gebhart/patrepeval huggingface dataset:
Standardized workflow for precise mid- and high-throughput proteomics of blood biofluids (2021)

Abstract Background Accurate discovery assay workflows are critical for identifying authentic circulating protein biomarkers in diverse blood matrices. Maximizing the commonalities in the proteomic workflows between different biofluids simplifies the approach and increases the likelihood for reproducibility. We developed a workflow that allows flexibility for high and mid-throughput analysis for three blood-based proteomes: naive plasma, plasma depleted of the 14 most abundant proteins, and dried blood. Methods Optimal conditions for sample preparation and DIA-MS analysis were established in plasma then automated and adapted for depleted plasma and whole blood. The MS workflow was modified to facilitate sensitive high-throughput or deep profile analysis with mid-throughput analysis. Analytical performance was evaluated from 5 complete workflows repeated over 3 days as well as a linearity analysis of a 5–6-point dilution curve. Result Using our high-throughput workflow, 74%, 93%, 87% of peptides displayed an inter-day CV&lt;30% in plasma, depleted plasma and whole blood. While the mid-throughput workflow had 67%, 90%, 78% of peptides in plasma, depleted plasma and whole blood meeting the CV&lt;30% standard. Lower limits of detection and quantitation were determined for proteins and peptides observed in each biofluid and workflow. Combining the analysis of both high-throughput plasma fractions exceeded the number of reliably identified proteins for individual biofluids in the mid-throughput workflows. Conclusion The workflow established here allowed for reliable detection of proteins covering a broad dynamic range. We envisage that implementation of this standard workflow on a large scale will facilitate the translation of candidate markers into clinical use.
Supplementary Table 3 from Targeting HER2 with Trastuzumab Deruxtecan: A Dose-Expansion, Phase I Study in Multiple Advanced Solid Tumors (2023)

&lt;p&gt;. Inclusion and exclusion criteria for cohort 2d (advanced HER2-expressing non-breast/non-gastric or HER2-mutant solid tumors)&lt;/p&gt;
Continuous production of LiCoO2fine crystals for lithium batteries by hydrothermal synthesis under supercritical condition (2001)

Abstract Specific features of supercritical hydrothermal crystallization synthesis (SHCS) by a rapid heating flow type method are reviewed. The attractive features of the method are (i) quantitative production of ultrafine particles, and (u) control of particle morphology or crystal structure by varying the pressure, temperature or reaction atmosphere (reducing or oxidizing). In this study, we use this method to continuously produce LiCoOz fine crystals that are used as for the cathode materials of rechargeable lithium ion batteries. LiOH and Co(NO& were chosen as starting materials. For oxidizing Co(II) to Co(III), O2 was introduced into the reactor after decomposing HzOz aqueous solution in a preheating tubing. LiCoO2 particles were formed in a single phase at supercritical conditions. scanning electron micrographs showed that the particle size was in the range of 500 to 1,000 nm in diameter. Electrochemical characterization was performed by a constant current discharge and charge test. Little decrease in the discharge capacity suggests high stability of the LiCoOz crystals prepared by this method.
A coaxial dual-receiver wireless power transfer system with bipolar coils to eliminate cross-coupling and achieve a controllable power distribution (2019)

This paper proposes a dual-receiver wireless power transfer system that uses bipolar coils as a transmitter and receivers. Compared with a traditional dual-receiver system with unipolar coils, the proposed system can effectively and conveniently eliminate cross-coupling between the receivers, and another significant feature of the system is the ease of changing the received power of the two receiver loads by changing the relative angle of the bipolar coils. The mutual inductance of the bipolar coils is modelled by Newman's formula. Then a system design method to eliminate the influence of cross-coupling and realize controllable power allocation is proposed.
Collision prediction at intersection in sensor network environment (2006)

This paper presents several algorithms to predict collisions among vehicles at intersection, where the information about the movement of vehicles within interesting region is exchanged via sensor network and local broadcasting. We additionally propose algorithms to predict collisions at access road, which is important as well. Experiments show that these algorithms give very accurate results with about 0.5 average false warnings at access road on highway. In comparison with access road, they give relatively more false warning reports at intersection
Role of Cationic Proteins in the Airway: Hyperresponsiveness Due to Airway Inflammation (1994)

