gebhart/patrepeval huggingface dataset:
A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function (2012)

The ability of a protein to carry out a given function results from fundamental physicochemical properties that include the protein's structure, mechanism of action, and thermodynamic stability. Traditional approaches to study these properties have typically required the direct measurement of the property of interest, oftentimes a laborious undertaking. Although protein properties can be probed by mutagenesis, this approach has been limited by its low throughput. Recent technological developments have enabled the rapid quantification of a protein's function, such as binding to a ligand, for numerous variants of that protein. Here, we measure the ability of 47,000 variants of a WW domain to bind to a peptide ligand and use these functional measurements to identify stabilizing mutations without directly assaying stability. Our approach is rooted in the well-established concept that protein function is closely related to stability. Protein function is generally reduced by destabilizing mutations, but this decrease can be rescued by stabilizing mutations. Based on this observation, we introduce partner potentiation, a metric that uses this rescue ability to identify stabilizing mutations, and identify 15 candidate stabilizing mutations in the WW domain. We tested six candidates by thermal denaturation and found two highly stabilizing mutations, one more stabilizing than any previously known mutation. Thus, physicochemical properties such as stability are latent within these large-scale protein functional data and can be revealed by systematic analysis. This approach should allow other protein properties to be discovered.
Stretch-tuneable dielectric mirrors and optical microcavities (2010)

We demonstrate how tuneable Distributed Bragg Reflectors (DBRs) and resonant micro-cavities can be built by a scalable layer assembly of the transparent utility rubbers polydimethylsiloxane and polystyrene-polyisoprene. Stretching the devices by more than 60% leads to an affine contraction of the layer thicknesses thereby tuning both DBR and cavity modes across the entire visible spectrum. Such rapidly- and reversibly- stretch-tuneable cavities can be used in tuneable micro-lasers and for quantitative optical strain sensing applications.
Explicit MPC for LPV Systems: Stability and Optimality (2012)

This paper considers high-speed control of constrained linear parameter-varying systems using model predictive control. Existing model predictive control schemes for control of constrained linear parameter-varying systems typically require the solution of a semi-definite program at each sampling instance. Recently, variants of explicit model predictive control were proposed for linear parameter-varying systems with polytopic representation, decreasing the online computational effort by orders of magnitude. Depending on the mathematical structure of the underlying system, the constrained finite-time optimal control problem can be solved optimally, or close-to-optimal solutions can be computed. Constraint satisfaction, recursive feasibility and asymptotic stability can be guaranteed a priori by an appropriate selection of the terminal state constraints and terminal cost. The paper at hand gathers previous developments and provides new material such as a proof for the optimality of the solution, or, in the case of close-to-optimal solutions, a procedure to determine a bound on the suboptimality of the solution.
Semiconductor diode matrix for isotope localization (1969)

A semiconductor matrix has been developed using lithium-drifted diodes, and successfully applied to two-dimensional radiation localization. It is based on the construction of an array of individual detection regions upon a single silicon diode by orthogonal partitioning of the p and n regions. In the matrix formation, parallel grooves, 0.5 mm wide, were cut into both the p and n faces of a silicon diode, penetrating the intrinsic region. The measured resistance achieved across all grooves is at least 109 ohms, as a result of chemical etching and surface treatment. The isolation of the electrode regions bounded by the grooves on the p and n sides of the device permits row and column addressing of charge pulses from ionizing radiations. By interconnecting the rows and interconnecting the columns of a number of such units, larger areas can be monitored. A resolution of (3*3) mm has been achieved. The configuration is considered suitable for the construction of a gamma camera.
PenBase, the shrimp antimicrobial peptide penaeidin database: Sequence-based classification and recommended nomenclature (2005)

Antimicrobial peptides play a major role in innate immunity. The penaeidins, initially characterized from the shrimp Litopenaeus vannamei, are a family of antimicrobial peptides that appear to be expressed in all penaeid shrimps. As of recent, a large number of penaeid nucleotide sequences have been identified from a variety of penaeid shrimp species and these sequences currently reside in several databases under unique identifiers with no nomenclatural continuity. To facilitate research in this field and avoid potential confusion due to a diverse number of nomenclatural designations, we have made a systematic effort to collect, analyse, and classify all the penaeidin sequences available in every database. We have identified a common penaeidin signature and subsequently established a classification based on amino acid sequences. In order to clarify the naming process, we have introduced a 'penaeidin nomenclature' that can be applied to all extant and future penaeidins. A specialized database, PenBase, which is freely available at , has been developed for the penaeidin family of antimicrobial peptides, to provide comprehensive information about their properties, diversity and nomenclature.
Recent developments in office design (1996)

