gebhart/patrepeval huggingface dataset:
A Systematic Literature Review on Fault Prediction Performance in Software Engineering (2011)

Background: The accurate prediction of where faults are likely to occur in code can help direct test effort, reduce costs, and improve the quality of software. Objective: We investigate how the context of models, the independent variables used, and the modeling techniques applied influence the performance of fault prediction models. Method: We used a systematic literature review to identify 208 fault prediction studies published from January 2000 to December 2010. We synthesize the quantitative and qualitative results of 36 studies which report sufficient contextual and methodological information according to the criteria we develop and apply. Results: The models that perform well tend to be based on simple modeling techniques such as Naive Bayes or Logistic Regression. Combinations of independent variables have been used by models that perform well. Feature selection has been applied to these combinations when models are performing particularly well. Conclusion: The methodology used to build models seems to be influential to predictive performance. Although there are a set of fault prediction studies in which confidence is possible, more studies are needed that use a reliable methodology and which report their context, methodology, and performance comprehensively.
Ascorbic Acid Induces Alkaline Phosphatase, Type X Collagen, and Calcium Deposition in Cultured Chick Chondrocytes (1989)

During the process of endochondral bone formation, proliferating chondrocytes give rise to hypertrophic chondrocytes, which then deposit a mineralized matrix to form calcified cartilage. Chondrocyte hypertrophy and matrix mineralization are associated with expression of type X collagen and the induction of high levels of the bone/liver/kidney isozyme of alkaline phosphatase. To determine what role vitamin C plays in these processes, chondrocytes derived from the cephalic portion of 14-day chick embryo sternae were grown in the absence or presence of exogenous ascorbic acid. Control untreated cells displayed low levels of type X collagen and alkaline phosphatase activity throughout the culture period. However, cells grown in the presence of ascorbic acid produced increasing levels of alkaline phosphatase activity and type X collagen mRNA and protein. Both alkaline phosphatase activity and type X collagen mRNA levels began to increase within 24 h of ascorbate treatment; by 9 days, the levels of both alkaline phosphatase activity and type X collagen mRNA were 15-20-fold higher than in non-ascorbate-treated cells. Ascorbate treatment also increased calcium deposition in the cell layer and decreased the levels of types II and IX collagen mRNAs; these effects lagged significantly behind the elevation of alkaline phosphatase and type X collagen. Addition of beta-glycerophosphate to the medium increased calcium deposition in the presence of ascorbate but had no effect on levels of collagen mRNAs or alkaline phosphatase. The results suggest that vitamin C may play an important role in endochondral bone formation by modulating gene expression in hypertrophic chondrocytes.
Backward flow in a surface tension driven micropump (2008)

A surface tension driven micropump harnessing the pressure difference generated by drops of different curvature radii proves to be a simple and attractive passive method to drive fluid flow in microdevices. Here we observed the appearance of backward flow when the initial sizes of the droplets at the inlet and outlet ports are similar. To explain this phenomenon several hypotheses have been investigated. Consideration of the inertia of the fluid in the channel revealed that it alone is insufficient to explain the observed backward flow. We discovered that rotational flow inside the outlet droplet could be a source of inertia, explaining the generation of the backward flow. In addition, we have experimentally determined that the ratio of the volumes of the initial outlet drop and inlet drop correlates with the occurrence of the backward flow.
Blood Volume Measurement at the Bedside Using ICG Pulse Spectrophometry (1998)

In most patients, the pulse method provides bedside measurement of BV without blood sampling (except for hemoglobin determination), with an estimated error less than 10%. In 10-30% of tests the method failed because of motion distortion of the record during the 10-min data collection period or because of insufficient pulse amplitude in the test tissue.
Thermionic energy conversion plasmas (1991)

The author provides a perspective of the nature and scientific characterization of the unique plasmas occurring in the various modes of thermionic converter operation associated with different application requirements. The basic plasma types associated with various modes of converter operation are described, with emphasis on identification and semi-quantitative characterization of the dominant physical processes and utility of each plasma type. Their characteristic advantages are identified with particular applications. The author is concerned primarily with the physics of the various types of plasma employed to conform to the constraints of particular options and applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Silencing of directional migration in roundabout4 knockdown endothelial cells (2008)

