gebhart/patrepeval huggingface dataset:
Greenhouse Gas Emissions Modeling: A Tool for Federal Facility Decommissioning (2011)

The increasing incidence of azole resistance in Aspergillus fumigatus causing invasive aspergillosis (IA) in immunocompromised/hematological patients emphasizes the need to improve the detection of resistance-mediating cyp51A gene mutations from primary clinical samples, particularly as the diagnosis of invasive aspergillosis is rarely based on a positive culture yield in this group of patients. We generated primers from the unique sequence of the Aspergillus fumigatus cyp51A gene to establish PCR assays with consecutive DNA sequence analysis to detect and identify the A. fumigatus cyp51A tandem repeat (TR) mutation in the promoter region and the L98H and M220 alterations directly in clinical samples. After testing of the sensitivity and specificity of the assays using serially diluted A. fumigatus and human DNA, A. fumigatus cyp51A gene fragments of about 150 bp potentially carrying the mutations were amplified directly from primary clinical samples and subsequently DNA sequenced. The determined sensitivities of the PCR assays were 600 fg, 6 pg, and 4 pg of A. fumigatus DNA for the TR, L98H, and M220 mutations, respectively. There was no cross-reactivity with human genomic DNA detectable. Sequencing of the PCR amplicons for A. fumigatus wild-type DNA confirmed the cyp51A wild-type sequence, and PCR products from one azole-resistant A. fumigatus isolate showed the L98H and TR mutations. The second azole-resistant isolate revealed an M220T alteration. We consider our assay to be of high epidemiological and clinical relevance to detect azole resistance and to optimize antifungal therapy in patients with IA.
Representation-Oblivious Error Correction by Natural Redundancy (2019)

Storage systems have a strong need for substantially improving their error correction capabilities, especially for long-term storage where the accumulating errors can exceed the decoding threshold of error-correcting codes (ECCs). In this work, a new scheme is presented that uses deep learning to perform soft decoding for noisy files based on their natural redundancy. The soft decoding result is then combined with ECCs for substantially better error correction performance. The scheme is representation-oblivious: it requires no prior knowledge on how data are represented (e.g., mapped from symbols to bits, compressed, and combined with meta data) in different types of files, which makes the solution more convenient to use for storage systems. Experimental results confirm that the scheme can substantially improve the ability to recover data for different types of files even when the bit error rates in the files have significantly exceeded the decoding threshold of the ECC. The code of this work has been publicly released.
Two-Wavelength Digital Holography (2007)

With two-wavelength digital holography, 3D images of diffuse objects are generated by computing the phase difference between coherent images recorded at two wavelengths. Results are presented that show robust, fine resolution 3D imaging.
An Approximation Algorithm for the Minimum Breakpoint Linearization Problem (2009)

In the recent years, there has been a growing interest in inferring the total order of genes or markers on a chromosome, since current genetic mapping efforts might only suffice to produce a partial order. Many interesting optimization problems were thus formulated in the framework of genome rearrangement. As an important one among them, the minimum breakpoint linearization (MBL) problem is to find the total order of a partially ordered genome that minimizes its breakpoint distance to a reference genome whose genes are already totally ordered. It was previously shown to be NP-hard, and the algorithms proposed so far are all heuristic. In this paper, we present an {m(2)+m/2}-approximation algorithm for the MBL problem, where m is the number of gene maps that are combined together to form a partial order of the genome under investigation.
[Molecular predictive markers of EGFR-targeted therapy in metastatic colorectal cancer]. (2011)

The monoclonal antibodies panitumumab and cetuximab that target the epidermal growth factor receptor are effective in approximately 10% and 20% of EGFR expressing, chemotherapy resistant metastatic colorectal cancer patients in monotherapy and in combination with chemotherapy, respectively. The evidence that EGFR expression by immunohistochemistry does not predict clinical outcome in EGFR targeted treatment has led to an intensive search for additional predicitive biomarkers. Oncogenic activation of signalling pathways downstream of the EGFR, such as mutation of KRAS, BRAF, or PIK3CA oncogenes, or inactivation of the PTEN tumor supressor gene is central to the progression of colorectal cancer. Tumor KRAS mutation, which may be present in 35%-45% of patients with colorectal cancer, is now recognized as an important predictive marker of resistance to cetuximab or panitumumab treatment and is also widely used in clinical practice. Among tumors carrying wild-type KRAS, mutations of BRAF or PIK3CA or loss of PTEN expression may be associated with resistance to the anti-EGFR monoclonal antibody treatment. On the other hand, EGFR ligands overexpression detected in tumor tissue is a promising positive predictive marker. There are also some initial observations that gene expression profiling could also contribute to clinical decision-making about the cetuximab and panitumumab treatments. These observations require further validation in prospective clinical trials before incorporation into clinical practice.
Functional Analysis of<i>α</i>-DOX2, an Active<i>α</i>-Dioxygenase Critical for Normal Development in Tomato Plants (2009)

