gebhart/patrepeval huggingface dataset:
Photoperiodic Time Measurement in tau Mutant Hamsters (1997)

Photoperiodic regulation of testicular function was investigated in homozygous tau mutant hamsters; these animals have an innate circadian period of about 20 h. In 20-h light:dark (LD) cycles, the minimum photoperiod required to prevent testicular regression was between 10.0 and 11.5 h per 20-h cycle (equivalent to 12.0-13.8 circadian hours). This was proportionally similar to the minimum photoperiod necessary to prevent regression in wild-type hamsters maintained in 24-h LD cycles. To examine the shape of the photoperiodic photosensitivity curve in homozygous tau mutant hamsters, the authors measured the effects of different T cycles on testicular maintenance. Entrainment to LD 1:18.0 and LD 1:20.5 partially or completely prevented gonadal regression in homozygous tau mutant hamsters, but LD 1:19.4 did not prevent regression. When considered in terms of circadian time, the photoperiodic photosensitivity curve for homozygous tau mutant hamsters was similar to that described previously for wild-type hamsters. The results indicate that, as in wild-type hamsters, photoperiodic regulation of reproduction is regulated by circadian photosensitivity in homozygous tau mutant hamsters. Because tau mutant hamsters measure day length against a time base of 20 h, the circadian pacemaker that measures day length might be the same as that which generates circadian rhythmicity in locomotor activity. The authors' data leave open the question of whether the tau mutation has had effects on the control of reproduction that are not directly attributable to its effects on the period of the circadian oscillator.
An Integrated Helmet and Neck Support (iHANS) for Racing Car Drivers: A Biomechanical Feasibility Study (2012)

A new form of head and neck protection for racing car drivers is examined. The concept is one whereby the helmet portion of the system is attached, by way of a quick release clamp, to a collar-like platform which is supported on the driver's shoulders. The collar, which encircles the back and sides of the driver's neck, is held in place by way of the on-board restraint belts. The interior of the helmet portion of the assembly is large enough to provide adequate volitional head motion. The overall objective of the design is to remove the helmet from the wearer's head and thereby to mitigate the deleterious features of helmet wearing such as neck fatigue, poor ventilation and aerodynamic buffeting. Just as importantly, by transferring the weight of the helmet and all attendant reaction forces associated with inertial and impact loads to the shoulder complex (instead of to the neck), reduced head and neck injury probability should be achievable. This paper describes the concept development and the evolution of various prototype designs. Prototypes have been evaluated on track and sled tested in accordance with contemporary head neck restraint systems practice. Also discussed is a series of direct impact tests. In addition, low mass high velocity ballistic tests have been conducted and are reviewed herein. It is concluded that this new concept indeed does address most of the drawbacks of the customary helmet and that it generally can reduce the probability of head and neck injury.
Laparoscopic cholecystectomy and choledochoscopy for the treatment of cholelithiasis and choledocholithiasis. (1992)

A 33-year-old woman with symptomatic cholelithiasis underwent laparoscopic cholecystectomy. Preoperative evaluation did not suggest the presence of choledocholithiasis, but intraoperative cholangiography showed a totally obstructing stone in the distal common bile duct. Laparoscopically directed, transperitoneal choledochoscopy was performed by passing a 9.4 F flexible ureteroscope through the cystic duct into the distal common bile duct. A single calculus was visualized and removed with a basket. The patient was discharged the next day, returned to full activity within 1 week, and has done well in the subsequent postoperative interval. The management of incidentally discovered common bile duct stones during performance of laparoscopic cholecystectomy is discussed.
Cover Picture: Efficient Encapsulation of Fluorinated Drugs in the Confined Space of Water‐Dispersible Fluorous Supraparticles (Angew. Chem. Int. Ed. 51/2017) (2017)

A Passion for Fluorine transport of fluorinated drugs in aqueous environments requires stable, water-dispersible carriers. In their Communication on page 16186 ff., P. Metrangolo and F. Baldelli Bombelli et al. describe a passionfruit-like supraparticle filled with fluorinated gold nanoparticles, which is coated by the vegetable protein hydrophobin II. The fluorous confined space of the supraparticle permits encapsulation of millions of fluorinated drug molecules. A Passion for Fluorine transport of fluorinated drugs in aqueous environments requires stable, water-dispersible carriers. In their Communication on page 16186 ff., P. Metrangolo and F. Baldelli Bombelli et al. describe a passionfruit-like supraparticle filled with fluorinated gold nanoparticles, which is coated by the vegetable protein hydrophobin II. The fluorous confined space of the supraparticle permits encapsulation of millions of fluorinated drug molecules. Supramolecular Gels Lithium–Sulfur Batteries Metal–Organic Frameworks
Certified DNA Reference Materials to Compare HER2 Gene Amplification Measurements Using Next-Generation Sequencing Methods (2016)

