gebhart/patrepeval huggingface dataset:
Fluorine in Drug Design: A Case Study with Fluoroanisoles (2015)

Anisole and fluoroanisoles display distinct conformational preferences, as evident from a survey of their crystal structures. In addition to altering the free ligand conformation, various degrees of fluorination have a strong impact on physicochemical and pharmacokinetic properties. Analysis of anisole and fluoroanisole matched molecular pairs in the Pfizer corporate database reveals interesting trends: 1) PhOCF3 increases log D by ~1 log unit over PhOCH3 compounds; 2) PhOCF3 shows lower passive permeability despite its higher lipophilicity; and 3) PhOCF3 does not appreciably improve metabolic stability over PhOCH3 . Emerging from the investigation, difluoroanisole (PhOCF2 H) strikes a better balance of properties with noticeable advantages of log D and transcellular permeability over PhOCF3 . Synthetic assessment illustrates that the routes to access difluoroanisoles are often more straightforward than those for trifluoroanisoles. Whereas replacing PhOCH3 with PhOCF3 is a common tactic to optimize ADME properties, our analysis suggests PhOCF2 H may be a more attractive alternative, and greater exploitation of this motif is recommended.
Optical Implementation of Semantic Networks Based on Association (1990)

An optical system combining a semantic network technique and an associative network architecture is presented. In the optical implementation of the associative system, an MSLM is used to store an optimum weight matrix. The optimum weight matrix is calculated by a dynamic learning rule.
Crystallization Kinetics of Maleated Polypropylene/Clay Hybrids (2004)

The isothermal crystallization kinetics of maleic anhydride grafted polypropylene (mPP) in hybrids with unmodified or organically modified montmorillonite (MMT), which have been prepared by melt intercalation in a mixer, has been investigated by using time-resolved wide-angle X-ray scattering (WAXS) and differential scanning calorimetry (DSC). WAXS and transmission electron microscopy (TEM) showed that the mPP/unmodified MMT hybrids formed macrophase-separated mixtures rather than intercalated nanocomposites, while mPP/organically layered silicate (OLS) hybrids formed exfoliated nanocomposites. The crystallization rate of mPP/unmodified silicate hybrids became faster with the MMT addition because agglomerated silicates in the mPP matrix act as nucleating agents. On the other hand, the crystallization rate of the mPP/OLS hybrids was slowed with the OLS addition. This retardation of the mPP crystallization is probably due to the presence of well-dispersed exfoliated silicates as diffusion or displacement barriers for crystallization. Interestingly, these well-dispersed exfoliated silicates change the crystal orientation as well as the crystallization kinetics of mPP in mPP/OLS nanocomposites, showing larger (040) peak than (110) peak for the α form crystal in WAXS profiles.
Drug Design of GPCR Ligands Using Physicogenetics and Chemogenomics - Principles and Case Studies (2011)

An efficient computational method for hit and lead identification is described. The method that incorporate ligand information from physicogenetically related 7TM receptors, i.e. receptors with similar physicochemical features in the ligand binding pockets, have been developed to aid the construction of pharmacophore queries for mining of vendor and in-house databases to produce small focused libraries for a specific GPCR target. The physicogenetically related targets could be complementary to phylogenetically derived receptors and convey more relevance for the structure-based design approaches suitable for GPCR targets associated with no or limited ligand information. The approach is useful not only in identification of hits but also in the hit-to-lead process as constructed homology receptor models, SAR information and pharmacophore features are collectively utilized in the design of proprietary new lead series. This site-directed drug discovery approach of making smaller receptor-specific libraries displays important advantages over conventional HTS-based generation of hits. The methodology has been exemplified with the CRTH2 receptor, which was associated with minimal ligand information, to produce a small diverse library containing several useful hit series which were further converted into drugable lead series. The use of ligand and QSAR information in scaffold hopping was exemplified with MCH1R antagonists, which had been obtained via chemogenomics-enriched design. Finally, an example on how ligand relationships can be used in identifying receptor relationships was given with CCR2 antagonists to highlight the 3D relationships of GPCR targets not directly evident from either phylogenetic or physicogenetic relationships.
Mast cell leukemia (2012)

