In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images.

Microscopy is a central method in life sciences. Many popular methods, such as antibody labeling, are used to add physical fluorescent labels to specific cellular constituents. However, these approaches have significant drawbacks, including inconsistency; limitations in the number of simultaneous labels because of spectral overlap; and necessary perturbations of the experiment, such as fixing the cells, to generate the measurement. Here, we show that a computational machine-learning approach, which we call "in silico labeling" (ISL), reliably predicts some fluorescent labels from transmitted-light images of unlabeled fixed or live biological samples. ISL predicts a range of labels, such as those for nuclei, cell type (e.g., neural), and cell state (e.g., cell death). Because prediction happens in silico, the method is consistent, is not limited by spectral overlap, and does not disturb the experiment. ISL generates biological measurements that would otherwise be problematic or impossible to acquire.

From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology.

Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.

Short QT intervals in African lions.

The cardiac conduction system in large carnivores, such as the African lion (Panthera leo), represents a significant knowledge gap in both veterinary science and in cardiac electrophysiology. Short QT intervals have been reported from zoo-kept, anaesthetized lions, and our goal was to record the first ECGs from wild, conscious lions roaming freely, and compare them to zoo-kept lions under the hypothesis that short QT is unique to zoo-kept lions. Macroscopic and histological examinations were performed on heart tissue removed from nine healthy zoo lions. ECGs were recorded from the nine anaesthetized zoo-kept lions, and from 15 anaesthetized and conscious wild lions in Africa. Our histological and topographical description of the lion's heart matched what has previously been published. In conscious lions, the ECG recordings revealed a mean heart rate of 70 ± 4 beats/min, with faster heart rates during the night. PQ and QT intervals were heart rate dependent in the conscious lions. Interestingly, QT intervals recorded in wild lions were markedly longer than QT intervals from zoo lions (398 ± 40 vs. 297 ± 9 ms, respectively; P < 0.0001). Anaesthesia or heart rate did not account for this difference. We provide a comprehensive description of the cardiac anatomy and electrophysiology of wild and zoo-kept lions. QT intervals were significantly shorter in zoo lions, suggesting functional disparities in cardiac electrophysiology between wild and zoo-kept lions, potentially related to physical fitness. These findings underscore the plasticity of cardiac electrophysiology and may be of value when reintroducing endangered species into the wild and when managing lions in human care.

Effects of non-digestible carbohydrates on gut microbiota and microbial metabolites: a randomised, controlled dietary intervention in healthy individuals.

The gut microbiome is impacted by certain types of dietary fibre. However, the type, duration, and dose needed to elicit gut microbial changes, and whether these changes also influence microbial metabolites, remains unclear. This study investigated the effects of supplementing healthy participants with two types of non-digestible carbohydrates (resistant starch (RS) and polydextrose (PD)), on the stool microbiota and microbial metabolite concentrations in plasma, stool, and urine, as secondary outcomes in the Dietary Intervention Stem Cells and Colorectal Cancer (DISC) Study.The DISC Study was a double-blind, randomised controlled trial that supplemented healthy participants with RS and/or PD or placebo for 50 days in a 2*2 factorial design. DNA was extracted from stool samples collected pre- and post-intervention, and V4 16S rRNA gene sequencing was used to profile the gut microbiota. Metabolite concentrations were measured in stool, plasma, and urine by high-performance liquid chromatography.A total of 58 participants with paired samples available were included. After 50 days, no effects of RS or PD were detected on composition of the gut microbiota diversity (alpha- and beta-diversity), on genus relative abundance, or on metabolite concentrations. However, Drichlet's multinomial mixture clustering-based approach suggests that some participants changed microbial enterotype post-intervention.The gut microbiome and faecal, plasma, and urinary microbial metabolites were stable in response to a 50-day fibre intervention in middle aged adults. Larger and longer studies, including those which explore the effects of specific fibre sub-types, may be required to determine the relationships between fibre intake, the gut microbiome, and host-health.

