gebhart/patrepeval huggingface dataset:
An intermolecular mechanism of T cell help for the production of antibodies to the bacterial pathogen, Chlamydia trachomatis (1993)

Antibodies that neutralize infectivity are directed at the antigenically variant major outer membrane protein (MOMP) of Chlamydia trachomatis. A vaccine for chlamydia will need to include T cell determinants that elicit T helper (Th) cells which provide help to MOMP-specific B cells. A limited number of determinants on MOMP are able to elicit Th cells and sequence diversity in the MOMP molecule may alter T cell recognition of these determinants. We investigated whether two sequence invariant proteins of C. trachomatis that are both abundant and immunogenic could elicit T cell help for the production of antibody to MOMP. We found that outer membrane protein 2 (OMP2) but not outer membrane protein 3 (OMP3) was able to prime BALB/c mice for an anamnestic anti-MOMP response following boost with the intact organism. This demonstration of an intermolecular mechanism of T cell help in a bacterial system has important implications for the development of a chlamydial vaccine as well as the design of vaccines for other antigenically variant non-viral pathogens.
Detection of Clonal and Subclonal Copy-Number Variants in Cell-Free DNA from Patients with Breast Cancer Using a Massively Multiplexed PCR Methodology (2015)

We demonstrate proof-of-concept for the use of massively multiplexed PCR and next-generation sequencing (mmPCR-NGS) to identify both clonal and subclonal copy-number variants (CNVs) in circulating tumor DNA. This is the first report of a targeted methodology for detection of CNVs in plasma. Using an in vitro model of cell-free DNA, we show that mmPCR-NGS can accurately detect CNVs with average allelic imbalances as low as 0.5%, an improvement over previously reported whole-genome sequencing approaches. Our method revealed differences in the spectrum of CNVs detected in tumor tissue subsections and matching plasma samples from 11 patients with stage II breast cancer. Moreover, we showed that liquid biopsies are able to detect subclonal mutations that may be missed in tumor tissue biopsies. We anticipate that this mmPCR-NGS methodology will have broad applicability for the characterization, diagnosis, and therapeutic monitoring of CNV-enriched cancers, such as breast, ovarian, and lung cancer.
Thermal stability ofNb∕a−NbxSi1−x∕NbJosephson junctions (2007)

As a high-resistivity normal-metal barrier for superconducting Josephson junctions, metal-silicon alloys appear to be a good replacement for noble metals and have been applied to the development of quantum voltage standard circuits. We observed that the electrical properties of Nb-based junctions made with amorphous ${\mathrm{Nb}}_{x}{\mathrm{Si}}_{1\ensuremath{-}x}$ barriers were slowly evolving over time when stored at room temperature. After systematically investigating both junctions and thin films, we have concluded that the changes in junction electrical parameters are due to changes in the amorphous ${\mathrm{Nb}}_{x}{\mathrm{Si}}_{1\ensuremath{-}x}$ and not due to barrier-electrode interface effects. The resistivity of amorphous ${\mathrm{Nb}}_{x}{\mathrm{Si}}_{1\ensuremath{-}x}$ increases after heat treatment at temperatures as low as $80\phantom{\rule{0.2em}{0ex}}\ifmmode^\circ\else\textdegree\fi{}\mathrm{C}$ when the Nb concentration is less than 33%, that of $\mathrm{Nb}{\mathrm{Si}}_{2}$. Furthermore, we found that annealed barriers behave similarly to barriers with the Nb concentration intentionally reduced to obtain smaller critical current and larger normal resistance with the same barrier thickness, as explained by our ${I}_{c}\text{\ensuremath{-}}{R}_{n}$ relation developed based on the dirty-limit superconductor--normal-metal--superconductor Josephson junction theory. To explain these effects, we adopt and corroborate a microscopic picture based on alloy phase stability that was previously demonstrated by others. We also successfully demonstrate a method to stabilize junctions made with ${\mathrm{Nb}}_{x}{\mathrm{Si}}_{1\ensuremath{-}x}$ barriers by intentionally annealing wafers during fabrication.
Cloning and characterization of a cDNA encoding gibberellin 20‐oxidase from rice (Oryza sativa) seedlings (1997)

