gebhart/patrepeval huggingface dataset:
New T2T assembly of Cryptosporidium parvum IOWA annotated with reference genome gene identifiers (2023)

<i>Cryptosporidium parvum</i> is a significant pathogen causing gastrointestinal infections in humans and animals, that is spread through the ingestion of contaminated food and water. Despite its global impact on public health, generating a <i>C. parvum</i> genome sequence has always been challenging due to a lack of <i>in vitro</i> cultivation systems and challenging sub-telomeric gene families. A gapless telomere to telomere genome assembly has been created for <i>Cryptosporidium parvum</i> IOWA obtained from Bunch Grass Farms, named here as CpBGF. There are 8 chromosomes that total 9,259,183 bp. The new hybrid assembly which was generated with Illumina and Oxford Nanopore resolves complex sub-telomeric regions of chromosomes 1, 7 and 8. To facilitate ease of use and consistency with the literature, whenever possible, chromosomes have been oriented and genes in this annotation have been given the same gene IDs used in the current reference genome sequence generated in 2004. The annotation of this assembly utilized considerable RNA expression evidence, thus, untranslated regions, long noncoding RNAs and antisense RNAs are annotated. The CpBGF genome assembly serves as a valuable resource for understanding the biology, pathogenesis, and transmission of <i>C. parvum</i>, and it facilitates the development of diagnostics, drugs, and vaccines against cryptosporidiosis.
Bypassing Tor Exit Blocking with Exit Bridge Onion Services (2020)

Tor exit blocking, in which websites disallow clients arriving from Tor, is a growing and potentially existential threat to the anonymity network. This paper introduces HebTor, a new and robust architecture for exit bridges---short-lived proxies that serve as alternative egress points for Tor. A key insight of HebTor is that exit bridges can operate as Tor onion services, allowing any device that can create outbound TCP connections to serve as an exit bridge, regardless of the presence of NATs and/or firewalls. HebTor employs a micropayment system that compensates exit bridge operators for their services, and a privacy-preserving reputation scheme that prevents freeloading. We show that HebTor effectively thwarts server-side blocking of Tor, and we describe the security, privacy, and legal implications of our design.
Identification of a free boundary arising in a magneto-hydrodynamics system (1997)

We study the free boundary problem to identify the plasma region in a stationary tokamak machine using the magnetic flux function. Uniqueness has been proved and the free boundary has been explicitly computed in the case where the domain is an n-dimensional ball. We also derive an energy distribution identity which is applicable to identify the location of the free boundary for more general domains in two-dimensional space.
X-linked Charcot-Marie-Tooth disease, Arts syndrome, and prelingual non-syndromic deafness form a disease continuum: evidence from a family with a novel PRPS1 mutation (2014)

Our findings demonstrate that CMTX5, Arts syndrome and DFN2 are phenotypic clusters on an intrafamilial continuum, including overlapping phenotypes even within individuals. The respective phenotypic presentation seems to be determined by the exact PRPS1 mutation and the residual enzyme activity, the latter being largely influenced by the degree of skewed X-inactivation. Finally, our findings show that brain atrophy might be more common in PRPS1-disorders than previously thought.
Controlled Expansion of Peripheral Nerves (1991)

The inherent disadvantages of nerve grafting have made it necessary to find alternative techniques for treating segmental nerve loss. This study compares the techniques of nerve grafting and nerve expansion/repair for the management of nerve injuries with segmental nerve loss in an animal model. Bilateral segmental sciatic nerve defects were created in eight dogs. On one side a 2-cm segment was excised and replaced with a nerve graft; on the other side a 2-cm defect was created with ligatures and the nerve underwent preliminary expansion and then repair. Eighteen months later nerve conduction velocity (NCV), gastrocnemius contraction force (GCF), and muscle weight (GMW) were determined for the seven surviving animals. NCV for the expanded repair was 58.66 ± 34.18 m/sec and 47.73 ± 7.93 for the grafted repair (p = 0.4); GCF was 619.04 ± 353.70 gm for the expanded repair and 726.80 ± 415.78 gm (p = 0.2) for the grafted repair; and GMW was 82.80 ± 5.68 gm for the expanded repair and 109.55 ± 20.63 gm (p = 0.02) for the grafted repair. The data suggest that: 1) conventional tissue expansion techniques can be used successfully to repair segmental peripheral nerve defects; 2) NCV and GCF are comparable for grafting and expansion/repair techniques although GMW is significantly higher in the grafted group; and 3) nerve expansion/repair may prove to be a useful alternative to grafting.
Survey of Metallic Multilayer Studies (2003)

