Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlation between controlled lung collapse and early lung injury in dogs

A new type of pulmonary sequestration ventilator was used to compare the relationship between controlled lung collapse and early lung injury in thoracic surgery for dogs. Eighteen experimental dogs were randomly divided into three groups (G1-G3 groups). After general anesthesia, the shunt balance in lung was controlled and the pulmonary sequestration tube was placed in the femoral artery and vein, and the Swan-Ganz tube was placed into the right internal jugular vein as well. Two-lung ventilation (TLV) was first performed for 20 min, followed by one-lung ventilation (OLV). The degree of collapse was 100% (G1), 90% (G2), and 50% (G3). Blood samples were extracted from femoral artery and jugular vein prior to collapse (T0), and at 30 (T1), 60 (T2), and 120 (T3) min after collapse for blood gas analysis to determine the shunt ratio (Qs/Qt). Blood samples were also subjected to enzyme linked immunosorbent assay (ELISA) to determine serum tumor necrosis factor-α (TNF-α), intercellular immune adhesion molecule-1 (ICAM-1) and interleukin-6 (IL-6) levels. Arterial blood pressure, heart rate, pulmonary artery pressure and other physiological indicators were monitored during the experiment. Lung tissues were collected at T3 to calculate the wet/dry weight ratio (W/D). Histopathological changes were observed and compared by microscopic observation and blind scoring of pathological section after hematoxylin and eosin (H&E) staining. There were no significant differences in the physiological indexes between the two groups during TLV (P>0.05). Mean pulmonary arterial pressure (MPAP) in G2 and G3 groups was significantly more stable than that in G1 group after OLV (P<0.05); shunt ratio Qs/Qt, W/D, and serum TNF-α, ICAM-1 and IL-6 levels in the lung were decreased; and the degrees of pulmonary edema, hemorrhage, inflammatory cell infiltration and lung injury were also decreased. There was no statistically significant difference in each index at each time-point between G2 and G3 groups (P>0.05). Compared with complete lung collapse (collapse degree: 100%), controlled lung collapse (collapse degree: 90% and 50%) can better reduce the intraoperative lung injury, but there was no significant difference between the collapse degrees of 90 and 50%.
Myopia prevalence and risk factors in children

Purpose To evaluate the prevalence and risk factors for pediatric myopia in a contemporary American cohort. Methods A cross-sectional study of pediatric patients enrolled in the Kaiser Permanente Southern California health plan was done. Eligible patients were 5- to 19-years old between January 1, 2008, through December 31, 2013, and received an ophthalmologic or optometric refraction. Electronic medical records were reviewed for demographic data, refraction results, and exercise data. Prevalence and relative risks of myopia (defined as ≤−1.0 diopter) were characterized. Age, sex, race/ethnicity, median neighborhood income, and minutes of exercise per day were examined as risk factors. Results There were 60,789 patients who met the inclusion criteria, of which 41.9% had myopia. Myopia was more common in older children (14.8% in 5- to 7-year olds, 59.0% in 17- to 19-year olds). Asian/Pacific Islander patients (OR 1.64, CI 1.58–1.70) had an increased rate of myopia compared to White patients as did African Americans to a lesser extent (OR 1.08, CI 1.03–1.13). Median neighborhood household income of $25,000–40,000 was associated with lower rates of myopia (OR 0.90, CI 0.83–0.97) compared to median neighborhood household incomes less than $25,000. Having at least 60 min of daily exercise was associated with lower prevalence of myopia (OR 0.87, CI 0.85–0.89). Discussion Myopia was common in this large and diverse Southern Californian pediatric cohort. The prevalence of myopia increases with age. Asian children are at highest risk for myopia. Exercise is associated with a lower rate of myopia and represents an important potentially modifiable risk factor that may be a target for future public health efforts.
bcGST - an interactive bias-correction method to identify over-represented gene-sets in boutique arrays

Motivation: Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes are important tools in Gene Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene set selection bias induced during the construction of these platforms. Results: We propose bcGST, a bias-corrected Gene Set Test by introducing bias correction terms in the contingency table needed for calculating the Fisher’s Exact Test (FET). The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and TCGA cancer studies. Availability: The bcGST method is made available as a Shiny web application at http://shiny.maths. usyd.edu. au/bcGST/ Contact: kevin.wang@sydney.edu. au
Diagnostic Biomarkers: Are We Moving from Discovery to Clinical Application?

