gebhart/patrepeval huggingface dataset:
Switching in amorphous-silicon devices (1994)

The phenomena of nonvolatile switching in amorphous-hydrogenated-silicon thin-film devices are explained by a theory based on the presence of charged inclusions in the film, having originated from the initial forming treatments. The inclusions almost penetrate the film, and are able to move under applied fields of sufficient magnitude, and in a direction determined by the applied polarity. The differences between analog and digital switching are ascribed to differences in the homogeneity of the inclusions, being affected by the nature of the top contact.
Necessary and Sufficient Conditions for Dynamical Structure Reconstruction of LTI Networks (2008)

This paper formulates and solves the network reconstruction problem for linear time-invariant systems. The problem is motivated from a variety of disciplines, but it has recently received considerable attention from the systems biology community in the study of chemical reaction networks. Here, we demonstrate that even when a transfer function can be identified perfectly from input-output data, not even Boolean reconstruction is possible, in general, without more information about the system. We then completely characterize this additional information that is essential for dynamical reconstruction without appeal to ad-hoc assumptions about the network, such as sparsity or minimality.
Hypermutation of hepatitis B virus genomes by APOBEC3G, APOBEC3C and APOBEC3H (2008)

Hepatitis B virus (HBV) is a DNA virus that causes liver disease and replicates by reverse transcription of an RNA template. Previous studies have reported that HBV genomes bearing G-->A hypermutation are present at low frequency in human serum. These mutations are most likely due to the activity of apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like (APOBEC) cytosine deaminases, cellular proteins known to confer innate immunity against retroviruses by generating lethal hypermutations in viral genomes. This study assessed APOBEC3G, APOBEC3C and APOBEC3H, three members of this protein family present in human liver, for their ability to edit HBV genomes. Transfection of human HepG2 hepatoma cells with a plasmid encoding the APOBEC3C protein resulted in abundant G-->A mutations in the majority of newly formed HBV genomes. By contrast, transfection of APOBEC3G- and APOBEC3H-encoding plasmids only marginally increased hypermutation rates above the level caused by the cytosine deaminases naturally present in HepG2 cells. APOBEC3G- and APOBEC3H-mediated hypermutation, however, was clearly revealed by transfection of chicken LMH hepatoma cells, which lack endogenous cytosine deaminases. These results indicate that APOBEC3G, APOBEC3C and APOBEC3H have the ability to edit HBV DNA and that each protein is likely to contribute to various degrees to the generation of modified genomes in human liver cells.
Correlation of particles size with mixed current (im) in electroless deposition of nano silver metal onto polyurethane catheter surface (2019)

Electroless deposition of nano-size silver metal onto polyurethane (PU) catheter is investigated. Grain size of the deposit is regulated by monitoring mixed potential, Em that indicates the deposition mechanism and mixed current, im which determines the deposition rate. It is demonstrated that these two parameters can be regulated through [Ag+] and/or [N2H4]. At relatively higher [Ag+] rate is under anodic control, whereas, at a lower [Ag+], diffusion of Ag+ controls the process (cathodic control). Lower the value of im, lower is the size of deposit, achieved under cathodic diffusion control mechanism. Size of the deposit lowers further by reducing deposition time. Silver particles of 48 nm are achieved within 5 min of deposition time at 0.1 M [N2H4] and 0.0001 M [AgNO3]. Average crystallite size measured from the XRD is around 13 nm and there are uniformly spread agglomerated spherical particles with some distributed cubic ones observed in the SEM.
Can prebiotics and probiotics improve therapeutic outcomes for undernourished individuals? (2013)

