gebhart/patrepeval huggingface dataset:
The use of dirty bedding for detection of murine pathogens in sentinel mice. (1989)

Sentinel Swiss (CD-1) mice, housed without filter bonnets, were seronegative for mouse hepatitis virus (MHV) for 8 consecutive months in an experimental colony of CD-1 mice. MHV titers had been detected sporadically in sentinel mice housed in this colony during a 2 year period. In an effort to determine whether MHV was still present in the colony, two methods of exposing sentinel mice to an animal room environment were compared under routine husbandry practices. Eight cages (12 mice per cage; 2 cages per rack) of experimental virus antibody free sentinel mice, housed without filter bonnets, were placed on the bottom shelf of 4 of 12 racks in the room. Twice each week, four cages of sentinel mice received a composite sample of dirty bedding (bedding used previously by mice in the room). The remaining four cages of experimental sentinels received fresh non-used bedding. Sentinel mice were bled at monthly intervals for MHV serology. After 4 months, mice from two cages which received dirty bedding seroconverted to MHV and mice from one cage were positive for Myobia musculi (mites). Three weeks later, all four cages of mice which received dirty bedding were positive for MHV and three were positive for mites. In contrast, only two of four cages of mice which received fresh bedding were positive for MHV and all were negative for mites. These findings indicate the importance of exposing sentinel mice to dirty bedding and that MHV and mites may go undetected for several months in a mouse colony when the incidence levels are low where standard sanitation procedures are used.
UAV-Aided Jamming for Secure Ground Communication With Unknown Eavesdropper Location (2020)

This paper investigates unmanned aerial vehicle (UAV)-aided jamming technique for enabling physical layer keyless security in scenarios where the exact eavesdropper location is unknown. We assume that the unknown eavesdropper location is within an ellipse characterizing the coverage region of the transmitter. By sequentially optimizing the transmit power, the flight path of the UAV and its jamming power, we aim at maximizing the average secrecy rate with arbitrary eavesdropper location. Simulation results demonstrate that the optimal flight path obtains better secrecy rate performance compared to that using direct UAV flight path encasing the transmitter and the legitimate receiver. Most importantly, even with the unknown eavesdropper location, we obtained a secrecy rate that is comparable to a scenario when the eavesdropper's location is known. However, the average secrecy rate with the unknown eavesdropper location varies depending on the proximity of the eavesdropper to the known location of the transmitter. We also observe that due to the UAV-aided jamming, the average secrecy rate stabilizes at some point even though the average received envelope power of the eavesdropper increases. This essentially demonstrates the effectiveness of the proposed scheme.
Thermostable virus portal proteins as reprogrammable adapters for solid-state nanopore sensors (2018)

Nanopore-based sensors are advancing the sensitivity and selectivity of single-molecule detection in molecular medicine and biotechnology. Current electrical sensing devices are based on either membrane protein pores supported in planar lipid bilayers or solid-state (SS) pores fabricated in thin metallic membranes. While both types of nanosensors have been used in a variety of applications, each has inherent disadvantages that limit its use. Hybrid nanopores, consisting of a protein pore supported within a SS membrane, combine the robust nature of SS membranes with the precise and simple engineering of protein nanopores. We demonstrate here a novel lipid-free hybrid nanopore comprising a natural DNA pore from a thermostable virus, electrokinetically inserted into a larger nanopore supported in a silicon nitride membrane. The hybrid pore is stable and easy to fabricate, and, most importantly, exhibits low peripheral leakage allowing sensing and discrimination among different types of biomolecules.
Exploratory analysis on the usage of Pi-score algorithm over endoscopic stone treatment step 1 protocol (2021)

Our exploratory study demonstrates that Pi-score can be effectively adapted to EST s1. Our algorithm successfully provided an objective score that equals the average performance improvement scores assigned by of a cohort of experts, in relation to a small amount of training attempts.
p53 Mutations in Chondrosarcoma (1998)

