gebhart/patrepeval huggingface dataset:
Mitochondrial oxidative stress in cancer-associated fibroblasts drives lactate production, promoting breast cancer tumor growth (2011)

Increasing chronological age is the most significant risk factor for cancer. Recently, we proposed a new paradigm for understanding the role of the aging and the tumor microenvironment in cancer onset. In this model, cancer cells induce oxidative stress in adjacent stromal fibroblasts. This, in turn, causes several changes in the phenotype of the fibroblast including mitochondrial dysfunction, hydrogen peroxide production, and aerobic glycolysis, resulting in high levels of L-lactate production. L-lactate is then transferred from these glycolytic fibroblasts to adjacent epithelial cancer cells and used as "fuel" for oxidative mitochondrial metabolism. Here, we created a new pre-clinical model system to directly test this hypothesis experimentally. To synthetically generate glycolytic fibroblasts, we genetically-induced mitochondrial dysfunction by knocking down TFAM using an sh-RNA approach. TFAM is mitochondrial transcription factor A, which is important in functionally maintaining the mitochondrial respiratory chain. Interestingly, TFAM-deficient fibroblasts showed evidence of mitochondrial dysfunction and oxidative stress, with the loss of certain mitochondrial respiratory chain components, and the over-production of hydrogen peroxide and L-lactate. Thus, TFAM-deficient fibroblasts underwent metabolic reprogramming towards aerobic glycolysis. Most importantly, TFAM-deficient fibroblasts significantly promoted tumor growth, as assayed using a human breast cancer (MDA-MB-231) xenograft model. These increases in glycolytic fibroblast driven tumor growth were independent of tumor angiogenesis. Mechanistically, TFAM-deficient fibroblasts increased the mitochondrial activity of adjacent epithelial cancer cells in a co-culture system, as seen using MitoTracker. Finally, TFAM-deficient fibroblasts also showed a loss of caveolin-1 (Cav-1), a known breast cancer stromal biomarker. Loss of stromal fibroblast Cav-1 is associated with early tumor recurrence, metastasis, and treatment failure, resulting in poor clinical outcome in breast cancer patients. Thus, this new experimental model system, employing glycolytic fibroblasts, may be highly clinically relevant. These studies also have implications for understanding the role of hydrogen peroxide production in oxidative damage and "host cell aging," in providing a permissive metabolic microenvironment for promoting and sustaining tumor growth.
Benign breast changes and the risk for subsequent breast cancer: an update of the 1985 consensus statement. Cancer Committee of the College of American Pathologists. (1998)

The Cancer Committee of the College of American Pathologists has prepared an update of the consensus statement on premalignant breast lesions and breast cancer risk that was originally published in the Archives of Pathology & Laboratory Medicine in 1986. The objective of this publication is to better define the relative breast cancer risk associated with specific histologic abnormalities by incorporating data derived from recent case-control studies. Explanatory notes are used to document and explain specific risk classifications. In addition to refining the degree of risk associated with individual lesions, such as fibroadenoma and atypical hyperplasia, this update includes a discussion of age-specific breast cancer risk and provides examples that can be used when counseling patients.
Codon reassignment in the Escherichia coli genetic code (2010)

Most organisms, from Escherichia coli to humans, use the 'universal' genetic code, which have been unchanged or 'frozen' for billions of years. It has been argued that codon reassignment causes mistranslation of genetic information, and must be lethal. In this study, we successfully reassigned the UAG triplet from a stop to a sense codon in the E. coli genome, by eliminating the UAG-recognizing release factor, an essential cellular component, from the bacterium. Only a few genetic modifications of E. coli were needed to circumvent the lethality of codon reassignment; erasing all UAG triplets from the genome was unnecessary. Thus, UAG was assigned unambiguously to a natural or non-natural amino acid, according to the specificity of the UAG-decoding tRNA. The result reveals the unexpected flexibility of the genetic code.
Solvent Microextraction with Simultaneous Back-Extraction for Sample Cleanup and Preconcentration:  Preconcentration into a Single Microdrop (1998)

