Miracle-dz/UniFAR-FTUs huggingface dataset:
The optimal design of clinical trials with potential biomarker effects: A novel computational approach

As a future trend of healthcare, personalized medicine tailors medical treatments to individual patients. It requires to identify a subset of patients with the best response to treatment. The subset can be defined by a biomarker (eg, expression of a gene) and its cutoff value. Topics on subset identification have received massive attention. There are over two million hits by keyword searches on Google Scholar. However, designing clinical trials that utilize the discovered uncertain subsets/biomarkers is not trivial and rarely discussed in the literature. This leads to a gap between research results and real‐world drug development. To fill in this gap, we formulate the problem of clinical trial design into an optimization problem involving high‐dimensional integration, and propose a novel computational solution based on Monte Carlo and smoothing methods. Our method utilizes the modern techniques of general purpose computing on graphics processing units for large‐scale parallel computing. Compared to a published method in three‐dimensional problems, our approach is more accurate and 133 times faster. This advantage increases when dimensionality increases. Our method is scalable to higher dimensional problems since the precision bound of our estimated study power is a finite number not affected by dimensionality. To design clinical trials incorporating the potential biomarkers, users can use our software "DesignCTPB". This software can be found on Github and will be available as an R package on CRAN. Although our research is motivated by the design of clinical trials, the method can be used widely to solve other optimization problems involving high‐dimensional integration.
Image Embedded Segmentation: Uniting Supervised and Unsupervised Objectives for Segmenting Histopathological Images

This paper presents a new regularization method to train a fully convolutional network for semantic tissue segmentation in histopathological images. This method relies on the benefit of unsupervised learning, in the form of image reconstruction, for network training. To this end, it puts forward an idea of defining a new embedding that allows uniting the main supervised task of semantic segmentation and an auxiliary unsupervised task of image reconstruction into a single one and proposes to learn this united task by a single generative model. This embedding generates an output image by superimposing an input image on its segmentation map. Then, the method learns to translate the input image to this embedded output image using a conditional generative adversarial network, which is known as quite effective for image-to-image translations. This proposal is different than the existing approach that uses image reconstruction for the same regularization purpose. The existing approach considers segmentation and image reconstruction as two separate tasks in a multi-task network, defines their losses independently, and combines them in a joint loss function. However, the definition of such a function requires externally determining right contributions of the supervised and unsupervised losses that yield balanced learning between the segmentation and image reconstruction tasks. The proposed approach provides an easier solution to this problem by uniting these two tasks into a single one, which intrinsically combines their losses. We test our approach on three datasets of histopathological images. Our experiments demonstrate that it leads to better segmentation results in these datasets, compared to its counterparts.
Unconventional relaxation of hydrodynamic modes in anharmonic chains under strong pressure fluctuations

We develop an effective numerical scheme to capture hydrodynamic (HD) modes in general classical anharmonic chains. This scheme is based on the HD theory suggested by Ernst–Hauge–van Leeuwen, which takes full role of pressure fluctuations into account. With this scheme we show that the traditional pictures given by the current nonlinear fluctuating HD theory are valid only when the system’s pressure is zero and the pressure fluctuations are weak. For nonvanishing pressure, the HD modes can, however, respond to small and large pressure fluctuations and relax in some distinct manners. Our results shed new light on understanding thermal transport from the perspective of HD theory.
Evaluation of methanol‐grown bacteria and hydrocarbon‐grown yeast as sources of protein for poultry: Studies with young chicks

1. In a series of five trials, conducted with broiler chicks during the starting period, two types of dietary single‐cell protein were tested: Pruteen (PR), a protein concentrate produced from methanol‐utilising bacteria, and a Lavera‐type yeast (LA) utilising the normal paraffins of heavy gas oil. 2. The inclusion of 90 to 150 g PR or LA/kg diet depressed growth rate by 14 to 16% and 9 to 10%, respectively. This effect was slightly counteracted (about 6 percentage units) by the addition of L‐arginine. 3. The growth depression can be explained completely in the case of PR or almost completely in that of LA on the basis of reduced food intake, without a decided effect on food utilisation. 4. The reduced consumption of PR‐containing diets is not due to a petroleum‐ether‐soluble factor, nor to the high and low concentrations of sodium and potassium, respectively, in PR.
Cross-Domain Few-Shot Learning with Meta Fine-Tuning

