gebhart/patrepeval huggingface dataset:
Loss of PTEN expression leading to high Akt activation in human multiple myelomas (2000)

Mouse plasma cell tumor (PCT) and human multiple myeloma (MM) are terminal B-cell malignancies sharing many similarities. Our recent work demonstrated that activation of the insulin-like growth factor receptor (IGF-IR)/insulin receptor substrate (IRS)/phosphatidylinositol 3' kinase (PI 3'K) pathway was evident in the tumor lines derived from both species. Although PI 3'K activity was higher in mouse tumor lines than that in human tumors, activation of Akt serine/threonine kinase was markedly lower in mouse lines. This discrepancy prompted us to test the status of PTEN tumor suppressor gene, as it has been shown to be a negative regulator of PI 3'K activity. Although all the mouse lines expressed intact PTEN, 2 of the 4 human lines (Delta47 and OPM2) possessing the highest Akt activity lost PTEN expression. Sequencing analysis demonstrated that the PTEN gene contains a deletion spacing from exon 3 to exon 5 or 6 in the Delta47 line and from exon 3 to 7 in the OPM2 line. Restoration of PTEN expression suppressed IGF-I-induced Akt activity, suggesting that loss of PTEN is responsible for uncontrolled Akt activity in these 2 lines. Despite the expression of PTEN with the concomitant low Akt activity in all mouse PCT lines, their p70S6K activities were generally higher than those in 3 human MM lines, arguing for specific negative regulation of Akt, but not p70S6K by PTEN. These results suggest that p70S6K and Akt may be differentially used by the plasma cell tumors derived from mice and humans, respectively.
Centering Single Cells in Microgels via Delayed Crosslinking Supports Long-Term 3D Culture by Preventing Cell Escape (2017)

Single-cell-laden microgels support physiological 3D culture conditions while enabling straightforward handling and high-resolution readouts of individual cells. However, their widespread adoption for long-term cultures is limited by cell escape. In this work, it is demonstrated that cell escape is predisposed to off-center encapsulated cells. High-speed microscopy reveals that cells are positioned at the microgel precursor droplets' oil/water interface within milliseconds after droplet formation. In conventional microencapsulation strategies, the droplets are typically gelled immediately after emulsification, which traps cells in this off-center position. By delaying crosslinking, driving cells toward the centers of microgels is succeeded. The centering of cells in enzymatically crosslinked microgels prevents their escape during at least 28 d. It thereby uniquely enables the long-term culture of individual cells within <5-µm-thick 3D uniform hydrogel coatings. Single cell analysis of mesenchymal stem cells in enzymatically crosslinked microgels reveals unprecedented high cell viability (>90%), maintained metabolic activity (>70%), and multilineage differentiation capacity (>60%) over a period of 28 d. The facile nature of this microfluidic cell-centering method enables its straightforward integration into many microencapsulation strategies and significantly enhances control, reproducibility, and reliability of 3D single cell cultures.
Respiratory Syncytial Virus G Protein CX3C Motif Impairs Human Airway Epithelial and Immune Cell Responses (2013)

Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory infection in infants and young children and causes disease in the elderly and persons with compromised cardiac, pulmonary, or immune systems. Despite the high morbidity rates of RSV infection, no highly effective treatment or vaccine is yet available. The RSV G protein is an important contributor to the disease process. A conserved CX3C chemokine-like motif in G likely contributes to the pathogenesis of disease. Through this motif, G protein binds to CX3CR1 present on various immune cells and affects immune responses to RSV, as has been shown in the mouse model of RSV infection. However, very little is known of the role of RSV CX3C-CX3CR1 interactions in human disease. In this study, we use an in vitro model of human RSV infection comprised of human peripheral blood mononuclear cells (PBMCs) separated by a permeable membrane from human airway epithelial cells (A549) infected with RSV with either an intact CX3C motif (CX3C) or a mutated motif (CX4C). We show that the CX4C virus induces higher levels of type I/III interferon (IFN) in A549 cells, increased IFN-α and tumor necrosis factor alpha (TNF-α) production by human plasmacytoid dendritic cells (pDCs) and monocytes, and increased IFN-γ production in effector/memory T cell subpopulations. Treatment of CX3C virus-infected cells with the F(ab')2 form of an anti-G monoclonal antibody (MAb) that blocks binding to CX3CR1 gave results similar to those with the CX4C virus. Our data suggest that the RSV G protein CX3C motif impairs innate and adaptive human immune responses and may be important to vaccine and antiviral drug development.
Bone morphogenetic protein (BMP) for fracture healing in adults (2010)

