A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

Unbiased next-generation sequencing (NGS) approaches enable comprehensive pathogen detection in the clinical microbiology laboratory and have numerous applications for public health surveillance, outbreak investigation, and the diagnosis of infectious diseases. However, practical deployment of the technology is hindered by the bioinformatics challenge of analyzing results accurately and in a clinically relevant timeframe. Here we describe SURPI (“sequence-based ultrarapid pathogen identification”), a computational pipeline for pathogen identification from complex metagenomic NGS data generated from clinical samples, and demonstrate use of the pipeline in the analysis of 237 clinical samples comprising more than 1.1 billion sequences. Deployable on both cloud-based and standalone servers, SURPI leverages two state-of-the-art aligners for accelerated analyses, SNAP and RAPSearch, which are as accurate as existing bioinformatics tools but orders of magnitude faster in performance. In fast mode, SURPI detects viruses and bacteria by scanning data sets of 7–500 million reads in 11 min to 5 h, while in comprehensive mode, all known microorganisms are identified, followed by de novo assembly and protein homology searches for divergent viruses in 50 min to 16 h. SURPI has also directly contributed to real-time microbial diagnosis in acutely ill patients, underscoring its potential key role in the development of unbiased NGS-based clinical assays in infectious diseases that demand rapid turnaround times.

Managing data transfers in computer clusters with orchestra

Cluster computing applications like MapReduce and Dryad transfer massive amounts of data between their computation stages. These transfers can have a significant impact on job performance, accounting for more than 50% of job completion times. Despite this impact, there has been relatively little work on optimizing the performance of these data transfers, with networking researchers traditionally focusing on per-flow traffic management. We address this limitation by proposing a global management architecture and a set of algorithms that (1) improve the transfer times of common communication patterns, such as broadcast and shuffle, and (2) allow scheduling policies at the transfer level, such as prioritizing a transfer over other transfers. Using a prototype implementation, we show that our solution improves broadcast completion times by up to 4.5X compared to the status quo in Hadoop. We also show that transfer-level scheduling can reduce the completion time of high-priority transfers by 1.7X.

Fractionated half-body irradiation (HBI) for the rapid palliation of widespread, symptomatic, metastatic bone disease: a randomized Phase III trial of the International Atomic Energy Agency (IAEA)

PURPOSE

To find the fastest and most effective/efficient method to economically deliver fractionated half-body irradiation (HBI) for widespread (WS), symptomatic, metastatic bone cancer.

METHODS AND MATERIALS

A Phase III trial with 3 HBI arms: (Arm A) Control (15 Gy/5 fractions/5 days); (Arm B) Hyperfractionation (HF) (8 Gy/2 fractions/1 day); (Arm C) Accelerated HF (12 Gy/4 fractions/2 days). Six countries randomized 156 patients (all with WS bone metastases): 51, 56, and 49 patients to Arms A, B, and C, respectively. There were 72 (46%) breast, 50 (32%) prostate, 9 (6%) lung, and 25 (16%) miscellaneous primary tumors. Initial performance status (PS) was 1-2 in 101 (65%) and PS 3-4 in 55 (35%). The lower, upper, and middle halves of the body were treated 79, 68, and 9 times.

RESULTS

Pain relief was seen in 91% of patients (45% complete [CR] and 46% partial [PR]) within 3-8 days. Overall (OS), median (MST), and pain-free (PFS) survival was 174, 150, and 122 days. Breast tumors had a higher OS (279 days) than that of other primary tumors, but when analyzed by treatment, was not significantly different than prostate tumors in Arm A. No survival differences were found in patients with PS 1-2 vs. 3-4, CR vs. PR, bone with/without visceral metastases, or by the number of metastases (< or > 15 bone lesions). Quality of life (QOL) assessed by the percent of the remaining life free of pain was 71%; furthermore significant improvements in PS, pain, and narcotic scores were seen after HBI. Toxicity was very acceptable (41% none, 50% mild/moderate, 12% severe but transitory); more was seen with upper HBI.

