gebhart/patrepeval huggingface dataset:
Adiponutrin Gene Expression in 3T3-L1 Adipocytes is Downregulated by Troglitazone (2003)

Thiazolidinedione compounds (TZDs) are increasingly useful in the treatment of type 2 diabetes [1]. TZDs are able to diminish insulin resistance and improve many of the associated symptoms. It is thought that the improvement of glucose homeostasis may be brought about by TZDs acting as ligands of PPARγ in adipose tissue and changing either plasma concentrations of adipocyte-derived metabolites such as fatty acids or secreted adipocytokines. PPARγ comprises transcription factors that modulate the expression of a cohort of target genes involved in adipocyte differentiation, glucose metabolism and lipid metabolism. The majority of genes that have so far been confirmed to be direct targets of TZD-activated PPARγ in adipose tissue encode proteins involved in lipid metabolism and its regulation, including adipocytokines [2]. It is not clear whether the antidiabetic potential of TZDs is related to their adipogenic actions or to their inhibitory or stimulatory effects on expression of specific genes. Identification of new target genes will provide further insights into the molecular mechanism of TZDs and in addition may reveal novel genes that are involved in glucose and lipid homeostasis. This paper reports that the recently identified gene adiponutrin [5] is downregulated by TZDs.
Initial clinical trial of the macrophage activator muramyl tripeptide-phosphatidylethanolamine encapsulated in liposomes in patients with advanced cancer. (1990)

A phase I clinical trial of the macrophage activator, muramyl tripeptide-phosphatidylethanolamine has been carried out in 37 patients (47 courses) at doses of 0.01-6.0 mg/m2 intravenously twice weekly for 4 weeks. Activation of peripheral blood monocytes and drug toxicity were used as the parameters to monitor the trial. Toxicity was acute systemic responses of fever, chills, and hypertension without a clear dose response. No major organ-related toxicity was seen. A dose of 4.0 mg/m2 biweekly produced activation of blood monocytes; a dose of 6.0 mg/m2 produced inhibition. There was one complete response of 3 months duration in a patient with renal cell carcinoma with pulmonary metastases. The optimum dose for phase II studies is in the range of 1-4 mg/m2 twice weekly for 4 weeks, a dose that is well tolerated.
Population Pharmacokinetic Model of Human Insulin Following Different Routes of Administration (2010)

Multiple-compartment disposition of insulin has been demonstrated following intravenous administration; however, because of slow absorption and flip-flop kinetics, meal-time insulin pharmacokinetics have been described by a 1-compartment model. Technosphere insulin (TI) is an inhaled human insulin with rapid absorption and a distinct second compartment in its pharmacokinetics. The aim of this analysis was to develop a pharmacokinetic model for insulin administered via the intravenous, subcutaneous, and inhalation routes. A 2-compartment pharmacokinetic model with 1 (inhaled) or 2 sequential (subcutaneous) first-order absorption processes and first-order elimination was developed using data from 2 studies with a total of 651 concentrations from 16 healthy volunteers. Insulin was administered intravenously (5 U), subcutaneously (10 U), and via inhalation (25, 50, and 100 U). The data were modeled simultaneously with NONMEM VI, using ADVAN6 subroutine with FO. Typical values were clearance, 43.4 L/h; volume of distribution in the central compartment, 5.0 L; intercompartmental clearance, 23.9 L/h; volume of distribution in the peripheral compartment 30.7 L; TI first-order absorption rate constant, 2.35 h⁻¹; and first-order absorption rate constants associated with subcutaneously administered insulin, 0.63 and 1.04 h⁻¹, respectively. Absorption rate after subcutaneous dosing was found to decrease with increasing body mass index. Insulin pharmacokinetics were found to be consistent with 2-compartment disposition, regardless of route of administration, with insulin curve differences attributable to absorption differences.
Plasmacytoid dendritic cells resident in human thymus drive natural Treg cell development (2010)

