gebhart/patrepeval huggingface dataset:
Effects of amino acid substitutions in the F helix of bacteriorhodopsin. Low temperature ultraviolet/visible difference spectroscopy. (1988)

Site-specific mutagenesis in combination with low temperature UV/visible difference spectroscopy has been used to investigate the role of individual amino acids in the structure and function of bacteriorhodopsin (bR). We examined the effects of eight single amino acid substitutions, all in the putative F helix, on the absorption of bR as well as formation of the K and M intermediates. Both the absorbance spectra and the photocycle difference spectra of Escherichia coli expressed bR as well as the mutants S183A, P186G, and E194Q all closely resembled the corresponding purple membrane spectra. In contrast the Pro-186----Leu substitution resulted in the loss of the normal photocycle and a large blue shift in the bR state lambda max. Thus, Pro-186 appears to play a critical role in maintaining the normal protein-chromophore interactions, although the pyrrolidine ring is not essential since proline could be replaced by glycine at this position. The mutants W182F, W189F, and S193A did not appear to be directly involved in the bathochromic shift of bR since they all had lambda max's close to that of purple membrane and produced intermediates similar to K and M. However, alterations in the UV and visible difference spectra as well as the appearance of some irreversibility in the photoreactions indicate that these mutants have altered protein-chromophore interactions during the photocycle. Unlike the other mutants examined, Y185F exhibited a red-shifted form of bR and K raising the possibility that Tyr-185 is directly involved in color regulation. In addition, UV difference peaks previously associated with a tyrosine deprotonation were absent in Y185F indicating that Tyr-185 undergoes protonation changes during the photocycle in agreement with recent Fourier transform infrared difference measurements (Braiman, M.S., Mogi, T., Stern, L. J., Hackett, N., Chao, B. H., Khorana, H.G., and Rothschild, K. J. (1988) Proteins: Structure, Function, and Genetics 3, 219-229). Our results suggest that Trp-182, Tyr-185, Pro-186, Trp-189, and Ser-193, all of which are within a 100 degrees segment of the F helix, are part of a retinal-binding pocket.
Non-sterilizing, Infection-Permissive Vaccination With Inactivated Influenza Virus Vaccine Reshapes Subsequent Virus Infection-Induced Protective Heterosubtypic Immunity From Cellular to Humoral Cross-Reactive Immune Responses (2020)

Conventional influenza vaccines aim at the induction of virus-neutralizing antibodies that provide with sterilizing immunity. However, influenza vaccination often confers protection from disease but not from infection. The impact of infection-permissive vaccination on the immune response elicited by subsequent influenza virus infection is not well-understood. Here, we investigated to what extent infection-permissive immunity, in contrast to virus-neutralizing immunity, provided by a trivalent inactivated virus vaccine (TIV) modulates disease and virus-induced host immune responses after sublethal vaccine-matching H1N1 infection in a mouse model. More than one TIV vaccination was needed to induce a serum HI titer and provide sterilizing immunity upon homologous virus infection. However, single TIV administration provided infection-permissive immunity, characterized by lower viral lung titers and faster recovery. Despite the presence of replicating virus, single TIV vaccination prevented induction of pro-inflammatory cyto- and chemokines, alveolar macrophage depletion as well as the establishment of lung-resident B and T cells after infection. To investigate virus infection-induced cross-protective heterosubtypic immune responses in vaccinated and unvaccinated animals, mice were re-infected with a lethal dose of H3N2 virus 4 weeks after H1N1 infection. Single TIV vaccination did not prevent H1N1 virus infection-induced heterosubtypic cross-protection, but shifted the mechanism of cross-protection from the cellular to the humoral branch of the immune system. These results suggest that suboptimal vaccination with conventional influenza vaccines may still positively modulate disease outcome after influenza virus infection, while promoting humoral heterosubtypic immunity after virus infection.
Open Access Repository-Scale Propagated Nearest Neighbor Suspect Spectral Library for Untargeted Metabolomics (2022)

