gebhart/patrepeval huggingface dataset:
Broader Tropism and Higher Cytopathicity for CD4+T Cells of a Syncytium-Inducing Compared to a Non-Syncytium-Inducing HIV-1 Isolate as a Mechanism for Accelerated CD4+T Cell Declinein Vivo (1996)

The emergence of syncytium-inducing (SI) HIV-1 isolates in infected individuals precedes an accelerated CD4+ T cell decline and is associated with high virus load and rapid disease progression. The exact mechanism by which SI HIV-1 variants may cause this enhanced clinical progression is unknown. Here we demonstrate that an SI HIV-1 isolate had a broader tropism for CD4+ T cell clones (TCC) compared to a macrophage-tropic non-syncytium-inducing (NSI) HIV-1 isolate. Whereas the NSI isolate replicated poorly in 6 of 12 TCC and completely failed to replicate in 3 of 12 TCC, the SI isolate replicated efficiently in all 12 TCC tested. Restriction for replication occurred early in the viral replication cycle, before provirus formation. Infection of TCC with the SI but not with the NSI HIV-1 isolate resulted in massive death of T cells, independent of the extent of virus replication and proportion of infected cells. The high cytopathicity and broader tropism of the SI isolate for primary CD4+ T cells may be directly related to the increased rate of CD4 cell decline and rapid disease progression in carriers of SI variants.
Location of the mycolyl ester substituents in the cell walls of mycobacteria (1991)

The question of the precise location of mycolic acids, the single most distinctive cell wall entity of members of the Mycobacterium genus, has now been addressed. The free hydroxyl functions of the arabinogalactan component of the mycobacterial cell wall were O-methylated under conditions in which the mycolyl esters were not cleaved. Subsequent replacement of the mycolyl functions with O-ethyl groups resulted in an acid- and base-stable differentially O-alkylated surrogate polysaccharide, more amenable to analysis. Complete hydrolysis, reduction, acetylation, and gas chromatography/mass spectrometry revealed the unexpected finding that the mycolyl substituents were selectively and equally distributed on the 5-hydroxyl functions of terminal- and 2-linked arabinofuranosyl (Araf) residues. Further analysis of the O-alkylated cell wall through partial acid hydrolysis, NaB[2H]4 reduction, pentadeuterioethylation, and gas chromatography/mass spectrometry demonstrated that the mycolyl units are clustered in groups of four on the previously recognized nonreducing terminal pentaarabinosyl unit [beta-Araf-(1----2)-alpha-Araf)2-3, 5-alpha-Araf. However, only about two-thirds of the available pentasaccharide units are so substituted. Thus, the antigenicity of the arabinan component of mycobacterial cell walls may be explained by the fact that about one-third of the pentaarabinosyl units are not mycolyated and are available for interaction with the immune system. On the other hand, the extreme hydrophobicity and impenetrability of the mycobacterial cell may be explained by the same motif also acting as the fulerum for massive esterified paraffin residues. New fundamental information on the structure of mycobacterial cell walls will aid in our comprehension of its impenetrability to antibiotics and role in immunopathogenesis and persistence of disease.
Persistence Increases in the Absence of the Alarmone Guanosine Tetraphosphate by Reducing Cell Growth (2016)

Most bacterial cells are stressed, and as a result, some become tolerant to antibiotics by entering a dormant state known as persistence. The key intracellular metabolite that has been linked to this persister state is guanosine tetraphosphate (ppGpp), the alarmone that was first linked to nutrient stress. In Escherichia coli, ppGpp redirects protein production during nutrient stress by interacting with RNA polymerase directly and by inhibiting several proteins. Consistently, increased levels of ppGpp lead to increased persistence; but, the mechanism by which elevated ppGpp translates into persistence has not been determined. Hence, we explored persistence in the absence of ppGpp so that the underlying mechanism of persister cell formation could be explored. We found that persister cells still form, although at lower levels, in the absence of ppGpp. Additionally, the toxin/antitoxin systems that we investigated (MqsR, MazF, GhoT, and YafQ) remain able to increase persistence dramatically in the absence of ppGpp. By overproducing each E. coli protein from the 4287 plasmid vectors of the ASKA library and selecting for increased persistence in the absence of ppGpp (via a relA spoT mutant), we identified five new proteins, YihS, PntA, YqjE, FocA, and Zur, that increase persistence simply by reducing cell growth.
Design and synthesis of polymers for light‐emitting diodes (1998)

Polymers with aromatic ϕ-conjugated moieties were utilized as electroluminescent materials. In order to meet the requirements for light-emitting diodes (LED), the design and synthesis of electroluminescent polymers had to be developed and viewed in this review. Focus is on polymers with arylene vinylene, arylene ethinylene, phenylene, thiophene and arylene amine moieties as light-emitting, hole-transporting and electron-transporting materials in LED devices. An attempt has been made to arrange a structural classification of electroluminescent polymers in nonsegmented and segmented polymers. © 1998 John Wiley & Sons, Ltd.
N-Doping of Graphene Through Electrothermal Reactions with Ammonia (2009)

