Genome-wide association and polygenic risk score estimation of type 2 diabetes mellitus in Kinh Vietnamese-A pilot study.

A genome-wide association study (GWAS) is a powerful tool in investigating genetic contribution, which is a crucial factor in the development of complex multifactorial diseases, such as type 2 diabetes mellitus. Type 2 diabetes mellitus is a major healthcare burden in the Western Pacific region; however, there is limited availability of genetic-associated data for type 2 diabetes in Southeast Asia, especially among the Kinh Vietnamese population. This lack of information exacerbates global healthcare disparities. In this study, 997 Kinh Vietnamese individuals (503 with type 2 diabetes and 494 controls) were prospectively recruited and their clinical and paraclinical information was recorded. DNA samples were collected and whole genome genotyping was performed. Standard quality control and genetic imputation using the 1000 Genomes database were executed. A polygenic risk score for type 2 diabetes was generated in different models using East Asian, European, and mix ancestry GWAS summary statistics as training datasets. After quality control and genetic imputation, 107 polymorphisms reached suggestive statistical significance for GWAS (≤5 × 10-6) and rs11079784 was one of the potential markers strongly associated with type 2 diabetes in the studied population. The best polygenic risk score model predicting type 2 diabetes mellitus had AUC = 0.70 (95% confidence interval = 0.62-0.77) based on a mix of ancestral GWAS summary statistics. These data show promising results for genetic association with a polygenic risk score estimation in the Kinh Vietnamese population; the results also highlight the essential role of population diversity in a GWAS of type 2 diabetes mellitus.

Geographic Accessibility and Completion of Initial Low-Dose CT-Based Lung Cancer Screening in an Urban Safety-Net Population.

BACKGROUND: Recent modifications to low-dose CT (LDCT)-based lung cancer screening guidelines increase the number of eligible individuals, particularly among racial and ethnic minorities. Because these populations disproportionately live in metropolitan areas, we analyzed the association between travel time and initial LDCT completion within an integrated, urban safety-net health care system. METHODS: Using Esri's StreetMap Premium, OpenStreetMap, and the r5r package in R, we determined projected private vehicle and public transportation travel times between patient residence and the screening facility for LDCT ordered in March 2017 through December 2022 at Parkland Memorial Hospital in Dallas, Texas. We characterized associations between travel time and LDCT completion in univariable and multivariable analyses. We tested these associations in a simulation of 10,000 permutations of private vehicle and public transportation distribution. RESULTS: A total of 2,287 patients were included in the analysis, of whom 1,553 (68%) completed the initial ordered LDCT. Mean age was 63 years, and 73% were underrepresented minorities. Median travel time from patient residence to the LDCT screening facility was 17 minutes by private vehicle and 67 minutes by public transportation. There was a small difference in travel time to the LDCT screening facility by public transportation for patients who completed LDCT versus those who did not (67 vs 66 min, respectively; P=.04) but no difference in travel time by private vehicle for these patients (17 min for both; P=.67). In multivariable analysis, LDCT completion was not associated with projected travel time to the LDCT facility by private vehicle (odds ratio, 1.01; 95% CI, 0.82-1.25) or public transportation (odds ratio, 1.14; 95% CI, 0.89-1.44). Similar results were noted across travel-type permutations. Black individuals were 29% less likely to complete LDCT screening compared with White individuals. CONCLUSIONS: In an urban population comprising predominantly underrepresented minorities, projected travel time is not associated with initial LDCT completion in an integrated health care system. Other reasons for differences in LDCT completion warrant investigation.

Early-onset gout and rare deficient variants of the lactate dehydrogenase D gene.

