Miracle-dz/UniFAR-FTUs huggingface dataset:
A Fast Image Deformity Correction Algorithm for Underwater Turbulent Image Distortion

An algorithm correcting distortion based on estimating the pixel shift is proposed for the degradation caused by underwater turbulence. The distorted image is restored and reconstructed by reference frame selection and two–dimensional pixel registration. A support vector machine-based kernel correlation filtering algorithm is proposed and applied to improve the speed and efficiency of the correction algorithm. In order to validate the algorithm, laboratory experiments on a controlled simulation system of turbulent water and field experiments in rivers and oceans are carried out, and the experimental results are compared with traditional, theoretical model-based and particle image velocimetry-based restoration and reconstruction algorithms. Using subjective visual evaluation, image distortion has been effectively suppressed; based on an objective performance statistical analysis, the measured values are better than the traditional and formerly studied restoration and reconstruction algorithms. The method proposed in this paper is also much faster than the other algorithms. It can be concluded that the proposed algorithm can effectively improve the de-distortion effect of the underwater turbulence degraded image, and provide potential techniques for the accurate operation of underwater target detection in real time.
Evaluation of a deep learning-based pelvic synthetic CT generation technique for MRI-based prostate proton treatment planning

The purpose of this work is to validate the application of a deep learning-based method for pelvic synthetic CT (sCT) generation that can be used for prostate proton beam therapy treatment planning. We propose to integrate dense block minimization into 3D cycle-consistent generative adversarial networks (cycleGAN) framework to effectively learn the nonlinear mapping between MRI and CT pairs. A cohort of 17 patients with co-registered CT and MR pairs were used to test the deep learning-based sCT generation method by leave-one-out cross-validation. Image quality between the sCT and CT images, gamma analysis passing rate, dose-volume metrics, distal range displacement, and the individual pencil beam Bragg peak shift between sCT- and CT-based proton plans were evaluated. The average mean absolute error (MAE) was 51.32 ± 16.91 HU. The relative differences of the statistics of the PTV dose-volume histogram (DVH) metrics in between sCT and CT were generally less than 1%. Mean values of dose difference, absolute dose difference (in percent of the prescribed dose) were −0.07% ± 0.07% and 0.23% ± 0.08%. Mean gamma analysis pass rate of 1 mm/1%, 2 mm/2%, 3 mm/3% criteria with 10% dose threshold were 92.39% ± 5.97%, 97.95% ± 2.95% and 98.97% ± 1.62% respectively. The median, mean and standard deviation of absolute maximum range differences were 0.09 cm and 0.23 ± 0.25 cm. The median and mean Bragg peak shifts among the 17 patients were 0.09 cm and 0.18 ± 0.07 cm. The image similarity, dosimetric and distal range agreement between sCT and original CT suggests the feasibility of further development of an MRI-only workflow for prostate proton radiotherapy.
Participation in Community Preparedness Programs in Human Services Organizations and Faith-Based Organizations — New York City, 2018

Community-based organizations have a long history of engagement with public health issues; these relationships can contribute to disaster preparedness (1,2). Preparedness training improves response capacity and strengthens overall resilience (1). Recognizing the importance of community-based organizations in community preparedness, the Office of Emergency Preparedness and Response in New York City's (NYC's) Department of Health and Mental Hygiene (DOHMH) launched a community preparedness program in 2016 (3), which engaged two community sectors (human services and faith-based). To strengthen community preparedness for public health emergencies in human services organizations and faith-based organizations, the community preparedness program conducted eight in-person preparedness trainings. Each training focused on preparedness topics, including developing plans for 1) continuity of operations, 2) emergency management, 3) volunteer management, 4) emergency communications, 5) emergency notification systems, 6) communication with persons at risk, 7) assessing emergency resources, and 8) establishing dedicated emergency funds (2,3). To evaluate training effectiveness, data obtained through online surveys administered during June-September 2018 were analyzed using multivariate logistic regression. Previously described preparedness indicators among trained human services organizations and faith-based organizations were compared with those of organizations that were not trained (3). Participation in the community preparedness program training was associated with increased odds of meeting preparedness indicators. NYC's community preparedness program can serve as a model for other health departments seeking to build community preparedness through partnership with community-based organizations.
Supplemental Intraoperative Oxygen Does Not Promote Acute Kidney Injury or Cardiovascular Complications After Noncardiac Surgery: Subanalysis of an Alternating Intervention Trial

