gebhart/patrepeval huggingface dataset:
Hydrolysis of poly(hydroxybutyrate‐co‐hydroxyvalerate) nanoparticles (2012)

Abstract Poly(hydroxybutyrate‐ co ‐hydroxyvalerate) (PHBV) is a natural polyester known for its biocompatibility and biodegradability. The hydrolysis of PHBV nanoparticles (90–150 nm) and microparticles (33–58 µm) was investigated. Particles were formulated from preformed polymer(s) by miniemulsification/solvent evaporation technique to obtain nanoparticles or by emulsification/solvent evaporation technique to obtain microparticles. The morphology of the nanoparticles was studied by Field Emission Gun‐Scanning Electron Microscopy (FEG‐SEM). The kinetics of PHBV degradation was followed by gel permeation chromatography. After storage of PHBV nanoparticles for 25 days at 37 °C, the M n and M w of PHBV was reduced up to 85 and 80%, respectively. PHBV nanoparticles stored at 4 °C presented a much lower molecular weight reduction. © 2012 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013
Microwave-Assisted Green Solid-Phase Peptide Synthesis Using γ-Valerolactone (GVL) as Solvent (2018)

The increasing demand for synthetic peptides in various research fields raises a challenge, namely, the development of greener methods for their preparation. Here we report on an ecofriendly solid-phase peptide synthesis (SPPS) methodology. Substitution of the hazardous solvent DMF by the biomass-derived organic solvent γ-valerolactone (GVL), together with the application of microwave-assisted automated SPPS, allowed the synthesis of peptides with a wide range of lengths and high purity using polystyrene- and polyethylene-glycol-based resins. The yields achieved were comparable to those obtained with standard methodologies. To date, this is the greenest approach reported in terms of the solvent used, waste generated, and energy efficiency.
Mobile Ultrasound Plane Wave Beamforming on iPhone or iPad using Metal- based GPU Processing (2015)

Mobile and cost effective ultrasound devices are being used in point of care scenarios or the drama room. To reduce the costs of such devices we already presented the possibilities of consumer devices like the Apple iPad for full signal processing of raw data for ultrasound image generation. Using technologies like plane wave imaging to generate a full image with only one excitation/reception event the acquisition times and power consumption of ultrasound imaging can be reduced for low power mobile devices based on consumer electronics realizing the transition from FPGA or ASIC based beamforming into more flexible software beamforming. The massive parallel beamforming processing can be done with the Apple framework “Metal” for advanced graphics and general purpose GPU processing for the iOS platform. We were able to integrate the beamforming reconstruction into our mobile ultrasound processing application with imaging rates up to 70 Hz on iPad Air 2 hardware.
Transmembrane topography of the nicotinic acetylcholine receptor: immunochemical tests contadict theoretical predictions based on hydrophobicity profiles (1986)