OBJECTIVES: To investigate whether the lactate dehydrogenase D (LDHD) gene deficiency causes juvenile-onset gout. METHODS: We used whole-exome sequencing for two families and a targeted gene-sequencing panel for an isolated patient. d-lactate dosages were analysed using ELISA. RESULTS: We demonstrated linkage of juvenile-onset gout to homozygous carriage of three rare distinct LDHD variants in three different ethnicities. In a Melanesian family, the variant was (NM_153486.3: c.206C>T; rs1035398551) and, as compared with non-homozygotes, homozygotes had higher hyperuricaemia (P = 0.02), lower fractional clearance of urate (P = 0.002), and higher levels of d-lactate in blood (P = 0.04) and urine (P = 0.06). In a second, Vietnamese, family, very severe juvenile-onset gout was linked to homozygote carriage of an undescribed LDHD variant (NM_153486.3: c.1363dupG) leading to a frameshift followed by a stop codon, p.(AlaGly432fsTer58). Finally, a Moroccan man, with early-onset and high d-lactaturia, whose family was unavailable for testing, was homozygous for another rare LDHD variant [NM_153486.3: c.752C>T, p.(Thr251Met)]. CONCLUSION: Rare, damaging LDHD variants can cause autosomal recessive early-onset gout, the diagnosis of which can be suspected by measuring high d-lactate levels in the blood and/or urine.

Decision tree learning in Neo4j on homogeneous and unconnected graph nodes from biological and clinical datasets.

BACKGROUND: Graph databases enable efficient storage of heterogeneous, highly-interlinked data, such as clinical data. Subsequently, researchers can extract relevant features from these datasets and apply machine learning for diagnosis, biomarker discovery, or understanding pathogenesis. METHODS: To facilitate machine learning and save time for extracting data from the graph database, we developed and optimized Decision Tree Plug-in (DTP) containing 24 procedures to generate and evaluate decision trees directly in the graph database Neo4j on homogeneous and unconnected nodes. RESULTS: Creation of the decision tree for three clinical datasets directly in the graph database from the nodes required between 0.059 and 0.099 s, while calculating the decision tree with the same algorithm in Java from CSV files took 0.085-0.112 s. Furthermore, our approach was faster than the standard decision tree implementations in R (0.62 s) and equal to Python (0.08 s), also using CSV files as input for small datasets. In addition, we have explored the strengths of DTP by evaluating a large dataset (approx. 250,000 instances) to predict patients with diabetes and compared the performance against algorithms generated by state-of-the-art packages in R and Python. By doing so, we have been able to show competitive results on the performance of Neo4j, in terms of quality of predictions as well as time efficiency. Furthermore, we could show that high body-mass index and high blood pressure are the main risk factors for diabetes. CONCLUSION: Overall, our work shows that integrating machine learning into graph databases saves time for additional processes as well as external memory, and could be applied to a variety of use cases, including clinical applications. This provides user with the advantages of high scalability, visualization and complex querying.

Smartphone clip-on instrument and microfluidic processor for rapid sample-to-answer detection of Zika virus in whole blood using spatial RT-LAMP.

Rapid, simple, inexpensive, accurate, and sensitive point-of-care (POC) detection of viral pathogens in bodily fluids is a vital component of controlling the spread of infectious diseases. The predominant laboratory-based methods for sample processing and nucleic acid detection face limitations that prevent them from gaining wide adoption for POC applications in low-resource settings and self-testing scenarios. Here, we report the design and characterization of an integrated system for rapid sample-to-answer detection of a viral pathogen in a droplet of whole blood comprised of a 2-stage microfluidic cartridge for sample processing and nucleic acid amplification, and a clip-on detection instrument that interfaces with the image sensor of a smartphone. The cartridge is designed to release viral RNA from Zika virus in whole blood using chemical lysis, followed by mixing with the assay buffer for performing reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) reactions in six parallel microfluidic compartments. The battery-powered handheld detection instrument uniformly heats the compartments from below, and an array of LEDs illuminates from above, while the generation of fluorescent reporters in the compartments is kinetically monitored by collecting a series of smartphone images. We characterize the assay time and detection limits for detecting Zika RNA and gamma ray-deactivated Zika virus spiked into buffer and whole blood and compare the performance of the same assay when conducted in conventional PCR tubes. Our approach for kinetic monitoring of the fluorescence-generating process in the microfluidic compartments enables spatial analysis of early fluorescent "bloom" events for positive samples, in an approach called "Spatial LAMP" (S-LAMP). We show that S-LAMP image analysis reduces the time required to designate an assay as a positive test, compared to conventional analysis of the average fluorescent intensity of the entire compartment. S-LAMP enables the RT-LAMP process to be as short as 22 minutes, resulting in a total sample-to-answer time in the range of 17-32 minutes to distinguish positive from negative samples, while demonstrating a viral RNA detection as low as 2.70 × 102 copies per µl, and a gamma-irradiated virus of 103 virus particles in a single 12.5 µl droplet blood sample.

