gebhart/patrepeval huggingface dataset:
Overexpression of a Protein Phosphatase 2C from Beech Seeds in Arabidopsis Shows Phenotypes Related to Abscisic Acid Responses and Gibberellin Biosynthesis (2006)

A functional abscisic acid (ABA)-induced protein phosphatase type 2C (PP2C) was previously isolated from beech (Fagus sylvatica) seeds (FsPP2C2). Because transgenic work is not possible in beech, in this study we overexpressed this gene in Arabidopsis (Arabidopsis thaliana) to provide genetic evidence on FsPP2C2 function in seed dormancy and other plant responses. In contrast with other PP2Cs described so far, constitutive expression of FsPP2C2 in Arabidopsis, under the cauliflower mosaic virus 35S promoter, produced enhanced sensitivity to ABA and abiotic stress in seeds and vegetative tissues, dwarf phenotype, and delayed flowering, and all these effects were reversed by gibberellic acid application. The levels of active gibberellins (GAs) were reduced in 35S:FsPP2C2 plants, although transcript levels of AtGA20ox1 and AtGA3ox1 increased, probably as a result of negative feedback regulation, whereas the expression of GASA1 was induced by GAs. Additionally, FsPP2C2-overexpressing plants showed a strong induction of the Responsive to ABA 18 (RAB18) gene. Interestingly, FsPP2C2 contains two nuclear targeting sequences, and transient expression assays revealed that ABA directed this protein to the nucleus. Whereas other plant PP2Cs have been shown to act as negative regulators, our results support the hypothesis that FsPP2C2 is a positive regulator of ABA. Moreover, our results indicate the existence of potential cross-talk between ABA signaling and GA biosynthesis.
The impact of dual energy CT on pseudo enhancement of kidney lesions (2010)

Renal lesion detection and characterization using Computed Tomography is an important application in genitourinary radiology. Although in general the detection of renal lesions has been shown to be exceedingly accuratce, the detection of benign renal cysts is still problematic. Under certain circumstances, the attenuation values inside a cyst increase incorrectly with an increase in the iodine concentration in the surrounding soft tissue. This so called pseudoenhancement complicates the classification of cysts and creates severe difficulties to distinguish a benign nonenhancing lesion from an enhancing mass. In the present study, the standard procedure based on a single energy 120 kV mode is compared to three dual energy modes available on the Siemens Somatom Definition Flash scanner. In order to simulate the kidney and the lesions, several plastic rods were placed inside a small container filled with different iodine concentrations. This phantom is then positioned inside water tanks of different sizes. The rods simulating the lesions are made out of a special plastic with constant HU value throughout the relevant X-ray energy range. During the project, three important aspects have been discovered: 1) for normal situations, a 100/140 Sn kV mode on the Siemens Flash scanner is similar to the traditional single energy 120 kV mode. 2) For small patient sizes, all dual energy modes show a reduction of pseudoenhancement. 3) For larger patients, only the 100/140 Sn kV mode results in a reduction of pseudoenhancement. Both the 80/140 kV and the 80/140 Sn kV mode show a worse performance than the 120 kV single energy mode in a very large phantom size.
Flash Photolysis in Aqueous Periodate‐Solutions (1982)

Abstract In the flash photolysis of periodate in the pH‐range 2.44 to 4.90 using conductometric detection three reactions are observed with time constants of the order 10 −4 s, 10 −2 s and 1 s (at 298 K and pH = 3). The fastest reaction is attributed to the general acid catalyzed hydration reaction of IO − 4 to H 4 IO − 6 . The two slower reactions are due to the hydrolysis of I 2 O 8 and I 2 O 6 . The relative amounts of these latter reactions depend on the concentration of oxygen in the solution. Oxygen atoms formed rapidly by the photolysis of periodate are scavenged by oxygen with the production of ozone. Ozone oxidizes IO 3 to IO 4 which dimerizes to I 2 O 8 .
Intramolecular Cyclopropanation of Glycals:  Studies toward the Synthesis of Canadensolide, Sporothriolide, and Xylobovide (2001)

