gebhart/patrepeval huggingface dataset:
Survival analysis of genome-wide gene expression profiles of prostate cancers identifies new prognostic targets of disease relapse. (2003)

Current models of prostate cancer classification are poor at distinguishing between tumors that have similar histopathological features but vary in clinical course and outcome. Here, we applied classical survival analysis to genome-wide gene expression profiles of prostate cancers and preoperative prostate-specific antigen (PSA) levels from each patient, to identify prognostic markers of disease relapse that provide additional predictive value relative to PSA concentration. Three of approximately 200 probesets showing strongest correlation with relapse were identified as the gene for the putative calcium channel protein, trp-p8, with loss of trp-p8 mRNA expression associated with a significantly shorter time to PSA relapse-free survival. We observed subsequently that trp-p8 is lost in the transition to androgen independence in a prostate cancer xenograft model and in prostate cancer tissue from patients treated preoperatively with antiandrogen therapy, suggesting that trp-p8 is androgen regulated, and its loss may be associated with more advanced disease. The identification of trp-p8 and other proteins implicated in the phosphatidylinositol signal transduction pathway that are associated with prostate cancer outcome, both here and in other published work, suggests an integral role for this pathway in prostate carcinogenesis. Thus, our findings demonstrate that multivariable survival analysis can be applied to gene expression profiles of prostate cancers with censored follow-up data and used to identify molecular markers of prostate cancer relapse with strong predictive power and relevance to the etiology of this disease.
High Sensitivity Atomic Magnetometers and Their Applications (2007)

I will review recent progress in optical magnetometry techniques using spin-polarized alkali-metal atoms and discuss their applications for detection of nuclear magnetic resonance, biological magnetic fields, rotation sending, and fundamental physics tests.
Emerging landscape of oncogenic signatures across human cancers (2013)

Cancer therapy is challenged by the diversity of molecular implementations of oncogenic processes and by the resulting variation in therapeutic responses. Projects such as The Cancer Genome Atlas (TCGA) provide molecular tumor maps in unprecedented detail. The interpretation of these maps remains a major challenge. Here we distilled thousands of genetic and epigenetic features altered in cancers to ∼500 selected functional events (SFEs). Using this simplified description, we derived a hierarchical classification of 3,299 TCGA tumors from 12 cancer types. The top classes are dominated by either mutations (M class) or copy number changes (C class). This distinction is clearest at the extremes of genomic instability, indicating the presence of different oncogenic processes. The full hierarchy shows functional event patterns characteristic of multiple cross-tissue groups of tumors, termed oncogenic signature classes. Targetable functional events in a tumor class are suggestive of class-specific combination therapy. These results may assist in the definition of clinical trials to match actionable oncogenic signatures with personalized therapies.
A modified histochemical technique to visualize acetylcholinesterase-containing axons. (1985)

An improved histochemical method for light microscopic demonstration of acetylcholinesterase (AChE) has been developed. Axonal, dendritic, and perikaryal staining are well delineated, both in areas of low AChE content, such as cerebral cortex, and in areas of high AChE content, such as neostriatum. Axonal staining, including arborizations, stands out against a clear background devoid of diffuse reaction product.
Reconciling pastoral agriculture and nature conservation: developing a co-management approach in the English uplands (2012)

The article assesses the influence of the Common Agricultural Policy (CAP) on the pastoral farming systems in a National Park within the south west of England and more recent attempts to use innovative and participatory techniques to reconcile pastoral farming systems with wildlife management. The paper confirms evidence that the economic sustainability of farm businesses in the UK involved in pastoral farming is reducing, and that wildlife-orientated schemes are changing traditional farming systems in a way that might not be in the long-term interest of wildlife. The data gathered raise questions about the cost-effectiveness of the current environmental approaches, which are government-run with centrally determined prescriptions relating to the natural resource and wildlife. Drawing on the concept of co-management, an alternative approach is identified and explored with both farmers and nature conservation regulators. This approach places more emphasis upon adjusting the traditional farming system of this marginal type of farming to align with the sustainable management of a fragile ecosystem.
Preparation of Oriented Zeolite UTD-1 Membranes via Pulsed Laser Ablation (1998)

