gebhart/patrepeval huggingface dataset:
Anomalous spectral weight in photoemission spectra of the hole-doped Haldane chainY2−xSrxBaNiO5 (2003)

In this paper, we present photoemission experiments on the hole-doped Haldane chain compound ${\mathrm{Y}}_{2\ensuremath{-}x}{\mathrm{Sr}}_{x}{\mathrm{BaNiO}}_{5}.$ By using the photon-energy dependence of the photoemission cross section, we identified the symmetry of the first ionization states $(d$ type). Hole doping in this system leads to a significant increase in the spectral weight at the top of the valence band without any change in the vicinity of the Fermi energy. This behavior, not observed in other charge-transfer oxides at low doping level, could result from the inhomogeneous character of the doped system and from a Ni $3d--\mathrm{O}2p$ hybridization enhancement due to the shortening of the relevant Ni-O distance in the localized hole-doped regions.
The Cysteine-rich Domain of Snake Venom Metalloproteinases Is a Ligand for von Willebrand Factor A Domains (2006)

Snake venom metalloproteinases (SVMPs) are members of the Reprolysin family of metalloproteinases to which the ADAM (a disintegrin and metalloproteinase) proteins also belong. The disintegrin-like/cysteine-rich domains of the ADAMs have been implicated in their function. In the case of the SVMPs, we hypothesized that these domains could function to target the metalloproteinases to key extracellular matrix proteins or cell surface proteins. Initially we detected interaction of collagen XIV, a fibril-associated collagen with interrupted triple helices containing von Willebrand factor A (VWA) domains, with the PIII SVMP catrocollastatin. Next we investigated whether other VWA domain-containing matrix proteins could support the binding of PIII SVMPs. Using surface plasmon resonance, the PIII SVMP jararhagin and a recombinant cysteine-rich domain from a PIII SVMP were demonstrated to bind to collagen XIV, collagen XII, and matrilins 1, 3, and 4. Jararhagin was shown to cleave these proteins predominantly at sites localized at or near the VWA domains suggesting that it is the VWA domains to which the PIII SVMPs are binding via their cysteine-rich domain. In light of the fact that these extracellular matrix proteins function to stabilize matrix, targeting the SVMPs to these proteins followed by their specific cleavage could promote the destabilization of extracellular matrix and cell-matrix interactions and in the case of capillaries could contribute to their disruption and hemorrhage. Although there is only limited structural homology shared by the cysteine-rich domains of the PIII SVMPs and the ADAMs our results suggest an analogous function for the cysteine-rich domains in certain members of the expanded ADAM family of proteins to target them to VWA domain-containing proteins.
Abstract 16278: Discordant Lipid Phenotype and Other Determinants of Statin Response in the Pravastatin Inflammation/crp Evaluation (PRINCE) Trial (2020)

Introduction: Wide variability in LDL-C change is observed with statins, yet determinants of statin response are uncertain. Methods: Participants were selected from the primary prevention cohort of the Pravastatin Inflammation/CRP Evaluation double-blind trial that randomized participants to pravastatin 40 mg/d or placebo over 24 weeks. Baseline and 24-week levels of LDL-C and 15 other biomarkers were measured in 495 participants. We defined optimal statin response as &gt;=30% LDL-C reduction and suboptimal response as &lt;30% reduction. Sub-optimal hs-CRP response was defined as &gt;=median (14%) decline in hs-CRP from baseline to 24 weeks and non-response as no decrease or an increase in hs-CRP. χ 2 , t-tests and ANOVA were used to compare variables across optimal statin response (N=166) and suboptimal response (N=287). Multivariable logistic regression models evaluated associations of determinants of statin response. Forward selection identified variables that associated with response. Xgboost was used to train and validate the models using 2/3 and 1/3 of the data respectively. Results: Significant determinants of optimal statin response included older age, and higher baseline levels of LDL-C and triglyceride-rich lipoproteins. By contrast, female sex, alcohol intake &gt;=1 drink/day, diabetes, higher baseline levels of apo B and lipoprotein(a) were associated with decreased response, as was hs-CRP non-response (Table). Race, baseline hs-CRP and sub-optimal hs-CRP response, smoking, HDL-C and BMI had no significant effect on statin LDL-C response. Training and validation of models predicted suboptimal LDL-C response with an AUC of 0.71. Similarly, training and validation of models using Xgboost yielded an AUC of 0.85. Conclusion: This study identified discordant lipid phenotype and other determinants of moderate-intensity statin response and suggests other pathways of CVD risk beyond those addressed by statin treatment that require further investigation.
Preliminary data revealing efficacy of Streptococcus salivarius K12 (SSK12) in Periodic Fever, Aphthous stomatitis, Pharyngitis, and cervical Adenitis (PFAPA) syndrome: A multicenter study from the AIDA Network PFAPA syndrome registry (2023)

