gebhart/patrepeval huggingface dataset:
Structure of the complex of porcine pancreatic elastase with a trimacrocyclic peptide inhibitor FR901451 (2005)

Porcine pancreatic elastase (PPE) resembles the attractive drug target leukocyte elastase, which has the ability to degrade connective tissue in the body. The crystal structure of PPE complexed with a novel trimacrocyclic peptide inhibitor, FR901451, was solved at 1.9 A resolution. The inhibitor occupied the subsites S3 through S3' of PPE and induced conformational changes in the side chains of Arg64 and Arg226, which are located at the edges of the substrate-binding cleft. Structural comparison of five PPE-inhibitor complexes, including the FR901451 complex and non-ligated PPE, reveals that the residues forming the S2, S1, S1' and S2' subsites in the cleft are rigid, but the two arginine residues playing a part in the S3 and S3' subsites are flexible. Structural comparison of PPE with human leukocyte elastase (HLE) implies that the inhibitor binds to HLE in a similar manner to the FR901451-PPE complex. This structural insight may help in the design of potent elastase inhibitors.
Loop-free multipath routing using generalized diffusing computations (2002)

A new distributed algorithm for the dynamic computation of multiple loop-free paths from source to destination in a computer network or Internet are presented, validated, and analyzed. According to this algorithm, which is called DASM (diffusing algorithm for shortest multipath), each router maintains a set of entries for each destination in its routing table, and each such entry consists of a set of tuples specifying the next router and distance in a loop-free path to the destination. DASM guarantees instantaneous loop freedom of multipath routing tables by means of a generalization of Dijkstra and Scholten's diffusing computations. With generalized diffusing computations, a node in a directed acyclic graph (DAG) defined for a given destination has multiple next nodes in the DAG and is able to modify the DAG without creating a directed loop. DASM is shown to be loop-free at every instant, and its average performance is analyzed by simulation and compared against an ideal link-state algorithm and the diffusing update algorithm (DUAL).
Automated leak localization performance without detailed demand distribution data (2018)

Automatic leak localization has been suggested to reduce the time and personnel efforts needed to localize (small) leaks. Yet, the available methods require a detailed demand distribution model for successful calibration and good leak localization performance. The main aim of this work was to analyze whether such a detailed demand distribution is needed. Two demand distributions were used: a factorized distribution that distributes the inflow demand proportionally across the consumption nodes according to individual billing data, and a uniform distribution that equally distributes demand across all consumption nodes. The performance of the automatic leak localization method, using both demand distribution models, was compared. A new measure for leak localization performance that is based on the percentage of false positive nodes is proposed. It was possible to localize the leaks with both demand distribution models, although performance varied depending on the timing and duration of the measurement.
Using a Marchenko-redatumed Reflection Response as an Exact Boundary Condition (2016)

Summary Marchenko Redatuming enables the creation of both virtual sources and receivers at an arbitrary depth level in the subsurface using only reflection data recorded at the surface and an estimate of the background velocity model. In this work, we perform full-waveform, target oriented modeling for a sub-domain of a 1D synthetic model using a combination of Marchenko-redatumed reflection responses and exact boundary conditions. We apply Marchenko redatuming to the two ends of the target region yielding Green’s functions for virtual sources and receivers at these positions, which illuminate the unknown embedding medium from below and above, respectively. Applying some simple processing steps to these Green’s functions enables us to use them as so-called exact boundary conditions for the target region. This procedure is aimed at establishing a link between the numerically modelled target region and the embedding background medium in order to include all interactions with the background medium. It appears that we can correctly account for the interactions without knowing the background medium in detail.
Performance analysis of buffered Banyan networks (1991)

The authors give a classification of the most common Banyan networks and outline an analysis approach for the rather general class of delta-b networks with multiple buffers. On the basis of this approach, they discuss the effects of the approximation involved and present a refined analysis algorithm for the special case of a single buffered delta-2 network. The results of both algorithms are compared with simulation results to assess their accuracy. The comparison shows clearly that the accuracy of the analysis is mainly determined by the modeling of the dependencies between consecutive clock cycles.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Extraordinary permittivity modulation in zinc oxide for dynamic nanophotonics (2021)

Dynamic control over the permittivity of materials enables control over the amplitude, phase, and polarization of light. Thus, to realize practical tunable devices, it is important to perform a detailed dynamic characterization of technology-relevant materials with substantially tunable optical properties. In this work, we demonstrate extraordinarily large, unity-order permittivity modulation in zinc oxide through interband pumping. The large permittivity changes actively enable large reflectance modulation in both lithography-free mirrors (70% at 31.6 mJ/cm2 pump) and nanodisk resonators (55% at 7.6 mJ/cm2 pump fluence). The relaxation time for this response is 20 ps. We explore the physical origins of the permittivity modulation and determine the physical limits. The results of this study will advance the realization of ultrafast dynamic optical devices for optical switching, beam-steering, and spectroscopy.
Flow in a Simulated Turbine Blade Cooling Channel With Spatially Varying Roughness Caused by Additive Manufacturing Orientation (2021)

