gebhart/patrepeval huggingface dataset:
Conformable formation of high quality ultra-thin amorphous Ta/sub 2/O/sub 5/ gate dielectrics utilizing water assisted deposition (WAD) for sub 50 nm damascene metal gate MOSFETs (2002)

A conformable formation process of ultra-thin Ta/sub 2/O/sub 5/ gate dielectrics, which is applicable to 50 nm damascene gate MOSFETs, was developed. Assisted by H/sub 2/O, perfect conformability was successfully realized even in the narrow gate groove (50 nm), while maintaining a low gate leakage. An excellent device performance of S-factor 72 mV/decade was obtained in 90 nm MOSFET with amorphous Ta/sub 2/O/sub 5/ gate dielectrics of T/sub eff/ 1.6 nm.
Regulation of the interferon-inducible IFI-78K gene, the human equivalent of the murine Mx gene, by interferons, double-stranded RNA, certain cytokines, and viruses (1989)

The interferon-inducible gene (IFI-78K gene) that codes for a human protein, p78, of 78,000 Mr is the equivalent of the mouse Mx gene encoding Mx protein. The IFI-78K gene is located on chromosome 21 together with the alpha/beta interferon (IFN-alpha/beta) receptor. The p78 protein is important since it may be involved in resistance to influenza viruses. The regulation of the IFI-78K gene was studied in human diploid cells by using a cDNA probe to p78 mRNA and specific monoclonal antibodies to p78 protein. The IFI-78K gene, a normally quiescent gene, is transcriptionally regulated by IFN-alpha, and its induction does not require protein synthesis. The rate of transcription measured in a run-on assay increased rapidly but transiently. The level of p78 mRNA increased up to 8 h, declining slowly afterwards. The p78 protein, undetectable in untreated cells, accumulated up to 16 h, and its amount remained stable for at least 36 h after the addition of IFN-alpha. Cytokines such as tumor necrosis factor, interleukin-1 alpha, and interleukin-1 beta activated the IFI-78K gene at concentrations comparable to that of IFN-alpha. However, gene activation by these cytokines required protein synthesis. Poly(rI)-poly(rC) induced the IFI-78K gene directly at the transcriptional level without requirement for protein synthesis. Newcastle disease virus, influenza virus, and to a lesser extent vesicular stomatitis virus also induced the IFI-78K gene in the absence of any protein synthesis. Induction of transcription by viruses was markedly enhanced by pretreatment of cells with IFN-gamma (which by itself is a poor inducer of the IFI-78K gene), resulting in accumulation of p78 protein during the course of infection; this suggests that IFN-gamma programs cells to full antiviral activity upon virus infection.
A single low dose of human recombinant interleukin 1 accelerates the recovery of neutrophils in mice with cyclophosphamide-induced neutropenia. (1989)

The actions of the cytokine interleukin 1 (IL-1) in hematopoiesis involve induction of colony-stimulating factor (CSF) production on accessory cells in the hematopoietic microenvironment and synergy with CSF on early hematopoietic progenitor cells. We have used these properties to accelerate hematologic reconstitution in granulocytopenic mice. Mice with cyclophosphamide-induced granulocytopenia were injected i.p. at day 0 with a single dose (8-800 ng) of human recombinant IL-1 alpha. At daily intervals thereafter during a period of 7 days mice were sacrificed and blood granulocytes and bone marrow cellularity were assessed. Mice receiving a single dose of 80 or 800 ng IL-1 had significantly (p less than 0.05) higher blood granulocyte counts at days 4 and 5 than control animals receiving heat-activated IL-1. This activity of IL-1 was not affected by injection of the cyclooxygenase inhibitor ibuprofen. Bone marrow cellularity, as assessed in histological sections of femurs, was significantly greater (p less than 0.05) at day 2 in mice treated with 80 or 800 ng IL-1. These results show that a single low dose of IL-1 may be used to accelerate the reconstitution of granulocytes following granulocytopenia induced with chemotherapy.
Carbohydrate-binding protein 35. I. Properties of the recombinant polypeptide and the individuality of the domains (1993)

