gebhart/patrepeval huggingface dataset:
Typing Hepatitis B Virus by Homology in Nucleotide Sequence: Comparison of Surface Antigen Subtypes (1988)

The complete nucleotide sequences of the DNA of three hepatitis B virus (HBV) genomes of subtype adw, cloned from plasma samples of asymptomatic carriers living in the mainland and Okinawa Prefecture of Japan and Indonesia were determined. All three comprised 3215 bp and differed in sequence by only 3.9 to 5.6%. When these isolates were compared with the reported sequences of two HBV genomes of the same subtype derived from American carriers, however, the differences were greater (8.3 to 9.3% to an extent comparable with the nucleotide divergence between an HBV genome of subtype adw and that of a heterotypic subtype, such as adr, ayw or ayr. A total of 18 HBV genomes of various subtypes, including the three described here, 10 reported previously and five unpublished ones, were classified into four groups based on an inter-group divergence in nucleotide sequence of 8% or greater: group A (two adw genomes), group B (four adw), group C (three adw, four adr and one ayr) and group D (four ayw). Thus, the nine genomes of HBV subtype adw were distributed into three groups with considerably different sequences. These results indicate that the four major antigenically defined subtypes of envelope polypeptide do not reflect true genotypic variation of HBV. The fact that d to y, as well as w to r, subtypic change can be induced by an A----G point mutation at nucleotides 365 and 479 in the S gene, respectively, supports this view.
Covalent linkage to beta2-microglobulin enhances the MHC stability and antigenicity of suboptimal CTL epitopes. (1999)

Many CTL epitopes of clinical importance, particularly those derived from tumor Ags, display relatively poor MHC binding affinity and stability. Because in vivo immunogenicity, and thus the efficacy of peptide-based vaccines, is thought to be determined by MHC/peptide complex stability, there is a need to develop a simple strategy for enhancing the binding of suboptimal epitopes. Toward this goal, the ability to enhance suboptimal peptides through covalent linkage to beta2-microglobulin (beta2m) was explored. Two suboptimal variants of a high-affinity Db-restricted influenza nucleoprotein peptide were covalently linked, via a polypeptide spacer, to the amino terminus of human beta2m and the recombinant fusion proteins expressed in Escherichia coli. When compared with their uncoupled counterparts, the beta2m-linked epitopes display enhanced MHC stabilization and antigenicity. Thus, tethering epitopes to beta2m provides a simple method for augmenting the biological activity of suboptimal peptides and could be useful in the design of peptide-based vaccines or immunotherapeutics.
The North‐West Diabetes Foot Care Study: incidence of, and risk factors for, new diabetic foot ulceration in a community‐based patient cohort (2002)

More than 2% of community-based diabetic patients develop new foot ulcers each year. The neuropathy disability score, 10 g monofilament and palpation of foot pulses are recommended as screening tools in general practice.
High SEMA4C expression promotes the epithelial-mesenchymal transition and predicts poor prognosis in colorectal carcinoma (2020)

Semaphorin 4C (SEMA4C), is an important regulator of axonal guidance and aggravates tumor development. However, the roles and prognostic value of SEMA4C in colorectal cancer (CRC) remain unclear. Here, bioinformatics analyses of transcriptome data from multiple CRC patient datasets and immunohistochemical staining of a CRC tissue microarray (TMA) (n=83) showed that SEMA4C mRNA and protein expression were higher in CRC tissues than normal colorectal tissues. SEMA4C mRNA and protein expression correlated with pathologic stage and metastasis in CRC patients. Higher SEMA4C expression was associated with shorter overall survival, consensus molecular subtype 4 (CMS4), and DNA hypomethylation of SEMA4C in CRC patients. Multivariate Cox regression analyses revealed that SEMA4C expression was an independent prognostic predictor in CRC patients. Gene set expression analysis (GSEA) illustrated that SEMA4C expression had remarkable correlations with epithelial-mesenchymal transition (EMT) as well as hedgehog, Wnt/β-catenin, TGF-β, and Notch signaling pathways. Receiver operating characteristic (ROC) curve analysis demonstrated that SEMA4C expression accurately distinguished between the CMS4 and CMS1-3 subtypes of CRC patients. By inhibiting EMT, SEMA4C silencing reduced <i>in vitro</i> proliferation, migration, and invasion by CRC cells. These findings suggest that SEMA4C is a CMS4-associated gene that enhances CRC progression by inducing EMT.
Latest advances in supercapacitors: from new electrode materials to novel device designs (2017)