Abstract Despite the increasing availability of tandem mass spectrometry (MS/MS) community spectral libraries for untargeted metabolomics over the past decade, the majority of acquired MS/MS spectra remain uninterpreted. To further aid in interpreting unannotated spectra, we created a nearest neighbor suspect spectral library, consisting of 87,916 annotated MS/MS spectra derived from hundreds of millions of public MS/MS spectra. Annotations were propagated based on structural relationships to reference molecules using MS/MS-based spectrum alignment. We demonstrate the broad relevance of the nearest neighbor suspect spectral library through representative examples of propagation-based annotation of acylcarnitines, bacterial and plant natural products, and drug metabolism. Our results also highlight how the library can help to better understand an Alzheimer’s brain phenotype. The nearest neighbor suspect spectral library is openly available through the GNPS platform to help investigators hypothesize candidate structures for unknown MS/MS spectra in untargeted metabolomics data.
Emerging standards at &#x223C;10 Gbps for wireline communications and associated integrated circuit design and validation (2009)

We first review the signaling and jitter requirements for emerging high-speed wireline communication standards at ~10 Gbps, including CEI 11G, XLAUI/CAUI, XFI, and SFP+. We then present an FPGA transceiver architecture and subsystem/circuit blocks for clocking and timing generation, transmitter buffer, and receiver CDR and DFE, all designed and manufactured with 40-nm process node. Lastly, we present the signal/jitter transmitter output and receiver-tolerance measurement results at 10.3125 Gbps, with an ultra-low random jitter at ~550 fs.
A 3D microfluidic platform incorporating methacrylated gelatin hydrogels to study physiological cardiovascular cell–cell interactions (2013)

The cardiovascular system is particularly well-suited to modelling with microfluidic technologies, and much progress has been made to create microfluidic devices that mimic the microvasculature. In contrast, microfluidic platforms that model larger blood vessels and heart valves are lacking, despite the clear potential benefits of improved physiological relevance and enhanced throughput over traditional cell culture technologies. To address this need, we developed a bilayer membrane microfluidic device to model the vascular/valvular three-dimensional environment. Key features of the platform include physiologically-relevant spatial arrangement of multiple cell types, fluid flow over an endothelial monolayer, a porous membrane that permits heterotypic cell interactions while maintaining cell compartmentalization, and a photopolymerizable gelatin methacrylate (gel-MA) hydrogel as a physiologically-relevant subendothelial 3D matrix. Processing guidelines were defined for successful in-channel polymerization of gel-MA hydrogels that were mechanically stable, had physiologically-relevant elastic moduli of 2-30 kPa, and supported over 80% primary cell viability for at least four days in culture. The platform was applied to investigate shear stress-regulated paracrine interactions between valvular endothelial cells and valvular interstitial cells. The presence of endothelial cells significantly suppressed interstitial cell pathological differentiation to α-smooth muscle actin-positive myofibroblasts, an effect that was enhanced when the endothelium was exposed to flow-induced shear stress. We expect this versatile organ-on-a-chip platform to have broad utility for mechanistic vascular and valvular biology studies and to be useful for drug screening in physiologically-relevant 3D cardiovascular microenvironments.
ChemInform Abstract: SYNTH. FUNKTIONALISIERTER PHOSPHORINANONE (1973)

Abstract Die Synthese von in α‐Stellung zum P‐Atom funktionalisierten Phosphorinanonen, wie (IX)‐(XI), wird beschrieben.
β ‐Catenin activation contributes to the pathogenesis of adenomyosis through epithelial–mesenchymal transition (2013)

Adenomyosis is defined by the presence of endometrial glands and stroma within the myometrium. Despite its frequent occurrence, the precise aetiology and physiopathology of adenomyosis is still unknown. WNT/β-catenin signalling molecules are important and should be tightly regulated for uterine function. To investigate the role of β-catenin signalling in adenomyosis, the expression of β-catenin was examined. Nuclear and cytoplasmic β-catenin expression was significantly higher in epithelial cells of human adenomyosis compared to control endometrium. To determine whether constitutive activation of β-catenin in the murine uterus leads to development of adenomyosis, mice that expressed a dominant stabilized β-catenin in the uterus were used by crossing PR-Cre mice with Ctnnb1(f(ex3)/+) mice. Uteri of PR(cre) (/+) Ctnnb1(f(ex3)/+) mice displayed an abnormal irregular structure and highly active proliferation in the myometrium, and subsequently developed adenomyosis. Interestingly, the expression of E-cadherin was repressed in epithelial cells of PR(cre) (/+) Ctnnb1(f(ex3)/+) mice compared to control mice. Repression of E-cadherin is one of the hallmarks of epithelial-mesenchymal transition (EMT). The expression of SNAIL and ZEB1 was observed in some epithelial cells of the uterus in PR(cre) (/+) Ctnnb1(f(ex3)/+) mice but not in control mice. Vimentin and COUP-TFII, mesenchymal cell markers, were expressed in some epithelial cells of PR(cre) (/+) Ctnnb1(f(ex3)/+) mice. In human adenomyosis, the expression of E-cadherin was decreased in epithelial cells compared to control endometrium, while CD10, an endometrial stromal marker, was expressed in some epithelial cells of human adenomyosis. These results suggest that abnormal activation of β-catenin contributes to adenomyosis development through the induction of EMT.
A Cost-Effective WDM-PON Configuration Employing Innovative Bi-directional Amplification (2007)

