Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerating Species Recognition and Labelling of Fish From Underwater Video With Machine-Assisted Deep Learning

Machine-assisted object detection and classification of fish species from Baited Remote Underwater Video Station (BRUVS) surveys using deep learning algorithms presents an opportunity for optimising analysis time and rapid reporting of marine ecosystem statuses. Training object detection algorithms for BRUVS analysis presents significant challenges: the model requires training datasets with bounding boxes already applied identifying the location of all fish individuals in a scene, and it requires training datasets identifying species with labels. In both cases, substantial volumes of data are required and this is currently a manual, labour-intensive process, resulting in a paucity of the labelled data currently required for training object detection models for species detection. Here, we present a “machine-assisted” approach for i) a generalised model to automate the application of bounding boxes to any underwater environment containing fish and ii) fish detection and classification to species identification level, up to 12 target species. A catch-all “fish” classification is applied to fish individuals that remain unidentified due to a lack of available training and validation data. Machine-assisted bounding box annotation was shown to detect and label fish on out-of-sample datasets with a recall between 0.70 and 0.89 and automated labelling of 12 targeted species with an F1 score of 0.79. On average, 12% of fish were given a bounding box with species labels and 88% of fish were located and given a fish label and identified for manual labelling. Taking a combined, machine-assisted approach presents a significant advancement towards the applied use of deep learning for fish species detection in fish analysis and workflows and has potential for future fish ecologist uptake if integrated into video analysis software. Manual labelling and classification effort is still required, and a community effort to address the limitation presented by a severe paucity of training data would improve automation accuracy and encourage increased uptake.
Stability of crop pollinator occurrence is influenced by bee community composition

Bees provide a vital ecosystem service to agriculture by contributing to the pollination of many leading global crops. Human wellbeing depends not only on the quantity of agricultural yields, but also on the stability and resilience of crop production. Yet a broad understanding of how the diversity and composition of pollinator communities may influence crop pollination service has previously been hindered by a scarcity of standardized data. We used outputs from Bayesian occupancy detection models to examine patterns in the inter-annual occupancy dynamics of the bee pollinator communities of four contrasting crops (apples, field bean, oilseed and strawberries) in Great Britain between 1985 and 2015. We compared how the composition and species richness of different crop pollinator communities may affect the stability of crop pollinator occurrence. Across the four crops, we found that the inter-annual occupancy dynamics of the associated pollinator communities tended to be more similar in smaller communities with closely related pollinator species. Our results indicate that crop pollinator communities composed of a small number of closely related bee species show greater variance in mean occupancy compared to crops with more diverse pollinator communities. Lower variance in the occurrence of crop pollinating bee species may lead to more stable crop pollination services. Finally, whilst our results initially indicated some redundancy within most crop pollinator communities, with no, or little, increase in the variance of overall mean occupancy when species were initially removed, this was followed by a rapid acceleration in the variance of crop pollinator occurrence as each crop's bee pollinator community was increasingly depreciated. High inter-annual variations in pollination services have negative implications for crop production and food security. High bee diversity could ensure more stable and resilient crop pollination services, yet current agri-environment schemes predominantly benefit a limited suite of common species. Management may therefore benefit from targeting a wider diversity of solitary species in order to safeguard crop pollination service in the face of increasing environmental change.
Grand Challenges in Imaging Applications

It is my honor to be the inaugural Specialty Chief Editor of Imaging Applications, one of the sections of the new journal Frontiers in Image Processing. This section features original research work, tutorial and review articles and welcomes submissions from academic and industry researchers that seek to develop new applications of image and video processing. Topics of interest covered by this section include, but are not limited to:
Neoadjuvant Anlotinib and chemotherapy followed by minimally invasive esophagectomy in patients with locally advanced esophageal squamous cell carcinoma: Short-term results of an open-label, randomized, phase II trial

