gebhart/patrepeval huggingface dataset:
Comparative Genome Analysis of Clostridium difficile Using DNA Microarrays (2010)

Clostridium difficile is a pathogen on the move, as evidenced by the rapid transcontinental spread of the so-called hypervirulent 027 strains, followed by the emergence of further PCR ribotypes such as 017, 078 and 106. This provides a rare opportunity to study the evolution of virulence in action. However, to fully exploit this opportunity, robust phylogenetic methods on a diverse set of characterised strains are required to provide a reference evolutionary framework to study C. difficile epidemiology, ecology and virulence. Traditional phylogenetic classification of bacteria to study evolutionary relatedness is based on the characterisation of a limited number of genes, rRNA or signature sequences. However, due to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast. By contrast, whole genome sequencing comparisons allow all genes to be compared. Nevertheless, whole-scale genome sequencing remains an expensive endeavour and such comparisons are limited to only a handful of strains. DNA microarrays represent an alternative technology for whole genome comparisons enabling a "birds eye view" of all the genes absent or present in a given genome as compared to the reference genome on the microarray.
Direct model-based tomographic reconstruction of the complex refractive index (2016)

X-ray propagation-based phase contrast tomography (XPCT) has become popular as a method for tomographically reconstructing the complex refractive index of a material from single distance measurements. XPCT has two major advantages over traditional X-ray computed tomography (CT): It can be used at higher cone-beam magnifications, and it typically produces higher contrast. However, current XPCT reconstruction algorithms are limited to near-field diffraction, which limits both their use and the quality of reconstructions. In this paper, we present a model-based iterative reconstruction (MBIR) algorithm called complex refractive index tomographic iterative reconstruction (CRITIR). CRITIR is based on a non-linear physics based model for X-ray propagation and a prior model for the complex refractive index of the object being imaged. Unlike conventional methods, CRITIR is designed to work within and beyond the near-field diffraction region. We use simulation to show that our algorithm accurately reconstructs the object while the conventional methods result in inaccurate reconstructions with blurry edges beyond the near-field region.
Degenerate four wave mixing in large mode area hybrid photonic crystal fibers (2013)

Spontaneous degenerate four wave mixing (FWM) is investigated in large mode area hybrid photonic crystal fibers, in which photonic bandgap guidance and index guidance is combined. Calculations show the parametric gain is maximum on the edge of a photonic bandgap, for a large range of pump wavelengths. The FWM products are observed on the edges of a transmission band experimentally, in good agreement with the numerical results. Thereby the bandedges can be used to control the spectral positions of FWM products through a proper fiber design. The parametric gain control combined with a large mode area fiber design potentially allows for power scaling of light at wavelengths not easily accessible with e.g. rare earth ions.
ChemInform Abstract: Enantioselective Total Synthesis of Didesepoxyrhizoxin. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Membrane interaction of TNF is not sufficient to trigger increase in membrane conductance in mammalian cells (1999)

Tumor necrosis factor TNF can trigger increases in membrane conductance of mammalian cells in a receptor-independent manner via its lectin-like domain. A lectin-deficient TNF mutant, lacking this activity, was able to bind to artificial liposomes in a pH-dependent manner, but not to insert into the bilayer, just like wild type TNF. A peptide mimicking the lectin-like domain, which can still trigger increases in membrane currents in cells, failed to interact with liposomes. Thus, the capacity of TNF to trigger increases in membrane conductance in mammalian cells does not correlate with its ability to interact with membranes, suggesting that the cytokine does not form channels itself, but rather interacts with endogenous ion channels or with plasma membrane proteins that are coupled to ion channels.
Genetic Disorders of Motor Neurons (1999)

Disorders of the motor neuron are etiologically and clinically heterogeneous and cause serious disability and death. Whereas mendelian inheritance can be demonstrated in a subset of these disorders, the genetic contribution to the sporadic forms of motor neuron degeneration are not well understood. In families with spinal muscular atrophy, Kennedy disease and amyotrophic lateral sclerosis, genetic linkage analysis and positional cloning have proven to be extremely productive. The genetics of these neurodegenerative disorders are reviewed.
Extreme-ultraviolet secondary electron blur at the 22-nm half pitch node (2011)

