gebhart/patrepeval huggingface dataset:
Preface (2014)

In a bid to develop synthetic molecules and materials that are capable of biomimicry, there has been intensive research in the fields of synthetic receptor technologies, smart materials, synthetic biology and smart indicators for the past 20 to 30 years. The development of synthetic receptors continues to grow rapidly. Novel molecular architectures, with ever improving selective binding properties, for biomolecules, are constantly being described, and in some cases providing much-needed physical insights into the nature of non-covalent interactions and molecular recognition. Such receptor systems are also being used for increasingly esoteric applications, often with real practical applications, particularly as specific sensors for single analytes and for sensor arrays for multi-analyte mixtures. This book aims to capture key developments at the synthetic receptor/biology/detection science interface.
IL-37 is associated with osteoarthritis disease activity and suppresses proinflammatory cytokines production in synovial cells (2017)

The objective of this study is to investigate the correlation between IL-37 level and osteoarthritis activity and to determine the anti-inflammatory effects of IL-37 in peripheral blood mononuclear cells (PBMCs) and synovial cells (SCs) from osteoarthritis (OA) patients, which including 32 patients with erosive inflammatory OA (EIOA) and 40 patients with primary generalized OA (PGOA), 40 age and sex matched healthy volunteers were recruited as healthy controls (HCs). The protein and relative mRNA levels of IL-37 were significant increased in the blood of EIOA patients compared with those of PGOA patients and HCs. Serum IL-37 levels of OA patients were positively correlated with VAS score, as well as with CRP, ESR in blood. Positive correlations were also observed among IL-37 with IL-1β, TNF-α and IL-6 in synovial cells. Furthermore, the expression of IL-1β, TNF-α and IL-6 in PBMCs and SCs from EIOA patients was suppressed by IL-37 in vitro. In conclusion, our results indicated that IL-37 increased in EIOA patients and was positively correlated with disease activity, the pro-inflammatory cytokines such as IL-1β, TNF-α and IL-6 in PBMCs and synovial cells from EIOA patients were restrained by recombinant IL-37. Thus, IL-37 may serve as a novel therapeutic target for the treatment of OA inflammation.
Some sampling effects of pairwise correlated observations on likelihood ratio tests for the difference between two means (1993)

We study the effects of the inclusion of pairs of correlated observations in a sample on likelihood ratio tests for the difference in two means. In particular, we assess how the inclusion of correlated data pairs (e.g., such as data inadvertently collected from sib-pairs) affects the sample size requirements necessary for the implementation of a Likelihood Ratio (LR) test for the difference between two means. Our results suggest that correlated data pairs beneficially or adversely effect sample size requirements for an LR test to a degree functionally related to the mixture parameters dictating their relative frequencies in the larger sample on which the test will be performed, the strength of the correlation between the observations, and the size of imbalances in the sample with respect to the number of observations in each group. The relevance and implications of the results for genetic and epidemiologic research are discussed.
Anti-differentiating approximation algorithms:A case study with min-cuts, spectral, and flow (2014)

We formalize and illustrate the general concept of algorithmic anti-differentiation: given an algorith-mic procedure, e.g., an approximation algorithm for which worst-case approximation guarantees are available or a heuristic that has been engi-neered to be practically-useful but for which a pre-cise theoretical understanding is lacking, an algo-rithmic anti-derivative is a precise statement of an optimization problem that is exactly solved by that procedure. We explore this concept with a case study of approximation algorithms for finding locally-biased partitions in data graphs, demon-strating connections between min-cut objectives, a personalized version of the popular PageRank vector, and the highly effective “push ” procedure for computing an approximation to personalized PageRank. We show, for example, that this lat-ter algorithm solves (exactly, but implicitly) an `1-regularized `2-regression problem, a fact that helps to explain its excellent performance in prac-tice. We expect that, when available, these im-plicit optimization problems will be critical for rationalizing and predicting the performance of many approximation algorithms on realistic data. 1.
SB‐656104‐A, a novel selective 5‐HT7 receptor antagonist, modulates REM sleep in rats (2003)

