gebhart/patrepeval huggingface dataset:
Towards Automated Experiments in Software Intensive Systems (2018)

Context: Delivering software that has value to customers is a primary concern of every software company. One of the techniques to continuously validate and deliver value in online software systems is the use of controlled experiments. The time cost of each experiment iteration, the increasing growth in the development organization to run experiments and the need for a more automated and systematic approach is leading companies to look for different techniques to automate the experimentation process. Objective: The overall objective of this thesis is to analyze how to automate different types of experiments and how companies can support and optimize their systems through automated experiments. This thesis explores the topic of automated online experiments from the perspectives of the software architecture, the algorithms for the experiment execution and the experimentation process, and focuses on two main application domains: the online and the embedded systems domain. Method: To achieve the objective, we conducted this research in close collaboration with industry using a combination of different empirical research methods: case studies, literature reviews, simulations and empirical evaluations. Results and conclusions: This thesis provides five main results. First, we propose an architecture framework for automated experimentation that can be used with different types of experimental designs in both embedded systems and web-facing systems. Second, we identify the key challenges faced by embedded systems companies when adopting controlled experimentation and we propose a set of strategies to address these challenges. Third, we develop a new algorithm for online experiments. Fourth, we identify restrictions and pitfalls of different algorithms for automating experiments in industry and we propose a set of guidelines to help practitioners select a technique that minimizes the occurrence of these pitfalls. Fifth, we propose a new experimentation process to capture the details of a trustworthy experimentation process that can be used as basis for an automated experimentation process. Future work: In future work, we plan to investigate how embedded systems can incorporate experiments in their development process without compromising existing real-time and safety requirements. We also plan to analyze the impact and costs of automating the different parts of the experimentation process.
Immature rat seminiferous tubules reconstructed in vitro express markers of Sertoli cell maturation after xenografting into nude mouse hosts (2009)

Sertoli cells undergo a maturation process during post-natal testicular development that leads to the adult-type Sertoli cell, which is required for spermatogenesis. Understanding Sertoli cell maturation is therefore necessary to gain insight into the underlying causes of impaired spermatogenesis and male infertility. The present study characterized the cellular and molecular differentiation of Sertoli cells in a xenograft model of mammalian testicular development. Immature rat Sertoli cells were cultured in a three-dimensional culture system to allow the formation of cord-like structures. The in vitro Sertoli cell cultures were then grafted into nude mice. Sertoli cell proliferation, morphological differentiation and mRNA expression of Sertoli cell maturation markers were evaluated in xenografts. Sertoli cell proliferation significantly decreased between 1 and 4 weeks (6.7 +/- 0.9 versus 1.2+/- 0.1%, P < 0.001), and was maintained at low levels thereafter. Sertoli cell cord-like structures significantly decreased between 1 and 4 weeks (59.6 versus 21%, P < 0.05), whereas Sertoli cell tubules were more frequently observed after 4 weeks (13.3 versus 73.1%, P < 0.05). Furthermore, expression of androgen binding protein, transferrin and follicle stimulating hormone receptor, markers for mature Sertoli cells, was detected after 1 week of grafting and increased significantly thereafter. We conclude from these results that rat Sertoli cells continue maturation after xenografting to the physiological environment of a host. This model of in vitro tubule formation will be helpful in future investigations addressing testicular maturation in the mammalian testis.
Increasing Turbocharged Engine Operating Ranges Through Use of a Booster System (2007)

