gebhart/patrepeval huggingface dataset:
Global Gene Expression Approaches to Mode-of-Action Studies with Natural Product-Based Pesticides (2006)

Natural products represent a vast repository of potential pesticides, some with novel molecular target sites. Wholegenome DNA microarrays seem a promising tool for identifying novel target sites, as microarrays enable monitoring the effects of a toxicant on the expression of every gene of an organism, providing clues about the targeted pathway or process. Examples of microarray studies of fungicide effects on Saccharomyces cerevisiae (baker's yeast), and of the effects of a natural herbicide on the dicot Arabidopsis thaliana, are presented. The results support a role for microarray studies in identifying molecular target sites and understanding the responses of plants to xenobiotics.
Tetramer identification of functional mouse mucosal associated invariant T cells (INC6P.352) (2014)

Abstract Mucosal associated invariant T (MAIT) cells have a semi-invariant TCR Vα chain, and their development is dependent upon the commensal flora and the expression of MR1. MAIT cells are activated in vitro in an MR1-restricted manner by cells infected with diverse strains of bacteria suggesting a widely shared antigen. Such an antigen was recently defined by the observation that human MR1 binds bacterial riboflavin metabolites (ribityllumazines, RL antigens) that are capable of activating MAIT cells. Recently MR1/RL tetramers were constructed allowing us to compare MR1-dependency and function of mouse MAIT cell subsets in invariant TCR Vα19-Jα33 (Vα19i) transgenic (Tg) mice. Although significant numbers of tetramer+ cells were detected in both MR1+/+ and MR1-/- Vα19i Tg mice, only tetramer+ cells from MR1+/+ and not MR1-/- Vα19i Tg mice had predominant expression of CD69, NK1.1 and Vβ6/8 and displayed robust in vitro responses to IL-12+IL-18 or RL Ag. In addition, tetramer+ MAIT cells expressing CD4, CD8 or neither developing in MR1+/+ Vα19i Tg mice had disparate cytokine profiles in response to RL Ag. Most notably, after mycobacterial infection all MAIT cell subsets decreased in the blood regardless of whether they express NK1.1 and/or Vβ6/8; however, only the NK1.1+Vβ6/8+ subset predominated in the lung airways of infected MR1+/+ Vα19i Tg mice. These findings present evidence for the functional diversity of MAIT cell responses to innate cytokines, RL Ag and bacterial infection.
Water- PUF: An Insider Threat Resistant PUF Enrollment Protocol Based on Machine Learning Watermarking (2021)

The demand for Internet of Things services is increasing exponentially, and consequently a big number of devices are being deployed. To efficiently authenticate these services, the use of Physical Unclonable Functions (PUF) has been introduced as a promising solution that is suitable for the resource-constraint nature of these devices. A growing number of PUF architectures has been demonstrated mathematically clonable through Machine Learning (ML) modeling techniques. The use of ML PUF models has been recently proposed to authenticate the IoT objects. This procedure facilitates the scalability of the authentication process by reducing the storage space required for each device. Nonetheless, the leakage scenario of the PUF model to an adversary due to an insider threat within the organization is not supported by the existing solutions. Hence, the security of these PUF model-based enrollment proposals can be compromised. In this paper, we propose an enrollment solution that exploits a ML PUF model in the authentication process, called Water-PUF. Our enrollment scheme is based on a specifically designed black-box watermarking technique for PUF models with a binary output response. This procedure prevents an adversary from relying on the watermarked model in question or another derivative model to bypass the authentication. Therefore, any leakage of the watermarked PUF model that is used for the enrollment does not affect the correctness of the protocol. The Water- PUF design is validated by a number of simulations against numerous watermark suppression attacks to assess the robustness of our proposal.
Discrepancies between cortical and behavioural long‐term readouts of hyperalgesia in awake freely moving rats (2016)

The present findings provide direct evidence that chronic recordings in S1 in awake animals can offer a powerful, and much sought for, translational model of the perception of pain magnitude during hyperalgesia. WHAT DOES THIS STUDY ADD?: In a novel animal model, chronic recordings of nociceptive activity in primary somatosensory cortex (S1) in awake freely moving rats are compared to behavioural readouts during UVB-induced hyperalgesia. Evoked activity in rat S1 replicates altered pain perception in humans during development of hyperalgesia, but withdrawal reflexes do not.
A 3-Phase Resonant Switched Capacitor Converter Delivering 7.7 W at 85% Efficiency Using 1.1 nH PCB Trace Inductors (2015)

