gebhart/patrepeval huggingface dataset:
Effects of Modifications of Residues in Position 3 of Dynorphin A(1−11)-NH2on κ Receptor Selectivity and Potency (1996)

Tyrosine1 and phenylalanine4 in dynorphin A (Dyn A) have been reported to be important residues for opioid agonist activity and for potency at kappa receptors. The glycine residues in the 2 and 3 positions of dynorphin A may affect the relative orientation of the aromatic rings in positions 1 and 4, but their flexibility precludes careful analysis. To examine these effects on dynorphin A, we previously have synthesized the linear analogues [D-Ala3]Dyn A(1-11)-NH2 (2) and [Ala3]Dyn A(1-11)-NH2 (3) and reported their biological activities. Analogues 2 and 3 displayed affinities for the central kappa opioid receptor (IC50 = 0.76 and 1.1 nM, respectively) similar to that of Dyn A(1-11)-NH2 (1) (IC50 = 0.58 nM) and greatly enhanced selectivities for kappa vs mu and kappa vs delta receptors (IC50 ratios of 350 and 1300 for 2, and 190 and 660 for 3, respectively). These results suggest that the structure and lipophilicity of the amino acid present in position 3 of Dyn A(1-11)-NH2 as well as the conformational changes they induce in the message sequence of dynorphin have important effects on potency and selectivity for kappa opioid receptors. To further investigate structure-activity relationships involving the residue at the 3 position of Dyn A(1-11)-NH2, a series of Dyn A analogues with aromatic, charged, and aliphatic side chain substitutions at the 3 position was designed, synthesized, and evaluated for their affinities for kappa, mu, and delta opioid receptors. It was found that analogues with lipophilic amino acids at the 3 position of Dyn A(1-11)-NH2 generally displayed higher affinity but similar selectivities for the kappa receptor than analogues with charged residues at the same position. It is suggested that the structural, configurational, and steric/lipophilic effects of amino acids at position 3 of Dyn A(1-11)-NH2 may play an important role in potency and selectivity for the kappa receptor.
ChemInform Abstract: Recent Advances in Phosphorescent Pt(II) Complexes Featuring Metallophilic Interactions: Properties and Applications (2015)

Abstract Review: 104 refs.
Investigation of Elastic Modulus of Xanthan and Locust Bean Gum at Different Concentrations of Mixture Using Cascade Model (2013)

Abstract Small amplitude oscillatory shear tests were performed to measure the elastic modulus of 1:1 xanthan–locust bean gum ( X / L ) mixed gels prepared with different total polymer concentrations (C = 0.1% to 3%). The critical concentration of X / L mixture was determined to be 0.15%. Based on the elasticity exponent ( t ) values, the concentration–modulus power–law relationship suggested the existence of two concentration regimes – a low concentration regime (0.15 ≤ C ≤ 0.5%) with t low = 3.88 and a high concentration regime (0.5 ≤ C ≤ 3.0%) with t high = 1.47. The elastic active network chain of X / L mixed gels was determined by the cascade model, and compared with the similar calculation based on the classical rubber elastic theory. The cascade model clearly showed the existence of nonideality parameter and enthalpic contribution to the X / L mixed gel. Practical applications The concentration dependence at the highest interaction might be useful for developing highly concentrated xanthan and locust bean gum mixture gels. Most studies of xanthan and locust bean gum mixtures focused only on the lower concentration regime. In this study the modulus at a higher concentration increased but eventually saturated.
SQL: The Complete Reference, Second Edition (2002)

Learn all you need to know about SQL with this one-stop resource. Updated to include information on Web services and XML, this complete guide also comes with a Windows 2000- and XP- compatible CD containing 4 databases (SQL Server 2000, IBM DB2 Version 7.2, Sybase, and mySQL).
Table of contents