Early in this century, extensive research was carried out regarding the worker in the industrial setting with the physical environment as the focus. In the 1930s, the focus became the social environment. Several developments have recently brought the physical environment into prominence and, in particular, the office as a work setting. The US economy has shifted from production to the provision of information and services, with 80 per cent of the workforce predicted to be in the office work setting by the year 2000, compared with 53 per cent today. The work environment is also changing due to advances in technology. This research is in its infancy; and the relationship of the work setting and behaviour, and how it affects productivity, is said to be complex.The existing data suggest that non‐supportive design has negative effects on work and workers, and design appropriate to the work has positive ones. In fact, many businesses have begun changing their design and organizational cultures with positive results. Only time and more observation can reveal what will result from these changes.
The development of a spatially uniform fast ionization wave in a large discharge volume (1998)

A high-voltage nanosecond breakdown in the form of a fast ionization wave (FIW) has been obtained and investigated in a large discharge volume (of 40 l). For various regimes in the air pressure range -4 Torr the velocity of breakdown front propagation and energy absorption by the plasma were measured. A high level of spatial uniformity and reproducibility of the discharge was demonstrated. The possibility of propagation of FIWs in electrodeless systems was shown. It is demonstrated that the FIW propagates quasi-spherically in a free-boundary space until the reduced electric field in the wavefront is close to or exceeds the electron run-away threshold, otherwise the FIW loses its homogeneity and becomes transformed into a streamer corona discharge.
Plasma Membrane Proteins and Glycoproteins Induced by Human Cytomegalovirus Infection of Human Embryonic Fibroblasts (1986)

An analysis of the plasma membrane proteins of human embryonic fibroblasts (HEF) infected with human cytomegalovirus strain AD169 (HCMV) was performed using in vitro radioactive labelling techniques followed by PAGE. Of the 12 virus-induced proteins detected in infected cells, glycoproteins of mol. wt. 34000 (34K), 53K to 55K, 60K to 63K, 70K to 72K, 98K to 103K and 145K to 150K and proteins of 130K to 133K and 260K to 270K were considered significant. The 60K to 63K, 70K to 72K and 130K to 133K components were detectable at early stages of infection (8 h), although only the latter two were labelled by surface iodination. The others only appeared in the membrane from 48 h to 80 h after infection. Serological studies indicated that the 34K, 70K to 72K, 98K to 103K and 145K to 150K components may be HCMV-specified virion constituents, as these glycoproteins reacted with antibodies raised against virions and extracted envelope glycoproteins. Of immunological importance was the exposure on the cell surface of the protein moieties of 70K to 72K and 130K to 133K proteins at 8 h and 53K to 55K, 60K to 63K, 70K to 72K and 145K to 150K components at 80 to 90 h after infection. Pooled human immune sera contained antibodies which reacted with these exposed proteins, as well as with three other virus-induced membrane components of 230K to 240K, 98K to 103K and 78K to 80K.
Challenges in Silicon Photonics Process Technology (2017)

In this paper we discuss the specific challenges of process integration of Si-Photonics for the current and future applications, including lithography, etching and heterogeneous materials integration.
First-trimester screening for trisomy 21 in twin pregnancy: does the addition of biochemistry make an improvement? (2005)

The Combined Test appears to maintain the detection rate achieved by NT screening for trisomy 21 in twin pregnancies, but false-positive rates and invasive diagnostic procedures are reduced.
Cyber attack modeling and simulation for network security analysis (2007)

Cyber security methods are continually being developed. To test these methods many organizations utilize both virtual and physical networks which can be costly and time consuming. As an alternative, in this paper, we present a simulation modeling approach to represent computer networks and intrusion detection systems (IDS) to efficiently simulate cyber attack scenarios. The outcome of the simulation model is a set of IDS alerts that can be used to test and evaluate cyber security systems. In particular, the simulation methodology is designed to test information fusion systems for cyber security that are under development.
Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets (2020)

Abstract The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assays are being used by clinical, research, and public health laboratories. However, it is currently unclear if results from different tests are comparable. Our goal was to evaluate the primer-probe sets used in four common diagnostic assays available on the World Health Organization (WHO) website. To facilitate this effort, we generated RNA transcripts to be used as assay standards and distributed them to other laboratories for internal validation. We then used (1) RNA transcript standards, (2) full-length SARS-CoV-2 RNA, (3) pre-COVID-19 nasopharyngeal swabs, and (4) clinical samples from COVID-19 patients to determine analytical efficiency and sensitivity of the qRT-PCR primer-probe sets. We show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 virus copies per reaction, except for the RdRp-SARSr (Charité) confirmatory primer-probe set which has low sensitivity. Our findings characterize the limitations of currently used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2.
Wireless Readout of Passive <i>LC</i> Sensors (2009)