Thin films of the high silica zeolite UTD-1 have been prepared by using pulsed laser ablation onto polished silicon and for the first time on porous stainless steel disks. A post hydrothermal treatment of the laser deposited films in a UTD-1 synthesis gel results in oriented crystal growth. Densely packed planklike crystals of UTD-1 grow from the laser deposited film resulting in the ultra-large pores of UTD-1 oriented perpendicular to the support. The oriented UTD-1 membrane grown on porous stainless steel was evaluated for the room temperature separation of a n-heptane/toluene mixture, and selective permeation of the paraffin was observed.
Sterilisation of canine anterior cruciate allografts by gamma irradiation in argon. Mechanical and neurohistological properties retained one year after transplantation (1995)

Bone-ACL-bone allograft transplantation is a potential solution to the problem of reconstruction of the anterior cruciate ligament (ACL), but sterilisation by gamma irradiation or ethylene oxide causes degradation of the graft. We have studied the biomechanical and histological properties of deep-frozen canine bone-ACL-bone allografts sterilised by gamma irradiation (2.5 Mrad) under argon gas protection. Particular attention was paid to their collagen structure and neuroanatomy compared with those of non-irradiated allografts. We used 60 skeletally mature foxhounds. In 30 animals one ACL was replaced by an irradiated allograft and in the other 30 a non-irradiated graft was used. In both groups the graft was augmented by a Kennedy Ligament Augmentation Device. Examination of the allografts at 3, 6 and 12 months after implantation included mechanical testing, histology, collagen morphometry, neuroanatomical morphology (silver and gold chloride stain) and studies of the microvasculature (modified Spalteholz technique). At 12 months the irradiated ACL allografts failed at a mean maximum load of 718.3 N, 63.8% of the strength of the normal canine ACL. The non-irradiated allografts failed at 780.1 N, 69.1% of normal. All the allografts showed a well-orientated collagen structure one year after transplantation and there was no difference between the irradiated grafts and the others. The silver staining technique demonstrated Golgi tendon organs and free nerve endings within both groups of allografts. As in the normal ACL these structures were most commonly found near the surface of the graft and at its bony attachments. At 12 months the irradiated allografts showed slight hypervascularity compared with the non-irradiated grafts.(ABSTRACT TRUNCATED AT 250 WORDS)
Radioimmunoguided surgery in colorectal cancer using a genetically engineered anti-CEA single-chain Fv antibody. (2000)

In radioimmunoguided surgery (RIGS), a radiolabeled antibody is given i.v. before surgery and a hand-held gamma-detecting probe is used to locate tumor in the operative field. The rapid blood clearance and good tumor penetration of single-chain Fv antibodies (scFv) offer potential advantages over larger antibody molecules used previously for RIGS. A Phase I clinical trial is reported on RIGS with scFv (MFE-23-his) to carcinoembryonic antigen (CEA). Thirty-four patients undergoing surgery for colorectal carcinoma (17 primary tumors, 16 liver metastases, and 1 anastomotic recurrence) and 1 patient with liver metastases of pancreatic carcinoma received 125I-labeled MFE-23-his scFv (125I-MFE-23-his) 24, 48, 72, or 96 h before operation. 125I-MFE-23-his showed biexponential blood clearance with alpha and beta half-lives of 0.32 and 10.95 h, respectively. The abdomen was scanned during surgery with a hand-held gamma detecting probe (Neoprobe Corp.). 125I-MFE-23-his showed good tumor localization; comparison with histology showed overall accuracy of 84%. Highest median ratios for tumor:normal tissue and tumor:blood were recorded 72 or 96 h after scFv injection for patients undergoing resection of liver metastases. High levels of radioactivity were found in the kidneys. Five patients had grade 1 fever, and three had a grade 1 rise in blood pressure according to the Common Toxicity Criteria. There was a significant correlation between these ratios and those measured in excised tissues using a laboratory gamma counter (P < 0.001). MFE-23-his scFv antibody localizes in CEA-producing carcinomas. The short interval between injection and operation, the lack of significant toxicity, and the relatively simple production in bacteria make MFE-23-his scFv suitable for RIGS.
Vaccinia Virus A36R Membrane Protein Provides a Direct Link between Intracellular Enveloped Virions and the Microtubule Motor Kinesin (2004)

