gebhart/patrepeval huggingface dataset:
Staphylococcus aureus Metabolic Adaptations during the Transition from a Daptomycin Susceptibility Phenotype to a Daptomycin Nonsusceptibility Phenotype (2015)

Staphylococcus aureus is a major cause of nosocomial and community-acquired infections. The success of S. aureus as a pathogen is due in part to its many virulence determinants and resistance to antimicrobials. In particular, methicillin-resistant S. aureus has emerged as a major cause of infections and led to increased use of the antibiotics vancomycin and daptomycin, which has increased the isolation of vancomycin-intermediate S. aureus and daptomycin-nonsusceptible S. aureus strains. The most common mechanism by which S. aureus acquires intermediate resistance to antibiotics is by adapting its physiology and metabolism to permit growth in the presence of these antibiotics, a process known as adaptive resistance. To better understand the physiological and metabolic changes associated with adaptive resistance, six daptomycin-susceptible and -nonsusceptible isogenic strain pairs were examined for changes in growth, competitive fitness, and metabolic alterations. Interestingly, daptomycin nonsusceptibility coincides with a slightly delayed transition to the postexponential growth phase and alterations in metabolism. Specifically, daptomycin-nonsusceptible strains have decreased tricarboxylic acid cycle activity, which correlates with increased synthesis of pyrimidines and purines and increased carbon flow to pathways associated with wall teichoic acid and peptidoglycan biosynthesis. Importantly, these data provided an opportunity to alter the daptomycin nonsusceptibility phenotype by manipulating bacterial metabolism, a first step in developing compounds that target metabolic pathways that can be used in combination with daptomycin to reduce treatment failures.
Correction: Stimuli-responsive magnetic nanoparticles for tumor-targeted bimodal imaging and photodynamic/hyperthermia combination therapy (2016)

Correction for ‘Stimuli-responsive magnetic nanoparticles for tumor-targeted bimodal imaging and photodynamic/hyperthermia combination therapy’ by Kyoung Sub Kim, et al., Nanoscale, 2016, DOI: 10.1039/c6nr02273a.
Physiological and transcriptomic responses of water spinach (Ipomoea aquatica) to prolonged heat stress (2020)

The prolonged heat stress resulted in a reduced antioxidant capacity while the role of antioxidant capacity in a prolonged thermotolerance of water spinach was not predominant. Transcriptome analysis and the measurement of carbohydrates as well as the gene expression evaluation indicated that the response of the metabolic pathway such as carbohydrate and phenylpropanoid biosynthesis to heat stress may be a key player in thermo resistance.
Breed Differences in Allele Frequency of the Dopamine Receptor D4 Gene in Dogs (2001)

We previously reported that the dog dopamine receptor D4 (DRD4) gene is polymorphic as observed in humans, and four alleles were identified based on the number and/or order of the 12 and 39 bp sequences located in the homologous region of human DRD4. To assess the diversity of the DRD4 gene in dogs we examined the allelic variations in four breeds (beagle, golden retriever, Shetland sheepdog, and shiba) employing the polymerase chain reaction (PCR). As a result, we found three novel alleles and determined the DNA sequences of these alleles. The beagle shared four alleles, including 396, 435, 447a, and 447b, with the 435 (52.6%) and 447a (39.5%) alleles being common. The golden retriever had the 435 and 447a alleles, and the 435 allele was frequent (73.3%). In the Shetland sheepdog, the 435, 447a, and 498 alleles were observed, of which the 447a allele was most frequent (82.5%). The shiba had five alleles-447a, 447b, 486, 498, and 549-and the 447b allele was most common (55.4%). These findings suggest that the allele frequency varied among the four dog breeds, and analysis of the DRD4 polymorphism may therefore be useful for elucidating the relationships among dog breeds.
Nuclear assembly of polyomavirus capsids in insect cells expressing the major capsid protein VP1 (1991)