Plant alpha-dioxygenases initiate the synthesis of oxylipins by catalyzing the incorporation of molecular oxygen at the alpha-methylene carbon atom of fatty acids. Previously, alpha-DOX1 has been shown to display alpha-dioxygenase activity and to be implicated in plant defense. In this study, we investigated the function of a second alpha-dioxygenase isoform, alpha-DOX2, in tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana). Recombinant Slalpha-DOX2 and Atalpha-DOX2 proteins catalyzed the conversion of a wide range of fatty acids into 2(R)-hydroperoxy derivatives. Expression of Slalpha-DOX2 and Atalpha-DOX2 was found in seedlings and increased during senescence induced by detachment of leaves. In contrast, microbial infection, earlier known to increase the expression of alpha-DOX1, did not alter the expression of Slalpha-DOX2 or Atalpha-DOX2. The tomato mutant divaricata, characterized by early dwarfing and anthocyanin accumulation, carries a mutation at the Slalpha-DOX2 locus and was chosen for functional studies of alpha-DOX2. Transcriptional changes in such mutants showed the up-regulation of genes playing roles in lipid and phenylpropanoid metabolism, the latter being in consonance with the anthocyanin accumulation. Transgenic expression of Atalpha-DOX2 and Slalpha-DOX2 in divaricata partially complemented the compromised phenotype in mature plants and fully complemented it in seedlings, thus indicating the functional exchangeability between alpha-DOX2 from tomato and Arabidopsis. However, deletion of Atalpha-DOX2 in Arabidopsis plants did not provoke any visible phenotypic alteration indicating that the relative importance of alpha-DOX2 in plant physiology is species specific.
Material Properties of Fluoropolymers and Perfluoroalkyl-based Polymers (2006)

All of the unique properties imparted by fluorocarbons can be traced back to a single origin: the nature of the C—F bond. These properties include low surface tension, excellent thermal and chemical stability, low coefficient of friction, and low dielectric constant. However, not all of these properties are possessed by the entire inventory of available fluorocarbons. The fluorocarbons can be assigned to two major categories: (1) fluoropolymers, which are materials that are comprised mainly of C—F bonds and include such examples as PTFE, and (2) fluorochemicals (FA) based on the perfluoroalkyl group, which are materials that generally have fewer C—F bonds and often exist as derivatives of other classes of molecules (e.g., acrylates, alcohols, esters). In addition, the properties that dictate the uses of fluorocarbons can be classified into: (1) bulk properties (e.g., thermal and chemical stability, dielectric constant) and (2) surface properties (e.g., low surface tension, low coefficient of friction). The types of materials available and properties imparted are not exclusive and overlap substantially. From this array of fluorocarbons and attributes, a large variety of unique materials can be constructed.
User profiling in personal information agents: a survey (2005)

Personal information agents have emerged in the last decade to help users to cope with the increasing amount of information available on the Internet. These agents are intelligent assistants that perform several information-related tasks such as finding, filtering and monitoring relevant information on behalf of users or communities of users. In order to provide personalized assistance, personal agents rely on representations of user information interests and preferences contained in user profiles. In this paper, we present a summary of the state-of-the-art in user profiling in the context of intelligent information agents. Existing approaches and lines of research in the main dimensions of user profiling, such as acquisition, learning, adaptation and evaluation, are discussed.
Biosensor surface functionalization by a simple photochemical immobilization of antibodies: experimental characterization by mass spectrometry and surface enhanced Raman spectroscopy (2019)

Surface functionalization is a key step in biosensing since it is the basis of an effective analyte recognition. Among all the bioreceptors, antibodies (Abs) play a key role thanks to their superior specificity, although the available immobilization strategies suffer from several drawbacks. When gold is the interacting surface, the recently introduced Photochemical Immobilization Technique (PIT) has been shown to be a quick, easy-to-use and very effective method to tether Abs oriented upright by means of thiols produced via tryptophan mediated disulphide bridge reduction. Although the molecular mechanism of this process is quite well identified, the detailed morphology of the immobilized antibodies is still elusive due to inherent difficulties related to the microscopy imaging of Abs. The combination of Mass Spectrometry, Surface-Enhanced Raman Spectroscopy and Ellman's assay demonstrates that Abs irradiated under the conditions in which PIT is realized show only two effective disulphide bridges available for binding. They are located in the constant region of the immunoglobulin light chain so that the most likely position Ab assumes is side-on, i.e. with one Fab (i.e. the antigen binding portion of the antibody) exposed to the solution. This is not a limitation of the recognition efficiency in view of the intrinsic flexibility of the Ab structure, which makes the free Fab able to sway in the solution, a feature of great importance in many biosensing applications.
Evaluation of low prophylactic forceps in pre term and low birth weight babies. (1999)