1 (6-((R)-2-[2-[4-(4-Chloro-phenoxy)-piperidin-1-yl]-ethyl]-pyrrolidine-1-sulphonyl)-1H-indole hydrochloride) (SB-656104-A), a novel 5-hydroxytryptamine (5-HT(7)) receptor antagonist, potently inhibited [(3)H]-SB-269970 binding to the human cloned 5-HT(7(a)) (pK(i) 8.7+/-0.1) and 5-HT(7(b)) (pK(i) 8.5+/-0.2) receptor variants and the rat native receptor (pK(i) 8.8+/-0.2). The compound displayed at least 30-fold selectivity for the human 5-HT(7(a)) receptor versus other human cloned 5-HT receptors apart from the 5-HT(1D) receptor ( approximately 10-fold selective). 2 SB-656104-A antagonised competitively the 5-carboxamidotryptamine (5-CT)-induced accumulation of cyclic AMP in h5-HT(7(a))/HEK293 cells with a pA(2) of 8.5. 3 Following a constant rate iv infusion to steady state in rats, SB-656104 had a blood clearance (CL(b)) of 58+/-6 ml min(-1) kg(-1) and was CNS penetrant with a steady-state brain : blood ratio of 0.9 : 1. Following i.p. administration to rats (10 mg kg(-1)), the compound displayed a t(1/2) of 1.4 h with mean brain and blood concentrations (at 1 h after dosing) of 0.80 and 1.0 micro M, respectively. 4 SB-656104-A produced a significant reversal of the 5-CT-induced hypothermic effect in guinea pigs, a pharmacodynamic model of 5-HT(7) receptor interaction in vivo (ED(50) 2 mg kg(-1)). 5 SB-656104-A, administered to rats at the beginning of the sleep period (CT 0), significantly increased the latency to onset of rapid eye movement (REM) sleep at 30 mg kg(-1) i.p. (+93%) and reduced the total amount of REM sleep at 10 and 30 mg kg(-1) i.p. with no significant effect on the latency to, or amount of, non-REM sleep. SB-269970-A produced qualitatively similar effects in the same study. 6 In summary, SB-656104-A is a novel 5-HT(7) receptor antagonist which has been utilised in the present study to provide further evidence for a role for 5-HT(7) receptors in the modulation of REM sleep.
Regioregular Polymer Analogous Thionation of Naphthalene Diimide–Bithiophene Copolymers (2018)

Polymer analogous thionation of the n-type conjugated polymer PNDIT2 is investigated using Lawesson’s reagent (LR). Detailed high-temperature NMR spectroscopic investigations show that due to the copolymer structure, two out of the four available carbonyl groups present in the naphthalene diimide (NDI) comonomer are sterically less hindered and react preferentially. This leads to regioselective thionation in the trans-configuration even for a large excess of LR. For high degrees of O/S conversion, signals of minor intensity show up in addition pointing to undesired side reactions. These signals could not be eliminated despite further optimized reaction conditions including different aromatic solvents and reaction temperatures. Compared to PNDIT2, the resulting 2S-trans-PNDIT2 features strong aggregation, lower solubility, an 80 nm bathochromic shift of the charge-transfer band, a by 0.22 eV lower LUMO energy level, a lower thermal stability, and higher melting temperatures (Tm). As the combination of the lower thermal stability and higher melting points renders the characterization of thermal transitions challenging, fast scanning calorimetry (flash-DSC) is successfully used to determine Tm. With increasing O/S conversion, Tm first increases but then decreases, which is ascribed to a combined effect of stronger main chain interactions and increasing chemical defects. Microstructural order and field-effect electron mobilities decrease with increasing O/S conversion compared to PNDIT2.
On Ray Reordering Techniques for Faster GPU Ray Tracing (2020)

We study ray reordering as a tool for increasing the performance of existing GPU ray tracing implementations. We focus on ray reordering that is fully agnostic to the particular trace kernel. We summarize the existing methods for computing the ray sorting keys and discuss their properties. We propose a novel modification of a previously proposed method using the termination point estimation that is well-suited to tracing secondary rays. We evaluate the ray reordering techniques in the context of the wavefront path tracing using the RTX trace kernels. We show that ray reordering yields significantly higher trace speed on recent GPUs (1.3 − 2.0 ×), but to recover the reordering overhead in the hardware-accelerated trace phase is problematic.
The neuropeptide Substance P facilitates the transition from an inflammatory to proliferation phase‐associated responses in dermal fibroblasts (2022)

