gebhart/patrepeval huggingface dataset:
The enigmatic role of fungal annexins: the case of Cryptococcus neoformans (2019)

Abstract Annexins are multifunctional proteins that bind to phospholipid membranes in a calcium-dependent manner. Annexins play a myriad of critical and well-characterized roles in mammals, ranging from membrane repair to vesicular secretion. The role of annexins in the kingdoms of bacteria, protozoa and fungi have been largely overlooked. The fact that there is no known homologue of annexins in the model organism may contribute to this gap in knowledge. However, annexins are found in most medically important fungal pathogens, with the notable exception of Candida albicans. In this study we evaluated the function of the one annexin gene in Cryptococcus neoformans , a causative agent of cryptococcosis. This gene CNAG_02415, is annotated in the C. neoformans genome as a target of calcineurin through its transcription factor Crz1, and we propose to update its name to cryptococcal annexin, AnnexinC1. C. neoformans strains deleted for AnnexinC1 revealed no difference in survival after exposure to various chemical stressor relative the wild type, as well as no major alteration in virulence or mating. The only alteration observed in strains deleted for AnnexinC1 was a small increase in the titan cells formation in vitro . The preservation of annexins in many different fungal species suggests an important function, and therefore the lack of a strong phenotype for annexin-deficient C. neoformans is suggestive of either redundant genes that can compensate for the absence of AnnexinC1 function or novel functions not revealed by standard assays of cell function and pathogenicity. Importance Cryptococcus neoformans is the deadliest human fungal pathogen, causing almost 200,000 deaths each year. Treatment of this lethal infection is lengthy, and in some patients therapy is not curative and patients require lifelong therapy. Fundamental research in this yeast is needed so that we can understand mechanisms of infection and disease and ultimately devise better therapies. In this work we investigated a fungal representative of the annexin family of proteins, specifically in the context of virulence and mating. We find that the cryptococcal annexin does not seem to be involved in virulence or mating but affects generation of titan cells, enlarged yeast cells that are detected in the lungs of mammalian hosts. Our data provides new knowledge in an unexplored area of fungal biology.
Infected Total Knee Arthroplasty; Two-stage Reimplantation With a Gastrocnemius Rotational Flap (1997)

This study reviews a consecutive series of 21 patients undergoing two-stage reimplantation total knee arthroplasty for late chronic infection. All 21 patients had late chronic infections, and 20 of 21 patients were compromised hosts. Seven different organisms were isolated at the time of prosthetic resection. Staphylococcus coagulase negative species was the most frequently isolated organism. At the time of reimplantation, a medial gastrocnemius rotational flap was rotated over the proximal tibia and knee for wound closure. The average explantation time was 25 weeks (range, 7-76 weeks), and no methylmethacrylate spacers were used. At an average 17-month followup (range, 5.1-33.1 months) all reimplanted total knee replacements remained in place with one patient having recurrent infection. At reimplantation, 11 patients had positive bacterial cultures from tissue specimens. Sixteen of the 33 (40%) positive cultures were from specimens taken from the medullary canal. At followup, the average Knee Society Score was 77.4 (range, 40-100). The lack of a methylmethacrylate spacer and a long explantation time were considered important factors in diminishing functional performance and determining the need for a gastrocnemius flap. A medial gastrocnemius rotational flap should be considered at the time of reimplantation total knee arthroplasty if the soft tissue envelope about the knee is compromised and cannot be closed without undue tension.
Genetic characterisation of isolates of Listeria monocytogenes from man, animals and food (1993)

Multilocus enzyme electrophoresis was used to assess genetic relationships between 95 isolates of Listeria monocytogenes, most of which were isolated in Australia and New Zealand from man, animals and food. The isolates were separable into two major genetic divisions; the majority of those from human patients and animals were in division I, and the majority from those foods that were not specifically associated with human listeriosis were in division II. Isolates in division I were virulent, whereas many isolates from food were probably less virulent and did not pose a large threat to human health. However, isolates from certain foods, particularly paté, were indistinguishable from those causing disease in man, and the consumption of these products represented a clear risk factor for infection. Isolates from infected human patients in Australia and New Zealand belonged to the same clone of serotype 4b that has been responsible for major epidemics in the northern hemisphere. However, a separate clone of serotype 1/2b strains, present in both Australia and New Zealand, was responsible for two major outbreaks that occurred in Western Australia in 1978-80 and 1990-91.
Using the Simulated Colonoscopy to Assess Force Measurement (2012)