Abstract Because of the effects of gravity acting on the melt region created during the laser sintering process, additively manufactured surfaces that are pointed upward have been shown to exhibit roughness characteristics different from those seen on surfaces that point downward. For this investigation, the roughness internal flow tunnel (RIFT) and computational fluid dynamics models were used to investigate flow in channels with different roughness on opposing walls of the channel. Three rough surfaces were employed for the investigation. Two of the surfaces were created using scaled, structured-light scans of the upskin and downskin surfaces of an Inconel 718 component which was created at a 45 deg angle to the printing surface and documented by Snyder et al. (2015). A third rough surface was created for the RIFT investigation using a structured-light scan of a surface similar to the Inconel 718 downskin surface, but a different scaling was used to provide larger roughness elements in the RIFT. The resulting roughness dimensions (Rq/Dh) of the three surfaces used were 0.0064, 0.0156, and 0.0405. The friction coefficients were measured over the range of 10,000 &amp;lt; ReDh &amp;lt; 70,000 for each surface opposed by a smooth wall and opposed by each of the other rough walls. At multiple ReDh values, x-array hot-film anemometry was used to characterize the velocity and turbulence profiles for each roughness combination. The friction factor variations for each rough wall opposed by a smooth wall approached complete turbulence. However, when rough surfaces were opposed, the surfaces did not reach complete turbulence over the Reynolds number range investigated. The results of inner variable analysis demonstrate that the roughness function (ΔU+) becomes independent of the roughness condition of the opposing wall providing evidence that Townsend’s hypothesis holds for the relative roughness values expected for additively manufactured turbine blade cooling passages.
ChemInform Abstract: Imaging Beyond the Proteome (2012)

Abstract Review: [recent development of emerging technologies that enable imaging beyond the proteome, i.e.
The native sequence determines sidechain packing in a protein, but does optimal sidechain packing determine the native sequence? (1997)

Globular proteins have highly compact structures and the corresponding packing interactions are widely considered as the principal determinant of the native structure. It is therefore important that theoretical approaches to protein design explicitly take in account packing, which requires that a full atomic representation of the designed protein is maintained. As a first step towards this goal, we have developed in this report an inverse folding algorithm with the aim of specifically designing amino acid sequences which optimise sidechain packing for a given protein fold. The design is performed by a global Monte Carlo optimisation in sequence space, with constant amino acid composition and a full-atom representation of the various protein models. Packing is defined by a Lennard-Jones potential. The program was tested by designing stable sequence variants for the chymotrypsin inhibitor fold. The final protein models showed an increase in intramolecular atomic contacts and a decrease in the overall volume compared to the native structure. Starting from the backbone only of the target structure, the algorithm did gradually retrieve reliable though limited sequence information. Higher compatibility might be achieved by improving the potential, however our results suggest that packing interactions are an essential element of a yet-to-be-defined successful energy function for protein design.
EEPROM Compact Model with SILC Simulation Capability (2006)

The objective of this paper is to present a EEPROM compact model suitable for SILC simulation. The SILC module allows simulating the retention capability of the cell after stress. Test chip array distribution and standard tunnel capacitor are used to extract the SILC module parameters. Thus the extraction procedure is detailed. The description of the complete model is presented. A simulation example is given and validated versus measurements.
Reproducibility of PET measurement for presynaptic dopaminergic functions using L-[β-11C]DOPA and [18F]FE-PE2I in humans (2013)

We found good test-retest reproducibility for the kref values of L-[β-(11)C]DOPA and that for the BPND of [(18)F]FE-PE2I in the striatum and midbrain, indicating the reliability of clinical investigation using PET with L-[β-(11)C]DOPA and [(18)F]FE-PE2I.
ChemInform Abstract: Fluostatins A and B, New Inhibitors of Dipeptidyl Peptidase III, Produced by Streptomyces sp. TA‐3391. Part 2. Structure Determination. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Solution Aggregate Structures of Donor Polymers Determine the Morphology and Processing Resiliency of Non-Fullerene Organic Solar Cells (2023)