BACKGROUND Despite considerable research investment, moving from biomarker discovery to clinical application has presented unique challenges. We aimed to evaluate progress toward clinical application of a sample of molecular- and "omics"-based diagnostic tests over a 10-year period. METHODS We used Scopus to locate studies, published before the December 31, 2016, citing 107 original-research articles published in 2006 that assessed the diagnostic value of a molecular- or "omics"-based test. We identified diagnostic studies of the same test and disease and determined whether the article represented progress in the validation of the molecular test. We classified the types of progress: (a) clinical validation (measuring diagnostic accuracy in a series of patients similar to the population in which the test will be used in practice), (b) technical improvement, (c) extended diagnostic application (modification of the diagnostic question attended initially by the test), (d) economic evaluation, or (e) clinical use or implementation. RESULTS In the 10-year period analyzed, 4257 articles cited the 107 diagnostic studies; 118 (2.8%) were diagnostic studies of the same test, and of these papers, 25 (21.2%) did not constitute progress toward validation of the test for use in clinical practice (potential research waste). Of the 107 molecular- or "omics"-based tests described in 2006, only 28 (26.2%) appeared to have made progress toward clinical application. Only 4 (9.1%) of 44 proteomics-based tests had made progress toward clinical application. CONCLUSIONS Articles evaluating molecular- or "omics"-based diagnostic tests are numerous in biomedical journals. Few tests have made progress toward clinical application in the 10 years following their discovery.
Canonical and Compact Point Cloud Representation for Shape Classification

We present a novel compact point cloud representation that is inherently invariant to scale, coordinate change and point permutation. The key idea is to parametrize a distance field around an individual shape into a unique, canonical, and compact vector in an unsupervised manner. We firstly project a distance field to a $4$D canonical space using singular value decomposition. We then train a neural network for each instance to non-linearly embed its distance field into network parameters. We employ a bias-free Extreme Learning Machine (ELM) with ReLU activation units, which has scale-factor commutative property between layers. We demonstrate the descriptiveness of the instance-wise, shape-embedded network parameters by using them to classify shapes in $3$D datasets. Our learning-based representation requires minimal augmentation and simple neural networks, where previous approaches demand numerous representations to handle coordinate change and point permutation.
Impact of neutrophil–lymphocyte ratio on long-term outcome in patients with craniopharyngioma

Abstract Neutrophil–lymphocyte ratio (NLR) is a poor prognostic factor in many tumors including glioblastoma multiforme (GBM), colorectal, and prostate cancer. The aim of this study was to investigate the prognostic value of preoperative NLR in patients with craniopharyngioma. Around 149 patients of craniopharyngioma surgically were treated at the Department of Neurosurgery, West China Hospital from January 2008 to December 2010, including 84 males and 65 females aged from 6 to 70 years were retrospectively reviewed, and preoperative NLR was analyzed. Overall survival (OS), progression free survival (PFS), and quality of life (QOL) were evaluated. The 5-year OS and PFS rates were 81.21% and 75.84%. Preoperative NLR was significantly correlated with OS (HR = 1.44, 95% CI 1.16–1.79, P = .001) and PFS (HR = 1.46, 95% CI 1.22–1.74, P < .001). The best cut-off value of NLR was found to be 4 based on the receiver operator characteristics (ROC) curve. Patients with NLR ≥4 had a significantly worse QOL (P = .039), lower OS rate (P = .009), and PFS rate (P < .001). Preoperative NLR may be a simple, readily available, and valid predictor of long-term outcome in craniopharyngioma. We suggest that the NLR can provide effective guidance to neurosurgeons for more information about the tumor and prognostic evaluation.
Studying Dynamics in Argumentation with Rob

