gebhart/patrepeval huggingface dataset:
Amyloid-Beta Protein Clearance and Degradation (ABCD) Pathways and their Role in Alzheimer’s Disease (2015)

Amyloid-β proteins (Aβ) of 42 (Aβ42) and 40 aa (Aβ40) accumulate as senile plaques (SP) and cerebrovascular amyloid protein deposits that are defining diagnostic features of Alzheimer's disease (AD). A number of rare mutations linked to familial AD (FAD) on the Aβ precursor protein (APP), Presenilin-1 (PS1), Presenilin- 2 (PS2), Adamalysin10, and other genetic risk factors for sporadic AD such as the ε4 allele of Apolipoprotein E (ApoE-ε4) foster the accumulation of Aβ and also induce the entire spectrum of pathology associated with the disease. Aβ accumulation is therefore a key pathological event and a prime target for the prevention and treatment of AD. APP is sequentially processed by β-site APP cleaving enzyme (BACE1) and γ-secretase, a multisubunit PS1/PS2-containing integral membrane protease, to generate Aβ. Although Aβ accumulates in all forms of AD, the only pathways known to be affected in FAD increase Aβ production by APP gene duplication or via base substitutions on APP and γ-secretase subunits PS1 and PS2 that either specifically increase the yield of the longer Aβ42 or both Aβ40 and Aβ42. However, the vast majority of AD patients accumulate Aβ without these known mutations. This led to proposals that impairment of Aβ degradation or clearance may play a key role in AD pathogenesis. Several candidate enzymes, including Insulin-degrading enzyme (IDE), Neprilysin (NEP), Endothelin-converting enzyme (ECE), Angiotensin converting enzyme (ACE), Plasmin, and Matrix metalloproteinases (MMPs) have been identified and some have even been successfully evaluated in animal models. Several studies also have demonstrated the capacity of γ-secretase inhibitors to paradoxically increase the yield of Aβ and we have recently established that the mechanism is by skirting Aβ degradation. This review outlines major cellular pathways of Aβ degradation to provide a basis for future efforts to fully characterize the panel of pathways responsible for Aβ turnover.
Depth Map Design and Depth-based Effects With a Single Image (2017)

We present a novel pipeline to generate a depth map from a single image that can be used as input for a variety of artistic depth-based effects. In such a context, the depth maps do not have to be perfect but are rather designed with respect to a desired result. Consequently, our solution centers around user interaction and relies on a scribble-based depth editing. The annotations can be sparse, as the depth map is generated by a diffusion process, which is guided by image features. Additionally, we support a variety of controls, such as a non-linear depth mapping, a steering mechanism for the diffusion (e.g., directionality, emphasis, or reduction of the influence of image cues), and besides absolute, we also support relative depth indications. We demonstrate a variety of artistic 3D results, including wiggle stereoscopy and depth of field.
Nanofiber Membranes with Controllable Microwells and Structural Cues and Their Use in Forming Cell Microarrays and Neuronal Networks (2010)

Neural scaffolds: A method for fabricating electrospun nanofiber membranes with arrayed microwells and aligned structural cues on their surfaces by using a collector assembled from stainless steel beads is reported. It is demonstrated that formation of cell microarrays and neuronal networks can be achieved using this novel class of nanofiber scaffolds.
Solaris 8 : network administrator certification : training guide : exam 310-043 (2002)

1. Introduction to Computer Networks. 2. The TCP/IP Protocol. 3. Routing in TCP/IP Networks. 4. Ports and Sockets. 5. Configuring and Managing DHCP. 6. Network Management with SNMP. 7. Configuring and Managing Domain Name Server. 8. Network Time Protocol. 9. Introduction to IPv6. 10. Point-to-Point Protocol. 11. Electronic Mail.
Efficient NFV deployment in data center networks (2015)

NFV is a new network concept that moves network functions from network appliances to virtual machines. Users can customize their own services by setting ordered traffic paths through network function virtual machines they want. Though this idea is flexible and scalable, it brings additional growth in east-west traffic. In this paper, we focus on NFV deployment in data center networks. An user has multiple VMs in a data center and wants to have some network functions for these VMs. According to the user's requirements and traffic flows, we design a heuristic NFV deployment algorithm for VNF allocation, VNF placement and traffic dispatching. We set a traffic model and evaluate our algorithm by simulation. We also give some further research directions in this paper.
Self-Biased Low Loss Conductor Featured With Skin Effect Suppression for High Quality RF Passives (2012)

