gebhart/patrepeval huggingface dataset:
Cooperative self-assembly of SH2 domain fragments restores phosphopeptide binding (1993)

Multifunctional proteins frequently can be subdivided into discrete functional domains. Selected cytoplasmic proteins involved in signal transduction contain catalytic domains in addition to protein binding modules termed Src homology (SH) domains; SH2 domains bind phosphotyrosyl peptide sequences. Even as isolated modules, SH2 domains have the intrinsic capacity to fold properly and retain sequence selectivity for binding. Following limited digestion with trypsin, the 14-kDa SH2 domains of Src and PI 3-kinase p85 were split at a lysine within the flexible, phosphotyrosine-binding (BC) loop into 5- and 9-kDa fragments. Whereas the purified fragments did not exhibit cooperative unfolding or phosphopeptide binding, when combined they spontaneously reassembled to restore specific phosphopeptide binding and the unique spectroscopic signatures of bound and free intact SH2 domains. Like fragments of intact proteins, we now show that fragments of SH2 domains, and therefore protein modules, possess the intrinsic capacity for self-assembly with restoration of function. Analyses of fragment structures may provide insights into pathways of module folding, which will facilitate a more global understanding of how complex, multifunctional proteins fold.
Cyclin‐dependent kinase 5 influences Rohon‐Beard neuron survival in zebrafish (2006)

Cyclin-dependent kinase 5 (cdk5), a member of the cyclin-dependent kinase family, is expressed predominantly in post-mitotic cell populations. Unlike the other cdks, cdk5 is abundant and most active in differentiated neurons. Here, we describe the function of a cdk5 ortholog in zebrafish. Cdk5 catalytic activity is meager but present in early stages of development. However, at 24 h post-fertilization (hpf), the activity is remarkably higher and continues to be high through 48 and 72 hpf. Knocking down cdk5 by micro-injection of a specific siRNA resulted in decreased cdk5 protein level accompanied by reduced kinase activity. In the cdk5 siRNA-injected embryos, the number of primary sensory Rohon-Beard (RB) neurons was significantly reduced and there were more apoptotic cells in the brain. These phenotypes were rescued by co-injection of cdk5 mRNA. Within the first two days of development, RB neurons undergo apoptosis in zebrafish. To examine whether cdk5 has a role in RB neuron survival, cdk5 mRNA was injected into the one- to two-cell embryos. In these embryos, RB neuron apoptosis was inhibited compared with the uninjected control embryos. These results suggest that in zebrafish, cdk5 influences RB neuron survival and potentially regulates early neuronal development.
Intra-operative Augmented Reality mit magnetischer Navigation und multitexturbasiertem Volume Rendering in der minimal-invasiven Chirurgie (2001)

Lehrstuhl fur Graphische Datenverarbeitung, Universitat Erlangen-Nurnberg Siemens Medical Solutions, Grundlagenentwicklung, Erlangen Institut fur minimal invasive interdisziplinare Therapie und Intervention, Klinikum rechts der Isar, TU Munchen Chirurgische Klinik und Poliklinik, Klinikum rechts der Isar, TU Munchen Email: scheuering@informatik.uni-erlangen.de http://www9.informatik.uni-erlangen.de/Persons/Scheuering
Cover Image (2022)

COVER ILLUSTRATION Neural changes accompanying dosage intensive treatments targeting voice or articulation in patients with Parkinson's dysphonia. Voice treatment (yellow) targeted larynx and respiration while articulation treatment (blue) targeted mouth and lips. Behaviorally, voice treatment but not articulation treatment resulted in improvement in voice quality. However, treatment target specific changes in the speech motor network were observed during a reading task immediately following each treatment. Brain areas altered by voice treatment are shown in yellow and brain areas showing changes following articulation treatment are shown in blue. Left hemisphere activations are clear and right hemisphere activations are checkered. Voice treatment increased activity in left premotor and bilateral auditory cortices while articulation treatment increased activity in bilateral premotor and left insular cortices. The intensive dosage contributed to persistent changes at 7-month follow up. These results indicate that dysphonia and the speech motor network can be differentially modified by treatment targets, while intensive dosage contribute to long lasting effects of speech treatments.
Oxygen gas, O2(g), by near-ambient pressure XPS (2019)