In the natural gas industry a large portion of the engines used for compression are lean-burn engines. When these engines operate at low equivalence ratios, oxides of nitrogen (NOX) can be minimized. The lean-burn engines are turbocharged to deliver high air flow to the engine. However, varying ambient temperatures alter the mass flow rate of air delivered to the engine, changing the equivalence ratio the engine fires at. This may cause an engine to be de-rated, or taken off line reducing the gas throughput. This problem can be partially offset by the installation of a turbocharger booster system to increase the available energy at the turbocharger turbine inlet. One method to boost the energy available to drive the turbocharger is to increase the temperature of the exhaust before it enters the turbine via a relatively small dry low NOX burner. A turbocharger booster system was designed, prototyped, installed, and tested at the National Gas Machinery Laboratory (NGML) turbocharger test and research facility (TTRF). The test data show that the addition of a turbocharger booster system increased the speed of the turbocharger without increasing the emission levels. The increase in speed translates to an increased pressure ratio and mass flow rate of air produced by the compressor. By controlling the booster system, constant air flow rate can be achieved regardless of ambient conditions. This paper provides test results that show how the system can be used to increase an engine’s operating range and mitigate ambient effects.
Supplementary Figure 3 from Global Levels of Specific Histone Modifications and an Epigenetic Gene Signature Predict Prostate Cancer Progression and Development (2023)

Supplementary Figure 3 from Global Levels of Specific Histone Modifications and an Epigenetic Gene Signature Predict Prostate Cancer Progression and Development
Mud Dauber Nests as Sources of Spiders in Mercury Monitoring Studies (2021)

Identifying ecosystems where biota may be contaminated with hazardous levels of methylmercury (MeHg) is a challenge. One widely used approach for determining site-specific MeHg contamination is to monitor MeHg contamination in sentinel species. Terrestrial shoreline spiders that consume emergent aquatic insects (e.g., midges and mayflies) have been proposed as sentinels of MeHg contamination of aquatic ecosystems. The purpose of the present study was to determine whether a novel sampling technique, collection of spiders from nests of mud dauber wasps (Sphecidae), would be an efficient method for capturing MeHg-contaminated shoreline spiders for use as sentinels in ecological risk assessments. Mud dauber nests were collected near the Clear Fork of the Trinity River in Fort Worth, Texas (USA) on 3 dates from 4 human-made structures. Nests contained 627 unconsumed spiders from 5 families: Araneidae, Salticidae, Thomisidae, Oxyopidae, and Theridiidae. Methylmercury concentrations ranged from 12.2 to 56.3 ng/g wet weight in Thomisidae and Araenidae, respectively. Methylmercury concentrations of the spiders were generally low relative to risk thresholds for adult birds, but a few families of spiders could pose a risk to nestlings. Although mud dauber nests have been recognized as a source of spiders for biodiversity studies, the present study is the first to demonstrate the potential use of spiders collected from mud dauber nests for ecotoxicology studies. Environ Toxicol Chem 2021;40:1335-1340. © 2021 SETAC.
Modulation of chemotherapy resistance in regional therapy: a novel therapeutic approach to advanced extremity melanoma using intra-arterial temozolomide in combination with systemicO6-benzylguanine (2006)

This study investigated whether the therapeutic index of regional melanoma therapy using parenteral temozolomide could be improved by chemomodulation with O6-benzylguanine (O6BG), an inhibitor of the DNA repair enzyme O6-alkylguanine-DNA alkyltransferase (AGT). Using a nude rat s.c. human melanoma xenograft model of the extremity, tumors were analyzed for AGT level 2 to 3 hours after the i.p. injection of 3.5 to 70.0 mg/kg O6BG to inhibit AGT activity. Survival studies were conducted using animals that were treated with a 15-minute isolated limb infusion with 10% DMSO in PBS (control), temozolomide alone, or temozolomide in conjunction with single or multiple doses of i.p. O6BG. Tumor volume and toxicity level were monitored every other day. Administration of 3.5 mg/kg O6BG depleted tumor AGT activity by 93.5% (P < 0.01). Groups treated with regional temozolomide alone (350 mg/kg), systemic temozolomide with O6BG, or vehicle combined with O6BG showed no significant tumor responses compared with controls. Whereas use of regional temozolomide alone at a higher dose (750 mg/kg) showed some degree of tumor response, regional temozolomide given in conjunction with multiple dosages of O6BG showed a marked (P < 0.01) reduction in tumor growth with minimal toxicity. Our findings suggest that AGT modulation by the administration of O6BG in combination with temozolomide regional chemotherapy leads to a significant improvement in melanoma antitumor responses. Clinical trials using chemotherapy modulation may improve response rates in future regional infusion and perfusion drug trials.
[A Case of Simultaneous Recurrence of Colon Cancer at the Drain Placement and Anastomotic Sites Postoperatively]. (2018)