CONCLUSION

In terms of response, time to response, OS, MST, PFS, QOL, and toxicity, schedules for Arms A and C were similar for all but prostate primaries. Schedule for Arm B, which delivered the lowest biologic dose in the shortest time, had significantly worse results in pain relief, OS, MST, PFS, and QOL. Results indicate that, for most primary tumor types (except prostate), delivering two HBI daily doses of 3 Gy in 2 consecutive days is as effective as delivering a daily dose of 3 Gy for 5 consecutive days. Thus, this is a faster and much more convenient HBI schedule for the palliation of pain in widespread cancer.

Machine Learning to Classify Intracardiac Electrical Patterns During Atrial Fibrillation: Machine Learning of Atrial Fibrillation

BACKGROUND

Advances in ablation for atrial fibrillation (AF) continue to be hindered by ambiguities in mapping, even between experts. We hypothesized that convolutional neural networks (CNN) may enable objective analysis of intracardiac activation in AF, which could be applied clinically if CNN classifications could also be explained.

METHODS

We performed panoramic recording of bi-atrial electrical signals in AF. We used the Hilbert-transform to produce 175 000 image grids in 35 patients, labeled for rotational activation by experts who showed consistency but with variability (kappa [κ]=0.79). In each patient, ablation terminated AF. A CNN was developed and trained on 100 000 AF image grids, validated on 25 000 grids, then tested on a separate 50 000 grids.

RESULTS

In the separate test cohort (50 000 grids), CNN reproducibly classified AF image grids into those with/without rotational sites with 95.0% accuracy (CI, 94.8%-95.2%). This accuracy exceeded that of support vector machines, traditional linear discriminant, and k-nearest neighbor statistical analyses. To probe the CNN, we applied gradient-weighted class activation mapping which revealed that the decision logic closely mimicked rules used by experts (C statistic 0.96).

CONCLUSIONS

CNNs improved the classification of intracardiac AF maps compared with other analyses and agreed with expert evaluation. Novel explainability analyses revealed that the CNN operated using a decision logic similar to rules used by experts, even though these rules were not provided in training. We thus describe a scaleable platform for robust comparisons of complex AF data from multiple systems, which may provide immediate clinical utility to guide ablation. Registration: URL: https://www.clinicaltrials.gov; Unique identifier: NCT02997254. Graphic Abstract: A graphic abstract is available for this article.

Machine Learned Cellular Phenotypes in Cardiomyopathy Predict Sudden Death

RATIONALE

Susceptibility to VT/VF (ventricular tachycardia/fibrillation) is difficult to predict in patients with ischemic cardiomyopathy either by clinical tools or by attempting to translate cellular mechanisms to the bedside.

OBJECTIVE

To develop computational phenotypes of patients with ischemic cardiomyopathy, by training then interpreting machine learning of ventricular monophasic action potentials (MAPs) to reveal phenotypes that predict long-term outcomes.

METHODS AND RESULTS

We recorded 5706 ventricular MAPs in 42 patients with coronary artery disease and left ventricular ejection fraction ≤40% during steady-state pacing. Patients were randomly allocated to independent training and testing cohorts in a 70:30 ratio, repeated K=10-fold. Support vector machines and convolutional neural networks were trained to 2 end points: (1) sustained VT/VF or (2) mortality at 3 years. Support vector machines provided superior classification. For patient-level predictions, we computed personalized MAP scores as the proportion of MAP beats predicting each end point. Patient-level predictions in independent test cohorts yielded c-statistics of 0.90 for sustained VT/VF (95% CI, 0.76-1.00) and 0.91 for mortality (95% CI, 0.83-1.00) and were the most significant multivariate predictors. Interpreting trained support vector machine revealed MAP morphologies that, using in silico modeling, revealed higher L-type calcium current or sodium-calcium exchanger as predominant phenotypes for VT/VF.

CONCLUSIONS

Machine learning of action potential recordings in patients revealed novel phenotypes for long-term outcomes in ischemic cardiomyopathy. Such computational phenotypes provide an approach which may reveal cellular mechanisms for clinical outcomes and could be applied to other conditions.