This study identifies specific components of the Robo signaling apparatus that work together to guide directional migration of endothelial cells.
Synthesis of Substituted Azaindenes: Synthesis of New Pyrazolo[1,5-a]pyrimidine Derivatives (1990)

Abstract Several new pyrazolo[1,5-a]pyrimidines were synthesized via the reaction of 4,5-disubstituted 3-aminopyrazoles 1a–d with 3-dimethylaminopropiophenone, cinnamaldehyde, benzylideneacetophenone and tetracyanoethylene.
Tumor-selective radiopharmaceutical targeting via receptor-mediated endocytosis of gallium-67-deferoxamine-folate. (1996)

Receptor-mediated endocytosis of radiolabeled folate-conjugates may offer a suitable mechanism for selectively delivering radiopharmaceuticals to tumors for diagnostic imaging and/or radiation therapy.
Nutritional Effects of Tannins in Animal Feeds (1988)

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Human Cytomegalovirus (HCMV) UL82 Gene Product (pp71) Relieves hDaxx-Mediated Repression of HCMV Replication (2006)

This study examines the role of the cellular protein hDaxx in controlling human cytomegalovirus (HCMV) immediate-early (IE) gene expression and viral replication. Using permissive cell lines that either overexpress hDaxx or are depleted of hDaxx expression by the use of short hairpin RNA, we demonstrate that hDaxx functions as a repressor of HCMV IE gene expression and replication. In addition, we demonstrate that the impaired growth phenotype associated with the UL82 (pp71) deletion mutant is abolished when hDaxx knockdown cells are infected, suggesting that pp71 functions to relieve hDaxx-mediated repression during HCMV infection.
A New High Activity Anti-CD22 Chimeric Antigen Receptor (CAR) Targeting B Cell Leukemia. (2012)

Abstract Abstract 2611 CD22 is expressed on the surface of B cell hematologic malignancies such as acute lymphoblastic leukemia (ALL). CD22 is a Siglec family lectin present on B cells, starting at the pre-B cell stage of development, but is not expressed on plasma cells. CD22 consists of 7 extracellular Ig domains and is found in 2 isoforms, one of which is missing the second and third N-terminal Ig domains. We generated CAR modified T cells containing anti-CD22 extracellular binding motifs fused to intracellular signaling domains for T cells activation (CD3 zeta) or costimulation (CD28 or 4-1BB). The binding motifs were derived from scFvs that targeted a membrane distal epitope of CD22, Ig domain 3, (BL22 and a higher affinity HA22 motif) or that bound a more membrane proximal, Ig domains 5–7, of CD22 (m971). The CAR constructs we generated were second-generation (CD28 and CD3 zeta; or, 4-1BB and CD3 zeta) or third generation (CD28, 4-1BB and CD3 zeta signaling domains). A CH2CH3 spacer domain from IgG1 was added in some constructs to examine the impact of extending the scFv-derived binding domain away from the transduced T cell membrane. In vitro cellular cytotoxicity and cytokine release experiments with 4 B cell-ALL cell lines (REH, SEM, NALM6, KOPN8) as well as the CD22 (+)ve Daudi and Raji cell lines were performed. Our results demonstrate that addition of the CH2CH3 domain did not improve tumor lysis and that standard affinity BL22 and higher affinity HA22-derived scFv epitopes were equivalent. With regard to signaling domains, second generation constructs were better than third generation constructs both in vitro and in vivo. In comparison between second generation constructs, CD28 containing domains outperformed 4-1BB with regard to lytic activity and cytokine release. Most surprising was the activity of the m971-derived scFv binding epitope. m971-CAR had significantly higher killing activity, a far more robust cytokine release profile, and superior in vivo activity. NSG mice were injected i.v. with 0.5× 106 NALM6-GL cells (pre-B cell ALL line engineered to express luciferase). Three days later, when disease was evident, mice were treated with 1×107 CAR+ T cells, and then followed by bioluminescent imaging to measure disease burden. The m971 CAR was significantly more potent at tumor clearance than our previously developed most active construct expressing the HA22-derived scFv domain (Figure 1). Disease progressed rapidly when non-transduced T cells were used (mock). We are currently examining the activity of different signaling domains on m971 CAR efficacy in vivo and directly comparing the anti-CD22 m971 CAR to the CD19 CAR currently being evaluated in clinical trials. These studies will guide future anti-CD22 CAR-based anti-leukemia immunotherapy trials. Disclosures: No relevant conflicts of interest to declare.
Leukemia, Lymphoma, and Osteosarcoma Induced in the Syrian Golden Hamster by Simian Virus 40 (1972)