A woman in her 70s presented to our hospital with abdominal pain and right lower abdominal mass. Colonoscopy revealed circumferential ascending colon cancer. She underwent right hemicolectomy, D3 lymphadenectomy, and ileocolonic functional end-to-end anastomosis. The tumorwas pathologically diagnosed as T4aN1M0, Stage Ⅲa. Nine months afterthe first surgery, tumor marker levels increased, and detailed examination yielded a diagnosis of isolated recurrence at the site of drain removal in the abdominal wall. The tumor was resected without exposure. Four months after the second surgery, the tumor recurred in the abdominal wall. Furthermore, colonoscopy revealed anastomotic recurrence. Both recurrent tumors at the anastomotic site and in the abdominal wall were resected. No more recurrence has been detected to date. In this case, a possible cause of recurrence is implantation of cancer cells. Sufficient consideration should be given to innovations in intraoperative maneuvers and surgical wound protection, among others.
Odorless Benzenethiols in Synthesis of Thioglycosides and Application for Glycosylation Reactions. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Hydrogen sulfide as a vasculoprotective factor (2013)

Hydrogen sulfide is a novel mediator with the unique properties of a gasotransmitter and many and varied physiological effects. Included in these effects are a number of cardiovascular effects that are proving beneficial to vascular health. Specifically, H2S can elicit vasorelaxation, prevention of inflammation and leukocyte adhesion, anti-proliferative effects and anti-thrombotic effects. Additionally, H2S is a chemical reductant and nucleophile that is capable of inhibiting the production of reactive oxygen species, scavenging and neutralising reactive oxygen species and boosting the efficacy of endogenous anti-oxidant molecules. These result in resistance to oxidative stress, protection of vascular endothelial function and maintenance of blood flow and organ perfusion. H2S has been shown to be protective in hypertension, atherosclerosis and under conditions of vascular oxidative stress, and deficiency of endogenous H2S production is linked to cardiovascular disease states. Taken together, these effects suggest that H2S has a physiological role as a vasculoprotective factor and that exogenous H2S donors may be useful therapeutic agents. This review article will discuss the vascular effects and anti-oxidant properties of H2S as well as examine the protective role of H2S in some important vascular disease states.
Transplantation of Corneal Stroma Reconstructed with Gelatin and Multipotent Precursor Cells from Corneal Stroma (2011)

Transplantation of Corneal Stroma Reconstructed with Gelatin and Multipotent Precursor Cells from Corneal Stroma
RENAL ALLOGRAFT REJECTION (1995)

Renal tubular epithelial cells can be induced to express potentially immunogenic levels of class II MHC antigens but fail to stimulate the activation of allospecific T lymphocytes. The current series of experiments was performed to determine whether the failure of lymphocyte activation in this system is caused by defective T cell costimulation. It was found that cultured renal epithelial cells expressed class II MHC antigens and the immunoregulatory adhesion molecules intercellular adhesion molecule-1, vascular cell adhesion molecule-1, and lymphocyte function-associated antigen-3 after stimulation with IFN-gamma, but that the B7 ligand for CD28 was not expressed. Mixed cell culture experiments were set up in which lymphocytes were mixed with IFN-gamma-treated allogeneic renal cells. Lymphoproliferation and IL-2 production were only observed if bivalent anti-CD28 antibodies were titrated into these cultures. The requirement for antigen stimulation was retained by these lymphocytes, as no proliferation was observed after stimulation by class II MHC antigen nonexpressing, resting renal cells. Further experiments demonstrated that the effectiveness of the anti-CD28 antibody-mediated signal was enhanced by cross-linking with a secondary anti-kappa-chain antibody. These data are consistent with the concept that a costimulatory signal generated by ligation of CD28 is of central importance to the development of an immune response to alloantigen. Furthermore, these results indicate that tubular epithelial cells within a rejecting renal allograft are unlikely to initiate direct activation of infiltrating allospecific lymphocytes.
ATM-deficiency in the absence of T cells promotes the development of B cell lymphomas with dependence on NF-kB (TUM7P.927) (2014)

