gebhart/patrepeval huggingface dataset:
Targetable activating mutations are very frequent in GCB and ABC diffuse large B‐cell lymphoma (2013)

Diffuse large B cell lymphoma (DLBCL) is an aggressive and heterogeneous malignancy that can be divided in two major subgroups, germinal center B-cell-like (GCB) and activated B-cell-like (ABC). Activating mutations of genes involved in the BCR and NF-κB pathways (CD79A, CD79B, MYD88, and CARD11) or in epigenetic regulation (EZH2) have been recently reported, preferentially in one of the two DLBCL subtypes. We analyzed the mutational status of these five recurrently mutated genes in a cohort of 161 untreated de novo DLBCL. Overall, 93 mutations were detected, in 61 (38%) of the patients. The L265P MYD88 mutation was the most frequent MYD88 variant (n = 18), observed exclusively in the ABC subtype. CD79A/CD79B ITAM domains were targeted in ABC DLBCL (12/77; 16%), whereas CARD11 mutations were equally distributed in the two subtypes. The EZH2 Y641 substitution was found almost exclusively in the GCB subgroup (15/62; 24%). Twenty cases (12%) displayed two activating mutations, including the most frequent CD79/MYD88 variants combination (n = 8) which is observed exclusively in the ABC subtype. When considering only ABC DLBCL patients treated by rituximab plus chemotherapy, the presence of an activating NF-κB mutation was associated with an unfavorable outcome (3-years OS 26% for mutated cases versus 67% for the cases without mutations, P = 0.0337). Our study demonstrates that activating and targetable mutations are observed at a very high frequency in DLBCL at the time of diagnosis, indicating that sequencing of a limited number of genes could help tailor an optimal treatment strategy in DLBCL.
Complications of thalassemia major and their treatment (2011)

The life of patients with thalassemia has improved both in duration and in quality in industrialized countries. Complications are still common and include heart disease (heart failure and arrhythmias), chronic liver hepatitis, which can evolve in cirrhosis and, rarely, in hepatocellular carcinoma, endocrine problems (hypogonadism, hypothyroidism, diabetes, hypoparathyroidism), stunted growth, osteoporosis, thrombophilia and pseudoxanthoma elasticum. The incidence of complications is decreasing in younger cohorts of patients who have been transfused with blood that has been screened for viruses and thanks to the introduction of new oral iron chelators and imaging methods. The accurate measurement of iron deposits allows better management of iron overload. In addition, therapy for several complications is available. Specialized competence in treating patients with thalassemia is of great importance.
Choline and carnitine acetyltransferases of heart (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCholine and carnitine acetyltransferases of heartHelen L. White and Joyce Chen WuCite this: Biochemistry 1973, 12, 5, 841–846Publication Date (Print):February 27, 1973Publication History Published online1 May 2002Published inissue 27 February 1973https://pubs.acs.org/doi/10.1021/bi00729a009https://doi.org/10.1021/bi00729a009research-articleACS PublicationsRequest reuse permissionsArticle Views93Altmetric-Citations112LEARN 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
Display of Polyhistidine Peptides on the Escherichia coli Cell Surface by Using Outer Membrane Protein C as an Anchoring Motif (1999)

A novel cell surface display system was developed by employing Escherichia coli outer membrane protein C (OmpC) as an anchoring motif. Polyhistidine peptides consisting of up to 162 amino acids could be successfully displayed on the seventh exposed loop of OmpC. Recombinant cells displaying polyhistidine could adsorb up to 32.0 micromol of Cd(2+) per g (dry weight) of cells.
DEFENSE-RELATED PROTEINS IN HIGHER PLANTS (1990)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Coronary CT Angiography: Use in Patients With Chest Pain Presenting to Emergency Departments (2018)

Use of CCTA in EDs has increased rapidly, but far more MPI examinations are still being performed. This finding suggests that recently acquired evidence is not yet being fully acted upon.
The bacteriophage λ O and P protein initiators promote the replication of single-stranded DNA (1984)