In our preceding paper [Ratnam, M., Sargent, P. B., Sarin, V., Fox, J. L., Le Nguyen, D., Rivier, J., Criado, M., & Lindstrom, J. (1986) Biochemistry (preceding paper in this issue)], we presented results from peptide mapping studies of purified subunits of the Torpedo acetylcholine receptor which suggested that the sequence beta 429-441 is on the cytoplasmic surface of the receptor. Since this finding contradicts earlier theoretical models of the transmembrane structure of the receptor, which placed this sequence of the beta subunit on the extracellular surface, we investigated the location of the corresponding sequence (389-408) and adjacent sequences of the alpha subunit by a more direct approach. We synthesized peptides including the sequences alpha 330-346, alpha 349-364, alpha 360-378, alpha 379-385, and alpha 389-408 and shorter parts of these peptides. These peptides corresponded to a highly immunogenic region, and by using 125I-labeled peptides as antigens, we were able to detect in our library of monoclonal antibodies to alpha subunits between two and six which bound specifically to each of these peptides, except alpha 389-408. We obtained antibodies specific for alpha 389-408 both from antisera against the denatured alpha subunit and from antisera made against the peptide. These antibodies were specific to alpha 389-396. In binding assays, antibodies specific for all of these five peptides bound to receptor-rich membrane vesicles only after permeabilization of the vesicles to permit access of the antibodies to the cytoplasmic surface of the receptors, suggesting that the receptor sequences which bound these antibodies were located on the intracellular side of the membrane. Electron microscopy using colloidal gold to visualize the bound antibodies was used to conclusively demonstrate that all of these sequences are exposed on the cytoplasmic surface of the receptor. These results, along with our previous demonstration that the C-terminal 10 amino acids of each subunit are exposed on the cytoplasmic surface, show that the hydrophobic domain M4 (alpha 409-426), previously predicted from hydropathy profiles to be transmembranous, does not, in fact, cross the membrane. Further, these results show that the putative amphipathic transmembrane domain M5 (alpha 364-399) also does not cross the membrane. Our results thus indicate that the transmembrane topology of a membrane protein cannot be deduced strictly from the hydropathy profile of its primary amino acid sequence. We present a model for the transmembrane orientation of receptor subunit polypeptide chains which is consistent with current data.
Learning to Separate Domains in Generalized Zero-Shot and Open Set Learning: a probabilistic perspective (2018)

This paper studies the problem of domain division which aims to segment instances drawn from different probabilistic distributions. Such a problem exists in many previous recognition tasks, such as Open Set Learning (OSL) and Generalized Zero-Shot Learning (G-ZSL), where the testing instances come from either seen or novel/unseen classes of different probabilistic distributions. Previous works focused on either only calibrating the confident prediction of classifiers of seen classes (W-SVM), or taking unseen classes as outliers. In contrast, this paper proposes a probabilistic way of directly estimating and fine-tuning the decision boundary between seen and novel/unseen classes. In particular, we propose a domain division algorithm of learning to split the testing instances into known, unknown and uncertain domains, and then conduct recognize tasks in each domain. Two statistical tools, namely, bootstrapping and Kolmogorov-Smirnov (K-S) Test, for the first time, are introduced to discover and fine-tune the decision boundary of each domain. Critically, the uncertain domain is newly introduced in our framework to adopt those instances whose domain cannot be predicted confidently. Extensive experiments demonstrate that our approach achieved the state-of-the-art performance on OSL and G-ZSL benchmarks.
A biomechanical study of the meniscofemoral ligaments and their contribution to contact pressure reduction in the knee (2008)

The aim of this study was to test the hypothesis that the meniscofemoral ligaments (MFLs) of the human knee assist the lateral meniscal function in reducing tibiofemoral contact pressure. Five human cadaveric knee joints were loaded in axial compression in extension using a 4-degree of freedom rig in a universal materials testing machine. Contact pressures pre- and post-sectioning of the MFLs were measured using pressure sensitive film. Sectioning the MFLs increased the contact pressure significantly in the joints for two of the four measures. In addition to their known function in assisting the posterior cruciate ligament (PCL) to resist tibiofemoral posterior drawer, the MFLs also have a significant role in reducing contact stresses in the lateral compartment. Their retention in PCL and meniscal surgery is therefore to be advised.
An Efficient Competition-based Skip Motion Vector Coding Scheme Based on the Context-based Adaptive Choice of Motion Vector Predictors (2010)

The demand for high quality of multimedia applications, which far surpasses the rapid evolution of transmission and storage technologies, makes better compression coding capabilities ever increasingly more important. In order to provide enhanced video coding performance, this paper proposes an efficient competition-based motion vector coding scheme. The proposed algorithm adaptively forms the motion vector predictors based on the contexts of scene characteristics such as camera motion and nearby motion vectors, providing more efficient candidate predictors than the previous competition-based motion vector coding schemes which resort to the fixed candidates optimized by extensive simulations. Up to 200% of compression gain was observed in the experimental results for the proposed scheme applied to the motion vector selection for skip mode processing.
Multi-tier caching of dynamic content for database-driven web sites (2002)