Postoperative radiotherapy in the management of cancer of the maxillary sinus

This report comprises 149 patients with carcinoma of the maxillary sinus treated with radical surgery and postoperative radiotherapy (5500 to 6000 cGy in 6 weeks) between 1963 and 1980 at the Instituto Nacional de Enfermedades Neoplasicas of Lima. Permanent local control was observed in 67.1% of the cases with a 5-year actuarial survival of 36.2% and a corrected survival for death not due to cancer of 42.3%. The ultimate local and distant failures were 61%. Data were analyzed regarding stage of the disease, radiotherapeutic technique and its influence on local control, complications, and patterns of relapse. The data indicate that the stage of the tumor influences survival. Because of the natural history of this disease, local control is paramount.

Local control of osteogenic sarcoma by radiation and chemotherapy

Sixteen patients with osteogenic sarcoma of limbs were treated with high dose methotrexate followed by leucovorin rescue, adriamycin and radiotherapy to the primary tumor. A post-treatment surgical biopsy was performed in 15 of the 16 patients. In 12 of 15 patients (80%), the follow-up biopsy was negative for active tumor. Complications of treatment were myelosuppression (16 cases), moist desquamation (13 cases), soft tissue necrosis (2 cases) local infection (2 cases), fibrosis (9 cases) and bone fracture (4 cases). The mean survival time in this group of patients was 712 days.

Incidence of regional lymph node metastasis in operable osteogenic sarcoma

Records of 182 consecutive patients with the diagnosis of operable osteogenic sarcoma, treated between 1954 through 1980 by the Breast, Bone and Mixed Tumors Department of the Instituto Nacional de Enfermedades Neoplasicas (Lima, Peru), were reviewed to study the incidence of regional lymph node metastases in this disease. All the patients included in this study had radical surgery, which means the complete resection of the bone where the tumor is located, including the proximal joint, which permitted excision of the regional lymph nodes. Nineteen patients (10.4%) had evidence of sarcoma metastatic to draining lymph nodes. A comprehensive analysis of the literature shows that the incidence of metastasis to the lymph nodes in this study, is higher than those cited in a review of the literature, probably due to the policy in the management of osteogenic sarcoma in our institution, during the period of study.

Impact of gestational diabetes mellitus on fetal cardiac morphology and function: cohort comparison of second- and third-trimester fetuses

OBJECTIVES

To assess differences in cardiac morphology and function in fetuses of mothers with gestational diabetes mellitus (GDM) compared to controls, and to assess whether, in women with GDM, fetal cardiac changes are accentuated with advancing gestational age.

METHODS

We studied 112 women with GDM and 224 women with uncomplicated pregnancy at 24-40 weeks' gestation. In all fetuses, a standard four-chamber oblique view was obtained and offline speckle-tracking analysis was performed to measure right and left endocardial global longitudinal strain (GLS) and tricuspid and mitral annular plane systolic excursion. Global sphericity index was also calculated. Echocardiographic parameters were compared between GDM fetuses and controls at two gestational time periods of 24 + 0 to 32 + 0 weeks and 32 + 1 to 40 + 1 weeks.

RESULTS

At 24 + 0 to 32 + 0 weeks, we phenotyped 43 fetuses from mothers with GDM and 71 from uncomplicated pregnancies, and, at 32 + 1 to 40 + 1 weeks, we phenotyped 69 fetuses from mothers with GDM and 153 from women with uncomplicated pregnancy. In fetuses of mothers with GDM, compared to controls, right ventricular functional indices were consistently lower both at 24 + 0 to 32 + 0 weeks and at 32 + 1 to 40 + 1 weeks. Right ventricular GLS was reduced in the GDM group at 24 + 0 to 32 + 0 weeks (adjusted mean difference, 0.7%; 95% CI, 0.3-1.1%) and at 32 + 1 to 40 + 1 weeks (adjusted mean difference, 0.9%; 95% CI, 0.6-1.1%). Fetal left ventricular global longitudinal function was similar in GDM pregnancies compared with controls, with the exception of the contractility of the left ventricular basal segment, which was reduced. Global sphericity index was reduced in GDM pregnancies only at 32 + 1 to 40 + 1 weeks (adjusted mean difference, -0.4; 95% CI, -0.7 to 0.1).