The issue of handling dynamics is a central problem in Argumentation Theory. In order to understand how dynamics work, we extended the ConArg suite with Rob , a tool that is able to display Abstract Argumentation Frameworks and their corresponding sets of extensions, in a way suitable to understand what happens to the semantics when a modiﬁcation to the graph occurs. In particular, Rob allows to inspect for a particular framework all the corresponding sets of extensions, and for every extension all the frameworks which admit it for some semantics.
Radiation tolerance of La-doped nanocrystalline steel under heavy-ion irradiation at different temperatures

Nanostructured materials have great potential for use as structural materials in advanced nuclear reactors due to the high density of grain boundaries that can serve as sinks to absorb irradiation-induced defects. In the present study, the irradiation tolerance of a La-doped nanocrystalline 304 austenitic stainless steel (NC-La) with a grain size of about 40 nm was investigated under an irradiation of 6 MeV Au ions to 1.5 × 1016 ions cm−2 at 600 °C and room temperature. Compared to its coarse-grained counterpart, in La-doped nanocrystalline steel no visible voids were observed at high-temperature irradiation, and no significant difference in extended defects, such as irradiation-induced dislocation loops or clusters, were found between irradiated and unirradiated areas at room temperature irradiation. Furthermore, the nano grain remains stable under irradiation, and no significant grain growth occurs at both irradiation temperatures. The excellent irradiation tolerance of the La-doped nanocrystalline alloys is attributed to the abundant grain boundaries and enhanced stability of nano grains induced by the Zener pinning effect and La segregation on grain boundaries. This study therefore demonstrates the superior irradiation tolerance of the La-doped nanocrystalline steel.
Interdevice variability of central corneal thickness measurement

Purpose To evaluate variability of central corneal thickness measurement (CCT) devices using a hitherto unprecedented number of CCT devices. Methods CCT was measured consecutively in 122 normal corneas of 61 subjects with seven different devices using three distinct measurement technologies: Scheimpflug, Ultrasound, and Optical Coherence Tomography (OCT). Per device deviation from the mean CCT value per eye was used to determine which of the devices performed best, compared to the mean value. Results Cirrus OCT yielded the lowest deviation. Deviations of the individual devices from the mean CCT of each eye were (OS/OD) 12.8±5.0/14.9±9.4 μm for Topcon noncontact specular microscopy (NCSM), 11.3±5.9/10.6±7.3 μm for Pentacam, 10.7±5.2/10.4±4.8 μm for Spectralis OCT, 6.0±3.9/6.2±4.9 μm for Topcon DRI OCT, 5.1±3.4/5.9±10.3 μm for AngioVue OCT, 4.8±4.1/5.7±4.6 μm for US pachymetry, and 4.2±3.2/5.7±4.6 μm for Cirrus OCT. The maximum differences between US pachymetry and the other devices were very high (up to 120 μm). Conclusion Central corneal thickness may be under- or overestimated due to high interdevice variations. Measuring CCT with one device only may lead to inappropriate clinical and surgical recommendations. OCT showed superior results.
Haem oxygenase-1 inhibits neointimal hyperplasia in rat by histone deacetylase 2

Abstract It has been reported that haem oxygenase-1 (Hmox1) induction attenuates neointimal thickening. Here we further investigated the potential mechanisms regulating this important pathological process. We revealed that histone deacetylase 2 (HDAC2) was induced following Hmox1 induction under 1% oxygen treatment and this induction was attenuated after the treatment of siRNA against Hmox1. Interestingly, this HDAC2 induction was dependent on Hmox1 protein as well as its enzymatic activity, and was regulated by carbon monoxide released from haem degradation. Furthermore, histone deacetylase inhibitor, trichostatin A, successfully abrogated the inhibitory effects of vascular smooth muscle migration and proliferation by Hmox1 induction in vitro. In a rat carotid balloon injury model, similar results were observed by measuring neointimal thickening. As such, we concluded that Hmox1 inhibits neointimal hyperplasia via HDAC2 in rats.
Perfluorinated Chemicals as Emerging Environmental Threats to Kidney Health: A Scoping Review.