NITES, a nocturnal bladder score to aid diagnosis during the transition to older age care.

BACKGROUND: As adults transition to older age, bothersome nocturnal lower urinary tract symptoms (LUTS) become common. There is need for a reliable assessment metric to detect and measure specific symptoms. OBJECTIVE: To subject the nocturnal LUTS score for older individuals, Nocturia, Incontinence, Toileting and Enuresis Symptom Score (NITES), to psychometric analysis. MATERIAL AND METHODS: Factor analysis of the metric was conducted with completed questionnaires from 151 older individuals who were either admitted to a tertiary hospital or attending an outpatient continence clinic. Test re-test reliability involved 18 older community dwelling individuals attending a Geriatrician clinic completing the metric at two timepoints separated by at least 1 week. Intra-class correlation coefficients were determined for reliability of each factor and item. RESULTS: The NITES metric was completed by 98 hospitalized older individuals and 53 attending a continence clinic (mean age 83.2 years [SD 7.0]). Factor analysis demonstrated that one item had a floor effect and two items had poor endorsement. After test re-test reliability analysis, a further three items were removed: one due to poor correlation between timepoints and two demonstrating inadequate internal consistency. The final NITES metric is comprised of three factors: Sleep 4-items, Incontinence 4-items, and Personal Bother 2-items. A 4-item short form for symptom screening was extracted from the longer measure. CONCLUSION: The final NITES metric is a 10-item questionnaire with an embedded 4-item short symptom screen. It has utility utilized to detect nocturnal bladder symptoms in both community dwelling and hospitalized older adults.

Characteristics of geriatric rehabilitation inpatients with nocturia: RESORT.

INTRODUCTION: Nocturnal lower urinary tract symptoms (nLUTS) are common in geriatric rehabiliation inpatients but have not been well described. The aim of this study was to compare patient characteristics stratified by self-reported nocturia severity in geriatric rehabilitation inpatients. METHODS: The REStORing health of acutely unwell adulTs (RESORT) is an observational, longitudinal, prospective inception cohort of geriatric rehabilitation inpatients who underwent a Comprehensive Geriatric Assessment (CGA) at admission and discharge. Nocturia was captured by item 7 of the American Urology Association Symptom Score (AUASS) and dichotomised as ≤1 void and >1 void at night as per the International Continence Society definition. Differences in demographic, functional and medical characteristics of the inpatients with and without nocturia >1 were compared. RESULTS: Overall, 641 inpatients completed the nocturia item (mean age 82.6 (SD 7.7) years, 59.9% female). Nocturia occurred > once per night in 57.4%; mean number of episodes was 1.96 (SD 1.38), ranging from 0-5. There was no change in nocturia severity between admission and discharge. Daily urinary incontinence, urinary urgency and comorbid illness were independently associated with multiple nocturia episodes. A history of falls within the last year, difficulty climbing stairs pre-admission, higher faecal incontinence score, impaired quality of life domains, higher levels of anxiety and depression were significantly more common in inpatients with multiple episodes of nocturia compared to no or only one episode of nocturia Conclusion: Bladder symptoms, poor functional status and frailty markers were associated with repeated episodes of nocturia. Targeted intervention may reduce the severity of nocturia, with potential to improve sleep quality, impact therapeutic gains and influence discharge destination.

The Influence of the Extracorporeal Membrane Oxygenation Circuit and Components on Anticoagulation Management: The Pediatric Extracorporeal Membrane Oxygenation Anticoagulation CollaborativE Consensus Conference.

