gebhart/patrepeval huggingface dataset:
Neuropathology and Virus in Brain of SARS-CoV-2 Infected Non-Human Primates (2020)

Abstract Neurological manifestations are a significant complication of coronavirus infection disease-19 (COVID-19). Understanding how COVID-19 contributes to neurological disease is needed for appropriate treatment of infected patients, as well as in initiating relevant follow-up care after recovery. Investigation of autopsied brain tissue has been key to advancing our understanding of the neuropathogenesis of a large number of infectious and non-infectious diseases affecting the central nervous system (CNS). Due to the highly infectious nature of the etiologic agent of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is a paucity of tissues available for comprehensive investigation. Here, we show for the first time, microhemorrhages and neuropathology that is consistent with hypoxic injury in SARS-CoV-2 infected non-human primates (NHPs). Importantly, this was seen among infected animals that did not develop severe respiratory disease. This finding underscores the importance of vaccinating against SARS-CoV-2, even among populations that have a reduced risk for developing of severe disease, to prevent long-term or permanent neurological sequelae. Sparse virus was detected in brain endothelial cells but did not associate with the severity of CNS injury. We anticipate our findings will advance our current understanding of the neuropathogenesis of SARS-CoV-2 infection and demonstrate SARS-CoV-2 infected NHPs are a highly relevant animal model for investigating COVID-19 neuropathogenesis among human subjects.
Secure Multicast in a WAN (1999)

A secure reliable multicast protocol enables a process to send a message to a group of recipients such that all correct destinations receive the same message, despite the malicious efforts of fewer than a third of the total number of processes, including the sender. This has been sh own to be a useful tool in building secure distributed services, albeit with a cost that typically grows linearly with the size of the system. For very large networks, for which this is prohibitive, we present two approaches for reducing the cost: First, we show a protocol whose cost is on the order of the number of tolerated failures. Secondly, we show how relaxing the consistency requirement to a probabilistic guarantee can reduce the associated cost, effectively to a constant.
Transcriptional repressor CopR: Structure model-based localization of the deoxyribonucleic acid binding motif (2000)

The plasmid pIP501 encoded transcriptional repressor CopR is one of the two regulators of plasmid copy number. CopR binds as a dimer to a nearly palindromic operator with the consensus sequence 5'-CGTG. Intermediate sequence searches revealed a significant structural relationship between CopR and the bacteriophage P22 c2 and the 434 c1 repressors. In this report we describe the experimental verification of a CopR homology model, which is based on a fairly low-sequence identity of 13.8% to P22 c2 repressor. A model for the complex of CopR with the deoxyribonucleic acid (DNA) target was built on the basis of experimental footprinting data, the above-mentioned CopR homology model, and the crystal structure of the 434 c1 repressor-DNA complex. Site-directed mutagenesis was used to test the function of amino acids involved in sequence and nonsequence-specific DNA recognition and amino acids important for correct protein folding. CD measurements were performed to detect structural changes caused by the mutations. Exchanges of residues responsible for sequence-specific DNA recognition reduced binding to a nonspecific level. Mutations of amino acids involved in nonspecific DNA binding lead to decreased binding affinity while maintaining selectivity. Substitution of amino acids necessary for proper folding caused dramatic structural changes. The experimental data support the model of CopR as a helix-turn-helix protein belonging to the lambda repressor superfamily.
System support for providing integrated services from networked multimedia storage servers (2001)

In this paper, we describe our experience in building an integrated multimedia storage system, Prism. Our current Linux-based implementation of Prism provides three levels of service: deadline guarantees for periodic applications, best-effort better response times for interactive applications and starvation-free throughput guarantees for aperiodic applications. Prism separates resource allocation from resource scheduling. Resource allocation is controlled across the service classes by a system-wide policy and service class specific admission controllers. Resource scheduling is done at the resources. This separation allows Prism to be deployed even when the storage system is separated on a network from the file system.We report on the important aspects of Prism architecture, innovations required to build Prism on top of Linux and lessons learned during the implementation and testing of Prism. We present experimental results to show that Prism achieves its goals in supporting multiple service classes within a single system. We compare Prism against standard Linux operating system to show the impact of our approach.
Elimination of atrioventricular nodal reentrant tachycardia using discrete slow potentials to guide application of radiofrequency energy. (1992)