A soluble enzyme system that specifically initiates lambda dv plasmid DNA replication at a bacteriophage lambda replication origin [Wold et al. (1982) Proc. Natl. Acad. Sci. USA 79, 6176-6180] is also capable of replicating the single-stranded circular chromosomes of phages M13 and phi X174 to a duplex form. This chain initiation on single-stranded templates is novel in that it is absolutely dependent on the lambda O and P protein chromosomal initiators and on several Escherichia coli proteins that are known to function in the replication of the lambda chromosome in vivo, including the host dnaB, dnaG (primase), dnaJ and dnaK replication proteins. Strand initiation occurs at multiple sites following an O and P protein-dependent pre-priming step in which the DNA is converted into an activated nucleoprotein complex containing the bacterial dnaB protein. We propose a scheme for the initiation of DNA synthesis on single-stranded templates in this enzyme system that may be relevant to strand initiation events that occur during replication of phage lambda in vivo.
Stomatal Patterning and Differentiation by Synergistic Interactions of Receptor Kinases (2005)

Coordinated spacing and patterning of stomata allow efficient gas exchange between plants and the atmosphere. Here we report that three ERECTA (ER)-family leucine-rich repeat-receptor-like kinases (LRR-RLKs) together control stomatal patterning, with specific family members regulating the specification of stomatal stem cell fate and the differentiation of guard cells. Loss-of-function mutations in all three ER-family genes cause stomatal clustering. Genetic interactions with a known stomatal patterning mutant too many mouths (tmm) revealed stoichiometric epistasis and combination-specific neomorphism. Our findings suggest that the negative regulation of ER-family RLKs by TMM, which is an LRR receptor-like protein, is critical for proper stomatal differentiation.
Fermi-Level Tuning of EpitaxialSb2Te3Thin Films on Graphene by Regulating Intrinsic Defects and Substrate Transfer Doping (2012)

High-quality Sb2Te3 films are obtained by molecular beam epitaxy on a graphene substrate and investigated by in situ scanning tunneling microscopy and spectroscopy. Intrinsic defects responsible for the natural p-type conductivity of Sb2Te3 are identified to be the Sb vacancies and Sb(Te) antisites in agreement with first-principles calculations. By minimizing defect densities, coupled with a transfer doping by the graphene substrate, the Fermi level of Sb2Te3 thin films can be tuned over the entire range of the bulk band gap. This establishes the necessary condition to explore topological insulator behaviors near the Dirac point.
REACTION OF 1-ACETYL-3-DICYANOMETHYLENE-1,3 - DIHYDRO-2H-INDOL-2-ONE WITH SOME NUCLEOPHILIC REAGENTS : SYNTHESIS OF SOME INDOL AND QUINOLINE DERIVATIVES (2000)

Article REACTION OF 1-ACETYL-3-DICYANOMETHYLENE-1,3 - DIHYDRO-2H-INDOL-2-ONE WITH SOME NUCLEOPHILIC REAGENTS : SYNTHESIS OF SOME INDOL AND QUINOLINE DERIVATIVES was published on June 1, 2000 in the journal Heterocyclic Communications (volume 6, issue 3).
Matrix Metalloproteinases and the Thyroid (2000)

Matrix metalloproteinases (MMPs) are proteolytic enzymes that degrade components of the extracellular matrix (ECM) and basement membrane. They play a critical role in many physiological and pathological processes, such as tumor metastasis. The original concept-that MMP activity during metastasis is restricted solely to invasion of the basement membrane and destruction of ECM components-has been modified to encompass multiple aspects of tumor progression: tumor establishment, growth, angiogenesis, intravasation, extravasation, and almost all metastatic steps. Moreover, the role of tissue inhibitors of matrix metalloproteinases (TIMPs), originally believed to exhibit anti-invasion properties solely by virtue of their inhibition of MMPs, has been extended to include their multiple biological effects, such as growth promotion. In thyroid neoplasia as well, MMPs, in particular MMP-2, seem to be associated with metastatic potential. It would seem that similar and divergent patterns regulate MMP and TIMP gene expression in benign and malignant human thyrocytes, in many instances in agreement with the concept of MMPs playing the role of stimulating, and TIMPs inhibiting cell invasion.
A method for de novo nucleic acid diagnostic target discovery (2014)

