Miracle-dz/UniFAR-FTUs huggingface dataset:
Graphical Presentations of Clinical Data in a Learning Electronic Medical Record

Abstract Background Complex electronic medical records (EMRs) presenting large amounts of data create risks of cognitive overload. We are designing a Learning EMR (LEMR) system that utilizes models of intensive care unit (ICU) physicians' data access patterns to identify and then highlight the most relevant data for each patient. Objectives We used insights from literature and feedback from potential users to inform the design of an EMR display capable of highlighting relevant information. Methods We used a review of relevant literature to guide the design of preliminary paper prototypes of the LEMR user interface. We observed five ICU physicians using their current EMR systems in preparation for morning rounds. Participants were interviewed and asked to explain their interactions and challenges with the EMR systems. Findings informed the revision of our prototypes. Finally, we conducted a focus group with five ICU physicians to elicit feedback on our designs and to generate ideas for our final prototypes using participatory design methods. Results Participating physicians expressed support for the LEMR system. Identified design requirements included the display of data essential for every patient together with diagnosis-specific data and new or significantly changed information. Respondents expressed preferences for fishbones to organize labs, mouseovers to access additional details, and unobtrusive alerts minimizing color-coding. To address the concern about possible physician overreliance on highlighting, participants suggested that non-highlighted data should remain accessible. Study findings led to revised prototypes, which will inform the development of a functional user interface. Conclusion In the feedback we received, physicians supported pursuing the concept of a LEMR system. By introducing novel ways to support physicians' cognitive abilities, such a system has the potential to enhance physician EMR use and lead to better patient outcomes. Future plans include laboratory studies of both the utility of the proposed designs on decision-making, and the possible impact of any automation bias.
Development of a dynamic in vitro stretch model of the alveolar interface with aerosol delivery

We describe the engineering design, computational modeling, and empirical performance of a moving air–liquid interface (MALI) bioreactor for the study of aerosol deposition on cells cultured on an elastic, porous membrane which mimics both air–liquid interface exposure conditions and mechanoelastic motion of lung tissue during breathing. The device consists of two chambers separated by a cell layer cultured on a porous, flexible membrane. The lower (basolateral) chamber is perfused with cell culture medium simulating blood circulation. The upper (apical) chamber representing the air compartment of the lung is interfaced to an aerosol generator and a pressure actuation system. By cycling the pressure in the apical chamber between 0 and 7 kPa, the membrane can mimic the periodic mechanical strain of the alveolar wall. Focusing on the engineering aspects of the system, we show that membrane strain can be monitored by measuring changes in pressure resulting from the movement of media in the basolateral chamber. Moreover, liquid aerosol deposition at a high dose delivery rate (>1 µl cm−2 min−1) is highly efficient (ca. 51.5%) and can be accurately modeled using finite element methods. Finally, we show that lung epithelial cells can be mechanically stimulated under air–liquid interface and stretch‐conditions without loss of viability. The MALI bioreactor could be used to study the effects of aerosol on alveolar cells cultured at the air–liquid interface in a biodynamic environment or for toxicological or therapeutic applications.
Morphological dependent effect of cell-free formed supramolecular fibronectin on cellular activities

Abstract Fibrillar fibronectin (FFN), an active form of fibronectin (FN), plays important roles in various cellular processes. Our goal is to investigate effect of FFN morphology on cellular behaviors. Plasma FN at two concentrations was cross-linked into FFN by dialysis against 2 M urea followed by morphological analysis under Scanning Electron Microscopy. To evaluate effect of FFN morphology, fibroblasts were cultured on FN or different FFNs. Fibroblast behaviors including adhesion, spreading, and migration were evaluated. Our data showed that FN fibrillogenesis was dependent on FN concentration. At high concentrations (0.75 mg/mL), large FFN approximately 2.167 + 0.875 µm in diameter were formed with attached nodular structures and rough surface. In contrast, smooth surface FFN fibrils with diameter of 1.886 + 0.412 µm were formed from FN at 0.25 mg/mL. Cellular assays revealed morphological dependent biological effects of different FFNs. Fibroblast separately adhered to native FN and remained spherical while on FFN, cells attached with higher quantity and showed spreading morphology. A synergistic ligand interaction of integrin α5β1 and αvβ3 was observed in cell adhering on FFN. Cell migration results showed that large FFN decreased migration rate while small FFN did not. Taken together, our data draws new attention towards controlling biological function of FN by its fibrillar structure.
ElaStick: A Handheld Variable Stiffness Display for Rendering Dynamic Haptic Response of Flexible Object