Near-ambient pressure x-ray photoelectron spectroscopy (NAP-XPS) is a less traditional form of XPS that allows samples to be analyzed at relatively high pressures, i.e., greater than 2500 Pa. With NAP-XPS, XPS can probe moderately volatile liquids, biological samples, porous materials, and/or polymeric materials that outgas significantly. In this submission, we show the survey, O 1s, valence band, and O KLL Auger NAP-XPS spectra of oxygen gas, O2, a material that would be difficult to analyze by conventional XPS. A small N 1s signal from N2(g) is also observed in the survey spectrum. The O 1s narrow scan is fit to Gaussian-Lorentzian sum functions. The Lorentzian character of this synthetic line shape was varied to obtain the best fit. Since it is likely that O2(g) will be present in other NAP-XPS analyses, these data should serve as a useful reference for other researchers.
State of the Art and Uses for the Biopharmaceutics Drug Disposition Classification System (BDDCS): New Additions, Revisions, and Citation References (2022)

The Biopharmaceutics Drug Disposition Classification system (BDDCS) is a four-class approach based on water solubility and extent of metabolism/permeability rate. Based on the BDDCS class to which a drug is assigned, it is possible to predict the role of metabolic enzymes and transporters on the drug disposition of a new molecular entity (NME) prior to its administration to animals or humans. Here, we report a total of 1475 drugs and active metabolites to which the BDDCS is applied. Of these, 379 are new entries, and 1096 are revisions of former classification studies with the addition of references for the approved maximum dose strength, extent of the systemically available drug excreted unchanged in the urine, and lowest solubility over the pH range 1.0-6.8 when such information is available in the literature. We detail revised class assignments of previously misclassified drugs and the literature analyses to classify new drugs. We review the process of solubility assessment for NMEs prior to drug dosing in humans and approved dose classification, as well as the comparison of Biopharmaceutics Classification System (BCS) versus BDDCS assignment. We detail the uses of BDDCS in predicting, prior to dosing animals or humans, disposition characteristics, potential brain penetration, food effect, and drug-induced liver injury (DILI) potential. This work provides an update on the current status of the BDDCS and its uses in the drug development process.
Nanophotonic front electrodes for perovskite solar cells (2015)

In less than 3 years' time, a vast progress in power conversion efficiencies of organometal halide perovskite solar cells has been achieved by optimization of the device architecture, charge transport layers, and interfaces. A further increase in these efficiencies is expected from an improvement in the optical properties via anti-reflection coatings and nanophotonic light management concepts. In this contribution, we report on the development and implementation of a nanophotonic front electrode for perovskite solar cells. The nanostructures were replicated via the versatile and large-area compatible UV-nanoimprint lithography. The shallow design of the used transparent and conductive nanostructures enabled easy integration into our solution-based baseline process. Prototype methylammonium lead iodide perovskite solar cells show an improvement of 5% in short-circuit current density and an improvement from 9.6% to 9.9% in power conversion efficiency compared to the flat reference device.
Abstract 3823: Platinum anti-cancer drugs attenuate T cell-mediated immune suppression through STAT6/PD-L2 (2010)