Novel bi-directional amplifier is employed in a WDM-PON system to increase power margin for both downstream and upstream signals. After 100-km SSMF transmission, the power-penalty for all channels at 10Gbit/s is less than 0.8 dB.
Acetoin and Phenylacetylcarbinol Formation by the Pyruvate Decarboxylases ofZymomonas MobilisandSaccharomyces CarlsbergensisStephanie Bringer-Meyer (1988)

Cell suspensions of Zymomonas mobilis and Saccharomyces carlsbergensis and the pyruvate decarboxylases from the two organisms were compared with respect to their efficiencies of acyloin formation. Although Z. mobilis contained five times more pyruvate decarboxylase activity than yeast, sugar-fermenting suspensions of Z. mobilis produced, in the presence of benzaldehyde, 4–5 times less phenylacetylcarbinol than the yeast. The pyruvate decarboxylases of both organisms catalyzed acetoin and phenylacetylcarbinol synthesis from pyruvate and acetaldehyde or benzaldehyde, but the affinity of the Z. mobilis pyruvate decarboxylase towards the aldehyde reactants was lower than that of the yeast enzyme. Because of the limited solubility of benzaldehyde, neither enzyme could be saturated with this substrate for phenyl-acetylcarbinol synthesis. Studies with 2-toluidinonaphthalene-6-sulfonate and substrate analogues showed that the catalytic sites of pyruvate decarboxylase from Z. mobilis were less lipophilic than those of the enzyme from yeast. This difference could explain the lower affinity for benzaldehyde of the Z. mobilis enzyme.
On the correct determination of reference values for serum antibodies against pigeon serum antigen using a group of healthy blood donors. (1997)

An enzymatic immunoassay was developed in order to evaluate the statistical distribution of IgG serum antibodies against pooled pigeon sera antigen in 102 healthy blood donors (HBD). A non-normal distribution was obtained as demonstrated by abnormal values of skewness (2.02) and kurtosis (6.50). A cut-off point (0.120) was determined from the mean plus 2 standard deviations of the optical density values obtained in the HBD group. This value was able to segregate 94% of subjects. However, when calculation of the mean less 2 SD was performed to delimit 95% of the samples, an aberrant negative value was obtained. In contrast, when the nonparametric method of percentile calculation was applied, an optical density value of 0.130 discriminated 97.5% of samples. In addition, the interval between p97.5 and p2.5 delimited 95% of samples. We conclude that when reference values and cut-off point are determined from an enzymatic immunoassay, careful analysis of the statistical distribution of reference values is necessary in order to avoid the inappropriate application of parametric procedures as demonstrated in this study for antibodies against pigeon serum antigens.
Cost trade-offs of various design for test techniques (2002)

Test cost is becoming a major factor in today's complex chip designs. One approach to lower test cost is to have the product test, or help test, itself. There are a wide variety of Design-for-Test techniques that have been developed for this purpose. A number of these techniques are evaluated against various related cost issues.
Concussion in Professional Football: Location and Direction of Helmet Impacts—Part 2 (2003)

The location, direction, and severity of helmet impacts causing concussion in the National Football League have been defined from analysis of game video and laboratory reconstruction. These conditions define the circumstances in which helmets need to reduce head injury risks in professional football.
Quantitative cardiac perfusion: a noninvasive spin-labeling method that exploits coronary vessel geometry. (1996)