Mast cell leukemia (MCL) is a very rare form of aggressive systemic mastocytosis accounting for < 1% of all mastocytosis. It may appear de novo or secondary to previous mastocytosis and shares more clinicopathologic aspects with systemic mastocytosis than with acute myeloid leukemia. Symptoms of mast cell activation-involvement of the liver, spleen, peritoneum, bones, and marrow-are frequent. Diagnosis is based on the presence of ≥ 20% atypical mast cells in the marrow or ≥ 10% in the blood; however, an aleukemic variant is frequently encountered in which the number of circulating mast cells is < 10%. The common phenotypic features of pathologic mast cells encountered in most forms of mastocytosis are unreliable in MCL. Unexpectedly, non-KIT D816V mutations are frequent and therefore, complete gene sequencing is necessary. Therapy usually fails and the median survival time is < 6 months. The role of combination therapies and bone marrow transplantation needs further investigation.
The Use of AES-192 and AES-256 in Secure RTP (2011)

Advanced Encryption Standard (AES) with 192-and 256-bit keys within the Secure RTP (SRTP) protocol. It details counter mode encryption for SRTP and Secure Realtime Transport Control Protocol (SRTCP) and a new SRTP Key Derivation Function (KDF) for AES-192 and AES-256.
FK506 and Sildenafil Promote Erectile Function Recovery After Cavernous Nerve Injury Through Antioxidative Mechanisms (2007)

Both FK506 and sildenafil protect erectile function after CN injury by decreasing oxidative stress-associated tissue damage. FK506 may act through increased GPX activity. Further research is required to elucidate mechanisms associated with the beneficial effect of sildenafil.
Natural antisense transcripts as drug targets (2022)

The recent discovery of vast non-coding RNA-based regulatory networks that can be easily modulated by nucleic acid-based drugs has opened numerous new therapeutic possibilities. Long non-coding RNA, and natural antisense transcripts (NATs) in particular, play a significant role in networks that involve a wide variety of disease-relevant biological mechanisms such as transcription, splicing, translation, mRNA degradation and others. Currently, significant efforts are dedicated to harnessing these newly emerging NAT-mediated biological mechanisms for therapeutic purposes. This review will highlight the recent clinical and pre-clinical developments in this field and survey the advances in nucleic acid-based drug technologies that make these developments possible.
Semantic Image Retrieval in Magnetic Resonance Brain Volumes (2012)

Practitioners in the area of neurology often need to retrieve multimodal magnetic resonance (MR) images of the brain to study disease progression and to correlate observations across multiple subjects. In this paper, a novel technique for retrieving 2-D MR images (slices) in 3-D brain volumes is proposed. Given a 2-D MR query slice, the technique identifies the 3-D volume among multiple subjects in the database, associates the query slice with a specific region of the brain, and retrieves the matching slice within this region in the identified volumes. The proposed technique is capable of retrieving an image in multimodal and noisy scenarios. In this study, support vector machines (SVM) are used for identifying 3-D MR volume and for performing semantic classification of the human brain into various semantic regions. In order to achieve reliable image retrieval performance in the presence of misalignments, an image registration-based retrieval framework is developed. The proposed retrieval technique is tested on various modalities. The test results reveal superior robustness performance with respect to accuracy, speed, and multimodality.
Using Intentional Magnetic Saturation for HFI Based Self-Sensing with SPMSMs (2018)

High-frequency injection (HFI) is widely used for zero-to-low speed self-sensing with machines with inductive saliency. The HFI algorithm uses inductive saliency in the d and q-axes to estimate the permanent magnet (PM) rotor position. Surface permanent magnet synchronous machines (SPMSMs), which are designed without inductive saliency, are not suitable for HFI based self-sensing. In this paper, a method to enable classically designed SPMSMs for HFI based self-sensing at zero-to-low speed is introduced utilizing intentional magnetic saturation under flux-intensifying operation. With properly chosen HFI operating spaces inducing inductive saliency, a smooth startup in the zero-to-low speed region can be achieved. To generalize the idea, a lumped parameter magnetic circuit is developed. The magnetic saturability of fractional slot concentration winding (FSCW) and distribution winding (DW) SPMSMs are compared.
GaAs-based integrated fluorescence bio-sensors: Progress towards high rejection of laser excitation light (2008)