In this paper, we tackle the new Cross-Domain Few-Shot Learning benchmark proposed by the CVPR 2020 Challenge. To this end, we build upon state-of-the-art methods in domain adaptation and few-shot learning to create a system that can be trained to perform both tasks. Inspired by the need to create models designed to be fine-tuned, we explore the integration of transfer-learning (fine-tuning) with meta-learning algorithms, to train a network that has specific layers that are designed to be adapted at a later fine-tuning stage. To do so, we modify the episodic training process to include a first-order MAML-based meta-learning algorithm, and use a Graph Neural Network model as the subsequent meta-learning module. We find that our proposed method helps to boost accuracy significantly, especially when combined with data augmentation. In our final results, we combine the novel method with the baseline method in a simple ensemble, and achieve an average accuracy of 73.78% on the benchmark. This is a 6.51% improvement over existing benchmarks that were trained solely on miniImagenet.
NEST-TREE USE BY NORTHERN AND SOUTHERN FLYING SQUIRRELS IN CENTRAL ONTARIO

Abstract Little is known about nest use by flying squirrels (Glaucomys) in partially harvested forests, especially for northerly populations where cavity use is prevalent. We used radiotelemetry to examine nest use by 24 southern flying squirrels (G. volans) in 2003 in logged and unlogged hardwood forests, and by 18 northern flying squirrels (G. sabrinus) in 2004 in conifer forests, in Algonquin Provincial Park, Ontario, Canada. Of 76 nest trees used by G. volans, 71% were in declining trees and 22% were in snags. Sixty tree nests used by G. sabrinus included 28% snags, 46% declining trees, and 25% healthy trees, although nearly one-half of nests of G. sabrinus that were used on more than 3 occasions were in snags. G. volans used larger-diameter trees and American beech (Fagus grandifolia) more often than expected by chance, whereas G. sabrinus used trembling aspen (Populus tremuloides), white birch (Betula papyrifera), and yellow birch (B. alleghaniensis) more than expected by chance. Both species used a high proportion of cavity nests, few external nests, and trees that were decayed or diseased. We found indications that nest supply was limited in recently harvested sites, where there were fewer cavity trees and snags; however, G. volans may compensate by using abandoned yellow-bellied sapsucker nests and by nesting in aggregations. Hardwood snags and decaying trees appear to provide crucial nesting habitats for both squirrel species, particularly for females.
Isolation of Motil Aeromonases and to determine antimicrobial susceptibility from farms of Trout

Bu calismada; Mart Mayis 2000 ve Kasim 2000 Mart 2001 tarihleri arasinda, alabalik isletmelerinden toplanan 73 adet balik ornegi ile 22 adet su ornegi motil Areomonas’lar yonunden incelendi. Suslarin 18 farkli antibiyotige karsi duyarliliklari arastirildi. Arastirmada 95 ornekten 52 motil Aeromonas (%41.0) izole edildi. Bu izolatlardan 21 sus (%40.3) Aeromonas hydrophila, 24 sus (%46.1) Aeromonas caviae ve 7 sus (%13.4) Aeromonas sobria olarak identifiye edildi. Balik orneklerinden 34 izolasyon (%35.6) yapildi. Bu izolatlardan 15 sus (%44.1) Aeromonas hydrophila, 14 sus (%41.1) Aeromonas caviae ve 5 sus (%14.7) Aeromonas sobria olarak identifiye edildi. Su orneklerinden 18 izolasyon (%59.0) yapildi. Bu izolatlardan 6 sus (%33.3) Aeromonas hydrophila, 10 sus (%55.5) Aeromonas caviae ve 2 sus (%11.1) Aeromonas sobria olarak identifiye edildi. Arastirmada incelenen balik materyallerinin ic organlarindan izolasyon yapilamazken, calismada tespit edilen motil Aeromonas suslarinin tamami baliklarin solungaclarindan ve sudan izole edildi. Antibiyotiklere duyarlilik testinde tum izolatlar; Ciprofloxacin ve enrofloxacin’e siddetli derecede (%96’nin uzerinde), amikacin’e yuksek derecede (%92.3), oxolinic acid, flumequin, cefoperazone+sulbactam, imipenem, mezlocillin, piperacillin ve cefotaxim’e orta derecede (%76.9 ile %84.6 arasinda), neomycine, nalidixic acid, sulphonamide, nitrofurantoin ve trimethoprim’e az (%26.9 ile %61.5 arasinda) duyarli bulunmustur. Oxytetracycline, streptomycin ve carbenicillin’e yuksek derecede direnc tespit edilmistir.
Seletividade de coroa-de-cristo (Euphorbia splendens) a diferentes classes de herbicidas para manejo de plantas daninhas em jardinagem.

