Unsupervised Activity Segmentation by Joint Representation Learning and Online Clustering

We present a novel approach for unsupervised activity segmentation, which uses video frame clustering as a pretext task and simultaneously performs representation learning and online clustering. This is in contrast with prior works where representation learning and clustering are often performed sequentially. We leverage temporal information in videos by employing temporal optimal transport. In particular, we incorporate a temporal regularization term which preserves the temporal order of the activity into the standard optimal transport module for computing pseudo-label cluster assignments. The temporal optimal transport module enables our approach to learn effective representations for unsupervised activity segmentation. Furthermore, previous methods require storing learned features for the entire dataset before clustering them in an offline manner, whereas our approach processes one mini-batch at a time in an online manner. Extensive evaluations on three public datasets, i.e. 50-Salads, YouTube Instructions, and Breakfast, and our dataset, i.e., Desktop Assembly, show that our approach performs on par or better than previous methods for unsupervised activity segmentation, despite having significantly less memory constraints.Comment: Preprint. Under revie

In vitro effect of seed bio-priming techniques on seed germination and seedling vigour of few vegetable crops

Bio-priming can also be viewed as a new technique of seed treatment using biological agents to stimulate germination of seed and growth of the plant and further protecting the seed from soil-and seed-borne pathogens. The present investigation was carried out in vitro conditions on seed germination and seedling vigour of few vegetable crops viz.  tomato (Solanum lycopersicum L.), brinjal (Solanum melongena L.), onion (Allium cepa L.) and chilli (Capsicum annuum L.), during 2015 and 2016. The treatments comprised viz. T1: Non primed seeds (Control), T2: Seed treatment with Carbendazim 2.5g/kg seed, T3: Hydro-priming for 6 hrs, T4: Hydro-priming for 12 hrs, T5: Hydro-priming for 18 hrs, T6: Biopriming with Trichoderma  viride for 6 hrs, T7: Biopriming with T.viride for 12 hrs, T8: Biopriming with T.viride for 18 hrs, T9: Biopriming with Trichoderma harzianum for 6 hrs, T10: Biopriming with T. harzianum for  12 hrs, T11: Biopriming with T. harzianum for 18 hrs, T12: Biopriming with Pseudomonas fluorescens for 6 hrs, T13: Biopriming with P. fluorescens for 12 hrs and T14: Biopriming with P. fluorescens for 18 hrs.  The results revealed that maxiumum germination percentage (92.92, 90.77,83.00 and 86.33), seedling length (32.38 cm, 29.35 cm, 31.75 and 31.60 cm), seedling fresh weight (2.07 g, 4.01 g, 3.05 g and 2.04 g),  seedling dry weight (0.42 g, 0.86 g, 0.62 g and 0.42 g) and seedling vigour index (3008.11, 2664.00, 2635.00 and 2728.00) were recorded in T10 (bio priming with T. harzianum for 12 hrs) in tomato (S. lycopersicum L.), brinjal (S. melongena L.), onion (A. cepa L.) and chilli (C. annuum L.), respectively. Thus, it indicated that priming of seeds of these crops with T. harzianum/P. fluorescens/ T. viride  for 12 hrs was very effective with respect to their vegetative growth along with the quality yield

Higher or Lower Hemoglobin Transfusion Thresholds for Preterm Infants

Background: Limited data suggest that higher hemoglobin thresholds for red-cell transfusions may reduce the risk of cognitive delay among extremely-low-birth-weight infants with anemia. Methods: We performed an open, multicenter trial in which infants with a birth weight of 1000 g or less and a gestational age between 22 weeks 0 days and 28 weeks 6 days were randomly assigned within 48 hours after delivery to receive red-cell transfusions at higher or lower hemoglobin thresholds until 36 weeks of postmenstrual age or discharge, whichever occurred first. The primary outcome was a composite of death or neurodevelopmental impairment (cognitive delay, cerebral palsy, or hearing or vision loss) at 22 to 26 months of age, corrected for prematurity. Results: A total of 1824 infants (mean birth weight, 756 g; mean gestational age, 25.9 weeks) underwent randomization. There was a between-group difference of 1.9 g per deciliter (19 g per liter) in the pretransfusion mean hemoglobin levels throughout the treatment period. Primary outcome data were available for 1692 infants (92.8%). Of 845 infants in the higher-threshold group, 423 (50.1%) died or survived with neurodevelopmental impairment, as compared with 422 of 847 infants (49.8%) in the lower-threshold group (relative risk adjusted for birth-weight stratum and center, 1.00; 95% confidence interval [CI], 0.92 to 1.10; P = 0.93). At 2 years, the higher- and lower-threshold groups had similar incidences of death (16.2% and 15.0%, respectively) and neurodevelopmental impairment (39.6% and 40.3%, respectively). At discharge from the hospital, the incidences of survival without severe complications were 28.5% and 30.9%, respectively. Serious adverse events occurred in 22.7% and 21.7%, respectively. Conclusions: In extremely-low-birth-weight infants, a higher hemoglobin threshold for red-cell transfusion did not improve survival without neurodevelopmental impairment at 22 to 26 months of age, corrected for prematurity

