gebhart/patrepeval huggingface dataset:
Solid‐State Foaming by Oxide Reduction and Expansion: Tailoring the Foamed Metal Microstructure in the Cu–CuO System with Oxide Content and Annealing Conditions (2015)

A new method of introducing porosity into solid metals was investigated using mixtures of Cu and CuO. The process involves distributing oxides through the Cu matrix (e.g., mechanical milling, as used here) and then reducing those oxides during annealing. The most distinguishing characteristic of this process is that pores develop within individual powder particles. In this study, we varied the oxide content (0–7 at% O), annealing temperature (400, 600, and 800 °C), and annealing time (up to 3 h) to investigate their effect on the foamed metal microstructure. In general, we find that the amount of porosity within the powder particles (or bulk part) can be controlled by varying of oxide content and annealing parameters. The maximum porosity of 47.4% corresponds to intermediate conditions of both temperature and oxide content (600 °C and ≈3 at% CuO, respectively). The pore size and grain size are small (&lt;5 μm) in comparison with other solid‐state foaming techniques and are not highly sensitive to the annealing parameters used in the present study. The unique mechanisms and opportunities associated with this oxide reduction and expansion process are discussed for the Cu–CuO system as well as extensions to other metal systems.
About the Impact of Defect Phases on the Thermoelectric Properties of Cr<sub>3</sub>S<sub>4–<i>x</i></sub>Se<sub><i>x</i></sub> (2023)

Phase relations in Cr 3 S 4 and the substituted system Cr 3 S 4– x Se x are studied to determine the influence of chemical substitutions on the thermoelectric properties. In addition to the expected equilibrium phase crystallizing in the monoclinic space group I 2/ m , some samples exhibit a defect phase with Cr 2 S 3 ‐like structure. The defect phase can be observed in a few samples prior to sintering, with the majority being phase‐pure Cr 3 S 4 . The defect phase can, however, be introduced in phase‐pure samples through in situ heating. It can be proven that the defect phase has an influence on the thermoelectric properties, by lowering the electrical and thermal conductivity, while increasing the Seebeck coefficient. Substitution in the anion lattice of Cr 3 S 4 with Se lowers the thermal conductivity. The improvement is mainly achieved through a reduction of the electronic contribution to the thermal conductivity, leading to total values as low as 1.6 Wm −1 K −1 for the substituted system in comparison to the pristine material 2.3 Wm −1 K −1 .
Mechanical Characterization of Open Cell Aluminum Foams Using X-ray Computed Tomography (2018)

Open-cell aluminum foams show excellent potential for use in a variety of applications. In order to accelerate the use of aluminum foams in engineering industry, it is important to accurately understand the relationship between the manufacturing processes and the resulting foam properties. Two tests are developed to support development of finite element (FE) models that will be used to design foam geometries optimized to meet specific design criteria. A bulk crush test is created for small foam blocks which uses in situ X-ray computed tomography (CT) imaging. A tensile experiment is developed to test individual foam ligaments, which measures the aluminum’s mechanical behavior and will be used to improve the simulation’s accuracy beyond what is possible using published bulk material properties of aluminum.
Clonal diversity of Salmonella enterica serotype Typhi isolated from patients with typhoid fever in Tehran (2007)

In this study, antimicrobial susceptibility test and genetic typing were used to characterize 15 Salmonella enterica serotype Typhi (S. Typhi) isolates recovered from sporadic cases of typhoid fever in Tehran, Iran during 2004. Antimicrobial susceptibility test showed that all isolates were susceptible to 20 antimicrobials examined in this study. Analysis of insertion elements showed that 2 IS200 types with 10 and 11 copies were present. 11 of the 15 isolates were found to possess 10 IS200 elements residing on fragments from 23 to 2.3 kb. Comparison of the RiboPrinter (automated ribotyping) patterns of S. Typhi showed that 60% (9/15) of the isolates belonged to a single ribotype. PCR based random amplified polymorphic DNA analysis (RAPD) and enterobacterial repetitive intergenic consensus (ERIC) and pulsed-field gel electrophresis (PFGE) were also performed. ERIC and RAPD-PCR method showed 2 and 3 genotyping patterns amongst the isolates, respectively. The PFGE typing was carried out by using XbaI restriction enzyme, and 7 restriction patterns were observed. Overall, the molecular typing methods applied in this study showed that the isolated S. Typhi populations were highly polyclonal as shown by PFGE.
Diversified Therapeutic Phage Cocktails from Close Relatives of the Target Bacterium (2020)