Chondrosarcoma is a primary bone tumor that has several different grades and variants. We evaluated 48 chondrosarcomas for p53 overexpression and p53 mutations. p53 expression was evaluated with immunohistochemistry using monoclonal antibodies PAb421, PAb1801, and PAb240. p53 mutations were identified with single-strand conformational polymorphism (SSCP) and DNA sequencing in selected cases. Immunohistochemistry revealed nuclear staining with PAb421 and PAb1801 in the spindle cell portion of one dedifferentiated chondrosarcoma. SSCP analysis was abnormal only in the case with positive immunostaining and localized the mutation to exons 7 and 8. DNA sequence analysis identified a point mutation of G to C in codon 276, resulting in an amino acid substitution of proline for alanine. This point mutation has been reported previously in other tumors but not in chondrosarcoma. Assimilation of our results with previous studies suggests that p53 mutations are present in a minority of chondrosarcomas but when present, are in higher grade chondrosarcomas and their variants.
2016 update on APBioNet’s annual international conference on bioinformatics (InCoB) (2016)

InCoB became since its inception in 2002 one of the largest annual bioinformatics conferences in the Asia-Pacific region with attendance ranging between 150 and 250 delegates depending on the venue location. InCoB 2016 in Singapore was attended by almost 220 delegates. This year, sessions on structural bioinformatics, sequence and sequencing, and next-generation sequencing fielded the highest number of oral presentation. Forty-four out 96 oral presentations were associated with an accepted manuscript in supplemental issues of BMC Bioinformatics, BMC Genomics, BMC Medical Genomics or BMC Systems Biology. Articles with a genomics focus are reviewed in this editorial. Next year's InCoB will be held in Shenzen, China from September 20 to 22, 2017.
Bloch domain walls in transverse patterns in type-II optical parametric oscillators (2005)

Summary form only given. We show that the presence of a birefringent and/or dichroic mirror into a type-II optical parametric oscillator (OPO) yields to a new kind of domain walls. In these walls the field amplitude remains constant while the phase rotates when going from one domain to the neighboring one. These domain walls are similar to Bloch walls in magnetic systems. They appear here for positive or null detunings, where the zero wavenumber is selected. Idler and signal fields show a similar pattern.
[Effects of calcium and vitamin D-fortified milk on physical development in school girls aged 10 to 12 years]. (2003)

Calcium and vitamin D-fortified milk supplementation could promote their physical development in girls aged 10 - 12 years.
A Role for IL-18 in Neutrophil Activation (2001)

IL-18 expression and functional activity has been identified in several autoimmune and infectious diseases. To clarify the potential role of IL-18 during early innate immune responses, we have explored the capacity of IL-18 to activate neutrophils. Human peripheral blood-derived neutrophils constitutively expressed IL-18R (alpha and beta) commensurate with the capacity to rapidly respond to IL-18. IL-18 induced cytokine and chemokine release from neutrophils that was protein synthesis dependent, up-regulated CD11b expression, induced granule release, and enhanced the respiratory burst following exposure to fMLP, but had no effect upon the rate of neutrophil apoptosis. The capacity to release cytokine and chemokine was significantly enhanced in neutrophils derived from rheumatoid arthritis synovial fluid, indicating differential responsiveness to IL-18 dependent upon prior neutrophil activation in vivo. Finally, IL-18 administration promoted neutrophil accumulation in vivo, whereas IL-18 neutralization suppressed the severity of footpad inflammation following carrageenan injection. The latter was accompanied by reduction in tissue myeloperoxidase expression and suppressed local TNF-alpha production. Together, these data define a novel role for IL-18 in activating neutrophils and thereby promoting early innate immune responses.
Melt‐Processed Multiphasic Ceramic Waste Forms (2014)

This chapter contains sections titled: Introduction Experimental Procedure Results and Discussions Conclusion Acknowledgements
Widely linear block-diagonalization type precoding in massive mimo systems with IQ imbalance (2015)

