gebhart/patrepeval huggingface dataset:
Is Antagonism of E/Z-Guggulsterone at the Farnesoid X Receptor Mediated by a Noncanonical Binding Site? A Molecular Modeling Study (2005)

Guggulsterone 1, the active principle of guggulipid, has been used in ethnic medicine for thousands of years for its antinflammatory and antilipidemic activities. The activities of 1 are apparently mediated by its interaction with an array of nuclear receptors, including endocrine steroid receptors and metabolic lipid receptors. Although relatively weak, the activity at the metabolic farnesoid X receptor (FXR) is particularly intriguing, as 1 is, so far, the only antagonist known for this receptor, with a peculiar ability of gene selective modulation. We report here a systematic study aimed at identifying the potential binding pocket of 1 at FXR. Although 1 could be docked into the canonical binding site, we identified a novel, so far undescribed binding pocket, localized near the loop region between helix 1 and helix 2. This novel binding pocket may explain some of the peculiar characteristics of 1 when acting at FXR.
Programmed Delayed Splicing: A Mechanism for Timed Inflammatory Gene Expression (2018)

SUMMARY Inflammation involves timed gene expression, suggesting that the fine-tuned onset, amplitude, and termination of expression of hundreds of genes is of critical importance to organismal homeostasis. Recent study of post-transcriptional regulation of inflammatory gene expression led to the suggestion of a regulatory role for pre-mRNA splicing. Here, using a hybrid capture approach to purify incompletely spliced, chromatin-associated pre-mRNAs, we use deep sequencing to study pre-mRNA splicing of the NF-kB transcriptome. By freezing transcription and examining subsequent splicing of complete transcripts, we find many introns splice tens to hundreds of times slower than average. Investigating the basis of these delays, we focused on evolutionarily conserved introns with suboptimal splice donor sequences and found that strengthening these donor sites by as few as two nucleotides in minigene reporter assays markedly increased gene expression for several targets. This suggests that such sites can act as timing elements that both delay mRNA production and limit expression amplitude. To broaden this mechanistic view, we applied deep learning sequence-to-function models with feature attribution to identify additional regulatory sequences—both intronic and exonic—that may contribute to delayed splicing through mechanisms independent of donor site strength. This integrated approach revealed non-canonical motifs enriched in slow-splicing introns, pointing to a broader repertoire of cis-elements that can fine-tune transcript maturation during inflammation. Together, these findings support a model in which the temporal regulation of pre-mRNA splicing serves as a layer of control in inflammatory gene expression, and raise the possibility that similar timing mechanisms operate in other rapid-response transcriptional programs.
A Convenient One-Pot Completely Stereoselective Synthesis of trans-4-Hydroxystilbenes and Its Derivatives and X-Ray Structure of Its Precursor (2003)

Abstract The synthesis of E-isomer of 4-Hydroxystilbene and its derivatives 3 by reductive elimination of the carbonyl function in 2-phenyl-1-(4-hydroxyphenyl)ethan-1-one and its derivatives 2 and the X-ray structure of 2a are described.
From Architecture to Implementation of a Wireless, Multiple Antenna Testbed (2005)

This paper describes the design and development of a wireless, multiple antenna testbed. The discussed wireless testbed, built with off-the-shelf components, is fully calibrated and has been used in many field trials. The author addresses the complete design flow from the frequency plan and the decision of the architecture to the actual implementation on multiple PCBs. The decisions are often driven by the availability of components on the market. A big challenge in multiple antenna systems is the distribution of the controlling and data signals, which significantly increases the complexity compared to single antenna systems. Most of the ideas discussed are kept very general and can be applied to any kind of wireless testbed.
Efficient chemical synthesis of human complement protein C3a (2013)

We report the total chemical synthesis of human C3a by one-pot native chemical ligation of three unprotected peptide segments, followed by efficient in vitro folding that yielded the anaphylatoxin C3a in high yield and excellent purity. Synthetic C3a was fully active and its crystal structure at 2.1 Å resolution showed 3 helices and a C-terminal turn motif.
1,3-Dichloro-1,1,3,3-tetraisopropyldisiloxane (2006)