Studies on artificially structured multilayers by the author's group for about 20 years are briefly surveyed. In many combinations of metallic elements, establishment of nanoscale superstructures has been confirmed, which suggests the potensial to create new materials. The novel phenomenon, giant magnetoresistance (GMR), was found first in Fe/Cr multilayers and the technical application of the GMR principle has been successfully realized as the spin-valve recording head. Perspectives for further studies on magnetic multilayers are also mentioned.
Requirements for benchmarking personal image retrieval systems (2006)

It is now common to have accumulated tens of thousands of personal ictures. Efficient access to that many pictures can only be done with a robust image retrieval system. This application is of high interest to Intel processor architects. It is highly compute intensive, and could motivate end users to upgrade their personal computers to the next generations of processors. A key question is how to assess the robustness of a personal image retrieval system. Personal image databases are very different from digital libraries that have been used by many Content Based Image Retrieval Systems.<sup>1</sup> For example a personal image database has a lot of pictures of people, but a small set of different people typically family, relatives, and friends. Pictures are taken in a limited set of places like home, work, school, and vacation destination. The most frequent queries are searched for people, and for places. These attributes, and many others affect how a personal image retrieval system should be benchmarked, and benchmarks need to be different from existing ones based on art images, or medical images for examples. The attributes of the data set do not change the list of components needed for the benchmarking of such systems as specified in<sup>2</sup>: - data sets - query tasks - ground truth - evaluation measures - benchmarking events. This paper proposed a way to build these components to be representative of personal image databases, and of the corresponding usage models.
Clinical effects and possible mechanisms of action of stannous fluoride. (1994)

Stannous fluoride was frequently used as a vehicle for fluoride in preparations used in caries prophylaxis in the 1960s and 1970s. At present it is not much used, although extensive research during the last two decades has established that stannous fluoride possesses several interesting properties which demonstrate that it deserves to be used in the prophylaxis against both gingivitis and caries. In the following, a review of the clinical properties of stannous fluoride is presented, together with a discussion of its merits compared with other fluoride vehicles in current use.
Porous silicon technology for integrated microsystems (2006)

With the development of micro systems, there is an increasing demand for integrable porous materials. In addition to those conventional applications, such as filtration, wicking, and insulating, many new micro devices, including micro reactors, sensors, actuators, and optical components, can benefit from porous materials. Conventional porous materials, such as ceramics and polymers, however, cannot meet the challenges posed by micro systems, due to their incompatibility with standard micro-fabrication processes. In an effort to produce porous materials that can be used in micro systems, porous silicon (PS) generated by anodization of single crystalline silicon has been investigated. In this work, the PS formation process has been extensively studied and characterized as a function of substrate type, crystal orientation, doping concentration, current density and surfactant concentration and type. Anodization conditions have been optimized for producing very thick porous silicon layers with uniform pore size, and for obtaining ideal pore morphologies. Three different types of porous silicon materials: meso porous silicon, macro porous silicon with straight pores, and macro porous silicon with tortuous pores, have been successfully produced. Regular pore arrays with controllable pore size in the range of 2µm to 6µm have been demonstrated as well. Localized PS formation has been achieved by using oxide/nitride/polysilicon stack as masking materials, which can withstand anodization in hydrofluoric acid up to twenty hours. A special etching cell with electrolytic liquid backside contact along with two process flows has been developed to enable the fabrication of thick macro porous silicon membranes with though wafer pores. For device assembly, Si-Au and In-Au bonding technologies have been developed. Very low bonding temperature (~200 degrees C) and thick/soft bonding layers (~6µm) have been achieved by In-Au bondi ng technology, which is able to compensate the potentially rough surface on the porous silicon sample without introducing significant thermal stress. The application of the porous silicon material in micro systems has been demonstrated in a micro gas chromatograph system by two indispensable components: an integrated vapor source and an inlet filter, wherein porous silicon performs the basic functions of porous media: wicking and filtration. By utilizing a macro porous silicon wick, the calibration vapor source was able to produce a uniform and repeatable vapor generation for n-decane with less than a 0.1% variation in 9 hours, and less than a 0.5% variation in rate over 7 days. With engineered porous silicon membranes the inlet filter was able to show a depth
Web Tracking: Mechanisms, Implications, and Defenses (2015)

