gebhart/patrepeval huggingface dataset:
Pre-clinical and clinical treatment of breast cancer with antiprogestins (1994)

Antiprogestins form a new potential treatment modality for breast cancer and their mode of action has been assessed in vitro on several breast cancer cell lines, in vivo in rats with dimethylbenzanthracene (DMBA)-induced mammary tumours and in vivo in patients with metastatic breast cancer. In vitro in serum-free medium, the progestin Org 2058 and antiprogestins RU486 and Org 31710 caused a dose-dependently stimulated MCF7 cell growth. Both antiprogestins dose-dependently inhibited the oestrogen-stimulated proliferation of progesterone receptor (PgR)-rich T-47D cells in DCC medium. Inhibition by Org 31710 plateaued at 10(-8) M (74% inhibition), compared with RU486 at up to 10(-6) M (53% inhibition). No inhibition was observed at doses of 10(-12)-10(-6) M of both antiprogestins in the absence of oestradiol. The proliferation of the ZR-75.1 and MDA-MB-231 cell lines was not or only marginally affected by either antiprogestin. Rats with DMBA-induced mammary tumours given prophylactic treatment with RU486 displayed a doubled latency period. Antiprogestins were slightly more effective than tamoxifen or progestins in rats with existing tumours. Org 31710 sometimes showed a somewhat more pronounced inhibitory effect than the antiprogestins Org 31806 and RU486. Combined antiprogestational and anti-oestrogenic treatment showed striking additive growth inhibitory effects resulting in clear tumour remissions, in the presence of very strong suppression of oestrogen and PgRs. The growth inhibitory effect of luteinizing hormone-releasing hormone agonists was potentiated by antiprogestins.(ABSTRACT TRUNCATED AT 250 WORDS)
Tunable anchoring groups@acridone-linked triphenylamine based pendant chromophores and their effects on the photovoltaic performance as sensitizers for dye-sensitized solar cells (2016)

In this study, a series of pendant chromophores bearing methacrylate polymers with different anchoring/acceptor groups were synthesized for use as sensitizers in the dye-sensitized solar cells.
A cyclin-dependent kinase inhibitor inducing cancer cell differentiation: Biochemical identification using Xenopus egg extracts (1999)

Cellular differentiation is a complex process involving growth arrest, exit from the cell cycle, and expression of differentiated cell-type-specific functions. To identify small molecules promoting this process, a chemical library was screened by using a myeloid leukemic cell line that retained the potential to differentiate in culture. In the presence of a purine derivative, aminopurvalanol (AP), cells acquired phenotypic characteristics of differentiated macrophages and became arrested in the cell cycle with a 4N DNA content. AP also inhibited mitosis in Xenopus egg extracts, suggesting that it acted on an evolutionarily conserved cell cycle regulatory pathway. Affinity chromatography and biochemical reconstitution experiments with Xenopus egg extracts identified cyclin-dependent kinase (CDK) 1-cyclin B as a target of the compound. Although AP potently inhibited immunoprecipitates of both human CDK1 and CDK2 from human leukemic cell extracts, our results indicate that the compound preferentially targets the G2/M-phase transition in vivo.
Genetically Engineered Attenuated Herpes Simplex Viruses (1991)

Two recombinant herpes simplex viruses, of type 1 background, were constructed with two large deletions and duplicate sets (type 1 and type 2) of the genes coding for glycoproteins D, G, and E. One recombinant (R7020) is thymidine kinase-positive, and the other (R7017) is thymidine kinase-negative. Evaluation in rodents indicated that these viruses are genetically stable, capable of establishing latency, protective against severe herpetic diseases, and protective against the establishment of latency. In Aotus monkeys, R7020 replicates at the site of inoculation but does not disseminate in the body. It can reactivate from the latent state but without causing recurrent lesions, even in immunosuppressed monkeys.
Increasing Incidence of Multiply Recurrent Clostridium difficile Infection in the United States (2017)

National Institute of Diabetes and Digestive and Kidney Diseases and National Institute of Allergy and Infectious Diseases.
Therapeutic aspects of IgA nephropathy: an overview (2002)