The cDNA clone for carbohydrate-binding protein 35 (CBP35) was engineered into the bacterial expression vector pIN III ompA2, which directs the secretion of the expressed protein into the periplasmic space. Recombinant CBP35 was purified from this system, at a level of approximately 50 mg/liter of bacterial culture. Digestion of recombinant CBP35 with collagenase D, followed by purification using saccharide-specific affinity chromatography yielded a M(r) approximately 16,000 polypeptide, corresponding to the COOH-terminal domain (residues 118-264) of the CBP35 polypeptide. This indicates that the COOH-terminal half of CBP35 contains the carbohydrate recognition domain, consistent with its sequence homology to other S-type lectins. The NH2-terminal domain (residues 1-137) was derived by site-directed mutagenesis of the cDNA, in which stop codons are inserted in place of Gly138 and Gly139, and expression of the mutant cDNA in the same pIN III ompA2 system. The purified NH2-terminal domain failed to bind to saccharide-specific affinity resins. Differential scanning calorimetry of rCBP35 and its individual domains yielded transition temperatures of approximately 39 and approximately 56 degrees C for the NH2- and COOH-terminal domains, respectively. Lactose binding by the COOH-terminal domain shifted the transition temperature to 65 degrees C, whereas sucrose failed to yield the same effect. These results suggest that the individual domains of the CBP35 polypeptide are folded independently.
β‐amyloid burden is not associated with rates of brain atrophy (2007)

These findings suggest that rate of brain volume loss is not determined by the amount of insoluble Abeta in the gray matter.
A high-throughput x-ray microtomography system at the Advanced Photon Source (2001)

A third-generation synchrotron radiation source provides enough brilliance to acquire complete tomographic data sets at 100 nm or better resolution in a few minutes. To take advantage of such high-brilliance sources at the Advanced Photon Source, we have constructed a pipelined data acquisition and reconstruction system that combines a fast detector system, high-speed data networks, and massively parallel computers to rapidly acquire the projection data and perform the reconstruction and rendering calculations. With the current setup, a data set can be obtained and reconstructed in tens of minutes. A specialized visualization computer makes rendered three-dimensional (3D) images available to the beamline users minutes after the data acquisition is completed. This system is capable of examining a large number of samples at sub-μm 3D resolution or studying the full 3D structure of a dynamically evolving sample on a 10 min temporal scale. In the near future, we expect to increase the spatial resolution to below 100 nm by using zone-plate x-ray focusing optics and to improve the time resolution by the use of a broadband x-ray monochromator and a faster detector system.
Efficient Delivery of dsRNA and DNA in Cultured Silkworm Cells for Gene Function Analysis Using PAMAM Dendrimers System (2019)

<b>:</b> Polyamidoamine (PAMAM) dendrimers are emerging as intriguing nanovectors for nucleic acid delivery because of their unique well-defined architecture and high binding capacity, which have been broadly applied in DNA- and RNA-based therapeutics. The low-cost and high-efficiency of PAMAM dendrimers relative to traditional liposomal transfection reagents also promote their application in gene function analysis. In this study, we first investigated the potential use of a PAMAM system in the silkworm model insect. We determined the binding property of G5-PAMAM using dsRNA and DNA in vitro, and substantially achieved the delivery of dsRNA and DNA from culture medium to both silkworm BmN and BmE cells, thus leading to efficient knockdown and expression of target genes. Under treatments with different concentrations of G5-PAMAM, we evaluated its cellular cytotoxicity on silkworm cells, and the results show that G5-PAMAM had no obvious toxicity to cells. The presence of serum in the culture medium did not affect the delivery performance of DNA and dsRNA by G5-PAMAM, revealing its convenient use for various purposes. In conclusion, our data demonstrate that the PAMAM system provides a promising strategy for delivering dsRNA and DNA in cultured silkworm cells and promote its further application in individuals.
Chemotherapy and chemosensitization of transgenic mice which express the human multidrug resistance gene in bone marrow: efficacy, potency, and toxicity. (1991)