Part I: An Overview of SQL
1: Introduction
2: A Quick Tour of SQL
3: SQL in Perspective
4: Relational Databases
Part II: Retrieving Data
5: SQL Basics
6: Simple Queries
7: Multitable Queries (Joins)
8: Summary Queries
9: Subqueries and Query Expressions
Part III: Updating Data
10: Database Updates
11: Data Integrity
12: Transaction Processing
Part IV: Database Structure
13: Creating a Database
14: Views
15: SQL Security
16: The System Catalog
Part V: Programming with SQL
17: Embedded SQL
18: Dynamic SQL *
19: SQL APIs
Part VI: SQL Today and Tomorrow
20: Database Processing and Stored Procedures
21: SQL and Data Warehousing
22: SQL and Application Servers
23: SQL Networking and Distributed Databases
24: SQL and Objects
25: SQL and XML
26: The Future of SQL
Part VII: Appendixes
A: The Sample Database
B: Database Vendor Profiles
C: SQL Syntax Reference
D: SQL Call-Level Interface
E: SQL Information Schema Standard
F: CD-ROM Installation Guide
Gene‐encoded nanoparticle vaccine platforms for in vivo assembly of multimeric antigen to promote adaptive immunity (2023)

Nanoparticle vaccines are a diverse category of vaccines for the prophylaxis or treatment of various diseases. Several strategies have been employed for their optimization, especially to enhance vaccine immunogenicity and generate potent B-cell responses. Two major modalities utilized for particulate antigen vaccines include using nanoscale structures for antigen delivery and nanoparticles that are themselves vaccines due to antigen display or scaffolding-the latter of which we will define as "nanovaccines." Multimeric antigen display has a variety of immunological benefits compared to monomeric vaccines mediated through potentiating antigen-presenting cell presentation and enhancing antigen-specific B-cell responses through B-cell activation. The majority of nanovaccine assembly is done in vitro using cell lines. However, in vivo assembly of scaffolded vaccines potentiated using nucleic acids or viral vectors is a burgeoning modality of nanovaccine delivery. Several advantages to in vivo assembly exist, including lower costs of production, fewer production barriers, as well as more rapid development of novel vaccine candidates for emerging diseases such as SARS-CoV-2. This review will characterize the methods for de novo assembly of nanovaccines in the host using methods of gene delivery including nucleic acid and viral vectored vaccines. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Therapeutic Approaches and Drug Discovery > Emerging Technologies.
Emergence of muscle and neural hematopoiesis in humans (2002)

During human development, hematopoiesis is thought to be compartmentalized to the fetal circulation, liver, and bone marrow. Here, we show that combinations of cytokines together with bone morphogenetic protein-4 and erythropoietin could induce multiple blood lineages from human skeletal muscle or neural tissue. Under defined serum-free conditions, the growth factors requirements, proliferation, and differentiation capacity of muscle and neural hematopoiesis were distinct to that derived from committed hematopoietic sites and were uniquely restricted to CD45(-)CD34(-) cells expressing the prominin AC133. Our study defines epigenetic factors required for the emergence of hematopoiesis from unexpected tissue origins and illustrates that embyronically specified microenvironments do not limit cell fate in humans.
Corticosteroid-resistant bone marrow-derived B lymphocyte progenitor for long term in vitro cultures. (1986)

A long-term in vitro culture system derived from murine bone marrow cells can successfully support the growth of B cell precursors, pre-B cells, and IgM-expressing B cells. Intermediates in the B cell developmental pathway are known to have differential sensitivities to the toxic effects of corticosteroids. We demonstrate here that long term B lineage cultures can be established with the corticosteroid-resistant cell population from bone marrow. Kinetics for the establishment and growth of cultures derived from corticosteroid-treated marrow are similar to those observed with control cultures. Cells obtained from both sets of cultures have similar morphologies and ranges of phenotypic markers. These results indicate that the cell responsible for the outgrowth of the long term B lineage cultures is corticosteroid resistant and is likely to be earlier in the B lymphocyte lineage than steroid-sensitive pre-B cells.
A Consolidated System for Robust Multi-Document Entity Risk Extraction and Taxonomy Augmentation (2019)

