gebhart/patrepeval huggingface dataset:
Superantigen genes in group A streptococcal isolates and their relationship with emm types (2008)

Superantigens are important virulence factors in the pathogenesis of invasive disease caused by group A streptococcus (GAS). There has been a recent re-emergence of this disease worldwide. A number of novel superantigens have been described recently. This study investigated 107 isolates of GAS for possession of each of the 11 currently known superantigen genes to determine the prevalence, co-occurrence and genetic restriction amongst different emm types of GAS. The results were compared with those in previously published studies. Superantigen genes were not randomly distributed amongst GAS isolates. Certain combinations of superantigen genes were more common and the majority of emm types showed restricted superantigen profiles. This is the first prevalence study of GAS isolates to include the complete range of known superantigen genes and their restriction amongst emm types. This study contributes to the understanding of the relationship between superantigen genes and emm types, and highlights the importance of comprehensive studies in different populations.
Total Anomalous Pulmonary Venous Connection (2012)

This chapter covers total anomalous pulmonary venous connection, with sections on embryology, classification, anatomy and associated lesions, natural history, diagnosis, operative management and anesthetic considerations, and results.
Polymer film with optically controlled form and actuation (2005)

A low power laser beam is used to induce large and fast variations in the shape of a polymer film due to photoinduced contraction and expansion of the polymer film surface subject to the beam. The direction of the photoinduced bend or twist of the polymer can be reversed by changing the polarization of the beam. Thus the film orientation could be varied within +/-70 masculine. The phenomenon is a result of optically induced reorientation of azobenzene moieties in the polymer network.
Dibromotris(trimethylphosphine)nickel(II) (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDibromotris(trimethylphosphine)nickel(II)Ben B. Chastain, Devon W. Meek, E. Billig, J. E. Hix Jr., and Harry B. GrayCite this: Inorg. Chem. 1968, 7, 11, 2412–2414Publication Date (Print):November 1, 1968Publication History Published online1 May 2002Published inissue 1 November 1968https://pubs.acs.org/doi/10.1021/ic50069a044https://doi.org/10.1021/ic50069a044research-articleACS PublicationsRequest reuse permissionsArticle Views94Altmetric-Citations10LEARN 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-Alertsclose Get e-Alerts
Developing and validating COVID-19 adverse outcome risk prediction models from a bi-national European cohort of 5594 patients (2021)

Patients with severe COVID-19 have overwhelmed healthcare systems worldwide. We hypothesized that machine learning (ML) models could be used to predict risks at different stages of management and thereby provide insights into drivers and prognostic markers of disease progression and death. From a cohort of approx. 2.6 million citizens in Denmark, SARS-CoV-2 PCR tests were performed on subjects suspected for COVID-19 disease; 3944 cases had at least one positive test and were subjected to further analysis. SARS-CoV-2 positive cases from the United Kingdom Biobank was used for external validation. The ML models predicted the risk of death (Receiver Operation Characteristics-Area Under the Curve, ROC-AUC) of 0.906 at diagnosis, 0.818, at hospital admission and 0.721 at Intensive Care Unit (ICU) admission. Similar metrics were achieved for predicted risks of hospital and ICU admission and use of mechanical ventilation. Common risk factors, included age, body mass index and hypertension, although the top risk features shifted towards markers of shock and organ dysfunction in ICU patients. The external validation indicated fair predictive performance for mortality prediction, but suboptimal performance for predicting ICU admission. ML may be used to identify drivers of progression to more severe disease and for prognostication patients in patients with COVID-19. We provide access to an online risk calculator based on these findings.
Relative error’s quadratic dependence on the electric current and the methods for its compensation in fiber optic current sensor systems (2022)

We find that the relative error of a fiber optic current sensor (FOCS) increases quadratically with the electric current to be measured, causing unacceptable inaccuracy for direct current (DC) measurements beyond 100 kA. We prove analytically and confirm experimentally that such a nonlinear relative error escalation (REE) mainly originates from the residual linear birefringence of the spun fiber used in the FOCS. We propose and demonstrate that by first measuring residual linear birefringence, together with the circular birefringence of the spun fiber, the REE of the FOCS can be significantly reduced from -1.22% to -0.15% at 200 kA DC by a compensation scheme using the measured birefringences in the quadratic expression we derived. Further reduction of the REE to -0.02% at 200 kA DC can be obtained if the quadratic relation between the REE and the current under test is experimentally obtained. Our work points to a new direction for drastically improving the accuracy of FOCS at large currents and shall prove beneficial for scientists and engineers working in the field of current sensing.
Performance of Space Orthogonal Resource Transmit Diversity for Delay Spreads in PUCCH Using Cyclic Shift CDMA (2011)

