gebhart/patrepeval huggingface dataset:
Low-Energy Electron Diffractive Imaging Based on a Single-Atom Electron Source (2015)

Imaging of the atomic structures of two-dimensional materials and organic materials is a challenge for current electron microscopes because of low imaging contrast and high radiation damage for highenergy electrons. It has been a general trend to develop electron microscopy of lower energies. Thanks to the progress in aberration-correction techniques, transmission electron microscopes with voltages down to 15-40 kV have recently been demonstrated. However, it becomes very difficult to achieve atomic resolution when the electron energy is reduced below 10 keV. An alternative approach is phase retrieval imaging, which requires a sufficiently coherent source, detection of high-angle diffracted patterns with a sufficient resolution, and a sufficiently small detection area on the sample. There is no need to fabricate high-quality lenses with a large numerical aperture. In this work, we propose several experimental schemes of low-energy electron coherent diffractive imaging (CDI). A great advantage of low energy electrons over high-energy electrons and x-ray is that the cross-sections of interaction with the atomic potentials are very large, so that the diffraction pattern has good signal-to-noise ratios even at high scattering angles and thus high-resolution images can be reconstructed.
Chemoselective Isomerization of Secondary-Type Propargylic Alcohols to Propargylic/Allenic Bromides, and Brominated Dienes with Appel-Type Reaction Conditions (2009)

Herein is described the chemoselective isomerization of secondary-type propargylic alcohols to allenic bromides, propargylic bromides and brominated dienes under Appel-type reaction conditions containing Ph3P, CBr4 and additives.
Infrared Spectroscopy, a Tool for Probing Bacterial Peptidoglycan (1982)

Infrared spectroscopic measurements are used to obtain insights into the three-dimensional architecture of peptidoglycan (murein), the rigid component of almost all bacterial cell walls. The infrared spectra of various types of peptidoglycans (including all chemotypes and examples of the so called A and B groups) were compared to each other and to those obtained from crystalline chitin. All peptidoglycans investigated exhibited very similar infrared spectra. In particular the conformationally sensitive amide A, I and II absorption bands were found to be constantly centered around 3300 cm-1, 1657 cm-1 and 1534 cm-1 respectively; furthermore, the spectral region between 1200 cm-1 and 800 cm-1, characterized by several strong absorption bands connected to complex sugar ring modes, proved to be remarkably uniform. Additionally the infrared spectra remained significantly constant between -175 degrees C and + 75 degrees C and turned out to be rather independent of sample preparation (solvent replacement, freeze-drying and film producing). An analysis of band half-widths revealed no high crystalline state of order of peptidoglycan. On the basis of band positions and half-widths of amide bands, regular conformations like alpha helices of beta pleated sheets could be excluded. Several distinctive, fingerprint-like spectral features of the various murein samples permitted a facile identification of individual peptidoglycans. Moreover, infrared spectroscopy seems to be very promising as an analytical tool, e.g. for tracing variations of cell wall structure, detecting conformational changes and estimating crosslinking indices in a quick and simple way. The comparative analysis of amide band positions and band half-widths yielded substantial differences between infrared spectra of chitin and murein, thus rejecting previous models based on the assumption of a nearly crystalline chitin-like structure of the glycan chains of murein.
Fringing Field Effect of the Liquid-Crystal-on-Silicon Devices (2002)

The fringing field has an important effect on the contrast ratio of liquid-crystal-on-silicon (LCOS) display devices. Computer simulation results of five commonly employed LC operating modes are compared: mixed-mode twisted nematic (MTN) cell, 45 twisted nematic cell, vertical alignment (VA) cell, film-compensated homogeneous cell, and fringe-field switching cell. The slope of the pixel electrodes is found to make an important contribution to the brightness and contrast ratio of each mode. Simulation results indicate that the VA mode has the best contrast ratio when all the pixels are on and off. However, the MTN cell shows the smallest fringing field effect when alternating pixels are switched on and off.
Odor Recognition in Multiple E-Nose Systems With Cross-Domain Discriminative Subspace Learning (2017)

