gebhart/patrepeval huggingface dataset:
Functional Analysis of Alkane Hydroxylases from Gram-Negative and Gram-Positive Bacteria (2002)

We have cloned homologs of the Pseudomonas putida GPo1 alkane hydroxylase from Pseudomonas aeruginosa PAO1, Pseudomonas fluorescens CHA0, Alcanivorax borkumensis AP1, Mycobacterium tuberculosis H37Rv, and Prauserella rugosa NRRL B-2295. Sequence comparisons show that the level of protein sequence identity between the homologs is as low as 35%, and that the Pseudomonas alkane hydroxylases are as distantly related to each other as to the remaining alkane hydroxylases. Based on the observation that rubredoxin, an electron transfer component of the GPo1 alkane hydroxylase system, can be replaced by rubredoxins from other alkane hydroxylase systems, we have developed three recombinant host strains for the functional analysis of the novel alkane hydroxylase genes. Two hosts, Escherichia coli GEc137 and P. putida GPo12, were equipped with pGEc47 Delta B, which encodes all proteins necessary for growth on medium-chain-length alkanes (C(6) to C(12)), except a functional alkane hydroxylase. The third host was an alkB knockout derivative of P. fluorescens CHA0, which is no longer able to grow on C(12) to C(16) alkanes. All alkane hydroxylase homologs, except the Acinetobacter sp. ADP1 AlkM, allowed at least one of the three hosts to grow on n-alkanes.
STM-64 linearly repeatered optical transmissionexperimentusing forward error correcting codes (1995)

STM-64 (10 Gbit/s) nonregenerative transmission experiments using forward error correcting codes have been conducted for the first time. Bit errors caused by dispersion in the transmission line and optical noise of Er-doped fibre amplifiers were successfully corrected by using (18880, 18865) and (2370, 2358) shortened Hamming codes.
Artificial Trading for US Wholesale Electric Power Market (2004)

In the US wholesale power market, electric power producers trade among themselves as well as with power-marketing and power-distribution companies. The wholesale power market comprises the world’s largest commodity market. The growth in power trading is due to the ongoing deregulation of the electric power industry. Most of deregulation scenarios indicate a further separation of power production from transmission and retailing, along with production and retailing, opened to more competition. Unfortunately, the power trading mechanism is not clearly investigated in the level that we can understand and predict a price change in the wholesale market. This study investigates such an exploration of the price change in the US power market. Computer software developed by Sueyoshi and Tadiparthi (2004) includes various analytical and numerical techniques and forecasting methods. Using the computer software, we investigate how traders determine power prices in the wholesale market and how the price change is occurring under different economic and engineering environments.
High-Q UHF micromechanical radial-contour mode disk resonators (2005)

A micromechanical, laterally vibrating disk resonator, fabricated via a technology combining polysilicon surface-micromachining and metal electroplating to attain submicron lateral capacitive gaps, has been demonstrated at frequencies as high as 829 MHz and with Q's as high as 23 000 at 193 MHz. Furthermore, the resonators have been demonstrated operating in the first three radial contour modes, allowing a significant frequency increase without scaling the device, and a 193 MHz resonator has been shown operating at atmospheric pressure with a Q of 8,880, evidence that vacuum packaging is not necessary for many applications. These results represent an important step toward reaching the frequencies required by the RF front-ends in wireless transceivers. The geometric dimensions necessary to reach a given frequency are larger for this contour-mode than for the flexural-modes used by previous resonators. This, coupled with its unprecedented Q value, makes this disk resonator a choice candidate for use in the IF and RF stages of future miniaturized transceivers. Finally, a number of measurement techniques are demonstrated, including two electromechanical mixing techniques, and evaluated for their ability to measure the performance of sub-optimal (e.g., insufficiently small capacitive gap, limited dc-bias), high-frequency, high-Q micromechanical resonators under conditions where parasitic effects could otherwise mask motional output currents. [1051].
Xunzi's moral analysis of war and some of its contemporary implications (2015)