An area showing slow potentials is present at the perinodal region in humans. In patients with AVNRT, application of radiofrequency energy renders tachycardia noninducible through the preferential modification of the anterograde slow pathway. With present clinical methods, the exact origin and significance of these physiological potentials cannot be specified.
Chamfered-edge laser cleaving of transparent materials (2022)

We report on the separation of glass substrates with customized edge contours including C-shapes. To achieve single-pass laser modifications along the entire contour geometry a processing optics is presented where a multitude of foci are simultaneously distributed inside a specific volume using a large-working-volume focusing unit. Tangential angles of the focus trajectory to the surface can be almost arbitrarily chosen and amount to even less than 45-deg in case of aiming for chamfered edges. After having induced laser modifications along the desired edge geometry, separation is done chemically in the present case. The glass articles, thus fabricated, meet the demands of the display industry in terms of bending strength and surface quality.
Identification of Novel Fibrosis Modifiers by In Vivo siRNA Silencing (2017)

Fibrotic diseases contribute to 45% of deaths in the industrialized world, and therefore a better understanding of the pathophysiological mechanisms underlying tissue fibrosis is sorely needed. We aimed to identify novel modifiers of tissue fibrosis expressed by myofibroblasts and their progenitors in their disease microenvironment through RNA silencing in vivo. We leveraged novel biology, targeting genes upregulated during liver and kidney fibrosis in this cell lineage, and employed small interfering RNA (siRNA)-formulated lipid nanoparticles technology to silence these genes in carbon-tetrachloride-induced liver fibrosis in mice. We identified five genes, Egr2, Atp1a2, Fkbp10, Fstl1, and Has2, which modified fibrogenesis based on their silencing, resulting in reduced Col1a1 mRNA levels and collagen accumulation in the liver. These genes fell into different groups based on the effects of their silencing on a transcriptional mini-array and histological outcomes. Silencing of Egr2 had the broadest effects in vivo and also reduced fibrogenic gene expression in a human fibroblast cell line. Prior to our study, Egr2, Atp1a2, and Fkbp10 had not been functionally validated in fibrosis in vivo. Thus, our results provide a major advance over the existing knowledge of fibrogenic pathways. Our study is the first example of a targeted siRNA assay to identify novel fibrosis modifiers in vivo.
Short Term Implications of Organic Additives on Properties of Sandy and Clay Soils and Plants Grown on Them. (2022)

Rates of 0 , 10 , 20 and 40 gkg-1 of two sources of organic additives i.e. biogas manure and pigeon manure were applied to 3 soils ( sand , light clay and heavy clay) in 2 experiments . The first was an incubation one in which the soils were incubated with the organic additive without growing plant and the second was in soils grown with maize (Zea mays) . The duration was 60 days. Additives improved soil properties and plant growth. Moisture retained at field capacity (FC and wilting point (WP and available water (AW) increased. Soil organic matter (SOM) and cation exchange capacity (CEC) increased.. Maize growth yield as well as uptake of NPK increased.
Harvesting raindrop energy: theory (2008)

At present, the energy autonomy of a microsystem is limited by the lifespan of the battery. Hence the development of an energy harvesting concept, whereby the energy needed to power the sensor is taken from the operating environment. However, there is no single solution suitable for all types of environment. In this paper, we look at a still unexploited source of energy: rain. Our system recovers the vibration energy from a piezoelectric flexible structure impacted by a water drop. This paper describes in detail the theoretical study undertaken to optimize the mechanical system.
Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancer (2018)

