gebhart/patrepeval huggingface dataset:
A Study on Detection of Anti-Patterns in Object-Oriented Systems (2014)

Software quality is an important issue in the development of software systems. The extent to which the software possesses a desired set of quality attributes such as testability, performance, maintainability, and manageability indicates the success of the design and the overall quality of the software system. These attributes are adversely affected by antipatterns. These design smells, the symptoms of code smells, are introduced during software development that constrains the evolution of system by making it difficult for engineers to bring changes. Researchers and practitioners put a great effort to detect these anti-patterns to reduce costs, effort and resources. Their detection is important because it allows refactoring or removing them from systems. Consequently, it improves software quality and usability. This paper discusses various manual, semi-automated and SVM based anti-pattern detection techniques for object-oriented systems, so that researchers can get a clear and concise view about them. The limitations and advantages (over previous approaches) of some detection techniques are also compared in this paper.
Nanosized cationic hydrogels for drug delivery: preparation, properties and interactions with cells (2019)

A new family of nanoscale materials on the basis of dispersed networks of cross-linked ionic and nonionic hydrophilic polymers is being developed. One example is the nanosized cationic network of cross-linked poly(ethylene oxide) (PEO) and polyethyleneimine (PEI), PEO-cl-PEI nanogel. Interaction of anionic amphiphilic molecules or oligonucleotides with PEO-cl-PEI results in formation of nanocomposite materials in which the hydrophobic regions from polyion-complexes are joined by the hydrophilic PEO chains. Formation of polyion-complexes leads to the collapse of the dispersed gel particles. However, the complexes form stable aqueous dispersions due to the stabilizing effect of the PEO chain. These systems allow for immobilization of negatively charged biologically active compounds such as retinoic acid, indomethacin and oligonucleotides (bound to polycation chains) or hydrophobic molecules (incorporated into nonpolar regions of polyion–surfactant complexes). The nanogel particles carrying biological active compounds have been modified with polypeptide ligands to enhance receptor-mediated delivery. Efficient cellular uptake and intracellular release of oligonucleotides immobilized in PEO-cl-PEI nanogel have been demonstrated. Antisense activity of an oligonucleotide in a cell model was elevated as a result of formulation of oligonucleotide with the nanogel. This delivery system has a potential of enhancing oral and brain bioavailability of oligonucleotides as demonstrated using polarized epithelial and brain microvessel endothelial cell monolayers.
Lipophilization of somatostatin analog RC‐160 with long chain fatty acid improves its antiproliferative and antiangiogenic activity <i>in vitro</i> (2000)

The therapeutic potential of the somatostatin analogue RC-160 having antiproliferative activity, is limited by its short serum half life. To overcome this limitation, fatty acids namely butanoic acid and myristic acid were conjugated to the N-terminal residue of RC-160. The lipophilized derivatives of RC-160 were synthesized, purified by reverse phase HPLC and characterized by ES-mass spectroscopy. The antiproliferative activity of lipophilized derivatives of RC-160 on the growth of MIA-PaCa2 (human pancreatic carcinoma), DU145 (human prostate carcinoma), ECV304 (human umbilical chord endothelioma), as well as their antiangiogenic activity was evaluated in vitro. The relative stability of myristoyl-RC-160 towards degradation by proteases and serum was also determined. Myristoyl-RC-160 exhibited significantly higher antiproliferative efficacy than RC-160, on the above cell lines (P<0.01). Receptor binding assays, demonstrated that the affinity of RC-160 towards somatostatin receptors remains unaltered by myristoylation. Unlike RC-160, the myristoylated derivative was found to have significantly greater resistance to protease and serum degradation (P<0.01). Myristoyl-RC-160 exhibited significantly greater antiproliferative activity on ECV304, than RC-160 (P<0.01). Myristoyl RC-160 could also inhibit capillary tube formation more efficiently than RC-160 in a dose dependent manner, suggesting that it possessed enhanced antiangiogenic activity in vitro (P<0.001). Lipophilization of RC-160 with long chain fatty acids like myristic acid endows it with improved antiproliferative and antiangiogenic activity, stability and therapeutic index. British Journal of Pharmacology (2000) 109, 101 - 109
Host Cell–Induced Components of the Sulfate Assimilation Pathway Are Major Protective Antigens of Mycobacterium tuberculosis (2012)