Major basic protein (MBP) is a highly cationic protein found in the granules of eosinophils. It has been postulated that MBP may participate in the pathogenesis of airway hyperresponsiveness exhibited by asthmatic patients. Accordingly, we have employed a rat system to investigate the effect of human MBP instillation on airway responsiveness and the possible role of cationic charge in the determination of this effect. Major basic protein caused a significant increase in airway responsiveness to inhaled methacholine. Two polycations, poly-L-arginine and poly-L-lysine, also increased airway responsiveness to inhaled methacholine. Moreover, two other very different cationic proteins, platelet factor 4 (PF4) and cathepsin G were also capable of inducing airway hyperresponsiveness. These effects were dependent on their positive charge, since the charge--and, hence the effect--of these proteins was neutralized with low molecular weight heparin. In addition, other polyanions, such as low molecular weight heparin, albumin, or dextran sulfate, were also effective. We investigated whether two synthetic cationic proteins, poly-L-arginine and poly-L-lysine, could modify epithelial-dependent responses using a perfused guinea pig tracheal tube preparation. With an intact epithelium, methacholine was some 150 times less potent when applied intraluminally than when applied extraluminally. Perfusion of the luminal surface with cationic proteins increased the potency of intraluminally applied methacholine without modifying the responses to extraluminally applied methacholine. Cationic proteins also attenuated the relaxant effects of intraluminally applied KCl. These effects occurred in the absence of any overt epithelial cell damage. Our data demonstrates that cationic proteins can modify epithelial-dependent responses in the airways.(ABSTRACT TRUNCATED AT 250 WORDS)
Zinc rescues obesity‐induced cardiac hypertrophy via stimulating metallothionein to suppress oxidative stress‐activated BCL10/CARD9/p38 MAPK pathway (2017)

Obesity often leads to obesity-related cardiac hypertrophy (ORCH), which is suppressed by zinc-induced inactivation of p38 mitogen-activated protein kinase (p38 MAPK). In this study, we investigated the mechanisms by which zinc inactivates p38 MAPK to prevent ORCH. Mice (4-week old) were fed either high fat diet (HFD, 60% kcal fat) or normal diet (ND, 10% kcal fat) containing variable amounts of zinc (deficiency, normal and supplement) for 3 and 6 months. P38 MAPK siRNA and the p38 MAPK inhibitor SB203580 were used to suppress p38 MAPK activity in vitro and in vivo, respectively. HFD activated p38 MAPK and increased expression of B-cell lymphoma/CLL 10 (BCL10) and caspase recruitment domain family member 9 (CARD9). These responses were enhanced by zinc deficiency and attenuated by zinc supplement. Administration of SB203580 to HFD mice or specific siRNA in palmitate-treated cardiomyocytes eliminated the HFD and zinc deficiency activation of p38 MAPK, but did not significantly impact the expression of BCL10 and CARD9. In cultured cardiomyocytes, inhibition of BCL10 expression by siRNA prevented palmitate-induced increased p38 MAPK activation and atrial natriuretic peptide (ANP) expression. In contrast, inhibition of p38 MAPK prevented ANP expression, but did not affect BCL10 expression. Deletion of metallothionein abolished the protective effect of zinc on palmitate-induced up-regulation of BCL10 and phospho-p38 MAPK. HFD and zinc deficiency synergistically induce ORCH by increasing oxidative stress-mediated activation of BCL10/CARD9/p38 MAPK signalling. Zinc supplement ameliorates ORCH through activation of metallothionein to repress oxidative stress-activated BCL10 expression and p38 MAPK activation.
Linewidth enhancement factor and high temperature performance of 1.48 mu m strained InGaAs-InGaAsP multiquantum well laser (1991)

