gebhart/patrepeval huggingface dataset:
Residual Convolutional Neural Network for the Determination of <i>IDH</i> Status in Low- and High-Grade Gliomas from MR Imaging (2017)

<b>Purpose:</b> Isocitrate dehydrogenase (<i>IDH</i>) mutations in glioma patients confer longer survival and may guide treatment decision making. We aimed to predict the <i>IDH</i> status of gliomas from MR imaging by applying a residual convolutional neural network to preoperative radiographic data.<b>Experimental Design:</b> Preoperative imaging was acquired for 201 patients from the Hospital of University of Pennsylvania (HUP), 157 patients from Brigham and Women's Hospital (BWH), and 138 patients from The Cancer Imaging Archive (TCIA) and divided into training, validation, and testing sets. We trained a residual convolutional neural network for each MR sequence (FLAIR, T2, T1 precontrast, and T1 postcontrast) and built a predictive model from the outputs. To increase the size of the training set and prevent overfitting, we augmented the training set images by introducing random rotations, translations, flips, shearing, and zooming.<b>Results:</b> With our neural network model, we achieved IDH prediction accuracies of 82.8% (AUC = 0.90), 83.0% (AUC = 0.93), and 85.7% (AUC = 0.94) within training, validation, and testing sets, respectively. When age at diagnosis was incorporated into the model, the training, validation, and testing accuracies increased to 87.3% (AUC = 0.93), 87.6% (AUC = 0.95), and 89.1% (AUC = 0.95), respectively.<b>Conclusions:</b> We developed a deep learning technique to noninvasively predict <i>IDH</i> genotype in grade II-IV glioma using conventional MR imaging using a multi-institutional data set. <i>Clin Cancer Res; 24(5); 1073-81. ©2017 AACR</i>.
The Gamblers’ Den (1994)

It all starts in 1979 with a General Election, the result of which has had a significance for British political, economic and cultural life only rivalled by that of the very coming to power of the Labour Party in 1945. Indeed, this comparison is particularly apt, for in both instances the assumption of power was accompanied by a conscious intent of change that would challenge the otherwise largely consensual nature of post-war government. In many ways, the programme initiated by that first Thatcher administration, and continued waywardly but insistently ever since, was based on the deconstruction of that post-1945 structure that has largely shaped, for better or worse, the subsequent state of the nation. Very little has been the same since, and the British theatre is no exception. The roots of the theatrical crisis and the direct cause of its continuing malaise must be seen as a direct result of wider government monetarist policy, as must the particular ways in which it has developed.
Structural and Functional Analysis of Caspase Active Sites (2003)

Amino acid sequences of caspases 1, 3, 7, and 8 were aligned with their published three-dimensional (3D) structures. The resultant alignment was used as a template to compare the primary structures of caspases 2, 4−6, and 9−11 to build 3D homology models. The structural models were subsequently refined and validated using structure−activity relationship data obtained from an array of substrate-like inhibitors. All caspases were shown to have identical S1 and catalytic dyad architecture but diverse S2−S4 structures. S2 pockets of these 11 caspases can be briefly categorized into two groups: Csp3, -6, and -7 as one and Csp1, -2, -4, -5, -8, -9, -10, and -11 as the other. S2 pockets of Csp3, -6, and -7 are smaller than those of the other eight caspases, and are limited to binding small P2 residues such as Ala and Val. At the S3 site, the presence of a conserved Arg in all caspases suggests that Glu would be a universally preferred P3 residue. Csp8 and Csp9 have an additional Arg in this pocket that can further enhance the binding of a P3 Glu, whereas Csp2 has a Glu adjacent to the conserved Arg. As such, Csp2 is the only caspase that can accommodate both positively and negatively charged P3. At S4, Csp1, -4, -5, and -11 are closely related with respect to their structures and binder preferences; all have a large hydrophobic pocket and prefer large hydrophobic residues such as Trp. S4 of Csp2, -3, and -7 represents an opposite group with a conformation that is highly specific in binding an Asp. The S4 structures of Csp6, -8, -9, and -10 appear to be hybrids of the two extremes, and have little specificity for any P4. Information revealed from this work provides a guide for designing potent caspase inhibitors with desirable specificity.
PROSPECTS OF IMPROVING ENERGY CONSUMPTION OF THE MULT-STAGE FLASH DISTILLATION PROCESS 1 (2001)