In recent years, there has been a push towards high-density and monolithic DC-DC converters to support applications such as performance and mobile computing, consumer electronics, and renewable energy. Switched capacitor (SC) converters have started to gain traction for a number of these applications, but are still subject to fundamental limitations that drive them towards expensive process options and high switching frequencies. Variable regulation is challenging with the SC approach, and comes at the cost of lower power density and efficiency. This work presents a resonant switched capacitor (ReSC) topology that addresses some of these challenges by introducing a small amount of inductance in series with the flying capacitor, eliminating charge-sharing losses and thus allowing efficient operation in a low-cost process option. The three-phase interleaved topology can deliver up to 7.7 W at 85% efficiency (power density of 0.91 W/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> or 6.4 kW/in <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ) using a bootstrapped n-channel power train and single-digit nH inductors embedded in a flip-chip assembly. We also present the first implementation of efficient, fully-variable conversion ratios in a silicon ReSC integrated circuit without reconfiguration or gain-hopping .
Water Concentration in Self-etching Primers Affects their Aggressiveness and Bonding Efficacy to Dentin (2005)

Water is required to ionize acid resin monomers for demineralization of tooth substrates. We tested the null hypothesis that altering the water concentration in two-step self-etching primers has no effect on their aggressiveness and bonding efficacy to dentin. Five experimental self-etching primers were prepared with resin-water-ethanol volume ratios of 9-0-1, 8-1-1, 7-2-1, 5-4-1, and 3-6-1. They were applied to smear-layer-covered dentin, followed by a bonding resin and composite build-ups for microtensile bond testing and TEM examination of tracer penetration. Increasing water concentration from 0-60 vol% improved acidic monomer ionization that was manifested as increasing hybrid layer thickness. However, significantly higher bond strength was observed in the 7-2-1 group, with minimal nanoleakage in the corresponding hybrid layer. When self-etching primers are formulated, a balance must be achieved to provide sufficient water for adequate ionization of the acidic monomers, without lowering the resin concentration too much, to optimize their bonding efficacy to dentin.
Visual Guidance of Natural Behavior (2022)

The essentially active nature of vision is revealed in the complex interplay of head, body, and eye movements as humans gather information to guide their actions in the natural visual world. This dynamic perception–action cycle has long been appreciated but has been difficult to investigate due to limitations in the available instrumentation both to measure eye and body movements and to present realistic stimuli in the context of active behavior. Technological developments have opened up a wider range of natural contexts where some degree of experimental control is possible, and the last two decades have ushered in a variety of insights that would otherwise be difficult to achieve in more constrained environments. Within the context of natural vision, humans make continuous sequences of sensorimotor decisions to satisfy behavioral goals, and vision provides the relevant information for making good decisions in order to achieve those goals. The components of a good decision include the task demands, the rewards and costs associated with the task, uncertainty about the state of the world, and information stored in memory. Natural behavior offers a rich domain for investigation, because it is remarkably stable and leads to novel questions, and the behavioral context helps specify the momentary visual computations and their temporal progression.
Reliable medical recommendation systems with patient privacy (2013)

One of the concerns patients have when confronted with a medical condition is which physician to trust. Any recommendation system that seeks to answer this question must ensure that any sensitive medical information collected by the system is properly secured. In this article, we codify these privacy concerns in a privacy-friendly framework and present two architectures that realize it: the Secure Processing Architecture (SPA) and the Anonymous Contributions Architecture (ACA). In SPA, patients submit their ratings in a protected form without revealing any information about their data and the computation of recommendations proceeds over the protected data using secure multiparty computation techniques. In ACA, patients submit their ratings in the clear, but no link between a submission and patient data can be made. We discuss various aspects of both architectures, including techniques for ensuring reliability of computed recommendations and system performance, and provide their comparison.
Economic Impact of Training and Career Decisions on Urological Surgery (2013)