[69304-37-6] C12H28Cl2OSi2 (MW 315.43) InChI = 1S/C12H28Cl2OSi2/c1-9(2)16(13,10(3)4)15-17(14,11(5)6)12(7)8/h9-12H,1-8H3 InChIKey = DDYAZDRFUVZBMM-UHFFFAOYSA-N (simultaneous protection of the 3′- and 5′-hydroxyl functions of furanose nucleosides;1, 2 protecting group for carbohydrates;3, 4 protecting group reagent for open-chain polyhydroxy compounds;5 preparation of cyclic bridged peptides6) Alternate Names: TIPSCl, TIPDSCl2. Physical Data: bp 70 °C/0.5 mmHg; d 0.986 g cm−3. Solubility: insoluble in water, 0.3M TsOH in dioxane, 10% TFA in chloroform, 5M NH3 in dioxane–water (4∶1), or isobutylamine–methanol (1∶9), or tertiary amines (Et3N, pyridine). Form Supplied in: liquid; commercially available. Preparative Method: can be prepared starting from Trichlorosilane by treatment with i-PrMgCl, H2O, and Acetyl Chloride.7 Alternatively, it can be prepared by the reaction of 1,1,3,3-tetraisopropyldisiloxane with CCl4 in the presence of catalytic PdCl2.8 This method is also suitable for its in situ preparation. Handling, Storage, and Precautions: the liquid is corrosive and insoluble in water.
On the Feasibility of Informative Biosignature Measurements Using an Enceladus Plume Organic Analyzer (2021)

Abstract The icy moons of Saturn and Jupiter are high priority locations in which to search for biomarkers of life elsewhere in our solar system. In particular, the ice plumes that jet out through the ice surface at Enceladus provide an enticing opportunity to sample the organic components of its subsurface ocean for possible biosignatures while ameliorating challenges of planetary protection. Extensive high- and hypervelocity light gas gun experiments, the first to model the Enceladus ice plume encounter accurately, have demonstrated that organic-rich ice particles can be efficiently captured using plume transits at and below 3 km s −1 without significant organic destruction. Realistic scenarios for the amount of ice captured and for the ability of organic chemical analysis instruments, especially microfluidic capillary electrophoresis with laser-induced fluorescence, to produce meaningful detection levels for biosignatures are then presented and compared with results from terrestrial models. This analysis indicates that an Enceladus plume fly-by mission carrying microfluidic instrumentation is capable of biosignature measurements with a sensitivity and analytical capability that is highly informative about the extent of extraterrestrial biological processes.
New errorprediction techniques forturbo-coded OFDM systems andimpact on adaptivemodulation and coding (2005)

Thispaperdeals withPacket Error Rate(PER)prediction andits impact onAdaptive Modulation andCoding (AMC)for anOFDM turbo codedtransmission onamultipath channel. Wecompare four LinkQuality Metrics (LQM),including the Signal toNoiseRatio (SNR), thecapacity, andtwoLQM whichwedesigned toexploit thesoft outputs oftheturbodecoder. Since error prediction isusedtoperform AMC, weassess thethroughput performance ofarealistic system employing eachofthefour LQM.Thecomparison showsthat while SNRperforms poorly andcapacity remains suboptimum, thetwometrics exploiting soft outputs approach thethroughputwhichwouldbeachieved byperfect PERprediction.
Geometry-Driven Charge Accumulation in Electrokinetic Flows between Thin, Closely Spaced Laminates (2012)

Fluid flows through anisotropic media are found in a wide variety of geophysical and biological systems. The macroscale behavior of these systems depends on the microstructure, which in turn may depend on local and global physical processes. Classically, geometric restrictions are needed to model these systems on the largest length scale, and we are interested in developing effective models which relax these restrictions. To explore the development of these multiscale models, we consider an array of closely spaced, purely dielectric rigid laminates with nonuniform thickness. The laminate thickness and spacing varies on a length scale much longer than the characteristic thickness of the laminates. In the spacing between the laminates, an electrically conducting fluid is driven by an applied electric field through electroosmosis and electrophoresis along with an applied pressure gradient. Debye layers occur at the laminate-fluid interface, which are assumed to be much smaller than the laminate thickness. From a modification of the classical homogenization approach that relies on a physical microscale constraint in place of a geometric constraint, we derive an effective set of equations that describe the fluid pressure, the anion and cation concentrations in the fluid, and the electric potential. Anisotropic dispersion effects in the electric field are included, and electroneutrality in the fluid is not imposed. We find that gradients in the laminate spacing can lead to charge accumulation when electroosmosis and the electrophoresis induced from the anisotropic dispersion effects balance.
Identification of a Novel Voltage-driven Organic Anion Transporter Present at Apical Membrane of Renal Proximal Tubule (2003)

