Miracle-dz/UniFAR-FTUs huggingface dataset:
Relating Whole-plant Photosynthesis to Physiological Acclimations at Leaf and Cellular Scales under Drought Stress in Bedding Plants

Bedding plants are at increased risk for exposure to drought stress during production because they are grown in small containers. Physiological mechanisms of bedding plants at leaf and cellular scales that regulate whole-plant photosynthesis under drought conditions are not well understood. This information can be useful for screening bedding plant cultivars with improved drought-tolerance and generate guidelines to mitigate drought stress during production. We subjected drought-sensitive salvia (Salvia splendens ‘Bonfire Red’) and drought-tolerant vinca (Catharanthus roseus ‘Cooler Peppermint’) to gradual drought stress inside whole-plant gas exchange chambers. Substrate water content (Θ), whole-plant net photosynthesis (Pn_avg), whole-plant respiration (Rd_avg), and daily carbon gain (DCG) were measured continuously, whereas stomatal conductance (gS) to water, leaf water (ΨL), osmotic (ΨS), and turgor (ΨP) potentials were measured at the start and end of the drought phase. In addition, ΨS was measured before exposure to stress and after thoroughly rehydrating plants. Dark-adapted quantum efficiency (dark-adapted ΦPSII) was measured after rehydrating plants. The results indicated that, at whole-plant scale, vinca continued to uptake water at lower Θ levels than the Θ level that resulted in wilting of salvia. There were no differences in Rd_avg; however, Pn_avg and DCG of salvia decreased at a higher Θ level than that of vinca. This indicated that salvia experienced drought stress at a higher Θ level than did vinca. At the leaf scale, there were no differences in ΨL; however, a more negative ΨS (P = 0.06) and significantly higher ΨP were observed in vinca (compared to salvia) under drought conditions. In addition, ΨS was not different between species before exposure to drought, whereas ΨS of rehydrated leaves after exposure to drought in vinca was significantly lower than that in salvia. Moreover, ΨS of rehydrated leaves after exposure to drought was significantly lower than that observed before exposure to drought in vinca. This indicated osmotic adjustment (OA) in vinca under drought conditions. Dark-adapted ΦPSII was lower in salvia than in vinca after exposure to drought, indicating damage to photosynthetic mechanisms. Our results suggested that increased OA likely helped to maintain higher ΨP under drought conditions and continuation of water uptake at lower Θ in vinca compared to salvia. In addition, healthier photosynthetic mechanisms of vinca (compared to salvia) under drought conditions likely resulted in its higher Pn_avg and DCG at lower Θ. Screening for OA and dark-adapted ΦPSII may be useful for developing drought-tolerant bedding plant cultivars.
Quantitative assessment of tumor-infiltrating neutrophils to predict immunotherapy responses in metastatic melanoma.

e21039 Background: Tumor-infiltrating neutrophils (TINs) and their myeloid precursors play an important role in cancer biology. While activated neutrophils have been shown to kill tumor cells, there is growing evidence that neutrophils may also support tumor progression by impairing T cell-dependent anti-tumor immunity. We hypothesized that low TINs would be associated with better responses to immunotherapy (IO). Methods: Pretreatment biopsies from 15 metastatic melanoma (MM) pts treated with anti-CTL4 and anti-PD-1 therapy from 2012-17 were collected and stained with myeloperoxidase (MPO). Slides were scanned at 40x magnification on the Aperio ScanScope AT Turbo brightfield instrument (Leica Biosystems) at a resolution of 0.25 microns per pixel. To indicate the region of analysis, the digital pen tool was used to trace a minimum 85% of tumor. Ten fixed-sized boxes were placed on the hottest staining region in a second annotation layer on the image. The boxes equaled 1mm2 in total area. If the tumor tracing had an area of 1mm2, or less, boxes were not placed on the image. The selected tissue was analyzed using an Aperio imaging quatification algorithm . The number of 3+ cells were considered positive for neutrophils and used in subsequent calculations. Quality control review was performed on a subset of cases by Anatomic Pathologists. Response to therapy was assessed using the Response Evaluation Criteria In Solid Tumors (RECIST). Overall survival (OS) was calculated using the Kaplan Meier method. Results: The median number of treatment lines before the biopsy was 1 (range 0-2). The treatment immediately following the biopsy consisted of ipilimumab (n = 10, 66.6%), pembrolizumab (n = 4, 26.6%), ipilimumab/nivolumab (n = 1, 6.6%). The median number of neutrophils in the biopsy hotspot was 92/mm2 (range 6-219) for the entire cohort. For patients achieving PR and CR after 4 cycles of therapy, the median neutrophils were 36/mm2 (IQ 14-78) while the median was 106/mm2 (IQ 60-138) for patients who had progressive disease,( p = 0.04). There was no correlation between the numbers of neutrophils in the biopsy with the absolute neutrophil count in the peripheral blood (R value: 0.012). Conclusions: Decreased TINs are significantly associated with better responses to IO in MM pts. Measurements of TINs may help to select patients who are likely to benefit from anti-CTL4 and anti-PD-1 therapy. Additionally, exploration of whether combining therapies that decrease neutrophils intratumorally should be explored.
Array methods in statistics with applications to the modelling and forecasting of mortality

