gebhart/patrepeval huggingface dataset:
An empirical study of the robustness of two module clustering fitness functions (2005)

Two of the attractions of search-based software engineering (SBSE) derive from the nature of the fitness functions used to guide the search. These have proved to be highly robust (for a variety of different search algorithms) and have yielded insight into the nature of the search space itself, shedding light upon the software engineering problem in hand.This paper aims to exploit these two benefits of SBSE in the context of search based module clustering. The paper presents empirical results which compare the robustness of two fitness functions used for software module clustering: one (MQ) used exclusively for module clustering. The other is EVM, a clustering fitness function previously applied to time series and gene expression data.The results show that both metrics are relatively robust in the presence of noise, with EVM being the more robust of the two. The results may also yield some interesting insights into the nature of software graphs.
Troubleshooting coupled in vitro transcription–translation system derived from Escherichia coli cells: synthesis of high-yield fully active proteins (2006)

Cell-free coupled transcription-translation systems with bacterial lysates are widely used to synthesize recombinant proteins in amounts of several mg per ml. By using reporter green fluorescence protein (GFP) we demonstrate that proteins are synthesized with an unsatisfyingly low-active fraction of (50 +/- 20)%. One reason is probably the T7 polymerase used, being up to eight times faster than the intrinsic transcriptase and thus breaking the coupling between transcription and translation in bacterial systems. The active fraction of the synthesized protein was improved by using either a slower T7 transcriptase mutant or lowering the incubation temperature to 20 degrees C. A drop of protein synthesis observed after 7 h incubation time was not due to a shortage of nucleotide triphosphates, but rather to a shortage of amino acids. Accordingly, a second addition of amino acids after 10 h during an incubation at 20 degrees C led to synthesis of up to 4 mg/ml of GFP with virtually 100% activity.
Quantitation of minimal residual disease in Philadelphia chromosome positive chronic myeloid leukaemia patients using real‐time quantitative RT‐PCR (1998)

We used a recently developed system for real-time quantitative polymerase chain reaction (PCR) to determine residual disease in patients with chronic myeloid leukaemia. The expression of the Bcr-Abl hybrid oncogene was determined and normalized by using the PBGD housekeeping gene product as endogenous reference. The sensitivity and reproducibility of the assay was tested on cell line K562. A dilution of Bcr-Abl-positive cell line K562 remained positive at up to 250 fg of RNA. 10 copies of Bcr-Abl DNA in water could still be detected. The dynamic range of the method spanned six orders of magnitude. Analysis of 10 identical assays on K562 RNA resulted in a variation of 15%. To test the feasibility of normalization of Bcr-Abl dosage by the PBGD product, we compared the efficiencies of the RT-PCRs in 150 patient analyses. We concluded that PBGD was a suitable and stringent quality control standard. Three patients who were treated with donor leucocyte infusions for chronic myeloid leukaemia who had relapsed after bone marrow transplantation were followed over time. The normalized Bcr-Abl dosage was compared to the results of cytogenetics. Cytogenetic analysis was negative below a normalized Bcr-Abl dose of about 3 x 10(-2). This semi-automated method is fast, sensitive and accurate and enables a high throughput of samples.
Depth-profiling XPS analysis of He-plasma treated amorphous InGaZnO thin films for use in top-gate coplanar thin-film transistors (2019)

Abstract A low-resistance amorphous InGaZnO (a-InGaZnO) film obtained with helium (He) plasma treatment is commonly used as the source/drain regions of top-gate planar thin-film transistors. Here we discuss some experimental results for the low-resistance a-InGaZnO films, focusing on depth profiling analysis of X-ray photoelectron spectroscopy signals. We show that the effect of He plasma treatment, which is generation of considerable oxygen vacancies, extends for the entire thickness (over 70 nm) of a-InGaZnO film. We also show that a significantly In-rich layer may be formed beneath the a-InGaZnO surface, depending on the He plasma power density.
[Research and development of medical case database: a novel medical case information system integrating with biospecimen management]. (2010)

