gebhart/patrepeval huggingface dataset:
Impact of Active Control on Passive Safety Response Characteristics of Sodium-Cooled Fast Reactors: II—Model Implementation and Simulations (2017)

Advanced reactors are often claimed to be passively safe against unprotected upset events. In common practice, these events are not considered in the context of the plant control system, i.e., the reactor is subjected to classes of unprotected upset events while the normally programmed response of the control system is assumed not to be present. However, this approach constitutes an oversimplification since, depending on the upset involving the control system, an actuator does not necessarily go in the same direction as needed for safety. In this work, dynamic simulations are performed to assess the degree to which the inherent self-regulating plant response is safe from active control system override. The simulations are meant to characterize the resilience of the plant to unprotected initiators. The initiators were represented and modeled as an actuator going to a hard limit. Consideration of failure is further limited to individual controllers as there is no cross-connect of signals between these controllers. The potential for passive safety override by the control system is then relegated to the single-input single-output controllers. The results show that when the plant control system is designed by taking into account and quantifying the impact of the plant control system on accidental scenarios there is very limited opportunity for the preprogrammed response of the control system to override passive safety protection in the event of an unprotected initiator.
The polyomavirus puzzle: is host immune response beneficial in controlling <scp>BK</scp> virus after adult hematopoietic cell transplantion? (2014)

BK virus (BKV), a ubiquitous human polyomavirus, usually does not cause disease in healthy individuals. BKV reactivation and disease can occur in immunosuppressed individuals, such as those who have undergone renal transplantation or hematopoietic cell transplantation (HCT). Clinical manifestations of BKV disease include graft dysfunction and failure in renal transplant recipients; HCT recipients frequently experience hematuria, cystitis, hemorrhagic cystitis (HC), and renal dysfunction. Studies of HCT patients have identified several risk factors for the development of BKV disease including myeloablative conditioning, acute graft-versus-host disease, and undergoing an umbilical cord blood (uCB) HCT. Although these risk factors indicate that alterations in the immune system are necessary for BKV pathogenesis in HCT patients, few studies have examined the interactions between host immune responses and viral reactivation in BKV disease. Specifically, having BKV immunoglobulin-G before HCT does not protect against BKV infection and disease after HCT. A limited number of studies have demonstrated BKV-specific cytotoxic T cells in healthy adults as well as in post-HCT patients who had experienced HC. New areas of research are required for a better understanding of this emerging infectious disease post HCT, including prospective studies examining BK viruria, viremia, and their relationship with clinical disease, a detailed analysis of urothelial histopathology, and laboratory evaluation of systemic and local cellular and humoral immune responses to BKV in patients receiving HCT from different sources, including uCB and haploidentical donors.
Understanding the Species Selectivity of Myeloid Cell Leukemia-1 (Mcl-1) Inhibitors (2018)

To test for on target toxicity of a new chemical entity, it is important to have comparable binding affinities of the compound in the target proteins from humans and the test species. To evaluate our myeloid cell leukemia-1 (Mcl-1) inhibitors, we tested them against rodent Mcl-1 and found a significant loss of binding affinity when compared to that seen with human Mcl-1. To understand the affinity loss, we used sequence alignments and structures of human Mcl-1/inhibitor complexes to identify the important differences in the amino acid sequences. One difference is human L246 (F226 in rat, F227 in mouse) in the ligand binding pocket. Mutating rat F226 to a Leu restores affinity, but the mouse F227L mutant still has a ligand affinity that is lower than that of human Mcl-1. Another mutation of mouse F267, located ∼12 Å from the ligand pocket, to the human/rat cysteine, F267C, improved the affinity and combined with F227L resulted in a mutant mouse protein with a binding affinity similar to that of human Mcl-1. To help understand the structural components of the affinity loss, we obtained an X-ray structure of a mouse Mcl-1/inhibitor complex and identified how the residue changes reduced compound complementarity. Finally, we tested Mcl-1 of other preclinical animal models (canine, monkey, rabbit, and ferret) that are identical to humans in terms of these two residues and found that their Mcl-1 bound our compounds with affinities comparable to that of human Mcl-1. These results have implications for understanding ligand selectivity for similar proteins and for the interpretation of preclinical toxicology studies with Mcl-1 inhibitors.
Unambiguity of Python Language Elements for Static Analysis (2021)