BACKGROUND AND OBJECTIVES Per- and polyfluoroalkyl substances (PFASs) are a large group of manufactured nonbiodegradable compounds. Despite increasing awareness as global pollutants, the impact of PFAS exposure on human health is not well understood, and there are growing concerns for adverse effects on kidney function. Therefore, we conducted a scoping review to summarize and identify gaps in the understanding between PFAS exposure and kidney health. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We systematically searched PubMed, EMBASE, EBSCO Global Health, World Health Organization Global Index, and Web of Science for studies published from 1990 to 2018. We included studies on the epidemiology, pharmacokinetics, or toxicology of PFAS exposure and kidney-related health, including clinical, histologic, molecular, and metabolic outcomes related to kidney disease, or outcomes related to the pharmacokinetic role of the kidneys. RESULTS We identified 74 studies, including 21 epidemiologic, 13 pharmacokinetic, and 40 toxicological studies. Three population-based epidemiologic studies demonstrated associations between PFAS exposure and lower kidney function. Along with toxicology studies (n=10) showing tubular histologic and cellular changes from PFAS exposure, pharmacokinetic studies (n=5) demonstrated the kidneys were major routes of elimination, with active proximal tubule transport. In several studies (n=17), PFAS exposure altered several pathways linked to kidney disease, including oxidative stress pathways, peroxisome proliferators-activated receptor pathways, NF-E2-related factor 2 pathways, partial epithelial mesenchymal transition, and enhanced endothelial permeability through actin filament modeling. CONCLUSIONS A growing body of evidence portends PFASs are emerging environmental threats to kidney health; yet several important gaps in our understanding still exist.
DEEP eye contact detector: Robust eye contact bid detection using convolutional neural network

Eye contact (mutual gaze) is a foundation of human communication and social interactions; therefore, it is studied in many ﬁelds such as psychology, social science, and medicine. To support these application of eye-contact detection, much effort has been made for automated eye-contact detection by using image recognition techniques; however, they are difﬁcult to use when facial-landmark tracking is not possible due to facial occlusions. To solve this issue, this paper proposes robust algorithms of detecting eye contacts leveraged using deep neural net to ﬁnd the eye-contact skills needed for care-givers in dementia care. Since our algorithms do not depend on facial-landmark tracking and only use the images around the eyes, they are robust against facial occlusions and/or image noise. We prepared two eye contact facial image datasets and conﬁrmed the performance of the proposed algorithms. The results show that our method are robust against facial occlusion in which a person is wearing a facemask or the person’s face is partially outside the camera viewing area. This study shows the potential to be able to obtain the eye-contact status only from the images around eyes.
Using information and communication technology in the recovery after a coronary artery bypass graft surgery: patients’ attitudes

