gebhart/patrepeval huggingface dataset:
Substrate recognition by the protein disulfide isomerases (2007)

Protein folding in the endoplasmic reticulum is often associated with the formation of native disulfide bonds. Their primary function is to stabilize the folded structure of the protein, although disulfide bond formation can also play a regulatory role. Native disulfide bond formation is not trivial, so it is often the rate-limiting step of protein folding both in vivo and in vitro. Complex coordinated systems of molecular chaperones and protein folding catalysts have evolved to help proteins attain their correct folded conformation. This includes a family of enzymes involved in catalyzing thiol-disulfide exchange in the endoplasmic reticulum, the protein disulfide isomerase (PDI) family. There are now 17 reported PDI family members in the endoplasmic reticulum of human cells, but the functional differentiation of these is far from complete. Despite PDI being the first catalyst of protein folding reported, there is much that is still not known about its mechanisms of action. This review will focus on the interactions of the human PDI family members with substrates, including recent research on identifying and characterizing their substrate-binding sites and on determining their natural substrates in vivo.
Time-domain Transfer Path Analysis for Transient Phenomena Applied to Tip-in/Tip-out (Shock &amp; Jerk) (2012)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Tip-in/Tip-out of the accelerator pedal generates transient torque oscillations in the driveline. These oscillations may be amplified by P/T, suspension and body modes and will eventually be sensible at the receiver side in the vehicle, for example at the seat or at the steering-wheel.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;The forces that are active during this transient excitation are influenced by non-linear effects in both the suspension and the power train mounts. In order to understand the contribution of each of these forces to the total interior target response (e.g. seat rail vibration) a detailed investigation is performed.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;Traditional force identification methods are not suitable for low-frequent, transient phenomena like tip-in/tip-out. Mount stiffness method can not be used because of non-linear effects in the P/T and suspension mounts. Application of matrix inversion method based on trimmed body vibration transfer functions is not possible due to numerical condition problems.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;This paper describes how the forces resulting from the Tip-in/Tip-out excitation are identified in the time-domain using a time-domain TPA-model. This force-identification is fully based on experimental data. The operational data includes strain signals and is acquired during on-road operational measurements and transfer functions are acquired in trimmed-body FRF-measurements.&lt;/div&gt;&lt;div class="htmlview paragraph"&gt;With the identified forces the time-domain contributions to the total target response can be identified and evaluated at each time-step of the transient phenomenon. This differs from the classical frequency domain TPA - in which the path-contributions represent the averaged frequency content over a certain amount of time and not the contributions at a specific time-step.&lt;/div&gt;&lt;/div&gt;
Low-loss Non-volatile Phase-change Integrated Photonics at 1550nm and 750nm (2021)

The phase shifting effect and low loss of Sb 2 S 3 are verified experimentally for the first time on SOI and SiN integrated photonics platform using microring resonators at the telecom C-band and near visible wavelengths.
Proteinase-K-Resistant Prion Protein Isoforms in Gerstmann-Sträussler-Scheinker Disease (Indiana Kindred) (1996)

Gerstmann-Straussler-Scheinker (GSS) disease is a cerebral prion protein (PrP) amyloidosis associated with mutations in the PrP gene (PRNP). A GSS disease variant with mutation at codon 198 (F198S) has been studied in a large Indiana kindred. Biochemical investigations showed that the amyloid protein consists of 11 and 7 kDa fragments of PrP. Immunohistochemical studies showed that in addition to amyloid, these patients accumulate PrP deposits which are neither fluorescent nor birefringent when stained with thioflavin S and Congo red. In the present paper, we analyzed proteinase-K (PK)-resistant PrP in 7 patients with GSS F198S disease. Immunoblots of PK-treated brain extracts show prominent bands of ca. 27–29, 18–19, and 8 kDa. Immunohistochemistry and thioflavin-S-fluorescence show that the amyloid deposits are conspicuous in the cerebellum but sparse in the caudate nucleus. However, immunoblot analysis reveals PK-resistant PrP bands of similar intensity in both regions. Treatment with PK and PNGase F generates a pattern similar to that of PK alone. Our findings suggest that brain extracts from GSS F198S disease contain 3 prominent nonglycosylated PK-resistant PrP fragments forming a pattern not previously described in other prion diseases, which may in part explain the pathology of this GSS disease variant.
Advances in engineering near-infrared luminescent materials (2021)