Polyomavirus normally assembles in the nucleus of infected mouse cells. Sf9 insect cells expressing the polyomavirus major capsid protein VP1 were examined by electron microscopy. Capsidlike particles of apparently uniform size were found in the nucleus. Immunogold electron microscopy demonstrated abundant VP1 in the cytoplasm which was not assembled into any recognizable higher-order structure. Cytoplasmic VP1 assembled after the cells were treated with the calcium ionophore ionomycin. Purified VP1 aggregates were shown by negative staining and cryoelectron microscopy to consist predominantly of particles similar to the empty T = 7 viral capsid. Thus, polyomavirus VP1 can assemble in vivo into capsids independent of other viral proteins or DNA. Nuclear assembly may result from increased available calcium in this subcellular compartment.
The Usefulness of CO2Laser-assisted Phonomicrosurgery Using a Computer-guided Scanner in Benign Vocal Fold Mucosal Disorders (2012)

Although no significant difference was observed between the two groups, CO 2 laser assisted phonomicrosurgery using CGS allows for performance of more accurate and delicate incision with a controllable depth of beam penetration.
A 1mm 3 2Mbps 330fJ/b transponder for implanted neural sensors (2011)

An implanted fully-integrated 65nm CMOS 1.1mm × 1.1mm × 0.8mm remotely-powered wireless transponder for implantable neural sensors provides 5uW for sensor interfaces, while consuming 3uW and transmitting 2Mbps at 330fJ/b without violating exposure limitations. This is accomplished by combining a time-multiplexed power and data transmission scheme with a reflective impulse transmitter architecture.
1(5)-Cyanosemibullvalene from barrelene. Spectral and crystal structure analysis of the marked equilibrium preference exerted by an efficient .pi.-electron acceptor substituent (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1(5)-Cyanosemibullvalene from barrelene. Spectral and crystal structure analysis of the marked equilibrium preference exerted by an efficient .pi.-electron acceptor substituentLeo A. Paquette, William E. Volz, Mark A. Beno, and Gary G. ChristophCite this: J. Am. Chem. Soc. 1975, 97, 9, 2562–2563Publication Date (Print):April 1, 1975Publication History Published online1 May 2002Published inissue 1 April 1975https://pubs.acs.org/doi/10.1021/ja00842a054https://doi.org/10.1021/ja00842a054research-articleACS PublicationsRequest reuse permissionsArticle Views46Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
NUTRIENT SUPPLEMENTATION OF MUSHROOM COMPOST AT CASING: VEGETABLE OILS (1966)

Supplementation of compost at casing with various ground seeds caused greater increases in mushroom yield than their respective seed oil meals when supplemented and compared at equivalent rates of nitrogen addition.Supplementation with various refined and crude seed oils increased mushroom yield, particularly in the first break or flush of mushrooms. This constitutes evidence for a relationship between lipid metabolism and the initiation of fruiting in the cultivated mushroom, Agaricus bisporus (Lange) Sing.
The Mechanism of Trichloroethylene Oxidation by Toluene Dioxygenase: Implications for Bioremediation (1991)

The oxidation of trichloroethylene (TCE) by toluene dioxygenase in vivo and in vitro has been investigated. In a previous study, the initial rate of TCE oxidation by Pseudomonas putida Fl declined rapidly. This was shown in vivo, in the present study, to be due to toluene dioxygenase-dependent activation of TCE to produce reactive intermediates. Carbon-14 label from metabolism of radioactive TCE was incorporated into proteins, small molecules, DNA, RNA, and lipid. Alkylation of proteins, including toluene dioxygenase, caused metabolic poisoning and the loss of TCE-degrading ability. P'. putida was able to recover from TCE-mediated cytotoxicity. Toluene dioxygenase enzyme components were purified from recombinant E. coli strains by the use of conventional chromatographic methods. The major products of TCE oxidation by purified toluene dioxygenase have been identified as formic acid and glyoxylic acid. An additional minor product was shown to result from the alkylation of reduced pyridine dinucleotide (NADPH) by a reactive TCE intermediate generated by the toluene dioxygenase catalyzed reaction. Experiments with 14C-TCE showed that enzyme inactivation was due to non-specific alkylation of the proteins by diffusible reactive intermediates. A recombinant E. coli expressing cloned toluene dioxygenase genes oxidized TCE. The rate of TCE oxidation by the E. coli strain was slower than that of P. putida Fl but the rates were sustained for a longer time. The use of recombinant strains or gratuitously induced P. putida Fl could have important implications for bioremediation. Furthermore, a greater understanding of the mechanism of toluene dioxygenase inactivation will be crucial for developing optimum systems for TCE-biotreatment.
SKIP Prediction for Fast Rate Distortion Optimization in H.264 (2007)