New therapies to control tuberculosis are urgently required because of the inability of the only available vaccine, BCG, to adequately protect against tuberculosis. Here we demonstrate that proteins of the Mycobacterium tuberculosis sulfate-assimilation pathway (SAP) represent major immunogenic targets of the bacillus, as defined by strong T-cell recognition by both mice and humans infected with M. tuberculosis. SAP proteins displayed increased expression when M. tuberculosis was resident within host cells, which may account in part for their ability to stimulate anti-M. tuberculosis host immunity. Vaccination with the first enzyme in this pathway, adenosine-5'-triphosphate sulfurylase, conferred significant protection against murine tuberculosis and boosted BCG-induced protective immunity in the lung. Therefore, we have identified SAP components as a new family of M. tuberculosis antigens, and we have demonstrated that these components are promising candidate for inclusion in new vaccines to control tuberculosis in humans.
Diastereoselective Synthesis of <i>N</i>-Protected β-Amino-α-hydroxyacids (Norstatines) from Urethane <i>N</i>-Carboxyanhydrides (UNCAs) (1999)

β-Amino-α-hydroxyacids (norstatines) are prepared from urethane N-protected carboxyanhydrides (UNCAs); the key step is the diastereoselective reduction of a keto-acetylenic compound, which lead is, with syn diastereoselectivity, to the corresponding propargylic alcohol.
Evaluation of Assertion Support for the Java Programming Language. (2002)

There is some evidence, that assertion techniques, i.e., preconditions, postconditions and invariants have a positive effect on the overall software quality. Unfortunately only a limited number of commercially relevant programming languages support assertion techniques (e.g., Eiffel). Even modern programming languages like Java have very limited built-in support for assertions. Nevertheless a number of systems exist for the the Java programming language, that support assertion techniques in different ways (language extensions, preprocessors, metaprogramming approaches). In order to make these different approaches comparable we developed a set of criteria and used these criteria to evaluate these systems.
Fusion of protoplasts and genetic recombination of Brevibacterium flavum. (1979)

Protoplasts of Brevibacterium flavum cells were obtained by treatment with 0.3 units of penicillin per ml during exponential growth, and followed by lysozyme treatment in a hypertonic medium. Protoplasts of antibiotic-resistant and auxotrophic strains were fused by a modified polyethyleneglycol technique, and allowed to revert to bacillary form on selective media. The clones were analyzed and recombinants were found not to segregate.
Syntheses of β-<scp>D</scp>-arabinofurano[1′,2′:4,5]oxa(thia)zolidines (1985)

Treatment of 2,2′-anhydro-1-(3,5-diacetoxy-β-D-arabinofuranosyl)-5,6-dihydrouracil (13) and its 2-thio analogue (17) with refluxing 80% AcOH gives 3-propionamido-(3,5-diacetoxy-1,2-dideoxy-β-D-arabinofurano)[1′,2′:4,5]oxazolidin-2-one (15) and 3-carboxyethyl-(3,5-diacetoxy-1,2-dideoxy-β-D-arabinofurano)[1′,2′:4,5]thiazolidin-2-imine (24), respectively. While the appearance of compound (15) indicates the occurrence of an unusual C(2)–N(3) bond cleavage of (13) the 2-thio analogue (17) yields compound (24), the product of an N(3)–C(4) ring opening. The latter product gives first methoxy-carbonylethyl(3,5-diacetoxy-1,2-dideoxy-β-D-arabinofurano)[1′,2′:4,5]thiazolidin-2-imine hydrochloride (26) by reaction with methanolic HCl and subsequently the corresponding thiazolidine-2-thione (27) on reaction with H2S in DMF.The synthesis of the 1-(3,5-diacetoxy-2-acetylthio-β-D-arabinofuranosyl) derivative of 2-O-methyl-5,6-dihydrouracil (22) and 5,6-dihydroisocytosine (23) is also described.
Kiloampere and microsecond electron beams from ferroelectric cathodes (1998)

