is a widely recommended treatment for mild persistent asthma in children. There is concern that, similar to systemic corticosteroids, inhaled corticosteroids may have adverse effects on bone health. Objective To determine whether there is an increased risk of bone fracture associated with inhaled corticosteroid use in children with asthma. Design, Setting, and Participants In this population-based nested case-control study, we used health administrative databases to identify a cohort of children aged 2 to 18 years with a physician diagnosis of asthma between April 1, 2003, and March 31, 2014, who were eligible for public drug coverage through the Ontario Drug Benefit Program (Ontario, Canada). We matched cases of first fracture after asthma diagnosis to fracture-free controls (ratio of 1 to 4) based on date of birth (within 1 year), sex, and age at asthma diagnosis (within 2 years). We used a 1-year lookback period to ascertain history of inhaled corticosteroid use. Multivariable conditional logistic regression was used to obtain an odds ratio (OR) with 95% confidence interval for fracture, comparing no inhaled corticosteroid use vs current, recent, and past use. Exposures Inhaled corticosteroid use during the child’s 1-year lookback period, measured as current user if the prescription was filled less than 90 days prior to the index date, recent user (91-180 days), past user (181-365 days), or no use. Main Outcomes and Measures First emergency department visit for fracture after asthma diagnosis, identified using International Statistical Classification of Diseases and Related Health Problems, 10th Revision codes. Results This study included 19 420 children (61.0% male; largest proportion of children, 31.5%, were aged 6-9 years at their index date). The multivariable regression results did not show a significant association between first fracture after asthma diagnosis and current use (OR, 1.07; 95% CI, 0.97-1.17), recent use (OR, 0.96; 95% CI, 0.86-1.07), or past use (OR, 1.00; 95% CI, 0.91-1.11) of inhaled corticosteroids, compared with no use, while adjusting for sociodemographic factors and other medication use. However, use of systemic corticosteroids in the 1-year lookback period resulted in greater odds of fracture (OR, 1.17; 95% CI, 1.04-1.33). Conclusions and Relevance Systemic corticosteroids, but not inhaled corticosteroids, were significantly associated with increased odds of fracture in the pediatric asthma population.
Work-Family Conflict and Employee Well-Being Over Time: The Loss Spiral Effect

Objective: The development of work-family conflict over time was analyzed using Conservation of Resources Theory. Method: The reciprocal effect between work-family conflict and employee well-being was tested with cross-lagged analyses on the basis of three waves. The sample comprised 713 employees of a Portuguese service organization. Results: Structural equation modeling analyses, with sex, age, and parental demand controlled, indicated that the work-family conflict at T1 and T2 decreases the employee psychological well-being at T2 and T3, respectively. Furthermore, employee psychological well-being at T2 had a longitudinal cross-lagged effect on work-family at T3. We concluded that employee psychological well-being at T2 predicted work-family at T3, which was a subsequent outcome of work-family conflict on T1. Conclusions: This paper highlighted the importance of organizations to consider work-family conflict to ensure employees’ well-being because they develop reciprocal relationship with a loss spiral effect.
Revising the Structural Diversity of Ribosomal Proteins Across the Three Domains of Life

Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes, and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations that reside within seemingly conserved segments of ribosomal proteins. We then illustrate that these variations reflect an apparent adaptation of ribosomal proteins to the specific environments and lifestyles of living species. Finally, we show that most of these structural variations reside within nonglobular extensions of ribosomal proteins-protein segments that are thought to promote ribosome biogenesis by stabilizing the proper folding of ribosomal RNA. We show that although the extensions are thought to be the most ancient peptides on our planet, they are in fact the most rapidly evolving and most structurally and functionally diverse segments of ribosomal proteins. Overall, our work illustrates that, despite being long considered as slowly evolving and highly conserved, ribosomal proteins are more complex and more specialized than is generally recognized.
Changes in morphology and metabolism enable Mn‐oxidizing bacteria from mid‐oceanic ridge environment to counter metal‐induced stress

Mn‐oxidizing potential of two metal‐tolerant bacterial strains – Halomonas meridiana and Marinobacter algicola isolated from the South West Indian Ridge waters were compared at varying concentrations of Mn (II), i.e., 1, 10, and 100 μmol and mmol L−1. Accompanying changes in their morphology and metabolism were also determined. At concentrations >1 mmol L−1 Mn (II), Mn‐oxidizing potential of M. algicola was 2–7 times greater than that of H. meridiana. Scanning electron microscopy revealed that exposure to elevated metal content prompted bacterial cells especially those of M. algicola to been enveloped in exopolymeric material and form aggregates. Energy dispersive spectrometric analysis showed that exopolymeric material acts as a nucleation site for Mn deposition and oxide formation which occurs in the form of microspherical aggregates. These features show striking resemblance to biogenically produced Fe‐Mn oxide deposits from Lau Basin. Surprisingly, diffractograms of auto‐oxidized and bacterially formed Mn‐oxide showed similarities to the hydrothermal vein mineral Rhodochrosite indicating that it can also be produced biotically. Elongation of cells by up to 4× the original size and distortion in cell shape were evident at Mn (II) concentrations >100 μmol L−1. Marked differences in C‐substrate utilization by the test strains were also observed in presence of Mn (II). A shift in use of substrates that are readily available in oceanic waters like N‐acetyl‐d‐glucosamine to those that can be used under changing redox conditions (d‐cellobiose) or in the presence of metal ions (d‐arabinose, l‐asparagine) were observed. These findings highlight the significant role of autochthonous bacteria in transforming reduced metal ions and aiding in the formation of metal oxides. Under natural or laboratory conditions, the mode of bacterially generated Mn‐oxide tends to remain the same.
From DNA sequence to chromatin organization: the fundamental role of genomic long-range correlations.

Understanding how chromatin is spatially and dynamically organized in the nucleus of eukaryotic cells and how this affects genome functions is one of the main challenges of cell biology. In this review, we show that when using concepts, methodologies, numerical and experimental techniques coming from physics and signal processing, we are able to extract, directly from the DNA sequence, structural and dynamical informations on chromatin condensationdecondensation mechanisms that are likely to play a fundamental role in regulating many molecular processes involved in nuclear functions.