gebhart/patrepeval huggingface dataset:
Multitask Classification of Breast Cancer Pathological Images Using SE-DenseNet (2019)

Breast cancer has always been the main killer of women. The constantly development of Convolutional Neural Network (CNN) greatly improved the possibility of early diagnostics of breast cancer owing to its high efficiency and accuracy. In this paper, we apply the architecture of Densely Connected Convolutional Network (DenseNet), and then assimilate into Squeeze-and-Excitation Network (SeNet) to perform multitask classification on Camelyon16 which is a set of images of hematoxylin and eosin (H&E) stained breast histology microscopy. Whole-slide images (WSIs) are generally stored in a multi-resolution pyramid, our dataset contains patches of Camelyon16 under ×5, ×20, ×40 three magnifications. Our multitask is to identify the magnification of the patch and distinguish whether the extracted patch belongs to metastatic tumor area of WSIs at the same time by link two classifiers at the end of the same network. Whether on multitask or a single subtask, our network has showed excellent performance, SE-DenseNet-40 has even achieved an accuracy of 92.92% on CIFAR-10.
Abstract 2163: Combined targeting of MEK and MCL-1 induces apoptosis and tumor regression of KRAS mutant NSCLC (2017)

Abstract There are currently no effective targeted therapeutic strategies for KRAS mutant non-small cell lung cancer (NSCLC). Single agent MEK inhibitors have demonstrated showed disappointing clinical activity, partly due to inability to induce a robust apoptotic response. Combining MEK inhibitors with BCL-XL/BCL-2 inhibitors may be effective for a subset of KRAS mutant cancers that are dependent on BCL-XL for survival, however this combination is unlikely to be an effective strategy for cancers dependent on MCL-1. We investigated the effect of combining the MEK inhibitor trametinib with a novel MCL-1 inhibitor (compound A), which possesses potent and selective anti-MCL-1 activity in vitro and in vivo, on KRAS mutant cancers. In contrast to colorectal cancer models, which are largely sensitive to combined MEK + BCL-XL inhibition, a subset of cell line and patient-derived mouse xenograft (PDX) KRAS mutant NSCLC models were significantly more sensitive to MEK + MCL-1 inhibition compared to MEK + BCL-XL. To model potential clinical strategies, we tested intermittent dosing regimens and unexpectedly discovered a method strategy for dramatically sensitizing KRAS mutant NSCLC cells to the MEK + MCL-1 combination. These studies provide rationale for the clinical evaluation of combined MEK + MCL-1 inhibitors for KRAS mutant NSCLC. Citation Format: Aaron N. Hata, Faria M. Siddiqui, Maria Gomez-Caraballo, Samantha J. Bilton, Daria Timonina, Varuna Nangia, Angela Coxon, Sean Caenepeel, Paul Hughes. Combined targeting of MEK and MCL-1 induces apoptosis and tumor regression of KRAS mutant NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2163. doi:10.1158/1538-7445.AM2017-2163
Identification of a degrading enzyme in human serum that hydrolyzes a C‐terminal core sequence of neuromedin U (2015)

Neuromedin U (NMU), an anorexigenic peptide, has attracted attention as a candidate for development of drugs against obesity. We recently developed several potent hexapeptidic agonists derived from NMU that share a common Pro-Arg-Asn-NH2 (PRN) sequence at their C-termini and found that the amide bond between Arg and Asn is rapidly degraded in serum. In this study, we determined that the key enzyme responsible for this biodegradation was thrombin. Both irreversible and reversible thrombin inhibitors (PPACK and argatroban, respectively) enhanced the serum stability of both hexapeptidic agonists and human NMU itself as an inherent ligand. In addition, rapid degradation did not occur in citrated human plasma because thrombin was not activated under these conditions. Furthermore, we found that an N-terminal 2-thienylacetyl group in hexapeptidic agonists enhanced recognition by thrombin. These findings will be valuable for future investigations of the biological functions of NMU in vivo. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 440-445, 2016.
Tendons and Ligaments: Connecting Developmental Biology to Musculoskeletal Disease Pathogenesis (2017)

