Miracle-dz/UniFAR-FTUs huggingface dataset:
Application of deep learning model (DeepCOVID-19) for detecting COVID-19 cases using chest x-ray images

By the time of the abstract, the coronavirus COVID-19 is affecting 213 countries with more than 9.4 million cases, and more than 480 thousand deaths. In the US it has been confirmed that there are more than 2.4 million COVID-19 cases and approximately 123 thousand related deaths, according to Worldometer. The Wuhan originated COVID-19 has become a global challenge since late December 2019. As control measures lift, life and businesses start going to open, the coronavirus pandemic continues to grow. In this research, we propose a Deep Learning model that recognizes COVID-19 cases using X-ray images (DeepCOVID-19). The model would help physicians to be more confident by having a second opinion in assessing patients. An implementation of the model would help countries where there is shortage of test kits, while X-ray devices are widely available.
Can we make a more efficient U-Net for blood vessel segmentation?

Blood vessel segmentation is an important step in the automated diagnosis of ophthalmic disease from retinal fundus images. The UNet is a popular encoder-decoder architecture widely used in biomedical pixel-wise seg- mentation problems. In this paper, we analyze how the UNet can be used in a more computationally efficient way. Pre-trained weights are used to initialize the network and 3 different architectures are used to compare and analyze the efficacy of the models in terms of both computational cost and performance. Three different deep architectures (VGG16, ResNet34, DenseNet121) are discussed and their efficiencies are compared for the blood vessel segmentation task. Resnet34 architecture achieved highest sensitivity of 0.849 and accuracy and specificity of 0.961, 0.9843 with number of parameters as low as 510178 compared to normal UNet with 34525168 parameters and a sensitivity of 0.756.
Unaltered Brain GABA Concentrations and Resting fMRI Activity in Functional Dyspepsia With and Without Comorbid Depression

Background GABA-deficit characterizes depression (MDD), which is highly comorbid with Functional Dyspepsia (FD). We examined brain GABA concentrations and resting activities in post-prandial distress subtype FD (FD-PDS) patients with and without MDD. Methods 24 female age/education-matched FD-PDS with comorbid MDD (FD-PDS-MDD), non-depressed FD-PDS, and healthy controls each were compared on GABA concentrations, resting fMRI (fALFF) in bilateral pregenual anterior cingulate (pgACC), left dorsolateral prefrontal cortex (DLPFC), insula, and somatosensory cortex (SSC). Results FD-PDS-MDD patients had mild though elevated depressive symptoms. FD-PDS patients had generally mild dyspeptic symptoms. No significant between-group differences in GABA or fALFF were found. No significant correlations were found between GABA and depressive/dyspeptic symptoms after Bonferroni correction. In patients, GABA correlated positively with left insula fALFF (r = 0.38, Bonferroni-corrected p = .03). Conclusion We did not find altered GABA concentrations or brain resting activity in FD-PDS or its MDD comorbidity. The neurochemical link between MDD and FD remains elusive.
Near-Infrared Reflectance Spectroscopy in Precision Feed Formulation

Abstract Because of the problems inherent in determining the digestible amino acid content of batches of feedstuffs used for the formulation of feeds, feed manufactures routinely over-formulate for digestible amino acids. A producer wishing to assure that no more than 20% of the batches of feed produced are nutritionally inadequate must over-formulate by 7.5% for a feed containing 65% maize, 25% soybean meal, and 5% poultry by-products when using randomly-selected batches of these feedstuffs. Selecting batches based on protein content allows for a reduction of this safety margin to 6.3%, since protein is a predictor, albeit a poor one, for digestible amino acid content. Near-Infrared Reflectance Spectroscopy (NIRS) was evaluated as a tool to directly predict the digestible amino acid content of animal meals with the objective to develop a nutritionally relevant quality control tool. Using a database containing 78 animal meals, we developed calibrations that explained 70-90% of the variation in digestible amino acid content. Achieving such a degree of accuracy for all feedstuffs of interest would permit over-formulation to be reduced to 3%. The precision of NIRS technology and its short sample analysis time would give feed mills an efficient, economical quality control tool for producing feeds that more accurately match the nutritional profile calculated.
The general law of dynamics in nonlinear manifolds and Noether’s theorem