This project tackles the antibiotic resistance crisis, developing a new method for discovering numerous efficacious bacteriophages for therapeutic cocktails against bacterial pathogens. The phage therapy approach to infectious disease, recently rekindled in U.S. medicine, requires numerous phages for each bacterial pathogen. Our approach 1) uses Sandia-unique software to identify dormant phages (prophages) integrated into bacterial chromosomes, 2) identifies prophage-laden bacteria that are close relatives of the target pathogenic strain to be killed, and 3) engineers away properties of these phages that are undesirable for therapy. We have perfected our phage-finding software, implemented our phage therapy strategy by targeting the pathogen Pseudomonas aeruginosa, and prepared new software to assist the phage engineering. We then turned toward Burkholderia pathogens, aiming to overcome the difficulty to transform these bacteria with a novel phage conjugation approach. Our work demonstrates the validity of a new approach to phage therapy for killing antibiotic resistant pathogens.
β-Arrestin-1 Protein Represses Diet-induced Obesity (2011)

Diet-related obesity is a major metabolic disorder. Excessive fat mass is associated with type 2 diabetes, hepatic steatosis, and arteriosclerosis. Dysregulation of lipid metabolism and adipose tissue function contributes to diet-induced obesity. Here, we report that β-arrestin-1 knock-out mice are susceptible to diet-induced obesity. Knock-out of the gene encoding β-arrestin-1 caused increased fat mass accumulation and decreased whole-body insulin sensitivity in mice fed a high-fat diet. In β-arrestin-1 knock-out mice, we observed disrupted food intake and energy expenditure and increased macrophage infiltration in white adipose tissue. At the molecular level, β-arrestin-1 deficiency affected the expression of many lipid metabolic genes and inflammatory genes in adipose tissue. Consistently, transgenic overexpression of β-arrestin-1 repressed diet-induced obesity and improved glucose tolerance and systemic insulin sensitivity. Thus, our findings reveal that β-arrestin-1 plays a role in metabolism regulation.
The Effect of Business Characteristics on the Methods of Knowledge Protections (2012)

Intellectual property (IP) protection has been suggested to be essential in protecting innovation in product-dominant companies. However, with the development of service industries, the ineffectiveness in IP protection becomes manifest. Meanwhile, other knowledge protecting methods enable companies to maintain their competency without formal protection. This study examines the effectiveness of different means of knowledge protection. Specifically, business is classified according to companies’ offering nature, serving mode and consider about their business hardware. The effectiveness of protection methods is analyzed among these business types. Interviews were conducted with senior managers of 39 companies in China and Singapore. It is demonstrated that the choice of knowledge protecting method does not depend mainly on whether a company provides products or services, but on how the company produces and provides its offerings. It is found that the core competency of companies largely affects their attitude on whether to protect their offerings. It is found that in weak appropriability regimes, companies apply for patents not for their knowledge protection function, but for other benefits, such as getting awards or tax reductions, and improving reputation among customers.
Exogenous hormone use, reproductive factors and risk of intrahepatic cholangiocarcinoma among women: results from cohort studies in the Liver Cancer Pooling Project and the UK Biobank (2020)

This study suggests that hysterectomy and long-term oral contraceptive use may be associated with an increased ICC risk.
Carbon–carbon bond forming reactions with substrates absorbed non-covalently on a cellulose chromatography paper support (2006)

Reactions and purifications, including carbon-carbon bond forming reactions, can be carried out on a cellulose support on which the substrates are non-covalently absorbed.
Asymmetric Hydrovinylation of 1-Vinylcycloalkenes. Reagent Control of Regio- and Stereoselectivity (2012)

