gebhart/patrepeval huggingface dataset:
The α10 helix of DevR, the Mycobacterium tuberculosis dormancy response regulator, regulates its DNA binding and activity (2016)

The crystal structures of several bacterial response regulators provide insight into the various interdomain molecular interactions potentially involved in maintaining their 'active' or 'inactive' states. However, the requirement of high concentrations of protein, an optimal pH and ionic strength buffers during crystallization may result in a structure somewhat different from that observed in solution. Therefore, functional assessment of the physiological relevance of the crystal structure data is imperative. DevR/DosR dormancy regulator of Mycobacterium tuberculosis (Mtb) belongs to the NarL subfamily of response regulators. The crystal structure of unphosphorylated DevR revealed that it forms a dimer through the α5/α6 interface. It was proposed that phosphorylation may trigger extensive structural rearrangements in DevR that culminate in the formation of a DNA-binding competent dimeric species via α10-α10 helix interactions. The α10 helix-deleted DevR protein (DevR∆α10 ) was hyperphosphorylated but defective with respect to in vitro DNA binding. Biophysical characterization reveals that DevR∆α10 has an open but less stable conformation. The combined cross-linking and DNA-binding data demonstrate that the α10 helix is essential for the formation and stabilization of the DNA-binding proficient DevR structure in both the phosphorylated and unphosphorylated states. Genetic studies establish that Mtb strains expressing DevR∆α10 are defective with respect to dormancy regulon expression under hypoxia. The present study highlights the indispensable role of the α10 helix in DevR activation and function under hypoxia and establishes the α10-α10 helix interface as a novel target for developing inhibitors against DevR, a key regulator of hypoxia-triggered dormancy.
Resolving Cell Population Heterogeneity: Real-Time PCR for Simultaneous Multiplexed Gene Detection in Multiple Single-Cell Samples (2009)

Decoding the complexity of multicellular organisms requires analytical procedures to overcome the limitations of averaged measurements of cell populations, which obscure inherent cell-cell heterogeneity and restrict the ability to distinguish between the responses of individual cells within a sample. For example, defining the timing, magnitude and the coordination of cytokine responses in single cells is critical for understanding the development of effective immunity. While approaches to measure gene expression from single cells have been reported, the absolute performance of these techniques has been difficult to assess, which likely has limited their wider application. We describe a straightforward method for simultaneously measuring the expression of multiple genes in a multitude of single-cell samples using flow cytometry, parallel cDNA synthesis, and quantification by real-time PCR. We thoroughly assess the performance of the technique using mRNA and DNA standards and cell samples, and demonstrate a detection sensitivity of approximately 30 mRNA molecules per cell, and a fractional error of 15%. Using this method, we expose unexpected heterogeneity in the expression of 5 immune-related genes in sets of single macrophages activated by different microbial stimuli. Further, our analyses reveal that the expression of one 'pro-inflammatory' cytokine is not predictive of the expression of another 'pro-inflammatory' cytokine within the same cell. These findings demonstrate that single-cell approaches are essential for studying coordinated gene expression in cell populations, and this generic and easy-to-use quantitative method is applicable in other areas in biology aimed at understanding the regulation of cellular responses.
A longitudinal analysis of hepatitis C virus replication following liver transplantation (1996)

Gane, E. J.; Naoumov, N. V.; Qian, K. P.; Mondelli, M. U.; Maertens, G.; Portmann, B. C.; Lau, J. Y.N.; Williams, R.
The color stability of maxillofacial silicones: A systematic review and meta analysis (2021)

Although there has been extensive amount of research in this field, an ideal maxillofacial silicone exhibiting good color stability in various human and environmental aging conditions is yet to be identified. Human and environmental aging conditions have an adverse effect on the color stability and addition of TiO<sub>2</sub> nano particle seems to improve the same.
A Novel Transparent Cross-Linked Poly(methyl methacrylate)-Based Copolymer with Enhanced Mechanical, Thermal, and Flame-Retardant Properties (2014)