Purpose: The Colon Force Monitor (CFM) is a novel, hand-held device that measures forces on the colonoscope. Previous in vivo studies have shown that maximum forces vary between experts and even between cases for a single expert. However, these forces have not been measured on a simulator, an increasingly utilized training tool. We used the SimbionixTM simulator to examine whether experts have a unique signature force application pattern and how the force pattern develops with repetition of cases. Methods: Two experts completed 3 simulated colonoscopy cases a total of 5 times each using the CFM. Statistical analysis was used to analyze the two experts. Results: When comparing max force applied, as measured by the CFM device, compared to max force applied, as measured by the simulator, there is a significant absolute difference in forces measured (p=0.04). When evaluating the max forces applied by each expert, there is a significant difference in the max force applied by expert 1 in case 1 compared to case 2 compared to case 3 (p=0.02). For expert 2, however, there is no significant difference in max forces applied for case 1 compared to case 2 compared to case 3 (p=0.10). When graphing the max force applied by each expert in each case, for expert 1, the values do not appear to approach an asymptote. However, expert 1 has a narrow range of max forces with all max forces between 20 and 30 N. When graphing the max force applied by each expert in each case, for expert 2, the values appear to approach an asymptote. Conclusion: The simulator may be used as a model to assess measurement of force applied to the colonoscope during colonoscopy; however, the measurement of maximum force obtained by the simulator does not correlate with the measurement of maximum force obtained by the CFM device. Likely the CFM device is better able to measure force parameters during colonoscopy. Experts may have a signature maximum force that they apply to the colonoscope during colonoscopy that is learned as they perform repeating trials on the simulator. In this pilot study of 2 experts, one demonstrated approach toward an asymptote while the other did not. Expert 2 appeared to approach his asymptote after approximately 5 total cases out of 15 cases suggesting that the current methods used may allow quantification of an individual's signature force profile. Further research is necessary to assess this finding, and to study the development of the novice's signature force profile on simulated cases. Disclosure: Aleksandr Pasechnik - Employee: Artann Laboratories Armen Sarvazyan PhD - Employee: Artann Laboratories Louis Y Korman, MD - Co-holder of CFM device patent.
Equivalent Oxide Thickness Reduction for High-k Gate Stacks by Optimized Rare-Earth Silicate Reactions (2009)

Equivalent oxide thickness (EOT) scaling still remains one of the main facilitators to increase transistor performance. The use of rare-earth (RE) elements has been shown to effectively increase permittivity of the gate-stack interfacial layer between substrate and high- dielectric, reducing its EOT contribution. In this paper, we have studied the optimal RE-to- ratio using as a test case. Capacitance–voltage and leakage current–voltage measurements were performed on Pt-gated capacitors with a -doped gate stack and varying ratios of to after a anneal. Optimal EOT-leakage performance was found for a -to- ratio of .
A dual-mode simultaneous bilateral optical imaging system for breast cancer detection (2010)

System design, performance characteristics and representative clinical findings are described for a second generation dynamic near-infrared optical tomography breast imager that examines both breasts simultaneously under conditions of rest and controlled provocation. Novel elements of the system include incorporation of high-density optical sensing heads (8192 channels) that include feedback-controlled force-sensing articulating members, their capacity to conform to a wide range of breast sizes, and the ability to perform opto-mechanical scans in the seated position. The new sensor heads employ a set of stepper linear motors to adjust the applied force with high spatial selectivity and rapid response time, and strain gauges to provide for active control. A user interface has been developed to support two different modes of sensing head control. In both modes, optical measurements from all sensing channels are continuously recorded. In all, the developed system provides three sets of measurements: optical, applied force, and deformation. The high sensor density combined with fine articulation supports exploration of the hemodynamic response of the breast under a wide range of protocols together with measures of Young's modulus and quasi-elastic plastic deformation. Representative clinical findings obtained from healthy and tumor breasts at rest and during controlled provocations are presented.
Device and circuit considerations for high performance SOI technologies (2002)

Summary form only given. The insatiable need for higher performance microprocessors has driven the development of high-speed deep-submicron Silicon On Insulator (SOI) CMOS technology. SOI 1.8 V microprocessors are currently produced in IBM's manufacturing line at 220 nm groundrules, and microprocessors are being developed for 1.5 V-180 nm and 1.2 V-130 nm SOI technologies. These technologies are based on partially-depleted (PD) SOI CMOS transistor designs because fully-depleted SOI transistor designs require excessively thin SOI films for short-channel threshold voltage control and also need alternate workfunction gate materials to achieve required transistor thresholds. Inherent to PD-SOI CMOS transistors is a floating body that needs to be accounted for in transistor design, manufacturing, and circuit design.
The CD4−CD8−MAIT cell subpopulation is a functionally distinct subset developmentally related to the main CD8+MAIT cell pool (2018)

