gebhart/patrepeval huggingface dataset:
Successional development of sulfate‐reducing bacterial populations and their activities in an activated sludge immobilized agar gel film (2002)

A combination of fluorescence in situ hybridization (FISH), microprofiles, and denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA fragments followed by hybridization analysis with specific probes was applied to investigate successional development of sulfate-reducing bacteria (SRB) community structure and in situ sulfide production activity within an activated sludge immobilized agar gel film. In this model biofilm system, since biases arising from biofilm heterogeneity can be ignored, the population dynamics of SRB in the agar gel is directly related to physiological capability and in situ activity of SRB. Microelectrode measurements showed that an anoxic zone was already developed at the beginning (0 day), a first sulfide production of 0.054 mumol H2S m(-2) x s(-1) was detected during the first week, and the rate increased gradually to 0.221 mumol H2S m(-2) x s(-1) in the fifth week. The most active sulfide production zone moved upward to the chemocline and intensified with time to form a narrow zone with high volumetric sulfide production rates. This result coincided with the shift of the spatial distributions of SRB populations determined by FISH. In situ hybridization with probe SRB385 for mainly general SRB of the delta Proteobacteria plus some gram-positive bacteria and probe 660 for Desulfobulbus indicated that the most abundant populations of SRB were primarily restricted to near the oxic/anoxic interface (chemocline). A close observation of the development of the vertical distributions of SRB populations revealed that the cell numbers of Desulfobulbus tripled (from 0.5 x 10(8) to 1.5 x 10(8) cells cm(-3)) near the oxic/anoxic interface. Similar growth (from 1.0 x10(8) to 4.5 x 10(8) cells cm(-3)) of Desulfovibrio-like SRB that hybridized with probe SRB385 was observed. PCR-DGGE followed by hybridization analysis revealed that one Desulfobulbus strain was detected from the beginning, and another strain appeared after 1 week, coinciding with the first detected sulfide production. In addition, three strains hybridizing with probe 687 (possibly Desulfovibrio) were also dominant SRB in the agar gel.
Chemical Modifications to RNA: A New Layer of Gene Expression Regulation (2017)

The first chemical modification to RNA was discovered nearly 60 years ago; to date, more than 100 chemically distinct modifications have been identified in cellular RNA. With the recent development of novel chemical and/or biochemical methods, dynamic modifications to RNA have been identified in the transcriptome, including N<sup>6</sup>-methyladenosine (m<sup>6</sup>A), inosine (I), 5-methylcytosine (m<sup>5</sup>C), pseudouridine (Ψ), 5-hydroxymethylcytosine (hm<sup>5</sup>C), and N<sup>1</sup>-methyladenosine (m<sup>1</sup>A). Collectively, the multitude of RNA modifications are termed epitranscriptome, leading to the emerging field of epitranscriptomics. In this review, we primarily focus on recently reported chemical modifications to mRNA; we discuss their chemical properties, biological functions, and mechanisms with an emphasis on their high-throughput detection methods. We also envision that future tools, particularly novel chemical biology methods, could further facilitate and enable studies in the field of epitranscriptomics.
Site-specific labeling of DNA sequences containing phosphorothioate diesters (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSite-specific labeling of DNA sequences containing phosphorothioate diestersJacqueline A. Fidanza, Hiroaki Ozaki, and Larry W. McLaughlinCite this: J. Am. Chem. Soc. 1992, 114, 14, 5509–5517Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ja00040a004https://doi.org/10.1021/ja00040a004research-articleACS PublicationsRequest reuse permissionsArticle Views794Altmetric-Citations79LEARN 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
Selective accumulation of low density lipoproteins in damaged arterial wall. (1983)