A novel cross-linked poly(methyl methacrylate) (PMMA)-based copolymer was first synthesized by bulk copolymerization of methyl methacrylate (MMA) and 1-oxo-2,6,7-trioxa-1-phosphabicyclo[2.2.2]octane-4-acrylate (PEPAA) at low temperature (80 °C), which is a facile and green method. The structure of PEPAA was confirmed by FTIR, 1H NMR, and 31P NMR. The morphology and structure of copolymers were characterized using FTIR and SEM. Due to the chain transfer during copolymerization, a cross-linked network is successfully introduced into the copolymers and the gel fraction increases as the PEPAA content increases, as evinced by the results from Soxhlet extraction and DMA. The copolymers exhibit relatively high transparency and significant improvements to the mechanical properties, thermal properties, and fire retardancy when compared to PMMA. From the mechanism analysis, the cross-linked network plays a key role in the improvements to the mechanical properties and thermal properties. For enhanced fire retardancy, char formation during degradation caused by PEPAA is the main factor.
High Hydrostatic Pressure Effects on Perpendicular Transport in GaAs–AlAs Superlattices (1993)

We report perpendicular transport measurement on a series of GaAs-AlAs superlattices in the presence of applied hydrostatic pressure up to 11Kbar. The calculation of the minibands widths and their relative position was performed taking into account a K.P model, which allowed the determination of the direct or indirect characteristic for each sample. Considering the relative fast rate in energy (approximately 12meV/Kbar) of the Γ miniband relatively to the X states we interpreted the pressure effects with a good qualitative agreement.
BoilerModel: a qualitative model-based reasoning system implemented in Ada (1991)

Effective, inexpensive, and realistic on-going training is required to keep all Naval personnel proficient in their fields. Nowhere is this more true than in steam propulsion engineering plants. The complex systems of valves, piping, and components require continual refresher for watchstanders to perform their jobs safely. BoilerModel is a qualitative expert system designed using model-based reasoning principles and implemented in Ada. It accurately models a 1200 psi D-type boiler and its associated peripherals. The use of fundamental intra-component relationships (first principles) and constraint propagation result in compact code because there is no need for the extensive rule base found in conventional expert systems. Implementation in Ada permits the use of concurrent tasking to simulate simultaneous valve propagation found in real-world boiler systems. Additionally Ada's portability allows BoilerModel to be compiled and run on virtually any machine, thereby making it an affordable and attractive complement to shipboard engineering training.
Chemical and Morphological Changes of Historical Lead Objects as a Result of the Use of Electrolytic Reduction as a Stabilization Treatment (2006)

This paper focuses on the evaluation of the treatment related to chemical and morphological changes of corroded lead artifacts when using electrolytic reduction as a stabilization method. Synchrotron radiation X-ray diffraction and X-ray photoelectron spectroscopy were used to study the chemical changes of the corrosion layer and on the top nanometer of surface, respectively. Neutron tomography and scanning electron microscopy were used to visualize potential morphological changes on millimeter and micrometer level, respectively. The results of this study have shown that electrolytic reduction is a reliable way to stabilize and conserve active corroded lead artifacts. The corrosion products are actually converted into metallic lead, while the morphological changes due to the treatment are limited.
Plausible Proxy Mining With Credibility for Unsupervised Person Re-Identification (2022)

One effective way to address unsupervised person re-identification is to use a clustering-based contrastive learning approach. Existing state-of-the-art methods adopt clustering algorithms ( <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">e.g.</i> , DBSCAN) and camera ID information to divide all person images into several camera-aware proxies. Then, for each person image, the extracted feature representation is pulled closer to the centroids of its pseudo-positive proxies (the proxies that share the same pseudo-identity label with this image) and pushed away from the centroids of other pseudo-negative proxies (the proxies that share the different pseudo-identity label with this image). However, the quality of the proxy centroid is significantly affected by the proxy impurity issue and thus deteriorates the learned feature representations. On the premise that we cannot introduce superior supervision signals by thoroughly solving the proxy impurity issue, for a person image, identifying its plausible proxies: the pseudo-negative proxies which potentially include its wrongly-clustered instances (the instances with the same ground-truth identity with this image), and further fixing the resulted incorrect supervision signals become an urgent and challenging problem. This paper proposes a simple yet effective approach to address this problem. With a given image, our method can effectively locate its plausible proxies. Then we introduce credibility to measure how much we should treat the centroid of each mined plausible proxy as a positive supervision signal rather than entirely negative. Extensive experiments on three widely-used person re-ID datasets validate the effectiveness of our proposed approach. Codes will be available at: <uri xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/Dingyuan-Zheng/PPCL</uri> .
CipA ofAcinetobacter baumanniiIs a Novel Plasminogen Binding and Complement Inhibitory Protein (2015)