BACKGROUND: Perioperative hyperoxia has been recommended by the World Health Organization and the Centers for Disease Control and Prevention for the prevention of surgical site infections. Based on animal studies and physiological concerns, the kidneys and heart may be at risk from hyperoxia. We therefore conducted 2 unplanned subanalyses of a previous alternating cohort trial in which patients having colorectal surgery were assigned to either 30% or 80% inspired intraoperative oxygen. Specifically, we tested 2 coprimary hypotheses: (1) hyperoxia increases the incidence of acute kidney injury (AKI) within 7 postoperative days (PODs); and (2) hyperoxia worsens a composite of myocardial injury, in-hospital cardiac arrest, and 30-day mortality. METHODS: The underlying controlled trial included 5749 colorectal surgeries in 4481 patients, with the exposure alternating between 30% and 80% fraction of inspired oxygen (Fio2) during general anesthesia at 2-week intervals over a period of 39 months. AKI was defined as a 1.5-fold increase in creatinine from the preoperative level to the highest value measured during the initial 7 PODs. Myocardial injury was defined by fourth-generation troponin-T level >0.03 ng/mL. We assessed the effect of 80% vs 30% oxygen on the outcomes using generalized estimating equation (GEE) logistic models that adjusted for the possible within-patient correlation across multiple potential operations for a patient on different visits. RESULTS: For the AKI outcome, 2522 surgeries were allocated to 80% oxygen and 2552 to 30% oxygen. Hyperoxia had no effect on the primary outcome of postoperative AKI, with an incidence of 7.7% in the 80% oxygen group and 7.7% in the 30% oxygen group (relative risk = 0.99; 95% confidence interval [CI], 0.82–1.2; P = .95). One thousand six hundred forty-seven surgeries (all with scheduled troponin monitoring) were analyzed for the composite cardiovascular outcome. Hyperoxia had no effect on the collapsed composite of myocardial injury, cardiac arrest, and 30-day mortality, nor on any of its components (estimated relative risk = 0.71; 95% CI, 0.44–1.16; P = .17). CONCLUSIONS: We found no evidence that intraoperative hyperoxia causes AKI or cardiovascular complications in adults undergoing colorectal surgery. Consequently, we suggest that clinicians select intraoperative inspired oxygen fraction based on other considerations.
Squat and Bench Press Force-Velocity Profiling in Male and Female Adolescent Rugby Players.

Alonso-Aubin, DA, Chulvi-Medrano, I, Cortell-Tormo, JM, Picón-Martínez, M, Rial-Rebullido, T, and Faigenbaum, AD. Squat and bench press force-velocity profiling in male and female adolescent rugby players. J Strength Cond Res XX(X): 000-000, 2019-Power development is critical for enhancing rugby performance because there is a close relationship between power and sport-specific skills. The aim of this study was to examine the force-velocity profiling generated by adolescent rugby players in the squat and bench press exercises and to compare sex-related differences. Subjects were 46 men (age: 14.48 ± 1.31 years; body height: 1.65 ± 0.09 m; and body mass: 58.07 ± 13.01 kg) and 41 women (age: 14.93 ± 2.76 years; body height: 1.63 ± 0.12 m; and body mass: 59.23 ± 12.66 kg) who were recruited from a national amateur rugby league team. Maximal strength, power, and velocity were assessed on the squat and bench press exercises using a Smith Machine and a linear power transducer with intensities ranging from 40 to 80% 1 repetition maximum (1RM) on the squat and 50-80% 1RM on the bench press. 1 repetition maximum squat and bench press performance were 104.26 ± 30.83 and 46.97 ± 13.59 kg, respectively, for men and 115.17 ± 41.42 and 45.85 ± 16.71 kg, respectively, for women. The maximum squat power results for men and women were 521.91 ± 298.75 and 591.26 ± 352.69 N, respectively, and the maximum bench press power results for men and women were 190.26 ± 150.54 and 326.16 ± 195.57 N, respectively. Significant sex-related differences (p < 0.001) were found on the squat exercise for maximum (40%), mean (40-50%), and time to maximum velocities (40-80%) as well as time to maximum power (80%). On the bench press exercise, significant sex-related differences (p < 0.001) were found for power and time to maximum velocity (40%-60%-70%-80%). These results may aid in the design of strength and conditioning programs for adolescent rugby players by targeting training prescriptions toward enhancing strength or velocity.
Exploring the impact of social network change: Experiences of older adults ageing in place