The solution-state aggregation of conjugated polymers is critical to the morphology and device performance of bulk heterojunction (BHJ) organic solar cells (OSCs). However, the detailed structures of polymer solution-state aggregates and their impact on the morphology and device performance of OSCs remain largely unexplored. Herein, we utilize a benzodithiophene-based donor polymer (PM7) and its ester-functionalized derivatives (PM7 D1 and D2) with reduced backbone rigidity as our model systems to demonstrate how a polymer solution-state aggregate structure impacts the morphology and processing resiliency of OSCs. Using X-ray scattering and microscopic imaging techniques, we ascertain that PM7 solution forms a combination of semi-crystalline fiber aggregates and amorphous polymer chain network aggregates, whereas PM7 D1 and D2 solutions primarily form amorphous network aggregates through sidechain associations. Interestingly, when the solution temperature is increased, the fiber aggregates of PM7 break down while the polymer network aggregates remain stable. Due to this temperature-dependent behavior of the fiber aggregates, blade-coated devices fabricated from the PM7 donor polymer and non-fullerene acceptor, ITIC-4F, lead to highly processing temperature-sensitive performance, whereas PM7 D1 and D2 polymers exhibit improved processing temperature resiliency. More importantly, we report that amorphous, network-like aggregates are conducive to superior device performance in blade-coated OSCs owing to the formation of blend films with short π–π stacking distance, small domain spacing, and face-on preferred molecular orientation. In contrast, we find that fiber-like aggregates lead to large π–π stacking distance, large domain spacing, and isotropic molecular orientation in the blend film, which deteriorate the device performance.
Dynamic Power Analysis under Laser Stimulation: A New Dynamic Laser Simulation Approach (2010)

Abstract Dynamic Laser Stimulation (DLS) techniques proved to be very efficient in soft defect localization bringing a lot of information about the device internal behavior. We need to use external parameter measurements such as frequency, delay, voltage etc to perform these techniques. So they can't be used to study internal signal propagation problems in latched device since signals are resynchronized. We will show that we can use the power analysis coupled with DLS techniques set up to characterize soft defect when we don't have a direct access to monitored signal propagation such as in some transistor transition issues. Laser stimulation in addition of power analysis is used to decrypt security codes in security chip, but in failure analysis it is a new way to reach internal information in order to localize soft defects.
Reactive Ion Beam Etching and Overgrowth Process in the Fabrication of InGaN Inner Stripe Laser Diodes (1998)

Dry etching and overgrowth process techniques have been developed for the fabrication of InGaN inner stripe laser diodes. The dry etch damage at the etched surface and the overgrown interface was estimated using X-ray photoelectron spectroscopy (XPS) and Rutherford backscattering spectrometry (RBS). As a result, the etch damage at the overgrown interface was shown to be repaired during the overgrowth. Groove stripes formed on the GaN layer by reactive ion beam etching (RIBE) were overgrown by GaN using metalorganic chemical vapor deposition (MOCVD). The morphology of the overgrown surface was observed by scanning electron microscopy (SEM). The grooves of widths less than 10 µm were buried completely at 1100°C and smooth, flat surfaces were obtained. We have fabricated the InGaN inner stripe (IS) lasers and reported on the first pulsed lasing operation of InGaN inner stripe lasers, fabricated by dry etching and overgrowth techniques.
Surface photochemistry: the effects of temperature on the singlet quenching of pyrene adsorbed on silica gel by 2-bromonaphthalene (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSurface photochemistry: the effects of temperature on the singlet quenching of pyrene adsorbed on silica gel by 2-bromonaphthalenePaul De Mayo, Lalgudi V. Natarajan, and William R. WareCite this: J. Phys. Chem. 1985, 89, 16, 3526–3530Publication Date (Print):August 1, 1985Publication History Published online1 May 2002Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/j100262a020https://doi.org/10.1021/j100262a020research-articleACS PublicationsRequest reuse permissionsArticle Views81Altmetric-Citations22LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Efficient Private Publish-Subscribe Systems (2014)

We address the problem of privacy in publish-subscribe(pub-sub) systems that typically expose some form of published content and subscriber interest, at least to the infrastructure responsible for subscription matching and content delivery. In our recent work, we proposed P3S, a pub-sub middleware designed to protect the privacy of subscriber interest and confidentiality of published content. P3S combined Cipher text Policy Attribute Based Encryption(CP-ABE) with Predicate Based Encryption (PBE) in its novel system architecture to achieve the desired level of content (payload and metadata) confidentiality, and subscription privacy. In this work, we build upon P3S to achieve the strongest possible subscription privacy where clear text subscription is visible only to the subscriber. Furthermore, we add support for subscription policy enforcement, improve the expressiveness of predicates by allowing disjunctions of conjunction, and improve the efficiency of the underlying cryptography through enhanced cryptographic construction and optimized implementation of cryptographic primitives. To the best of our knowledge, this paper presents the first comprehensive and practical implementation of a real-time privacy preserving pub-sub system, demonstrated on a large-scale test bed featuring up to 90 subscribers with robust, scalable and efficient performance. Our code and test bed specifications are freely available for research and experimentation purposes.
New database compression assists in the IBM z14 processor (2018)

