gebhart/patrepeval huggingface dataset:
Inhibition Assay of Biomolecules based on Fluorescence Resonance Energy Transfer (FRET) between Quantum Dots and Gold Nanoparticles (2005)

An inhibition assay method was developed based on the modulation in the FRET efficiency between quantum dots (QDs) and gold nanoparticles (AuNPs) in the presence of the molecules which inhibit the interactions between QD- and AuNP-conjugated biomolecules. For the functionalization, AuNPs were first stabilized by chemisorption of n-alkanethiols and then capped with the first generation polyamidoamine (G1 PAMAM) dendrimers. By employing a streptavidin-biotin couple as a model system, avidin was quantitatively analyzed as an inhibitor by sensing the change in photoluminescence (PL) quenching of SA-QDs by biotin-AuNPs. The detection limit for avidin was about 10 nM. It is anticipated that the PL quenching-based sensing system can be used for the quantitative analysis and high throughput screening of molecules which inhibit the specific biomolecular interactions.
Pesticides: Amounts Applied and Amounts Reaching Pests (1986)

Journal Article Pesticides: Amounts Applied and Amounts Reaching Pests Get access David Pimentel, David Pimentel Search for other works by this author on: Oxford Academic Google Scholar Lois Levitan Lois Levitan Search for other works by this author on: Oxford Academic Google Scholar BioScience, Volume 36, Issue 2, February 1986, Pages 86–91, https://doi.org/10.2307/1310108 Published: 01 February 1986
Resistance of Mice Deficient in IL-4 to Retrovirus-Induced Immunodeficiency Syndrome (MAIDS) (1993)

The murine acquired immunodeficiency syndrome (MAIDS) is induced by a defective murine leukemia virus and has many symptoms similar to those found in patients infected with the human immunodeficiency virus. The presence of both B cells and CD4+ T cells is critical for the development of the disease. Furthermore, a Th2 cytokine response dominates during the progression of the disease. When interleukin-4 (IL-4)-deficient mice that are defective in Th2 cytokine responses were infected, there was no lethality, and the development of the T cell abnormalities associated with MAIDS was delayed. These data suggest that IL-4 or a Th2 response is involved in the development of retrovirus-induced immunodeficiency in mice.
Parvovirus Expresses a Small Noncoding RNA That Plays an Essential Role in Virus Replication (2017)

Human bocavirus 1 (HBoV1) belongs to the species <i>Primate bocaparvovirus</i> of the genus <i>Bocaparvovirus</i> of the <i>Parvoviridae</i> family. HBoV1 causes acute respiratory tract infections in young children and has a selective tropism for the apical surface of well-differentiated human airway epithelia (HAE). In this study, we identified an additional HBoV1 gene, bocavirus-transcribed small noncoding RNA (BocaSR), within the 3' noncoding region (nucleotides [nt] 5199 to 5338) of the viral genome of positive sense. BocaSR is transcribed by RNA polymerase III (Pol III) from an intragenic promoter at levels similar to that of the capsid protein-coding mRNA and is essential for replication of the viral DNA in both transfected HEK293 and infected HAE cells. Mechanistically, we showed that BocaSR regulates the expression of HBoV1-encoded nonstructural proteins NS1, NS2, NS3, and NP1 but not NS4. BocaSR is similar to the adenovirus-associated type I (VAI) RNA in terms of both nucleotide sequence and secondary structure but differs from it in that its regulation of viral protein expression is independent of RNA-activated protein kinase (PKR) regulation. Notably, BocaSR accumulates in the viral DNA replication centers within the nucleus and likely plays a direct role in replication of the viral DNA. Our findings reveal BocaSR to be a novel viral noncoding RNA that coordinates the expression of viral proteins and regulates replication of viral DNA within the nucleus. Thus, BocaSR may be a target for antiviral therapies for HBoV and may also have utility in the production of recombinant HBoV vectors.<b>IMPORTANCE</b> Human bocavirus 1 (HBoV1) is pathogenic to humans, causing acute respiratory tract infections in young children. In this study, we identified a novel HBoV1 gene that lies in the 3' noncoding region of the viral positive-sense genome and is transcribed by RNA polymerase III into a noncoding RNA of 140 nt. This bocavirus-transcribed small RNA (BocaSR) diverges from both adenovirus-associated (VA) RNAs and Epstein-Barr virus-encoded small RNAs (EBERs) with respect to RNA sequence, representing a third species of this kind of Pol III-dependent viral noncoding RNA and the first noncoding RNA identified in autonomous parvoviruses. Unlike the VA RNAs, BocaSR localizes to the viral DNA replication centers of the nucleus and is essential for expression of viral nonstructural proteins independent of RNA-activated protein kinase R and replication of HBoV1 genomes. The identification of BocaSR and its role in virus DNA replication reveals potential avenues for developing antiviral therapies.
Unifying Messaging, Queuing, Streaming and Light Weight Compute for Online Event Processing (2019)