This spin-labeling method provides quantitative estimates of myocardial arterial perfusion in this model and may hold promise for clinical applications.
Planetary Gearbox Fault Diagnosis Using a Single Piezoelectric Strain Sensor (2014)

Planetary gearboxes are widely used in the drivetrain of helicopters and wind turbines. Any planetary gearbox failure could lead to breakdown of the whole drivetrain and major loss of helicopters and wind turbines. Therefore, planetary gearbox fault diagnosis is an important topic in prognostics and health management (PHM). Planetary gearbox fault diagnosis has been done mostly through vibration analysis over the past years. Vibration signals theoretically have the amplitude modulation effect caused by time variant vibration transfer paths due to the rotation of planet carrier and sun gear, and therefore their spectral structure is complex. It is difficult to diagnose planetary gearbox faults via vibration analysis. Strain sensor signals on the other hand have less amplitude modulation effect. Thus, it is potentially easy and effective to diagnose planetary gearbox faults via stain sensor signal analysis. In this paper, a research investigation on planetary gearbox fault diagnosis via strain sensor signal analysis is reported. The investigation involves using time synchronous average technique to process signals acquired from a single piezoelectric strain sensor mounted on the housing of a planetary gearbox and extracting condition indicators for fault diagnosis. The reported investigation includes analysis results on a set of seeded fault tests performed on a planetary gearbox test rig in a laboratory. The results have showed a satisfactory planetary gearbox fault diagnostic performance using strain sensor signal analysis.
Computation and visualization of photonic quasicrystal spectra via Bloch’s theorem (2008)

Previous methods for determining photonic quasicrystal (PQC) spectra have relied on the use of large supercells to compute the eigenfrequencies and/or local density of states. In this paper, we present a method by which the energy spectrum and the eigenstates of a PQC can be obtained by solving Maxwell's equations in higher dimensions for any PQC defined by the standard cut-and-project construction, to which a generalization of Bloch's theorem applies. In addition, we demonstrate how one can compute band structures with defect states in the same higher-dimensional superspace. As a proof of concept, these general ideas are demonstrated for the simple case of one-dimensional quasicrystals, which can also be solved by simple transfer-matrix techniques.
Genomic signatures of chromosomal instability and osteosarcoma progression detected by high resolution array CGH and interphase FISH (2008)

Osteosarcoma (OS) is characterized by an unstable karyotype which typically has a heterogeneous pattern of complex chromosomal abnormalities. High-resolution array comparative genomic hybridization (CGH) in combination with interphase fluorescence in situ hybridization (FISH) analyses provides a complete description of genomic imbalances together with an evaluation of the contribution of cell-to-cell variation to copy number changes. There have been no analyses to date documenting genomic signatures consistent with chromosomal instability mechanisms in OS tumors using array CGH. In this study, we utilized high-resolution array CGH to identify and characterize recurrent signatures of genomic imbalances using ten OS tumors. Comparison between the genomic profiles identified tumor groups with low, intermediate and high levels of genomic imbalance. Bands 6p22-->p21, 8q24 and 17p12--> p11.2 were consistently involved in high copy gain or amplification events. Since these three locations have been consistently associated with OS oncogenesis, FISH probes from each cytoband were used to derive an index of cellular heterogeneity for copy number within each region. OS with the highest degree of genomic imbalance also exhibited the most extreme cell-to-cell copy number variation. Significantly, the three OS with the most imbalance and genomic copy number heterogeneity also had the poorest response to preoperative chemotherapy. This genome wide analysis is the first utilizing oligonucleotide array CGH in combination with FISH analysis to derive genomic signatures of chromosomal instability in OS tumors by studying genomic imbalance and intercellular heterogeneity. This comprehensive genomic screening approach provides important insights concerning the mechanisms responsible for generating complex genomes. The resulting phenotypic diversity can generate tumors with a propensity for an aggressive disease course. A better understanding of the underlying mechanisms leading to OS tumor development could result in the identification of prognostic markers and therapeutic targets.
Desynchronizing anti-resonance effect ofm:nON–OFF coordinated reset stimulation (2011)