In this paper, we propose an odor recognition framework for multiple electronic noses (E-noses), machine olfaction odor perception systems. Straight to the point, the proposed transferring odor recognition model is called cross-domain discriminative subspace learning (CDSL). General odor recognition problems with E-nose are single domain oriented, that is, recognition algorithms are often modeled and tested on the same one domain data set (i.e., from only one E-nose system). Different from that, we focus on a more realistic scenario: the recognition model is trained on a prepared source domain data set from a master E-nose system A, but tested on another target domain data set from a slave system B or C with the same type of the master system A. The internal device parameter variance between master and slave systems often results in data distribution discrepancy between source domain and target domain, such that single-domain-based odor recognition model may not be adapted to another domain. Therefore, we propose domain-adaptation-based odor recognition for addressing the realistic recognition scenario across systems. Specifically, the proposed CDSL method consists of three merits: 1) an intraclass scatter minimizationand an interclass scatter maximization-based discriminative subspace learning is solved on source domain; 2) a data fidelity and preservation constraint of the subspace is imposed on target domain without distortion; and 3) a minipatch feature weighted domain distance is minimized for closely connecting the source and target domains. Experiments and comparisons on odor recognition tasks in multiple E-noses demonstrate the efficiency of the proposed method.
Binary optimization by momentum annealing (2019)

One of the vital roles of computing is to solve large-scale combinatorial optimization problems in a short time. In recent years, methods have been proposed that map optimization problems to ones of searching for the ground state of an Ising model by using a stochastic process. Simulated annealing (SA) is a representative algorithm. However, it is inherently difficult to perform a parallel search. Here we propose an algorithm called momentum annealing (MA), which, unlike SA, updates all spins of fully connected Ising models simultaneously and can be implemented on GPUs that are widely used for scientific computing. MA running in parallel on GPUs is 250 times faster than SA running on a modern CPU at solving problems involving 100 000 spin Ising models.
The Deleterious Consequences of Right Ventricular Apical Pacing: Time to Seek Alternate Site Pacing (2006)

Not only is spontaneous permanent LBBB harmful to our patients, but the iatrogenic variety produced by right ventricular apical pacing during conventional permanent pacing may also be deleterious to some patients. The compelling evidence presented herein cannot be ignored; it may dictate a change of attitude toward right ventricular apical pacing directing our attention to alternate sites of ventricular pacing and avoidance of the right ventricular apex.
Exploiting dynamic timing slack for energy efficiency in ultra-low-power embedded systems (2016)

Many emerging applications such as the internet of things, wearables, and sensor networks have ultra-low-power requirements. At the same time, cost and programmability considerations dictate that many of these applications will be powered by general purpose embedded microprocessors and microcontrollers, not ASICs. In this paper, we exploit a new opportunity for improving energy efficiency in ultra-low-power processors expected to drive these applications -- dynamic timing slack. Dynamic timing slack exists when an embedded software application executed on a processor does not exercise the processor's static critical paths. In such scenarios, the longest path exercised by the application has additional timing slack which can be exploited for power savings at no performance cost by scaling down the processor's voltage at the same frequency until the longest exercised paths just meet timing constraints. Paths that cannot be exercised by an application can safely be allowed to violate timing constraints. We show that dynamic timing slack exists for many ultra-low-power applications and that exploiting dynamic timing slack can result in significant power savings for many ultra-low-power processors. We also present an automated methodology for identifying dynamic timing slack and selecting a safe operating point for a processor and a particular embedded software. Our approach for identifying and exploiting dynamic timing slack is non-speculative, requires no programmer intervention and little or no hardware support, and demonstrates potential power savings of up to 32%, 25% on average, over a range of embedded applications running on a common ultra-low-power processor, at no performance cost.
Supplementary Tables 1 - 2, Figure 1 - 11 from Activity of the Monocarboxylate Transporter 1 Inhibitor AZD3965 in Small Cell Lung Cancer (2023)

