Using neural networks to improve simulations in the gray zone

Machine learning represents a potential method to cope with the gray zone problem of representing motions in dynamical systems on scales comparable to the model resolution. Here we explore the possibility of using a neural network to directly learn the error caused by unresolved scales. We use a modified shallow water model which includes highly nonlinear processes mimicking atmospheric convection. To create the training dataset, we run the model in a high- and a low-resolution setup and compare the difference after one low-resolution time step, starting from the same initial conditions, thereby obtaining an exact target. The neural network is able to learn a large portion of the difference when evaluated on single time step predictions on a validation dataset. When coupled to the low-resolution model, we find large forecast improvements up to 1 d on average. After this, the accumulated error due to the mass conservation violation of the neural network starts to dominate and deteriorates the forecast. This deterioration can effectively be delayed by adding a penalty term to the loss function used to train the ANN to conserve mass in a weak sense. This study reinforces the need to include physical constraints in neural network parameterizations

Recruiting and retaining participants in three randomised controlled trials of psychological interventions conducted on acute psychiatric wards; Top ten tips for success

BACKGROUND: It is essential to conduct randomised controlled trials of psychological interventions on acute psychiatric wards to build a robust evidence base for clinical practice. AIMS: This paper aims to share strategies from three different in-patient trials that successfully recruited and retained participants, to disseminate good practice for the conduct of future trials in this challenging and complex clinical setting. METHOD: We present strategies from three in-patient trials of psychological interventions: TULIPS (Talk, Understand, Listen for Inpatient Settings), amBITION (Brief Talking Therapies on Wards) and INSITE (Inpatient Suicide Intervention and Therapy Evaluation). All studies recruited participants from acute in-patient wards, initiated therapy within the in-patient setting and followed up on participants post-discharge. RESULTS: We summarise our recommendations for good practice in the form of ten top tips for success, based on our collective experience of conducting trials on psychiatric wards. Key themes relate to the importance of relationships between the research team and clinical staff; good stakeholder involvement and getting early buy-in from the team; and adapting to the particular demands of the clinical setting. CONCLUSIONS: Sharing good practice recommendations can help reduce research waste arising from poor recruitment and/or retention in future in-patient clinical trials

Spatio-temporal dynamics of Marbled Murrelet hotspots during nesting in nearshore waters along the Washington to California coast

The Marbled Murrelet, Brachyramphus marmoratus, is a federally listed alcid that forages in nearshore waters of the Pacific Northwest, and nests in adjacent older-forest conifers within 40-80 km of shore. To estimate abundance and distribution of murrelets, we conduct at-sea surveys from May to July each year, starting in 2000 and continuing to present. We record numbers of individuals sighted by using distance-based transects and compute annual estimates of density after adjusting for detectability. At-sea transects are subdivided into 5-km segments, and we summarized mean and variance of density at each segment in Puget Sound and along the coast from the Canadian border South to San Francisco Bay. We used a boosted regression tree analysis to investigate the contributions of marine and terrestrial attributes on murrelet abundance in each segment. We observed that terrestrial attributes, especially the amount and pattern of suitable nesting habitat in proximity to each segment, made the strongest contribution, but that marine attributes also helped explain variation in murrelet abundance. Hotspots of murrelet abundance therefore reflect not only suitable marine foraging habitat but proximity of suitable inland nesting habitat

Toll-like receptor gene variants and bacterial vaginosis among HIV-1 infected and uninfected African women.

Bacterial vaginosis (BV) is a common vaginal syndrome associated with altered microflora that increases the risk of preterm delivery and acquisition of sexually transmitted diseases. The cause of BV is unknown although toll-like receptors (TLRs), that are central to innate immune responses, may be important. We evaluated associations between TLR SNPs and BV among HIV-1 infected and uninfected African women. Logistic regression was used to assess associations between SNPs (N=99) in TLRs 2-4, 7-9 and BV (as classified by Nugent's criteria). Among HIV-1 uninfected women, TLR7 rs5743737 and TLR7 rs1634323 were associated with a decreased risk of BV, whereas TLR7 rs179012 was associated with an increased risk. TLR2 SNP rs3804099 was associated with a decreased risk of BV among HIV-1 infected women. Our findings indicate that there may be differences in TLR association with BV among HIV-1 infected and HIV-1 uninfected women

SpeechNet: Weakly Supervised, End-to-End Speech Recognition at Industrial Scale

End-to-end automatic speech recognition systems represent the state of the art, but they rely on thousands of hours of manually annotated speech for training, as well as heavyweight computation for inference. Of course, this impedes commercialization since most companies lack vast human and computational resources. In this paper, we explore training and deploying an ASR system in the label-scarce, compute-limited setting. To reduce human labor, we use a third-party ASR system as a weak supervision source, supplemented with labeling functions derived from implicit user feedback. To accelerate inference, we propose to route production-time queries across a pool of CUDA graphs of varying input lengths, the distribution of which best matches the traffic's. Compared to our third-party ASR, we achieve a relative improvement in word-error rate of 8% and a speedup of 600%. Our system, called SpeechNet, currently serves 12 million queries per day on our voice-enabled smart television. To our knowledge, this is the first time a large-scale, Wav2vec-based deployment has been described in the academic literature.Comment: Accepted to EMNLP 2022 Industry Track; 9 pages, 7 figure

An accurate, nontraumatic ultrasonic method to monitor myocardial wall thickening in patients undergoing cardiac surgery