We introduce a hybrid human-automated system that provides scalable entity-risk relation extractions across large data sets. Given an expert-defined keyword taxonomy, entities, and data sources, the system returns text extractions based on bidirectional token distances between entities and keywords and expands taxonomy coverage with word vector encodings. Our system represents a more simplified architecture compared to alerting focused systems - motivated by high coverage use cases in the risk mining space such as due diligence activities and intelligence gathering. We provide an overview of the system and expert evaluations for a range of token distances. We demonstrate that single and multi-sentence distance groups significantly outperform baseline extractions with shorter, single sentences being preferred by analysts. As the taxonomy expands, the amount of relevant information increases and multi-sentence extractions become more preferred, but this is tempered against entity-risk relations become more indirect. We discuss the implications of these observations on users, management of ambiguity and taxonomy expansion, and future system modifications.
HMM‐based text segmentation using variational Bayes learning and its application to audio‐visual indexing (2007)

Abstract Recent progress in large‐vocabulary continuous speech recognition (LVCSR) has raised the possibility of applying information retrieval techniques to the resulting text. This paper presents a novel unsupervised text segmentation method. Assuming a generative model of a text stream as a left‐to‐right hidden Markov model (HMM), text segmentation can be formulated as model parameter estimation and model selection using the text stream. The formulation is derived based on the variational Bayes framework, which is expected to work well with highly sparse data such as text. The effectiveness of the proposed method is demonstrated through a series of experiments, where broadcast news programs are automatically transcribed and segmented into separate news stories. © 2007 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 90(12): 1–11, 2007; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/ecjb.20421
Store operation with conditional push of a tag value to a queue (2023)

According to one embodiment, a method for a store operation with a conditional push of a tag value to a queue is provided. The method includes configuring a queue that is accessible by an application, setting a value at an address in a memory device including a memory and a controller, receiving a request for an operation using the value at the address and performing the operation. The method also includes the controller writing a result of the operation to the address, thus changing the value at the address, the controller determining if the result of the operation meets a condition and the controller pushing a tag value to the queue based on the condition being met, where the tag value in the queue indicates to the application that the condition is met.
Supplementary Figure 5 from Interleukin-6 and Oncostatin-M Synergize with the PI3K/AKT Pathway to Promote Aggressive Prostate Malignancy in Mouse and Human Tissues (2023)

&lt;p&gt;PDF file - 3842K, Loss of PTEN results in increased expression of total AKT, ERK1/2 and STAT3 in transformed epithelial tissues.&lt;/p&gt;
Genome-wide analysis of long-term evolutionary domestication in Drosophila melanogaster (2016)

Experimental evolutionary genomics now allows biologists to test fundamental theories concerning the genetic basis of adaptation. We have conducted one of the longest laboratory evolution experiments with any sexually-reproducing metazoan, Drosophila melanogaster. We used next-generation resequencing data from this experiment to examine genome-wide patterns of genetic variation over an evolutionary time-scale that approaches 1,000 generations. We also compared measures of variation within and differentiation between our populations to simulations based on a variety of evolutionary scenarios. Our analysis yielded no clear evidence of hard selective sweeps, whereby natural selection acts to increase the frequency of a newly-arising mutation in a population until it becomes fixed. We do find evidence for selection acting on standing genetic variation, as independent replicate populations exhibit similar population-genetic dynamics, without obvious fixation of candidate alleles under selection. A hidden-Markov model test for selection also found widespread evidence for selection. We found more genetic variation genome-wide, and less differentiation between replicate populations genome-wide, than arose in any of our simulated evolutionary scenarios.
Data from <i>S</i>-nitrosylation of the Mitochondrial Chaperone TRAP1 Sensitizes Hepatocellular Carcinoma Cells to Inhibitors of Succinate Dehydrogenase (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;i&gt;S&lt;/i&gt;-nitrosoglutathione reductase (GSNOR) represents the best-documented denitrosylase implicated in regulating the levels of proteins posttranslationally modified by nitric oxide on cysteine residues by &lt;i&gt;S&lt;/i&gt;-nitrosylation. GSNOR controls a diverse array of physiologic functions, including cellular growth and differentiation, inflammation, and metabolism. Chromosomal deletion of GSNOR results in pathologic protein &lt;i&gt;S&lt;/i&gt;-nitrosylation that is implicated in human hepatocellular carcinoma (HCC). Here we identify a metabolic hallmark of aberrant &lt;i&gt;S&lt;/i&gt;-nitrosylation in HCC and exploit it for therapeutic gain. We find that hepatocyte GSNOR deficiency is characterized by mitochondrial alteration and by marked increases in succinate dehydrogenase (SDH) levels and activity. We find that this depends on the selective &lt;i&gt;S&lt;/i&gt;-nitrosylation of Cys&lt;sup&gt;501&lt;/sup&gt; in the mitochondrial chaperone TRAP1, which mediates its degradation. As a result, GSNOR-deficient cells and tumors are highly sensitive to SDH inhibition, namely to α-tocopheryl succinate, an SDH-targeting molecule that induced RIP1/PARP1-mediated necroptosis and inhibited tumor growth. Our work provides a specific molecular signature of aberrant &lt;i&gt;S&lt;/i&gt;-nitrosylation in HCC, a novel molecular target in SDH, and a first-in-class therapy to treat the disease. &lt;i&gt;Cancer Res; 76(14); 4170–82. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Antifungal susceptibility, genotyping, resistance mechanism, and clinical profile of Candida tropicalis blood isolates (2019)

