gebhart/patrepeval huggingface dataset:
Ultrasensitive Measurement of Hotspot Mutations in Tumor DNA in Blood Using Error-Suppressed Multiplexed Deep Sequencing (2012)

Detection of cell-free tumor DNA in the blood has offered promise as a cancer biomarker, but practical clinical implementations have been impeded by the lack of a sensitive and accurate method for quantitation that is also simple, inexpensive, and readily scalable. Here we present an approach that uses next-generation sequencing to quantify the small fraction of DNA molecules that contain tumor-specific mutations within a background of normal DNA in plasma. Using layers of sequence redundancy designed to distinguish true mutations from sequencer misreads and PCR misincorporations, we achieved a detection sensitivity of approximately 1 variant in 5,000 molecules. In addition, the attachment of modular barcode tags to the DNA fragments to be sequenced facilitated the simultaneous analysis of more than 100 patient samples. As proof-of-principle, we showed the successful use of this method to follow treatment-associated changes in circulating tumor DNA levels in patients with non-small cell lung cancer. Our findings suggest that the deep sequencing approach described here may be applied to the development of a practical diagnostic test that measures tumor-derived DNA levels in blood.
Operon mer: bacterial resistance to mercury and potential for bioremediation of contaminated environments. (2003)

Mercury is present in the environment as a result of natural processes and from anthropogenic sources. The amount of mercury mobilized and released into the biosphere has increased since the beginning of the industrial age. Generally, mercury accumulates upwards through aquatic food chains, so that organisms at higher trophic levels have higher mercury concentrations. Some bacteria are able to resist heavy metal contamination through chemical transformation by reduction, oxidation, methylation and demethylation. One of the best understood biological systems for detoxifying organometallic or inorganic compounds involves the mer operon. The mer determinants, RTPCDAB, in these bacteria are often located in plasmids or transposons and can also be found in chromosomes. There are two classes of mercury resistance: narrow-spectrum specifies resistance to inorganic mercury, while broad-spectrum includes resistance to organomercurials, encoded by the gene merB. The regulatory gene merR is transcribed from a promoter that is divergently oriented from the promoter for the other mer genes. MerR regulates the expression of the structural genes of the operon in both a positive and a negative fashion. Resistance is due to Hg2+ being taken up into the cell and delivered to the NADPH-dependent flavoenzyme mercuric reductase, which catalyzes the two-electron reduction of Hg2+ to volatile, low-toxicity Hg0. The potential for bioremediation applications of the microbial mer operon has been long recognized; consequently, Escherichia coli and other wild and genetically engineered organisms for the bioremediation of Hg2+-contaminated environments have been assayed by several laboratories.
H-ras Oncogene Mutation and Human Papillomavirus Infection in Oral Carcinomas (1994)

These results suggest a stronger association between HPV infection and activation of the H-ras gene in oral verrucous carcinomas. These results continue to confirm the multihit hypothesis of tumorigenesis and suggest that in some cases of oral cancer at least two of these events are H-ras gene mutation and HPV infection.
Trim5α protein restricts both HIV-1 and murine leukemia virus (2004)

Replication of HIV-1 and N-tropic murine leukemia virus (N-MLV) is restricted in a number of different primate cells. In some cell lines, cross-saturation experiments suggest that the two viruses are interacting with the same restriction factor. Recently, Trim5alpha protein from rhesus monkey was found to restrict HIV-1. We have confirmed this result and have shown that Trim5alpha from two African green monkey cell lines, Vero and CV-1, also restricts HIV-1. In addition, we show that human, rhesus, and African green monkey Trim5alpha can restrict N-MLV. By using a panel of MLV capsid mutants, subtle differences in the anti-MLV activity were identified among the different primate Trim5alpha cDNAs. Trim1 isolated from humans and green monkeys was also found to restrict N-MLV. We hypothesize that the Trim family of proteins plays a widespread role in innate immunity to viral infection.
Virus Throttling for Instant Messaging (2004)

Virus Throttling is a technique to slow the spread of worms and viruses by targeting their propagation. It works by preventing an infected machine infecting many others. This then results in fewer machines becoming infected and less traffic generated by the virus. The technique has been shown to work well for worms that spread over many TCP/IP protocols as well as email. This paper applies the technique to Instant Messaging. Worms and viruses that spread over Instant Messaging are a growing but significant threat. They have the potential to spread very rapidly causing widespread damage. While there have been few Instant Messaging viruses in the wild, they are likely to become more of a problem in the future, particularly as many enterprises are adopting Instant Messaging for internal use.
A Prize Worth Having: The IMF and Price Stability (2006)