Abstract It has become evident that many immune inhibitory mechanisms in the tumor micro-environment prevent the development of effective T cell responses against the tumor cells in cancer patients. Therapeutic interventions aimed at blocking these pathways have been shown to result in enhanced anti-tumor immunity, but they lack direct cytotoxic effects. Cancer chemotherapeutic drugs have these direct cytotoxic anti-tumor effects and although for some anti-cancer drugs indirect activation of the immune system via induction of an immunogenic type of tumor cell death has been described, their effect on inhibitory pathways in anti-tumor immunity is unknown. We investigated the effect of a wide array of chemotherapeutics on dendritic cell (DC) function and on tumor cell immunogenicity. Using allogeneic and antigen-specific in vitro models, we found that when DCs were matured/activated in the presence of platinum-based chemotherapy, they showed strongly enhanced T cell stimulatory capacity. Programmed death receptor-ligand 2 (PD-L2) expression by DC was markedly reduced upon platinum exposure. The enhanced T cell stimulatory capacity by DC upon platinum exposure was abrogated in the presence of PD-L2 blocking antibodies. This was also observed when the regulator of PD-L2 expression, signal transducer and activator of transcription 6 (Stat6), was knocked down using siRNA. In addition, we found that STAT6 was dephosphorylated in tumor cells by platinum compounds, leading to marked downregulation of PD-L2, resulting in enhanced recognition by tumor-specific T cells. In line with these in vitro findings, we found enhanced Th1 cytokine secretion and T cell proliferative responses in cancer patients upon treatment with platinum-based chemotherapy, confirming the in vivo occurrence of platinum-induced immune deviation. Our findings show that treatment with platinum compounds not only results in enhanced T cell stimulation by DC, but at the same time enhances the sensitivity of the tumor for lysis by cytotoxic T cells. This novel double action of platinum compounds may initiate combinations with other immune stimulatory compounds to increase clinical efficacy. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3823.
Abstract B36: Interrogating cellular metabolism to improve therapy for EGFR mutant NSCLC (2016)

Abstract Tyrosine kinase inhibitors (TKIs) that target the EGFR are the standard of care for patients with EGFR mutant non-small lung cancer (NSCLC). However, TKIs are not curative; most patients with EGFR-mutant NSCLC treated with EGFR TKIs develop resistance within 9 to 14 months. The tumor microenvironment is thought to influence the fitness of cancer cells and drive the evolution of a tumor, but the effect of altered environmental conditions on oncogenic signaling and therapeutic response is not well understood. In the present study, we used the Operetta® High Content Imaging System to track cell dynamics over time and found that microenvironmental stress, specifically nutrient starvation, had a differential effect on growth rates of TKIs sensitive and resistant cells. Furthermore, we discovered that TKIs sensitive and resistant cells have differential metabolic signaling in response to this microenvironmental stress. To further interrogate cellular metabolism in TKIs sensitive and resistant cells, we utilized fluorescence lifetime imaging microscopy (FLIM), a state-of-the-art live-cell imaging technique to measure the autofluorescence lifetime of metabolic coenzyme NADH, the principle electron acceptor in glycolysis and electron donor in oxidative phosphorylation. Taken together, our data suggest that TKIs sensitive and resistant cells have adopted different metabolic strategies to cope with stressful environmental conditions, and interrogating tumor metabolic adaptations would inform the design of new therapeutic strategies to delay or prevent the outgrowth of resistant clones during treatment of EGFR mutant NSCLC. Citation Format: Chun-Te Chiang, Chi-Li Chiu, Cosimo Arnesano, Scott E. Fraser, David B. Agus, Dan L. Ruderman, Shannon M. Mumenthaler. Interrogating cellular metabolism to improve therapy for EGFR mutant NSCLC. [abstract]. In: Proceedings of the AACR Special Conference: Function of Tumor Microenvironment in Cancer Progression; 2016 Jan 7–10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2016;76(15 Suppl):Abstract nr B36.
Ultralow‐frequency magnetohydrodynamics in boundary‐constrained geomagnetic flux coordinates (2002)

A new method is described for constructing geomagnetic flux coordinates, constrained by magnetospheric and ionospheric boundary surfaces. The technique is especially useful for computing boundary value solutions in a geometry defined by a realistic, three‐dimensional geomagnetic field with boundary conditions specified on surfaces oriented arbitrarily relative to the background magnetic field. An adaptable algorithm for calculating the metric tensor for a general class of geomagnetic flux coordinate systems is presented. Application to ultralow‐frequency wave propagation in the magnetosphere is illustrated by solving the equations of linear, one‐fluid magnetohydrodynamics for the driven field line resonance in a dipolar geomagnetic field bounded by a spherical ionosphere. A novel diagnostic for energy flow in the driven resonance problem shows that MHD wave power flows “radially” inward as a compressional wave from the boundary driver to the resonant flux surface, is diverted azimuthally at the resonant surface, and becomes field‐aligned in the resonant surface by coupling to the magnetically guided Alfvén wave at locations where the shear mode is in azimuthal phase quadrature with the compressional driver.
Efficient demethylation of aromatic methyl ethers with HCl in water (2021)