In this paper the Arrhenius behavior of blur upon extreme ultraviolet (EUV) exposure is investigated through variation of the post-exposure bake (PEB) temperature. In this way, thermally activated parameters that contribute to blur (such as acid/base diffusion) can be separated from nonthermally activated parameters (such as secondary electron blur). The experimental results are analyzed in detail using multiwavelength resist modeling based on the continuum approach and through fitting of the EUV data using stochastic resist models. The extracted blur kinetics display perfectly linear Arrhenius behavior, indicating that there is no sign for secondary electron blur at 22-nm half pitch. At the lowest PEB setting the total blur length is ∼4 nm, indicating that secondary electron blur should be well below that. The stochastic resist model gives a best fit to the current data set with parameters that result in a maximum probability of acid generation at 2.4 nm from the photon absorption site. Extrapolation of the model predicts that towards the 16-nm half pitch the impact on sizing dose is minimal and an acceptable exposure latitude is achievable. In order to limit the impact on linewidth roughness at these dimensions it will be required to control acid diffusion to ∼5 nm.
Progressive joint source-channel coding in feedback channels (1999)

It is well known that Shannon's separation result does not hold under finite computation or finite delay constraints, thus joint source-channel coding is of great interest for practical reasons. For progressive source-channel coding systems, efficient codes have been proposed for feedforward channels and the important problem of rate allocation between the source and channel codes has been solved. For memoryless channels with feedback, the rate allocation problem was studied by Chande et al. (1998). In this paper, we consider the case of fading channels with feedback. Feedback routes are provided in many existing standard wireless channels, making rate allocation with feedback a problem of considerable practical importance. We address the question of rate allocation between the source and channel codes in the forward channel, in the presence of feedback information and under a distortion cost function. We show that the presence of feedback shifts the optimal rate allocation point, resulting in higher rates for error-correcting codes and smaller overall distortion. Simulations on both memoryless and fading channels show that the presence of feedback allows up to 1 dB improvement in PSNR compared to the similarly optimized feedforward scheme.
Anisotropy of the Third Order Nonlinear Optical Susceptibility in a Degenerate Ground State Conjugated Polymer;Trans-(CH)x (1988)

Abstract The promise of conducting polymers as fast response nonlinear optical materials has been recently ernphaized1-3. Polymers such as polyacetylene, polythiophene and the soluble (and processible) poly(3alkylthienylenes) contain a high density of welectrons, and they are known to exhibit photoinduced absorption and photoinduced bleaching, indicating major shifts of oscillator strength upon photoexcitation2-4. For polyacetylene, these nonlinear effects have been studied in detail in the picosecond5a-b and subpicosecond5c time regime and correlated with the photoproduction of charge carriers through fast photoconductivity measuremenkm6. The data have demonstrated ul-tra-fast response with nonlinear shifts in oscillator strength occurring at times of the order of 10−13 seconds. These resonant nonlinear optical properties are intrinsic; they originate from the nonlinearity of the self-localized photoexcitations7 which characterize this class of polymers: solitons, polarons and bipolarons4.
Hematopoietic Stem-Cell Transplantation for Advanced SystemicMastocytosis (2014)

