gebhart/patrepeval huggingface dataset:
Homology model of the dengue 2 virus NS3 protease: putative interactions with both substrate and NS2B cofactor. (1999)

The crystal structure coordinates of the hepatitis C virus NS3 protease (HCVpro) were used to develop an homology model of the dengue 2 virus NS3 protease (DEN2pro). The amino acid sequence of DEN2pro accommodates the same alpha-helices, beta-sheets and protein-binding domains as its HCVpro counterpart, but the model predicts a number of significant differences for DEN2pro and its interactions with substrates and cofactor. Whereas HCVpro contains a Zn2+-binding site, there is no equivalent metal-binding motif in DEN2pro. It is possible that the structural role played by the zinc ion may be provided by a salt bridge between Glu93 and Lys145. The two-component viral protease comprises NS3 and a virus-encoded cofactor, NS4A for HCV and NS2B for DEN2. Previous studies have identified a central 40 amino acid cofactor domain of the dengue virus NS2B that is required for protease activity. Modelling of the putative interactions between DEN2pro and its cofactor suggests that a 12 amino acid hydrophobic region within this sequence (70GSSPILSITISE81) may associate directly with NS3. Modelling also suggests that the substrate binds in an extended conformation to the solvent-exposed surface of the protease, with a P1-binding site that is significantly different from its HCV counterpart. The model described in this study not only reveals unique features of the flavivirus protease but also provides a structural basis for both cofactor and substrate binding that should prove useful in the early design and development of inhibitors.
10-propargyl-10-deazaaminopterin: an antifolate with activity in patients with previously treated non-small cell lung cancer. (2003)

The broad applicability of this new antifolate with limited toxicity and proven efficacy in NSCLC encourage further development of this compound. Several trials are now underway combining PDX with other chemotherapeutic agents and testing its efficacy in other cancers.
Human oligodendrocytes from embryonic stem cells: conserved SHH signaling networks and divergent FGF effects (2009)

Human embryonic stem cells (hESCs) offer a platform to bridge what we have learned from animal studies to human biology. Using oligodendrocyte differentiation as a model system, we show that sonic hedgehog (SHH)-dependent sequential activation of the transcription factors OLIG2, NKX2.2 and SOX10 is required for sequential specification of ventral spinal OLIG2-expressing progenitors, pre-oligodendrocyte precursor cells (pre-OPCs) and OPCs from hESC-derived neuroepithelia, indicating that a conserved transcriptional network underlies OPC specification in human as in other vertebrates. However, the transition from pre-OPCs to OPCs is protracted. FGF2, which promotes mouse OPC generation, inhibits the transition of pre-OPCs to OPCs by repressing SHH-dependent co-expression of OLIG2 and NKX2.2. Thus, despite the conservation of a similar transcriptional network across vertebrates, human stem/progenitor cells may respond differently to those of other vertebrates to certain extrinsic factors.
Frequency of UL97 Phosphotransferase Mutations Related to Ganciclovir Resistance in Clinical Cytomegalovirus Isolates (1995)

Cytomegalovirus (CMV) isolates from subjects who received ganciclovir therapy were tested for susceptibility to ganciclovir by a plaque reduction assay. Results were correlated with restriction enzyme and sequence analysis of the CMV UL97 phosphotransferase gene. Of the 30 isolates, 20 had one or more mutations in UL97 affecting amino acid encoding at codons 460, 520, or 591-596. All 20 were resistant to ganciclovir, with an IC50 of > 6.0 microM (range, 6.7-50.0). The remaining 10 isolates had no mutations at these loci; 8 were susceptible to ganciclovir while the other 2 were borderline resistant (IC50s, 6.6 and 7.2 microM). None of 40 control CMV isolates from untreated subjects contained any amino acid changes at these loci. The three most common mutations at codons 460, 594, and 595 were detected by restriction digest analysis in 16 (80%) of 20 isolates and in 16 (73%) of 22 isolates with ganciclovir IC50s > 6.0 microM. These results indicate that the majority of ganciclovir-resistant clinical isolates contain diagnostically useful mutations in UL97.
Maintenance Rituximab after CVP Results in Superior Clinical Outcome in Advanced Follicular Lymphoma (FL): Results of the E1496 Phase III Trial from the Eastern Cooperative Oncology Group and the Cancer and Leukemia Group B. (2005)

