gebhart/patrepeval huggingface dataset:
Diphosphine Oxide−Brφnsted Acid Complexes as Novel Hydrogen-Bonded Self-Assembled Molecules (2000)

Novel hydrogen-bonded supramolecules based on interactions between an acid and a base have been prepared from (R,R)-1,2-bis(1-adamantylmethylphosphinyl)ethane (1) and tetrafluoroboric acid. Both linear and cyclic structures have been observed. Recrystallization from CH2Cl2−AcOEt gave the linear supramolecule 2. The structure of 2 was confirmed by single-crystal X-ray analysis. On the other hand, cyclic dimer 3 was produced by recrystallization from CHCl3−AcOEt. The structure of 3 was estimated by electron spray ionization mass spectrometry and single crystal X-ray analysis. Significantly different enantioselectivities were observed in asymmetric protonation reactions of these two supramolecules with silyl enolates.
Comparison of Amplitude Recovery Dynamics of Two Limit Cycle Oscillator Models of the Human Circadian Pacemaker (2005)

At an organism level, the mammalian circadian pacemaker is a two-dimensional system. For these two dimensions, phase (relative timing) and amplitude of the circadian pacemaker are commonly used. Both the phase and the amplitude (A) of the human circadian pacemaker can be observed within multiple physiological measures--including plasma cortisol, plasma melatonin, and core body temperature (CBT)--all of which are also used as markers of the circadian system. Although most previous work has concentrated on changes in phase of the circadian system, critically timed light exposure can significantly reduce the amplitude of the pacemaker. The rate at which the amplitude recovers to its equilibrium level after reduction can have physiological significance. Two mathematical models that describe the phase and amplitude dynamics of the pacemaker have been reported. These models are essentially equivalent in predictions of phase and in predictions of amplitude recovery for small changes from an equilibrium value (A = 1), but are markedly different in the prediction of recovery rates when A < 0.6. To determine which dynamic model best describes the amplitude recovery observed in experimental data; both models were fit to CBT data using a maximum likelihood procedure and compared using Akaike's Information Criterion (AIC). For all subjects, the model with the lower recovery rate provided a better fit to data in terms of AIC, supporting evidence that the amplitude recovery of the endogenous pacemaker is slow at low amplitudes. Experiments derived from model predictions are proposed to test the influence of low amplitude recovery on the physiological and neurobehavioral functions.
Immersion lithography exposure systems: today's capabilities and tomorrow’s expectations (2005)

In less than two years immersion lithography has been developed from curiosity to viable technology for IC manufacturing. With water as immersion fluid ArF immersion offers the potential to extend conventional optical lithography to at least the 45-nm node. By slightly modifying “dry lenses” it is possible to use the immersion option as enhancement for the focus window. With immersion the DOF can be increased with 50% and more. ASML has developed and shipped ArF immersion TWINSCAN systems with lens NA’s of 0.75 and of 0.85. In the near future immersion systems with 0.93 NA and >1.1NA will become available. In this paper we discuss the experimental results obtained on the TWINSCAN immersion systems. In the first part we discuss the experimental results obtained with the 0.75 NA and 0.85 NA immersion systems. It is demonstrated that basic system performance is maintained in case of immersion, while the imaging performance is improved significantly. We present data on resolution capability, full wafer CD uniformity, lens aberrations and single machine overlay. In the last part of the paper we will give an outlook to the next generations of immersion systems. This will include a discussion on the possible use of high index fluids and what resolution can be reached ultimately.
ChemInform Abstract: A Facile One‐Pot Synthesis of Homopropargylic Alcohols from Terminal Acetylenes. (1993)

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.
Dissection of the Fusarium I2 Gene Cluster in Tomato Reveals Six Homologs and One Active Gene Copy (1998)