This paper investigates the block error rate (BLER) performance of space orthogonal-resource transmit diversity (SORTD) against delay spreads for the physical uplink control channel (PUCCH) in the Long-Term Evolution (LTE) uplink using discrete Fourier transform (DFT)-precoded orthogonal frequency division multiple access (OFDMA). Channel estimation accuracy using a reference signal (RS) becomes a bottleneck to achieving a high diversity gain from SORTD under the highly channel-loaded conditions. This is because the inter-code interference due to frequency selectivity deteriorates the channel estimation accuracy particularly in a longer delay spread channel. Hence, we investigate the combined effect of SORTD and hybrid RS multiplexing using block spread (BS) and cyclic shift (CS) for a larger number of multiplexed PUCCHs such as K = 12. Computer simulation results show that SORTD particularly combined with hybrid RS multiplexing is effective in decreasing the required received signal-to-noise power ratio (SNR) that satisfies the target BLER for the PUCCH in the LTE uplink.
Oncogenic Role of miR-15a-3p in 13q Amplicon-Driven Colorectal Adenoma-to-Carcinoma Progression (2015)

Progression from colorectal adenoma to carcinoma is strongly associated with an accumulation of genomic alterations, including gain of chromosome 13. This gain affects the whole q arm and is present in 40%-60% of all colorectal cancers (CRCs). Several genes located at this amplicon are known to be overexpressed in carcinomas due to copy number dosage. A subset of these genes, including the mir-17~92 cluster, are functionally involved in CRC development. The present study set out to explore whether apart from mir-17~92, other miRNAs located at the 13q amplicon show a copy number dependent dosage effect that may contribute to 13q-driven colorectal adenoma-to-carcinoma progression. Integration of publically available miRNA expression, target mRNA expression and DNA copy number data from 125 CRCs yielded three miRNAs, miR-15a, -17, and -20a, of which high expression levels were significantly correlated with a 13q gain and which influenced target mRNA expression. These results could be confirmed by qRT-PCR in a series of 100 colon adenomas and carcinomas.Functional analysis of both mature miRNAs encoded by mir-15a, i.e. miR-15a-5p and miR-15a-3p, showed that silencing of miR-15a-3p significantly inhibited viability of CRC cells. Integration of miR-15a expression levels with mRNA expression data of predicted target genes identified mitochondrial uncoupling protein 2 (UCP2) and COP9 signalosome subunit 2 (COPS2) as candidates with significantly decreased expression in CRCs with 13q gain. Upon silencing of miR-15a-3p, mRNA expression of both genes increased in CRC cells, supporting miR-15a-3p mediated regulation of UPC2 and COPS2 expression. In conclusion, significant overexpression of miR-15a-3p due to gain of 13q is functionally relevant in CRC, with UCP2 and COPS2 as candidate target genes. Taken together our findings suggest that miR-15a-3p may contribute to adenoma-to-carcinoma progression.
MIST: Multiple Instance Spatial Transformer Networks (2018)

We propose a deep network that can be trained to tackle image reconstruction and classification problems that involve detection of multiple object instances, without any supervision regarding their whereabouts. The network learns to extract the most significant top-K patches, and feeds these patches to a task-specific network -- e.g., auto-encoder or classifier -- to solve a domain specific problem. The challenge in training such a network is the non-differentiable top-K selection process. To address this issue, we lift the training optimization problem by treating the result of top-K selection as a slack variable, resulting in a simple, yet effective, multi-stage training. Our method is able to learn to detect recurrent structures in the training dataset by learning to reconstruct images. It can also learn to localize structures when only knowledge on the occurrence of the object is provided, and in doing so it outperforms the state-of-the-art.
Water-induced lipid changes in oat processing (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTWater-induced lipid changes in oat processingKirsi H. Liukkonen, Ad. Montfoort, and Simo V. LaaksoCite this: J. Agric. Food Chem. 1992, 40, 1, 126–130Publication Date (Print):January 1, 1992Publication History Published online1 May 2002Published inissue 1 January 1992https://pubs.acs.org/doi/10.1021/jf00013a024https://doi.org/10.1021/jf00013a024research-articleACS PublicationsRequest reuse permissionsArticle Views301Altmetric-Citations30LEARN 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-Alertsclose Get e-Alerts
Three Third Generation Attacks on the Format Preserving Encryption Scheme FF3. (2021)