This review highlights a paucity of data on the use of BMP in fracture healing as well as considerable industry involvement in currently available evidence. There is limited evidence to suggest that BMP may be more effective than controls for acute tibial fracture healing, however, the use of BMP for treating nonunion remains unclear. The limited available economic evidence indicates that BMP treatment for acute open tibial fractures may be more favourable economically when used in patients with the most severe fractures.
Enhanced inhibitive effects of combination of rofecoxib and octreotide on the growth of human gastric cancer (2004)

Our previous studies indicated that cyclooxygenase-2 inhibitor or octreotide could suppress the proliferation of gastric adenocarcinoma in vitro or in vivo. The present study was aimed to find whether rofecoxib combined with octreotide could enhance the inhibitive effects on the growth of gastric cancer. The effect of rofecoxib or octreotide on proliferation of gastric cancer cell line was determined by 3H-thymidine ribotide incorporation. The TdT-mediated dUTP nick end-labeling assay was used to detect the apopotosis. To determine their synergic antineoplastic effects, the interaction between rofecoxib and octreotide on SGC-7901 cell was evaluated by the median effect plot. After orthotopical implantion of xenografts of human gastric cancer in stomach, nude mice were given rofecoxib plus octreotide for 8 weeks. Cyclooxygenase-2 in gastric cancer tissues was measured by immunohistochemistry. Combination of rofecoxib and octreotide presented synergistic effect (combination index < 1) in the majority of responses. The inhibitory rate for xenografts in nude mice was 89.7% in rofecoxib group. Combination of rofecoxib and octreotide enhanced inhibitory rate to 98.8%. The combination greatly increased the apoptotic index (78.20% +/- 6.45%) of the xenografts as compared with that of using rofecoxib alone (46.60% +/- 3.42%); the difference was very significant (p < 0.001). Rofecoxib could inhibit the activity of cyclooxygenase-2 in the tissue of gastric adenocarcinomas of nude mice. Our results indicate that combination of rofecoxib and octreotide significantly enhances the antiproliferative effect in gastric adenocarcinoma, which might have potential therapeutic value.
Beyond the adaptive matched filter: nonlinear detectors for weak signals in high-dimensional clutter (2007)

For known signals that are linearly superimposed on gaussian backgrounds, the linear adaptive matched filter (AMF) is well-known to be the optimal detector. The AMF has furthermore proved to be remarkably effective in a broad range of circumstances where it is not optimal, and for which the optimal detector is not linear. In these cases, nonlinear detectors are theoretically superior, but direct estimation of nonlinear detectors in high-dimensional spaces often leads to flagrant overfitting and poor out-of-sample performance. Despite this difficulty in the general case, we will describe several situations in which nonlinearity can be effectively combined with the AMF to detect weak signals. This allows improvement over AMF performance while avoiding the full force of dimensionality's curse.
The relationship between dopamine D2 receptor polymorphism at the Taq1 A locus and therapeutic response to nemonapride, a selective dopamine antagonist, in schizophrenic patients (2000)

