gebhart/patrepeval huggingface dataset:
Rapid evolutionary adaptation to elevated salt concentrations in pathogenic freshwater bacteria Serratia marcescens (2014)

Rapid evolutionary adaptions to new and previously detrimental environmental conditions can increase the risk of invasion by novel pathogens. We tested this hypothesis with a 133-day-long evolutionary experiment studying the evolution of the pathogenic Serratia marcescens bacterium at salinity niche boundary and in fluctuating conditions. We found that S. marcescens evolved at harsh (80 g/L) and extreme (100 g/L) salt conditions had clearly improved salt tolerance than those evolved in the other three treatments (ancestral conditions, nonsaline conditions, and fluctuating salt conditions). Evolutionary theories suggest that fastest evolutionary changes could be observed in intermediate selection pressures. Therefore, we originally hypothesized that extreme conditions, such as our 100 g/L salinity treatment, could lead to slower adaptation due to low population sizes. However, no evolutionary differences were observed between populations evolved in harsh and extreme conditions. This suggests that in the study presented here, low population sizes did not prevent evolution in the long run. On the whole, the adaptive potential observed here could be important for the transition of pathogenic S. marcescens bacteria from human-impacted freshwater environments, such as wastewater treatment plants, to marine habitats, where they are known to infect and kill corals (e.g., through white pox disease).
TonB Is Required for Intracellular Growth and Virulence ofShigella dysenteriae (2000)

To assess the importance of TonB-dependent iron transport systems to growth of Shigella in vivo, a tonB mutant of Shigella dysenteriae was isolated and tested in cultured cells. The tonB mutant invaded epithelial cells, but did not form plaques in confluent monolayers of Henle cells, indicating an inability of this mutant to spread from cell to cell. The rate of intracellular multiplication of the tonB mutant was reduced significantly compared to that of the wild type. The loss of virulence in the tonB mutant was not due to loss of either Shu or Ent, the TonB-dependent systems which allow for transport of heme and ferrienterobactin, respectively. A shuA mutant lacking the outer membrane receptor for heme, an entB mutant defective in enterobactin synthesis, and a shuA entB double mutant each were able to invade cultured cells, multiply intracellularly, and form wild-type plaques. The ability of S. dysenteriae to access iron during intracellular growth was assessed by flow cytometric analysis of an iron- and Fur-regulated shuA-gfp reporter construct. Low levels of green fluorescent protein expression in the intracellular environment were observed in all strains, indicating that iron is available to intracellular bacteria, even in the absence of TonB-dependent iron transport. The failure of the tonB mutant to grow well in an iron-replete intracellular environment suggests that TonB plays a role in addition to heme- and siderophore-mediated iron acquisition in vivo, and this function is required for the intracellular growth and intercellular spread of S. dysenteriae.
A Novel Method for the Preparation of Macrolides from ω-Hydroxycarboxylic Acids (1994)

Abstract An efficient method for the synthesis of macrolides directly from ω-hydroxycarboxylic acids is established by using 4-(trifluoromethyl)benzoic anhydride and a catalytic amount of active titanium(IV) salts together with chlorotrimethylsilane under mild conditions.
Structure guided discovery of inhibitors of indoleamine 2,3-dioxygenase (IDO1) (2015)

