gebhart/patrepeval huggingface dataset:
A statistical deformation model based regularizer for registration of histology and MRI (2014)

Free form deformation (FFD) is a popular algorithm for non-linear image registration because of its ability to accurately recover deformations. However, due to the unconstrained elastic registration, FFD may introduce unrealistic deformations, especially when differences between template and target image are large, thereby necessitating a regularizer to constrain the registration to a physically meaning transformation. Prior knowledge in the form of a Statistical Deformation Model (SDM) in a registration scheme has been shown to function as an effective regularizer. With a similar underlying premise, in this paper, we present a novel regularizer for FFD that leverages knowledge of known, valid deformations to train a statistical deformation model (SDM). At each iteration of the FFD registration, the SDM is utilized to calculate the likelihood of a given deformation occurring and appropriately influence the similarity metric to limit the registration to only realistic deformations. Qualitative evaluation of the SDM regularizer was performed for registration of ex vivo pseudo-whole mount histology (WMH) and in vivo prostate MRI to quantify multiprotocol MRI signatures of prostate cancer (CaP). Knowledge from a training set of 6 deformation fields gathered from a single patient study is used to deliver accurate overlays of prostate histology and MRI.
Structural gene for NAD synthetase in Salmonella typhimurium (1988)

We have identified the structural gene for NAD synthetase, which catalyzes the final metabolic step in NAD biosynthesis. This gene, designated nadE, is located between gdh and nit at 27 min on the Salmonella typhimurium chromosome. Mutants of nadE include those with a temperature-sensitive lethal phenotype; these strains accumulate large internal pools of nicotinic acid adenine dinucleotide, the substrate for NAD synthetase. Native gel electrophoresis experiments suggest that NAD synthetase is a multimeric enzyme of at least two subunits and that subunits from Escherichia coli and S. typhimurium interact to form an active heteromultimer.
ChemInform Abstract: Structure of a Carboxylate‐Bridged Tetraazamacrocyclic Complex of Cobalt(III). (1990)

Abstract A new macrocyclic ligand, containing a carefully selected pendant group and the title Co(III) complex (VIII) of it are prepared.
Isolation of Phage Lysins That Effectively Kill Pseudomonas aeruginosa in Mouse Models of Lung and Skin Infection (2019)

Multidrug resistance (MDR) is rapidly increasing in prevalence among isolates of the opportunistic pathogen <i>Pseudomonas aeruginosa</i>, leaving few treatment options. Phage lysins are cell wall hydrolases that have a demonstrated therapeutic potential against Gram-positive pathogens; however, the outer membrane of Gram-negative bacteria prevents most lysins from reaching the peptidoglycan, making them less effective as therapeutics. Nevertheless, a few lysins from Gram-negative bacterial phage can penetrate the bacterial outer membrane with the aid of an amphipathic tail found in the molecule's termini. In this work, we took a phylogenetic approach to systematically identify those lysins from <i>P. aeruginosa</i> phage that would be most effective therapeutically. We isolated and performed preliminary characterization of 16 lysins and chose 2 lysins, PlyPa03 and PlyPa91, which exhibited >5-log killing activity against <i>P. aeruginosa</i> and other Gram-negative pathogens (particularly <i>Klebsiella</i> and <i>Enterobacter</i>). These lysins showed rapid killing kinetics and were active in the presence of high concentrations of salt and urea and under pH conditions ranging from 5.0 to 10.0. Activity was not inhibited in the presence of the pulmonary surfactant beractant (Survanta). While neither enzyme was active in 100% human serum, PlyPa91 retained activity in low serum concentrations. The lysins were effective in the treatment of a <i>P. aeruginosa</i> skin infection in a mouse model, and PlyPa91 protected mice in a lung infection model, making these lysins potential drug candidates for Gram-negative bacterial infections of the skin or respiratory mucosa.
Optimal Torque-Vectoring Control Strategy for Energy Efficiency and Vehicle Dynamic Improvement of Battery Electric Vehicles with Multiple Motors (2023)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;Electric vehicles comprising multiple motors allow the individual wheel torque allocation, i.e. torque-vectoring. Powertrain configurations with multiple motors provide additional degree of freedom to improve system level efficiencies while ensuring handling performances and active safety. However, most of the works available on this topic do not simultaneously optimize both vehicle dynamic performance and energy efficiency while considering the real-time implementability of the controller. In this work, a new and systematic approach in designing, modeling, and simulating the main layers of a torque-vectoring control framework is introduced. The high level control combines the actions of an adaptive Linear Quadratic Regulator (A-LQR) and of a feedforward controller, to shape the steady-state and transient vehicle response by generating the reference yaw moment. A novel energy efficient torque allocation method is proposed as a low level controller. The torque is allocated on each wheel by solving a quadratic programming problem. The latter is solved in real-time to guarantee the desired yaw moment and the requested driver power demand while minimizing the system losses. The objective function of the quadratic problem accounts for the efficiency map of the electric machine as well as the dissipations due to tire slip phenomena. The torque-vectoring is evaluated in a co-simulation environment. Matlab/Simulink is used for the control strategy and VI-CarRealTime for the vehicle model and driver. The vehicle model represents a high performance pure electric SUV with four e-motors. The performance of the proposed controller is assessed using open loop maneuvers and in closed loop track lap scenarios. The results demonstrate that the proposed controller enhances the vehicle’s performance in terms of handling. Additionally, a significant improvement in energy saving in a wide range of lateral acceleration conditions is: presented. Moreover, the control strategy is validated using rapid control prototyping, thus guaranteeing a deterministic real-time implementation.&lt;/div&gt;&lt;/div&gt;
Sperm Proteasome as a Putative Egg Coat Lysin in Mammals (2014)