SSK12 prophylaxis given for at least 6.00 months was found to reduce febrile flares of PFAPA syndrome: in particular, it halved the total number per year of fever flares, shortened the duration of the single febrile episode, lowered body temperature by 1°C in the febrile flare, provided a steroid-sparing effect, and significantly reduced the accompanying symptoms related to the syndrome.
Role of electron polarization in nuclear spin diffusion (2023)

Dynamic nuclear polarization (DNP) is capable of boosting signals in nuclear magnetic resonance by orders of magnitude by creating out-of-equilibrium nuclear spin polarization. The diffusion of nuclear spin polarization in the vicinity of paramagnetic dopants is a crucial step for DNP and remains yet not well understood. In this paper, we show that the polarization of the electron spin largely controls the rate of proton spin diffusion in a DNP sample at 1.2 K and 7 T; at increasingly high electron polarization, spin diffusion vanishes. We rationalize our results using a 2 nucleus--1 electron model and Lindblad's master equation, which generalizes preexisting models in the literature and qualitatively accounts for the experimental observed spin diffusion dynamics.
Scenario-based configuration management for flexible experimentation infrastructures (2009)

Configuration management is a key issue in flexible networking experimentation infrastructures (i.e., testbeds). However, manual procedures have several drawbacks (such as high time consumption in tedious and mechanic operations or the probability of introducing human errors). Moreover, inter-testbed scenario reutilization (i.e., the same network configuration replicated from one testbed to another) is difficult to achieve. In order to solve this limitations, automatic mechanisms are desirable in order to make testbeds profitable tools for their users. Our work describes one of such approaches, defining a model-driven methodology for automatic testbed reconfiguration. It is based in a high-level testbed-independent model (thus being applicable to any testbed in general) which is used to describe desired experimentation scenarios. Those scenarios are then particularized to testbed-specific models for automatic deployment and management by model-based tools. The paper also provides practical use cases applying the methodology in two different situations (VNUML-based virtual testbeds and the GMPLS-enabled optical networking ADRENALINE testbed <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">reg</sup> ) thus assessing the feasibility and generality of our solution.
Ion implantation of porous silicon (1994)

We have investigated the properties of light-emitting porous silicon after ion implantation and successive annealing through continuous-wave photoluminescence (CWPL) and time dependent photoluminescence (TDPL) spectroscopies. Implantation was performed with phosphorus, boron and silicon ions of different doses and energies. Low dose dopant implantation keeps or even increases the CWPL intensity and increases the TDPL decay time. High dose dopant implantation and silicon self-implantation reduce the CWPL intensity and slightly decrease the TDPL decay time.
Knowledge-Based Question Answering as Machine Translation (2014)

A typical knowledge-based question answering (KB-QA) system faces two challenges: one is to transform natural language questions into their meaning representations (MRs); the other is to retrieve answers from knowledge bases (KBs) using generated MRs. Unlike previous methods which treat them in a cascaded manner, we present a translation-based approach to solve these two tasks in one unified framework. We translate questions to answers based on CYK parsing. Answers as translations of the span covered by each CYK cell are obtained by a question translation method, which first generates formal triple queries as MRs for the span based on question patterns and relation expressions, and then retrieves answers from a given KB based on triple queries generated. A linear model is defined over derivations, and minimum error rate training is used to tune feature weights based on a set of question-answer pairs. Compared to a KB-QA system using a state-of-the-art semantic parser, our method achieves better results.
Overexpression of virD1 and virD2 genes in Agrobacterium tumefaciens enhances T-complex formation and plant transformation (1990)