Abstract Social networks are sources of support and contribute to the well‐being of older adults who are ageing in place. As social networks change, especially when accompanied by health decline, older adults’ sources of support change and their well‐being is challenged. Previous studies predominantly used quantitative measures to examine how older adults’ social networks change. Alternatively, this study explores the impact of changing social networks on older adults’ lives by examining their personal experiences. We held four focus groups, two with a total of 14 older adults who are ageing in place and receiving home care and two with a total of 20 home‐care nurses from different regions and organisations in the Netherlands. Subsequently, an expert team of home‐care professionals and managers discussed and verified the results. Procedures for grounded theory building were used for analysis. We revealed four themes of high‐impact experiences: (a) struggling with illness/death of the spouse; (b) working out a changing relationship with (grand)children; (c) regretting the loss of people they have known for so long and (d) feeling dependent and stressed when helpers enter the network. Also, network dynamics were found to follow three consecutive stages: (a) awareness of social network change; (b) surprise when social network change actually occurs and (c) acceptance and adjusting to new circumstances. Together, the four themes of experiences and three stages of network change form an integrative model of the role of social network dynamics for older adults’ lives when ageing in place.
Identification of Molecular Targets of Dietary Grape-Mediated Chemoprevention of Ultraviolet B Skin Carcinogenesis: A Comparative Quantitative Proteomics Analysis.

We recently showed that dietary grape powder (GP) imparts considerable protection against ultraviolet B (UVB)-mediated skin carcinogenesis in SKH-1 mice. To determine molecular mechanisms of this response, we employed tandem mass tag (TMT) quantitative global proteomics approach on skin tumors from mice exposed to 180 mJ/cm2 UVB twice per week and fed control or 5% GP diet. We found 2,629 proteins modulated by GP feeding, with 34 identified using stringent cutoffs (false discovery rate (FDR) q-value ≤0.1, fold change ≥1.2, p-value ≤0.05, ≥3 unique peptides). Ingenuity Pathway Analysis helped identify seven proteins involved in protein ubiquitination, including the deubiquitinase UCHL5 and 6 subunits of the 20S proteasome (PSMA1,3,4,6 and PSMB4,7). A second data set without the FDR q-value identified 239 modulated proteins, seven of which are involved in protein ubiquitination. Further, 14 proteins involved in acute phase response signaling were modulated >1.5-fold, including acute phase proteins APCS, FGA, FGB, HP, HPX, and RBP1. Evaluation of upstream regulators found inhibition of ERK1/2 phosphorylation and NF-κB p65, and an increase in IκBα in GP-treated tumors. Overall, our data suggested that GP consumption may mitigate tumorigenesis by enhancing protein ubiquitination and degradation caused by oxidative stress, and manipulates an otherwise tumor-promoting anti-inflammatory environment.
Complete Genome Sequence of Escherichia-Infecting Phage CEC_KAZ_2018, Isolated from Soil

Avian pathogenic Escherichia coli (APEC) bacteria are one of the main problems of the poultry industry. An effective way to combat colibacillosis is to use a phage preparation that lyses the bacteria. Here, we report the isolation of an E. coli-infecting phage, CEC_KAZ_2018, isolated from soil. ABSTRACT Avian pathogenic Escherichia coli (APEC) bacteria are one of the main problems of the poultry industry. An effective way to combat colibacillosis is to use a phage preparation that lyses the bacteria. Here, we report the isolation of an E. coli-infecting phage, CEC_KAZ_2018, isolated from soil.
An Easy and Reliable Strategy for Making Type I Interferon Signature Analysis Comparable among Research Centers