In H.264, the optimal coding mode for each macroblock (MB) is selected by exhaustively searching all MB modes in the multiple reference frames. The exhaustive mode search has a very high computational complexity. This paper proposes three different approaches along with their combination to reduce the complexity of the rate-distortion optimized mode decision process in H.264. These approaches are based on transform-domain properties and spatio-temporal correlation in video sequences. Experimental results demonstrate that the proposed methods achieve around 5-7 times improvement in average speedup with good prediction quality and comparable bitrate.
Genetic variation in ST6GAL1 is a determinant of capecitabine and oxaliplatin induced hand‐foot syndrome (2022)

Cancer patients treated with capecitabine and oxaliplatin (XELOX) often develop hand-foot syndrome (HFS) or palmar-plantar erythrodysesthesia. Genetic variation in ST6GAL1 is a risk factor for type-2 diabetes (T2D), a disease also associated with HFS. We analysed genome-wide association data for 10 toxicities in advanced colorectal cancer (CRC) patients from the COIN and COIN-B trials. One thousand and fifty-five patients were treated with XELOX ± cetuximab and 745 with folinic acid, fluorouracil and oxaliplatin ± cetuximab. We also analysed rs6783836 in ST6GAL1 with HFS in CRC patients from QUASAR2. Using UK Biobank data, we sought to confirm an association between ST6GAL1 and T2D (17 384 cases, 317 887 controls) and analysed rs6783836 against markers of diabetes, inflammation and psoriasis. We found that 68% of patients from COIN and COIN-B with grade 2-3 HFS responded to treatment as compared to 58% with grade 0-1 HFS (odds ratio [OR] = 1.1, 95% confidence interval [CI] = 1.02-1.2, P = 2.0 × 10<sup>-4</sup> ). HFS was also associated with improved overall survival (hazard ratio = 0.92, 95% CI = 0.84-0.99, P = 4.6 × 10<sup>-2</sup> ). rs6783836 at ST6GAL1 was associated with HFS in patients treated with XELOX (OR = 3.1, 95% CI = 2.1-4.6, P = 4.3 × 10<sup>-8</sup> ) and was borderline significant in patients receiving capecitabine from QUASAR2, but with an opposite allele effect (OR = 0.66, 95% CI = 0.42-1.03, P = .05). ST6GAL1 was associated with T2D (lead SNP rs3887925, OR = 0.94, 95% CI = 0.92-0.96, P = 1.2 × 10<sup>-8</sup> ) and the rs6783836-T allele was associated with lowered HbA1c levels (P = 5.9 × 10<sup>-3</sup> ) and lymphocyte count (P = 2.7 × 10<sup>-3</sup> ), and psoriasis (P = 7.5 × 10<sup>-3</sup> ) beyond thresholds for multiple testing. In conclusion, HFS is a biomarker of treatment outcome and rs6783836 in ST6GAL1 is a potential biomarker for HFS with links to T2D and inflammation.
Development of a Vaccine against Murine Cytomegalovirus (MCMV), Consisting of Plasmid DNA and Formalin-Inactivated MCMV, That Provides Long-Term, Complete Protection against Viral Replication (2002)

We previously demonstrated that immunization of mice with plasmid DNAs (pDNAs) expressing the murine cytomegalovirus (MCMV) genes IE1-pp89 and M84 provided synergistic protection against sublethal viral challenge, while immunization with plasmids expressing putative virion proteins provided no or inconsistent protection. In this report, we sought to augment protection by increasing the breadth of the immune response. We identified another MCMV gene (m04 encoding gp34) that provided strong and consistent protection against viral replication in the spleen. We also found that immunization with a DNA pool containing 10 MCMV genes that individually were nonprotective elicited reproducible protection against low to intermediate doses of challenge virus. Moreover, inclusion of these plasmids into a mixture with gp34, pp89, and M84 DNAs provided even greater protection than did coimmunization with pp89 and M84. The highest level of protection was achieved by immunization of mice with the pool of 13 pDNAs, followed by formalin-inactivated MCMV (FI-MCMV). Immunization with FI-MCMV elicited neutralizing antibodies against salivary gland-derived MCMV, and of greatest importance, mice immunized with both the combined pDNA pool and FI-MCMV had undetectable levels of virus in the spleen and salivary glands after challenge. Intracellular cytokine staining of splenocytes from pDNA- and FI-MCMV-immunized mice showed that pDNA immunization elicited high levels of pp89- and M83-specific CD8(+) T cells, whereas both pDNA and FI-MCMV immunizations generated strong CD8(+)-T-cell responses against virion-associated antigens. Taken together, these results show that immunization with pDNA and inactivated virus provides strong antibody and cell-mediated immunity against CMV infection.
만성 B형 바이러스성 간염환자들에 대한 lamivudine 1년 치료 효과에 대한 전향적 연구 (2000)