Graphene is readily p-doped by adsorbates, but for device applications, it would be useful to access the n-doped material. Individual graphene nanoribbons were covalently functionalized by nitrogen species through high-power electrical joule heating in ammonia gas, leading to n-type electronic doping consistent with theory. The formation of the carbon-nitrogen bond should occur mostly at the edges of graphene where chemical reactivity is high. X-ray photoelectron spectroscopy and nanometer-scale secondary ion mass spectroscopy confirm the carbon-nitrogen species in graphene thermally annealed in ammonia. We fabricated an n-type graphene field-effect transistor that operates at room temperature.
Biosynthesis of the Prosthetic Group of Citrate Lyase (2000)

Citrate lyase (EC 4.1.3.6) catalyzes the cleavage of citrate to acetate and oxaloacetate and is composed of three subunits (alpha, beta, and gamma). The gamma-subunit serves as an acyl carrier protein (ACP) and contains the prosthetic group 2'-(5' '-phosphoribosyl)-3'-dephospho-CoA, which is attached via a phosphodiester linkage to serine-14 in the enzyme from Klebsiella pneumoniae. In this work, we demonstrate by genetic and biochemical studies with citrate lyase of Escherichia coli and K. pneumoniae that the conversion of apo-ACP into holo-ACP is dependent on the two proteins, CitX (20 kDa) and CitG (33 kDa). In the absence of CitX, only apo-ACP was synthesized in vivo, whereas in the absence of CitG, an adenylylated ACP was produced, with the AMP residue attached to serine-14. The adenylyltransferase activity of CitX could be verified in vitro with purified CitX and apo-ACP plus ATP as substrates. Besides ATP, CTP, GTP, and UTP also served as nucleotidyl donors in vitro, showing that CitX functions as a nucleotidyltransferase. The conversion of apo-ACP into holo-ACP was achieved in vitro by incubation of apo-ACP with CitX, CitG, ATP, and dephospho-CoA. ATP could not be substituted with GTP, CTP, UTP, ADP, or AMP. In the absence of CitG or dephospho-CoA, AMP-ACP was formed. Remarkably, it was not possible to further convert AMP-ACP to holo-ACP by subsequent incubation with CitG and dephospho-CoA. This demonstrates that AMP-ACP is not an intermediate during the conversion of apo- into holo-ACP, but results from a side activity of CitX that becomes effective in the absence of its natural substrate. Our results indicate that holo-ACP formation proceeds as follows. First, a prosthetic group precursor [presumably 2'-(5' '-triphosphoribosyl)-3'-dephospho-CoA] is formed from ATP and dephospho-CoA in a reaction catalyzed by CitG. Second, holo-ACP is formed from apo-ACP and the prosthetic group precursor in a reaction catalyzed by CitX.
Sequential injection immunoassay utilizing immunomagnetic beads (1992)

A novel sequential injection immunoassay (SIIA) method is described which utilizes immunomagnetic beads to investigate short-time antibody binding. The method is versatile and flexible and may therefore be adapted to many different applications. Initial results for a competitive assay are also presented. The immunomagnetic bead reactor is created within the flowing stream by retaining immunomagnetic beads with an electromagnet to form an open tube reactor. Thus, the spent beads may be discharged after each analysis. This eliminates the problems of instability of reaction surfaces and eliminates the need for additional time traditionally required for regeneration of the solid-reacting phase in order to not only save time and increase sampling frequency but also to provide each individual sampling cycle with a fresh, uniform portion of beads. The spent beads are collected off line and may be regenerated later. Short-time binding kinetic studies demonstrate linear initial binding under 1 min, which then begins to reach saturation in approximately 10 min. Competitive binding assays of monoclonal mouse IgG (MRC OX-19) to polyclonal sheep anti-mouse IgG immobilized to the immunomagnetic beads show reproducible linear displacement in 30-120-s reactions. Fluorescence detection is utilized with a detection limit of 155 ng/mL, and since the reaction time is typically 2 min or shorter, the sampling frequency is 30 samples/h.
Theory, Production and Mechanism of Formation of Monodispersed Hydrosols (1950)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTheory, Production and Mechanism of Formation of Monodispersed HydrosolsVictor K. LaMer and Robert H. DinegarCite this: J. Am. Chem. Soc. 1950, 72, 11, 4847–4854Publication Date (Print):November 1, 1950Publication History Published online1 May 2002Published inissue 1 November 1950https://pubs.acs.org/doi/10.1021/ja01167a001https://doi.org/10.1021/ja01167a001research-articleACS PublicationsRequest reuse permissionsArticle Views27290Altmetric-Citations2991LEARN 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
Likelihood-enhanced fast translation functions (2005)