A common form of multidrug resistance in human cancer results from expression of the MDR1 gene which encodes a plasma membrane energy-dependent multidrug efflux pump. We have engineered transgenic mice which express this multidrug transporter in their bone marrow cells and demonstrated that peripheral WBC of these animals provide a rapid and reliable system for assessing the bioactivity of agents that reverse multidrug resistance. Immunocytochemical analysis of bone marrow smears suggests that the activation of the MDR1 transgene has probably occurred at a very early stage of bone marrow differentiation since most bone marrow cells express the transporter. Expression of this transgene in bone marrow produces about 10-fold resistance to leukopenia induced by taxol compared to normal bone marrow. Chemosensitization of MDR1 mice to daunomycin and taxol, measured by a fall in WBC, is detectable at a dose as low as 0.01 mg/kg R-verapamil. A dose of 0.5 mg/kg R-verapamil reduces the WBC by nearly 50%. Chemosensitization of MDR-transgenic mice with 5 mg/kg R-verapamil, which is highly effective in reversing MDR and readily tolerated by mice, necessitates a reduction of the maximum tolerated dose of most chemotherapeutic agents by only 20%. In addition, detailed histopathological examination shows that treatment of mice with chemotherapeutic drugs and R-verapamil does not change the organ-related toxicity pattern but only moderately accentuates inherent toxic side effects of the chemotherapeutic agents. We conclude that MDR1-transgenic mice represent a valid model for evaluating efficacy, potency, and toxicity associated with chemotherapy and chemosensitization of multidrug-resistant cells in animals.
Anomaly detection in dynamic networks: a survey (2015)

Anomaly detection is an important problem with multiple applications, and thus has been studied for decades in various research domains. In the past decade there has been a growing interest in anomaly detection in data represented as networks, or graphs, largely because of their robust expressiveness and their natural ability to represent complex relationships. Originally, techniques focused on anomaly detection in static graphs, which do not change and are capable of representing only a single snapshot of data. As real‐world networks are constantly changing, there has been a shift in focus to dynamic graphs, which evolve over time. In this survey, we aim to provide a comprehensive overview of anomaly detection in dynamic networks, concentrating on the state‐of‐the‐art methods. We first describe four types of anomalies that arise in dynamic networks, providing an intuitive explanation, applications, and a concrete example for each. Having established an idea for what constitutes an anomaly, a general two‐stage approach to anomaly detection in dynamic networks that is common among the methods is presented. We then construct a two‐tiered taxonomy, first partitioning the methods based on the intuition behind their approach, and subsequently subdividing them based on the types of anomalies they detect. Within each of the tier one categories—community, compression, decomposition, distance, and probabilistic model based—we highlight the major similarities and differences, showing the wealth of techniques derived from similar conceptual approaches. WIREs Comput Stat 2015, 7:223–247. doi: 10.1002/wics.1347 This article is categorized under: Algorithms and Computational Methods &gt; Algorithms Data: Types and Structure &gt; Graph and Network Data Statistical Learning and Exploratory Methods of the Data Sciences &gt; Pattern Recognition
Designed Enediynes: A New Class of DNA-Cleaving Molecules with Potent and Selective Anticancer Activity (1992)

The rational design and biological actions of a new class of DNA-cleaving molecules with potent and selective anticancer activity are reported. These relatively simple enediyne-type compounds were designed from basic chemical principles to mimic the actions of the rather complex naturally occurring enediyne anticancer antibiotics, particularly dynemicin A. Equipped with locking and triggering devices, these compounds damage DNA in vitro and in vivo on activation by chemical or biological means. Their damaging effects are manifested in potent anticancer activity with remarkable selectivities. Their mechanism of action involves intracellular unlocking and triggering of a Bergman reaction, leading to highly reactive benzenoid diradicals that cause severe DNA damage. The results of these studies demonstrate the potential of these de novo designed molecules as biotechnology tools and anticancer agents.
Enhanced interaction of L-selectin with the high endothelial venule ligand via selectively oxidized sialic acids. (1993)

The selectins are adhesion receptors that play key roles in leukocyte trafficking. Each has an N-terminal C-type lectin domain that binds to specific carbohydrates in a calcium-dependent manner. L-selectin recognizes sulfated, sialylated ligands on lymph node high endothelial venules. This recognition is abolished by strong periodate oxidation under conditions that destroy oligosaccharides. In contrast, mild periodate oxidation, which selectively oxidizes the side chain of sialic acid residues without affecting the underlying oligosaccharide, markedly enhances this interaction. The enhancement is calcium dependent, indicating that lectin recognition is maintained. Reduction of the sialic acid aldehydes generated by mild periodate to alcohol groups abolishes this effect. Covalent cross-linking of the oxidized ligand to L-selectin can be demonstrated, suggesting Schiff base formation between lysine residues of the selectin and the newly formed aldehydes. Such selectively oxidized sialylated ligands could be used to probe the lectin domains of the selectins and to identify lysine residues near the binding site. Also, this approach could be used to design drugs for disrupting leukocyte-endothelial interactions leading to pathological inflammation.
Brentuximab vedotin for relapsed or refractory non-Hodgkin lymphoma: Preliminary results from a phase II study. (2012)