We report experimental results of the operation of two ferroelectric cathodes of relatively large size. The first cathode had a diameter of 10.2 cm and was built in the Pierce cathode geometry by Integrated Applied Physics (IAP). It achieved emission currents of up to 1.2 kA (15.3 A/cm/sup 2/) at voltages up to 100 kV, in 150 ns pulses. The second cathode had an annular shape with a diameter of 11.4 cm and a width of 0.25 cm. It was built at the Massachusetts Institute of Technology to produce an annular electron beam for use in a Gyrotron microwave source. It operated at currents of up to 10 A (1.1 A/cm/sup 2/) at 8 kV, in 5 /spl mu/s pulses. Detailed operating characteristics for each of these electron sources are reported. These results indicate that ferroelectric cathodes can be used to produce electron beams of large area and size, with high total operating current and pulse lengths of several microseconds. These sources should be suitable for use in future microwave generation experiments.
Experimental Analysis of Sources of Error in Evolutionary Studies Based on Roche/454 Pyrosequencing of Viral Genomes (2012)

Factors affecting the reliability of Roche/454 pyrosequencing for analyzing sequence polymorphism in within-host viral populations were assessed by two experiments: 1) sequencing four clonal simian immunodeficiency virus (SIV) stocks and 2) sequencing mixtures in different proportions of two SIV strains with known fixed nucleotide differences. Observed nucleotide diversity and frequency of undetermined nucleotides were increased at sites in homopolymer runs of four or more identical nucleotides, particularly at AT sites. However, in the mixed-strain experiments, the effects on estimated nucleotide diversity of such errors were small in comparison to known strain differences. The results suggest that biologically meaningful variants present at a frequency of around 10% and possibly much lower are easily distinguished from artifacts of the sequencing process. Analysis of the clonal stocks revealed numerous rare variants that showed the signature of purifying selection and that elimination of variants at frequencies of less than 1% reduced estimates of nucleotide diversity by about an order of magnitude. Thus, using a 1% frequency cutoff for accepting a variant as real represents a conservative standard, which may be useful in studies that are focused on the discovery of specific mutations (such as those conferring immune escape or drug resistance). On the other hand, if the goal is to estimate nucleotide diversity, an optimal strategy might be to include all observed variants (even those at less than 1% frequency), while masking out homopolymer runs of four or more nucleotides.
Label-Free Single Exosome Detection Using Frequency-Locked Microtoroid Optical Resonators (2015)

Recently exosomes have attracted interest due to their potential as cancer biomarkers. We report the real-time, label-free sensing of single exosomes in serum using microtoroid optical resonators. We use this approach to assay the progression of tumors implanted in mice by specifically detecting low concentrations of tumor-derived exosomes. Our approach measures the adsorption of individual exosomes onto a functionalized silica microtoroid by tracking changes in resonant frequency of the microtoroid. When exosomes land on the microtoroid, they perturb its refractive index in the evanescent field and thus shift its resonance frequency. Through digital frequency locking, we are able to rapidly track these shifts with accuracies of better than 10 attometers (one part in 10^(11)). Samples taken from tumor-implanted mice from later weeks generated larger frequency shifts than those from earlier weeks. Analysis of these shifts shows a distribution of unitary steps, with the maximum step having a height of ∼1.2 fm, corresponding to an exosome size of 44 ± 4.8 nm. Our results demonstrate the development of a minimally invasive tumor “biopsy” that eliminates the need to find and access a tumor.
Dementia and mild cognitive impairment in patients with Parkinson's disease (2009)

clinical-neurological assessment; modified Hoehn and Yahr staging scale (HYS); standard neuropsychological battery of CERAD (Consortium to Establish a Registry for Alzheimer' Disease); Pfeffer questionnaire; and Clinical Dementia Rating. A comparison was made with a control group (CG), consisting of 26 individuals with similar age and educational level but without cognitive impairment. The PD patients showed an inferior performance in the CERAD battery when compared to the CG. Three PD sub-groups were characterised according to cognition: no cognitive impairment--15 cases; mild cognitive impairment--10; dementia--7 cases. There was a significant association between motor disability (HYS) and the occurrence of dementia. Dementia and mild cognitive impairment frequently occur in PD patients and should be investigated in a routine way.
Development of coherent Doppler lidar at CRL (2003)