Previous work demonstrated that intracellular enveloped vaccinia virus virions use microtubules to move from the site of membrane wrapping to the cell periphery. The mechanism and direction of intracellular virion movement predicted that viral proteins directly or indirectly interact with the microtubule motor protein kinesin. The yeast two-hybrid assay was used to test for interactions between the light chain of kinesin and the cytoplasmic tails from five viral envelope proteins. We found that the N-terminal tetratricopeptide repeat region of the kinesin light chain (KLC-TPR) interacted with the cytoplasmic tail of the viral A36R protein. A series of C- and N-terminal truncations of A36R further defined a region from residues 81 to 111 that was sufficient for interaction with KLC-TPR. Interactions were confirmed by using pull-down assays with purified glutathione S-transferase (GST)-A36R and (35)S-labeled KLC-TPR. The defined region on A36R for interaction with kinesin overlaps the recently defined region (residues 91 to 111) for interaction with the A33R envelope protein. The yeast three-hybrid system was used to demonstrate that expression of A33R interrupted the interaction between A36R and KLC-TPR, indicating that the binding of A36R is mutually exclusive to either A33R or kinesin. Pull-down assays with purified GST-A36R and (35)S-labeled KLC-TPR in the presence of competing A33R corroborated these findings. Collectively, these results demonstrated that the viral A36R protein interacts directly with the microtubule motor protein kinesin and that the viral protein A33R may regulate this interaction.
A General and Mild Ullmann-Type Synthesis of Diaryl Ethers (2004)

[reaction: see text] An efficient method for the synthesis of diaryl ethers under particularly mild conditions is described. Inexpensive ligands were found to greatly accelerate the Ullmann-type coupling of aryl bromides or iodides with phenols. A series of diaryl ethers were obtained with excellent yields in acetonitrile in the presence of Cs(2)CO(3) and catalytic copper(I) oxide. The reaction tolerates substrates with unfavorable substitution patterns, such as sterically hindered coupling partners or electron-rich aryl halides.
Prime-boost regimens with adjuvanted synthetic long peptides elicit T cells and antibodies to conserved regions of HIV-1 in macaques (2011)

The present results encourage evaluation of the SLP.HIVconsv vaccine modality in human volunteers along the currently trialled pSG2.HIVconsv DNA, ChAdV63.HIVconsv and MVA.HIVconsv vaccines. These results are discussed in the context of the RV144 trial outcome.
Pruritus in patients with chronic liver disease and serum autotaxin levels in patients with primary biliary cholangitis (2019)

The frequency of pruritus was high in patients with chronic liver disease. Reduction of liver function is associated with severe pruritus based on the large number of patients with chronic liver disease. Serum autotaxin is useful for assessing liver fibrosis and severity of cholangitis; however, it is not a predictive marker for severe pruritus in patients with PBC.
Lipophilicity-antifungal activity relationships for some isoflavonoid phytoalexins (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLipophilicity-antifungal activity relationships for some isoflavonoid phytoalexinsAnna Arnoldi and Lucio MerliniCite this: J. Agric. Food Chem. 1990, 38, 3, 834–838Publication Date (Print):March 1, 1990Publication History Published online1 May 2002Published inissue 1 March 1990https://pubs.acs.org/doi/10.1021/jf00093a052https://doi.org/10.1021/jf00093a052research-articleACS PublicationsRequest reuse permissionsArticle Views252Altmetric-Citations26LEARN 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
The Office Marathon: Robust navigation in an indoor office environment (2010)