Abstract E1496 is a phase III trial designed to evaluate the ability of 2 years (yr) of maintenance rituximab (MR) to prolong progression-free survival (PFS) after CVP (cyclophosphamide 1 G/m2 day [d] 1, vincristine 1.4 mg/m2 [max = 2 mg] d 1, prednisone 100 mg/m2 d 1–5) chemotherapy in stage III–IV follicular grade 1 and 2 and small lymphocytic lymphoma. After CVP treatment to maximum response, (6–8 cycles), stable and responding patients (pt) were randomized to MR (375 mg/m2 weekly x 4) every 6 months x 4 or observation (OBS). Stratification factors included histology, response and residual disease after CVP. With 3-yr median follow-up, survivals (from time of randomization, one-sided logrank p values) for all pt (n=304) favored MR for PFS (p = 3 x 10–8; hazard rate {HR} = 0.38 [0.28;0.54, 95% confidence intervals]) and OS (p = 0.09; HR = 0.66 [0.36–1.22]). Because the large majority of pt have FL and because rituximab efficacy is notably greater in FL, we focused in this report on the 237 FL pt. Median age was 58 yr, 65% were stage IV, 64% had marrow disease, 64% had high tumor burden and 37% had high-risk disease by the follicular lymphoma prognostic index. PFS after randomization was significantly longer for MR vs OBS (p = 3 x 10-7; HR = 0.39 [0.27;0.57]). The estimated PFS at 4 yr (~4.5 yr after start of treatment) was 56% for MR vs 33% for OBS. Differences in PFS were significant within the predefined strata and the differences were most significant in favor of MR for pt with high initial tumor burden and minimal residual disease after CVP. Overall survival was superior for MR (p = 0.03; HR = 0.51 [0.25;1.04]. Estimated OS at 4 yr (~4.5 years after start of treatment) was 88% for MR vs 72% for OBS. Of 33 deaths, 21 occurred on the OBS arm. These data demonstrate that maintenance rituximab not only significantly delays disease progression in FL compared with OBS but that a substantial proportion of patients treated with MR remain disease-free at 4 years after the completion of CVP. These are the first data to strongly suggest a survival benefit with a therapy that includes rituximab and CVP and the first to strongly suggest a survival benefit with maintenance rituximab in FL.
Degos Disease (2011)

Degos disease is a lethal small vessel angiopathy targeting the skin, gastrointestinal tract, and central nervous system, potentially developing in the setting of known autoimmune disease, although forme fruste primary variants exist. Its pathogenetic basis is unknown. Four cases of Degos disease were encountered in archival material, representing 2 men, ages 38 and 43 years, and 2 females, ages 48 and 2 years; 3 patients died of disease. All had characteristic skin lesions with gastrointestinal involvement; other affected organs included brain in one and pericardium and pleura in another. Skin biopsies showed pauci-inflammatory thrombogenic microangiopathy with endothelial cell injury. Extracutaneous organs demonstrated fibromucinous occlusive arteriopathy. Prominent vascular C5b-9 was seen in the skin, gastrointestinal tract, and brain. All cases had evidence of high expression of interferon-α (based on tissue expression of MXA, a type I interferon-inducible protein), endothelial tubuloreticular inclusions, and an interferon gene signature in peripheral blood mononuclear cells. The MXA expression paralleled the pattern of C5b-9 deposition. Degos disease is a distinct vascular injury syndrome whereby a dysregulated interferon-α response in concert with membranolytic attack complex deposition may contribute to the unique vascular changes. Understanding the pathophysiology of the disease process could lead to more directed therapies, including terminal complement inhibition with agents such as eculizumab.
High Efficiency Composite Metal Oxide‐Polymer Electroluminescent Devices: A Morphological and Material Based Investigation (2008)

Composite metaloxide polymer based electroluminescent diodes are designed to obtain air stable operation along with sub-volt turn on and high brightness. We investigate different structures (mesoporous and compact) and different materials (TiO2 and ZnO) for electron injecting layers, and employ MoO3 for hole injecting layers. The highest efficiencies, close to 3 Cd A−1, are achieved using compact ZnO.
Progression and enhancement of metastatic potential after exposure of tumor cells to chemotherapeutic agents. (2001)