Global wind profiling with a space-borne Doppler lidar is expected to bring big progress in the studies on global climate change and Numerical Weather Prediction. A feasibility study has been done for an eye-safe 2micron coherent Doppler lidar aiming at demonstration of the technology onboard the Japanese Experiment module of the International Space Station. We are now developing an airborne coherent Doppler lidar system to measure wind profile under a jet plane for simulation of the Doppler lidar measurement in space. This system is also operated in the ground to develop algorithm of the wind measurements and the results of the wind profiles are compared with those derived from other instruments.
Deep Scrotal Temperature and the Effect on it of Clothing, Air Temperature, Activity, Posture and Paraplegia (1982)

Two new techniques for measuring deep scrotal temperature are described. Paraplegic men in wheelchairs have deep scrotal temperatures averaging about 0.9 degrees C higher than normal sitting men, and those whose scrotal temperatures are very high usually lack motile spermatozoa. In the author, deep scrotal temperatures at constant air temperature are 0.5 degrees C lower wearing boxer shorts than wearing Y-fronts, and 1.2 degrees C lower wearing scrotal slit underpants than wearing boxer shorts; they are 1.6 degrees C lower sitting with thighs apart than sitting with thighs together, and 0.5 degrees C lower running than sitting with thighs apart. From such observations, means of lowering paraplegic deep scrotal temperatures can be designed.
On the output SNR of the speech-distortion weighted multichannel Wiener filter (2005)

In this letter, we prove that the output signal-to-noise ratio (SNR) after noise reduction with the speech-distortion weighted multichannel Wiener filter is always larger than or equal to the input SNR, for any filter length, for any value of the tradeoff parameter between noise reduction and speech distortion, and for all possible speech and noise correlation matrices.
Serum ceramides increase the risk of Alzheimer disease (2012)

Results from this preliminary study suggest that particular species of serum ceramides are associated with incident AD and warrant continued examination in larger studies.
Lag correction model and ghosting analysis for an indirect‐conversion flat‐panel imager (2007)

Cone-beam digital tomosynthesis (CBDT) is a new approach that was recently proposed for rapid tomographic imaging of soft-tissue targets in the radiotherapy treatment room. One of the potential problems in implementing CBDT using, for example, megavoltage (MV) X rays is the possibility of artifacts caused by image lag and ghosting of the X-ray detector used. In the present work, we developed a model to correct for image lag with indirect-conversion flat-panel imagers (FPIs) used for MV-CBDT. This model is based on measurement and analysis of image lag in an indirect-conversion FPI irradiated with a 6-MV X-ray beam. Our results demonstrated that image lag is amenable to correction. In addition, we measured the ghosting effect for an indirect-conversion FPI and found it to be insignificant.
Effect of temperature and surfactant on biomass growth and higher-alcohol production during syngas fermentation by Clostridium carboxidivorans P7 (2020)

Abstract Hexanol–butanol–ethanol fermentation from syngas by Clostridium carboxidivorans P7 is a promising route for biofuel production. However, bacterial agglomeration in the culture of 37 °C severely hampers the accumulation of biomass and products. To investigate the effect of culture temperature on biomass growth and higher-alcohol production, C. carboxidivorans P7 was cultivated at both constant and two-step temperatures in the range from 25 to 37 °C. Meanwhile, Tween-80 and saponin were screened out from eight surfactants to alleviate agglomeration at 37 °C. The results showed that enhanced higher-alcohol production was contributed mainly by the application of two-step temperature culture rather than the addition of anti-agglomeration surfactants. Furthermore, comparative transcriptome revealed that although 37 °C promoted high expression of genes involved in the Wood–Ljungdahl pathway, genes encoding enzymes catalyzing acyl-condensation reactions associated with higher-alcohol production were highly expressed at 25 °C. This study gained greater insight into temperature-effect mechanism on syngas fermentation by C. carboxidivorans P7.
G Protein-coupled Receptor Kinase and β-Arrestin-mediated Desensitization of the Angiotensin II Type 1A Receptor Elucidated by Diacylglycerol Dynamics (2006)