En este ensayo se evalúan los beneficios que trae un entorno de baja inflación a la economía mundial. Para comenzar, se resumen los principales costos de la inflación: cómo distorsiona los cálculos de rentabilidad, alentando los proyectos a corto plazo a expensas de la inversión de largo plazo y restando valor a las señales de precios relativos. Luego se analiza cuánto han avanzado muchos países en los últimos años en sus esfuerzos por lograr una baja inflación. El nuevo entorno de baja inflación ha reportado beneficios considerables: más crecimiento global, mayor estabilidad y menor vulnerabilidad. También se evalúa la contribución que hace el FMI para que los países miembros logren un entorno de baja inflación, resaltando el importante apoyo que presta el organismo a las iniciativas de reformas de política. Para finalizar, se analizan los desafíos que depara el futuro a los economistas y a las autoridades de gobierno: asegurar los beneficios de una baja inflación, determinar hasta dónde deben ir las políticas para bajar la inflación y expandir las fronteras del conocimiento sobre la transición hacia un esquema de metas de inflación.
Bidirectional transmission using an erbium-doped fiber amplifier without optical isolators (1995)

We present bidirectional transmission experiments with an erbium-doped fiber amplifier (EDFA) without optical isolators. It is shown that the amplifier does not increase the bidirectional crosstalk from Rayleigh backscattering, provided that the gain of the amplifier is smaller than the transmission losses of the fibers connected to it.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Histopathologic changes of macula lutea retinae in elderly Chinese autopsy eyes (2000)

Purpose To investigate the histopathologic changes of macula lutea retinae in the elderly Chinese population,and to provide information for the cause of visiual disturbance in an autopsy study. Methods Two hundred and twelve eyes from 108 consecutive cases of postmortem (mean age of 78.4 years old) sections of the area of macula lutea retinae were studied by histopathology. Results Among the 212 eyes,hard drusen were found in 36.3% of eyes and soft drusen in 19.3% of eyes.The eyes with both of the above mentioned 2 types of drusens were found to be combined with RPE atrophy and RPE detachment;and subretinal neovascularization were found in 5.7% of these eyes and they were associated with obvious RPE atrophy and photoreceptor loss;3.2% eyes had posterior scleral staphyloma showing thinning of the sclera and choroid,RPE atrophy and apparent photoreceptor loss;2.4%eyes showed CME with the history of cataract surgery. Conclusion The macular affections,age related macular degeneration,myopic macular degeneration and post operative cystoid macular edema are varying in number in the above mentioned order successively,in elderly Chinese at an autopsy study.
Hypoglossal Nerve Stimulation for Obstructive Sleep Apnea (2015)

Obstructive sleep apnea (OSA) is a very frequent affliction that affects about 1-5% of the adult population in its severe form. Continuous positive airway pressure (CPAP) is the most commonly used treatment and is highly effective, but its use is limited by low long-term adherence rates and overall poor acceptance among the patients. Therefore, there is a need for developing alternative approaches to OSA treatment, including a more 'natural' concept of maintaining an open airway through neuromodulation. Here we review the concept, scientific rationale, and technical details of hypoglossal nerve stimulation. We also review results of published clinical studies with several hypoglossal stimulation devices that are being investigated today. Hypoglossal nerve stimulation appears to be a very promising treatment for patients with moderate-to-severe OSA. If its efficacy is confirmed, it will probably be complementary with CPAP therapy and initially aimed at patients unable or unwilling to use CPAP. Once it becomes a standard therapy, its advantages might prove sufficient to challenge CPAP as the first-line therapy.
TLR Signaling in the Gut in Health and Disease (2005)

The human intestine has evolved in the presence of diverse enteric microflora. TLRs convert the recognition of pathogen-associated molecules in the gut into signals for anti-microbial peptide expression, barrier fortification, and proliferation of epithelial cells. Healing of injured intestinal epithelium and clearance of intramucosal bacteria require the presence of intact TLR signaling. Nucleotide oligomerization domain (Nod)1 and Nod2 are additional pattern recognition receptors that are required for defense against invasive enteric pathogens. Through spatial and functional localization of TLR and Nod molecules, the normal gut maintains a state of controlled inflammation. By contrast, patients with inflammatory bowel disease demonstrate inflammation in response to the normal flora. A subset of these patients carry polymorphisms in TLR and CARD15/NOD2 genes. A better understanding of the delicate regulation of TLR and Nod molecules in the gut may lead to improved treatment for enteric infections and idiopathic inflammatory bowel diseases.
Generation and synthetic applications of 2-lithio-1,3-dithianes (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneration and synthetic applications of 2-lithio-1,3-dithianesDieter Seebach and Elias J. CoreyCite this: J. Org. Chem. 1975, 40, 2, 231–237Publication Date (Print):January 1, 1975Publication History Published online1 May 2002Published inissue 1 January 1975https://pubs.acs.org/doi/10.1021/jo00890a018https://doi.org/10.1021/jo00890a018research-articleACS PublicationsRequest reuse permissionsArticle Views4268Altmetric-Citations513LEARN 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
Sample enrichment in high speed narrow bore capillary gas chromatography (1988)