Abstract The protein product of the ataxia-telangiectasia mutated gene, ATM, is a kinase that plays a central role in maintaining genomic integrity and protecting cells from oncogenic transformation. Mutations of the human ATM gene cause ataxia-telangiectasia, an autosomal recessive disorder that is associated with increased incidence of malignancies, especially lymphoid tumors. ATM-deficient mice have been useful tools to study thymic lymphomas, which occur at high frequency in these mice, but the early onset of these tumors has prevented analysis of other types of malignancies. In this study we generated ATM- and CD3ε-deficient mice that lacked T cells. These mice do not develop thymic lymphomas, but routinely develop early onset B cell lymphomas that express surface markers characteristic of mature activated B cells. These B cell lymphomas resemble human diffuse large B cell (DLBC) lymphomas and possess complex karyotypes with genetic amplifications, deletions and unbalanced translocations. Interestingly all lymphomas (10/10) contain an amplification of a 5Mb region on chromosome 18 containing MALT1. These lymphomas also express NF-kB and are dependent on MALT1 and NF-kB signaling for in vitro survival. As such they represent a mouse model for NF-kB- dependent human DLBC lymphomas of the ABC- subtype.
Analysis of MMC Energy-Based Control Structures for VSC-HVDC Links (2018)

An analysis of control structures for modular multilevel converters (MMCs) used in high-voltage direct current (HVDC) applications is addressed. In particular, this paper focuses on the case of a point-to-point link with master-slave control, considering an energy-based scheme (also known as closed loop or energy controlled) for the MMC, meaning that the internal energy of the converter is explicitly controlled. With such an approach, the MMC internal energy can be controlled independently of the energy of the HVDC link, and whereas the internal capacitance of the MMC depends on the converter's rating, the capacitance at the dc terminal depends on the cable length. Therefore, several possibilities regarding the outer control structure (internal energy and dc voltage) arise, affecting the overall dynamics differently. Whereas for a long link, the classic control structures should perform well, for shorter links the transient performance might not be acceptable and other alternatives shall be used instead. Different control structures are presented and evaluated in this paper through small-signal and frequency-domain analysis, and validated through time-domain simulation with MATLAB Simscape Power Systems.
Application Level Interoperability between Clouds and Grids (2009)

SAGA is a high-level programming interface which provides the ability to develop distributed applications in an infrastructure independent way. In an earlier paper, we discussed how SAGA was used to develop a version of MapReduce which provided the user with the ability to control the relative placement of compute and data, whilst utilizing different distributed infrastructure. In this paper, we use the SAGA-based implementation of MapReduce, and demonstrate its interoperability across clouds and grids. We discuss how a range of cloud adaptors have been developed for SAGA. The major contribution of this paper is the demonstration - possibly the first ever, of interoperability between different clouds and grids, without any changes to the application. We analyse the performance of SAGA-MapReduce when using multiple, different, heterogeneous infrastructure concurrently for the same problem instance; However, we do not strive to provide a rigorous performance model, but to provide a proof-of-concept of application-level interoperability and illustrate its importance.
Regularity-constrained pre- and post-filtering for block DCT-based systems (2003)