Background : The aims of our study was to explore the effectiveness of 1 year treatment of lamivudine in Korean patients with chronic liver disease caused by chronic infection of HBV. Methods : Thirty patients with chronic infection of HBV were included in this study who were diagnosed at Hanyang University Hospital from January 1998 to August 1999. They received 150mg of lamivudine per oral once daily for 1 year with follow-up of liver function test, serum HBV-bDNA and serologic markers for hepatitis B virus every two months. Results : The mean values of ALT, AST, and GGT decreased significantly after 6 months treatment, but after 10∼12 months treatment, 6 out of 30 cases(20%) tended to flare-up or return to pretreatment state. Nevertheless, their levels revealed no statistically significant changes after 12 months. No case show disappearance of HBsAg. HBeAg seroconversion occurred in 10 among 27 patients(37%). The mean of HBV-bDNA decreased from 1,776.0 pg/mL(2.5∼17,000) to 10.8 pg/mL (2.5∼67) after 6 months, but tended to rise to 317.9 pg/mL(2.5∼5,900) after 12 months. After 10∼12 months treatment, 11 cases out of 30 showed breakthrough or incomplete suppression of HBV DNA replication. Stepwise-logistic regression analysis proved the high baseline ALT was the only predictable factor for loss of HBeAg by lamivudine with an odds ratio of 1.0518(95% confidence interval: 1.0052∼1.1007)(p=0.0291). Conclusion : Treatment of lamivudine showed improvement in normalization of ALT and reduction of HBV-bDNA after 6months. But after 10∼12 months treatment, one third cases of them tended to flare-up or return to pretreatment state. And the group with high baseline ALT is not only suitable for indication of lamivudine therapy but also predictable factor of disappearance of HBeAg after 12months treatment with lamivudine.(Korean J Med 59:20-29, 2000)
Data from Adding Umbralisib and Ublituximab (U2) to Ibrutinib in Patients with CLL: A Phase II Study of an MRD-Driven Approach (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Ibrutinib has transformed the management of chronic lymphocytic leukemia (CLL), though its use is limited by toxicity and resistance. In this study, we utilized an “add on” approach for patients who had been treated with ibrutinib in the front-line or relapsed/refractory settings with detectable MRD. Umbralisib and ublituximab (U2) were added on to ibrutinib, patients were treated until achieving undetectable-MRD (U-MRD), and then they entered a period of treatment-free observation (TFO).&lt;/p&gt;Patients and Methods:&lt;p&gt;Patients were eligible if they received ibrutinib in any line of therapy for at least 6 months and had detectable MRD (flow cytometry, &lt;1 cell in 10&lt;sup&gt;–4&lt;/sup&gt; cutoff for U-MRD). U2 was added to ibrutinib, and patients were monitored serially for MRD. Once U-MRD was achieved or a total of 24 cycles were administered, patients entered a period of TFO. The primary study objective was rate of U-MRD. Secondary endpoints included safety and durability of clinical benefit after treatment discontinuation.&lt;/p&gt;Results:&lt;p&gt;Twenty-eight patients were enrolled of whom 27 were evaluable for efficacy. Patients received ibrutinib for a median of 21 months (range 7–67) prior to study enrollment. Fourteen patients (52%) have achieved U-MRD per protocol whereas 78% had at least one U-MRD evaluation. Seventeen patients (63%) have entered TFO after a median of 6.4 months on triplet therapy. Progression-free survival at 12 months was estimated at 95%. Grade ≥3 adverse events were hypertension 7%, diarrhea 4%, and increased ALT/AST 4%.&lt;/p&gt;Conclusions:&lt;p&gt;This triplet approach utilizes the addition of U2 to ibrutinib as an MRD-driven time-limited therapy. This therapy was well tolerated and effective. TFO following this therapy appears durable in ongoing follow-up.&lt;/p&gt;&lt;/div&gt;
Joint Statement of Editors of Journals Publishing Thermophysical Property Data (2009)