Static analysis is a technique for gathering some meaningful information during compilation-time and using it for further processing. This technique is applied in bug finding, code comprehension and in many other areas. However, static analysis gives a static view of the source and provides limited information about the dynamic behavior of a program. This limitation is generally considered to be a major barrier for dynamically typed languages, like Python, since in many situations it is hard to derive the most basic properties of variables or functions, sometimes we can’t even find the location of their definition. In this paper we present our experimental results that show this is not necessary a hard barrier in practical industrial projects. We analyzed open-source Python libraries, including the Python Standard Library itself as part of the CodeCompass code comprehension framework, and found that in a high number of the cases it was possible to decide the mentioned important features in unambiguous way. The consistent coding conventions make it possible to reduce unambiguity in static analysis of dynamic languages.
Simulation of Non-Linear Ultrasonic Wave through an Interface Including Imperfections (2006)

A numerical modeling of an interface including a local imperfection and simulation of the ultrasonic wave propagation through the interface are described in this paper. We propose an imperfection model with the interface condition depending on displacement‐stress states. This phenomenon generates superharmonics in the transmitted wave through the interface. The interface model is incorporated into a time domain boundary element method and transmitted waveforms are calculated. Simulation results show that the amplitude ratio of superharmonic waves changes according to the initial opening gap and the length of the imperfection area.
Probing photoexcited free carrier dynamics of two-dimensional MXene, Nb2C, using ultrafast terahertz spectroscopy (2023)

Discovered in 2013, 2D niobium carbide (Nb<sub>2</sub>C), a member of the MXene family, has been shown to have many extraordinary properties, such as high photothermal conversion efficiency, strong electron-phonon interactions, strong optical absorption in the near-infrared, and even saturable optical absorption. These unique properties of Nb<sub>2</sub>C render this MXene potentially useful for a variety of applications, including photonic and optoelectronic devices and even photothermal cancer therapy. Here, we employ both terahertz time-domain spectroscopy (TDS) and time-resolved terahertz spectroscopy (TRTS) to investigate intrinsic and photoinduced conductivity and dynamics of optically injected charge carriers with 1.55 eV excitations in order to understand the photoinduced processes taking place in Nb<sub>2</sub>C. We find that the photoinduced conductivity in this MXene shows an initial rapid decay over a picosecond time scale, followed by a much longer-lived component that lasts for nanoseconds. We also observe that the long-range conductivity is strongly limited by the nanoflake boundaries.
Rotating cylindrical and spherical triboelectric generators (2023)

A generator includes a first member, a second member and a sliding mechanism. The first member includes a first electrode and a first dielectric layer affixed to the first electrode. The first dielectric layer includes a first material that has a first rating on a triboelectric series. The second member includes a second material that has a second rating on the triboelectric series that is different from the first rating. The second member includes a second electrode. The second member is disposed adjacent to the first dielectric layer so that the first dielectric layer is disposed between the first electrode and the second electrode. The sliding mechanism is configured to cause relative movement between the first member and the second member, thereby generating an electric potential imbalance between the first electrode and the second electrode.
Cat infected by a bat variant rabies virus in a 29-year disease-free highly populated urban area of Southern Brazil. (2012)

Introduction: After 29 years, rabies in a cat was detected in Curitiba, Southern Brazil. Methods: The virus was identified by immunofluorescence antibody test (FAT) in central nervous system (CNS) samples, and inoculation in adult mice. Results: Direct Immunofluorescence was negative, but Biological Testwas positive and virus characterized as variant 4 (from non-hematophagous bat). Conclusions: Reappearance of rabies alerts for sylvatic-aerial risk of infection and the necessity of bat monitoring in historically rabies-free areas. Key words: Feline rabies. Non-hematophagous bat. Epidemiological surveillance.
Long‐Term Results of Cryoablation with a New Cryoprobe to Eliminate Chronic Atrial Fibrillation Associated with Mitral Valve Disease (2005)