The multi-stage flash (MSF) distillation process in the Arab Gulf Region is superceding other conventional desalting processes. Although the MSF process was introduced more than forty years ago, the development of the process has been evolutionary rather than revolutionary. Research and development efforts were mainly directed towards the control of scale formation on heat transfer tubes by developments and dose rate optimization of scale inhibiting chemicals and adoption of on-line sponge ball cleaning. Other areas of R&D are selection of appropriate construction materials, increase of unit capacity and improvements of the quality and variety of control and instrumentation. The MSF process is an energy intensive process that is associated with high irreversibility. Although coupling the water production with power generation in a dual purpose arrangement reduces the specific fuel energy consumption for water production to around 60 kWh/m 3 which is 50 percent less than that required by single purpose water production desalting plant, it is still much larger than that required by an ideal reversible desalination process. The specific energy consumption of the MSF process can be reduced either by the use of innovative modifications in conventional power cycles and/or by reducing the irreversibility of the MSF process through the improvements in the design and operating features of the distiller.
Recent progress in the consideration of flavoring ingredients under the Food Additives Amendment. 15. GRAS substances. (1990)

Liste des composes aromatiques generalement consideres comme sans danger par un jury d'expert de l'Association des fabricants d'aromes et d'extraits (Etats Unis)
On the computational power of Elman-style recurrent networks (1995)

Recently, Elman (1991) has proposed a simple recurrent network which is able to identify and classify temporal patterns. Despite the fact that Elman networks have been used extensively in many different fields, their theoretical capabilities have not been completely defined. Research in the 1960's showed that for every finite state machine there exists a recurrent artificial neural network which approximates it to an arbitrary degree of precision. This paper extends that result to architectures meeting the constraints of Elman networks, thus proving that their computational power is as great as that of finite state machines.
Human Papillomavirus and Immunosuppression (2014)

Chronic immunosuppression for various reasons is an important risk factor for persistent infections with human papillomaviruses (HPV) and HPV-associated disease. Anogenital cancers and their precursor lesions play an important role in modern HIV medicine. Anal intraepithelial neoplasia and anal cancer are especially prevalent in HIV-positive men who have sex with men, and experts have advocated screening similarly to cervical cancer screening for this high-risk group. HPV-induced skin warts are a frequent problem of organ transplant recipients (OTRs) and a severe manifestation (generalized verrucosis) of certain primary immunodeficiencies. HIV-positive individuals are very often affected by genital warts (condylomata acuminata). Iatrogenic immunosuppression in OTRs allows more active replication of the commensal β-papillomavirus spectrum in the entire skin. A high viral DNA load in plucked eyebrow hairs was shown to imply a significant risk for the development of cutaneous squamous cell carcinoma. This may explain the up to 250-fold increased risk of OTRs to develop precancerous actinic keratoses and skin cancer.
Balancing network performance and network security in a smart grid application (2016)

A key aspect of realizing the future smart grid communication solution is a balanced approach between the network performance and the network security during the network deployment. A high security communication flow path is not useful when the network path cannot support capacity and reachability requirements. The deployment phase in communication network can facilitate an optimal network path by focusing on both the network performance and the network security at the same time. In this paper, we describe a use case of smart grid application where security, network capacity and reachability needs to be optimal for successful network operation. We explain our proposed balancing approach of the network performance and the network security which can be useful for the optimal smart grid secure system design.
The Optimal Steering Control System using Imperialist Competitive Algorithm on Vehicles with Steer-by-Wire System (2015)