CONCLUSIONS

The offspring of women with GDM are at high risk for development of cardiovascular disease in childhood and early adulthood. Our study demonstrates that GDM is associated with a reduction mainly in fetal right ventricular function, compared to controls, and this response is not exaggerated with increasing gestational age. Further studies are needed to determine whether fetuses with the observed alterations in cardiac function are those at highest risk for subsequent development of cardiovascular disease. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.

Multi-resource fair queueing for packet processing

Middleboxes are ubiquitous in today's networks and perform a variety of important functions, including IDS, VPN, firewalling, and WAN optimization. These functions differ vastly in their requirements for hardware resources ( e.g. , CPU cycles and memory bandwidth). Thus, depending on the functions they go through, different flows can consume different amounts of a middlebox's resources. While there is much literature on weighted fair sharing of link bandwidth to isolate flows, it is unclear how to schedule multiple resources in a middlebox to achieve similar guarantees. In this paper, we analyze several natural packet scheduling algorithms for multiple resources and show that they have undesirable properties. We propose a new algorithm, Dominant Resource Fair Queuing (DRFQ), that retains the attractive properties that fair sharing provides for one resource. In doing so, we generalize the concept of virtual time in classical fair queuing to multi-resource settings. The resulting algorithm is also applicable in other contexts where several resources need to be multiplexed in the time domain.

Rod-cone differences in response to retinal ischemia in rabbit

Two series of experiments are reported on incremental increases of ischemia and monitoring of recovery from total ischemia of varying duration. In the first, rods show hyper-responses and cones do not; changes in amplitude and delays appear at higher levels of ischemia in cones than they do in rods. In the second series, cones do not recover up to control values with total ischemias of 30 min or more, while rods do recover and even show hyper-responses. Cones appear more resistant than rods to ischemia, but once affected do not recover as well as rods. Discussion proposes that these differences are specific to receptor systems of each rather than secondary to vascularization patterns.

Postoperative whole lung irradiation with or without adriamycin in osteogenic sarcoma

Thirty-six patients with histologically proven osteogenic sarcoma of the extremities, treated between September 1975 and April 1978, are the subject of this report. The primary tumor was treated with radical surgery. Patients received 2000 cGy whole lung irradiation postoperatively in an attempt to control micrometastases to the lung. Twenty-nine of the patients were given Adriamycin (60 mg/m2 IV every 6 weeks for a total dose of 550 mg/m2) in addition to the irradiation. The median, disease-free interval was 118 days for the seven patients treated with lung irradiation only. The median overall survival for these patients is 241 days, with one patient alive with disease. All patients developed lung metastasis. For the 29 patients treated with postoperative lung irradiation and Adriamycin, the median disease-free interval was 372 days, and the median overall survival is 843 days. Nineteen of the patients recurred (65.5%). The differences are statistically significant (p less than or equal to 0.003, median disease-free survival and p less than or equal to 0.03, median survival). This study supports the role of whole lung irradiation plus Adriamycin, in the control of micrometastases in osteogenic sarcoma of the extremities and suggests that additional clinical trials are warranted.

Effects of dextromethorphan on ischemia induced electroretinogram changes in rabbit

The present study was undertaken to determine whether dextromethorphan (DM), a potent N-methyl-D-aspartate antagonist, could attenuate the effects of ischemia on rabbit ERG. Retinal ischemia was induced by increasing intraocular pressure to 120 mm Hg for 30, 60, or 90 min. DM was intravenously administered before ischemia and maintained throughout the entire experimental period. ERGs were recorded prior to, during, and after ischemia. The results indicate that the b-wave hyperresponses and the delays in implicit times induced by 30 min. ischemia were suppressed by the administration of DM. Similar findings were obtained when ischemia lasted for 60 min, except that DM did not improve delayed implicit times, suggesting that cellular injury is still present. ERG changes resulting from 90 min ischemia were not reversed by DM treatment. Effects of DM treatment on a-wave were less prominent. Together, our results further support that DM can to some extent alleviate ischemic injury in the rabbit retina.