Purpose Advanced systemic mastocytosis (SM), a fatal
hematopoietic malignancy characterized by drug resistance, has
no standard therapy. The effectiveness of allogeneic
hematopoietic stem-cell transplantation (alloHCT) in SM remains
unknown. Patients and Methods In a global effort to define the
value of HCT in SM, 57 patients with the following subtypes of
SM were evaluated: SM associated with clonal hematologic
non–mast cell disorders (SM-AHNMD; n = 38), mast cell leukemia
(MCL; n = 12), and aggressive SM (ASM; n = 7). Median age of
patients was 46 years (range, 11 to 67 years). Donors were
HLA-identical (n = 34), unrelated (n = 17), umbilical cord
blood (n = 2), HLA-haploidentical (n = 1), or unknown (n = 3).
Thirty-six patients received myeloablative conditioning (MAC),
and 21 patients received reduced-intensity conditioning (RIC).
Results Responses in SM were observed in 40 patients (70%),
with complete remission in 16 patients (28%). Twelve patients
(21%) had stable disease, and five patients (9%) had primary
refractory disease. Overall survival (OS) at 3 years was 57%
for all patients, 74% for patients with SM-AHNMD, 43% for those
with ASM, and 17% for those with MCL. The strongest risk factor
for poor OS was MCL. Survival was also lower in patients
receiving RIC compared with MAC and in patients having
progression compared with patients having stable disease or
response. Conclusion AlloHCT was associated with long-term
survival in patients with advanced SM. Although alloHCT may be
considered as a viable and potentially curative therapeutic
option for advanced SM in the meantime, given that this is a
retrospective analysis with no control group, the definitive
role of alloHCT will need to be determined by a prospective
trial.
Transcriptome analysis reveals similarities between human blood CD3− CD56bright cells and mouse CD127+ innate lymphoid cells (2017)

For many years, human peripheral blood natural killer (NK) cells have been divided into functionally distinct CD3<sup>-</sup> CD56<sup>bright</sup> CD16<sup>-</sup> and CD3<sup>-</sup> CD56<sup>dim</sup> CD16<sup>+</sup> subsets. Recently, several groups of innate lymphoid cells (ILC), distinct from NK cells in development and function, have been defined in mouse. A signature of genes present in mouse ILC except NK cells, defined by Immunological Genome Project studies, is significantly over-represented in human CD56<sup>bright</sup> cells, by gene set enrichment analysis. Conversely, the signature genes of mouse NK cells are enriched in human CD56<sup>dim</sup> cells. Correlations are based upon large differences in expression of a few key genes. CD56<sup>bright</sup> cells show preferential expression of ILC-associated IL7R (CD127), TNFSF10 (TRAIL), KIT (CD117), IL2RA (CD25), CD27, CXCR3, DPP4 (CD26), GPR183, and MHC class II transcripts and proteins. This could indicate an ontological relationship between human CD56<sup>bright</sup> cells and mouse CD127<sup>+</sup> ILC, or conserved networks of transcriptional regulation. In line with the latter hypothesis, among transcription factors known to impact ILC or NK cell development, GATA3, TCF7 (TCF-1), AHR, SOX4, RUNX2, and ZEB1 transcript levels are higher in CD56<sup>bright</sup> cells, while IKZF3 (AIOLOS), TBX21 (T-bet), NFIL3 (E4BP4), ZEB2, PRDM1 (BLIMP1), and RORA mRNA levels are higher in CD56<sup>dim</sup> cells.
Tuning Optical Properties of Conjugated Molecules by Lewis Acids: Insights from Electronic Structure Modeling (2019)

Understanding and controlling the optoelectronic properties of organic semiconductors at the molecular level remains a challenge due to the complexity of chemical structures and intermolecular interactions. A common strategy to address this challenge is to utilize both experimental and computational approaches. In this contribution, we show that density functional theory (DFT) calculation is a useful tool to provide insights into the bonding, electron population distribution, and optical transitions of adducts between conjugated molecules and Lewis acids (CM-LA). Adduct formation leads to relevant modifications of key properties, including a red shift in optical transitions and an increase in charge carrier density and charge mobility, compared to the parent conjugated molecules. We show that electron density transfer from the CM to the LA, which was hypothesized to cause the experimental red shift in absorption spectra upon LA binding, can be quantified and interpreted by population analysis. Experimental red shifts in optical transitions for all molecular families can also be predicted by time-dependent DFT calculations with different density functionals. These detailed insights help to optimize a priori design guidelines for future applications.
Lysogeny of Streptococcus pneumoniae with MM1 Phage: Improved Adherence and Other Phenotypic Changes (2006)