Tendons and ligaments provide connections between muscle and bone or bone and bone to enable locomotion. Damage to tendons and ligaments caused by acute or chronic injury or associated with aging and arthritis is a prevalent cause of disability. Improvements in approaches for the treatment of these conditions depend on a better understanding of tendon and ligament development, cell biology, and pathophysiology. This review focuses on recent advances in the discovery of transcription factors that control ligament and tendon cell differentiation, how cell and extracellular matrix homeostasis are altered in disease, and how this new insight can lead to novel therapeutic approaches. © 2017 American Society for Bone and Mineral Research.
SNP analysis using catacleave probes (2008)

CataCleave probes are catalytically cleavable fluorescence probes having a chimeric deoxyribonucleic acid (DNA)-ribonucleic acid (RNA)-DNA structure that can be used for real-time detection of single nucleotide polymorphisms (SNPs), insertions, and deletions. Fluorescent donor emission is normally quenched by Förster resonance energy transfer (FRET). Upon binding to the target, if the RNA/DNA hybrid is correctly base-paired, ribonuclease (RNase) H will cleave the RNA moiety and the probe fragments will dissociate. FRET is lost and the donor fluorescence signal is recovered. A single-base mismatch within the hybrid region causes probe cleavage to be significantly reduced. We designed CataCleave probes to detect SNPs located in the insulin-like growth factor 2 (IGF-2) gene and at position 702 within the NOD2/CARD15 gene. Probes were also designed to detect a six-basepair deletion in the amelogenin gene and a partially methylated target DNA. Discrimination between wild-type and SNP is demonstrated for both genes in homogeneous reactions under isothermal and temperature cycling conditions. These probes were also able to identify a multibase deletion and methylated DNA. Cleavage rates were proportional to target concentration. Probe length and position of fluorescent labels may also be modified for use in multiplexing high-throughput SNP assays. This represents a novel method for the detection of SNPs.
The Rac GTPase effector p21-activated kinase is essential for hematopoietic stem/progenitor cell migration and engraftment (2013)

The p21-activated kinases (Paks) are serine/threonine kinases that are major effectors of the Rho guanosine 5'\x{2011}triphosphatase, Rac, and Cdc42. Rac and Cdc42 are known regulators of hematopoietic stem and progenitor cell (HSPC) function, however, a direct role for Paks in HSPCs has yet to be elucidated. Lin(-)Sca1(+)c-kit(+) (LSK) cells from wild-type mice were transduced with retrovirus expressing Pak inhibitory domain (PID), a well-characterized inhibitor of Pak activation. Defects in marrow homing and in vitro cell migration, assembly of the actin cytoskeleton, proliferation, and survival were associated with engraftment failure of PID-LSK. The PID-LSK demonstrated decreased phosphorylation of extracellular signal-regulated kinase (ERK), whereas constitutive activation of ERK in these cells led to rescue of hematopoietic progenitor cell proliferation in vitro and partial rescue of Pak-deficient HSPC homing and engraftment in vivo. Using conditional knock-out mice, we demonstrate that among group A Paks, Pak2(-/-) HSPC show reduced homing to the bone marrow and altered cell shape similar to PID-LSK cells in vitro and are completely defective in HSPC engraftment. These data demonstrate that Pak proteins are key components of multiple engraftment-associated HSPC functions and play a direct role in activation of ERK in HSPCs, and that Pak2 is specifically essential for HSPC engraftment.
E EARNING MANAGEMENT: THE EFFECT OF MANAGEMENT OVERCONFIDENCE AND CORPORATE GOVERNANCE (2022)

Many studies have discussed the determinants of earning management. However, most of these studies discuss external factors of management such as audit quality and quality of disclosure and as a determinant of earning management. Study that tries to examine the intrinsic factors such as managerial overconfidence effect on earning management has not been widely conducted, especially in companies listed on IDX, Indonesia. This study aims to examine the effect of managerial overconfidence on earning management in companies listed on IDX. Furthermore, this study also aims to determine the moderating effect of corporate governance mechanisms on the relationship between managerial overconfidence. By using data analysis with the SEMPLS technique, the present study has succeeded to prove that managerial overconfidence affect earning management. Furthermore, this study also successfully provide evidence that corporate governance mechanisms such as independent audit committees and audit committee activities moderate the relationship between managerial overconfidence and earning management.
Antibody reactivity with new antigens revealed in multi‐transgenic triple knockout pigs may cause early loss of pig kidneys in baboons (2020)