Steer-by-wire is the electrical steering systems on vehicles that are expected with the development of an optimal control system can improve the dynamic performance of the vehicle. This paper aims to optimize the control systems, namely Fuzzy Logic Control (FLC) and the Proportional, Integral and Derivative (PID) control on the vehicle steering system using Imperialist Competitive Algorithm (ICA). The control systems are built in a cascade, FLC to suppress errors in the lateral motion and the PID control to minimize the error in the yaw motion of the vehicle. FLC is built has two inputs (error and delta error) and single output. Each input and output consists of three Membership Function (MF) in the form of a triangular for language term "zero" and two trapezoidal for language term "negative" and "positive". In order to work optimally, each MF optimized using ICA to get the position and width of the most appropriate. Likewise, in the PID control, the constant at each Proportional, Integral and Derivative control also optimized using ICA, so there are six parameters of the control system are simultaneously optimized by ICA. Simulations performed on vehicle models with 10 Degree Of Freedom (DOF), the plant input using the variables of steering that expressed in the desired trajectory, and the plant outputs are lateral and yaw motion. The simulation results showed that the FLC-PID control system optimized by using ICA can maintain the movement of vehicle according to the desired trajectory with lower error and higher speed limits than optimized with Particle Swarm Optimization (PSO).
Structural and functional properties of the evolutionarily ancient Y‐box family of nucleic acid binding proteins (1994)

The Y-box proteins are the most evolutionarily conserved nucleic acid binding proteins yet defined in bacteria, plants and animals. The central nucleic acid binding domain of the vertebrate proteins is 43% identical to a 70-amino-acid-long protein (CS7.4) from E. coli. The structure of this domain consists of an antiparallel five-stranded beta-barrel that recognizes both DNA and RNA. The diverse biological roles of these Y-box proteins range from the control of the E. coli cold-shock stress response to the translational masking of messenger RNA in vertebrate gametes. This review discusses the organization of the prokaryotic and eukaryotic Y-box proteins, how they interact with nucleic acids, and their biological roles, both proven and potential.
A cell-based high-throughput screening assay for Farnesoid X receptor agonists. (2007)

A stable and sensitive cell-based high-throughput screening model can be used in high-throughput screening for FXR agonists from the synthetic and natural compound library.
Hollow Capsules of Reduced Graphene Oxide Nanosheets Assembled on a Sacrificial Colloidal Particle (2010)

We introduce a novel and versatile approach for preparing hollow multilayer capsules of graphene oxide nanosheets. Positively charged reduced graphene oxide (rGO-NH3+) and negatively charged reduced graphene oxide (rGO-COO−) were used as building blocks for the layer-by-layer assembly of graphene multilayer films onto polystyrene (PS) colloids. After removing the PS colloids with THF treatment, hollow graphene capsules with necessary physical and chemical stabilities were prepared successfully. Furthermore, we expand this approach in incorporating a new functionality such as gold nanoparticles into a hollow graphene capsule. SEM and TEM analyses suggest the successful preparation of multilayers of hollow graphene capsules and integration of gold nanoparticles into a hollow graphene capsule.
Inverse Relationship between Human Papillomavirus-16 Infection and Disruptive<i>p53</i>Gene Mutations in Squamous Cell Carcinoma of the Head and Neck (2008)

Although HPV16 and mutated p53 may coexist in a subset of HNSCCs, HPV16 and disruptive p53 mutations seem to be nonoverlapping events. A less calamitous genetic profile, including the absence of disruptive p53 mutations, may underlie the emerging clinical profile of HPV16-positive HNSCC such as improved patient outcome.
The Neuroendocrine-Derived Peptide Parathyroid Hormone–Related Protein Promotes Prostate Cancer Cell Growth by Stabilizing the Androgen Receptor (2009)