Receptor desensitization progressively limits responsiveness of cells to chronically applied stimuli. Desensitization in the continuous presence of agonist has been difficult to study with available assay methods. Here, we used a fluorescence resonance energy transfer-based live cell assay for the second messenger diacylglycerol to measure desensitization of a model seven-transmembrane receptor, the Gq-coupled angiotensin II type 1(A) receptor, expressed in human embryonic kidney 293 cells. In response to angiotensin II, we observed a transient diacylglycerol response reflecting activation and complete desensitization of the receptor within 2-5 min. By utilizing a variety of approaches including graded tetracycline-inducible receptor expression, mutated receptors, and overexpression or short interfering RNA-mediated silencing of putative components of the cellular desensitization machinery, we conclude that the rate and extent of receptor desensitization are critically determined by the following: receptor concentration in the plasma membrane; the presence of phosphorylation sites on the carboxyl terminus of the receptor; kinase activity of G protein-coupled receptor kinase 2, but not of G protein-coupled receptor kinases 3, 5, or 6; and stoichiometric expression of beta-arrestin. The findings introduce the use of the biosensor diacylglycerol reporter as a powerful means for studying Gq-coupled receptor desensitization and document that, at the levels of receptor overexpression commonly used in such studies, the properties of the desensitization process are markedly perturbed and do not reflect normal cellular physiology.
Genomic analysis in <i>Escherichia coli</i> demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay (2003)

Previous work has shown that simultaneous inactivation of polynucleotide phosphorylase (PNPase) and RNase II (both 3' 5' exonucleases) in Escherichia coli leads to the loss of cell viability and the accumulation of partially degraded mRNA species. In order to help to distinguish how these two enzymes globally affect the abundance and decay of mRNAs, we have carried out a genome-wide analysis of the steady-state levels of E. coli transcripts using deletion mutations in either rnb or pnp. The data show that, in exponentially growing cells, inactivation of PNPase leads to an increase in the steady-state level of more expressed mRNAs (17.3%) than inactivation of RNase II (7.3%). In contrast, the steady-state levels of a large number of E. coli mRNAs (31%) are decreased in the absence of RNase II, including almost all the ribosomal protein genes, suggesting that a major function of this enzyme is to protect specific mRNAs from the activity of other ribonucleases. Array data were confirmed by Northern analysis of 12 individual mRNAs. A comparison between the steady-state levels and the half-lives of individual mRNAs indicates that there may be a direct interaction between transcription and mRNA decay for some of the transcripts. In addition, results are presented to show significant phenotypic differences between the pnp-7 point mutant and the pnp delta 683 deletion allele.
Expression of listeriolysin and phosphatidylinositol‐specific phospholipase C is repressed by the plant‐derived molecule cellobiose in <i>Listeria monocytogenes</i> (1993)

The primary habitat of the intracellular pathogen Listeria monocytogenes is considered to be soil and decaying vegetation. As an opportunistic pathogen it must be able to recognize its entry into host tissue and, in response, co-ordinately induce the expression of virulence factors. No signature molecule, which facilitates this regulation, has been identified for any human pathogen. Our studies have demonstrated for the first time that the expression of major virulence determinants in L. monocytogenes can be repressed by an environmentally ubiquitous molecule. Transcriptional hlyA and plcA fusions to luxAB were used to monitor virulent gene expression in the presence of various disaccharides. These studies revealed that the expression of listeriolysin O and phosphatidylinositol-specific phospholipase C is repressed specifically by the plant-derived disaccharide, cellobiose.
Protein identification using MS/MS data (2011)

The subject of this tutorial is protein identification and characterisation by database searching of MS/MS Data. Peptide Mass Fingerprinting is excluded because it is covered in a separate tutorial. Practical aspects of database searching are emphasised, such as choice of sequence database, effect of mass tolerance, and how to identify post-translational modifications. The relationship between sensitivity and specificity is discussed, as is the challenge of using peptide match information to infer which proteins were present in the sample. Since these tutorials are introductory in nature, most references are to reviews, rather than primary research papers. Some familiarity with mass spectrometry and protein chemistry is assumed. There is an accompanying slide presentation, including speaker notes, and a collection of web-based, practical exercises, designed to reinforce key points. This Tutorial is part of the International Proteomics Tutorial Programme (IPTP 6).