The ancient Chinese expression for 'punitive expedition' is zheng or zhengfa, which connote 'conquest and subjugation'. This chapter reappraises early Chinese ideas, especially the Daoist one, on punitive expeditions with the intention that those ethical debates should be revisited to look at discourses of just war and world order in the twenty-first century. It focuses on the Daoist position as represented by Laozi and Zhuangzi. One of the contested issues within the framework of contemporary just war theory is 'humanitarian intervention'. The chapter argues that the differences between Confucianism and Daoism with regard to their political views and positions on war and peace may be approached from two related yet different models of 'harmony' in early Chinese philosophy, namely the music model and the culinary model. These two models point to two different ways of understanding what constitutes harmony and harmonization.
Cerebrospinal Fluid lnterleukin-6, Prostaglandin E2 and Autoantibodies in Patients with Neuropsychiatric Systemic Lupus Erythematosus and Central Nervous System Infections (1994)

Cerebrospinal fluid (CSF) from patients with a variety of central nervous system (CNS) disorders was assayed for cytokines, prostaglandins, and autoantibodies. CSF interleukin-6 (IL-6) in patients with CNS infection (374.24 +/- 92.61 pg/mL) and neuropsychiatric systemic lupus erythematosus (NP-SLE) (71.40 +/- 5.89 pg/mL) were significantly higher than in patients with CNS inflammation (33.92 +/- 29.36 pg/mL) or controls (non-inflammatory CNS diseases) (4.35 +/- 3.00 pg/mL). Interleukin-1 beta, interferon alpha, and tumor necrosis factor alpha were undetectable in these samples: CSF prostaglandin E2 (PGE2) also exhibited similar patterns as IL-6. CSF immunoglobulin G (IgG) in patients with NP-SLE (8.84 +/- 1.80 mg/dL) was much higher than in patients with CNS infection (4.65 +/- 3.09 mg/dL), CNS inflammation (2.54 +/- 1.24 mg/dL), or controls (2.11 +/- 1.03 mg/dL). CSF autoantibodies against calf thymus antigens were present in patients with NP-SLE but not in patients with CNS infection as demonstrated by immunoblot. These results suggest that high IL-6 and PGE2 in CSF favors the diagnosis of CNS infection, while modestly elevated IL-6, high IgG, and autoantibodies against calf thymus antigens in CSF are the features of NP-SLE.
Color Manipulation of Mechanoluminescence from Stress‐Activated Composite Films (2013)

The prospective application of luminescence to imaging devices is shown using a combination of color-tunable and patternable mechanoluminescent materials. A white light source is demonstrated by using an alternative color tuning method, induced under high vibration conditions. As the implementation is fairly straightforward, it is expected that the present results will find a number of potential uses in current industrial applications.
Selective Sintering of Metal Nanoparticle Ink for Maskless Fabrication of an Electrode Micropattern Using a Spatially Modulated Laser Beam by a Digital Micromirror Device (2014)

We demonstrate selective laser sintering of silver (Ag) nanoparticle (NP) ink using a digital micromirror device (DMD) for the facile fabrication of 2D electrode pattern without any conventional lithographic means or scanning procedure. An arbitrary 2D pattern at the lateral size of 25 μm × 25 μm with 160 nm height is readily produced on a glass substrate by a short exposure of 532 nm Nd:YAG continuous wave laser. The resultant metal pattern exhibits low electrical resistivity of 10.8 uΩ · cm and also shows a fine edge sharpness by the virtue of low thermal conductivity of Ag NP ink. Furthermore, 10 × 10 star-shaped micropattern arrays are fabricated through a step-and-repeat scheme to ensure the potential of this process for the large-area metal pattern fabrication.
Biomedical applications of polyhydroxyalkanoates, an overview of animal testing andin vivoresponses (2006)

Polyhydroxyalkanoates (PHAs) have been established as biodegradable polymers since the second half of the twentieth century. Altering monomer composition of PHAs allows the development of polymers with favorable mechanical properties, biocompatibility and desirable degradation rates, under specific physiological conditions. Hence, the medical applications of PHAs have been explored extensively in recent years. PHAs have been used to develop devices, including sutures, nerve repair devices, repair patches, slings, cardiovascular patches, orthopedic pins, adhesion barriers, stents, guided tissue repair/regeneration devices, articular cartilage repair devices, nerve guides, tendon repair devices, bone-marrow scaffolds, tissue engineered cardiovascular devices and wound dressings. So far, various tests on animal models have shown polymers, from the PHA family, to be compatible with a range of tissues. Often, pyrogenic contaminants copurified with PHAs limit their pharmacological application rather than the monomeric composition of the PHAs and thus the purity of the PHA material is critical. This review summarizes the animal testing, tissue response, in vivo molecular stability and challenges of using PHAs for medical applications. In future, PHAs may become the materials of choice for various medical applications.
Delivery of Multiple Transgenes to Plant Cells (2007)