&lt;p&gt;PDF file - 1117K, Supplemental Table 1 - p53, RB and Myc status of the SCLC cell line panel investigated. Supplemental Table 2 - Characteristics of SCLC patients represented in the TMA. Supplemental Figure 1 - Structure of AZD3965. Supplemental Figure 2 - Effect of MCT1 overexpression on AZD3965 sensitivity in NCI-H1048 cells. Supplemental Figure 3 - Representative cell cycle profiles of normoxic and hypoxic SCLC cell lines treated with AZD3965. Supplemental Figure 4 - The effect of AZD3965 treatment on autophagy assessed by LC3 western blotting. Supplemental Figure 5 - Correlation between hypoxic MCT4 expression and AZD3965 sensitivity. Supplemental Figure 6 - MCT1 and MCT4 IHC of COR-L103 xenografts. Supplemental Figure 7 - Validation of MCT1 and MCT4 IHC staining. Supplemental Figure 8 - Representative images of MCT1, MCT4 and CA IX IHC staining in the SCLC TMA. Supplemental Figure 9 - Inter-scorer correlation of MCT1, MCT4 and CA IX TMA staining and distribution of MCT1, MCT4 and CA IX staining score across the TMA. Supplemental Figure 10 - Correlation between MCT4 and CA IX staining in the SCLC TMA. Supplemental Figure 11 - Effect of CA IX expression, stage and serum LDH on SCLC patient survival.&lt;/p&gt;
Synthesis and DPPH Radical Scavenging Activity of Prenylated Phenol Derivatives (2012)

The synthesis of twenty six prenylated phenols derivatives is reported. These compounds were obtained under mild conditions via Electrophilic Aromatic Substitution (EAS) coupling reactions between phenol derivatives containing electron-donor subtituents and 3-methyl-2-buten-1-ol using BF(3)×OEt(2). Dialkylations were also produced with this method. The formation of a chroman ring by intramolecular cyclization between a sp2 carbon from the prenyl group with the hydroxyl substituent in the ortho position occurred with some phenols. All the synthesized compounds were evaluated as antioxidants according to a DPPH radical scavenging activity assay. IC(50) values of five synthesized compounds indicated they were as good antioxidants as Trolox™.
Serum Vitamin D Depends Less on Latitude Than on Skin Color and Dietary Intake During Early Winter in Northern Europe (2015)

Insufficient vitamin D status was common during early winter in children living in Sweden, particularly in those with dark skin. Although, higher dietary vitamin D intake in northern than southern Sweden attenuated the effects of latitude, a northern country of living combined with darker skin and vitamin D intake below recommendations are important risk factors for vitamin D insufficiency.
Inhibitors of Intestinal Barrier Dysfunction (2008)

In the past decade, literature has increasingly pointed to a proximal intestinal barrier dysfunction and inappropriate paracellular permeability increase that precedes and correlates with inflammatory markers and/or disease expression in inflammatory bowel disease, celiac disease and irritable bowel syndrome. Exogenous and endogenous stimuli are known to induce paracellular permeability and disrupt barrier function. Recent identification of regulatory pathways that induce cytoskeletal reorganization, tight junction disassembly and paracellular permeability provide targets for therapeutic intervention in celiac disease. Here we review the identity, function and regulation of these pathways and propose various approaches to therapeutic intervention in celiac disease with the aim of inhibiting intestinal barrier dysfunction.
Induction of Functional Mesenchymal Stem Cells from Rabbit Embryonic Stem Cells by Exposure to Severe Hypoxic Conditions (2012)

Embryonic stem cells (ESCs) have the potential to be used as an unlimited cell source for cell transplantation therapy, as well as for studying mechanisms of disease and early mammalian development. However, applications involving ESCs have been limited by the lack of reliable differentiation methods in many cases. Mesenchymal stem cells (MSCs) have also emerged as a promising cell source, but as suggested in recent studies, these cells display limited potential for proliferation and differentiation, thereby limiting their usefulness in the clinic and in the laboratory. Unfortunately, effective methods for induction of MSCs from pluripotent stem cells have not been established, and the development of such methods remains a major challenge facing stem cell biologists. Oxygen concentration is one of the most important factors regulating tissue development. It has profound effects on cell metabolism and physiology and can strongly influence stem cell fate. Here we demonstrate that severelow O(2) concentrations (1%) can function as a selective pressure for removing undifferentiated pluripotent cells during the induction of MSCs from rabbit ESCs (rESCs) and that MSCs induced under severe hypoxic conditions function as normal MSCs; that is, they repopulate after cloning, express specific markers (vimentin, CD29, CD90, CD105, and CD140a) and differentiate into adipocytes, osteoblasts, and chondrocytes. Furthermore, we demonstrate that these cells can contribute to cartilage regeneration in an in vivo rabbit model for joint cartilage injury. These results support the notion that exposing ESCs to severe hypoxic conditions during differentiation can be used as a strategy for the preparation of functional MSCs from ESCs.
<title>Optical area I/O enhanced FPGA with 256 optical channels per chip</title> (2000)