The VirD1 and VirD2 proteins encoded by an inducible locus of the virulence (vir) region of the Agrobacterium tumefaciens Ti plasmid are required for site-specific nicking at T-DNA border sites. We have determined the nucleotide sequence of a 3.6-kilobase-pair fragment carrying the virD locus from nopaline Ti plasmid pTiC58. In contrast to the previous report (Hagiya et al., Proc. Natl. Acad. Sci. USA 82:2669-2673, 1985), we found that the first three open reading frames were capable of encoding polypeptides of 16.1, 49.7, and 21.4 kilodaltons. Deletion analysis demonstrated that the N-terminal conserved domain of VirD2 was absolutely essential for its endonuclease activity. When extra copies of the virD1 and virD2 genes were present in an A. tumefaciens strain carrying a Ti plasmid, increased amounts of T-strand and nicked molecules could be detected at early stages of vir induction. Such strains possessed the ability to transform plants with higher efficiency.
Rapid and Sensitive Detection Method of a Bacterium by Using a GFP Reporter Phage (2002)

A rapid, sensitive, and convenient method for detecting a specific bacterium was developed by using a GFP phage. Here we describe a model system that utilizes the temperate Escherichia coli-restricted bacteriophage lambda, which was genetically modified to express a reporter gene for GFP to identify the colon bacillus E. coli in the specimen. E. coli infected with GFP phage was detected by GFP fluorescence after 4-6 hr of incubation. The results show that a few bacteria in a specimen can be detected under fluorescence microscopy equipped with a sensitive cooled CCD camera. When E. coli and Mycobacterium smegmatis were mixed in a solution containing GFP phage, only E. coli was infected, indicating the specificity of this method. The method has the following advantages: 1) Bacteria from biological samples need not be purified unless they contain fluorescent impurities; 2) The infection of GFP phage to bacteria is specific; 3) The fluorescence of GFP within infected bacteria enables highly sensitive detection; 4) Exogenous substrates and cofactors are not required for fluorescence. Therefore this method is suitable for any phage-bacterium system when bacteria-specific phages are available.
Tax Evasion and Fraud Detection: A Theoretical Evaluation of Taiwan’s Business Tax Policy for Internet Auctions (2010)

Only registered businesses can charge and collect taxes on goods and services made in Taiwan. As auction sites are places where individuals can conduct business activities for profit without paying business taxes, Taiwan’s tax authority has ruled that profit-seeking individuals must register as businesses and pay taxes. However, the anonymity of sellers on Internet auction platforms poses challenges to the ability of the tax authority to enforce this ruling. This paper examines business tax policy for online auctions in Taiwan and then assesses the prospects of taxing sales on online auctions using a game theory model. Analytical results suggest that seller anonymity will allow a vendor to continue to disguise business identity and the tax authority will not aggressively pursue tax evaders.
Molecular Breeding of a Yeast that Produces Human Compatible Glycoproteins. (2001)

出芽酵母 Saccharomyces cerevisiae は、遺伝子操作や培養が容易な真核生物であり、有用タンパク質などの分泌発現系としては優れたものである。しかしながら、糖タンパク質の生産においては、マンノース30-100残基という大きな糖外鎖がN-結合型糖鎖に結合することから、ヒトに対する抗原性の付与やタンパク質の活性低下などの問題を引き起こしている。我々は、この酵母のN-結合型糖外鎖の除去及び哺乳類型糖鎖合成に必要な遺伝子の酵母への導入を行い、ヒトに適合できる糖タンパク質を生産可能な酵母の分子育種を行ってきた。この研究において、我々は、酵母の大きな糖外鎖を形成するのに必要なマンノース転移酵素をコードするOCH1遺伝子の単離と破壊に成功すると共に、同じく酵母特有のマンノースリン酸転移に関わる遺伝子MNN4とMNN6の単離と破壊に成功した。このことにより、ほぼ完全に酵母特有の糖外鎖の形成を取り除くことに成功した。さらに、哺乳類型糖鎖の、混成型や複合型糖鎖を酵母で合成可能とするために、様々な糖転移酵素、糖分解酵素、糖ヌクレオチド輸送体などの遺伝子の単離と酵母での発現を試みてきた。その成果をここに紹介する。
Multicast authentication in fully adversarial networks (2004)

We study a general version of the multicast authentication problem where the underlying network, controlled by an adversary, may drop chosen packets, rearrange the order of the packets in an arbitrary way, and inject new packets into the transmitted stream. Prior work on the problem has focused on less general models, where random, rather than adversarially-selected packets may be dropped and altered, or no additional packets may be injected into the stream. We describe an efficient and scalable authentication scheme that is based on a novel combination of error-correcting codes with standard cryptographic primitives. We prove the security of our scheme and analyze its performance in terms of the computational effort at the sender and receiver and the communication overhead. We also discuss specific design and implementation choices and compare our scheme with previously proposed approaches.
NDLGS project update March 2, 2011 (2011)