This paper describes a navigation system that allowed a robot to complete 26.2 miles of autonomous navigation in a real office environment. We present the methods required to achieve this level of robustness, including an efficient Voxel-based 3D mapping algorithm that explicitly models unknown space. We also provide an open-source implementation of the algorithms used, as well as simulated environments in which our results can be verified.
Phase II and pharmacokinetic study of aziridinylbenzoquinone [2,5-diaziridinyl-3,6-bis(carboethoxyamino)-1,4-benzoquinone, diaziquone, NSC 182986] in high-grade gliomas. (1983)

2,5-Diaziridinyl-3,6-bis(carboethoxyamino)-1,4-benzoquinone (AZQ; Diaziquone, NSC 182986) is a rationally designed antitumor drug possessing sufficient lipid solubility to allow penetration into the central nervous system. Thirty-one patients with high-grade glioma and progressive disease following radiation, with or without previous chemotherapy, have been treated with 144 cycles of drug, consisting of 20 mg/sq m given as an i.v. infusion on Days 1 and 8 of a 28-day cycle. Responses were measured by serial computer tomography scanning. Of the 28 evaluable patients, 6 (21%) had limited improvement (10 to 40% reduction in tumor size) on computer tomography scan, 10 (36%) had disease stabilization, and 12 (43%) had progressive disease. The drug was well tolerated clinically, with little acute toxicity. The major toxicity was myelosuppression, which appeared cumulative, using this dose regimen. AZQ was measurable in both tumor tissue and tumor cyst fluid in patients on therapy. Plasma samples taken during the period of infusion confirm that 50% or more of the total AZQ exposure occurs during the infusion period. AZQ behaves as intended by design and demonstrates activity in this poor-prognosis group of patients.
Is the "drug holiday" harmful? (1976)

The “drug holiday” has been recently supposed to be necessary in order to protect psychotic patients who have been taking neuroleptics for a long time against the occurance of tardive dyskinesia. But from the fact that neuroleptics have some hormonal, metabolic and autonomic nervous effects besides mental ones, it is reasonable to assume that sudden intermittent withdrawal of neuro-leptics (“drug holiday”) is followed by rebound phenomena such as changes of blood pressure, increase of blood free fatty acids, increase of blood serotonin, and increase of growth-hormone release-inhibiting hormone etc. These rebound phenomena may be consistent with the ischemic heart diseases, the kinds of embolism, and the sudden deaths that are supposed to have a higher incidence among psychotic patients: and the obesity and diabetes that are supposed to be caused by neuroleptics. It remains, however, to be investigated how to decide and decrease the dosage of psychotropic drugs more safely.
Removal of Group B Streptococci Colonizing the Vagina and Oropharynx of Mice with a Bacteriophage Lytic Enzyme (2004)

Group B streptococci (GBS) are the leading cause of neonatal meningitis and sepsis worldwide. The current treatment strategy is limited to intrapartum antibiotic prophylaxis in pregnant women to prevent early-onset neonatal diseases, but considering the potential for antibiotic resistance, the risk of losing control over the disease is high. To approach this problem, we have developed a bacteriophage (phage) lytic enzyme to remove colonizing GBS. Bacteriophage muralytic enzymes, termed lysins, are highly evolved molecules designed to degrade the cell wall of host bacteria to release phage particles from the bacterial cytoplasm. Several different lysins have been developed to specifically kill bacterial pathogens both on mucosal surfaces and in blood and represent a novel approach to control infection. A lysin cloned from a phage infecting GBS was found to contain two putative catalytic domains and one putative binding domain, which is similar to the domain organization of some staphylococcal phage lysins. The lysin (named PlyGBS) was recombinantly expressed in Escherichia coli, and purified PlyGBS efficiently killed all tested GBS serotypes in vitro. In a mouse model, a single dose of PlyGBS significantly reduced bacterial colonization in both the vagina and oropharynx. As an alternative strategy for intrapartum antibiotic prophylaxis, this approach may be used to reduce vaginal GBS colonization in pregnant women before delivery or to decontaminate newborns, thus reducing the incidence of GBS-associated neonatal meningitis and sepsis.
Lymphocyte membrane IgG and secreted IgG are structurally and allotypically distinct. (1980)