A preconcentration technique which employs a microliter-size liquid membrane has been developed in order to obtain a large enrichment factor (EF) in a short time. The 30-μL n-octane liquid membrane, confined inside a small Teflon ring, is layered over 1.60 mL of aqueous source phase (sample), which is buffered at pH 13. The receiving phase is either a 1.00- or a 0.50-μL aqueous drop buffered at pH 2.1, that is suspended in the 30-μL membrane phase directly from the tip of a microsyringe needle. When the sample solution is stirred, basic analytes are extracted into the organic membrane phase and back-extracted simultaneously into the microdrop because they are neutral at high pH and protonated at low pH. After extracting for a prescribed time, the microdrop is taken back into the syringe needle and injected directly into an HPLC for quantification. In 15 min, the EFs in the 1.00-μL receiving drop are about 500 for methamphetamine, mephentermine, and methoxyphenamine, and about 160 for 2-phenylethylamine. Enrichment factors are approximately doubled for the same 15-min extraction time by using a 0.50-μL receiving drop. The reasons for this significant increase in EF with decreasing drop volume are discussed on the basis of a previously derived kinetic model.
Current Treatment of Juvenile Rheumatoid Arthritis (2002)

Prognostic factors in juvenile rheumatoid arthritis (JRA) include polyarticular onset, polyarticular disease course, and rheumatoid factor positivity; in the systemic onset subtype, persistence of systemic features at 6 months after onset confers a worse prognosis. Timely diagnosis and appropriate aggressive treatment of patients with poor prognostic features improve quality of life and outcome. After nonsteroidal anti-inflammatory drugs, methotrexate is the most commonly used second-line agent. However, approximately one third of patients do not respond to methotrexate adequately. Randomized, placebo-controlled, clinical trials in patients with JRA are few, but one such trial with the tumor necrosis factor inhibitor etanercept shows that this drug is effective and well-tolerated. Other recently approved agents for rheumatoid arthritis, including infliximab, leflunomide, celecoxib, and rofecoxib, have not been adequately studied in pediatric patients, and the role of these agents in children with JRA remains to be determined.
A complete secure customer centric anonymous payment in a digital ecosystem (2012)

In this paper, we propose a secure customer centric mobile payment scenario in which the merchant is disconnected from acquirer due to lack of internet connection and still can be used for mobile transaction. Our protocol protects the real identity of the customer during the transaction flow. The proposed protocol is based on symmetric key cryptography which further reduces computation at all the entities of the protocol. The protocol satisfies all the security requirements met by the existing standard protocols like SET, iKP, Kungpisdan et al and Tellez et al. Based on the author knowledge, the proposed protocol is the first protocol which satisfies all the cases of Non Repudiation. All the above mentioned protocols satisfies only Non Repudiation of Origin, where as our proposed protocol satisfies Non repudiation of Receipt, Non repudiation of Submission, Non repudiation of Delivery.
Storage Allocation in Bounded Time (2003)

The correctness of a real-time system is very much dependent on the time at which a specific task is completed. Hence, satisfying a storage allocation request within bounded time is important. Fragmentation of the heap after repeated allocations and deallocations is a major issue for real-time systems, as most allocators depend on garbage collection for defragmentation of the heap, which might not finish in time to honor deadlines. We present the storage requirement for a defragmentation-free binary-buddy allocator. We also study a localized defragmentation algorithm to satisfy a single allocation request, within bounded time, instead of requiring defragmentation of the entire heap. We prove that the cost of the algorithm is within twice the optimal cost. Results are presented from applying the defragmentation algorithm, with different heap sizes, on various programs. The amount of storage relocated with our defragmentation algorithm is compared with other compaction algorithms. Also, the amount of storage relocated by selecting a minimally occupied block is compared with the policy of selecting a block randomly.
Purification, Cloning, and Expression of a Cytidine 5′-Monophosphate -Acetylneuraminic Acid Synthetase from (1996)