During animal and human fertilization, the fertilizing spermatozoon creates and passes through a fertilization slit in the vitelline coat (VC) of the oocyte. It has been hypothesized that the penetration of the mammalian VC, the zona pellucida (ZP), is aided by a proteolytic enzyme capable of locally degrading ZP proteins. This putative “zona lysin” is predicted to reside within the sperm head acrosome and be released or exposed by ZP-induced acrosomal exocytosis. Evidence has been accumulating in favor of the 26S proteasome, the ubiquitin-dependent multi-subunit protease acting as the putative vitelline coat/zona lysin in humans and animals. To confirm this hypothesis, three criteria must be met: (1) the sperm receptor on the ZP must be ubiquitinated, (2) proteasomes must be present, exposed, and enzymatically active in the sperm acrosome, and (3) sperm proteasomes must be able to degrade the sperm receptor on the egg coat/ZP during fertilization. This review discusses recent data from a number of mammalian and nonmammalian models addressing these predictions. These data shed light on the mechanisms controlling sperm interactions with VC and on the evolutionary conservation of the proteasome-assisted fertilization mechanisms.
On-package multiprocessor ground-referenced single-ended interconnect (2023)

A system of interconnected chips comprising a multi-chip module (MCM) includes a first processor chip, a second processor chip, and an MCM package configured to include the first processor chip, the second processor chip, and an interconnect circuit. The first processor chip is configured to include a first ground-referenced single-ended signaling (GRS) interface circuit. A first set of electrical traces fabricated within the MCM package and configured to couple the first GRS interface circuit to the interconnect circuit. The second processor chip is configured to include a second GRS interface circuit. A second set of electrical traces fabricated within the MCM package and configured to coupled the second GRS interface circuit to the interconnect circuit.
Titanium and Zirconium Complexes That Contain the Tridentate Diamido Ligands [(i-PrN-o-C6H4)2O]2-([i-PrNON]2-) and [(C6H11N-o-C6H4)2O]2-([CyNON]2-) (1999)