The generation of natural regulatory T cells (nTregs) is crucial for the establishment of immunologic self-tolerance and the prevention of autoimmunity. Still, the origin of nTregs and the mechanisms governing their differentiation within the thymus are poorly understood, particularly in humans. It was recently shown that conventional dendritic cells (cDCs) in human thymus were capable of inducing nTreg differentiation. However, the function of plasmacytoid DCs (pDCs), the other major subset of thymic DCs, remains unknown. Here we report that pDCs resident in the human thymus, when activated with CD40 ligand (CD40L) plus interleukin-3, efficiently promoted the generation of CD4(+)CD25(+)Foxp3(+) nTregs from autologous thymocytes. The progenitors of these nTregs were selectively found within CD4(+)CD8(+) thymocytes that had accomplished positive selection, as judged by their CD69(hi)TCR(hi) phenotype. Supporting the involvement of the CD40-CD40L pathway in pDC-induced nTreg generation, we show that positively selected CD4(+)CD8(+) progenitors specifically transcribed CD40L in vivo and up-regulated CD40L expression on T-cell receptor engagement, thereby promoting the activation of pDCs. Finally, evidence is provided that nTregs primed by pDCs displayed reciprocal interleukin-10/transforming growth factor-beta cytokine expression profiles compared with nTregs primed by cDCs. This functional diversity further supports a nonredundant tolerogenic role for thymic pDCs in the human thymus.
Overlapping functions of the starch synthases SSII and SSIII in amylopectin biosynthesis in Arabidopsis (2008)

SSII and SSIII have partially redundant functions in determination of amylopectin structure, and these roles cannot be substituted by any other conserved SS, specifically SSI, GBSSI, or SSIV. Even though SSIII is not required for the normal abundance of glucan chains of DP12 to DP18, the enzyme clearly is capable of functioning in production such chains. The role of SSIII in producing these chains cannot be detected simply by analysis of an individual mutation. Competition between different SSs for binding to substrate could in part explain the specific distribution of glucan chains within amylopectin.
Preliminary investigations of three-dimensional microwave tomography using different data sets (2012)

Owing to the extensive amount of computing resources required for solving the non-linear microwave inverse scattering problems, previous numerical studies have mainly been focus on two-dimensional inverse scattering problem. In three-dimensional cases, the vectorial nature of electromagnetic waves has to be properly handled. In this paper, preliminary investigations of using vertical and horizontal components of the scattered near-field are considered. The forward data is first evaluated quantitatively and image reconstruction using the two different sets of data from the same scattering problem is performed.
The Mechanism of Rabbit Platelet Aggregation Induced by 2,5-Di-(tert-butyl)-l,4-benzohydroquinone, an Inhibitor of Endoplasmic Reticulum Ca2+-ATPase (1997)

2,5-Di-(tert-butyl)-1,4-benzohydroquinone (tBuBHQ), an inhibitor of endoplasmic reticulum Ca2+-ATPase, caused aggregation accompanied by a marked increase in intracellular Ca2+ concentrations ([Ca2+]i) in washed rabbit platelets. Treatment of platelets with SK&F96365 or removal of extracellular Ca2+ inhibited both Ca2+ influx and platelet aggregation induced by tBuBHQ. These responses of platelets to tBuBHQ were also inhibited by genistein. Western blots using antibody against phosphorylated amino acid residues revealed that tBuBHQ activated tyrosine kinase independently of extracellular Ca2+. These results suggest that tBuBHQ induces Ca2+ influx into platelets probably through activation of tyrosine kinase, resulting in platelet aggregation.
Generation of the Single Chain Antibody Fragment Conserves the Idiotypic Profile of the Anti‐CD30 Monoclonal Antibody HRS3 (1998)

Recombinant single chain antibody fragments (scFv) derived by combining immunoglobulin VL and VH regions provide valuable antibody-like reagents. A number of them are shown to have retained the antigen specificity of the parental monoclonal antibody (MoAb). Little is known about the idiotypic profile of scFv fragments compared with that of the parental MoAb. To address this question we analysed the idiotypic profile of a scFv that was derived by phage-display techniques from the anti-CD30 MoAb HRS3. We assayed (i) binding of HRS3-scFv to recombinant CD30-Fc antigen and to four different anti-idiotypic MoAbs defining at least three different idiotopes on HRS3, and (ii) cross-competition with the parental MoAb HRS3 and the closely related anti-CD30 MoAb HRS4. The assays revealed that the HRS3-scFv fragment exhibits the same specificity for both CD30 antigen and the tested anti-idiotypic MoAbs compared with the parental MoAb demonstrating that the recombinant scFv fragment has retained the complete idiotope of the parental MoAb.
Chromosome region 8p11-p21: Refined mapping and molecular alterations in breast cancer (1998)