Clinical and urodynamic features of secondary tethered cord syndrome: How can they be found longitudinally?

PURPOSE: Secondary tethered cord syndrome (TCS) can be diagnosed with signs of progressive deterioration in urological or neuro-orthopedic systems following primary untethering surgery. Though urological deterioration is a common secondary TCS manifestation, a paucity of diagnostic criteria makes diagnoses challenging. A detailed description of urological deterioration may help diagnose secondary TCS. Thus, the clinical and urodynamic features of the current secondary TCS cases were described. MATERIALS AND METHODS: Fifty-one patients who had undergone reuntethering for secondary TCS experienced improvement or stabilization of progressive problems. Moreover, their clinical and videourodynamic changes were longitudinally described. RESULTS: Loss of postoperative spontaneous voiding was the first urological secondary TCS sign for those who could void spontaneously. Urological problems mostly occurred during elementary school (6-12 years). Major urological presentations were recalcitrant urinary tract infection or urinary incontinence. Follow-up videourodynamic studies revealed typical changes, from acontractile bladder to overactive and low-complaint bladders. While detrusor overactivity did not always occur during the progression, detrusor sphincter dyssynergia was always present in all patients with urological deterioration. All patients postoperatively showed significant urodynamic improvement regardless of preoperative bladder dysfunction. This included four cases of restoring spontaneous voiding. Nine patients experienced newly appearing nonprogressive neuro-orthopedic complications despite their urological improvement. CONCLUSIONS: Urological deterioration should prompt secondary TCS suspicion, and changes in clinical patterns and videourodynamic studies helped diagnose it. However, reuntethering can effectively address urological problems at the cost of some neuro-orthopedic functions in some patients.

Estimation of Water Depth on Road Surfaces Using Accelerometric Signals.

The paper presents an experimental study conducted to evaluate the feasibility of using accelerometers as an indirect means to estimate water depths on road surfaces. It makes use of the vibration of the vehicle's wheel arch due to water droplets projected by a tire rolling on a wet road surface. A trailer equipped with a wheel and towed by a van was used. The test setups to spread water on the road surface and before the test wheel, measure the water depth and visualize the water spray are described. The test program, conducted on a test track closed to the traffic, includes three surfaces and two speeds. Visualization of water flows by means of high-speed cameras makes it possible to choose a suitable location for the accelerometers. It turns out that signals provided by the accelerometers are affected by the trailer's movement; a filtering method has been successfully developed to remove noises. Results show a tight relationship between the mean amplitude of accelerometric signals and actual water depths. Discussions are made in terms of effects of the vehicle speed and the road surface texture. Perspectives for using the developed system to improve passenger safety under autonomous driving conditions are presented.

Conception of a High-Level Perception and Localization System for Autonomous Driving.

This paper describes the conception of a high level, compact, scalable, and long autonomy perception and localization system for autonomous driving applications. Our benchmark is composed of a high resolution lidar (128 channels), a stereo global shutter camera, an inertial navigation system, a time server, and an embedded computer. In addition, in order to acquire data and build multi-modal datasets, this system embeds two perception algorithms (RBNN detection, DCNN detection) and one localization algorithm (lidar-based localization) to provide real-time advanced information such as object detection and localization in challenging environments (lack of GPS). In order to train and evaluate the perception algorithms, a dataset is built from 10,000 annotated lidar frames from various drives carried out under different weather conditions and different traffic and population densities. The performances of the three algorithms are competitive with the state-of-the-art. Moreover, the processing time of these algorithms are compatible with real-time autonomous driving applications. By providing directly accurate advanced outputs, this system might significantly facilitate the work of researchers and engineers with respect to planning and control modules. Thus, this study intends to contribute to democratizing access to autonomous vehicle research platforms.