SUMMARY: IgA nephropathy (IgAN) is the cause of end‐stage renal failure in 15–20% of patients within 10 years from the apparent onset of the disease and in 30–40% of individuals within 20 years. the degree of renal lesions, serum creatinine, severe proteinuria and microhematuria are independent prognostic indicators. No specific therapy has been definitely established, although several approaches have been experimented. the most important aspects of each randomized controlled trial (RCT) available in the literature were analysed regarding the treatment of IgAN with corticosteroids, cytotoxic agents and fish oil. Their quality was evaluated according to the Consolidated Standards of Reporting Trials (CONSORT) statement, an analysis was performed of heterogeneity between trials and finally these results were used to obtain a meta‐analysis adjusted for the duration of follow up. Regarding the quality assessment of the considered trials, the analysis showed that the majority of RCT lack key information, particularly in their methods and results sections. Because a wide heterogeneity existed among RCT, the meta‐analysis was performed with both fixed and random methods to obtain the most reliable results. the present study showed that only corticosteroid treatment may be beneficial for the outcome of renal function, while this is only partially true for fish‐oil treatment and not true for cytotoxic agents. These statements are in concordance with previously published meta‐analyses. Furthermore, when the results of meta‐analysis on the effect of treatment for corticosteroids, cytotoxic agents and fish oil were adjusted for the duration of follow up, it was found that their effects decreased and became null as follow up increased. In conclusion, further RCT are necessary, including more homogeneous groups of IgAN patients and therapeutic regimens with a long‐term follow up. It is necessary to state that the results of meta‐analysis must be used with care and not as a surrogate for sound decision‐making. They should not be considered as absolute, and this is particularly true in fields such as nephrology in which the number of patients enrolled in individual studies is very small and the duration of follow up is very short.
Therapeutic vaccine for acute and chronic motor neuron diseases: Implications for amyotrophic lateral sclerosis (2003)

Therapeutic vaccination with Copaxone (glatiramer acetate, Cop-1) protects motor neurons against acute and chronic degenerative conditions. In acute degeneration after facial nerve axotomy, the number of surviving motor neurons was almost two times higher in Cop-1-vaccinated mice than in nonvaccinated mice, or in mice injected with PBS emulsified in complete Freund's adjuvant (P < 0.05). In mice that express the mutant human gene Cu/Zn superoxide dismutase G93A (SOD1), and therefore simulate the chronic human motor neuron disease amyotrophic lateral sclerosis, Cop-1 vaccination prolonged life span compared to untreated matched controls, from 211 +/- 7 days (n = 15) to 263 +/- 8 days (n = 14; P < 0.0001). Our studies show that vaccination significantly improved motor activity. In line with the experimentally based concept of protective autoimmunity, these findings suggest that Cop-1 vaccination boosts the local immune response needed to combat destructive self-compounds associated with motor neuron death. Its differential action in CNS autoimmune diseases and neurodegenerative disorders, depending on the regimen used, allows its use as a therapy for either condition. Daily administration of Cop-1 is an approved treatment for multiple sclerosis. The protocol for non-autoimmune neurodegenerative diseases such as amyotrophic lateral sclerosis, remains to be established by future studies.
A mechanism of covalent substrate binding in the x-ray structure of subunit K of the Escherichia coli dihydroxyacetone kinase (2003)

Dihydroxyacetone (Dha) kinases are homologous proteins that use different phosphoryl donors, a multiphosphoryl protein of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system in bacteria, ATP in animals, plants, and some bacteria. The Dha kinase of Escherichia coli consists of three subunits, DhaK and DhaL, which are colinear to the ATP-dependent Dha kinases of eukaryotes, and the multiphosphoryl protein DhaM. Here we show the crystal structure of the DhaK subunit in complex with Dha at 1.75 A resolution. DhaK is a homodimer with a fold consisting of two six-stranded mixed beta-sheets surrounded by nine alpha-helices and a beta-ribbon covering the exposed edge strand of one sheet. The core of the N-terminal domain has an alpha/beta fold common to subunits of carbohydrate transporters and transcription regulators of the phosphoenolpyruvate-dependent carbohydrate:phosphotransferase system. The core of the C-terminal domain has a fold similar to the C-terminal domain of the cell-division protein FtsZ. A molecule of Dha is covalently bound in hemiaminal linkage to the N epsilon 2 of His-230. The hemiaminal does not participate in covalent catalysis but is the chemical basis for discrimination between short-chain carbonyl compounds and polyols. Paralogs of Dha kinases occur in association with transcription regulators of the TetR/QacR and the SorC families, pointing to their biological role as sensors in signaling.
Tandem Duplication Producing a Novel Oncogenic BRAF Fusion Gene Defines the Majority of Pilocytic Astrocytomas (2008)