Background Clinical benefits of neoadjuvant Anlotinib for locally advanced esophageal squamous cell carcinoma (ESCC) remains unclear. This study evaluated the efficacy and safety of neoadjuvant Anlotinib plus chemotherapy followed by minimally invasive esophagectomy (MIE) for the treatment of patients with locally advanced ESCC. Methods Patients with locally advanced ESCC were randomly assigned to neoadjuvant Anlotinib combined with chemotherapy (Anlotinib group) or neoadjuvant chemoradiotherapy alone (nCRT group) with an allocation ratio of 1:1. The primary endpoint was the R0 surgical resection rate. Secondary endpoints included postoperative pathologic stage, complete response (CR) rate, and safety. Safety was assessed by adverse events (AEs) and postoperative complications. Results From August 2019 to August 2021, 93 patients were assigned to the nCRT or Anlotinib group. Of the 93 patients, 79 underwent MIE and were finally included in the per-protocol set (nCRT group: n=39; Anlotinib group: n=40). The R0 resection rate was 97.4% for nCRT versus 100.0% for Anlotinib group (p>0.05). Compared with the nCRT group, patients in the Anlotinib group had shorter total operation duration (262.2 ± 39.0 vs. 200.7 ± 25.5 min, p=0.010) and less blood loss (161.3 ± 126.7 vs. 52.4 ± 39.3 mL, p<0.001). No significant differences were found in the postoperative pathologic stage between the Anlotinib group and nCRT group (all p>0.05). Besides, the incidences of AEs (80.0% vs. 92.3%) and postoperative complications (22.5% vs. 30.8%) were similar between the two groups (all p>0.05). Conclusions Neoadjuvant Anlotinib plus chemotherapy had a similar safety profile and pathologic response, but better surgical outcomes than nCRT for locally advanced ESCC.
A New Definition for Intracranial Compliance to Evaluate Adult Hydrocephalus After Shunting

The clinical application of intracranial compliance (ICC), ∆V/∆P, as one of the most critical indexes for hydrocephalus evaluation was demonstrated previously. We suggest a new definition for the concept of ICC (long-term ICC) where there is a longer amount of elapsed time (up to 18 months after shunting) between the measurement of two values (V1 and V2 or P1 and P2). The head images of 15 adult patients with communicating hydrocephalus were provided with nine sets of imaging in nine stages: prior to shunting, and 1, 2, 3, 6, 9, 12, 15, and 18 months after shunting. In addition to measuring CSF volume (CSFV) in each stage, intracranial pressure (ICP) was also calculated using fluid–structure interaction simulation for the noninvasive calculation of ICC. Despite small increases in the brain volume (16.9%), there were considerable decreases in the ICP (70.4%) and CSFV (80.0%) of hydrocephalus patients after 18 months of shunting. The changes in CSFV, brain volume, and ICP values reached a stable condition 12, 15, and 6 months after shunting, respectively. The results showed that the brain tissue needs approximately two months to adapt itself to the fast and significant ICP reduction due to shunting. This may be related to the effect of the “viscous” component of brain tissue. The ICC trend between pre-shunting and the first month of shunting was descending for all patients with a “mean value” of 14.75 ± 0.6 ml/cm H2O. ICC changes in the other stages were oscillatory (nonuniform). Our noninvasive long-term ICC calculations showed a nonmonotonic trend in the CSFV–ICP graph, the lack of a linear relationship between ICC and ICP, and an oscillatory increase in ICC values during shunt treatment. The oscillatory changes in long-term ICC may reflect the clinical variations in hydrocephalus patients after shunting.
Signaling networks controlling ID and E protein activity in T cell differentiation and function