Online event processing are abound ranging from web and mobile applications to data processing. Such event processing applications often require the ability to ingest, store, dispatch and process events. Until now, supporting all of these needs has required different systems for each task -- stream processing engines, messaging queuing middleware, and pub/sub messaging systems. This has led to the unnecessary complexity for the development of such applications and operations leading to increased barrier to adoption in the enterprises.
Validation of tumor‐associated macrophage ferritin light chain as a prognostic biomarker in node‐negative breast cancer tumors: A multicentric 2004 national PHRC study (2011)

Novel prognostic biomarkers are imperatively needed to help direct treatment decisions by typing subgroups of node-negative breast cancer patients. Large screening of different biological compartments, such as the proteome, by means of high throughput techniques may greatly help scientists to find such markers. The present retrospective multicentric study included 268 node-negative breast cancer patients. We used a proteomic approach of SELDI-TOF-MS screening to identify differentially expressed cytosolic proteins with prognostic impact. The screening cohort was composed of 198 patients. Seventy supplementary patients were included for validation. Immunohistochemistry (IHC) and immunoassay (IA) were run to confirm the prognostic role of the marker identified by SELDI-TOF-MS screening. IHC was also used to explore links between selected marker and epithelial-mesenchymal transition (EMT)-like, proliferation and macrophage markers. Ferritin light chain (FTL) was identified as an independent prognostic marker (HR = 1.30-95% CI: 1.10-1.50, p = 0.001). Validation step by means of IHC and IA confirmed the prognostic value of FTL level. CD68 IHC showed that FTL was stored in tumor-associated macrophages (TAM), which exhibit an M2-like phenotype. We report here, first, the validation of FTL as a breast tumor prognostic biomarker in node-negative patients, and second, the fact that FTL is stored in TAM.
New development of integrated CT simulation system for radiation therapy planning. (1993)

In order to put more accurate radiotherapy into practice, a radiotherapy planning system using CT, which is named CT simulation system, has been developed and introduced at Kobe University Hospital. The CT simulation system consists of a CT scanner, an image processing work-station, and a laser marking system. The target area of radiation is determined on each CT axial image or scout view in the work-station. Three-dimensional treatment planning is feasible on the basis of the two-dimensional tumor information in CT axial images. After setting treatment parameters, the contour of the radiation field on beam's eye view and the iso-center position are calculated by computer. This system makes it possible to choose an appropriate irradiation method and an optimal dose distribution. In the present study we examined the fundamental capability of this system. The laser marking system proved to have a very high degree of accuracy. The outcome of a phantom test raised the strong possibility that this system may be applied clinically. In addition to these basic findings, this paper describes preliminary clinical observations that support the good reproducibility of the radiation field projected with the CT simulator. In conclusion, this system is of high value for radiation therapy planning.
Two-dimensional block diagonal LMS adaptive algorithm (1993)

This paper is concerned with the development of a two-dimensional (2-D) adaptive filtering using block diagonal least mean squared (BDLMS) method. In this adaptive filtering scheme, the image is scanned and processed block by block in a diagonal fashion, and the filter weights are adjusted once per each block rather than once per each pixel. As a result, this method takes into account the correlations of the pixels along both vertical and horizontal directions. The properties of this 2-D adaptive filter, including convergence behavior, adaptation speed, and adaptation accuracy, have been studied. Simulation results are presented which indicate the effectiveness of the 2-D BDLMS when used for image enhancement and estimation applications.
Sex and strain differences in adult mouse cardiac repolarization: importance of androgens (2004)