Data presented in this report indicate short-term in vitro treatment of nonmetastatic MCF-7 breast carcinoma cells with the chemotherapeutic agents-, Adriamycin and/or 5-fluoro-2'-deoxyuridine (FUdR), induced changes in the expressed phenotype. Cells treated sequentially with Adriamycin and FUdR expressed a metastatic phenotype. The results also show short-term exposure of MCF-7 cells to either Adriamycin or FUdR rapidly increases, in a dose-dependent manner, the release of the angiogenic cytokine, interleukin-8(IL-8), which is released at consistently higher levels in metastatic cell lines. Cell populations surviving a single treatment with either one or both of these chemotherapeutic agents continue to stably release IL-8. Survivors of sequential treatment with Adriamycin and FUdR (MCF-7 A/F) release the most IL-8 and express the greatest phenotypic variance from the parental, MCF-7 cells. Parental MCF-7 cells and MCF-7 A/F cells both form primary tumors when used in an orthotopic tumor model; however, the MCF-7 A/F tumors have a more rapid initial growth phase in situ and give rise to spontaneous lung metastases within 10 weeks. A cell line that is established from lung metastases releases more IL-8, has a higher cloning efficiency, and forms looser colonies in monolayer than do their parental cells. These experiments indicate the in vitro exposure of tumor cells to chemotherapeutic agents either selects more aggressive cells or enhances the metastatic potential of the surviving cells.
Rescue of p53 Function by Small-Molecule RITA in Cervical Carcinoma by Blocking E6-Mediated Degradation (2010)

Proteasomal degradation of p53 by human papilloma virus (HPV) E6 oncoprotein plays a pivotal role in the survival of cervical carcinoma cells. Abrogation of HPV-E6-dependent p53 destruction can therefore be a good strategy to combat cervical carcinomas. Here, we show that a small-molecule reactivation of p53 and induction of tumor cell apoptosis (RITA) is able to induce the accumulation of p53 and rescue its tumor suppressor function in cells containing high-risk HPV16 and HPV18 by inhibiting HPV-E6-mediated proteasomal degradation. RITA blocks p53 ubiquitination by preventing p53 interaction with E6-associated protein, required for HPV-E6-mediated degradation. RITA activates the transcription of proapoptotic p53 targets Noxa, PUMA, and BAX, and repressed the expression of pro-proliferative factors CyclinB1, CDC2, and CDC25C, resulting in p53-dependent apoptosis and cell cycle arrest. Importantly, RITA showed substantial suppression of cervical carcinoma xenografts in vivo. These results provide a proof of principle for the treatment of cervical cancer in a p53-dependent manner by using small molecules that target p53.
Bacterial virulence: can we draw the line? (2001)

The molecular approach to microbial pathogenesis has resulted in an impressive amount of data on bacterial virulence genes. Bacterial genome sequences rapidly add candidate virulence genes to electronic databases. The interpretation of this overwhelming information is obscured because every gene involved in pathogenicity is called a virulence gene, regardless of its function in the complex process of virulence. This review summarizes the changing concept of bacterial virulence and the detection and identification strategies followed to recognize virulence genes. A refined definition of virulence genes is proposed in which the function of the gene in the virulence process is incorporated. We propose to include the life-style of bacteria in the assessment of their putative virulence genes. A universal nomenclature in analogy to the EC enzyme numbering system is proposed. These recommendations would lead to a better insight into bacterial virulence and a more precise annotation of (putative) virulence genes, which would enable more efficient use of electronic databases.
Ultrasensitive DNA Detection Using Oligonucleotide−Silver Nanoparticle Conjugates (2008)

Oligonucleotide-gold nanoparticle (OGN) conjugates are powerful tools for the detection of target DNA sequences due to the unique properties conferred upon the oligonucleotide by the nanoparticle. Practically all the research and applications of these conjugates have used gold nanoparticles to the exclusion of other noble metal nanoparticles. Here we report the synthesis of oligonucleotide-silver nanoparticle (OSN) conjugates and demonstrate their use in a sandwich assay format. The OSN conjugates have practically identical properties to their gold analogues and due to their vastly greater extinction coefficient both visual and absorption analyses can occur at much lower concentrations. This is the first report of OSN conjugates being successfully used for target DNA detection and offers improved sensitivity which is of interest to a range of scientists.
The Oscillatory Potentials of the Dark-Adapted Electroretinogram in Retinopathy of Prematurity (2007)