8070 Background: Brentuximab vedotin is a CD30-directed antibody-drug conjugate approved for the treatment of Hodgkin lymphoma and systemic anaplastic large cell lymphoma (ALCL) after failure of other therapies. Based on the high objective response rate observed in patients with systemic ALCL, a type of non-Hodgkin lymphoma that is characterized by homogeneous CD30 expression, a study was initiated in other non-Hodgkin lymphomas that express the CD30 target. Methods: A phase 2 open-label single-arm study is underway in patients with relapsed or refractory CD30-positive non-Hodgkin lymphoma, excluding ALCL (NCT01421667). Brentuximab vedotin is administered IV at 1.8 mg/kg every 3 weeks until disease progression or unacceptable toxicity. The primary endpoint is objective response rate assessed by the Revised Response Criteria for Malignant Lymphoma (Cheson 2007). Tumor specimens are assessed by central lab in order to characterize the relationship of CD30 expression with antitumor activity. Results: Ten patients (age range 28–83; 5 M, 5 F) have enrolled to date. Diagnoses include diffuse large B-cell lymphoma (DLBCL, n=2), EBV-positive DLBCL of the elderly (n=3), primary mediastinal B-cell lymphoma (n=2), peripheral T-cell lymphoma NOS (n=2), and angioimmunoblastic T-cell lymphoma (AITL). Patients had received 1–6 prior chemotherapy regimens; 3 patients had prior stem cell transplants. Of 6 patients who have completed the cycle 2 response assessment, 2 attained complete remission, 1 with DLBCL (90% CD30+) and 1 with AITL (8% CD30+), 1 had stable disease, and 3 had progressive disease. Treatment-related serious adverse events observed to date were rash, febrile neutropenia, and mastoiditis. Conclusions: Preliminary results suggest that brentuximab vedotin may have antitumor activity in patients with relapsed or refractory CD30-expressing non-Hodgkin lymphomas, in addition to the efficacy previously observed in systemic ALCL. Updated study results will be presented.
Baroreflex sensitivity, clinical correlates, and cardiovascular mortality among patients with a first myocardial infarction. A prospective study. (1988)

Experimental studies have shown that among dogs with a healed myocardial infarction, depressed baroreflex sensitivity (BRS) identifies a subgroup at higher risk for sudden death. We have examined the relation among BRS, several clinical cardiovascular variables, and subsequent mortality in 78 patients below the age of 65 years who have had a first myocardial infarction. BRS was assessed by calculating the regression line relating phenylephrine-induced increases in systolic blood pressure to the attendant changes in the RR interval. A reduced BRS primarily reflects an impairment in the vagal efferent component of the baroreceptor reflexes. The BRS of the entire population was 7.8 +/- 4.9 msec/mm Hg. BRS was lower among patients with an inferior myocardial infarction (6.1 +/- 3.3 vs. 8.9 +/- 5.8 msec/mm Hg, p = 0.03), with a three- versus a one-vessel disease (4.8 +/- 2.7 vs. 7.1 +/- 3.1 msec/mm Hg, p = 0.04), and with episodes of ventricular tachycardia (5.1 +/- 3.0 vs. 8.3 +/- 5.1, p = 0.03). There was no correlation between BRS and left ventricular ejection fraction or with mean pulmonary capillary wedge pressure at peak exercise, but a correlation (r = 0.35, p less than 0.001) was present with exercise tolerance. During the 24 months mean follow-up period, there were six cardiovascular deaths (7.6%), and four were sudden.(ABSTRACT TRUNCATED AT 250 WORDS)
Disturbed Peripheral B Lymphocyte Homeostasis in Systemic Lupus Erythematosus (2000)