It has become clear in recent years that the human intestinal microbiota plays an important role in maintaining health and thus is an attractive target for clinical interventions. Scientists and clinicians have become increasingly interested in assessing the ability of probiotics and prebiotics to enhance the nutritional status of malnourished children, pregnant women, the elderly, and individuals with non-communicable disease-associated malnutrition. A workshop was held by the International Scientific Association for Probiotics and Prebiotics (ISAPP), drawing on the knowledge of experts from industry, medicine, and academia, with the objective to assess the status of our understanding of the link between the microbiome and under-nutrition, specifically in relation to probiotic and prebiotic treatments for under-nourished individuals. These discussions led to four recommendations: (1) The categories of malnourished individuals need to be differentiated To improve treatment outcomes, subjects should first be categorized based on the cause of malnutrition, additional health-concerns, differences in the gut microbiota, and sociological considerations. (2) Define a baseline "healthy" gut microbiota for each category Altered nutrient requirement (for example, in pregnancy and old age) and individual variation may change what constitutes a healthy gut microbiota for the individual. (3) Perform studies using model systems to test the effectiveness of potential probiotics and prebiotics against these specific categories These should illustrate how certain microbiota profiles can be altered, as members of different categories may respond differently to the same treatment. (4) Perform robust well-designed human studies with probiotics and/or prebiotics, with appropriate, defined primary outcomes and sample size These are critical to show efficacy and understand responder and non-responder outcomes. It is hoped that these recommendations will lead to new approaches that combat malnutrition. This report is the result of discussion during an expert workshop titled "How do the microbiota and probiotics and/or prebiotics influence poor nutritional status?" held during the 10th Meeting of the International Scientific Association for Probiotics and Prebiotics (ISAPP) in Cork, Ireland from October 1-3, 2012. The complete list of workshop attendees is shown in Table 1.
Benefits and limitations of immersion lithography (2004)

Liquid immersion has been used for more than 100 years to increase the numeric aperture (NA) and resolution in optical microscopy. We explore the benefits and limitations of immersion technology in lithography. Immersion optical lithography has the potential to extend the resolution below 40 nm. The theory of immersion is decribed. Simulations show that a 193-nm immersion system at NA = 0.95 can double the depth of focus as compared to a dry system. Also, an immersion 193-nm system at NA = 1.05 has slightly more depth of focus than a 157-nm dry system at NA = 0.85. However, the exposure latitude at 193 nm is decreased due to the impact of polarization in imaging. Design schemes are presented to realize an immersion step and scan system. Two configuration approaches are proposed and explored. A localized shower type solution may be preferred over a bath type solution, because the impact on the step and scan platform design is significantly less. However, scanning over the wafer edge becomes the main design challenge with a shower solution. Studies are presented that look at the interaction of immersion fluids with the lens and the photoresist. Water seems to be a likely candidate, as it does not impact productivity of the step and scan system; however, focus and aberration levels need to be carefully controlled. For 157 nm, per-fluor-polyether (PFPE) materials are currently being studied, but their characteristics may limit the productivity of the exposure system. Further research on fluid candidates for 157-nm immersion is required.
Towards Conceptualizing Information Transparency and its Role in Internet Consumers' Concerns: A Literature Review (2014)

In recent years, calls for a safer online shopping environment are growing louder. Empirical studies on consumers’ expectations of ethical e-commerce practices have found that the top concerns among e-shoppers revolved around security of transactions, privacy protection of personal data, deception and reliability issues. Consumer generally desire richer and truthful information to make purchase decisions. By addressing the information needs of consumers, transparency presents itself as a promising concept for firms to leverage towards strategizing its role in ethical practices. This paper revisits the consumer-perceived ethical issues in e-commerce literature, presents the disclosure paradox faced by e-seller firms, reviews the various conceptualizations of transparency in multidisciplinary literature and suggests extending the transparency strategy to map to consumers’ informational needs and concerns.
Awakening from the Twentieth Century (1996)

Benjamin was concerned with how public space, the city of Berlin, had entered into his unconscious and, for all his protected, bourgeois upbringing, held sway over his imagination. . . . He wrote: ' As Proust begins his life story with awakening, so must every work of history begin with awakening ; indeed , it actually must be concerned with nothing else. This work is concerned with awakening from
Theory of ferromagnetic resonance driven by the combined action of spin-transfer torque and voltage-controlled magnetic anisotropy (2017)