We present experimental data for artificial metaconductors exhibiting skin effect suppression at microwave frequencies. The metaconductor consists of a stack comprising twelve periods of alternating ferromagnetic (Permalloy) and normal metal (Cu) layers. Near the effective antiferromagnetic resonant frequency the average in-plane magnetic permeability of the stack approaches zero, leading to an increase in the skin depth. Compared to a Cu-based device, up to 70% loss reduction has been achieved by a metaconductor based coplanar wave guide at ~ 10 GHz without changing the propagation wavelength. Moreover, unlike conventional magnetic devices, no external magnetic bias is required due to the large magnetic anisotropy present in the ferromagnetic layers.
Activated Macrophages in Experimental Subretinal Neovascularization (With 1 color plate) (1990)

Laser-induced subretinal neovascularization (SRN) in monkey retinas was investigated by immunohistochemical techniques to identify the presence and location of activated macrophages. Retinal lesions were examined 3, 8 and 14 days after intensive argon laser treatment, and the distribution of interleukin-1 (IL-1)-containing cells in the lesions was determined by the orthogonal reconstruction of serial sections. Macrophages were present in the subretinal space of day 3 and day 8 lesions. These IL-1-containing cells were distributed about the area of rupture of Bruch's membrane and were quite common in lesions taken 3 days following laser treatment. While still apparent, the number was decreased at 8 days, and none were found 14 days after laser treatment. The temporal and spatial distribution of IL-1-staining macrophages paralleled the development of SRN, suggesting a relationship between the presence of activated macrophages and the initiation of neovascularization in this model.
Cloning and Transcriptional Activity of the Mouse Omi/HtrA2 Gene Promoter (2016)

HtrA serine peptidase 2 (HtrA2), also named Omi, is a pro-apoptotic protein that exhibits dramatic changes in expression levels in a variety of disorders, including ischemia/reperfusion injury, cancer, and neurodegeneration. In our study, Omi/HtrA2 protein levels were high in the heart, brain, kidney and liver, with elevated heart/brain expression in aging mice. A similar expression pattern was observed at the mRNA level, which suggests that the regulation of Omi/HtrA2 is predominately transcriptional. Promoter binding by transcription factors is the main influencing factor of transcription, and to identify specific promoter elements that contribute to the differential expression of mouse Omi/HtrA2, we constructed truncated Omi/HtrA2 promoter/luciferase reporter vectors and analyzed their relative luciferase activity; it was greatest in the promoter regions at -1205~-838 bp and -146~+93 bp, with the -838~-649 bp region exhibiting negative regulatory activity. Bioinformatics analysis suggested that the Omi/HtrA2 gene promoter contains a CpG island at -709~+37 bp, and eight heat shock transcription factor 1 (HSF1) sites, two Sp1 transcription factor (SP1)sites, one activator protein (AP) site, seven p53 sites, and four YY1 transcription factor(YY1) sites were predicted in the core areas. Furthermore, we found that p53 and HSF1 specifically binds to the Omi/HtrA2 promoter using chromatin immunoprecipitation analysis. These results provide a foundation for understanding Omi/HtrA2 regulatory mechanisms, which could further understanding of HtrA-associated diseases.
The organizational antecedents of a firm’s supply chain agility for risk mitigation and response (2008)