A novel transport protein with the properties of voltage-driven organic anion transport was isolated from pig kidney cortex by expression cloning in Xenopus laevis oocytes. A cDNA library was constructed from size-fractionated poly(A)+ RNA and screened for p-aminohippurate (PAH) transport in high potassium medium. A 1856-base pair cDNA encoding a 467-amino acid peptide designated as OATV1 (voltage-driven organic anion transporter 1) was isolated. The predicted amino acid sequence of OATV1 exhibited 60-65% identity to those of human, rat, rabbit, and mouse sodium-dependent phosphate cotransporter type 1 (NPT1), although OATV1 did not transport phosphate. The homology of this transporter to known members of the organic anion transporter family (OAT family) was about 25-30%. OATV1-mediated PAH transport was affected by the changes in membrane potential. The transport was Na+-independent and enhanced at high concentrations of extracellular potassium and low concentrations of extracellular chloride. Under the voltage clamp condition, extracellularly applied PAH induced outward currents in oocytes expressing OATV1. The current showed steep voltage dependence, consistent with the voltage-driven transport of PAH by OATV1. The PAH transport was inhibited by various organic anions but not by organic cations, indicating the multispecific nature of OATV1 for anionic compounds. This transport protein is localized at the apical membrane of renal proximal tubule, consistent with the proposed localization of a voltage-driven organic anion transporter. Therefore, it is proposed that OATV1 plays an important role to excrete drugs, xenobiotics, and their metabolites driven by membrane voltage through the apical membrane of the tubular epithelial cells into the urine.
Revisiting Polyfluoroarenes as Radical Acceptors: Radical C–F Bond Borylation of Polyfluoroarenes with N-Heterocyclic Carbene Boranes and Synthesis of Borane-Containing Liquid Crystals (2020)

Polyfluoroarenes work as good radical acceptors in the thermal radical reaction with N-heterocyclic carbene boranes (NHC-boranes) in the presence of di-<i>tert</i>-butyl peroxide. In this reaction, a C-F bond of polyfluoroarenes is substituted with an NHC-boryl group to provide <i>B</i>-aryl NHC-borane derivatives. The developed synthetic method was applied to the synthesis of novel borane-containing liquid crystalline molecules having highly thermal stability.
Radiometric model for coaxial single- and multimode optical emission from double-clad fiber (2018)

Double-clad fibers (DCFs) are versatile waveguides supporting a single-mode core surrounded by a multimode inner cladding. DCFs are increasingly used for multimodal biomedical applications, such as imaging or therapy, for which the core is typically used for coherent illumination and the inner cladding, to support a concurrent modality. Proper optimization is, however, critical to ensure high optical performance and requires accurate modeling of coaxial single- and multimode output beams. In this paper, we present an approach based on geometrical optics and radiometry, which provides a simple and efficient modeling tool for designing and optimizing DCF-based systems. A radiometric definition of single- and multimode output beams in terms of irradiance and radiant intensity allows for the modeling of the energy distribution along the beams' propagation. We confirmed the validity of the model through comparison with experimental measurements and demonstrate the use of the model for optimizing a catheter for concurrent OCT and laser coagulation.
Joint Optimization of Robot Design and Motion Parameters using the Implicit Function Theorem (2017)