ADVERTISEMENT RETURN TO ISSUEPREVEditorialNEXTJoint Statement of Editors of Journals Publishing Thermophysical Property DataPeter T. Cummings, Theo de Loos, John P. O’Connell, W. M. (Mickey) Haynes, Daniel G. Friend, Andreas Mandelis, Kenneth N. Marsh, Paul L. Brown, Robert Chirico, Anthony R. H. Goodwin, Jiangtao Wu, Ronald D. Weir, J. P. Martin Trusler, Agilio Pádua, V. Rives, C. Schick, S. Vyazovkin, and Lee D. HansenView Author InformationFluid Phase EquilibriaInternational Journal of ThermophysicsJournal of Chemical and Engineering DataThe Journal of Chemical ThermodynamicsThermochimica ActaCite this: J. Chem. Eng. Data 2009, 54, 1, 2–3Publication Date (Web):January 8, 2009Publication History Received12 December 2008Published online8 January 2009Published inissue 8 January 2009https://doi.org/10.1021/je8009607Copyright © This article not subject to U.S. Copyright. Published 2009 by the American Chemical SocietyRIGHTS & PERMISSIONSArticle Views1889Altmetric-Citations17LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (29 KB) Get e-AlertsSUBJECTS:Salts,Theoretical and computational chemistry,Thermodynamics,Solvents,Software Get e-Alerts
[Combined multiple organ resection in 16 patients with adenocarcinoma of the body or tail of the pancreas]. (2005)

Radical combined multiple organ resection may be performed actively in appropriately selected patients.
Raman Study Of Ge/Si Strained Layer Superlattices Grown On Different Substrate Orientations (1989)

We present the growth and characterization of Ge/Si strained layer superlattices grown on different substrate orientations. Prior to the growth of the superlattices, a relaxed thick GexSi1-x buffer layer is grown on Si substrate to symmetrize the strain distribution and thus maintain pseudomorphic growth of the superlattices. The effective Ge fraction x is used to define the degree of interface mixing of these superlattices. It is found that for samples grown on the same orientaion, the degree of interface mixing is higher for samples with smaller period lengths. The samples grown on (110) and (111) substrates also have a higher degree of interface mixing than those grown on (100) substrates. The thermal stability of these Ge/Si strained layer superlattice samples is also studied.
In Situ Rapid Thermal Oxidation and Reduction of Copper Thin Films and Their Applications in Ultralarge Scale Integration (2001)

Copper is widely accepted as a next-generation metallization material for ultralarge-scale integration (ULSI) because of its low resistivity and high electromigration resistance. It is well known that Cu oxidizes easily at low temperatures. This characteristic has impeded the application of Cu in integrated circuits. However, the high oxidation rate of Cu and high reduction rate of its oxides at low temperature can be exploited for some potential applications. This paper presents the kinetic studies of Cu film oxidation and in situ reduction of its oxide films. The Cu oxidation experiments were performed in dry and wet oxygen at temperatures from 100 to 600°C for oxidation times from 10 to 718 s. Scanning electron microscopy, Rutherford backscattering spectrometry, spectroscopic ellipsometry and reflectometry, and X-ray photoelectron spectroscopy were used for analyzing the chemical composition of the processed material and determining the oxidation/reduction kinetics of the films. The results showed that the oxide phase is CuO at higher temperature and at lower temperature (<400°C). In situ reduction of copper oxide was studied using secondary ion mass spectroscopy, indicating that the reduction of Cu oxides proceeds from the interface to the surface with a high reduction rate. The infrared reflectivity of Cu surface is over 99%. This is a problem when the Cu process is performed in a rapid thermal processing (RTP) system, since most of the radiation from the lamps is consequently reflected by the Cu surface. An improved process, called shield-enhanced RTP, results in higher lamp power efficiency and better within wafer temperature uniformity. © 2001 The Electrochemical Society. All rights reserved.