An analytical study of the spectral line shape of ferromagnetic resonance (FMR) detected by spin rectification effect and driven by the combined action of spin-transfer torque (STT) and voltage-controlled magnetic anisotropy (VCMA) is developed. The system under consideration consists of a magnetic tunnel junction (MTJ). Explicit expressions for the symmetric and asymmetric components of the rectified voltage are derived, where the role of the VCMA, in-plane STT, and field-like torque is clearly identified and discussed. Typical geometrical configurations are particularly analyzed and compared with recent experimental results. The analytical findings show that the change of sign in the FMR response upon reversal of the magnetization is completely due to VCMA. By distinguishing in-plane, out-of-plane, and full magnetization reversal processes, it is shown that the VCMA induces a change of sign in the symmetric part for the in-plane and out-of-plane magnetization reversal, while the asymmetric part change its sign under a full and in-plane reversion of the magnetization. Explicit expressions of the symmetric and asymmetric contributions of the spectral line shape allow us to detect under what conditions the STT and VCMA can increase or decrease the FMR spectral line shape. The proposed theory allows access to a better understanding of the physics behind ferromagnetic resonance phenomena, promoting potential applications in STT+VCMA-based MTJs.
Design of Constant Force Compliant Mechanisms (2014)

Abstract—Compliant mechanisms realize mechanism functions by utilizing the elastic deformations of flexible components rather than the relative motions of rigid joints. The advantages of compliant mechanisms stem from the removal or replacement of rigid joints, which include the elimination of backlash, friction, wear and lubrication, the reduction of vibration and noise, the decreased manufacturing and assembly cost, and the increased precision. Because of the integrated motion and force behavior and the nonlinearities of large deformations, designing compliant mechanisms is much more challenging than rigid mechanisms. Constant force compliant mechanisms produce an output force that does not change for a large range of input motion and have many different applications. A method is introduced in this paper for designing constant force compliant mechanisms. A designed constant force compliant mechanism is modelled as a network of variable width spline curves which are defined by their interpolation circles. The design of constant force compliant mechanisms is systematized as optimizing the independent parameters of the variable width spline curves. The presented method is demonstrated by the design of a constant force compliant mechanism in the paper. Keywords—compliant mechanism; constant force; design; spline interpolation; interpolation circle. I.
Kallistatin Modulates Immune Cells and Confers Anti-Inflammatory Response To Protect Mice from Group A Streptococcal Infection (2013)

Group A streptococcus (GAS) infection may cause severe life-threatening diseases, including necrotizing fasciitis and streptococcal toxic shock syndrome. Despite the availability of effective antimicrobial agents, there has been a worldwide increase in the incidence of invasive GAS infection. Kallistatin (KS), originally found to be a tissue kallikrein-binding protein, has recently been shown to possess anti-inflammatory properties. However, its efficacy in microbial infection has not been explored. In this study, we transiently expressed the human KS gene by hydrodynamic injection and investigated its anti-inflammatory and protective effects in mice via air pouch inoculation of GAS. The results showed that KS significantly increased the survival rate of GAS-infected mice. KS treatment reduced local skin damage and bacterial counts compared with those in mice infected with GAS and treated with a control plasmid or saline. While there was a decrease in immune cell infiltration of the local infection site, cell viability and antimicrobial factors such as reactive oxygen species actually increased after KS treatment. The efficiency of intracellular bacterial killing in neutrophils was directly enhanced by KS administration. Several inflammatory cytokines, including tumor necrosis factor alpha, interleukin 1β, and interleukin 6, in local infection sites were reduced by KS. In addition, KS treatment reduced vessel leakage, bacteremia, and liver damage after local infection. Therefore, our study demonstrates that KS provides protection in GAS-infected mice by enhancing bacterial clearance, as well as reducing inflammatory responses and organ damage.
A real-time performance measurement system for arterial traffic signals (2008)

University of Minnesota Ph.D. dissertation. September 2008. Major: Civil Engineering. Advisor: Henry X. Liu. 1 computer file (PDF); xix, 154 pages.
Enhanced performance of 450 nm GaN laser diodes with an optical feedback for high bit-rate visible light communication (2018)

First report on significant performance improvement of 450 nm blue edge-emitting laser in terms of optical linewidth (~6.5 times), modulation bandwidth (~16%) and SMSR (~7.4 times) by employing self-injection locking scheme.
Collateral sensitivity of human melanoma multidrug-resistant variants to the polyamine analogue, N1,N11-diethylnorspermine. (1994)