The purpose of this study was to examine the performance of a new cryoprobe in the treatment of chronic atrial fibrillation (AF) associated with mitral valve disease. The study included 66 patients undergoing mitral valve replacement. The mean AF duration was 9.0 +/- 9.0 years and mean left atrial (LA) was diameter 57 +/- 10 mm. Cryoablation (-60 degrees C) was applied to four pulmonary vein (PV) orifices over 2-3 minute. The spherical tip (2-cm in diameter) of the cryoprobe is capable of ablating the left atrium near the PV, as well as the PV ostium with a single cryoablation. After cryoablation, mitral valve surgery or a combined surgical procedure were performed in 66 patients. There were no intraoperative complications. Sinus rhythm was restored in 60 patients (91%) immediately after the operation. Recurrent AF was treated with antiarrhythmic drugs and/or direct current cardioversion in 43 patients (72%). At discharge, 48 patients (72%) were in sinus rhythm. During a mean follow-up period of 31 +/- 16 months, 40 patients (61%) were in sinus rhythm with (29) or without antiarrhythmic drugs (11). In patients in sinus rhythm at the end of the follow-up period, the duration of preoperative AF duration was significantly shorter (P < 0.05) and the preoperative LA diameter and cardiothoracic ratio were significantly smaller than in patients who were in AF (both for P < 0.005). Using this new cryoprobe, sinus rhythm was restored and maintained in 61% of patients with chronic AF and mitral valve disease with a 12-15 minute cryoablation procedure.
Integrated semantic-syntactic video event modeling for search and retrieval (2003)

This paper proposes to integrate text-based database models (commonly used in the database and information retrieval literature) and low-level video features, such as object-based motion features (commonly used in image processing and computer vision), within a single framework to describe video events for fast and effective browsing and retrieval using a mixture of textual and low-level descriptors. The instantiations of the model are expressed as graphs. Users can formulate flexible queries that can be translated into such graphs. Alternatively, users can input query graphs by editing an abstract model (model template) derived either from a model database or from an example scene in the media database. Search and retrieval is accomplished by matching the query graph with those instantiated models in the database. The proposed approach allows for integrated textual and low-level, descriptor-based video search, where the integration is enabled by the model. Examples and experimental results are provided to demonstrate the effectiveness of the proposed integrated modeling and querying framework.
Investigation of Ion Mobility coupled with mass spectrometry (IM-MS) for the screening of pesticide residues in food (2011)

Pesticide residue analysis requires methods that can determine hundreds of compounds at low levels in complex food matrices. This challenge has given rise to multi residue methods, the only efficient analytical approach. This type of analytical method entails a “generic” extraction followed by a soft or no purification step to avoid any analytes looses. With over a 1000 active compounds with different physico-chemical properties, gas and liquid chromatography are used as complementary separative techniques.
Halogenated Monoterpenes from <i>Plocamium </i><i>costatum </i>and Their Biological Activity (1999)

From the dichloromethane solubles of the temperate red alga Plocamium costatum, one new [1,4-dibromo-2,3,6-trichloro-3, 7-dimethyl-7-octene] (1) and three previously reported polyhalogenated monoterpenes (2-4), and the known phytol derivative 3,7,11,15-tetramethylhexadec-1-en-3-ol (1-phyten-3-ol, 5) were isolated. The structure of 1 was deduced from its spectroscopic data. For compound 3, complete 1H and 13C NMR data are reported for the first time. The CH2Cl2 extract and compounds 3 and 5 deterred settlement of barnacle larvae, suggesting a potential ecological role of these isolates.
T‐Cell Immunity to Oncogenic Proteins Including Mutated <i>RAS</i> and Chimeric <i>BCR‐ABL</i>a (1993)