During progression to an androgen-independent state following androgen ablation therapy, prostate cancer cells continue to express the androgen receptor (AR) and androgen-regulated genes, indicating that AR is critical for the proliferation of hormone-refractory prostate cancer cells. Multiple mechanisms have been proposed for the development of AR-dependent hormone-refractory disease, including changes in expression of AR coregulatory proteins, AR mutation, growth factor-mediated activation of AR, and AR protein up-regulation. The most prominent of these progressive changes is the up-regulation of AR that occurs in >90% of prostate cancers. A common feature of the most aggressive hormone-refractory prostate cancers is the accumulation of cells with neuroendocrine characteristics that produce paracrine factors and may provide a novel mechanism for the regulation of AR during advanced stages of the disease. In this study, we show that neuroendocrine-derived parathyroid hormone-related protein (PTHrP)-mediated signaling through the epidermal growth factor receptor (EGFR) and Src pathways contributes to the phenotype of advanced prostate cancer by reducing AR protein turnover. PTHrP-induced accumulation of AR depended on the activity of Src and EGFR and consequent phosphorylation of the AR on Tyr(534). PTHrP-induced tyrosine phosphorylation of AR resulted in reduced AR ubiquitination and interaction with the ubiquitin ligase COOH terminus of Hsp70-interacting protein. These events result in increased accumulation of AR and thus enhanced growth of prostate cancer cells at low levels of androgen.
Composite curing with high energy electron beams (1996)

Curing of fiber-reinforced polymer composites using high energy electron beams (EB) offers significant advantages for fabricating a variety of aerospace and ground vehicle components. The EB curing process greatly reduces the time required to cross-link the polymer matrix compared to conventional heat curing. The process allows curing at room temperature for high throughput and reduced residual stresses, without the release of volatile organics. Science Research Laboratory (SRL) has developed a new generation of pulsed linear induction accelerators which allow reliable, cost efficient production of high average power electron beams with the necessary parameters for high energy electron beam curing of advanced composites. This paper describes results of EB composite curing experiments, with application to aerospace and ground vehicle components. The paper includes a discussion of processing and material property issues and a description of SRL composite curing equipment.
Resource optimization and deadlock prevention while generating streaming architectures from ordinary programs (2011)

This paper presents a methodology for generating streaming architectures from ordinary programs. It automatically identifies streaming relationships and translates them into parallel computational kernels connected with customized stream buffers. New optimizations are introduced that reduce resource utilization by automatically generating lower bounds on stream buffer sizes. The approach also statically analyzes the design for deadlock and determines appropriate strategies to guarantee prevention. The experimental results show 19-325% improvement in performance and 15-62% reduction in area over non-streaming designs of several software-defined radio applications. This framework allows system-level designers to develop optimized reconfigurable streaming architectures for FPGAs at compile-time.
The time-variable photoplethysmographic signal; dependence of the heart synchronous signal on wavelength and sample volume (1995)

The photoplethysmorgraphic signal (PPG) from forearm skin and the ECG were recorded simultaneously from healthy subjects. The optical signal was derived with a fibre-optic probe which consisted of 61 fibre pairs. The peak-to-peak averaged a.c.-signal was calculated. The dependency of this signal and the signal-to-noise ratio (SNR) on the light wavelength and on sample volume was studied. The light intensities used at 560 nm were 0.015 and 0.029 mWmm-2 and at 940 nm we used 0.029, 1.37 and 2.77 mWmm-2. A theoretical model for calculation of the sample volumes was also developed. The amplitude and SNR of the a.c.-signal at 560 nm is larger than at 940 nm at the same intensity (0.029 mWmm-2). At 940 nm using 1.37 and 2.77 mWmm-2 the a.c.-signal increased with the number of fibre pairs (volume) while the SNR was little affected. At 560 nm it is suggested that the major contribution to the a.c.-signal is pulsations in the ascending arterioles and at 940 nm from pulsations in the larger vessels deeper in the tissue volume under study.
2D Digital Filter Implementation on a FPGA (2011)