Degenerate oligonucleotide primers based on the amino acid sequences of gibberellin (GA) 20‐oxidases from pumpkin and Arabidopsis were used in nested polymerase chain reactions to generate an internal cDNA fragment from rice ( Oryza satiya L.) seedlings. Using this fragment as a probe, a full‐length cDNA (pOs20ox) was isolated from a cDNA library constructed from rice seedlings. The deduced amino acid sequence of Os20ox showed good identity (42–55%) with the GA 20‐oxidases from pumpkin and Arabidopsis . Recombinant Os20ox protein, produced in Escherichia coli , catalyzed the conversion of GA 12 and GA 53 to GA 9 and GA 20 , respectively. In contrast to the enzyme from immature pumpkin seeds, the recombinant rice GA 20‐oxidase did not produce the tricarboxylic acids GA 25 and GA 17 from GA 12 and GA 53 , respectively. The conversion rate of GA 53 was higher than that of GA 12 . which is consistent with the relatively high abundance of 13‐hydroxylated GAs in rice seedlings. Os20ox mRNA accumulated at higher levels in seedlings of two GA‐deficient dwarf mutants than in normal plants. Treatment with uniconazole‐P. an inhibitor of GA biosynthesis, increased abundance of the mRNA, while exogenously applied GA 3 decreased it. These results suggest that the expression of the Os20ox gene is regulated by the level of physiologically active GA.
PetaBricks (2009)

It is often impossible to obtain a one-size-fits-all solution for high performance algorithms when considering different choices for data distributions, parallelism, transformations, and blocking. The best solution to these choices is often tightly coupled to different architectures, problem sizes, data, and available system resources. In some cases, completely different algorithms may provide the best performance. Current compiler and programming language techniques are able to change some of these parameters, but today there is no simple way for the programmer to express or the compiler to choose different algorithms to handle different parts of the data. Existing solutions normally can handle only coarse-grained, library level selections or hand coded cutoffs between base cases and recursive cases.
A 1,000x improvement in computer systems by bridging the processor-memory gap (2017)

For over 4 decades the gap between computer processing speed and memory access has grown at about 50% per year, to more than 1,000x today. This provides an excellent opportunity to enhance the single-core system performance. An innovative 3D integration technology combined with re-architecting the integrated memory device is proposed to bridge the gap and enable a 1,000 x improvement in computer systems. The proposed technology utilizes processes that are widely available and could be integrated in products within a very short time.
Mechanism of UV endonuclease V cleavage of abasic sites in DNA determined by carbon-13 labeling (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMechanism of UV endonuclease V cleavage of abasic sites in DNA determined by carbon-13 labelingMuthiah. Manoharan, Abhijit. Mazumder, Stephen C. Ransom, John A. Gerlt, and Philip H. BoltonCite this: J. Am. Chem. Soc. 1988, 110, 8, 2690–2691Publication Date (Print):April 1, 1988Publication History Published online1 May 2002Published inissue 1 April 1988https://pubs.acs.org/doi/10.1021/ja00216a074https://doi.org/10.1021/ja00216a074research-articleACS PublicationsRequest reuse permissionsArticle Views150Altmetric-Citations53LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Structure and stability of gamma-crystallins. Denaturation and proteolysis behavior. (1987)

The denaturation behavior of bovine lens gamma-crystallin fractions II, III, and IV and their susceptibility to proteolysis in vitro was compared to determine whether differences in their stability could play a role in cataract formation. Tertiary and secondary structure changes induced by increasing concentrations of urea, guanidine hydrochloride, and sodium dodecyl sulfate and by increasingly alkaline pH were followed by near-UV and far-UV circular dichroism, Trp fluorescence emission, and exposure of sulfhydryl groups. Major differences were found in the denaturation and proteolysis behavior of the three gamma-crystallin fractions. In general, the unfolding of gamma-II and gamma-III crystallins is rather gradual, suggesting the presence of intermediate unfolding states; in contrast, the order-disorder transition of gamma-IV crystallin is abrupt. The gamma-IV crystallin fraction is the most stable in urea and guanidine hydrochloride, but is most susceptible to nonspecific proteolysis and alkaline pH denaturation. Differences in denaturation and proteolysis behavior are attributed to the inherent differences in the tertiary structures of these crystallins.
Optimal strategies for the chemical and enzymic synthesis of bihelical deoxyribonucleic acids (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptimal strategies for the chemical and enzymic synthesis of bihelical deoxyribonucleic acidsGary J. Powers, Russell L. Jones, George A. Randall, Marvin H. Caruthers, J. H. Van de Sande, and H. G. KhoranaCite this: J. Am. Chem. Soc. 1975, 97, 4, 875–884Publication Date (Print):February 1, 1975Publication History Published online1 May 2002Published inissue 1 February 1975https://pubs.acs.org/doi/10.1021/ja00837a030https://doi.org/10.1021/ja00837a030research-articleACS PublicationsRequest reuse permissionsArticle Views62Altmetric-Citations18LEARN 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
BAM Receptors Regulate Stem Cell Specification and Organ Development Through Complex Interactions With CLAVATA Signaling (2008)