The process of malignant transformation can be ascribed to a series of characteristics and definable mutations of genes which encode proteins that control cell growth and differentiation. During the course of malignant transformation the cancer-related genes are altered by a variety of mechanisms including translocations, deletions, and point mutations which commonly result in the expression of aberrant proteins. Our laboratory has focused on determining the extent to which cancer-specific proteins expressed by aberrant cancer-related genes can function as tumor-specific antigens. The current paper reviews our studies with two prototype cancer-specific proteins, mutated p21ras protein and chimeric p210bcr-abl protein. Ras protooncogenes are activated by point mutation in approximately 20% of human malignancies. The mutations occur primarily at codons 12 or 61 and result in the expression of p21ras proteins with single substituted amino acids. Only a limited number of amino acid substitutions occur. Murine studies demonstrate that immunization with synthetic peptides corresponding to the mutated segment can elicit both class II restricted CD4+ helper/inducer T-cell responses and class I restricted CD8+ cytotoxic T-cell responses specific for mutated p21ras protein. In addition, the existence in vivo of tumors expressing mutated ras proteins can be detected by assaying for T-cell immunity to the mutated segment of ras protein. Preliminary human studies show that some patients with colon cancer have existent antibody responses to p21ras protein, implying the possible existence of autochthonous T-cell immunity to mutated ras proteins in those patients. In chronic myelogenous leukemia the human c-abl protooncogene from chromosome 9 is translocated to the specific breakpoint cluster (bcr) region on chromosome 22. The translocation results in the formation of a bcr-abl fusion gene that encodes at 210-kD chimeric protein. The joining region segment of chimeric bcr-abl protein is composed of a unique combination of c-abl and bcr amino acids and is expressed only by malignant cells. Studies demonstrate that immunization of mice with synthetic peptides corresponding to the joining region segment can elicit class II restricted CD4+ T-cell responses to p210bcr-abl proteins. Preliminary studies show that bcr-abl peptides can bind in the groove of both murine and human class I MHC molecules and can elicit bcr-abl peptide-specific cytotoxic T lymphocytes (CTL). Whether bcr-abl peptide-specific CTL can lyse cells expressing bcr-abl protein is a yet unknown. In summary, the results of the studies reviewed confirm that cancer-specific oncogenic proteins can serve as tumor-specific antigens.
Computational Insights into the Sequence-Activity Relationships of the NGF(1–14) Peptide by Molecular Dynamics Simulations (2022)

The Nerve Growth Factor (NGF) belongs to the neurothrophins protein family involved in the survival of neurons in the nervous system. The interaction of NGF with its high-affinity receptor TrkA mediates different cellular pathways related to Alzheimer's disease, pain, ocular dysfunction, and cancer. Therefore, targeting NGF-TrkA interaction represents a valuable strategy for the development of new therapeutic agents. In recent years, experimental studies have revealed that peptides belonging to the N-terminal domain of NGF are able to partly mimic the biological activity of the whole protein paving the way towards the development of small peptides that can selectively target specific signaling pathways. Hence, understanding the molecular basis of the interaction between the N-terminal segment of NGF and TrkA is fundamental for the rational design of new peptides mimicking the NGF N-terminal domain. In this study, molecular dynamics simulation, binding free energy calculations and per-residue energy decomposition analysis were combined in order to explore the molecular recognition pattern between the experimentally active NGF(1-14) peptide and TrkA. The results highlighted the importance of His4, Arg9 and Glu11 as crucial residues for the stabilization of NGF(1-14)-TrkA interaction, thus suggesting useful insights for the structure-based design of new therapeutic peptides able to modulate NGF-TrkA interaction.
Automatic pupil detection on retro-illumination lens images from a population-based study (2012)

Automatic detection of the pupil is an important step in cataract assessment. This paper proposes a new pupil detection method which addresses the challenges faced in current methods employed for this task. We evaluate the performance of the proposed method against the current methods on a large population-based image dataset of more than 9000 images from the Singapore Malay Eye Study (SiMES) database. The accuracy achieved is 98.60% for the proposed method for SiMES-1. A modified version of the method was applied on the follow-up SiMES-2 dataset, obtaining an accuracy of 97.25%. The results are encouraging towards a fully automatic cataracts detection and assessment.
Revealing the Surface Corrosion Chemistry and Kinetic Stabilization at Photoelectrochemical Interfaces for Solar-Driven Water-Splitting (2020)