Brain tumors are the most common solid tumors of childhood, and pilocytic astrocytomas (PA) are the most common central nervous system tumor in 5 to 19 year olds. Little is known about the genetic alterations underlying their development. Here, we describe a tandem duplication of approximately 2 Mb at 7q34 occurring in 66% of PAs. This rearrangement, which was not observed in a series of 244 higher-grade astrocytomas, results in an in-frame fusion gene incorporating the kinase domain of the BRAF oncogene. We further show that the resulting fusion protein has constitutive BRAF kinase activity and is able to transform NIH3T3 cells. This is the first report of BRAF activation through rearrangement as a frequent feature in a sporadic tumor. The frequency and specificity of this change underline its potential both as a therapeutic target and as a diagnostic tool.
Basal Insulin Therapy in Type 2 Diabetes (2005)

Patients with type 2 diabetes mellitus are usually treated initially with oral antidiabetic agents, but as the disease progresses, most patients eventually require insulin to maintain glucose control. Optimal insulin therapy should mimic the normal physiologic secretion of insulin and minimize the risk of hypoglycemia. This article discusses the role of insulin therapy in patients with type 2 diabetes, emphasizing long-acting insulin agents designed to approximate physiologic basal insulin secretion and provide control over fasting plasma glucose. Clinical trials of recently developed long-acting insulins are reviewed herein, with emphasis on studies that combined basal insulin with oral agents or with short-acting insulins in a basal-bolus approach. The normal physiologic pattern of insulin secretion by pancreatic beta cells consists of a sustained basal insulin level throughout the day, superimposed after meals by relatively large bursts of insulin that slowly decay over 2 to 3 hours (bolus insulin). Basal support with long-acting insulin is a key component of basal-bolus therapy for patients with diabetes who require insulin with or without the addition of oral agents. Newer long-acting agents such as insulin glargine provide a steadier and more reliable level of basal insulin coverage and may have significant advantages over traditional long-acting insulins as part of a basal-bolus treatment strategy.
Angiopoietin-3 Is Tethered on the Cell Surface via Heparan Sulfate Proteoglycans (2004)

Angiopoietins are a family of factors that play important roles in angiogenesis, and their receptor, Tie-2 receptor tyrosine kinase, is expressed primarily by endothelial cells. Three angiopoietins have been identified so far, angiopoietin-1 (Ang-1), angiopietin-2 (Ang-2), and angiopoietin-3 (Ang-3). It has been established that Ang-1 and Tie-2 play essential roles in embryonic angiogenesis. We have demonstrated recently that, unlike Ang-2, Ang-1 binds to the extracellular matrix, which regulates the availability and activity of Ang-1 (Xu, Y., and Yu, Q. (2001) J. Biol. Chem. 276, 34990-34998). However, the role and biochemical characteristics of Ang-3 are unknown. In our current study, we demonstrated that, unlike Ang-1 and Ang-2, Ang-3 is tethered on cell surface via heparan sulfate proteoglycans (HSPGs), especially perlecan. The cell surface-bound Ang-3 is capable of binding to its receptor, Tie-2; suggesting HSPGs concentrate Ang-3 on the cell surface and present Ang-3 to its receptor to elicit specific local reaction. Mutagenesis experiment revealed that the coiled-coil domain of Ang-3 is responsible for its binding to the cell surface. In addition, we demonstrated that the cell surface-bound Ang-3 but not soluble Ang-3 induces retraction and loss of integrity of endothelial monolayer, indicating the binding of Ang-3 to the cell surface via HSPGs is required for this bioactivity of Ang-3.
Feasibility of global gene expression analysis in testicular biopsies from infertile men (2003)

