gebhart/patrepeval huggingface dataset:
Characterization of two hepatitis B virus populations isolated from a hepatitis B surface antigen-negative patient (2002)

In a study of surface antigen-negative, but weakly hepatitis B virus (HBV) DNA-positive, patients, we were able to amplify and clone whole HBV genomes from the serum of a cirrhotic patient. Sequencing showed that the patient harbored two different HBV populations, one of genotype A and the other of genotype D, with the genotype D genome apparently predominating. The surface antigen of the genotype A virus is heavily mutated, especially in the extracellular << determinant a >> region, with several mutations that have not been previously described. The genotype D virus is a precore mutant. Both genomes possess the common A1762T-G1764A double mutation of the basal core promoter (BCP), and the genotype D virus is also mutated in the << TATA box >> of the large surface antigen promoter. Biological characterization showed that the genotype A genome was fully replication-competent, whereas the genotype D genome replicated poorly. The small surface antigen of the genotype A virus was only very weakly recognized by commercial tests. The small surface antigen of the genotype D virus could be recognized by the tests, but it was mainly retained within transfected cells, probably because of an excess of large surface antigen. In conclusion, the cryptic nature of this double HBV infection is characterized by the predominance of the replication-deficient genotype D virus over the replication-competent genotype A virus.
Deep Brain Stimulation (DBS) : Current and Emerging Applications (2014)

Deep brain stimulation (DBS) is a safe and effective treatment for medically refractory movement disorders such as Parkinson's disease, essential tremor and dystonia. The success of DBS in treating movement disorders with over 100,000 patient implants has revived interest in the use of DBS for the neurosurgical management of refractory conditions including epilepsy, psychiatric disorders (obsessive compulsive disorder, major depressive disorder, addictions, and eating disorders), neuropathic chronic pain, headaches, cognitive disorders, and traumatic brain injury. This manuscript provides a review of the current application of DBS surgery in movement disorders, psychiatric and other conditions. Additionally, an overview of the recent advances in our understanding of the neural circuitry underpinning the pathophysiology of these disorders is provided. The use of imaging and the latest surgical techniques to target these structures will be highlighted. Furthermore, new technology such as the introduction of the “closed loop system”, smart DBS devices, responsive brain stimulation and emerging neuromodulation approaches will be discussed.
Proteomic analyses of different human tumour-derived chaperone-rich cell lysate (CRCL) anti-cancer vaccines reveal antigen content and strong similarities amongst the vaccines along with a basis for CRCL's unique structure: CRCL vaccine proteome leads to unique structure (2013)

We conclude that it is feasible to prepare and characterise CRCL from a variety of different tissue sources; a substantial portion of the protein content is identical among the different CRCLs, while the overall compositions also suggest high overlaps in functional categories. The protein content indicates the presence of antigens and implies a potential structure, which we believe may play a role in CRCL's ability to stimulate innate antigen presenting cell activation.
Mechanical and Chemical Stability of Monolayer Black Phosphorous Studied by Density Functional Theory Simulations (2018)

Simulations based on electronic density functional theory have been employed to study the stability of phosphorene under mechanical stress as well as oxidative conditions. To understand the mechanical response, biaxial strain was applied along zigzag and armchair directions, and the potential energy surface was generated. Poisson’s ratio and Young’s modulus were calculated along each direction revealing the anisotropic response of the material. Under large strain conditions, several stable or metastable phases were identified including transformation from black phosphorus to white phosphorus and polymeric phases. To evaluate the chemical stability, surface mixing energies of phosphorene oxide were calculated as a function of oxygen coverage. Results indicate the formation of PO3 and PO4 chains at oxygen coverage above 0.5 monolayers, suggesting a multistep oxidation process that leads ultimately to the formation of P2O5. Ab initio molecular dynamics simulations with an additional water molecule revealed the hydrophobic nature of pristine black phosphorus in comparison to the hydrophilic nature of oxidized black phosphorus.
A Fully Integrated 2$\,\times\,$2 Power Amplifier for Dual Band MIMO 802.11n WLAN Application Using SiGe HBT Technology (2009)

