gebhart/patrepeval huggingface dataset:
On the specificity of antibiotics targeting the large ribosomal subunit (2011)

The peptidyltransferase center of the large ribosomal subunit is responsible for catalyzing peptide bonds. This active site is the target of a variety of diverse antibiotics, many of which are used clinically. The past decade has seen a plethora of structures of antibiotics in complex with the large ribosomal subunit, providing unprecedented insight into the mechanism of action of these inhibitors. Ten distinct antibiotics (chloramphenicol, clindamycin, linezolid, tiamulin, sparsomycin, and five macrolides) have been crystallized in complex with four distinct ribosomal species, three bacterial, and one archaeal. This review aims to compare these structures in order to provide insight into the conserved and species-specific modes of interaction for particular members of each class of antibiotics. Coupled with the wealth of biochemical data, a picture is emerging defining the specific functional states of the ribosome that antibiotics preferentially target. Such mechanistic insight into antibiotic inhibition will be important for the development of the next generation of antimicrobial agents.
RNase III mediated cleavage of the coding region of <i>mraZ</i> mRNA is required for efficient cell division in <i>Corynebacterium glutamicum</i> (2015)

The Corynebacterium glutamicum R cgR_1959 gene encodes an endoribonuclease of the RNase III family. Deletion mutant of cgR_1959 (Δrnc mutant) showed an elongated cell shape, and presence of several lines on the cell surface, indicating a required of RNase III for maintaining normal cell morphology in C. glutamicum. The level of mraZ mRNA was increased, whereas cgR_1596 mRNA encoding a putative cell wall hydrolase and ftsEX mRNA were decreased in the Δrnc mutant. The half-life of mraZ mRNA was significantly prolonged in the Δrnc and the Δpnp mutant strains. This indicated that the degradation of mraZ mRNA was performed by RNase III and the 3'-to-5' exoribonuclease, PNPase. Northern hybridization and primer extension analysis revealed that the cleavage site for mraZ mRNA by RNase III is in the coding region. Overproduction of MraZ resulted in an elongated cell shape. The expression of ftsEX decreased while that of cgR_1596 unchanged in an MraZ-overexpressing strain. An electrophoretic mobility shift assay and a transcriptional reporter assay indicate that MraZ is a transcriptional repressor of ftsEX in C. glutamicum. These results indicate that RNase III is required for efficient expression of MraZ-dependent ftsEX and MraZ-independent cgR_1596.
CD2-CD4-CD8- lymph node T lymphocytes in MRL <i>lpr/lpr</i> mice are derived from a CD2+CD4+CD8+ thymic precursor. (1993)

MRL lpr/lpr (lymphoproliferative, lpr) mice demonstrate an age-dependent lymphoproliferation and development of autoimmunity. Characteristic of the lymphoproliferation in these mice is the accumulation of large numbers of CD4-CD8-(CD4-8-),CD3+ T lymphocytes in their lymph nodes. The development of the CD4-8- cells, which also aberrantly express B220 and CD44 (Pgp-1) but are CD2-, has been shown to be thymus dependent. An unusual feature of lpr CD4-8-T lymphocytes is that although they appear unresponsive to stimulation, as defined by proliferation and IL-2 production, they have undergone thymic negative selection. As thymic deletion normally occurs at the CD4+CD8+ (CD4+8+) stage, this raises the dilemma that lpr CD4-8- T lymphocytes have either previously been CD4+8+, or they are able to undergo thymic selection as CD4-8- cells. We have addressed this question by examining the methylation status of the CD8 gene in MRL lpr CD4-8- lymph node cells. Demethylation of the CD8 gene has been shown to be an indicator of previous CD8 expression. We find that the CD8 gene in lpr CD4-8- lymph node cells, as well as in the abnormal B220+ CD4-8- lpr thymocytes, is demethylated, suggesting that these cells have previously expressed CD8. In addition, we find that the lpr CD4+8+ thymocyte population contains an increased percentage of atypical B220+, CD44+ cells that are virtually all CD2+. Taken together, these data are consistent with the lpr CD2-CD4-8- population of LNC having arisen from a CD2+ CD4+8+ thymic stage of differentiation.
Review of the development and applications of the Wiebe function: A tribute to the contribution of Ivan Wiebe to engine research (2010)