An N-acetylneuraminic acid cytidylyltransferase (EC 2.7.7.43) (CMP-NeuAc synthetase) was isolated from a Haemophilus ducreyi strain 35000 cell lysate and partially characterized. The enzyme catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases. Previous studies have shown that the outer membrane lipooligosaccharides of H. ducreyi contain terminal sialic acid attached to N-acetyllactosamine and that this modification is likely important to its pathogenesis. Therefore, to investigate the role of sialic acid in H. ducreyi pathogenesis, the gene encoding the CMP-NeuAc synthetase was cloned using degenerate oligonucleotide probes derived from NH2-terminal sequence data, and the nucleotide sequence was determined. The derived amino acid sequence of the CMP-NeuAc synthetase gene has homology to other CMP-NeuAc synthetases and to a lesser extent to CMP-2-keto-3-deoxy-D-manno-octulosonic acid synthetases. The gene was cloned into a T7 expression vector, the protein expressed in Escherichia coli, and purified to apparent homogeneity by anion exchange, Green 19 dye, and hydrophobic interaction chromatography. The final step yielded 20 mg of pure protein/liter of culture. The protein has a predicted molecular mass of 25440.6 Da, which was confirmed by electrospray mass spectrometry (Mexpt = 25439.9 +/- 1.4 Da). The enzyme appears to exist as a dimer by size exclusion chromatography. In contrast to other bacterial CMP-NeuAc synthetases, the H. ducreyi enzyme exhibited a different substrate specificity, being capable of also using N-glycolylneuraminic acid as a substrate.
Cloning and Functional Expression of mCCR2, a Murine Receptor for the C-C Chemokines JE and FIC (1996)

The C-C chemokines human monocyte chemoattractant protein-1 and -3 (MCP-1 and MCP-3) and mouse JE and FIC are potent activators of monocytes. Several receptors for MCP-1 and MCP-3 have been cloned from human monocytic cell lines, and one of these receptors, CCR2B, binds both MCP-l and MCP-3. Thus far, no murine receptors for JE or FIC have been reported. We have cloned a novel murine C-C chemokine receptor, designated mouse CCR2 (mCCR2), from the mouse monocyte cell line WEHI265.1. The predicted 373-amino acid sequence of mCCR2 shows highest identity (80%) with CCR2B. When stably expressed in human embryonic kidney 293 cells, mCCR2 specifically bound 125I-JE with high affinity. FIC was less potent than JE in competing 125I-JE binding to mCCR2-expressing cells, while three other mouse chemokines, MIP-1alpha, C10, and N51/KC, did not compete. mccr2 mRNA expression was detected in elicited peritoneal macrophages as well as in several mouse organs. The cloning of mCCR2 provides an important tool to investigate monocyte/macrophage responses to JE and FIC, to identify other targets for their action, and potentially to study models of CCR2 function in the mouse.
Micrornas As A Potential Magic Bullet In Cancer (2006)

Genes that control cell differentiation and development are frequently mutated in human cancer. Micro (mi)RNAs are small regulatory RNAs that are emerging as important regulators of cell division/differentiation and human cancer genes. In this review, the miRNA cancer connection is discussed and the possibility of using this novel, but potentially powerful new therapy, involving miRNAs, to treat cancers is speculated on. For example, lung cancer is the major cause of cancer deaths in the USA, but existing therapies fail to treat this disease in the overwhelming majority of cases. The let-7 miRNA is one of a number of 'oncomirs', natural miRNA tumor suppressors in lung tissue, which may prove useful in treating lung cancer or enhancing current treatments for lung cancer.
Targeting a Therapy-Resistant Cancer Cell State Using Masked Electrophiles as GPX4 Inhibitors (2018)

SUMMARY We recently discovered that inhibition of the lipid peroxidase GPX4 can selectively kill cancer cells in a therapy-resistant state through induction of ferroptosis. Although GPX4 lacks a conventional druggable pocket, covalent small-molecule inhibitors are able to overcome this challenge by reacting with the GPX4 catalytic selenocysteine residue to eliminate enzymatic activity. Unfortunately, all currently-reported GPX4 inhibitors achieve their activity through reactive chloroacetamide groups. We demonstrate that such chloroacetamide-containing compounds are poor starting points for further advancement given their promiscuity, instability, and low bioavailability. Development of improved GPX4 inhibitors, including those with therapeutic potential, requires the identification of new electrophilic chemotypes and mechanisms of action that do not suffer these shortcomings. Here, we report our discovery that nitrile oxide electrophiles, and a set of remarkable chemical transformations that generates them in cells from masked precursors, provide an effective strategy for selective targeting of GPX4. Our results, which include structural insights, target engagement assays, and diverse GPX4-inhibitor tool compounds, provide critical insights that may galvanize development of improved compounds that illuminate the basic biology of GPX4 and therapeutic potential of ferroptosis induction. In addition, our discovery that nitrile oxide electrophiles engage in highly selective cellular interactions and are bioavailable in their masked forms may be relevant for targeting other currently undruggable proteins, such as those revealed by recent proteome-wide ligandability studies.
Transgenic T-cell receptor immunotherapy for cancer: building on clinical success (2020)