Certain N-alkylated analogues of the natural polyamine spermine, such as N1,N11-diethylnorspermine (DENSPM), rapidly deplete intracellular polyamine pools by down-regulating the biosynthetic enzymes, ornithine decarboxylase and S-adenosylmethionine decarboxylase, and by potently up-regulating the polyamine catabolizing enzyme, spermidine/spermine N1-acetyltransferase. On the basis of previously reported antitumor activity in human tumor xenograft model systems, DENSPM is currently undergoing Phase I clinical trials against human melanoma and other solid tumors. The antiproliferative activity of this analogue against the multidrug resistance (MDR) phenotype was examined in three MDR sublines of human melanoma RPMI-7932 cells, which were shown to be 2-to 10-fold resistant to classical MDR agents. These MDR lines had been separately derived using different selecting agents (Lemontt et al., Cancer Res., 48: 6344-6353, 1988). Subline functional resistance due to P-glycoprotein was confirmed by decreased retention of rhodamine 123 relative to parent cells as detected by flow cytometry. Although the three sublines were 2- to 10-fold less sensitive than the parent line to classical MDR-type agents, they were found in dose-response studies to be significantly more sensitive to DENSPM than the parent line. In addition, they showed a distinct cytotoxic response after a 48-h treatment with 10 microM DENSPM, which was not apparent in the parent line. Growth sensitivity of the sublines to the ornithine decarboxylase inhibitor, alpha-difluoromethylornithine, or the S-adenosylmethionine decarboxylase inhibitor, CGP-48664, was found to be similar to parent cells. The ratio of the key biosynthetic enzyme activities for ornithine decarboxylase and S-adenosylmethionine decarboxylase was found to be 3.5- to 5-fold higher in all three sublines, due mainly to increases in the former enzyme. This imbalance produced unusually high putrescine pools. Although DENSPM down-regulation of decarboxylase activities and potent up-regulation of spermidine/spermine N1-acetyltransferase activity occurred similarly in both parent and variant lines, polyamine depletion was greater in the variant lines. Collateral sensitivity of the MDR sublines to DENSPM is partially attributable to the finding that analogue (and spermidine) uptake in the sublines was about 2-fold higher (after 2 h) than in the parent cells. The presence of disturbances in polyamine homeostasis and increased sensitivity to DENSPM in three independently selected cell line variants suggests that they may be generally associated with the MDR phenotype in human melanoma and possibly other tumor cells. The collateral sensitivity of human melanoma MDR variants to DENSPM represents a possible therapeutic indication which should be considered during the ongoing clinical evaluation of this drug.
Tyrosinemia: the Quebec experience. (1996)

Tyrosinemia, a genetic disorder of the liver and kidneys, is caused by reduced activity of fumarylacetoacetate hydrolase (FAH), the final enzyme in the degradation of tyrosine. The consequent presence of succinylacetone in urine or blood is pathognomonic of tyrosinemia and is used as a confirmatory test in the Quebec neonaral screening program. Due to a complex founder effect, the province of Quebec has an unusually high prevalence of tyrosinemia, particularly in the Saguenay-Lac Saint-Jean region (where the prevalence is 1 in 1850). Tyrosinemia has several different clinical presentations, ranging from acute liver failure with severe coagulopathy early in life, to slowly progressing cirrhosis with multiple nodules and variable renal dysfunction, to normal liver function with renal failure. Hepatocarcinoma has been found in approximately one third of cases. FAH complementary DNA has been cloned and mapped to chromosome 15q23-q25. The mutation observed in Quebec is a splice mutation at intron 12. This mutation is common and has been observed in other areas of the world as well, although more than 20 mutations causing tyrosinemia have now been described. Liver transplantation remains the definitive treatment. The author's team has carried out 28 liver transplantations (including 2 combined liver-kidney transplantations) in 25 children. The overall survival rate has been 92%; two children died as a result of primary nonfunction. The primary indications for transplantation were hepatic nodules (in 14 cases), neurological crises (6) and hepatic (3) or renal failure (2). An abnormal glomerular filtration rate (GFR) of less than 80 mL/min per 1.73 m2 was documented before transplantation in 54% of the cases. The rate normalized after liver transplantation in most patients, with rapid improvement in tubular function. However, patients with a severely low rate (less than 55 mL/min per 1.73 m2) before transplantation still had borderline renal function and poor growth after the transplantion, despite normal liver function. Therefore, for children with a consistently low GFR, careful consideration should be given to performing a combined liver-kidney transplantation, and a renal biopsy should form part of the pretransplantation evaluation.
ChemInform Abstract: THE STRUCTURE OF BENULIN, A NEW PENTACYCLIC TRITERPENE HEMIKETAL ISOLATED FROM BURSERA ARIDA (BURSERACEAE) (1977)