Leukemia, lymphoma, and osteogenic and anaplastic sarcomas develop in Syrian golden hamsters inoculated intravenously at 3 weeks of age with simian virus 40, which is a popova virus. Previously, only RNA and herpes DNA viruses have been recognized as capable of inducing leukemia and lymphoma in mammals. The significance of these findings is emphasized in relation to the nature of viral agents that may be involved in analogous diseases of man.
Skeletal Muscle Satellite Cells Are Committed to Myogenesis and Do Not Spontaneously Adopt Nonmyogenic Fates (2011)

The developmental potential of skeletal muscle stem cells (satellite cells) remains controversial. The authors investigated satellite cell developmental potential in single fiber and clonal cultures derived from MyoD(iCre/+);R26R(EYFP/+) muscle, in which essentially all satellite cells are permanently labeled. Approximately 60% of the clones derived from cells that co-purified with muscle fibers spontaneously underwent adipogenic differentiation. These adipocytes stained with Oil-Red-O and expressed the terminal differentiation markers, adipsin and fatty acid binding protein 4, but did not express EYFP and were therefore not of satellite cell origin. Satellite cells mutant for either MyoD or Myf-5 also maintained myogenic programming in culture and did not adopt an adipogenic fate. Incorporation of additional wash steps prior to muscle fiber plating virtually eliminated the non-myogenic cells but did not reduce the number of adherent Pax7+ satellite cells. More than half of the adipocytes observed in cultures from Tie2-Cre mice were recombined, further demonstrating a non-satellite cell origin. Under adipogenesis-inducing conditions, satellite cells accumulated cytoplasmic lipid but maintained myogenic protein expression and did not fully execute the adipogenic differentiation program, distinguishing them from adipocytes observed in muscle fiber cultures. The authors conclude that skeletal muscle satellite cells are committed to myogenesis and do not spontaneously adopt an adipogenic fate.
ATR inhibition selectively sensitizes G 1 checkpoint-deficient cells to lethal premature chromatin condensation (2001)

Premature chromatin condensation (PCC) is a hallmark of mammalian cells that begin mitosis before completing DNA replication. This lethal event is prevented by a highly conserved checkpoint involving an unknown, caffeine-sensitive mediator. Here, we have examined the possible involvement of the caffeine-sensitive ATM and ATR protein kinases in this checkpoint. We show that caffeine's ability to inhibit ATR (but not ATM) causes PCC, that ATR (but not ATM) prevents PCC, and that ATR prevents PCC via Chk-1 regulation. Moreover, mimicking cancer cell phenotypes by disrupting normal G(1) checkpoints sensitizes cells to PCC by ATR inhibition plus low-dose DNA damage. Notably, loss of p53 function potently sensitizes cells to PCC caused by ATR inhibition by a small molecule. We present a molecular model for how ATR prevents PCC and suggest that ATR represents an attractive therapeutic target for selectively killing cancer cells by premature chromatin condensation.
Antibacterials. Synthesis and structure-activity studies of 3-aryl-2-oxooxazolidines. 2. The "A" group (1990)