The theory of continuous dynamical systems, undergoing motions in a nonlinear configuration manifold, is formulated and developed with a coordinatefree variational approach. The starting point is a new formulation of Hamilton’s action principle in the velocity-time phase-space in which piecewise regularity of the trajectory is assumed and testing variations which are infinitesimal isometries of the trajectory are allowed for. It is shown that localization yields a new general differential law of dynamics and the related jump conditions at singular points. An extended version of Noether’s theorem follows as a simple corollary. The Lagrange’s law is recovered by assuming a torsion-free connection on the configuration manifold.
Towards Automatic EEG Signal Denoising by Quality Metric Optimization

Electroencephalography (EEG) signals are widely used in areas such as: mental disease research, psychological evaluation and Affective Computing. One of the obstacles faced by researchers is related to EEG noise filtering. Involuntary muscle activity, such as eye-blinks and mandibular movements, insert noise into the signal which has a negative impact on its quality thus may result in misleading conclusions. Consequently, this study proposes an approach to remove noise in EEG signals based on a deep learning strategy that optimizes quality assessment algorithms. Furthermore, our methodology trains a model that learns how to optimize algorithms of quality assessment. In such manner, EEG signal users will not need human interference to extract noise which saves time and resources. To evaluate the robustness of our approach, we compare it with a baseline band-pass filter in terms of Peak Signal-to-Noise Ratio (PSNR), Structural Similarity index (SSIM) and quality scores. Our approach has demonstrated superior performance over the baseline technique in terms of PSNR and considering the second quality score applied. These are still preliminary results, yet they show great potential for continued development. Furthermore, this approach provides a new perspective on how to build deep learning methodologies in order to remove noise in EEG signals.
Mangrove biogeography : the role of quaternary environmental and sea-level change

Mangroves and corals have broadly similar pat- terns of global distribution with a major disjunction between New World and Old World populations. However, while palaeogeographic interpretations of present coral dis- tributions have emphasized the role of environmental and sea-level fluctuations during the Quatemary, the traditional explanation of mangrove distributions has invoked gradual dispersal over the Tertiary and Quatemary from a Southeast Asian centre of origin. The distribution of mangroves at their latitudinal limits and on oceanic islands is examined. These observations together with palynological evidence for substantial changes in mangrove extent in the Holocene are used to suggest that sea-level fluctuations in particular have caused major disruptions to mangrove distributions during the Quatemary. Many species of mangroves have re- colonized oceanic islands during the Holocene and their present distribution is, at least in part, a function of their successful transoceanic dispersal to these islands. Although little evidence of Pleistocene distributions of mangroves is preserved, environmental and especially sea-level fluctuations are likely to have played a similar role in the biogeography of mangroves as they have in influencing the biogeography of corals.
On the Optimal Calculation of the Rice Coding Parameter

In this article, we design and evaluate several algorithms for the computation of the optimal Rice coding parameter. We conjecture that the optimal Rice coding parameter can be bounded and verify this conjecture through numerical experiments using real data. We also describe algorithms that partition the input sequence of data into sub-sequences, such that if each sub-sequence is coded with a different Rice parameter, the overall code length is minimised. An algorithm for finding the optimal partitioning solution for Rice codes is proposed, as well as fast heuristics, based on the understanding of the problem trade-offs.
Vegetation-pollen-climate relationships for the arcto-boreal region of North America and Greenland