Several genes, most of them unknown, of the short arm of chromosome 8 are involved in malignant diseases. Numerous studies have implicated a portion of the 8p11-p21 region as the location of one or more tumor suppressor genes involved in a variety of human cancers, including breast cancer. We and others have reported linkage analyses suggesting the presence of a putative breast cancer susceptibility gene. Furthermore, several oncogenes of the 8p11-p12 region are involved in reciprocal translocations in myeloproliferative and myelodysplastic disorders and in amplification in breast cancer. To facilitate the analysis of the 8p11-p21 region and the cloning of candidate oncogenes and tumor suppressor genes, a high-resolution physical and transcriptional map was established with 39 yeast artificial chromosomes and 94 markers, including so-called sequence-tagged sites and expressed sequence-tagged sites derived from either known genes or expressed sequence tags corresponding to unidentified transcripts. In addition, four novel transcripts were identified and localized precisely within the map. This transcription map provides a detailed description of gene order for the 8p11-p21 region and will be helpful in the identification of candidate genes for diseases. From this basis, we refined the mapping of two types of molecular alterations that occur at 8p11-p21 in sporadic breast cancers, i.e., amplification and deletion.
Role of C-peptide in human physiology (2000)

The C-peptide of proinsulin is important for the biosynthesis of insulin but has for a long time been considered to be biologically inert. Data now indicate that C-peptide in the nanomolar concentration range binds specifically to cell surfaces, probably to a G protein-coupled surface receptor, with subsequent activation of Ca(2+)-dependent intracellular signaling pathways. The association rate constant, K(ass), for C-peptide binding to endothelial cells, renal tubular cells, and fibroblasts is approximately 3. 10(9) M(-1). The binding is stereospecific, and no cross-reaction is seen with insulin, proinsulin, insulin growth factors I and II, or neuropeptide Y. C-peptide stimulates Na(+)-K(+)-ATPase and endothelial nitric oxide synthase activities. Data also indicate that C-peptide administration is accompanied by augmented blood flow in skeletal muscle and skin, diminished glomerular hyperfiltration, reduced urinary albumin excretion, and improved nerve function, all in patients with type 1 diabetes who lack C-peptide, but not in healthy subjects. The possibility exists that C-peptide replacement, together with insulin administration, may prevent the development or retard the progression of long-term complications in type 1 diabetes.
Novel ZrInZnO Thin‐film Transistor with Excellent Stability (2008)

Novel ZrInZnO semiconductor materials to resolve transistor instability for active-matrix organic light-emitting diodes are proposed. The ZrInZnO film is preprared using a cosputtering method, and presents a nanocrystal structure embedded in an amorphous matrix. The thin-film transistors fabricated have good electrical performances as well as excellent stability under long-term bias stresses.
Quantitative and Mechanistic Studies of A&#946; Immunotherapy (2009)

There is substantial and compelling evidence that aggregation and accumulation of amyloid beta protein (Abeta) plays a pivotal role in the development of Alzheimer's disease (AD); thus, numerous strategies to prevent Abeta aggregation and accumulation or to facilitate removal of preexisting deposits of Abeta are being evaluated as ways to treat or prevent AD. Pre-clinical studies in mice demonstrate the therapeutic potential of altering Abeta deposition by inducing a humoral immune response to fibrillar Abeta42 (fAbeta42) or passively administering anti-Abeta antibodies (Abs), and both passive and active anti-Abeta immunotherapeutic approaches are now being tested in humans. Although a variety of mechanisms have been postulated regarding how Abeta immunotherapy might work to attenuate or in some circumstances clear Abeta from the brain, no mechanism has been definitively proven or disproven. Herein, we will review the various mechanisms that have been postulated. In addition we will discuss how a more thorough understanding of the pharmacokinetics of anti-Abeta Abs and their effects on Abeta levels and turnover provides insight into both the therapeutic potential and limitation of Abeta immunotherapy. We will conclude with a discussion of additional experimentation required to better understand the mechanism of action of anti-Abeta Abs in AD and optimize antibody (Ab) mediated therapy for AD.
Use of Reverse Transcriptase Polymerase Chain Reaction for Diagnosis and Staging of Alveolar Rhabdomyosarcoma, Ewing Sarcoma Family of Tumors, and Desmoplastic Small Round Cell Tumor (2001)