In this thesis we investigate the application of array methods for the smoothing of multi-dimensional arrays with particular reference to mortality data. A broad outline follows. We begin with an introduction to smoothing in one dimension, followed by a discussion of multi-dimensional smoothing methods. We then move on to review and develop the array methods of Currie et al. (2006), and show how these methods can be applied in additive models even when the data do not have a standard array structure. Finally we discuss the Lee-Carter model and show how we fulfilled the requirements of the CASE studentship. Our main contributions are: firstly we extend the array methods of Currie et al. (2006) to cope with more general covariance structures; secondly we describe an additive model of mortality which decomposes the mortality surface into a smooth twodimensional surface and a series of smooth age dependent shocks within years; thirdly we describe an additive model of mortality for data with a Lexis triangle structure. To Susie I love you. Acknowledgements The help and support of lots of people has enabled me to complete this thesis. I’d like to thank Rajeev Shah, Simon Spencer and Tony Leandro at the CMI for supporting the project and providing the data. Discussions and collaborations with the following people have helped me improve my understanding and helped me formulate new ideas: Giancarlo Camarda, Maria Durban, Paul Eilers, Jutta Gampe, Phillippe Lambert, Stephen Richards, and Richard Willets; special thanks to Richard for being such an understanding boss. I’d like to thank the following house-mates and office-mates for making my time in Edinburgh so much fun: Gudmund, Ellen, Bjorn, Breeda, Cian, Two-Dogs, and Katie. Thanks to Mum, Dad, Rich, Dan, and Mona for being so supportive and keeping me on track. Most of all I’d like to thank my supervisor, Iain. Thank you for inspiring me with your beautiful ideas about arrays; and special thanks for all your kindness, patience, and support while I have been writing up.
Size Selection of Alternative Prey Relative to the Abundance of Primary Prey: Pine Marten Hunting for Frogs

According to optimal foraging theory, a predator should select the most beneficial prey in terms of energy gain relative to handling time. For the pine marten (Martes martes), rodents such as bank voles are the primary prey; however, the pine marten can switch to a variety of secondary prey items (e.g., birds, fruit and frogs) when the rodent abundance is low. We measured frog ilia found in pine marten scats during several consecutive years to assess whether the body mass of consumed frogs varied with changes in rodent abundance. Rodent density was inversely related to the frequency of occurrence of frogs in the marten's diet. Moreover, during the years with low rodent abundance, pine martens ate smaller frogs than in the years with high rodent availability. The average frog weight (18 g) during the years with high rodent density was similar to average vole weight, suggesting that prey of this size has an optimal ratio of foraging effort to energetic gain. During the lean years, martens preyed on frogs smaller than the average vole weight, and during spring this frog size-group is usually the most abundant in the environment. Our results suggest that functional responses of predators to low abundance of primary prey involve not only a prey-switch but also a decrease in the size of secondary prey consumed. Fluctuations in the proportion of frogs eaten in relation to yearly rodent density can affect both marten and frog population demography.
Interaction of Tomatoes (Solanum lycopersicum L.) Transformed by rapA1 Gene with Pseudomonas sp. 102 Bacteria Resistant to High Cadmium Concentrations as a Basis for Effective Symbiotic Phytoremediation System