Plasmodium vivax malaria in a Romanian traveller returning from Greece, August 2011

In August 2011, a Plasmodium vivax malaria infection was diagnosed in a Romanian traveller returning from Greece. This case together with several reports over the past decade of autochthonous cases in Greece highlight that malaria should be considered as differential diagnosis in symptomatic travellers returning from this country. Travellers may serve as sentinels of emerging vector-borne diseases.

Radiotherapy in the management of locally advanced breast cancer

A retrospective study of 484 patients with locally advanced cancer of the breast treated with irradiation alone revealed a partial or complete response in 64% of the patients, with a mean duration of 13 months. The 5-year survival was 21.9% for the entire group of patients; 32% for patients responding, and 5% for non-responding patients. The data suggests that the size of the tumor and the age of the patients influence the quality of response. The results indicate that radiotherapy adequately controls local disease in a significant number of patients but systemic treatment is needed for better disease control.

Long-term follow-up of radiation accident patients in Peru: review of two cases

Overexposure to radioactive sources used in radiotherapy or industrial radiography may result in severe health consequences. This report assesses the initial clinical status and the medical and psychological long-term follow-up of two radiation accident patients from Peru during the mid-to-late 1990s: one patient exposed to a radiotherapy (60)Co source in Arequipa, the other patient to a (192)Ir source in Yanango. Commonalities and differences are described. The main causes in both accidents were human error and the failure to apply appropriate safety guidelines and standard operating procedures. Education and training of the personnel working with radiation sources are essential to prevent accidents. The experience gained from the medical management of the two patients is valuable for future treatment of such patients.

Optimally designing games for behavioural research

Computer games can be motivating and engaging experiences that facilitate learning, leading to their increasing use in education and behavioural experiments. For these applications, it is often important to make inferences about the knowledge and cognitive processes of players based on their behaviour. However, designing games that provide useful behavioural data are a difficult task that typically requires significant trial and error. We address this issue by creating a new formal framework that extends optimal experiment design, used in statistics, to apply to game design. In this framework, we use Markov decision processes to model players' actions within a game, and then make inferences about the parameters of a cognitive model from these actions. Using a variety of concept learning games, we show that in practice, this method can predict which games will result in better estimates of the parameters of interest. The best games require only half as many players to attain the same level of precision.

Dextromethorphan attenuates the effects of ischemia on rabbit electroretinographic oscillatory potentials

Dextromethorphan has been shown to protect against ischemic tissue damage. We investigated the effects of dextromethorphan on electroretinographic oscillatory potentials in retinal ischemia. Retinal ischemia was induced in rabbits by increasing intraocular pressure to 120 mm Hg for 30, 60 or 90 minutes. Dextromethorphan was intravenously administered before ischemia and maintained throughout the whole period of experiments. Oscillatory potentials were recorded before and during ischemia as well as 4 hours of recirculation after ischemia. As expected, all oscillatory potentials were decreased after 60 and 90 minutes of ischemia. However, after 30 minutes of ischemia followed by 4 hours of recirculation, amplitudes of P2 were elevated whereas those of P3 and P4 were decreased with normal P1 amplitudes. Dextromethorphan administration diminished the effects of 30 minutes of ischemia on oscillatory potentials and partially attenuated the effects of 60 minutes of ischemia, whereas the effects of 90 minutes of ischemia could not be reversed by dextromethorphan treatment. These results indicate that electroretinographic oscillatory potentials could be useful indicators to evaluate retinal function in the ischemic condition and that dextromethorphan can attenuate the effects of relatively short periods of ischemia on rabbit electroretinographic oscillatory potentials.

