gebhart/patrepeval huggingface dataset:
A New Bacmid for Customized Protein Glycosylation Pathway Engineering in the Baculovirus-Insect Cell System (2021)

One attractive feature of the baculovirus-insect cell system (BICS) is the baculoviral genome has a large capacity for genetic cargo. This enables construction of viral vectors designed to accept multigene insertions, which has facilitated efforts to produce recombinant multisubunit protein complexes. However, the large genetic capacity of baculovirus vectors has not yet been exploited for multistep pathway engineering. Therefore, we created PolyBac, which is a novel baculovirus shuttle vector, or bacmid, that can be used for this purpose. PolyBac was designed to accept multiple transgene insertions by three different mechanisms at three different sites within the baculovirus genome. After constructing and characterizing PolyBac, we used it to isolate nine derivatives encoding various combinations of up to eight different protein <i>N</i>-glycosylation pathway functions, or glycogenes. We then used these derivatives, which were designed to progressively extend the endogenous insect cell pathway, to assess PolyBac's utility for protein glycosylation pathway engineering. This assessment was enabled by engineering each derivative to produce a recombinant influenza hemagglutinin (rH5), which was used to probe the impact of each glycoengineered PolyBac derivative on the endogenous insect cell pathway. Genetic analyses of these derivatives confirmed PolyBac can accept large DNA insertions. Biochemical analyses of the rH5 products showed each had distinct <i>N</i>-glycosylation profiles. Finally, the major <i>N</i>-glycan on each rH5 product was the predicted end product of the engineered <i>N</i>-glycosylation pathways encoded by each PolyBac derivative. These results generally indicate that PolyBac has utility for multistep metabolic pathway engineering and directly demonstrate that this new bacmid can be used for customized protein glycosylation pathway engineering in the BICS.
Surgical Management of Stones: American Urological Association/Endourological Society Guideline, PART I (2016)

Proper treatment selection, which is directed by patient- and stone-specific factors, remains the greatest predictor of successful treatment outcomes. This Guideline is intended for use in conjunction with the individual patient's treatment goals. In all cases, patient preferences and personal goals should be considered when choosing a management strategy.
Virtual Private Services: Coordinated Policy Enforcement for Distributed Applications (2007)

Large scale distributed applications combine network access with multiple storage and computational elements. The distributed responsibility for resource control creates new security issues, caused by the complexity of the operating environment. In particular, policies at multiple layers and locations force conventional mechanisms such as firewalls and compartmented file storage into roles where they are clumsy and failure-prone. Our approach relies on two functional divisions. First, we split policy specification and policy enforcement, providing local autonomy within the constraints of the global security policy. Second, we create virtual security domains each with its own security policy. Every domain has an associated set of privileges and permissions restricting it to the resources it needs to use and the services it must perform. Virtual private services ensure security and privacy policies are adhered to through coordinated policy enforcement points.
A Crosstalk-Harnessed Signaling Enhancement that Eliminates Common-Mode Encoding (2021)

This paper presents an encoding variation on the Crosstalk-Harnessed Signaling (CHS) technique, aimed towards eliminating the common-mode eigenvector included in the Hadamard matrix for CHS encoding/decoding. This is accomplished by either removing the eigenvector or making it differential by concatenating matrices in a diagonal fashion, or by adding columns to the matrix; this results in a non-square matrix that delivers a larger number of signals to be routed in the interface. Simulation results show the signaling/routing overhead translates in a significantly higher performance for high-speed parallel interfaces with very high routing integration levels.
STUDY OF THE ANOMALOUS CAPILLARY BAGLEY FACTOR BEHAVIOR OF THREE TYPES OF WHEAT FLOUR DOUGHS AT TWO MOISTURE CONTENTS (2002)

