Miracle-dz/UniFAR-FTUs huggingface dataset:
A deep learning-based system for identifying differentiation status and delineating the margins of early gastric cancer in magnifying narrow-band imaging endoscopy

Abstract Background Accurate identification of the differentiation status and margins for early gastric cancer (EGC) is critical for determining the surgical strategy and achieving curative resection in EGC patients. The aim of this study was to develop a real-time system to accurately identify differentiation status and delineate the margins of EGC on magnifying narrow-band imaging (ME-NBI) endoscopy. Methods 2217 images from 145 EGC patients and 1870 images from 139 EGC patients were retrospectively collected to train and test the first convolutional neural network (CNN1) to identify EGC differentiation status. The performance of CNN1 was then compared with that of experts using 882 images from 58 EGC patients. Finally, 928 images from 132 EGC patients and 742 images from 87 EGC patients were used to train and test CNN2 to delineate the EGC margins. Results The system correctly predicted the differentiation status of EGCs with an accuracy of 83.3 % (95 % confidence interval [CI] 81.5 % – 84.9 %) in the testing dataset. In the man – machine contest, CNN1 performed significantly better than the five experts (86.2 %, 95 %CI 75.1 % – 92.8 % vs. 69.7 %, 95 %CI 64.1 % – 74.7 %). For delineating EGC margins, the system achieved an accuracy of 82.7 % (95 %CI 78.6 % – 86.1 %) in differentiated EGC and 88.1 % (95 %CI 84.2 % – 91.1 %) in undifferentiated EGC under an overlap ratio of 0.80. In unprocessed EGC videos, the system achieved real-time diagnosis of EGC differentiation status and EGC margin delineation in ME-NBI endoscopy. Conclusion We developed a deep learning-based system to accurately identify differentiation status and delineate the margins of EGC in ME-NBI endoscopy. This system achieved superior performance when compared with experts and was successfully tested in real EGC videos.
Genomic Landscape of Mutational Biases in the Pacific Oyster Crassostrea gigas

Abstract Mutation is a driving force of evolution that has been shaped by natural selection and is universally biased. Previous studies determined genome-wide mutational patterns for several species and investigated the heterogeneity of mutational patterns at fine-scale levels. However, little evidence of the heterogeneity of mutation rates over large genomic regions was shown. Hence, the mutational patterns of different large-scale genomic regions and their association with selective pressures still need to be explored. As the second most species-rich animal phylum, little is known about the mutational patterns in Mollusca, especially oysters. In this study, the mutational bias patterns are characterized by using whole-genome resequencing data in the Crassostrea gigas genome. I studied the genome-wide relative rates of the pair mutations and found that the predominant mutation is GC -> AT, irrespective of the genomic regions. This analysis reveals that mutational biases were associated with gene expression levels across the C. gigas genome. Genes with higher expression levels and breadth expression patterns, longer coding length, and more exon numbers had relatively higher GC -> AT rates. I also found that genes with larger dN/dS values had relatively higher GC -> AT rates. This work represents the first comprehensive research on the mutational biases in Mollusca species. Here, I comprehensively investigated the relationships between mutational biases with some intrinsic genetic factors and evolutionary indicators and proposed that selective pressures are important forces shaping the mutational biases across the C. gigas genome.
Brain Data Mining for Epileptic Seizure-Detection

Humans are suffering from various neurological disorders, due to the sedentary life style with stress and anxiety. Epilepsy is one of them, which is the second most prevalent neurological disorder after brain stroke. It has affected 65 million people, which are approximately 1% of global population, with 80% of the patients being from developing countries. At every moment, a human brain generates signals, which communicate with each other. Once this communication breaks down or any abnormal events occur, this causes a seizure. As such, a person starts to behave abnormally for a few moments. It triggers a sudden uncontrolled disruption to the normal electrical activity of the brain and affects a particular point or the whole region of the brain. Different monitoring devices are available to monitor this unusual behaviour such as EEG and ECoG. Both of these are popularly used to reveal these brain signals. Though being detected by these monitoring devices, some challenges still exist such as accurate seizure detection, quick seizure detection, and localization. If the duration of these recordings are long, then the chances of missing seizure cases are very high. In order to solve these challenges, we took advantage of techniques which is dominant and widely used in different domains including health. This research work is application oriented and is intended to solve the aforementioned challenges. Firstly, we process raw brain signals (ECoG and EEG) data by exploring their statistical features. This is because signal data provides different statistical features, thereby, it helps in seizure detection. Secondly, after examining the multiple classifiers performance, we have found the suitable and best classifier (i.e., decision forest), which is capable of detecting seizures from EEG and
Degree of tapering of xylem conduits in stems and roots of small Pinus cembra and Larix decidua trees