Abstract Not Provided
Reflection-canceling of slotted waveguide antenna by using a circular pit (2002)

A slot cut on a metal waveguide produces scattered fields in the internal region as well as the external region. It causes reflection in the waveguides and deteriorates the VSWR of the antenna. This paper proposes a novel technique to cancel the reflection by placing a pit on the bottom of the waveguide. Only the original slots exist on the aperture and the pit is in the waveguide. Thus, the radiation pattern design by the slots and the pit design for reflection cancelling can be conducted independently. We design a circular pit for a transverse slot in a rectangular waveguide. The analysis and design are validated by experiments. These results are applicable for parallel plates such as radial lines as well.
Hepatic Metabolism Affects the Atropselective Disposition of 2,2′,3,3′,6,6′-Hexachlorobiphenyl (PCB 136) in Mice (2014)

To understand the role of hepatic vs extrahepatic metabolism in the disposition of chiral PCBs, we studied the disposition of 2,2',3,3',6,6'-hexachlorobiphenyl (PCB 136) and its hydroxylated metabolites (HO-PCBs) in mice with defective hepatic metabolism due to the liver-specific deletion of cytochrome P450 oxidoreductase (KO mice). Female KO and congenic wild type (WT) mice were treated with racemic PCB 136, and levels and chiral signatures of PCB 136 and HO-PCBs were determined in tissues and excreta 3 days after PCB administration. PCB 136 tissue levels were higher in KO compared to WT mice. Feces was a major route of PCB metabolite excretion, with 2,2',3,3',6,6'-hexachlorobiphenyl-5-ol being the major metabolite recovered from feces. (+)-PCB 136, the second eluting PCB 136 atropisomers, was enriched in all tissues and excreta. The second eluting atropisomers of the HO-PCBs metabolites were enriched in blood and liver; 2,2',3,3',6,6'-hexachlorobiphenyl-5-ol in blood was an exception and displayed an enrichment of the first eluting atropisomers. Fecal HO-PCB levels and chiral signatures changed with time and differed between KO and WT mice, with larger HO-PCB enantiomeric fractions in WT compared to KO mice. Our results demonstrate that hepatic and, possibly, extrahepatic cytochrome P450 (P450) enzymes play a role in the disposition of PCBs.
Absence of JAK2V617F Mutated Endothelial Colony‐Forming Cells in Patients With JAK2V617F Myeloproliferative Neoplasms and Splanchnic Vein Thrombosis (2020)

Supplemental Digital Content is available in the text
Characterization of myeloid leukemias with monoclonal antibodies 3C5 and MY9 (1985)

The expression of two membrane antigens identified by the monoclonal antibodies (McAb) My9 and 3C5 has been investigated in cells from 80 acute leukemias. My9 was positive in the blasts of 33 out of the 38 (87 per cent) cases of acute myeloid leukemia (AML) tested, regardless of FAB subtype, and in 13 of 18 (72 per cent) cases of chronic granulocytic leukemia (CGL) in myeloid blast crisis. The reactivity of 3C5 was confined to myeloblastic (M1) AML, 85 per cent of cases, and to lymphoblastic leukemia (ALL) of B-lineage, 70 per cent of cases, including CGL in lymphoid transformation. My9 was negative in ALL except for an unusual case. The phenotype My9+, 3C5+ was seen exclusively in M1 (69 per cent) and M2 (14 per cent) AML. Ultrastructural analysis with the immunogold method in combination with the myeloperoxidase (MPO) reaction showed that expression of My9 increased in parallel with MPO activity whereas 3C5 was expressed mainly in myeloblasts with little MPO content. We conclude that the use of these two McAb will contribute to the diagnosis and classification of AML and may throw some light to the pathogenesis of biphenotypic acute leukemias, including TdT + AML.
Author response: An alternative splicing program promotes adipose tissue thermogenesis (2016)