These data suggest that neoantigens associated with mTg Tri-KO promote acute xenograft rejection in a pig-to-baboon VT + K XTx model. The screening assays may be useful to select "safe" recipients to receive mTg Tri-KO kidneys.
Demonstration of Aluminum-Air Fuel Cells in a Road Vehicle (1989)

<div class="htmlview paragraph">This paper discusses recent progress in the application of aluminum-air fuel cell technology to road vehicles. Preliminary road tests were conducted to compare the performance of an aluminum-air/lead-acid hybrid battery energy source with that of a conventional lead-acid-only energy source. One of Unique Mobility's Electrek hatchback vehicles was converted into a highly instrumented testbed for testing the aluminum-air/lead-acid hybrid. Tests showed that at least a doubling of the range was achieved in an all-electric vehicle using the aluminum-air/lead-acid hybrid approach. The demonstration provided focus to necessary future developments in aluminum-air fuel cell engineering for vehicle applications. Test data are presented, as well as projections on future developments of the aluminum-air fuel cell as a vehicle power source.</div>
Volume Rendering on Server GPUs for Enterprise-Scale Medical Applications (2010)

We describe a system for volume rendering via ray casting, targeted at medical data and clinicians. We discuss the benefits of server vs client rendering, and of GPU vs CPU rendering, and show how we combine these two advantages using nVidia’s Tesla hardware and CUDA toolkit. The resulting system allows hopsital-acquired data to be visualized on-demand and in real-time by multiple simultaneous users, with low latency even on low bandwidth networks and on thin clients. Each GPU serves multiple clients, and our system scales to many GPUs, with data distribution and load balancing, to create a fully scalable system for commercial deployment. To optimize rendering performance, we present our novel solution for empty space skipping, which improves on previous techniques used with CUDA. To demonstrate the flexibility of our system, we show several new visualization techniques, including assisted interaction through automatic organ detection and the ability to toggle visibility of pre-segmented organs. These visualizations have been deemed by clinicians to be highly useful for diagnostic purposes. Our performance results indicate that our system may be the best-value option for hospitals to provide ubiquitous access to state-of-the-art 3D visualizations.
Valley splitting in strained silicon quantum wells modeled with 2° miscuts, step disorder, and alloy disorder (2007)

Valley splitting (VS) in strained SiGe∕Si∕SiGe quantum wells grown on (001) and 2° miscut substrates is computed in a magnetic field. Calculations of flat structures significantly overestimate, while calculations of perfectly ordered structures underestimate experimentally observed VS. Step disorder and confinement alloy disorder raise the VS to the experimentally observed levels. Atomistic alloy disorder is identified as the critical physics, which cannot be modeled with analytical effective mass theory. NEMO-3D is used to simulate up to 106 atoms, where strain is computed in the valence-force field and electronic structure in the sp3d5s* model.
Combination of analytical and finite element methods to obtain acoustic fields in complex structures driven by piezoelectric multi-layered transducers (2002)

This paper presents a method to obtain the acoustic field in complex structures driven at a plane by a multi-layered piezoelectric transducer of simple geometry. The Finite Element Method (FEM) is used in the complex structure to compute the fields and the acoustic impedance presented to the transducer. This procedure is computer intensive, but is obtained only once for a frequency range. The electric impedance of the transducer loaded with the computed acoustic impedance is obtained with the chain matrix, a fast analytical method, and FEM. These two approaches were applied to a steel tube driven through a coupler by a power transducer. Measured and calculated electric impedances are compared.
Palmitoleic Acid Enrichment of Seabuckthorn (Hippophaë rhamnoides L.) Pulp Oil by Crystallization Process (2008)

Abstract Seabuckthorn pulp oil was fractionated using a crystallization process with acetone under controlled cooling rate of 0.25°C/min without agitation at different crystallization temperatures ranging from − 15 to 15°C. The obtained liquid (LF) and solid (SF) fractions were analyzed for their fatty acid and triacylglycerol compositions and their melting profiles were characterized. Fractionation at − 15°C yielded about 20% of LF where palmitoleic acid represented 53% of total lipids. The SF fraction was mainly rich in palmitic acid. LF were richer in triacylglycerol with acyl carbon numbers of 50 and 52 (C50 and C52) than SF, which contained a higher amount of C48. The melting curves of LF and SF showed multiple endothermic transitions.
Deep Kernel Learning (2015)