Strain and gender differences observed in mouse cardiac repolarization can be explained by different androgen levels. As a consequence, androgens are major regulatory factors in cardiac repolarization and special attention should be paid to the hormonal status of the animal when studying hormonal regulation of cardiac repolarization.
Cord Blood Leptin and Adiponectin as Predictors of Adiposity in Children at 3 Years of Age: A Prospective Cohort Study (2009)

Lower cord blood leptin levels are associated with smaller size at birth but more pronounced weight gain in the first 6 months of life and higher BMI at 3 years of age. Cord blood adiponectin levels are also directly associated with birth weight for gestational age, inversely associated with weight gain in the first 6 months of life, and predict an increase in central adiposity at age 3 years.
Effects of insulin on perfused liver from streptozotocin-diabetic and untreated rats: carbon-13 NMR assay of pyruvate kinase flux (1987)

The effects of insulin in vitro on perfused liver from streptozotocin-diabetic rats and their untreated littermates during gluconeogenesis from either [3-13C]alanine + ethanol or [2-13C]pyruvate + NH4Cl + ethanol were studied by 13C NMR. A 13C NMR determination of the rate of pyruvate kinase flux under steady-state conditions of active gluconeogenesis was developed; this assay includes a check on the reuse of recycled pyruvate. The preparations studied provided gradations of pyruvate kinase flux within the confines of the assay's requirement of active gluconeogenesis. By this determination, the rate of pyruvate kinase flux was 0.74 +/- 0.04 of the gluconeogenic rate in liver from 24-h-fasted controls; in liver from 12-h-fasted controls, relative pyruvate kinase flux increased to 1.0 +/- 0.2. In diabetic liver, this flux was undetectable by our NMR method. Insulin's hepatic influence in vitro was greatest in the streptozotocin model of type 1 diabetes: upon treatment of diabetic liver with 7 nM insulin in vitro, a partial reversal of many of the differences noted between diabetic and control liver was demonstrated by 13C NMR. A major effect of insulin in vitro upon diabetic liver was the induction of a large increase in the rate of pyruvate kinase flux, bringing relative and absolute fluxes up to the levels measured in 24-h-fasted controls. By way of comparison, the effects of ischemia on diabetic liver were studied by 13C NMR to test whether changes in allosteric effectors under these conditions could also increase pyruvate kinase flux. A large increase in this activity was demonstrated in ischemic diabetic liver.
A monoclonal antibody to a membrane glycoprotein binds only to activated platelets. (1984)

Rearrangements of membrane glycoproteins are believed to occur during platelet activation, but these changes have not been well defined. We have developed a monoclonal antibody, named S12, which demonstrates dramatically enhanced binding to platelets after thrombin activation. Unstimulated gel-filtered platelets from 12 normal individuals bound only 800 +/- 470 (S.D.) 125I-S12 molecules/cell, while platelets stimulated with 0.5 unit/ml of thrombin bound 9,600 +/- 2,600 molecules/cell (KD = 1.5 nM). Increasing thrombin concentrations produced similar increases in platelet 125I-S12 binding and [14C]serotonin secretion. S12 binding was not dependent on divalent cations. ADP and epinephrine, which caused no [14C]serotonin secretion, had little or no effect on S12 binding. We isolated the S12 binding protein by affinity chromatography of Lubrol PX-solubilized human platelet membranes on S12-agarose. When analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the isolated protein stains with both periodic acid-Schiff and Coomassie Blue and has an apparent molecular weight of 138,000 (unreduced) and 148,000 (reduced). After radioiodination of intact platelets the protein was also labeled, with apparently equal intensity in both control and thrombin-stimulated cells. The protein's staining, radiolabeling properties, and mobility on sodium dodecyl sulfate gels relative to glycoprotein IIb-IIIa fit previously defined criteria for membrane glycoprotein IIa. Our studies provide further evidence for alterations in membrane glycoproteins after platelet stimulation and suggest that S12 may serve as a useful probe of in vivo platelet activation.
Maintenance of Epstein–Barr virus (EBV) oriP -based episomes requires EBV-encoded nuclear antigen-1 chromosome-binding domains, which can be replaced by high-mobility group-I or histone H1 (2001)