E and inhibitor of DNA binding (ID) proteins are involved in various cellular developmental processes and effector activities in T cells. Recent findings indicate that E and ID proteins are not only responsible for regulating thymic T cell development but also modulate the differentiation, function, and fate of peripheral T cells in multiple immune compartments. Based on the well-established E and ID protein axis (E-ID axis), it has been recognized that ID proteins interfere with the dimerization of E proteins, thus restricting their transcriptional activities. Given this close molecular relationship, the extent of expression or stability of these two protein families can dynamically affect the expression of specific target genes involved in multiple aspects of T cell biology. Therefore, it is essential to understand the endogenous proteins or extrinsic signaling pathways that can influence the dynamics of the E-ID axis in a cell-specific and context-dependent manner. Here, we provide an overview of E and ID proteins and the functional outcomes of the E-ID axis in the activation and function of multiple peripheral T cell subsets, including effector and memory T cell populations. Further, we review the mechanisms by which endogenous proteins and signaling pathways alter the E-ID axis in various T cell subsets influencing T cell function and fate at steady-state and in pathological settings. A comprehensive understanding of the functions of E and ID proteins in T cell biology can be instrumental in T cell-specific targeting of the E-ID axis to develop novel therapeutic modalities in the context of autoimmunity and cancer.
CD28 and chemokine receptors: Signalling amplifiers at the immunological synapse

T cells are master regulators of the immune response tuning, among others, B cells, macrophages and NK cells. To exert their functions requiring high sensibility and specificity, T cells need to integrate different stimuli from the surrounding microenvironment. A finely tuned signalling compartmentalization orchestrated in dynamic platforms is an essential requirement for the proper and efficient response of these cells to distinct triggers. During years, several studies have depicted the pivotal role of the cytoskeleton and lipid microdomains in controlling signalling compartmentalization during T cell activation and functions. Here, we discuss mechanisms responsible for signalling amplification and compartmentalization in T cell activation, focusing on the role of CD28, chemokine receptors and the actin cytoskeleton. We also take into account the detrimental effect of mutations carried by distinct signalling proteins giving rise to syndromes characterized by defects in T cell functionality.
PD-L1 expression on circulating tumor cells can be a predictive biomarker to PD-1 inhibitors combined with radiotherapy and antiangiogenic therapy in advanced hepatocellular carcinoma

Aim A programmed death 1 (PD-1) inhibitor coupled with radiotherapy and antiangiogenic therapy is a potential therapeutic strategy for advanced hepatocellular carcinoma (HCC). We aimed to determine if circulating tumor cells (CTCs) positive for programmed death-ligand 1 (PD-L1) could be employed as a predictive biomarker in HCC patients receiving triple therapy. Methods In this study, HCC patients received a PD-1 inhibitor in combination with intensity-modulated radiotherapy (IMRT) and antiangiogenic therapy. Following IMRT, the PD-1 inhibitor was administrated once every 3 weeks, while the antiangiogenic drug was given once a day. Treatment was continued until the disease progressed. Two mL of peripheral blood was collected at baseline, 1 month, and 3 months after treatment for CTC enrichment using the CytoSorter® system with a CytoSorter™ CTC PD-L1 Kit (Watson Biotech., China). Result A total of 47 HCC patients receiving the triple therapy were enrolled in this study. Patients with < 2 PD-L1+ CTCs at baseline had a higher objective response rate (ORR) and longer overall survival (OS) than those with ≥ 2 PD-L1+ CTCs (56.5% vs. 16.7%, p = 0.007; not reach vs. 10.8 months, p = 0.001, respectively). The count of PD-L1+ CTCs was found to be an independent predictive biomarker of OS. Furthermore, the objective response was more likely to be achieved in patients with a dynamic decrease in PD-L1+ CTC counts at 1 month after treatment. Conclusions Our study demonstrated that PD-L1+ CTCs could be a predictive biomarker for HCC patients receiving PD-1 inhibitors in combination with IMRT and antiangiogenic therapy.
Quiet ego is associated with positive attitudes toward Muslims