Abstract Today’s marketplace is characterized by intense competitive pressures as well as high levels of turbulence and uncertainty. Organizations require agility in their supply chains to provide superior value as well as to manage disruption risks and ensure uninterrupted service to customers. Thus the cultivation of agility is approached as a risk management initiative that enables a firm to respond rapidly to marketplace changes, as well as anticipated and actual disruptions in the supply chain. Agility is of value for both risk mitigation and response. This research investigates the impact of two cultural antecedents, market orientation and learning orientation, and three organizational practices, all aimed at augmenting the supply chain agility of a firm. A firm’s supply chain agility (FSCA) is defined as the capability of the firm, both internally and in conjunction with its key suppliers and customers, to adapt or respond in a speedy manner to marketplace changes as well as to potential and actual disruptions, contributing to the agility of the extended supply chain. The two cultural antecedents of market and learning orientations are posited to affect the organizational practices of internal integration, external integration with key suppliers and customers, and external flexibility, and eventually impact the firm’s supply chain agility. The external flexibility elements considered are volume and mix flexibility. In addition, the specific organizational characteristics and practices exhibited by firms with high levels of supply chain agility are also investigated. Through the use of the structural equation modeling technique, partial least squares (PLS), it is shown that strong linkages exist among the cultural antecedents, the three organizational practices considered, and the firm’s supply chain agility. All three organizational practices, internal integration, external integration with key suppliers and customers, and external flexibility are shown to have significant positive impact on the firm’s supply chain agility. Market orientation is shown to significantly impact both internal and external supply chain integration, along with the two elements of external flexibility. Learning orientation, on the other hand, is shown to have a strong and direct influence only on the level of internal integration. Firms with high levels of external integration are also shown to have high levels of internal integration, consistent with past research. Internal and external integration efforts are also seen to be unrelated to the levels of external flexibility present. The results serve to establish a set of key drivers for augmenting supply chain agility as a risk management initiative.
Anti–IL-20 Monoclonal Antibody Suppresses Breast Cancer Progression and Bone Osteolysis in Murine Models (2012)

IL-20 is a proinflammatory cytokine involved in rheumatoid arthritis, atherosclerosis, and stroke. However, little is known about its role in breast cancer. We explored the function of IL-20 in tumor growth and metastasis, as well as in clinical outcome. Tumor expression of IL-20 was assessed by immunohistochemical staining among 198 patients with invasive ductal carcinoma of the breast, using available clinical and survival data. IL-20 expression was associated with advanced tumor stage, greater tumor metastasis, and worse survival. Reverse transcription quantitative polymerase chain reaction showed that clinical breast tumor tissue expressed higher levels of IL-20 and its receptors than did nontumorous breast tissue. IL-20 was also highly expressed in breast cancer bone-metastasis tissue. In vitro, IL-20 upregulated matrix metalloproteinase-9, matrix metalloproteinase-12, cathepsin K, and cathepsin G, and enhanced proliferation and migration of breast cancer cells, which were inhibited by anti-IL-20 mAb 7E. In vivo, we generated murine models to evaluate the therapeutic potential of 7E, using luminescence intensity, radiological scans, and micro-computed tomography. 7E reduced tumor growth, suppressed bone colonization, diminished tumor-mediated osteolysis, and lessened bone density decrement in mice injected with breast cancer cells. In conclusion, our results suggest that IL-20 plays pivotal roles in the tumor progression of breast cancer. IL-20 expression in breast cancer tissue is associated with a poor clinical outcome. Anti-IL-20 mAb 7E suppressed bone colonization and decreased osteolytic bone lesions. Therefore, IL-20 may be a novel target in treating breast tumor-induced osteolysis.
Nearest-Neighbor-Based Active Learning for Rare Category Detection (2018)

Rare category detection is an open challenge for active learning, especially in the de-novo case (no labeled examples), but of significant practical importance for data mining - e.g. detecting new financial transaction fraud patterns, where normal legitimate transactions dominate. This paper develops a new method for detecting an instance of each minority class via an unsupervised local-density-differential sampling strategy. Essentially a variable-scale nearest neighbor process is used to optimize the probability of sampling tightly-grouped minority classes, subject to a local smoothness assumption of the majority class. Results on both synthetic and real data sets are very positive, detecting each minority class with only a fraction of the actively sampled points required by random sampling and by Pelleg’s Interleave method, the prior best technique in the sparse literature on this topic.
Medusa: A Scalable MR Console Using USB (2011)