Abstract Die Struktur von Benulin wird zu (I) aufgeklärt.
A Novel Approach of Lung Tumor Segmentation Using a 3D Deep Convolutional Neural Network (2021)

Cancer is one of the most life-threatening diseases in the world, and lung cancer is the leading cause of death worldwide. If not detected at an early stage, the survival rate of lung cancer patients can be very low. To treat patients in later stages, one needs to analyze the tumour region. For accurate diagnosis of lung cancer, the first step is to detect and segment the tumor. In this chapter, an approach for segmentation of a lung tumour is presented. For pre-processing of lung CT images, simple image processing like morphological operations is used, and for tumour segmentation task, a 3D convolutional neural network (CNN) is used. The CNN architecture consists of a 3D encoder block followed by 3D decoder block just like U-Net but with deformable convolution blocks. For this study, two datasets have been used; one is the online-available NSCLC Radiomics dataset, and the other is collected from an Indian local hospital. The approach proposed in this chapter is evaluated in terms of dice coefficient. This approach is able to give significant results with a dice coefficient of 77.23%.
Construction of cohorts of similar patients from automatic extraction of medical concepts (2022)

Abstract Objective: We aimed to provide an automated end-to-end extraction of cohorts of similar patients from electronic health records for systemic diseases. Materials and Methods: Our multistep algorithm includes a named-entity recognition step, a multilabel classification using Medical Subject Headings ontology and the computation of patient similarity. A selection of cohorts of similar patients on a priori annotated phenotypes was performed. Six phenotypes were selected for their clinical significance: P1-osteoporosis, P2-nephritis in systemic erythematosus lupus, P3-interstitial lung disease in systemic sclerosis, P4-lung infection, P5-obstetric antiphospholipid syndrome, and P6-Takayasu stroke. We used a training set of 151 clinical notes and an independent validation set of 256 clinical notes, with annotated phenotypes, both extracted from the Assistance Publique-Hôpitaux de Paris data warehouse. We evaluated the precision of the 3 patients closest to the index patient for each phenotype with the precision-at-3, and the recall and average precision. Results: For P1-P4, the precision-at-3 ranged from 0.85 to 0.99, the recall ranged from 0.53 to 0.83, and the average precision ranged from 0.58 to 0.88, respectively. P5-P6 phenotypes could not be analysed due to a limited number of phenotypes. Conclusion: Using a method close to clinical reasoning, we built a scalable and interpretable end-to-end algorithm to extract cohorts of similar patients.
Facial biometrics for 2D barcodes (2012)

This paper proposes a novel use of 2D barcodes to store biometric data, in particular for facial recognition, which represents one of the least invasive biometric techniques. To accomplish this, we deploy 2D color barcodes, which allow larger storage capabilities than traditional 2D barcodes. To improve the quality of facial recognition, we combine local feature descriptors, such as SURF descriptors, together with shape landmarks identified through statistical models for discriminating faces. The biometric information can be secured through digital signature algorithms, in order to protect biometric data from malicious tampering. The use of color barcodes is crucial in this setting, as traditional barcodes cannot store a suitable number of SURF descriptors for discriminating faces and cannot even afford to store an additional cryptographic payload. We report the results of an experimental evaluation of our system on real-world data sets (i.e., a face database).