We examine modem pollen, vegetation and climate relationships for the arcto-boreal region of North America using isopollen maps, scatter diagrams and re- sponse surfaces. These analyses are based on an array of 1119 modern pollen sites extending from Alaska to Green- land (excluding the Pacific-Cordillera region of western North America) and north of 42? N latitude. The pollen sum consists of thirty-one taxa selected for their abundance on the modern landscape or significance as indicators of par- ticular vegetation types. Response surfaces were calculated using a locally weighted-average procedure in order to display the percentages of the various taxa as a function of one to three climate variables. The isopoll maps accurately reflect taxa abundance and range limits, although the actual percentage at these limits may vary. Pollen of the major boreal taxa have optima at 10-20? C and dry (Pinus), moist (Abies) and intermediate (Picea) values of precipitation. Monospecific pollen taxa and those where the species have similar ecologies show a simple climate optimum, whereas pollen taxa with several species, such as Betula, show multiple optima. Each boreal taxon, even those with similar ranges, has a unique surface, suggesting that community level responses to climatic change, whether past or future, are likely to be complex and variable throughout North America.
A NEUROMORPHIC CHIP THAT IMITATES THE ON SLUGGISH SUSTAIN GANGLION CELL SET IN THE RETINA OF RABBITS

The mammalian retina is comprised of five different kinds of cells, for each kind can be divided into more types. Besides transducing the visual world into neural signals, these cells are in charge of 0.3% of the visual function of the brain. In this research, we try to understand the retinal functions from the engineering point of view. In this thesis, a new design methodology is proposed to implement CMOS neuromorphic chips which imitate the ON sluggish sustain ganglion cell set of rabbits’ retinas. A retinal chip based on the biological model derived from the mammalian retina is proposed. The retinal chip contains a focal plane sensory array of 32x32 similar basic cells that perform the functions. Each basic cell contains photo-input, photoreceptor, horizontal cell, on bipolar cell, off bipolar cell, amacrine cell and ganglion cell. ESD protection circuit for I/O pads, address decoders and readout circuits are also included in this chip. Finally, the results of HSPICE simulation and chip measurement are compared with that of the original model to examine the consistency and the difference for further improvement. The
Metabolic Rates of Female Viviparous Lizards (Sceloporus jarrovi) throughout the Reproductive Cycle: Do Pregnant Lizards Adhere to Standard Allometry?

The standard metabolic rate (SMR) of viviparous female lizards (Sceloporus jarrovi) was measured at different times during the reproductive cycle at 30°C. The pattern of change in rate of O₂ consumption (V̇o2) during pregnancy is sigmoidal. Oxygen consumption increases slowly during the first two-thirds of pregnancy and rapidly during the last trimester, with a slight plateau before parturition. Immediately following parturition, V̇o2 decreases sharply and is not different from V̇o2 of nonreproductive females. The SMRs of early, middle, and late pregnant lizards is 80%, 98%, 140%, respectively, of that expected of nonreproductive lizards, after adjusting SMR for body mass. Deviations from standard allometry are due mostly to changes in litter metabolism. Litter metabolism is low during early pregnancy because litter mass consists mostly of metabolically inert yolk. At the end of gestation most of the mass of a litter consists of metabolically active embryos, which have nearly twice the mass-specific metabolic rate of the female's somatic mass. It can no longer be assumed that gravid or pregnant lizards conform to inter-or intraspecific allometric equations relating V̇o2 to body mass. When constructing energy budgets for female squamates, investigators should take into account changes in maternal V̇o2 during pregnancy, as well as the litter's contribution to that change.
Cys-Oxidation of Protein Tyrosine Phosphatases: Its Role in Regulation of Signal Transduction and Its Involvement in Human Cancers