Acinetobacter baumannii is an emerging opportunistic pathogen, responsible for up to 10% of gram-negative, nosocomial infections. The global increase of multidrug-resistant and pan-resistant Acinetobacter isolates presents clinicians with formidable challenges. To establish a persistent infection,A. baumannii must overcome the detrimental effects of complement as the first line of defense against invading microorganisms. However, the immune evasion principles underlying serum resistance inA. baumannii remain elusive. Here, we identified a novel plasminogen-binding protein, termed CipA. Bound plasminogen, upon conversion to active plasmin, degraded fibrinogen and complement C3b and contributed to serum resistance. Furthermore, CipA directly inhibited the alternative pathway of complement in vitro, irrespective of its ability to bind plasminogen. A CipA-deficient mutant was efficiently killed by human serum and showed a defect in the penetration of endothelial monolayers, demonstrating that CipA is a novel multifunctional protein that contributes to the pathogenesis ofA. baumannii.
Measuring Structural and Electronic Effects on Keto–Enol Equilibrium in 1,3-Dicarbonyl Compounds (2016)

Nuclear magnetic resonance (NMR) spectroscopy is an integral part of the undergraduate chemistry curriculum. In addition to structure determination, NMR spectroscopy is used to analyze chemical reactions and equilibria in situ. Determination of the position of equilibria is well-suited to NMR analysis in the undergraduate laboratory as an extension of peak identification and signal integration, and the determination of keto–enol equilibrium remains a popular undergraduate laboratory experiment. Several factors affect the position of keto–enol equilibrium, defined here as Ke/k = [enol]/[keto], including structure (steric bulk, conjugation, electron-withdrawing/donating groups, resonance), temperature, and solvent. A judiciously selected set of compounds that have a common 1,3-dicarbonyl moiety with progressively changing ligands at the 1 and 3 positions is presented. This array allows students to investigate structure–function relationships that affect keto–enol equilibrium in a cumulative fashion and affords instructors a broad selection of compounds for study in both introductory and advanced laboratory courses using a variety of pedagogic approaches.
A global database of lake surface temperatures collected by in situ and satellite methods from 1985–2009 (2015)

Global environmental change has influenced lake surface temperatures, a key driver of ecosystem structure and function. Recent studies have suggested significant warming of water temperatures in individual lakes across many different regions around the world. However, the spatial and temporal coherence associated with the magnitude of these trends remains unclear. Thus, a global data set of water temperature is required to understand and synthesize global, long-term trends in surface water temperatures of inland bodies of water. We assembled a database of summer lake surface temperatures for 291 lakes collected in situ and/or by satellites for the period 1985-2009. In addition, corresponding climatic drivers (air temperatures, solar radiation, and cloud cover) and geomorphometric characteristics (latitude, longitude, elevation, lake surface area, maximum depth, mean depth, and volume) that influence lake surface temperatures were compiled for each lake. This unique dataset offers an invaluable baseline perspective on global-scale lake thermal conditions as environmental change continues.
Estudio y tratamiento en 51 casos de membranas neovasculares subretinianas secundarias a degeneración macular asociada a la edad (1996)