1-Vinylcycloalkenes undergo highly regio- and enantioselective (>98% ee) 1,4-hydrovinylation (HV) when treated with ethylene (1 atm) at room temperature in the presence of [(S,S)-2,4-bis-diphenylphosphinopentane (BDPP)]CoCl(2) (0.05 equiv) and methylaluminoxane. The minor 1,2-HV products, seen only in 1-vinylcyclohexene (~15%) and 1-vinylcycloheptene (2%), are formed as racemic mixtures. The corresponding Ni(II)-catalyzed HV reactions of these substrates give mostly the 1,2-adducts. Racemic 4-tert-butyl-1-vinylcyclohexene, when treated with Co[(S,S)-(BDPP)]Cl(2) and ethylene, undergoes a rare enantiodivergent reaction giving two diastereomers each in >98% ee.
Mobile backhaul transport streamlined through SDN (2015)

In this paper, we describe the integration of Software Defined Networking (SDN) in the mobile backhaul as a disruptive approach to streamline the transport network. In this work we leverage SDN to optimize the mobile backhaul transport by removing all mobile specific tunnelling and replace it with more efficient MPLS or Carrier Grade Ethernet deployed either over electrical or optical networks. The paper also presents the testbed with complete end to end system including off the shelf base stations, SDN enabled mobile backhaul switches and virtualize network elements (i.e. Mobility Management Entity (MME), Serving/Packet Gateway (S/P-GW)) running on the cloud. This testbed is currently accepted as European Telecommunication Standards (ETSI) Proof of Concept and the results are used to describe the benefits for operators and end users. Moreover, an initial design of services based on the proposed virtualized mobile network architecture is proposed. The results of the testbed show the benefits for mobile operators in terms of Capital Expenditure (CAPEX) and Operational Expenditure (OPEX) savings but more importantly the development of services that benefit from optimal usage of resources.
Recombination mechanisms in InAs/InP quantum dash lasers studied using high hydrostatic pressure (2004)

Abstract Two types of InAs quantum dash lasers grown on InP substrates with lasing wavelengths of 1.52 μm and 1.76 μm were studied. In both laser types the threshold current density, J th , was about 2 kA/cm 2 at room temperature and had a similar temperature sensitivity ( T 0 was about 80 K in the range T = 120–250 K, and T 0 = 60–70 K from 250 to 300 K). Measurements of the spontaneous emission from a window milled in a substrate contact showed that J rad , the radiative part of J th , is almost temperature independent and less than 5% of J th at T = 295 K, demonstrating that the relatively large value of J th and its temperature sensitivity must be due to non‐radiative recombination processes. However, despite the similar temperature behaviour of the lasers, their pressure dependences were very different showing that in the 1.52 μm lasers, pressure independent defect related recombination outside the dashes due to thermal carrier spill‐over or thermal leakage dominates, while in the 1.76 μm quantum dash laser 60% of J th is due to Auger recombination. (© 2004 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Supplemental Methods and Figure Legends from BRAF&lt;sup&gt;V600E&lt;/sup&gt; Co-opts a Conserved MHC Class I Internalization Pathway to Diminish Antigen Presentation and CD8&lt;sup&gt;+&lt;/sup&gt; T-cell Recognition of Melanoma (2023)

&lt;p&gt;Supplemental Methods and Figure Legends&lt;/p&gt;
IgG Subclass Profile of Serum Antigliadin Antibodies and Antibody‐Dependent Cell‐Mediated Cytotoxicity in Young Children with Coeliac Disease (2001)

Recently, sera from children with active coeliac disease were found to efficiently induce antibody-dependent cell-mediated cytotoxicity (ADCC) of gliadin-coated cells. In the present study, the subclass profile of immunoglobulin (Ig)G antigliadin antibodies in sera from young children, with or without coeliac disease, was determined and related to the ADCC-mediating capacity of the same sera. In addition, IgG subclasses were selectively depleted from sera and the effect on ADCC-mediating was studied. Children with untreated coeliac disease had high antigliadin antibody activities of all four IgG subclasses. However, they had a particularly high proportion of IgG1 antigliadin antibodies (ratio IgG1/IgG) compared with healthy references or coeliac children in remission. In contrast, children who had high serum antigliadin antibody activity but no histological signs of enteropathy (disease references), showed significantly lower proportions of antigliadin antibodies of the IgG1 as well as the IgG3 subclass compared with healthy references or untreated coeliac children. Regression analysis showed that IgG1 and IgG3 antigliadin antibody activity correlated positively to ADCC-mediating capacity, and depletion of IgG1 from sera profoundly diminished ADCC. The results suggest that gliadin-specific antibodies of predominantly the IgG1 subclass mediate tissue-damaging immune reactions like ADCC, and may, thus, contribute to the disease process of coeliac disease.
Reverse Genetics as a Tool for Detection of Negative-Stranded RNA Viruses (2014)