To meet the needs of management of medical case information and biospecimen simultaneously, we developed a novel medical case information system integrating with biospecimen management. The database established by MS SQL Server 2000 covered, basic information, clinical diagnosis, imaging diagnosis, pathological diagnosis and clinical treatment of patient; physicochemical property, inventory management and laboratory analysis of biospecimen; users log and data maintenance. The client application developed by Visual C++ 6.0 was used to implement medical case and biospecimen management, which was based on Client/Server model. This system can perform input, browse, inquest, summary of case and related biospecimen information, and can automatically synthesize case-records based on the database. Management of not only a long-term follow-up on individual, but also of grouped cases organized according to the aim of research can be achieved by the system. This system can improve the efficiency and quality of clinical researches while biospecimens are used coordinately. It realizes synthesized and dynamic management of medical case and biospecimen, which may be considered as a new management platform.
Phenotypic plasticity in fungi: a review with observations onAureobasidium pullulans (2009)

Phenotypic plasticity in fungi is reviewed in the context of observations on phenotypic changes in the colony morphology of the fungus Aureobasidium pullulans. The variation in colony form is shown to depend on (i) the types of single carbon substrates (sugars and sugar alcohols) used in the growth medium, (ii) colony age, (iii) incubation temperature, (iv) light cycle and (v) substrate type. Expanding colonies grow in a developmental sequence that show synchronize growth phase shifts as well as unusual transitions from homogeneous to sectored, yeast to mycelial and giant to microcolonial growth forms. Epigenetic influences on phenotypic switches are suggested to be potential causes of form changes. The desirable properties of a model organism for studying phenotypic plasticity are discussed and past work on the yeast-mycelial transition of fungi is reviewed.
[Case report: reversible acute renal failure following therapy with both ketorolac (non-selective non-steroidal anti-inflammatory drug NSAID) and celecoxib (COX-2 selective) in the same patient]. (2003)

The case we report seems to confirm that, in patients at risk, the renal adverse effects of non-selective NSAIDs and of COX-2 Inhibitors could be the same due to the similar physiological role of COX-1 and COX-2-dependent prostaglandins.
Diphtheria Toxin Binds to the Epidermal Growth Factor (EGF)-like Domain of Human Heparin-binding EGF-like Growth Factor/Diphtheria Toxin Receptor and Inhibits Specifically Its Mitogenic Activity (1995)

The membrane anchored form of human heparin-binding epidermal growth factor-like growth factor (HB-EGF) acts as the diphtheria toxin (DT) receptor. Transfection of human HB-EGF cDNA into mouse LC cells, L cells stably expressing DRAP27, conferred sensitivity to DT, but transfection of mouse HB-EGF cDNA did not. To define the essential regions of HB-EGF that serve as the functional DT receptor, we examined the sensitivity to DT and DT binding of cells expressing several human/mouse HB-EGF chimeras. It was found that DT binds to the EGF-like domain of the human HB-EGF. However, mouse HB-EGF does not serve as a functional DT receptor due to non-conserved amino acid substitutions in this domain. In addition, CRM197, a non-toxic mutant of DT, inhibited strongly the mitogenic activity of the secreted form of human HB-EGF, but not of mouse HB-EGF and other EGF receptor-binding growth factors. These results confirmed further that DT interacts with the EGF-like domain of HB-EGF and that this interaction is specific for human HB-EGF. The membrane anchored form of human heparin-binding epidermal growth factor-like growth factor (HB-EGF) acts as the diphtheria toxin (DT) receptor. Transfection of human HB-EGF cDNA into mouse LC cells, L cells stably expressing DRAP27, conferred sensitivity to DT, but transfection of mouse HB-EGF cDNA did not. To define the essential regions of HB-EGF that serve as the functional DT receptor, we examined the sensitivity to DT and DT binding of cells expressing several human/mouse HB-EGF chimeras. It was found that DT binds to the EGF-like domain of the human HB-EGF. However, mouse HB-EGF does not serve as a functional DT receptor due to non-conserved amino acid substitutions in this domain. In addition, CRM197, a non-toxic mutant of DT, inhibited strongly the mitogenic activity of the secreted form of human HB-EGF, but not of mouse HB-EGF and other EGF receptor-binding growth factors. These results confirmed further that DT interacts with the EGF-like domain of HB-EGF and that this interaction is specific for human HB-EGF.
Molecular Cloning of Monkey Histamine H4 Receptor (2005)