The wound healing process is a product of three successive and overlapping phases of inflammation, proliferation and remodelling. Considerable efforts have been invested in deconstructing the intercellular crosstalk that orchestrates tissue repair, and we investigated the role of neuropeptides released from peripheral neurons upon injury in mediating these interactions. Amongst the most abundant of these neuropeptides secreted by nerves in the skin, is Substance P (SP). Given the role of dermal fibroblasts in coordinating multiple processes in the wound healing program, the effect of SP on human dermal fibroblasts of different ages was evaluated. The use of a substrate that recapitulates the mechanical properties of the in vivo tissue revealed novel effects of SP on dermal fibroblasts, including a block in inflammatory cytokine expression. Moreover, SP can promote expression of some extracellular matrix components and generates signals that regulate angiogenesis. Interestingly, the response of fibroblasts to SP was reduced concomitant with donor age. Altogether, SP acts to inhibit the inflammatory responses and promote proliferation-associated responses in an age-dependent manner in dermal fibroblasts, suggesting a role as a molecular switch between the inflammatory and proliferative phases of the wound healing response.
THE USE OF IONIZATION CHAMBERS AS SECONDARY STANDARDS OF X-RAY EXPOSURE (1958)

The use or calibrated ionization chambers to determine the total amount of energy transported by a well collimated bremsstrahlung beam, with a peak energy between 18 and 170 Mev, is discussed. Three chambers are described which have been used for this purpose, and their relative merits are discussed. The first chamber is an r-thinble which was calibrated calorimetrically between 18.2 and 36.7 Mev. The other two chambers are flat chambers, designed to intercept the entire beam. They were calibrated calorimetrically in the same energy range, and in addition, they were calibrated with a total absorption crystal spectrometer at a variety or energies up to 170 Mev. These calibration are all presented, and compared with those obtained in other laboatories, where possible. (auth)
Contrast enhanced magnetic resonance imaging of the liver (2008)

Dynamic contrast enhanced magnetic resonance imaging (DCE MRI) is a useful tool to characterise and stage a disease. Here we investigate the application of DCE MRI to the liver, an organ subject to large excursions during normal breathing. For DCE MRI it is important to have an estimate of the longitudinal relaxation time parameter T1. We show that by using a T1 mapping approach, which takes into account inaccuracies in transmitted flip angles, we obtain a smoother T1 map, resulting in a more consistent parameter estimation for the subsequent analysis. The dynamic imaging protocol described enables the acquisition of high resolution unblurred images by simulating the normal breathing cycle. The contrast enhanced data is aligned, first rigidly, then non-rigidly, and input to a two-compartment pharmacokinetic model. We observe that rigid registration markedly improves the parameter estimation, but is insufficient in clinically important heterogeneous areas.
Characterization of a Fe/Y[subscript 2]O[subscript 3] metal/oxide interface using neutron and x-ray scattering (2014)

The structure of metal/oxide interfaces is important to the radiation resistance of oxide dispersion-strengthened steels. We find evidence of gradual variations in stoichiometry and magnetization across a Fe/Y[subscript 2]O[subscript 3] metal/oxide heterophase interface using neutron and x-ray reflectometry. These findings suggest that the Fe/Y[subscript 2]O[subscript 3] interface is a transitional zone approximately ∼64 Å-thick containing mixtures or compounds of Fe, Y, and O. Our results illustrate the complex chemical and magnetic nature of Fe/oxide interfaces and demonstrate the utility of combined neutron and x-ray techniques as tools for characterizing them.
CD44 isoform-cytoskeleton interaction in oncogenic signaling and tumor progression (1998)