To determine whether damaged arterial wall selectively accumulates lipoproteins, normocholesterolemic rabbits were injected with human radiolabeled low density lipoproteins, high density lipoproteins, and/or albumin 24 hr to 12 weeks after balloon-catheter de-endothelialization of the abdominal aorta. When 125I-labeled low density lipoproteins and 99mTc-labeled albumin were injected simultaneously, the amount of 125I-low density lipoprotein present 24 hr later in abdominal aortas increased steadily, for several weeks, above the amount present at 24 hr in control animals. The increase correlated closely with the degree of re-endothelialization and correlated closely with the degree of re-endothelialization and reached an average maximum for the whole abdominal aorta of three times control when re-endothelialization was between 75 and 85% complete. By contrast, the amounts of 99mTc-albumin or 125I-labeled high density lipoprotein in balloon-damaged abdominal aortas, and the amounts of 125I-low density lipoprotein, 125I-high density lipoprotein, or 99mTc-albumin in undamaged thoracic aortas of injured animals showed no such increase. As early as 2 weeks after de-endothelialization, en face radioautographs made following injection of 125I-labeled low density lipoproteins revealed localized areas of greatest radioactivity around the leading edges of regenerating endothelial islands, broad areas of intermediate radioactivity corresponding to the de-endothelialized areas, and very like radioactivity in the re-endothelialized areas. This pattern occurred rarely with 125I-labeled high density lipoproteins and not at all with 125I-labeled albumin. The results suggest that low density lipoproteins are selectively accumulated by the healing rabbit aorta and that the accumulation is greatest in regions where the endothelium is actively regenerating.
Chiral Monodentate Phosphines and Bulky Carboxylic Acids: Cooperative Effects in Palladium‐Catalyzed Enantioselective C(sp3)–H Functionalization (2012)

LCSA
Taxonomic Study of Bacillus coagulans Hammer 1915 with a Proposal for Bacillus smithii sp. nov. (1988)

Guanine-plus-cytosine (G+C) content determinations, deoxyribonucleic acid (DNA) relatedness estimations, and phenotypic similarity analyses of 90 strains identified previously as Bacillus coagulans Hammer 1915 revealed that 52 (group 1) strains were Bacillus coagulans sensu stricto; 30 of the remaining organisms segregated into two distinct DNA relatedness groups, one consisting of 26 (group 2) strains and the other of 4 (group 4) organisms. Five (group 3) strains were Bacillus licheniformis, and three (group 5) strains were B. stearothermophilus. Because group 2 was a major cluster of strains which did not correspond in their characteristics to any previously known group, efforts were made to determine its taxonomic position. Group 2, with G+C contents ranging from 37 to 40 mol%, was compared with other species generally characterized as having G+C contents ranging from 37 to 44 mol% or capable of growing at 50°C or both (namely, Bacillus alcalophilus, Bacillus azotoformans, Bacillus badius, Bacillus firmus, Bacillus globiformis, Bacillus laterosporus, Bacillus macquariensis, Bacillus marinus, Bacillus megaterium, Bacillus pumilus, and Bacillus subtilis). Low DNA relatedness values and poor matching of phenotypic characteristics strongly indicated that group 2 organisms are strains of a new species, for which the name Bacillus smithii is proposed. The type strain of the new species is strain NRRL NRS-173.
Enhanced sensitivity fibre optic long period grating temperature sensor (2002)

Surrounding a long period grating, fabricated in a standard optical fibre, with a material with a high thermo-optic coefficient enhances the temperature sensitivity of a long period grating. Temperature sensitivities as high as 19nm/°C are reported over a temperature range of 1.1°. The temperatures at which the LPG exhibits enhanced sensitivity may be tailored by a suitable choice of material.
Functional heterogeneity of mutant rhodopsins responsible for autosomal dominant retinitis pigmentosa. (1991)