Near-infrared (NIR) luminescent materials have emerged as a growing field of interest, particularly for imaging and optics applications in biology, chemistry, and physics. However, the development of materials for this and other use cases has been hindered by a range of issues that prevents their widespread use beyond benchtop research. This review explores emerging trends in some of the most promising NIR materials and their applications. In particular, we focus on how a more comprehensive understanding of intrinsic NIR material properties might allow researchers to better leverage these traits for innovative and robust applications in biological and physical sciences.
Pathologic Q Waves and Prolonged QTc Time in Preoperative ECG Are Predictive for Perioperative Cardiovascular Events (2014)

Aims: The value of ECG in the perioperative risk stratification under modern treatment options is uncertain. The main objective of the present analysis was to determine the usefulness of a pre-operative ECG derivation for evaluating the risk of perioperative morbidity and mortality. Methods: We performed a secondary analysis of the prospective, international, multicenter, observational “No-Risk” Study (N-terminal B-type natriuretic peptide [NT-proBNP] for the assessment of the perioperative cardiac risk after major noncardiac surgery) to determine the prognostic value of 12-lead ECG. Inclusion criteria were age >55 years and at least one of the following cardiovascular risk factors: arterial hypertension, diabetes mellitus, dyslipidemia, active smoking, and family history positive for coronary heart disease. The combined primary endpoint included total mortality, acute myocardial infarction (NSTEMI and STEMI), cardiopulmonary resuscitation, heart failure, and asystole or ventricular fibrillation during hospitalization. ECGs from 616 patients enrolled from 2006 to 2009 prior to noncardiac surgery in the No-Risk Study were analyzed. Results: The mean age was 67.6 (±8.1) years; 300 (48.7%) patients were male. Fourteen (2.3%) patients suffered from the combined primary endpoint while in the hospital. In Kaplan-Meier analyses, a pathologic Q wave and QTc > 500 ms were significantly related to the incidence of the primary endpoint (p p = 0.042, respectively), whereas other ECG parameters such as LBBB, RBBB, PQ interval, QRS interval, and others were not related to worse in-hospital outcome. Conclusion: The 12-lead ECG is still an important diagnostic tool for perioperative risk assessment of cardiovascular events in noncardiac surgery in patients at risk.
2-(2-Bromo-4,5-dimethoxyphenyl)-2-(dimethylamino)acetonitrile (1997)

The regioselective synthesis, spectrometric data (1H and 13C NMR, and MS) and the X-ray crystal structure determination of the title compound, C12H15BrN2O2, are reported. In spite of the presence of a Br atom ortho to the bulky α-aminonitrile group, normal molecular dimensions have been found.
Effect of Dose Size on Bioavailability of Acylated and Nonacylated Anthocyanins from Red Cabbage (<i>Brassica oleracea</i> L. Var. <i>capitata</i>) (2007)

Recent studies indicate that anthocyanin intake conveys a variety of health benefits, which depend on absorption and metabolic mechanisms that deliver anthocyanins and their bioactive metabolites to responsive tissues. The anthocyanin bioavailability of red cabbage (Brassica oleracea L. var. capitata) was evaluated as reflected by urinary excretion of anthocyanins and anthocyanin metabolites. Twelve volunteers consumed 100, 200, and 300 g of steamed red cabbage (containing 1.38 micromol of anthocyanins/g of cabbage) in a crossover design. Anthocyanin concentration in cabbage extract and urine was measured by HPLC-MS/MS. Six nonacylated and 30 acylated anthocyanins were detected in red cabbage, and 3 nonacylated anthocyanins, 8 acylated anthocyanins, and 4 metabolites were present in urine. Mean 24 h excretion of intact anthocyanins increased linearly from 45 (100 g dose) to 65 nmol (300 g dose) for acylated anthocyanins and from 52 (100 g dose) to 79 nmol (300 g dose) for nonacylated anthocyanins. Urinary recovery of intact anthocyanins (percent of anthocyanin intake) decreased linearly from 0.041% (100 g dose) to 0.020% (300 g dose) for acylated anthocyanins and from 0.18% (100 g dose) to 0.09% (300 g dose) for nonacylated anthocyanins. Anthocyanin metabolites consisted of glucuronidated and methylated anthocyanins. The results show that red cabbage anthocyanins were excreted in both intact and metabolized forms and that recovery of nonacylated anthocyanins in urine was >4-fold that of acylated anthocyanins.
A JFET-Based Radiation-Hardened Sensing and Communications Electronic System for Dry Cask Instrumentation (2021)