The I2 locus in tomato confers resistance to race 2 of the soil-borne fungus Fusarium oxysporum f sp lycopersici. The selective restriction fragment amplification (AFLP) positional cloning strategy was used to identify I2 in the tomato genome. A yeast artificial chromosome (YAC) clone covering approximately 750 kb encompassing the I2 locus was isolated, and the AFLP technique was used to derive tightly linked AFLP markers from this YAC clone. Genetic complementation analysis in transgenic R1 plants using a set of overlapping cosmids covering the I2 locus revealed three cosmids giving full resistance to F. o. lycopersici race 2. These cosmids shared a 7-kb DNA fragment containing an open reading frame encoding a protein with similarity to the nucleotide binding site leucine-rich repeat family of resistance genes. At the I2 locus, we identified six additional homologs that included the recently identified I2C-1 and I2C-2 genes. However, cosmids containing the I2C-1 or I2C-2 gene could not confer resistance to plants, indicating that these members are not the functional resistance genes. Alignments between the various members of the I2 gene family revealed two significant variable regions within the leucine-rich repeat region. They consisted of deletions or duplications of one or more leucine-rich repeats. We propose that one or both of these leucine-rich repeats are involved in Fusarium wilt resistance with I2 specificity.
WormBase 2017: molting into a new stage (2017)

WormBase (http://www.wormbase.org) is an important knowledge resource for biomedical researchers worldwide. To accommodate the ever increasing amount and complexity of research data, WormBase continues to advance its practices on data acquisition, curation and retrieval to most effectively deliver comprehensive knowledge about Caenorhabditis elegans, and genomic information about other nematodes and parasitic flatworms. Recent notable enhancements include user-directed submission of data, such as micropublication; genomic data curation and presentation, including additional genomes and JBrowse, respectively; new query tools, such as SimpleMine, Gene Enrichment Analysis; new data displays, such as the Person Lineage browser and the Summary of Ontology-based Annotations. Anticipating more rapid data growth ahead, WormBase continues the process of migrating to a cutting-edge database technology to achieve better stability, scalability, reproducibility and a faster response time. To better serve the broader research community, WormBase, with five other Model Organism Databases and The Gene Ontology project, have begun to collaborate formally as the Alliance of Genome Resources.
Enhancers of Host Immune Tolerance to Bacterial Infection Discovered Using Linked Computational and Experimental Approaches (2022)

Current therapeutic strategies against bacterial infections focus on reduction of pathogen load using antibiotics; however, stimulation of host tolerance to infection in the presence of pathogens might offer an alternative approach. Computational transcriptomics and Xenopus laevis embryos are used to discover infection response pathways, identify potential tolerance inducer drugs, and validate their ability to induce broad tolerance. Xenopus exhibits natural tolerance to Acinetobacter baumanii, Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pneumoniae bacteria, whereas Aeromonas hydrophila and Pseudomonas aeruginosa produce lethal infections. Transcriptional profiling leads to definition of a 20-gene signature that discriminates between tolerant and susceptible states, as well as identification of a more active tolerance response to gram negative compared to gram positive bacteria. Gene pathways associated with active tolerance in Xenopus, including some involved in metal ion binding and hypoxia, are found to be conserved across species, including mammals, and administration of a metal chelator (deferoxamine) or a HIF-1α agonist (1,4-DPCA) in embryos infected with lethal A. hydrophila increased survival despite high pathogen load. These data demonstrate the value of combining the Xenopus embryo infection model with computational multiomics analyses for mechanistic discovery and drug repurposing to induce host tolerance to bacterial infections.
<title>Validity-weighted model vector-based retrieval of video</title> (2003)

Model vector-based retrieval is a novel approach for video indexing that uses a semantic model vector signature that describes the detection of a fixed set of concepts across a lexicon. The model vector basis is created using a set of independent binary classifiers that correspond to the semantic concepts. The model vectors are created by applying the binary detectors to video content and measuring the confidence of detection. Once the model vectors are extracted, simple techniques can be used for searching to find similar matches in a video database. However, since confidence scores alone do not capture information about the reliability of the underlying detectors, techniques are needed to ensure good performance in the presence of varying qualities of detectors. In this paper, we examine the model vector-based retrieval framework for video and propose methods using detector validity to improve matching performance. In particular, we develop a model vector distance metric that weighs the dimensions using detector validity scores. In this paper, we explore the new model vector-based retrieval method for video indexing and empirically evaluate the retrieval effectiveness on a large video test collection using different methods of measuring and incorporating detector validity indicators.
Lattice dynamics and thermoelectric properties of nanocrystalline silicon–germanium alloys (2015)