Xylem conduits increase in size from the apex downwards. While conduit tapering in the stem has often been reported to converge towards a common pattern among all plants, information on conduit tapering in small plants and roots is extremely scarce. We selected 10 small trees (height < 3 m) of Pinus cembra L. and Larix decidua Miller along an altitudinal gradient and measured diameter and conduit dimensions along stems and roots in the last annual ring. Sections of 10 µm were cut from wooden disks taken at different heights in the stem and in the roots and then stained with safranine. Slides were observed under a microscope, the lumen areas of conduits were measured and mean hydraulic diameters (Dh) calculated. Dh increased from stem tip (Dh at 1 cm from the apex averaged 10.75 µm; s = 2.33) to base (Dh from 20.70 to 30.54 µm), following a power trajectory (i.e., Dh = a·Lb, with L being the distance from the tip). Such degrees of conduit tapering may have a considerable effect in minimizing the hydraulic .
Diabetes is not a risk factor for myocardial infarction in patients without coronary artery disease: A study from the Western Denmark Heart Registry

Background: Diabetes is considered a risk factor for myocardial infarction. However, we have previously found that diabetes was not a short-term risk factor for myocardial infarction in the absence of obstructive coronary artery disease. Methods: We conducted a cohort study of patients undergoing coronary angiography from 2003 to 2012 and followed them by cross-linking Danish health registries. Patients were stratified according to coronary artery disease and diabetes. Endpoints included myocardial infarction, cardiac death, all-cause death and coronary revascularization. Results: 86,202 patients were included in total (diabetes: n = 12,652). Median follow-up was 8.8 years. Using patients with neither coronary artery disease nor diabetes as reference (cumulative myocardial infarction incidence 2.6%), the risk of myocardial infarction was low and not substantially increased for patients with diabetes alone (3.2%; hazard ratio 1.202, 95% confidence interval 0.996−1.451), was increased for patients with coronary artery disease alone (9.3%; hazard ratio 2.75, 95% confidence interval 2.52−3.01) and was highest for patients with both coronary artery disease and diabetes (12.3%; hazard ratio 3.79, 95% confidence interval 3.43−4.20). Similar associations were observed for cardiac death and coronary revascularization. Conclusion: Diabetes patients without coronary artery disease by coronary angiography have a low risk of myocardial infarction, not substantially increased compared to patients with neither coronary artery disease nor diabetes. In the presence of coronary artery disease, however, diabetes increases the risk of myocardial infarction.
Discovery of Ranking Fraud for Mobile Apps

In this paper, we provide a holistic view of ranking fraud and propose a ranking fraud detection system for mobile Apps. Specifically, we first propose to accurately locate the ranking fraud by mining the active periods, namely leading sessions, of mobile Apps. Furthermore, we investigate three types of evidences, i.e., ranking based evidences, rating based evidences and review based evidences, by modeling Apps’ ranking, rating and review behaviors through statistical hypotheses tests. In addition, we propose an optimization based aggregation method to integrate all the evidences for fraud detection.
Effect of Different Reducing Agents on Aromatic Compounds, Antioxidant and Chromatic Properties of Sauvignon Blanc Wine

Sulfur dioxide (SO2) is widely the most used enological additive with reductive, antiseptic and dissolving properties. According to increasing health concerns and the gradual decrease in total SO2 concentrations allowed in wine, alternative and supplementary agents for preservation are being investigated. For this reason, the current study was focused on the impact of different commercial reductive agents on white wine antioxidant activity and chemical composition. The effect of additives that combine sulfites, ascorbic acid and enological tannins were compared against standard 5% sulfurous acid (H2SO3) during the pre-fermentative treatments of Sauvignon Blanc must (Vitis vinifera L.). The basic parameters of quality, free amino-nitrogen and total polyphenoliccompounds in must were analyzed. Gas chromatography and spectrophotometric methods were used to investigate the overall volatile composition, antioxidant and chromatic parameters in wines. The obtained results undoubtedly pointed out the positive effect of sulfuric acid on the fermentation dynamics. Furthermore, application of combined reducing additives with potassium metabisulfite, L-ascorbic acid, gallotannins and ellagitannins, resulted in a higher antioxidant capacity and increased concentration of aromatic compounds and their odor activity values in Sauvignon Blanc wine.
TETRALEC, Artificial Tetrameric Lectins: A Tool to Screen Ligand and Pathogen Interactions