Candida tropicalis is one of the major candidaemia agents, associated with the highest mortality rates among Candida species, and developing resistance to azoles. Little is known about the molecular mechanisms of azole resistance, genotypic diversity, and the clinical background of C. tropicalis infections. Consequently, this study was designed to address those questions. Sixty-four C. tropicalis bloodstream isolates from 62 patients from three cities in Iran (2014-2019) were analyzed. Strain identification, antifungal susceptibility testing, and genotypic diversity analysis were performed by MALDI-TOF MS, CLSI-M27 A3/S4 protocol, and amplified fragment length polymorphism (AFLP) fingerprinting, respectively. Genes related to drug resistance (ERG11, MRR1, TAC1, UPC2, and FKS1 hotspot9s) were sequenced. The overall mortality rate was 59.6% (37/62). Strains were resistant to micafungin [minimum inhibitory concentration (MIC) ≥1 μg/ml, 2/64], itraconazole (MIC > 0.5 μg/ml, 2/64), fluconazole (FLZ; MIC ≥ 8 μg/ml, 4/64), and voriconazole (MIC ≥ 1 μg/ml, 7/64). Pan-azole and FLZ + VRZ resistance were observed in one and two isolates, respectively, while none of the patients were exposed to azoles. MRR1 (T255P, 647S), TAC1 (N164I, R47Q), and UPC2 (T241A, Q340H, T381S) mutations were exclusively identified in FLZ-resistant isolates. AFLP fingerprinting revealed five major and seven minor genotypes; genotype G4 was predominant in all centers. The increasing number of FLZ-R C. tropicalis blood isolates and acquiring FLZ-R in FLZ-naive patients limit the efficiency of FLZ, especially in developing countries. The high mortality rate warrants reaching a consensus regarding the nosocomial mode of C. tropicalis transmission.
Benefits of additive manufacturing and micro and nano surface texture modifications on mechanical strength and infection resistance of skin–implant interfaces in rats (2020)

Patients find existing exo-prostheses utilizing traditional socket connections uncomfortable and irritating, as they do not provide the dexterity and proprioception which is often expected by active patients. Transcutaneous osseointegrated implants are a potential solution, but carry risk of infection at the skin–implant interface. Histological and observational studies previously demonstrated that textured implants have both improved epidermal ingrowth and decreased skin retraction. This study aimed to determine effects on mechanical integration, barrier to bacterial colonization, and infection of the skin–implant interface using additive manufacturing and post-manufactured surface modifications. In this study, titanium alloy implants were made by either computer numerical control machining (CNC) or electron beam melting (EBM). Implants in each group were left either unaltered (CNC-control and EBM-control), acid etched (CNC-micro and EBM-micro), or oxidatively treated (CNC-nano and EBM-nano) creating six distinct surface textures. This study was divided into two phases, each utilizing 10 rats. Six implants—one of each texture—randomized for position were placed in each rat. Phase 1 animals healed for three weeks and skin-implant mechanical pull-off strength was measured. Phase 2 animals were challenged by S. aureus inoculation during the three-week healing process and serial dilutions of the sonicated implants were performed to quantify bacterial colonization. The three EBM implant groups had 830% greater force at pull-off compared to the three CNC groups. Additionally, the pull-off force of EBM-micro implants was 101% and 83% stronger, respectively, than EBM-nano and EBM-control implants. There was negligible mechanical attachment of skin to any CNC implant. Bacterial colonization counts were collectively 63% ( P &lt; 0.05) lower for EBM implants relative to CNC implants. CNC-control implants exhibited 90% ( P &lt; 0.01) greater bacterial colonization than EBM-controls. No significant differences in bacterial colonization were noted between the other implant groups. Both manufacturing technique and post-manufacturing surface texture modification affected the skin-implant interface’s mechanical integration and effectiveness as a barrier to infection. EBM manufacturing produced markedly superior transcutaneous implants compared to machining.
136 ADDITION OF LOW DENSITY LIPOPROTEIN TO CHEMICALLY DEFINED PORCINE EMBRYO CULTURE MEDIUM CAN PARTIALLY REPLACE BOVINE SERUM ALBUMIN (2007)