Choice of specialty has a dramatic impact on future earnings, as does the decision to pursue a fellowship or choose private vs academic practice. Additional years of training and forgone wages have a tremendous impact on monetary outcomes. There is also no guarantee that fellowship training will translate into a more financially valuable career. The differential in income between private practice and academics was lowest for urologists.
Expression of interleukin 6 and its specific receptor by untreated and PMA-stimulated human erythroid and megakaryocytic cell lines. (1991)

Different human hematopoietic cell lines were analyzed for the presence of interleukin 6 (IL-6) and IL-6 receptor (IL-6-R). Both IL-6 mRNA and secreted active IL-6 protein were detectable in untreated cell lines with erythroid or megakaryoblastic features (K562, HEL, KU 812, MEG-01, and Dami), but they were not expressed constitutively in other leukemic cell lines (KG1, HL60, and U937). IL-6-R production, studied by the presence of its mRNA and specific binding sites for iodinated recombinant IL-6, was detected in most cell lines except K562, HEL, and Dami. Therefore, only KU 812 and MEG-01 coexpress both IL-6 and IL-6-R. After phorbol ester myristate acetate (PMA) treatment, all the cell lines studied expressed or overexpressed IL-6. In the erythroid K562 cell line, IL-6-R was not detectable before induction, but was promptly expressed after stimulation with PMA, suggesting that some of the new features of K562 cells induced by PMA may be mediated by IL-6. However, neutralizing antibodies against IL-6 did not block either the growth arrest or the loss of the erythroid phenotype induced by PMA. The presence of IL-6 and IL-6-R in erythroid and megakaryocytic leukemic cell lines suggests that their synthesis may occur during normal hematopoietic differentiation.
A comprehensive workflow for target adaptive sampling long-read sequencing applied to hereditary cancer patient genomes (2023)

Abstract Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic rate by overcoming the limitations of short-read sequencing. In addition, Oxford Nanopore Technologies (ONT) offers a computationally-driven target enrichment technology, adaptive sampling, which enables intensive analysis of targeted gene regions at low cost. In this study, we developed an efficient computational workflow for target adaptive sampling long-read sequencing (TAS-LRS) and evaluated it through application to 33 genomes collected from suspected hereditary cancer patients. Our workflow can identify single nucleotide variants with nearly the same accuracy as the short-read platform and elucidate complex forms of structural variations. We also newly identified SVAs affecting the APC gene in two patients with familial adenomatous polyposis, as well as their sites of origin. In addition, we demonstrated that off-target reads from adaptive sampling, which are typically discarded, can be effectively used to accurately genotype common SNPs across the entire genome, enabling the calculation of a polygenic risk score. Furthermore, we identified allele-specific MLH1 promoter hypermethylation in a Lynch syndrome patient. In summary, our workflow with TAS-LRS can simultaneously capture monogenic risk variants including complex structural variations, polygenic background as well as epigenetic alterations, and will be an efficient platform for genetic disease research and diagnosis.
Diagenetic signature of the Mid-Paleocene exposure surface in the southeastern Pyrenean platform (2010)

From Danian to Thanetian, the South-Pyrenean carbonate platform underwent the most important Paleocene marine level fall of approximately 60 m magnitude. The palaeoenvironmental setting related to the highstand systems tract was defined thanks to detailed petrographical descriptions of the sedimentary facies. These conditions are based on a “hypersaline lagoon and prograding subtidal sabhka” model. The descriptions of diagenetical processes show that the lowstand period is underlined by the following six major diagenetic stages: early processes related to depositional environment, meteoric karstification, meteoric cementation, mixed corrosion and precipitation, and burial. We propose this sequence such as the diagenetic signature of the Mid-Paleocene subaerial exposure.
Telomerization of butadiene with starch in water: role of the surfactants (2010)

Nowadays, the preparation of bio-based polymers remains a challenging issue. The modification of starch by hydrophobic chemical substitutions results in an innovative material. We introduced the hydrophobic part of the derivative via catalytic butadiene telomerization using exclusively water as solvent in the presence of surfactants. In this paper, we describe the influence of the nature of the surfactant on the reaction, CTAB (cetyltrimethylammonium bromide) giving the best reactivity. Moreover, some physicochemical properties of modified starches are evaluated showing their hydrophobic behaviours.
NULL-METHOD IN IMMERSION REFRACTOMETRY FOR BIOPHYSICAL MEASUREMENT OF CRYPTOSPORIDIUM AND GIARDIA LAMBLIA (2011)