It is well known that the traditional block transform can only have at most one degree of regularity. In other words, by retaining only one subband, these transforms, including the popular discrete cosine transform (DCT), can only capture the constant signal. The ability to capture polynomials of higher orders is critical in smooth signal approximation, minimizing blocking effects. This paper presents the theory, design, and fast implementation of regularity constrained pre-/post-filters for block-based decomposition systems. We demonstrate that simple pre-/post-filtering modules added to the current block-based infrastructure can help the block transform capture not only the constant signal but the ramp signal as well. Moreover, our proposed framework can be used to generate various fast symmetric M-band wavelets with up to two degrees of regularity.
Classification of Partially Labeled Malicious Web Traffic in the Presence of Concept Drift (2014)

Attacks to Web systems have shown an increasing trend in the recent past. A contributing factor to this trend is the deployment of Web 2.0 technologies. While work related to characterization and classification of malicious Web traffic using supervised learning exists, little work has been done using semi-supervised learning with partially labeled data. In this paper an incremental semi-supervised algorithm (CSL-Stream) is used to classify malicious Web traffic to multiple classes, as well as to analyze the concept drift and concept evolution phenomena. The work is based on data collected in duration of nine months by a high-interaction honeypot running Web 2.0 applications. The results showed that on completely labeled data semi-supervised learning performed only slightly worse than the supervised learning algorithm. More importantly, multiclass classification of the partially labeled malicious Web traffic (i.e., 50% or 25% labeled sessions) was almost as good as the classification of completely labeled data.
Serotonin Uptake in Blood Platelets of Acute Schizophrenics-Reply (1983)

<h3>In Reply.—</h3> Modai et al are correct in pointing out that their method permits the assessment of active uptake of serotonin. We apologize for our misunderstanding of their means of estimating passive diffusion. However, the use of only a single tube to assess passive diffusion and of duplicate tubes to assess total uptake is questionable, because the data on passive diffusion contribute as much to the measurement of active uptake as do those on total uptake. The important issue of whether schizophrenic patients suffering acute exacerbation have decreased active uptake of serotonin in their platelets requires further study, because we cannot confirm the report by Modai et al of low uptake in schizophrenics. S. Stahl, MD, PhD, and P. Berger, MD, of Stanford (Calif) University also have not found decreased uptake of serotonin in the platelets of schizophrenics not receiving medication (oral communication, Nov 15, 1981). There could be some differences between
Measurable residual disease monitoring provides insufficient lead-time to prevent morphologic relapse in the majority of patients with core-binding factor acute myeloid leukemia (2020)

Core-binding factor acute myeloid leukemia is characterized by t(8;21) or inv(16) and the fusion proteins RUNX1-RUNX1T1 and CBFB-MYH11. International guidelines recommend monitoring for measurable residual disease every 3 months for 2 years after treatment. However, it is unknown if serial molecular monitoring can predict and prevent morphologic relapse. We conducted a retrospective single-center study of 114 patients in complete remission who underwent molecular monitoring with RT-qPCR of RUNX1-RUNX1T1 or CBFB-MYH11 transcripts every 3 months. Morphologic relapse was defined as re-emergence of >5% blasts and molecular relapse as ≥1 log increase in transcript level between 2 samples. Over a median follow-up time of 3.7 years (range 0.2-14.3), remission persisted in 71 (62.3%) patients but 43 (37.7%) developed molecular or morphologic relapse. Patients who achieved <3 log reduction in RUNX1-RUNX1T1 or CBFB-MYH11 transcripts at end of chemotherapy had a significantly higher risk of relapse compared to patients who achieved ≥3 log reduction (61.1% vs. 33.7%, p=0.004). The majority of relapses (74.4%, n=32) were not predicted by molecular monitoring and occurred rapidly with <100 days from molecular to morphologic relapse. Molecular monitoring enabled the detection of impending relapse and permitted pre-emptive intervention prior to morphologic relapse in only 11 (25.6%) patients. The current practice of molecular monitoring every 3 months provided insufficient lead-time to identify molecular relapses and prevent morphologic relapse in the majority of patients with core-binding factor acute myeloid leukemia treated at our institution. Further research is necessary to determine the optimal monitoring strategies for these patients.