OBJECTIVES: To derive systematic-review informed, modified Delphi consensus regarding the influence of extracorporeal membrane oxygenation (ECMO) circuit components on anticoagulation practices for pediatric ECMO for the Pediatric ECMO Anticoagulation CollaborativE. DATA SOURCES: A structured literature search was performed using PubMed, EMBASE, and Cochrane Library (CENTRAL) databases from January 1988 to May 2021. STUDY SELECTION: Management of ECMO anticoagulation in the setting of different ECMO circuit components. DATA EXTRACTION: Two authors reviewed all citations independently, with a third independent reviewer resolving conflicts. Twenty-nine references were used for data extraction and informed recommendations, evidence-based consensus statements, and good practice statements. Evidence tables were constructed using a standardized data extraction form. DATA SYNTHESIS: Risk of bias was assessed using the Quality in Prognosis Studies tool. The evidence was evaluated using the Grading of Recommendations Assessment, Development and Evaluation system. Forty-eight experts met over 2 years to develop evidence-based recommendations and, when evidence was lacking, expert-based consensus statements or good practice statements for the influence of ECMO circuit and components on anticoagulation management. A web-based modified Delphi process was used to build consensus via the Research And Development/University of California Appropriateness Method. Consensus was defined as greater than 80% agreement. One good practice statement, 2 weak recommendations, and 2 consensus statements are presented. CONCLUSIONS: The incorporation of new component technologies into clinical practice has outpaced clinical investigations of anticoagulation strategies for pediatric ECMO. Future investigations should leverage academic and industrial collaborations, translational platforms, and modern biostatistical methods to improve patient outcomes.

Executive Summary: The Pediatric Extracorporeal Membrane Oxygenation Anticoagulation CollaborativE (PEACE) Consensus Conference.

OBJECTIVES: To present recommendations and consensus statements with supporting literature for the clinical management of neonates and children supported with extracorporeal membrane oxygenation (ECMO) from the Pediatric ECMO Anticoagulation CollaborativE (PEACE) consensus conference. DATA SOURCES: Systematic review was performed using PubMed, Embase, and Cochrane Library (CENTRAL) databases from January 1988 to May 2021, followed by serial meetings of international, interprofessional experts in the management ECMO for critically ill children. STUDY SELECTION: The management of ECMO anticoagulation for critically ill children. DATA EXTRACTION: Within each of eight subgroup, two authors reviewed all citations independently, with a third independent reviewer resolving any conflicts. DATA SYNTHESIS: A systematic review was conducted using MEDLINE, Embase, and Cochrane Library databases, from January 1988 to May 2021. Each panel developed evidence-based and, when evidence was insufficient, expert-based statements for the clinical management of anticoagulation for children supported with ECMO. These statements were reviewed and ratified by 48 PEACE experts. Consensus was obtained using the Research and Development/UCLA Appropriateness Method. Results were summarized using the Grading of Recommendations Assessment, Development, and Evaluation method. We developed 23 recommendations, 52 expert consensus statements, and 16 good practice statements covering the management of ECMO anticoagulation in three broad categories: general care and monitoring; perioperative care; and nonprocedural bleeding or thrombosis. Gaps in knowledge and research priorities were identified, along with three research focused good practice statements. CONCLUSIONS: The 91 statements focused on clinical care will form the basis for standardization and future clinical trials.

Extracorporeal cardiopulmonary resuscitation outcomes for children with out-of-hospital and emergency department cardiac arrest.