Differences between OPs in healthy rats and healthy humans were substantial, suggesting that OPs in rat models of ROP are unlikely to provide insight into the effects of ROP on human OPs. Indeed, neither ROP model studied showed a pattern of effects similar to that in human ROP.
Learning message-passing inference machines for structured prediction (2011)

Nearly every structured prediction problem in computer vision requires approximate inference due to large and complex dependencies among output labels. While graphical models provide a clean separation between modeling and inference, learning these models with approximate inference is not well understood. Furthermore, even if a good model is learned, predictions are often inaccurate due to approximations. In this work, instead of performing inference over a graphical model, we instead consider the inference procedure as a composition of predictors. Specifically, we focus on message-passing algorithms, such as Belief Propagation, and show how they can be viewed as procedures that sequentially predict label distributions at each node over a graph. Given labeled graphs, we can then train the sequence of predictors to output the correct labeling s. The result no longer corresponds to a graphical model but simply defines an inference procedure, with strong theoretical properties, that can be used to classify new graphs. We demonstrate the scalability and efficacy of our approach on 3D point cloud classification and 3D surface estimation from single images.
Clinical heterogeneity of ATP13A2 linked disease (Kufor-Rakeb) justifies a PARK designation (2007)

In this issue of Neurology , Di Fonzo and colleagues describe the identification of a Brazilian patient with juvenile parkinsonism who carries a homozygous missense mutation in ATP13A2 .1 Mutation of this gene has been recently shown to underlie the autosomal recessive, l-dopa–responsive, pallido-pyramidal disease Kufor-Rakeb syndrome (KRS).

KRS was originally described by Al Din and colleagues in 1994, when they reported the clinical and radiologic features of five siblings born of a consanguineous marriage and living with their parents in the small homestead of Kufor-Rakeb in Jordan.2 Onset occurred between the ages of 12 and 15 years with lethargy and bradyphrenia evolving over several months culminating in social withdrawal and removal from schooling. Difficulties with walking due to stiffness and postural abnormalities started at around the same time. Within 2 years of onset problems with swallowing and articulating had appeared and assistance was required in several everyday tasks. Cognitive decline continued with slowness of thinking, perseveration, and utilization behavior …
Numerical Simulation of CO2 Flood Performance (1984)

Abstract A multicomponent, three-phase, three-dimensional (3D) reservoir simulator has been developed for predicting miscible flood performance with particular emphasis on CO2 flooding. Several features, not all normally found represented in either a black-oil or compositional simulator, are represented in the simulator described here. These features include (1) heavy-end dropout and concomitant reduction in phase mobility, (2) water blocking of oil from an invading solvent, (3) viscous instability (fingering) at the CO2 displacement front, (4) miscible/immiscible transition as a function of pressure and composition, and (5) loss of CO2 to the aqueous phase. The solution scheme employs an implicit in pressure, explicit in saturation and composition time integration scheme (IMPES). This scheme allows for ready use of a second-order correct spatial discretization. We have found that for field applications, a numerical grid fine enough to represent waterflood performance accurately is usually sufficient for representing CO2-miscible-type processes as well. The program automatically employs a stabilized Runge-Kutta time discretization to alleviate the usual stability limitations imposed by the IMPES procedure. Up to 49 times the usual stable timestep size can be employed for seven times as much computing work. Work required to simulate a given time period when stability is limiting was improved overall by a factor of seven. To date, we have not encountered a pattern flood displacement simulation where the increased timestep size provided by the Runge-Kutta scheme has not been adequate to maintain stability for timesteps chosen so as to limit truncation error. The CO2 flood simulator described has been in application for 4 years. The simulator has been used for design of CO2 EOR projects and interpretation of CO2 injectivity tests in several low-temperature west Texas San Andres dolomite reservoirs as well as high-temperature sandstone reservoirs. In addition to CO2 applications, the simulator has been used for the design of liquefied petroleum gas/dry gas flooding processes and for examining the effect of injection gas composition on oil recovery performance for immiscible gas drives.
Functional Consequences of Changing Proline Residues in the Phenylalanine-Specific Permease of Escherichia coli (1998)

