Miracle-dz/UniFAR-FTUs huggingface dataset:
Polyp Detection in Colonoscopy Videos by Bootstrapping Via Temporal Consistency

Computer-aided polyp detection during colonoscopy is beneficial to reduce the risk of colorectal cancers. Deep learning techniques have made significant process in natural object detection. However, when applying those fully supervised methods to polyp detection, the performance is greatly depressed by the deficiency of labeled data. In this paper, we propose a novel bootstrapping method for polyp detection in colonoscopy videos by augmenting training data with temporal consistency. For a detection network that is trained on a small set of annotated polyp images, we fine-tune it with new samples selected from the test video itself, in order to more effectively represent the polyp morphology of current video. A strategy of selecting new samples is proposed by considering temporal consistency in the test video. Evaluated on 11954 endoscopic frames of the CVC-ClinicVideoDB dataset, our method yields great improvement on polyp detection for several detection networks, and achieves state-of-the-art performance on the benchmark dataset.
ScenarioSA: A Dyadic Conversational Database for Interactive Sentiment Analysis

Interactive sentiment analysis is an emerging, yet challenging, subtask of the natural language processing problem. It aims to discover the affective state and sentimental change of each person in a conversation, and has attracted an increasing attention from both academia and industry. Existing sentiment analysis approaches are insufficient in modelling the interactions among people. However, the development of new approaches are critically limited by the lack of labelled interactive sentiment datasets. In this paper, we present a new conversational database that we have created and made publicly available, namely ScenarioSA, for interactive sentiment analysis. We manually label 2,214 multi-turn English conversations collected from various websites that provide online communication services. In comparison with existing sentiment datasets, ScenarioSA (1) is no longer limited to one specific domain but covers a wide range of topics and scenarios; (2) describes the interactions between two speakers of each conversation; and (3) reflects the sentimental evolution of each speaker over the course of a conversation. Finally, we propose an extension of interactive attention networks that could model the interactions, and compare various strong sentiment analysis algorithms on ScenarioSA, demonstrating the need of novel interactive sentiment analysis models and the potential of ScenarioSA to facilitate the development of such models.
Assessing the Suitability of Traditional Botnet Detection against Contemporary Threats

Botnets are groups of compromised devices used by malicious actors to perpetrate various forms of cyber-attacks. The Internet of Things involves the use and operation of (often small, low power) devices such as household appliances, industrial sensors and actuators, and media devices. Contemporary botnets have been known to target IoT devices for use in their attacks. Traditional botnet detection techniques may not be adequate in detecting contemporary botnet threats. BotMiner is one such technique. This paper discusses the attempted recreation of BotMiner and the limitations found in the context of IoT-based Botnet detection.
Settlement of juveniles of pearl oyster (Pinctada imbricata) on artificial collectors in Caraguatatuba, Sao Paulo, Brazil

In Southeastern Brazil, there is good cultivation potential for the pearl oyster Pinctada imbricata, which is often found on mussel ropes or seed collectors across the north coast of Sao Paulo State. Despite this, very few studies have focused on the biology of this species in Brazil. This research aimed to partially address this lack of information by evaluating the optimal season and preferred depth range (surface, first and second metres of depth) for the settlement of juvenile P. imbricata on artificial collectors. Two replicate artificial collectors made from braided fishing nets and comprising of horizontally and vertically suspended lines were deployed at Cocanha Beach, Brazil, and left in situ for a period of 5 months. At the end of the deployment period, the density of juveniles was significantly greater on the surface than the first and second metres of depth. It was also found that the period from November to March was more favourable for the placement of collectors and settlement of juveniles. Furthermore the results of the study confirm that is feasible to capture juvenile P. imbricata using artificial collectors to provide a continuous supply of commercial cultures.
Adaptive Weighted Minimax-Concave Penalty Based Dictionary Learning for Brain MR Images