Magnetic resonance imaging (MRI) pulse sequence consoles typically employ closed proprietary hardware, software, and interfaces, making difficult any adaptation for innovative experimental technology. Yet MRI systems research is trending to higher channel count receivers, transmitters, gradient/shims, and unique interfaces for interventional applications. Customized console designs are now feasible for researchers with modern electronic components, but high data rates, synchronization, scalability, and cost present important challenges. Implementing large multichannel MR systems with efficiency and flexibility requires a scalable modular architecture. With Medusa, we propose an open system architecture using the universal serial bus (USB) for scalability, combined with distributed processing and buffering to address the high data rates and strict synchronization required by multichannel MRI. Medusa uses a modular design concept based on digital synthesizer, receiver, and gradient blocks, in conjunction with fast programmable logic for sampling and synchronization. Medusa is a form of synthetic instrument, being reconfigurable for a variety of medical/scientific instrumentation needs. The Medusa distributed architecture, scalability, and data bandwidth limits are presented, and its flexibility is demonstrated in a variety of novel MRI applications.
Expressing and Describing Surprise (2017)

This paper re-examines the well-established distinction between expression and description of emotion as regards surprise. First, the authors show that the expression of surprise does not involve the use of surprise lexemes, but rather mirative utterances and specific syntactic constructions (while the description of surprise involves surprise lexemes). Second, the investigation of the corpus data indicates that surprise lexemes – namely the noun surprise and the adjective surprised – differ from other emotion lexemes in that they do not systematically refer to the emotional state of an experiencer. The noun surprise can have such a state reading but can also evaluate a source seen as a salient unexpected referent. As for the adjective surprised, it may serve various argumentative strategies. These uses reflect the epistemic rather than emotional nature of surprise, which sets it apart from other emotions.
Osteogenic protein-1 (Bone morphogenetic protein-7) protects against renal injury following ischemia in rats (1997)

Osteogenic protein-1 (OP-1/BMP-7), a member of TGF-B superfamily of proteins, is required for the kidney development and OP-1/BMP-7 null mutation mice die shortly after birth due to renal failure. In the present study, we examined the ability of systemically administered recombinant human OP-1 to modulate the degree of injury following ischemia and reperfusion in rats. Pharmacokinetic studies indicate that high serum levels of OP-1 were achieved after IV injection followed by a steadily decline with a halflife of about 30 minutes. Bioavailability studies show that 125-I-OP-1 specifically bound to plasma membrane fractions of the kidney and about 140 and 270 ng OP-1/g of tissue was available to the medulla or cortex, respectively, when 250 ug/kg bw of 125-I-OP-1 was injected. Evaluation of therapeutic effects indicate that OP-1 significantly suppresses blood urea nitrogen and serum creatinine levels and effectively increases the survival rate when applied within 16 hours after injury. Additional histochemical and molecular analyses demonstrate that OP-1: 1) improves renal hemodynamic properties as shown by increased glomerular filtration rate, 2) maintains the integrity of vascular smooth muscle cells in the S3 zone as qualified by expression of smooth muscle alpha-actin, 3) suppresses inflammation by downregulating the expression of intercellular adhesive molecule, I-CAM, in vascular endothelium, 4) minimizes infarction and cell necrosis, and 5) reduces programmed cell death during the recovery phase. These data collectively indicate that OP-1 averts damage associated with ischemia and reperfusion to kidney and, as such, may provide a basis for the treatment of acute renal failure.
Adrenergic receptor genotype influences heart failure severity and β-blocker response in children with dilated cardiomyopathy (2014)

Our study identifies genetic risk markers that may help in the identification of patients at risk for developing decompensated HF and who may benefit from early institution of β-blocker therapy before progression to decompensated HF.
Cardiac balanced steady-state free precession MRI at 0.35 T: a comparison study with 1.5 T (2018)

This study demonstrates that cardiac bSSFP imaging is highly feasible at 0.35 T.
Estimation of Missing Data Using Computational Intelligence and Decision Trees (2007)

This paper introduces a novel paradigm to impute missing data that combines a decision tree with an auto-associative neural network (AANN) based model and a principal component analysis-neural network (PCA-NN) based model. For each model, the decision tree is used to predict search bounds for a genetic algorithm that minimize an error function derived from the respective model. The models' ability to impute missing data is tested and compared using HIV sero-prevalance data. Results indicate an average increase in accuracy of 13% with the AANN based model's average accuracy increasing from 75.8% to 86.3% while that of the PCA-NN based model increasing from 66.1% to 81.6%.
Autoantibodies against Glial Fibrillary Acidic Protein (GFAP) in Cerebrospinal Fluids from Pug Dogs with Necrotizing Meningoencephalitis (2007)