We introduce scalable deep kernels, which combine the structural properties of deep learning architectures with the non-parametric flexibility of kernel methods. Specifically, we transform the inputs of a spectral mixture base kernel with a deep architecture, using local kernel interpolation, inducing points, and structure exploiting (Kronecker and Toeplitz) algebra for a scalable kernel representation. These closed-form kernels can be used as drop-in replacements for standard kernels, with benefits in expressive power and scalability. We jointly learn the properties of these kernels through the marginal likelihood of a Gaussian process. Inference and learning cost $O(n)$ for $n$ training points, and predictions cost $O(1)$ per test point. On a large and diverse collection of applications, including a dataset with 2 million examples, we show improved performance over scalable Gaussian processes with flexible kernel learning models, and stand-alone deep architectures.
Blockade of advanced glycation end-product formation restores ischemia-induced angiogenesis in diabetic mice (2003)

We hypothesized that formation of advanced glycation end products (AGEs) associated with diabetes reduces matrix degradation by metalloproteinases (MMPs) and contributes to the impairment of ischemia-induced angiogenesis. Mice were treated or not with streptozotocin (40 mg/kg) and streptozotocin plus aminoguanidine (AGEs formation blocker, 50 mg/kg). After 8 weeks of treatment, hindlimb ischemia was induced by right femoral artery ligature. Plasma AGE levels were strongly elevated in diabetic mice when compared with control mice (579 +/- 21 versus 47 +/- 4 pmol/ml, respectively; P < 0.01). Treatment with aminoguanidine reduced AGE plasma levels when compared with untreated diabetic mice (P < 0.001). After 28 days of ischemia, ischemic/nonischemic leg angiographic score, capillary density, and laser Doppler skin-perfusion ratios were 1.4-, 1.5-, and 1.4-fold decreased in diabetic mice in reference to controls (P < 0.01). Treatment with aminoguanidine completely normalized ischemia-induced angiogenesis in diabetic mice. We next analyzed the role of proteolysis in AGE formation-induced hampered neovascularization process. After 3 days of ischemia, MMP-2 activity and MMP-3 and MMP-13 protein levels were increased in untreated and aminoguanidine-treated diabetic mice when compared with controls (P < 0.05). Despite this activation of the MMP pathway, collagenolysis was decreased in untreated diabetic mice. Conversely, treatment of diabetic mice with aminoguanidine restored collagenolysis toward levels found in control mice. In conclusion, blockade of AGE formation by aminoguanidine normalizes impaired ischemia-induced angiogenesis in diabetic mice. This effect is probably mediated by restoration of matrix degradation processes that are disturbed as a result of AGE accumulation.
Galileo Open Service Authentication: A Complete Service Design and Provision Analysis (2015)

GNSS authentication, and in particular Navigation Message Authentication (NMA), has been already studied in the scientific literature. However, not many references that analyse the assets at risk, existing threats, mitigation actions, and residual risks through standard risk assessment processes, are available. In this paper, we outline how to use such processes to justify the design and selection of some configurable options for the service specification and operational procedures of GNSS Navigation Message Authentication (NMA) using the Galileo Open Service signals. The proposed NMA scheme is based on the TESLA protocol as proposed in [1]. 

To motivate the design of the service, we first identify the categories of users and associated risks of attack. We then summarize the mitigation capability against these attacks provided by the TESLA solution referred herein.

We define the cryptographic parameters to use for the service in the foreseeable future. We also identify further mitigations that the receiver manufacturer or service user might need to consider to ensure security of the position and/or the time fixes according to their risk aversion. These might include a trusted local clock reference, a process to verify or challenge digital certificates and statistical analysis of symbol recovery. 

We then define crypto parameters and procedures that affect the quality of service for different users, as a function of several system performance scenarios. 