Previous studies have demonstrated that subjects with one or two A1 alleles of dopamine D2 receptor (DRD2) polymorphism at the Taq1 A locus have lower DRD2 density than those with no A1 allele. The present study aimed to examine whether the Taq1 A DRD2 genotypes are related to therapeutic response to nemonapride, a selective dopamine antagonist, in schizophrenic patients. The subjects were 25 acutely exacerbated schizophrenic inpatients who had received no medication for at least 1 month before the study. The fixed dose (18 mg/day) of nemonapride was administered to each patient for 3 weeks. The clinical status was prospectively monitored by the Brief Psychiatric Rating Scale (BPRS) before, and 3 weeks after, the treatment. The Taq1 A genotypes (A1 and A2 alleles) were determined by the polymerase chain reaction method. Three patients were homozygous for the A1 allele, 11 were heterozygous for the A1 and A2 alleles, and 11 were homozygous for the A2 allele. The patients with one or two A1 alleles (n = 14) showed significantly higher percentage improvement in total BPRS and positive symptoms than those with no A1 allele (n = 11) after 3-week treatment while the percentage improvement in other subgrouped symptoms (negative, anxiety-depression, excitement and cognitive symptoms) was similar between the two genotype groups. The present results suggest that the Taq1 A DRD2 polymorphism is related to early therapeutic response to nemonapride in schizophrenic patients, possibly by modifying the efficiency of DRD2 antagonism of the drug in the central nervous system.
Bundled execution of recurring traces for energy-efficient general purpose processing (2011)

Technology scaling has delivered on its promises of increasing device density on a single chip. However, the voltage scaling trend has failed to keep up, introducing tight power constraints on manufactured parts. In such a scenario, there is a need to incorporate energy-efficient processing resources that can enable more computation within the same power budget. Energy efficiency solutions in the past have typically relied on application specific hardware and accelerators. Unfortunately, these approaches do not extend to general purpose applications due to their irregular and diverse code base. Towards this end, we propose BERET, an energy-efficient co-processor that can be configured to benefit a wide range of applications. Our approach identifies recurring instruction sequences as phases of "temporal regularity" in a program's execution, and maps suitable ones to the BERET hardware, a three-stage pipeline with a bundled execution model. This judicious off-loading of program execution to a reduced-complexity hardware demonstrates significant savings on instruction fetch, decode and register file accesses energy. On average, BERET reduces energy consumption by a factor of 3-4X for the program regions selected across a range of general-purpose and media applications. The average energy savings for the entire application run was 35% over a single-issue in-order processor.
Synthesis of Acid-Labile PEG and PEG-Doxorubicin-Conjugate Nanoparticles via Brush-First ROMP (2014)

A panel of acid-labile bis-norbornene cross-linkers was synthesized and evaluated for the formation of acid-degradable brush-arm star polymers (BASPs) via the brush-first ring-opening metathesis polymerization (ROMP) method. An acetal-based cross-linker was identified that, when employed in conjunction with a poly(ethylene glycol) (PEG) macromonomer, provided highly controlled BASP formation reactions. A combination of this new cross-linker with a novel doxorubicin (DOX)-<i>branch</i>-PEG macromonomer provided BASPs that simultaneously degrade and release cytotoxic DOX in vitro.
In-depth analysis of subclass-specific conformational preferences of IgG antibodies (2014)

IgG subclass-specific differences in biological function and in vitro stability are often referred to variations in the conformational flexibility, while this flexibility has rarely been characterized. Here, small-angle X-ray scattering data from IgG1, IgG2 and IgG4 antibodies, which were designed with identical variable regions, were thoroughly analysed by the ensemble optimization method. The extended analysis of the optimized ensembles through shape clustering reveals distinct subclass-specific conformational preferences, which provide new insights for understanding the variations in physical/chemical stability and biological function of therapeutic antibodies. Importantly, the way that specific differences in the linker region correlate with the solution structure of intact antibodies is revealed, thereby visualizing future potential for the rational design of antibodies with designated physicochemical properties and tailored effector functions. In addition, this advanced computational approach is applicable to other flexible multi-domain systems and extends the potential for investigating flexibility in solutions of macromolecules by small-angle X-ray scattering.
Increased expression in Escherichia coli of a synthetic gene encoding human somatomedin C after gene duplication and fusion (1987)

A synthetic gene coding for human somatomedin C (SMC) was inserted into an Escherichia coli plasmid vector that contains the bacteriophage lambda pL promoter. Intracellular accumulation of the gene product after induction of the promoter was found to be low. A 200-fold greater yield was obtained with a similar plasmid containing two translationally fused copies of the SMC gene. A series of such tandem genes truncated at their 3' ends were generated with nuclease Bal 31. These gave intermediate expression levels that correlated with the expected sizes of their gene products. Comparison of RNAs extracted from cells containing either the monomer or tandem SMC gene constructions showed that there was no significant difference in expression at the transcriptional level. Pulse-chase experiments demonstrated that the tandem SMC protein was far more stable than the monomer SMC product.
Gene Expression Following Direct Injection of DNA into Liver (1994)