We have demonstrated that there are structurally distinct membrane and secreted IgG2a immunoglobulin molecules. The membrane heavy chain is both larger and more acidic than the secreted molecule. This difference is not a result of different N-glycosidic-linked oligosaccharide chains. The membrane heavy chain also is antigenically different from its secreted homologue. This is based on the fact that secreted IgG2a molecules express an allotypic determinant absent on membrane molecules. We discussed the genetic control and gene organization of membrane and secreted immunoglobulin heavy chain sequences and suggest mechanisms controlling the expression of the simian virus 40 genome as models for alternate gene expression of membrane and secreted heavy chain polypeptide chains from the same DNA sequence. The possible biological significance of the membrane immunoglobulin acting as a recognition site for regulatory T cells also is discussed. The difference between membrane and secreted immunoglobulin is proposed as a possible explanation for the manner in which T cells interact with IgG on memory B cells in the presence of a large excess of IgG present in body fluids.
Use of a reamplification protocol improves sensitivity of detection of Mycobacterium tuberculosis in clinical samples by amplification of DNA (1991)

We have compared the sensitivity and specificity of quantitative mycobacterial culture against results obtained by using the polymerase chain reaction for the detection of DNA from organisms of the Mycobacterium tuberculosis complex in 82 clinical specimens from patients suspected of having tuberculosis. Two amplification protocols were used, a standard amplification protocol, which amplifies a segment of the gene coding for the 65-kDa antigen, and a protocol in which the initial amplification products are reamplified with a second set of nested oligonucleotide primers. Although the standard amplification protocol gave positive results for 18 of 18 samples which grew greater than 100 CFU/ml and gave positive results in 4 of 35 specimens from patients with tuberculosis which were negative by culture, only 1 of 6 samples which grew less than 100 CFU/ml was positive. This lack of sensitivity could not be explained by the presence of inhibitors of Taq polymerase present in the original samples. In contrast, the reamplification protocol gave positive results for 24 of 24 samples which were positive by culture as well as for 13 of 35 samples from patients with tuberculosis which were negative by culture (overall sensitivity, 63%, P less than 0.02, compared with the standard amplification protocol and routine culture). Two of 23 samples from patients not diagnosed as having tuberculosis gave positive results when the standard amplification protocol was used, but no additional false-positive results were seen with the reamplification protocol (overall specificity, 91%). We conclude that the use of a reamplification protocol improves the sensitivity of detection of mycobacterial DNA in clinical samples without sacrificing specificity. The sensitivity of this approach appears to be superior to that of standard culture techniques.
Towards Software Defined Autonomic Terabit Optical Networks (2014)

This paper presents an Optical SDN architecture and implementation enabled for virtual optical networks, supporting adaptive and cognitive algorithms to enhance QoT. The paper also shows experimental results of a software-defined autonomic flexible transponder.
Creation of nanopores on graphene planes with MgO template for preparing high-performance supercapacitor electrodes (2014)

Creation of nanopores on graphene planar sheets is of great significance in promoting the kinetic diffusion of electrolyte and enhancing the utilization efficiency of graphene planar sheets. Herein, we developed a facile chemical vapor deposition strategy to prepare highly porous graphene with flake-like MgO as template and ferrocene as the carbon precursor. The graphene layers show a highly porous structure with small mesopores of 4-8 nm, large mesopores of 10-20 nm and additional macropores of 100-200 nm. These nanopores on graphene sheets provide numerous channels for fast ion transport perpendicular to the 2D basal plane, while the good powder conductivity ensures an effective electron propagation within the 2D graphene plane. As a result, a specific capacitance of 303 F g(-1), an areal capacitance up to 17.3 μF cm(-2) and a nearly tenfold shorter time constant were achieved when compared with those of nonporous and stacked graphene electrodes. The method demonstrated herein would open up an opportunity to prepare porous graphene for a wide applications in energy storage, biosensors, nanoelectronics and catalysis.