Haptic controllers have an important role in providing rich and immersive Virtual Reality (VR) experiences. While previous works have succeeded in creating handheld devices that simulate dynamic properties of rigid objects, such as weight, shape, and movement, recreating the behavior of flexible objects with different stiffness using ungrounded controllers remains an open challenge. In this paper we present ElaStick, a variable-stiffness controller that simulates the dynamic response resulting from shaking or swinging flexible virtual objects. This is achieved by dynamically changing the stiffness of four custom elastic tendons along a joint that effectively increase and reduce the overall stiffness of a perceived object in 2-DoF. We show that with the proposed mechanism, we can render stiffness with high precision and granularity in a continuous range between 10.8 and 71.5Nmm/degree. We estimate the threshold of the human perception of stiffness with a just-noticeable difference (JND) study and investigate the levels of immersion, realism and enjoyment using a VR application.
On-chip metalenses based on one-dimensional gradient trench in the broadband visible.

Metasurfaces are composed of flat, ultrathin subwavelength nanoantennas with strong capability in manipulating light propagation by modulations on its phase, amplitude, and polarization. For instance, the invention of two-dimensional (2D) metalenses has enabled light focusing and imaging in three-dimensional (3D) free space with miniaturized thickness and device size at a planar surface. However, such inherent form of 2D arrays and focusing functionality at 3D optical free-space limits the degree of freedom for light propagation and manipulation along a 2D planar surface and eventually the possibility of on-chip photonic system integration. Here, we theoretically study and demonstrate a new type of planar on-chip metalens, which enables light focusing and strong localization at a 2D surface. The planar on-chip architecture design is based on the one-dimensional (1D) length or width gradient trench metalens (GTM), which could yield the elaborately engineered phase shift for propagating light within the on-chip waveguide at the visible wavelength of 500 nm. By generating 1D phase arrangement at the nanoscale, a miniature on-chip metalens with ∼3×0. 5µm dimension could achieve light focusing on a 2D waveguide surface with the flexibility to design scalable focal lengths and ultra-high numerical aperture of up to ∼0.99. Additionally, GTM metalens designs could also exhibit overlapped high depth-of-focus, which consequently could behave as achromatic-like lensing at the selected focal plane. Furthermore, we manifest that the focusing functionality can also be subject to dynamically tuning and switching on-and-off with TE/TM polarization change or waveguide index alteration. We believe this new form of on-chip 1D metalens holds potential applications including on-chip light manipulation functionality of focusing and diverging, optical on-chip sensing, next-generation on-chip optical communication, signal processing as well as imaging devices, etc.
Vision impairment, vision correction, and cognitive decline among middle-aged and older Chinese: results from the China health and retirement longitudinal study