[reaction: see text] The first examples of copper-catalyzed intramolecular cyclopropanations of glycal-derived diazoacetates are reported. The new cyclopropanes are converted into advanced intermediates for the synthesis of bislactone natural products. Synthetic highlights include the selective monodeprotection of a di-tert-butylsilylene ether and a zinc-mediated ring opening cascade reaction.
LTE Handover performance evaluation based on power budget handover algorithm (2014)

LTE (Long Term Evolution) is a fourth generation cellular network technology that provides improved performance related to data rate, coverage and capacity compared to legacy cellular systems. In this context, one of the main goals of LTE is to provide fast and seamless handover from one cell to another to meet a strict delay requirement while simultaneously keeping network management simple. Hence, the decision to trigger a handover is a crucial component in the design process of handover, since the success and the efficiency, to a large extent, depends on the accuracy and timeliness of the decision. The design of an efficient and successful handover requires a careful selection of HO parameters and the optimal setting of these. The LTE standard supports two parameters to trigger the handover and select the target cell: hysteresis margin and Time-to-Trigger (TTT) The research topic of this thesis which is “LTE Handover Performance Evaluation Based on Power Budget Handover Algorithm”, focuses on different combinations or settings of HOM and TTT values to evaluate the handover performance based on Reference Signal Received Power (RSRP) measurement within certain deployment scenarios, such as different UE speeds, system loads and cell sizes. The Power Budget Handover Algorithm (PBHA) picks the best hysteresis and time-to-trigger combinations to evaluate the system performance in terms of number of handovers, signal-to-interference plus noise ratio (SINR), throughput, delay and packet lost for UE's which are about to perform the handover.
Design of Anisotropic Thermal Conductivity in Multilayer Printed Circuit Boards (2015)

The design of anisotropic thermal conductivity in multilayer printed circuit boards (PCB) is studied, where the flow of heat is manipulated through the informed layout of circuit board electrothermal traces. Three representative circuit board configurations are considered to illustrate the basic method. A baseline circuit board (Configuration 1) comprising a heat-generating device in thermal communication with a heat sensitive device by the way of a standard electrical trace connection is studied first to characterize heat flow due to conduction and convection. Building off of this baseline structure, the thermal management advantages and disadvantages of a closed heat shield for anisotropic PCB thermal conductivity are explored using the second circuit board (Configuration 2). The design of the third multilayer circuit board (Configuration 3) with optimized anisotropic PCB thermal conductivity for enhanced heat flow control is simultaneously explored. It is experimentally shown that, for PCBs subject to free convection and power densities on the order of 1-10 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , the design technique allows for noticeable (-10 °C) reduction in the temperature of the heat sensitive device without a significant (<;3 °C) increase in the heat-generating device temperature. The experimental heat transfer results are verified through simulations that further confirm and explain the functionality and limitations of the heat flow control concept. The effect of Joule heating is also investigated numerically. A conceptual framework for electrothermal codesign of multilayer PCBs with integrated heat flow control and more device-dense packaging is proposed.
Imaging and Identification of Waterborne Parasites Using a Chip-Scale Microscope (2014)

We demonstrate a compact portable imaging system for the detection of waterborne parasites in resource-limited settings. The previously demonstrated sub-pixel sweeping microscopy (SPSM) technique is a lens-less imaging scheme that can achieve high-resolution (<1 µm) bright-field imaging over a large field-of-view (5.7 mm×4.3 mm). A chip-scale microscope system, based on the SPSM technique, can be used for automated and high-throughput imaging of protozoan parasite cysts for the effective diagnosis of waterborne enteric parasite infection. We successfully imaged and identified three major types of enteric parasite cysts, Giardia, Cryptosporidium, and Entamoeba, which can be found in fecal samples from infected patients. We believe that this compact imaging system can serve well as a diagnostic device in challenging environments, such as rural settings or emergency outbreaks.
Cancer treatment and survivorship statistics, 2019 (2019)