In patients with active systemic lupus erythematosus (SLE), a marked B lymphocytopenia was identified that affected CD19(+)/CD27(-) naive B cells more than CD19(+)/CD27(+) memory B cells, leading to a relative predominance of CD27-expressing peripheral B cells. CD27(high)/CD38(+)/CD19(dim)/surface Ig(low)/CD20(-)/CD138(+) plasma cells were found at high frequencies in active but not inactive SLE patients. Upon immunosuppressive therapy, CD27(high) plasma cells and naive CD27(-) B cells were markedly decreased in the peripheral blood. Mutational analysis of V gene rearrangements of individual B cells confirmed that CD27(+) B cells coexpressing IgD were memory B cells preferentially using V(H)3 family members with multiple somatic mutations. CD27(high) plasma cells showed a similar degree of somatic hypermutation, but preferentially employed V(H)4 family members. These results indicate that there are profound abnormalities in the various B cell compartments in SLE that respond differently to immunosuppressive therapy.
GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences (2017)

Our Gaussian model aims to simplify the complex interaction between nucleotides. The model is computed not by the linear statistical method but by the Gaussian energy distribution and accumulation. The parameters of Gaussian function are not arbitrarily designated but deliberately chosen by optimizing the biological statistics. By using the pseudopotential analysis on CpG islands, the novel model is validated on both the real and artificial data sets.
Complete nucleotide sequence of immunogenic protein MPB70 from Mycobacterium bovis BCG (1989)

The extracellular protein MPB70 is a heat-stable immunogenic protein which was found in the culture filtrate of Mycobacterium bovis BCG Japanese. We determined the complete nt and aa sequences of MPB70 and correlated with the previously reported data. The N-terminal sequence revealed that the signal peptide (SP) consisted of 30 aa and that the mature protein had 163 aa with a molecular weight of 16 305. The SP displayed a characteristic feature of an Ala-rich property which would be efficient in a SP function.
Acute Myeloid Leukemia: The Challenge of Capturing Disease Variety (2008)

The difference between success and failure of treatment of acute myeloid leukemia (AML) is largely determined by genotypic leukemia-specific differences among patients. The diversity of AML genotypes result from somatic genetic alterations settling down in succession in an individual's leukemia clone during the development of the disease. Gene mutations, gene expression abnormalities and other molecular alterations (e.g., microRNA variations) affect critical functions in AML cells, and may exert profound effects on the therapeutic response and outcome of the disease. Prototypes of common clinically significant gene aberrations involve transcription factors, signaling molecules and growth factor receptors. The expanding knowledge in this area allowing for risk stratified therapy decisions and the development of targeted drug therapy, is becoming an increasingly important part of the modern individualized clinical management of AML. This chapter highlights recent insights into the diagnostic, prognostic and therapeutic impact of chromosomal (e.g., the so-called monosomal karyotype) as well as particular genomic abnormalities, and presents examples of decision algorithms for individualized therapy.
Docosahexaenoic acid and neurologic development in animals (2006)

Feeding dams a diet enriched with DHA during gestation and lactation has been associated with improvements in neurologic development of their puppies. Also, feeding diets or supplements containing DHA may improve memory or learning in young dogs.
Regulation of angiogenesis by scatter factor (1997)

Scatter factor (SF, hepatocyte growth factor) is a cytokine that stimulates motility, proliferation, and morphogenesis of epithelia. These responses are transduced through a tyrosine kinase receptor that is encoded by a proto-oncogene (c-met). SF is a potent angiogenic molecule, and its angiogenic activity is mediated, in part, through direct actions on endothelial cells. These include stimulation of cell motility, proliferation, protease production, invasion, and organization into capillary-like tubes. SF also stimulates the proliferation of smooth muscle cells and pericytes, cell types that also participate in the formation of capillaries and other microvessels. SF is chronically overexpressed in tumors, and it is postulated SF may function as a tumor angiogenesis factor. SF production in tumors may be due, in part, to an abnormal tumor: stroma interaction in which tumor cells secrete soluble proteins (SF-inducing factors) that stimulate stromal cell SF production and in part to autocrine production by the tumor cells themselves. Recent studies suggest a linkage between tumor suppressors (anti-oncogenes) and inhibition of angiogenesis. We hypothesize that tumor suppressor gene mutations may contribute to activation of an SF-->c-met signalling pathway, leading to an invasive and angiogenic tumor phenotype. Modulation of this pathway may provide clinically useful methods of enhancing or inhibiting angiogenesis.