This paper presents an on-chip null-method immersion refractometer for the measurement of size, shape and refractive index of protozoa in treated water. The key features of the on-chip immersion refractometer include (1) multiple single cyst trapping sites, which enable the measurement of multiple sample per test; and (2) zig-zag micromixer, which enables the refractive index variation of external medium as the key component of immersion refractometry. The results show that Cryptosporidium parvum oocysts have size of 3 to 7 μm, spherical with ovality lower than 0.3, and refractive index of 1.418. Giardia lamblia cysts have size of 8 to 12 μm, oval with ovality higher than 0.3, and refractive index of 1.433. The refractive indices of the samples are measured with high precision of < 10 -3 .
The opsonizing ligand on Salmonella typhimurium influences incorporation of specific, but not azurophil, granule constituents into neutrophil phagosomes. (1989)

Phagosomes were purified from human neutrophils ingesting Salmonella typhimurium opsonized with adsorbed normal human serum or with rabbit IgG. Constituents within the phagosome were endogenously labeled by supplying the cells with 125INa during phagocytosis. Lactoferrin and vitamin B12 binding protein (TC1 and TC3), markers for specific granules, were present in the phagosomes from neutrophils ingesting S. typhimurium opsonized with IgG but were 3.5- to 5-fold less prominent in phagosomes from cells phagocytosing Salmonella bearing C3 fragments only. In contrast, iodinated azurophilic granule components, most prominently defensins, were the major constituents in phagosomes prepared under both opsonization conditions. Furthermore, labeled complement (CR1 and CR3) and immunoglobulin (Fc gamma RIII) receptors were incorporated in the phagosome regardless of the ligand mediating phagocytosis. These results suggest that the ligand-receptor interactions mediating phagocytosis influence incorporation of neutrophil-specific granule contents into phagosomes.
Allergic Bronchopulmonary Aspergillosis Masquerading as Pulmonary Tuberculosis (2004)

We present an unusual pediatric patient with severe allergic bronchopulmonary aspergillosis that masqueraded as pulmonary tuberculosis. After antituberculous therapy, the patient's pulmonary disease flared, prompting an aggressive diagnostic evaluation. Radiographic findings included nodular pulmonary densities with superimposed infiltrates. Lung biopsy showed evidence of acute and chronic inflammation with necrotizing granulomas, giant cells, tissue eosinophilia and rare hyphal elements.
Auf dem Weg zur verlässlichen und quantitativen SERS‐Spektroskopie: von Schlüsselparametern zur guten analytischen Praxis (2019)

Abstract Experimentelle Resultate, die in verschiedenen Laboren weltweit von Wissenschaftlern mithilfe der oberflächenverstärkten Raman‐Streuung (SERS, surface‐enhanced Raman scattering) erhalten wurden, können beträchtlich voneinander abweichen. Wir, ein internationales Team von Wissenschaftlerinnen und Wissenschaftlern mit langjähriger SERS‐Expertise, präsentieren hier unsere Sichtweise auf dieses Thema mit Betrachtungen hinsichtlich verlässlichem und quantitativem SERS. Die zentrale Idee dieses Gemeinschaftsunterfangens ist es, auf die oft in der Literatur anzutreffenden Schlüsselparameter und Stolperfallen hinzuweisen. Im Hinblick darauf bieten wir Empfehlungen zu folgenden Themen an: a) die Charakterisierung von festen und kolloidalen SERS‐Substraten durch korrelative Elektronen‐ und optische Mikroskopie und Spektroskopie, b) zur Bestimmung des SERS‐Verstärkungsfaktors (EF, enhancement factor) inklusive geeigneter Raman‐Reporter/Sonden‐Moleküle und schließlich c) zur guten analytischen Praxis. Die Autorinnen und Autoren hoffen, dass sowohl Newcomer als auch Spezialisten von diesen Empfehlungen profitieren, um die Inter‐Labor‐Vergleichbarkeit von experimentellen SERS‐Resultaten zu erhöhen und zur weiteren Etablierung von SERS als einer analytischen Methode beizutragen.
Climate change scenarios, their impacts and implications on Indian cardamom-coffee hot spots; one of the two in the world (2022)