Numerous studies have documented the use of microarray analysis to identify patterns of global gene expression that distinguish normal development from that of the diseased state. Yet, there are no reports that compare global gene expression in the fertile and infertile human testis. Here, we report an initial study of global gene expression in testicular biopsies from several men with different infertility phenotypes. We found that microarray analysis of small biopsy samples was suitable for profiling expression of genes known to function in germ cell development and also identified expression of novel genes. Since it is now common for infertile men with spermatogenic failure to use intracytoplasmic sperm injection (ICSI) to achieve biological paternity, we hypothesize that molecular screening of testicular biopsies with microarrays may be suitable: (1) to categorize the molecular phenoytpes of infertile testes in a manner similar to standard morphologic analysis and (2) to initiate larger studies of gene expression in the infertile testes that may identify genetic signatures from biopsies that allow prediction of outcomes.
Paradigms for computational nucleic acid design (2004)

The design of DNA and RNA sequences is critical for many endeavors, from DNA nanotechnology, to PCR-based applications, to DNA hybridization arrays. Results in the literature rely on a wide variety of design criteria adapted to the particular requirements of each application. Using an extensively studied thermodynamic model, we perform a detailed study of several criteria for designing sequences intended to adopt a target secondary structure. We conclude that superior design methods should explicitly implement both a positive design paradigm (optimize affinity for the target structure) and a negative design paradigm (optimize specificity for the target structure). The commonly used approaches of sequence symmetry minimization and minimum free-energy satisfaction primarily implement negative design and can be strengthened by introducing a positive design component. Surprisingly, our findings hold for a wide range of secondary structures and are robust to modest perturbation of the thermodynamic parameters used for evaluating sequence quality, suggesting the feasibility and ongoing utility of a unified approach to nucleic acid design as parameter sets are refined further. Finally, we observe that designing for thermodynamic stability does not determine folding kinetics, emphasizing the opportunity for extending design criteria to target kinetic features of the energy landscape.
Cloning, sequencing, and expression of the Pseudomonas putida protocatechuate 3,4-dioxygenase genes (1993)

The genes that encode the alpha and beta subunits of protocatechuate 3,4-dioxygenase (3,4-PCD [EC 1.13.11.3]) were cloned from a Pseudomonas putida (formerly P. aeruginosa) (ATCC 23975) genomic library prepared in lambda phage. Plaques were screened by hybridization with degenerate oligonucleotides designed using known amino acid sequences. A 1.5-kb SmaI fragment from a 15-kb primary clone was subcloned, sequenced, and shown to contain two successive open reading frames, designated pcaH and pcaG, corresponding to the beta and alpha subunits, respectively, of 3,4-PCD. The amino acid sequences deduced from pcaHG matched the chemically determined sequence of 3,4-PCD in all except three positions. Cloning of pcaHG into broad-host-range expression vector pKMY319 allowed high levels of expression in P. putida strains, as well as in Proteus mirabilis after specific induction of the plasmid-encoded nahG promoter with salicylate. The recombinant enzyme was purified and crystallized from P. mirabilis, which lacks an endogenous 3,4-PCD. The physical, spectroscopic, and kinetic properties of the recombinant enzyme were indistinguishable from those of the wild-type enzyme. Moreover, the same transient enzyme intermediates were formed during the catalytic cycle. These studies establish the methodology which will allow mechanistic investigations to be pursued through site-directed mutagenesis of P. putida 3,4-PCD, the only aromatic ring-cleaving dioxygenase for which the three-dimensional structure is known.
Screening for Breast Cancer: An Update for the U.S. Preventive Services Task Force (2009)

Mammography screening reduces breast cancer mortality for women aged 39 to 69 years; data are insufficient for older women. False-positive mammography results and additional imaging are common. No benefit has been shown for clinical breast examination or breast self-examination.
Zinc and Alzheimer's Disease (1995)

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Management of an acute primary headache. (1998)

Effective management of primary (benign) headaches generally depends upon proper diagnosis and rational use of medications. Successful treatment requires adequate dosing plus choosing the optimal route for drug delivery. When oral remedies fail, transnasal, rectal, or parenteral therapy may succeed. While cure of headaches is not currently possible, control is possible for the majority of sufferers. Most patients can adequately treat their headaches without resorting to the doctor's office or emergency room. Many therapies may not only relieve head pain, but also alleviate associated symptoms.
Mitochondrial Membrane Potential in Axons Increases with Local Nerve Growth Factor or Semaphorin Signaling (2008)

