gebhart/patrepeval huggingface dataset:
Construction of thousands of single cell genome sequencing libraries using combinatorial indexing (2016)

Abstract Single cell genome sequencing has proven to be a valuable tool for the detection of somatic variation, particularly in the context of tumor evolution and neuronal heterogeneity. Current technologies suffer from high per-cell library construction costs which restrict the number of cells that can be assessed, thus imposing limitations on the ability to quantitatively measure genomic heterogeneity within a tissue. Here, we present Single cell Combinatorial Indexed Sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single cell libraries for the purpose of somatic copy number variant detection. In total, we constructed libraries for 16,698 single cells from a combination of cultured cell lines, frontal cortex tissue from Macaca mulatta , and two human adenocarcinomas. This novel technology provides the opportunity for low-cost, deep characterization of somatic copy number variation in single cells, providing a foundational knowledge across both healthy and diseased tissues.
Voclosporin: a novel calcineurin inhibitor for the treatment of lupus nephritis (2022)

Voclosporin is a CNI with a consistent pharmacokinetic-pharmacodynamic relationship resulting from enhanced calcineurin binding and reduced drug and metabolite load. This profile permits therapeutic efficacy in LN at a dose associated with relatively low calcineurin inhibition, and therefore a potentially improved safety profile. Pivotal trials demonstrated a significant benefit of adding voclosporin to standard therapy, with rapid reduction in proteinuria, and a clinically meaningful and significantly higher CRR rate at 1 year. At approved doses for LN, potential advantages of voclosporin versus historical experience with CNIs include lack of need for therapeutic drug monitoring, benign metabolic, lipid and electrolyte profile, and no impact on mycophenolate mofetil levels.
Conjugate Vaccine Production Technology (2014)

Polysaccharide–protein conjugate vaccines have proven to be effective in preventing diseases caused by encapsulated pathogens. The licensed conjugate vaccines have been prepared for the most part from polysaccharides that were previously licensed as vaccines. Because of the success of conjugates, they are supplanting their polysaccharide counterparts. Our understanding of the technology of conjugate design has evolved over the last 20 years; nevertheless, there remains only a limited repertoire of reactions used in the manufacture of conjugate vaccines. These conjugation reactions are described in this chapter. The potency of polysaccharide and polysaccharide–protein conjugate vaccines is associated with their physicochemical characteristics. The characterization of conjugate vaccines is discussed.
Two-Photon Laser-Assisted Device Alteration in Silicon Integrated Circuits using a 1.28-μm Femtosecond Raman-Soliton Fiber Laser (2013)

By inducing two-photon absorption to perturb the switching characteristics of sensitive transistors located within the active layer of a proprietary 28-nm silicon test chip, we demonstrate time-resolved nonlinear laser-assisted device alteration.
8*10 Gb/s transmission through 280 km of dispersion-managed fiber (1993)

Eight WDM channels each operating at 10 Gb/s were transmitted through 280 km of dispersion-shifted fiber concatenated with small amounts of conventional fiber. No degradations from optical nonlinearities were observed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Indium phosphide passivation using thin layers of cadmium sulfide (1995)

The electrical properties of the silicon dioxide/n-type (100) InP interface were significantly improved by thin interlayers of chemical bath deposited CdS. The CdS layer and CdS/InP interface were investigated with x-ray photoelectron spectroscopy (XPS) and photoluminescence (PL). XPS data showed reduction of native oxides and the prevention of subsequent substrate oxide growth following CdS layer deposition. PL spectra, measured between 1.0 and 1.3 μm, indicate a reduction in phosphorus vacancies. Metal–insulator–semiconductor (MIS) capacitors fabricated with CdS-treated InP substrates displayed interface-state densities below 1×1011 eV−1 cm−2 when determined from the difference between the high- and low-frequency capacitance data.
Palladium-Catalyzed C–N Coupling of Pyrazole Amides with Triazolo- and Imidazopyridine Bromides in Ethanol (2021)