This paper reports simple yet precise equations for automated wireless measurement of the resonance frequency, <formula formulatype="inline" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex Notation="TeX">$Q$</tex></formula> -factor, and coupling coefficient of inductively coupled passive resonant <emphasis emphasistype="italic" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">LC</emphasis> circuits. This allows remote sensing of all physical and chemical quantities that can be measured with capacitance transducers. Formerly reported front-end circuit concepts for wireless sensor readout, i.e., phase dip measurement and the dip meter, are subsequently discussed. It is shown that, due to fundamental system limitations, the formerly reported circuit concepts are not applicable if the distance between the sensor and the readout electronic circuit becomes too small, resulting in large coupling coefficients. Therefore, we present an improved concept for an analog front-end circuit of the readout system that overcomes these limitations and hence allows wireless sensor readout under a wider range of operating distances.
3-D Generic Elastic Models for Fast and Texture Preserving 2-D Novel Pose Synthesis (2012)

This paper provides an in-depth analysis on face shape alignment for pose insensitive face recognition. The dissimilarity between two face images can be modeled as the difference in intensity between these two images, obtained by warping these faces onto the same shape. In order to achieve this, we must first align both face images independently to obtain a sparse 2-D shape representation. We achieve this by using a Combination of ASMs and AAMs (CASAAMs). We then exchange these two shapes and obtain new intensity (texture) faces based on these exchanged shapes. This allows us to align the two faces with increased pixel-level correspondence while simultaneously achieving a certain degree of pose correction. In order to account for large pose variation, it becomes necessary to model the underlying 3-D face structure for the synthesis of novel 2-D poses. However, in many real-world scenarios, only a single image of the subject is provided and acquisition of the 3-D model is not always feasible. To tackle this common real-world scenario, we propose a novel approach for modeling faces, called 3D Generic Elastic Model (3D-GEM), which can be deformed from a single 2-D image. Our analysis shows that 3-D depth information of human faces does not dramatically change across people, indicating that precise depth information of a person is not needed to generate useful novel 2-D poses. This is a significant discovery that makes our method feasible. We thus demonstrate that our 3-D face model can be efficiently produced by using a generic depth model which can be elastically deformed based on input facial features. This face model can then be rotated in 3-D in order to synthesize any arbitrary 2-D facial pose. Experimental results show that 3-D faces modeled by our proposed work effectively handle large 3-D pose changes in face alignment and they can be used for achieving pose tolerant face recognition. We also provide comparative results of face synthesis obtained by an actual 3-D face scanner and our approach, showing our proposed modeling approach is both effective and efficient.
Mode and Site of Analgesic Action of Epidural Buprenorphine in Humans (1996)

This study was designed to clarify the site of analgesic action of epidural buprenorphine and its spinal segmental analgesia.Fifty patients undergoing gastrectomy were randomly assigned to five groups according to the dose of buprenorphine and route of administration: epidural saline group, epidural buprenorphine 2- and 4-micro gram/kg groups, and intravenous buprenorphine 2- and 4-micro gram/kg groups. The changes in pressure pain threshold (PPT) and visual analog scale (VAS) were compared within groups of patients receiving either buprenorphine, 2 or 4 micro gram/kg epidurally, and between groups of patients receiving buprenorphine 2 or 4 micro gram/kg either epidurally or intravenously. The PPT near the surgical incision was significantly greater (P < 0.05) in the epidural buprenorphine group compared to the intravenous group during the middle period (between 2 and 6 h after administration) of analgesia obtained after administration of buprenorphine. VAS response significantly (P < 0.05) decreased in the epidural group compared to the intravenous group at the same dose. In the smaller dose buprenorphine epidural group, PPT at the forehead (an index of systemic analgesia) exceeded the preoperative value during the 12 h after administration of buprenorphine. PPT near the surgical incision decreased by 30% from the preoperative value and did not exceed the preoperative value throughout the study. PPT at the forehead significantly exceeded the PPT changes measured near the surgical incision (an index of regional analgesia) (P < 0.05). In the larger dose buprenorphine epidural group, during the early period (up to 2 h after administration), PPT at the forehead increased by 30%-40%, while PPT near the surgical incision decreased by 10%-25% compared to the preoperative value (P < 0.01). However, in the middle period, there were no significant differences in the changes between PPT at the forehead and near the surgical incision. In the late period (more than 6 h after administration), PPT at the forehead maintained the level of preoperative value, whereas PPT near the surgical incision decreased by more than 25% from the preoperative value (P < 0.01). VAS value significantly (P < 0.01) decreased in the larger dose buprenorphine epidural group compared with that in the smaller dose group during the middle period. The larger dose of epidural buprenorphine provided better analgesia than the smaller dose. We conclude that epidural buprenorphine acts predominantly at the supraspinal region and produces spinal segmental analgesia in a dose-related manner. (Anesth Analg 1996;83:530-6)
Realizing super-steep subthreshold slope with conventional FDSOI CMOS at low-bias voltages (2010)