The linewidth enhancement factor alpha in strained InGaAs-InGaAsP multiquantum well (MQW) lasers emitting near 1.48 mu m has been experimentally determined. The measured alpha at the lasing wavelength is found to be 2 compared to a value of 5.5 and 3.5 typically observed in InGaAsP-InP regular double heterostructure (DH) lasers and MQW lasers, respectively. The small alpha shows that single wavelength strained MQW lasers have smaller chirp width under modulation and also smaller CW linewidth. The carrier lifetime at threshold in these strained MQW lasers does not decrease as rapidly with increasing temperature as is observed for regular InGaAsP-InP DH lasers. This indicates a smaller nonradiative carrier loss due to Auger recombination in strained quantum wells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of diffraction gratings by use of a tabletop soft-x-ray laser (2001)

We have demonstrated the use of a high-repetition-rate 46.9-nm tabletop laser to characterize diffraction gratings designed for grazing-incidence operation in the soft-x-ray spectral region. The efficiencies for various diffraction orders were measured as a function of angle of incidence and compared with the results of model simulations. This measurement technique provides benchmarks with which to improve electromagnetic codes used in the design of soft-x-ray diffraction gratings. The results illustrate the potential of compact tabletop soft-x-ray lasers for use as a new tool for characterization of short-wavelength optics at the manufacturer's site.
Threshold for Tonic Motor Effects from Random Waveform in a Rat Experimental Model of Frontal Cortex Stimulation (2019)

The random waveform was better tolerated than the other waveforms and may allow for the use of higher stimulation voltage without side effects.
Future trends in total digital control of variable speed drives for industrial applications (2002)

The essential rudiments of digital control hardware and software as well as the potential extension of this technology to a dedicated CAD/CAE (computer-aided design/engineering) environment for design of motor drive systems are discussed. These systems, which are intensely application-dependent, have been traditionally designed and manufactured using combinations of logic controllers, computers, power circuits, and analog control boards connected together to achieve the final goal. The proposed CAD environment strives to consolidate the drive systems design requirements in such a way as to allow implementation of these designs within a framework of a standard library of hardware and software. The end result is a production environment where all designs are optimally manufacturable.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Left Ventricular Pressure Measurement During Noninvasive Transcutaneous Cardiac Pacing (1989)

In a pacemaker-dependent patient, the hemodynamic response during external transcutaneous and endocardial sequential pacing was evaluated by left ventricular pressure monitoring. A single ventricular pacing mode with hemodynamic effect of atrioventricular asynchrony was shown during external pacing.
Analytical finite element matrix elements and global matrix assembly for hierarchical 3-D vector basis functions within the hybrid finite element boundary integral method (2014)

Abstract. A hybrid higher-order finite element boundary integral (FE-BI) technique is discussed where the higher-order FE matrix elements are computed by a fully analytical procedure and where the gobal matrix assembly is organized by a self-identifying procedure of the local to global transformation. This assembly procedure applys to both, the FE part as well as the BI part of the algorithm. The geometry is meshed into three-dimensional tetrahedra as finite elements and nearly orthogonal hierarchical basis functions are employed. The boundary conditions are implemented in a strong sense such that the boundary values of the volume basis functions are directly utilized within the BI, either for the tangential electric and magnetic fields or for the asssociated equivalent surface current densities by applying a cross product with the unit surface normals. The self-identified method for the global matrix assembly automatically discerns the global order of the basis functions for generating the matrix elements. Higher order basis functions do need more unknowns for each single FE, however, fewer FEs are needed to achieve the same satisfiable accuracy. This improvement provides a lot more flexibility for meshing and allows the mesh size to raise up to λ/3. The performance of the implemented system is evaluated in terms of computation time, accuracy and memory occupation, where excellent results with respect to precision and computation times of large scale simulations are found.
MALE-RESTRICTED EXPRESSION OF H-Y ANTIGEN ON PREIMPLANTATION MOUSE EMBRYOS (1984)

The H-Y (male) antigen is detectable on 50% of eight-cell mouse embryos. We show that 82% of the offspring resulting from the transfer of (C57BL/6 X A/J)F1 embryos surviving treatment with H-Y antibody and complement to the uteruses of pseudopregnant mice are female. The increased ratio of female-to-male births indicates that the H-Y-bearing embryos are male.
Estrogen and Progesterone Receptors in the Organs of Prenatal Cynomolgus Monkey and Laboratory Mouse1 (1986)