The high sensitivity and specificity of RT-PCR for the characteristic fusion transcripts of pediatric sarcomas make it an ideal method to aid in the routine staging of these patients. In addition, the 100% sensitivity of RT-PCR in detection of micrometastasis makes it useful for follow-up and detection of minimal residual disease. However, the clinical significance of molecularly-detectable disease remains unknown. Further studies should aim to elucidate the therapeutic and prognostic implications of micrometastases detected by RT-PCR alone.
RNA Based Vaccines (2002)

The recognition that CD8(+) T-cell mediated Th1 immune responses were necessary to produce immunity to intracellular and transformed self pathogens led to intense interest in the delivery of nucleic acids, DNA, or RNA encoding candidate antigens, as vaccines. Antigen presenting cells (APC) encounter most protein and vaccine immunogens as extracellular proteins and, thus, present them on major histocompatibility complex (MHC) class II molecules leading to the activation of CD4(+) T cells. Protein antigens encoded by nucleic acids delivered to dendritic cell (DC) are produced inside the cell and, thus, can stimulate MHC class I mediated activation of CD8(+) T-cell immune responses. Unfortunately, DCs are not readily transfected with DNA (Akbari et al., 1999) resulting in the requirement for high concentrations of DNA and repeated immunizations to achieved immune responses. RNA, on the other hand, is readily taken up and expressed by DC, making it an alternative vaccine candidate. In this article, we will discuss immune responses developed, interactions between APC and RNA that activate and dictate DC activation, and preliminary studies using RNA in vivo and in vitro to develop protective immunity.
d-Galactose induces cellulase gene expression in Hypocrea jecorina at low growth rates (2006)

Lactose (1,4-O-beta-d-galactopyranosyl-d-glucose) is a soluble and economic carbon source for the industrial production of cellulases or recombinant proteins by Hypocrea jecorina (anamorph Trichoderma reesei). The mechanism by which lactose induces cellulase formation is not understood. Recent data showed that the galactokinase step is essential for cellulase induction by lactose, but growth on d-galactose alone does not induce cellulases. Consequently, the hypothesis was tested that d-galactose may be an inducer only at a low growth rate, which is typically observed when growing on lactose. Carbon-limited chemostat cultivations of H. jecorina were therefore performed at different dilution rates with d-galactose, lactose, galactitol and d-glucose. Cellulase gene expression was monitored by using a strain carrying a fusion between the cbh2 (encoding cellobiohydrolase 2, Cel6A) promoter region and the Aspergillus niger glucose oxidase gene and by identification of the two major cellobiohydrolases Cel7A and Cel6A. The results show that d-galactose indeed induces cbh2 gene transcription and leads to Cel7A and Cel6A accumulation at a low (D=0.015 h(-1)) but not at higher dilution rates. At the same dilution rate, growth on d-glucose did not lead to cbh2 promoter activation or Cel6A formation but a basal level, lower than that observed on d-galactose, was detected for the carbon-catabolite-derepressible Cel7A. Lactose induced significantly higher cellulase levels at 0.015 h(-1) than d-galactose and induced cellulases even at growth rates up to 0.042 h(-1). Results of chemostats with an equimolar mixture of d-galactose and d-glucose essentially mimicked the behaviour on d-galactose alone, whereas an equimolar mixture of d-galactose and galactitol, the first intermediate of a recently described second pathway of d-galactose catabolism, led to cellulase induction at D=0.030 h(-1). It is concluded that d-galactose indeed induces cellulases at low growth rate and that the operation of the alternative pathway further increases this induction. However, under those conditions lactose is still a superior inducer for which the mechanism remains to be clarified.
StimDust: A 6.5mm3, wireless ultrasonic peripheral nerve stimulator with 82% peak chip efficiency (2018)

