Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain Tumor-Enhancement Visualization and Morphometric Assessment: A Comparison of MPRAGE, SPACE, and VIBE MRI Techniques

Fifty-four contrast-enhancing tumors (38 gliomas and 16 metastases) were assessed using MPRAGE, VIBE, and SPACE techniques randomly acquired after gadolinium-based contrast agent administration on a 3T scanner. Enhancement conspicuity was assessed quantitatively by calculating the contrast rate and contrast-to-noise ratio, and qualitatively, by consensus visual comparative ratings. Compared with MPRAGE, both SPACE and VIBE obtained higher contrast rate, contrast-to-noise ratio, and visual conspicuity ratings in both gliomas and metastases. The authors conclude that superior conspicuity for brain tumor enhancement can be achieved using SPACE and VIBE techniques, compared with MPRAGE. BACKGROUND AND PURPOSE: Postgadolinium MR imaging is crucial for brain tumor diagnosis and morphometric assessment. We compared brain tumor enhancement visualization and the “target” object morphometry obtained with the most commonly used 3D MR imaging technique, MPRAGE, with 2 other routinely available techniques: sampling perfection with application-optimized contrasts by using different flip angle evolutions (SPACE) and volumetric interpolated brain examination (VIBE). MATERIALS AND METHODS: Fifty-four contrast-enhancing tumors (38 gliomas and 16 metastases) were assessed using MPRAGE, VIBE, and SPACE techniques randomly acquired after gadolinium-based contrast agent administration on a 3T scanner. Enhancement conspicuity was assessed quantitatively by calculating the contrast rate and contrast-to-noise ratio, and qualitatively, by consensus visual comparative ratings. The total enhancing tumor volume and between-sequence discrepancy in the margin delineation were assessed on the corresponding 3D target objects contoured with a computer-assisted software for neuronavigation. The Wilcoxon signed rank and Pearson χ2 nonparametric tests were used to investigate between-sequence discrepancies in the contrast rate, contrast-to-noise ratio, visual conspicuity ratings, tumor volume, and margin delineation estimates. Differences were also tested for 1D (Response Evaluation Criteria in Solid Tumors) and 2D (Response Assessment in Neuro-Oncology) measurements. RESULTS: Compared with MPRAGE, both SPACE and VIBE obtained higher contrast rate, contrast-to-noise ratio, and visual conspicuity ratings in both gliomas and metastases (P range, <.001–.001). The between-sequence 3D target object margin discrepancy ranged between 3% and 19.9% of lesion tumor volume. Larger tumor volumes, 1D and 2D measurements were obtained with SPACE (P range, <.01–.007). CONCLUSIONS: Superior conspicuity for brain tumor enhancement can be achieved using SPACE and VIBE techniques, compared with MPRAGE. Discrepancies were also detected when assessing target object size and morphology, with SPACE providing more accurate estimates.
Challenges and Opportunities to Improve the Clinician Experience Reviewing Electronic Progress Notes

Abstract Background High-quality clinical notes are essential to effective clinical communication. However, electronic clinical notes are often long, difficult to review, and contain information that is potentially extraneous or out of date. Additionally, many clinicians write electronic clinical notes using customized templates, resulting in notes with significant variability in structure. There is a need to understand better how clinicians review electronic notes and how note structure variability may impact clinicians' note-reviewing experiences. Objective This article aims to understand how physicians review electronic clinical notes and what impact section order has on note-reviewing patterns. Materials and Methods We conducted an experiment utilizing an electronic health record (EHR) system prototype containing four anonymized patient cases, each composed of nine progress notes that were presented with note sections organized in different orders to different subjects (i.e., Subjective, Objective, Assessment, and Plan, Assessment, Plan, Subjective, and Objective, Subjective, Assessment, Objective, and Plan, and Mixed). Participants, who were mid-level residents and fellows, reviewed the cases and provided a brief summary after reviewing each case. Time-related data were collected and analyzed using descriptive statistics. Surveys were administered and interviews regarding experiences reviewing notes were collected and analyzed qualitatively. Results Qualitatively, participants reported challenges related to reviewing electronic clinical notes. Experimentally, time spent reviewing notes varied based on the note section organization. Consistency in note section organization improved performance (e.g., less scrolling and searching) compared with Mixed section organization when reviewing progress notes. Discussion Clinicians face significant challenges reviewing electronic clinical notes. Our findings support minimizing extraneous information in notes, removing information that can be found in other parts of the EHR, and standardizing the display and order of note sections to improve clinicians' note review experience. Conclusion Our findings support the need to improve EHR note design and presentation to support optimal note review patterns for clinicians.
A systematic review of the validity and reliability of patient-reported experience measures.