EBV-encoded nuclear antigen-1 (EBNA-1) binding to a cis-acting viral DNA element, oriP, enables plasmids to persist in dividing human cells as multicopy episomes that attach to chromosomes during mitosis. In investigating the significance of EBNA-1 binding to mitotic chromosomes, we identified the basic domains of EBNA-1 within amino acids 1-89 and 323-386 as critical for chromosome binding. In contrast, the EBNA-1 C terminus (amino acids 379-641), which includes the nuclear localization signal and DNA-binding domain, does not associate with mitotic chromosomes or retain oriP plasmid DNA in dividing cell nuclei, but does enable the accumulation of replicated oriP-containing plasmid DNA in transient replication assays. The importance of chromosome association in episome maintenance was evaluated by replacing EBNA-1 amino acids 1-378 with cell proteins that have similar chromosome binding characteristics. High-mobility group-I amino acids 1-90 or histone H1-2 could substitute for EBNA-1 amino acids 1-378 in mediating more efficient accumulation of replicated oriP plasmid, association with mitotic chromosomes, nuclear retention, and long-term episome persistence. These data strongly support the hypothesis that mitotic chromosome association is a critical factor for episome maintenance. The replacement of 60% of EBNA-1 with cell protein is a significant step toward eliminating the need for noncellular protein sequences in the maintenance of episomal DNA in human cells.
Cell vacuolization induced by Helicobacter pylori: Inhibition by bafilomycins A1, B1, C1 and D (1993)

All available bafilomycins (A1, B1, C1 and D) inhibit and revert macroscopic vacuolization induced by Helicobacter pylori cell-free extracts. Bafilomycin A1 displays the highest activity, followed by bafilomycin B1, C1 and D. The different potency of bafilomycins correlates with their ability to inhibit the vacuolar-type ATPase (V-ATPase) and to dissipate the membrane pH gradient of intracellular acidic organelles. These results suggest that bafilomycins should be considered as possible therapeutic agents in the treatment of gastritis.
XCo: Explicit Coordination for Preventing Congestion in Data Center Ethernet (2010)

Cluster-based storage systems increasingly use commodity communication technologies, such as Fibre Channel over Ethernet (FCoE), for accessing stored data over the network. Data is striped over multiple storage nodes, and storage traffic often shares the network with non-storage traffic. In such conditions, storage clients can experience severely degraded performance, such as TCP throughput collapse and network congestion due to competing network traffic. Furthermore, consolidation of multiple virtual machines (VMs) onto fewer physical nodes can worsen the performance of network storage systems. The root cause of this performance problem is that network traffic from multiple sources can cause transient overloads in the switch buffers. In this paper, we make the case that virtualization opens up a new set of opportunities to alleviate and solve such performance problems experienced by network storage in particular, and data center Ethernet in general. We present an architecture, called XCo, for explicit coordination of network traffic among VMs in a data center Ethernet that is inexpensive, fully transparent, currently feasible, and complementary to any switch-level hardware support. We present experimental evidence via proof-of-concept implementation and evaluation to support this claim and describe the challenges and opportunities in a complete solution.
Cytotoxic activity of the maytansinoid immunoconjugate B-B4–DM1 against CD138+ multiple myeloma cells (2004)