An efficient palladium-catalyzed coupling between a pyrazole amide and a heteroaryl bromide was developed to enable the streamlined synthesis of a lead candidate for schizophrenia treatment. Process robustness and scalability were achieved using ethanol as a solvent. The Xantphos ligand employed in the catalytic system was found to be key to prevent common side reactions arising from the alcoholic solvent. The scope of the methodology was investigated and is presented.
From Lignocellulosic Biomass to Furans via 5‐Acetoxymethylfurfural as an Alternative to 5‐Hydroxymethylfurfural (2015)

A facile pathway to furan derivatives from lignocellulosic biomass via 5-acetoxymethylfurfural (AMF) was developed. AMF possesses advantageous properties due to its less-hydrophilic acetoxymethyl group relative to the hydroxymethyl group of 5-hydroxymethylfurfural (HMF). The hydrophobicity and chemical stability of AMF allowed practical isolation and purification to afford a highly pure product of up to 99.9 %. AMF was produced in good to excellent yields under mild conditions from 5-chloromethylfurfural (CMF) and alkylammonium acetates, both of which could be obtained directly from lignocellulosic biomass. Heterogeneous reactions with polymer-supported alkylammonium acetates were also established; this showed the feasibility of a continuous process for this pathway. AMF could be transformed into various promising furanic compounds, such as 2,5-furandicarboxylic acid (FDCA), 2,5-furandimethanol (FDM), and 5-hydroxymethyl-2-furanoic acid (HFA), in high yields.
Genome Wide Sequencing Compared to Candidate Gene Association Studies for Predisposition to Substance Abuse a Subset of Reward Deficiency Syndrome (RDS): Are we throwing the Baby Out with the Bathwater? (2014)

In 1990 Blum, Noble and associates utilized a candidate approach to associate the first genetic polymorphic association with severe alcoholism that was published in JAMA. This experiment was based on a “blue print” of the reward circuitry proposed as the “brain Reward Cascade”. Impairment of this system leads to aberrant substance seeking behavior. Over the last five years newer and more sophisticated techniques have been developed, including whole genome sequencing, as well as exome sequencing. While there are different schools of thought regarding appropriate approaches to dissecting a very complex disorder known as Reward Deficiency Syndrome (RDS) as an umbrella term for all addictions, future approaches may combine both genome sequencing with gene candidates. Importantly, GWAS/WES generally provides the most value for highly penetrant, rare alleles and as such may not currently be as informative as the candidate gene approach. However, since there is convergence of GWAS and neurotransmitter clusters including specific genes (e.g. DRD1, DRD2, DAt1, etc.) albeit small contributions for each gene, thousands of studies have elucidated risk alleles to RDS behaviors. Thus, we are proposing herein that we should not hasten to “throw out the baby with the bathwater”, because genetic addiction risk stratification depends upon the current candidate gene analysis.
Sound Radiation From a Finite Cylinder (1996)

Abstract A formulation is derived which expresses the radiated acoustic pressure in terms of the tangential and normal components of the particle velocity at the surface of a vibrating object. The boundary condition at an impermeable surface requires that the normal component of the particle velocity be equal to that of the surface velocity, which is usually specified for acoustic radiation problem. The tangential component of the particle velocity is different from that of the surface velocity, but can be determined by using an intensity probe. In this paper, both the tangential and normal components of the particle velocity at the surface of a vibrating object are assumed specified. Hence the radiated acoustic pressure can be obtained by direct integrations of these known quantities over the surface. The formulation thus derived is validated on sound radiation from a right cylinder of finite length.
Assessment of Cumulative Lifetime Seaway Loads for Ships (2002)

ABSTRACT This paper presents a reliability‐based design methodology for primary seaway loadings on surface ships. The goal for such a design methodology is to have one consistent method for developing extreme primary hull girder loads for reliability‐based strength design criteria as well as lifetime exceedance loads for reliability‐based fatigue strength design criteria. The primary hull girder loads, i.e., vertical bending, lateral bending, and torsion, include contributions from both the low frequency (wave‐induced) and the high frequency (slam‐induced) domains for vertical and lateral bending. The contributions of secondary loads, such as hydrostatic and dynamic pressure loads, are important but are beyond the scope of this paper. A method is presented for calculating lifetime seaway loads as functions of ship and seaway parameters. The method is embodied in a PC based computer program called SPECTRA.
Hexagonal vs Rhombohedral Graphite: the Effect of Crystal Structure on Electrochemical Intercalation of Lithium Ions (1998)