We present a novel computational approach to optimizing the morphological design of robots.Our framework takes as input a parameterized robot design and a motion plan consisting of trajectories for end-effectors, as well as optionally, for its body.The algorithm we propose is used to optimize design parameters, namely link lengths and the placement of actuators, while concurrently adjusting motion parameters such as joint trajectories, actuator inputs, and contact forces.Our key insight is that the complex relationship between design and motion parameters can be established via sensitivity analysis if the robot's movements are modeled as spatio-temporal solutions to optimal control problems.This relationship between form and function allows us to automatically optimize robot designs based on specifications expressed as a function of range of motion or actuator forces.We evaluate our model by computationally optimizing two simulated robots that employ linear actuators: a manipulator and a large quadruped.We further validate our framework by optimizing the design of a small quadrupedal robot and testing its performance using a hardware implementation.
Determinants for further wishes for cosmetic and reconstructive interventions in 1652 patients with surgical treated carcinomas of the oral cavity (2017)

The wish for CRS depends on diverse functional psychosocial and psychological parameters. Hence, it has to be issued during conversation to improve rehabilitation. A decision on the medical treatment can be of greater satisfaction if the surgeon knows the patients' needs and is able to compare them with the medical capabilities. The informed consent between doctor and patient in regard to these findings is necessary.
Engineered plant biomass particles coated with biological agents (2023)

Plant biomass particles coated with a biological agent such as a bacterium or seed, characterized by a length dimension (L) aligned substantially parallel to a grain direction and defining a substantially uniform distance along the grain, a width dimension (W) normal to L and aligned cross grain, and a height dimension (H) normal to W and L. In particular, the L.times.H dimensions define a pair of substantially parallel side surfaces characterized by substantially intact longitudinally arrayed fibers, the W.times.H dimensions define a pair of substantially parallel end surfaces characterized by crosscut fibers and end checking between fibers, and the L.times.W dimensions define a pair of substantially parallel top and bottom surfaces.
Coordinated Position Control of Multi-Axis Mechanical Systems (1998)

Position coordination of multi-axis mechanical systems is studied. Under the assumption that the coordination objective can be represented by smooth functions of the positions of the multiple axes control systems, a necessary coupling effect can be introduced to each axis by the proper choice of a Lyapunov-like function. The resulting, control law requires the knowledge of the desired trajectories and their time derivatives as well as actual position and velocity information. Implementation of the proposed control algorithm on a CNC feed drive system shows significant improvement in dimensional accuracy during high speed contouring.
Structural Approaches to Cancer Drug Development (2015)

The design of a new CSF1R inhibitor reveals how medicinal chemists can now examine drug interactions with three-dimensional forms of key proteins and predict modifications of an inhibitor that will enhance potency for a specific protein conformation.
Transient thermal analysis of an ACF package assembly process (2001)

Transient thermal simulation was performed to analyze thermal response of the assembly process for a package using anisotropic conductive film (ACF). The main purpose of the study is to simulate the actual assembly and manufacturing process, in order to provide a first-hand approximation and insight of the thermal behavior of the package and ACF film during the process. Two assembly processes were modeled: a simplified process where the package was fixed at two different temperatures during assembly, and a detailed process where the package experienced a ramping heating process, followed by a constant temperature curing process. A full convection-conduction case was conducted first. The results indicate a weak hydrodynamic field and radiation effects, hence for computational purposes (reduced CPU time), it was decided to model the process using a conduction-only investigation. Results from the detailed process modeling indicated that during the initial ramping, within 0.02 s, the die and nozzle head experienced a small temperature drop due to the cooling effect of the ACF material and substrate. The ACF material also displayed a steep increase in temperature after contacting the die, followed by a short decay, then ramped up again. At the end of the 10-s ramping process, the ACF reached a temperature of almost 203/spl deg/C, while the die was at 206/spl deg/C. During the 5 s of curing, all parts reached steady state in less than 2 s.
Investigation on Crystallization of CH3NH3PbI3 Perovskite and Its Intermediate Phase from Polar Aprotic Solvents (2018)