OBJECTIVE: Data suggest extracorporeal cardiopulmonary resuscitation (ECPR) improves survival in adult patients with refractory cardiac arrest; however, ECPR outcomes in pediatric patients with out-of-hospital cardiac arrest (OHCA) is lacking. The primary aim of this study was to characterize pediatric patients who experience OHCA or cardiac arrest in the ED (EDCA). The secondary aim was to examine associations of cardiac arrest and location of ECPR cannulation with mortality. METHODS: We performed a retrospective analysis of the Extracorporeal Life Support Organization registry. We included pediatric patients (age > 28 days to <18 years) who received ECPR for refractory OHCA or EDCA between 2010 and 2019. Patient, cardiac arrest, and ECPR cannulation characteristics were summarized. We examined associations of location of cardiac arrest and ECPR cannulation with in-hospital mortality using multivariable logistic regression. RESULTS: We analyzed data from 140 pediatric patients. 66 patients (47%) experienced OHCA and 74 patients (53%) experienced EDCA. Overall survival to hospital discharge was 31% (20% OHCA survival vs. 41% EDCA survival, p = 0.008). In adjusted analyses, OHCA was associated with 3.9 times greater odds of mortality (95% confidence interval [CI] 1.61, 9.81) when compared to compared to EDCA. The location of ECPR cannulation was not associated with mortality (odds ratio 1.8, 95% CI 0.75, 4.3). CONCLUSIONS: The use of ECPR for pediatric patients with refractory OHCA is associated with poor survival compared to patients with EDCA. Location of ECPR cannulation does not appear to be associated with mortality.

Social mindfulness and prosociality vary across the globe.

Humans are social animals, but not everyone will be mindful of others to the same extent. Individual differences have been found, but would social mindfulness also be shaped by one's location in the world? Expecting cross-national differences to exist, we examined if and how social mindfulness differs across countries. At little to no material cost, social mindfulness typically entails small acts of attention or kindness. Even though fairly common, such low-cost cooperation has received little empirical attention. Measuring social mindfulness across 31 samples from industrialized countries and regions (n = 8,354), we found considerable variation. Among selected country-level variables, greater social mindfulness was most strongly associated with countries' better general performance on environmental protection. Together, our findings contribute to the literature on prosociality by targeting the kind of everyday cooperation that is more focused on communicating benevolence than on providing material benefits.

Variable trends in the distribution of Atlantic cod (Gadus morhua) in the Celtic seas.

Despite decades of active fisheries management, many stocks of Atlantic cod in its southern range are in a depleted state and mortality estimates remain high. Recovery of these stocks, as defined by management areas, could be confounded by cod distributions shifting outside of these areas. Here, we assess data from internationally coordinated trawl surveys to investigate the distribution of three cod stocks in the Celtic Seas ecoregion, Irish Sea, Celtic Sea, and West of Scotland, from 1985 to 2021. We mapped cod densities, analyzed trends in mean weighted depth and bottom temperature, and calculated the center of gravity and equivalent area of the stocks. The distribution of the West of Scotland stock shifted north and east, spilling into the North Sea, while the Irish Sea and Celtic Sea stocks shifted west. Each stock showed decreasing trends in equivalent area, but there were no clear trends in the average depth occupied by the fish. There was no apparent relationship between temperature and the distribution of cod, as bottom temperature varied little from 1993 to 2021. Although Irish Sea cod showed a shift into warmer water, this was due to changes in survey distribution. The shift in distribution of the West of Scotland cod stock towards the North Sea whilst impairing local recovery provides further justification for the recent definition of its incorporation into a larger stock unit that includes the northwest of the North Sea. The Irish Sea and Celtic Sea cod stocks are neither shifting northwards, nor into deeper waters, but remained within current boundaries. This suggests that recent temperature conditions did not affect their distribution, but this may change as temperatures increase towards the limit for reproduction.

Morphological profiling of tubercle bacilli identifies drug pathways of action.

Morphological profiling is a method to classify target pathways of antibacterials based on how bacteria respond to treatment through changes to cellular shape and spatial organization. Here we utilized the cell-to-cell variation in morphological features of Mycobacterium tuberculosis bacilli to develop a rapid profiling platform called Morphological Evaluation and Understanding of Stress (MorphEUS). MorphEUS classified 94% of tested drugs correctly into broad categories according to modes of action previously identified in the literature. In the other 6%, MorphEUS pointed to key off-target activities. We observed cell wall damage induced by bedaquiline and moxifloxacin through secondary effects downstream from their main target pathways. We implemented MorphEUS to correctly classify three compounds in a blinded study and identified an off-target effect for one compound that was not readily apparent in previous studies. We anticipate that the ability of MorphEUS to rapidly identify pathways of drug action and the proximal cause of cellular damage in tubercle bacilli will make it applicable to other pathogens and cell types where morphological responses are subtle and heterogeneous.