ABSTRACT The flow properties of wheat flour dough were evaluated using a capillary rheometer as a function of flour type (soft, hard and durum wheat flours) and dough moisture content (43 and 48% wb). The description of experimental flow properties was conducted using the classical Bagley approach and assuming linear relationships between pressure drop and L/D ratio (R 2 ranging from 0.795 to 0.993). The entrance pressure drop (P o ) increased (from 40 to 1870 kPa) with an increase in shear rate (from 40 to 1333 s −1 ) and a decrease in dough moisture content. Shear viscosities (7 to 160 Pa.s) and elongational viscosities (41 to 2840 kPa.s) demonstrated shear‐thinning behaviors that were characterized using power law models. Elongational and shear flows were compared by the Trouton ratio. The characterization of the capillary flow behavior for wheat flour dough was then discussed in regard with a possible nonlinear behavior of Bagley plots and related to possible changes in dough structure (i. e. dough hardening, strain hardening and dough deorientation).
Contents / Preface (2008)

Initially conceived as a strategy to remedy inherited genetic disorders, gene therapy has been successfully applied in the last decade to ameliorate the renal function compromised by progressive renal diseases and to prevent kidney allograft rejection in experimental animals. In the present book, world-renowned experts are presenting new insights into viral and non-viral systems used to effect gene delivery, one chapter being dedicated to the new field of RNA interference (RNAi). This latter method may be successfully used in renal ischemia-reperfusion injury, trauma and transplantation. In the near future, gene therapy might also prove to be a new strategy to target molecules involved in tissue damage and inflammation processes that underlie ARF. So far, gene transfer has been successfully applied in experimental glomerulonephritis and interstitial fibrosis, and studies in larger animals are keenly awaited. Also covered are issues related to transplantation, which is the therapy of choice in many end-stage organ failures. Transfer of genes whose protein products have immunomodulatory properties have proven beneficial in treating acute and chronic graft rejection, one of the problems not satisfactorily solved by current anti-rejection drugs. Gene therapy thus may become a reality in clinical transplantation once its efficacy in larger animals has been demonstrated. Last but not least, a possible benefit of targeted gene therapy in renal cancer or HIV-associated nephropathy is explored. Covering a wide spectrum of topics, this publication provides a valuable overview of current developments and issues.
Gender in Domestic Programming: from Bricolage to Séances d'Essayage (2006)

Developments in ubiquitous computing mean that domestic appliances are increasingly programmable, providing new opportunities for end-user control and configuration. Unfortunately home programming, just as with end-user programming in professional contexts, is associated with stereotypically masculine learning styles. This is likely to result in future inequalities surrounding domestic technology. This paper summarises recent experimental evidence regarding the role of self-efficacy in learning through experimentation, demonstrates that similar genderlinked behaviour can be found in both domestic and professional contexts, and recommends a new approach to promoting such experimentation among women.
Practical Power Analysis Attacks to RSA on a Large IP Portfolio SoC (2009)

The RSA algorithm is the most widely used public-key cryptosystem. For this reason it is important to protect RSA-based cryptosystems from the threat of side channels attacks and particularly from power analysis.This article presents the application of power analysis attacks based on real power measurements and describes the main experimental results obtained by attacking software implementations of the RSA algorithm executed on an ARM 926 processor running at 266 MHz. Few practical results of similar type are reported in the literature, and none of them targets a complex SoC running at such a high frequency as that considered in this paper.
On-die instrumentation to solve challenges for 28nm, 28Gbps timing variability and stressing (2012)

Moving to the latest submicron node is required for digital scaling but causes many challenges for analog design. Additionally, scaling pushes the need for higher bandwidth. Data rates up to 28Gbps require effectively dealing with random variations and layout dependent effects. On-die instrumentation (ODI) is an effective means to alleviate many of the challenges, as well as characterize and margin performance. This paper covers two of the ODI techniques used in the design of a wide range 28nm, 28Gbps transceiver.
Peripheral Display Architectures (2020)

Chapter 5 showed that the performance of the human peripheral vision system is different from the central foveated region. The peripheral region might lack dramatically in angular resolution and color depth, but is more sensitive to clutter, jitter, aliasing and other display phenomenon than the foveated region. These peripheral display effects can reduce the visual experience for a wide-FOV HMD user.
Design and Evaluation of Compliant Constant-Force Mechanisms (1996)