Supplementary data are available at Bioinformatics online.
<b>Detection of inducible prostaglandin H synthase-2 in cells in the exudate of rat carrageenin-induced </b><b>pleurisy </b> (1994)

Pleurisy was induced in rats by intrapleural injection of 0.2 ml of 2% /l-carrageenin. Prostaglandin H synthase (PGHS)-2 was detected using immunoblot analysis in cells of the pleural exudate 5 h after carrageenin injection, and waned at 19 h. PGHS-1 was also detected, but was maintained at similar levels in cells before and after carrageenin injection. The level of PGHS-2 was markedly suppressed by pretreatment of rats with anti-inflammatory dose of dexam ethasone (3 mg/ kg, i.p.) 2 h before carrageenin injection. Furthermore, only PGHS-l, but not PGHS-2, was detected in the microsomal fraction of the lung, stomach and kidney of pleurisy-affected and non-affected normal rats. These results suggest the involvement of
On single-deletion-correcting codes (2002)

This paper gives a brief survey of binary single-deletion-correcting codes. The Varshamov-Tenengolts codes appear to be optimal, but many interesting unsolved problems remain. The connections with shift-register sequences also remain somewhat mysterious.
Solid Phase Microextraction (1999)

Solid Phase Microextraction (SPME) uses a small volume of sorbent dispersed typically on the surface of small fibres, to isolate and concentrate analytes from sample matrix. After contact with sample, analytes are absorbed or adsorbed by the fibre phase (depending on the nature of the coating) until an equilibrium is reached in the system. The amount of an analyteextracted by the coating at equilibrium is determined by the magnitude of the partition coefficient of the analyte between the sample matrix and the coating material. After the extraction step, the fibres are transferred, with the help of a syringe-like handling device, to analytical instrument, for separation and quantitation of target analytes. This technique integrates sampling, extraction and sample introduction and is a simple way of facilitating on-site monitoring. Applications of this technique include environmental monitoring, industrial hygiene, process monitoring, clinical, forensic, food, flavour, fragrance and drug analyses, in laboratory and on-site analysis.
Diagnosis and Management of Onychomycosis (2016)

Onychomycosis is a fungal infection, and, as such, one of the goals of treatment should be eradication of the infective agent. Despite this, in contrast to dermatologists, many podiatric physicians do not include antifungals in their onychomycosis treatment plans. Before initiating treatment, confirmation of mycologic status via laboratory testing (eg, microscopy with potassium hydroxide preparation, histopathology with periodic acid-Schiff staining, fungal culture, and polymerase chain reaction) is important; however, more podiatric physicians rely solely on clinical signs than do dermatologists. These dissimilarities may be due, in part, to differences between specialties in training, reimbursement patterns, or practice orientation, and to explore these differences further, a joint podiatric medicine-dermatology roundtable was convened. In addition, treatment options have been limited owing to safety concerns with available oral antifungals and relatively low efficacy with previously available topical treatments. Recently approved topical treatments-efinaconzole and tavaborole-offer additional options for patients with mild-to-moderate disease. Debridement alone has no effect on mycologic status, and it is recommended that it be used in combination with an oral or topical antifungal. There is little to no clinical evidence to support the use of lasers or over-the-counter treatments for onychomycosis. After a patient has achieved cure (absence of clinical signs or absence of fungus with minimal clinical signs), lifestyle and hygiene measures, prophylactic/maintenance treatment, and proactive treatment for tinea pedis, including in family members, may help maintain this status.
Transdifferentiation of myoblasts by the adipogenic transcription factors PPAR gamma and C/EBP alpha. (1995)