CD44, a major hyaluronan receptor, exists as several isoforms and is widely distributed in different cells and tissues. The isoforms of CD44, such as CD44s (the standard form), CD44E (the epithelial form) and CD44v (variant isoforms) (arise from differential splicing of one to ten (or eleven) variable exons that encode portions of the membrane proximal extracellular domain. The molecular diversity of CD44 isoforms is further compounded by differential biosynthetic processes and post-translational modifications [e.g. N-/O-glycosylation or glycosaminoglycan (GAG) addition]. This structural arrangement, which occurs within either the invariant region or the extracellular domain of the variant region, is important for CD44-mediated communication between extracellular matrix materials [ECM-hyaluronic acid (HA), collagen and fibronectin] and intracellular protein components (e.g cytoskeletal proteins and various regulatory enzymes). The 15 amino acid sequence [e.g. NSGNGAVEDRKPSGL (in human) or NGGNGTVEDRKPSEL (in mouse)] residing in the cytoplasmic domain of CD44 isoforms is the ankyrin-binding domain of this family of transmembrane glycoproteins. Biochemical analyses plus in vitro mutagenesis indicate that the ankyrin-binding domain is required for CD44-mediated "outside-in" and "inside-out" cell activation events. Furthermore, CD44s-cytoskeleton interaction is tightly coupled with signal transducing molecules (e.g. p185HER2 or Src kinases) during oncogenic signaling. Moreover, the transmembrane linkage between CD44v isoforms (CD44v10 and CD44v3) and the cytoskeleton up-regulates invasive and metastatic-specific tumor phenotypes [e.g. matrix degradation (MMPs) activities, tumor cell invasion and migration]. These findings strongly suggest that the interaction between CD44 isoforms and the cytoskeleton plays a pivotal role in the onset of oncogenesis and tumor progression.
Increased limb involvement in murine collagen-induced arthritis following treatment with anti-interferon-gamma (1993)

We have tested the effect of administering H22, a hamster neutralizing MoAb to murine interferon-gamma (IFN-gamma) in collagen-induced arthritis. Mice were immunized with human type II collagen in adjuvant on day 1 and boosted with soluble collagen on day 21. H22 was administered (250 micrograms, intraperitoneally) either during the induction of arthritis (on days 0, 6, 13 and 20) or around the time of disease manifestation (on days 21, 28, 35 and 42). Control mice received either an isotype-matched non-neutralizing MoAb or saline. Both treatment regimes gave similar results. Treatment with H22 did not significantly affect the incidence of arthritis, time of onset, degree of oedema, histopathological severity, or level of anti-type II collagen IgG. However, a highly significant increase (P < 0.01) in the number of limbs affected by arthritis was observed in the H22-treated group, irrespective of whether the antibody was administered during the induction of arthritis, or during the time of clinical manifestation of disease. From these results it was concluded that anti-IFN-gamma treatment caused an increase in the number of arthritic lesions, but did not affect the severity of each individual lesion.
The components of crop productivity: measuring and modeling plant metabolism. (1995)

Several investigators in the CELSS program have demonstrated that crop plants can be remarkably productive in optimal environments where plants are limited only by incident radiation. Radiation use efficiencies of 0.4 to 0.7 g biomass per mol of incident photons have been measured for crops in several laboratories. Some early published values for radiation use efficiency (1 g mol-1) were inflated due to the effect of side lighting. Sealed chambers are the basic research module for crop studies for space. Such chambers allow the measurement of radiation and CO2 fluxes, thus providing values for three determinants of plant growth: radiation absorption, photosynthetic efficiency (quantum yield), and respiration efficiency (carbon use efficiency). Continuous measurement of each of these parameters over the plant life cycle has provided a blueprint for daily growth rates, and is the basis for modeling crop productivity based on component metabolic processes. Much of what has been interpreted as low photosynthetic efficiency is really the result of reduced leaf expansion and poor radiation absorption. Measurements and models of short-term (minutes to hours) and long-term (days to weeks) plant metabolic rates have enormously improved our understanding of plant environment interactions in ground-based growth chambers and are critical to understanding plant responses to the space environment.
[Three-dimensional analysis of the early correction of anterior crossbite using eruption guidance appliance]. (2018)

The anterior cross bite in mixed dentition could be corrected by eruption guidance appliance, and at the same time, the normal overjet and overbite were established, and the teeth were aligned.
Estudo da biodegradação do acido 2,4-diclorofenoxiacetico em formulações de liberação controlada (1996)

