gebhart/patrepeval huggingface dataset:
Dimeric anthracene-based mechanophore particles for damage precursor detection in reinforced epoxy matrix composites (2016)

The problem of catastrophic damage purveys in any material application, and minimizing its occurrence is paramount for general health and safety. We have successfully synthesized, characterized, and applied dimeric 9-anthracene carboxylic acid (Di-AC)-based mechanophore particles to form stress sensing epoxy matrix composites. As Di-AC had never been previously applied as a mechanophore and thermosets are rarely studied in mechanochemistry, this created an alternative avenue for study in the field. Under an applied stress, the cyclooctane-rings in the Di-AC particles reverted back to their fluorescent anthracene form, which linearly enhanced the overall fluorescence of the composite in response to the applied strain. The fluorescent signal further allowed for stress sensing in the elastic region of the stress–strain curve, which is considered to be a form of damage precursor detection. Overall, the incorporation of Di-AC to the epoxy matrix added much desired stress sensing and damage precursor detection capabilities with good retention of the material properties.
Enhanced DNA detection using a multiple pulse pumping scheme with time-gating (MPPTG) (2018)

Fluorescence signal enhancement induced by the binding of intercalators to DNA has been broadly utilized in various DNA detection methods. In most instances the increase in fluorescence intensity is associated with a concomitant increase of fluorescence lifetime. This increase of the fluorescence lifetime presents an additional opportunity to increase detection sensitivity. In this paper, we present a new approach to significantly enhance the sensitivity in detecting minute DNA concentrations. The approach is based on simultaneous use of time-gated detection and multi-pulse pumping. By using a calibrated burst of short pulses we greatly enhance the contribution of long-lived fluorescence species, thus enabling easy time-gated detection. Using a classic DNA intercalator - Ethidium Bromide (EtBr) - as an example with our novel multi-pulse pumping and time-gated detection technique, we were able to increase detection sensitivity over 70-fold with only 3 pulse excitation. This approach is generic and can be used with any analytical probe (exhibiting about 10 times change in lifetime) that shows an increase in fluorescence signal and fluorescence lifetime upon binding to a target.
A Novel Force Modeling Scheme for Needle Insertion Using Multiple Kalman Filters (2011)

In this paper, the interaction force between a surgical needle and soft tissue is studied. The force is modeled using a novel nonlinear dynamic model. Encouraged by the LuGre model for representing friction forces, the proposed model captures all stages of needle-tissue interaction, including puncture, cutting, and friction forces. An estimation algorithm for identifying the parameters of the model is presented. This online approach, which is based on sequential extended Kalman filtering, enables us to characterize the total contact force using an efficient mathematical model. The algorithm compares the axial force measured at the needle base with its expected value and then adapts the model parameters to represent the actual interaction force. While the nature of this problem is very complex, the use of multiple Kalman filters makes the system highly adaptable for capturing the force evolution during an interventional procedure in standard operating conditions. To evaluate the performance of our model, experiments were performed on artificial phantoms.
Depth-based Local Search Heuristics for Boolean Circuit Satisfiability (2010)

We propose a structure-exploiting heuristic for the justification-based stochastic local search (SLS) method CRSat for Boolean circuit satisfiability. Experimental evaluation shows that the proposed depth-based heuristic significantly improved the performance of CRSat on structural instances arising from industrial applications. A proof of probabilistically approximate completeness (PAC) of CRSat relies on the same kind of variable ordering as the one imposed by the depth-based heuristic, and hence provides a theoretical motivation for the heuristic. Furthermore, we compare the behavior of (depth-based) CRSat to that of the justification-based SLS method BC SLS driven by justification frontiers.
Simplified Tracking of a Soy Allergen in Processed Food Using a Monoclonal Antibody-Based Sandwich ELISA Targeting the Soybean 2S Albumin Gly m 8 (2019)