The use of transgenic technologies for the genetic manipulation of plant species has had a profound impact on basic plant research and biotechnology. Overexpression of heterogonous genes, for example, is widely used for the introduction of novel traits into transgenic crop plants. Overexpression can also be used in combination with down-regulation and controlled expression (e.g. induced, developmentally regulated, or tissue specific) studies as a tool for basic plant research and for functional analysis of native genes in various model plants. Two crucial components are required for the transient and/or stable expression of
Teratogenesis of holoprosencephaly (2002)

Teratogenic causes of holoprosencephaly are critically assessed. A brief general review of holoprosencephaly is followed by four tables summarizing etiologic factors. Subjects evaluated here include: 1) maternal diabetes; 2) ethyl alcohol; 3) retinoic acid; 4) mutated genes and teratogens involving the sonic hedgehog signaling network and cholesterol biosynthesis; and 5) cholesterol trafficking, sterol adducts, target tissue response, and sterol sensing domain.
An embedded overlay concept for microsystems packaging (2000)

An embedded overlay concept for packaging hybrid components containing microelectromechanical systems (MEMS) is described. This packaging process is a derivative of the chip-on-flex (COF) process currently used for microelectronics packaging. COF is a high performance, multichip packaging technology in which die are encased in a molded plastic substrate and interconnects are made via a thin-film structure formed over the components. A laser ablation process has been developed which enables selected areas of the COF overlay to be efficiently ablated with minimal impact to the packaged MEMS devices. Analysis and characterization of the ablation procedures used in the standard COF process was performed to design a new procedure which minimized the potential for heat damage to exposed MEMS devices. The COF/MEMS packaging technology is well-suited for many microsystem packaging applications such as micro-optics and radio frequency (RF) devices.
Correction: Rapamycin Inhibits IGF-1-Mediated Up-Regulation of MDM2 and Sensitizes Cancer Cells to Chemotherapy (2013)

The Murine Double Minute 2 (MDM2) protein is a key regulator of cell proliferation and apoptosis that acts primarily by inhibiting the p53 tumor suppressor. Similarly, the PI3-Kinase (PI3K)/AKT pathway is critical for growth factor-mediated cell survival. Additionally, it has been reported that AKT can directly phosphorylate and activate MDM2. In this study, we show that IGF-1 up-regulates MDM2 protein levels in a PI3K/AKT-dependent manner. Inhibition of mTOR by rapamycin or expression of a dominant negative eukaryotic initiation factor 4E binding protein 1 (4EBP1) mutant protein, as well as ablation of eukaryotic initiation factor 4E (eIF4E), efficiently abolishes IGF-1-mediated up-regulation of MDM2. In addition, we show that rapamycin effectively inhibits MDM2 expression and sensitizes cancer cells to chemotherapy. Taken together, this study reveals a novel mechanism by which IGF-1 activates MDM2 via the mTOR pathway, and that pharmacologic inhibition of mTOR combined with chemotherapy may be more effective in treatment of a subset of cancers harboring increased MDM2 activation.
A novel transcription property of SP6 and T7 RNA polymerases: dependence on template structure (1985)

The in vitro synthesis of extraneous RNA sequences by SP6 and T7 RNA polymerases from specific DNA templates is described. Transcription of templates prepared by digestion with restriction enzymes that leave 3' protruding ends resulted in the production of significant amounts of long, template-sized RNA transcripts which hybridized to vector DNA. Sequences copied from the noncoding template strand were among the extraneous transcripts. The presence of these sequences in probe preparations were detected in Southern and RNase protection hybridization assays. In contrast, transcription of DNA templates with blunt or 5' protruding ends yielded few RNA products as extraneous sequences.
Elevated Concentrations of CSF Corticotropin-Releasing Factor-Like Immunoreactivity in Depressed Patients (1984)