Cerebrospinal fluids (CSFs) from 9 Pug dogs with necrotizing meningoencephalitis (NME: Pug dog encephalitis) were examined to identify the antigens for anti-astrocyte autoantibodies. Each CSF exhibited a positive reaction to the cytoplasm of cultured canine astrocytes by an indirect fluorescent antibody test. In an immunoblotting analysis on normal canine brain proteins, eight of 9 CSFs showed a common band of 52 kDa, corresponding to glial fibrillary acidic protein (GFAP), and all of 9 CSFs reacted with purified bovine GFAP. From these results, GFAP is one of the common autoantigens in Pug dogs with NME. On the other hand, the reactivity of CSFs to chymotrypsin-digested bovine GFAP fragments were variable among dogs, indicating that the antibodies in the CSFs recognized different epitopes on GFAP.
Asymmetric catalysis with bifunctional cinchona alkaloid-based urea and thiourea organocatalysts (2008)

Cinchona alkaloid derivatives modified to include a (thio)urea component have emerged in the last three years as readily accessible, robust and tunable bifunctional organocatalysts for a range of synthetically useful transformations. The origins of these catalysts and the major developments in their application in enantioselective synthesis are reviewed.
A Deep SE(3)-Equivariant Model for Learning Inverse Protein Folding (2022)

Abstract In this work, we establish a framework to tackle the inverse protein design problem; the task of predicting a protein’s primary sequence given its backbone conformation. To this end, we develop a generative SE(3)-equivariant model which significantly improves upon existing autoregressive methods. Conditioned on backbone structure, and trained with our novel partial masking scheme and side-chain conformation loss, we achieve state-of-the-art native sequence recovery on structurally independent CASP13, CASP14, CATH4.2, and TS50 test sets. On top of accurately recovering native sequences, we demonstrate that our model captures functional aspects of the underlying protein by accurately predicting the effects of point mutations through testing on Deep Mutational Scanning datasets. We further verify the efficacy of our approach by comparing with recently proposed inverse protein folding methods and by rigorous ablation studies.
Dressed up (2018)

Honeypots have been widely employed to track attackers' activities and divert potential threats against real assets. A critical challenge of honeypot research is how to better integrate deceptive honeypots as part of an overall production network. Conventional honeypots are typically deployed as separate assets near those they are protecting---they are not in the direct line of fire. Such a setup does not effectively protect real assets since attackers do not require a full network scan to identify certain production hosts.
A MOSFET with Si-implanted gate-SiO/sub 2/ insulator for nonvolatile memory applications (1992)

A MOSFET with Si-implanted gate-SiO/sub 2/ insulator (MEmory-Insulator Transistor, MEIT) is fabricated and investigated, especially with emphasis on its feasibility for nonvolatile memory applications for the first time. A high-dose Si/sup +/ implantation to thermal SiO/sub 2/ introduces excess-Si sites acting as traps responsible for a memory effect. As a result, a large V/sub T/ window of approximately 10 V is achieved by applying small electric fields of 3-5 MV/cm to the MEIT insulator for write/erase programming. By taking advantage of the memory effect, it is found that MEIT achieves sufficient programming characteristics as a flash E/sup 2/PROM as well as simplicity of the single poly-Si-gate process. Most of all, the V/sub T/ window is scarcely degraded, at least, up to 10/sup 7/ write/erase cycles. Although further investigation is needed, MEIT is promising for nonvolatile memory applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Developing Microsoft Excel 5 solutions: Expert development strategies using the Microsoft Excel 5 Object Model and Visual Basic for applications (1995)

An extraordinary new feature in Microsoft Excel 5 called Visual Basic for Applications (VBA) makes it easy for anyone with an understanding of VBA to build powerful business solutions with the Microsoft Excel engine. This insider's guide introduces VBA and Microsoft Excel 5 as a full-fledged development environment and shows the best methods for building quality data access and decison-making tools.