We demonstrate progress towards a GaAs-based integrated fluorescence bio-sensor capable of rivaling the performance of large-format fluorescence imaging systems by using a dielectric stack to filter the excitation light.
Materials and architectures for efficient harvesting of singlet and triplet excitons for white light emitting OLEDs (2023)

The present invention relates to organic light emitting devices (OLEDs), and more specifically to OLEDS that emit light using a combination of fluorescent emitters and phosphorescent emitters for the efficient utilization of all of the electrically generated excitons.
Development of an extremely selective e-nose employing a single polycyclic aromatic hydrocarbon-based chemFET (2011)

In this study, we introduce a novel synthetically designed polycyclic aromatic hydrocarbon (PAH) chemFET. The chemFET device operates by employing voltage dependent back-gate measurements, wherein the drain current (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> ) is monitored while the gate voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> ) applied to the device is swept backward and forward between -40V and +40V. Using this device, we demonstrate that an extremely selective e-nose can be developed by extracting the most suitable features from the I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">d</sub> -V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</sub> characteristic curves of a single chemFET. The accuracy of the identification of eight different volatile organic compounds (VOCs) surpassed 91%.
Merged two-stage power converterarchitecture with softcharging switched-capacitor energy transfer (2008)

This paper presents a two-stage architecture that combines a large step-down switched-capacitor transformation stage with a high-bandwidth magnetic regulation stage. The proposed design is particularly well-suited for an integrated CMOS process, as it makes use of the available on-die device characteristics. In such a process, the two-stage architecture presented offers high efficiency, high power density, and high- bandwidth regulation. We show that by merging the switched-capacitor stage and the regulation stage in a specific manner, further performance improvements can be attained. When the fast-switching regulation stage is used to provide soft charging of the switched-capacitor stage, a substantial improvement in performance is possible. An experimental prototype, implemented using discrete components, validates the approach.
Differential Antigenic Hierarchy Associated with Spontaneous Recovery from Hepatitis C Virus Infection: Implications for Vaccine Design (2006)

Because these data comprehensively define the breadth, specificity, and threshold of the T cell response associated with spontaneous recovery from HCV infection, they have important implications in the development of multigenic vaccine candidates for this common infection.
Hydrolytic Degradation of 3D-Printed Poly (Lactic Acid) Structures (2021)

Hydrolytic degradation of commercially available 3D printing filament, i.e. poly (lactic acid) with broad molecular weight distribution was induced by incubating 3D-printed parts in deionized water at 3 temperatures. Small changes in orthogonal dimensions occurred due to relaxation of printing stresses, but no mass or volume loss were detected over the time-frame of the experiments. Molecular weight decreased while polydispersity remained constant. The most sensitive measure of degradation was found to be nondestructive, small-amplitude oscillatory tensile measurements. A rapid decay of tensile storage modulus was found with an exponential decay time constant of about an hour. This work demonstrates that practical monitoring of commercially available PLA degradation can be achieve with linear viscoelastic measurements of modulus.
Synthese piretanidanaloger 1,3,4‐Triazole (1983)

Abstract Die Synthese der piretanidanalogen 1,3,4‐Triazole 2a und 2b wird beschrieben. Bei Schutz der Carboxyl‐ und der Sulfonamidgruppe gelingt der Aufbau des Triazolrings durch Cyclokondensation der Amine 3a und 3b mit Diformylhydrazin in einem Reaktionsschritt.
Pharmacological Modulation of Calcium Homeostasis in Familial Dilated Cardiomyopathy: An In Vitro Analysis From an RBM20 Patient‐Derived iPSC Model (2016)