Background Patients who have undergone a coronary artery bypass graft (CABG) surgery are exposed to physical and mental problems after discharge from the specialist hospital and are often in need of post-discharge support and follow-up. Aim This study aimed to explore the attitudes of CABG patients toward using information and communication technology (ICT) during the first year of recovery after discharge from hospital. Methods A cross-sectional design utilizing an electronic survey was employed. The sample consisted of 197 patients who had undergone a CABG surgery during 2015. The questionnaire included questions about follow-up needs, contacts with health professionals, use of the Internet, and attitudes toward using ICT in the recovery phase. Results Mean age of the participants was 67.3 years; 18.3% were women. A total of 48.2% of the patient group was satisfied with the pre-discharge information. Only 27% had contacted the hospital after discharge. Whereas 58.4% of the participants had used the Internet to acquire information, only 30.4% found this information to be useful. Many patients (40%) reported that they could benefit from online health information and Skype meetings with professionals. More than 30% reported that nutritional guidance on the Internet could be motivating for choosing healthy diets, and 42.6% reported that Internet-based illustrative videotapes could be motivating for undertaking physical training. Conclusion ICT can be useful and resource-saving for patients who have undergone a CABG surgery, as well as for the health care services. The technology must be appropriately tailored, with regard to content and design, to be helpful for patients.
Optimal Procurement Mechanisms for Assembly

We consider an OEM’s contracting mechanism to procure multiple inputs from different suppliers to be assembled into its product under simultaneous and sequential contracting. We derive optimal mechanisms under both contracting scenarios, and show that they can be implemented by simple tiered-pricing contracts which are widely used in industry assembly settings. We find that optimal simultaneous and sequential procurement mechanisms for assembly are revenue-equivalent for all parties, despite them having different asymmetric information structures. All results are extended to general convex costs and concave revenues, confirming that the results capture fundamental properties of optimal procurement mechanisms for assembly.
Psychometric Properties of Assessments of Cognition in Infants With Cerebral Palsy or Motor Impairment: A Systematic Review

Objective Approximately 50% of people with cerebral palsy have a cognitive impairment. However, many tools used to assess cognition in infants require almost normal fine motor ability, and thus may not accurately reflect cognitive abilities of infants with cerebral palsy or other motor impairments. This systematic review aimed to evaluate the psychometric properties of cognitive assessment tools for infants aged 0-24 months with motor impairments and to make recommendations about the most appropriate cognitive assessment tools for the purpose of discrimination, prediction, and evaluation. Method A systematic review was conducted. CINAHL, Embase, ERIC, Medline, PsycINFO, and SCOPUS databases were searched to identify studies reporting on 1 or more psychometric properties of a standardized cognitive assessment tool or questionnaire in a sample/subsample of infants with motor impairment. Of the 4,480 articles reviewed, 9 assessment tools were identified in 20 publications, which met our inclusion criteria. Articles were appraised using the COnsensus-based Standards for the selection of health Measurement INstruments to assess study rigor. The GRADE framework was applied to develop recommendations for clinical practice. Results The Mayes Motor-Free Compilation, Fagan Test of Infant Intelligence, and Bayley-III Low Motor/Vision have predictive and/or discriminative utility in this population. The Mullen Scales of Early Learning was the only tool with psychometric research available examining responsivity to change. Conclusions Assessment tools with low-motor/motor-free accommodations have greater accuracy in estimating cognitive abilities of infants with motor impairment than conventional norm-referenced tests. There, however, remains a significant paucity of research in this area.
BER performances of downlink and uplink NOMA in the presence of SIC errors over fading channels

Non-orthogonal multiple access (NOMA) is a strong candidate for next generation radio access networks due to its ability of serving multiple users using the same time and frequency resources. Therefore, researchers in academia and industry have been recently investigating the error performances and capacity of NOMA schemes. The main drawback of NOMA techniques is the interference among users due to the its non-orthogonal access nature, that is usually solved by interference cancellation techniques such as successive interference cancellation (SIC) at the receivers. On the other hand, the interference among users may not be completely eliminated in the SIC process due to the erroneous decisions in the receivers usually caused by channels. In this study, for the first time in the literature, the authors derive an exact closed-form bit error rate (BER) expressions under SIC error for downlink NOMA over Rayleigh fading channels. Besides, they derive one-degree integral form exact BER expressions and closed-form approximate expressions for uplink NOMA. Then, the derived expressions are validated by simulations. The numerical results are depicted to reveal the effects of error during SIC process on the performance for various cases such as power allocation for downlink and channel quality difference for uplink.