Effects of calcitonin gene-related peptide on the rabbit electroretinogram

In order to better understand the role of Calcitonin gene-related peptide (CGRP) in mammalian retina, the dose related effects of human CGRP (hCGRP) on rabbit electroretinogram (ERG) were examined in the present study. CGRP was administered intraocularly in doses of 0.1, 1.0 and 10.0 micrograms. ERG A- and B-wave as well as oscillatory potentials (P1, P2, P3 and P4) were recorded. The highest dose of CGRP (10.0 micrograms) significantly increased the amplitudes of the A-wave and OP components (P1, P2, P3 and P4) produced by relatively high stimulus intensity. The same dose of the peptide also enhanced B-wave amplitude at all intensities studied. The effects of the intermediate dose of CGRP (1.0 microgram) on the B-wave amplitudes were dependent on stimulus intensities. B-wave amplitudes at high stimulus intensities were not affected by 1.0 microgram of CGRP but were significantly increased with relatively lower stimulus intensities. The amplitudes of P3, one of OP components, were significantly increased. However, amplitudes of A-wave and other OP components (P1, P2 and P4) were not affected by 1.0 microgram CGRP. The lowest dose of the peptide (0.1 microgram) did not affect any amplitudes of ERG components. Implicit times of A-wave, B-wave and OP components were not significantly affected by the different doses of CGRP. Taken together, these results indicate that CGRP may play a functional role in modulating retinal responses to photic stimulation.

Pattern and flash electroretinogram following increased intraocular pressure in pigeons

We have observed an increase in time to peak and a decrease in amplitude for both the pattern electroretinogram (PERG) and the electroretinogram (ERG) in pigeons following an elevation in intraocular pressure (IOP). The changes in PERG were highly correlated to the changes in ERG. However, they differed in that significant changes from baseline values occurred at lower levels of IOP for PERG than ERG for the amplitude, and in some cases for the time to peak.

Stressor-induced alterations of the splenic plaque-forming cell response: strain differences and modification by propranolol

The effects of stressor application on the splenic plaque-forming cell (PFC) response was assessed in two strains of mice: the BALB/cByJ strain, which is highly responsive to stressors; and the more hardy DBA/2J strain. Both strains exhibited a peak PFC response 120 h following administration of sheep red blood cells (SRBC; 5 x 106 cells). Stressor exposure reduced the immune response; however, the appearance of such an outcome was dependent upon the time at which the stressor was applied relative to SRBC inoculation. In DBA/2J mice, foot-shock applied either immediately after SRBC inoculation or at the time of the peak immune response (120 h) resulted in suppression of the PFC response. In BALB/cByJ mice, both stressor severities provoked an immunosuppression when applied 120 h after inoculation, but when applied 96 h after immunization only foot-shock reduced the PFC response. At other intervals, the stressors were without effect. Pretreatment with the beta-norepinephrine antagonist propranolol precluded the immunosuppression elicited by a stressor applied 96 h after inoculation, but did not affect the reduction of the PFC response elicited by a stressor applied 120 h after inoculation. It is suggested that several factors may contribute to stressor-provoked alterations of the immune response, and that the contribution of these factors vary over the course of an immune response being mounted.

Selective effects of retinal dopamine depletion on partial ischemia-induced electroretinographic hyperresponses in rabbits

The interaction of retinal dopamine depletion and partial ischemia on the a- and b-wave amplitudes and implicit times of the electroretinogram was examined in adult pigmented rabbits. Seven days after 6-hydroxydopamine treatment, which resulted in a depletion of the amine, partial retinal ischemia was induced by raising the intraocular pressure. As expected, moderate elevation of intraocular pressure produced increases in both a- and b-wave amplitudes. Amplitude hyperresponses were significantly reduced in dopamine-depleted retinas. These reductions were more prominent with relatively lower intensities. However, response delays were not shortened but lengthened by 6-hydroxydopamine pretreatment. Together, these results point to a selective role of dopamine in partial retinal ischemia induced by moderate elevation of intraocular pressure in rabbits.