A Pseudomonas sp. 102 strain, which is highly resistant to toxic effects of cadmium and has plant growth-promoting activity, can significantly increase growth parameters and biomass of tomato plants, including those observed under toxic effects of cadmium. The greatest positive effect was observed in plants transformed with the bacterial adhesin gene rapA1, the product of which is important for colonization of plant roots by bacteria. It was also shown that shoots of transgenic tomato plants accumulated the greatest amount of cadmium during inoculation with Pseudomonas sp. 102. The ability to extract high concentrations of cadmium and accumulate a large biomass under stress opens up prospects for the further use of associative interactions between tomato and Pseudomonas for phytoremediation. phytoremediation, cadmium, tomato, Pseudomonas, inoculation, agglutinins, This study was carried out using the equipment of the Biomika Centre for Collective Use of the Institute of Biochemistry and Genetics (Ufa Federal Research Centre, Russian Academy of Sciences) as part of the government task (project no. AAAA-A16-1160203500284). This study was supported by the Russian Foundation for Basic Research (project nos. 18-34-20004 and 18-34-00033) and 18-344-0033 mol_a_ved and 34-00033 mol_a).
Learners' Perspectives on Networked Collaborative Interaction with Native Speakers of Spanish in the US

In this paper, I discuss a network-based collaborative project that focused on the learning conditions non-native speakers (NNSs) of Spanish perceived to be necessary to satisfactoraly communicate with native speakers (NSs). Data from online discussions, end-of-semester surveys, and final oral interviews are presented and discussed. The results of this study demonstrated that the NNS and NS online collaboration promoted the scaffolding by which the NSs assisted the NNSs in composing meaning (ideas) and form (grammar). In addition, the NNSs praised the unique learning condition of being exposed to a wide range of functional language discourse produced by the NSs. Students perceived that open-ended questions for two-way exchange were meaningful for them because they were encouraged to use specific vocabulary and structures during the discussions. In spite of the positive conditions and benefits created by networked collaborative interaction (NCI), it was found that there were some major issues that are crucial for NCI. This study demonstrates that learners' language proficiency, computer skills, and age differences are important factors to be considered when incorporating institutional NCI as these may linguistically and socially affect the quality of online negotiation and students' motivation toward NCI. Practical ideas for further research are suggested.
CMOS Image Sensor.

新しく登場したCMOSイメージセンサを, すでに撮像素子として確固たる地位を確立しているCCDイメージセンサと比較することにより, その可能性を検討し, これからの技術課題を述べる. 課題を解決できると, CCDセンサと同等またはそれ以上の性能を実現し, 大きな市場を形成すると予想できる. CMOSセンサの可能性としてシステムオンチップの現状についても触れる.
Automated breast cancer lesion detection on breast MRI using artificial intelligence.

e14612 Background: Over 40,000 women in the US will die from breast cancer. Early detection of cancer is crucial and is a potential avenue to improve survival. The objective of this research study is to develop a convoluted neural network (CNN), a subset of artificial intelligence, in order to enhance computerized detection of breast lesions on MRIs. Methods: This is an institutional review board approved retrospective study with post contrast MRI data from 238 patients. Breast tumor segmentation was automated with a hybrid 3D/2D CNN designed adapted from U-net, a popular neural network architecture in biomedical image analysis. T1 post-contrast MRI volumes were used to train the network. The data set was separated into training (80%) and validation (20%) sets. Re-sampling and normalization using z-scores were applied to each volume before training. Contracting and expanding arms of the model consist of successive convolutions followed by batch normalization and ReLU operations. Ground truth was established through manual segmentation and previously conducted readings of the images used to train our network. Results: A 5-fold cross validation was performed for analysis. The Dice similarity coefficient was used to assess segmentation accuracy. The hybrid 3D/2D U-Net architecture yielded a Dice score of 0.753 and a Pearson correlation of 0.548 for the breast tumor segmentation. Conclusions: These results demonstrated the feasibility for artificial intelligence applications in accurately identifying the presence of lesions on breast MRI images.
Mammographic density in asymptomatic menopausal women: correlation with clinical and sonographic findings