Embryo culture media typically contain undefined biologicals such as BSA. Our goal is to develop chemically defined culture media that are based on the biology and physiology of the embryo. To that end we evaluated the presence of message in embryos at various stages of development and determined that the message for the low density lipoprotein receptor (LDLR) increased from the germinal vesicle and 4-cell stage to the blastocyst stage of porcine embryogenesis. Thus, this study was conducted to determine if the addition of low density lipoprotein (LDL) would enhance the development and quality of in vitro produced porcine embryos in an already chemically defined culture medium. Slaughterhouse ovaries were aspirated, cumulous–oocyte complexes (COC) identified, and the COC were matured for 42 h in M199 base medium supplemented with EGF, FSH, and LH. Metaphase II oocytes were then selected. Fertilization was then preformed in modified Tris buffered medium and cocultured with 0.25 × 106/mL frozen thawed porcine semen for 5 h. The presumptive zygotes were then transferred to either porcine zygote medium with 0.3% BSA or 0.1% PVA (PZM3, PZM4). After 28 h, cleaved embryos were then sorted into six treatment groups (1. PZM3, 2. PZM3 + 20 µg mL–1 LDL, 3. PZM4, 4. PZM4 + 10 µg mL–1 LDL, 5. PZM4 + 20 µg mL–1 LDL, 6. PZM4 + 50 µg mL–1 LDL). The embryos were cultured in 5%O2 5%CO2 90%N until day 7. The percentage of development to the blastocyst stage was determined and analyzed with the SAS Proc GENMOD Procedure (a–c P = 0.05). The percentage blastocyst was 51.3 ± 0.09a, 51.6 ± 0.09a, 33.1 ± 0.99c, 35.8 ± 0.09c, 36.9 ± 0.09c, and 41.3 ± 0.06b, for treatments 1–6, respectively. Culture in PZM4 (without BSA) significantly reduced development. However, addition of 50 µg mL–1 of LDL to PZM4 improved development above PZM4 alone. We interpret these data to indicate that a high concentration of LDL in the PZM4 media did improve embryo development and that LDL could partially substitute for BSA. Differential staining was performed on the blastocysts, and preliminary results suggest that the ICM to trophectoderm ratio in the high LDL treatment group is closer to the ratio found in in vivo produced embryos. This project was supported by USDA CSREES NRI (2006-35203-17282) and Food for the 21st Century .
Chronic black tea extract consumption improves endothelial function in ovariectomized rats (2015)

The present study reveals the novel benefits of chronic BT consumption to reverse endothelial dysfunction and favorably modifying cholesterol profile in a rat model of estrogen deficiency and provides insights into developing BT as beneficial dietary supplements for postmenopausal women.
Zero voltage switching Forward-Flyback Converter with efficient active LC snubber circuit (2014)

This paper describes a Boundary Mode Forward-Flyback Converter (BMFFC) with zero-voltage switching that is able to process power efficiently. The theoretical analysis and operating principle of the BMFFC are presented in detail. A non-dissipative LC snubber that recycles energy to the input source is employed in order to suppress the voltage spike caused by the leakage inductance of the transformer. The relatively large snubber capacitor also significantly reduces turn-off loss. Following a detailed design procedure, a 200W prototype with a 25-50VDC input and 230VDC output was constructed and tested in order to evaluate the performance of the BMFFC.