Abstract Compliant constant-force mechanisms combine the effects of mechanical advantage and stored strain energy of flexible members to obtain constant output forces for a large range of input displacements. This paper extends and compliments previous work by accomplishing the following: i) dimensional synthesis is performed for a number of compliant constant-force mechanism configurations, ii) a simplified method of determining the magnitude of the constant output force is presented, and iii) experimental validation of the theory is addressed by reporting the results of testing three constant-force configurations. The results of i) and ii) are presented in a manner to be easily used by engineers designing such mechanisms. The results of iii) show that the mechanisms do follow a nearly constant force for a large input displacement, as predicted.
Performance Analysis of LDM-Based Distributed Congestion Control of 5G NR V2X in Urban Environments (2022)

본 논문은 3GPP LTE C-V2X(Cellular-Vehicular to Everything)의 사이드링크에서 채널 혼잡에 의해 발생하는 성능 열화를 극복하기 위해 제안했던 LDM(Local Dynamic Map) 기반 분산혼잡제어를, 5G NR(New Radio) V2X의 사이드링크에 최적화하고 이의 성능을 분석하였다. 특히, 혼잡도가 불균일한 도심환경에서 분산혼잡제어의 성능을 비교 분석하였다.
A frequency compensated real time DSP GMSK modem (1998)

Due to the character of the original source materials and the nature of batch digitization, quality control issues may be present in this document. Please report any quality issues you encounter to digital@library.tamu.edu, referencing the URI of the item.
Regulatory ecotoxicity testing of engineered nanoparticles: are the results relevant to the natural environment? (2013)

Engineered nanoparticles (ENPs) will be released to the environment during use or following the disposal of ENP-containing products and concerns have been raised over the risks of ENPs to the environment. Many studies have explored the toxicity of ENPs to aquatic organisms but these studies have usually been performed with little understanding of the ENPs' behaviour in the test media and the relationship between behaviour in the media to behaviour in natural waters. This study evaluated and compared the aggregation behaviour of four model gold nanoparticle (NP) types (coated with neutral, negative, positive and amphoteric cappings) in standard ecotoxicity test media and natural waters. The effects of humic acid (HA) and test organisms on aggregation were also investigated. In standard media, positive and neutral NPs were stable, whereas amphoteric and negative NPs generally showed substantial aggregation. In natural waters, amphoteric NPs were generally found to be stable, neutral and positive NPs showed substantial aggregation while negative NPs were stable in some waters and unstable in others. HA addition stabilised the amphoteric NPs, destabilised the positive NPs and had no effect on stability of negative NPs. The presence of invertebrates generally lowered the degree of particle aggregation while macrophytes had no effect. Given the dramatically different behaviours of ENPs in various standard media and natural waters, current regulatory testing may either under- or overestimate the toxicity of nanomaterials to aquatic organisms. Therefore, there is a pressing need to employ ecotoxicity media which better represent the behaviour of ENPs in natural system.
A microbiological study of gastro-enteritis in Black infants. (1977)

A survey was carried out to determine the aetiological agents responsible for acute gastro-enteritis in Black infants. Bacteriological examination of 191 patients and 178 age-matched controls showed that salmonellae and shigellae together accounted for only 15% of cases and were harboured by almost 7% of controls. Seropositive 'enteropathogenic' Escherichia coli was an important cause of diarrhoea, especially in the summer months. Enterotoxin-producing E. coli was not a significant cause of gastro-enteritis in this study. This study suggests that routine serotyping of E. coli from infantile gastro-enteritis should be continued until the relationship of serotype and enterotoxigenicity with enteropathogenicity has been established. Rotaviruses were detected by electron microscopy in 14,4% of children. The clinical features associated with the different infectious agents are described.
Retrospective Analysis on the Feasibility and Efficacy of Docetaxel-Cisplatin Therapy for Recurrent Endometrial Cancer. (2016)

DP therapy was fully feasible and demonstrated efficacy for patients with recurrent endometrial cancer.
All Digital-RF SATCOM Transceiver Provides the Modular Open Systems Architecture Required to Meet HC3 GRA (2007)