Format-Preserving Encryption (FPE) schemes accept plaintexts from any finite set of values (such as social security numbers or birth dates) and produce ciphertexts that belong to the same set. They are extremely useful in practice since they make it possible to encrypt existing databases or communication packets without changing their format. Due to industry demand, NIST had standardized in 2016 two such encryption schemes called FF1 and FF3. They immediately attracted considerable cryptanalytic attention with decreasing attack complexities. The best currently known attack on the Feistel construction FF3 has data and memory complexity of \({O}(N^{11/6})\) and time complexity of \({O}(N^{17/6})\), where the input belongs to a domain of size \(N \times N\).
Programmable Metamaterials & Metasurfaces for Ultra-Compact Multi-Functional Photonics (2019)

We demonstrate the design and experimental verification of several examples of programmable metamaterials and metasurfaces. Such devices offer the advantage of high-density integration and versatility.
Broadband optical studies of 1D and 3D photonic crystals (2005)

Supercontinuum based sources and measurement techniques are developed, enabling optical ultra-broadband studies of nano-scale photonic crystal devices and integrated photonic circuits over 1.2 - 2.0 micron wavelength range. Experiments involving 1-D periodic photonic crystal microcavity waveguides and 3-D periodic photonic crystals with embedded point defects are described. Experimental findings are compared with rigorous electromagnetic simulations.
Monitoring flap for buried free tissue transfer: its importance and reliability. (2002)

To improve the success rate of microsurgical flap transfers into a buried area, it is important to monitor the circulation of the flap during the early stage. A monitoring flap includes such advantages as simplicity, reliability, noninvasiveness, and the ability to continuously monitor the vascular status of various buried flaps. This article describes experiences related to the importance and reliability of a monitoring flap. A total of 109 flaps in 99 patients were treated with buried free flaps, including a monitoring flap, between 1990 and 1999. Forty-nine patients received a tubed free radial forearm flap with a skin-monitoring flap, and six received a free jejunal flap with a jejunal segment monitoring flap for the reconstruction of the esophagus. Vascularized fibular grafts with a skin monitoring flap or peroneus longus muscle monitoring flap were used for reconstructing the mandible in six patients and for treating osteonecrosis of the femoral head in 48 flaps in 38 patients. Monitoring flap abnormalities were indicated in 14 flaps; therefore, immediate revisions were performed on the pedicle of the monitoring flap and microanastomosis site. Among these 14 flaps, nine showed true thrombosis and five showed false-positive thrombosis. Among the nine flaps that showed true thrombosis, five were salvaged and four were finally lost. The false-positive thrombosis in the five flaps was attributed to torsion or tension of the perforator of the monitoring flap in three flaps, an unclear determination in one flap because the monitoring flap size was too small, and damage to the perforator in the last flap. The total thrombosis rate was 8.3 percent (nine of 109), and the failure rate of the free tissue transfer was 3.7 percent (four of 109). The overall sensitivity of the monitoring flap was 100 percent, the predictive value of a positive test was 64 percent (nine of 14), and false-positive results occurred in 36 percent (five of 14). The salvage rate was 55.6 percent. To improve the reliability of a monitoring flap, it is recommended that the size of the flap be larger than 1 x 2 cm to assess the arterial status, and that a perforator with the appropriate caliber be selected. When a monitoring flap is fixed to a previous incision line or a newly created wound, any torsion or tension of the perforator should be avoided. In conclusion, the current results suggest that a monitoring flap is a simple, extremely useful, and reliable method for assessing the vascular status of a buried free flap.
Condensation of Semiconductor Microcavity Exciton Polaritons (2002)

A phase transition from a classical thermal mixed state to a quantum-mechanical pure state of exciton polaritons is observed in a GaAs multiple quantum-well microcavity from the decrease of the second-order coherence function. Supporting evidence is obtained from the observation of a nonlinear threshold behavior in the pump-intensity dependence of the emission, a polariton-like dispersion relation above threshold, and a decrease of the relaxation time into the lower polariton state. The condensation of microcavity exciton polaritons is confirmed.
Scattered refractive index profiles of thin silicon oxide film on silicon substrate (1997)

Randomly scattered depth profiles of refractive index are experimentally observed on thin silicon dioxide films on silicon substrates by means of conventional ellipsometry and gradually chemical etching. Computer simulations with an abrupt model and random uncertainties in ellipsometric angles Ψ and Δ show very similar behavior as experiments, and the distribution of the measured profile in the near interface region is in good agreement with 0.02° standard deviation in Ψ. Simulations also indicate that even very small errors in Ψ, as small as 0.001°, can result in divergent depth profile of the refractive index in the near interface region.
Transalar encephalocele associated with Wegener granulomatosis and meningeal enhancement: case report. (2005)