Abstract Reduction of the column diameter has proved to be a highly efficient tool to increase the speed of analysis. Unfortunately, the requirements for instrumental design with respect to sample input band width, low dead volume interfacing, and time constants of detection and registration systems are the more critical the smaller the inside diameter. Recently we reported input band widths as low as 1 ms [1] for gaseous samples at ppm concentration levels, without any preconcentration, in a study with narrow bore columns and thermal conductivity detection. In this study a simple versatile micro on‐column cold trap/thermodesorption enrichment system for narrow bore columns is introduced and evaluated. The combination of considerable sample enrichment and preservation of the compatibility of the required input band width with column dimensions is critically examined. The process of thermodesorption (reinjection) which is the most critical step, is particularly emphasized. The system consists of a short aluminum coated fused silica or metal capillary with a low mass and a low cost electrical heating. Input band widths down to 1 ms are obtained without extreme demands on electrical power (300 watt). The potential of the system is illustrated with some extremely fast separations.
Coupling site-directed mutagenesis with high-level expression: large scale production of mutant porins fromE. coli (1998)

Combination of an origin repair mutagenesis system with a new mutS host strain increased the efficiency of mutagenesis from 46% to 75% mutant clones. Overexpression with the T7 expression system afforded large quantities of proteins from mutant strains. A series of E. coli BE host strains devoid of major outer membrane proteins was constructed, facilitating the purification of mutant porins to homogeneity. This allowed preparation of 149 porin mutants in E. coli used in detailed explorations of the structure and function of this membrane protein to high resolution.
TARGETING AND COVALENT MODIFICATION OF CELL WALL AND MEMBRANE PROTEINS HETEROLOGOUSLY EXPRESSED IN THE DIATOM CYLINDROTHECA FUSIFORMIS (BACILLARIOPHYCEAE) (1999)

Diatoms are unicellular organisms encased by silica‐based cell walls that display species‐specific structures. Morphogenesis of diatom cell walls is believed to be controlled by a polysaccharide/protein‐matrix that remains associated with mature cell walls. Recently, a family of calcium‐binding glycoproteins, the frustulins, has been identified as major diatom cell wall component. Here we describe a transformation‐based approach to investigate intracellular targeting and function of frustulins. When ε‐frustulin from the diatom Navicula pelliculosa is expressed in Cylindrotheca fusiformis, it is correctly targeted into the cell wall. Furthermore, the unique N‐terminus of ε‐frustulin was properly modified, indicating that C. fusiformis and N. pelliculosa contain homologous frustulin‐processing proteases. In a different transformation experiment, a modified version of the Chlorella kessleri hexose/H + symporter bearing a bacterial biotinyl‐acceptor domain was expressed in C. fusiformis. The transporter became biotinylated in vivo and was functionally incorporated into the plasma membrane, allowing C. fusiformis to take up 14 C‐glucose and 14 C‐glucosamine. Stage‐specific radioactive labeling with this transformant revealed that secretion of frustulins is strongly enhanced during cell wall development. The data presented in this study demonstrate for the first time functional expression of a membrane protein and correct targeting of a cell wall protein heterologously expressed in a diatom cell.
Functional mapping of a trans-activating gene required for expression of a baculovirus delayed-early gene (1986)