Abstract Graphite samples with different crystalline characteristics were evaluated as negative materials for lithium ion batteries. Conversely to non crystalline coke materials, they were found to experience exfoliation problems to a variable extent during the first electrochemical reduction process. A clear correlation was found between their rhombohedral phase content and their resistance to exfoliation. Key Words: graphitelithiumintercalationexfoliation
Cable Fault Detection: Optical Fiber Current Sensor Cable Link Noise Reduction (2020)

In fiber optic current sensors, two main parts, the sensor head unit and the drive/control/chassis unit, are connected by optical fiber cable links. The fiber link carries measurement information from the sensor to an electronics chassis faraway. The optical cable can be wrapped around the main high voltage/current conductors to reduce cost. However, a fiber wrapped around the conductor will have an induced Faraday effect due to the power conductor magnetic field. This creates an unwanted current signal pickup. Also, vibrational pickup due to the macro and micro bend loss of this fiber cable is present as well. These unwanted signals interfere with electric current measurement in a very problematic and erratic way. We have demonstrated by employing optical depolarizers in the sensor fiber link a method of reducing unwanted vibrational and current pickup in the sensor.
Accurate bit-error-rate estimation for OFDM based telecommunication systems schemes in the presence of nonlinear distortions (2002)

This paper proposes a quasi analytical method for estimating the Bit-Error-Rate (BER) of Orthogonal Frequency Domain Multiplexing (OFDM) modulation schemes suffering from nonlinear distortions somewhere in the transmission path. The presented method splits the different transmitted signals into different classes according to their crest factor. Signals with a high crest factor will in general suffer more from nonlinear distortion than signals with a low crest factor. Dividing the signals according to their crest factor makes it possible to use whatever appropriate BER estimation method. The classes of signals that suffer from a large BER can, for example, be simulated more efficiently using a Monte-Carlo simulation, while low BER estimation can be done more efficiently using a quasi analytical method. Hence, the overall method requires only a relative small number of experiments. The method is verified on both simulations and measurements.
Backscattering Mueller Matrix Analysis for Biomedical Optical Diagnostics (1998)

We report on the development of a method that records spatially dependent intensity patterns of polarized light that is diffusely backscattered from highly scattering media. It is demonstrated that these intensity patterns can be used to differentiate turbid media, such as polystyrene-sphere and biological-cell suspensions. Our technique employs polarized light from a He-Ne laser, which is focused onto the surface of the scattering medium. A surface area of approximately 4×4 cm centered on the light input point is imaged through polarization-analysis optics onto a CCD camera. One can observe a large variety of intensity patterns by varying the polarization state of the incident laser light and changing the analyzer configuration to detect different polarization components of the back-scattered light. Introducing the Mueller-matrix concept for diffusely backscattered light, a framework is provided to select a subset of measurements that comprehensively describe the optical properties of backscattering media.
The SoftRouter Architecture (2004)

In urrent routers, implementations of the \nontrol and for-warding fun\ntions are \nolo\nated and tightly integrated by stati asso\niation of \nontrol and forwarding elements. In this paper, we present the SoftRouter ar\nhite\nture that permits dynami\n asso\niation between \nontrol and forward-ing elements, and separates the implementation of \non-trol plane fun\ntions from pa\nket forwarding fun\ntions. In this ar\nhite\nture, all \nontrol plane fun\ntions are imple-mented on general purpose servers \nalled the \nontrol el-ements (CE&apos;s) that \nould be multiple hops away from the forwarding elements (FEs). A network element (NE) or a router is formed using dynami\n binding between the CEs and the FEs. We argue that this \nexibility results in sev-eral benets in\nluding in\nreased reliability, in\nreased s\nal-ability, in\nreased se\nurity, ease of adding new fun\ntionality, and de\nreased \nost. 1.
MLR: a recovery method for multi-level systems (1992)