Web sites have gradually shifted from delivering just static html pages and images to customized, user-specific content and plethora of online services. The new features and facilities are made possible by dynamic content which is produced at request time. Multi-tiered database-driven web sites form the predominant infrastructure for most structured and scalable approaches to dynamic content delivery. However, even with these scalable approaches, the request-time computation and high resource demands for dynamic content generation result in significantly higher latencies and lower throughputs than for sites with just static content.\nThis thesis proposes the caching of dynamic content as the solution for improving the performance of web sites with significant amount of dynamic content. This work shows that there is significant locality in the data accesses and computations for content generation which can be exploited by caching to improve performance. This work introduces a novel multi-tier caching architecture that incorporates multiple, independent caching components to enable easy deployment and effective performance over the prevalent multi-tiered database-driven architecture for dynamic content delivery.\nThe dynamic content infrastructure and the proposed caching strategy is evaluated with e-commerce workloads from the TPC-W benchmark. The evaluation of the system without caching shows that content generation overheads are dominated by the database component for e-commerce workloads. With multi-tier caching, each caching component overcomes specific overheads during content generation while the combination provides overall improvements in performance significantly greater than the individual contributions. The increased peak throughputs with caching range from 1.58 to 8.72 times the peak throughputs without caching at similar or significantly reduced average response times. At the same load as for the peak throughputs without caching, the response times were reduced by 90% to 97% with caching. The evaluations also establish the effectiveness of the strategy in relation to variation in platform and site configurations. Overall, the proposed multi-tier caching strategy brings about dramatic improvements in performance for dynamic content delivery.
Towards a Two-Tier Hierarchical Infrastructure: An Offline Payment\n System for Central Bank Digital Currencies (2020)

Digital payments traditionally rely on online communications with several\nintermediaries such as banks, payment networks, and payment processors in order\nto authorize and process payment transactions. While these communication\nnetworks are designed to be highly available with continuous uptime, there may\nbe times when an end-user experiences little or no access to network\nconnectivity.\n The growing interest in digital forms of payments has led central banks\naround the world to explore the possibility of issuing a new type of\ncentral-bank money, known as central bank digital currency (CBDC). To\nfacilitate the secure issuance and transfer of CBDC, we envision a CBDC design\nunder a two-tier hierarchical trust infrastructure, which is implemented using\npublic-key cryptography with the central bank as the root certificate authority\nfor generating digital signatures, and other financial institutions as\nintermediate certificate authorities. One important design feature for CBDC\nthat can be developed under this hierarchical trust infrastructure is an\noffline capability to create secure point-to-point offline payments through the\nuse of authorized hardware. An offline capability for CBDC as digital cash can\ncreate a resilient payment system for consumers and businesses to transact in\nany situation.\n We propose an offline payment system (OPS) protocol for CBDC that allows a\nuser to make digital payments to another user while both users are temporarily\noffline and unable to connect to payment intermediaries (or even the Internet).\nOPS can be used to instantly complete a transaction involving any form of\ndigital currency over a point-to-point channel without communicating with any\npayment intermediary, achieving virtually unbounded throughput and real-time\ntransaction latency.\n
Selective retinal therapy with a continuous line scanning laser (2010)