Abstract The lattice dynamics and thermoelectric properties of sintered phosphorus‐doped nanostructured silicon–germanium alloys obtained by gas‐phase synthesis were studied. Measurements of the density of phonon states by inelastic neutron scattering were combined with measurements of the elastic constants and the low‐temperature heat capacity. A strong influence of nanostructuring and alloying on the lattice dynamics was observed. The thermoelectric transport properties of samples with different doping as well as samples sintered at different temperature were characterized between room temperature and C. A peak figure of merit at C is observed and is comparatively insensitive to the aforementioned parameter variations.
A Novel Clinically Translatable Fluorescent Nanoparticle for Targeted Molecular Imaging of Tumors in Living Subjects (2011)

The use of quantum dots (QDs) in biomedical research has grown tremendously, yet successful examples of clinical applications are absent due to many clinical concerns. Here, we report on a new type of stable and biocompatible dendron-coated InP/ZnS core/shell QD as a clinically translatable nanoprobe for molecular imaging applications. The QDs (QD710-Dendron) were demonstrated to hold several significant features: near-infrared (NIR) emission, high stability in biological media, suitable size with possible renal clearance, and ability of extravasation. More importantly, a pilot mouse toxicity study confirmed that QD710-Dendron lacks significant toxicity at the doses tested. The acute tumor uptake of QD710-Dendron resulted in good contrast from the surrounding nontumorous tissues, indicating the possibility of passive targeting of the QDs. The highly specific targeting of QD710-Dendron-RGD(2) to integrin α(v)β(3)-positive tumor cells resulted in high tumor uptake and long retention of the nanoprobe at tumor sites. In summary, QD710-Dendron and RGD-modified nanoparticles demonstrate small size, high stability, biocompatibility, favorable in vivo pharmacokinetics, and successful tumor imaging properties. These features satisfy the requirements for clinical translation and should promote efforts to further investigate the possibility of using QD710-Dendron-based nanoprobes in the clinical setting in the near future.
PTP/IP - transport layer for picture transfer protocol (2005)

PTP (picture transfer protocol) is a standard for connectivity of digital photography devices. We describe how PTP can be extended to work over generic TCP/IP networks. This provides a significantly more flexible applications infrastructure for networked digital photography.
8.1: Invited Paper : Optical and System Considerations for Mobile Touch Screen Applications (2013)

Abstract The tradeoffs of a mobile computer industrial design include pixel density, optical effects, ambient lighting influence, touch screen weight and power. In this paper, we analyzed the significance of these based on human eye's acuity, contrast sensitivity, focusing ability and lighting condition.
Can routinely collected data be used for research on bipolar disorder? data from the St. Göran bipolar project (2012)

Landén, M; Rydén, E; Johansson, A; Wetterberg, L; Jakobsson, J; Pålsson, E; Ekman, C J; Sellgren, C; Olsson, S; Erhardt, S; Båve, U
The measured creatinine generation rate in CAPD suggests only 78% of prescribed dialysis is delivered. (1993)

The creatinine generation was measured (GCr) in 132 continuous ambulatory peritoneal dialysis (CAPD) patients from the product of total daily peritoneal plus renal creatinine clearance and plasma creatinine (CpCr) plus the product of estimated gut clearance of 0.036 L/kg/day and CpCr. The creatinine generation was also predicted (PGCr) from gender, age, and weight. The mean ratio of MGCr/PGCr was 1.29. Analysis of these data suggests that on average, only 78% of the prescribed dialysis is actually delivered in CAPD patients. Further studies are suggested for the verification of the assumed gut creatinine clearance.
Competitive Compliance with Blockchain (2019)