The enzyme indoleamine 2,3‐dioxygenase‐1 (IDO1) plays a critical role in the regulation of the immune system. IDO1 expression is commonly upregulated in cancer, resulting in a suppressed immune system in patients. Clinical observations that patients with high IDO1‐expressing tumours have a poor prognosis have promoted the discovery of novel inhibitors of IDO1 for development as potential anti‐cancer agents to restore tumour immunity. Work in this thesis used differential scanning fluorimetry and enzyme inhibition assays to screen a fragment library for novel IDO1 inhibitors. Thirty‐five small compounds that interacted with and inhibited the IDO1 enzyme were identified, and included compounds from the chemical classes: benzothiazoles, benzimidazoles, benzoxazoles, indoles, indan‐1‐ones, quinolines, naphthalenes, coumarins, biphenyls, phenols, 4‐phenylimidazole, pyridines, hydroxyamidines and phenylpyruvic acids. Spectroscopic studies show that these compounds interact with the haem complex present in the IDO1 active site. Of these, 4‐phenylimidazole and a hydrazine‐containing benzothiazole compound were found to bind to both the Fe(II) and Fe(III) forms of IDO1. Compounds in the hydrazine sub‐class found within the benzothiazole class of fragments in the library were found to be the most potent inhibitors (phenylhydrazine, IC50:0.3 M). A pharmacophore model was developed based on the predicted binding mode of inhibitory fragments. The use of Goldscore, Chemscore, ChemPLP and Astex Statistical Potential (ASP) scoring functions for sampling and rescoring were assessed to find a docking protocol that enriched for IDO1 inhibitory compounds from a dataset. Goldscore/Chemscore docking achieved a seven‐fold enrichment of IDO1 inhibitors in the top‐scoring 5% of compounds from the dataset. This docking protocol was subsequently applied to a set of over 14, 000 phenylhydrazine‐containing compounds. The selection of compounds based on fitness score and on parameters described in the pharmacophore model identified ten potent IDO1 inhibitors (IC50:0.2‐2.4 M). Crystals of IDO1 were also produced for X‐ray crystallographic analysis of protein‐inhibitor interactions. Although extensive optimisation of conditions for crystal production was undertaken, they failed to produce well‐diffracting crystals. Overall, these studies have identified the hydrazine‐containing compounds as a novel IDO1 inhibitory chemotype that may be a useful scaffold for the further lead development.
Dentin Extracellular Matrix (ECM) Proteins: Comparison to Bone ECM and Contribution to Dynamics of Dentinogenesis (2003)

Dentinogenesis involves the initial odontoblastic synthesis of a collagen-rich extracellular matrix (ECM) and predentin that is converted to dentin when the collagen fibrils become mineralized. Since the width of predentin is rather uniform, we postulate that extracellular events regulate dentinogenesis. Similarly, osteogenesis involves an initial unmineralized osteoid that is mineralized and converted to bone. To gain insights into these two processes, we compared ECM proteins in bone with those in dentin, focusing upon the sialic acid (SA)-rich proteins. We observed qualitative similarities between the SA-rich proteins, but distinct differences in the amounts of osteopontin (OPN) and dentin sialoprotein (DSP). OPN, a predominant protein in bone, was found in much smaller amounts in dentin. Conversely, DSP was abundant in dentin ECM, but found sparingly in bone. Molecular cloning experiments indicate that coding sequences for DSP and dentin phosphoprotein (DPP) are found on the same mRNA. We believe that the initial form of the precursor protein DSPP is inactive in influencing the mineralization process and that it must be activated by cleavage of peptide bonds in conserved regions. Thus, unknown proteinases would act on DSPP, possibly at the mineralization front, and liberate active DPP, which plays an initiation and regulatory role in the formation of apatite crystals. This post-translational processing reaction would represent an important control point in dentinogenesis. Recently, we identified uncleaved DSPP in dentin extracts, which should allow us to test portions of our hypothesis.
Biosensors from conjugated polyelectrolyte complexes (2001)

A charge neutral complex (CNC) was formed in aqueous solution by combining an orange light emitting anionic conjugated polyelectrolyte and a saturated cationic polyelectrolyte at a 1:1 ratio (per repeat unit). Photoluminescence (PL) from the CNC can be quenched by both the negatively charged dinitrophenol (DNP) derivative, (DNP-BS(-)), and positively charged methyl viologen (MV(2+)). Use of the CNC minimizes nonspecific interactions (which modify the PL) between conjugated polyelectrolytes and biopolymers. Quenching of the PL from the CNC by the DNP derivative and specific unquenching on addition of anti-DNP antibody (anti-DNP IgG) were observed. Thus, biosensing of the anti-DNP IgG was demonstrated.
Triangle order optimization for graphics hardware computation culling (2006)