The CLAVATA1 (CLV1) receptor kinase regulates stem cell specification at shoot and flower meristems of Arabidopsis. Most clv1 alleles are dominant negative, and clv1 null alleles are weak in phenotype, suggesting additional receptors functioning in parallel. We have identified two such parallel receptors, BAM1 and BAM2. We show that the weak nature of the phenotype of clv1 null alleles is dependent on BAM activity, with bam clv mutants exhibiting severe defects in stem cell specification. Furthermore, BAM activity in the meristem depends on CLV2, which is required in part for CLV1 function. In addition, clv1 mutants enhance many of the Bam(-) organ phenotypes, indicating that, contrary to current understanding, CLV1 function is not specific to the meristem. CLV3 encodes a small, secreted peptide that acts as the ligand for CLV1. Mutations in clv3 lead to increased stem cell accumulation. Surprisingly, bam1 and bam2 mutants suppress the phenotype of clv3 mutants. We speculate that in addition to redundant function in the meristem center, BAM1 and BAM2 act to sequester CLV3-like ligands in the meristem flanks.
Identification of a new catenin: the tyrosine kinase substrate p120cas associates with E-cadherin complexes. (1994)

p120cas is a tyrosine kinase substrate implicated in ligand-induced receptor signaling through the epidermal growth factor, platelet-derived growth factor, and colony-stimulating factor receptors and in cell transformation by Src. Here we report that p120 associates with a complex containing E-cadherin, alpha-catenin, beta-catenin, and plakoglobin. Furthermore, p120 precisely colocalizes with E-cadherin and catenins in vivo in both normal and Src-transformed MDCK cells. Unlike beta-catenin and plakoglobin, p120 has at least four isoforms which are differentially expressed in a variety of cell types, suggesting novel means of modulating cadherin activities in cells. In Src-transformed MDCK cells, p120, beta-catenin, and plakoglobin were heavily phosphorylated on tyrosine, but the physical associations between these proteins were not disrupted. Association of p120 with the cadherin machinery indicates that both Src and receptor tyrosine kinases cross talk with proteins important for cadherin-mediated cell adhesion. These results also strongly suggest a role for p120 in cell adhesion.
PlasmaLyte (2011)

PlasmaLyte is a family of balanced crystalloid solutions with multiple different formulations available worldwide according to regional clinical practices and preferences. It closely mimics human plasma in its content of electrolytes, osmolality, and pH. These solutions also have additional buffer capacity and contain anions such as acetate, gluconate, and even lactate that are converted to bicarbonate, CO2, and water. The advantages of PlasmaLyte include volume and electrolyte deficit correction while addressing acidosis. It shares the same problems as most other crystalloid fluids (fluid overload, edema with weight gain, lung edema, and worsening of the intracranial pressure). A unique concern is that most formulations contain magnesium, which may affect peripheral vascular resistance, heart rate, and worsen organ ischemia. There are few studies on its use in trauma or hypovolemic shock. There is no evidence that PlasmaLyte is superior to other crystalloids for the prehospital management of traumatic hypovolemia.
Catalytic conjugate addition promoted by the copper(I)-monothiobinaphthol system. Part 3. Comparison of three thiolate-based catalytic systems (1999)

Monothiobinaphthol (MTB, 2-hydroxy-2′-mercapto-1,1′-binaphthyl undergoes S-alkylation with BuBr and α,ω-dihalides to afford thioether species. The precursor to MTB, 2-(N,N-dimethylcarbamoyloxy)-2′-(N,N-dimethylcarbamoylthio)-1,1′-binaphthyl, undergoes anionic Fries rearrangement of the O-aryl carbamate to afford a crystallographically characterised amido species. Hydrolysis of this species affords the 3-C(O)NMe2 analogue of MTB. These MTB-based ligand systems have been tested in asymmetric conjugate addition reactions of cyclic and acyclic enones and compared with 1,1′-bi(2-thionaphthol). Active catalysts are formed in all cases but only low enantioselectivities are realised (0–55% ee). Full conditions for the separation of the enantiomeric conjugate addition products are reported.
CAMP: a useful resource for research on antimicrobial peptides (2009)

