gebhart/patrepeval huggingface dataset:
Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces (2021)

Circular tandem repeat proteins ('cTRPs') are de novo designed protein scaffolds (in this and prior studies, based on antiparallel two-helix bundles) that contain repeated protein sequences and structural motifs and form closed circular structures. They can display significant stability and solubility, a wide range of sizes, and are useful as protein display particles for biotechnology applications. However, cTRPs also demonstrate inefficient self-assembly from smaller subunits. In this study, we describe a new generation of cTRPs, with longer repeats and increased interaction surfaces, which enhanced the self-assembly of two significantly different sizes of homotrimeric constructs. Finally, we demonstrated functionalization of these constructs with (1) a hexameric array of peptide-binding SH2 domains, and (2) a trimeric array of anti-SARS CoV-2 VHH domains. The latter proved capable of sub-nanomolar binding affinities towards the viral receptor binding domain and potent viral neutralization function.
Effects of ruxolitinib cream on pruritus and quality of life in atopic dermatitis: Results from a phase 2, randomized, dose-ranging, vehicle- and active-controlled study (2020)

RUX cream provides a clinically meaningful reduction in itch and QoL burden.
A comparison of statistical methods for the detection of hepatocellular carcinoma based on serum biomarkers and clinical variables (2013)

In addition to multiple biomarkers, the incorporation of age and gender into statistical models significantly improved their predictive performance in the detection of HCC.
A fully-differential switched capacitor chopper stabilized high-pass filter (mirrored integrator) (2004)

This work presents a new design for fully differential, high-pass switched-capacitor (SC) filter. The frequency dependence of the filter transfer function is the mirrored image (around one-half of the Nyquist frequency) of the low-pass integrator transfer function, thus we refer to the new filter as the "mirrored integrator" (MI). The MI will be a key element in the design of Nyquist band signal processing applications such as two-path band-pass /spl Sigma//spl Delta/ analog to digital converters (ADC's) and high-pass /spl Sigma//spl Delta/ ADC's. A chopper stabilization method is inherently employed in the design to suppress the DC offset and 1/f noise of the opamp.
Management of application complexes in multitier clustered systems [Technical forum] (2003)

In this Technical Forum article, we describe a generalized management framework for application complexes in multitiered cluster environments. The application complexes can be viewed as distinct autonomic computing entities that live together in thecluster. The management framework was implemented on a rack-mounted cluster of servers using the IBM Director management tool.
MCS: Buffered Clos-network switch with in-sequence packet forwarding (2012)

Multi-stage buffered Clos-network switches suffer from out-of-sequence packet forwarding. This paper proposes a three-stage memory memory memory (MMM) Clos-network switch, called the MCS switch, which provides in-sequence packet forwarding while maintaining high throughput. The proposed MCS switch adopts the oldest-cell-first selection for arbitrations at the first and second stages and an iterative matching scheme at the third-stage of the switch to provide in-sequence packet service. It keeps the properties of a buffered Clos-network switch, such as small configuration time and relaxed time synchronization among different switch modules and stages. The performance of the proposed switch is analyzed through computer simulation. Simulation results show that the performance of the proposed switch under both uniform and nonuniform traffic is comparable to that of a switch without in-sequence packet service.
Novel Co-processing Methodology To Enable Direct Compression of a Poorly Compressible, Highly Water-Soluble Active Pharmaceutical Ingredient for Controlled Release (2018)

Herein we introduce an innovative process for the preparation of a directly compressible active pharmaceutical ingredient (API) and excipient agglomerates for an extended-release formulation of a highly water soluble drug, demonstrated with metformin HCl. Metformin is poorly compressible and currently employs wet granulation for tablet manufacturing, resulting in long cycle times. We have co-processed metformin HCl with hydroxypropyl methylcellulose (HPMC) and sodium carboxymethylcellulose (NaCMC) in a solvent medium to generate agglomerates that were tableted via direct compression, thereby reducing the drug product manufacturing cycle time and cost while maintaining the extended-release dissolution profile. The intimate mixing of HPMC and NaCMC with metformin HCl through co-processing reduces the risk of segregation during downstream handling and tableting. Additionally, this process reduced the excipient load required to achieve the target dissolution profile and bioequivalence, leading to reduced tablet mass and size with a 1000 mg drug load.
A Broadband Tracking YIG-Tuned Mixer for a State-of-the-Art Spectrum Analyzer (1987)