Reactive oxygen species (ROS) are currently viewed as secondary messengers that control signal transduction through the post-translational modifications of Cys-oxidation in targeting proteins. The physiological levels of ROS are generated in response to stimulation induced by extracellular ligands. Due to the labile feature of ROS, the effect of protein oxidation is normally transient. Such a character is essential for the precise control of redox-dependent signaling homeostasis. Nevertheless, studies have shown that under pathological conditions, such as certain types of cancer, the cellular ROS are produced in a ligand-independent manner. Interestingly, the generation of ROS is required for the development of transformed phenotype and tumors, suggesting that the constitutive oxidation of signaling modulators might contribute to the uncontrolled signaling cascades, further leading to pathological consequences. Emerging evidence has revealed that protein tyrosine phosphatases (PTPs), which regulate tyrosine phosphorylation-dependent signal transduction through tyrosine dephosphorylation of substrates, are highly susceptible to oxidation. Interestingly, oxidation of catalytic Cys residue results in enzymatically inactivated form of PTPs, concomitant with an enhanced tyrosine phosphorylation level in cells. The primary focus of this review is to comprehend recent studies that greatly advanced our understanding towards redox-dependent regulation of cell signaling through Cys oxidation of endogenous PTPs. The rational implication of this mechanism in contributing to the development and maintenance of cell transformation is discussed.
Diet Induced Inflammation and Potential Consequences on Fetal Development

The significance of diet induced inflammation in gestational tissue (chorioamnionitis) on fetal growth and development is emerging as an important area of research. Role of infection and intrauterine inflammation in preterm deliveries has been extensively explored, but, implication of sterile inflammation (not associated with infection) on fetal development has received little attention. Inflammation is generally thought to be the result of a local or systemic infection or products of infection; conversely, inflammation may result from high calorie intake or from diets low in micronutrients. While systemic inflammation is widely proposed as the predisposing factor for the increasing incidence of non-communicable diseases such as diabetes mellitus and cardiovascular diseases in adults, accumulating evidences now suggest that low grade intrauterine inflammation might impair linear growth and adversely affect myogenesis and adipogenesis that might have lasting effects on offspring. Given that intrauterine inflammation is frequently present, its origin and impact on fetal development needs attention. The public health implications of nutrition-mediated inflammation is of particular importance in India, which is burdened with problem of over-nutrition coupled with undernutrition and micronutrient malnutrition. Studies to unearth the link between nutrition and inflammation and its impact on fetal growth and development are needed. This review explores the potential consequences of intrauterine inflammation on fetal growth and development.
Deep Learning-based Object Detection for Crop Monitoring in Soybean Fields

In this paper, a soybean flower/seedpod detection system is built for collecting growing state information by introducing convolutional neural networks, aiming that observed plant states (e.g., #flowers and #seedpods) are used to predict the crop yields of soybeans by combining the environment information in future. To predict the crop yields (i.e., quantity of seedpods) precisely, it is considered important to know how the number of flowers are translated over time and how such flower transients can affect the final yields of soybeans. However, there has not existed a way to measure the number of flowers in real environments. For this purpose, We propose a deep learning approach to automatically detect flower and seedpod regions from images which are taken in real soybean fields without environmental control. Various object detection methods are compared, including RetinaNet, Faster R-CNN, and Cascade R-CNN. Ablation studies are provided to analyze how these methods perform on both flower and seedpod across different parameters. In our experimental results, Cascade R-CNN gives the best average precision (AP) of 89.6, while RetinaNet and Faster R-CNN give AP of 83.3 and 88.7, respectively. Cascade RCNN also attains the highest accuracy in detecting small objects, which are not easily detected by other models. With accurate detection, the system is expected to contribute to constructing high-performance measurement for soybean flowers and seedpods, which ultimately leads to better pipeline in evaluating plant status.
Zidovudine or azidothymidine

In 1964, Jerome Horwitz synthesized the drug zidovudine, commonly abbreviated ZDV, otherwise known as azidothymidine, or AZT, at Wayne State University School of Medicine in Detroit, Michigan. Horwitz and his colleagues originally developed zidovudine to treat cancers caused by retroviruses. In 1983, Nobel Prize in Physiology or Medicine [6] recipients Françoise BarréSinoussi and Luc Montagnier [7] discovered a new retrovirus [8], the human immunodeficiency virus, or HIV, at the Pasteur Institute in Paris, France. HIV weakens the immune system and can be passed from a pregnant woman to her fetus [9] in utero, or in the womb [10]. In 1984, scientist Marty St. Clair and her team determined that zidovudine could help treat HIV. Zidovudine was the first medicine discovered to help treat HIV and prevent the transmission of HIV from affected pregnant women to fetuses in the womb [10] by blocking the virus from passing through the placenta [11].
BOBCAT (LYNX RUFUS) HOME RANGE SIZE AND HABITAT USE IN NORTHWEST WISCONSIN