For inherited cardiomyopathies, abnormal sensitivity to intracellular calcium (Ca(2+) ), incurred from genetic mutations, initiates subsequent molecular events leading to pathological remodeling. Here, we characterized the effect of β-adrenergic stress in familial dilated cardiomyopathy (DCM) using human-induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (CMs) from a patient with RBM20 DCM. Our findings suggest that β-adrenergic stimulation accelerated defective Ca(2+) homeostasis, apoptotic changes, and sarcomeric disarray in familial DCM hiPSC-CMs. Furthermore, pharmacological modulation of abnormal Ca(2+) handling by pretreatment with β-blocker, carvedilol, or Ca(2+) -channel blocker, verapamil, significantly decreased the area under curve, reduced percentage of disorganized cells, and decreased terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick-end labeling (TUNEL)-positive apoptotic loci in familial DCM hiPSC-CMs after β-adrenergic stimulation. These translational data provide patient-based in vitro analysis of β-adrenergic stress in RBM20-deficient familial DCM hiPSC-CMs and evaluation of therapeutic interventions to modify heart disease progression, which may be personalized, but more importantly generalized in the clinic.
Use of common time base for checkpointing and rollback recovery in a distributed system (1993)

An approach to checkpointing and rollback recovery in a distributed computing system using a common time base is proposed. A common time base is established in the system using a hardware clock synchronization algorithm. This common time base is coupled with the idea of pseudo-recovery points to develop a checkpointing algorithm that has the following advantages: reduced wait for commitment for establishing recovery lines, fewer messages to be exchanged, and less memory requirement. These advantages are assessed quantitatively by developing a probabilistic model.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Variable-Length Sparse Feedback Codes for Point-to-Point, Multiple Access, and Random Access Channels (2021)

This paper investigates variable-length stop-feedback codes for memoryless channels in point-to-point, multiple access, and random access communication scenarios. The proposed codes employ $L$ decoding times $n_1, n_2, \dots, n_L$ for the point-to-point and multiple access channels and $KL + 1$ decoding times for the random access channel with at most $K$ active transmitters. In the point-to-point and multiple access channels, the decoder uses the observed channel outputs to decide whether to decode at each of the allowed decoding times $n_1, \dots, n_L$, at each time telling the encoder whether or not to stop transmitting using a single bit of feedback. In the random access scenario, the decoder estimates the number of active transmitters at time $n_0$ and then chooses among decoding times $n_{k, 1}, \dots, n_{k, L}$ if it believes that there are $k$ active transmitters. In all cases, the choice of allowed decoding times is part of the code design; given fixed value $L$, allowed decoding times are chosen to minimize the expected decoding time for a given codebook size and target average error probability. The number $L$ in each scenario is assumed to be constant even when the blocklength is allowed to grow; the resulting code therefore requires only sparse feedback. The central results are asymptotic approximations of achievable rates as a function of the error probability, the expected decoding time, and the number of decoding times. A converse for variable-length stop-feedback codes with uniformly-spaced decoding times is included for the point-to-point channel.
Fragmentation of an alkali metal-attached peptide probed by collision-induced dissociation Fourier transform mass spectrometry and computational methodology (1999)

Collision-induced dissociation of metal-cationized N-CBZ-Gly-Pro-Gly-Pro-Ala was studied by Fourier transform mass spectrometry. Lithium-, sodium-, potassium- and rubidium-cationized peptide species were generated by matrix-assisted laser desorption/ionization (MALDI) using 2,5-dihydroxybenzoic acid as matrix, together with appropriate metal salts. The experimental mass spectrometric results were interpreted with the aid of Monte Carlo conformational searches using the Amber(*) force field, together with ab initio molecular orbital calculations with Gaussian-94 for the singly lithium- and potassium-cationized peptides. It is concluded that metal coordination plays a key role in guiding the gas-phase fragmentation of the cationized peptide. In contrast to lithium and sodium, potassium and rubidium apparently do not coordinate to the C-terminal carbonyl. When the peptide is cationized with the two smaller alkali metals, losses corresponding to alanine and CBZ are observed, while the coordination of potassium and rubidium results in only CBZ loss upon dissociation.
Deep CG2Real: Synthetic-to-Real Translation via Image Disentanglement (2020)