A switched. YIG-tuned filter/mixer/discriminator has been developed for a microwave spectrum analyzer to eliminate tuning problems associated with magnetically tuned filters. Such problems arise from nonlinear hysteresis and eddy current delay. The new broadband component (2.7 to 22 GHz) contains a triple YIG sphere tuned preselector. a fundamental mixer using a GaAs monolithic diode IC. and a YIG-tuned discriminator. The output of the YIG discriminator is a voltage proportional to the difference between the RF signal applied to it and the ferrite resonant frequency. This voltage provides a feedback signal to the control circuits driving the main magnet of the YIG-tuned filter/mixer to correct for tuning error. The result is a microwave spectrum analyzer setting a new standard in amplitude accuracy and sensitivity.
Microwave plasma reactor design for diamond synthesis at high pressures and high power densities (2010)

Summary form only given. It is now widely recognized the CVD synthesized diamond quality and growth rates can be improved by using high power density microwave discharges operating at pressures above 180 Torr. However at high pressures these discharges separate from the walls of the discharge chamber and become freely floating taking on shapes that are related to the shape of the impressed electromagnetic fields. Discharges can even move about the discharge chamber as they react to buoyant forces and to convective forces caused by the gas flows. Thus at high pressures microwave discharges behave very differently from the typical low pressure discharge and require new methods of discharge control and microwave applicator and plasma reactor design. In particular the high pressure plasma reactor system must be able control the size, the spatial location and the shape of the very hot, and spatially non-uniform microwave discharge in such a manner to enable optimal diamond synthesis at high pressures and power densities. The engineering challenge is to develop reactor designs and associated process methods that are both robust and optimized for high pressure and high power density operation and thereby take advantage of the improved deposition chemistry and physics that exist in the high pressure regime. The design and development of two new microwave plasma reactors is described. Each of these reactors is excited with a hybrid "TM013 plus TEM001" mode, and robustly operated in the 200-400 Torr pressure regime. The reactor applicators are tunable and their electromagnetic fields are focused just above the substrate and can be varied and modified by reactor tuning. An intense microwave discharge with absorbed variable power densities of 150-600 W/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> is produced. The adaptable design allows the control of the discharge size, shape and position and thereby allows in situ process optimization; i.e. the discharge can be positioned over the substrate for optimized synthesis. The experimental single crystal diamond (SCD) and polycrystalline diamond (PCD) synthesis performance of these reactors over the 200-400 Torr pressure regime is compared to the performance of commercial reactors operating at lower pressures and lower power densities. In particular, high quality SCD and PCD is synthesized with deposition rates that exceed 100 microns/hr and reactor power efficiencies range from 6 -25 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> of diamond per kW-h over a 25 mm diameter synthesis area as pressure, power density and gas chemistry are varied. The ability to extend these designs to even higher pressures will also be discussed.
Mesenchymal Stem Cell-Mediated Functional Tooth Regeneration in Swine (2006)

Mesenchymal stem cell-mediated tissue regeneration is a promising approach for regenerative medicine for a wide range of applications. Here we report a new population of stem cells isolated from the root apical papilla of human teeth (SCAP, stem cells from apical papilla). Using a minipig model, we transplanted both human SCAP and periodontal ligament stem cells (PDLSCs) to generate a root/periodontal complex capable of supporting a porcelain crown, resulting in normal tooth function. This work integrates a stem cell-mediated tissue regeneration strategy, engineered materials for structure, and current dental crown technologies. This hybridized tissue engineering approach led to recovery of tooth strength and appearance.
Parallel Information Transfer in a Multi-Node Quantum Information Processor (2011)

We describe a method for coupling disjoint quantum bits (qubits) in different local processing nodes of a distributed node quantum information processor. An effective channel for information transfer between nodes is obtained by moving the system into an interaction frame where all pairs of cross-node qubits are effectively coupled via an exchange interaction between actuator elements of each node. All control is achieved via actuator-only modulation, leading to fast implementations of a universal set of internode quantum gates. The method is expected to be nearly independent of actuator decoherence and may be made insensitive to experimental variations of system parameters by appropriate design of control sequences. We show, in particular, how the induced cross-node coupling channel may be used to swap the complete quantum states of the local processors in parallel.
<title>Digital Mammography: Development Of A Computer-Aided System For Detection Of Microcalcifications</title> (1987)

One of the potential advantages of digital radiography is that it allows computerized methods to be applied in the analysis of image abnormalities. In this study, automated detection of microcalcifications in digital mammograms was investigated. We employed a spatial filtering technique to suppress the structured background in a mammogram while enhancing the microcalcifications. Signal-extraction techniques based on the physical characteristics of microcalcifications were then used to isolate clustered microcalcifications from the remaining noise background. To obtain test mammograms with known signal locations for evaluation of the detection accuracy of the computer method, we employed Monte Carlo techniques to generate simulated microcalcification clusters which were then superimposed on normal mammograms. The results indicate that the computer method can achieve a true-positive cluster detection rate of approximately 85% at a false-positive detection rate of one cluster per image for microcalcifications of average subtlety. Detection accuracy is expected to increase if the parameters of the image-processing and signal-extraction techniques are optimized further.
Crystal structure of rhodopsin in complex with a mini-G<sub>o</sub>sheds light on the principles of G protein selectivity (2018)

Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-G<sub>o</sub> protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.
Improving T-wave alternans measurement quality by reducing noise and artifacts (2005)

We adopted the time domain method for T-wave alternans (TWA) measurement from BD Nearing and RL Verrier, Harvard Medical School, Boston, MA, USA, developed techniques for noise and artifact rejection, and made it more suitable for processing of ECG data, acquired with standard electrodes during exercise stress testing and Holter monitoring. New techniques are cubic alignment, nonlinear filtering, and intra class variability in the odd and even median beats. During the development stage 64 simulated ECGs with different amplitudes, heart rates, QT intervals, TWA levels, and different noise types and levels were used. With these ECGs the expected TWA values were known. Their agreement with the measured values was very high. In addition, we used 90 real Holter, 1416 bicycle and treadmill exercise test ECGs with annotated visible TWA episodes for development and verification of the TWA algorithm.
A Lithology-lndependent Porosity Model Using Three Neutron Measurements: Part II—Applications and Error Analysis (1993)

Abstract A lithology independent porosity model, N3LIP, using three neutron measurements, thermal and epithermal neutron porosity and thermal absorption cross section, was developed and presented at the 33rd SPWLA annual logging symposium (reference 1). This model considers any formation, regardless of its mineralogical composition, as two major regions. The first region is the pore space which is filled with fluid, while the second, the matrix, is the rest of the formation. N3LIP deals with the second region, the matrix, as a black box. The model calculates matrix diffusion length, which is the most lithology dependent parameter of a formation, without a need to know its lithological composition. This matrix diffusion length is calculated using two different techniques while iterating on porosity. The final solution, porosity, is deterrnined by analyzing the difference of the diffusion lengths. In Part I (reference 1), the methodology of N3LIP was described in detail and applied to some artificial logs generated using SNUPAR (reference 2) as a forward model. Here, the applications of this model to actual reservoirs are presented, and an error analysis of the calculated porosity is discussed. N3LIP has been used to calculate porosity in two different types of reservoirs, shaly sandstone and carbonates. The shaly sand reservoirs are Kuparuk in the North Slope and Long Beach in California, while the carbonate reservoir is Sycamore in the Permian Basin. Due to concerns of the environmental effects on the calculated neutron measurements, especially the borehole rugosity on the epithermal tool, the uncertainty in the calculated porosity using N3LIP in those reservoirs has been studied by applying uncertainties to the logs that have been used. The effect of these uncertainties are presented and discussed in detail.
Bov-tA Short Interspersed Nucleotide Element Sequences in Circulating Nucleic Acids from Sera of Cattle with Bovine Spongiform Encephalopathy (BSE) and Sera of Cattle Exposed to BSE (2005)

Circulating nucleic acids (CNA) are known to be enriched in repetitive DNA sequences in humans. Here, bovine sera CNA were analyzed to determine if cell stress-related short interspersed nucleotide elements (SINEs) could be detected in sera from cattle associated with bovine spongiform encephalopathy (BSE). Nucleic acids were extracted, amplified, cloned, and sequenced from the sera of protease-resistant prion protein (PrP(res))-positive cattle (n = 2) and sera from BSE-cohort cows (n = 6); 150 out of 163 clones revealed the presence of, on average, an 80-bp sequence from the 3' region of Bov-tA SINE. A PCR protocol was developed that differentially identified SINE-associated CNA in BSE-exposed versus normal cattle. CNA were extracted from a serum vesicular fraction after controlled blood collection and processing procedures. Sera from four confirmed cases of BSE, 137 BSE-exposed cohort animals associated with eight confirmed BSE cases, and 845 healthy, PrP(res)-negative control cows were tested. All four sera from confirmed BSE cases were repeatedly reactive in the assay. BSE-exposed cohorts had a 100-fold higher occurrence of repeatedly reactive individuals per cohort (average = 63%; range = 33% to 91%), compared to healthy controls (average = 0.6%; P < 0.001). This study shows that BSE-confirmed and cohort animals possess a unique profile of SINE-associated serum CNA that can be utilized as a marker that highly correlates to BSE exposure.
Mailbox-Based vs. Log-Based Query Completion for Mail Search (2017)

Recent research studies on mail search have shown that the longer the query, the better the quality of results, yet a majority of mail queries remain very short and searchers struggle with formulating queries. A known mechanism to assist users in this task is query auto-completion, which has been highly successful in Web search, where it leverages huge logs of queries issued by hundreds of millions of users. This approach cannot be applied directly to mail search as personal query logs are small, mailboxes are not shared and other users' queries are not necessarily generalizable to all. We therefore propose here to leverage the mailbox content in order to generate suggestions, taking advantage of mail-specific features. We then compare this approach to a recent study that augments an individual user's mail search history with query logs from "similar users'', where the similarity is driven by demographics. Finally we show how combining both types of approaches allows for better suggestions quality but also increases the chance that the desired message be retrieved. We validate our claims via a manual qualitative evaluation and large scale quantitative experiments conducted on the query log of Yahoo Mail.
On driver's braking behavior in car following (2007)