Histamine H(4) receptor is considered as a novel therapeutic target for allergic diseases. To enhance the knowledge about species difference, which is essential for drug discovery research, monkey H(4) receptor was identified. Monkey H(4) receptor was characterized to have comparable similarity with its human counterpart. Discovery of monkey H(4) receptor will contribute to a better interpretation of effective drug discovery.
Human methylenetetrahydrofolate reductase pharmacogenomics: gene resequencing and functional genomics (2006)

5,10-Methylenetetrahydrofolate reductase (MTHFR) is an important enzyme in the folate metabolic pathway. Common genetic polymorphisms in the human MTHFR gene are associated with individual variation in the efficacy and toxicity of chemotherapeutic agents, such as methotrexate and 5-fluorouracil. However, the full range of polymorphisms and intragene haplotypes in the human MTHFR gene remains unclear. Furthermore, cellular mechanisms by which common, naturally occurring nonsynonymous coding single nucleotide polymorphisms (cSNPs) might alter the function of this enzyme have not been defined. The present study focused on the systematic identification and investigation of common polymorphisms and haplotypes in the MTHFR gene using a genotype-to-phenotype strategy, followed by functional genomic studies. Specifically, we resequenced exons, splice junctions and portions of the 5'-flanking region (5'-FR) of the human MTHFR gene using 240 DNA samples from four ethnic groups. A total of 65 polymorphisms were observed, 11 of which were nonsynonymous cSNPs. We then performed functional genomic studies with constructs for wild-type and 15 variant allozymes (some with multiple alterations in amino acid sequence) using a mammalian expression system. Activity for the variant allozymes ranged from 13% to 149% of wild-type activity. Levels of immunoreactive protein for the allozymes ranged from 31% to 120% of wild-type and were significantly correlated with enzyme activity (Rp=0.85, P<0.0001), suggesting that a major mechanism by which nonsynonymous cSNPs influence the function of this gene is by alteration in the quantity of protein. These observations represent steps towards an understanding of molecular genetic mechanisms responsible for variation in MTHFR function that may contribute to individual differences in drug efficacy and toxicity, as well as disease risk.
Analysis of glucocorticoid unresponsive cell variants using a mouse glucocorticoid receptor complementary DNA clone. (1986)

We have used a glucocorticoid receptor cDNA isolated from a mouse lymphoma cell line to characterize receptor mRNA and genomic sequences present in wild type and mutant rat hepatoma (HTC) and mouse thymoma (S49 and WEHI7) cells. Wild type rat and mouse cell lines contain two receptor mRNAs, 5 and 7 kilobase pairs (kb) in length, which differ in the length of their 3'-untranslated regions. Levels of receptor mRNA present in mutant HTC, WEHI7, and S49 cells of the r- (receptorless) phenotype are decreased compared to wild type cells. This decreased level of receptor mRNA parallels the decreased level of total immunoreactive receptor protein found in these cells. S49 nt- (nuclear transfer minus) cells contain receptor mRNA levels which parallel their hormone binding and immunoreactive receptor levels. Cells of the r- and nt- phenotype contain no detectable deletions or rearrangements of the receptor gene. We conclude that r- cells have lesions which affect the expression of receptor mRNA. Surprisingly, HTC cells of the r- phenotype differ from WEHI7 and S49 r- cells in that HTC r- cells contain a lower level of receptor DNA than does their parental wild type cell line. Although these cells may contain multiple lesions, it appears that loss of receptor genomic sequences is responsible, in part, for the phenotype of the HTC r- cells. The S49 nti (nuclear transfer increase) cells produce glucocorticoid receptors of molecular weights 40,000 and 94,000. These cells produce, in addition to the wild type 5- and 7-kb receptor mRNAs, two other receptor messages 5.5 and 3.5 kb in length. RNA blot analysis using various portions of our receptor cDNA indicates that these are 5' truncated messages and suggests that the 40-kDa nti receptor is truncated at its NH2-terminal end. These data also indicate that the hormone and DNA-binding regions of the receptor are located in the COOH-terminal half of the protein.
Mechanism of impaired glucose-potentiated insulin secretion in diabetic 90% pancreatectomy rats. Study using glucagonlike peptide-1 (7-37). (1996)