A fully monolithic 2 times 2(2 times 5 GHz-band, 2 times 2.4 GHz-band) power amplifier (PA) implemented in a 0.18 mum Silicon Germanium (SiGe) HBT process has been developed for a dual band MIMO 802.11n WLAN system. In order to achieve the required performance for the 5 GHz band while maintaining a high level of integration, different approaches have been investigated. A special Through-Wafer-Via (TWV) process on Si wafer was developed and utilized for this 2 times 2 PA. From fabricated 2 times 2 chip measurement results, both 5 GHz-band and 2.4 GHz-band PAs show above 17 dBm linear power output for -28 dB EVM and more than 18 dBm with >14% efficiency for 5 GHz-band and 19% efficiency for 2.4 GHz-band at -25 dB EVM linear output.
On Trigonometric Formulations of Polynomial Equations (2006)

The displacement analysis of open and closed kinematic chains is based on polynomial equations whose variables are functions of relative joint displacements. The objective of this paper is to investigate new and interesting properties of the transformations between the canonical cosine-sine polynomials and the even degree tan-half angle polynomials associated with displacement kinematics. Using a homogeneous coordinate formulation, it is shown that the coefficients of the polynomials are linearly related by a projective transformation whose elements can be defined recursively. The canonical cosine-sine polynomial is then transformed to a cosine or a sine polynomial which can be rooted by usual techniques. However, all real roots are bracketed between −1 and +1 which can have numerical advantages over a corresponding tan-half angle polynomial for which the entire real axis must be searched. It is also demonstrated how polynomial solutions corresponding to circular points at infinity in the tan-half angle, which are typically introduced as extraneous roots via algebraic elimination, may be easily factored out by the transformation to the cosine-sine formulation.
Characterization of the recombinant human prostanoid DP receptor and identification of L‐644,698, a novel selective DP agonist (1998)

1. A human embryonic kidney cell line [HEK 293(EBNA)] stably expressing the human recombinant prostaglandin D2 (PGD2) receptor (hDP) has been characterized with respect to radioligand binding and signal transduction properties by use of prostanoids and prostanoid analogues. Radioligand binding studies included saturation analyses, the effects of nucleotide analogues, the initial rate of ligand-receptor association and equilibrium competition assays. In addition, adenosine 3':5'-cyclic monophosphate (cyclic AMP) generation in response to ligand challenge was also measured, as this is the predominant hDP signalling pathway. 2. L-644,698 ((4-(3-(3-(3-hydroxyoctyl)-4-oxo-2-thiazolidinyl) propyl) benzoic acid) (racemate)) was identified as a novel ligand having high affinity for hDP with an inhibitor constant (Ki) of 0.9 nM. This Ki value was comparable to the Ki values obtained in this study for ligands that have previously shown high affinity for DP: PGD2 (0.6 nM), ZK 110841 (0.3 nM), BW245C (0.4 nM), and BW A868C (2.3 nM). 3. L-644,698 was found to be a full agonist with an EC50 value of 0.5 nM in generating cyclic AMP following activation of hDP. L-644,698 is, therefore, comparable to those agonists with known efficacy at the DP receptor (EC50): PGD2 (0.5 nM), ZK 110841 (0.2 nM) and BW245C (0.3 nM). 4. L-644,698 displayed a high degree of selectivity for hDP when compared to the family of cloned human prostanoid receptors: EP1 (> 25,400 fold), EP2 (approximately 300 fold), EP3-III (approximately 4100 fold), EP4 (approximately 10000 fold), FP (> 25,400 fold), IP (> 25,400 fold) and TP (> 25,400 fold). L-644,698 is, therefore, one of the most selective DP agonists as yet described. 5. PGJ2 and delta12-PGJ2, two endogenous metabolites of PGD2, were also tested in this system and shown to be effective agonists with Ki and EC50 values in the nanomolar range for both compounds. In particular, PGJ2 was equipotent to known DP specific agonists with a Ki value of 0.9 nM and an EC50 value of 1.2 nM.
Viktor Nikolaevich Ivanov: the Director of the Leningrad Institute of Chemistry and Pharmacy in the 1950s (2021)