This paper is a companion to a recent paper on fast rotation functions [Storoni et al. (2004), Acta Cryst. D60, 432-438], which showed how a Taylor-series expansion of the maximum-likelihood rotation function leads to improved likelihood-enhanced fast rotation functions. In a similar manner, it is shown here how linear and quadratic Taylor-series expansions and least-squares approximations of the maximum-likelihood translation function lead to likelihood-enhanced translation functions, which can be calculated by FFT and which are more sensitive to the correct translation than the traditional correlation-coefficient fast translation function. These likelihood-enhanced translation targets for molecular-replacement searches have been implemented in the program Phaser using the Computational Crystallography Toolbox (cctbx).
Identification of deleterious mutations within three human genomes (2009)

Each human carries a large number of deleterious mutations. Together, these mutations make a significant contribution to human disease. Identification of deleterious mutations within individual genome sequences could substantially impact an individual's health through personalized prevention and treatment of disease. Yet, distinguishing deleterious mutations from the massive number of nonfunctional variants that occur within a single genome is a considerable challenge. Using a comparative genomics data set of 32 vertebrate species we show that a likelihood ratio test (LRT) can accurately identify a subset of deleterious mutations that disrupt highly conserved amino acids within protein-coding sequences, which are likely to be unconditionally deleterious. The LRT is also able to identify known human disease alleles and performs as well as two commonly used heuristic methods, SIFT and PolyPhen. Application of the LRT to three human genomes reveals 796-837 deleterious mutations per individual, approximately 40% of which are estimated to be at <5% allele frequency. However, the overlap between predictions made by the LRT, SIFT, and PolyPhen, is low; 76% of predictions are unique to one of the three methods, and only 5% of predictions are shared across all three methods. Our results indicate that only a small subset of deleterious mutations can be reliably identified, but that this subset provides the raw material for personalized medicine.
GPR using an array antenna for landmine detection (2003)

ABSTRACT We propose a new ground‐penetrating radar (GPR) methodology for buried land‐mine detection. A GPR system using an antenna array was used for common‐midpoint (CMP) data acquisition. This system uses an array of ten Vivaldi antennae and operates from 30 MHz to 6 GHz. The moveout of the CMP data was corrected and the data were stacked to suppress ground clutter. The system was tested in the laboratory and we showed that it images buried mine‐like targets with a high resolution. A model of a plastic land‐mine of Type‐72 was buried in soil consisting of a mixture of gravel and crushed rocks and could be detected by the proposed technique. CMP processing applied to the array signal effectively suppresses the clutter from rough ground surfaces and inhomogeneous soil. We found that the migration algorithm is effective in suppressing ground clutter, but it is even more effective if it is combined with the CMP technique.
A phase I study in paediatric patients to evaluate the safety and pharmacokinetics of SPI-77, a liposome encapsulated formulation of cisplatin (2001)

Pre-clinical studies indicate that cisplatin encapsulated in STEALTH((R))liposomes (SPI-77) retains anti-tumour activity, but has a much reduced toxicity, compared to native cisplatin. A phase I study was conducted to determine the toxicity and pharmacokinetics of SPI-77 administered to children with advanced cancer not amenable to other treatment. Paediatric patients were treated at doses ranging from 40 to 320 mg m(-2)by intravenous infusion every 4 weeks. Blood samples taken during, and up to 3 weeks after, administration and plasma and ultrafiltrate were prepared immediately. Urine was collected, when possible, for 3 days after administration. SPI-77 administration was well tolerated with the major toxicity being an infusion reaction which responded to modification of the initial infusion rate of SPI-77. Limited haematological toxicity and no nephrotoxicity were observed. No responses to treatment were seen during the course of this phase I study. Measurement of total plasma platinum showed that cisplatin was retained in the circulation with a half life of up to 134 h, with maximum plasma concentrations approximately 100-fold higher than those reported following comparable doses of cisplatin. Comparison of plasma and whole blood indicated that cisplatin was retained in the liposomes and there was no free platinum measurable in the ultrafiltrate. Urine recovery was less than 4% of the dose administered over 72 h. Results from this phase I study indicate that high doses of liposomal cisplatin can safely be given to patients, but further studies are required to address the issue of reformulation of liposomally bound cisplatin.
Genetic variants in the repeat region of MHC class I for miniature pig (Brief Report) (2009)