Mucosa-associated invariant T (MAIT) cells are unconventional innate-like T cells that recognize microbial riboflavin metabolites presented by the MHC class I-like protein MR1. Human MAIT cells predominantly express the CD8α coreceptor (CD8<sup>+</sup>), with a smaller subset lacking both CD4 and CD8 (double-negative, DN). However, it is unclear if these two MAIT cell subpopulations distinguished by CD8α represent functionally distinct subsets. Here, we show that the two MAIT cell subsets express divergent transcriptional programs and distinct patterns of classic T cell transcription factors. Furthermore, CD8<sup>+</sup> MAIT cells have higher levels of receptors for IL-12 and IL-18, as well as of the activating receptors CD2, CD9, and NKG2D, and display superior functionality following stimulation with riboflavin-autotrophic as well as riboflavin-auxotrophic bacterial strains. DN MAIT cells display higher RORγt/T-bet ratio, and express less IFN-γ and more IL-17. Furthermore, the DN subset displays enrichment of an apoptosis gene signature and higher propensity for activation-induced apoptosis. During development in human fetal tissues, DN MAIT cells are more mature and accumulate over gestational time with reciprocal contraction of the CD8<sup>+</sup> subset. Analysis of the T cell receptor repertoire reveals higher diversity in CD8<sup>+</sup> MAIT cells than in DN MAIT cells. Finally, chronic T cell receptor stimulation of CD8<sup>+</sup> MAIT cells in an in vitro culture system supports the accumulation and maintenance of the DN subpopulation. These findings define human CD8<sup>+</sup> and DN MAIT cells as functionally distinct subsets and indicate a derivative developmental relationship.
700nm pitch Cu/SiCN wafer-to-wafer hybrid bonding (2022)

Wafer-to-wafer (W2W) hybrid bonding has gained more attention as the Artificial intelligence (AI) and big data machine learning (ML) applications required higher interconnect densities. This paper presents our research to demonstrated Cu/SiCN W2W hybrid bonding down to PAD Pitch 700nm. We have proven good Cu-Cu connectivity performance in both long daisy chains and kelvin resistor devices. Atomic Force Microscope (AFM) measurement is used to analyze the pre-bonding materials properties, namely Cu PAD height, dielectric surface profile and roughness. This enables, together with good W2W hybrid bonding overlay control, high electrical yield.
Search for new resonances in Wγ and Zγ final states in pp collisions at √s = 8 TeV with the ATLAS detector (2014)

This Letter presents a search for new resonances decaying to final states with a vector boson produced in association with a high transverse momentum photon, V gamma, with V = W(-&gt; l nu) or Z(-&gt; l(+)l(-)), where l = mu or mu. The measurements use 20.3fb(-1) of proton-proton collision data at a center-of-mass energy of root s = 8 TeV recorded with the ATLAS detector. No deviations from the Standard Model expectations are found, and production cross section limits are set at 95% confidence level. Masses of the hypothetical a(T) and omega(T) states of a benchmark Low Scale Technicolor model are excluded in the ranges [275, 960] GeV and [200, 700]boolean OR[750, 890] GeV, respectively. Limits at 95% confidence level on the production cross section of a singlet scalar resonance decaying to Z gamma final states have also been obtained for masses below 1180GeV. Published by Elsevier B. V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/3.0/).
Schwarzian Derivatives and Zeros of Solutions to Second Order Linear Differential Equations (1991)

Let A be entire.Suppose that there exists an unbounded quasidisk D such that A is sufficiently small in D. We prove that then any nontrivial solution to y" + Ay = 0 has at most one zero in D. We show that if A = Q exp P where P and Q are polynomials, one can usually take D to be an angle of opening x/n where n is the degree of P .
Rotavirus excretion and immune status of piglets during suckling and after weaning (1985)

Pasteurella multocida is one of the infectious agents responsible for respiratory di- seases in the pig in which mainly capsular groups A and D have been isolated. According to most authors strains of type A play a major role in pneumopathies, while those of type D generally produce nasal lesions. Pathogenicity of Pasteurella l1I ultocida depends on its serotype and on the presence of a thermolabile exotoxin. Several tests are suggested to study the dermonecrotic properties of this toxin : intradermic injection in guinea pigs, lethality in mice, experimental infection in SPF piglets and cytopathogenic effect in cell cultures.
Phytochemical composition and antioxidant evaluation of Pelargonium sidoides DC. root extract and proanthocyanidins (2018)