Analytical functions approximating the burn rate in internal combustion engines are useful and cost-effective tools for engine cycle simulations. Most functions proposed to date are based on the law of normal distribution of a continuous random variable. The best known of these is the Wiebe function, which is used to predict the burn fraction and burn rate in internal combustion engines operating with different combustion systems and fuels. These include direct injection (DI) and indirect injection (IDI) diesel engines, classical spark ignition (SI) engines and gasoline direct injection (GDI) engines, engines with homogeneous charge compression ignition (HCCI) and premixed charge compression ignition (PCCI). This paper is a tribute to the lasting legacy of the Wiebe function and to the man behind it, Ivan Ivanovitch Wiebe. It includes a historical background to the development of the function in the mid 1950s in the Soviet Union, the controversy that surrounded its introduction, a description of the method used to arrive at the final formulation, and an overview of the many applications as prescriptive or predictive single-, double- and multi-function combustion models in engine research.
A survey of buoyant density of microorganisms in pure cultures and natural samples. (1985)

Values of buoyant density of microorganisms reported in literature are widely divergent because of techniques used. Many of these involve centrifugation in density gradients formed by substances with high osmolarity which dehydrate the cells. In order to better understand the ranges of variation of density of microbial cells several approaches were taken. Firstly, samples from several natural aquatic habitats were taken and the densities of the microorganisms present determined. Secondly, experiments were performed with selected microorganisms to maximize density changes by forcing them to accumulate intracytoplasmic inclusions of dense materials or to loose their capsules. Finally, the relevant literature was reviewed. It could be demonstrated that most microorganisms have a density around 1.080 pg microns-3 when measured in low osmolarity media such as Percoll. However, many species are able to modify their density by as much as 7% (for instance, from 1.097 to 1.022 pg microns-3 in Thiocapsa roseopersicina, and similar variations in other bacteria), by incorporating substances into inclusions (sulfur, carbon, phosphorous storage materials, etc.), or by making capsules and/or gas vesicles. The relevance of buoyant density determinations for several aspects of microbial ecology and physiology is discussed.
Interference Suppression Strategy for Cell-Edge Users in the Downlink (2011)

In this paper we focus on the cell-edge users whose performance is severely limited by the interfering signals of diverse rates and strengths. In contrast to the suboptimal single-user detection, we propose an interference suppression strategy based on a low complexity matched filter (MF) based receiver. This proposed receiver exploits the structure of dominant interference in the detection process, instead of assuming it to be Gaussian and merging it in noise. This receiver is also characterized by the reduction of one complex dimension in the detection process thereby making it low complexity receiver structure. For comparison purposes, we also include the analysis of MMSE receiver and show that while MMSE detection loses one diversity order in the presence of one interferer, the proposed receiver recuperates the lost order of diversity. We further show that MMSE detection suffers from a coding loss as the interference gets stronger while the proposed receiver exhibits a coding gain as either the interference gets stronger or its modulation order decreases. Based on these results, we further propose a novel fractional frequency reuse (FFR) scheme for cellular systems.
Myogenin contains two domains conserved among myogenic factors. (1990)

Previously, three structurally related proteins, MyoD, myogenin, and Myf5, have been identified, and each of them was found to convert C3H10T1/2 fibroblasts to myoblasts when their respective cDNAs were expressed under the control of a viral promoter. Here, we describe the cloning and DNA sequencing of myogenin cDNAs from chicken and mouse. They encode polypeptides highly homologous to each other, but the polypeptide sequences we have obtained are not homologous in the carboxyl-terminal 70 amino acids with those previously reported for mouse, rat, and human because of a single base deletion in the previously reported cDNAs. Determination of genomic sequence coding for myogenin revealed that the mouse myogenin cDNA presented here corresponds to a correct transcript of the gene, and the nucleotide sequence of the previously reported cDNA is incorrect. A comparison of chicken and mouse myogenins with other myogenic regulatory factors, MyoD and Myf-5, identified a domain with an interesting feature located in the carboxyl terminus of these proteins in addition to the myc homology domain previously reported.
A Complete Optical Character Recognition Methodology for Historical Documents (2008)