We describe an automatic preprocessing algorithm that reorders triangles in a mesh so as to enable the graphics hardware to efficiently cull vertex and pixel processing at rendering time.Our method starts by dividing the mesh into planar clusters which are subsequently sorted into a view-independent order which greatly reduces overdraw. The result is an increase in the opportunities for early Z-culling, reducing pixel processing time. The clusters are then optimized for mesh locality. This produces high rates of vertex cache hits, reducing vertex processing time.We have found that our method brings the overdraw rates of a wide range of models close to that of front-to-back order, while preserving state of the art vertex cache performance. This results in higher frame rates for pixel-bound applications with no penalty to vertex-bound applications.
원저 : 땅콩 알레르기의 생쥐모델에서 Bifidobacterium (strain BGN4)의 항알레르기 효과 (2006)

목 적 : 땅콩알레르기의 생쥐모델을 이용하여 bifidobacreria(BGN4)의 위장관 투여에 의한 항원 특이적 IgE 항체 생산 조절과 비장세포의 항원 특이적 사이토카인 생성에 미치는 영향을 알아보기 위하여 본 연구를 시행하였다. 방 법 : 연구자들이 이미 확립한 IgE-매개성 땅콩 알레르기의 생쥐모델을 이용하였다. 이전의 연구 결과 가장 적절한 IgE, 생성 반응과 항원 특이적 사이토카인 생성이 유도된 땅콩 감작 농도인 1 ㎎/dose/mouse의 용량으로 실험 제 1, 2, 3, 7, 21일에 땅콩의 조항원을 위장관을 통하여 감작시켰다. 이 모델을 이용하여, BGN4가 제1형 알레르기 면역반응에 미치는 영향을 보기 위하여 BGN4의 경구 치료시기에 따라 실험군을 4군으로 나누어 진행하였다. 제1군은 땅콩 감작 전 2주간 BGN4를 투여한 군(pre/PN), 제2군은 땅콩 감작 전 2주 및 감작 시작 후 2주간의 총 4주간 BGN4를 투여한 군(Pre＋Post/PN), 제3군은 땅콩 감작 전 2주간 PBS만 투여한 양성대조군(PBS/PN), 제4군은 땅콩 감작 및 BGN4 치료를 하지 않은 음성 대조군(naive)이었다. 연령 4주의 female C3H/HeJ strain의 생쥐를 각 군당 3-4마리씩 이용하여 동일한 실험을 2회씩 반복 하였다. 각 군별로 4군간 실험 주별 혈청 땅콩 특이 IgE 농도를 비교하였고, 실험 4주에 얻은 비장세포의 72시간 배양을 통한 땅콩 특이적 IL-4, IL-10, IL-12, IFN-γ의 생성량을 비교 분석하였다. 결 과 : 땅콩의 위장관 감작이 끝난 후 땅콩 특이 IgE의 농도는 제1군(pre/PN)과 제 3군(PBS/PN)에 비하여 제2군(pre＋post/PN)에서 의미 있게 감소하였다. 그러나 땅콩 항원 자극에 따른 비장세포의 증식능은 감소하지 않았다. 한편 비장세포배양 부유액에서의 IL-4, INF-γ 및 IL-10은 제1군과 2군에서 모두 감소하였고, 특히 IL-4의 생성 감소 및 IFN-γ/IL-4 ratio 증가는 혈청 땅콩 특이 IgE 생성의 감소와 비례하였다. IL-12는 감작 항원 자극에 의해서는 BGN4 감작 전 투여 및 감작기간 중 지속투여군인 제2군에서만 의미 있는 농도로 생성되었으며, Con A 자극에 의한 IL-12의 생성은 제2군 뿐 아니라 BGN4 전처치군인 제1군에서도 증가하였다. 결 론 : 땅콩의 감작 과정 중 BGN4를 감작기간 동안 투여함으로서 항원 특이 IgE 생성의 감소, 비장 세포 항원 특이적 IL-12 생성 증가, IFN-γ/IL-4 ratio 증가가 관찰되었다. 투여 시기와 용량에 대한 추가적인 연구가 필요하지만, 이러한 결과는 BGN4가 IgE-매개성 알레르기 면역반응에 대한 면역조절 기능을 가지고 있음을 시사한다.
Wyner-Ziv coding based on TCQ and LDPC codes (2004)