The number of cancer survivors continues to increase in the United States because of the growth and aging of the population as well as advances in early detection and treatment. To assist the public health community in better serving these individuals, the American Cancer Society and the National Cancer Institute collaborate every 3 years to estimate cancer prevalence in the United States using incidence and survival data from the Surveillance, Epidemiology, and End Results cancer registries; vital statistics from the Centers for Disease Control and Prevention's National Center for Health Statistics; and population projections from the US Census Bureau. Current treatment patterns based on information in the National Cancer Data Base are presented for the most prevalent cancer types. Cancer-related and treatment-related short-term, long-term, and late health effects are also briefly described. More than 16.9 million Americans (8.1 million males and 8.8 million females) with a history of cancer were alive on January 1, 2019; this number is projected to reach more than 22.1 million by January 1, 2030 based on the growth and aging of the population alone. The 3 most prevalent cancers in 2019 are prostate (3,650,030), colon and rectum (776,120), and melanoma of the skin (684,470) among males, and breast (3,861,520), uterine corpus (807,860), and colon and rectum (768,650) among females. More than one-half (56%) of survivors were diagnosed within the past 10 years, and almost two-thirds (64%) are aged 65 years or older. People with a history of cancer have unique medical and psychosocial needs that require proactive assessment and management by follow-up care providers. Although there are growing numbers of tools that can assist patients, caregivers, and clinicians in navigating the various phases of cancer survivorship, further evidence-based resources are needed to optimize care.
Quantitative assessment of liver fibrosis: a novel automated image analysis method (2006)

The presented AQS is considered to be a novel approach in the domain of automatic liver fibrosis quantification. It is a true quantification and intelligent approach that attempts to utilize the current semiquantitative methods of liver fibrosis assessment to turn them into real quantitative ones with significant reduction in variability and subjectivity. We propose that our method can be adopted by a panel of expert liver pathologists and software to be developed and used on a wide scale.
Fast and memory efficient feature detection using multiresolution probabilistic boosting trees (2011)

This paper presents a highly optimized algorithm for fast feature detection in 3D volumes. Rapid detection of structures and\nlandmarks in medical 3D image data is a key component for many medical applications. To obtain a fast and memory efficient\nclassifier, we introduce probabilistic boosting trees (PBT) with partial cascading and classifier sorting. The extended PBT\nis integrated into a multiresolution scheme, in order to improve performance and works on block cache data structure which\noptimizes the memory footprint. We tested our framework on real world clinical datasets and showed that classical PBT can be\nsignificantly speeded up even in an environment with limited memory resources using the proposed optimizations.
Dual-Bed Gasification of Petcoke: Model Development and Validation (2010)

In this work, the problem of modeling a previously proposed dual-bed gasification scheme [Sudiro et al., Energy Fuels 2008, 22, 3894−3901] is addressed. The process consists of a combustor and a gasifier, which are thermally coupled by the circulation of an inert solid, to use air instead of pure oxygen in the combustor. The coal gasification reactor is modeled, taking into account both chemical kinetics and mass transfer between gas phase and char particles. First, the model is developed and validated with reference literature and experimental data for conventional coal gasification using oxygen in both entrained-flow and fluid-bed gasifiers. A series of sensitivity analyses is performed with regard to a conventional gasifier fed by petcoke, and the effects of residence time and oxygen/carbon mass ratio in the feed are investigated over three process variables: char conversion at the gasifier exit, temperature at the gasifier exit, and amount of useful syngas (H2 and CO) produced, in terms of N m3 per ton of petcoke. Finally, the model is extended for application to the dual-bed process. Results from this simulation are compared to those obtained under equilibrium conditions, with an energetically equivalent syngas throughput.
The collagen content of the gubernaculum during testicular descent in the pig fetus. (1989)