This articles surveys the existing literature on the methods currently used by web services to track the user online as well as their purposes, implications, and possible user's defenses. A significant majority of reviewed articles and web resources are from years 2012-2014. Privacy seems to be the Achilles' heel of today's web. Web services make continuous efforts to obtain as much information as they can about the things we search, the sites we visit, the people with who we contact, and the products we buy. Tracking is usually performed for commercial purposes. We present 5 main groups of methods used for user tracking, which are based on sessions, client storage, client cache, fingerprinting, or yet other approaches. A special focus is placed on mechanisms that use web caches, operational caches, and fingerprinting, as they are usually very rich in terms of using various creative methodologies. We also show how the users can be identified on the web and associated with their real names, e-mail addresses, phone numbers, or even street addresses. We show why tracking is being used and its possible implications for the users (price discrimination, assessing financial credibility, determining insurance coverage, government surveillance, and identity theft). For each of the tracking methods, we present possible defenses. Apart from describing the methods and tools used for keeping the personal data away from being tracked, we also present several tools that were used for research purposes - their main goal is to discover how and by which entity the users are being tracked on their desktop computers or smartphones, provide this information to the users, and visualize it in an accessible and easy to follow way. Finally, we present the currently proposed future approaches to track the user and show that they can potentially pose significant threats to the users' privacy.
Discovering Point Lights with Intensity Distance Fields (2018)

We introduce the light localization problem. A scene is illuminated by a set of unobserved isotropic point lights. Given the geometry, materials, and illuminated, appearance of the scene, the light localization problem is to completely recover the number, positions, and intensities of the lights. We first present a scene transform that identifies likely light positions. Based on this transform, we develop an iterative algorithm to locate remaining lights and determine all light intensities. We demonstrate the success of this method in a large set of 2D synthetic scenes, and show that it extends to 3D, in both synthetic scenes and real-world scenes.
Initial Field Installation of Manganese Indicators of Reduction in Soils, Brooks Range, Alaska (2010)

Ten manganese indicators of reduction in soils (MIRIS) and five iron reduction indicator in soils (FIRIS) tubes were installed in a calcareous fen wetland on the south face of the Brooks Range in northern Alaska. Tubes were set in five groups of two MIRIS and one FIRIS across a landscape transect with hydric soils experiencing high pH/Eh conditions at the wetland, and one set of six MIRIS tubes was installed in a well‐drained mid‐slope position. The wetland MIRIS displayed oxide paint removal within 4 d, whereas the FIRIS installed at the same location for 6 wk (recommended installation interval for FIRIS) displayed &lt;10% oxide removal in four of the five locations and experienced concentration of the iron oxide on the upper 10 cm of the tube. Three of the five FIRIS also had pyrite (FeS 2 ) formation on 10 to 20% of their surface areas. After 7 d of installation in the upland, MIRIS did not experience significant removal, indicating that the MIRIS oxide removal in the wetland was due to reduction alone. The rapid removal of MIRIS oxide in high pH/Eh conditions in comparison with the limited removal of oxide from FIRIS supports the idea that MIRIS is a suitable tool to determine the presence of reducing conditions in wetlands unfavorable to Fe reduction. The experiment also showed that pyrite formation on FIRIS should be considered as a proxy for oxide removal in high pH conditions that inhibit Fe reduction.
Acquired Immune Deficiency Syndrome and Systemic Lupus Erythematosis (2008)