This study evaluates the effects of exposure duration, beam diameter, and power on the safety, selectivity, and healing of retinal lesions created using a continuous line scanning laser. A 532 nm laser (PASCAL<sup>TM</sup>) with retinal beam diameters of 40 and 66 &mu;m was applied to 60 eyes of 30 Dutch-Belted rabbits. Retinal exposure duration varied from 15 to 60 &mu;s. Lesions were acutely assessed by ophthalmoscopy and fluorescein angiography (FA). RPE flatmounts were evaluated with live-dead fluorescent assay (LD). Histological analysis was performed at 1 hour, 1 and 3 days, 1 and 2 weeks, and 1 and 2 months following laser treatment. Ophthalmoscopic visibility (OV) of the lesions corresponded to photoreceptor damage on histological analysis at 1 hour. In subvisible lesions, FA and LD yielded similar thresholds of RPE damage. The ratios of the threshold of rupture and of OV to FA visibility (measures of safety and selectivity) increased with decreasing duration and beam diameter. Above the threshold of OV, histology showed focal RPE damage and photoreceptor loss at one day without inner retinal effects. By one week, continuity of photoreceptor and RPE layers was restored. By 1 month, photoreceptors appeared normal while hypertrophy and hyperpigmentation of the RPE persisted. Retinal therapy with a fast scanning continuous laser achieves selective targeting of the RPE and, at higher power, of the photoreceptors. The damage zone in the photoreceptor layer is quickly filled-in, likely due to photoreceptor migration from adjacent zones. Continuous scanning laser can treat large retinal areas within standard eye fixation time.
APOBEC3G Incorporation into Human Immunodeficiency Virus Type 1 Particles (2004)

APOBEC3G is promiscuous with respect to its antiretroviral effect, requiring that it be packaged into diverse retrovirus particles. Here, we show that most virally encoded human immunodeficiency virus type 1 particle components are dispensable for APOPEC3G incorporation. However, replacement of the nucleocapsid (NC) Gag domain with a leucine zipper abolished APOBEC3G incorporation. Moreover, coprecipitation analysis showed that APOBEC3G-Gag interaction requires NC and nonspecific RNA. These observations suggest that APOBEC3G exploits an essential property of retroviruses, namely, RNA packaging, to infiltrate particles. Because it is, therefore, difficult to evolve specific sequences that confer escape from APOBEC3G, these findings may explain why lentiviruses evolved an activity that induces its destruction.
Reductive N-Alkylation of Nitroarenes: A Green Approach for the N-Alkylation of Natural Products (2012)

A simple, mild, cost-effective, and green approach for the reductive mono-N-alkylation of nitroarenes has been developed. HOAc/Zn are utilized as the reducing system together with a carbonyl compound as an alkyl source in methanol. Excellent yields were obtained with stoichiometric control of mono- over dialkylated products. Application to five complex natural products demonstrated the practical utility of the method.
ROHINI: A robotic flower system for intuitive smart home interface (2010)

ROHINI is a humanoid type flower robot that mediates interactions between occupants and various devices and equipments embedded in a smart home environment. Traditional interfaces such as remote controllers, switches or buttons at home lack of intuitive and natural interactions needed to provide a highly sophisticated monitoring and control of various smart home operations. ROHINI, a rose-like anthropomorphic robot is equipped with biometric sensing system(voice recognition), flower bud and stem motion control systems as well as voice synthesis and color change actuation mechanism to respond to both occupants' and environmental demands. ROHINI can listen to the user's voice to recognize verbal command or question and then respond to it based on simple embedded conversational rules. ROHINI also could open or close its rose petals, change its flower bud color through embedded LED, bends its stem at each joint that has step motors and rotate clockwise or counter-clockwise through its rotating base panel. ROHINI has high potential to be a one of the unique robotic home service interface through which a user or group of users could monitor real time context of a smart home and control various indoor devices which constitute smart home environment.
Global illumination of glossy environments using wavelets and importance (1996)

We show how importance-driven refinement and a wavelet basis can be combined to provide an efficient solution to the global illumination problem with glossy and diffuse reflections. Importance is used to focus the computation on the interactions having the greatest impact on the visible solution. Wavelets are used to provide an efficient representation of radiance, importance, and the transport operator. We discuss a number of choices that must be made when constructing a finite element algorithm for glossy global illumination. Our algorithm is based on the standard wavelet decomposition of the transport operator and makes use of a four-dimensional wavelet representation for spatially and angularly varying radiance distributions. We use a final gathering step to improve the visual quality of the solution. Features of our implementation include support for curved surfaces as well as texture-mapped anisotropic emission and reflection functions.
Intrapericardial Delivery of Amiodarone Rapidly Achieves Therapeutic Levels in the Atrium (2013)