Whereas <i>VHL</i> inactivation is a primary event in clear cell renal cell carcinoma (ccRCC), the precise mechanism(s) of how this interacts with the secondary mutations in tumor suppressor genes, including <i>PBRM1</i>, <i>KDM5C</i>/<i>JARID1C</i>, <i>SETD2</i>, and/or <i>BAP1</i>, remains unclear. Gene expression analyses reveal that VHL, PBRM1, or KDM5C share a common regulation of interferon response expression signature. Loss of HIF2α, PBRM1, or KDM5C in <i>VHL-/-</i>cells reduces the expression of interferon stimulated gene factor 3 (ISGF3), a transcription factor that regulates the interferon signature. Moreover, loss of SETD2 or BAP1 also reduces the ISGF3 level. Finally, ISGF3 is strongly tumor-suppressive in a xenograft model as its loss significantly enhances tumor growth. Conversely, reactivation of ISGF3 retards tumor growth by PBRM1-deficient ccRCC cells. Thus after <i>VHL</i> inactivation, HIF induces ISGF3, which is reversed by the loss of secondary tumor suppressors, suggesting that this is a key negative feedback loop in ccRCC.
Palladium(II)‐Catalyzed Site‐Selective C(sp3)−H Alkynylation of Oligopeptides: A Linchpin Approach for Oligopeptide–Drug Conjugation (2017)

Abstract The palladium(II)‐catalyzed C(sp 3 )−H alkynylation of oligopeptides was developed with tetrabutylammonium acetate as a key additive. Through molecular design, the acetylene motif served as a linchpin to introduce a broad range of carbonyl‐containing pharmacophores onto oligopeptides, thus providing a chemical tool for the synthesis and modification of novel oligopeptide–pharmacophore conjugates by C−H functionalization. Dipeptide conjugates with coprostanol and estradiol were synthesized by this method for potential application in targeted drug delivery to tumor cells with overexpressed nuclear hormone receptors.
Anisotropy of ultrasonic backscatter and attenuation from human calcaneus: Implications for relative roles of absorption and scattering in determining attenuation (2000)

Although bone sonometry has been demonstrated to be useful in the diagnosis of osteoporosis, much remains to be learned about the processes governing the interactions between ultrasound and bone. In order to investigate these processes, ultrasonic attenuation and backscatter in two orientations were measured in 43 human calcaneal specimens in vitro at 500 kHz. In the mediolateral (ML) orientation, the ultrasound propagation direction is approximately perpendicular to the trabecular axes. In the anteroposterior (AP) orientation, a wide range of angles between the ultrasound propagation direction and trabecular axes is encountered. Average attenuation slope was 18% greater while average backscatter coefficient was 50% lower in the AP orientation compared with the ML orientation. Backscatter coefficient in both orientations approximately conformed to a cubic dependence on frequency, consistent with a previously reported model. These results support the idea that absorption is a greater component of attenuation than scattering in human calcaneal trabecular bone.
Funcational assay platform to identify novel inhibitors of receptor tyrosine kinases (2005)

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Continuous shape sensitivity of incompressible Navier-Stokes flows (1998)

Direct and adjoint continuous shape sensitivity analysis of time independent and dependent NavierStokes flows in the fixed and rotating frames of reference are discussed in this paper. First-order shape sensitivity equations for several common types of boundary conditions are derived. The shape sensitivities of domain integral types of objective and constraint functions are shown to be only dependent on the boundary shape, boundary and initial conditions, and their corresponding design sensitivities. As a result, the need to obtain a design velocity field in the flow domain is eliminated. In addition, shape sensitivity analysis of Navier-Stokes flows may be conducted in a more efficient manner.
Real-time FTIR monitoring and modeling Bacillus amyloliquefaciens spore germination: Effect of temperature and sub-lethal treatment by nonthermal plasma (2022)