Soybean allergens in food samples are currently detected in most cases using enzyme-linked immunosorbent assays (ELISAs) based on antibodies raised against bulk soybean proteins or specifically targeting soybean trypsin inhibitor, conglycinin, or glycinin. The various commercial ELISAs lack standardized reference material, and the results are often inaccurate because the antibodies cross-react with proteins from other legumes. Furthermore, the isolation of allergenic proteins involves laborious denaturing extraction conditions. To tackle these challenges, we have developed a novel sandwich ELISA based on monoclonal antibodies raised against the soybean 2S albumin Gly m 8 and a recombinant Gly m 8 reference protein with native-analogous characteristics. The antibodies do not cross-react with other legume proteins, and the extraordinary stability and solubility of Gly m 8 allows it to be extracted even from complex matrices after processing. The Gly m 8 ELISA therefore achieves greater specificity and reproducibility than current ELISA tests.
Tracking and removal of suspended matter from underwater video images (2017)

We propose a method for obtaining clear underwater images by tracking the motion of suspended matter from video images captured in water and by separating the images into foreground and background. We assume that input images are the superposition of a foreground and a background, and constructed a transition model and the observation model. An input image is divided into patches and tracking of the foreground in each patch is performed while applying Kalman filter to separate the input images into the foreground and the background. From the result of the experiment using simulated images, we confirmed that the background images were successfully estimated and a region that was moving slowly was also recognized as a part of the background.
Purinergic Signaling in Oral Tissues (2022)

The role of the purinergic signal has been extensively investigated in many tissues and related organs, including the central and peripheral nervous systems as well as the gastrointestinal, cardiovascular, respiratory, renal, and immune systems. Less attention has been paid to the influence of purines in the oral cavity, which is the first part of the digestive apparatus and also acts as the body's first antimicrobial barrier. In this review, evidence is provided of the presence and possible physiological role of the purinergic system in the different structures forming the oral cavity including teeth, tongue, hard palate, and soft palate with their annexes such as taste buds, salivary glands, and nervous fibers innervating the oral structures. We also report findings on the involvement of the purinergic signal in pathological conditions affecting the oral apparatus such as Sjögren's syndrome or following irradiation for the treatment of head and neck cancer, and the use of experimental drugs interfering with the purine system to improve bone healing after damage. Further investigations are required to translate the results obtained so far into the clinical setting in order to pave the way for a wider application of purine-based treatments in oral diseases.
<scp><i>VPT</i></scp>‐like genes modulate <i>Rhizobium</i>–legume symbiosis and phosphorus adaptation (2023)

Although vacuolar phosphate transporters (VPTs) are essential for plant phosphorus adaptation, their role in Rhizobium-legume symbiosis is unclear. In this study, homologous genes of VPT1 (MtVPTs) were identified in Medicago truncatula to assess their roles in Rhizobium-legume symbiosis and phosphorus adaptation. MtVPT2 and MtVPT3 mainly positively responded to low and high phosphate, respectively. However, both mtvpt2 and mtvpt3 mutants displayed shoot phenotypes with high phosphate sensitivity and low phosphate tolerance. The root-to-shoot phosphate transfer efficiency was significantly enhanced in mtvpt3 but weakened in mtvpt2, accompanied by lower and higher root cytosolic inorganic phosphate (Pi) concentration, respectively. Low phosphate induced MtVPT2 and MtVPT3 expressions in nodules. MtVPT2 and MtVPT3 mutations markedly reduced the nodule number and nitrogenase activity under different phosphate conditions. Cytosolic Pi concentration in nodules was significantly lower in mtvpt2 and mtvpt3 than in the wildtype, especially in tissues near the base of nodules, probably due to inhibition of long-distance Pi transport and cytosolic Pi supply. Also, mtvpt2 and mtvpt3 could not maintain a stable cytosolic Pi level in the nodule fixation zone as the wildtype under low phosphate stress. These findings show that MtVPT2 and MtVPT3 modulate phosphorus adaptation and rhizobia-legume symbiosis, possibly by regulating long-distance Pi transport.
Rho Kinase (ROCK) Inhibitors (2007)