The estrogen and progesterone receptors of several organs of the prenatal cynomolgus macaque and the fetal mouse were studied using a combination of the dextran-coated charcoal technique and high-performance liquid chromatography. This procedure permitted the concurrent measurement of both receptors in minute amounts of tissue. Estrogen receptors, but not progesterone receptors, were found in the fetal monkey and mouse uteri. No estrogen or progesterone receptors were detected in the lungs, liver, kidney, heart, brain, adrenal gland, or limbs of mouse or monkey fetuses. The nonspecific binding of radioactive ORG-2058 was not displaced by unlabeled progesterone, 17 alpha-hydroxyprogesterone caproate, or ORG-2058. Because the steroid receptors that are indispensable mediators of steroid hormone action were absent from the nonreproductive tissues, prenatal development of these organs and tissues cannot be adversely influenced by exposure to estradiol, progesterone, or their synthetic analogues.
Photoinhibition of Photosynthesis and its Recovery in the Green Alga <italic>Chlamydomonas reinhardii</italic> (1987)

Photoinhibition of photosynthesis and its recovery was studied in the unicellular green alga Chlamydomonas reinhardii. Exposure of the algae for 90 min to photosynthetic photon flux densities (PPFD) above the level where photosynthesis approaches saturation (200 μE.m−2.s−1), resulted in photoinhibition; 50% inhibition at about 1,100 μE.m−2.s−1. The time course of inhibition revealed a rapid initial decline of photosynthesis which below 1,000 μE.m−2.s−1, levelled out after 30 min to reach a steady-state plateau. The recovery process was found to be rapid, reaching completion from 50% inhibition within one hour. In the presence of the plastid translation inhibitor chloramphenicol, PPFDs even well below light saturation of photosynthesis induced severe photoinhibition. Chloramphenicol also prevented recovery, whether or not present during the photoinhibitory treatment. Thus, even under rate limiting light levels plants are dependent on continuous chloroplast protein synthesis to replace photodamaged protein. The plastid transcription inhibitor rifampicin did not promote photoinhibition nor did it prevent recovery. The cytoplasmic translation inhibitor cydoheximide only slightly increased the susceptibility to photoinhibition at very high PPFDs. Our results suggest that at PPFDs up to about four times the light saturation of photosynthesis, the repair function suffices to balance the rate of damage, which confers a steady-state level of photodamage. Our data also suggest that this repair process requires continuous translation of chloroplast messenger(s) of high stability.
Related Articles from Targeting the Hedgehog Pathway in Cancer: Can the Spines Be Smoothened? (2023)

Related Articles from Targeting the Hedgehog Pathway in Cancer: Can the Spines Be Smoothened?
Relevance feedback and inference networks (1993)

Relevance feedback, which modifies queries using judgements of the relevance of a few, highly-ranked documents, has historically been an important method for increasing the performance of information retrieval systems. In this paper, we extend the inference network model introduced by Turtle and Croft to include relevance feedback techniques. The difference between relevance feedback on text abstracts and full text collections is studied. Preliminary results for relevance feedback on the structured queries supported by the inference net model are also reported.
Peripheral nerve injury fails to induce growth of lesioned ascending dorsal column axons into spinal cord scar tissue expressing the axon repellent Semaphorin3A (2001)