In this paper, we propose widely-linear blockdiagonalization (BD) type precoding techniques to alleviate the impact of IQ imbalance in the downlink Massive multi-input multi-output (MIMO) systems. We first introduce a real-valued signal model and then develop widely-linear BD (WL-BD) type precoding algorithms, i.e., WL-BD, widely linear regularized BD (WL-RBD) and widely linear simplified generalized MMSE channel inversion (WL-S-GMI). We also present analysis of the sum-rate and multiplexing gain achieved by the proposed WLBD for scenarios with and without IQ imbalance. Numerical results verify the analysis and show that WL-BD type precoding methods significantly outperform their conventional counterparts with IQ imbalance and approach the ideal case.
Agricultural Recycling of Sewage Sludge and the Environment (1996)

Potentially Toxic Elements (PTEs) in sewage sludge and sludge-treated soils effects of PTEs on the yield of agricultural crops human dietary intake of PTEs from agricultural crops by soil ingestion factors influencing bioavailability of PTEs to crop plants ingestion of PTEs by grazing livestock - implications for animal health and the human food chain mobility of PTEs in soil and impacts on water quality effects of PTEs on soil fertility and natural ecosystems nutrients organic pollutants Appendix: Legislation and codes of practice.
Changes in 3-, 2-Monochloropropandiol and Glycidyl Esters during a Conventional Baking System with Addition of Antioxidants (2020)

Shortening derived from palm oil is widely used in baking applications. However, palm oil and the related products are reported to contain high levels of monochloropropandiol (MCPD) ester and glycidyl ester (GE). MCPD and glycidol are known as process contaminants, which are carcinogenic and genotoxic compounds, respectively. The objective was to evaluate the effects of antioxidant addition in palm olein and stearin to the content of MCPD esters and GE in baked cake. Butylated hydroxyanisole (BHA), rosemary extract and tocopherol were used to fortify the samples at 200 mg/kg and in combinations (400, 600 and 800 mg/kg rosemary or tocopherol combined with 200 mg/kg BHA). The MCPD esters and GE content, radical formation and the quality of the fats portion were analyzed. The results showed that palm olein fortified with rosemary extract yielded less 2-MCPD ester. The GE content was lower when soft stearin was fortified with rosemary. ESR spectrometry measurements showed that the antioxidants were effective to reduce radical formation. The synergistic effects of combining antioxidants controlled the contaminants formation. In conclusion, oxidation stability was comparable either in the single or combined antioxidants. Tocopherol in combination with BHA was more effective in controlling the MCPD esters and GE formation.
Influence of Transient Thermal Response of Solid Wall on Bubble Dynamics in Pool Boiling (2014)

Numerical simulation of single bubble pool boiling process including transient thermal response of solid wall is performed using the ghost fluid method and the level set method for the sharp interface representation. The results show that non-physical initial condition in the numerical simulation deeply affects the process of bubble growth, and then multicycle simulation is necessary to eliminate its influence. It is shown by the present results that two nucleate criteria, i.e. constant waiting time and constant nucleate superheat, for determining the appearance time for the subsequent bubble lead to the same quasi-steady process of bubble growth if they are matched with each other. A periodically expanding and receding thermal “hollow” can be observed inside solid wall underneath the growing bubble. The recovery of the temperature on the nucleate site and the thermal boundary layer near the heating surface is influenced by transient heat conduction inside solid wall, which can affect evidently bubble thermal dynamics and heat transfer.
Artificial Neural Networks and Support Vector Machines for Water Demand\n Time Series Forecasting (2007)

Water plays a pivotal role in many physical processes, and most importantly\nin sustaining human life, animal life and plant life. Water supply entities\ntherefore have the responsibility to supply clean and safe water at the rate\nrequired by the consumer. It is therefore necessary to implement mechanisms and\nsystems that can be employed to predict both short-term and long-term water\ndemands. The increasingly growing field of computational intelligence\ntechniques has been proposed as an efficient tool in the modelling of dynamic\nphenomena. The primary objective of this paper is to compare the efficiency of\ntwo computational intelligence techniques in water demand forecasting. The\ntechniques under comparison are the Artificial Neural Networks (ANNs) and the\nSupport Vector Machines (SVMs). In this study it was observed that the ANNs\nperform better than the SVMs. This performance is measured against the\ngeneralisation ability of the two.\n
Caracterização do transcriptoma e parede celular de três espécies de Eucalyptus com importância industrial (2012)