This paper considers TCQ and LDPC codes for the quadratic Gaussian Wyner-Ziv problem. After TCQ of the source input X, LDPC codes are used to implement Slepian-Wolf coding of the quantized source input Q(X) given the side information Y at the decoder. Assuming ideal Slepian-Wolf coding in the sense of achieving the theoretical limit H (Q(X)|Y), it is shown that Slepian-Wolf coded TCQ (SWC-TCQ) performs 0.2 dB away from the Wyner-Ziv distortion-rate function D/sub WZ/*(R) at high rate. This result mirrors that of entropy-coded TCQ in classic source coding and establishes the connection between performances of high-rate Wyner-Ziv coding and classic source coding. Practical designs with TCQ, irregular LDPC codes (for Slepian-Wolf coding) and optimal estimation at the decoder perform 0.83 dB away from D/sub WZ/*(R) at medium bit rates (e.g., /spl ges/ 2.3 b/s). With 2-D trellis-coded vector quantization, the performance gap to D/sub WZ/*(R) is only 0.66 dB at 1.0 b/s and 0.47 dB at 3.3 b/s.
The role of Ca-organic interactions in soil aggregate stability .III. Mechanisms and models (1989)

Serial additions of glucose after drying-wetting cycles led to substantial aggregation of the surface soil from a red-brown earth. Addition of glucose and Ca compounds resulted in up to 80% of the soil bound in particles &amp;gt;2000µm with only a small portion of the soil in particles 4 0 µm. Treatment of the soils with Na4P2O7 caused dispersion of most of the clay but did not disrupt larger aggregates. More disaggregation was caused by treatments with HCI (0.02 M and 0.1 M), indicating the presence of pyrophosphate-resistant binding mechanisms which were presumed to be due to Ca bridging. Addition of Ca to the soil reduced the efficiency of extraction of organic materials by NaOH. This effect was eliminated by a pretreatment with 1 M HCl, indicating a 'bridging' effect of Ca between polycarboxylic macromolecules (humic acids) and clays. The role of Ca in clay and organic matter flocculation, the bridging of clay aggregates to organic materials and interactions of these colloidal aggregates with the biologic cycle is illustrated in some pictorial models.
Pharmacokinetics and metabolism of omeprazole in animals and man - an overview (1985)

The pharmacokinetics of omeprazole have been studied to varying extent in the mouse, rat, dog and in man. The drug is rapidly absorbed in all these species. The systemic availability is relatively high in the dog and in man provided the drug is protected from acidic degradation in the stomach. In man the fraction of the oral dose reaching the systemic circulation was found to increase from an average of 40.3 to 58.2% when the dose was raised from 10 to 40 mg, suggesting some dose-dependency in this parameter. The drug distributes rapidly to extra-vascular sites. The volume of distribution, V beta, in man is comparable to the volume of the extracellular water. The penetration into the red cells is low, the ratio between the concentration in whole blood and in plasma being about 0.6. Omeprazole is bound to about 95% to proteins in human plasma. The binding is lower in the dog and rat (90 and 87%, respectively). Omeprazole is eliminated almost completely by metabolism and no unchanged drug has been recovered in the urine in the species studied. Two metabolites, characterised as the sulfone and sulfide of omeprazole, have been identified and quantified in human plasma. The mean elimination half-life in man and in the dog is about 1 hour, whereas half-lives in the range of 5 to 15 minutes have been recorded in the mouse. In two studies in man, the mean total body clearance was 880 and 1097 ml X min-1, indicating that omeprazole belongs to the group of high clearance drugs. In the dog, too, the drug appears to be rapidly cleared from the blood, the mean total body clearance being about 10.5 ml X min-1 X kg-1. In the rat and dog, 20 to 30% of an i.v. or oral dose of omeprazole is excreted as metabolites in the urine and the remaining fraction is recovered in the faeces within three days after the administration. In man, the excretion of radioactivity via the kidneys is much more efficient and the recoveries in the excreta are approximately the reverse of those in the rat and dog. In vitro studies with rat liver microsome preparations suggest that omeprazole and cimetidine inhibit cytochrome P-450-mediated metabolic reactions to about the same extent in equimolar concentrations. However, since the molar daily dose of cimetidine will be 25 to 50 times higher than that of omeprazole, the latter might have less influence on the mixed function oxidase system than cimetidine.(ABSTRACT TRUNCATED AT 400 WORDS)
Coherent control of the population transfer in complex solvated molecules at weak excitation. An experimental study (2005)