Interferon-stimulated genes (ISGs) are a set of genes whose transcription is induced by interferon (IFN). The measure of the expression of ISGs enables calculating an IFN score, which gives an indirect estimate of the exposition of cells to IFN-mediated inflammation. The measure of the IFN score is proposed for the screening of monogenic interferonopathies, like the Aicardi-Goutières syndrome, or to stratify subjects with systemic lupus erythematosus to receive IFN-targeted treatments. Apart from these scenarios, there is no agreement on the diagnostic value of the score in distinguishing IFN-related disorders from diseases dominated by other types of cytokines. Since the IFN score is currently measured in several research hospitals, merging experiences could help define the potential of scoring IFN inflammation in clinical practice. However, the IFN score calculated at different laboratories may be hardly comparable due to the distinct sets of IFN-stimulated genes assessed and to different controls used for data normalization. We developed a reliable approach to minimize the inter-laboratory variability, thereby providing shared strategies for the IFN signature analysis and allowing different centers to compare data and merge their experiences.
A novel POU domain class 3 transcription factor 4 mutation causes X-linked non-syndromic hearing loss in a Chinese family

bers, including five patients (four males: II: 2, II: 7, III: To the Editor: POU domain class 3 transcription factor 4 or BRN-4 (POU3F4) is a causative gene of non-syndromic 4, and III: 5; and one female: II: 1) with HL and nine X-linked hearing loss (HL), which is characterized by inner ear anomalies. To date, six X-linked non-syndromic HL loci (DFNX1-6) have been mapped to chromosome X and five of these genes have been identified: phosphoribosyl pyrophosphate synthetase 1 (PRPS1) (DFNX1, OMIM: 304500), POU3F4 (DFNX2, OMIM: 304400), small muscle protein, X-linked (SMPX) (DFNX4, OMIM: 300066), apoptosis-inducing factor, mitochondria-associated, 1 (AIFM1) (DFNX5, OMIM: 300614), and collagen, type IV alpha-6 (COL4A6) (DFNX6, OMIM; 300914). POU3F4mutation accounts for nearly 50% of all cases of DFNX. The human POU3F4 gene is located in the Xq21.1 region with only one exon, encoding 361 amino acids. POU3F4 belongs to a superfamily of POU domain transcription factors, comprised of a POU-specific domain (75 amino acids) and a POU-homeodomain (63 amino acids), both of which influence DNA binding and specificity. The POU3F4 protein is involved in the development of the middle ear and inner ear, as well as some areas of the brain before birth. However, HL is the only clinical phenotype observed in DFNX2 patients. So far, 72 different mutations in the coding region (57 mutations) and the putative regulatory element region (15 mutations) of the POU3F4 gene have been reported to be associated with non-syndromic HL in families with DFNX2. In this study, a new non-sense mutation in POU3F4 was analyzed and found to be associated with non-syndromic X-linked inheritance HL in a Chinese Han family.
THADA_rs13429458 Minor Allele Increases the Risk of Polycystic Ovary Syndrome in Asian, but Not in Caucasian Women: A Systematic Review and Meta-Analysis

Abstract Polycystic ovary syndrome (PCOS) is a highly prevalent disease in young women that also features increased insulin resistance. Genetic factors have a strong relationship with the etiology of PCOS. We assessed whether carrying THADA rs13429458 is associated with the development of PCOS by meta-analysis and whether the association is influenced by ethnicity. Articles were searched using PubMed, EMBASE, Cochrane Library, Korean scientific database, and Chinese and Indian medical databases to identify all eligible studies for evaluating the association of THADA rs13429458 and PCOS risk. The association was assessed in five genetic random effects models including the allelic (AG), recessive (RG), dominant (DG), homozygous (HMG), and heterozygous (HTG) genetic models. Subgroup analyses stratified by ethnicity (Asians and non-Asians) were assessed. Nine articles were selected and 1 association analysis of Korea PCOS study met Hardy–Weinberg equilibrium criteria. A set of 38 224 PCOS women and 120 173 healthy women were included. The AG and RG showed heterogeneity in the overall and Asian subjects, but the other genetic model did not exhibit heterogeneity in all subjects. AG, RG, DG, and HMG, but not HTG, exhibited publication bias in total subjects but there was no publication bias in all genetic models among Asians and non-Asians. The overall effect of THADA_rs13429458 on PCOS risk showed significant positive associations in pooling 10 studies. In sub-group analysis only Asians, but not non-Asians, had a positive association (AG: OR=1.24, p=0.001; RG: OR=1.32, p=0.002; DG: OR, 1.70, p<0.00001; HMG: OR, 1.71, p=0.002; HTG: OR=1.34, p=0,006). In conclusions, young Asian women with the minor allele (C) for THADA rs13429458 were at increased risk of PCOS.
Remote control of microtubule plus-end dynamics and function from the minus-end