Dry spent fuel casks are enclosed in stainless-steel and concrete walls to prevent release of the contained hazardous radioactive material into the surrounding environment.Due to the lengthy storage duration, monitoring the structural health conditions of the cask through measurements of internal temperature, pressure, radiation, humidity, and gas distribution and concentration is crucial to ensure the safe containment of the enclosed spent fuels.Placing electrically active sensors inside this harsh environment requires supporting electronics for signal conditioning, amplification, and data transmission to the canister exterior.Commercially available space-rated electronics, typically rated to 300 -1000 krad (Si), would become inoperable during the first few years of the monitoring duration.However, JFET devices are inherently resistant to large doses of ionizing radiation (100 Mrad (Si)) due to the absence of the SiO2 gate-oxides present in MOSFET devices and the SiO2 overlays in BJTs which create charge traps.Using the inherent radiation tolerance offered by JFETs, Oak Ridge National Laboratory has designed a radiation-hardened JFET-based sensing and communication system, suitable for use in spent fuel containment vessels or casks.This electronic system is comprised of multiple sensing oscillators, amplifiers and filters for signal conditioning, a local oscillator for carrier generation, a Gilbert cell mixer, and an output amplifier for driving ultrasonic transducers.Frequency orthogonality is exploited to enable the use multiple sensors using a single transmitter.By driving a high-temperature, radiation-resistant piezoelectric transducer near resonance, this system is designed to transmit through a 2-inch stainless-steel barrier.Presently, the JFET-based sensing and communications system has survived to 1 Mrad (Si) total ionizing dose.
The Dissemination of Time-Varying Information over Networked Agents with Gossiping (2022)

We consider information dissemination over a network of gossiping agents (nodes). In this model, a source keeps the most up-to-date information about a time-varying binary state of the world, and n receiver nodes want to follow the information at the source as accurately as possible. When the information at the source changes, the source first sends updates to a subset of m≤n nodes. After that, the nodes share their local information during the gossiping period to disseminate the information further. The nodes then estimate the information at the source using the majority rule at the end of the gossiping period. To analyze information dissemination, we introduce a new error metric to find the average percentage of nodes that can accurately obtain the most up-to-date information at the source. We characterize the equations necessary to obtain the steady-state distribution for the average error. Through numerical results, we first show that when the source’s transmission capacity m is limited, gossiping can be harmful as it causes incorrect information to disseminate. We then find the optimal gossip rates to minimize the average error for a fixed m.
A Speech-Driven Second Screen Application for TV Program Discovery (2014)

In this paper, we present a speech-driven second screen application for TV program discovery. We give an overview of the application and its architecture. We also present a user study along with a failure analysis. The results from the study are encouraging, and demonstrate our application’s effectiveness in the target domain. We conclude with a discussion of follow-on efforts to further enhance our application.
BONSAI Garden: parallel knowledge discovery system for amino acid sequences. (1995)

We have developed a machine discovery system BONSAI which receives positive and negative examples as inputs and produces as a hypothesis a pair of a decision tree over regular patterns and an alphabet indexing. This system has succeeded in discovering reasonable knowledge on transmembrane domain sequences and signal peptide sequences by computer experiments. However, when several kinds of sequences are mixed in the data, it does not seem reasonable for a single BONSAI system to find a hypothesis of a reasonably small size with high accuracy. For this purpose, we have designed a system BONSAI Garden, in which several BONSAI's and a program called Gardener run over a network in parallel, to partition the data into some number of classes together with hypotheses explaining these classes accurately.
Understanding robustness of mobile networks through temporal network measures (2011)