Com objetivo de avaliar a seletividade da coroa-de-cristo ( Euphorbia splendes ) para diferentes classes de herbicidas, tres experimentos foram realizados, em condicoes de campo, na Fazenda Modelo da ESAPP/SP (2001/2002). Os tratamentos do Experimento 1 foram (em e.a. ou i.a.): glyphosate (1,44 kg.ha-1); sulfosate (1,44kg.ha-1); amonio-glufosinato (0,48 kg.ha-1); paraquat (0,60 kg.ha-1); glyphosate + flumioxazin (1,44 + 0,06 kg.ha-1); glyphosate + carfentrazone-ethyl (1,44 + 0,06 kg.ha-1) e testemunha. No Experimento 2:carfentrazone-ethyl (0,12 kg.ha-1); 2,4-D (1,30 kg.ha-1); isoxaflutole (0,06 kg.ha-1); nicosulfuron (0,06 kg.ha-1); metsulfuron-methyl (0,0024 kg.ha-1); lactofen (0,180 kg.ha-1); chlorimuron-ethyl (0,02 kg.ha-1); bentazon (1,25 kg.ha-1) e testemunha. No Experimento 3 foram testados: fluazifop-p-butyl (0,25 kg.ha-1); sethoxydim (1,25 kg.ha-1); haloxyfop-methyl (0,06 kg.ha-1); clethodim + fenoxaprop-p-ethyl (0,11 kg.ha-1); quizalofop-p-ethyl (0,10 kg.ha-1); clethodim (0,12 kg.ha-1); propaquizafop (0,12 kg.ha-1); tepraloxydim (0,40 kg.ha-1); butroxydim (0,10 kg.ha-1) e testemunha. No Experimento 1, nenhum tratamento foi seletivo, causando danos visiveis de fitointoxicacao a partir dos 7 dias apos aplicacao. No Experimento 2, apenas o metsulfuron-methyl apresentou seletividade a coroa-de-cristo, para as folhas e inflorescencias; sendo o isoxaflutole, nicosulfuron, chlorimuron-ethyl e bentazon improprios apenas no que diz respeito a preservacao de flores. No Experimento 3, todos os tratamentos indicaram seletividade a coroa-de-cristo, observando-se apenas injurias as flores para os herbicidas fluazifop-p-butil e sethoxydim e propaquizafop.
GENOMES OF THE AUSTRALIAN WILD SPECIES OF COTTON. II. THE DESIGNATION OF A NEW G GENOME FOR GOSSYPIUM BICKII

Gossypium bickii Prokh. is distinct from the C genome species, although it was tentatively placed in this genome. A comparison of the karyotypes of G. bickii and G. sturtianum Willis separates G. bickii sharply from G. sturtianum, the standard species for the C genome. Karyotypic differences are evident in centromere position of the chromosomes, chromosome size, and the lack of satellites or secondary constrictions in G. bickii. A clear separation of G. bickii from G. sturtianum and other Gossypium species is also demonstrated in previous studies of phenetic analysis, flower flavonoids, DNA content, and electrophoresis of seed proteins, esterases, leucine aminopeptidases, and catalases. G. bickii is placed in a new G genome and is assigned to the 2G1 subgenome.
Extubation and the Risks of Coughing and Laryngospasm in the Era of Coronavirus Disease-19 (COVID-19)

The coronavirus disease-19 (COVID-19) pandemic has prompted new interest among anesthesiologists and intensivists in controlling coughing and expectoration of potentially infectious aerosolized secretions during intubation and extubation. However, the fear of provoking laryngospasm may cause avoidance of deep or sedated extubation techniques which could reduce coughing and infection risk. This fear may be alleviated with clear understanding of the mechanisms and effective management of post-extubation airway obstruction including laryngospasm. We review the dynamic function of the larynx from the vantage point of head-and-neck surgery, highlighting two key concepts: 1. The larynx is a complex organ that may occlude reflexively at levels other than the true vocal folds; 2. The widely held belief that positive-pressure ventilation by mask can “break” laryngospasm is not supported by the otorhinolaryngology literature. We review the differential diagnosis of acute airway obstruction after extubation, discuss techniques for achieving smooth extubation with avoidance of coughing and expectoration of secretions, and recommend, on the basis of this review, a clinical pathway for optimal management of upper airway obstruction including laryngospasm to avoid adverse outcomes.
Nonalcoholic fatty liver disease, a potential risk factor of non-specific ST-T segment changes: data from a cross-sectional study