The temporal regulation of an early gene of the baculovirus Autographa californica nuclear polyhedrosis virus was examined. We constructed a plasmid (plasmid 39CAT) in which the bacterial gene for chloramphenicol acetyltransferase was placed under the control of the promoter for the gene for a A. californica nuclear polyhedrosis virus 39,000-dalton protein (39K). A transient expression assay of plasmid 39CAT revealed that the 39K gene was expressed in infected cells but not in uninfected cells, indicating that the 39K gene should be classified as a delayed-early gene. The 39K promoter also efficiently directed the synthesis of chloramphenicol acetyltransferase when the plasmid was cotransfected with viral DNA which had been restricted with several restriction enzymes. To map the location of the gene(s) required for the synthesis of 39K, plasmid 39CAT was cotransfected with purified restriction fragments of A. californica nuclear polyhedrosis virus DNA. Fragments which mapped between 90.7 and 100.8 map units induced plasmid 39CAT. Plasmid pEcoRI-B, containing EcoRI fragment B (90 to 100 map units), activated plasmid 39CAT. Functional mapping of plasmid pEcoRI-B indicated that the essential region was located between 95.0 and 97.5 map units. The 5' end of this gene was mapped, and the chloramphenicol acetyltransferase gene was inserted under the control of its promoter. Transient assay experiments indicated that the trans-acting regulatory gene was expressed in uninfected cells and is therefore an immediate-early gene. This gene was named IE-1.
Security Protocols for version 2 of the Simple Network Management Protocol (SNMPv2) (1993)

It is the purpose of this document, Security Protocols for SNMPv2, to
define one such authentication and one such privacy protocol.
[STANDARDS-TRACK]
Development and Characterization of a Novel, Graded Model of Clip Compressive Spinal Cord Injury in the Mouse: Part 1. Clip Design, Behavioral Outcomes, and Histopathology (2002)

In order to take advantage of various genetically manipulated mice available to study the pathophysiology of spinal cord injury (SCI), we adapted an extradural clip compression injury model to the mouse (FEJOTA mouse clip). The dimensions of the modified aneurysm clip blades were customized for application to the mouse spinal cord. Three clips with different springs were made to produce differing magnitudes of closing force (3, 8, and 24 g). The clips were calibrated regularly to ensure that the closing force remained constant. The surgical procedure involved a laminectomy at T3 and T4, followed by extradural application of the clip at this level for 1 min to produce SCI. Three injury severities (3, 8, and 24 g), sham (passage of dissector extradurally at T3-4), and transection control groups were examined (n = 12/group). Quantitative behavioural assessments using the Basso, Beattie, and Bresnahan (BBB; H > 46; df = 4; p < 0.001; Kruskal-Wallis one-way ANOVA) and inclined plane (IP; F = 123; df = 4; p < 0.0001; two-way repeated measures ANOVA) tests showed a significant graded increase in neurological deficits with increasing severity of injury. By day 14, the motor recovery of the mice plateaued. Qualitative examination of the injury site morphology indicated that microcystic cavitation, degenerating axons, and robust astrogliosis were characteristic of the murine response to clip compressive SCI. Morphometric analyses of H&E/Luxol Fast Blue stained sections at every 50 microm from the injury epicenter indicated that with greater injury severity there was a progressive decrease in residual tissue (F = 220, df = 3; p < 0.0001; two-way ANOVA). In addition, statistically significant differences were found in the amount of residual tissue at the injury epicenter between all of the injury severities (p < 0.05, SNK test). This novel, graded compressive model of SCI will facilitate future studies of the pathological mechanisms of SCI using transgenic and knockout murine systems.
Ultrasonic hydrogenation of soybean oil (1983)

Abstract The rate of hydrogenation of soybean oil with either copper chromite or nickel catalysts increased more than a hundredfold with the aid of ultrasonication. In a continuous reaction system, the selectivity with copper catalyst for linolenate reduction was somewhat lower when ultrasonic energy was applied than when not applied. With ultrasonic energy, 87% hydrogenation of linolenate in soybean oil was obtained in 9 sec at 115 psig H 2 with 1% copper chromite at 181 C and 77% linolenate hydrogenation with 0.025% nickel. Without ultrasonic energy, only 59% linolenate hydrogenation was obtained in 240 sec with copper chromite at 198 C and 500 psig H 2 and 68% linolenate hydrogenation in 480 sec with nickel at 200 C and 115 psig H 2 . This innovation may offer an important advantage in increasing the activity of commercial catalysts, particularly copper chromite, for fats and oil hydrogenation.
The Polybromination of Alkylbenzenes1 (1946)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Polybromination of Alkylbenzenes1G. F. Hennion and James G. AndersonCite this: J. Am. Chem. Soc. 1946, 68, 3, 424–426Publication Date (Print):March 1, 1946Publication History Published online1 May 2002Published inissue 1 March 1946https://pubs.acs.org/doi/10.1021/ja01207a023https://doi.org/10.1021/ja01207a023research-articleACS PublicationsRequest reuse permissionsArticle Views478Altmetric-Citations19LEARN 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