Chronic hyperglycemia causes a near-total disappearance of glucose-induced insulin secretion. To determine if glucose potentiation of nonglucose secretagogues is impaired, insulin responses to 10(-9) M glucagonlike peptide-1 (GLP-1) (7-37) were measured at 2.8, 8.3, and 16.7 mM glucose with the in vitro perfused pancreas in rats 4-6 wk after 90% pancreatectomy (Px) and sham-operated controls. In the controls, insulin output to GLP-1 was > 100-fold greater at 16.7 mM glucose versus 2.8 mM glucose. In contrast, the increase was less than threefold in Px, reaching an insulin response at 16.7 mM glucose that was 10 +/- 2% of the controls, well below the predicted 35-40% fractional beta-cell mass in these rats. Px and control rats then underwent a 40-h fast followed by pancreas perfusion using a protocol of 20 min at 16.7 mM glucose followed by 15 min at 16.7 mM glucose/10(-9) M GLP-1. In control rats, fasting suppressed insulin release to high glucose (by 90%) and to GLP-1 (by 60%) without changing the pancreatic insulin content. In contrast, in Px the insulin response to GLP-1 tripled in association with a threefold increase of the insulin content, both now being twice normal when stratified for the fractional beta-cell mass. The mechanism of the increased pancreas insulin content was investigated by assessing islet glucose metabolism and proinsulin biosynthesis. In controls with fasting, both fell 30-50%. In Px, the degree of suppression with fasting was similar, but the attained levels both exceeded those of the controls because of higher baseline (nonfasted) values. In summary, chronic hyperglycemia is associated with a fasting-induced paradoxical increase in glucose-potentiated insulin secretion. In Px rats, the mechanism is an increase in the beta-cell insulin stores, which suggests a causative role for a lowered beta-cell insulin content in the impaired glucose-potentiation of insulin secretion.
Collaborative Bacteriostatic Activity of Bovine Lactoferrin with Lysozyme againstEscherichia coliO111 (1989)

Journal Article Collaborative Bacteriostatic Activity of Bovine Lactoferrin with Lysozyme against Escherichia coli O111 Get access Takashi Suzuki, Takashi Suzuki Food Research and Development Laboratory, Morinaga Milk Industry Co., Ltd., 4–4–22 Meguro, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Koji Yamauchi, Koji Yamauchi Nutritional Science Laboratory, Morinaga Milk Industry Co., Ltd., 4–4–22 Meguro, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Kozo Kawase, Kozo Kawase Nutritional Science Laboratory, Morinaga Milk Industry Co., Ltd., 4–4–22 Meguro, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Mamoru Tomita, Mamoru Tomita Nutritional Science Laboratory, Morinaga Milk Industry Co., Ltd., 4–4–22 Meguro, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Isao Kiyosawa, Isao Kiyosawa Department of Agricultural Chemistry, Faculty of Agriculture, Tamagawa University, 6–1–1 Tamagawagakuen, Machida-shi, Tokyo 194, Japan Search for other works by this author on: Oxford Academic Google Scholar Shigeo Okonogi Shigeo Okonogi Food Research and Development Laboratory, Morinaga Milk Industry Co., Ltd., 4–4–22 Meguro, Meguro-ku, Tokyo 153, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 53, Issue 6, 1 June 1989, Pages 1705–1706, https://doi.org/10.1080/00021369.1989.10869524 Published: 01 June 1989 Article history Received: 19 October 1988 Published: 01 June 1989
MMSE and adaptive prediction of time-varying channels for OFDM systems (2005)

We propose decision-directed channel predictors for orthogonal frequency-division multiplexing (OFDM) communications over time-varying channels. Channel prediction is capable of yielding up-to-date channel state information even without regular transmission of pilot symbols. It is thus potentially useful for delay-free equalization, antenna combining, space-time decoding, adaptive modulation, adaptive power control, and adaptive transmit antenna diversity. We derive a minimum mean-square error channel predictor and its efficient discrete Fourier transform implementation. Furthermore, we develop adaptive predictors that do not require any statistical prior knowledge and are able to track nonstationary channel and noise statistics. Simulation results involving an OFDM receiver in which channel prediction is used for delay-free equalization demonstrate the excellent performance of the proposed techniques even for fast time-varying channels.
Phosphoramidate Dinucleosides as Hepatitis C Virus Polymerase Inhibitors (2008)