A variety of five- and six-coordinate titanium and zirconium dialkyl complexes that contain the [(i-PrN-o-C6H4)2O]2- ([i-PrNON]2-) ligand have been prepared, among them [i-PrNON]Ti(CH2CHMe2)2, [i-PrNON]Ti(CH2CMe3)2, [i-PrNON]Zr(CH2CH3)2, and [i-PrNON]Zr(CH2CHMe2)2. These species serve as sources of complexes such as {[i-PrNON]Ti(PMe3)2}2(μ-N2), [i-PrNON]Ti(CHCMe3)(PMe3)2, [i-PrNON]Zr(CH2CHMe2)2(PMe3), and [i-PrNON]Zr(H2CCMe2)(PMe3)2. The reaction between [i-PrNON]Ti(CH2CMe3)2 and Me2PCH2CH2PMe2 in the absence of dinitrogen yields (i-PrNC6H4)(i-PrNC6H4O)Ti(dmpe), a pseudooctahedral species in which one aryl−oxygen bond has been cleaved. In all structurally characterized complexes in which the [i-PrNON]2- ligand is intact, it adopts a mer configuration in which the donor oxygen atom is planar. Analogous dialkyl complexes [CyNON]MR2 (Cy = cyclohexyl; M = Zr, R = Me, Et, i-Bu, CH2CMe3, allyl; M = Ti, R = Me, CH2CMe3, i-Bu) have also been prepared. Decomposition of [i-PrNON]Zr(CH2CH3)2 in the absence of phosphine has been found to proceed in a first-order manner to yield {[i-PrNON]Zr(CH2CH3)}2(μ-C2H4) via rate-limiting β-hydrogen abstraction to give transient [i-PrNON]Zr(CH2CH2) followed by either intermolecular selective β-hydrogen transfer or ethyl group transfer from [i-PrNON]Zr(CH2CH3)2 to [i-PrNON]Zr(CH2CH2), as suggested by 2H and 13C labeling studies. Decompositions of [i-PrNON]ZrR2 complexes are dramatically accelerated in the presence of PMe3. One equivalent of PMe3 is proposed to bind to give a pseudooctahedral adduct, [i-PrNON]ZrR2(PMe3), in which the two alkyl (R) groups are pushed close to one another and β-hydrogen abstraction is thereby accelerated. Consistent with the relatively uncrowded coordination sphere in [i-PrNON]2- or [CyNON]2- complexes, activated dialkyls will only oligomerize 1-hexene. Compounds whose structures have been determined include [i-PrNON]Ti(CH2CHMe2)2, [i-PrNON]ZrMe2, [i-PrNON]Zr(H2CCHMe2)2(PMe3), [i-PrNON]Zr(CH2CMe2)(PMe3)2, [i-PrNON]Ti(PMe3)2]2(μ-N2), [i-PrNON]Ti(CHCMe3)(PMe3)2, and (i-PrNC6H4)(i-PrNC6H4O)Ti(dmpe).
Thermal Disorder in Finite-Length Carbon Nanowire (2023)

Enhancement in chemisorption is one of the active research areas in carbon materials. To remedy the thermally degraded chemisorption at high temperatures, we report a comprehensive study of kink structures in free-standing monoatomic carbon nanowires upon heating. Our Monte Carlo simulation considers multi-monoatomic carbon chains laterally interacted by the Van der Waals force. Our study reveals that the carbon nanowires maintain their linearity regardless of chain length at low temperatures, but this is not the case at high temperatures. Disordered kink structure is observed in the short carbon chains, especially above the Peierls transition temperature. The severe kink structure might increase the possibility of attaching negatively charged atoms, thereby contributing to the development of next-generation materials for chemisorption at high temperatures. We have also provided an important inspection that any physical property of the finite-length carbon chain predicted by ab-initio calculation should reconsider the atomic rearrangement due to the thermal instability at high temperatures.
Real-Time Fingerprint Analysis&amp;Authentication for Embedded Appliances (2007)

A complete fingerprint analysis system is described. The design and architecture of a loadable device driver for a USB fingerprint sensor is described. Image processing filters to enhance the raw image data and to extract key points from fingerprint images are also described. Finally a novel pattern matching technique which allows fast authentication is described. The results of initial reliability testing and some example applications of fingerprint authentication in CE appliances are given.
An Efficient Route to 3,3′‐Biindolinylidene‐diones by Iron‐Catalyzed Dimerization of Isatins (2022)

Iron-catalyzed dimerization of various isatin derivatives is described for the efficient synthesis of 3,3'-biindolinylidene-diones (isoindigos). The reaction provides easy access to self-coupled and cross-coupled 3,3'-indolinylidene-diones that have high relevance to biology and materials. This Fe(0)- or Fe(II)-catalyzed dimerization reaction tolerates a wide range of functionalities, such as fluoro, chloro, bromo, alkenyl, nitrile, ether, ester, pyrrolyl, indolyl and carbazolyl groups, including cyclic and acyclic alkyls as well as an alkyl-bearing fatty-alcohol moiety. Especially, the coupling between two distinct isatins provided excellent selectivity for the cross-dimerization with trace of self-couplings. The single-crystal X-ray diffraction study established the molecular structure of eight dimerized products. A preliminary mechanistic study of the Fe-catalyzed dimerization supported the radical pathway for the reaction.
Effects on Rainbow Trout Fry of a Metals-Contaminated Diet of Benthic Invertebrates from the Clark Fork River, Montana (1994)