Contracture of collagen fibres in the gubernaculum has been suggested as a mechanism responsible for fetal descent of the testis. We measured the collagen content of the gubernaculum, fetal thigh muscle and umbilical cord tissue by assaying its hydroxyproline and protein content in 194 male pig fetuses between 60 and 109 days of gestation. During the period of testicular descent (80-90 days of gestation), a decrease occurred in the hydroxyproline/wet mass and protein/wet mass of the gubernaculum, but not of fetal striated muscle or umbilical cord tissue, reflecting an increase in the water content of the gubernaculum during this period. An increase occurred in the hydroxyproline/protein concentration of the gubernaculum and fetal striated muscle, but not of umbilical cord tissue, denoting an accumulation of collagen in the gubernaculum after descent of the testis. In view of the absence of a firm distal attachment of the gubernaculum in the pig fetus, the increase in its collagen content is probably not a cause of descent by exerting traction on the testis, but merely reflects the involution of the gubernaculum noted after descent.
DeepDetectNet vs RLAttackNet: An adversarial method to improve deep learning-based static malware detection model (2020)

Deep learning methods are being increasingly widely used in static malware detection field because they can summarize the feature of malware and its variants that have never appeared before. But similar to the picture recognition model, the static malware detection model based on deep learning is also vulnerable to the interference of adversarial samples. When the input feature vectors of the malware detection model is based on static features of Windows PE (Portable Executable, PE) file, the model is vulnerable to gradient-based attacks. Regarding the issue above, a method of adversarial sample generation is proposed, which can summarize the blind spots of the original detection model. However, the existing malware adversarial sample generation method is not universal and low in generation efficiency due to the need for human control and difficulty in maintaining a normal file format. In response to these problems, this paper proposes a novel method of automatic adversarial samples generation based on deep reinforcement learning. Firstly, a static PE malware detection model based on deep learning called DeepDetectNet is constructed, the original AUC of which can reach 0.989. Then, an adversarial sample generation model based on reinforcement learning called RLAttackNet is implemented, which generates malware samples that can bypass DeepDetectNet. Finally, when we re-input the adversarial samples into the previously trained DeepDetectNet, the original defects of DeepDetectNet can be reinforced. Experimental results show that the RLAttackNet proposed in this paper can generate about 19.13% of malware samples bypass DeepDetectNet. When DeepDetectNet is retrained with these adversarial samples, the AUC value improves from 0.989 to 0.996 and attack success rate has a significant drop, from 19.13% to 3.1%, compared with the original model.
Actions in the Eye: Dynamic Gaze Datasets and Learnt Saliency Models for Visual Recognition (2013)

Systems based on bag-of-words models from image features collected at maxima of sparse interest point operators have been used successfully for both computer visual object and action recognition tasks. While the sparse, interest-point based approach to recognition is not inconsistent with visual processing in biological systems that operate in `saccade and fixate' regimes, the methodology and emphasis in the human and the computer vision communities remains sharply distinct. Here, we make three contributions aiming to bridge this gap. First, we complement existing state-of-the art large scale dynamic computer vision annotated datasets like Hollywood-2 and UCF Sports with human eye movements collected under the ecological constraints of the visual action recognition task. To our knowledge these are the first large human eye tracking datasets to be collected and made publicly available for video, vision.imar.ro/eyetracking (497,107 frames, each viewed by 16 subjects), unique in terms of their (a) large scale and computer vision relevance, (b) dynamic, video stimuli, (c) task control, as opposed to free-viewing. Second, we introduce novel sequential consistency and alignment measures, which underline the remarkable stability of patterns of visual search among subjects. Third, we leverage the significant amount of collected data in order to pursue studies and build automatic, end-to-end trainable computer vision systems based on human eye movements. Our studies not only shed light on the differences between computer vision spatio-temporal interest point image sampling strategies and the human fixations, as well as their impact for visual recognition performance, but also demonstrate that human fixations can be accurately predicted, and when used in an end-to-end automatic system, leveraging some of the advanced computer vision practice, can lead to state of the art results.
Plasmid encoded antibiotic resistance: acquisition and transfer of antibiotic resistance genes in bacteria (2008)