OBJECTIVE: To evaluate mammographic breast density in asymptomatic menopausal women in correlation with clinical and sonographic findings. MATERIALS AND METHODS: Mammograms and clinical and sonographic findings of 238 asymptomatic patients were retrospectively reviewed in the period from February/2022 to June/2006. The following variables were analyzed: mammographic density patterns, sonographic findings, patients' age, parity, body mass index and use of hormone replacement therapy. RESULTS: Age, parity and body mass index showed a negative correlation with breast density pattern, while use of hormone replacement therapy showed a positive correlation. Supplementary breast ultrasonography was performed in 103 (43.2%) patients. Alterations which could not be visualized at mammography were found in 34 (33%) of them, most frequently in women with breast density patterns 3 and 4. CONCLUSION: The authors concluded that breast density patterns were influenced by age, parity, body mass index and time of hormone replacement therapy. Despite not having found any malignant abnormality in the studied cases, the authors have observed a predominance of benign sonographic abnormalities in women with high breast density patterns and without mammographic abnormalities, proving the relevance of supplementary ultrasonography to identify breast lesions in such patients.
Energy-Efficient Opportunistic Interference Alignment With MMSE Receiver

This paper introduces a refined opportunistic interference alignment (OIA) technique that uses minimum mean square error (MMSE) detection at the receivers in multiple-input multipleoutput multi-cell uplink networks. In the OIA scheme under consideration, each user performs the optimal transmit beamforming and power control to minimize the level of interference generated to the other-cell base stations, as in the conventional energy-efficient OIA. The result showed that owing to the enhanced receiver structure, the OIA scheme shows much higher sum-rates than those of the conventional OIA with zero-forcing detection for all signal-to-noise ratio regions.
Proteomic Prediction of Breast Cancer Risk: A Cohort Study

Abstract : Our objective is to develop and test proteomic methods for the prediction of breast cancer risk. Our underlying hypothesis is that proteomic analysis of serum will identify proteins differentially expressed in women who do versus those who do not develop invasive breast cancer, and that these differences will be identifiable prior to the clinical presentation of breast cancer. Our work is being conducted in two phases, a training phase and a test phase. Both phases will be conducted as case-control studies nested in a population-based cohort of women who were members of Kaiser Permanente. These serum specimens were collected between 1986 and 1992. We have finalized our cohort definition, finalized the definition of cases and controls, finalized the criteria for matching controls to cases, selected the cases and controls, and pulled and aliquotted the serum specimens. For the proteomic analysis, the serum sample is loaded onto an immunoaffinity column to deplete 12 abundant proteins, and the flow-through fraction is collected and subjected to tryptic digestion. Then the peptides are labeled with iTRAQ reagents and fractionated by cation exchange chromatography (SCX). Six pooled SCX fractions are separately loaded onto a reverse phase column and followed by MALDI-TOF/TOF analyses. The data are automatically processed, combined, and searched against a human protein database. This procedure has been thoroughly tested for reproducibility, quantitation, and complexity and the routine collection of case/control data has been initiated. By applying this high-resolution proteomic approach to a prospective setting, this ongoing project should enhance our ability to identify those women at increased risk of breast cancer and intervene before they progress to cancer. Furthermore, it is expected to provide insight into the biological processes underlying breast cancer development through the identification of protein markers of disease and disease susceptibility genes.
Medicinal properties and growth of Merwilla natalensis.