Acute injury or illness related to the inhalation of vaping aerosols among children and adolescents across Canada: A cross-sectional survey of Canadian paediatricians.

Background: Vaping prevalence rates have increased among Canadian youth. Evidence suggests that vaping poses significant health risks to children and adolescents. Objectives: The objectives of the study were to investigate epidemiological characteristics of acute injury/illness cases due to the inhalation of vaping aerosols among children and adolescents across Canada and to explore factors contributing to severe cases. Methods: Data from the 2019 Canadian Paediatric Surveillance Program cross-sectional survey on vaping-related injury/illness were used. Analyses focused on injury/illness cases (n=71) among children and adolescents aged 0 to 17 years who presented to participating paediatricians for a harm related to the inhalation of vaping aerosols. We conducted descriptive analyses and performed logistic regression to explore associations between severe presentations requiring hospitalization or intensive care unit (ICU) admission and selected case characteristics. Results: Of the 71 reported injury/illness cases related to inhalation of vaping aerosols, 56% of patients were male, and 68% were aged 15 to 17 years. Nicotine vaping was reported in 42% of cases, and cannabis vaping in 24%. Fifty-four per cent presented with respiratory distress, 18% with symptoms of nicotine toxicity, and 41% required hospitalization and/or admission to the ICU. Cases presenting with respiratory distress were more likely to be hospitalized/admitted to the ICU (odds ratio [OR]=5.37, 95% confidence interval [CI]:1.76 to 16.39). Conclusions: The inhalation of vaping aerosols among children and adolescents may contribute to acute injury/illness. Clear associations between study variables and severe cases could not be established due to a small sample size. Additional research is needed to determine predictors and preventable risk factors of severe vaping-related injuries.

A cross-sectional study of 502 patients found a diffuse hyperechoic kidney medulla pattern in patients with severe gout.

We have previously shown that ultrasonography can detect hyperechogenic crystal deposits in the kidney medulla of patients with gout. In this cross-sectional study we investigated the frequency and clinical correlates of hyperechogenic kidney medulla in 502 consecutive primary consultants for gout (ACR/EULAR criteria) at the Vien Gut medical center in Ho Chi Minh City, Vietnam. None of these patients received urate-lowering drugs. Kidney medulla echogenicity on B-mode ultrasonography was compared to that of the kidney cortex. Overall, 36% patients showed a hyperechoic pattern of Malpighi pyramids. On univariate analysis, the pattern was significantly associated with age, estimated gout duration, steroid-dependency, clinical tophi, urate arthropathy, double contour thickness at the scanned joints, coronary heart disease, arterial hypertension, hyperuricemia, proteinuria, leukocyturia, and decreased estimated glomerular filtration rate. On multivariable analysis, the hyperechoic pattern was associated with estimated disease duration, clinical tophi, urate arthropathy, double contour thickness and decreased estimated glomerular filtration rate. No hyperechoic pattern was observed in 515 consecutive consultants without gout. Thus, hyperechoic kidney medulla was frequently demonstrated in Vietnamese patients with tophaceous gout and associated with features of tubulointerstitial nephritis. This finding revives the hypothesis of microcrystalline nephropathy of gout, predominantly seen in untreated gouty patients, which could be an important target for urate-lowering therapy.

Evaluation of chronic toxicity of cyclocreatine in beagle dogs after oral gavage administration for up to 23 weeks.