The process of building a protein from the information encoded in a gene begins when the gene is copied to form a pre-messenger RNA molecule. This molecule is then edited to produce a final messenger RNA that is “translated” to form the protein. Different segments of the pre-messenger RNA molecule can be removed to create different messenger RNAs. This “alternative splicing” enables a single gene to produce multiple protein variants, allowing a diverse range of processes to be performed by cells. Fat cells store energy in the form of fats and can release this energy as heat in a process called thermogenesis. This helps to regulate the body’s metabolism and prevent obesity. Vernia et al. now find that that feeding mice a high-fat diet causes widespread changes in alternative splicing in fat cells. Further bioinformatics analysis revealed that the NOVA family of splicing factors – proteins that bind to the pre-messenger RNAs to control alternative splicing – contribute to the alternative splicing of around a quarter of the genes whose splicing changes in response to a fatty diet. Mice whose fat cells were deficient in the NOVA splicing factors displayed increased thermogenesis. As a consequence, when these animals were fed a high-fat diet, they gained less weight than animals in which NOVA proteins were present. Their metabolic activity was also better, meaning they were less likely to show the symptoms of pre-diabetes. Moreover, the activity of certain genes that are known to promote thermogenesis was greater in the fat cells that were deficient in NOVA proteins. Overall, the results presented by Vernia et al. suggest that the normal role of NOVA proteins is to carry out an alternative splicing program that suppresses thermogenesis, which in turn may promote obesity. Drugs that are designed to target NOVA proteins and increase thermogenesis may therefore help to treat metabolic diseases and obesity. The next step is to identify the protein variants that are generated by NOVA proteins and work out how they contribute to thermogenesis.
A 1 GHz sample rate, 256-channel, 1-bit quantization, CMOS, digital correlator chip (1992)

This paper describes the development of a digital correlator chip with the following features: 1 Giga-sample/second; 256 channels; 1-bit quantization; 32-bit counters providing up to 4 seconds integration time at 1 GHz; and very low power dissipation per channel. The improvements in the performance-to-cost ratio of the digital correlator chip are achieved with a combination of systolic architecture, novel pipelined differential logic circuits, and standard 1.0 micron CMOS process.
Mixed-Integer Linear Programming for Optimal Scheduling of Autonomous Vehicle Intersection Crossing (2018)

We propose an urban traffic management scheme for an all connected vehicle environment. If all the vehicles are autonomous, for example, in smart city projects or future's dense city centers, then such an environment does not need a physical traffic signal. Instead, an intersection control server processes data streams from approaching vehicles, periodically solves an optimization problem, and assigns to each vehicle an optimal arrival time that ensures safety while significantly reducing number of stops and intersection delays. The scheduling problem is formulated as a mixed-integer linear program (MILP), and is solved by IBM CPLEX optimization package. The optimization outputs (scheduled access/arrival times) are sent to all approaching vehicles. The autonomous vehicles adjust their speed accordingly by a proposed trajectory planning algorithm with the aim of accessing the intersection at their scheduled times. A customized traffic microsimulation environment is developed to determine the potentials of the proposed solution in comparison to two baseline scenarios. In addition, the proposed MILP-based intersection control scheme is modified and simulated for a mixed traffic consisting of autonomous and human-controlled vehicles, all connected through a wireless communication to the intersection controller of a signalized intersection.
Novel enzymatic approach to the synthesis of flavonoid glycosides and their esters (2000)

Flavonoids such as (+)catechin can be efficiently solubilised in supersaturated solutions prepared with donor glycosides, e.g., p-nitrophenyl glycosides, di- and higher oligosaccharides, and poly(ethylene glycol) dimethyl ether in sufficiently high concentration for their efficient enzymatic glycosylation. Under these conditions several glycosidases readily accept (+)catechin as substrate and the target glycosides were prepared in one step in up to 26% yields. The regioselectivity of the reaction depends on the enzyme and substrate combination used; three positions, 5, 7, and 4', in the flavonoid can be glycosylated. The resulting and similar flavonoid glycosides were further modified by regioselective acylation with vinyl esters of arylpropenoic acids using lipases as biocatalyst. The efficiency of acylation was found to diminish in the order of vinyl cinnamate > vinyl ferulate > vinyl coumarate. This work demonstrates the feasibility of assembling complex flavonoid glycoside esters in just two steps by sequential use of commercially available glycosidases and lipases.
Convergent production of 2,5-furandicarboxylic acid from biomass and CO2 (2019)

We report a rationally designed process for complete lignocellulose conversion and CO<sub>2</sub> utilization to convergently produce 2,5-furandicarboxylic acid (FDCA) that can be used in bioplastics and resins.