We present a 6.5mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , 10mg, wireless peripheral nerve stimulator. The stimulator is powered and controlled through ultrasound from an external transducer and utilizes a single 750×750×750μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> piezocrystal for downlink communication, powering, and readout, reducing implant volume and mass. An IC with 0.06mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> active circuit area, designed in TSMC 65nm LPCMOS process, converts harvested ultrasound to stimulation charge with a peak efficiency of 82%. A custom wireless protocol that does not require a clock or memory circuits reduces on-chip power to 4μW when not stimulating. The encapsulated stimulator was cuffed to the sciatic nerve of an anesthetized rodent and demonstrated full-scale nerve activation in vivo. We achieve a highly efficient and temporally precise wireless peripheral nerve stimulator that is the smallest and lightest to our knowledge.
Comparative Genomics of BCG Vaccines by Whole-Genome DNA Microarray (1999)

Bacille Calmette-Guérin (BCG) vaccines are live attenuated strains of Mycobacterium bovis administered to prevent tuberculosis. To better understand the differences between M. tuberculosis, M. bovis, and the various BCG daughter strains, their genomic compositions were studied by performing comparative hybridization experiments on a DNA microarray. Regions deleted from BCG vaccines relative to the virulent M. tuberculosis H37Rv reference strain were confirmed by sequencing across the missing segment of the H37Rv genome. Eleven regions (encompassing 91 open reading frames) of H37Rv were found that were absent from one or more virulent strains of M. bovis. Five additional regions representing 38 open reading frames were present in M. bovis but absent from some or all BCG strains; this is evidence for the ongoing evolution of BCG strains since their original derivation. A precise understanding of the genetic differences between closely related Mycobacteria suggests rational approaches to the design of improved diagnostics and vaccines.
Epstein-Barr virus-associated non-Hodgkin's lymphoma in patients infected with the human immunodeficiency virus [see comments] (1993)

Lymphoproliferations associated with Epstein-Barr virus (EBV) commonly arise in settings of immune dysfunction, including human immunodeficiency virus (HIV) infection. In this study, EBV was associated with 39 of 59 (66%) HIV-related systemic lymphomas. Unlike the lymphoproliferations that arise in the setting of transplantation, the HIV-related lymphomas were monoclonal, as evaluated by Ig heavy chain rearrangements and EBV termini analysis, and associated (40%) with c-MYC rearrangements. Furthermore, analysis of multiple lymphoma tissues from one autopsy showed evidence that a single lymphoma clone was responsible for dissemination. The latent EBV nuclear antigen (EBNA- 1) transcripts detected in the HIV-related lymphomas were characteristic of the pattern found in Burkitt lymphoma (g1 EBNA1) and not in transplant-related lymphoproliferations. However, unlike Burkitt lymphoma, EBV latent membrane-associated protein (LMP) transcripts were also detected, thereby constituting an EBV expression pattern (g1 EBNA1+, LMP+) not previously observed in B-cell lymphomas. These findings demonstrate a high frequency of EBV-associated lymphomas in the setting of HIV infection that are distinct from the lymphoproliferations that arise during iatrogenic transplant-associated immuno-suppression or in the general population. However, it is also apparent that HIV-related lymphomas are biologically heterogeneous, which may reflect the multiple mechanisms or steps necessary for eventual malignant transformation.
Fast-Start (2001)

Availability requirements for database systems are more stringent than ever before with the widespread use of databases as the foundation for ebusiness. This paper highlights Fast-Start ™ Fault Recovery , an important availability feature in Oracle, designed to expedite recovery from unplanned outages. Fast-Start allows the administrator to configure a running system to impose predictable bounds on the time required for crash recovery. For instance, fast-start allows fine-grained control over the duration of the roll-forward phase of crash recovery by adaptively varying the rate of checkpointing with minimal impact on online performance. Persistent transaction locking in Oracle allows normal online processing to be resumed while the rollback phase of recovery is still in progress, and fast-start allows quick and transparent rollback of changes made by uncommitted transactions prior to a crash.