OBJECTIVES To identify patient-reported experience measures (PREMs), assess their validity and reliability, and assess any bias in the study design of PREM validity and reliability testing. DATA SOURCES/STUDY SETTING Articles reporting on PREM development and testing sourced from MEDLINE, CINAHL and Scopus databases up to March 13, 2018. STUDY DESIGN Systematic review. DATA COLLECTION/EXTRACTION METHODS Critical appraisal of PREM study design was undertaken using the Appraisal tool for Cross-Sectional Studies (AXIS). Critical appraisal of PREM validity and reliability was undertaken using a revised version of the COSMIN checklist. PRINCIPAL FINDINGS Eighty-eight PREMs were identified, spanning across four main health care contexts. PREM validity and reliability was supported by appropriate study designs. Internal consistency (n = 58, 65.2 percent), structural validity (n = 49, 55.1 percent), and content validity (n = 34, 38.2 percent) were the most frequently reported validity and reliability tests. CONCLUSIONS Careful consideration should be given when selecting PREMs, particularly as seven of the 10 validity and reliability criteria were not undertaken in ≥50 percent of the PREMs. Testing PREM responsiveness should be prioritized for the application of PREMs where the end user is measuring change over time. Assessing measurement error/agreement of PREMs is important to understand the clinical relevancy of PREM scores used in a health care evaluation capacity.
Alternative oxidase confers nutritional limitation on Drosophila development

Abstract The mitochondrial alternative oxidase, AOX, present in most eukaryotes apart from vertebrates and insects, catalyzes the direct oxidation of ubiquinol by oxygen, by‐passing the terminal proton‐motive steps of the respiratory chain. Its physiological role is not fully understood, but it is proposed to buffer stresses in the respiratory chain similar to those encountered in mitochondrial diseases in humans. Previously, we found that the ubiquitous expression of AOX from Ciona intestinalis in Drosophila perturbs the development of flies cultured under low‐nutrient conditions (media containing only glucose and yeast). Here we tested the effects of a wide range of nutritional supplements on Drosophila development, to gain insight into the physiological mechanism underlying this developmental failure. On low‐nutrient medium, larvae contained decreased amounts of triglycerides, lactate, and pyruvate, irrespective of AOX expression. Complex food supplements, including treacle (molasses), restored normal development to AOX‐expressing flies, but many individual additives did not. Inhibition of AOX by treacle extract was excluded as a mechanism, since the supplement did not alter the enzymatic activity of AOX in vitro. Furthermore, antibiotics did not influence the organismal phenotype, indicating that commensal microbes were not involved. Fractionation of treacle identified a water‐soluble fraction with low solubility in ethanol, rich in lactate and tricarboxylic acid cycle intermediates, which contained the critical activity. We propose that the partial activation of AOX during metamorphosis impairs the efficient use of stored metabolites, resulting in developmental failure.
Current best practices in single‐cell RNA‐seq analysis: a tutorial

Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single‐cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up‐to‐date workflow to analyse one's data. Here, we detail the steps of a typical single‐cell RNA‐seq analysis, including pre‐processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell‐ and gene‐level downstream analysis. We formulate current best‐practice recommendations for these steps based on independent comparison studies. We have integrated these best‐practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github. com/theislab/single-cell-tutorial. This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines.
Commercially produced complementary foods in Bandung City, Indonesia, are often reported to be iron fortified but with less than recommended amounts or suboptimal forms of iron

Abstract Commercially produced complementary foods (CPCF) that are iron fortified can help improve iron status of young children. We conducted a review of 217 CPCF sold in 42 stores in Bandung, Indonesia, in 2017. There were 95 (44%) infant cereals, 71 (33%) snacks or finger foods (biscuits or cookies, puffs, and noodles or crackers), 35 (16%) purees, and 16 (7%) other foods for which we obtained label information. Nearly 70% of CPCF reported iron content on their labels, but only 58% of products were reported to be fortified with iron according to ingredient lists. Among iron‐fortified products, only one fifth indicated a specific type of iron used as the fortificant, but all of these were recommended by the World Health Organization for fortifying complementary foods. Infant cereal was more likely to contain added iron (81%) compared with snacks or finger food (58%) and purees (14%) and had higher iron content per median serving size (cereal = 3.8 mg, snacks or finger food = 1.3 mg, mixed meals = 2.7 mg, and purees = 0.9 mg). Infant cereal was most likely to meet the recommended daily intakes for iron (41% for infants 6–12 months of age and 66% for children 12–36 months) compared with snacks or finger food (infants = 14%, children = 22%), mixed meals (infants = 28%, children = 46%), or purees (infants = 9%, children = 15%). Regulations on fortification of complementary foods need to specify minimum levels and forms of iron and require reporting in relation to requirements by child age and serving size. Monitoring and enforcement of regulations will be essential to ensure compliance.
Proceedings of the Workshop on Computational Approaches to Arabic Script-based Languages

Recently, there has been a surge of interest in the study of the languages of the Middle East, especially Arabic, Persian (Farsi), Pashto, Kurdish and Urdu. This sudden and urgent interest is manifested by the availability of funding for rapid development of practical systems for processing large volumes of data in these languages. Computational applications for proper name identification, entity recognition, categorization, information retrieval, summarization, machine translation and other implementations are currently in high demand. This comes at a time when advances in formal and computational linguistics over the last fifty years are being consolidated, while work on machine learning and statistical methods has been showing great promise. There exists a considerable body of work in computational linguistics specifically targeted to these middle eastern languages. Much of the research and development has been the result of initiatives by individual research establishments or industry firms. Furthermore, the usage of the Arabic script gives rise to certain issues that are common to all these languages despite their being of distinct language families. Hence, these languages share properties such as the absence of capitalization, right to left direction, lack of clear word boundaries, complex word structure, a high degree of ambiguity due to non-representation of short vowels in the writing system, and related encoding issues.
Prevalence, duration, and content of television advertisements for breast milk substitutes and commercially produced complementary foods in Phnom Penh, Cambodia and Dakar, Senegal

Abstract Promotion of breast milk substitutes (BMS) and inappropriate marketing of commercially produced complementary foods (CPCF), including through television, can negatively influence infant and young child feeding. The World Health Organization International Code of Marketing of Breast‐milk Substitutes and subsequent relevant World Health Assembly (WHA) resolutions prohibit such advertising and require manufacturers and distributors to comply with its provisions; however, such regulations at national level may vary. Advertisements require Ministry of Health approval in Cambodia but are not regulated in Senegal. Television stations were monitored for 13 months in Phnom Penh and for 3 months in Dakar to assess advertisements for BMS and CPCF. Ten television channels (out of 16) in Phnom Penh and four (out of 20) in Dakar aired advertisements for BMS. Three and five channels, respectively, aired advertisements for CPCF. All BMS advertised in Phnom Penh were for children over 1 year of age. BMS products for children 6+ months of age and 1+ years of age were advertised in Dakar. Average air time for BMS advertisements was 189.5 min per month in Phnom Penh and 29.7 min in Dakar. Air time for CPCF advertisements averaged 3.2 min per month and 13.6 min, respectively. Fewer than half of BMS advertisements and three quarters of CPCF advertisements explicitly stated an age of use for products. Nutrition and health claims were common across BMS advertisements. This study illustrates the need to adopt, regulate, monitor, and enforce legislation prohibiting BMS promotion, as well as to implement regulations to prevent inappropriate promotion of CPCF.
Anthropogenic noise and the bioacoustics of terrestrial invertebrates