The Rho kinase (ROCK) isoforms, ROCK1 and ROCK2, were initially discovered as downstream targets of the small GTP-binding protein Rho. Because ROCKs mediate various important cellular functions such as cell shape, motility, secretion, proliferation, and gene expression, it is likely that this pathway will intersect with other signaling pathways known to contribute to cardiovascular disease. Indeed, ROCKs have already been implicated in the regulation of vascular tone, proliferation, inflammation, and oxidative stress. However, it is not entirely clear how ROCKs are regulated, what some of their downstream targets are, and whether ROCK1 and ROCK2 mediate different cellular functions. Clinically, inhibition of ROCK pathway is believed to contribute to some of the cardiovascular benefits of statin therapy that are independent of lipid lowering (ie, pleiotropic effects). To what extent ROCK activity is inhibited in patients on statin therapy is not known, but it may have important clinical implications. Indeed, several pharmaceutical companies are already actively engaged in the development of ROCK inhibitors as the next generation of therapeutic agents for cardiovascular disease because evidence from animal studies suggests the potential involvement of ROCK in hypertension and atherosclerosis.
Experimental Approach for Thermal Contact Resistance Estimation at the Glass / Metal Interface (2013)

An experimental device is designed and developed in order to estimate thermal conditions at the Glass / Metal contact interface. The device is made of two parts: the upper part contains the tool (piston) made of bronze and a heating device to raise the temperature of the piston to 700° C. The lower part is composed of a lead crucible and a glass sample. The assembly is provided with a heating system, an induction furnace of 6 kW for heating the glass up to 950° C. Both parts are put in contact through a mechanical system consisting of a pneumatic cylinder sliding on a column and a pump providing the required pressure in the enclosure. The developed experimental procedure has permitted the estimation of the Thermal Contact Resistance TCR using a developed measurement principle based on an inverse technique. The semi-transparent character of the glass has been taken into account by an additional radiative heat flux and an equivalent thermal conductivity. After the set-up tests, reproducibility experiments for a specific contact pressure have been carried out. Results shows a good repeatability of the registered and estimated parameters such as the piston surface temperature, heat flux density and TCR. The maximum dispersion of the estimated TCR doesn’t exceed 6%.Copyright © 2013 by ASME
Synthesis of a Lightweight Nanocomposite Based on Polyaniline 3D Hollow Spheres Integrated Milled Carbon Fibers for Efficient X-Band Microwave Absorption (2020)

In the present study, the milled carbon fiber (MCF) and conductive polyaniline (PANI) are impregnated in the epoxy matrix to synthesize a lightweight nanocomposite, providing efficient microwave absorption in the X band. The PANI 3D hollow spheres are uniquely synthesized by removing the polystyrene (PS) core structure of PS/PANI composites. The MCF and as-synthesized PANI hollow spheres are characterized by Raman spectroscopy, X-ray diffraction (XRD), and field emission scanning electron microscopy (FESEM). The FESEM analysis confirmed the formation of 3D hollow PANI conductive spheres, which exhibited numerous porosity and high roughness on PANI sphere surfaces. The XRD revealed that the size reduction of carbon fibers down to the micro level resulted into more graphitic carbon. The MCF- and PANI-impregnated epoxy nanocomposites are evaluated by reflectivity measurements for their microwave absorption capabilities, exclusively in the X band. The correlation of the results shows that the ratio of MCF and PANI fillers in the epoxy matrix can be customized to obtain the desired microwave absorption performance of the synthesized nanocomposite. A maximum absorption value of −49.3 dB (99.998% absorption) as well as 1.7 GHz −10 dB effective bandwidth is achieved using a nanocomposite sample of 1.8 mm thickness comprising 4 wt % MCF and 1 wt % PANI filler loadings. The strong microwave absorption in the present situation for a very thin sample using just 5% of the total filler results into quite a lightweight composite, which basically originates from the electric/dipolar polarization in the interfacial polarization dominant in the micron length fibers and hollow 3D PANI spherical structures. The hollow 3D morphology here improves the impedance matching of the resulting nanocomposite sample due to multiple reflections and scattering of EM waves inside the structure, which substantially increases the reflection loss of EM waves in the specified frequency band. The novelty of this work lies in synthesizing the PANI/MCF-based filler for the first time and using it to develop a lightweight nanocomposite, which is found to be quite an efficient microwave absorber, especially for X band applications.
Hematoma location and morphology of anticoagulation-associated intracerebral hemorrhage (2019)