A celulose e o polimero mais abundante do planeta e esta presente principalmente na parede secundaria de celulas vegetais maduras. O conhecimento dos mecanismos moleculares envolvidos na sua biossintese, bem como a regulacao deste processo e recente e ainda elementar, apesar da sua grande importância. O Eucalyptus e o genero florestal mais plantado no mundo, especialmente por ser materia-prima para fabricacao de celulose. Investimentos em pesquisas e desenvolvimento estao sendo realizados pelo setor florestal, no intuito de aumentar os ganhos de produtividade de celulose atraves da pesquisa na area da biologia molecular. Os dados analisados desmostram que a expressao genica das especies estudadas (E. globulus, E. grandis e E. urophylla) difere em genes essenciais para a formacao dos compostos da parede celular e por fim da madeira. Os dados moleculares sao condizentes com dados diferenciais aqui encontrados em relacao a composicao dos acucares da parede. Os resultados gerados pela analise de composicao da parede por diferentes tecnicas, incluindo a recentemente desenvolvida mostram uma grande diversidade e quantidade dos carboidratos da parede celular diferentemente distribuidos no xilema das especies Eucalyptus globulus, grandis e urophylla, bem como em folha. Tais resultados apresentam um grande avanco para o entendimento da composicao das paredes celulares de tais especies. Assim, o objetivo do presente trabalho foi correlacionar os dados moleculares, com dados highthroughput do Perfil Glicomico para entender a composicao e arquitetura da parece celular. Espera-se que esses dados possam contribuir para o entendimento da xilogenese e de como os genes trabalham para gerar arvores com caracteristicas tao distintas, podendo direcionar o melhoramento das mesmas. 
Abstract
Comparing and combining implicit ligand sampling with multiple steered molecular dynamics to study ligand migration processes in heme proteins (2011)

The ubiquitous heme proteins perform a wide variety of tasks that rely on the subtle regulation of their affinity for small ligands like O2, CO, and NO. Ligand affinity is characterized by kinetic association and dissociation rate constants, that partially depend on ligand migration between the solvent and active site, mediated by the presence of internal cavities or tunnels. Different computational methods have been developed to study these processes which can be roughly divided in two strategies: those costly methods in which the ligand is treated explicitly during the simulations, and the free energy landscape of the process is computed; and those faster methods that use prior computed Molecular Dynamics simulation without the ligand, and incorporate it afterwards, called implicit ligand sampling (ILS) methods. To compare both approaches performance and to provide a combined protocol to study ligand migration in heme proteins, we performed ILS and multiple steered molecular dynamics (MSMD) free energy calculations of the ligand migration process in three representative and well theoretically and experimentally studied cases that cover a wide range of complex situations presenting a challenging benchmark for the aim of the present work. Our results show that ILS provides a good description of the tunnel topology and a reasonable approximation to the free energy landscape, while MSMD provides more accurate and detailed free energy profile description of each tunnel. Based on these results, a combined strategy is presented for the study of internal ligand migration in heme proteins.
Hydration in semicrystalline polymers: Small‐angle neutron scattering studies of the effect of drawing in nylon‐6 fibers (1994)

Abstract Water absorbed by nylons appears to be partitioned into interlamellar and interfibrillar spaces. The amount of water in the interfibrillar region remains essentially unchanged with increasing draw ratio, whereas that in the interlamellar regions decreases with draw ratio; the latter accounts for the decrease in the water uptake in the drawn fibers. These results suggest that the amount of the amorphous material in the interfibrillar regions remains unchanged during drawing, and the increase in the crystallinity during drawing results from the incorporation of the amorphous chain segments in the interlamellar regions into the crystalline lamellae. Further, the interfibrillar water is more tightly bound than the interlamellar water. The length of the longitudinal channels into which water diffuses is about the same as that of the fibrils, and increases from ca. 1500 to 2000 Å upon drawing. The longitudinal channels are highly oriented even in undrawn fibers, and their misorientation increases from 5° to 15° upon drawing. These channels can be described as surface fractals of dimension 3.4–3.6. © 1994 John Wiley &amp; Sons, Inc.
Surface emission from MBE and MOVPE grown quantum cascade lasers (2005)