The National Institute of Standards and Technology (NIST) Standard Reference Materials 2373 is a set of genomic DNA samples prepared from five breast cancer cell lines with certified values for the ratio of the HER2 gene copy number to the copy numbers of reference genes determined by real-time quantitative PCR and digital PCR. Targeted-amplicon, whole-exome, and whole-genome sequencing measurements were used with the reference material to compare the performance of both the laboratory steps and the bioinformatic approaches of the different methods using a range of amplification ratios. Although good reproducibility was observed in each next-generation sequencing method, slightly different HER2 copy numbers associated with platform-specific biases were obtained. This study clearly demonstrates the value of Standard Reference Materials 2373 as reference material and as a calibrator for evaluating assay performance as well as for increasing confidence in reporting HER2 amplification for clinical applications.
CuO Nanopetals Based Electrochemical Sensor for Selective Ag+ Measurements (2012)

The electrochemical sensing activity of cupric oxide (CuO) nanopetals was investigated for the detection of silver (I) ions (Ag+). The CuO nanopetals were synthesized on a large area glass substrat ...
Development of Fiber Laser Weld Parameters for Stainless Steel and Refractory Metals (2009)

Laser welds were made in 21-6-9 stainless steel, vanadium and tantalum using LLNL's new 6kW fiber laser to target 1 mm penetration depths. The materials were machined into flat coupon samples with standard step-joint geometries, and were welded in a continuous wave mode. The laser was characterized using the Primes laser beam diagnostic system so that the beams can be reproduced in the future. The optical configuration consisted of a 200 {micro}m fiber, 200 mm collimator and 250 mm focusing lens, which delivered electron-beam level power densities in the 5 to 20 kW/mm2 range. The three different materials required different power densities to produce the desired penetration, and this report summarizes the results of this screening study that was directed at developing a first approximation to the proper welding parameters for future work. The results show that 1 mm penetrations can be achieved using a 400W beam for 21-6-9 stainless steel, a 600W beam for vanadium, and a 1,100W beam for tantalum using sharp focus and a travel speed of 40 inch/min. Future welds should incorporate a trailing gas shield to prevent discoloration of the surface and to prevent oxygen and nitrogen pickup in the welds.
Novel Small Molecules Targeting the Intrinsically Disordered Structural Ensemble of α-Synuclein Protect Against Diverse α-Synuclein Mediated Dysfunctions (2019)

Abstract The over-expression and aggregation of α-synuclein (αSyn) are linked to the onset and pathology of Parkinson’s disease. Native monomeric αSyn exists in an intrinsically disordered ensemble of interconverting conformations, which has made its therapeutic targeting by small molecules highly challenging. Nonetheless, here we successfully target the monomeric structural ensemble of αSyn and thereby identify novel drug-like small molecules that impact multiple pathogenic processes. Using a surface plasmon resonance high-throughput screen, in which monomeric αSyn is incubated with microchips arrayed with tethered compounds, we identified novel αSyn interacting drug-like compounds. Because these small molecules could impact a variety of αSyn forms present in the ensemble, we tested representative hits for impact on multiple αSyn malfunctions in vitro and in cells including aggregation and perturbation of vesicular dynamics. We thereby identified a compound that inhibits αSyn misfolding and is neuroprotective, multiple compounds that restore phagocytosis impaired by αSyn overexpression, and a compound blocking cellular transmission of αSyn. Our studies demonstrate that drug-like small molecules that interact with native αSyn can impact a variety of its pathological processes. Thus, targeting the intrinsically disordered ensemble of αSyn offers a unique approach to the development of small molecule research tools and therapeutics for Parkinson’s disease.
Viscous-inviscid analysis of transonic and low Reynolds number airfoils (1986)

A method of accurately calculating transonic and low Reynolds number airfoil flows, implemented in the viscous-inviscid design/analysis code ISES, is presented. The Euler equations are discretized on a conservative streamline grid and are strongly coupled to a two-equation integral boundary-layer formulation, using the displacement thickness concept. A transition prediction formulation of the e type is derived and incorporated into the viscous formulation. The entire discrete equation set, including the viscous and transition formulations, is solved as a fully coupled nonlinear system by a global Newton method. This is a rapid and reliable method for dealing with strong viscous-inviscid interactions, which invariably occur in transonic and low Reynolds number airfoil flows. The results presented demonstrate the ability of the ISES code to predict transitioning separation bubbles and their associated losses. The rapid airfoil performance degradation with decreasing Reynolds number is thus accurately predicted. Also presented is a transonic airfoil calculation involving shock-induced separation, showing the robustness of the global Newton solution procedure. Good agreement with experiment is obtained, further demonstrating the performance of the present integral boundary-layer formulation.
Virtual machine provisioning, code management, and data movement design for the Fermilab HEPCloud Facility (2017)