To achieve high concurrency in a database system has meant building a system that copes well with important special cases. Recent work on multi-level systems suggest a systematic path to high concurrency. A multi-level system using locks permits restrictive low level locks of a subtransaction to be replaced with less restrictive high level locks when sub-transactions commit, enhancing concurrency. This is possible because sub-transactions can be undone via high level compensation actions rather than by restoring a prior lower level state. We describe a recovery scheme, called Multi-Level Recovery (MLR) that logs this high level undo operation with the commit record for the subtransaction that it compensates, posting log records to only a single log. A variant of the method copes with nested transactions, and both nested and multi-level transactions can be treated in a unified fashion.
Highly sensitive optical response of optical fiber long period gratings to nanometer-thick ionic self-assembled multilayers (2005)

Ionic self-assembled multilayers deposited on long period fiber gratings (LPGs) yield dramatic resonant-wavelength shifts, even with nanometer-thick films. Fine control of the refractive index and the thickness of these films was achieved by altering the relative fraction of the anionic and cationic materials combined with layer-by-layer deposition. We demonstrate the feasibility of this highly controllable deposition technique for fine-tuning grating properties. In addition a variety of biological and chemical sensing agents can easily be incorporated into these films, which makes this an attractive platform for realization of high-performance LPG-based sensors.
Phosphoramidates as Steering Elements for Highly Selective Access to Complementary Imidazo[1,2-<i>a</i>]pyrimidine Isomers (2019)

We report that selective <i>N</i>-phosphorylation of aminoimidazoles results in a key steering element that controls isomeric selectivity in the condensation of β-ethoxy acrylamides and aminoimidazoles to furnish imidazo[1,2-<i>a</i>]pyrimidines. We identified conditions that provide highly selective (99:1) phosphorylation at the endo- or exocyclic nitrogen. Either the 2-amino or 4-amino isomer of the (benzo)imidazo[1,2-<i>a</i>]pyrimidine products could be isolated in 64-95% yield. Mass spectrometric analysis and computational studies give insight into the mechanism of this exceptionally selective transformation.
Quantitative Assessment of Artifacts on Cardiac Magnetic Resonance Imaging of Patients With Pacemakers and Implantable Cardioverter-Defibrillators (2011)

In contrast to patients with right-sided PM/ICD and left-sided PM, the anterior and apical left ventricle can be affected by susceptibility artifacts in patients with left-sided ICD. Artifact reduction methodologies will be necessary to improve the performance of CMR in patients with left sided ICD systems.
Comparative Performance of Two Prototypes of a Passive Solar Heat Pipe System (2014)

Thermal performance of an improved passive solar heat pipe system was directly compared to that of a previous prototype. Simulated and experimental results for the first prototype established baseline performance. Subsequently, potential improvements were simulated, and a second prototype was built and tested along side the first. The system uses heat pipes for high rates of heat transfer into the building, and limited losses in the reverse direction. The evaporator section of each heat pipe is attached to a glass-covered absorber on the outside of a south wall, and the slightly elevated condenser section is either immersed in water in a thermal storage tank or exposed to air in the room. Two-phase flow occurs in the heat pipe only when the evaporator is warmer than the condenser, creating a thermal diode effect. Computer simulations showed that system performance could be improved by using thicker insulation between the absorber and the storage tanks, and by switching from a copper to a rubber adiabatic section, which both reduced heat losses to ambient from the storage tanks. Early morning heating was improved by exposing one of five condensers directly to room air, which also improved overall system efficiency. A copper solar absorber soldered to the copper evaporator section improved heat conduction compared to the previous aluminum absorber bonded to the copper evaporator. Together these modifications improved simulated annual solar fraction by 20.8%. The new prototype incorporating these changes was tested along side the previous prototype in a two-room passive solar test facility during January through February of 2013. Temperatures were monitored with thermocouples at multiple locations throughout the systems, in each room and outdoors. Insolation was measured by four pyranometers attached to the building. Results showed that the design modifications implemented for the new model increased thermal gains to storage and to the room, and decreased thermal losses to ambient. The load-to-collector ratio for the experiments was 2.7 times lower than for the simulations, which decreased the potential for experimental improvements compared to the simulated improvements. However, average daily peak efficiency for the new system was 85.0%, compared to 80.7% for the previous system. Furthermore, the average storage temperature over the entire testing period for the new model was 13.4% higher than that of the previous model, while the average room temperature over the same period was 24.6% greater for the new system.
Plasma Process. Polym. 3/2009 (2009)