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

Microbiology and the microbiome in bronchiectasis

The microbiology in bronchiectasis has been historically defined by culture-based analysis of the airway microbiome and to date has largely focused on the detection and eradication of specific bacterial pathogens. Although central to our current understanding of disease, microbial culture alone masks the holistic complexity of the microbiome and does not account for potential microbial interactions that define specific clinical phenotypes such as frequent exacerbators. Advances in next-generation sequencing including their analytical technologies can further complement and build upon our current understanding of the microbiology and microbiome in bronchiectasis providing improved patient stratification with prognostic significance.Ministry of Health (MOH)National Medical Research Council (NMRC)This research is funded by Singapore Ministry of Health’s National Medical Research Council under its Clinician-Scientist Individual Research Grant (MOH-000141) (S.H.C.) and Clinician Scientist Award (MOH-000710) (S.H.C.). S.H.C is on advisory boards for CSL Behring and Boehringer Ingelheim and has received personal fees from AZ, all outside of the submitted work. M.M.A

Aging and the microbiome: implications for asthma in the elderly?

In the elderly, asthma remains a clinical challenge. Recognition, diagnosis and treatment are all complex. Influenced by processes, such as aging, the identification of an ‘asthma microbiome’ presents a further challenge. This editorial discusses aging and the ‘asthma microbiome’ separately and then evaluates their potential relationship. Current evidence suggests that differences in the airway microbiome are associated with asthma, however, whether such associations are comparable or different for late-onset disease is yet to be established. Microbes are now linked to fundamental physiological processes, such as aging, based on data from invertebrate systems. This will likely confer implications for asthma in the elderly, and it is crucial that such emerging scientific data are considered in the context of aging, asthma and late-onset disease.Accepted versio

Aspergillus Species in Bronchiectasis: Challenges in the Cystic Fibrosis and Non-cystic Fibrosis Airways

Bronchiectasis is a chronic irreversible airway abnormality associated with infectious agents that either cause or superinfect the airways. While the role of bacteria is well studied, much remains to be determined about fungi in both cystic fibrosis- and non-cystic fibrosis-related bronchiectasis. The airway is constantly exposed to inhaled ambient moulds of which Aspergillus represent the most ubiquitous. In a normal healthy host, this situation is of little consequence. The presence of anatomical or immunological abnormalities such as those in bronchiectasis leads to a range of fungal-related pathologies from asymptomatic airway colonization to fungal sensitization, allergic bronchopulmonary aspergillosis or chronic pulmonary aspergillosis. These entities are difficult to recognize, diagnose and treat due in part to a lack of validated biomarkers. Our true understanding of the complex relationships that regulate fungal-host interactions is still in its infancy and, several questions remain. This includes if fungal epidemiology in bronchiectasis is uniform across countries, and to what extent immunopathological mechanisms-related to fungal airway infections-occurs in different disease states. Specific triggers to allergic or infectious responses to Aspergillus require further exploration. How transition occurs between allergic and invasive phenotypes and their respective biomarkers is also important. Whether anti-fungal treatment is warranted in all cases and what the optimal management strategy is, particularly when treatment should commence and its expected duration remains unclear. Further research is clearly necessary and should be prioritized to better understand the clinical effects and impact of Aspergillus in the setting of bronchiectasis.NMRC (Natl Medical Research Council, S’pore)MOH (Min. of Health, S’pore)Accepted versio

The airway microbiome: present and future applications

Accelerated by developments in DNA sequencing technologies, our understanding of the respiratory microbiome is advancing at pace, providing unprecedented opportunities for clinical translation. Building on the early observations of sub-clinical micro-aspiration in healthy individuals, and initial culture independent microbiome studies in respiratory disease, recent work reveals an expansive microbial ecosystem that encompasses bacterial, fungal and viral constituents. This has led to major paradigm shifts including the potential importance of airway microbial networks in chronic respiratory disease states. As a complex organ system, with varying topology and a mucosal surface area exceeding that of the gut, the respiratory tract is recognized as a key site of host-microbe interaction. The airway experiences dynamic and continuous microbial exposures on breathing, shaped by climate and environmental surroundings, and is further influenced by sub clinical micro-aspiration of resident upper-airway microbes. The respiratory microbiome exists as an ecological gradient from upper to lower airway, interacting with host epithelia in balance between immune homeostasis and pathology. Current models posit that a balanced host-microbe interaction establishes in early life with a protective immune response that become dysregulated in respiratory disease. Characterization of microbial aberration as early indicators of deteriorating respiratory health is therefore a fundamental concept underpinning its potential clinical applications. Detecting microbial dysbiosis from otherwise ‘healthy microbiomes’ represents a potential opportunity for personalized phenotyping, stratification and therapeutic intervention. Despite such promise, this relatively nascent field has inherent challenges that need addressing as we seek to translate research gains in our understanding of the airway microbiome into tangible clinical applications for respiratory medicine

Applying next-generation sequencing and multi-omics in chronic obstructive pulmonary disease

Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.Ministry of Health (MOH)National Medical Research Council (NMRC)Published versionThis research is supported by the Singapore Ministry of Health’s National Medical Research Council under its Clinician Scientist Award (MOH-000710) (S.H.C) and the Open Fund-Individual Research Grant (MOH-000955) (S.H.C)