The synthesis and structure-activity relationship (SAR) studies of the effect of varying the "A" group in a series of 5-(acetamidomethyl)oxazolidonone antibacterials (2) are described. Compounds 2 were principally prepared either by the six-step synthesis described previously (J. Med. Chem. 1989, 32, 1673) or by elaboration of the synthetic intermediate 2 (A = H) via electrophilic aromatic substitution or elaboration of the intermediate 2 (A = I) by transition metal catalyzed carbon-carbon bond-forming reactions. Antibacterial evaluation of compounds 2 with A = alkyl, ethenyl, ethynyl, hydroxyalkyl, aldo and keto, oximinoakyl, carboalkoxy, nitro, amino, halo and psi-halo, alkylthio, alkylsulfinyl, and alkysulfonyl against Staphylococcus aureus and Enterococcus faecalis led to the identification of several SAR trends. In several series of homologues (alkyl, ketyl, aximinoalkyl, amino, halo and psi-halo, and alkythio), antibacterial activity increased with increasing lipophilicity. But in series with where A is a substituent with a trior tetrasubstituted (substituent larger than H) quaternary atom attached directly to the aromatic ring (hydroxyalkyl, alkylsulfinyl, alkylsufonyl), the activity peaked at the member of the series with the "tert-butyl" connectivity pattern. Conjugated electron-withdrawing substituents also had increased activity relative to nonconjugated analogues of comparable lipophilicity.
Pediatric Intestinal Failure–Associated Liver Disease Is Reversed With 6 Months of Intravenous Fish Oil (2013)

A limited duration of FO appears to be safe and effective in reversing IFALD.
Epidermal Growth Factor Receptor Mutants from Human Lung Cancers Exhibit Enhanced Catalytic Activity and Increased Sensitivity to Gefitinib (2007)

Somatic mutations within the epidermal growth factor receptor (EGFR) kinase domain are detected in 10% to 30% of human non-small cell lung cancers and are correlated with striking clinical responses in a subset of patients treated with EGFR kinase inhibitors, such as gefitinib and erlotinib. Cell-based studies suggest that these mutant EGFRs promote increased autophosphorylating activity on a subset of EGFR COOH-terminal tyrosines and the consequent engagement of a subset of downstream effectors. Because EGFR function is regulated at multiple levels in vivo, and it is therefore difficult to assess the direct consequences of these mutations on EGFR enzyme function, we measured EGFR catalytic activity in in vitro kinase assays using purified recombinant proteins corresponding to the cytoplasmic domain of wild-type and two frequently detected EGFR mutants (DelL747-P753insS and L858R). Both mutants exhibit substantially increased autophosphorylating activity relative to wild-type EGFR, and they exhibit distinct reaction kinetics. In addition, the mutant kinases are more sensitive to kinase inhibition by gefitinib, which seems to reflect their increased drug affinity. These findings suggest that the altered signaling properties and drug sensitivity of these EGFR mutants that have been observed in vivo largely result from differences in the catalytic properties of the kinase. In addition, we find that the T790M secondary "drug resistance mutation" of EGFR, which frequently arises in relapsed patients that initially responded to treatment, confers enhanced kinase activity to primary activating EGFR alleles and may, therefore, be oncogenic in some contexts.
An integrated flow cytometry-based platform for isolation and molecular characterization of circulating tumor single cells and clusters (2018)

Comprehensive molecular analysis of rare circulating tumor cells (CTCs) and cell clusters is often hampered by low throughput and purity, as well as cell loss. To address this, we developed a fully integrated platform for flow cytometry-based isolation of CTCs and clusters from blood that can be combined with whole transcriptome analysis or targeted RNA transcript quantification. Downstream molecular signature can be linked to cell phenotype through index sorting. This newly developed platform utilizes in-line magnetic particle-based leukocyte depletion, and acoustic cell focusing and washing to achieve >98% reduction of blood cells and non-cellular debris, along with >1.5 log-fold enrichment of spiked tumor cells. We could also detect 1 spiked-in tumor cell in 1 million WBCs in 4/7 replicates. Importantly, the use of a large 200μm nozzle and low sheath pressure (3.5 psi) minimized shear forces, thereby maintaining cell viability and integrity while allowing for simultaneous recovery of single cells and clusters from blood. As proof of principle, we isolated and transcriptionally characterized 63 single CTCs from a genetically engineered pancreatic cancer mouse model (n = 12 mice) and, using index sorting, were able to identify distinct epithelial and mesenchymal sub-populations based on linked single cell protein and gene expression.
Induction machine diagnostics using zero sequence components (2005)