Cyclocreatine (LUM-001) was evaluated for chronic toxicity (23 weeks) in beagle dogs to support clinical development in patients with creatine transporter deficiency (CTD) disorder. Deionized water (vehicle control) or cyclocreatine was administered by oral gavage twice daily (12 ± 1 h apart) at 20, 40 and 75 mg/kg/dose followed by a recovery period. Due to severe toxicity, the study was terminated earlier than the planned 39 weeks of dosing. Animals in the 20, 40 and 75 mg/kg/dose groups completed 160, 106, and 55 days of dosing, respectively, followed by 30, 55 and 106 days of a recovery period, respectively. Three (25%), 7 (58%), and 7 (58%) animals were euthanized and/or found dead in the 40, 80, and 150 mg/kg/day dose groups, respectively. Clinical signs observed were inappetence, frequent emesis, stool abnormalities, weight loss, lethargy and respiratory distress. Histopathological evaluation revealed congestion, edema, cellular infiltration, fibrin, and/or hemorrhage in the lungs of all dose groups. Additionally, animals in all cyclocreatine treatment groups had perinuclear cytoplasmic vacuoles in the heart, kidneys, skeletal and smooth muscles. After the recovery period, the vacuoles were still observed in the cardiac and renal tissues. Cyclocreatine was absorbed rapidly with mean Tmax within 1 to 2 h and half-life ranged between 2.17 and 2.79 h on Day 1, however, on the final day of dosing, it ranged between 5.80 and 8.77 h (males) and 10.3 to 13.1 h (females). To conclude, in this study the lungs, kidneys, heart, skeletal and smooth muscles were identified as the target organs of cyclocreatine toxicity in beagle dogs.

Gold-Catalyzed Access to Isophosphinoline 2-Oxides.

Gold(I)-catalyzed reactions of electron-poor alkynes are still a challenging process. A straightforward synthesis of phosphorus-based heterocycles, namely, 2-phenyl 1H-isophosphinoline 2-oxides 1, is reported. The reaction used PPh3AuCl precatalyst in combination with triflic acid under microwave activation and afforded isophosphinoline 2-oxides 1 in moderate to quantitative yields through a fully regioselective 6-endo-dig hydroarylation cyclization, paving the way toward an effective synthesis of phosphorus heterocycles.

Prevalence, species distribution and antifungal susceptibility of Candida albicans causing vaginal discharge among symptomatic non-pregnant women of reproductive age at a tertiary care hospital, Vietnam.

BACKGROUND: Vaginal candidiasis is frequent in women of reproductive age. Accurate identification Candida provides helpful information for successful therapy and epidemiology study; however, there are very limited data from the Vietnam have been reported. This study was performed to determine the prevalence, species distribution of yeast causing vaginal discharge and antifungal susceptibility patterns of Candida albicans among symptomatic non-pregnant women of reproductive age. METHODS: Vaginal discharge samples were collected from 462 women of reproductive age in Hanoi, Vietnam between Sep 2019 and Oct 2020. Vaginal swabs from these patients were examined by direct microscopic examination (10% KOH). CHROMagar™ Candida medium and Sabouraud dextrose agar supplemented with chloramphenicol (0.5 g/l) were used to isolate yeast, and species identification was performed using morphological tests and molecular tools (PCR and sequencing). Antifungal susceptibility testing was determined according to the Clinical and Laboratory Standards Institute guidelines (M27-A3 and M27-S4). RESULTS: The prevalence of vaginal yeast colonization in non-pregnant women was 51.3% of 462 participants. Nine different yeast species were identified. Among these isolates, C. albicans (51.37%) was the most frequent, followed by C. parapsilosis (25.88%), C. glabrata (11.37%), C. tropicalis (4.31%), C. krusei (3.92%), C. africana (1.57%), Saccharomyces cerevisiae (0.78%), C. nivariensis (1 isolates, 0.39%), and C. lusitaniae (1 isolates, 0.39%), respectively. Among C. albicans, all 46 isolates were 100% susceptible to micafungin, caspofungin, and miconazole. The susceptibility rates to amphotericine B, 5-flucytosine, fluconazole, itraconazole and voriconazole were 95.65, 91.30, 91.30, 82.61 and 86.95%, respectively. CONCLUSIONS: The prevalence of VVC among symptomatic non-pregnant women of reproductive age in Vietnam was higher than many parts of the world. The high frequency of non-albicans Candida species, which were often more resistant to antifungal agents, was a notable feature. Resistance rates of vaginal C. albicans isolates to antifungal agents was low. Our findings suggest that continued surveillance of changes in species distribution and susceptibility to antifungals should be routinely screened and treated.

Ultrasonographic cystometry for neurogenic bladder using elastography.