We have investigated the hypothesis that the chemorepellent Semaphorin3A may be involved in the failure of axonal regeneration after injury to the ascending dorsal columns of adult rats. Following transection of the thoracic dorsal columns, fibroblasts in the dorsolateral parts of the lesion site showed robust expression of Semaphorin3A mRNA. In addition, dorsal root ganglion (DRG) neurons with projections through the dorsal columns to the injury site persistently expressed both Semaphorin3A receptor components, neuropilin-1 and plexin-A1. These ascending DRG collaterals failed to invade scar regions occupied by Semaphorin3A-positive fibroblasts, even in animals which had received conditioning lesions of the sciatic nerve to enhance regeneration. Other axon populations in the dorsal spinal cord were similarly unable to penetrate Semaphorin3A-positive scar tissue. These data suggest that Semaphorin3A may create an exclusion zone for regenerating dorsal column fibres and that enhancing the intrinsic regenerative response of DRG neurons has only limited effects on axonal regrowth. Tenascin-C and chondroitin sulphate proteoglycans were also detected at the injury site, which was largely devoid of central nervous system (CNS) myelin, showing that several classes of inhibitory factors, including semaphorins, with only partially overlapping spatial and temporal patterns of expression are in a position to participate in preventing regenerative axonal growth in the injured dorsal columns. Interestingly, conditioning nerve injuries enabled numerous ascending DRG axons to regrow across areas of strong tenascin-C and chondroitin sulphate proteoglycan expression, while areas containing Semaphorin3A and CNS myelin were selectively avoided by (pre)primed axonal sprouts.
Machine Learning-Based Unbalance Detection of a Rotating Shaft Using Vibration Data (2020)

Fault detection at rotating machinery with the help of vibration sensors offers the possibility to detect damage to machines at an early stage and to prevent production downtimes by taking appropriate measures. The analysis of the vibration data using methods of machine learning promises a significant reduction in the associated analysis effort and a further improvement in diagnostic accuracy. Here we publish a dataset which is used as a basis for the development and evaluation of algorithms for unbalance detection. For this purpose, unbalances of various sizes were attached to a rotating shaft using a 3D-printed holder. In a speed range from approx. 630 RPM to 2330 RPM, three sensors were used to record vibrations on the rotating shaft at a sampling rate of 4096 values per second. A development and an evaluation dataset are available for each unbalance strength. Using the dataset recorded in this way, fully connected and convolutional neural networks, Hidden Markov Models and Random Forest classifications on the basis of automatically extracted time series features were tested. With a prediction accuracy of 98.6 % on the evaluation dataset, the best result could be achieved with a fully-connected neural network that receives the scaled FFT-transformed vibration data as input.
A Digital CMOS PWCL With Fixed-Delay Rising Edge and Digital Stability Control (2006)

A digital pulsewidth control loop (PWCL) with a fixed-delay rising edge and digital stability control is proposed for multiphase clock applications. In the duty-cycle tracking mode, the linear range of the input duty cycle was measured to be 28%-70%, with a maximum linearity deviation of 0.5%. In the duty-cycle correction mode, the correction range of the input duty cycle was measured to be 25%-75%, with the output duty cycle within 50 plusmn 0.4%. The chip was fabricated by using a 0.25-mum CMOS process with a 2.5-V supply. The chip area and the power consumption were 200 mumtimes250 mum and 18 mW at an input clock frequency of 1.0 GHz, respectively
The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly (2013)

Techniques for assembly of designed DNA sequences are important for synthetic biology. So far, a few methods have been developed towards high-throughput seamless DNA assembly in vitro, including both the homologous sequences-based system and the type IIS-mediated system. Here, we describe a novel method designated 'MASTER Ligation', by which multiple DNA sequences can be seamlessly assembled through a simple and sequence-independent hierarchical procedure. The key restriction endonuclease used, MspJI, shares both type IIM and type IIS properties; thus, it only recognizes the methylation-specific 4-bp sites, (m)CNNR (R = A or G), and cuts DNA outside of the recognition sequences. This method was tested via successful assembly of either multiple polymerase chain reaction amplicons or restriction fragments of the actinorhodin biosynthetic cluster of Streptomyces coelicolor (∼29 kb), which was further heterologously expressed in a fast-growing and moderately thermophilic strain, Streptomyces sp. 4F.
Dynamic models of human motion (2002)

This paper describes experiments in human motion understanding, defined here as estimation of the physical state of the body (the Plant) combined with interpretation of that part of the motion that cannot be predicted by the plant alone (the Behavior). The described behavior system operates in conjunction with a real-time, fully-dynamic, 3-D person tracking system that provides a mathematically concise formulation for incorporating a wide variety of physical constraints and probabilistic influences. The framework takes the form of a non-linear recursive filter that enables pixel-level, probabilistic processes to take advantage of the contextual knowledge encoded in the higher-level models. Results are shown that demonstrate both qualitative and quantitative gains in tracking performance.