The upper Clark Fork River in northwestern Montana has received mining wastes from the Butte and Anaconda areas since 1880. These wastes have contaminated areas of the river bed and floodplain with tailings and heavy metal sludge, resulting in elevated concentration of metals in surface water, sediments, and biota. Rainbow trout Oncorhynchus mykiss were exposed immediately after hatching for 91 d to cadmium, copper, lead, and zinc in water at concentrations simulating those in Clark Fork River. From exogenous feeding (21 d posthatch) through 91 d, fry were also fed benthic invertebrates from the Clark Fork River that contained elevated concentrations of arsenic, cadmium, copper, and lead. Evaluations of different combinations of diet and water exposure indicated diet-borne metals were more important than water-borne metals – at the concentrations we tested – in reducing survival and growth of rainbow trout. Whole-body metal concentrations (μg/g, wet weight) at 91 d in fish fed Clark Fork invertebrates without exposure to Clark Fork water were arsenic, 1.4; cadmium, 0.16; and copper, 6.7. These were similar to concentrations found in Clark Fork River fishes. Livers from fish on the high-metals diets exhibited degenerative changes and generally lacked glycogen vacuolation. Indigenous Clark Fork River invertebrates provide a concentrated source of metals for accumulation into young fishes, and probably were the cause of decreased survival and growth of age-0 rainbow trout in our laboratory exposures.
Delineation of Lipopolysaccharide (LPS)-binding Sites on Hemoglobin (2011)

Hemoglobin (Hb) functions as a frontline defense molecule during infection by hemolytic microbes. Binding to LPS induces structural changes in cell-free Hb, which activates the redox activity of the protein for the generation of microbicidal free radicals. Although the interaction between Hb and LPS has implications for innate immune defense, the precise LPS-interaction sites on Hb remain unknown. Using surface plasmon resonance, we found that both the Hb α and β subunits possess high affinity LPS-binding sites, with K(D) in the nanomolar range. In silico analysis of Hb including phospho-group binding site prediction, structure-based sequence comparison, and docking to model the protein-ligand interactions showed that Hb possesses evolutionarily conserved surface cationic patches that could function as potential LPS-binding sites. Synthetic Hb peptides harboring predicted LPS-binding sites served to validate the computational predictions. Surface plasmon resonance analysis differentiated LPS-binding peptides from non-binders. Binding of the peptides to lipid A was further substantiated by a fluorescent probe displacement assay. The LPS-binding peptides effectively neutralized the endotoxicity of LPS in vitro. Additionally, peptide B59 spanning residues 59-95 of Hbβ attached to the surface of Gram-negative bacteria as shown by flow cytometry and visualized by immunogold-labeled scanning electron microscopy. Site-directed mutagenesis of the Hb subunits further confirmed the function of the predicted residues in binding to LPS. In summary, the integration of computational predictions and biophysical characterization has enabled delineation of multiple LPS-binding hot spots on the Hb molecule.
Directed 2D‐to‐3D Pattern Transfer Method for Controlled Fabrication of Topologically Complex 3D Features in Silicon (2010)

A process that allows control over the 3D motion of catalyst nanostructures during metal-assisted chemical etching by their local pinning prior to etching is demonstrated. The pinning material acts as a fulcrum for rotation of the catalyst structures resulting in etching of silicon features with rotational geometry.
Optimization of the performance of an air–cathode MFC by changing solid retention time (2016)

