gebhart/patrepeval huggingface dataset:
Modeling botulinum neurotoxin type A using 3D printing technology (2010)

The Clostridium botulinum bacteria produce 7 different neurotoxin serotypes (types A–G) that cause botulism, and these are the most toxic proteins known to man. Botulism develops if a person ingests the toxin, or if the Clostridium bacteria grow in the intestines or wounds in the host and toxin is released. The toxin paralyzes victims by blocking the nerve's ability to communicate with muscle fibers by inhibiting the release of acetylcholine at the synaptic clefts of neuromuscular junctions. The BoNT/A crystal structure solved by the Stevens Lab revealed three domains that are involved in catalytic cleavage of SNARE proteins, translocation of the catalytic domain, and cell receptor binding (Lacy and Stevens 1998). BoNT/A's zinc‐dependant catalytic domain cuts and disables SNAP‐25, one of the major SNARE fusion proteins required for acetylcholine vesicle docking to the presynaptic membrane. Without acetylcholine to properly signal muscle contraction, breathing muscles become paralyzed and the victim eventually suffocates. Although the potential use of BoNT/A as a bioweapon is a major concern, it is also effectively used for numerous therapeutic and cosmetic purposes. The North San Diego Girls Cooperative SMART Team (Students Modeling A Research Topic) developed a model of BoNT/A using 3D printing technology.
CuI/TBHP: A versatile reagent system for the synthesis of 5-iodomethyl-2-aryl-4,5-dihydrooxazoles from N-allylarylamides (2018)

Herein, a novel reagent system using CuI/TBHP is described for the facile conversion of easily accessible N-allylarylamides into 5-iodomethyl-2-aryl-4,5-dihydrooxazoles in moderate to good yields. In this communication we describe CuI as the iodine source for the first time towards the intramolecular iodooxygenation of N-allylarylamides.
ChemInform Abstract: Regioselective Cyclopentane Ring Formation Mediated by Titanocene Chloride. (1991)

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.
Investigating Li Microstructure Formation on Li Anodes for Lithium Batteries by in Situ 6Li/7Li NMR and SEM (2015)

The growth of lithium microstructures during battery cycling has, to date, prohibited the use of Li metal anodes and raises serious safety concerns even in conventional lithium-ion rechargeable batteries, particularly if they are charged at high rates. The electrochemical conditions under which these Li microstructures grow have, therefore, been investigated by in situ nuclear magnetic resonance (NMR), scanning electron microscopy (SEM), and susceptibility calculations. Lithium metal symmetric bag cells containing LiPF6 in EC/DMC electrolytes were used. Distinct 7Li NMR resonances were observed due to the Li metal bulk electrodes and microstructures, the changes in peak positions and intensities being monitored in situ during Li deposition. The changes in the NMR spectra, observed as a function of separator thickness and porosity (using Celgard and Whatmann glass microfiber membranes) and different applied pressures, were correlated with changes in the type of microstructure, by using SEM. Isotopically enriched 6Li metal electrodes were used against natural abundance predominantly 7Li metal counter electrodes to investigate radiofrequency (rf) field penetration into the Li anode and to confirm the assignment of the higher frequency peak to Li dendrites. The conclusions were supported by calculations performed to explore the effect of the different microstructures on peak position/broadening, the study showing that Li NMR spectroscopy can be used as a sensitive probe of both the amount and type of microstructure formation.
Genetic Evidence of a Precisely Tuned Dysregulation in the Hypoxia Signaling Pathway during Oncogenesis (2020)

The classic model of tumor suppression implies that malignant transformation requires full 'two-hit' inactivation of a tumor suppressor gene. However, more recent work in mice has led to the proposal of a "continuum" model that involves more fluid concepts such as gene dosage-sensitivity and tissue specificity. Mutations in the tumor suppressor gene VHL are associated with a complex spectrum of conditions. Homozygotes or compound heterozygotes for the R200W germline mutation in VHL have Chuvash polycythemia, whereas heterozygous carriers are free of disease. Individuals with classic, heterozygous VHL mutations have von Hippel-Lindau disease and are at high risk of multiple tumors (e.g. CNS hemangioblastomas, pheochromocytoma, renal cell carcinoma). We report here an atypical family bearing two VHL gene mutations in cis (R200W and R161Q), together with phenotypic analysis, structural modeling, functional and transcriptomic studies of these mutants in comparison to classical mutants involved in the different VHL phenotypes. We demonstrate that the complex pattern of disease manifestations observed in VHL syndrome is perfectly correlated with a gradient of pVHL dysfunction in hypoxia signaling pathways. Thus, by studying naturally occurring familial mutations, our work validates in humans the "continuum" model of tumor suppression.
Redox Proteomics Analyses of the Influence of Co-Expression of Wild-Type or Mutated LRRK2 and Tau on C. elegans Protein Expression and Oxidative Modification: Relevance to Parkinson Disease (2012)

These results suggest that changes in LRRK2 expression or activity lead to corresponding changes in mitochondrial function, autophagy, and protein translation. These findings are discussed with reference to the pathophysiology of PD.
Urologic oncology: extraordinary opportunities for discovery: highlights from the 2nd annual winter meeting of the society of urologic oncology december 1-2, 2001, bethesda, MD. (2003)