The effects of preconception and early gestation SARS-CoV-2 infection on pregnancy outcomes and placental pathology.

OBJECTIVE: To evaluate if peri-pregnancy timing of a PCR+ test for SARS-CoV-2 RNA affects pregnancy outcomes and placental pathology. METHODS: This is a retrospective cohort study conducted in a tertiary center. Pregnancy outcomes and placental pathology were compiled for women who tested positive for SARS-CoV-2 RNA from a nasopharyngeal swab assessed by RT-PCR. The population comprised four groups that were PCR+ preconception (T0) or in the 1st (T1), 2nd (T2), or 3rd (T3) trimester of pregnancy. A fifth, control group (TC) tested PCR- for SARS-CoV-2 before delivery. RESULTS: Seventy-one pregnancies were studied. The T0 group exhibited lower gestational ages at delivery, had infants with the lowest birth weights, the highest rate of pregnancy loss before 20 weeks. Features of maternal vascular malperfusion and accelerated villous maturation were prominent findings in the histopathology of placentas from women PCR+ for SARS-CoV-2 RNA, especially in the T0 and the T1 groups. CONCLUSION: Women at highest risk for pregnancy complications are those who test PCR+ for viral RNA preconception or during first trimester of pregnancy.

Improving the Efficacy of ACR TI-RADS Through Deep Learning-Based Descriptor Augmentation.

Thyroid nodules occur in up to 68% of people, 95% of which are benign. Of the 5% of malignant nodules, many would not result in symptoms or death, yet 600,000 FNAs are still performed annually, with a PPV of 5-7% (up to 30%). Artificial intelligence (AI) systems have the capacity to improve diagnostic accuracy and workflow efficiency when integrated into clinical decision pathways. Previous studies have evaluated AI systems against physicians, whereas we aim to compare the benefits of incorporating AI into their final diagnostic decision. This work analyzed the potential for artificial intelligence (AI)-based decision support systems to improve physician accuracy, variability, and efficiency. The decision support system (DSS) assessed was Koios DS, which provides automated sonographic nodule descriptor predictions and a direct cancer risk assessment aligned to ACR TI-RADS. The study was conducted retrospectively between (08/2020) and (10/2020). The set of cases used included 650 patients (21% male, 79% female) of age 53 ± 15. Fifteen physicians assessed each of the cases in the set, both unassisted and aided by the DSS. The order of the reading condition was randomized, and reading blocks were separated by a period of 4 weeks. The system's impact on reader accuracy was measured by comparing the area under the ROC curve (AUC), sensitivity, and specificity of readers with and without the DSS with FNA as ground truth. The impact on reader variability was evaluated using Pearson's correlation coefficient. The impact on efficiency was determined by comparing the average time per read. There was a statistically significant increase in average AUC of 0.083 [0.066, 0.099] and an increase in sensitivity and specificity of 8.4% [5.4%, 11.3%] and 14% [12.5%, 15.5%], respectively, when aided by Koios DS. The average time per case decreased by 23.6% (p = 0.00017), and the observed Pearson's correlation coefficient increased from r = 0.622 to r = 0.876 when aided by Koios DS. These results indicate that providing physicians with automated clinical decision support significantly improved diagnostic accuracy, as measured by AUC, sensitivity, and specificity, and reduced inter-reader variability and interpretation times.

Waitlist and posttransplant outcomes of critically ill infants awaiting heart transplantation managed without ventricular assist device support.