We performed a series of successful experiments for the optimization of the population transfer from the ground to the first excited state in a complex solvated molecule (rhodamine 101 in methanol) using shaped excitation pulses at very low intensities (1 absorbed photon per 100-500 molecules per pulse). We found that the population transfer can be controlled and significantly enhanced by applying excitation laser pulses with crafted pulse shapes. The optimal shape was found in feedback-controlled experiments using a genetic search algorithm. The temporal profile of the optimal excitation pulse corresponds to a comb of subpulses regularly spaced by approximately 150 fs, whereas its spectrum consists of a series of well-resolved peaks spaced apart by approximately 6.5 nm corresponding to a frequency of 220 cm(-1). This frequency matches very well with the frequency modulation of the population kinetics (period of approximately 150 fs), observed by excitation with a short (approximately 20 fs) transform-limited laser pulse directly after excitation. In addition, an antioptimization experiment was performed under the same conditions. The difference in the population of the excited state for the optimal and antioptimal pulses reaches approximately 30% even at very weak excitation. The results of optimization are reproducible and have clear physical meaning.
Structural (shape-maintaining) role of the cell surface glycoprotein of Halobacterium salinarium. (1976)

The obligate halophile, Halobacterium salinarium, maintains a rod-shaped morphology under normal growth conditions. Lactoperoxidase(EC 1.11.1.7;donor:hydrogen-peroxide oxidoreductase)-catalyzed iodination and treatment with proteolytic enzymes were used to demonstrate that the recently described envelope glycoprotein (Mescher, M.F. & Strominger, J.L. (1976) J. Biol. Chem. 251, 2005-2014) is the only major cell surface component of this organism. The morphological changes that accompany alteration of the structure of the glycoprotein by growth in the presence of bacitracin or its removal with proteolytic enzymes strongly suggest that it forms a rigid matrix at the cell surface and is responsible for maintenance of the characteristic rod shape.
TREATMENT OF RHEUMATOID ARTHRITIS WITH BLACKCURRANT SEED OIL (1994)

The objective of this study was to assess the clinical efficacy and side effects of blackcurrant seed oil (BCSO), in a randomized, double-blind, placebo controlled, 24-week trial in patients with RA and active synovitis. BCSO is rich in gammalinolenic acid (GLA) and alphalinolenic acid (ALA). Both GLA and eicosapentaenoic acid which derives from ALA suppress inflammation and joint tissue injury in animal models. Treatment with BCSO resulted in reduction in signs and symptoms of disease activity in patients with RA (P < 0.05). In contrast, patients given a placebo showed no change in disease. Overall clinical responses (significant change in four measures) were no better in the treatment group than in the placebo group. No patients withdrew from BCSO treatment because of adverse reactions. However, many patients withdrew because BCSO and its placebo had to be administered in 15 large capsules daily. Nonetheless, the study indicates that BCSO is a potentially effective treatment for active RA. However, means must be found to reduce the size and number of capsules taken, so that larger studies of longer duration in RA patients can be done.
Particle Morphology Analysis of Biomass Material Based on Improved Image Processing Method (2017)