We report the first demonstration of a super-steep subthreshold slope (SS) (the smallest ever reported experimentally) with ultra-thin BOX (UTBOX) FDSOI standard CMOS transistors. Record steep SS of 72μV/dec for L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> =25nm and 58μV/dec for L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> =55nm at room temperature are achieved with low voltages. The device also exhibits high ON-state current (~100μA/μm), as compared to other devices from this class. As a result, I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> ratio of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> is realized with 0.5V gate swing for L <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> =55nm MOSFETs. The excellent reliability is also demonstrated.
Therapeutic Intervention with Breast Cancer Metastasis (2002)

Metastatic disease, mainly to the lungs, liver, bone, and brain, is the most common cause of death from breast cancer, despite advances in surgical and clinical management. Two basic principles govern the process of metastasis. First, that tumors are heterogeneous populations of cells, and second, that the process is a sequence of events that depends on tumor cell properties and interactions with the microenvironment at the site of metastasis. Inhibitors targeted at any of these different steps have the potential to inhibit metastatic progression, and examples of key therapeutic targets include overexpression of growth factor receptors, angiogenic factors, matrix metalloproteases, and integrin receptors. The identification of molecular targets for therapy of breast cancer metastasis will be accelerated by DNA array technology, and their selection for use should include evaluation of interactions between tumor cells and normal tissue components. These sorts of inhibitors are likely to target both cancer and normal cell functions, for example, inhibitors of matrix metalloproteases that can potentially inhibit both tumor cell invasion and angiogenesis. The use of appropriate animal models will be necessary to determine the impact of targeted inhibitors on the growth and development of breast cancer metastasis.
Equivalent bandwidth for heterogeneous sources in ATM networks (2002)

Considers the problem of equivalent bandwidth in ATM networks. On/off source models are assumed. Most prior work on this topic assumes that the on/off periods are independent and are exponentially or geometrically distributed. The present authors permit the on and off periods to be dependent and generally distributed. As a specific example, simulated video sources are considered: during a frame of fixed duration, the source generates cells at its constant peak rate for a random active period, which is bounded by the frame length. No cells are generated during the remainder of the frame (off period). The sum of the on and off periods is equal to the frame length and, hence, the on and off periods are dependent. The authors present an accurate approximation for computing the equivalent bandwidth for heterogeneous sources, especially for a mixture of voice and simulated video sources. Simulation was performed to verify the accuracy of the approximate results. It is found that the approximation is accurate over a wide range of system parameters. Numerical results indicate that the linear approximation method underestimates the equivalent bandwidth required, these results agree with the previous simulation studies reported in the literature. For the simulated video sources, the required equivalent bandwidth obtained is compared with that obtained by modeling the simulated video sources as two-state on/off sources. It is observed that the two-state on/off source model overestimates the required bandwidth for the simulated video sources.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Mixed Cation FA<i><sub>x</sub></i>PEA<sub>1–</sub><i><sub>x</sub></i>PbI<sub>3</sub> with Enhanced Phase and Ambient Stability toward High‐Performance Perovskite Solar Cells (2016)

In this work, different from the commonly explored strategy of incorporating a smaller cation, MA + and Cs + into FAPbI 3 lattice to improve efficiency and stability, it is revealed that the introduction of phenylethylammonium iodide (PEAI) into FAPbI 3 perovksite to form mixed cation FA x PEA 1–x PbI 3 can effectively enhance both phase and ambient stability of FAPbI 3 as well as the resulting performance of the derived devices. From our experimental and theoretical calculation results, it is proposed that the larger PEA cation is capable of assembling on both the lattice surface and grain boundaries to form quais‐3D perovskite structures. The surrounding of PEA + ions at the crystal grain boundaries not only can serve as molecular locks to tighten FAPbI 3 domains but also passivate the surface defects to improve both phase and moisture stablity. Consequently, a high‐performance (PCE:17.7%) and ambient stable FAPbI 3 solar cell could be developed.