BACKGROUND: Infants listed for heart transplant are at high risk for waitlist mortality. While waitlist mortality for children has decreased in the current era of increased ventricular assist device use, outcomes for small infants supported by ventricular assist device remain suboptimal. We evaluated morbidity and survival in critically ill infants listed for heart transplant and managed without ventricular assist device support. METHODS: Critically ill infants (requiring ≥1 inotrope and mechanical ventilation or ≥2 inotropes without mechanical ventilation) listed between 2008 and 2019 were included. During the study period, infants were managed primarily medically. Mechanical circulatory support, specifically extracorporeal membrane oxygenation, was utilized as "rescue therapy" for decompensating patients. RESULTS: Thirty-two infants were listed 1A, 66% with congenital heart disease. Median age and weight at listing were 2.2 months and 4.4 kg, with 69% weighing <5 kg. At listing, 97% were mechanically ventilated, 41% on ≥2 inotropes, and 25% under neuromuscular blockade. Five patients were supported by ECMO after listing. A favorable outcome (transplant or recovery) was observed in 84%. One-year posttransplant survival was 92%. Infection was the most common waitlist complication occurring in 75%. Stroke was rare, occurring in one patient who was supported on ECMO. Renal function improved from listing to transplant, death, or recovery (eGFR 70 vs 87 ml/min/1.73m2 , p = .001). CONCLUSION: A strategy incorporating a high threshold for mechanical circulatory support and acceptance of prolonged mechanical ventilation and neuromuscular blockade can achieve good survival and morbidity outcomes for critically ill infants listed for heart transplant.

Ex vivo comparison of different thoracoabdominal stapler sizes for typhlectomy in canine cadavers.

OBJECTIVE: To determine the influence of staple size on leakage pressure of typhlectomy sites in canine cadavers. STUDY DESIGN: Randomized, experimental cadaveric study. ANIMALS: Twenty-four fresh canine cadavers. METHODS: Ileocecocolic segments were exteriorized following right paracostal laparotomy after euthanasia. Cecal base length and wall thickness were measured. Each cecum was randomly assigned to 1 of 3 groups (TA 30 V3 2.5 mm, TA 60 3.5 mm, and TA 60 4.8 mm). The cecal base was stapled and the cecum was removed. A 10 cm segment including the stapled cecal excision site was tested for initial leak pressure. RESULTS: The mean ± standard deviation body weights across the groups were 18.7 ± 6.1 kg, 16.2 ± 7.5 kg, and 14.2 ± 5.5 kg for the TA 30 V3 2.5 mm, TA 60 3.5 mm, and TA 60 4.8 mm groups, respectively (P = .48). There were no differences for mean cecal base length or wall thickness. Mean initial leak pressure (ILP) across groups was 182 ± 111 mmHg (TA 30 V3 2.5 mm), 112 ± 57 mmHg (TA 60 3.5 mm), and 77 ± 60 mmHg (TA 60 4.8 mm) (P = .78). CONCLUSION: Each stapler size that was evaluated resulted in a mean ILP in excess of typical intraluminal pressures under normal circumstances. There were no differences among groups. CLINICAL SIGNIFICANCE: The results of this cadaveric study support the use of any of the stapler sizes evaluated in similarly sized dogs. A prospective study is needed to be able to correlate stapler size and clinical outcome.

Histopathology of Third Trimester Placenta from SARS-CoV-2-Positive Women.

Background: This study aims to investigate whether maternal SARS-CoV-2 status affects placental pathology. Methods: A retrospective case-control study was conducted by reviewing charts and slides of placentas delivered between April 1 to July 24, 2020. Clinical history of "COVID-19" was searched in Pathology Database (CoPath). Controls were matched with SARS-CoV-2-negative women with singleton deliveries in the 3rd-trimester. Pathological features were extracted from placental pathology reports. Results: Twenty-one 3rd trimester placentas from SARS-CoV-2-positive women were identified and compared to 20 placentas from SARS-CoV-2-negative women. There were no significant differences in individual or group gross or microscopic pathological features. Within the SARS-CoV-2+ group, there are no differences between symptomatic and asymptomatic women. Conclusion: Placentas from SARS-CoV-2-positive women do not demonstrate a specific pathological pattern. Pregnancy complicated with COVID-19 during the 3rd trimester does not have a demonstrable effect on placental structure and pathology.