In this paper a complete OCR methodology for recognizing historical documents, either printed or handwritten without any knowledge of the font, is presented. This methodology consists of three steps: The first two steps refer to creating a database for training using a set of documents, while the third one refers to recognition of new document images. First, a pre-processing step that includes image binarization and enhancement takes place. At a second step a top-down segmentation approach is used in order to detect text lines, words and characters. A clustering scheme is then adopted in order to group characters of similar shape. This is a semi-automatic procedure since the user is able to interact at any time in order to correct possible errors of clustering and assign an ASCII label. After this step, a database is created in order to be used for recognition. Finally, in the third step, for every new document image the above segmentation approach takes place while the recognition is based on the character database that has been produced at the previous step.
Co and Ni Incorporated γ-Al2O3 (110) Surface: A Density Functional Theory Study (2022)

Investigation into the state and mechanisms of the active metal substitution into the γ-Al2O3 support is the basis for design of many catalysts. Periodic density functional theory (DFT) +U calculations were used to investigate the surface properties of transition metals Co3+ and Ni3+ cations substitute for the Al3+ cations of γ-Al2O3 (110) surface. It was found that the substitution energy of one Al3+ substituted by Co3+ and Ni3+ are −61 and −57 kJ/mol, respectively. The Co and Ni preferentially substitute the tetrahedral Al sites instead of the octahedral Al sites. Using thermodynamics, the Al atoms in the top layer of γ-Al2O3 (110) can be 100% substituted by Co and Ni. Ni is easier to substitute the Al atom than Co. There is no obvious structural distortion that occurs after Co and Ni substituted all the top layer Al atoms. While the band gaps of the substituted surface become narrower, resulting in the increase of surface Lewis acidity. In addition, the oxygen vacancy formation energies of the Co and Ni substituted surface are 268 and 53 kJ/mol, respectively. The results provide interface structure and physical chemistry properties of metal-doped catalysts.
Multilevel bioluminescence tomography based on radiative transfer equation Part 1: l1 regularization (2010)

In this paper we study an l1-regularized multilevel approach for bioluminescence tomography based on radiative transfer equation with the emphasis on improving imaging resolution and reducing computational time. Simulations are performed to validate that our algorithms are potential for efficient high-resolution imaging. Besides, we study and compare reconstructions with boundary angular-averaged data, boundary angular-resolved data and internal angular-averaged data respectively.
Endothelial to mesenchymal transition: a precursor to post-COVID-19 interstitial pulmonary fibrosis and vascular obliteration? (2020)

We read with interest the recent editorial by Huertas et al. [1], highlighting the importance of endothelial cell dysfunction in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The authors have made some very fascinating insights, and we would like to take this discussion further, especially emphasising the role of endothelial cells in initiating post-infection pulmonary fibrosis and vascular remodelling. The angiotensin-converting enzyme 2 (ACE2) has been suggested as the primary receptor for mediating SARS-CoV-2 entry into the host cells. Apart from ACE2, the other key players that facilitate SARS-CoV-2 entry, includes transmembrane serine protease 2 (TMPRSS2), furin, sialic acid and the extracellular matrix metalloproteinase inducer (CD147) [1]. In their article, the authors provide compelling comprehensions from a study comparing post mortem lung tissues from patients who died from coronavirus disease 2019 (COVID-19), acute respiratory distress syndrome due to influenza A (H1N1) infection and those from age-matched, uninfected control lungs [1, 2]. A crucial inference was the connections between the significant increase in ACE2 positive endothelial cells and the substantial change in endothelial cell morphology, disruption of intercellular junctions, cell swelling, and the breakdown of the underlying basement membrane, all indicative of vascular structural modification in tune to the process of endothelial to mesenchymal transition (EndMT) [3]. Considering the implications for post-COVID-19 pulmonary fibrosis and vascular destruction seen in this infectious pathology, we believe that the role of EndMT in disease manifestation could be consequential. Endothelial to mesenchymal transition (EndMT) could lead to post-COVID-19 pulmonary fibrosis and vascular remodelling <https://bit.ly/2QqSKxT> Clifford Craig Foundation Launceston General Hospital, Lung Foundation Australia, The Alfred Hospital Melbourne and James Hogg Lung Registry, The University of British Columbia, Canada.
Design And Implementation Of A 10-Bit Sar Adc (2013)