Bobcats were radio-tagged and monitored to estimate and compare annual and seasonal patterns in home range size and habitat use in northwestern Wisconsin. Annual and seasonal male home ranges extensively overlapped those of other males and females, whereas females maintained more exclusive areas. Annual male home ranges (60.4 km2 ? 23.4 kM2) were 112% larger than those of females (28.5 km2 + 3.7 kM2). Females expanded and contracted their home ranges seasonally; the largest home ranges occurred in winter. Males shifted similar-sized ranges seasonally resulting in larger annual ranges. Male bobcats selected lowland conifer forests, and avoided upland conifer stands, upland deciduous forest and mixed savanna cover-types. Females exhibited similar preferences but also selected for lowland deciduous forests and avoided unforested areas. Seasonal shifts in habitat use were evident for males and females; both used lowland conifer stands more, and unforested areas and upland deciduous forests less, in winter. The selection of lowland coniferous forests by males and females during all seasons suggest these areas are important range components
THE DESIGN AND ANALYSIS OF NEW CMOS CURRENT READOUT INTRGRATED CIRCUIT FOR INFRARED DETECTOR ARRAY

In this thesis, new CMOS current readout design techniques are proposed, developed, and applied to the implementation of readout integrated circuit chip for infrared detector array. The readout circuit will be combined with the infrared detector chip developed by Chunghwa Telecom Lab to complete the entire IR image system. In the proposed structure a new readout structure is proposed called improved buffered gate modulation input (improved BGMI) circuit is adapted as the input stage. In the improved BGMI circuit, there is an integration capacitance in every pixel to improve the readout rate. Besides, high swing cascode current mirror is used in the new structure. Therefore the current gain is not sensitive to the Early effect and the output swing of the current mirror can be increased. Linearity is also improved by using the new circuit. A dynamic discharge output stage is also design and analyzed. It can improve the speed performance and consumes only dynamic power dissipation.
Production of Triterpenes from Cell Suspension Cultures of Solanum incanum L.

This paper describes the secondary metabolites produced by a cell suspension culture of Solanum incanum L. The investigation led to the characterization of five triterpenes, glut-5(6)-en-3β-ol (1), lupeol (2), betulin (3), betulinic acid (4) and betulinaldehyde (5). Their structures were determined on the basis of spectral analysis. Of these, betulinic acid, a potent anti-HIV agent, was found to be a major product. Glut-5(6)-en-3β-ol was a rare natural product.
Regeneration of plants from alginate-encapsulated shoots of Tylophora indica (Burm. f.) Merrill, an endangered medicinal plant

Summary A protocol has been developed for plant regeneration from encapsulated nodal segments of Tylophora indica. Nodal segments collected from a 2-year-old plant were encapsulated in calcium alginate beads. The best gel complex was achieved using 3% (w/v) sodium alginate and 100 mM CaCl2.2H2O. The maximum frequency (91%) of conversion of encapsulated beads into plantlets was achieved on Murashige and Skoog (MS) medium containing 2.5 µM 6-benzyladenine (BA) and 0.5 µM αnaphthalene acetic acid (NAA) after 6 weeks of culture. Encapsulated nodal segments stored at 4°C for 1 – 8 weeks also showed successful conversion, followed by development into complete plantlets when returned to regeneration medium. Conversion of encapsulated nodal segment into plantlets also occurred when the calcium alginate beads were sown directly into SoilriteTM moistened with ½2MS salts. Plants regenerated from encapsulated nodal segments could be hardened, acclimatised and established in soil, with a success rate of 90%. Encapsulation of vegetative propagules in calcium alginate beads could be useful for the exchange, storage and micropropagation of germplasm of this endangered medicinal plant.