A new index have been proposed to evaluate danger situation in car following based on the hypothesis that drivers evaluate collision risk for preceding car and decide braking behavior with change of area of a preceding car on the retina. Based on the index, braking behaviors in car following situation is analyzed. Decelerating profile of a test driver is modeled using the proposed index and the gap D based on the experimental results of the test driver with a real car. In addition, the results of laboratory experiments using a driving simulator support the results of the real car experiments. In addition, braking initiation timing of the test driver is characterized as a brake judgment line in the plane of the modified index and gap D and the characterization is applied to analyze change of the braking initiation timing according to the change of road condition.
A method of measuring a molten metal liquid pool volume (1990)

A broth microdilution method was used to examine the sensitivity of 75 Haemophilus paragallinarum isolates to six antimicrobial drugs (ampicillin, erythromycin, neomycin, penicillin, streptomycin, and tetracycline). A total of 55 of the isolates (73%) were sensitive to all six drugs. The remaining 20 isolates were resistant to streptomycin, with one of these isolates also being resistant to tetracycline and another also resistant to neomycin. No isolate showing antimicrobial drug resistance belonged to agglutinin serovar C, despite this being the single largest serovar (27 out of 75) in the study. No plasmids were detected among the 75 isolates, despite the use of five different plasmid-screening techniques.
8th International IUFRO Wood Drying Conference: Brasov-Romania, August 24-29, 2003 (2003)

The IUFRO 5.04.06 Wood Drying Conference was organised by the "Transilvania" University of Brasov - Faculty of Wood Industry and hosted by the Aro Palace Complex in Brasov (Romania). Over 100 scientists from 28 countries attended the meeting. Two Keynote Addresses: " The Role of Wood Anatomy in the Drying of Wood: "Great Oaks from Little Acorns Grow " by the Wood Drying Working Party Leader, Patrick PerrC (France) and " High-Frequency Heating Combined With Vacuum Drying Of Wood by Helmut Resch (Austria) was an excellent start of the technical program of over 80 oral presentations and 28 poster presentations. The topics of the 10 oral presentation sessions and the poster session covered modelling, stress and strain behaviour of wood, properties ofwood related to drying, fast drying procedures, applied drying, heat and mass transfer, kiln control, drying quality, colorations and general.
Human MHC Class I-restricted high avidity CD4<sup>+</sup>T cells generated by co-transfer of TCR and CD8 mediate efficient tumor rejection in vivo (2012)

In this study, we generated human MHC Class I-restricted CD4<sup>+</sup> T cells specific for Epstein-Barr virus (EBV) and cytomegalovirus (CMV), two herpesviridae associated with lymphoma, nasopharyngeal carcinoma and medulloblastoma, respectively. Retroviral transfer of virus-specific, HLA-A2-restricted TCR-coding genes generated CD4<sup>+</sup> T cells that recognized HLA-A2/peptide multimers and produced cytokines when stimulated with MHC Class II-deficient cells presenting the relevant viral peptides in the context of HLA-A2. Peptide titration revealed that CD4<sup>+</sup> T cells had a 10-fold lower avidity than CD8<sup>+</sup> T cells expressing the same TCR. The impaired avidity of CD4<sup>+</sup> T cells was corrected by simultaneously transferring TCR- and CD8-coding genes. The CD8 co-receptor did not alter the cytokine signature of CD4<sup>+</sup> T cells, which remained distinct from that of CD8<sup>+</sup> T cells. Using the xenogeneic NOD/SCID mouse model, we demonstrated that human CD4<sup>+</sup> T cells expressing a specific TCR and CD8 can confer efficient protection against the growth of tumors expressing the EBV or CMV antigens recognized by the TCR. In summary, we describe a robust approach for generating therapeutic CD4<sup>+</sup> T cells capable of providing MHC Class I-restricted immunity against MHC Class II-negative tumors in vivo.
High-density probe substrate for testing optical interconnects (2005)

The design, fabrication, and demonstration of a high-density probe substrate (100 /spl mu/m pitch) for testing chips with electrical and optical input/output (I/O) interconnects are presented. The primary purpose of this substrate is to provide nondamaging, temporary interconnections between the device-under-test (DUT) and the automated test equipment (ATE) during wafer probing - an essential step in the system-on-chip (SOC) manufacturing process. Optical probing of an array of polymer pillar-based optical I/O interconnects is demonstrated for the first time, to the authors' knowledge.