Notably, many significant breakthroughs for a new generation of supercapacitors have been reported in recent years, related to theoretical understanding, material synthesis and device designs. Herein, we summarize the state-of-the-art progress toward mechanisms, new materials, and novel device designs for supercapacitors. Firstly, fundamental understanding of the mechanism is mainly focused on the relationship between the structural properties of electrode materials and their electrochemical performances based on some in situ characterization techniques and simulations. Secondly, some emerging electrode materials are discussed, including metal-organic frameworks (MOFs), covalent organic frameworks (COFs), MXenes, metal nitrides, black phosphorus, LaMnO<sub>3</sub>, and RbAg<sub>4</sub>I<sub>5</sub>/graphite. Thirdly, the device innovations for the next generation of supercapacitors are provided successively, mainly emphasizing flow supercapacitors, alternating current (AC) line-filtering supercapacitors, redox electrolyte enhanced supercapacitors, metal ion hybrid supercapacitors, micro-supercapacitors (fiber, plane and three-dimensional) and multifunctional supercapacitors including electrochromic supercapacitors, self-healing supercapacitors, piezoelectric supercapacitors, shape-memory supercapacitors, thermal self-protective supercapacitors, thermal self-charging supercapacitors, and photo self-charging supercapacitors. Finally, the future developments and key technical challenges are highlighted regarding further research in this thriving field.
Comparison of the bonding power of various autologous fibrin tissue adhesives. (1997)

All three methods for manufacturing AFTA are effective in producing a reliable, stable fibrin glue. However, AFTA-E and AFTA-C demonstrate stronger bonding power than AFTA-A. In addition, all three forms of AFTA produce no undesirable tissue changes when injected into rat auricles.
Fast messages: efficient, portable communication for workstation clusters and MPPs (1997)

Illinois Fast Messages is a low level software messaging layer designed to meet the demands of high-performance network hardware. Implementations on a Cray T3D and a Myrinet-based workstation cluster demonstrate that FM can deliver much of the underlying hardware's performance to both higher-level messaging layers and applications.
Evolutionary wavelength division multiplexed schemes for broadband networks (1987)

Advances in optical transmission and electronic Integrated circuit technology have led to the emergence of the switched star network architecture1,2 In which high-capacity shared or concentrated optical feeder links radiate from a central service point to remote electronic switching points sited close to the subscriber. As information requirements expand at individual terminals, for example, through the growth of viewphone or video library services, additional feeder fibers are needed. Alternatively a wavelength division multiplex (WDM) scheme operating with channel spacings &gt; 1 nm and using free running single-mode or multimode lasers could be used to meet this growth without the need for additional fibers (Fig. 1). WDM also offers the advantage of allowing several switch points to be served by a single-feeder fiber and could allow direct optical channels to selected subscribers.
A Guide to the Chemical Basis of Drug Design (1983)

This book by a leading author in the field of medicinal chemistry deals with the chemical structure of biologically active compounds. Presents a unique historical overview of drug discovery and design using the historical facts of the pharmacology to reveal the serendipity of discovery and to point toward new structures that may be developed based on what has gone before.
Combined action of S-carvone and mild heat treatment on Listeria monocytogenes Scott A (2000)

The combined action of the plant-derived volatile, S-carvone, and mild heat treatment on the food-borne pathogen, Listeria monocytogenes, was evaluated. The viability of exponential phase cultures grown at 8 degrees C could be reduced by 1.3 log units after exposure to S-carvone (5 mmol l-1) for 30 min at 45 degrees C, while individual treatment with S-carvone or exposure to 45 degrees C for 30 min did not result in a loss in viability. Other plant-derived volatiles, namely carvacrol, cinnamaldehyde, thymol and decanal, were also found to reduce the viability of L. monocytogenes in combination with the same mild heat treatment at concentrations of 1.75 mmol l-1, 2.5 mmol l-1, 1.5 mmol l-1 and 2 mmol l-1, respectively. These findings show that essential oil compounds can play an important role in minimally processed foods, and can be used in the concept of Hurdle Technology to reduce the intensity of heat treatment or other individual hurdles.
Proteolysis of platelet receptors in humans and other species (2010)