This paper presents the development of a 38.5 kS/s 10-bit low power SAR ADC which is realized in MIMOS’s 0.35 µm CMOS process. The design uses a resistive DAC, a dynamic comparator with pre-amplifier and SAR digital logic to create 10 effective bits while consuming less than 7.8 mW with a 3.3 V power supply.
A Classification Based Framework to Predict Viral Threads (2015)

Online social media allows consumers to engage with each other and to create, share, discuss and modify user-generated content in a highly interactive way. Social media platforms have therefore become critical for companies trying to gauge the pulse of consumers, help identify issues faster, receive immediate feedback on products and offering etc. An effective social media strategy therefore requires companies to mine large volumes of structured unstructured and semi-structured online textual data in order to gain insights into the underlying traits of the consumers and prevailing public opinion. These insights can provide opportunities for market research, protection of brand reputation and a mechanism to gauge user preferences in an attempt to maximize customer satisfaction and consumer-brand engagement. In this paper, we propose and evaluate a classification based framework to predict thread lengths in online discussion forums in order to identify potential topics that may of interest to a particular online community. We identify and evaluate several key features of viral social media conversations through extensive experiments conducted on health 2.0 datasets. We also present a pharmaceutical industry based case study to illustrate how well the viral thread topics relate to real world events.
Characterization of a transforming N-ras gene in the human hepatoma cell line Hep G2: additional evidence for the importance of c-myc and ras cooperation in hepatocarcinogenesis. (1990)

The expression of the c-myc gene has previously been shown to be elevated and deregulated in the human hepatoma cell line Hep G2 (B. E. Huber and S. S. Thorgeirsson, Cancer Res., 47: 3414-3420, 1987). We now report that the Hep G2 N-ras gene is activated to a dominant-acting, transforming gene by a missense mutation in codon 61. Hep G2 DNA produced transformed foci when transfected into NIH 3T3 cells. Subsequent to a secondary round of transfection, Southern blot analysis of tumorigenic NIH 3T3 foci demonstrated the presence of human N-ras sequences. Nucleotide sequence analysis of one Hep G2 N-ras allele demonstrated that codons 12, 13, and 59 were normal and that codon 61 had a missense mutation (CAA to CTA). This mutation results in the incorporation of leucine instead of glutamine at residue 61 of the N-ras gene product, p21. N-ras sequences were amplified by the polymerase chain reaction from both Hep G2 genomic DNA and Hep G2 complementary DNA. Analysis of the amplified sequences demonstrated that only one Hep G2 N-ras allele exhibited the codon 61 mutation and that both the mutant and normal alleles were transcribed. Northern blot analysis demonstrated equivalent steady-state levels of N-ras transcripts in Hep G2 cells and normal human liver. The steady-state levels of N-ras and ornithine decarboxylase transcripts were positively correlated suggesting a positive relationship between N-ras expression and the replication rate of Hep G2 cells. c-Ki-ras and c-Ha-ras transcripts were not detected in either Hep G2 cells or normal human liver. Immunoprecipitation experiments using the monoclonal antibody Y13-259 demonstrated the presence of p21 in Hep G2 cells. Expression of a dominant-acting, transforming N-ras gene, in conjunction with the altered regulation of the c-myc gene, documents two important genetic lesions that could be responsible for the transformed phenotype of Hep G2 cells.
Application of Stereocontrolled Stepwise [3+2] Cycloadditions to the Preparation of Inhibitors of α<sub>4</sub>β<sub>1</sub>‐Integrin‐Mediated Hepatic Melanoma Metastasis (2005)