We tested the in vitro and in vivo antitumor activity of the maytansinoid DM1 (N(2')-deacetyl-N(2')-(3-mercapto-1-oxopropyl)-maytansine), a potent antimicrotubule agent, covalently linked to the murine monoclonal antibody (mAb) B-B4 targeting syndecan-1 (CD138). We evaluated the in vitro activity of B-B4-DM1 against a panel of CD138(+) and CD138(-) cell lines, as well as CD138(+) patient multiple myeloma (MM) cells. Treatment with B-B4-DM1 selectively decreased growth and survival of MM cell lines, patient MM cells, and MM cells adherent to bone marrow stromal cells. We further examined the activity of B-B4-DM1 in 3 human MM models in mice: (1) severe combined immunodeficient (SCID) mice bearing subcutaneous xenografts; (2) SCID mice bearing green fluorescent protein-positive (GFP(+)) xenografts; and (3) SCID mice implanted with human fetal bone (SCID-hu) and subsequently injected with patient MM cells. Tumor regression and inhibition of tumor growth, improvement in overall survival, and reduction in levels of circulating human paraprotein were observed in mice treated with B-B4-DM1. Although immunohistochemical analysis demonstrates restricted CD138 expression in human tissues, the lack of B-B4 reactivity with mouse tissues precludes evaluation of its toxicity in these models. In conclusion, B-B4-DM1 is a potent anti-MM agent that kills cells in an antigen-dependent manner in vitro and mediates in vivo antitumor activity at doses that are well tolerated, providing the rationale for clinical trials of this immunoconjugate in MM.
Direct interaction between the TnsA and TnsB subunits controls the heteromeric Tn7 transposase (2013)

The transposon Tn7 transposase that recognizes the transposon ends and mediates breakage and joining is heteromeric. It contains the Tn7-encoded proteins TnsB, which binds specifically to the transposon ends and carries out breakage and joining at the 3' ends, and TnsA, which carries out breakage at the 5' ends of Tn7. TnsA apparently does not bind specifically to DNA, and we have hypothesized that it is recruited to the ends by interaction with TnsB. In this work, we show that TnsA and TnsB interact directly and identify several TnsA and TnsB amino acids involved in this interaction. We also show that TnsA can stimulate two key activities of TnsB, specific binding to the ends and pairing of the Tn7 ends. The ends of Tn7 are structurally asymmetric (i.e., contain different numbers of TnsB-binding sites), and Tn7 also is functionally asymmetric, inserting into its specific target site, attachment site attTn7 (attTn7) in a single orientation. Moreover, Tn7 elements containing two Tn7 right ends can transpose, but elements with two Tn7 left ends cannot. We show here that TnsA + TnsB are unable to pair the ends of a Tn7 element containing two Tn7 left ends. This pairing defect likely contributes to the inability of Tn7 elements with two Tn7 left ends to transpose.
Prevalence, Diagnosis and Management of Pancreatic Cystic Neoplasms: Current Status and Future Directions (2015)

Cystic neoplasms of the pancreas are found with increasing prevalence, especially in elderly asymptomatic individuals. Although the overall risk of malignancy is very low, the presence of these pancreatic cysts is associated with a large degree of anxiety and further medical investigation due to concerns about malignancy. This review discusses the different cystic neoplasms of the pancreas and reports diagnostic strategies based on clinical features and imaging data. Surgical and nonsurgical management of the most common cystic neoplasms, based on the recently revised Sendai guidelines, is also discussed, with special reference to intraductal papillary mucinous neoplasm (IPMN; particularly the branch duct variant), which is the lesion most frequently identified incidentally. IPMN pathology, its risk for development into pancreatic ductal adenocarcinoma, the pros and cons of current guidelines for management, and the potential role of endoscopic ultrasound in determining cancer risk are discussed. Finally, surgical treatment, strategies for surveillance of pancreatic cysts, and possible future directions are discussed.
1-aminocyclobutane[11C]carboxylic acid, a potential tumor-seeking agent. (1979)

1-Aminocyclobutane[14C]carboxylic acid [C-14) ACBC] was incorporated preferentially by several tumor types in rats and hamsters. The agent was cleared rapidly from rat blood, attaining its maximum tissue concentrations within 30 min after i.v. injection. Carrier ACBC had little effect on the tissue distribution of (C-14) ACBC. This agent showed no affinity for a Staphylococcus aureus abscess in rats. The total excretion was low, 3.6% in 2 hr. (C-11) ACBC was synthesized in amounts up to 415 mCi (55% chemical yield) using our modified Bücherer-Strecker technique. Forty minutes were required for the two-step synthesis and chromatographic purification. ACBC was found to be nontoxic in three animal species. The radiation dose from (C-11) ACBC should be minimal. (C-11) ACBC thus appears to have good potential as a tumor-seeking agent, particularly when used with a positron emission computed tomograph.