Abstract In the past 5 years, metalloproteinase-mediated ectodomain shedding of platelet receptors has emerged as a new mechanism for modulating platelet function. By regulating surface expression of the platelet-specific receptors, glycoprotein (GP)VI that binds collagen, and GPIbα (the major ligand-binding subunit of the GPIb-IX-V complex) that binds von Willebrand factor (VWF) and other procoagulant and proinflammatory ligands, shedding not only irreversibly downregulates GPVI/GPIbα function, but generates proteolytic fragments that might be unique biomarkers or modulators in plasma. This is potentially significant because GPVI and GPIbα are involved in initiating thrombotic diseases such as heart attack and stroke, as well as autoimmune diseases where anti-platelet antibodies result in thrombocytopenia. Altered expression levels of GPIbα/GPVI are associated with both thrombotic propensity and platelet aging, suggesting an additional role in platelet clearance. Although emerging data are elucidating molecular mechanisms underlying GPIbα/GPVI shedding, evidence for the functional consequences of shedding in vivo , either clinically or in animal models, is far more limited. Here we consider recent published evidence for GPVI or GPIbα shedding in humans, nonhuman primates and mice, and whether conservation of sheddase cleavage sites across species points to a functional role for metalloproteolytic shedding in vivo .
Dihydroartemisinin Induces Apoptosis by a Bak-Dependent Intrinsic Pathway (2010)

The sesquiterpene lactone dihydroartemisinin (DHA), a semisynthetic derivative of the herbal antimalaria drug artemisinin, is cytotoxic to human tumor cells. Treatment of Jurkat T-lymphoma cells with DHA induced a breakdown of the mitochondrial transmembrane potential, release of cytochrome c, activation of caspases, and DNA fragmentation indicative of apoptosis induction. Although the absence of FADD or caspase-8 did not alter apoptosis rates in Jurkat cells, overexpression of dominant-negative caspase-9 or of antiapoptotic Bcl-xL or Bcl-2 largely decreased the cytotoxicity of DHA, demonstrating a role of the intrinsic death pathway. The proapoptotic Bcl-2 effector protein Bak and the Bcl-2 homology domain 3-only protein NOXA turned out to be important mediators of DHA-induced apoptosis in Jurkat cells. DHA treatment triggered the expression of NOXA and the activation of Bak. Furthermore, DHA-induced apoptosis was completely abrogated by loss of Bak and largely reduced in cells with siRNA-mediated downregulation of Bak or NOXA. Proapoptotic signaling of DHA also involved the formation of reactive oxygen species and membrane oxidation. Pretreatment with the lipophilic radical scavenger vitamin E or the hydrophilic radical scavengers glutathione and N-acetylcysteine reduced DHA-induced membrane oxidation and apoptosis, respectively. Oxidative changes also occurred in cells with disruption of the mitochondrial death pathway, suggesting a role of reactive oxygen species and oxidative membrane changes in death signaling upstream of the mitochondria. Interestingly, DHA increased the cytotoxic action of ionizing radiation and of the death receptor agonist tumor necrosis factor-related apoptosis-inducing ligand in Jurkat cells, suggesting a potential benefit of DHA in combined treatment strategies.
A proteinase inhibitor from Caesalpinia echinata (pau-brasil) seeds for plasma kallikrein, plasmin and factor XIIa (2004)