Authentication is essential for sharing information in IoT and its secondary use with AI-capable machines. The aim is to support humans in optimizing risk of supply chains for industrial manufacturing and service provisioning in a timely manner. The ultimate aim is sustainability. The problem for deciding on authentication is probably imperfect information on compliance. Its asymmetric implications of the meaning of contracts for secure information sharing may cause vulnerability of data breach and misuse. A traditional way to avoid harm of that asymmetry requires authentic and consistent sharing of audit information on violation of a certification policy to a centralized audit intelligence. This information sharing is, however, subject to the problem of single point of failure of the centralized audit intelligence. With our work on Security by Design, we show a non-central approach of clarifying accountability to reduce the risk caused by asymmetric implications of the meaning of contracts on authentication. Our signaling and screening scheme SK4SC provides personal digital evidences on compliance to multilateral policies on using information or in other words on trustworthiness. Blockchains are used to realize their symmetric distribution while users share risk on accountability with competition on incentives in a privacy-enhancing manner. Customer relationship management with royalty points, e.g., for eGovernment with taxation, is an example for using SK4SC as digital platform.
Training Deep Bidirectional LSTM Acoustic Model for LVCSR by a Context-Sensitive-Chunk BPTT Approach (2016)

This paper presents a study of using deep bidirectional long short-term memory (DBLSTM) recurrent neural network as acoustic model for DBLSTM-HMM based large vocabulary continuous speech recognition (LVCSR), where a context-sensitive-chunk (CSC) back-propagation through time (BPTT) approach is used to train DBLSTM by splitting each training sequence into chunks with appended contextual observations, and a CSC-based decoding method with possibly overlapped CSCs is used for recognition. Our approach makes mini-batch based training on GPU more efficient and reduces the latency of DBLSTM-based LVCSR from a whole utterance to a short chunk. Evaluations have been made on Switchboard-I benchmark task. In comparison with epoch-wise BPTT training, our method can achieve more than three times speedup on a single GPU card without degrading recognition accuracy. In comparison with a highly optimized DNN-HMM system trained by a frame-level cross entropy (CE) criterion, our CE-trained DBLSTM-HMM system achieves relative word error rate reductions of 9% and 5% on Eval2000 and RT03S testing sets, respectively. Furthermore, by running model averaging based parallel training of DBLSTM on a cluster of GPUs, CSC-BPTT incurs less accuracy degradation than epoch-wise BPTT while achieves a linear speedup.
Nucleic acid- based methods for detection of foodborne pathogens (2012)

These cultural methods, while proven to be reliable, may not necessarily be optimal for detection of foodborne pathogens due to the current fast-paced production and distribution practices of food products by the food-processing industry. The rapidity of the food production system has actually helped spur the development and application of alternative molecular and more rapid methods for detection of foodborne pathogens. Early accurate detection of pathogens along the food production chain (from raw ingredients to nished product) can aid in avoiding the transmission of foodborne disease to consumers, thereby further protecting public health and lowering the nancial burden on the health care system, as well as reducing economic losses to the food industry, which stem from costly product recalls, loss of reputation, and litigation costs.
De Novo Methylation of CpG Island Sequences in Human Fibroblasts Overexpressing DNA (Cytosine-5-)-Methyltransferase (1996)