Thirteen mutant rhodopsins responsible for autosomal dominant retinitis pigmentosa (ADRP) have been produced by transfection of cloned cDNA into tissue culture cells. Three mutants [class I: Phe-45----Leu, Gln-344----termination (deletion of C-terminal positions 344-348), and Pro-347----Leu] resemble wild-type rhodopsin in yield, regenerability with 11-cis-retinal, and plasma membrane localization. Ten mutants [class II: Thr-17----Met, Pro-23----His, Thr-58----Arg, Val-87----Asp, Gly-89----Asp, Gly-106----Trp, Arg-135----Leu, Arg-135----Trp, Tyr-178----Cys, and Asp-190----Gly] accumulate to significantly lower levels, regenerate with 11-cis-retinal variably or not at all, and are transported inefficiently to the plasma membrane, remaining primarily in the endoplasmic reticulum. These data suggest that there are at least two distinct biochemical defects associated with different rhodopsin mutants in ADRP.
Dicarboxylic acid promoted immortal copolymerization for controllable synthesis of low‐molecular weight oligo(carbonate‐ether) diols with tunable carbonate unit content (2012)

Abstract Low‐molecular weight oligo(carbonate‐ether) diols are important raw materials for polyurethane formation, which with tunable carbonate unit content (CU) may endow new thermal and mechanical performances to polyurethane. Herein, facile synthesis of oligo(carbonate‐ether) diols with number average molecular weight ( M n ) below 2000 g mol −1 and CU tunable between 40% and 75% are realized in high activity by immortal copolymerization of CO 2 /propylene oxide (PO) using zinc‐cobalt double metal cyanide complex (Zn‐Co‐DMCC) in the presence of sebacic acid (SA). M n of the oligomer is in good linear relationship to the mole ratio of PO and SA (PO/SA) and hence can be precisely controlled by adjusting PO/SA. Besides, the molecular weight distribution is quite narrow due to the rapid reversible chain transfer in the immortal copolymerization. High pressure and low temperature are favorable for raising CU. In all the reactions, the weight fraction of propylene carbonate ( W PC ) can even be controlled as low as 2.0 wt %, and the catalytic activity of Zn‐Co‐DMCC is above 1.0 kgg −1 cat. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012
Transcription at different salinities of Haloferax mediterranei sequences adjacent to partially modified PstI sites (1993)

Two genomic sequences from the halophilic archaeon Haloferax mediterranei, where we had found PstI restriction-pattern modifications depending on the salinity of the growth medium, have been studied. A markedly salt-dependent differential expression has been detected in the nearby regions. Two of the open reading frames characterized correspond to two of the differentially expressed transcripts. In both cases the PstI sites were included in purine-pyrimidine alternancies suggestive of Z-DNA structures and located in non-coding regions with frequent repetitive motifs. A long alternating adenine-thymine tract also appears in the upstream regions of one of these open reading frames. A possible role of local DNA configuration in osmoregulation in this organism is discussed.
Erratum: “Multilayer exchange spring media for magnetic recording” [Appl. Phys. Lett. 89, 113105 (2006)] (2006)

First Page
Carotid intima-media thickness and the risk of new vascular events in patients with manifest atherosclerotic disease: the SMART study (2006)

Common CIMT is associated with the occurrence of new vascular events, mostly for ischaemic stroke, in patients with manifest arterial disease. This relation does not appear to depend on the presence of plaques.
Rapid fabrication of microchannels using microscale plasma activated templating (μPLAT) generated water molds (2007)

Poly(dimethylsiloxane) (PDMS) is a common material used in fabricating microfluidic devices. The predominant PDMS fabrication method, soft lithography, relies on photolithography for fabrication of micropatterned molds. In this technical note, we report an alternative molding technique using microscale PLasma Activated Templating (microPLAT). The use of photoresist in soft lithography is replaced by patterned water droplets created using microPLAT. When liquid PDMS encapsulates patterned water and then solidifies, the cavities occupied by water become structures such as microchannels. Using this method, device fabrication is less time consuming, more cost efficient and flexible, and ideal for rapid prototyping. An additional important feature of the water-molding process is that it yields structural profiles that are difficult to achieve using photolithography.
Disease modification in partial epilepsy (2002)