This study uses real-time FTIR spectroscopy to probe biochemical changes occurring in spores of Bacillus amyloliquefaciens during nutrient germination at T = 23 − 50°C and after sub-lethal injury by treatment with a nonthermal plasma (NTP). The FTIR identifies several spore structural components (e.g., stretching bands of the COO− group of dipicolinic acid at 1378 and 1616 cm−1; C−N vibrations in the DPA ring at 1570 cm−1, etc.) that are correlated to steps occurring during germination. The increase in peak intensity at 1570 cm−1 is interrelated to spore germination as measured with optical density at 600 nm (OD600) of refractile spores at T = 23 − 50°C and after NTP treatment. For the OD600 germination kinetics data, the Weibull model accurately fit the observed dynamics with values for the rate parameters α = 18.1 − 52.9 s−1 and shape parameter β = 0.9 − 1.2, and the Weibull model's performance was assessed by satisfactory values of the accuracy factor (1.00 < Af ≤ 1.15) and the bias factor (Bf in the ranges of 0.90 − 1.05), with the NTP-treated spores being the lone exception (Af = 1.22, Bf = 1.06).
Gas Absorption and Pore Breathing of Metal-Organic Frameworks Studied Using in situ Environmental Transmission Electron Microscopy (ETEM) (2018)

Metal-organic frameworks (MOFs), a class of periodic mesoporous nanomaterials, exhibit promising small molecule adsorption properties for gas storage/separation, comparable to those of zeolites However, little is currently known about the fundamental mechanisms involved in functional gas absorption/release ("pore breathing") behavior of these nanostructures, which limits our ability to controllably design and bulk-produce MOFs that are optimized for specific gas storage or separation applications. The bulk gas-storage capacity and kinetics of uptake/release of porous materials, including MOFs, are routinely screened using bulk gas adsorption analysis, such as breakthrough analysis and dynamic loading, supported by (bulk) powder X-ray diffraction (PXRD) [2,3]. However, these techniques cannot reveal the underlying molecular-scale mechanisms that give rise to the observed bulk gas storage properties. At the fundamental level, gas adsorption(/release) into a mesoporous nanostructure is a molecular transport and lattice rearrangement phenomenon, and must be studied at this length scale (angstrom/nano-scale). In situ Environmental (E)TEM studies, which monitor and characterize nanostructures in gas/vapor environments, can provide unprecedented insight into the fundamental molecular transport and structural transformation processes directly related to bulk properties of gasstorage/release.
Cooperative Localization with Angular Measurements and Posterior Linearization (2019)

The application of cooperative localization in vehicular networks is attractive to improve accuracy and coverage. Conventional distance measurements between vehicles are limited by the need for synchronization and provide no heading information of the vehicle. To address this, we present a cooperative localization algorithm using posterior linearization belief propagation (PLBP) utilizing angle-of-arrival (AoA)-only measurements. Simulation results show that both directional and positional root mean squared error (RMSE) of vehicles can be decreased significantly and converge to a low value in a few iterations. Furthermore, the influence of parameters for the vehicular network, such as vehicle density, communication radius, prior uncertainty and AoA measurements noise, is analyzed.
Introduction (1995)

The fundamental nature of economic fluctuations is a point of obvious importance, but also one of the least understood questions in economics. Under dispute are not details, but the basic mechanisms underlying the business cycle phenomenon. Are these fluctuations of a sufficiently regular period to be called cycles, or rather irregular ups and downs? Are these movements the outcome of an endogenous process, or simply caused by exogenous shocks, such as import price increases, changes in foreign demand, switches of policy? Are the unpleasant concomitants of business cycles, like unemployment, a sign of coordination failures of a market economy, or, quite the reverse, optimal responses of economic agents to exogenous shocks?
Exploring Inter-feature and Inter-class Relationships with Deep Neural Networks for Video Classification (2014)

Videos contain very rich semantics and are intrinsically multimodal. In this paper, we study the challenging task of classifying videos according to their high-level semantics such as human actions or complex events. Although extensive efforts have been paid to study this problem, most existing works combined multiple features using simple fusion strategies and neglected the exploration of inter-class semantic relationships. In this paper, we propose a novel unified framework that jointly learns feature relationships and exploits the class relationships for improved video classification performance. Specifically, these two types of relationships are learned and utilized by rigorously imposing regularizations in a deep neural network (DNN). Such a regularized DNN can be efficiently launched using a GPU implementation with an affordable training cost. Through arming the DNN with better capability of exploring both the inter-feature and the inter-class relationships, the proposed regularized DNN is more suitable for identifying video semantics. With extensive experimental evaluations, we demonstrate that the proposed framework exhibits superior performance over several state-of-the-art approaches. On the well-known Hollywood2 and Columbia Consumer Video benchmarks, we obtain to-date the best reported results: 65.7% and 70.6% respectively in terms of mean average precision.
Radiographic and Clinical Outcomes in Total Hip Arthroplasty Utilizing a Porous Acetabular Shell Developed with Additive Manufacturing (2019)