It is our goal to demonstrate the viability of massively parallel optical interconnections between electronic VLSI chips. This is done through the development of the technology necessary for the realization of such interconnections, and the definition of a systems architecture in which these interconnections play a meaningful role. Field-programmable gate arrays (FPGA) have been identified as a class of general-purpose very large scale integration components that could benefit from the massive introduction of state-of-the-art optical inter-chip interconnections at the logic level. In this paper, we present the realization of a small-scale optoelectronic FPGA with 8 X 8 logic cells, containing two optical sources and two receivers per FPGA cell yielding a total of 256 links per chip. These FPGA chips designed to operate with information rates of 80 Mbit/s/link will be used in a three- chip demonstrator system as a test bed for the concepts above. We first identify the reason why we think optical interconnects can provide added value in FPGAs. The next sections briefly discuss the general architecture of our demonstrator system and the realization of the optoelectronic FPGA. We then present first measurement results followed by ongoing work and conclusions.
Social sensing (2011)

Adaptation requires a system to monitor its operational context to ensure that when changes occur, a suitable adaptation action is planned and taken at runtime. The ultimate goal of adaptation is that users get their dynamic requirements met efficiently and correctly. Context changes and users' judgment of the role of the system in meeting their requirements are drivers for adaptation. In many cases, these drivers are hard to identify by designers at design time and hard to monitor by the use of exclusively technological means by the system at runtime. In this paper, we propose Social Sensing as the activity performed by users who act as monitors and provide information needed for adaptation at runtime. Such information helps the system cope with technology limitations and designers' uncertainty. We discuss the motivation and foundations of Social Sensing and outline a set of research challenges to address in future work.
Sixteen CB11(CH3)n(CD3)12-n· radicals with fivefoldsubstitution symmetry: Spin distribution in CB11Me12 (2012)

The syntheses of all sixteen CB11(CH3)n(CD3)12-n. radicals with
fivefold substitution symmetry are described. The variation in
the width of their broad and featureless EPR signals is used to
deduce the relative values of the av. hyperfine coupling
consts. aH of the hydrogen atoms in the ipso (1), ortho (2-6),
meta (7-11), and para (12) Me groups: aH(i) : aH(o) : aH(m) :
aH(p) = (0.5 +/- 5.8) : (1.5 +/- 1.3) : (3.6 +/- 0.5) : (1.6
+/- 6.3). The values are in fair agreement with the results of
a B3LYP/EPRII calcn.
Short communication. PCR detection of DNA of bovine, ovine-caprine and porcine origin in feed as part of a bovine spongiform encephalopathy control program (2007)

The rapid identification of residues of mammalian materials in animal feedstuffs is important for the effective control of feed as a potential source of transmission of bovine spongiform encephalopathy (BSE). It is included in the monitoring program developed to avoid the appearance of this disease. In the present work a PCR analysis was tested for the detection of mammalian residues (bovine, caprine, ovine and porcine). The DNA extraction method utilised guanidium thiocianate, and primers flanking a conserved region of mitochondrial DNA were synthesized for each species. PCR tests were specific for each species and allowed detection in feedstuffs of levels as low as 1% of bovine DNA and 1.5% of ovine, caprine and porcine DNA. These PCR tests may allow the rapid detection of residues of these species constituting a powerful tool against BSE
Ocular cytotoxicity evaluation of medical devices such as contact lens solutions and benefits of a rinse step in cleaning procedure (2013)