Well-known predictors of prejudice toward Muslims include social dominance and authoritarianism. However, a gap exists for variables reflecting a rejection or mitigation of ideological motivations associated with prejudice toward Muslims. We examined if quiet ego was related to positive attitudes toward Muslims, and whether this could be explained by lower levels of authoritarianism, social dominance, and the motivation to express prejudice. We explored this possibility across two studies of adults in the United States (N = 376; N = 519). In Study 1, regression results showed quiet ego was directly associated with positive attitudes toward Muslims. Study 2 utilized path analyses and found that the direct relationship between quiet ego and positive attitudes toward Muslims was explained by associations between quiet ego and lower endorsement of authoritarianism, social dominance, and the internal motivation to express prejudice toward Muslims. Moreover, these associations held when accounting for several correlates of intergroup attitudes.
Robust humoral and cellular immune responses in long-term convalescent COVID-19 individuals following one-dose SARS-CoV-2 inactivated vaccination

COVID-19, caused by SARS-CoV-2, has resulted in hundreds of millions of infections and millions of deaths worldwide. Preliminary results exhibited excellent efficacy of SARS-CoV-2 vaccine in preventing hospitalization and severe disease. However, data on inactivated vaccine-induced immune responses of naturally infected patients are limited. Here, we characterized SARS-CoV-2 RBD-specific IgG (anti-S-RBD IgG) and neutralizing antibodies (NAbs) against SARS-CoV-2 wild type and variants of concerns (VOCs), as well as RBD-specific IgG-secreting B cells and antigen-specific T cells respectively in 51 SARS-CoV-2 recovered subjects and 63 healthy individuals. In SARS-CoV-2 recovered patients, a single dose vaccine is sufficient to reactivate robust anti-S-RBD IgG and NAbs. The neutralizing capacity against VOCs increased significantly post-vaccination no matter healthy individuals or SARS-CoV-2 recovered patients. In addition, RBD-specific IgG-secreting B cells in SARS-CoV-2 recovered patients were significantly higher than that in healthy vaccine recipients. After the vaccine booster, the frequencies of specific IFN-γ+ CD4+ T cell, IL-2+ CD4+ T cell, and TNF-α+ CD4+ T cell responses were significantly increased in SARS-CoV-2 recovered patients. Our data highlighted the safety and utility of SARS-CoV-2 inactivated vaccine and demonstrated that robust humoral and cellular immune response can be reactivated by one-dose inactivated vaccine in SARS-CoV-2 recovered patients.
Intermediate English as a Foreign Language learners’ formulaic language speaking proficiency: Where does the teaching of lexical chunks figure?

This research aims to investigate the impact of learning lexical chunks on the English as a Foreign Language (EFL) Saudi learners’ (aged 13 to 17) speaking fluency. The study uses an intervention with intermediate Saudi learners comprising lexical chunks based upon the books Collocation in Use and Common Idioms in English. Findings obtained from the post-test show that the experimental groups scored significantly better when compared to their performance in the pre-test of speaking fluency. On the contrary, the difference in the performance of the control group between the pre and post-tests is not significant as far as speaking fluency is concerned. The findings also show that the experimental group participants had favorable sentiments regarding explicit lexical chunk training. The research has theoretical and practical consequences in teaching and learning a foreign/second language.
Mindfulness, cognitive fusion, and self-compassion in patients with schizophrenia spectrum disorders—A cross-sectional study