Induction machine diagnostics using zero sequence components is presented in this paper. Electrical faults cause asymmetries in the phase impedances, producing a zero sequence voltage in wye-connected machines and a zero sequence current in delta-connected machines. The proposed measurement method identifies these well defined components in the zero sequence voltage/current and uses them to provide reliable information on the condition of the machine, with low sensitivity to the load level of the machine or variations in the phase voltage. The method can be used for the diagnosis of stator winding faults and broken rotor bars, and is valid both for line-connected and inverter-fed machines.
Acute repair of chondrocytes in the rabbit tibiofemoral joint following blunt impact using P188 surfactant and a preliminary investigation of its long-term efficacy (2009)

Recent studies have indicated that there may be a correlation between acute chondrocyte damage and joint degeneration reminiscent of early-stage osteoarthritis (OA). P188 surfactant has been shown to acutely restore the integrity of damaged chondrocytes; however, its long-term efficacy is unknown. The hypothesis of this study was that a single injection of P188 into a traumatized joint would acutely repair damaged cell membranes and maintain their viability in the long term. Twelve rabbits were divided into two groups, with and without P188, and sacrificed 4 days after tibiofemoral (TF) impact. Another six rabbits were sacrificed after 6 weeks and divided into two groups, with and without P188 treatment immediately posttrauma. Treatment with P188 increased the viable cell density 4 days posttrauma. A higher density of viable cells was also documented 6 weeks posttrauma in the treated versus untreated limb. The results of the current study confirm the acute efficacy of P188 treatment, and may suggest long-term efficacy of treatment, but additional studies are still needed to investigate the chronic implications of the acute repair of cells in the traumatized joint.
Recombination during transformation as a source of chimeric mammalian artificial chromosomes in yeast (YACs) (1994)

Mammalian DNAs cloned as artificial chromosomes in yeast (YACs) frequently are chimeras formed between noncontiguous DNAs. Using pairs of human and mouse YACs we examined the contribution of recombination during transformation or subsequent mitotic growth to chimeric YAC formation. The DNA from pairs of yeast strains containing homologous or heterologous YACs was transformed into a third strain under conditions typical for the development of YAC libraries. One YAC was selected and the presence of the second was then determined. Co-penetration of large molecules, as deduced from co-transformation of markers identifying the different YACs, was >50%. In approximately half the cells receiving two homologous YACs, the YACs had undergone recombination. Co-transformation depends on recombination since it was reduced nearly 10-fold when the YACs were heterologous. While mitotic recombination between homologous YACs is nearly 100-fold higher than for yeast chromosomes, the level is still much lower than observed during transformation. To investigate the role of commonly occurring Alu repeats in chimera formation, spheroplasts were transformed with various human YACs and an unselected DNA fragment containing an Alu at one end and a telomere at the other. When unbroken YACs were used, between 1 and 6% of the selected YACs could incorporate the fragment as compared to 49% when the YACs were broken. We propose that Alu's or other commonly occurring repeats could be an important source of chimeric YACs. Since the frequency of chimeras formed between YACs or a YAC and an Alu-containing fragment was reduced when a rad52 mutant was the recipient and since intra-YAC deletions are reduced, rad52 and possibly other recombination-deficient mutants are expected to be useful for YAC library development.
Streaming current generation in two‐phase flow conditions (2007)

Self‐potential (SP) signals that are generated under two‐phase flow conditions could be used to study vadose zone dynamics and to monitor petroleum production. These streaming‐potentials may also act as an error source in SP monitoring of vulcanological activity and in magnetotelluric studies. We propose a two‐phase flow SP theory that predicts streaming currents as a function of the pore water velocity, the excess of charge in the pore water, and the porosity. The source currents that create the SP signals are given by the divergence of the streaming currents, and contributions are likely to be located at infiltration fronts, at the water table, or at geological boundaries. Our theory was implemented in a hydrogeological modeling code to calculate the SP distribution during primary drainage. Forward and inverse modeling of a well‐calibrated 1D drainage experiment suggest that our theory can predict streaming potentials in the vadose zone.