Abstract. Recently, miniature pigs have been issued for xenotransplantation studies (CHARON et al. 2000) to verify what major factors are critical matters for immune responses in human. Major histocompatibility complex (MHC) knowing for high rate of mutations and responsible for systematic immune responses is essential to understand swine immunology. Numerous studies have documented the influence of swine leukocyte antigen (SLA) genes on immune responses, organ and cell transplantation success and disease resistance (SMITH et al. 2004). The satellite region in MHC can be used to identify individuals as well as breeds, and it is important to characterize and breed unique miniature pig lines for supporting organ transplantation studies. Up to the present moment, genetic variants including repeat units (CA14-20) located between the SLA-1 and SLA-5 genes are available with GenBank acc. no. AJ131112, AP009559, AP009558, AP009556, AP009555, and CU311184, but miniature pigs have not been reported.
Successful Islet Transplantation (2002)

Clinical islet transplantation is gaining acceptance as a potential therapy, particularly for subjects who have labile diabetes or problems with hypoglycemic awareness. The risks of the procedure and long-term outcomes are still not fully known. We have performed 54 islet transplantation procedures on 30 subjects and have detailed follow-up in 17 consecutive Edmonton protocol-treated subjects who attained insulin independence after transplantation of adequate numbers of islets. Subjects were assessed pretransplant and followed prospectively posttransplant for immediate and long-term complications related to the procedure or immunosuppressive therapy. The 17 patients all became insulin independent after a minimum of 9,000 islets/kg were transplanted. Of 15 consecutive patients with at least 1 year of follow-up after the initial transplant, 12 (80%) were insulin independent at 1 year. In 14 subjects who have maintained demonstrable C-peptide secretion, glucose control has been stable and glycemic lability and problems with hypoglycemic reactions have been corrected. After 2 of the 54 procedures, some thrombosis was detected in the portal vein circulation. Five subjects had bleeding related to the percutaneous portal vein access procedures: three required transfusion alone, and in one subject, who had a partial thrombosis of the portal vein, an expanding intrahepatic and subscapular hemorrhage occurred while on anticoagulation, requiring transfusion and surgery. Elevated liver function test results were found in 46% of subjects but resolved in all. Complications related to the therapy have been hypercholesterolemia requiring statin therapy in 65%; a rise in creatinine in two patients, both of whom had preexisting renal disease; a rise in protein in four, all of whom had preexisting proteinuria; and antihypertensive therapy increased or started in 53%. Three of the 17 patients have required retinal laser photocoagulation. There have been no cases of posttransplant lymphoproliferative disorder or cytomegalovirus infection, and no deaths. The acute insulin response to arginine correlated better with transplanted islet mass than acute insulin response to glucose (AIR(g)) and area under the curve for insulin (AUC(i)), but the AIR(g) and AUC(i) were more closely related to glycemic control. The AUC(i) directly posttransplant was lower in those who eventually became C-peptide deficient. Our results, with a maximum follow-up of 34 months, indicate that prolonged insulin independence can be achieved after islet transplantation. There are some risks associated acutely with the procedure, and hypercholesterolemia and hypertension are treatable concerns on longer-term follow-up. All patients with persisting C-peptide secretion have had a resolution of both glycemic lability and problems with hypoglycemic reactions. Apart from the rise in serum creatinine in two subjects, no serious consequences of immunosuppressive therapy have been encountered. Islet transplantation is a reasonable option in those with severe problems with glycemic lability or hypoglycemia.
Lung Cancer Immunotherapy (2005)

Recent insights into anti-tumor immunotherapy have led to a wave of clinical trials involving immunotherapy for lung cancer. Vaccines have evolved from nonspecific immune stimulants, like Bacillus Calmette-Guerin (BCG), to much more specific and potent strategies, some of which generate active immune responses against tumor-associated antigens. Understanding the mechanisms of anti-tumor immunity and identifying target antigens will likely improve these therapeutic strategies and provide them with a niche in the future of lung cancer therapy.
Cognitive control in media multitaskers (2009)

Chronic media multitasking is quickly becoming ubiquitous, although processing multiple incoming streams of information is considered a challenge for human cognition. A series of experiments addressed whether there are systematic differences in information processing styles between chronically heavy and light media multitaskers. A trait media multitasking index was developed to identify groups of heavy and light media multitaskers. These two groups were then compared along established cognitive control dimensions. Results showed that heavy media multitaskers are more susceptible to interference from irrelevant environmental stimuli and from irrelevant representations in memory. This led to the surprising result that heavy media multitaskers performed worse on a test of task-switching ability, likely due to reduced ability to filter out interference from the irrelevant task set. These results demonstrate that media multitasking, a rapidly growing societal trend, is associated with a distinct approach to fundamental information processing.
The Use of Herbal Preparations to Alleviate Climacteric Disorders and Risk of Postmenopausal Breast Cancer in a German Case-Control Study (2009)

Our findings support the hypothesis that HEP use protects from invasive breast cancer in postmenopausal women. Among conceivable modes of action, those independent of estrogen receptor-mediated pathways seem to be involved (i.e., cytotoxicity, apoptosis).