Reverse genetics (RG) was developed about 30 years ago andhas been used mainly for exploring the molecular biology andpathogenesis of RNA viruses. Using RG, the need for working withinfectious viral particles is obviated, thus making it possible toexplore dangerous viruses in almost any laboratory. Recently, RG-based detection systems for several negative-stranded RNA (NSRNA) viruses were developed. The novel detection techniques relyon short, extremely well-conserved sequences at the ends of theviral genome, so this detection method is unaﬀected by the diversityof the strains within a given viral family. Due to the use of the greenﬂuorescent protein or Luciferase reporter genes as a signal of viralreplication in vitro, these detection systems can serve as a platformtechnology for high-throughput screening of antiviral agents andneutralizing antibodies for NS RNA viruses.
Container-aided Integrative QTL and RNA-seq Analysis of Collaborative Cross Mice Supports Distinct Sex-Oriented Molecular Modes of Response in Obesity (2019)

Abstract Background: The CC mouse population is a valuable resource to study the genetic basis of complex traits, such as obesity. Although the development of obesity is influenced by environmental factors, the underlying genetic mechanisms play a crucial role in the response to these factors. The interplay between the genetic background and the gene expression pattern can provide further insight into this response, but we lack robust and easily reproducible workflows to integrate genomic and transcriptomic information in the CC mouse population. Results: We established an automated and reproducible integrative workﬂow to analyse complex traits in the CC mouse genetic reference panel at the genomic and transcriptomic levels. We implemented the analytical workﬂow to assess the underlying genetic mechanisms of host susceptibility to diet induced obesity and integrate these results with diet induced changes in the hepatic gene expression of susceptible and resistant mice. Hepatic gene expression diﬀers signiﬁcantly between obese and non-obese mice, with a signiﬁcant sex eﬀect, where male and female mice exhibit diﬀerent responses and coping mechanisms. Conclusion: Integration of the data showed that diﬀerent genes but similar pathways are involved in the genetic susceptibility and disturbed in diet induced obesity. Genetic mechanisms underlying susceptibility to high-fat diet induced obesity diﬀer in female and male mice. The clear distinction we observe in the systemic response to the high-fat diet challenge and to obesity between male and female mice points to the need for further research into distinct sex-related mechanisms in metabolic disease.
Gold Nanoparticles with Self-Assembled Cysteine Monolayer Coupled to Nitrate Reductase in Polypyrrole Matrix Enhanced Nitrate Biosensor (2013)

We have developed here a novel, highly sensitive and selective nitrate (NO– 3) biosensor by covalent immobilization of nitrate reductase (NaR) in self-assembled monolayer (SAM) of cysteine on gold nanoparticles (GNP)-polypyrrole (PPy) modified platinum electrode. Incorporation of GNP in highly microporous PPy matrix was confirmed by morphological scanning electron microscope (SEM) images. The electrochemical behavior of the NaR modified electrode exhibited the characteristic reversible redox peaks at the potential, –0.76 and –0.62 V versus Ag/AgCl. Further, the GNP-PPy nanocomposite enhanced the current response by 2-fold perhaps by enhancing the immobilization of NaR and also direct electron transfer between the deeply buried active site and the electrode surface. The common biological interferences like ascorbic acid, uric acid were not interfering with the NO– 3 measurement at low concentration levels. This biosensor showed a wide linear range of response over the concentration of NO– 3 from 1 μM to 1 mM, with higher sensitivity of 84.5 nA μM–1 and a detection limit of 0.5 μM. Moreover, the NO– 3 level present in the nitrate-rich beetroot juice and the NO– 3 release from the lipopolysaccharide treated human breast cancer cells were estimated.
Metalloporphyrin antioxidants ameliorate normal tissue radiation damage in rat brain (2010)

Metalloporphyrin antioxidants merit further exploration as adjunctive radioprotectants for cranial radiotherapy/radiosurgery applications, although the potential for tumour protection must be carefully considered.
Quantum Dipole in a Silicon Transistor: Quantum Simulation for Strongly Correlated System (2017)