Perovskite films are usually fabricated by a solution-processed method due to its low cost and ease of fabrication. The organic solvent plays multiple roles in the growth of perovskites. Here, we investigate the growth of methylammonium lead iodide perovskite and its intermediate phase from microdroplets containing various solvents. The perovskite intermediate phase inclines to grow in the direction of its (020) plane from polar aprotic solvents at low temperature. At high temperature, the growth of perovskites depends on the structure of solvent molecules. The intermediate phase still grows from the solvents with a short chain structure. It tends to form smooth films containing radial domains with dimensions in tens of microns, which consist of nanocrystals due to annealing effects. However, perovskite grains grow directly from the solvents with a ring structure. It tends to form smooth thin films by joining the large hexagonal perovskite crystals together. It provides a guidance to prepare high quality perovskite films for high performance optoelectronic devices.
An in situ Raman spectroscopy-based microfluidic “lab-on-a-chip” platform for non-destructive and continuous characterization of Pseudomonas aeruginosa biofilms (2015)

Pseudomonas aeruginosa biofilm was cultivated and characterized in a microfluidic "lab-on-a-chip" platform coupled with confocal Raman microscopy in a non-destructive manner. Biofilm formation could be quantified by this label-free platform and correlated well with confocal laser scanning microscopy. This Raman-microfluidic platform could also discriminate biofilms at different developmental stages.
Membrane-mediated structural transitions at the cytoplasmic face during integrin activation (2004)

Cytoplasmic face-mediated integrin inside-out activation remains a paradigm in transmembrane signal transduction. Emerging evidence suggests that this process involves dissociation of the complex between the integrin cytoplasmic tails; however, a dynamic image of how it occurs on the membrane surface remains elusive. We show here that, whereas membrane-proximal helices of integrin alpha/beta cytoplasmic tails associate in cytoplasm-like aqueous medium, they become partially embedded into membrane-mimetic micelles when unclasped. Membrane embedding induces substantial structural changes of the cytoplasmic tails as compared to their aqueous conformations and suggests there may be an upward movement of the membrane-proximal helices into the membrane during their separation. We further demonstrate that the beta3 tail exhibits additional membrane binding site at its C terminus containing the NPLY motif. Talin, a key intracellular integrin activator, recognizes this site as well as the membrane-proximal helix, thereby promoting cytoplasmic tail separation along the membrane surface. These data provide a structural basis of membrane-mediated changes at the cytoplasmic face in regulating integrin activation and signaling.
Improved Silanization Modification of a Silica Surface and Its Application to the Preparation of a Silica-Supported Polyoxometalate Catalyst (2003)

A hydrolyzed silane ((C2H5O)3Si−(CH2)3−NH2) was anchored on the surface of silica nanoparticles, forming silica-immobilized silane. After calcination, the silane-modified silica (M-silica) can attract heteropoly acid (HPA) efficiently. It has been shown that the presence of water in the atmosphere is necessary for the hydrolysis of silane molecules and is also essential for the silanization modification of the silica particles. The efficient silanization modification enabled the high loading ratio of HPA on the surface of the M-silica. The interaction between the NH2 groups in the silanes and the HPA molecules was demonstrated by results of control experiments. The catalytic properties of the M-silica-supported 12-tungstophoshoric acid (HPW) and 12-tungstosilic acid (HSiW) were tested by an oxidation reaction of hydrocarbon (cyclohexane and octane-1) using oxygen as oxidizers. A high conversion of more than 60% was obtained for the HPW/M-silica complex. To our knowledge, it is the highest conversion percentage obtained for the oxidation of cyclohexane.
Overwatch: learning patterns in code edit sequences (2022)

Integrated Development Environments (IDEs) provide tool support to automate many source code editing tasks. Traditionally, IDEs use only the spatial context, i.e., the location where the developer is editing, to generate candidate edit recommendations. However, spatial context alone is often not sufficient to confidently predict the developer’s next edit, and thus IDEs generate many suggestions at a location. Therefore, IDEs generally do not actively offer suggestions and instead, the developer is usually required to click on a specific icon or menu and then select from a large list of potential suggestions. As a consequence, developers often miss the opportunity to use the tool support because they are not aware it exists or forget to use it. To better understand common patterns in developer behavior and produce better edit recommendations, we can additionally use the temporal context, i.e., the edits that a developer was recently performing. To enable edit recommendations based on temporal context, we present Overwatch, a novel technique for learning edit sequence patterns from traces of developers’ edits performed in an IDE. Our experiments show that Overwatch has 78% precision and that Overwatch not only completed edits when developers missed the opportunity to use the IDE tool support but also predicted new edits that have no tool support in the IDE.