Abstract Objectives To investigate the associations between vision impairment (VI), vision correction (VC), and cognitive function. Method We included 20,677 participants aged ≥45 years from the China Health and Retirement Longitudinal Study (2011–2015). Participants were grouped into no VI, distance VI (DVI) only, near VI (NVI) only, or both distance and near VI (DNVI), and VI(+)/VC(−), VI(+)/VC(+), VI(−)/VC(−), or VI(−)/VC(+) further at baseline. Cognitive function at baseline and subsequently every two years was applied as a dependent variable in a generalized estimating equation model. Results DVI only, NVI only, and DNVI had significantly worse cognitive function over time than no VI (all p < .05). DNVI had significantly worse cognitive function over time than DVI only and NVI only (all p < .001). VI(+)/VC(+), VI(−)/VC(−), and VI(−)/VC(+) had significantly better cognitive function over time than VI(+)/VC(−) (all p < .05). VI(−)/VC(+) had significantly better cognitive function over time than VI(+)/VC(+) and VI(−)/VC(−) (all p < .05). Conclusion Cognitive function was worse in middle-aged and older Chinese with VI, especially in those with DNVI. VC was associated with better cognitive function over time regardless of the status of vision.
The complete mitochondrial genome of Florida gar (Lepisosteus platyrhincus)

Abstract Lepisosteus platyrhincus is a member of the family Lepisosteidae living in the Western Hemisphere. It is a primitive air-breathing fish with the special intermediate position of phylogeny and between elasmobranchs and teleosts. Herein, we first sequenced and assembled the complete mitochondrial genome of Lepisosteus platyrhincus. The total length of mitochondrion is 16 320 bp with GC content of 42.43%, containing 13 protein-coding genes, two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a 564 bp control region. The accuracy of the fresh sequences was verified by phylogenetic analysis. This mitochondrial genome provides potentially important resources for addressing taxonomic issues and studying molecular evolution.
The UMLS knowledge sources at 30: indispensable to current research and applications in biomedical informatics

This special issue is dedicated to the memory of Donald Allan Bror Lindberg, MD (1933–2019). An informatics pioneer, leader, and longest serving Director of the US National Library of Medicine (NLM), Dr. Lindberg conceived, initiated, and led the Unified Medical Language System (UMLS) effort in its formative years and provided sustained support for free dissemination and regular maintenance of the UMLS resources.
The Effect of Flipped Classroom Instruction on Enhancing English Grammar and Vocabulary Learning for Secondary Commercial Schools’ Graduates

The study aimed to investigate the effect of flipped classroom instruction on enhancing grammar and vocabulary learning of secondary commercial school graduates enrolled in a preparation course for obtaining a Commercial Diploma Equivalency Certificate (CDEC), Cairo University. The CDEC preparation course is designed in the light of EFL teaching goals specified by Ministry of Education for general secondary schools to prepare commercial school graduates for studying in higher education settings. The study used the quasi-experimental design. The sample of the study consisted of fifty-eight students assigned to two group; 29 controls, 29 experimental. Instruments included two equivalent grammar and vocabulary tests. The Implementation of the proposed program took a period of seven weeks. Despite drawbacks and challenges, results of the study revealed the positive impact of flipped classroom instruction on enhancing grammar and vocabulary learning for secondary commercial school graduates.
Voluntary Inhibition of Physiological Mirror Activity: An EEG-EMG Study

Abstract Physiological mirror activity (pMA), observed in healthy human adults, describes the involuntary co-activation of contralateral homologous muscles during unilateral limb movements. Here we provide novel evidence, using neuromuscular measurements (electromyography; EMG), that the amplitude of pMA can be voluntarily inhibited during unilateral isometric contractions of intrinsic hand muscles after informing human participants (10 male, 10 female) about its presence and establishing a basic understanding of pMA mechanisms through a standardized protocol. Importantly, significant suppression of pMA was observed immediately after participants were asked to inhibit it, despite the absence of any online feedback during task execution and without special training. Moreover, we observed that the decrease of pMA was specifically accompanied by an increase in relative frontal δ power recorded with electroencephalography (EEG). Correlation analysis further revealed an inverse association between the individual amplitude of pMA and frontal δ power that reached significance once participants started to inhibit. Taken together, these results suggest that δ power in frontal regions might reflect executive processes exerting inhibitory control over unintentional motor output, in this case pMA. Our results provide an initial reference point for the development of therapeutic applications related to the neurorehabilitation of involuntary movements which could be realized through the suppression of pMA observed in the elderly before it would fully manifest in undesirable overt movement patterns.
Pepsin in gastroesophageal and extraesophageal reflux: molecular pathophysiology and diagnostic utility