Neurons concentrate mitochondria at sites in the cell that have a high demand for ATP and/or calcium buffering. To accomplish this, mitochondrial transport and docking are thought to respond to intracellular signaling pathways. However, the cell might also concentrate mitochondrial function by locally modulating mitochondrial activity. We tested this hypothesis by measuring the membrane potential of individual mitochondria throughout the axons of chick sensory neurons using the dye tetramethylrhodamine methylester (TMRM). We found no difference in the TMRM mitochondrial-to-cytoplasmic fluorescence ratio (F(m)/F(c)) among three functionally distinct regions: axonal branch points, distal axons, and the remaining axon shaft. In addition, we found no difference in F(m)/F(c) among stationary, retrogradely moving, or anterogradely moving mitochondria. However, F(m)/F(c) was significantly higher in the lamellipodia of growth cones, and among a small fraction of mitochondria throughout the axon. To identify possible signals controlling membrane potential, we used beads covalently coupled to survival and guidance cues to provide a local stimulus along the axon shaft. NGF- or semaphorin 3A-coupled beads caused a significant increase in F(m)/F(c) in the immediately adjacent region of axon, and this was diminished in the presence of the PI3 (phosphatidylinositol-3) kinase inhibitor LY294002 [2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one] or the MAP (mitogen-activated protein) kinase inhibitor U0126 (1,4-diamino-2,3-dicyano-1,4-bis[2-amino-phenylthio]butadiene), demonstrating that signaling pathways downstream of both ligands affect the DeltaPsi(m) of mitochondria. In addition, general inhibition of receptor tyrosine kinase activity produced a profound global decrease in F(m)/F(c). Thus, two guidance molecules that exert different effects on growth cone motility both elicit local, receptor-mediated increases in membrane potential.
Electrical doping is paving the way for the implementation of OLEDs in consumer electronics (2007)

Abstract The great potential of organic light‐emitting diodes (OLEDs) to replace current display and lighting technologies is no longer questioned. Nevertheless, before large‐scale production can commence, considerable advances in the OLED technology are still necessary to satisfy the corresponding challenging requirements and to be competitive with firmly established alternative technologies. In this context, significant progress in diode performance, lifetime and stability is achieved by employing electrically doped charge‐transport layers. Thus, the so‐called PIN technology allows for an early, successful implementation of OLEDs in consumer applications.
Centralized flow coordination for proportional fairness in enterprise wireless mesh networks (2010)

IEEE 802.11-based Enterprise WMNs (Wireless Mesh Networks) is one of possible practical extensions of WMNs. However, the wide adoption of Enterprise WMNs is limited by the flow unfairness problem due to the complicated interference relationship between adjacent nodes. To overcome this limitation, we propose FlowNet that centrally coordinates flows to implement a centralized source rate control algorithm in the Enterprise WMNs. By the cooperative operation between flow signalling and flow balancing methods, FlowNet provides proportional fairness among multiple flows in the Enterprise WMNs.
Varying complexity in tree-structured image distribution models (2006)

Probabilistic models of image statistics underlie many approaches in image analysis and processing. An important class of such models have variables whose dependency graph is a tree. If the hidden variables take values on a finite set, most computations with the model can be performed exactly, including the likelihood calculation, training with the EM algorithm, etc. Crouse et al. developed one such model, the hidden Markov tree (HMT). They took particular care to limit the complexity of their model. We argue that it is beneficial to allow more complex tree-structured models, describe the use of information theoretic penalties to choose the model complexity, and present experimental results to support these proposals. For these experiments, we use what we call the hierarchical image probability (HIP) model. The differences between the HIP and the HMT models include the use of multivariate Gaussians to model the distributions of local vectors of wavelet coefficients and the use of different numbers of hidden states at each resolution. We demonstrate the broad utility of image distributions by applying the HIP model to classification, synthesis, and compression, across a variety of image types, namely, electrooptical, synthetic aperture radar, and mammograms (digitized X-rays). In all cases, we compare with the HMT.