C-type lectin receptor (CLR)/carbohydrate recognition occurs through low affinity interactions. Nature compensates that weakness by multivalent display of the lectin carbohydrate recognition domain (CRD) at the cell surface. Mimicking these low affinity interactions in vitro is essential to better understand CLR/glycan interactions. Here, we present a strategy to create a generic construct with a tetrameric presentation of the CRD for any CLR, termed TETRALEC. We applied our strategy to a naturally occurring tetrameric CRD, DC-SIGNR, and compared the TETRALEC ligand binding capacity by synthetic N- and O-glycans microarray using three different DC-SIGNR constructs i) its natural tetrameric counterpart, ii) the monomeric CRD and iii) a dimeric Fc-CRD fusion. DC-SIGNR TETRALEC construct showed a similar binding profile to that of its natural tetrameric counterpart. However, differences observed in recognition of low affinity ligands underlined the importance of the CRD spatial arrangement. Moreover, we further extended the applications of DC-SIGNR TETRALEC to evaluate CLR/pathogens interactions. This construct was able to recognize heat-killed Candida albicans by flow cytometry and confocal microscopy, a so far unreported specificity of DC-SIGNR. In summary, the newly developed DC-SIGNR TETRALEC tool proved to be useful to unravel novel CLR/glycan interactions, an approach which could be applied to other CLRs.
Nitrogen deposition in tropical forests from savanna and deforestation fires

We used satellite‐derived estimates of global fire emissions and a chemical transport model to estimate atmospheric nitrogen (N) fluxes from savanna and deforestation fires in tropical ecosystems. N emissions and reactive N deposition led to a net transport of N equatorward, from savannas and areas undergoing deforestation to tropical forests. Deposition of fire‐emitted N in savannas was only 26% of emissions – indicating a net export from this biome. On average, net N loss from fires (the sum of emissions and deposition) was equivalent to approximately 22% of biological N fixation (BNF) in savannas (4.0 kg N ha−1 yr−1) and 38% of BNF in ecosystems at the deforestation frontier (9.3 kg N ha−1 yr−1). Net N gains from fires occurred in interior tropical forests at a rate equivalent to 3% of their BNF (0.8 kg N ha−1 yr−1). This percentage was highest for African tropical forests in the Congo Basin (15%; 3.4 kg N ha−1 yr−1) owing to equatorward transport from frequently burning savannas north and south of the basin. These results provide evidence for cross‐biome atmospheric fluxes of N that may help to sustain productivity in some tropical forest ecosystems on millennial timescales. Anthropogenic fires associated with slash and burn agriculture and deforestation in the southern part of the Amazon Basin and across Southeast Asia have substantially increased N deposition in these regions in recent decades and may contribute to increased rates of carbon accumulation in secondary forests and other N‐limited ecosystems.
Barriopsis tectonae sp. nov. a new species of Botryosphaeriaceae from Tectona grandis (teak) in Thailand

Tectona grandis (teak) is an increasingly important timber resource globally. It is native to Asia, including Thailand. In this paper a new species of Barriopsis, B. tectonae sp. nov . , is described from a dead T. grandis branch collected in Thailand. Barriopsis tectonae can be differentiated from the two previously described species of Barriopsis ; B. fusca and B. iraniana, by its ascospore and conidial dimensions. Phylogenetic evaluation of the ITS, TEF1-α and BT genomic regions provide further evidence that B. tectonae is a novel species.
Spatial distribution of the cottony camellia scale, Pulvinaria floccifera (Westwood) (Hemiptera: Coccidae) in the tea orchards