AbstractMeasurement of systolic wall thickening by sonomicrometry provides an accurate index of regional left ventricular function, but the trauma of crystal insertion limits its widespread clinical use. The first clinical application of a 10 MHz ultrasonic Doppler probe that can be either sutured or applied by suction to the epicardium and can measure wall thickening at any depth of the left ventricular wall is described. In 18 dogs, measurements obtained with the suction probe correlated well (r = 0.97) with those of a previously validated sutured probe.To assess clinical feasibility, the probe was applied to the epicardium of patients undergoing coronary bypass surgery. Good quality wall thickening signals were obtained with no complications. Transmural left ventricular thickening fraction before bypass surgery was 34 ± 3% (mean value ± SE) at the mid-ventricular lateral wall, 33 ± 4% at the anterior basal wall and 26 ± 4% at the mid-ventricular posterior wall. Right ventricular thickening fraction averaged 25 ± 3%. Endocardial thickening fraction tended to exceed epicardial thickening fraction, although the difference attained statistical significance (p < 0.05) only at the anterior basal wall.On average, thickening fraction during the immediate postoperative period remained unchanged compared with the preoperutive values, but a marked individual variability was observed, with 7 of 15 patients exhibiting a decrease and 8 an increase. Exteriorization of the wires attached to the sutured probe allowed continuous in situ monitoring of wall thickening in the postoperative period and subsequent removal of the probe, in six patients the crystal was left in place for 48 to 72 h after surgery and then removed without complications; good wall thickening signals were obtained for the entire period during which the probe was implanted.Thus, the Doppler probe is an accurate, atraumatic method for measuring right and left ventricular regional function. Transmural, endocardial and epicardial function can be mapped at various sites during surgery, and postoperatively one can monitor serial changes of regional function and assess the effects of cardioplegia and other therapeutic interventions. This technique should be useful for both investigative and clinical purposes

Empowering HIV-infected women in lowresource settings: A pilot study evaluating a patient-centered HIV prevention strategy for reproduction in Kisumu, Kenya

Background: Female positive/male negative HIV-serodiscordant couples express a desire for children and may engage in condomless sex to become pregnant. Current guidelines recommend antiretroviral treatment in HIV-serodiscordant couples, yet HIV RNA viral suppression may not be routinely assessed or guaranteed and pre-exposure prophylaxis may not be readily available. Therefore, options for becoming pregnant while limiting HIV transmission should be offered and accessible to HIV-affected couples desiring children. Methods: A prospective pilot study of female positive/male negative HIV-serodiscordant couples desiring children was conducted to evaluate the acceptability, feasibility, and effectiveness of timed vaginal insemination. Eligible women were 18-34 years with regular menses. Prior to timed vaginal insemination, couples were observed for two months, and tested and treated for sexually transmitted infections. Timed vaginal insemination was performed for up to six menstrual cycles. A fertility evaluation and HIV RNA viral load assessment was offered to couples who did not become pregnant. Findings: Forty female positive/male negative HIV-serodiscordant couples were enrolled; 17 (42.5%) exited prior to timed vaginal insemination. Twenty-three couples (57.5%) were introduced to timed vaginal insemination; eight (34.8%) achieved pregnancy, and six live births resulted without a case of HIV transmission. Seven couples completed a fertility evaluation. Four women had no demonstrable tubal patency bilaterally; one male partner had decreased sperm motility. Five women had unilateral/bilateral tubal patency; and seven women had an HIV RNA viral load (≥ 400 copies/mL). Conclusion: Timed vaginal insemination is an acceptable, feasible, and effective method for attempting pregnancy. Given the desire for children and inadequate viral suppression, interventions to support safely becoming pregnant should be integrated into HIV prevention programs

Multi-proxy summer and winter precipitation reconstruction for southern Africa over the last 200 years

This study presents the first consolidation of palaeoclimate proxy records from multiple archives to develop statistical rainfall reconstructions for southern Africa covering the last two centuries. State-of-the-art ensemble reconstructions reveal multi-decadal rainfall variability in the summer and winter rainfall zones. A decrease in precipitation amount over time is identified in the summer rainfall zone. No significant change in precipitation amount occurred in the winter rainfall zone, but rainfall variability has increased over time. Generally synchronous rainfall fluctuations between the two zones are identified on decadal scales, with common wet (dry) periods reconstructed around 1890 (1930). A strong relationship between seasonal rainfall and sea surface temperatures (SSTs) in the surrounding oceans is confirmed. Coherence among decadal-scale fluctuations of southern African rainfall, regional SST, SSTs in the Pacific Ocean and rainfall in south-eastern Australia suggest SST-rainfall teleconnections across the southern hemisphere. Temporal breakdowns of the SST-rainfall relationship in the southern African regions and the connection between the two rainfall zones are observed, for example during the 1950s. Our results confirm the complex interplay between large-scale teleconnections, regional SSTs and local effects in modulating multi-decadal southern African rainfall variability over long timescales

Evidence for supporting cell mitosis in response to acoustic trauma in the avian inner ear

Acoustic overstimulation can lead to sensory cell (hair cell) loss in the auditory epithelium. Damaged hair cells in the organ of Corti (the mammalian auditory end-organ) degenerate and are replaced by non-sensory cells (supporting cells) which construct an irreversible scar. In birds, however, auditory hair cells which are damaged by acoustic trauma or ototoxic drugs may be replaced by new hair cells. As first step in determining the mechanism of hair cell regeneration, we developed an assay for cell divisions in the auditory epithelium after acoustic trauma. The results of these experiments demonstrate that supporting cells in damaged regions of the auditory epithelium incorporate the DNA-specific marker bromodeoxyuridine as early as one day after noise exposure. We provide direct evidence that following acoustic insult to the avian inner ear, supporting cells which reside within the sensory epithelium divide near the luminal surface and repopulate the epithelium. These results suggest that supporting cells participate in scar formation during hair cell degeneration, and produce new cells for regeneration.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47429/1/11068_2005_Article_BF01191727.pd