Particle morphology, including size and shape, is an important factor that significantly influences the physical and chemical properties of biomass material. Based on image processing technology, a method was developed to process sample images, measure particle dimensions, and analyse the particle size and shape distributions of knife-milled wheat straw, which had been preclassified into five nominal size groups using mechanical sieving approach. Considering the great variation of particle size from micrometer to millimeter, the powders greater than 250 <i>μ</i>m were photographed by a flatbed scanner without zoom function, and the others were photographed using a scanning electron microscopy (SEM) with high-image resolution. Actual imaging tests confirmed the excellent effect of backscattered electron (BSE) imaging mode of SEM. Particle aggregation is an important factor that affects the recognition accuracy of the image processing method. In sample preparation, the singulated arrangement and ultrasonic dispersion methods were used to separate powders into particles that were larger and smaller than the nominal size of 250 <i>μ</i>m. In addition, an image segmentation algorithm based on particle geometrical information was proposed to recognise the finer clustered powders. Experimental results demonstrated that the improved image processing method was suitable to analyse the particle size and shape distributions of ground biomass materials and solve the size inconsistencies in sieving analysis.
Pore-scale investigation of residual oil displacement in surfactant–polymer flooding using nuclear magnetic resonance experiments (2016)

Research on the Gangxi III area in the Dagang Oilfield shows that there was still a significant amount of oil remaining in oil reservoirs after many years of polymer flooding. This is a potential target for enhanced oil recovery (EOR). Surfactant–polymer (SP) flooding is an effective chemical EOR method for mobilizing residual oil and improving displacement efficiency macroscopically, but the microscopic oil displacement efficiency in pores of different sizes is unclear. Nuclear magnetic resonance (NMR) is an efficient method for quantifying oil saturation in the rock matrix and analyzing pore structures. In this paper, the threshold values of different pore sizes were established from the relationship between mercury injection curves and NMR T 2 spectrums. The distribution and migration of residual oil in different flooding processes was evaluated by quantitatively analyzing the change of the relaxation time. The oil displaced from pores of different sizes after the water flood, polymer flood, and the SP flood was calculated, respectively. Experimental results indicate that (1) the residual oil in medium pores contributed the most to the incremental oil recovery for the SP flood, ranging from 40 % to 49 %, and small pores usually contributed <30 %; (2) the residual oil after the SP flood was mainly distributed in small and medium pores; the residual oil in medium pores accounted for 47.3 %–54.7 %, while that trapped in small pores was 25.7 %–42.5 %. The residual oil in small and medium pores was the main target for EOR after the SP flood in oilfields.
Hepatitis delta virus (HDV) and woodchuck hepatitis virus (WHV) nucleic acids in tissues of HDV-infected chronic WHV carrier woodchucks (1989)

The molecular forms of genomic and antigenomic hepatitis delta virus (HDV) RNA and of woodchuck hepatitis virus (WHV) DNA and WHV RNA were studied in nonneoplastic liver (NL) tissues, hepatocellular carcinoma (HCC) tissues, and several extrahepatic tissues of chronic WHV carrier woodchucks acutely (two animals) and chronically (six animals) superinfected with HDV. HDV was shown to replicate in all NL and HCC tissues but not in any of the extrahepatic tissues analyzed, which included spleen, peripheral blood lymphocytes, kidney, ovary, testis, thymus, lung, and stomach. HDV RNA was present as species with molecular weights consistent with those of monomers, dimers, and trimers of both strand polarities, supporting the rolling circle model proposed for HDV RNA replication. WHV DNA levels in NL, HCC, spleens, and serum were 10- to 100-fold lower than the levels typically observed in chronic WHV carrier woodchucks not infected with HDV. WHV DNA replicative intermediates were rarely observed and only at very low levels, representing less than 10% of the total WHV DNA. By contrast, WHV RNA transcription was not significantly depressed and both primary WHV RNA transcripts, 2.3 and 3.6 kilobases, were observed in NL, HCC, spleens, and in one of the kidney tissues. In addition, a 2.6-kilobase WHV RNA transcript was found in the majority of the NL tissues.