Analizamos los signos oftalmoscopicos y angiograficos, asi como los resultados tras el tratamiento con laser de argon monocromatico verde de 51 casos de membranas neovasculares subretinianas (M. N.S.R.) secundarias a degeneracion macular asociada a la edad (D. M.A.E.) en un periodo de tres anos. De los 51 casos, 38 (74.5%) eran M.N.S.R. Atipicas u ocultas y 13 (25.5%) tipicas, con una relacion, pues, de 3/1. La agudeza visual (A. V.) oscilaba entre 0.8 y 0.01, con una A.V. Media de 0.1468: t0.204 en las atipicas y 0.2785: t0.329 en las tipicas (P<0.3636). De todos los signos oftalmoscopicos estudiados, en la comparacion de ambos tipos de M.N.S.R. Solo la hemorragia subretiniana perilesional mostro una diferencia estadisticamente significativa (P<0.00142) entre ambas, apareciendo en el 61.5% de las M.N.S.R. Tipicas. 43 M.N.S.R. Fueron sometidas a tratamiento con laser de argon, 12 (92.3%) tipicas y 31 (81.6%) atipicas. Se realizo la tecnica in-situ en 22 casos (43.1%) y la tecnica de Coscas en 21 (41.2%). Los resultados que obtuvimos fueron de ablacion en el 50% de las M.N.S.R. Tipicas y en el 58.1 de las atipicas, de persistencias de la lesion en el 50% de las tipicas y en el 38.7% de las atipicas, y de recurrencia en el 3.2% de las atipicas. La disminucion de A.V. Tras el tratamiento, aunque existio, no fue significativa (nivel de significacion = 0.194).
First in human implantation of the mechanical expanding Lotus® valve in degenerated surgical valves in mitral position (2015)

This study demonstrates for the first time the feasibility of transapical Lotus® Valve implantation in degenerated mitral bioprostheses. The controlled mechanical Lotus® valve expansion with remarkably stable hemodynamics throughout the procedure offers a new and valuable treatment option.
Intraoperative imaging device for glioblastoma multiforme surgery: Review of Raman‐based intraoperative imaging and introduction of a novel handheld probe technology (2021)

Abstract Glioblastoma multiforme (GBM) is a malignant primary brain tumor with poor prognosis. Degree of resection contributes greatly to improved prognosis. Review of the literature for intraoperative hand‐held Raman probes technology to enhance maximal gross total resection was conducted. Additionally, we introduce study of Raman shift of graphene, as the biosensing interface with tumor, to enhance the current model of hand‐held probes. Retrospective analysis of the literature was conducted using pubMed database to delineate various intraoperative hand‐held probes with a particular focus on Raman spectroscopic (RS) technology in neuronal tissue. Summary of our group's recent publications in this area is included. Literature review demonstrates ability of Raman Spectroscopy (RS) to distinguish normal glial tissue from that of pathologic tissue (GBM) with great accuracy, sensitivity, and specificity. Furthermore, addition of nano sensors, such as gold particles, has proven successful in enhancing the detection of tumor and normal brain interface. Our work has previously demonstrated graphene as a feasible biosensor to be used in conjunction with RS in detecting GBM cells. Intra operative handheld Raman probes (RP) have advanced overtime as an additive tool to help surgeons clearly distinguish tumor and normal brain interface. Optimal biosensors can significantly enhance the detection of such margins, thereby, aiding in more precise gross total resection.
Inkjet-printed paper-based SERS dipsticks and swabs for trace chemical detection (2012)

We demonstrate a paper-based surface swab and lateral-flow dipstick that includes an inkjet-printed surface-enhanced Raman spectroscopy (SERS) substrate for analyte detection. Due to capillary-action wicking of cellulose, the paper dipstick enables extremely simple and pump-free loading of liquid samples into the detection device, and in addition provides inherent analyte concentration within the detection volume. Furthermore, the flexible nature of the paper-based SERS device also enables it to act as a swab to collect analyte molecules directly from a large-area surface; the collected analyte molecules can then be focused into a small-volume SERS-active region by lateral-flow concentration. These capabilities are unseen in today's SERS substrates and microfluidic SERS devices. Using these novel lateral-flow paper SERS devices, we achieved detection limits as low as 95 fg of Rhodamine 6G (R6G), 413 pg of the organophosphate malathion, 9 ng of heroin, and 15 ng of cocaine. Moreover, the measurements show that the technique is quantitative and is repeatable across multiple swabs and dipsticks. The results reported here may lead to ultra-low-cost portable applications in trace chemical detection.
Circuitry uniking opiate-sensitive nociceptive modulatory systems in rostral ventromedial medulla, perlaoueductal gray and spinal cord (1990)