Stability is a crucial consideration for practical applications of integrated solar-fuel devices. For solar water-splitting reactions, the requirement of strong acidic/alkaline electrolytes poses serious concerns over the materials stability of semiconductors, electrocatalysts and membranes. Especially, the stability of semiconductor materials can be even more complicated due to its dependence on applied potentials, ambient environment and light/dark conditions etc. However, systematic understandings based on experimental results are lacking for many materials. Herein, we would like to address the material stability for a series of 3-5 semiconductors (InP, GaP and GaAs etc.) used as photocathodes for the hydrogen-evolution reaction (HER) at pH=0/14. To minimize any impact of ambient oxygen, the long-term corrosion evaluation experiments and post-electrochemistry XPS surface characterizations were carefully performed under air-free conditions. The electrode-to-electrolyte leaching of ions over time was quantitatively analyzed by ICP-MS. Combined with considerations of the Pourbaix diagram, both the thermodynamics and kinetics of existing corrosion reactions can be experimentally determined. Significant differences in material stability and surface conditions were revealed between bare semiconductor surfaces and semiconductor/catalyst interfaces, where a surface kinetic stabilization effect has been emphasized. Based on the current understanding, we demonstrate significant promises of these semiconductors to be used as robust light-absorbers for solar water-splitting.
Reconstruction of Zebrafish Early Embryonic Development by Scanned Light Sheet Microscopy (2008)

A long-standing goal of biology is to map the behavior of all cells during vertebrate embryogenesis. We developed digital scanned laser light sheet fluorescence microscopy and recorded nuclei localization and movement in entire wild-type and mutant zebrafish embryos over the first 24 hours of development. Multiview in vivo imaging at 1.5 billion voxels per minute provides "digital embryos," that is, comprehensive databases of cell positions, divisions, and migratory tracks. Our analysis of global cell division patterns reveals a maternally defined initial morphodynamic symmetry break, which identifies the embryonic body axis. We further derive a model of germ layer formation and show that the mesendoderm forms from one-third of the embryo's cells in a single event. Our digital embryos, with 55 million nucleus entries, are provided as a resource.
Reflexiones en torno a los cambios en el sistema de evaluación de la asignatura Política Económica (2015)

A pesar de los cambios que ha experimentado la docencia a raíz de la implantación del tratado de Bolonia continua siendo necesario plantear y planificar adecuadamente la valoración de los conocimientos y habilidades que el alumno desarrolla a lo largo del curso. Esta evaluación se ha ido enfocando cada vez más hacia la evaluación continua en la que los exámenes tradicionales son solo parte de los elementos para evaluar que se utilizan. En este cambio en el sistema de evaluación el profesor, que tiene que desarrollar cada vez más un perfil de guía en el aprendizaje que de docente, puede ayudarse de multitud de herramientas ya sean de carácter presencial o en línea, individual o grupal, tipo test o de desarrollo, etc… Todas estas tareas, ya sean puntuables o no para la calificación final, deben ir acompañadas de una retroalimentación hacia el alumno para que éste pueda apreciar cuáles son sus fortalezas y debilidades de cara a las siguientes pruebas. Del mismo modo los resultados obtenidos permiten al profesorado reflexionar sobre cuáles son las herramientas de evaluación más útiles para su docencia y contribuyen a la selección de las mejores para planificar el siguiente periodo académico. En este sentido, el presente trabajo se estructura en tres apartados. Tras la introducción, que tratará de enmarcar el nuevo contexto en el que opera la docencia universitaria, en el segundo apartado se analizarán los resultados obtenidos en la asignatura de Política Económica, que se imparte en el cuarto curso del grado en ADE de la Universidad de Alicante, en cuatro cursos académicos distintos tras un cambio en las herramientas de evaluación. Este análisis permitirá conocer si los cambios han conllevado mejores resultados y, por tanto, nos ofrecerá información sobre el sistema de evaluación más adecuado.