The liver is an attractive target tissue for gene therapy. Current approaches for hepatic gene delivery include retroviral and adenoviral vectors, liposome/DNA, and peptide/DNA complexes. This study describes a technique for direct injection of DNA into liver that led to significant gene expression. Gene expression was characterized in both rats and cats following injection of plasmid DNA encoding several different proteins. Luciferase activity was measured after injection of plasmid DNA encoding the luciferase gene (pCMVL), beta-galactosidase (beta-Gal) activity was evaluated in situ using plasmid DNA encoding Lac Z (pCMV beta), and serum concentration of secreted human alpha-1-antitrypsin was measured following injection of plasmid DNA encoding this protein (pRC/CMV-sHAT). Several variables, including injection technique, DNA dose, and DNA diluent, were investigated. Direct injection of pCMVL resulted in maximal luciferase expression at 24-48 hr. beta-Gal staining demonstrated that the majority of transfected hepatocytes were located near the injection site. Significant concentrations of human alpha-1-antitrypsin were detected in the serum of animals injected with pRC/CMV-sHAT. These findings demonstrate the general principle that direct injection of plasmid DNA into liver can lead to significant gene expression.
Feeding Response of Adult Helicoverpa zea (Lepidoptera: Noctuidae) to Commercial Phagostimulants (1994)

Journal Article Feeding Response of Adult Helicoverpa zea (Lepidoptera: Noctuidae) to Commercial Phagostimulants Get access J. D. Lopez, Jr., J. D. Lopez, Jr. Crop Insect Pests Management Research Unit, USDA-ARS, Rt. 5, Box 808, College Station, TX 77845 Search for other works by this author on: Oxford Academic PubMed Google Scholar P. D. Lingren P. D. Lingren Crop Insect Pests Management Research Unit, USDA-ARS, Rt. 5, Box 808, College Station, TX 77845 Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Economic Entomology, Volume 87, Issue 6, 1 December 1994, Pages 1653–1658, https://doi.org/10.1093/jee/87.6.1653 Published: 01 December 1994 Article history Received: 19 November 1993 Accepted: 18 May 1994 Published: 01 December 1994
A bi-directional quasi-optical lens amplifier (1997)

A 24-element bi-directional quasi-optical lens amplifier array is presented. The lens amplifier array is designed for X-band, and operates in transmission mode. Single-pole double-throw (SPDT) switches are used to switch between transmit and receive amplifiers. The lens amplifier array demonstrates gains of 5.5 dB at 10.1 GHz in receive mode, and 2 dB at 10.2 GHz in transmit mode, with more than 15-dB ON/OFF isolation. Several applications for the lens amplifier array are demonstrated: a quasi-optical transceiver front-end, reduction of multipath fading, and a multiuser frequency reuse application.
ADAMTS13 gene mutation in congenital thrombotic thrombocytopenic purpura with previously reported normal VWF cleaving protease activity (2003)

Deficiency of von Willebrand factor (VWF) cleaving protease ADAMTS13 is associated with the development of thrombotic thrombocytopenic purpura (TTP). A case of congenital TTP that was previously reported to have normal ADAMTS13 activity was analyzed at the molecular level. Reanalysis of plasma VWF cleaving protease activity using a different assay revealed that the patient had less than 0.1 U/L ADAMTS13 protease activity, while the parents were both partially deficient. Sequence analysis of DNA amplified by polymerase chain reaction showed that the patient was homozygous for a novel TT deletion in exon 15 of the ADAMTS13 gene resulting in a frameshift, while both parents were heterozygous for the same mutation. Taken together with other recent reports, all the cases of hereditary TTP studied by DNA sequence analysis to date appear to be due to mutations within the ADAMTS13 gene.
The Complete Genome Sequence of Escherichia coli DH10B: Insights into the Biology of a Laboratory Workhorse (2008)

Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified. We report the complete genomic sequence of DH10B by using reads accumulated from the bovine sequencing project at Baylor College of Medicine and assembled with DNAStar's SeqMan genome assembler. The DH10B genome is largely colinear with that of the wild-type K-12 strain MG1655, although it is substantially more complex than previously appreciated, allowing DH10B biology to be further explored. The 226 mutated genes in DH10B relative to MG1655 are mostly attributable to the extensive genetic manipulations the strain has undergone. However, we demonstrate that DH10B has a 13.5-fold higher mutation rate than MG1655, resulting from a dramatic increase in insertion sequence (IS) transposition, especially IS150. IS elements appear to have remodeled genome architecture, providing homologous recombination sites for a 113,260-bp tandem duplication and an inversion. DH10B requires leucine for growth on minimal medium due to the deletion of leuLABCD and harbors both the relA1 and spoT1 alleles causing both sensitivity to nutritional downshifts and slightly lower growth rates relative to the wild type. Finally, while the sequence confirms most of the reported alleles, the sequence of deoR is wild type, necessitating reexamination of the assumed basis for the high transformability of DH10B.
Mechanical properties of calcium phosphate based dental filling and regeneration materials (2003)

The objective of this study was to compare the mechanical properties of calcium phosphate cements (CPC) for possible dental applications with varied liquid and powder compositions under the same testing condition. Cements studied in this experiment were divided into two groups of CPC not containing polymer and polymeric CPC (PCPC). Cement powder was formed by combining equimolar amounts of dicalcium phosphate anhydrous and tetracalcium phosphate, or acrylic resin polymer powder mixture. The CPC specimens for the compressive strength (CS) and diametral tensile strength (DTS) measurements were prepared by mixing powder and liquid for 30 s with a powder/liquid ratio of 3:1, and subsequently packing the paste into a brass mould. The specimens were kept at 37 degrees C and 100% relative humidity for 24 h before measurements were conducted on a Universal Testing Machine with a cross-head speed of 1 mm min-1. The CS of CPC was 0.14-10.29 MPa and that of PCPC was 0.26-117.58 MPa. The DTS of CPC was 0.10-4.56 MPa and that of PCPC was 0.07-22.54 MPa. The CS and DTS were very diverse depending on the composition of powder and liquid. Some compositions showed higher values than commercial liners. Thus compositions of 2% carboxymethyl cellulose + 35% citric acid in phosphate buffered saline (PBS), 20% gelatin in PBS, 2% sodium alginate in PBS, 20-40% aqueous acrylic-maleic copolymer solution, and some of the HPMC and PMVE-Ma solutions exhibited promising formulae for dentine regenerating materials. Acrylic resin-PCPC group showed generally higher CS and DTS values. Based on this study, further studies on the reaction with odontoblast and resultant dentine regeneration should be performed using promising compositions.
Synthesis of pharmacologically active indoles. (1999)

Formylation of 6-methoxy-1-methyl and 5-methyl,2,3-diphenyl-1H-indole (Ib and IX) gave the 5- and 6- carboxaldehyde derivatives (II and X) respectively, which were treated with ethyl cyanoacetate to form the corresponding 2-cyano-3-substituted acrylic acid ethyl ester (III and XI). The latter compounds reacted with hydrazine hydrate, urea and thiourea to form the corresponding 5-amino-4-substituted 2,4,dihydropyrazol-3- one (IV), 6-indolyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile s (V and XII) and 6-indolyl-4-oxo-2-thixo-1,2,3,4-tetrahydropyrimidine-5-ca rbonitriles (VI and XIII). Reaction of the 5- and 6-carboxaldehyde derivatives with malononitrile afforded the 2-substituted malononitrile derivatives (VII and XIV). VII and XIV reacted readilly with aromatic ketones to give the 2-amino4,6-disubstituted nicotinonitriles (VIII a,b and XVa,b). The biological activity of compounds Ia, Ib, II, III, IX and X was tested for antiinflammatory, ulcerogenic and antispasmodic activities.