We consider adaptive weighted minimax-concave (WMC) penalty as a generalization of the minimax-concave penalty (MCP) and vector MCP (VMCP). We develop a computationally efficient algorithm for sparse recovery considering the WMC penalty. Our algorithm in turn employs the fast iterative soft-thresholding algorithm (FISTA) but with the key difference that the threshold is adapted from one iteration to the next. The new sparse recovery algorithm when used for dictionary learning has a better representation capability as demonstrated by an application to magnetic resonance image denoising. The denoising performance turns out to be superior to the state-of-the-art techniques considering the standard performance metrics namely peak signal-to-noise ratio (PSNR) and structural similarity index metric (SSIM).
Effects of long‐term atmospheric CO2 enrichment on the mineral concentration of Citrus aurantium leaves

summary Leaf mineral concentration of Citrus aurantium (sour orange tree) was measured at bi-monthly intervals from 30 to 85 months of exposure in a long-term study on the effects of a 300 μmol mol−1 enrichment of atmospheric CO2, under conditions of high nutrient and water supply. There were clear seasonal trends in the concentrations of most of the elements studied. There were initial decreases in the leaf concentrations of N and the xylem-mobile, phloem-immobile elements Mn, Ca and Mg, as well as a significant and sustained increase in the leaf concentration of B, and no changes in the concentrations of K, Fe, Na, P, S, Zn and Cu. Interestingly, the initial reductions in the leaf concentrations of Mn, N, Ca and Mg gradually disappeared with time.
Evaluation of the Aryl Hydrocarbon Receptor Response in LMH 3D Spheroids

In the present study, we investigated whether the immortalized chicken hepatocellular carcinoma cell line, leghorn male hepatoma (LMH), had a comparable aryl hydrocarbon receptor (AhR) response to primary chicken embryonic hepatocytes (CEHs) when used in a well‐established assay for chemical screening and prioritization. The LMH cells were grown as 2‐dimensional (2D) confluent cells and 3D spheroids to determine the optimal cell culture states for chemical screening. Cytochrome P450 1A4 and 1A5 (CYP1A) activity and gene expression were compared between CEHs and LMH cells grown in 2 culture states following exposure to the dioxin‐like compound 3,3′,4,4′,5‐pentachlorobiphenyl (PCB‐126). The CYP1A activity was measured using the ethoxyresorufin‐O‐deethylase (EROD) assay, and changes in mRNA expression associated with the AhR pathway were determined using a custom‐designed polymerase chain reaction array. Among LMH cell culture states (i.e., 2D vs 3D), EROD induction was observed only in 3D LMH spheroids. Similarly, 3D spheroids had the greatest number of changes in AhR‐related genes compared with confluent cells. Overall, these results suggest that LMH cells grown as 3D spheroids have a metabolic and gene expression profile that is comparable to that of CEH, and may represent a suitable animal‐free alternative for in vitro screening of chemicals. Environ Toxicol Chem 2020;39:1693–1701. © 2020 SETAC
The Intelligent Automated Pressure-Adjustable Orthosis for Patients with Adolescent Idiopathic Scoliosis (AIS): A Bi-Center Randomized Controlled Trial.

STUDY DESIGN Randomized controlled trial. OBJECTIVE To compare the effectiveness of the automated pressure-adjustable orthosis (PO) and conventional orthosis (CO) for treatment of adolescent idiopathic scoliosis (AIS). SUMMARY OF BACKGROUND DATA Orthosis wearing quality may influence its effectiveness for AIS. An automated PO aimed to provide a more optimized and consistent biomechanical environment. Clinical evaluation was conducted to study the effectiveness of this innovative orthosis. METHODS Patients with AIS who met the criteria (Age 10-14, Cobb 20°-40°, and Risser sign 0-2) were recruited from 2 clinics and randomly assigned to the PO and CO groups. Compliance sensors were embedded in both groups, while the PO group was set to adjust the interfacial pressure as prescribed automatically. Clinical assessments (radiology and quality of life, QoL) were conducted at the baseline, immediate after orthosis fitting and 1-year follow-up. Orthosis wearing compliance was tracked using thermo and pressure sensors. RESULTS Twenty-four patients were enrolled with one drop-out (PO, n = 11; CO, n = 12). Significant immediate in-orthosis correction was observed in the PO (11.0°±6.5°, 42.0%, p < 0.001) and CO (10.3°±5.3°, 37.6%, p < 0.001) groups. After 1 year, no patient with PO progressed while 2 with CO had progression > 5°. The mean daily wearing duration was 1.1 hours longer in the PO group as compared with the CO group (15.4 ± 4.5 vs 14.3 ± 3.8 hours). Moreover, the wearing quality within the targeted pressure was 33.9% higher in the PO group (56.5 ± 16.5% vs 23.1 ± 12.1%, p < 0.001). No significant difference in the QoL results was observed between two groups nor within both groups during the study period. CONCLUSION This study showed that the automated PO could enhance wearing quality when compared with the CO, thus offering a better biomechanical corrective effect in the study period without adverse effect on the patients' wearing quantity and QoL. LEVEL OF EVIDENCE 1.
Environment-Aware Coverage Optimization for Space-Ground Integrated Maritime Communications