The application of complex network theory to communication systems has led to several important results. Nonetheless, previous research has often neglected to take into account their temporal properties, which in many real scenarios play a pivotal role. Mainly because of mobility, transmission delays or protocol design, a communication network should not be considered only as a static entity. At the same time, network robustness has come extensively under scrutiny. Understanding whether networked systems can undergo structural damage and yet perform efficiently is crucial to both their protection against failures and to the design of new applications. In spite of this, it is still unclear what type of resilience we may expect in a network that continuously changes over time. In this work we present the first attempt to define the concept of temporal network robustness: we describe a measure of network robustness for time-varying networks and we show how it performs on different classes of random models by means of analytical and numerical evaluation. Particularly, we show how static approximation can wrongly indicate high robustness of fragile networks when adopted in mobile time-varying networks, while a temporal approach captures more accurately the system performance.
Binaural Loudness for Artificial-Head Measurements in Directional Sound Fields (2008)

The effect of the sound incidence angle on loudness was investigated for fifteen listeners who matched the loudness of sounds coming from five different incidence angles in the horizontal plane to that of the same sound with frontal incidence. The stimuli were presented via binaural synthesis by using head-related transfer functions measured for an artificial head. The results, which exhibited marked individual differences, show that loudness depends on the direction from which a sound reaches the listener. The average results suggest a relatively simple rule for combining the two signals at the ears of an artificial head for binaural loudness predictions.
Evaluation of the Prototype Surface Bypass for Salmonid Smolts in Spring 1996 and 1997 at Lower Granite Dam on the Snake River, Washington (2000)

In spring 1996 and 1997, we studied the prototype surface bypass and collector (SBC) at Lower Granite Dam on the Snake River in Washington. Our objectives were to determine the most efficient SBC configuration and to describe smolt movements and swimming behavior in the forebay. To do this, we used hydroacoustic and radiotelemetry techniques. The SBC was retrofitted onto the upstream face of the north half of the powerhouse to test the surface bypass method of diverting smolts from turbines. The SBC had three entrances, with mean velocities ranging from 0.37 to 1.92 m/s, and it discharged 113 m3/s through its outlet at Spill Bay 1, which was adjacent to the powerhouse. Different SBC configurations were created by altering the size and shape of entrances. During spring 1996 and 1997, river discharge was well above normal (123 and 154% of average, respectively). Powerhouse operations caused a strong downward component of flow upstream of the SBC. Many smolts (primarily steelhead and secondarily chinook salmon) were observed actively swimming upward in the water column. There were four times as many smolts diverted from turbines per unit volume of water with SBC flow than with spill flow, which indicated that the SBC may be an especially important bypass consideration in moderate- or low-flow years. The highest SBC efficiency (the proportion of total fish passing through the north half of the powerhouse by all routes that passed through the SBC) for any configuration tested was about 40%. Although no single SBC configuration stood out as the most efficient, the horizontal surface and maximum area configurations, or some combination of the two, are worth further investigation because they were moderately efficient.
Coupling of the Distal Hydrogen Bond Network to the Exogenous Ligand in Substrate-Bound, Resting State Human Heme Oxygenase (2009)