The overrepresentation of cerebellar ICH location and intraventricular extension in OAC-ICH might have mechanistic relevance for the underlying arteriopathy, pathophysiology, or bleeding pattern of OAC-ICH, and should be investigated further.
On the Two-User MISO Interference Channel With Single-User Decoding: Impact of Imperfect CSIT and Channel Dimension Reduction (2019)

This paper examines the Rayleigh fading multiple-input single-output interference channel with single-user decoding and limited channel state information (CSI) feedback. Its contribution is twofold. First, the achievable rate-region with imperfect CSI at the transmitters due to channel quantization errors is analyzed for the two-user case. An analytically tractable inner bound on that region is derived, which provides insights into the problem. Similarly to the case of perfect CSI at the transmitters, it can be shown that beamforming constitutes an optimal strategy for achieving the boundary points of the inner bound. Second, we present a novel CSI feedback scheme that reduces the cross-link CSI feedback overhead, and enhances throughput for any rate-limited feedback scheme. This feedback reduction is crucial when control channels for sharing information between transmitters and unintended receivers are rate limited. A distinguishing feature of the proposed scheme is that feedback is taken into account already at the channel estimation stage. While maintaining a high array gain in the direct channel towards the intended user, the scheme induces an effective low-dimensional cross-link channel, which can be quantized more accurately than the full-dimensional channel. This eventually leads to enhanced performance while maintaining a low CSI feedback overhead. Finally, the proposed feedback scheme is extended to the case of N>2 users and shown to provide a significant reduction in CSI feedback overhead in a practically oriented setting.
Particulate gold as an anti‐inflammatory mediator in bone allograft—An animal study (2010)

Morselized allograft is widely used when increased bone stock is needed in implant surgery. Gold ions liberated from metallic gold surfaces act in an anti-inflammatory manner by inhibiting cellular NF-κB-DNA binding and suppressing I-κ B-kinase activation. This study investigated the effect of 45-63 μm sized gold particles mixed in morselized allograft. It was hypothesized that bio-released gold ions would influence allograft reabsorption, increase mechanical stability, and further stimulate osseointegration. A pair of 10 mm long implants surrounded by a 2.5-mm gap was inserted in proximal part of each humerus in 10 sheep. Each gap was filled with morselized allograft with 1.29 mg gold particles or nothing. Observation time was 12 weeks. The gold ion liberation was visualized by autometallographic tracing and showed liberation of gold ions. Biomechanical push-out tests and stereological histomorphometric analyses showed no statistically significant differences in the two groups. Although particulate gold was primarily observed surrounded by bone marrow tissue, no obvious clinically relevant short-term effects could be measured using gold as an anti-inflammatory mediator. These findings show that the released gold ions have only influenced cells adjacent to the particles without influencing the fixation and illustrates gold ions' limited field of effect. We suggest a new design for orthopedic implants by introducing gold dots on the prosthesis surface. This aims at suppressing the inflammatory foci along the implant-bone zone and reduces the risk of chronic inflammation before aseptic loosening without affecting bone remodeling. This implant model will be investigated in further studies.
Double Knockouts Reveal that Protein Tyrosine Phosphatase 1B Is a Physiological Target of Calpain-1 in Platelets (2007)

Calpains are ubiquitous calcium-regulated cysteine proteases that have been implicated in cytoskeletal organization, cell proliferation, apoptosis, cell motility, and hemostasis. Gene targeting was used to evaluate the physiological function of mouse calpain-1 and establish that its inactivation results in reduced platelet aggregation and clot retraction potentially by causing dephosphorylation of platelet proteins. Here, we report that calpain-1 null (Capn1-/-) platelets accumulate protein tyrosine phosphatase 1B (PTP1B), which correlates with enhanced tyrosine phosphatase activity and dephosphorylation of multiple substrates. Treatment of Capn1-/- platelets with bis(N,N-dimethylhydroxamido)hydroxooxovanadate, an inhibitor of tyrosine phosphatases, corrected the aggregation defect and recovered impaired clot retraction. More importantly, platelet aggregation, clot retraction, and tyrosine dephosphorylation defects were rescued in the double knockout mice lacking both calpain-1 and PTP1B. Further evaluation of mutant mice by the ferric chloride-induced arterial injury model suggests that the Capn1-/- mice are relatively resistant to thrombosis in vivo. Together, our results demonstrate that PTP1B is a physiological target of calpain-1 and suggest that a similar mechanism may regulate calpain-1-mediated tyrosine dephosphorylation in other cells.
A FAST AND ACCURATE ALGORITHM FOR COMPARATIVE ANALYSIS OF METABOLIC PATHWAYS (2009)