The article is dedicated to the director of the Leningrad Chemical and Pharmaceutical Institute (now the Saint Petersburg Chemical and Pharmaceutical University), a specialist in the field of chemical absorbers, Viktor Nikolaevich Ivanov, who headed the university in 19511958. The contribution to the development of chemical science has been revealed, also the activities during the years of the defense of Leningrad in 19411944 have been traced. In addition to the Chemical and Pharmaceutical Institute, his teaching activities were associated with the Leningrad and Moscow State Universities. During the era of his directorship at the Chemical and Pharmaceutical Institute, he managed to significantly strengthen the teaching staff, including specialists in the humanities, the famous sociologist I. S. Kon, as well as construct a new building and create a medicinal plant nursery in Lembolovo.
LISA interferometry: recent developments (2006)

LISA, the Laser Interferometer Space Antenna, will be launched by NASA and ESA in the 2014 timeframe and will be the first gravitational wave observatory for the many fascinating sources at low frequencies (down to 10 -5 Hz). One of the challenges is to perform precision laser interferometry over a distance of 5 million km. This paper describes recent developments in the interferometer design.
3-Dimensional Computer Simulation of Plasma Confinement in a Resonant RF Cavity Aided by a Magnetic Mirror: Single Particle Trajectories (1978)

The 3-dimensional trajectories of a single, charged particle within the fields of a resonant microwave cavity and a DC magnetic mirror were computed. The RF fields were due to the TM011 mode of a cylindrical cavity which produces a closed, 3-dimensional, axisymmetric containment region in the center of the cavity. The mirror field was produced by current carrying rings at the ends of the cylinder. The combined fields were able to contain particles which would escape the RF containment well alone. Similarly, the loss cone angles at the ends of the mirror were decreased, a result noted by Gray [1] for a mirror simulated by parabolic magnetic fields aided by a 1-dimensional RF containment well.
ChemInform Abstract: Synthesis of an Immunogenic Template for the Generation of Catalytic Antibodies for (‐)‐Cocaine Hydrolysis. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Dualistic Assessment of Communication Technology Performance for Control of Large-scale Smart Distribution Grids (2016)

The integration of Distributed Energy Resources (DER) and functionalities such as Demand Side Management (DSM) or Automated Meter Reading (AMR) into the electrical grid is progressing with the move towards a more environmentally friendly, decentralized approach to power generation. As deployments of these Smart Grids become more pervasive, advanced monitoring and control schemes lead to an increased importance of communication infrastructures, as they are instrumental in achieving a manageable and stable distribution grid. Therefore the available choices in Information and Communication Technologies (ICT) have to be assessed regarding their capabilities to support the necessary control algorithms and thereby the overall use cases. In this work a dualistic approach employing simulations as well as physical testbeds is presented. This serves to achieve a comprehensive assessment of communication network performance supporting utilities in rollout decisions for large-scale Smart Distribution Grid deployments.
Precise Optical Modulation and Its Application to Optoelectronic Device Measurement (2021)

Optoelectronic devices which play important roles in high-speed optical fiber networks can offer effective measurement methods for optoelectronic devices including optical modulators and photodetectors. Precise optical signal modulation is required for measurement applications. This paper focuses on high-speed and precise optical modulation devices and their application to device measurement. Optical modulators using electro-optic effect offers precise control of lightwaves for wideband signals. As examples, this paper describes frequency response measurement of photodetectors using high-precision amplitude modulation and wavelength domain measurement of optical filters using fast optical frequency sweep. Precise and high-speed modulation can be achieved by active trimming which compensates device structure imbalance due to fabrication error, where preciseness can be described by on-off extinction ratio. A Mach-Zehnder modulator with sub Mach-Zehnder interferometors can offer high extinction-ratio optical intensity modulation, which can be used for precise optoelectronic frequency response measurement. Precise modulation would be also useful for multi-level modulation schemes. To investigate impact of finite extinction ratio on optical modulation, duobinary modulation with small signal operation was demonstrated. For optical frequency domain analysis, single sideband modulation, which shifts optical frequency, can be used for generation of stimulus signals. Rapid measurement of optical filters was performed by using an optical sweeper consisting of an integrated Mach-Zehnder modulator for optical frequency control and an arbitrary waveform generator for generation of a source frequency chirp signal.
Chip-Based Polyketide Biosynthesis and Functionalization (2006)