Skeletal muscle and adipose tissue development often has a reciprocal relationship in vivo, particularly in myodystrophic states. We have investigated whether determined myoblasts with no inherent adipogenic potential can be induced to transdifferentiate into mature adipocytes by the ectopic expression of two adipogenic transcription factors, PPAR gamma and C/EBP alpha. When cultured under optimal conditions for muscle differentiation, murine G8 myoblasts expressing PPAR gamma and C/EBP alpha show markedly reduced levels of the myogenic basic helix-loop-helix proteins MyoD, myogenin, MRF4, and myf5 and are completely unable to differentiate into myotubes. Under conditions permissive for adipogenesis including a PPAR activator, these cells differentiate into mature adipocytes that express molecular markers characteristic of this lineage. Our results demonstrate that a developmental switch between these two related but highly specialized cell types can be controlled by the expression of key adipogenic transcription factors. These factors have an ability to inhibit myogenesis that is temporally and functionally separate from their ability to stimulate adipogenesis.
Super self-aligned GaAs RF switch IC with 0.25 dB extremely low insertion loss for mobile communication systems (2001)

An extremely low loss switch IC has been implemented by using a 0.15 /spl mu/m-gate super self-aligned FET with reduced drain/source area. Both off-state-capacitance and the specific on-resistance of the implemented FET have been dramatically reduced by the novel device structure. The experimentally fabricated switch IC showed the low insertion loss of 0.25 dB at an added power of 35 dBm at a frequency of 0.9 GHz, which is the lowest value ever reported.
Screening for breast cancer (1993)

To be successful, screening procedures must have certain properties: simplicity, acceptability, reasonable costs, and adequate sensitivity. The evolution of mammography over the past 10 years has allowed the examination to fall within accepted standards for these properties, and it has become a widely accepted procedure. Its expanded use has resulted in an increase in the detection of early stage disease with a profound effect upon the treatment of the disease. Survival continues to correlate with cancer size and nodal involvement, and the increase in the number of early cases diagnosed eventually should be reflected in a decreasing mortality rate. Though the efficacy of screening mammography for women between the ages of 50 and 69 is well-established, its usefulness in women aged 40-49 has provoked considerable debate. Despite the disagreements concerning appropriate screening thresholds and intervals, the American Cancer Society and the American College of Radiology have concluded that sufficient evidence exists to maintain published guidelines.
Verifying an all fused silica miniature optical fiber tip pressure sensor performance with turbine engine field test (2005)

Pressure sensors are the key elements for industrial monitoring and control systems to lower equipment maintenance cost, improve fuel economy, reduce atmospheric pollution, and provide a safer workplace. However, the testing environment is usually harsh. For example, inside the turbine engine, temperatures might exceed 600°C and pressures might exceed 100psi (690kPa), where most current available sensors cannot survive. Moreover, due to the restricted space for installation, miniature size of the sensor is highly desirable. To meet these requirements, a novel type of all fused silica optic fiber tip pressure sensor with a 125&#956;m diameter was developed. It is a diaphragm based pressure sensor in which a Fabry-Perot interferometer is constructed by the end face of an optical fiber and the surface of a diaphragm connected by a short piece of hollow fiber. The FP cavity length and the interference pattern will change according to ambient pressure variation. Its main improvement with respect to previously developed optical sensors, such as those utilizing techniques of wet etching, anodic bonding and sol-gel bonding, is the fact that no chemical method is needed during the cavity fabrication. Its dynamic pressure performance was verified in a turbine engine field test, demonstrating not only that it can safely and reliably function near the fan of a turbine engine for more than two hours, but also that its performance is consistent with that of a commercial Kulite sensor.
Oxidative stress in health and disease: The therapeutic potential of Nrf2 activation (2011)