We report high power single mode surface emission from second order distributed feedback quantum cascade lasers. Two different laser materials are used for the lasers: MOVPE grown InGaAs/InAlAs and MBE grown GaAs/AlGaAs
Morphological awareness and its role in early word reading in English monolinguals, Spanish-English, and Chinese-English simultaneous bilinguals (2021)

Words’ morphemic structure and their orthographic representations vary across languages. How do bilingual experiences with structurally distinct languages influence children's morphological processes for word reading? Focusing on English literacy in monolinguals and bilinguals (N = 350, ages 5-9), we first revealed unique contributions of derivational (friend-li-est) and compound (girl-friend) morphology to early word reading. We then examined mechanisms of bilingual transfer in matched samples of Spanish-English and Chinese-English dual first language learners. Results revealed a principled cross-linguistic interaction between language group (Spanish vs. Chinese bilinguals) and type of morphological awareness. Specifically, bilinguals’ proficiency with the type of morphology that was less characteristic of their home language explained greater variance in their English literacy. These findings showcase the powerful effects of bilingualism on word reading processes in children who have similar reading proficiency but different language experiences, thereby advancing theoretical perspectives on literacy across diverse learners.
Cloning and characterization of KNR4, a yeast gene involved in (1,3)-beta-glucan synthesis. (1994)

k9 killer toxin from Hansenula mrakii was used to select a number of resistant mutants from Saccharomyces cerevisiae. Preliminary biochemical and genetic studies showed that some of them acquired structural defects in the cell wall. One of these mutants, the knr4-1 mutant, displays a number of cell wall defects, including osmotic sensitivity; sensitivity to cercosporamide, a known antifungal agent; and resistance to Zymolyase, a (1,3)-beta-glucanase. We report here the isolation and analysis of the KNR4 gene. DNA sequence analysis revealed an uninterrupted open reading frame which contains five potential start codons. The longest coding template encodes a protein of 505 amino acids with a calculated molecular mass of 57,044 Da. A data base search revealed 100% identity with a nuclear protein, SMI1p. Disruption of the KNR4 locus does not result in cell death; however, it leads to reduced levels of both (1,3)-beta-glucan synthase activity and (1,3)-beta-glucan content in the cell wall. The gene was mapped to the right arm of chromosome VII.
Isolation and mapping of a polymorphic DNA sequence (CJ52.15) on chromosome 11 [D11S383] (1989)

Journal Article Isolation and mapping of a polymorphic DNA sequence (CJ52.15) on chromosome 11 [D11S383] Get access C. Julier, C. Julier The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J. Gill, J. Gill The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Y. Nakamura, Y. Nakamura The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar G.M. Lathrop, G.M. Lathrop The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar J.-M. Lalouel, J.-M. Lalouel The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R. White R. White The Howard Hughes Medical Institute, University of Utah Medical SchoolSalt Lake City, UT 84132, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 23, 11 December 1989, Page 10149, https://doi.org/10.1093/nar/17.23.10149 Published: 11 December 1989
Comparison of the planned one‐ and elective two‐stent techniques in patients with coronary bifurcation lesions with or without acute coronary syndrome from the COBIS II Registry (2018)

Planned one-stenting reduced TLF in patients with ACS and it also might be beneficial in those without ACS for the treatment of coronary bifurcation lesions.
Factors Affecting the Sodium Permeability of Rat Erythrocytes (1981)

No difference was noted in Na+-Li+ counter-transport between SHR and WKY rats. Erythrocytes from rats with splenomegaly showed high cation permeability. Osmotic fragility, which was similar in SHR and WKY rats, was greater in Kyoto-derived rats than in other strains.