We present a method to improve the visual realism of low-quality, synthetic images, e.g. OpenGL renderings. Training an unpaired synthetic-to-real translation network in image space is severely under-constrained and produces visible artifacts. Instead, we propose a semi-supervised approach that operates on the disentangled shading and albedo layers of the image. Our two-stage pipeline first learns to predict accurate shading in a supervised fashion using physically-based renderings as targets, and further increases the realism of the textures and shading with an improved CycleGAN network. Extensive evaluations on the SUNCG indoor scene dataset demonstrate that our approach yields more realistic images compared to other state-of-the-art approaches. Furthermore, networks trained on our generated "real" images predict more accurate depth and normals than domain adaptation approaches, suggesting that improving the visual realism of the images can be more effective than imposing task-specific losses.
Analysis of volatile metabolites from cultured bacteria by gas chromatography/atmospheric pressure chemical ionization–mass spectrometry (2008)

An analytical system using gas chromatography/atmospheric pressure chemical ionization–mass spectrometry (GC/APCI-MS) was suitably set up for the analysis of volatile metabolites from cultured bacteria. The developed system was proved to have high sensitivity: the detection limit for a standard sample of indole was 17 pg (33 ppt (parts per trillion) for 100 mL gas sample). The system was extensively applied to rapid analysis of volatile metabolites from different bacteria: Escherichia coli, Streptococcus pneumoniae, and two strains of Staphylococcus aureus. A total of 156 metabolite peaks were peculiar to one of the species among 163 metabolite peaks found for all of the bacteria. The experimental results suggest that the GC/APCI-MS has the potential to distinguish bacterial pathogens rapidly by detecting bacterial volatile metabolites.
On understanding the influence sleep mode on packet delay variation in TDM-PONs (2014)

Sleep mode has been widely applied in TDM-Passive Optical Networks for maximizing energy saving. However, it can significantly influence QoS performance of traffic. In this article, we present an insightful study results which comprehend how delay variation performance of a flow can be influenced under different length of sleep intervals used in Optical Network Units.
P3‐470: Combined dietary vitamins B6, B12, and folic acid increase plasma choline levels in rats (2011)

Choline is an essential nutrient for humans and is required for the synthesis of choline-containing phospholipids, acetylcholine and the methyl-donor betaine. Choline is not only derived from the diet, but also from de novo synthesis, via sequential methylation of phosphatidylethanolamine to phosphatidylcholine (PC) by phosphatidylethanolamine-N-methyltransferase (PEMT). Choline is liberated from the newly formed PC and released into the bloodstream. Vitamin B6, B12, and folic acid supplementation may support the PEMT pathway by both enhancing regeneration of methionine and reducing homocysteine levels. An alternative pathway for regeneration of methionine from homocysteine is provided by betaine-homocysteine methyltransferase which utilizes choline. Hence, B-vitamins may not only increase endogenous choline synthesis through the PEMT pathway, but may also decrease choline utilization by the betaine-homocysteine methyltransferase pathway. We now studied whether B-vitamin supplementation affects plasma choline availability. Rats were fed different diets specific in vitamin B6, B12, and folic acid: 1) B-vitamin poor; 2) B-vitamin enriched. First, a mild B-vitamin deficiency was induced in all rats by feeding the B-vitamin poor diet for 4 weeks. Second, animals either continued on the B-vitamin poor diet or switched to the B-vitamin enriched diet for another 4 weeks. Third, rats were sacrificed and plasma was collected for analysis of free choline and total homocysteine. Dietary enrichment with B-vitamins significantly increased plasma choline levels up to 110% of control. In addition, the B-vitamin enriched diet significantly decreased plasma homocysteine levels. B-vitamins may be required to sustain optimal choline levels for precursor availability for synthesis of phospholipids and acetylcholine.