Caesalpinia echinata is a tree belonging to the Leguminosae family. The red color of the trunk, looking like burning wood ('brasa' in Portuguese), is the origin of the name Brazil. Seeds of leguminous plants contain high amounts of serine proteinase inhibitors that can affect different biological processes. Here we show that a protein isolated from seeds of C. echinata is able to inhibit enzymes that participate in blood coagulation and fibrinolysis. This inhibitor (CeKI) was purified to homogeneity by ion exchange and reversed-phase chromatography. SDS-PAGE indicated a single polypeptide chain with a molecular mass of 20 kDa. CeKI inhibits human plasma kallikrein ( K i =3.1 nM), plasmin ( K i =0.18 nM), factor XIIa ( K i =0.18 nM), trypsin ( K i =21.5 nM) and factor Xa ( K i =0.49 mM). CeKI inhibited kinin release from highmolecular- mass kininogen by kallikrein in vitro . The N-terminal sequence, determined by automatic Edman degradation, identified the inhibitor as a member of the Kunitz family. The secondary structure, determined by circular dichroism, is mainly a random coil followed by beta-sheet structure. The action of CeKI on enzymes of the blood-clotting intrinsic pathway was confirmed by prolongation of the activated partial thromboplastin time.
Free and glycosidically bound volatile compounds in fresh celery (Apium graveolens L.) (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFree and glycosidically bound volatile compounds in fresh celery (Apium graveolens L.)Jian Tang, Yuangang Zhang, Thomas G. Hartman, Robert T. Rosen, and Chi Tang HoCite this: J. Agric. Food Chem. 1990, 38, 10, 1937–1940Publication Date (Print):October 1, 1990Publication History Published online1 May 2002Published inissue 1 October 1990https://pubs.acs.org/doi/10.1021/jf00100a013https://doi.org/10.1021/jf00100a013research-articleACS PublicationsRequest reuse permissionsArticle Views371Altmetric-Citations38LEARN 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
TLE3 as a biomarker for taxane sensitivity in breast cancer (2008)

573 Background: The addition of taxanes (T) to chemotherapeutic regimens has not demonstrated a consistent therapeutic benefit in early stage breast cancer (Ward, HTA 2007). A recent study by Hayes, et al. suggested that HER2+ breast tumors may gain increased clinical benefit from treatment with T. The toxicity associated with T therapy compels a search for additional and or refined biomarkers of response. Methods: A dataset of IHC stains in 411 patients from Clearview Cancer Center (CCI) was mined to identify biomarkers of T response (Ring, JCO 2006). TLE3 staining with a polyclonal antibody was nominated as a candidate T-response predictor. The association with T sensitivity was tested by staining with anti-TLE3 antibody on an independent triple-negative (TN) validation cohort assembled at the Roswell Park Cancer Institute (RPCI). Results: TLE3 was identified as a candidate T sensitivity marker in the CCI cohort by identifying patients with improved five-year disease-free interval (DFI) in overall cohort (n=441, p<0.004), patients treated with CMF (n=72 p<0.02), or those treated with a AC+T regimen (n=65 p<0.04) but no association of staining with outcome in untreated patients (n=203 p=0.49) or those treated with a AC without T (n=66 p=0.97). In the RPCI TN validation cohort, TLE3 staining was significantly associated with improved five-year DFI in T treated patients (n=45 p<0.02) and all patients (n=81 p<0.015) but not AC treated patients (n=17 p=0.81). These associations were independent of grade, tumor size and nodal status in both cohorts. Conclusions: TLE3 staining is associated with improved DFI in taxane-treated patients in two independent cohorts. Given that the validation cohort was triple negative, it is unlikely that TLE3 is serving as a surrogate for ER or HER2 expression. TLE3 should be studied in large clinical trial cohorts to establish its role in taxane chemotherapy selection. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Applied Genomics Applied Genomics Applied Genomics Applied Genomics
Positron emission tomography for urological tumours (2003)

For urological tumours, positron emission tomography (PET) is currently most useful in testicular cancer. In patients with residual masses or raised marker levels after treatment, PET is both sensitive and specific for detecting recurrent disease, at suspected and unsuspected sites. Although fewer studies are available it also appears to be useful for staging at diagnosis, although this requires further investigation. Prostate cancer imaging has been more variable, with studies showing that PET cannot reliably differentiate between tumour and hypertrophy. It is not as good as a bone scan for defining bone metastases. In renal cancer, PET can be used to define the primary tumour, providing better staging of local recurrence than computed tomography (CT), and to define metastatic disease. There are few studies in bladder cancer, and despite excretion of the tracer via the bladder in early studies, it has better results than CT or magnetic resonance imaging for local staging; again it can detect metastases. Overall, the place of PET in urological tumours is developing, with the strongest areas undoubtedly being testicular and renal cancer. Tracers other than fluorodeoxyglucose are being examined and are providing further information.
The RNP motif protein family. (1992)