Animal lifestyle affects acceptable mass limits for attached tags.

Animal-attached devices have transformed our understanding of vertebrate ecology. To minimize any associated harm, researchers have long advocated that tag masses should not exceed 3% of carrier body mass. However, this ignores tag forces resulting from animal movement. Using data from collar-attached accelerometers on 10 diverse free-ranging terrestrial species from koalas to cheetahs, we detail a tag-based acceleration method to clarify acceptable tag mass limits. We quantify animal athleticism in terms of fractions of animal movement time devoted to different collar-recorded accelerations and convert those accelerations to forces (acceleration × tag mass) to allow derivation of any defined force limits for specified fractions of any animal's active time. Specifying that tags should exert forces that are less than 3% of the gravitational force exerted on the animal's body for 95% of the time led to corrected tag masses that should constitute between 1.6% and 2.98% of carrier mass, depending on athleticism. Strikingly, in four carnivore species encompassing two orders of magnitude in mass (ca 2-200 kg), forces exerted by '3%' tags were equivalent to 4-19% of carrier body mass during moving, with a maximum of 54% in a hunting cheetah. This fundamentally changes how acceptable tag mass limits should be determined by ethics bodies, irrespective of the force and time limits specified.

Batch equalization with a generative adversarial network.

MOTIVATION: Advances in automation and imaging have made it possible to capture a large image dataset that spans multiple experimental batches of data. However, accurate biological comparison across the batches is challenged by batch-to-batch variation (i.e. batch effect) due to uncontrollable experimental noise (e.g. varying stain intensity or cell density). Previous approaches to minimize the batch effect have commonly focused on normalizing the low-dimensional image measurements such as an embedding generated by a neural network. However, normalization of the embedding could suffer from over-correction and alter true biological features (e.g. cell size) due to our limited ability to interpret the effect of the normalization on the embedding space. Although techniques like flat-field correction can be applied to normalize the image values directly, they are limited transformations that handle only simple artifacts due to batch effect. RESULTS: We present a neural network-based batch equalization method that can transfer images from one batch to another while preserving the biological phenotype. The equalization method is trained as a generative adversarial network (GAN), using the StarGAN architecture that has shown considerable ability in style transfer. After incorporating new objectives that disentangle batch effect from biological features, we show that the equalized images have less batch information and preserve the biological information. We also demonstrate that the same model training parameters can generalize to two dramatically different types of cells, indicating this approach could be broadly applicable. AVAILABILITY AND IMPLEMENTATION: https://github.com/tensorflow/gan/tree/master/tensorflow_gan/examples/stargan. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Learning from incidents in medically assisted reproduction: the Notify Library as a learning tool.

Biovigilance is the systematic monitoring of serious adverse reactions and events (SARE) that ensures the quality and safety of tissues and cells for human application in medically assisted reproduction (MAR). The Notify Library is an open access database launched by the World Health Organization and supported by the Italian National Transplant Centre (CNT) that has collected information on documented adverse occurrences in transplantation, transfusion and MAR. It is not a SARE register, but rather a collection of SARE types identified primarily by review of published articles and case reports from national or regional vigilance programmes. The Notify Library includes many well-documented records of adverse occurrences in MAR treatment, representing a useful tool for MAR operators in the evaluation of the risks associated with the clinical application of reproductive tissues and cells. It is updated with new records when a new type of incident is reported for the first time. All incident types described might have teaching value during the risk management carried out by a MAR centre. Sharing lessons learned from these incidents represents an important didactic opportunity that can help MAR centres to improve their processes and to achieve higher standards of quality and safety.