For the past 40 years or so, oxidative stress has been increasingly recognized as a contributing factor in aging and in various forms of pathophysiology generally associated with aging. Our view of oxidative stress has been largely "superoxide-centric", as we focused on the pathological sources of this oxygen-derived free radical and the types of molecular havoc it can wreak, as well as on the protection provided by the antioxidant enzymes, especially the superoxide dismutases, catalases, and glutathione peroxidases. In the last decade our view of oxidative stress has broadened considerably, and it is now often seen as an imbalance that has its origins in our genes, and the ways in which gene expression is regulated. At the center of this new focus is the transcription factor called nuclear factor (erythroid-derived 2)-like 2, or Nrf2. Nrf2 is referred to as the "master regulator" of the antioxidant response, modulating the expression of hundreds of genes, including not only the familiar antioxidant enzymes, but large numbers of genes that control seemingly disparate processes such as immune and inflammatory responses, tissue remodeling and fibrosis, carcinogenesis and metastasis, and even cognitive dysfunction and addictive behavior. Thus, the dysregulation of Nrf2-regulated genes provides a logical explanation for the connections, both direct and indirect, between observable oxidative stress and perhaps 200 human diseases involving these various physiological processes, each reflecting a network involving many gene products. The evolutionary self-association of these many genes under the common control of Nrf2 suggests that the immune and inflammatory systems may present the largest demand for increased antioxidant protection, apart from constitutive oxidative stress resulting from mitochondrial oxygen consumption for metabolic purposes. Gene expression microarray data on human primary vascular endothelial cells and on the SK-N-MC human neuroblastoma-derived cell line have been obtained in response to the dietary supplement Protandim, a potent composition of highly synergistic phytochemical Nrf2 activators. Pathway analysis of results shows significant modulation by Protandim of pathways involving not only antioxidant enzymes, but of those related to colon cancer, cardiovascular disease, and Alzheimer disease.
Purification and Characterization of Interferon-??-Inducing Molecule of OK-432, a Penicillin-Killed Streptococcal Preparation, by Monoclonal Antibody Neutralizing Interferon-??-Inducing Activity of OK-432 (1993)

An immunoglobulin M mouse monoclonal antibody (MAb) to streptococcal preparation OK-432, TS-2, was generated. The TS-2 MAb showed positive reaction with butanol extract of OK-432 and fungal, branched (1-->3)-gamma-glucans (lentinan and schizophyllan) as well as lipoteichoic acids. Moreover, the interferon (IFN)-gamma-inducing activity of OK-432 was neutralized by TS-2 MAb. The affinity column of butanol extract of OK-432 on CNBr-activated Sepharose 4B-bound TS-2 antibody was prepared and the fractions containing IFN-gamma-inducing activity were eluted. The polysaccharide sample carrying the IFN-gamma-inducing activity with a molecular weight of 700,000 was destroyed by treatment with acid or sodium metaperiodate, but was stable to treatment with heat, alkali, pronase, or neuraminidase. Survival time of human salivary adenocarcinoma-bearing animals given a combination of the polysaccharide sample purified from butanol extract of OK-432 and TS-2 MAb was significantly shorter compared with that of the tumor-bearing animals given only the purified polysaccharide sample of OK-432. Moreover, a high level of effector cell activity in natural killer (NK) and lymphokine-activated killer (LAK) assays and significant increase of IFN-gamma-positive cells or asialo-GM1-positive cells were detected in the spleen cells from the animals given the polysaccharide sample purified from butanol extract of OK-432. These findings indicate that the polysaccharide sample purified by the affinity chromatography of butanol extract of OK-432 on CNBr-activated Sepharose 4B-bound TS-2 MAb carries the IFN-gamma-inducing activity of OK-432 and marked antitumor activity.
Structural Insights into Neonatal Fc Receptor-based Recycling Mechanisms (2014)

We report the three-dimensional structure of human neonatal Fc receptor (FcRn) bound concurrently to its two known ligands. More particularly, we solved the crystal structure of the complex between human FcRn, wild-type human serum albumin (HSA), and a human Fc engineered for improved pharmacokinetics properties (Fc-YTE). The crystal structure of human FcRn bound to wild-type HSA alone is also presented. HSA domain III exhibits an extensive interface of contact with FcRn, whereas domain I plays a lesser role. A molecular explanation for the HSA recycling mechanism is provided with the identification of FcRn His(161) as the only potential direct contributor to the corresponding pH-dependent process. At last, this study also allows an accurate structural definition of residues considered for decades as important to the human IgG/FcRn interaction and reveals Fc His(310) as a significant contributor to pH-dependent binding. Finally, we explain various structural mechanisms by which several Fc mutations (including YTE) result in increased human IgG binding to FcRn. Our study provides an unprecedented relevant understanding of the molecular basis of human Fc interaction with human FcRn.