The Fermilab HEPCloud Facility Project has as its goal to extend the current Fermilab facility interface to provide transparent access to disparate resources including commercial and community clouds, grid federations, and HPC centers. This facility enables experiments to perform the full spectrum of computing tasks, including data-intensive simulation and reconstruction. We have evaluated the use of the commercial cloud to provide elasticity to respond to peaks of demand without overprovisioning local resources. Full scale data-intensive workflows have been successfully completed on Amazon Web Services for two High Energy Physics Experiments, CMS and NOνA, at the scale of 58000 simultaneous cores. This paper describes the significant improvements that were made to the virtual machine provisioning system, code caching system, and data movement system to accomplish this work. The virtual image provisioning and contextualization service was extended to multiple AWS regions, and to support experiment-specific data configurations. A prototype Decision Engine was written to determine the optimal availability zone and instance type to run on, minimizing cost and job interruptions. We have deployed a scalable on-demand caching service to deliver code and database information to jobs running on the commercial cloud. It uses the frontiersquid server and CERN VM File System (CVMFS) clients on EC2 instances and utilizes various services provided by AWS to build the infrastructure (stack). We discuss the architecture and load testing benchmarks on the squid servers. We also describe various approaches that were evaluated to transport experimental data to and from the cloud, and the optimal solutions that were used for the bulk of the data transport. Finally, we summarize lessons learned from this scale test, and our future plans to expand and improve the Fermilab HEP Cloud Facility.
Skettching the delay: tracking temporally uncorrelated flow-level latancies (2011)

Packet delay is a crucial performance metric for real-time, network-based applications. Obtaining per-flow delay measurements is particularly important to network operators,
but is computationally challenging in high-speed links. Recently, passive delay measurement techniques have been proposed that outperform traditional active probing in terms of accuracy and network overhead. However, such techniques rely on the empirical observation that packet delays across different flows are temporally correlated, an assumption that is not met in presence of traffic prioritization, load balancing policies, or due to intricacies of the switch fabric. We present a novel data structure called Lossy Difference Sketch (LDS) that provides per-flow delay measurements without relying on any specific delay model. LDS obtains a notable accuracy improvement compared to the state of the art with a small memory footprint and network overhead. The data structure can be sized according to target accuracy requirements or to fit a low memory budget. We deploy an actual implementation of LDS in an opera-
tional research and education network and show that it obtains higher accuracy than temporal correlation-based techniques without exploiting any knowledge about the underlying delay model.
Integrated microdroplet-based system for enzyme synthesis and sampling (2013)

Microdroplet-based microfluidic devices are emerging as powerful tools for a wide range of biochemical screenings and analyses. Monodispersed aqueous microdroplets from picoliters to nanoliters in volume are generated inside microfluidic channels within an immiscible oil phase. This results in the formation of emulsions which can contain various reagents for chemical reactions and can be considered as discrete bioreactors. In this paper an integrated microfluidic platform for the synthesis, screening and sorting of libraries of an organophosphate degrading enzyme is presented. The variants of the selected enzyme are synthesized from a DNA source using in-vitro transcription and translation method. The synthesis occurs inside water-in-oil emulsion droplets, acting as bioreactors. Through a fluorescence based detection system, only the most efficient enzymes are selected. All the necessary steps from the enzyme synthesis to selection of the best genes (producing the highest enzyme activity) are thus integrated inside a single and unique device. In the second part of the paper, an innovative design of the microfluidic platform is presented, integrating an electronic prototyping board for ensuring the communication between the various components of the platform (camera, syringe pumps and high voltage power supply), resulting in a future handheld, user-friendly, fully automated device for enzyme synthesis, screening and selection. An overview on the capabilities as well as future perspectives of this new microfluidic platform is provided.
Age Effects on the Temporal Evolution of Isometric and Swallowing Pressure (2000)

Decreased lingual strength with age combined with unchanging swallowing pressure leads to a decreased "pressure reserve," perhaps leaving older individuals more at risk for dysphagia resulting from insults directly or indirectly to the swallowing system. Additionally, swallowing is generally "slowed" with age, apparently due to both central and peripheral factors, and this change may have an impact on bolus flow outcomes.
Intestinal microvascular responsiveness to norepinephrine in chronic portal hypertension (1991)