This study evaluates the use of prophylactic forceps for the delivery of preterm and low-birth-weight babies in India specifically the relationship of forceps application and spontaneous delivery to neonatal morbidity and mortality. The sample included a total of 81 cases of preterm and low-birth-weight babies delivered by a prophylactic low forceps with wide episiotomy over a period of 5 years from January 1994 to December 1998. An equal number of such babies delivered by normal spontaneous vaginal delivery were studied as a control group. All these babies were investigated in relation to maturity neonatal morbidity and mortality. In the results deliveries by prophylactic low forceps in preterm and low-birth-weight babies showed a better outcome than those delivered by normal spontaneous vaginal delivery. Fetal morbidity in the prophylactic low forceps group was 14.4% as compared to 27.7% in the control group. The incidence of fetal mortality was 3.7% in the forceps group as compared to 14.8% in the control group. Therefore the use of prophylactic low forceps with preterm and low-birth-weight babies is recommended if necessary for a better fetal outcome.
A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation (2015)

Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy.
Non‐Volatile Silicon Photonics Using Nanoscale Flash Memory Technology (2018)

Abstract Nonvolatile flash memory technology is widely used in our daily life. Following the recent progress in silicon photonics, there is now an opportunity to embed flash memories also in photonic applications. As of today, chip scale photonic devices, e.g., micro‐resonators, are becoming essential building blocks in modern silicon photonics. However, their properties, such as their resonance frequencies, fluctuate due to fabrication tolerances, significantly limiting their applicability. Here, by integrating the well‐established non‐volatile flash memory technology into silicon photonic circuitry, this major obstacle is tackled and electrical post trimming of such resonators is demonstrated. Specifically, the Metal‐Oxide‐Nitride‐Oxide‐Silicon (MONOS) structure is used to trap charges in the thin silicon nitride layer, located in close proximity to the silicon device layer. This enables accumulating charges in the silicon, modifying the effective index of the optical mode and consequently the resonance frequency. By doing so, a robust and CMOS compatible nonvolatile memory solution is provided, which not only allows for precise trimming of the resonance frequency of the photonic device, but can also be easily manufactured and commercialized. This approach paves the way for efficient utilization of photonic structures such as resonators and interferometers in chip scale silicon photonics and electro optic systems, with a wide range of applications spanning from filters, switches and modulators, to sensors, and even lasers.
Macrocyclization strategies in polyketide and nonribosomal peptide biosynthesis (2007)

Nonribosomal peptides and polyketides have attracted considerable attention in basic and applied research and have given rise to a multitude of therapeutic agents. The biological activity of many of these complex natural products, including for example the peptide antibiotics daptomycin and bacitracin or the polyketide anticancer agents epothilone and geldanamycin, specifically relies on the macrocyclization of linear acyl chains that form the backbone of these highly valuable molecules. The construction of the linear acyl precursors is accomplished by modular protein templates that follow comparable assembly line logic. As an enzymatic key step, macrocyclization is introduced after the consecutive condensation of amino acid or acyl-CoA building blocks by dedicated catalysts, and the mature product is released from the biosynthetic machinery. The diverse chain termination strategies of nonribosomal peptide and polyketide assembly lines, the structures and mechanisms of the versatile macrocyclization catalysts, and chemoenzymatic approaches for the development of new therapeutics are the focus of this review. Further, it is illustrated that macrocyclization is not restricted to secondary metabolites, but represents a commonly found structural motif of other biologically active proteins and peptides.
Toward automated intraocular laser surgery using a handheld micromanipulator (2014)

This paper presents a technique for automated intraocular laser surgery using a handheld micromanipulator known as Micron. The novel handheld manipulator enables the automated scanning of a laser probe within a cylinder of 4 mm long and 4 mm in diameter. For the automation, the surface of the retina is reconstructed using a stereomicroscope, and then preplanned targets are placed on the surface. The laser probe is precisely located on the target via visual servoing of the aiming beam, while maintaining a specific distance above the surface. In addition, the system is capable of tracking the surface of the eye in order to compensate for any eye movement introduced during the operation. We compared the performance of the automated scanning using various control thresholds, in order to find the most effective threshold in terms of accuracy and speed. Given the selected threshold, we conducted the handheld operation above a fixed target surface. The average error and execution time are reduced by 63.6% and 28.5%, respectively, compared to the unaided trials. Finally, the automated laser photocoagulation was demonstrated also in an eye phantom, including compensation for the eye movement.
Our theoretical frame (2016)