The possibility that hypersecretion of corticotropin-releasing factor (CRF) contributes to the hyperactivity of the hypothalamo-pituitary-adrenal axis observed in patients with major depression was investigated by measuring the concentration of this peptide in cerebrospinal fluid of normal healthy volunteers and in drug-free patients with DSM-III diagnoses of major depression, schizophrenia, or dementia. When compared to the controls and the other diagnostic groups, the patients with major depression showed significantly increased cerebrospinal fluid concentrations of CRF-like immunoreactivity; in 11 of the 23 depressed patients this immunoreactivity was greater than the highest value in the normal controls. These findings are concordant with the hypothesis that CRF hypersecretion is, at least in part, responsible for the hyperactivity of the hypothalamo-pituitary-adrenal axis characteristic of major depression.
A novel ligand delivery system to non-invasively visualize and therapeutically exploit the IL13Rα2 tumor-restricted biomarker (2012)

Our objective was to exploit a novel ligand-based delivery system for targeting diagnostic and therapeutic agents to cancers that express interleukin 13 receptor alpha 2 (IL13Rα2), a tumor-restricted plasma membrane receptor overexpressed in glioblastoma multiforme (GBM), meningiomas, peripheral nerve sheath tumors, and other peripheral tumors. On the basis of our prior work, we designed a novel IL13Rα2-targeted quadruple mutant of IL13 (TQM13) to selectively bind the tumor-restricted IL13Rα2 with high affinity but not significantly interact with the physiologically abundant IL13Rα1/IL4Rα heterodimer that is also expressed in normal brain. We then assessed the in vitro binding profile of TQM13 and its potential to deliver diagnostic and therapeutic radioactivity in vivo. Surface plasmon resonance (SPR; Biacore) binding experiments demonstrated that TQM13 bound strongly to recombinant IL13Rα2 (Kd∼5 nM). In addition, radiolabeled TQM13 specifically bound IL13Rα2-expressing GBM cells and specimens but not normal brain. Of importance, TQM13 did not functionally activate IL13Rα1/IL4Rα in cells or bind to it in SPR binding assays, in contrast to wtIL13. Furthermore, in vivo targeting of systemically delivered radiolabeled TQM13 to IL13Rα2-expressing subcutaneous tumors was demonstrated and confirmed non-invasively for the first time with 124I-TQM13 positron emission tomography imaging. In addition, 131I-TQM13 demonstrated in vivo efficacy against subcutaneous IL13Rα2-expressing GBM tumors and in an orthotopic synergeic IL13Rα2-positive murine glioma model, as evidenced by statistically significant survival advantage. Our results demonstrate that we have successfully generated an optimized biomarker-targeted scaffolding that exhibited specific binding activity toward the tumor-associated IL13Rα2 in vitro and potential to deliver diagnostic and therapeutic payloads in vivo.
Effectiveness, Tolerability, and Safety of Belimumab in Patients with Refractory SLE: a Review of Observational Clinical-Practice-Based Studies (2018)

The following changes are made for this article: (1.) Maddalena Larosa's given name and surname were inadvertently interchanged. The authorgroup section is now corrected. (2.) The author(s)' decision to opt for Open Choice.
Overexpression of cyclin D1 correlates with recurrence in a group of forty-seven operable squamous cell carcinomas of the head and neck. (1995)

We evaluated the prognostic significance of overexpression of cyclin D1 in 47 patients with surgically resected squamous cell carcinomas of the head and neck. Overexpression of cyclin D1 was detected immunohistochemically using an affinity-purified polyclonal antibody directed against the carboxyl-terminal part of the cyclin D1 protein, applied to formalin-fixed, paraffin-embedded tissue sections. Overexpression of cyclin D1 was found in 30 of 47 head and neck squamous cell carcinoma (HNSCC) cases and was associated with a more rapid and frequent recurrence of disease (P = 0.027). There was a 5-year disease-free interval of 47% for HNSCC patients with a strong overexpression of cyclin D1 and of 80% for cyclin D1-negative HNSCC patients. Overexpression of cyclin D1 was also associated with a shortened overall survival of these patients (P = 0.0095), with a 5-year survival of 60% for the cyclin D1 strongly positive cases and of 83% for cyclin D1-negative cases. Overexpression of cyclin D1 appears to indicate poor prognosis in operable HNSCC.
Abstract 880: Allogeneic CAR-T cell products containing 10 gene edits using CRISPR/Cas9 can retain full functionality in vivo and in vitro (2020)