Transalar encephaloceles are rare lesions that do not fit the standard classification of basal encephaloceles. Typically, these lesions present in adulthood, with nonspecific symptoms. We report here a case of a patient with Wegener disease in whom a large transalar encephalocele posterior to the sinus was noted when he was preoperative for left maxillary sinus surgery. The encephalocele demonstrated irregular peripheral enhancement along the margin--a very uncommon finding--as well as contrast enhancement of the basal meninges, which can be seen occasionally with Wegener granulomatosis.
BTLA, A T Cell Co-Inhibitory Receptor, Is A Potential Biomarker For Progressive Idiopathic Pulmonary Fibrosis (2012)

IPF has a heterogeneous course of disease in which some patients experience a slow or more stable course while others RATIONALE: experience rapid decline and early mortality. Currently we lack understanding of the mechanisms that underlie the pathogenesis responsible for the differences between stable IPF (S-IPF) and rapidly progressive IPF (RP-IPF). Previous studies examining whole genome expression arrays in PBMCs of IPF patients have demonstrated a signature that is predictive of progressive disease. The predominant pathways identified were altered gene expression in T cell activity and receptors. is to link these markers of The objective of our study progressive IPF to actual protein expression on peripheral lymphocytes, thereby determining potential mechanisms involved in disease progression. METHODS: We collected patient's peripheral blood mononuclear cells (PBMC) and classified patients as S-IPF or RP-IPF based on physiologic measures taken as part of their usual clinical care. We examined mRNA levels and cell surface protein expression by flow cytometry and correlated our findings with IPF severity, using the diffusing capacity of carbon monoxide (DLCO) as the physiological measurement. RESULTS: From our previous data sets, one of the T cell receptors with the highest alteration in gene expression patterns between S-IPF and RP-IPF was Band T-lymphocyte attenuator (BTLA), a surface co-inhibitory receptor on lymphocytes. A significant association was found between decreased BTLA mRNA levels and decreased predicted DLCO levels. Analysis of all samples demonstrated a significant and dramatically decreased BTLA surface expression on both peripheral CD4 and CD8 T cells, but not B cells, from RP-IPF patients compared to controls or S-IPF patients. CONCLUSION: Our data demonstrate that BTLA protein expression and mRNA levels are potential biomarkers and may have a predictive value for determining the patients most likely to rapidly progress. Decreased BTLA protein expression on peripheral blood T cells, may either be a cause of, or a result of, disease progression. Further, our data imply that the adaptive immune system, and T cells specifically, play a key role in the progression of IPF. Peripheral blood T cell biomarkers of rapid progression developed as a result of these efforts may be used in the development of personalized diagnostics. Furthermore, understanding these pathways may identify potential therapeutic targets and explain why the variability of disease course exists.
A design framework for real-time embedded systems with code size and energy constraints (2008)

Real-time embedded systems are typically constrained in terms of three system performance criteria: space, time, and energy. The performance requirements are directly translated into constraints imposed on the system's resources, such as code size, execution time, and energy consumption. These resource constraints often interact or even conflict with each other in a complex manner, making it difficult for a system developer to apply a well-defined design methodology in developing a real-time embedded system. Motivated by this observation, we propose a design framework that can flexibly balance the tradeoff involving the system's code size, execution time, and energy consumption. Given a system specification and an optimization criteria, the proposed technique generates a set of design parameters in such a way that a system cost function is minimized while the given resource constraints are satisfied. Specifically, the technique derives code generation decision for each task so that a specific version of code is selected among a number of different ones that have distinct characteristics in terms of code size and execution time. In addition, the design framework determines the voltage/frequency setting for a variable voltage processor whose supply voltage can be adjusted at runtime in order to minimize the energy consumption while execution performance is degraded accordingly. The proposed technique formulates this design process as a constrained optimization problem. We show that this optimization problem is NP-hard and then provide a heuristic solution to it. We show that these seemingly conflicting design goals can be pursued by using a simple optimization algorithm that works with a single optimization criteria. Moreover, the optimization is driven by an abstract system specification given by the system developer, so that the system development process can be automated. The results from our simulation show that the proposed algorithm finds a solution that is close to the optimal one with the average error smaller than 1.0%.