Pneumococcal prophages are extremely frequent, but no role in pathogenesis has so far been attributed to them. We isolated a variant of phage MM1, named MM1-1998, from a serotype 24 strain of Streptococcus pneumoniae. We created three isogenic strain pairs (serotypes 3, 4, and 24) that differed only by the lysogenic presence of the MM1-1998 phage and did a phenotypic comparison. Lysogeny led to improved adherence to inert surfaces and pharyngeal cells compared to that with the cured variants of the strains. We found that lysogeny with MM1-1998 coincided with a more transparent phenotype and phage curing with more opaque colonies in all strain pairs, and we discovered that transparency was associated with more successful and stable lysogeny. Since transparency alone was possibly responsible for the adherence difference, we further compared the TIGR4 lysogen with an equally transparent variant of TIGR4 in order to reassess the role of phage or transparency separately. The results revealed that improved adherence was independently associated with lysogeny with the MM1-1998 phage. Other phenotypic differences such as faster growth, increased autolysis, and decreased intracellular hemolytic activity were more likely due to transparency. By improving the adherence of pneumococci, this prophage may contribute to their fitness and possibly to their persistence in humans.
Page Classification for Print Imaging Pipeline (2025)

Digital copiers and printers are widely used nowadays. One of the most important things people care about is copying or printing quality. In order to improve it, we previously came up with an SVM-based classification method to classify images with only text, only pictures or a mixture of both based on the fact that modern copiers and printers are equipped with processing pipelines designed specifically for different kinds of images. However, in some other applications, we need to distinguish more than three classes. In this paper, we develop a more advanced SVM-based classification method using four more new features to classify 5 types of images which are text, picture, mixed, receipt and highlight.
Reliability and stability of SiC power mosfets and next-generation SiC MOSFETs (2014)

In this paper, we present reliability and stability data based on a large body of data accumulated from high volume production of SiC power MOSFETs. The SiC MOSFETs (Gen2, C2M) showed excellent body diode and threshold voltage stability after 1000 hours of accelerated stressing tests. Results from next generation SiC power MOSFET development efforts are also presented. A significant reduction in specific on-resistance was demonstrated, and a wide range of blocking voltages, from 900 V to 15 kV, has also been demonstrated.
Interactive Multimedia Reporting Technical Considerations: HIMSS-SIIM Collaborative White Paper (2022)

Despite technological advances in the analysis of digital images for medical consultations, many health information systems lack the ability to correlate textual descriptions of image findings linked to the actual images. Images and reports often reside in separate silos in the medical record throughout the process of image viewing, report authoring, and report consumption. Forward-thinking centers and early adopters have created interactive reports with multimedia elements and embedded hyperlinks in reports that connect the narrative text with the related source images and measurements. Most of these solutions rely on proprietary single-vendor systems for viewing and reporting in the absence of any encompassing industry standards to facilitate interoperability with the electronic health record (EHR) and other systems. International standards have enabled the digitization of image acquisition, storage, viewing, and structured reporting. These provide the foundation to discuss enhanced reporting. Lessons learned in the digital transformation of radiology and pathology can serve as a basis for interactive multimedia reporting (IMR) across image-centric medical specialties. This paper describes the standard-based infrastructure and communications to fulfill recently defined clinical requirements through a consensus from an international workgroup of multidisciplinary medical specialists, informaticists, and industry participants. These efforts have led toward the development of an Integrating the Healthcare Enterprise (IHE) profile that will serve as a foundation for interoperable interactive multimedia reporting.
Improving Dynamic Performance of Low-Inertia Systems through\n Eigensensitivity Optimization (2020)

An increasing penetration of renewable generation has led to reduced levels\nof rotational inertia and damping in the system. The consequences are higher\nvulnerability to disturbances and deterioration of the dynamic response of the\nsystem. To overcome these challenges, novel converter control schemes that\nprovide virtual inertia and damping have been introduced, which raises the\nquestion of optimal distribution of such devices throughout the network. This\npaper presents a framework for performance-based allocation of virtual inertia\nand damping to the converter-interfaced generators in a low-inertia system.\nThis is achieved through an iterative, eigensensitivity-based optimization\nalgorithm that determines the optimal controller gains. Two conceptually\ndifferent problem formulations are presented and validated on a 3-area, 12-bus\ntest system.\n
Front Matter: Volume 9303 (2015)