The PheP protein is a high-affinity phenylalanine-specific permease of the bacterium Escherichia coli. A topological model based on genetic analysis involving the construction of protein fusions with alkaline phosphatase has previously been proposed in which PheP has 12 transmembrane segments with both N and C termini located in the cytoplasm (J. Pi and A. J. Pittard, J. Bacteriol. 178:2650-2655, 1996). Site-directed mutagenesis has been used to investigate the functional importance of each of the 16 proline residues of the PheP protein. Replacement of alanine at only three positions, P54, P341, and P442, resulted in the loss of 50% or more activity. Substitutions at P341 had the most dramatic effects. None of these changes in transport activity were, however, associated with any defect of the mutant protein in inserting into the membrane, as indicated by [35S]methionine labelling and immunoprecipitation using anti-PheP serum. A possible role for each of these three prolines is discussed. Inserting a single alanine residue at different sites within span IX and the loop immediately preceding it also had major effects on transport activity, suggesting an important role for a highly organized structure in this region of the protein.
Heart Failure (2003)

Heart failure is a costly and deadly condition that currently affects nearly 5 million Americans. The incidence approaches 10 per 1000 population among persons older than 65 years of age. This review highlights current pathophysiological concepts and discusses available therapies for a range of patients — from those at risk to those with widespread disease.
Fresh versus old blood: are there differences and do they matter? (2013)

The medical effects of transfusing stored RBCs is an area of significant concern that has received substantial attention in recent years. Retrospective trials show all possible outcomes, including sequelae from transfusing older RBCs, no difference between older and fresher RBCs, and a benefit to older RBCs. Several prospective clinical trials are under way to further investigate potential untoward effects of stored RBCs. Thus far, the issue of potential sequelae from transfusing stored RBCs remains a highly controversial issue. However, what is not controversial is that RBC storage is an unnatural state during which a series of substantial changes take place to the stored RBCs. These changes result in the formation of cellular and chemical entities known to have biological activities in other settings, giving rise to several distinct hypotheses by which stored RBCs may alter recipient biology. Herein, the clinical background and basic science of RBC storage are reviewed, with a particular focus on factors that may complicate hypothesis testing and obfuscate underlying biologies. The complexity of the RBC storage lesion, donor-to-donor variation, and the diversity of recipient pathophysiologies remain a challenge to prospective trials assessing the safety of stored RBCs.
Comparative Proteomic Analysis of Advanced Serous Epithelial Ovarian Carcinoma: Possible Predictors of Chemoresistant Disease (2011)

To identify specific proteins associated with chemotherapeutic responses, we analyzed protein expression patterns in stage IIIc primary serous epithelial ovarian cancer tissues displaying differential responses to first-line postoperative adjuvant chemotherapy. The expression profiles of five chemoresistant tissues [progression-free survival (PFS) ≤12 months] and five chemosensitive tissues (PFS ≥48 months) were analyzed with 2D electrophoresis, and the spot intensities of differentially expressed proteins were quantified. To validate these proteins as markers for chemoresistant disease, we analyzed tissues from an additional 17 patients. All the patients were allocated to the over- or underexpressing group according to protein spot intensity, and survival analysis was performed. In chemoresistant tissues, four proteins (thioredoxin domain containing four, similar to RIKEN cDNA 1700016G05, tubulin α 1A chain, and the pyruvate dehydrogenase E1-β subunit precursor) were overexpressed, and seven proteins [keratin 1, vitamin D-binding protein, creatine kinase B, annexin V, SH3-containing guanine nucleotide exchange factor (SGEF), tryptophan-aspartate repeat protein-1 (WDR 1), and WDR 1 isoform 1] were underexpressed. The underexpression of keratin 1, creatine kinase B, annexin V, SGEF, WDR1, and WDR1 isoform 1 were significantly correlated with poor overall survival. A combination of keratin 1 and SGEF showed the highest sensitivity of 0.800, specificity of 0.917, PPV of 0.800, and NPV of 0.917 in predicting chemoresistant disease. These proteins may be useful as predictive markers of chemoresistant disease. However, further analyses in large-scale should be performed before they can be considered reliable predictive markers of chemoresistant disease.