In the north of Iran, near the Caspian Sea, about 35,627 ha is cultivated with tea plant, Camellia sinensis (L.) Kuntze on both plain and hilly land. The cottony camellia scale, Pulvinaria floccifera (Westwood) (Hemiptera: Coccidae) is one of the most important pests of tea orchards in the north of Iran. Spatial distribution is an important item in entomoecology and needs to be studied for many pest management programs. So, weekly sampling of P. floccifera population was carried out throughout the 2008-2010 season, in the tea gardens of the Tonekabon region of the Mazandaran province of Iran. Each cut branch of tea was determined as a sample unit and after primary sampling, sample size was calculated using the equation: N = (ts/dm)2, (d = 0.15, sample size = 50). The data acquired were used to describe the spatial distribution pattern of P. floccifera by Tylor's power law, Iwao's mean crowding regression, Index of Dispersion (ID), and Index of Clumping (IDM). Tylor's power law (R2 > 0.84) and Iwao's mean crowding regression (R2 > 0.82) indi- cated that spatial distribution of 1st and 2nd nymphal instars is aggregated, but the distribution of 3rd instars, adults, and egg ovisacs is uniform. A result of ID and IDM showed that distribution of 1st, 2nd, and 3rd instars, adults, and egg ovisacs were aggregative each time the sampling was done.
IDENTIFICATION OF A NOVEL CYTOCHROME P450 cDNA, CYP97E1, FROM THE MARINE DIATOM SKELETONEMA COSTATUM BACILLARIOPHYCEAE 1

Here we report identification of a 2269‐base pair full‐length cDNA, CYP97E1, encoding a novel cytochrome P450 protein from the marine diatom Skeletonema costatum. The CYP97E1 protein contains 659 amino acids (Mr 74,200) and is the largest P450 isoform described to date. Our BLAST homology search and parsimony analysis showed that CYP97E1 shared high sequence identity (>40%) and genetic relatedness, respectively, with the CYP97B isoforms from different plant species. CYP97E1 was predicted by PSORT (a protein localization site prediction program) to be a cytosolic protein. Northern hybridization analysis indicated that CYP97E1 expression in S. costatum was not significantly affected by 2,4‐dichlorophenol, suggesting that CYP97E1 may not be involved in 2,4‐dichlorophenol detoxification in this diatom.
SMALL‐SUBUNIT RIBOSOMAL DNA SEQUENCE ANALYSES AND A RECONSTRUCTION OF THE INFERRED PHYLOGENY AMONG SYMBIOTIC DINOFLAGELLATES (PYRROPHYTA) 1

The small‐subunit ribosomal RNA genes (SSU rDNA) from the four symbiotic dinoflagellates, Symbiodinium corculorum Trench isolated from the bivalve mollusc Corculum cardissa (from Belau, Western Caroline Is.), S. meandrinae Trench, from the scleractinian coral Meandrina meandrites (from famaica, W.I.), Gloeodinium viscum Banaszak et al. from the hydrocoral Millepora dichotoma (from the Gulf of Aqaba), and Amphidinium belauense Trench from the acoel flatworm Haplodiscus sp. (from Belau) have been amplified by the polymerase chain reaction, cloned, and sequenced. Following alignment of these complete sequences to homologous sequences from six other dinoflagellates, eight api‐complexans, six ciliates, six chromophytes and oomycetes, three ascomycetes, two rhodophytes, two chlorophytes, and two myxomycetes (with Physarum polycephalum as the outgroup), phylogenetic reconstruction was conducted using Fitch and Margoliash distance, DNA maximum likelihood, and Wagner parsimony methods, with bootstrap resampling. All methods generated trees with similar topologies. The inferred “across Kingdom” phylogeny reemphasizes previous reports that show that the dinoflagellates, the apicomplexans, and the ciliates share a common ancestry and that the dinoflagellates are distantly related to the chromophyte‐oömycete lineage. The evidence supports the concept of a polyphyletic origin of dinoflagellate‐invertebrate symbioses, as symbiotic dinoflagellates represent seven genera in at least four orders. The three symbiotic species, S. corculorum, S. meandrinae, and S. pilosum, consistent with their morphological and biochemical similarities, cluster most closely. Symbiodinium pulchrorum Trench, the symbiontfrom the Hawaiian sea anemone Aiptasia pulchella, is more distantly related to them. Gloeodinium viscum is not closely related to the Symbiodinium species. Amphidinium carterae (free‐living) and A. belauense (symbiotic) also appear to be distantly related to Symbiodinium. Some symbionts (e.g. S. corculorum, S. pilosum) from distant geographic locations (the Indo‐Pacific and Caribbean, respectively) were found to be very closely related, whereas S. pulchrorum and S. corculorum from the Pacific were found to be distantly related. Analyses of 10 additional symbiotic and nonsymbiotic dinoflagellates, using partial SSU rDNA sequences to generate a tentative dinoflagellate phylogeny, indicate that members of the genus Symbiodinium cluster with most of the other (free‐living) dinoflagellates in the genus Gymnodinium. The genus Amphidinium, as represented by A. carterae and A. belauense, appear to be distantly related to the other members of the Gymnodiniaceae. This analysis, combined with morphological and biochemical data, indicates that the symbionts S. pulchrorum (from Aiptasia pulchella) and S. bermudense Trench (from Aiptasia tagetes) from the Indo‐Pacific and Caribbean, respectively, are very closely related but are not identical.
Plan optimization with L0-norm and group sparsity constraints for a new rotational, intensity-modulated brachytherapy for cervical cancer