Merwilla natalensis (Planchon) Speta is ranked as one of the most commonly sold medicinal plants at most of the informal medicinal plant markets found throughout South Africa. The increasing demand for medicinal plants has resulted in overexploitation of many of the wild populations. Overharvesting has resulted in M. natalensis being declared vulnerable. Although this species is so popular, and reports state that the bulbs are used for a variety of ailments, very little is known about its pharmacological activity or phytochemical composition. Extracts were made from mature M. natalensis bulbs using hexane, dichloromethane, methanol and water. These extracts were screened for antibacterial, anticancer, anti-inflammatory, antischistosomal and anthelmintic activity. Antibacterial activity was evaluated using the minimal inhibitory concentration (MIC) assay. Methanol extracts displayed good antibacterial activity against both Gram-positive (Bacillus subtilis and Staphylococcus aureus) and Gram-negative (Escherichia coli and Klebsiella pneumoniae) bacteria. Anti-inflammatory activity was evaluated using the COX-1 and COX-2 bioassays. Dichloromethane extracts displayed the highest inhibitory activity against both COX-1 and -2 enzymes. (80% and 91 % inhibition respectively) Very good activity was displayed against the freeliving nematode Caenorhabditis elegans and the schistosomula worms of Schistosoma haematobium using microdilution techniques. Anticancer activity was evaluated using the biochemical induction assay (BIA) in which DNA-damaging properties are tested for. No activity was found using this assay, however, these results do not prove that M. natalensis does not have other anticancer properties. The phytochemical investigation of mature M. natalensis plants showed the bulbs to contain both saponins and bufadienolides. One of the bufadienolides had the same Rf value as proscillaridin A. Cytotoxicity tests reveal M. natalensis to be extremely cytotoxic, yet the bulbs are commonly sold at traditional medicine markets around South Africa. This cytotoxicity may be accredited to the presence of saponins within the bulbs. No alkaloids or tannins were detected in the bulbs. iii
Antioxidant activity characterization of a commercial juice (apple, strawberry and lemon thyme infusion) and comparison with its manufactured equivalent

Background: Natural juices are nowadays related with healthy food choices due to their antioxidant properties [1]. Yet processing fruit may alter some of its antioxidant properties [2]. It is, therefore, relevant to compare the total phenol content (TPC) and antioxidant activity (AA), of a commercial fruit juice with its manufactured equivalent. Methods: Ten independent samples of commercial juice (CJ) and ten samples of this equivalent manufactured juice (MJ) were analyzed. The TPC were determinate through the Folin-Ciocalteau test [3], and AA through FRAP and DPPH tests [4]. The t-Student test was applied to compare the TPC of the two juices, the two-way ANOVA was used to compare the AA of the two juices for the two tests and the Spearman coefficient to verify the correlation between TPC and AA. Results: Regarding comparison of the juices for TPC, the results revealed a significant difference between juices. A strong interaction between the 2 factors, juice and method was found, which influences the AA. The AA results revealed no significant difference between methods for MJ in spite of a difference for CJ, Table 1. The Spearman Correlation Coefficient obtained for the association between TPC and AA for FRAP and DPPH tests revealed a strong correlation (R = 0.891 and 0,891, respectively) with statistical significance (p < 0.01), for MJ. Regarding CJ, a weak correlation was found between TPC and AA in both methods (R = 0.479 for FRAP and R = 0.467 for DPPH), without statistical significance (p = 0.162 and p = 0.174 respectively). Conclusion: The results revealed significant differences between the commercial and manufactured juices, which is in accordance to the literature [5]. These results suggest an advantage for commercial juice in which concerns the antioxidant properties.
Control of Wild Cane in Soybeans

Greenhouse and field studies showed that α,α,α,-trifluro-2,6-dinitro-N,N-dipropyl-p-toluidine (trifluralin) gave better control of wild cane [Sorghum bicolor (L.) Moench] when incorporated in the soil above rather than below the wild cane seed. Of four herbicides studied in field experiments, trifluralin gave the best control of wild cane in soybeans (Glycine max L., var. Clark) followed by S-propyl dipropylthiocarbamate (vernolate). Herbicides were more effective than cultivation in controlling wild cane, but neither alone was adequate. A combination of cultivation plus herbicides markedly increased soybean yields on wild cane infested areas. These results show that an economical crop of soybeans can be produced on wild cane infested land.