O herbicida 2,4-D de grau tecnico (acido 2,4-diclorofenoxiacetico, 2,4-D livre), e o herbicida retido em formulacoes de liberacao controlada a base de lignina (2,4-D/FLC), foram submetidos a biodegradacao. Para isto foram empregados a bacteria Pseudomona putida, o fungo Phanerochaete chrysosporium, e microflora do solo. Diferentes taxas de degradacao foram observadas de acordo com as diferentes concentracoes iniciais do herbicida no meio. Nas concentracoes iniciais de 5, 10 e 20 mg/L de 2,4-D livre, P. chrysosporium, degradou 12, 45 e 56% do herbicida , respectivamente. A 40, 60 e 80 mg/L de 2,4-D, observou-se 35% de degradacao, e a 100 mg/L 25% de degradacao. Para as FLC observou-se 20,43, 46 e 42% de degradacao para 10, 20, 40 e 60 mg/L de 2,4-D, respectivamente. Os experimentos com P.putida e 2,4-D livre apresentaram 19% de degradacao a uma concentracao de 10 mg/L. Acima desta concentracao, nenhuma degradacao foi observada. Ja para a FLC a 10 e 100 mg/L de 2,4-D, foram observados 29 e 12% de degradacao, respectivamente. Os experimentos em solo foram realizados a concentracao constante de 9,4 Kg/ha de 2,4-D. Em solo sem estimulacao do crescimento dos microrganismos, o 2,4-D livre apresentou entre 7-10% de degradacao, e o solo com estimulacao, 44,5 4,5%. Ja o 2,4-D em FLC apresentou 17 3% e nenhuma degradacao para os solos com e sem estimulacao do crescimento inicial dos microrganismos, respectivamente. A ausencia de metabolitos da via degradativa do 2,4-D determinadas por cromatografia gasosa acoplada a espectrometria de massa, demonstrou que as condicoes empregadas nos ensaios de degradacao, favoreceram a mineralizacao do herbicida. O aumento da porosidade da FLC apos degradacao pelo fungo e pela bacteria, observado atraves de analise de microscopia eletronica de varredura, demonstrou que a formulacao sofreu alteracoes fisicas apos o processo de degradacao. A hidrolise da funcao ester entre o 2,4-D e lignina, foi observada atraves de analise por FTIR das FLC. Estas modificacoes fisicas e quimicas resultaram num aumento da velocidade de liberacao do herbicida da FLC. As constantes de difusao aparente do 2,4-D da FLC passaram de 9 dias para 17 e de 12 dias para 16 dias, apos tratamento com o fungo e a bacteria, respectivamente. A FLC atuou como uma barreira a biodegradacao do ingrediente ativo presente em seu interior. Porem, maiores ou menores taxas de degradacao do ingrediente ativo dependeram da concentracao inicial proporcionada pelo sistema de liberacao controlada.
Abstract
Analysis and Design of a New Self-Packaged Wideband Balun Bandpass Filter With the Functionality of Impedance Transformation (2019)

In this paper, a new self-packaged wideband balun with the high selective bandpass filtering response and impedance transformation characteristic is presented. By virtue of circuit transformations, corresponding two-port equivalent circuit with asymmetrical port impedances is put forward. The analysis results of this two-port network exhibit that the proposed new design is able to achieve a quasi-elliptic equal-ripple response with three transmission poles and four transmission zeros. In addition, the frequency response can be directly determined according to the desired design specifications of impedance transformation ratio k, ripple fractional bandwidth (FBW), and in-band return loss RL. For validation purposes, a demonstrated wideband balun bandpass filter (BPF) working at 2.0 GHz with 50-100-Ω impedance transformation has been implemented by utilizing the multilayer liquid-crystal polymer (LCP) bonded printed circuit board (PCB) lamination technology. Theoretical, simulated, and measured results are recorded in good agreement, well verifying the design method.
Parallel competition analysis of Saccharomyces cerevisiae strains differing by a single base using polymerase colonies (2003)

We describe a strategy to analyze the impact of single nucleotide mutations on protein function. Our method utilizes a combination of yeast functional complementation, growth competition of mutant pools and polyacrylamide gel immobilized PCR. A system was constructed in which the yeast PGK1 gene was expressed from a plasmid-borne copy of the gene in a PGK1 deletion strain of Saccharomyces cerevisiae. Using this system, we demonstrated that the enrichment or depletion of PGK1 point mutants from a mixed culture was consistent with the expected results based on the isolated growth rates of the mutants. Enrichment or depletion of individual point mutants was shown to result from increases or decreases, respectively, in the specific activities of the encoded proteins. Further, we demonstrate the ability to analyze the functional effect of many individual point mutations in parallel. By functional complementation of yeast deletions with human homologs, our technique could be readily applied to the functional analysis of single nucleotide polymorphisms in human genes of medical interest.