With the advent of immunotherapy as a realistic and promising option for cancer treatment, adoptive cellular therapies are gaining significant interest in the clinic. Whilst the recent successes of chimeric antigen receptor T-cell therapies for haematological malignancies are widely known, they have yet to show great success in solid cancers. However, immune cells transduced with T-cell receptors have been shown to traffic to and exert anti-cancer effects on solid tumour cells with some great successes. In this review, we explore the field of transgenic T-cell receptor immunotherapy, highlighting some of the key clinical trials which have paved the way for this type of cellular immunotherapy. Some trials have shown amazing clinical results, including long-term remissions and minimal toxicity, and can be looked at as an exemplar for this adoptive cell therapy. There have also been key trials where unexpected, fatal, off-tumour toxicity has occurred, and these trials have also been instrumental in shaping safer clinical trials, particularly regarding preclinical testing. In addition to previous trials, we analysed the current clinical trial space for T-cell receptor T-cell therapy, showing which trials are dominating in the clinic and which targets are being prioritised by researchers around the world. By looking at both past and current trials, we have been able to identify key drivers in developing transgenic T-cell receptor immunotherapy for the future.
Phosphorylation of membrane proteins at a cholinergic synapse. (1977)

Endogenous membrane protein kinase activity and protein kinase substrates have been found in membrane fractions enriched in the acetylcholine receptor that were prepared from the electric organ of Torpedo californica. Phosphorylation of four polypeptides is stimulated 9-fold by K+. The specific cholinergic ligand, carbachol, inhibited phosphorylation of these four polypeptides by 72% in the presence of 1mM Na+ and 100 mM K+. The 65,000-dalton component of the acetylcholine receptor in the membrane fraction appears to be phosphorylated by the endogenous protein kinase. These results suggest that protein phosphorylation may play an important role in synaptic events at nicotinic cholinergic synapses.
Age, Neuropathology, and Dementia (2009)

The association between the pathological features of Alzheimer's disease and dementia is stronger in younger old persons than in older old persons. Age must be taken into account when assessing the likely effect of interventions against dementia on the population.
Cyclosporin A protects striatal neurons in vitro and in vivo from 3-nitropropionic acid toxicity (2000)

The neuroprotective properties of cyclosporin A (CsA) are mediated by its ability to prevent mitochondrial permeability transition during exposure to high levels of calcium or oxidative stress. By using the mitochondrial toxin 3-nitropropionic acid (3NP), the present study assessed whether CsA could protect striatal neurons in vitro and in vivo. In vitro, 3NP produced a 20-30% reduction of striatal glutamic acid decarboxylase-immunoreactive (GAD-ir) neurons. A single treatment with CsA protected GAD-ir neurons from 3NP toxicity at lower (0.2 or 1.0 microM), but not at higher (5.0 microM) doses. Similar findings were seen when the cultures were treated twice with cyclosporin. In vivo experiments used the Lewis rat model of Huntington's disease (HD) in which a low 3NP dose was delivered subcutaneously through an osmotic minipump. Rats received unilateral or bilateral intrastriatal saline injections to disrupt the blood-brain barrier (BBB) and facilitate CsA reaching vulnerable neurons. In the first experiment, CsA treated 3NP-lesioned rats displayed significantly more dopamine-and adenosine-3;, 5;-monophosphate-regulated phosphoprotein (DARPP32-ir) neurons ipsilateral to BBB disruption compared to the contralateral intact striatum, indicating that disruption of the BBB maybe necessary for CsA's neuroprotective effects. In the second experiment, stereological counts of DARPP32-ir neurons revealed that CsA protected striatal neurons in a dose-dependent manner following bilateral disruption of the striatal BBB. Rats treated with the higher (15 or 20 mg/kg) but not lower (5 mg/kg) doses of CsA displayed greater numbers of DARRP32-ir striatal neurons relative to vehicle-treated 3NP-lesioned rats. Thus, under conditions in which CsA can gain access to striatal neurons, significant protection from 3NP toxicity is observed. Therefore, CsA or more lipophilic analogues of this compound, may be of potential therapeutic benefit by protecting vulnerable neurons from the primary pathological event observed in HD.
Robust Generation of Hemangioblastic Progenitors from Human Embryonic Stem Cells (2008)