In the last decades, third wave approaches in cognitive-behavioral therapies (CBT) have shown effectiveness in treating several mental disorders, including schizophrenia spectrum disorders (SSD). Three crucial processes associated with clinical changes in patients include mindfulness, psychological flexibility (PF) and self-compassion (SC). PF is generally assessed by cognitive fusion (CF), a negative formulated key process of PF. The current study encompasses a cross-sectional design to examine the interplay of mindfulness, CF, SC and symptom severity in SSD. It was hypothesized that mindfulness is negatively correlated with symptom severity, CF mediates the negative relation between mindfulness and symptom severity, and SC moderates the link between mindfulness and CF. In total, 79 persons with SSD were recruited at the Department of Psychiatry and Neurosciences at the Charité – Universitätsmedizin Berlin. Correlations, as well as moderated mediation analyses, were performed using the analysis modeling tool PROCESS with total symptom severity and negative symptom severity as outcome variables, measured by the Positive and Negative Syndrome Scale (PANSS) and the Self-Evaluation of Negative Symptoms Scale (SNS). Results show that the moderated mediation hypothesis was confirmed for negative symptom severity assessed by SNS, however, not for total symptom severity assessed by PANSS. In general, the association between mindfulness and CF was stronger for participants with higher SC scores in our data. Future studies should investigate the relationship between mindfulness, SC, and PF regarding symptom severity in SSD in longitudinal designs while considering the impact on different outcomes and differences regarding assessment tools.
Modes of Selection in Tumors as Reflected by Two Mathematical Models and Site Frequency Spectra

The tug-of-war model was developed in a series of papers of McFarland and co-authors to account for existence of mutually counteracting rare advantageous driver mutations and more frequent slightly deleterious passenger mutations in cancer. In its original version, it was a state-dependent branching process. Because of its formulation, the tug-of-war model is of importance for tackling the problem as to whether evolution of cancerous tumors is “Darwinian” or “non-Darwinian. ” We define two Time-Continuous Markov Chain versions of the model, including identical mutation processes but adopting different drift and selection components. In Model A, drift and selection process preserves expected fitness whereas in Model B it leads to non-decreasing expected fitness. We investigate these properties using mathematical analysis and extensive simulations, which detect the effect of the so-called drift barrier in Model B but not in Model A. These effects are reflected in different structure of clone genealogies in the two models. Our work is related to the past theoretical work in the field of evolutionary genetics, concerning the interplay among mutation, drift and selection, in absence of recombination (asexual reproduction), where epistasis plays a major role. Finally, we use the statistics of mutation frequencies known as the Site Frequency Spectra (SFS), to compare the variant frequencies in DNA of sequenced HER2+ breast cancers, to those based on Model A and B simulations. The tumor-based SFS are better reproduced by Model A, pointing out a possible selection pattern of HER2+ tumor evolution. To put our models in context, we carried out an exploratory study of how publicly accessible data from breast, prostate, skin and ovarian cancers fit a range of models found in the literature.
Dynamically upregulated mast cell CPA3 patterns in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

Background The mast cell-specific metalloprotease CPA3 has been given important roles in lung tissue homeostasis and disease pathogenesis. However, the dynamics and spatial distribution of mast cell CPA3 expression in lung diseases remain unknown. Methods Using a histology-based approach for quantitative spatial decoding of mRNA and protein single cell, this study investigates the dynamics of CPA3 expression across mast cells residing in lungs from control subjects and patients with severe chronic obstructive pulmonary disease (COPD) or idiopathic lung fibrosis (IPF). Results Mast cells in COPD lungs had an anatomically widespread increase of CPA3 mRNA (bronchioles p < 0.001, pulmonary vessels p < 0.01, and alveolar parenchyma p < 0.01) compared to controls, while granule-stored CPA3 protein was unaltered. IPF lungs had a significant upregulation of both mast cell density, CPA3 mRNA (p < 0.001) and protein (p < 0.05), in the fibrotic alveolar tissue. Spatial expression maps revealed altered mast cell mRNA/protein quotients in lung areas subjected to disease-relevant histopathological alterations. Elevated CPA3 mRNA also correlated to lung tissue eosinophils, CD3 T cells, and declined lung function. Single-cell RNA sequencing of bronchial mast cells confirmed CPA3 as a top expressed gene with potential links to both inflammatory and protective markers. Conclusion This study shows that lung tissue mast cell populations in COPD and IPF lungs have spatially complex and markedly upregulated CPA3 expression profiles that correlate with immunopathological alterations and lung function. Given the proposed roles of CPA3 in tissue homeostasis, remodeling, and inflammation, these alterations are likely to have clinical consequences.