Effects of chronic prehepatic portal hypertension on intestinal microvascular sensitivity to norepinephrine (NE) were studied. Normal and portal hypertensive rats were anesthetized, and the intestine was prepared for in vivo microscopic observation. The preparation was transferred to a video microscope and a first-, second-, or third-order submucosal arteriole (i.e., 1A, 2A, or 3A, respectively) selected for study. Microvascular diameter and arteriolar erythrocyte velocity were measured on-line, and arteriolar blood flow was subsequently calculated as the product of velocity and vessel cross-sectional area. Once steady-state conditions were reached, the preparation was exposed to incremental doses of NE and microvessel responses were recorded. Cumulative log dose-response curves relating the change in arteriolar blood flow and vessel diameter to NE concentration were constructed for each group of arterioles and the ED50 for maximal response obtained from each dose-response relationship. NE ED50 for 1A blood flow was significantly higher in portal hypertensive rats (2.57 +/- 0.25 microM) compared with control rats (1.48 +/- 0.19 microM). Analysis of the diameter responses of 1A, 2A, and 3A indicated that the loss of vascular NE sensitivity in chronic portal hypertension was localized to the terminal submucosal arterioles (2A and 3A). No differences in the diameter response of 1A were observed between normal and portal hypertensive rats. Separate experiments were conducted to test if glucagon, a known mediator of the hyperdynamic intestinal circulation in portal hypertension, could acutely alter NE responsiveness in normal animals.(ABSTRACT TRUNCATED AT 250 WORDS)
Toward a Secure Drone System: Flying With Real-Time Homomorphic Authenticated Encryption (2018)

Controlling or accessing remotely has become a prevalent form of operating numerous types of platforms and infrastructure. An exploding number of vehicles such as drones or cars, in particular, are being controlled wirelessly or connected through networks. This has brought unanimous concern that today's networked vehicle systems are vulnerable to attacks and the results could be fatal. Unfortunately, in contrast to active investigation on the security of the vehicles themselves, sensors, or communication channels, existing approaches for these real-time, safety-critical systems do not take controllers into enough consideration. In order to protect the controller that performs the arithmetic operations using sensor measurements and generates command signals, we adopt homomorphic cryptography for the controller. It removes risks associated with the management of the secret key inside the controller, by eliminating the need to encrypt and decrypt the data for the mathematical operation within the controller. Specifically, we propose an efficient linearly homomorphic authenticated encryption (LinHAE) scheme for the ground control center of a multi-rotor drone, in a manner that enables real-time operation for safe autonomous flight. To facilitate the linear scheme, we design the ground controller targeted to allow state update using additions and multiplications by a system-specific constant. The proposed LinHAE guarantees the security against eavesdropping and forgery attacks, unlike homomorphic encryption alone that does not provide means to check whether the received signal at the drone side is authentic or compromised. We introduce a LinHAE with security and computational tractability, and describe how it can fit into the standard architecture for drone systems and how the specific controller is implemented. Building on these ingredients, we report the first successful operation of a multi-rotor flying robot that autonomously flies under the ground controller with real-time homomorphic authenticated encryption.
SOME REFLECTIONS ON VIOLENCE AND NONVIOLENCE (1978)

(1978). SOME REFLECTIONS ON VIOLENCE AND NONVIOLENCE. Philosophical Papers: Vol. 7, No. 1, pp. 1-14.
Asymmetric electron transport realized by decoupling between molecule and electrode (2009)

We studied the contact coupling effect on the asymmetric electron transport in molecular junctions by the first-principles density functional theory incorporating with the non-equilibrium Green's function method. To realize the decoupling, a rigid saturated ring is inserted into the metallic electrode and conjugated molecular bridge (linear oligo phenylene ethynylene and cyclic porphine). As a tunneling barrier, the saturated ring reduces the conductance by 2-3 orders of magnitude. However, the electronic decoupling greatly improves the asymmetric electron transport. In the case of the linear system, the favorite direction of electron transport is from the strong coupling end to the weak coupling one with a rectification ratio of 5 at 2.0 V. In addition, the rectification performance is sensitive to the molecular proportion of the molecular wire length and the tunneling barrier width. When the same barrier is applied, shortening the length of conjugated part can reduce rectification performance. The mechanism of rectification is analyzed by means of the potential drop, the spatial distribution of the molecular orbitals and the transmission spectra.
ChemInform Abstract: Postsynthesis‐Treated Iron‐Based Metal—Organic Frameworks as Selective Catalysts for the Sustainable Synthesis of Nitriles. (2016)

Abstract Several solid catalysts are tested for the selective synthesis of nitriles by dehydration of aldoximes.
<title>Packed binary representations for fast motion estimation on general-purpose architectures</title> (1998)

Reduced representations have been used to decrease the memory bandwidth requirements of fast motion estimation schemes. Usually, this is achieved on special-purpose architectures that exploit the reduced representations to do several distortion calculations in parallel. In this paper, we present a generic fast implementation that its suitable for various general-purpose architectures. The algorithm uses a novel data structure that is based on packing and 'overlapping' the reduced representation data into the native word size of the processor. Efficient motion estimation schemes to minimize the memory bandwidth between the processor and cache by exploiting this data structure are developed. These schemes can be tailored with ease to suit different general-purpose processors and media processors.