Mammalian heme oxygenase (HO) possesses catalytically implicated distal ordered water molecules within an extended H-bond network, with one of the ordered water molecules (#1) providing a bridge between the iron-coordinated ligand and the catalytically critical Asp140, that, in turn, serves as an acceptor for the Tyr58 OH H-bond. The degree of H-bonding by the ligated water molecule and the coupling of this water molecule to the H-bond network are of current interest and are herein investigated by (1)H NMR. Two-dimensional NMR allowed sufficient assignments to provide both the H-bond strength and hyperfine shifts, the latter of which were used to quantify the magnetic anisotropy in both the ferric high-spin aquo and low-spin hydroxo complexes. The anisotropy in the aquo complex indicates that the H-bond donation to water #1 is marginally stronger than in a bacterial HO, while the anisotropy for the hydroxo complex reveals a conventional (d(xz), d(yz))(1) ground state indicative of only moderate to weak H-bond acceptance by the ligated hydroxide. Mapping out the changes of the H-bond strengths in the network during the ligated water --> hydroxide conversion by correcting for the effects of magnetic anisotropy reveals a very substantial change in H-bond strength for Tyr58 OH and lesser effects on nearby H-bonds. The effect of pH on the H-bonding network in human HO is much larger and transmitted much further from the iron than in a pathogenic bacterial HO. The implications for the HO mechanism of the H-bond of Tyr58 to Asp140 are discussed.
Immobilization of Lipase from <i>Thermomyces lanuginosus</i> in Magnetic Macroporous ZIF-8 Improves Lipase Reusability in Biodiesel Preparation (2021)

In recent years, metal-organic frameworks (MOFs) have emerged as a promising support for immobilizing enzymes due to their high designability and structural diversity. Previous studies show that MOFs with single-crystal-ordered macroporous structures can effectively improve the accessibility of large-size enzyme and reduce the mass transfer resistance compared to conventional MOFs. In order to further enhance the reusability of lipase immobilized on macroporous MOFs, modification of MOFs through some magnetic particles could be an efficient approach. In this work, magnetic macroporous zeolitic imidazolate framework-8 (ZIF-8), referred to as m-M-ZIF-8 (with an average macropore size of about 140 nm), was synthesized and used for the immobilization of <i>Thermomyces lanuginosus</i> lipase (TLL). It was found that enzyme loading and the specific enzyme activity of the immobilized lipase were greatly enhanced through this magnetic modification. The enzyme loading of TLL@C-ZIF-8, T LL@M-ZIF-8, and TLL@m-M-ZIF-8 was 0.060, 0.074, and 0.076 mg/mg respectively. Besides, the activity of 93.5% was maintained after the immobilized lipase being repeatedly used for five batches, which was much higher than that of the immobilized lipase without magnetic modification, which was only 73.4%.
An astronomical pattern‐matching algorithm for computer‐aided identification of whale sharks <i>Rhincodon typus</i> (2005)

Summary The formulation of conservation policy relies heavily on demographic, biological and ecological knowledge that is often elusive for threatened species. Essential estimates of abundance, survival and life‐history parameters are accessible through mark and recapture studies given a sufficiently large sample. Photographic identification of individuals is an established mark and recapture technique, but its full potential has rarely been exploited because of the unmanageable task of making visual identifications in large data sets. We describe a novel technique for identifying individual whale sharks Rhincodon typus through numerical pattern matching of their natural surface ‘spot’ colourations. Together with scarring and other markers, spot patterns captured in photographs of whale shark flanks have been used, in the past, to make identifications by eye. We have automated this process by adapting a computer algorithm originally developed in astronomy for the comparison of star patterns in images of the night sky. In tests using a set of previously identified shark images, our method correctly matched pairs exhibiting the same pattern in more than 90% of cases. From a larger library of previously unidentified images, it has to date produced more than 100 new matches. Our technique is robust in that the incidence of false positives is low, while failure to match images of the same shark is predominantly attributable to foreshortening in photographs obtained at oblique angles of more than 30°. We describe our implementation of the pattern‐matching algorithm, estimates of its efficacy, its incorporation into the new ECOCEAN Whale Shark Photo‐identification Library, and prospects for its further refinement. We also comment on the biological and conservation implications of the capability of identifying individual sharks across wide geographical and temporal spans. Synthesis and applications. An automated photo‐identification technique has been developed that allows for efficient ‘virtual tagging’ of spotted animals. The pattern‐matching software has been implemented within a Web‐based library created for the management of generic encounter photographs and derived data. The combined capabilities have demonstrated the reliability of whale shark spot patterns for long‐term identifications, and promise new ecological insights. Extension of the technique to other species is anticipated, with attendant benefits to management and conservation through improved understanding of life histories, population trends and migration routes, as well as ecological factors such as exploitation impact and the effectiveness of wildlife reserves.