We show that, for the selected parameters, multiconstellation NMA can be achieved in environments with a masking angle up to 40°. We also show that authentication using only validated signals presents good performance at 5° masking angle, for users requiring four satellites transmitting NMA. This performance may increase through an optimized downlink strategy.
An Experiment-Based Study of Formation Damage Using a Microetching Model Displacement Method (2022)

In the field of oil and gas exploration, drilling fluid is regarded as the essential "blood" for drilling, which mainly helps to control the formation pressure and remove cuttings from the well. During the drilling fluid cycle, the drilling fluid penetrates into the pores of the formation rock, thus blocking the rock pores and resulting in a decline in oil and gas recovery efficiency. Therefore, it is very important to understand the microscopic mechanism of formation damage caused by drilling fluid. However, as an important component of formation damage, the microscopic mechanism of fluid damage has not yet been clearly revealed. In this study, a new microetching model (MEM), along with displacement equipment, was designed. The pore network of rock samples was extracted from thin-section images and etched to a thin aluminum sheet by laser. Oil-based drilling fluid was used to displace the stratum water in the MEM. The displacement process was recorded by a camera and analyzed. A core flooding experiment, permeability measurement, and SEM observations were performed. The results show that, for low-porosity and low-permeability sandstone, the main forms of formation damage by drilling fluid include solid damage and liquid damage. Solid damage is mainly caused by the blockage of small pores and narrow throats with solid particles of the size 0.1~30.0 μm in drilling fluid, while liquid damage is mainly caused by the water lock and hydrocarbon lock effects formed by the oil-water two-phase interface, gas-water two-phase interface, or the oil-gas-water three-phase interface.
Impact of Network Address Translator Traversal on Delays in Peer-to-Peer Session Initiation Protocol (2010)

Peer-to-Peer Session Initiation Protocol (P2PSIP) is a distributed communication system being standardized in the Internet Engineering Task Force (IETF). Since it uses the peer-to-peer paradigm, P2PSIP faces the problems created by Network Address Translators (NATs); even peers located behind NATs need to be able to not only initiate connections to other peers but also accept connections initiated by other peers. In this paper, we study the impact of standardized NAT traversal solutions, namely Session Traversal Utilities for NAT (STUN), Traversal Using Relays around NAT (TURN), and Interactive Connectivity Establishment (ICE), on delays in P2PSIP overlay networks. These delays are studied from the viewpoint of wireless and wired nodes acting as clients in a P2PSIP overlay network running in the PlanetLab. The delays are also compared to those of the traditional client/server Session Initiation Protocol (SIP).
Improving the Detection of Stage I Pressure Ulcers by Enhancing Digital Color Images (2006)

It has been observed in previous studies that the detection of stage I pressure ulcers becomes more difficult by unaided visual inspection and/or by using currently available techniques with darker skin subjects, due to increased melanin content. This difficulty is indicated by the elevated proportion of black and hispanic patients developing more serious stage III and IV pressure ulcers compared to white patients. The ultimate goal of this project, undertaken by MARC at the University of Virginia, is to develop a low-cost, non-contact imaging-based stage I pressure ulcer detection system for use by support staff in assisted living and skilled nursing facilities to increase the ulcer detection rate over a wide range of skin colors. This paper describes an image enhancement procedure that improves the detection of pressure ulcers when applied to the color images of ulcer sites. Preliminary results clearly indicate that the enhanced images exhibit higher contrast and make the pressure ulcer site more conspicuous to the examiner. The experiments show promising results even for subjects with black and dark brown skin colors.
Cutting Edge: Novel Human Dendritic Cell- and Monocyte-Attracting Chemokine-Like Protein Identified by Fold Recognition Methods (2006)

Chemokines play an important role in the immune system by regulating cell trafficking in homeostasis and inflammation. In this study, we report the identification and characterization of a novel cytokine-like protein, DMC (dendritic cell and monocyte chemokine-like protein), which attracts dendritic cells and monocytes. The key to the identification of this putative new chemokine was the application of threading techniques to its uncharacterized sequence. Based on our studies, DMC is predicted to have an IL-8-like chemokine fold and to be structurally and functionally related to CXCL8 and CXCL14. Consistent with our predictions, DMC induces migration of monocytes and immature dendritic cells. Expression studies show that DMC is constitutively expressed in lung, suggesting a potential role for DMC in recruiting monocytes and dendritic cells from blood into lung parenchyma.