We demonstrate construction and novel compound synthesis from a synthetic metabolic pathway consisting of a type III polyketide synthase (PKS) known as 1,3,6,8-tetrahydroxynaphthalene synthase (THNS) from Streptomyces coelicolor and soybean peroxidase (SBP) in a microfluidic platform. THNS immobilized to Ni-NTA agarose beads is prepacked into a microfluidic channel, while SBP is covalently attached to the walls of a second microfluidic channel precoated with a reactive poly(maleic anhydride) derivative. The result is a tandem, two-step biochip that enables the synthesis of novel polyketide derivatives. The first microchannel, consisting of THNS, results in the conversion of malonyl-CoA to flaviolin in yields up to 40% with a residence time of 6 min. This conversion is similar to that obtained in several-milliliter batch reactions after 2 h. Linking this microchannel to the SBP microchannel results in biflaviolin synthesis. During the course of this work, we discovered that the substrate specificity of THNS could be manipulated by simply changing the reaction pH. As a result, the starter acyl-CoA specificity can be broadened to yield a series of truncated pyrone products. When combined with variations in the ratio of acyl-CoA and malonyl-CoA (extender substrate) feed rates, high yields of the pyrone products could be achieved, which is further structurally diversified from self- and cross-coupling in the SBP microchannel. The ability to rapidly evaluate the effects of reaction conditions and synthetic multienzyme pathways on a microfludic platform provides a new paradigm for performing metabolic pathway engineering, namely, the reconstruction of pathways for use in new compound discovery.
Receiver Offset Cancellation in 90-nm PLD Integrated SERDES (2007)

A wide-range transceiver was designed and fabricated in a 90-nm TSMC CMOS logic process. Each transceiver channel contains a transmitter and receiver with clock data recovery (CDR) circuit. The range of operation for this transceiver is from 622 Mbps to 6.5 Gbps. Voltage offsets in the receive path degrade the performance of the transceiver by putting a lower bound on the precision with which a data bit can be measured In addition to raising the minimum input voltage that can be correctly detected by the CDR, offsets in receive path cause duty cycle distortion, which, added with inter symbol interference (ISI), reduce the overall margin of data recovery directly worsening the bit error rate (BER). Presented in this paper is a methodology to cancel voltage offsets in the receive path with a soft intellectual property (IP) core programmed in the PLD.
Monoclonal antibodies for successful tumour imaging. (1984)

The monoclonal antibody HMFG-2 which is directed to an oligosaccharide determinant on a large molecular weight mucin-like molecule found in the human milk fat globule reacts positively with breast and ovarian carcinomas. The purified antibody, labelled with 123I has been used successfully to locate ovarian tumours and their metastases in 20 out of 22 patients tested. Here we discuss those features of a) the antibody, b) the antigenic site it reacts with, c) the radioactive label and d) the scanning technique, which have contributed to the successful application of HMFG-2 to the effective imaging of ovarian tumours.
Development of Interactive Visualization System for Unsteady Large-Scale Data Set (2004)

A parallel volume rendering system that incorporated a hardware compositor was developed to visualize unsteady large-scale data set in real-time. This rendering system is constructed by PC-cluster on a master-slave basis, and utilizes hardware functions of GPU on a modern graphics card. At first, a master node divides a data region into several sub-domains, and then each slave node renders the images for each domain. Generated images on each Slave-PC are gathered and overlapped each other according to a BSP tree, which is determined by the relation between an eye point and the position of each domain. This superimpose process is carried out on a composite hardware to minimize the transmission and synthesis time of the images. It was found that the present visualization system achieved enough interactivity with 10-15 fps for time varying data of 25.6GB.
A Modified Footplate for the Kerrison Rongeur (2010)