Abstract Hematologic malignancies have proven most responsive to CAR-T therapies. However, there is significant variability in the depth and duration of response to autologous CAR-T cells. Furthermore, CAR-T responses in solid malignancies have been minimal. T cells from cancer patients can be compromised by the disease and prior treatments, and the use of allogeneic CAR-T products could potentially provide a more robust therapy. However, even CAR-T cells from healthy donors may benefit from additional gene edits that could enhance effector function, increase durability, evade immune mechanisms and/or combat the tumor microenvironment. These types of additional CAR-T features are readily enabled by CRISPR/Cas9 technology. While recent clinical data has demonstrated the persistence of therapeutic T cells that had been edited with CRISPR, the extent of gene editing that therapeutic T cells can tolerate has not been fully described. Herein, we have generated CAR-T cells with 10 gene edits. Loss of function alleles were produced in 9 genes and a CAR cassette was knocked into the TRAC locus via homology-directed repair. CD19-directed CAR-T cells with these 10 gene edits were fully functional in vitro, as shown by their ability to expand and kill target cells and secrete cytokines while remaining non-transformed. These cells were also highly efficacious in an in vivo model of CD19+ malignancy. Importantly, these edits, which produced insertions and deletions in target genes, could be detected in the blood of mice several months post injection. These data demonstrate that CRISPR/Cas9 can be used to create highly edited allogeneic CAR-T cells, unlocking the potential to enhance many functions relevant to CAR-T health and anti-tumor activity. Citation Format: Brigid McEwan, Meghna Kuppuraju, Zinkal Padalia, Jonathan Terrett, Demetrios Kalaitzidis. Allogeneic CAR-T cell products containing 10 gene edits using CRISPR/Cas9 can retain full functionality in vivo and in vitro [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 880.
The Human Obesity Gene Map: The 1999 Update (2000)

This report constitutes the sixth update of the human obesity gene map incorporating published results up to the end of October 1999. Evidence from the rodent and human obesity cases caused by single gene mutations, Mendelian disorders exhibiting obesity as a clinical feature, quantitative trait loci (QTL) uncovered in human genome-wide scans and in crossbreeding experiments with mouse, rat, pig and chicken models, association and linkage studies with candidate genes and other markers is reviewed. Twenty-five human cases of obesity can now be explained by variation in five genes. Twenty Mendelian disorders exhibiting obesity as one of their clinical manifestations have now been mapped. The number of different QTLs reported from animal models reaches now 98. Attempts to relate DNA sequence variation in specific genes to obesity phenotypes continue to grow, with 89 reports of positive associations pertaining to 40 candidate genes. Finally, 44 loci have linked to obesity indicators in genomic scans and other linkage study designs. The obesity gene map depicted in Figure 1 reveals that putative loci affecting obesity-related phenotypes can be found on all autosomes, with chromosomes 14 and 21 showing each one locus only. The number of genes, markers, and chromosomal regions that have been associated or linked with human obesity phenotypes continues to increase and is now well above 200.
The alpha-1,3-galactosyltransferase knockout mouse (1996)

Organ xenografts in discordant combinations such as pig-to-man undergo hyperacute rejection due to the presence of naturally occurring human anti-pig xenoantibodies. The galactose [alpha](1,3)-galactose epitope on glycolipids and glycoproteins is the major porcine xenoantigen recognized by these xenoantibodies. This epitope is formed by[alpha](1,3)-galactosyltransferase, which is present in all mammals except man, apes, and Old World monkeys. We have generated mice lacking this major xenoantigen by inactivating the [alpha](1,3)-galactosyltransferase gene. These mice are viable and have normal organs but develop cataracts. Substantially less xenoantibody from human serum binds to cells and tissues of these mice compared with normal mice. Similarly, there is less activation of human complement on cells from mice lacking the galactose [alpha](1,3)-galactose epitope. These mice confirm the importance of the galactose[alpha](1,3)-galactose epitope in human xenoreactivity and the logic of continuing efforts to generate pigs that lack this epitope as a source of donor organs.
Simple and efficient subtractive hybridization screening. (1991)

A method of subtractive hybridization screening is presented that does not rely on the availability of large amounts of poly(A)+ RNA. The usefulness of this method is demonstrated by the isolation of cDNA clones that are unique or present at enhanced levels in cDNA libraries derived from a psoriatic skin cell line. A very high level of enrichment for rare cDNA sequences is possible as shown by the isolation of cDNA clones present at a frequency of less than one in one hundred thousand (0.001%). This method is particularly useful in experimental systems where the amount of RNA available is limited.