Bacteria have existed on Earth for three billion years or so and have become adept at protecting themselves against toxic chemicals. Antibiotics have been in clinical use for a little more than 6 decades. That antibiotic resistance is now a major clinical problem all over the world attests to the success and speed of bacterial adaptation. Mechanisms of antibiotic resistance in bacteria are varied and include target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Acquisition of genes needed to elaborate the various mechanisms is greatly aided by a variety of promiscuous gene transfer systems, such as bacterial conjugative plasmids, transposable elements and integron systems, that move genes from one DNA system to another and from one bacterial cell to another, not necessarily one related to the gene donor. Bacterial plasmids serve as the scaffold on which are assembled arrays of antibiotic resistance genes, by transposition (transposable elements and ISCR mediated transposition) and site-specific recombination mechanisms (integron gene cassettes).The evidence suggests that antibiotic resistance genes in human bacterial pathogens originate from a multitude of bacterial sources, indicating that the genomes of all bacteria can be considered as a single global gene pool into which most, if not all, bacteria can dip for genes necessary for survival. In terms of antibiotic resistance, plasmids serve a central role, as the vehicles for resistance gene capture and their subsequent dissemination. These various aspects of bacterial resistance to antibiotics will be explored in this presentation.
SVM-based Framework for the Robust Extraction of Objects from Histopathological Images Using Color, Texture, Scale and Geometry (2012)

The extraction of nuclei from Haematoxylin and Eosin (H&E) stained biopsies present a particularly steep challenge in part due to the irregularity of the high-grade (most malignant) tumors. To your best knowledge, although some existing solutions perform adequately with relatively predictable low-grade cancers, solutions for the problematic high-grade cancers have yet to be proposed. In this paper, we propose a method for the extraction of cell nuclei from H&E stained biopsies robust enough to deal with the full range of histological grades observed in daily clinical practice. The robustness is achieved by combining a wide range of information including color, texture, scale and geometry in a multi-stage, Support Vector Machine (SVM) based framework to replace the original image with a new, probabilistic image modality with stable characteristics. The actual extraction of the nuclei is performed from the new image using Mark Point Processes (MPP), a state-of-the-art stochastic method. An empirical evaluation on clinical data provided and annotated by pathologists shows that our method greatly improves detection and extraction results, and provides a reliable solution with high grade cancers. Moreover, our method based on machine learning can easily adapt to specific clinical conditions. In many respects, our method contributes to bridging the gap between the computer vision technologies and their actual clinical use for breast cancer grading.
Artificial photochemical nitrogen cycle to produce nitrogen and hydrogen from ammonia by platinized TiO2 and its application to a photofuel cell (2005)

Photochemical artificial nitrogen cycle was reported to produce dinitrogen and dihydrogen by photodecomposing ammonia with platinized TiO2, and its application to a photofuel cell with a nanoporous TiO2 film electrode, a new concept of a fuel cell to photochemically produce electricity and H2 from ammonia, was proposed.
Interpreting Adversarially Trained Convolutional Neural Networks (2019)

We attempt to interpret how adversarially trained convolutional neural networks (AT-CNNs) recognize objects. We design systematic approaches to interpret AT-CNNs in both qualitative and quantitative ways and compare them with normally trained models. Surprisingly, we find that adversarial training alleviates the texture bias of standard CNNs when trained on object recognition tasks, and helps CNNs learn a more shape-biased representation. We validate our hypothesis from two aspects. First, we compare the salience maps of AT-CNNs and standard CNNs on clean images and images under different transformations. The comparison could visually show that the prediction of the two types of CNNs is sensitive to dramatically different types of features. Second, to achieve quantitative verification, we construct additional test datasets that destroy either textures or shapes, such as style-transferred version of clean data, saturated images and patch-shuffled ones, and then evaluate the classification accuracy of AT-CNNs and normal CNNs on these datasets. Our findings shed some light on why AT-CNNs are more robust than those normally trained ones and contribute to a better understanding of adversarial training over CNNs from an interpretation perspective.