The use of two dimensional (2D) digital filters for real-time 2D data processing has found important practical applications in many areas, such as aerial surveillance, satellite\nimaging and pattern recognition. In the case of military operations, real-time image pro-cessing is extensively used in target acquisition and tracking, automatic target recognition and identi cation, and guidance of autonomous robots. Furthermore, equal opportunities exist in civil industries such as vacuum cleaner path recognition and mapping and car collision detection and avoidance. Many of these applications require dedicated hardware for signal processing. It is not efficient to implement 2D digital filters using a single processor for real-time applications due to the large amount of data. A multiprocessor\nimplementation can be used in order to reduce processing time.\nPrevious work explored several realizations of 2D denominator separable digital filters\nwith minimal throughput delay by utilizing parallel processors. It was shown that regardless of the order of the filter, a throughput delay of one adder and one multiplier can be\nachieved. The proposed realizations have high regularity due to the nature of the processors. In this thesis, all four realizations are implemented in a Field Programming Gate\nArray (FPGA) with floating point adders, multipliers and shift registers. The implementation details and design trade-offs are discussed. Simulation results in terms of performance, area and power are compared.\nFrom the experimental results, realization four is the ideal candidate for implementation on an Application Specific Integrated Circuit (ASIC) since it has the best performance, dissipates the lowest power, and uses the least amount of logic when compared to other realizations of the same filter size. For a filter size of 5 by 5, realization four can produce a throughput of 16.3 million pixels per second, which is comparable to realization one and about 34% increase in performance compared to realization one and two. For the given\n filter size, realization four dissipates the same amount of dynamic power as realization one, and roughly 54% less than realization three and 140% less than realization two. Furthermore, area reduction can be applied by converting floating point algorithms to fixed point algorithms. Alternatively, the denormalization and normalization stage of the floating point pipeline can be eliminated and fused together in order to save hardware resources.
Selected Reaction Monitoring (SRM) Analysis of Epidermal Growth Factor Receptor (EGFR) in Formalin Fixed Tumor Tissue (2012)

This report describes and evaluates the performance of a robust and reproducible SRM assay designed for measuring EGFR directly in FFPE patient tumor tissue with accuracy at extremely low (attomolar) levels. This assay can be used as part of a complementary or companion diagnostic strategy to support novel therapies currently under development and demonstrates the potential to identify candidates for EGFR-inhibitor therapy, predict treatment outcome, and reveal mechanisms of therapeutic resistance.
Severe acquired aplastic anemia in children: 11-year experience with bone marrow transplantation and immunosuppressive therapy. (1989)

We reviewed the management and outcome of severe acquired aplastic anemia in 36 patients younger than 18 years old between March 1977 and June 1987. In most patients, no cause could be found. The best therapeutic results were achieved with allogeneic bone marrow transplantation from histocompatible related donors (14 patients), with a cure rate of 79%. Bone marrow transplantation from mismatched related donors was attempted in two patients and failed in both. Immunosuppression using antithymocyte globulin and/or high-dose methylprednisolone represented an alternative treatment in the absence of a suitable bone marrow donor (12 patients) and induced complete remission in 25% of the patients. Children treated with supportive care only (eight patients) had a 75% mortality with a very short survival time. These data confirm the superiority of allogeneic bone marrow transplantation over immunosuppressive therapy in children with severe aplastic anemia.
Origin of low sodium capacity in graphite and generally weak substrate binding of Na and Mg among alkali and alkaline earth metals (2016)

It is well known that graphite has a low capacity for Na but a high capacity for other alkali metals. The growing interest in alternative cation batteries beyond Li makes it particularly important to elucidate the origin of this behavior, which is not well understood. In examining this question, we find a quite general phenomenon: among the alkali and alkaline earth metals, Na and Mg generally have the weakest chemical binding to a given substrate, compared with the other elements in the same column of the periodic table. We demonstrate this with quantum mechanics calculations for a wide range of substrate materials (not limited to C) covering a variety of structures and chemical compositions. The phenomenon arises from the competition between trends in the ionization energy and the ion-substrate coupling, down the columns of the periodic table. Consequently, the cathodic voltage for Na and Mg is expected to be lower than those for other metals in the same column. This generality provides a basis for analyzing the binding of alkali and alkaline earth metal atoms over a broad range of systems.