A method for the cleavage of aryl alkyl ethers is presented, involving hot pressurized water and catalytic mineral acid. The protocol is applicable on a variety of (biorenewable) substrates, not requiring mass-intensive work-up.
Extension of Matrix-Based Intra Prediction to 4:4:4 Chroma Formats (2021)

The final version of the Versatile Video Coding (VVC) standard incorporates the Matrix-Based Intra Prediction (MIP) tool. It consists of additional intra prediction modes which were derived from a data-driven training. These modes, in general, are applied to the luma component only. This paper describes how to apply the MIP modes to the chroma components in certain cases. In the generic case, if a chroma block uses the intra direct mode (DM), its intra mode is derived from the co-located luma block. If this luma block uses MIP, the chroma block uses the planar mode, because a MIP mode is not applicable for all block shapes. However, if the chroma format is 4:4:4 and single-tree coding is used, luma and chroma blocks share the same partitioning. The paper investigates the impact of using the MIP mode of the luma component when the chroma mode is the DM in these cases. This extension also harmonizes MIP with the Adaptive Color-Space Transform (ACT) for RGB-content, because the chroma mode of blocks using the ACT is inferred to be the DM. For the extended MIP tool in the Versatile Video Coding Test Model 11.2 (VTM-11.2) that implements the final VVC standard, bit-rate savings of 1.51%/0.60%/0.62% in terms of the Bj⊘ntegaard-Delta bit rate (BD-rate) are reported compared to the VTM-11.2 with MIP disabled for the All-Intra configuration and natural content in the RGB 4:4:4 format.
3-D camera based on conoscopic holography (1990)

The principle and the firstresults of a new 3D camera will be presented. This camera is based on a holographic technique named conoscopic holography. The simplicity of the technique, using only a crystal, waves plates and polarizers, and its compatibility with CCD sensors make possible the fabrication of low cost and flexible conoscopic vision systems. The first prototype is an tive rangefmder which will be developed into a profilometer and a 3D camera a resolution of 1 jnn and a precision of a 2-3 jim have already been obtained. The numerical processing is based on Fourier Transforms, quickly performed by available dedicied hardware.
Potent and Selective Cathepsin L Inhibitors Do Not Inhibit Human Osteoclast Resorption in Vitro (2001)

Cathepsins K and L are related cysteine proteases that have been proposed to play important roles in osteoclast-mediated bone resorption. To further examine the putative role of cathepsin L in bone resorption, we have evaluated selective and potent inhibitors of human cathepsin L and cathepsin K in an in vitro assay of human osteoclastic resorption and an in situ assay of osteoclast cathepsin activity. The potent selective cathepsin L inhibitors (K(i) = 0.0099, 0.034, and 0.27 nm) were inactive in both the in situ cytochemical assay (IC(50) > 1 micrometer) and the osteoclast-mediated bone resorption assay (IC(50) > 300 nm). Conversely, the cathepsin K selective inhibitor was potently active in both the cytochemical (IC(50) = 63 nm) and resorption (IC(50) = 71 nm) assays. A recently reported dipeptide aldehyde with activity against cathepsins L (K(i) = 0.052 nm) and K (K(i) = 1.57 nm) was also active in both assays (IC(50) = 110 and 115 nm, respectively) These data confirm that cathepsin K and not cathepsin L is the major protease responsible for human osteoclastic bone resorption.
16 Split Cord Malformations (2008)

Split cord malformations are rare form of occult spinal dysraphism in children. Split cord malformations are characterized by septum that cleaves the spinal canal in sagittal plane within the single or duplicated thecal sac. Although their precise incidence is unknown, split cord malformations are exceedingly rare and represent %3.8-5 of all congenital spinal anomalies. Characteristic neurological, urological, orthopedic clinical manifestations are variable and asymptomatic course is possible. Earlier diagnosis and surgical intervention for split cord malformations is associated with better long-term fuctional outcome. For this reason, diagnostic imaging is indicated for children with associated cutaneous and orthopedic signs. Additional congenital anomalies usually to accompany the split cord malformations. Earlier diagnosis, meticuolus surgical therapy and interdisciplinary careful evaluation and follow-up should be made for good prognosis.
Navigation Error Analysis in the ZUPT‐Aided Pedestrian Inertial Navigation (2021)