Contact lens care solutions are known to have toxic effects on the ocular surface. The ISO 10993-5 standard describes test methods to assess the cytotoxicity of medical devices, but it needs some improvements to discriminate contact lens care multipurpose solutions. First we evaluated the biological hazards associated with the use of ophthalmic solutions, running a collaborative study with the French medical agency to propose adapted tools to study contact lens care solutions' ocular cytotoxicity (human cell line, short incubation times, and no dilution of solutions to test). Then we took into account the potential risk of these ophthalmic solutions adsorbed on contact lenses and released on the ocular surface, highlighting the addition of a rinse step with unpreserved marine solution in the contact lens cleaning procedure to avoid side effects of contact lens care solutions.
Supplementary Figure 3 from A Live-Attenuated Listeria Vaccine (ANZ-100) and a Live-Attenuated Listeria Vaccine Expressing Mesothelin (CRS-207) for Advanced Cancers: Phase I Studies of Safety and Immune Induction (2023)

&lt;p&gt;PDF file - 61K&lt;/p&gt;
Identification of a new Schistosoma mansoni membrane-bound protein through bioinformatic analysis. (2006)

Progress in schistosome genome research has enabled investigators to move rapidly from genome sequences to vaccine development. Proteins bound to the surface of parasites are potential vaccine candidates, or they can be used for diagnosis. We analyzed 4342 proteins deduced from the Schistosoma mansoni transcriptome with bioinformatic computer programs. Thirty-four proteins had membrane-bound motifs. Within this group, we selected the Sm29 protein to be further characterized by in silico analysis. Sm29 was found to have a signal peptide made up of 26 amino acids, with a cleavage site between Ser26 and Val27. The glycosylation site search revealed three threonines (39, 132 and 133) with high probability of O-glycosylation and two asparagines (58 and 115) with high probability of N-glycosylation. Only one transmembrane helix was found in the C-terminal region of the protein from Leu169 to Lis191. The search for similarities and conserved motifs show that Sm29 is a protein with high identity to proteins present in S. japonicum (53, 52, 49, and 37% of identity) and it possesses disulfide-rich conserved domains. Apparently, Sm29 is a membrane bound protein, and it may be an important molecule in host-parasite interactions.
Software traceability with topic modeling (2010)

Software traceability is a fundamentally important task in software engineering. The need for automated traceability increases as projects become more complex and as the number of artifacts increases. We propose an automated technique that combines traceability with a machine learning technique known as topic modeling. Our approach automatically records traceability links during the software development process and learns a probabilistic topic model over artifacts. The learned model allows for the semantic categorization of artifacts and the topical visualization of the software system. To test our approach, we have implemented several tools: an artifact search tool combining keyword-based search and topic modeling, a recording tool that performs prospective traceability, and a visualization tool that allows one to navigate the software architecture and view semantic topics associated with relevant artifacts and architectural components. We apply our approach to several data sets and discuss how topic modeling enhances software traceability, and vice versa.
Investigation on the performance of space-time block coded ultrawide band communication systems: Research Articles (2005)

Ultrawide band (UWB) communication systems show many advantages over the conventional narrow band systems. In this paper, three UWB systems at the same transmission efficiency are investigated. The first one is a conventional system with only one transmit antenna (non-STBC). The second one is combined with the space-time block coding (STBC) over one symbol (STBC-1). The third system is combined with the STBC over two symbols (STBC-2), which is in accordance with Almouti's scheme. Both theoretical analysis and simulations show that the STBC-1 system performs the best. In addition, the adoption of the normalized modified Hermite polynomial based orthogonal pulses (NMHP) instead of the Gaussian pulse (GP) to represent the M-ary symbol constellation can increase the data rate and lead to an improvement of the signal to noise ratio (SNR) by about 10log10M dB at the bit error rate (BER) of 10-4 at any symbol constellation for any UWB system. The simulations in both flat-fading channels and frequency-selective channels have confirmed such improvement. Copyright © 2005 John Wiley & Sons, Ltd.
Electroencephalographic Characterization of an Adult Rat Model of Radiation‐Induced Cortical Dysplasia (2001)

Our results further characterize the in vivo EEG characteristics of the in utero radiation model of CD using long-term EEG monitoring. This model may be used to study the molecular and cellular changes in epileptogenic CD and to test the efficacy of newer antiepileptic medications.