Acknowledgement: The PELARGODONT Project (“Engineering and functionalization of delivery system with Pelargonium sidoides biologically active substance on inflamed periodontal surface area”) is financed under the M-ERA.NET 2 Programme, which has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 685451.
A hybrid optical packet and wavelength selective switching platform for high-performance data center networks (2011)

We propose and experimentally demonstrate for the first time a hybrid optical packet and wavelength selective switching platform for high-performance data center networks. This architecture based on cascaded silicon microrings and semiconductor optical amplifiers (SOAs) supports wavelength reconfigurable packet and circuit switching, and is highly scalable, energy efficient and potentially integratable. By combining the wavelength-selective behavior of the microring and the broadband behavior of the SOA switch, we are able to achieve fast switching transitions, high extinction ratios, and low driving voltages, which are all requirements for future optical high-performance data center networks. Routing correctness and error-free operation (<10(-12)) are verified for both 10-Gb/s and 40-Gb/s packets and streaming data with format transparency.
The Photochemistry of Pyrylium Salts:  New Photohydrations and Photoamidations of Heterocycles Leading to Bicyclic Oxazolines and Functionalized Cyclopentenes (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTThe Photochemistry of Pyrylium Salts: New Photohydrations and Photoamidations of Heterocycles Leading to Bicyclic Oxazolines and Functionalized CyclopentenesMatthew A. Clark, Ryan C. Schoenfeld, and Bruce GanemView Author Information Department of Chemistry and Chemical Biology Baker Laboratory, Cornell University Ithaca, New York 14853-1301 Cite this: J. Am. Chem. Soc. 2001, 123, 42, 10425–10426Publication Date (Web):October 2, 2001Publication History Received12 July 2001Published online2 October 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/ja0166040https://doi.org/10.1021/ja0166040rapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1015Altmetric-Citations13LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Ethers,Oxidation,Perchlorates,Photodissociation,Salts Get e-Alerts
Pure‐Silica‐Zeolite MFI and MEL Low‐Dielectric‐Constant Films with Fluoro‐Organic Functionalization (2008)

Abstract The synthesis of organic‐functionalized pure‐silica‐zeolites (PSZs) with MFI‐ and MEL‐type structures for low‐ k applications prepared through a direct‐synthesis method by adding a fluorinated silane to the synthesis solution is reported. The added fluorine functionality increases the hydrophobicity of the zeolites, which are characterized by scanning electron microscopy, X‐ray diffraction, 29 Si and 19 F solid‐state NMR spectroscopy, nitrogen adsorption, and thermogravimetric analysis. The functionalized zeolite powders have low water content and calcined spin‐on films prepared from the functionalized nanoparticle suspensions exhibit higher water contact angles and lower k values (2.1 and 1.8 for the functionalized MFI‐ and MEL‐type zeolites, respectively) than PSZ films. The use of a direct‐synthesis method to decrease the moisture adsorption in the films eliminates the extra post‐spin‐on silylation steps that are traditionally used to render the zeolite films hydrophobic.
Fabrication of Monodisperse Polymer Nanoparticles by Membrane Emulsification Using Ordered Anodic Porous Alumina (2009)

Uniformly sized droplets of photocurable monomer were obtained through membrane emulsification using highly ordered anodic porous alumina as a membrane. Subsequent polymerization of the monomer generated polymer particles, whose sizes could be controlled by changing the size of the pores in anodic porous alumina. The size distribution was very narrow owing to the uniformity of pore size in the anodic porous alumina used for the emulsification.
Search for new phenomena in events with a photon and missing transverse momentum inppcollisions ats=8  TeVwith the ATLAS detector (2015)

Results of a search for new phenomena in events with an energetic photon and large missing transverse momentum with the ATLAS experiment at the LHC are reported. Data were collected in proton-proton collisions at a center-of-mass energy of 8 TeV and correspond to an integrated luminosity of 20.3 fb -1 . The observed data are well described by the expected Standard Model backgrounds. The expected (observed) upper limit on the fiducial cross section for the production of events with a photon and large missing transverse momentum is 6.1 (5.3) fb at 95% confidence level. Exclusion limits are presented on models of new phenomena with large extra spatial dimensions, supersymmetric quarks, and direct pair production of dark-matter candidates.