Our software and the source code in C programming language is available at http://bioinformatics.cise.ufl.edu/pal.html.
Hearing Vital Signs: Mobile Audiometry in the Emergency Department for Evaluation of Sudden Hearing Loss (2020)

Emergency departments (EDs) are a common location for patients to present with sudden hearing loss (SHL). Unfortunately, high-quality, rapid quantitative measurement of hearing loss is challenging. Herein, we aim to evaluate the accuracy of tablet-based audiometry in patients complaining of SHL. Prospective tablet-based testing was completed in the ED in patients complaining of SHL. Air conduction thresholds (ACTs) obtained via tablet-based audiometry were compared to same-day measurements with a clinical-grade audiometer. Hearing loss (HL) was defined as >20 dB ACT for any frequency. In participant-level analysis, 30+ dB HL in 3 consecutive frequencies was used to define SHL. In the ED, mobile audiogram ACTs were within 5 dB (77%) and 10 dB (89.6%) of those determined by conventional audiometry. The sensitivity and specificity for mobile audiometry to detect 3 or more consecutive thresholds with 30+ dB HL were 100% and 62.5%, respectively. Findings have implications for increasing access to high-quality audiometry.
DECchip 21066: the Alpha AXP chip for cost-focused systems (2002)

The DECchip 21066 microprocessor is the first Alpha AXP architecture microprocessor to target cost-focused system applications and the second in a family of chips to implement the Alpha AXP architecture. The 21066 is a 0.675-micron, CMOS-based superscalar, super-pipelined processor using dual instruction issue. It incorporates a high level of system integration to provide best-in-class system performance for low-cost system applications. The 21066 integrates on-chip fully pipelined integer and floating-point processors, a high-bandwidth memory controller, an industry-standard Peripheral Component Interconnect (PCI) I/O controller, graphics-assisting hardware, internal instruction and data caches, and an external cache controller. This paper discusses the tradeoffs and results of the design, verification, and implementation of the 21066.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Beery VMI and brain volumetric relations in autism spectrum disorder. (2019)

Although diminished proficiency on tasks that require visual-motor integration (VMI) has been reported in individuals with autism spectrum disorder (ASD), very few studies have examined the association between VMI performance and neuroanatomical regions of interest (ROI) involved in motor and perceptual functioning. To address these issues, the current study included an all-male sample of 41 ASD (ages 3-23 years) and 27 typically developing (TD) participants (ages 5-26 years) who completed the Beery-Buktenica Developmental Test of Visual-Motor Integration (Beery VMI) as part of a comprehensive neuropsychological battery. All participants underwent 3.0 T magnetic resonance imaging (MRI) with image quantification (FreeSurfer software v5.3). The groups were statistically matched on age, handedness, and intracranial volume (ICV). ASD participants performed significantly lower on VMI and IQ measures compared with the TD group. VMI performance was significantly correlated with FSIQ and PIQ in the TD group only. No pre-defined neuroanatomical ROIs were significantly different between groups. Significant correlations were observed in the TD group between VMI and total precentral gyrus gray matter volume (<i>r</i> = .51, <i>p</i> = .006) and total frontal lobe gray matter volume (<i>r</i> = .46, <i>p</i> = .017). There were no significant ROI correlations with Beery VMI performance in ASD participants. At the group level, despite ASD participants exhibiting reduced visuomotor abilities, no systematic relation with motor or sensory-perceptual ROIs was observed. In the TD group, results were consistent with the putative role of the precentral gyrus in motor control along with frontal involvement in planning, organization, and execution monitoring, all essential for VMI performance. Given that similar associations between VMI and ROIs were not observed in those with ASD, neurodevelopment in ASD group participants may not follow homogenous patterns making correlations in these brain regions unlikely to be observed.