Recent studies showing a correlation between the levels of DNA (cytosine-5-)-methyltransferase (DNA MTase) enzyme activity and tumorigenicity have implicated this enzyme in the carcinogenic process. Moreover, hypermethylation of CpG island-containing promoters is associated with the inactivation of genes important to tumor initiation and progression. One proposed role for DNA MTase in tumorigenesis is therefore a direct role in the de novo methylation of these otherwise unmethylated CpG islands. In this study, we sought to determine whether increased levels of DNA MTase could directly affect CpG island methylation. A full-length cDNA for human DNA MTase driven by the cytomegalovirus promoter was constitutively expressed in human fibroblasts. Individual clones derived from cells transfected with DNA MTase (HMT) expressed 1- to 50-fold the level of DNA MTase protein and enzyme activity of the parental cell line or clones transfected with the control vector alone (Neo). To determine the effects of DNA MTase overexpression on CpG island methylation, we examined 12 endogenous CpG island loci in the HMT clones. HMT clones expressing > or = 9-fold the parental levels of DNA MTase activity were significantly hypermethylated relative to at least 11 Neo clones at five CpG island loci. In the HMT clones, methylation reached nearly 100% at susceptible CpG island loci with time in culture. In contrast, there was little change in the methylation status in the Neo clones over the same time frame. Taken together, the data indicate that overexpression of DNA MTase can drive the de novo methylation of susceptible CpG island loci, thus providing support for the idea that DNA MTase can contribute to tumor progression through CpG island methylation-mediated gene inactivation.
SU‐GG‐J‐89: Evaluation of the Internal Target Tracking Algorithms in a Commercial Research Fluoroscopic Toolkit (2008)

Purpose: A means of tracking internal target or structure motion in x‐ray images is important for monitoring motion at treatment. We evaluate the accuracy and robustness of several tracking algorithms in a commercial research toolkit with patient images. Method and Materials: Anterior/posterior view fluoroscopic images (10/s) over several respiratory cycles in the thorax or abdomen are acquired with a gantry‐mounted kV imaging system immediately after radiation treatment. We compare three tracking algorithms available in the research toolkit with manual tracking: single implanted fiducial or surgical clip, diaphragm, and markerless tracking of tumor in lung. The latter mode provides separation of moving features from stationary features in the images, for improved extraction of motion signals. For each algorithm, the position of the object in the superior‐inferior direction is compared to the manually determined one in each image in the sequence. We also determine the mean and variance discrepancy between algorithm and manual tracking. Intra‐observer variability is determined from repeated manual tracking of a subset of fluoro sequences. The percentage of images in which discrepancy is &lt;5mm is taken as a measure of algorithm robustness. Results: The mean and standard deviation of the algorithm‐manual difference were: Single Marker μ=0.53 mm, σ=0.92 mm, Diaphragm μ=0.88 mm, σ=1.4 mm, and markerless μ=2.06 mm, σ=1.68 mm. This compares with an intra‐observer variability mean of ⩽ 1 mm, 2 mm, and 3.5 mm respectively. The discrepancy between algorithmic and manual tracking exceeding the robustness threshold occurred 0%, 2%, and 3% of the time of the three algorithms respectively. Conclusion: For the algorithms examined, the toolkit agreement with manual tracking is consistent with or less than intra‐observer variation. Future plans are to evaluate the toolkit's performance with multiple fiducials in close proximity, and at other gantry orientations.
The optical soliton transmission amplified by bidirectional Raman pumps with nonconstant depletion (1991)

A numerical method to solve the coupled equations between the soliton and bidirectional Raman pump waves is proposed. The pump depletion due to the soliton is obtained without using the constant depletion approximation. With this method, the soliton propagation in a Raman-pumped fiber, can be solved accurately. It is found that the constant depletion approximation is valid at a small depletion rate, which requires low soliton power (or long pulsewidth), small material loss, and a short-pump period. In a periodically Raman-pumped fiber, there exists a stable signal energy which is very sensitive to the pump intensity. The stability of the soliton propagation with nonconstant pump depletion is studied. It is found that the stability predicted by the nonconstant depletion (NCD) and the constant depletion assumption (CDA) are generally different.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
High speed silicon photonic crystal waveguide modulator for low voltage operation (2007)

A high speed compact silicon modulator is experimentally demonstrated to work at a low driving voltage desirable for on-chip applications. As carrier injection is the only practical option for optical modulation in silicon, a lower limit of current density (∼104A∕cm2) exists for achieving gigahertz modulation in the p-i-n diode configuration. Exploiting the slow group velocity of light in photonic crystal waveguides, the interaction length of this Mach-Zehnder interferometer-type silicon modulator is reduced significantly compared to conventional modulators. The required high current density is achieved with a low voltage (2V) by scaling down the interaction length to 80μm.