GC dinucleosides exhibiting a phosphoramidate internucleosidic linkage with neutral, amphiphile, positively or negatively charged side chains were synthesized. Their potential inhibitory effect on the hepatitis C virus (HCV) NS5B polymerase was evaluated in vitro and in HCV replicon containing cells. Whereas the amphiphile and the positively charged analogues were found to be inactive, the neutral (1) and the negatively charged (4) ones inhibited enzyme activity when tested as a diastereoisomeric mixture. The most potent inhibitor proved to be the Sp isomer of the 5'-thiophosphorylated dinucleotide bearing the carboxylic side chain (8) (IC 50 of 25 microM in vitro and an EC 50 of 9 microM in HCV subgenomic replicon). Molecular modeling suggests that the phosphoramidate dinucleoside (8) is stabilized in the active site by interactions with magnesium ions and lysine and arginine residues of the polymerase.
A Single Point Mutation in Nonstructural Protein NS2 of Bovine Viral Diarrhea Virus Results in Temperature-Sensitive Attenuation of Viral Cytopathogenicity (2009)

For Bovine viral diarrhea virus (BVDV), the type species of the genus Pestivirus in the family Flaviviridae, cytopathogenic (cp) and noncytopathogenic (ncp) viruses are distinguished according to their effect on cultured cells. It has been established that cytopathogenicity of BVDV correlates with efficient production of viral nonstructural protein NS3 and with enhanced viral RNA synthesis. Here, we describe generation and characterization of a temperature-sensitive (ts) mutant of cp BVDV strain CP7, termed TS2.7. Infection of bovine cells with TS2.7 and the parent CP7 at 33 degrees C resulted in efficient viral replication and a cytopathic effect. In contrast, the ability of TS2.7 to cause cytopathogenicity at 39.5 degrees C was drastically reduced despite production of high titers of infectious virus. Further experiments, including nucleotide sequencing of the TS2.7 genome and reverse genetics, showed that a Y1338H substitution at residue 193 of NS2 resulted in the temperature-dependent attenuation of cytopathogenicity despite high levels of infectious virus production. Interestingly, TS2.7 and the reconstructed mutant CP7-Y1338H produced NS3 in addition to NS2-3 throughout infection. Compared to the parent CP7, NS2-3 processing was slightly decreased at both temperatures. Quantification of viral RNAs that were accumulated at 10 h postinfection demonstrated that attenuation of the cytopathogenicity of the ts mutants at 39.5 degrees C correlated with reduced amounts of viral RNA, while the efficiency of viral RNA synthesis at 33 degrees C was not affected. Taken together, the results of this study show that a mutation in BVDV NS2 attenuates viral RNA replication and suppresses viral cytopathogenicity at high temperature without altering NS3 expression and infectious virus production in a temperature-dependent manner.
Simultaneous separation and detection of cations and anions on a microfluidic device with suppressed electroosmotic flow and a single injection point (2010)

A rapid and simultaneous separation of cationic and anionic peptides and proteins in a glass microfluidic device that has been covalently modified with a neutral poly(ethylene glycol) (PEG) coating to minimize protein adsorption is presented. The features of the device allow samples that contain both anions and cations to be introduced from a central flow stream and separated in different channels with different outlets-all in the presence of low electroosmotic flow (EOF) imparted by the PEG coating. The analytes are electrophoretically extracted from a central hydrodynamic stream and electrophoretically separated in two different channels, in which pressure driven flow has been suppressed through the use of hydrodynamic restrictors. Having different outlets for the electrophoretic separation channels that are spatially separated from the injection enables coupling with further downstream functionalities or off-chip detection, such as mass spectrometry. A plug of charged analyte is hydrodynamically pumped to the sampling intersection and anions from the plug migrate electrophoretically toward the anode in one channel while cations migrate toward the cathode in the other channel due to suppressed EOF from the PEG coating. The separations presented here required less than a minute to complete and produced average separation efficiencies of up to about 3,500 plates from a separation length of 2 cm. The extraction efficiency of both cations and anions from the hydrodynamic stream is determined experimentally and compared with a previously reported model that was used to determine anion extraction efficiency. The extraction efficiency is determined to be 87% and 98% for the two sample mixtures analyzed, and the values predicted by the model are within 3.5% of the experimental data. It is anticipated that this basic approach for simultaneous separation of anions and cations with reduced EOF will be integrated into larger microfluidic systems because the design provides separate outlets that can feed downstream processes or linked to off-chip detection.