We discovered anomalous transport properties in a conventional Si based Metal-Oxide-Semiconductor Field-Effect-Transistor with a wide and narrow hole-channel at low temperatures. We found the quantum dipole formed at the thin gate interface is responsible for the phase transition. We discuss its potential to use for a quantum simulator as a test bed to examine various theoretical concepts in condensed-matter physics.
Estimation of residual magnetization by BEM. (1991)

A method of estimation for the residual magnetizations in a magnetic substance is presented. This method is based on inverse analysis using the threedimensional boundary element method. That is. the distribution of the residual magnetizations is calculated by the measured flux density near the surface as input-data. In this paper, the singularity of the system equations for a simple problem is examined. This method is applied to a model of the permanent magnet, and then it is indicated that our method is available for the estimation of the residual magnetization.
Proxy Mobile IPv6 indication and discovery (2008)

Proxy Mobile IPv6 is a network-based mobility protocol that enabling
mobility management for an IP host as it moves across different points
of attachment within the mobility domain. An IP host whose mobility is
being managed by the network is unaware of the access networks
capability to do mobility management on its behalf using Proxy Mobile
IPv6. This draft proposes mechanisms by which the host is informed of
Proxy Mobile IPv6 support, as well as how to actively discover such
capability in the network that host attaches to. The ability of the
host to discover or be aware of Proxy Mobile IPv6 support in the
access network enables better decision making in terms of the type of
mobility protocol used for IP mobility.
VEGF-trap Aflibercept Significantly Improves Long-term Graft Survival in High-risk Corneal Transplantation (2015)

In a clinically relevant model of high-risk corneal transplantation in which blood and lymphatic vessels are present and treatment begins at the time of transplantation, VEGF-trap is significantly more effective in improving long-term graft survival as compared to anti-VEGF-C and sVEGFR-3, but all approaches improve survival when compared to untreated control.
Classifying Breast Histopathology Images with a Ductal Instance-Oriented Pipeline (2020)

In this study, we propose the Ductal Instance-Oriented Pipeline (DIOP) that contains a duct-level instance segmentation model, a tissue-level semantic segmentation model, and three-levels of features for diagnostic classification. Based on recent advancements in instance segmentation and the Mask R-CNN model, our duct-level segmenter tries to identify each ductal individual inside a microscopic image; then, it extracts tissue-level information from the identified ductal instances. Leveraging three levels of information obtained from these ductal instances and also the histopathology image, the proposed DIOP outperforms previous approaches (both feature-based and CNN-based) in all diagnostic tasks; for the four-way classification task, the DIOP achieves comparable performance to general pathologists in this unique dataset. The proposed DIOP only takes a few seconds to run in the inference time, which could be used interactively on most modern computers. More clinical explorations are needed to study the robustness and generalizability of this system in the future.
Replication and integration of a <i>Vibrio cholerae</i> cryptic plasmid linked to the CTX prophage (1998)

We identified a 4.7kb cryptic plasmid in all ctxAB+ Vibrio cholerae strains we tested. An isolate of the V. cholerae classical biotype strain 0395 that harbours the cryptic plasmid at high copy number was found. Hybridization analysis demonstrated that sequences highly related or identical to this plasmid exist in all toxigenic strains of V. cholerae but were notably absent in all non-toxigenic environmental isolates that lacked the genes for toxin-co-regulated pili and the filamentous CTX prophage. Accordingly, we have named the cryptic plasmid pTLC for toxin-linked cryptic. The complete nucleotide sequence of pTLC from the high-copy-number isolate was determined. The largest open reading frame in the plasmid is predicted to encode a protein similar to the replication initiation protein (pII) of Escherichia coli F-specific filamentous phages. The nucleotide sequence of pTLC also facilitated the structural characterization of the DNA homologous to pTLC in other strains of V. cholerae. pTLC-related DNA exists in these strains as both low-copy-number, covalently closed circular DNA and tandemly duplicated, chromosomally integrated DNA. Remarkably, the chromosomally integrated form of pTLC is adjacent to the CTX prophage. The strain distribution, chromosomal location and DNA sequence of pTLC suggests that it may be a genetic element that plays some role in the biology of CTXphi, perhaps facilitating either its acquisition or its replication.