To satisfy the growing demand for broadband maritime communications, space-ground integrated maritime communication networks (MCNs) arise, which are envisioned to take full advantage of both satellites and terrestrial shore-based networks. In practice, due to the frequent beam hopping of satellites and the limited number of geographically available onshore base-station sites, the space-ground integrated MCN usually presents a highly non-cellular network structure, leading to both challenging blind zones and coverage areas with severe interference. In this paper, we optimize the coverage performance by exploiting the marine environment information. Particularly, the transmit antenna correlation is estimated using the location and mobility information of scatterers on the sea, such as lighthouses, reefs, islands, and vessels. The position and attitude information of satellites are also utilized for interference estimation. Based on that, we optimize the input covariance and precoding matrix to maximize the ergodic sum capacity for all mobile terminals within the coverage. It is a complicated non-convex problem, especially because the ergodic sum capacity is difficult to be expressed straightly without the expectation operator. We introduce an upper bound of the ergodic sum capacity using the path loss and the transmit antenna correlation estimated from the environment information, and then propose an iterative algorithm to solve the problem by solving a set of convex subproblems. The proposed environment-aware scheme is evaluated using the real-world geographic information of a coastal area of China. Simulation results demonstrate that the proposed scheme can greatly improve the ergodic sum capacity and the energy efficiency compared with existing approaches, and achieve dynamic coverage to match the non-cellular network structure.
Development and validation of a prediction model (AHC) for early identification of refractory thrombotic thrombocytopenic purpura using nationally representative data

Immune‐mediated thrombotic thrombocytopenic purpura (iTTP) is a rare and life‐threatening haematological emergency. Although therapeutic plasma exchange together with corticosteroids achieve successful outcomes, a considerable number of patients remain refractory to this treatment and require early initiation of intensive therapy. However, a method for the early identification of refractory iTTP is not available. To develop and validate a model for predicting the probability of refractory iTTP, a cohort of 265 consecutive iTTP patients from 17 large medical centres was retrospectively identified. The derivation cohort included 94 patients from 11 medical centres. For the validation cohort, we included 40 patients from the other six medical centres using geographical validation. An easy‐to‐use risk score system was generated, and its performance was assessed using internal and external validation cohorts. In the multivariable logistic analysis of the derivation cohort, three candidate predictors were entered into the final prediction model: age, haemoglobin and creatinine. The prediction model had an area under the curve of 0.886 (95% CI: 0.679–0.974) in the internal validation cohort and 0.862 (95% CI: 0.625–0.999) in the external validation cohort. The calibration plots showed a high agreement between the predicted and observed outcomes. In conclusion, we developed and validated a highly accurate prediction model for the early identification of refractory iTTP. It has the potential to guide tailored therapy and is a step towards more personalized medicine.
MORBILLIVIRUS INFECTION IN MANATEES