AIM: Ultrasound shear wave elastography (SWE) has been used to measure elasticity (Young's modulus: YM) in solid organs. It was reported to show a better correlation with intravesical pressure (Pves) than with compliance, supporting its potential use in noninvasive cystometry. Contrariwise, conceptually, YM should be more correlated with compliance than with Pves. To optimize the potential use of YM as a noninvasive urodynamic study, the relationship between YM, Pves, and compliance was reassessed in this study. METHOD: YM was serially measured using SWE along with bladder filling. To overcome problems inherent to current compliance measurements, modified dynamic compliance was developed from cystometry by a locally weighted scatter plot smoothing algorithm. Then it was matched with YM from SWE. YM was also correlated with Pves. Furthermore, to understand the nature of YM, which was measured by ultrasound, the bladder wall's modulus, which was the mathematical assessment of YM derived from cystometric data, was also calculated and compared. RESULTS: Thirty-two neurogenic bladder patients were included in this study. YM correlated with Pves (r = .72, p < .0001) better than with modified dynamic compliance (r = -0.43, p < .0001). The correlation of YM with Pves was even higher than that with the calculated bladder wall's modulus (r = .52, p < .0001). CONCLUSION: YM measured by SWE associates with Pves better than with compliance, confirming the results of previous studies. SWE reflects the integration of both the holding capability of the bladder wall and urine rather than either of one, implying its potential utilization in noninvasive cystometry.

Salivary flow rate and the risk of cognitive impairment among Korean elders: a cross-sectional study.

BACKGROUND: Salivary function has been suggested to be associated with cognitive impairment. However, the effect of salivary flow rate (SFR) on cognitive impairment remains unclear. This study aimed to investigate whether SFR is associated with cognitive impairment among Korean elders. METHODS: This cross-sectional study included 649 elders aged 65 and older in the Korean community-dwelling population. Cognitive impairment was assessed using the Mini-Mental Status Examination. Unstimulated SFR was measured and dichotomized. Denture status, age, sex, education level, smoking, drinking, diabetes, hypertension, and obesity were considered confounders. Multivariable logistic regression analysis was applied to assess the adjusted association. Stratified analysis by sex and denture status was performed to clarify the effect modification. RESULTS: Participants without cognitive impairment showed a higher SFR level than those with cognitive impairment (0.81 mL/min for non-cognitive impairment versus 0.52 mL/min for cognitive impairment, p < 0.001). After controlling for confounders, participants with low SFR (< 0.3 mL/min) were more likely to have cognitive impairment by 1.5 times than participants with normal SFR (odds ratio [OR] = 1.5, confidence interval [CI] = 1.05-2.10). The association of low SFR with cognitive impairment was higher in women and dentate participants: about 10% higher in women (OR = 1.63, CI = 1.07-2.50) and about 22% higher in dentate participants (OR = 1.82, CI = 1.41-2.90). CONCLUSIONS: Salivary flow rate is independently associated with cognitive impairment among Korean elders. The association was modified in females and dentate elders. Physicians and dentists should consider low SFR and cognitive impairment as a risk factor between them in clinics.

Use of an animal model of disease for toxicology enables identification of a juvenile no observed adverse effect level for cyclocreatine in creatine transporter deficiency.

In standard general toxicology studies in two species to support clinical development, cyclocreatine, a creatine analog for the treatment of creatine transporter deficiency, caused deaths, convulsions, and/or multi-organ pathology. The potential translatability of these findings to patients was evaluated by comparing toxicity of cyclocreatine in wild-type mice to creatine transporter-deficient mice, a model of the human disease. A biodistribution study indicated greater accumulation of cyclocreatine in the brains of wild-type mice, consistent with its ability to be transported by the creatine transporter. Subsequent toxicology studies confirmed greater sensitivity of wild-type mice to cyclocreatine-induced toxicity. Exposure at the no observed adverse effect level in creatine transporter-deficient (554 µg*hr/ml) mice exceeded exposure at the maximum tolerated dose in wild-type (248 µg*hr/ml) mice. When dosed at 300 mg/kg/day for 3 months, cyclocreatine-related mortality, convulsions, and multi-organ pathology were observed in wild-type mice whereas there were no adverse findings in creatine transporter-deficient mice. Brain vacuolation was common to both strains. Although transporter-deficient mice appeared to be more sensitive, the finding had no functional correlates in this strain. The results highlight the importance of considering models of disease for toxicology in cases where they may be relevant to assessing safety in the intended patient population.