This new method represents a significantly improved system for generating hemangioblasts from hESCs, and although simplified, results in an eightfold increase in cell yield.
Hierarchical storage management for relational databases (2002)

The author describes a prototype that integrates a database management system (DBMS) with a storage management system, allowing simple, cost-effective access to large volumes of data stored in a tape archive. The prototype study suggests that it is feasible from both technical and cost perspectives to store not just metadata, but large satellite images in a DBMS. The actual location of the data, whether in the DBMS, file system, or tape archive, is transparent to clients, allowing cost/performance optimization to be performed without affecting the interface to the client. Further, in common cases where database inserts can be bypassed, the performance of the prototype is equivalent to file system input/output (I/O).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Implications of special parking areas in a London Borough (1992)

Perspectives relatives a la nouvelle reglementation, donnant aux autorites locales la gestion des problemes de stationnement
Technology to Obtain Sustained Release Characteristics of Drugs after Delivered to the Colon (1999)

To determine the necessary technology by which sustained drug release is obtained after drug is delivered to the colon, two kinds of microcapsules were prepared and were filled in a pressure-controlled colon delivery capsule (PCDC). As a model drug 5-aminosalicylic acid (5-ASA) was used, because the target site of 5-ASA is the entire large intestine. 5-ASA was microencapsulated using a water-insoluble polymer, ethylcellulose (EC) or with pH-sensitive polymers, Eudragit L-100 or S-100 and encased in PCDC. The particle size of these microcapsules was around 800 microns and the loading efficiencies of 5-ASA were approximately 90%. In vitro dissolution tests were performed with the prepared microcapsules. The release rate of 5-ASA from the microcapsules was significantly prolonged as compared to 5-ASA powder, although there were no significant differences in the release rates between these microcapsules. By incorporating the 5-ASA microcapsules into PCDC, sustained release PCDCs for colon delivery were prepared and in vivo evaluation was performed using beagle dogs. As a fast release colon delivery system, PCDCs were prepared with 5-ASA powder suspended in suppository base. After oral administration of the test preparations to beagle dogs, plasma 5-ASA concentrations were measured and sustained release characteristics of 5-ASA from the test preparations were evaluated from the plasma 5-ASA concentration-time profiles. The first appearance time of 5-ASA into the systemic circulation after oral administration were 3 h for all the colon delivery preparations and it was thought that these test preparations were delivered to the colon. Both EC microcapsules and Eudragit S-100/RS-100 microcapsules in PCDC showed longer the mean residence time MRT, 8.2 +/- 0.6 h and 8.7 +/- 0.9 h, than Eudragit L-100/RS-100 microcapsules in PCDC where the MRT was 6.6 +/- 0.2 h. Since PCDCs containing 5-ASA powder exhibited a MRT of 7.0 +/- 1.0 h, these two types of preparations have suggested sustained release characteristics.
Classification of lymphoid neoplasms: the microscope as a tool for disease discovery (2008)

In the past 50 years, we have witnessed explosive growth in the understanding of normal and neoplastic lymphoid cells. B-cell, T-cell, and natural killer (NK)-cell neoplasms in many respects recapitulate normal stages of lymphoid cell differentiation and function, so that they can be to some extent classified according to the corresponding normal stage. Likewise, the molecular mechanisms involved the pathogenesis of lymphomas and lymphoid leukemias are often based on the physiology of the lymphoid cells, capitalizing on deregulated normal physiology by harnessing the promoters of genes essential for lymphocyte function. The clinical manifestations of lymphomas likewise reflect the normal function of lymphoid cells in vivo. The multiparameter approach to classification adopted by the World Health Organization (WHO) classification has been validated in international studies as being highly reproducible, and enhancing the interpretation of clinical and translational studies. In addition, accurate and precise classification of disease entities facilitates the discovery of the molecular basis of lymphoid neoplasms in the basic science laboratory.