The first evidence of exposure of free-ranging Florida manatees (Trichechus manatees latirostris) to a morbillivirus is reported. Blood samples were collected from 148 Florida manatees between 1977 and 1994. The sample included manatees that were under rehabilitation (n = 97), free-ranging (n = 40) and fresh necropsy specimens (n = 11). Serum from six animals (4%) neutralized porpoise and dolphin morbilliviruses to a higher titer than any other member of the Morbillivirus genus. Antibodies were not detected in sera from 12 free-ranging Antillean manatees (T. manatus manatus) from Guyana sampled in 1992 or from 12 hand-reared Amazonian manatees (T. inunguis) sampled in 1984. Immunoprecipitation studies using radio-labelled canine distemper virus protein and serum from Florida manatees showed precipitation of the nucleo-capsid (N) protein. The combination of low antibody titers and absence of clinical disease suggest that the Florida manatee is a dead-end host. Sporadic infection may occur following contact with another species in which infection is enzootic. Morbillivirus could, either by fatal infection or more insidious effects on the immune system or reproduction, pose a problem to this already threatened species.
Salinity and mineral nutrition effects on growth and accumulation of organic and Inorganic ions in two cultivated tomato varieties

Abstract A trial was conducted on the effect of salinity and method of fertilizer application on two varieties of cultivated tomato, i.e. VF 145 and Edkawi. Salinity ranged from 0.52 to 11 dS/m, and fertilizer was applied by either broadcasting in small doses or added with irrigation water. Weight of shoots, fruit yield, and sodium (Na), calcium (Ca), chloride (Cl), free proline contents in both developing and mature leaves, and total soluble salts and ascorbic acid contents in fruits were taken as evaluating criteria. Salinity depressed both growth and fruit yield, and simultaneously increased ion concentration in plant leaves. Sodium and Cl accumulated with salinity, being greater in mature leaves, while proline accumulation in developing leaves was much higher than in mature leaves. Total soluble salts and ascorbic acid were not affected. Liquid fertilization resulted in higher fruit yields than that obtained with the solid fertilizer treatments as well as better alleviating the depressive effects of s.
HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread

The female reproductive tract (FRT) is the most common site of infection during HIV transmission to women, but viral remodeling complicates characterization of cells targeted for infection. Here, we report extensive phenotypic analyses of HIV-infected endometrial cells by CyTOF, and use a ‘nearest neighbor’ bioinformatics approach to trace cells to their original pre-infection phenotypes. Like in blood, HIV preferentially targets memory CD4+ T cells in the endometrium, but these cells exhibit unique phenotypes and sustain much higher levels of infection. Genital cell remodeling by HIV includes downregulating TCR complex components and modulating chemokine receptor expression to promote dissemination of infected cells to lymphoid follicles. HIV also upregulates the anti-apoptotic protein BIRC5, which when blocked promotes death of infected endometrial cells. These results suggest that HIV remodels genital T cells to prolong viability and promote viral dissemination and that interfering with these processes might reduce the likelihood of systemic viral spread.
Misspecifying the covariance structure in a linear mixed model under MAR drop‐out

Misspecification of the covariance structure in a linear mixed model (LMM) can lead to biased population parameters' estimates under MAR drop‐out. In our motivating example of modeling CD4 cell counts during untreated HIV infection, random intercept and slope LMMs are frequently used. In this article, we evaluate the performance of LMMs with specific covariance structures, in terms of bias in the fixed effects estimates, under specific MAR drop‐out mechanisms, and adopt a Bayesian model comparison criterion to discriminate between the examined approaches in real‐data applications. We analytically show that using a random intercept and slope structure when the true one is more complex can lead to seriously biased estimates, with the degree of bias depending on the magnitude of the MAR drop‐out. Under misspecified covariance structure, we compare in terms of induced bias the approach of adding a fractional Brownian motion (BM) process on top of random intercepts and slopes with the approach of using splines for the random effects. In general, the performance of both approaches was satisfactory, with the BM model leading to smaller bias in most cases. A simulation study is carried out to evaluate the performance of the proposed Bayesian criterion in identifying the model with the correct covariance structure. Overall, the proposed method performs better than the AIC and BIC criteria under our specific simulation setting. The models under consideration are applied to real data from the CASCADE study; the most plausible model is identified by all examined criteria.
Primary central nervous system lymphoma: status and advances in diagnosis, molecular pathogenesis, and treatment