In this study, we investigated climatic parameters and predicted future changes in precipitation and atmospheric temperature levels based on RCP4. 5/8.5 scenarios in all cardamom-coffee hot spots of southern India. Our results showed more precipitation levels and patterns occurred in Cardamom hills (Kerala), followed by lower Puleny hills in Tamil Nadu. The least variation in precipitation levels has been noticed for temperate upper Puleny hills and Kodagu hills in Karnataka. RCP4.5/8.5 scenario analysis showed greater variability in precipitation, up to 180% increase and 90% decrease for all hot sports. The scenario analysis also predicted extreme temperature variations ranging from 0.5 to 8.5°C increase for the entire study region. A significant change in coffee yield and quality has been recorded over the last 30 years. Increased yield trends in coffee were noticed for Cardamom hills (CH) and Kodagu hills, but significantly lower coffee production was observed for lower Pulney hills. The mixed response of yield variability in coffee has been primarily attributed to the ongoing changing climatic factors. Ecophysiological studies of coffee, cardamom, and black pepper have proved that coffee would adapt well to future challenging climatic conditions, closely followed by cardamom and black pepper. Since all the coffee-cardamom hot spots in southern India undergoes considerable change in precipitation levels and pattern, necessary precautions, including water and irrigation management strategies, must be given utmost priority to increase the crop yield sustainability of these delicate cardamom-coffee hot spots in India.
Retinal Vascular Geometry in Asian Persons with Diabetes and Retinopathy (2012)

Retinal vascular parameters varied by diabetes and retinopathy status in this older Asian cohort. Our findings suggest that subtle alterations in retinal vascular architecture are influenced by diabetes.
Seismic-scale petrophysical interpretation and gas-volume estimation from simultaneous impedance inversion (2017)

Abstract Simultaneous impedance inversion was performed to obtain the seismic-scale P- and S-wave impedances as well as the bulk density volumes from seismic angle stacks at a siliciclastic turbidite offshore gas reservoir. To translate these variables into seismic-scale total porosity (φ), clay content, and water saturation (Sw), we used a deterministic rock-physics model established at the well. A crucial input into this model is the bulk modulus (Kf) of the brine/gas system. We need to link it to Sw at the seismic scale. This link can be one of simple mixing laws, such as harmonic and arithmetic. Alternately, it can be derived at the well by using upscaled variables and ensuring that they obey the well-data-driven rock-physics model. These different Kf-Sw relations produce different interpretations for φ and Sw thus allowing one to assess the variability in the estimates of the gas volume in place that is proportional to the product of φ and (1 − Sw).
Neutralizing Monoclonal Antibodies Block Chikungunya Virus Entry and Release by Targeting an Epitope Critical to Viral Pathogenesis (2015)

We evaluated the mechanism by which neutralizing human monoclonal antibodies inhibit chikungunya virus (CHIKV) infection. Potently neutralizing antibodies (NAbs) blocked infection at multiple steps of the virus life cycle, including entry and release. Cryo-electron microscopy structures of Fab fragments of two human NAbs and chikungunya virus-like particles showed a binding footprint that spanned independent domains on neighboring E2 subunits within one viral spike, suggesting a mechanism for inhibiting low-pH-dependent membrane fusion. Detailed epitope mapping identified amino acid E2-W64 as a critical interaction residue. An escape mutation (E2-W64G) at this residue rendered CHIKV attenuated in mice. Consistent with these data, CHIKV-E2-W64G failed to emerge in vivo under the selection pressure of one of the NAbs, IM-CKV063. As our study suggests that antibodies engaging the residue E2-W64 can potently inhibit CHIKV at multiple stages of infection, antibody-based therapies or immunogens that target this region might have protective value.
Method and system for piloting an aircraft during runway approach (2013)

Also published as US2013079958 (A1) US8818582 (B2) FR2980618 (A1) CN103018761 (A) CN103018761 (B)