Medullary off- and on-cells have been proposed to inhibit and facilitate, respectively, nociceptive transmission. Upon hearing the tail in lightly anesthetized rats, the tail flick (TF) reflex occurs only after off-cells decrease and on-cells increase their activity. Dipyrone (DIP) microinjection (100 μg/0.5 μl) into the periaqueductal gray (PAG) caused retardation in the off-cell pause, on-cell burst and corresponding TF. This effect was partly reverted by naloxone given i.v. (1 mg/kg) or microinjected into PAG (5 μg/0.5 μl). These results suggest that endogenous opioids are partly responsible for the central antinociceptive action of DIP, and that such action involves medullary off- and on-cells.
Two different modes of cyclin Clb2 proteolysis during mitosis in Saccharomyces cerevisiae (2000)

Sister chromatid separation and mitotic exit are triggered by the anaphase-promoting complex (APC/C) which is a multi-subunit ubiquitin ligase required for proteolytic degradation of various target proteins. Cdc20 and Cdh1 are substrate-specific activators of the APC/C. It was previously proposed that Cdh1 is essential for proteolysis of the yeast mitotic cyclin Clb2. We show that Clb2 proteolysis is triggered by two different modes during mitosis. A fraction of Clb2 is degraded during anaphase in the absence of Cdh1. However, a second fraction of Clb2 remains stable during anaphase and is degraded in a Cdh1-dependent manner as cells exit from mitosis. Most of cyclin Clb3 is degraded independently of Cdh1. Our data imply that degradation of mitotic cyclins is initiated by a Cdh1-independent mechanism.
2210 A Study on Alternative Tangential Force Modelling for High Speed Railway Vehicles (2005)

The modeling methods as dynamics analysis was considered about the wheel /rail tangential force which affects various running ability of high speed railway vehicles, such as running stability, comfort, curving negotiation, and safety to derailment. In the case of a high speed railway, the driving force which balances to the train resistance is needed, even when running at the constant speed. So the traction force and the spin, in the quasi- state running condition, influence the saturation characteristics of wheel/rail tangential force, and generate the error which cannot be disregarded to lateral oscillation analysis of driven vehicles. Two alternative models in consideration of traction force and the spin of wheel /rail tangential force are devised. As a result of verifying by comparison with a real vehicle run, the necessity of raising the accuracy of analysis further was accepted. Nevertheless, the second method would be fully equal to use as a good approximation.
Nuisance Regression of High-Frequency Functional Magnetic Resonance Imaging Data: Denoising Can Be Noisy (2016)

Recently, emerging studies have demonstrated the existence of brain resting-state spontaneous activity at frequencies higher than the conventional 0.1 Hz. A few groups utilizing accelerated acquisitions have reported persisting signals beyond 1 Hz, which seems too high to be accommodated by the sluggish hemodynamic process underpinning blood oxygen level-dependent contrasts (the upper limit of the canonical model is ∼0.3 Hz). It is thus questionable whether the observed high-frequency (HF) functional connectivity originates from alternative mechanisms (e.g., inflow effects, proton density changes in or near activated neural tissue) or rather is artificially introduced by improper preprocessing operations. In this study, we examined the influence of a common preprocessing step-whole-band linear nuisance regression (WB-LNR)-on resting-state functional connectivity (RSFC) and demonstrated through both simulation and analysis of real dataset that WB-LNR can introduce spurious network structures into the HF bands of functional magnetic resonance imaging (fMRI) signals. Findings of present study call into question whether published observations on HF-RSFC are partly attributable to improper data preprocessing instead of actual neural activities.