Abstract Primary central nervous system lymphoma (PCNSL) is a rare group of extra-nodal non-Hodgkin lymphoma which is confined to the central nervous system or eyes. This article aims to present a brief profile of PCNSL diagnosis and treatment in immunocompetent patients. The authors retrieved information from the PubMed database up to September 2019. The annual incidence of PCNSL increased over the last four decades. The prognosis of PCNSL has improved mainly due to the introduction and wide-spread use of high-dose methotrexate, which is now the backbone of all first-line treatment polychemotherapy regimens. Gene expression profiling and next-generation sequencing analyses have revealed mutations that induce activation of nuclear factor-κB, B cell antigen receptor, and Janus kinases/signal transducer and activator of transcription proteins signal pathways. Some novel agents are investigated in the treatment of relapsed PCNSL including immunotherapy and targeted therapy. In particular, lenalidomide and ibrutinib have demonstrated durable efficiency. Treatment of PCNSL has evolved in the last 40 years and survival outcomes have improved in most patient groups, but there is still room to improve outcome by optimizing current chemotherapy and novel agents.
Size-Dependent Growth in Two Zoanthid Species: A Constrast in Clonal Strategies

The widespread occurrence of genet fragmentation among modular, clonal organisms results in size—dependent life history patterns that are often independent of clonal age. In this study the size dependence of clonal growth rates was experimentally evaluated using two common coral reef cnidarians that inhabit shallow reef environments at Discovery Bay, Jamaica. As a result of the turbulent conditions associated with storms, these organisms commonly undergo fragmentation. The growth of aggregations of these clonal fragments in three small size classes (ranging over three orders of magnitude) was statistically evaluated against a null, exponential model that predicts that relative growth rates of small aggregations are size independent. Growth rates for Zoanthus solanderi were consistent with this model. Z. sociatus, on the other hand, exhibited size—dependent relative growth rates. The smallest aggregations of this species had the higher relative growth rates, which were sufficiently high to more than compensate for losses due to mortality. These results are consistent with other life history and distributional differences between these two species. Zoanthus sociatus has a higher rate of mortality, does not undergo sexual reproduction until reaching a larger aggregation size, and commonly has a higher vertical distribution (which may represent a spatial refuge from subtidal predators) than does Z. solanderi. The comparatively rapid relative growth rates of small aggregations of Z. sociatus may be the result of spatial constraints on growth in large aggregations and/or of higher relative energy allocations to growth in small aggregations. The incorporation of fragmentation into the life history strategy of clonal organisms has a range of predicted consequences. Among some organisms, fragmentation and associated adaptations may be rare and of little consequence. Among organisms that frequently fragment as a result of physical disturbances, natural selection should favor repair and regenerative processes as well as resistance to this source of mortality. At the extreme, fragmentation need not be associated with death and injury. Adaptations at the developmental and physiological level may involve genetically programmed production of asexual fragments and size—dependent shifts in energy allocations to growth, sexual reproduction, and energy reserves. The degree of interdependence of the processes controlling the dynamics of genets and fragmented modules may well depend on the relative importance of such adaptations.
ISING-GAN: Annotated Data Augmentation with a Spatially Constrained Generative Adversarial Network

Data augmentation is a popular technique with which new dataset samples are artificially synthesized to the end of assisting training of learning-based algorithms and avoiding overfitting. Methods based on generative adversarial networks (GANs) have recently rekindled interest in research on new techniques for data augmentation. With the current paper we propose a new GAN-based model for data augmentation, comprising a suitable Markov random field-based spatial constraint that encourages synthesis of spatially smooth outputs. Oriented towards use with medical imaging sets where a localization/segmentation annotation is available, our model can simultaneously also produce artificial annotations. We gauge performance numerically by measuring performance through U-Net trained to detect cells on microscopy images, by taking into account the produced augmented dataset. Numerical trials, as well as qualitative results validate the contribution of our model.