Cover: Plasma surface processing is used to overcome agglomeration of dry find powders and meet the demand for homogenously functionalized powder particle surfaces. The cover shows a scheme for a down‐stream reactor designed for efficient surface modification and functionalization of particulates. Further details can be found in the article by A. Sonnenfeld, A. Spillmann, C. Arpagaus, and Ph. Rudolf von Rohr * on page 170.
An Efficient Authentication Scheme for Access Control in Mobile Pay-TV Systems (2009)

In a mobile pay-TV system, a large number of messages are exchanged for mutual authentication purposes. In traditional authentication schemes, with one-to-one delivery, one authentication message per request is delivered from a head end system to subscribers. This results in the delivery of a large quantity of messages and therefore is inefficient and costly. Moreover, since most traditional schemes use an RSA-based signature for identity validation and nonrepudiation of communication, they suffer from high communication costs. Due to its wireless nature, mobile pay-TV is vulnerable to attacks during hand-off. As traditional schemes do not support hand-off authentication, they are insecure during hand-off. With these shortcomings, they are not suitable for mobile pay-TV. In this paper, we propose an innovative authentication scheme, in which, by providing one-to-many facility, only one authentication message for multiple requests is broadcasted from the head end system to subscribers. By employing bilinear property of pairing and elliptic curve cryptography, our scheme provides one-to-many facility in the case of multiple requests for the same service in a short period of time. This new scheme achieves better broadcast efficiency and performance on communication costs than traditional ones. Additionally, this scheme provides a hand-off authentication mechanism to protect the access of services while preventing attacks during hand-off; therefore, the scheme is more secure to support access control. Moreover, to provide anonymous authentication for protecting identity privacy, the scheme adopts an identity-based scheme while traditional schemes do not apply. The scheme inherits advantages of the identity-based scheme that a public key does not need to be certificated, the certification authority mechanism will not be needed and the key exchange overhead can be reduced. With these advantages of our scheme, it is well suited for mobile pay-TV system.
Supplementary Figure from Overcoming Taxane Resistance: Preclinical and Phase 1 Studies of Relacorilant, a Selective Glucocorticoid Receptor Modulator, with Nab-Paclitaxel in Solid Tumors (2023)

Supplementary Figure from Overcoming Taxane Resistance: Preclinical and Phase 1 Studies of Relacorilant, a Selective Glucocorticoid Receptor Modulator, with Nab-Paclitaxel in Solid Tumors
CHAPTER 3. Carbohydrate Vaccines (2013)

Carbohydrates started to catch the interest of immunologists in the early 20th century. Vaccines based on bacterial polysaccharides were proven effective to prevent infections, but were overshadowed by antibiotics for a long time. When antibiotic resistances emerged, polysaccharide vaccines rapidly gained importance. However, infants were not protected from infectious disease by vaccines consisting of pure polysaccharides. Protein conjugates of bacterial saccharides were introduced to overcome this challenge. Glycoconjugate vaccines induce immunological memory against pathogens, even in infants, and have become standard in childhood vaccination schedules. Despite the effectiveness of glycoconjugate vaccines, isolation of natural pathogen-derived glycans is often tedious, and numerous measures of quality control have to be taken. Synthetic oligosaccharides facilitate glycoconjugate vaccine manufacturing and serve as tools for detailed mechanistic studies on vaccine immunology. Chapter 3 provides insight into the production, mechanisms of action, and future directions of carbohydrate-based vaccines.