Purpose of review Gastroesophageal and extraesophageal reflux are prevalent and costly diseases. Recognition of the pathogenicity of nonacid reflux has stimulated interest in alternatives to acid-targeting diagnostics and therapeutics. Pepsin is the most deleterious enzyme in refluxate, eliciting inflammatory and carcinogenic effects irrespective of acid. Its presence in all refluxate and detection in saliva have situated pepsin as the most widely researched biomarker for reflux today. This review summarizes emerging findings regarding pepsin-mediated damage during reflux and developments in pepsin-targeting diagnostics. Recent findings New evidence supports a role for pepsin in epithelial--mesenchymal transition, an important process in carcinogenesis and fibrosis. The first global transcriptomic analysis of pepsin-exposed laryngeal cells was described, yielding evidence of a putative airway pepsin receptor. Evaluation of pepsin diagnostics highlighted the need for rigorous validation in which pepsin concentrations are corroborated by a secondary quantitative assay, and reflux is confirmed or excluded by multichannel intraluminal impedance pH testing. Standards for sample collection and storage, and normative and pathological values are lacking. Summary Progress continues to be made in our understanding of pepsin-mediated damage with implications for novel therapeutic strategies. Salivary pepsin diagnostics continue to garner interest; however, further work appears necessary to improve their accuracy and reproducibility.
Genome-based reclassification of Azospirillum brasilense Sp245 as the type strain of Azospirillum baldaniorum sp. nov.

Azospirillum sp. strain Sp245T, originally identified as belonging to Azospirillum brasilense, is recognized as a plant-growth-promoting rhizobacterium due to its ability to fix atmospheric nitrogen and to produce plant-beneficial compounds. Azospirillum sp. Sp245T and other related strains were isolated from the root surfaces of different plants in Brazil. Cells are Gram-negative, curved or slightly curved rods, and motile with polar and lateral flagella. Their growth temperature varies between 20 to 38 °C and their carbon source utilization is similar to other Azospirillum species. A preliminary 16S rRNA sequence analysis showed that the new species is closely related to A. brasilense Sp7T and A. formosense CC-Nfb-7T. Housekeeping genes revealed that Azospirillum sp. Sp245T, BR 12001 and Vi22 form a separate cluster from strain A. formosense CC-Nfb-7T, and a group of strains closely related to A. brasilense Sp7T. Overall genome relatedness index (OGRI) analyses estimated based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between Azospirillum sp. Sp245T and its close relatives to other Azospirillum species type strains, such as A. brasilense Sp7T and A. formosense CC-Nfb-7T , revealed values lower than the limit of species circumscription. Moreover, core-proteome phylogeny including 1079 common shared proteins showed the independent clusterization of A. brasilense Sp7T, A. formosense CC-Nfb-7T and Azospirillum sp. Sp245T, a finding that was corroborated by the genome clustering of OGRI values and housekeeping phylogenies. The DNA G+C content of the cluster of Sp245T was 68.4-68.6 %. Based on the phylogenetic, genomic, phenotypical and physiological analysis, we propose that strain Sp245T together with the strains Vi22 and BR12001 represent a novel species of the genus Azospirillum, for which the name Azospirillum baldaniorum sp. nov. is proposed. The type strain is Sp245T (=BR 11005T=IBPPM 219T) (GCF_007827915.1, GCF_000237365.1, and GCF_003119195.2).
Cannabis-related Hospitalizations Among Youth in Canada Before and After Cannabis Legalization