In eukaryotes, the organization and function of the microtubule cytoskeleton depend on the allocation of different roles to individual microtubules. For example, many asymmetrically dividing cells differentially specify microtubule behavior at old and new centrosomes. Here we show that yeast spindle pole bodies (SPBs, yeast centrosomes) differentially control the plus-end dynamics and cargoes of their astral microtubules, remotely from the minus-end. The old SPB recruits the kinesin motor protein Kip2, which then translocates to the plus-end of the emanating microtubules, promotes their extension and delivers dynein into the bud. Kip2 recruitment at the SPB depends on Bub2 and Bfa1, and phosphorylation of cytoplasmic Kip2 prevents random lattice binding. Releasing Kip2 of its control by SPBs equalizes its distribution, the length of microtubules and dynein distribution between the mother cell and its bud. These observations reveal that microtubule organizing centers use minus to plus-end directed remote control to individualize microtubule function.
Plumbagin attenuated oxygen-glucose deprivation/reoxygenation-induced injury in human SH-SY5Y cells by inhibiting NOX4-derived ROS-activated NLRP3 inflammasome

ABSTRACT Plumbagin (PLB), an alkaloid obtained from the roots of the plants of Plumbago genus, is an inhibitor of NADPH oxidase 4 (NOX4). This study aimed to investigate the beneficial effect of PLB against oxygen-glucose deprivation/reoxygenation (OGDR)-induced neuroinjury in human SH-SY5Y neuronal cultures. Our results showed that OGD/R stimulated NOX4 protein expression and reactive oxygen species (ROS) production in SH-SY5Y cells, whereas increased 4-hydroxynonenal (4-HNE) and malondialdehyde (MDA) production, resulting in the activation of the NLRP3 inflammasome. And PLB pretreatment reduced the ROS production by regulating the expression of NOX4 and downregulated NF-κB signaling which was induced by OGDR. Furthermore, PLB inhibited OGDR induced NLRP3 inflammasome activation but not PARP1. Overall, PLB improved OGDR induced neuroinjury by inhibiting NOX4-derived ROS-activated NLRP3 inflammasome. Graphical abstract Plumbagin treatment attenuated OGDR-induced neuronal cell injury by inhibiting NOX4-derived ROS-activated NLRP3 inflammasome and NF-κB activation.
Defining signatures of peripheral T-cell lymphoma with a targeted 20-marker gene expression profiling assay

Peripheral T-cell lymphoma comprises a heterogeneous group of mature non-Hodgkin lymphomas. Their diagnosis is challenging, with up to 30% of cases remaining unclassifiable and referred to as “not otherwise specified”. We developed a reverse transcriptase-multiplex ligation-dependent probe amplification gene expression profiling assay to differentiate the main T-cell lymphoma entities and to study the heterogeneity of the “not specified” category. The test evaluates the expression of 20 genes, including 17 markers relevant to T-cell immunology and lymphoma biopathology, one Epstein-Barr virus-related transcript, and variants of RHOA (G17V) and IDH2 (R172K/T). By unsupervised hierarchical clustering, our assay accurately identified 21 of 21 ALK-positive anaplastic large cell lymphomas, 16 of 16 extranodal natural killer (NK)/T-cell lymphomas, 6 of 6 hepatosplenic T-cell lymphomas, and 13 of 13 adult T-cell leukemia/lymphomas. ALK-negative anaplastic lymphomas (n=34) segregated into one cytotoxic cluster (n=10) and one non-cytotoxic cluster expressing Th2 markers (n=24) and enriched in DUSP22-rearranged cases. The 63 TFH-derived lymphomas divided into two subgroups according to a predominant TFH (n=50) or an enrichment in Th2 (n=13) signatures. We next developed a support vector machine predictor which attributed a molecular class to 27 of 77 not specified T-cell lymphomas: 17 TFH, five cytotoxic ALK-negative anaplastic and five NK/T-cell lymphomas. Among the remaining cases, we identified two cell-of-origin subgroups corresponding to cytotoxic/Th1 (n=19) and Th2 (n=24) signatures. A reproducibility test on 40 cases yielded a 90% concordance between three independent laboratories. This study demonstrates the applicability of a simple gene expression assay for the classification of peripheral T-cell lymphomas. Its applicability to routinely-fixed samples makes it an attractive adjunct in diagnostic practice.