This PDF file contains the front matter associated with SPIE Proceedings Volume 9303, including the Title Page, Copyright information, Table of Contents, Invited Panel Discussion, and Conference Committee listing.
Design of fully spatially coherent extreme-ultraviolet light sources (2004)

We demonstrate experimentally that, in order to generate fully spatially coherent extreme-ultraviolet (EUV) beams using high-harmonic generation, it is necessary to guide the driving laser beam over long interaction lengths in gas-filled hollow waveguides. Numerical simulations show that, in propagating the laser through a long plasma-filled guide, the laser beam forms a stable eigenmode with uniform spatial phase, even at very high levels of ionization. This results in a compact, highly spatially coherent, EUV source useful for applications in EUV metrology, microscopy, interferometry, and holography.
Artificial Connection Between Glucose Sensing and Insulin Delivery: Implications of Peritoneal Administration (1992)

The replacement of insulinogenic function in insulin-dependent diabetes has to restore the feedback between intracorporal glucose and insulin. This has been accomplished by the following approaches: (a) the so-called open-loop insulin treatment by means of injections or pumps, employing laboratory or other extracorporal analytical devices and closing the feedback at large intervals only; (b) transplantation of insulin producing tissue and the bioartificial pancreas, employing the natural beta-cell both for glucose sensing and insulin delivery; (c) implanted artificial drug delivery systems providing chemical feedback between intracorporal glucose and insulin release from a nonrefillable reservoir of limited capacity; (d) the intracorporal or paracorporal artificial beta-cell comprising a glucose sensor (electrochemical or other type) that permanently delivers the signal to the computer-controlled insulin pump. This artificial device works on the basis of an algorithm of glucose-dependent insulin provision, compensating for the lack of other regulators, for the site of insulin administration, which is usually posthepatic, and for the kinetic properties of sensing system, e.g., a subcutaneous inserted amperometric electrode. Present experimental studies show that the pharmacodynamics of peritoneally applied insulin may be implemented into a mathematical model of the overall glucose-insulin system. They include absorption nearly as fast as after intravenous application, predominant portal inflow and approximately 30% hepatic removal. Feedback-controlled peritoneal insulin administration by means of an artificial beta-cell working on peripheral-venous blood glucose monitoring results in normal glycemic profiles under basal conditions and during oral glucose loads, if the pharmacodynamic properties of the peritoneal route are implemented into the insulin dosage algorithm.
A Self-Assembling NHC-Pd-Loaded Calixarene as a Potent Catalyst for the Suzuki-Miyaura Cross-Coupling Reaction in Water (2020)

Nanoformulated calix[8]arenes functionalized with <i>N</i>-heterocyclic carbene (NHC)-palladium complexes were found to be efficient nano-reactors for Suzuki-Miyaura cross-coupling reactions of water soluble iodo- and bromoaryl compounds with cyclic triol arylborates at low temperature in water without any organic co-solvent. Combined with an improved one-step synthesis of triol arylborates from boronic acid, this remarkably efficient new tool provided a variety of 4'-arylated phenylalanines and tyrosines in good yields at low catalyst loading with a wide functional group tolerance.
ChemInform Abstract: SYNTHESIS AND BIOLOGICAL ACTIVITY OF POSITION 1 ANALOGS OF LH‐RH (1977)

Abstract Durch automatisierte Synthese an fester Phase wurden 6 LH‐RH‐Hormone mit einem in Position 1 geänderten Rest hergestellt: (Formyl‐sarcosin?‐LH‐RH, (Acetyl‐sarcosin?‐LH‐RH, (2‐Pyrrolidon‐4‐carbonsäure) 1 ‐LH‐RH, (N‐Methyl‐2‐pyrrolidon‐4‐carbonsäure) 1‐ LH‐RH, Hydroxyprolinl‐LH‐RH und (Cyclopentancarbonsäure?‐LH‐RH.