Supplemental Digital Content is available in the text Objectives: We investigated trends in cannabis-related hospitalizations among youth before and after legalization of recreational cannabis in Canada on October 17, 2018. Methods: We computed rates of cannabis-related hospitalizations and the proportion of substance-related hospitalizations involving cannabis by age and sex in the months before and after legalization in Quebec, Canada. Results: In boys aged 10 to 14 years, cannabis-related hospitalization rates increased from 5.2 per 100,000 one year before legalization [95% confidence interval (CI) 2.9–9.3] to 9.5 per 100,000 after legalization (95% CI 6.2–14.6), although the increase was not statistically significant. Cannabis was reported in 39.3% of substance-related hospitalizations in boys aged 10 to 14 years before legalization, compared with 70.0% after legalization, representing a difference of 30.7% (95% CI 2.8–58.6). There was no increase in cannabis-related hospitalizations among girls or boys aged 15 to 19 years. Conclusions: This study suggests that cannabis legalization in Canada did not increase the risk of short-term cannabis-related hospitalization among girls and older boys. However, legalization may have contributed to an increase in the risk in boys under 15 years. Further data are needed to clarify trends after legalization for younger adolescents.
Bioactive Phenolic Compounds of Two Medicinal Mushroom Species Trametes versicolor and Stereum subtomentosum as Antioxidant and Antiproliferative Agents

Medicinal mushrooms have tremendous potential in production of bioactive compounds with diverse bioactivities while the biochemical potential of some specific mushroom strains (autochthonous for the region) in production of specific bioactive agents may be of the main importance in a continuous search for novel strains with supreme activities all over the world.
Association between muscle strength and risk factors for metabolic syndrome in children and adolescents: a systematic review

Abstract The aim of this systematic review was to identify and summarize evidence for the association between muscle strength (MS) and metabolic syndrome (MetS), and MS and combinations of risk factors for MetS in children and adolescents. Five databases (Medline/PubMed, EBSCO, Scielo, Scopus, and Web of Knowledge) were searched up to November 2019 with complementary reference list searches. Inclusion criteria were studies that investigated the relationship between MS and MetS or MS and combinations of risk factors for MetS in children and adolescents (≤19 years of age). Risk of bias was assessed using standard procedures. From the total of 15,599 articles initially identified, 13 articles were included, representing 11,641 children and adolescents. Higher MS values were associated with lower risk for MetS or combinations of risk factors for MetS (n=11/13 studies). Of the total of included studies, about 23.1% (03/13) were longitudinal and all included studies were classified as having a moderate risk of bias. This review provides preliminary evidence for a beneficial relationship between MS and MetS among children and adolescents. Additionally, although the body of evidence points to the beneficial relationship between higher MS and lower risk for combination of factors for MetS in children and adolescents, this relationship is inconclusive.
Mus musculus papillomavirus 1 is a key driver of skin cancer development upon immunosuppression

Epidemiological and experimental data implicate cutaneous human papillomavirus infection as co‐factor in the development of cutaneous squamous cell carcinomas (cSCCs), particularly in immunocompromised organ transplant recipients (OTRs). Herein, we established and characterized a skin cancer model, in which Mus musculus papillomavirus 1 (MmuPV1) infection caused cSCCs in cyclosporine A (CsA)‐treated mice, even in the absence of UV light. Development of cSCCs and their precursors were observed in 70% of MmuPV1‐infected, CsA‐treated mice on back as well as on tail skin. Immunosuppression by systemic CsA, but not UV‐B irradiation, was a prerequisite, as immunocompetent or UV‐B–irradiated mice did not develop skin malignancies after infection. In the virus‐driven cSCCs the MmuPV1‐E6/E7 oncogenes were abundantly expressed, and transcriptional activity and productive infection demonstrated. MmuPV1 infection induced the expression of phosphorylated H2AX, but not degradation of proapoptotic BAK in the cSCCs. Transfer of primary cells, established from a MmuPV1‐induced cSCC from back skin, into athymic nude mice gave rise to secondary cSCCs, which lacked viral DNA, demonstrating that maintenance of the malignant phenotype was virus independent. This papillomavirus‐induced skin cancer model opens future investigations into viral involvement, pathogenesis, and cancer surveillance, aiming at understanding and controlling the high incidence of skin cancer in OTRs.