Background Non-specific ST-T segment changes are prevalent and are proven risk factors for early onset of cardiovascular diseases. They can increase all-cause mortality by 100∼200% and are candidate for early signs of cardiovascular changes. Nonalcoholic fatty liver disease (NAFLD) is prevalent worldwide and is one facet of a multisystem disease that confers substantial increases morbidity and mortality of nonalcoholic fatty liver-related cardiovascular diseases. It is unclear whether NAFLD is associated with non-specific ST-T changes warning early signs of cardiovascular changes. Therefore, we investigated this association. Methods A cross-sectional study was designed that included a sample consisting of 32,922 participants who underwent health examinations. Participants with missing information, excessive alcohol intake, viral hepatitis, chronic liver disease or established cardiovascular diseases were excluded. Electrocardiograms were used for analysis of non-specific ST-T segment changes. NAFLD was diagnosed by ultrasonographic detection of hepatic steatosis without other liver diseases. A multivariable logistic regression model was served to calculate the OR and 95% CI for non-specific ST-T segment changes. Results The prevalence of non-specific ST-T segment changes was 6.5% in participants with NAFLD, however, the prevalence of NAFLD was 42.9% in participants with non-specific ST-T segment changes. NAFLD was independently associated with non-specific ST-T segment changes (OR: 1.925, 95% CI: 1.727-2.143, P < 0.001). After adjusting for age, sex, heart rate, hypertension, body mass index, fasting glucose, total cholesterol, triglycerides, HDL-C, NAFLD remained an independent risk factor of non-specific ST-T segment changes (OR: 1.289, 95% CI: 1.122-1.480). Conclusion Non-specific ST-T segment changes were independently associated with the presence of NAFLD after adjusting for potential confounders.
NIR IS A NUCLEOLAR RNA-BINDING PROTEIN THAT IS INVOLVED IN CELL PROLIFERATION

A novel inhibitor of histone acetyltransferase repressor (NIR) is a histone acetylation inhibitor that associates with p53, p63 and histone complexes. Staining with anti-NIR antibodies revealed that the protein is localized at the nucleo- lus. The nucleolar localization of NIR was lost upon RNase treatment, whereas its localization was unaffected by treatment with DNase. These results indicate that NIR directly or indirectly binds RNA in the nucleolus. The expression of NIR pro- tein was higher in cancer cell lines than in non-cancer cell lines. The proliferation rate of human embryonic kidney 293T cells was higher following the ectopic expression of NIR than following the ectopic expression of green fluorescent protein (GFP). In summary, NIR is an RNA-associated protein that is involved in the cell proliferation regulation.
Cellulase activity of some phytopathogenic fungi isolated from diseased leaves of broad bean

Forty-five fungal species and two varieties belonging to the 23 genera were collected from 50 samples of diseased leaves of broad bean collected from Qena Governorate in Egypt on glucose-Czapek’s, dichloran-chloramphenicol-malt extract and dichloran-chloramphenicol-peptone agar at 28 °C. The most common genera were Alternaria, Aspergillus, Cladosporium, Fusarium, Mycosphaerella and Penicillium. The most prevalent species were Alternaria alternata, Aspergillus flavus, A. fumigatus, A. niger, Cladosporium cladosporioides, Fusarium merismoides, Mycosphaerella tassiana and Penicillium chrysogenum. Among the eight dematiaceous Hyphomycetes phytopathogenic fungi screened for their abilities to produce both exo- and endo-β-1,4-glucanase enzymes (C1 and Cx), five species had high C1 enzyme production and two species had high Cx enzyme production. However, two and three species were moderately active in producing C1 and Cx enzymes, respectively. The remaining species had low production of both C1 and Cx enzymes. The highest cellulase activity was recorded by Alternaria citri and Cochliobolus spicifer for C1 and by A alternata and A. citri for Cx enzyme. Maximum production of C1 enzyme by A. citri and C. spicifer was obtained after six days of incubation at 30 °C with an initial pH of 6 in a culture medium containing lactose and calcium nitrate as the carbon and nitrogen sources, respectively. The highest Cx enzyme production was by A. alternata and A. citri,which was recorded after eight days of incubation at 30 °C with an initial pH of 6 in a culture medium containing carboxymethyl cellulose and sodium or calcium nitrate as the carbon and nitrogen sources, respectively.
VARIATION IN NITROGEN PHYSIOLOGY AND GROWTH AMONG GEOGRAPHICALLY ISOLATED POPULATIONS OF THE GIANT KELP, MACROCYSTIS PYRIFERA (PHAEOPHYTA) 1