In this paper, we describe how the IBM z14 processor, together with Db2 for z/OS Version 12, can improve data compression rates and thus reduce data storage requirements and cost for large databases. The new processor improves on the compression hardware accelerator available in earlier IBM Z generations by adding new hardware algorithms that increase the compression ratio and extend the applicability to additional data structures in Db2 for z/OS databases. A new entropy coding step employed after Ziv–Lempel compression reduces the size of data compressed with the prior algorithms by 30% on average. Moreover, the new order-preserving compression algorithm enables database index compression, reducing index sizes by roughly 30%. This results in an overall improvement of 30% of the database size for many applications, with associated benefits in storage requirements, input/output bandwidth, and buffer pool efficiency.
Enhanced transduction of dendritic cells by FcγRI‐targeted adenovirus vectors (2007)

FcgammaRI-targeting significantly enhances the efficiency of Ad vector-mediated gene transfer in primary human DC, and results in an improved immune response to a vector-encoded antigen.
Splenosis mimicking metastatic abdominal and pelvic tumours in a 12-year-old female patient (2023)

Splenosis is a heterotopic autotransplantation of splenic tissue after rupture of the splenic capsule caused by injury or during elective splenectomy in the management of haematological diseases. Splenosis might cause nonspecific abdominal symptoms but is usually asymptomatic, and it is diagnosed accidentally as an abdominal tumour. It is rarely diagnosed in the paediatric population. We describe a 12-year-old female patient with hereditary spherocytosis admitted to the hospital 3 years after elective splenectomy and cholecystectomy. In medical imaging abdominal and pelvic tumours together with enlarged lymph nodes were found. During laparoscopic surgery many nodules were found with morphology similar to splenic tissue in the omentum, on the surface of small intestine, colon and peritoneum. Results of histopathological examination confirmed splenosis. Splenosis should be considered in differential diagnosis of abdominal tumours in paediatric patients with a history of elective splenectomy or spleen injury.
Privacy-protection solid-state storage (PP-SSS) system: Automatic lifetime management of internet-data's right to be forgotten (2015)

Recently, a new right, the “Right to be forgotten”, has been defined for privacy protection. One approach to protect personal information is to control the data's lifetime or expiration. Here, a privacy-protection solid-state storage (PP-SSS) system is proposed, in which personal data is automatically invalidated within the hardware itself. In the proposed data-lifetime management (DLM) scheme, the same physical memory cells can be programmed to have different data lifetimes.
Verifiable Delay Functions. (2018)

We study the problem of building a verifiable delay function (VDF). A \(\text {VDF}\)requires a specified number of sequential steps to evaluate, yet produces a unique output that can be efficiently and publicly verified. \(\text {VDF}\)s have many applications in decentralized systems, including public randomness beacons, leader election in consensus protocols, and proofs of replication. We formalize the requirements for \(\text {VDF}\)s and present new candidate constructions that are the first to achieve an exponential gap between evaluation and verification time.
Assessing the In Vivo Targeting Efficiency of Multifunctional Nanoconstructs Bearing Antibody-Derived Ligands (2013)

A great challenge in nanodiagnostics is the identification of new strategies aimed to optimize the detection of primary breast cancer and metastases by the employment of target-specific nanodevices. At present, controversial proof has been provided on the actual importance of surface functionalization of nanoparticles to improve their in vivo localization at the tumor. In the present paper, we have designed and developed a set of multifunctional nanoprobes, modified with three different variants of a model antibody, that is, the humanized monocolonal antibody trastuzumab (TZ), able to selectively target the HER2 receptor in breast cancer cells. Assuming that nanoparticle accumulation in target cells is strictly related to their physicochemical properties, we performed a comparative study of internalization, trafficking, and metabolism in MCF7 cells of multifunctional nanoparticles (MNP) functionalized with TZ or with alternative lower molecular weight variants of the monoclonal antibody, such as the half-chain (HC) and scFv fragments (scFv). Hence, to estimate to what extent the structure of the surface bioligand affects the targeting efficiency of the nanoconjugate, three cognate nanoconstructs were designed, in which only the antibody form was differentiated while the nanoparticle core was maintained unvaried, consisting of an iron oxide spherical nanocrystal coated with an amphiphilic polymer shell. In vitro, in vivo, and ex vivo analyses of the targeting efficiency and of the intracellular fate of MNP-TZ, MNP-HC, and MNP-scFv suggested that the highly stable MNP-HC is the best candidate for application in breast cancer detection. Our results provided evidence that, in this case, active targeting plays an important role in determining the biological activity of the nanoconstruct.