With the growth in antiepileptic drug treatment, the question arises as to what extent we are merely treating the symptom (i.e. the seizures) rather than the underlying disease process (i.e. epileptogenesis). Epileptogenicity can be considered as the process whereby structural and functional changes occur following an insult that in some cases result in epilepsy. Epileptogenicity also describes some of the changes and processes that contribute to the progression observed in some epilepsies. These processes have been modelled in animals mostly by the kindling model of epilepsy, in which repetition of subconvulsive stimuli results in a progressive epileptic state and eventually leads to spontaneous seizures. However, it is not clear that kindling has a human correlate, so models in which an initial insult (status epilepticus, hyperthermia, hypoxia, trauma) is followed by the development of lowered seizure threshold and, in some instances, spontaneous seizures have been used. These models seem to support the "second hit" hypothesis, in which there is an initial insult resulting in lowered seizure threshold, and then a later insult, the "second hit", that results in the expression of epilepsy. These models also support the concept of a latent period during which there could be targeted therapies to prevent the epileptogenic process. Although the occurrence of neuronal damage is one such target, neuronal damage is not necessary for epileptogenesis, and other mechanisms are at play. At the present time, it is not known whether targeted therapies may also affect compensatory processes, such as brain repair. Clearly, this would be a potential risk of such strategies. Epidemiological evidence and trials indicate that our present antiepileptic drugs are not effective in preventing epileptogenesis; antiepileptic drugs were, however, not designed for this purpose. Data from animal experiments suggest that treatment of non-convulsive status epilepticus following specific insults may prevent epileptogenesis. The relevance of this for the human condition remains uncertain, but non-convulsive status epilepticus is probably an under-recognized and probably under-treated condition. Perhaps one of the most salutary findings has been the observation of decreased childhood epilepsy with improved neonatal care. This highlights the importance of medical care at the time of an insult, and of prevention of the insults. This review discusses the data that support the concepts underlying epileptogenesis and the model systems that are presumed to reflect the human condition. Particular attention is paid to the potential for interrupting the processes underlying epileptogenesis.
Herbimycin B, a new benzoquinonoid ansamycin with anti-TMV and herbicidal activities. (1980)

A new benzoquinonoid ansamycin, herbimycin B was isolated from the culture broth of Streptomyces hygroscopicus No. AM-3672, a herbimycin A-producing strain. Herbimycin B showed potent anti-TMV activity. Herbicidal effect of herbimycin B was less than that of herbimycin A.
Studies in Chemotherapy. X. Antithyroid Compounds. Synthesis of 5- and 6- Substituted 2-Thiouracils from β-Oxoesters and Thiourea1 (1945)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStudies in Chemotherapy. X. Antithyroid Compounds. Synthesis of 5- and 6- Substituted 2-Thiouracils from β-Oxoesters and Thiourea1George W. Anderson, I. F. Halverstadt, Wilbur H. Miller, and Richard O. Roblin Jr.Cite this: J. Am. Chem. Soc. 1945, 67, 12, 2197–2200Publication Date (Print):December 1, 1945Publication History Published online1 May 2002Published inissue 1 December 1945https://pubs.acs.org/doi/10.1021/ja01228a042https://doi.org/10.1021/ja01228a042research-articleACS PublicationsRequest reuse permissionsArticle Views918Altmetric-Citations107LEARN 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
Native Client: A Sandbox for Portable, Untrusted x86 Native Code (2009)

This paper describes the design, implementation and evaluation of Native Client, a sandbox for untrusted x86 native code. Native Client aims to give browser-based applications the computational performance of native applications without compromising safety. Native Client uses software fault isolation and a secure runtime to direct system interaction and side effects through interfaces managed by Native Client. Native Client provides operating system portability for binary code while supporting performance-oriented features generally absent from Web application programming environments, such as thread support, instruction set extensions such as SSE, and use of compiler intrinsics and hand-coded assembler. We combine these properties in an open architecture that encourages community review and 3rd-party tools.
Role of antibiotics for treatment of inflammatory bowel disease (2016)