RNA-protein interactions play critical roles in a variety of important processes in the cell, such as mRNA splicing and translation. Many RNA binding proteins contain an approximately 80-aminoacid conserved sequence, the RNP motif, that has been shown in several cases to constitute the binding domain. As a class, RNP motif proteins bind many different RNAs with varying degrees of sequence specificity. A major area of current interest is the elucidation of the structure-function relationships in these proteins: the structure of the motif and the residues that are important for sequence-specific binding, the roles of the individual motifs in proteins with multiple RNP motifs, and the functions of other domains found in RNP motif proteins. Recent experiments have provided some insight into these issues and have paved the way for a more detailed understanding of this protein family.
Measurement of serum amyloid A1 (SAA1), a major isotype of acute phase SAA (2005)

Serum amyloid A (SAA), a plasma precursor of reactive amyloid deposits, is a multigene product. SAA1 and SAA2, with primary structures that are 93% identical (98 of 104 amino acids), behave as acute phase proteins, as demonstrated by their increasing levels in plasma. Heretofore, it has been understood that SAA1 predominates and functions as an isotype in plasma. However, accurate measurements differentiating the two isotypes have not been reported. In this study, using monoclonal antibodies specific for SAA1, we developed an enzyme-linked immunosorbent assay (ELISA) for SAA1. The levels and ratios of SAA1 in total SAA (TSAA) were investigated in healthy subjects and patients with rheumatoid arthritis (RA). The SAA1/TSAA ratio was 74 +/- 12% and 77 +/- 12% in healthy subjects and RA patients, respectively. In RA patients, the ratios were not influenced by SAA1 genotype, which has been proposed to affect plasma SAA values. The kinetics of SAA1 in inflamed patients undergoing hemodialysis was found to be parallel with total SAA and C-reactive protein. Finally, this study confirmed that SAA1 is a major isotype of acute phase SAA and may determine total SAA values. This specific assay could be used in the evaluation of SAA behavior in several clinical conditions.
The d3-Growth Hormone (GH) Receptor Polymorphism Is Associated with Increased Responsiveness to GH in Turner Syndrome and Short Small-for-Gestational-Age Children (2006)

Our data support the theory that there is increased responsiveness to high-dose rhGH in association with the d3-GHR genotype. The magnitude of this effect may depend on the primary origin of the short stature.
Child Mortality Following Standard, Medium or High Titre Measles Immunization in West Africa (1996)

The combined analysis showed a decreased survival related to high titre measles vaccine compared with standard titre vaccines, though solely among females. As a result of these studies from West Africa and a study from Haiti, WHO has recommended that high titre measles vaccine no longer be used.
Parallel gene synthesis in a microfluidic device (2007)

The ability to synthesize custom de novo DNA constructs rapidly, accurately and inexpensively is highly desired by researchers, as synthetic genes and longer DNA constructs are enabling to numerous powerful applications in both traditional molecular biology and the emerging field of synthetic biology. However, the current cost of de novo synthesis—driven largely by reagent and handling costs—is a significant barrier to the widespread availability of such technology. In this work, we demonstrate, to our knowledge, the first gene synthesis in a microfluidic environment. The use of microfluidic technology greatly reduces reaction volumes and the corresponding reagent and handling costs. Additionally, microfluidic technology enables large numbers of complex reactions to be performed in parallel. Here, we report the fabrication of a multi-chamber microfluidic device and its use in carrying out the syntheses of several DNA constructs. Genes up to 1 kb in length were synthesized in parallel at minute starting oligonucleotide concentrations (10–25 nM) in four 500 nl reactors. Such volumes are one to two orders of magnitude lower than those utilized in conventional gene synthesis. The identity of all target genes was verified by sequencing, and the resultant error rate was determined to be 1 per 560 bases.