This computational study is devoted to the optimal parameter calibration for coordinated reset (CR) stimulation, a stimulation technique suggested for an effective desynchronization of pathological neuronal synchronization. We present a detailed study of the parameter space of the CR stimulation method and show that CR stimulation can induce cluster states, desynchronization and oscillation death. The stimulation-induced cluster states (at CR offset) cause the longest desynchronizing post-stimulus transients, which constitute an essential part of the CR stimulation effect. We discover a desynchronization-related anti-resonance response of the stimulated oscillators induced by a periodic ON-OFF CR stimulation protocol with m cycles ON stimulation followed by n cycles OFF stimulation. The undesired collective oscillations are effectively desynchronized if the stimulation is administered at resonant frequencies of the controlled ensemble, which is in complete contrast to the typical effect of the usual periodic forcing.
Serving DNNs in Real Time at Datacenter Scale with Project Brainwave (2018)

To meet the computational demands required of deep learning, cloud operators are turning toward specialized hardware for improved efficiency and performance. Project Brainwave, Microsofts principal infrastructure for AI serving in real time, accelerates deep neural network (DNN) inferencing in major services such as Bings intelligent search features and Azure. Exploiting distributed model parallelism and pinning over low-latency hardware microservices, Project Brainwave serves state-of-the-art, pre-trained DNN models with high efficiencies at low batch sizes. A high-performance, precision-adaptable FPGA soft processor is at the heart of the system, achieving up to 39.5 teraflops (Tflops) of effective performance at Batch 1 on a state-of-the-art Intel Stratix 10 FPGA.
Einfluss von Hyaluronsäure auf die Funktion von natürlichem Surfactant (2023)

Hintergrund Die Surfactantsubstitution stellt noch immer den Goldstandard in der Behandlung des Atemnotsyndroms des Früh- und Neugeborenen dar. In der Vergangenheit konnte bereits gezeigt werden, dass Hyaluronsäure in vitro positive Effekte auf die Oberflächenaktivität von Surfactant hat. Gleichzeitig ist Hyaluronsäure als Bestandteil der Extrazellulärmatrix auch in der Lunge zu finden. Unsere Arbeit beleuchtet erstmals die physiologischen Zusammenhänge zwischen Hyaluronsäure und natürlichem Surfactant in humanen Fruchtwasserproben, die während operativen Entbindungen entnommen wurden.
Coarse wavelength division (de)multiplexer using an interleaved angled multimode interferometer structure (2013)

We have demonstrated a coarse wavelength (de)multiplexing structure on the silicon-on-insulator platform. It comprises two 4-channel angled multimode interferometers interleaved with an imbalanced Mach-Zehnder interferometer (MZI) leading to an 8-channel multiplexing device. The device requires only single lithography and etching steps for fabrication and has a good tolerance to fabrication errors in terms of waveguide width. The insertion loss and crosstalk achieved are 3-4 dB and –(15–20) dB, respectively. Potential is shown for achieving improved performance using larger waveguide bending radii in the MZI arms and/or (a) local heater(s) for refractive index tuning.
Identification of Fast-Rate Systems Using Slow-Rate Image Sensor Measurements (2013)

In this paper, we propose a method to identify the frequency response of a fast-rate motion system using measurements from a slow-rate image sensor. The integrative nature of the sensor produces a blurred image of the observed moving feature, e.g., of a laser beam deflected on a steering mirror, when the image moves much faster than the exposure period. The key concept of this paper is to extract the parameters describing the motion of the observed feature from the image blur by treating the image sensor as a nonlinear temporal-to-spatial transformation, under a known input excitation, i.e., a sinusoid. The output signal amplitude and phase characterize the frequency response of the system at the specific excitation frequency. This problem is posed as a nonlinear minimization: finding parameters to match the predicted spatial distribution with the measurement. The nonlinear mapping is shown to be noninvertible; therefore, the solution of the nonlinear minimization is nonunique. Two methods are proposed for avoiding this aliasing problem: 1) by imposing a continuity constraint and 2) by solving the minimization over two different exposure periods. The efficacy of the proposed frequency response identification approach for a multi-input/multioutput system is experimentally demonstrated by accurately obtaining the frequency response of a fast steering mirror up to 500 Hz using a 30-Hz CCD camera.
ChemInform Abstract: Stereoselective Synthesis of α‐Branched Amines by Nucleophilic Addition of Unstabilized Carbanions to Imines (2011)

Abstract Review: 242 refs.