Government software standards such as the Software Communications Architecture (SCA) have been proposed and are evolving to facilitate reuse and portability of both software waveforms and hardware. To date these steps have shown limited success in maximizing reuse and reducing costs for new applications. As a result, PM WINT HC3 has been defining a new modular Open Systems Architecture (OSA) that is designed to address these issues using a Government Reference Architecture (GRA) that provides for both hardware and software modularity and portability. An All Digital-RF transceiver design provides programmability and flexibility into a multiple band architecture that can be incorporated into modules that easily meet the HC3 GRA modular OSA requirement while providing many unique benefits. A system concept is presented which employs cryo-genically cooled superconductor microelectronic (SME) technology to enable a next-generation multiple band, multiple channel MILSATCOM system with the goal of achieving HC3 GRA modular OSA compliance simultaneously at frequencies covering the C, X, Ku, Ka and EHF bands. All Digital-RF technology brings revolutionary changes in the design and implementation of RF microwave electronics. For the first time, it becomes practical to implement high frequency RF functions in the digital domain - all accomplished with extreme low-noise performance and spectral purities with ultra-fast speeds otherwise unattainable with competing semiconductor technologies, analog or digital. These new Digital-RF "tools" lead directly to modular system designs that support multi-band and multi-channel operation from a single RF platform with much smaller antennas, increased capacities and flexibility.
Generative Street Addresses from Satellite Imagery (2018)

We describe our automatic generative algorithm to create street addresses from satellite images by learning and labeling roads, regions, and address cells. Currently, 75% of the world’s roads lack adequate street addressing systems. Recent geocoding initiatives tend to convert pure latitude and longitude information into a memorable form for unknown areas. However, settlements are identified by streets, and such addressing schemes are not coherent with the road topology. Instead, we propose a generative address design that maps the globe in accordance with streets. Our algorithm starts with extracting roads from satellite imagery by utilizing deep learning. Then, it uniquely labels the regions, roads, and structures using some graph- and proximity-based algorithms. We also extend our addressing scheme to (i) cover inaccessible areas following similar design principles; (ii) be inclusive and flexible for changes on the ground; and (iii) lead as a pioneer for a unified street-based global geodatabase. We present our results on an example of a developed city and multiple undeveloped cities. We also compare productivity on the basis of current ad hoc and new complete addresses. We conclude by contrasting our generative addresses to current industrial and open solutions. Keywords: road extraction; remote sensing; satellite imagery; machine learning; supervised learning; generative schemes; automatic geocoding
The 'Swiss cheese' instability of bacterial biofilms (2012)

We demonstrate a novel pattern that results in bacterial biofilms as a result of the competition between hydrodynamic forces and adhesion forces. After the passage of an air plug, the break up of the residual thin liquid film scrapes and rearranges bacteria on the surface, such that a Swiss cheese pattern of holes is left in the residual biofilm.
Figure S2 from RTK-Dependent Inducible Degradation of Mutant PI3Kα Drives GDC-0077 (Inavolisib) Efficacy (2023)

&lt;p&gt;Activity of GDC-0077 in combination with Palbociclib and/ or Fulvestrant&lt;/p&gt;
XACML profile and implementation for authorization interoperability between OSG and EGEE (2010)

The Open Science Grid (OSG) and the Enabling Grids for E-sciencE (EGEE) have a common security model, based on Public Key Infrastructure. Grid resources grant access to users because of their membership in a Virtual Organization (VO), rather than on personal identity. Users push VO membership information to resources in the form of identity attributes, thus declaring that resources will be consumed on behalf of a specific group inside the organizational structure of the VO. Resources contact an access policies repository, centralized at each site, to grant the appropriate privileges for that VO group. Before the work in this paper, despite the commonality of the model, OSG and EGEE used different protocols for the communication between resources and the policy repositories. Hence, middleware developed for one Grid could not naturally be deployed on the other Grid, since the authorization module of the middleware would have to be enhanced to support the other Grid's communication protocol. In addition, maintenance and support for different authorization call-out protocols represents a duplication of effort for our relatively small community. To address these issues, OSG and EGEE initiated a joint project on authorization interoperability. The project defined a common communication protocol and attribute identity profile for authorization call-out and provided implementation and integration with major Grid middleware. The activity had resonance with middleware development communities, such as the Globus Toolkit and Condor, who decided to join the collaboration and contribute requirements and software. In this paper, we discuss the main elements of the profile, its implementation, and deployment in EGEE and OSG. We focus in particular on the operations of the authorization infrastructures of both Grids.
Anti-tumor immune response after photodynamic therapy (2009)