Three geographically isolated populations of the giant kelp, Macrocystis pyrifera (L.) C. Ag. , were examined for responses to nitrate availability in batch culture experiments using juvenile sporophytes reared from spores in the laboratory. Although maximum rates of nitrate‐saturated growth were similar among groups, there were significant quantitative differences in the response to nitrate limitation that can be related to natural patterns of nutrient availability at these sites. Plants from Santa Catalina Island (most oligotrophic) achieved maximum growth rates at ambient nitrate concentrations that were lower than those for plants from Monterey Bay, California (most eutrophic), or Refugio State Beach (near Santa Barbara, California). Tissue nitrogen and amino acid concentrations were highest in plants cultured from Santa Catalina Island populations at all external nitrate concentrations, suggesting that differences in nitrate requirements for growth may reflect the efficiency of nitrate uptake and assimilation at subsaturating nitrate concentrations. Given the different physical environments from which these plants came, the data suggest that geographically isolated populations of M. pyrifera have undergone genetic divergence that can be explained by ecotypic adaptation to unique habitat conditions at these sites.
The activity of sulfono-γ-AApeptide helical foldamers that mimic GLP-1

The α-helix–mimicking sulfono-γ-AApeptides with entire unnatural backbone were reported as novel GLP-1R agonists. Existing long α-helix mimicking necessitates the retention of most natural amino acid residues to maintain their biological activity. Here, we report the exploration of helical sulfono-γ-AApeptides with entire unnatural backbones for their ability to structurally and functionally mimic glucagon-like peptide 1 (GLP-1). Our findings suggest that efficient construction of novel GLP-1 receptor (GLP-1R) agonists could be achieved with nanomolar potencies. In addition, the resulting sulfono-γ-AApeptides were also proved to display remarkable stability against enzymatic degradation compared to GLP-1, augmenting their biological potential. This alternative strategy of α-helix mimicking, as a proof of concept, could provide a new paradigm to prepare GLP-1R agonists.
Abstract 3836: Identification of PTPsigma as an autophagic phosphatase

Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL Macroautophagy is a dynamic process whereby portions of the cytosol are encapsulated in double-membrane vesicles and delivered to the lysosome for degradation. Phosphatidylinositol-3-phosphate (PI(3)P) is concentrated on autophagic vesicles and recruits effector proteins critical for this process. The production of PI(3)P by the class III phosphatidylinositol 3-kinase (PI3K), Vps34, has been well established; however, protein phosphatases which antagonize this early step in autophagy remain to be identified. To identify such enzymes, we screened human phosphatase genes by RNA interference (RNAi) and found that loss of PTPsigma, a dual-domain protein tyrosine phosphatase (PTP), increases cellular PI(3)P. The abundant PI(3)P-positive vesicles conferred by PTPsigma loss strikingly phenocopied those observed in amino acid-starved cells. Accordingly, we discovered that loss of PTPsigma hyperactivates both constitutive and induced autophagy. Finally, we found that PTPsigma localizes to PI(3)P-positive membranes in cells and this vesicular localization is enhanced during autophagy. Our findings propose a novel role for PTPsigma and provide insight into the regulation of autophagy. Mechanistic knowledge of this process is critical for understanding and targeting therapies for several human diseases, including cancer and Alzheimer's disease, in which abnormal autophagy may be pathological. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3836. doi:10.1158/1538-7445.AM2011-3836
Holy Basil Curl Leaf Disease Classification using Edge Detection and Machine Learning

Holy basil (Ocimum basilicum L.) is one of the most vital economic crops that has a significant impact on export earnings. However, the holy basil prices could be dropped due to a curl leaf disease caused by pests. Several previous studies focused on plant leaf disease detection based on the leaf color. Unfortunately, the leaf curl disease sometimes changes a shape of the leaf not the color so it cannot be detected with those schemes. We proposed a novel approach aims to automatically detect a curling leaf on holy basil. This paper presents a Neural Network (NN) model and Logistic Regression (LR) model to automatically detect a curling leaf on holy basil. To be able to detect the infected one not by colors but by its shape, we have applied edge detection algorithms which are Canny and Sobel model. To speed up processing time, images were resized and converted to grayscale before passing them to machine learning models. Moreover, NN and LR were modified with mini-batch technique in order to increase the speed of the processing time. The dataset contains 600 images of holy basil leaves with 300 images of healthy leaves and 300 images of infected leaves. The experimental results indicate that the proposed method effectively detects the curling leaves on holy basil.