Inflammatory bowel disease is thought to be caused by an aberrant immune response to gut bacteria in a genetically susceptible host. The gut microbiota plays an important role in the pathogenesis and complications of the two main inflammatory bowel diseases: Crohn's disease (CD) and ulcerative colitis. Alterations in gut microbiota, and specifically reduced intestinal microbial diversity, have been found to be associated with chronic gut inflammation in these disorders. Specific bacterial pathogens, such as virulent Escherichia coli strains, Bacteroides spp, and Mycobacterium avium subspecies paratuberculosis, have been linked to the pathogenesis of inflammatory bowel disease. Antibiotics may influence the course of these diseases by decreasing concentrations of bacteria in the gut lumen and altering the composition of intestinal microbiota. Different antibiotics, including ciprofloxacin, metronidazole, the combination of both, rifaximin, and anti-tuberculous regimens have been evaluated in clinical trials for the treatment of inflammatory bowel disease. For the treatment of active luminal CD, antibiotics may have a modest effect in decreasing disease activity and achieving remission, and are more effective in patients with disease involving the colon. Rifamixin, a non absorbable rifamycin has shown promising results. Treatment of suppurative complications of CD such as abscesses and fistulas, includes drainage and antibiotic therapy, most often ciprofloxacin, metronidazole, or a combination of both. Antibiotics might also play a role in maintenance of remission and prevention of post operative recurrence of CD. Data is more sparse for ulcerative colitis, and mostly consists of small trials evaluating ciprofloxacin, metronidazole and rifaximin. Most trials did not show a benefit for the treatment of active ulcerative colitis with antibiotics, though 2 meta-analyses concluded that antibiotic therapy is associated with a modest improvement in clinical symptoms. Antibiotics show a clinical benefit when used for the treatment of pouchitis. The downsides of antibiotic treatment, especially with recurrent or prolonged courses such as used in inflammatory bowel disease, are significant side effects that often cause intolerance to treatment, Clostridium dificile infection, and increasing antibiotic resistance. More studies are needed to define the exact role of antibiotics in inflammatory bowel diseases.
DsbC activation by the N-terminal domain of DsbD (2001)

The correct formation of disulfide bonds in the periplasm of Escherichia coli involves Dsb proteins, including two related periplasmic disulfide-bond isomerases, DsbC and DsbG. DsbD is a membrane protein required to maintain the functional oxidation state of DsbC and DsbG. In this work, purified proteins were used to investigate the interaction between DsbD and DsbC. A 131-residue N-terminal fragment of DsbD (DsbDalpha) was expressed and purified and shown to form a functional folded domain. Gel filtration results indicate that DsbDalpha is monomeric. DsbDalpha was shown to interact directly with and to reduce the DsbC dimer, thus increasing the isomerase activity of DsbC. The DsbC-DsbDalpha complex was characterized, and formation of the complex was shown to require the N-terminal dimerization domain of DsbC. These results demonstrate that DsbD interacts directly with full-length DsbC and imply that no other periplasmic components are required to maintain DsbC in the functional reduced state.
Major Groove Recognition of DNA by Carbohydrates (2006)

Because of the number of distinguishable interactions within the DNA major groove, there is considerable interest in discovering the governing factors involved in DNA recognition. Carbohydrates represent a class of DNAinteractive agents capable of binding the major groove due to their size and intricate distribution of hydrophobic and hydrophilic interactions within their molecular structure. To date a limited number of carbohydrates have been found to interact within the DNA major groove; the majority have been shown to bind within the minor groove. Representative carbohydrates that bind within the major groove include neocarzinostatin, nogalamycin, and a few aminoglycoside (neomycin) conjugates developed in our labs. An overview of the various DNA groove-binding carbohydrates is presented, with particular emphasis on novel aminoglycoside-based approaches in probing the molecular environment and requirements therein associated with the DNA major groove.