Abstract BACKGROUND This work is focused on the optimization of the performances of air‐cathode microbial fuel cells ( MFC ) by changing the solid retention time ( SRT ) of the suspended biomass culture. RESULTS Five MFCs inoculated with activated sludge obtained from a municipal wastewater treatment plant were fed with a highly‐concentrated acetate solution (10 000 ppm COD ) and operated over two‐month tests in order to determine how SRT may influence the performances of the bio‐electrogenic cells. The MFC operated at SRTs of 2.5 days was found to outperform the other cells, operated at SRT of 1.4, 5.0, 7.4 and 10.0 days. In order to evaluate the possibility of using SRT as a manipulated parameter for the regulation of the operation of MFC , the SRT of the other MFCs was changed from their initial value up or down to 2.5 days. CONCLUSIONS As a result of the change in the SRT , production of electricity of the cells increased significantly in all cases, highlighting the relevance of SRT control in the optimization of the performances of MFCs . By operating at SRT 2.5 days, the current density was 4.2 A m −2 , the COD consumption rate was 1.53 g COD d −1 L −1 and the COD transformed by electrogenic microorganisms was estimated at 1.5%. © 2016 Society of Chemical Industry
Automatic Identification of Tinnitus Malingering Based on Overt and Covert Behavioral Responses During Psychoacoustic Testing (2022)

Abstract Tinnitus, or ringing in the ears, is a prevalent condition that imposes a substantial health and financial burden on the patient and to society. The diagnosis of tinnitus, like pain, relies on patient self-report. Subjective self-report measures can complicate the distinction between actual and fraudulent claims and obscure accurate severity assessments. In this study, we combined tablet-based self-directed hearing assessments with neural network classifiers to objectively determine tinnitus severity, and to differentiate participants with tinnitus (N=24) from a malingering cohort, who were instructed to feign an imagined tinnitus percept (N=28). We identified clear differences between the groups, both in their overt rating of tinnitus severity but also covert differences in their fingertip movement trajectories on the tablet surface as they performed the reporting assay. Using only 10 minutes of data, we achieved 81% accuracy classifying patients vs malingerers (ROC AUC=0.88) with leave-one-participant-out cross validation. Objective measurements of tinnitus will improve estimates of tinnitus prevalence and help to prioritize and direct funds for tinnitus compensation.
Tyrosines in the MUC1 Cytoplasmic Tail Modulate Transcription via the Extracellular Signal-Regulated Kinase 1/2 and Nuclear Factor-κB Pathways (2006)

Much of the ability of the MUC1 oncoprotein to foster tumorigenesis and tumor progression likely originates from the interaction of its cytoplasmic tail with proteins involved in oncogenic signaling. Many of these interactions are regulated by phosphorylation, as the cytoplasmic tail contains seven highly conserved tyrosines and several serine/threonine phosphorylation sites. We have developed a cell line-based model system to study the effects of tyrosine phosphorylation on MUC1 signaling, with particular emphasis on its effects on gene transcription. COS-7 cells, which lack endogenous MUC1, were stably infected with wild-type MUC1 or a MUC1 construct lacking all seven tyrosines (MUC1 Y0) and analyzed for effects on transcription mediated by the extracellular signal-regulated kinase 1/2 (ERK1/2) and nuclear factor-kappaB (NF-kappaB) pathways. COS.MUC1 Y0 cells showed heightened active ERK1/2 with increased activator protein-1 (AP-1) and signal transducer and activator of transcription 3 (STAT3) transcriptional activity; there was also a simultaneous decrease in NF-kappaB transcriptional activity and nuclear localization. These changes altered the phenotype of COS.MUC1 Y0 cells, as this line displayed increased invasion and enhanced [(3)H]thymidine incorporation. Analysis of the three lines also showed significant differences in their cell cycle profile and bromodeoxyuridine incorporation when the cells were serum starved. These data support the growing evidence that MUC1 is involved in transcriptional regulation and link MUC1 for the first time to the NF-kappaB pathway.
Differential Program Verification for Approximate Computing (2013)

Approximate computing is an emerging area for trading off the accuracy of an application for improved performance, lower energy costs, and tolerance to unreliable hardware. However, care has to be taken to ensure that the approximations do not cause significant divergence from the reference implementation. Previous research has proposed various metrics to guarantee several relaxed notions of safety for the design and verification of such approximate applications. However, current approximation verification approaches often lack in either precision or automation. On one end of the spectrum, type-based approaches lack precision, while on the other, proofs in interactive theorem provers require significant manual effort. In this work, we apply automated differential program verification (as implemented in SymDiff) for reasoning about approximations. We show that mutual summaries naturally express many relaxed specifications for approximations, and SMT-based checking and invariant inference can substantially automate the verification of such specifications. We demonstrate that the framework significantly improves automation compared to previous work on using Coq, and improves precision when compared to path-insensitive analysis. Our results indicate the feasibility of applying automated verification to the domain of approximate computing in a cost-effective manner.