This chapter analyzes navigation errors in Zero-Velocity Update (ZUPT)-aided pedestrian inertial navigation due to Inertial Measurement Unit (IMU) noises. It presents a 2D biomechanical model to simulate human gait to better understand human walking dynamics and also to serve as the basis for the following numerical simulations. Human ambulatory gait models are multidimensional due to the complex kinematic and dynamic relations between many parts of human body involved during walking. The foot motion can be superimposed on top of the torso motion to obtain the foot motion in the navigation frame. The navigation errors in the ZUPT-aided navigation algorithm come mainly from two major sources: systematic modeling errors and IMU noises. The chapter presents verification of the analysis both numerically and experimentally. ZUPT-aided inertial navigation algorithm eliminates the velocity drift during pedestrian navigation, and therefore greatly reduces the overall navigation error compared to the navigation result without any aiding.
Life-History Characteristics of Japanese Medaka Oryzias latipes (2011)

Japanese Medaka, Oryzias latipes, is a widely used organism in biological investigations because of its high fecundity, small adult size, and ease of husbandry. However, many aspects of its life history have not been fully described. In this study we determine patterns of somatic growth, frequency of egg production, and competency of eggs. We also describe temporal aspects of reproductive output. We modeled the length-at-age relationship with a von Bertalanffy growth function and found mean parameter values: L∞ = 49.5 mm TL (total length), k = 0.010 dph−1 (days post hatch), and t0 = 3.3 mm TL. These estimates are used to predict longevity of 347 to 485 days. The weight-at-length relationship was described using a power curve and resulted in mean parameter estimates, a = 2.16 × 10−5 and b = 2.79. The mean proportion of eggs that hatched was 73% (95% confidence interval: 53 to 93%). We observed that 50% of larvae emerge from eggs at 3.5 days and 99% of larvae emerge at 7.5 days in incubation. Daily egg production increased to a maximum number (range: 8 to 48) of eggs at 92 days post hatch. Total egg production by individual females ranged from 38 to 141 eggs. We found a significant negative linear relationship (F = 34.7, P < 0.001, R2 = 0.28) between the number of eggs collected from an individual during a single egg deposition event (n = 91) and mean egg volume. However, there were large variations in the sizes of individual eggs within a clutch (median CV = 14.8). Our work provides previously unreported life-history information that can be used to effectively develop experiments in the laboratory and field, and increased understanding of this species.
On the behavior of renewable energy systems in buildings of three Saudi cities: Winter variabilities and extremes are critical (2023)

Integration of renewable energy systems emerges as a key enabler for future low-carbon electricity supply. To maintain a secure and effective supply, the design and operation of these systems must carefully account for the influence of weather variability on the availability of renewable energy resources and on energy demand. This study examines the impact of weather variability on the optimal design and operation of renewable energy systems for office buildings in Saudi Arabia. The building electricity demand is supplied by a photovoltaic/wind/battery storage system, with an additional connection to the grid. The optimization process then aims at finding the optimal capacities of the renewable energy system components, so as to strike a trade-off between life cycle cost and CO2 emissions by considering weather datasets with different levels of variability. The results show that accounting for the full weather variability, particularly the extreme weather events, leads to higher investment costs in fully renewable energy system, namely due to increased battery storage (up to 288%). Neglecting extreme events at the design stage, however, leads to a significant performance gap that could be compensated by grid integration, which adds to the overall CO2 emissions, for a negligible change in the system cost. Such extreme weather events are then associated with cloudy and high temperatures days, the impact of which drives down the photovoltaic power output and increases the demand for energy from the grid or from the storage. The study further examines the electricity price impacts on renewable energy system design and operation. With global weather variability challenges at the forefront, the paper findings draw insightful recommendations related to energy policy.