ABSTRACT Anthropogenic noise is an important issue of environmental concern owing to its wide-ranging effects on the physiology, behavior and ecology of animals. To date, research has focused on the impacts of far-field airborne noise (i.e. pressure waves) on vertebrates, with few exceptions. However, invertebrates and the other acoustic modalities they rely on, primarily near-field airborne and substrate-borne sound (i.e. particle motion and vibrations, respectively) have received little attention. Here, we review the literature on the impacts of different types of anthropogenic noise (airborne far-field, airborne near-field, substrate-borne) on terrestrial invertebrates. Using literature on invertebrate bioacoustics, we propose a framework for understanding the potential impact of anthropogenic noise on invertebrates and outline predictions of possible constraints and adaptations for invertebrates in responding to anthropogenic noise. We argue that understanding the impacts of anthropogenic noise requires us to consider multiple modalities of sound and to cultivate a broader understanding of invertebrate bioacoustics. Summary: We review the current literature on invertebrate bioacoustics and characteristics of anthropogenic noise to suggest a framework for understanding the potential impact of anthropogenic noise on terrestrial invertebrates.
Anthocyanins and Anthocyanin-Derived Products in Yeast-Fermented Beverages

The beverages obtained by yeast fermentation from anthocyanin-rich natural sources (grapes, berries, brown rice, etc.) retain part of the initial pigments in the maturated drink. During the fermentation and aging processes anthocyanins undergo various chemical transformations, which include reactions with glycolytic products (especially pyruvate and acetaldehyde) or with other compounds present in the complex fermentation milieu (such as vinylphenols obtained from cinnamic acids by means of a yeast decarboxylase) yielding pigments which can be more stable than the initial anthocyanins. Overall, these compounds contribute to the organoleptic traits of the mature product, but also to the overall chemical composition which make the yeast fermented beverages important sources of dietary antioxidants. In this review, we focused on the studies regarding the changes underwent by anthocyanins during yeast-mediated fermentation, on the approaches taken to enrich the fermented beverages in anthocyanins and their derived products, and on the interrelations between yeast and anthocyanin which were of relevance for obtaining a high-quality product containing optimum amounts of anthocyanin and anthocyanin-derived products.
Fractal geometry: A consolidated tool for imagination

Since the very first attempts performed by the human brain for acquiring information about the surrounding world, priority is usually given to the information received by visual channels, i.e. by the eyes. It is interesting the proportion of human cerebral cortex destined for processing the stimuli captured by the photo-sensors contained in the retina, ranging 55%. According to several authors (1-4), the human learning process involves the association of each stimulus received by the different transduction assemblies composing the five senses to an image or, even, to a specific intricate memory. This has derived in formulating research works about how the brain develops the processes of creation and imagination. Therefore, the complexity of the well-known capacity of children for drawing in the mind (or in a piece of paper) a picture of an imaginary creature, and defining how it smells, hears, tastes, and touches, is astonishing. Having fun making an imaginary creature does not necessarily imply an easy task for the human brain, especially if the thinker of such an imaginary creature goes deeper into deciding if the creature becomes an opponent or a friend. In turn, the learning process may result affected when the visual channels do not work properly. Some studies have shown that lack of visual experience delays the physiological development of cognitive, social and linguistic skills in blind children. Although this might signify a serious disadvantage for an adequate brain development, there exist reports indicating that cerebral processing of shapes, spatial perception and imagery occurs in the same way and in the same highly-specialised visual areas, despite the sensory channels through which the information is acquired, in both blind and non-blind individuals. Furthermore, it is possible to mention many examples of blind persons noticing some aspects that the non-blind ones do not recognise.
MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation

The linker of nucleoskeleton and cytoskeleton (LINC) complex is an essential multi-protein structure spanning the eukaryotic nuclear envelope. The LINC complex functions to maintain nuclear architecture, positioning, and mobility, along with specialized functions in meiotic prophase and chromosome segregation. Members of the LINC complex were recently identified in maize, an important scientific and agricultural grass species. Here we characterized Maize LINC KASH AtSINE-like2, MLKS2, which encodes a highly conserved SINE-group plant KASH protein with characteristic N-terminal armadillo repeats (ARM). Using a heterologous expression system, we showed that actively expressed GFP-MLKS2 is targeted to the nuclear periphery and colocalizes with F-actin and the endoplasmic reticulum, but not microtubules in the cell cortex. Expression of GFP-MLKS2, but not GFP-MLKS2ΔARM, resulted in nuclear anchoring. Genetic analysis of transposon-insertion mutations, mlks2-1 and mlks2-2, showed that the mutant phenotypes were pleiotropic, affecting root hair nuclear morphology, stomatal complex development, multiple aspects of meiosis, and pollen viability. In male meiosis, the mutants showed defects for bouquet-stage telomere clustering, nuclear repositioning, perinuclear actin accumulation, dispersal of late prophase bivalents, and meiotic chromosome segregation. These findings support a model in which the nucleus is connected to cytoskeletal F-actin through the ARM-domain, predicted alpha solenoid structure of MLKS2. Functional conservation of MLKS2 was demonstrated through genetic rescue of the misshapen nuclear phenotype of an Arabidopsis (triple-WIP) KASH mutant. This study establishes a role for the SINE-type KASH proteins in affecting the dynamic nuclear phenomena required for normal plant growth and fertility.
Functional Connectivity Associated with Health-Related Quality of Life in Children with Focal Epilepsy

BACKGROUND AND PURPOSE: Although functional connectivity has been linked to cognitive function in epilepsy, its relationship with physical, psychological, or social dysfunction is unknown. This study aimed to assess the relationship between network architecture from resting-state fMRI and health-related quality of life in children with medically intractable focal epilepsy. MATERIALS AND METHODS: Forty-seven children with nonlesional focal epilepsy were included; 22 had frontal lobe epilepsy and 15 had temporal lobe epilepsy. We computed graph metrics of functional connectivity, including network segregation (clustering coefficient and modularity) and integration (characteristic path length and participation coefficient). Health-related quality of life was measured using the Quality of Life in Childhood Epilepsy questionnaire. We examined the associations between graph metrics and the Quality of Life in Childhood Epilepsy total and domains scores, with age, sex, age at seizure onset, fMRI motion, and network density as covariates. RESULTS: There was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = −2.0; P = . 04] and social function [t(40) = −2.9; P = . 005]. There was a positive association between the mean participation coefficient and total Quality of Life in Childhood Epilepsy score [t(40) = 2.2; P = . 03] and cognition [t(40) = 3.8; P = . 0004]. In temporal lobe epilepsy, there was a negative relationship between the clustering coefficient and total Quality of Life in Childhood Epilepsy score [t(8) = −2.8; P = . 02] and social function [t(8) = −3.6; P = . 0075] and between modularity and total Quality of Life in Childhood Epilepsy score [t(8) = −2.5; P = . 04] and social function [t(8) = −4.4; P = . 0021]. In frontal lobe epilepsy, there was no association between network segregation and integration and Quality of Life in Childhood Epilepsy total or domain scores. CONCLUSIONS: Our findings indicate that there are other higher order brain functions beyond cognition, which may be linked with functional connectivity of the brain.