Tyrosyl-tRNA synthetase stimulates thrombopoietin-independent hematopoiesis accelerating recovery from thrombocytopenia.

New mechanisms behind blood cell formation continue to be uncovered, with therapeutic approaches for hematological diseases being of great interest. Here we report an enzyme in protein synthesis, known for cell-based activities beyond translation, is a factor inducing megakaryocyte-biased hematopoiesis, most likely under stress conditions. We show an activated form of tyrosyl-tRNA synthetase (YRSACT), prepared either by rationally designed mutagenesis or alternative splicing, induces expansion of a previously unrecognized high-ploidy Sca-1+ megakaryocyte population capable of accelerating platelet replenishment after depletion. Moreover, YRSACT targets monocytic cells to induce secretion of transacting cytokines that enhance megakaryocyte expansion stimulating the Toll-like receptor/MyD88 pathway. Platelet replenishment by YRSACT is independent of thrombopoietin (TPO), as evidenced by expansion of the megakaryocytes from induced pluripotent stem cell-derived hematopoietic stem cells from a patient deficient in TPO signaling. We suggest megakaryocyte-biased hematopoiesis induced by YRSACT offers new approaches for treating thrombocytopenia, boosting yields from cell-culture production of platelet concentrates for transfusion, and bridging therapy for hematopoietic stem cell transplantation.

Rotation equivariant and invariant neural networks for microscopy image analysis.

MOTIVATION: Neural networks have been widely used to analyze high-throughput microscopy images. However, the performance of neural networks can be significantly improved by encoding known invariance for particular tasks. Highly relevant to the goal of automated cell phenotyping from microscopy image data is rotation invariance. Here we consider the application of two schemes for encoding rotation equivariance and invariance in a convolutional neural network, namely, the group-equivariant CNN (G-CNN), and a new architecture with simple, efficient conic convolution, for classifying microscopy images. We additionally integrate the 2D-discrete-Fourier transform (2D-DFT) as an effective means for encoding global rotational invariance. We call our new method the Conic Convolution and DFT Network (CFNet). RESULTS: We evaluated the efficacy of CFNet and G-CNN as compared to a standard CNN for several different image classification tasks, including simulated and real microscopy images of subcellular protein localization, and demonstrated improved performance. We believe CFNet has the potential to improve many high-throughput microscopy image analysis applications. AVAILABILITY AND IMPLEMENTATION: Source code of CFNet is available at: https://github.com/bchidest/CFNet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PUMA - pooled uranium miners analysis: cohort profile.

OBJECTIVES: Epidemiological studies of underground miners have provided clear evidence that inhalation of radon decay products causes lung cancer. Moreover, these studies have served as a quantitative basis for estimation of radon-associated excess lung cancer risk. However, questions remain regarding the effects of exposure to the low levels of radon decay products typically encountered in contemporary occupational and environmental settings on the risk of lung cancer and other diseases, and on the modifiers of these associations. These issues are of central importance for estimation of risks associated with residential and occupational radon exposures. METHODS: The Pooled Uranium Miner Analysis (PUMA) assembles information on cohorts of uranium miners in North America and Europe. Data available include individual annual estimates of exposure to radon decay products, demographic and employment history information on each worker and information on vital status, date of death and cause of death. Some, but not all, cohorts also have individual information on cigarette smoking, external gamma radiation exposure and non-radiological occupational exposures. RESULTS: The PUMA study represents the largest study of uranium miners conducted to date, encompassing 124 507 miners, 4.51 million person-years at risk and 54 462 deaths, including 7825 deaths due to lung cancer. Planned research topics include analyses of associations between radon exposure and mortality due to lung cancer, cancers other than lung, non-malignant disease, modifiers of these associations and characterisation of overall relative mortality excesses and lifetime risks. CONCLUSION: PUMA provides opportunities to evaluate new research questions and to conduct analyses to assess potential health risks associated with uranium mining that have greater statistical power than can be achieved with any single cohort.