The aim of this work is to build a framework that comprehends inverse planning procedure and plan optimization algorithm tailored to a novel directional beam intensity-modulated brachytherapy (IMBT) of cervical cancer using a rotatable, single-channel radiation shield. Inverse planning is required for finding optimal beam emitting direction, source dwell position and dwell time, which begin with creating a kernel matrix for each structure based on Monte-Carlo simulated dose distribution in the rotatable shield. For efficient beam delivery and less transit dose, the number of source dwell positions and angles needs to be minimized. It can be solved by L0-norm regularization for fewest possible dwell points, and by group sparsity constraint in L2,p-norm (0≤p<1) besides L0-norm for fewest active applicator rotating angles. The dose distributions from our proposed algorithms were compared to those of conventional tandem-based intracavitary brachytherapy (ICR) plans for six cervical cancer patients. The algorithmic performance was evaluated in delivery efficiency and plan quality relative to the unconstrained algorithm. The proposed framework yielded substantially enhanced plan quality over the conventional ICR plans. The L0-norm and (group sparsity+L0-norm) constrained algorithms reduced the number of source dwell points by 60 and 70% and saved 5 and 8 rotational angles on average (7 and 11 angles for highly modulated cases), relative to the unconstrained algorithm, respectively. Though both algorithms reduced the optimal source dwell positions and angles, the group sparsity constrained optimization with L0-norm was more effective than the L0-norm constraint only, mainly because of considering physical constraints of the new IMBT applicator. With much fewer dwell points compared to the unconstrained, the proposed algorithms led to statistically similar plan quality in dose volume histograms and iso-dose lines. It also demonstrated that the plan optimized by rotating the applicator resulted in much better plan quality than that of conventional applicator-based plans.
Use of live oocyst vaccine in the control of turkey coccidiosis: Effect on performance and intestinal morphology

SUMMARY An experiment was conducted to determine the effects of different coccidiosis-preventing programs on performance and intestinal morphology of commercial turkeys. Three hundred fifteen1-d-old female commercial cross turkey poults (British United Turkeys, BUT Big 9) were distributed into 3 treatments with 5 replicates of 21 birds each. Three programs were evaluated from 1 to 70 d of age, where program 1 had no anticoccidial drug and no vaccination against coccidiosis; program 2 had an anticoccidial drug (maduramycin 1%, 5 ppm); and program 3 had a vaccination (commercial vaccine, 4 species of Eimeria). All the groups were challenged with a dose of oocysts sporulated (20,000/bird) of 2 species of Eimeria at 21 d of age. In the growing phase (d 0–28), BW, BW gain, and FCR were significantly greater in treated groups compared with control group. In the fattening phase, the performance was not affected by treatments. Treatments and coccidiosis challenge had no significant effects on intestinal villus height. These observations support other reports that confirm live oocyst vaccination can be used effectively as a preventive against avian coccidiosis in commercially reared turkeys.
Revision of the subgenus Ceratitis (Pardalaspis) Bezzi, 1918 (Diptera, Tephritidae, Ceratitini)

Abstract. The fruit fly genus Ceratitis (Diptera: Tephritidae) comprises several important pest species attacking a wide range of unrelated fruits. In this paper the subgenus Ceratitis (Pardalaspis) Bezzi is revised. Ten species are recognized of which five are described as new: C. (P.)hamata sp.n. , C. (P.)munroi sp.n. , C. (P.)serrata sp.n. , C. (P.)semipunctata sp.n. and C. (P.)zairensis sp.n. A key to both sexes is provided. All species are restricted to the Afrotropical Region and distributional and known host plant data are given.