Inhibitors of the interaction between protein VLA-4 and its natural ligand VCAM-1 have been designed, even though the structure of the protein remains unresolved. The rational design relied on the simulation of the steric and electronic properties of the active loop of VCAM-1, whose structure is known (see picture), and the inhibitors were readily prepared by stereoselective stepwise [3+2] cycloadditions.
Reliability-aware Dynamic Voltage Scaling for energy-constrained real-time embedded systems (2008)

The dynamic voltage scaling (DVS) technique is the basis of numerous state-of-the-art energy management schemes proposed for real-time embedded systems. However, recent research has illustrated the alarmingly negative impact of DVS on task and system reliability. In this paper, we consider the problem of processing frequency assignment to a set of real-time tasks in order to maximize the overall reliability, under given time and energy constraints. First, we formulate the problem as a non-linear optimization problem and show how to obtain the static optimal solution. Then, we propose on-line (dynamic) algorithms that detect early completions and adjust the task frequencies at run-time, to improve overall reliability. Our simulation results indicate that our algorithms perform comparably to a clairvoyant optimal scheduler that knows the exact workload in advance.
Downregulation of the Syk Signaling Pathway in Intestinal Dendritic Cells Is Sufficient To Induce Dendritic Cells That Inhibit Colitis (2016)

Helminthic infections modulate host immunity and may protect people in less-developed countries from developing immunological diseases. In a murine colitis model, the helminth Heligmosomoides polygyrus bakeri prevents colitis via induction of regulatory dendritic cells (DCs). The mechanism driving the development of these regulatory DCs is unexplored. There is decreased expression of the intracellular signaling pathway spleen tyrosine kinase (Syk) in intestinal DCs from H. polygyrus bakeri-infected mice. To explore the importance of this observation, it was shown that intestinal DCs from DC-specific Syk(-/-) mice were powerful inhibitors of murine colitis, suggesting that loss of Syk was sufficient to convert these cells into their regulatory phenotype. DCs sense gut flora and damaged epithelium via expression of C-type lectin receptors, many of which signal through the Syk signaling pathway. It was observed that gut DCs express mRNA encoding for C-type lectin (CLEC) 7A, CLEC9A, CLEC12A, and CLEC4N. H. polygyrus bakeri infection downmodulated CLEC mRNA expression in these cells. Focusing on CLEC7A, which encodes for the dectin-1 receptor, flow analysis showed that H. polygyrus bakeri decreases dectin-1 expression on the intestinal DC subsets that drive Th1/Th17 development. DCs become unresponsive to the dectin-1 agonist curdlan and fail to phosphorylate Syk after agonist stimulation. Soluble worm products can block CLEC7A and Syk mRNA expression in gut DCs from uninfected mice after a brief in vitro exposure. Thus, downmodulation of Syk expression and phosphorylation in intestinal DCs could be important mechanisms through which helminths induce regulatory DCs that limit colitis.
The Synthesis of Esters of Substituted Amino Phosphonic Acids<sup>1a</sup> (1952)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Synthesis of Esters of Substituted Amino Phosphonic Acids1aEllis K. FieldsCite this: J. Am. Chem. Soc. 1952, 74, 6, 1528–1531Publication Date (Print):March 1, 1952Publication History Published online1 May 2002Published inissue 1 March 1952https://pubs.acs.org/doi/10.1021/ja01126a054https://doi.org/10.1021/ja01126a054research-articleACS PublicationsRequest reuse permissionsArticle Views2255Altmetric-Citations493LEARN 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