Short-term intrapericardial delivery of amiodarone is a safe method for rapidly obtaining therapeutic atrial-tissue drug levels. When begun perioperatively, this method may prevent postoperative atrial fibrillation similarly to oral or intravenous amiodarone therapy. However, we have shown that pericardial administration avoids systemic drug distribution and thus may greatly decrease the systemic complicationsresulting from this drug.
FAM222A encodes a protein which accumulates in plaques in Alzheimer’s disease (2020)

Alzheimer's disease (AD) is characterized by amyloid plaques and progressive cerebral atrophy. Here, we report FAM222A as a putative brain atrophy susceptibility gene. Our cross-phenotype association analysis of imaging genetics indicates a potential link between FAM222A and AD-related regional brain atrophy. The protein encoded by FAM222A is predominantly expressed in the CNS and is increased in brains of patients with AD and in an AD mouse model. It accumulates within amyloid deposits, physically interacts with amyloid-β (Aβ) via its N-terminal Aβ binding domain, and facilitates Aβ aggregation. Intracerebroventricular infusion or forced expression of this protein exacerbates neuroinflammation and cognitive dysfunction in an AD mouse model whereas ablation of this protein suppresses the formation of amyloid deposits, neuroinflammation and cognitive deficits in the AD mouse model. Our data support the pathological relevance of protein encoded by FAM222A in AD.
Supplementary Video 2a from Unexpected Dissemination Patterns in Lymphoma Progression Revealed by Serial Imaging within a Murine Lymph Node (2023)

&lt;p&gt;MOV file - 6.2MB, Observation of behavior between control mouse and LNIWC implanted mouse (LNIWC mouse):Mouse videos were acquired on day 12 after implantation of either LNIWC or control mouse. No difference in behavior was observed between LNIWC-implanted mice and control mice without the LNIWC.&lt;/p&gt;
Control predicates are better than dummy variables for reasoning about program control (1988)

When explicit control predicates rather than dummy variables are used, the Owicki-Gries method for proving safety properties of concurrent programs can be strengthened, making it easier to construct the required program annotations.
Automated classification of breast pathology using local measures of broadband reflectance (2010)

We demonstrate that morphological features pertinent to a tissue's pathology may be ascertained from localized measures of broadband reflectance, with a mesoscopic resolution (100-μm lateral spot size) that permits scanning of an entire margin for residual disease. The technical aspects and optimization of a k-nearest neighbor classifier for automated diagnosis of pathologies are presented, and its efficacy is validated in 29 breast tissue specimens. When discriminating between benign and malignant pathologies, a sensitivity and specificity of 91 and 77% was achieved. Furthermore, detailed subtissue-type analysis was performed to consider how diverse pathologies influence scattering response and overall classification efficacy. The increased sensitivity of this technique may render it useful to guide the surgeon or pathologist where to sample pathology for microscopic assessment.
Real-time Sound Localization With a Binaural Head-system Using a Biologically-inspired Cue-triple Mapping (2006)

We present a sound localization system that operates in real-time, calculates three binaural cues (IED, UD, and ITD) and integrates them in a biologically inspired fashion to a combined localization estimation. Position information is furthermore integrated over frequency channels and time. The localization system controls a head motor to fovealize on and track the dominant sound source. Due to an integrated noise-reduction module the system shows robust localization capabilities even in noisy conditions. Real-time performance is gained by multi-threaded parallel operation across different machines using a timestamp-based synchronization scheme to compensate for processing delays
Supplementary Figure 1 from Regulatory T Cell–Resistant CD8<sup>+</sup> T Cells Induced by Glucocorticoid-Induced Tumor Necrosis Factor Receptor Signaling (2023)

Supplementary Figure 1 from Regulatory T Cell–Resistant CD8&lt;sup&gt;+&lt;/sup&gt; T Cells Induced by Glucocorticoid-Induced Tumor Necrosis Factor Receptor Signaling