This is a prospective data collection across seven centers in a non-randomized, post- market study where an additive manufactured cementless acetabular shell was used in primary total hip arthroplasty. There was a total of 254 hips/246 patients across seven centers. Clinical outcomes including all-cause survivorship, the Harris Hip Score (HHS), Lower Extremity Activity Scale (LEAS), Veterans Rand 12 (VR-12), EuroQol 5D (EQ- 5D) and radiographs were collected pre- and postoperatively. Radiographs were analyzed for presence of radiolucencies, migration and overall cup stability. All-cause survival rate was 99.61% and there were no reported radiolucencies greater than 2mm for any zone. There was a reduction in radiolucencies from the 6-week to 1-year postoperative timeframe. All cups reviewed at 1-year were stable with no radiolucencies in 96% of hips. These early results demonstrate the favorable properties of this shell and the use of additive manufacturing in orthopaedic surgery.
Plant Cuticle-Inspired Polyesters as Promising Green and Sustainable Polymer Materials (2021)

The plant cuticle is a hydrophobic barrier membrane found mainly on leaf surfaces and fruit skin. This work presents the structural and barrier properties of cuticle-inspired poly(hydroxyhexadecanoate) (PHHA), an ω-hydroxy fatty acid-derived biopolyester. PHHA was copolymerized and cross-linked with glycerol by melt polycondensation, and films were fabricated by compression molding. The study showed the effect of the addition of a trifunctional comonomer on the thermal, mechanical, and barrier properties. The neat PHHA, owing to its higher crystallinity, demonstrated the best water vapor barrier properties, but formed brittle films. The glycerol-copolymerized films, on the other hand, were flexible and displayed a good balance between barrier and mechanical properties. The water vapor transmission rate was overall similar to that of PLA, and limonene (a hydrophobic food component) uptake and diffusivity were lower than that of low-density polyethylene, the commonly used polymer for packaging. In addition, the polyester had UV-blocking properties. The way the films were made yielded a rough surface, mimicking the outer rough wax layer in plant cuticles with high water repellence. Hence, these cutin-inspired polyesters are promising for, e.g., water barrier (packaging/device) applications, provided means of efficient/sustainable production/isolation of the monomer is developed.
104 Development of Optical Door Sensor with Planar Detection Area for Elevators (2010)

We have developed a new optical door sensor that has a planar detection area with no gap. This sensor has two elongate light sources and two imaging units that are embedded in door posts of an elevator car. The sensor can detect a passenger's finger or a small object and prevent it form being pinched by the doors before door opening and during door closing. Additionally, the elongate light sources blink by red light to alert timings of the door moving to passengers.
Severe slugging in oil-well simulations using a drift flux code (2010)

To design and evaluate slugging control strategies, a simulator that is capable to simulate severe slugging accurately with limited CPU-needs is required; therefore a drift flux simulator was developed. The drift-flux simulator was used to simulate a field case. The pressure drop was predicted very well. However, an additional horizontal length was needed in the simulations to obtain slugging. This additional requirement is in-line with known shortcomings of multiphase models identified in literature. Aside this criterion, also a minimum hydraulic jump was required. The current drift-flux simulator is suitable for case specific control strategy development and testing. © BHR Group 2010.
70-Gb/s Multicore Multimode Fiber Transmissions for Optical Data Links (2010)

This letter describes a novel structure and crosstalk characteristics of a graded-index multicore fiber with seven cores arranged in a hexagonal array. A total of 70 Gb/s (7 × 10 Gb/s) is transmitted over a single 100-m seven-core multimode fiber (MMF) using tapered multicore fiber connectors and 850-nm vertical-cavity surface-emitting lasers, demonstrating high-speed multicore MMF transmissions for parallel optical data links.