Use of the Kerrison rongeur for bone removal in spinal surgery is associated with dural tears and cerebrospinal fluid (CSF) leaks. We report a modification of the Kerrison rongeur footplate designed to reduce the risk of dural tears. A novel footplate was designed by incorporating the following parameters: (1) tapering the footplate to deflect soft tissue downward during positioning of the rongeur underneath the bone, and (2) making the footplate longer and wider than the cutting element to prevent soft tissue from entering into the cutting surface. Stereolithography models of the modified footplate were made and tested in a cadaver. A stainless steel modified footplate was then incorporated into an existing Kerrison rongeur as a working prototype, and tested in 20 laminectomy cases to clinically validate its design. The modified footplate prevented soft tissue from entering the cutting surface of the Kerrison rongeur in the manner intended by its design. No dural tears or CSF leaks were encountered in any instance. Potential soft tissue compression caused by an increase in footplate dimensions was not a significant issue in the rongeur size tested. This modification, however, might not be practical in rongeurs larger than 3 mm. The risk of dural tears and cerebrospinal fluid leaks in spinal surgery may be reduced by this footplate modification of the Kerrison rongeur. Soft tissue compression may limit the incorporation of this modification to rongeurs of 3 mm or smaller. The promising results warrant further tests with a wider range of sizes.
Supplementary Data 1 from Investigation of Antigen-Specific T-Cell Receptor Clusters in Human Cancers (2023)

&lt;p&gt;Datasets generated in this study including: Supplementary file -15_antigens. Information for the 15 selected antigens for methodology performance evaluation. Supplementary file -TCRcount_correlation. Summary of association analysis between gene expression levels and clustered CDR3 count in each individual. Supplementary file -New_Group_genes. Summary of differential gene expression analysis between the single cells from new defined group and others, with fold change and FDR estimations. Supplementary file -Trm2vsTrm1_DETable. The differential expressed genes of Trm2vsTrm1. Supplementary file -CDR3_Cluster_Gene_Correlation: Summary of differential gene expression analysis between each CDR3 cluster and other TCGA tumors, with fold change and FDR estimations. Supplementary file -TCGAtcrClustered_iSMART. 4.6K iSMART clustered TCRs from TCGA tumor RNA-seq data.&lt;/p&gt;
Body Image Disturbances and Weight Bias After Obesity Surgery: Semantic and Visual Evaluation in a Controlled Study, Findings from the BodyTalk Project (2021)

OS patients are more psychologically burdened and have more difficulties in judging their bodies than overweight/obese peers. Their mental body representations seem not to be linked to their own BMI. Our findings provide helpful insight for the design of specific interventions in body image in obese and overweight people, as well as in OS.
Additional file 3: of Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks (2015)

1:1 C. elegans gene identifiers for the 1:1 orthologs conserved across the phylum Nematoda. These represent putative phylogenetic markers though their informative value remains to be tested. (TXT 7Â kb)
Multi Source Streaming for Robust Video Transmission in Mobile Ad-Hoc Networks (2006)

Video transmission over networks is getting increasingly important, thus upcoming network types like mobile ad-hoc networks (MANETs) can also become a suitable platform for exchanging/sharing real-time video streams. We present an approach using different sources with linear independent representations of a layered video stream for increasing the robustness in transmission. This approach is based on the scalable video coding (SVC) extensions of H.264/MPEG-4 AVC with different layers for assigning importance for transmission. Additionally a novel unequal packet loss protection (UPLP) scheme based on Raptor forward error correction codes is employed. This scheme allows for reception from different sources and benefits from it. While the reception of a single stream guarantees base quality at least, the combined reception enables play-back of video of full quality and/or lower error rates.
Brief announcement (2013)

The distributed systems research community has developed many provably correct algorithms and abstractions that are in wide use. However, practical implementations of distributed systems often contain many bugs, and practitioners spend much of their time troubleshooting these bugs. In this paper we present an algorithm, retrospective causal inference, to ease the burden of troubleshooting. We end by enumerating several open research problems related to the troubleshooting process.