Compartment Syndrome (CS) is a disease that has 2 etiologies, that of acute events and that of chronic. It occurs when the pressure in a fascia-encased compartment exceeds the profusion pressure in tissue. The end result, when left untreated, is muscle and nerve ischemia that can cause significant morbidity. Nerve paralysis, muscle necrosis and fibrosis and, when occurring in an extremity, loss of the limb are some of the potential outcomes of missed diagnosis. This case series involves 2 cases of CS that where caused by vasculitis with etiologies of human immunodeficiency virus and systemic lupus erythematosis. Autoimmune vasculitis has many systemic and local manifestations, but to our knowledge CS has not been described as one of its sequelae. The following is literature review and presentation of these 2 cases.
Exercise capacity in patients with hypertrophic cardiomyopathy: non-invasive hemodynamic responses to exercise and association with clinical and imaging variables (2013)

Background and aim: Hypertrophic cardiomyopathy (HCM) could be characterized by reduced exercise capacity. The intrinsic mechanisms affecting a reduced functional tolerance are not completely understood. The aim of the study was to determine the association between cardiopulmonary exercise test (CPET), non-invasively-determined hemodynamic variables, and clinical and echocardiographic variables and outcomes in patients with HCM. Methods: The study sample included 156 patients consecutively enrolled from 2007 to 2012 with a complete clinical assessment, including exercise echocardiography and CPX with impedence cardiography. Patients were followed for the composite outcome of cardiac-related death, heart transplant and functional deterioration leading to septal reduction (myectomy or alcholization). A Cox proportional hazard model was used to quantify determinants of the composite outcome. Results: Abnormalities in CPET parameters were commonly observed, with 39% (n=61) of our patients showing a reduced exercise tolerance (VO2 max < 80% of the predicted) and the 19% (n=30) characterized by an impaired ventilatory efficiency (VE/VCO2 > 34). The variables that were independently associated with peak VO2 (R2=0.65) were age (r=-0.32, p<0.001), male sex (r=0.31, p=0.001), E/E' (r=-0.24, p=0.014) and peak cardiac index (CI) (r=0.61, p<0.001). The variables most strongly associated (R2= 0.15) with VE/VCO2 slope were E/E' (r=0.23, p=0.021) and indexed left atrial volume (LAVi) (r=0.34, p=0.005). In our exploratory analysis, three variables were independently associated with the composite outcome (mean follow-up: 27±13 months): peak VO2 less than 80% of predicted (HR: 4.11 CI 1.46 to 11.59, p=0.008), VE/VCO2 slope > 34 (HR: 3.14 CI 1.26 to 7.87, p=0.014) and LAVi > 40 ml/m2 (HR: 3.32 CI 1.08 to 10.16, p=0.036). Conclusions: In HCM peak CI is the main determinant of exercise capacity, but is not significantly related to ventilatory efficiency. Peak VO2, ventilatory efficiency and LAVi are major independent predictors of short/medium-term outcomes in HCM and could be helpful in the prognostic stratification of these patients.
Orientation of erythrocytes in a strong static magnetic field (1993)

The frequency of exposure to strong magnetic fields has increased as the magnetic-resonance image-diagnostic technique (MRI) and passenger transport systems based on the principle of magnetic levitation have come into wider use. Accordingly, it has become necessary to more systematically assess their influence on the body and set strict guidelines on acceptable limits of magnetism exposure. Therefore, we have assessed the influence of an uniform static magnetic field (8 T in maximum) on normal erythrocytes. The erythrocytes were oriented with their disk plane parallel to the magnetic field direction. These erythrocytes were influenced even by 1 T and almost 100% of them were oriented when exposed to 4 T. Furthermore, the degree of orientation was not influenced by the state of hemoglobin (oxy: diamagnetic, deoxy and met: paramagnetic). The dependence of the measured degree of orientation on the intensity of the magnetic field was in good agreement with the theoretical equation for the magnetic orientation of diamagnetic substances. As a result of a numerical analysis based on the equation, the anisotropic diamagnetic susceptibility of erythrocytes was found to be delta chi = 8 x 10(-22) electromagnetic units/erythrocyte. It was almost in agreement with the calculated value delta chi = 6 x 10(-22) emu/erythrocyte estimated from the diamagnetism of the membrane constituents of erythrocyte.
A Useful Guide for X-Ray Stress Evaluation (XSE) (1983)