Antimicrobial peptides (AMPs) are gaining popularity as better substitute to antibiotics. These peptides are shown to be active against several bacteria, fungi, viruses, protozoa and cancerous cells. Understanding the role of primary structure of AMPs in their specificity and activity is essential for their rational design as drugs. Collection of Anti-Microbial Peptides (CAMP) is a free online database that has been developed for advancement of the present understanding on antimicrobial peptides. It is manually curated and currently holds 3782 antimicrobial sequences. These sequences are divided into experimentally validated (patents and non-patents: 2766) and predicted (1016) datasets based on their reference literature. Information like source organism, activity (MIC values), reference literature, target and non-target organisms of AMPs are captured in the database. The experimentally validated dataset has been further used to develop prediction tools for AMPs based on the machine learning algorithms like Random Forests (RF), Support Vector Machines (SVM) and Discriminant Analysis (DA). The prediction models gave accuracies of 93.2% (RF), 91.5% (SVM) and 87.5% (DA) on the test datasets. The prediction and sequence analysis tools, including BLAST, are integrated in the database. CAMP will be a useful database for study of sequence-activity and -specificity relationships in AMPs. CAMP is freely available at http://www.bicnirrh.res.in/antimicrobial.
A Highly Sensitive and Selective Catalytic DNA Biosensor for Lead Ions (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTA Highly Sensitive and Selective Catalytic DNA Biosensor for Lead IonsJing Li and Yi LuView Author Information Departments of Chemistry and Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 Cite this: J. Am. Chem. Soc. 2000, 122, 42, 10466–10467Publication Date (Web):October 4, 2000Publication History Received14 June 2000Published online4 October 2000Published inissue 1 October 2000https://pubs.acs.org/doi/10.1021/ja0021316https://doi.org/10.1021/ja0021316rapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views7383Altmetric-Citations614LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Fluorescence,Genetics,Ions,Metals,Sensors Get e-Alerts
Autocrine laminin-5 ligates α6β4 integrin and activates RAC and NFκB to mediate anchorage-independent survival of mammary tumors (2003)

Invasive carcinomas survive and evade apoptosis despite the absence of an exogenous basement membrane. How epithelial tumors acquire anchorage independence for survival remains poorly defined. Epithelial tumors often secrete abundant amounts of the extracellular matrix protein laminin 5 (LM-5) and frequently express alpha6beta4 integrin. Here, we show that autocrine LM-5 mediates anchorage-independent survival in breast tumors through ligation of a wild-type, but not a cytoplasmic tail-truncated alpha6beta4 integrin. alpha6beta4 integrin does not mediate tumor survival through activation of ERK or AKT. Instead, the cytoplasmic tail of beta4 integrin is necessary for basal and epidermal growth factor-induced RAC activity, and RAC mediates tumor survival. Indeed, a constitutively active RAC sustains the viability of mammary tumors lacking functional beta1 and beta4 integrin through activation of NFkappaB, and overexpression of NFkappaB p65 mediates anchorage-independent survival of nonmalignant mammary epithelial cells. Therefore, epithelial tumors could survive in the absence of exogenous basement membrane through autocrine LM-5-alpha6beta4 integrin-RAC-NFkappaB signaling.
Industrial Noise Control and Acoustics (2002)

Compiling strategies from more than 30 years of experience, this book provides numerous case studies that illustrate the implementation of noise control applications, as well as solutions to common dilemmas encountered in noise reduction processes. It offers methods for predicting the noise generation level of common systems such as fans, motors, c
Building a RAPPOR with the Unknown: Privacy-Preserving Learning of\n Associations and Data Dictionaries (2015)

Techniques based on randomized response enable the collection of potentially\nsensitive data from clients in a privacy-preserving manner with strong local\ndifferential privacy guarantees. One of the latest such technologies, RAPPOR,\nallows the marginal frequencies of an arbitrary set of strings to be estimated\nvia privacy-preserving crowdsourcing. However, this original estimation process\nrequires a known set of possible strings; in practice, this dictionary can\noften be extremely large and sometimes completely unknown.\n In this paper, we propose a novel decoding algorithm for the RAPPOR mechanism\nthat enables the estimation of "unknown unknowns," i.e., strings we do not even\nknow we should be estimating. To enable learning without explicit knowledge of\nthe dictionary, we develop methodology for estimating the joint distribution of\ntwo or more variables collected with RAPPOR. This is a critical step towards\nunderstanding relationships between multiple variables collected in a\nprivacy-preserving manner.\n
Gabapentin Attenuates Late but Not Early Postoperative Pain After Thyroidectomy with Superficial Cervical Plexus Block (2008)

Oral preoperative administration of gabapentin did not modify immediate pain management in thyroidectomy patients receiving SCPB, but prevented delayed neuropathic pain at 6 mo.
An evaluation of bone growth into porous high density polyethylene (1976)

The purpose of this investigation was to study bone growth into porous polyethylene rods as a function of time and pore structure. Previous studies have indicated the biocompatibility of solid polyethylene materials which are currently being used clinically. Porous polyethylene rods were implanted in the femurs of mongrel dogs which are sacrificed four, eight, and 16 weeks postoperatively. The implants were then sectioned and examined histologically and microadiographically. Quantitative techniques were employed to determine the amount of bone ingrowth as a function of time and pore size. The pore structures of the materials were evaluated using optical microscopy and mercury intrusion porosimetry. The results of this investigation have demonstrated that porous polyethylene is capable of accepting bone growth into pores as small as 40 mum. The optimum rate of bone ingrowth was observed in pore sizes of approximately 100 to 135 mum, with no increase in the rate of bone ingrowth observed in samples possessing larger pore sizes. No adverse tissue response was found at implant times up to 16 weeks in pore sizes of 100 mum or larger.