The authors set out their own distinctive analytical frame that combines elements of critical theory, psychosocial criminology and applied existential philosophy to produce a practical conceptual basis for work with the young people that youth workers will encounter on a daily basis. This involves the authors seeking to augment the existing youth work ‘canon’ with some key concepts from criminological thought, primarily around the study of desistance and masculinities. The authors seek to locate the criminological subject within a social context, whilst taking psychodynamic ideas of the “defended self” seriously, and existential philosophy which serves to foreground notions of self, choice and meaning within considerations of violent behaviour and desistance. These are then linked to what the authors see as 4 possible levels of meaningful response: personal/psychological, community/cultural, structural/symbolic and existential.
Modulation of Env Content in Virions of Simian Immunodeficiency Virus: Correlation with Cell Surface Expression and Virion Infectivity (2004)

Specific mutations were created in the cytoplasmic domain of the gp41 transmembrane protein of simian immunodeficiency virus strain 239 (SIV239). The resultant strains included a mutant in which Env residue 767 was changed to a stop codon, a double mutant in which positions 738 and 739 were changed to stop codons, another mutant in which a prominent endocytosis motif was changed from YRPV to GRPV by the substitution of tyrosine 721, and a final combination mutant bearing Q738stop, Q739stop, and Y721G mutations. The effects of these mutations on cell surface expression, on Env incorporation into virions, and on viral infectivity were examined. The molar ratio of Gag to gp120 of 54:1 that we report here for SIV239 virions agrees very well with the ratio of 60:1 reported previously by Chertova et al. (E. Chertova, J. W. Bess, Jr., B. J. Crise, R. C. Sowder II, T. M. Schaden, J. M. Hilburn, J. A. Hoxie, R. E. Benveniste, J. D. Lifson, L. E. Henderson, and L. O. Arthur, J. Virol. 76:5315-5325, 2002), although they were determined by very different methodologies. Assuming 1,200 to 2,500 Gag molecules per virion, this corresponds to 7 to 16 Env trimers per SIV239 virion particle. Although all of the mutations increased Env levels in virions, E767stop had the most dramatic effect, increasing the Env content per virion 25- to 50-fold. Increased levels of Env content in virions correlated strictly with higher levels of Env expression on the cell surface. The increased Env content with the E767stop mutation also correlated with an increased infectivity, but the degree of change was not proportional: the 25- to 50-fold increase in Env content only increased infectivity 2- to 3-fold. All of the mutants replicated efficiently in the CEMx174 and Rh221-89 cell lines. Although some of these findings have been reported previously, our findings show that the effects of the cytoplasmic domain of gp41 on the Env content in virions can be dramatic, that the Env content in virions correlates strictly with the levels of cell surface expression, and that the Env content in virions can determine infectivity; furthermore, our results define a particular change with the most dramatic effects.
Active Polymer Gel Actuators (2010)

Many kinds of stimuli-responsive polymer and gels have been developed and applied to biomimetic actuators or artificial muscles. Electroactive polymers that change shape when stimulated electrically seem to be particularly promising. In all cases, however, the mechanical motion is driven by external stimuli, for example, reversing the direction of electric field. On the other hand, many living organisms can generate an autonomous motion without external driving stimuli like self-beating of heart muscles. Here we show a novel biomimetic gel actuator that can walk spontaneously with a worm-like motion without switching of external stimuli. The self-oscillating motion is produced by dissipating chemical energy of oscillating reaction. Although the gel is completely composed of synthetic polymer, it shows autonomous motion as if it were alive.
Identification of genome wide host RNA biomarkers for infectious diseases (2020)

Existe una predisposicion genetica en humanos a la susceptibilidad y la gravedad de las enfermedades infecciosas. No todas las personas en contacto cercano con patogenos se infectan y desarrollan la enfermedad, en general, la mayoria de los pacientes muestran sintomas leves o moderados, y solo una minoria desarrolla una enfermedad grave. En la presente tesis nos centramos en el estudio de las firmas de expresion genica ya que el transcriptoma es un puente entre la informacion contenida dentro de nuestros genes y el fenotipo. Nuestros resultados suponen demuestran el potencial del uso de firmas trascriptomicas del huesped en la practica clinica como pruebas clinicas para diagnostico, pronostico o evaluacion de riesgos