Abstract This paper summarizes experiences available for the measurement of lattice strains in different materials with different wavelengths to evaluate stresses by means of X-rays. The recommendations given are based on previous statements. Some principles of fundamentals of X-ray physics for the recording of interference lines with Ω and ψ-diffractometers are dealt with. Methods applicable for the determination of the peak position of the interference lines, the assessment of linear and non-linear lattice strain distributions, and tine calculation of stresses are outlined. For iron, aluminium, copper, nickel and titanium the constants for practical X-ray stress evaluation (XSE) and the parameters of measurement are tabled.
Perception of stress and speaking style for selected elements of the s u s a s database (1999)

The susas database [J. H. L. Hansen and S. E. Bou-Ghazale, EUROSPEECH 97, 1743–1746 (1997)] is a collection of utterances recorded under conditions of simulated or actual stress, the purpose of which is to allow researchers to study the effects of stress and speaking style on the speech waveform. The aim of the present investigation was to assess the perceptual validity of the simulated portion of the database by determining the extent to which listeners classify its utterances according to their assigned labels. Seven listeners performed an eight-alternative, forced-choice, judging whether monosyllabic or disyllabic words spoken by talkers from three different accent classes (Boston, Generic Midwest, New York) were best classified as ‘‘angry,’’ ‘‘clear,’’ ‘‘fast,’’ ‘‘loud,’’ ‘‘neutral,’’ ‘‘question,’’ ‘‘slow,’’ or ‘‘soft.’’ Mean percentages of ‘‘correct’’ judgments were analyzed using a 3 (accent class)×2 (number of syllables)×8 (speaking style) repeated measures analysis of variance. Results indicated that, overall, listeners correctly classify the utterances only 58% of the time, and that percentage of correct classifications varies as a function of all three independent variables.
Optical performance characterisation of HERSCHEL/SPIRE (2006)

The Spectral and Photometric Imaging Receiver (SPIRE) is one of three scientific instruments on ESA's Herschel Space Observatory. The instrument covers 200 to 670 &#956;m with a three band photometric camera and a two band imaging Fourier Transform Spectrometer (IFTS). In this paper we discuss the performance of the optics of the instrument as determined during the pre-flight instrument testing to date. In particular we concentrate on the response of the instrument to a point source, the comparison between the visible light alignment and the infrared alignment and the effect of the optical performance on the overall instrument sensitivity. We compare the empirical performance of the instrument optics to that expected from elementary diffraction theory.
ChemInform Abstract: SYNTHESIS OF 1,1′‐, 2,2′‐, 1,2′‐, AND 2,6′‐BIAZULENES AND THEIR DERIVATIVES BY THE ULLMANN REACTION (1982)

Abstract Die Darstellung der Titelverbindungen (IIIc), (Vb), (VIIb) und (IX) sowie einer Reihe davon" abgeleiteter Verbindungen wird beschrieben.
Enantioselective Synthesis of the 5–6–7 Carbocyclic Core of the Gagunin Diterpenoids (2013)

A catalytic enantioselective double allylic alkylation reaction has been employed in the synthesis of the core of the gagunin diterpenoids. Enantioenriched material was advanced in 11 steps to afford the core of the highly oxygenated target, which includes two all-carbon quaternary stereocenters.
A Model to Characterize the D-T Layer of ICF Targets by Backlit Optical Shadowgraphy (2005)

A numerical model is presented in order to modelize the bright ring that appears in backlit optical shadowgraphy on a transparent hollow sphere with a solid deuterium-tritium layer inside. This novel model is based on computational calculations applied to the problem of the targets used in inertial confinement fusion.The model takes into account the influences of the optical imaging system (numerical aperture, source divergence, camera resolution, etc.) and the effect of the capsule itself, diameter, thickness, and refractive index, and allows one to analyze the inner surface of a capsule in terms of thickness and roughness.