Anti-tumor immunity is stimulated after PDT due a number of factors including: the acute inflammatory response caused by PDT, release of antigens from PDT-damaged tumor cells, priming of the adaptive immune system to recognize tumor-associated antigens (TAA), and induction of heat-shock proteins. The induction of specific CD8+ T-lymphocyte cells that recognize major histocompatibility complex class I (MHC-I) restricted epitopes of TAAs is a highly desirable goal in cancer therapy as it would allow the treatment of tumors that may have already metastasized. The PDT killed tumor cells may be phagocytosed by dendritic cells (DC) that then migrate to draining lymph nodes and prime naïve T-cells that recognize TAA epitopes. We have carried out in vivo PDT with a BPD-mediated vascular regimen using a pair of BALB/c mouse colon carcinomas: CT26 wild type expressing the naturally occurring retroviral antigen gp70 and CT26.CL25 additionally expressing beta-galactosidase (b-gal) as a model tumor rejection antigen. PDT of CT26.CL25 cured 100% of tumors but none of the CT26WT tumors (all recurred). Cured CT26.CL25 mice were resistant to rechallenge. Moreover mice with two bilateral CT26.CL25 tumors that had only one treated with PDT demonstrated spontaneous regression of 70% of untreated contralateral tumors. T-lymphocytes were isolated from lymph nodes of PDT cured mice that recognized a particular peptide specific to b-gal antigen. T-lymphocytes from LN were able to kill CT26.CL25 target cells in vitro but not CT26WT cells as shown by a chromium release assay. CT26.CL25 tumors treated with PDT and removed five days later had higher levels of Th1 cytokines than CT26 WT tumors showing a higher level of immune response. When mice bearing CT26WT tumors were treated with a regimen of low dose cyclophosphamide (CY) 2 days before, PDT led to 100% of cures (versus 0% without CY) and resistance to rechallenge. Low dose CY is thought to deplete regulatory T-cells (Treg, CD4+CD25+foxp3+) and potentiate immune response after PDT in the case of tumors that express self-antigens. These data suggest that PDT alone will stimulate a strong immune response when tumors express a robust antigen, and in cases where tumors express a self-antigen, T-reg depletion can unmask the immune response after PDT.
Moonlighting of Helicobacter pylori catalase protects against complement-mediated killing by utilising the host molecule vitronectin (2016)

Helicobacter pylori is an important human pathogen and a common cause of peptic ulcers and gastric cancer. Despite H. pylori provoking strong innate and adaptive immune responses, the bacterium is able to successfully establish long-term infections. Vitronectin (Vn), a component of both the extracellular matrix and plasma, is involved in many physiological processes, including regulation of the complement system. The aim of this study was to define a receptor in H. pylori that binds Vn and determine the significance of the interaction for virulence. Surprisingly, by using proteomics, we found that the hydrogen peroxide-neutralizing enzyme catalase KatA is a major Vn-binding protein. Deletion of the katA gene in three different strains resulted in impaired binding of Vn. Recombinant KatA was generated and shown to bind with high affinity to a region between heparin-binding domain 2 and 3 of Vn that differs from previously characterised bacterial binding sites on the molecule. In terms of function, KatA protected H. pylori from complement-mediated killing in a Vn-dependent manner. Taken together, the virulence factor KatA is a Vn-binding protein that moonlights on the surface of H. pylori to promote bacterial evasion of host innate immunity.