The 2nd Annual Winter Meeting of the Society of Urologic Oncology (SUO) was held in the Natcher Conference Center of the National Institutes of Health in Bethesda, Maryland on December 1–2, 2001. The SUO was created in 1984 to include members interested in the care of patients with malignant genitourinary disease. The SUO develops educational and research initiatives, one of which is this winter oncology meeting, which is jointly sponsored by the National Cancer Institute and the Society of Urologic Oncology. Physicians, scientists, fellows, and medical and urologic oncologists attended to listen to state-of-the-art lectures presented by experts from all over the United States and Canada. Furthermore, there was a poster session with 50 abstract presentations, many of which were presented by fellows in training, which was a forum for basic research. This meeting was designed to facilitate discussion of important issues among members of the urologic oncology community at the National Institutes of Health.

The meeting was broadly organized into three sessions devoted to the major urologic malignancies: transitional cell carcinoma (TCC), kidney cancer, and prostate cancer.
Laws of order (2011)

Building correct and efficient concurrent algorithms is known to be a difficult problem of fundamental importance. To achieve efficiency, designers try to remove unnecessary and costly synchronization. However, not only is this manual trial-and-error process ad-hoc, time consuming and error-prone, but it often leaves designers pondering the question of: is it inherently impossible to eliminate certain synchronization, or is it that I was unable to eliminate it on this attempt and I should keep trying? In this paper we respond to this question. We prove that it is impossible to build concurrent implementations of classic and ubiquitous specifications such as sets, queues, stacks, mutual exclusion and read-modify-write operations, that completely eliminate the use of expensive synchronization. We prove that one cannot avoid the use of either: i) read-after-write (RAW), where a write to shared variable A is followed by a read to a different shared variable B without a write to B in between, or ii) atomic write-after-read (AWAR), where an atomic operation reads and then writes to shared locations. Unfortunately, enforcing RAW or AWAR is expensive on all current mainstream processors. To enforce RAW, memory ordering--also called fence or barrier--instructions must be used. To enforce AWAR, atomic instructions such as compare-and-swap are required. However, these instructions are typically substantially slower than regular instructions. Although algorithm designers frequently struggle to avoid RAW and AWAR, their attempts are often futile. Our result characterizes the cases where avoiding RAW and AWAR is impossible. On the flip side, our result can be used to guide designers towards new algorithms where RAW and AWAR can be eliminated.
Efficient implementation of scatter-gather operations for large scale graph analytics (2016)

We developed a methodology to improve the cache behavior and overall performance of sparse linear algebra kernels used in graph analytics. Large scale graph processing typically has low performance because it cannot effectively use processor caches, resulting in high-latency for memory accesses. This is particularly true in a sparse linear algebra formulations of graph algorithms, which use well known kernels such as sparse-matrix vector multiply and sparse-matrix transposition. The proposed methodology partitions the inner loops of linear algebra kernels, and executes the iterations over these partitions in an independently ordered manner. This produces more cache-friendly access patterns, which reduce cache misses and improve performance. We first illustrate the technique through an example and then generalize it to multiple scenarios. Our evaluation shows that execution time of key computational kernels is reduced by 2- to 5-fold, when large graphs are considered. Most of the improvement in execution time comes from a significant reduction in cycles-per-instruction (CPI), even as the path length of the executed code increases.
Parental Alcohol History Differentially Predicts Offspring Disorders in Distinct Subgroups in Israel (2014)

Parental alcohol problems were related to substance use and psychiatric disorders differently in FSU and other Israelis, two groups with different alcohol consumption levels and drinking norms. We propose that, in social contexts that vary in the degree to which they constrain alcohol behavior, underlying genetic predispositions may manifest as different disorders.
Radiofluorinated N-Octanoyl Dopamine ([18F]F-NOD) as a Tool To Study Tissue Distribution and Elimination of NOD in Vitro and in Vivo (2016)

To mitigate pretransplantation injury in organs of potential donors, N-octanoyl dopamine (NOD) treatment might be considered as it does not affect hemodynamic parameters in braindead (BD) donors. To better assess optimal NOD concentrations for donor treatment, we report on the fast and facile radiofluorination of the NOD-derivative [<sup>18</sup>F]F-NOD [<sup>18</sup>F]5 for in vivo assessment of NOD's elimination kinetics by means of PET imaging. [<sup>18</sup>F]5 was synthesized in reproducibly high radiochemical yields and purity (>98%) as well as high specific activities (>20 GBq/μmol). Stability tests showed no decomposition of [<sup>18</sup>F]5 over a period of 120 min in rat plasma. In vitro, low cell association was found for [<sup>18</sup>F]5, indicating no active transport mechanism into cells. In vivo, [<sup>18</sup>F]5 exhibited a fast blood clearance and a predominant hepatobiliary elimination. As these data suggest that also NOD might be cleared fast, further pharmacokinetic evaluation is warranted.
Data from Fine Mapping of Chromosome 6q23-25 Region in Familial Lung Cancer Families Reveals <i>RGS17</i> as a Likely Candidate Gene (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; We have previously mapped a major susceptibility locus influencing familial lung cancer risk to chromosome 6q23-25. However, the causal gene at this locus remains undetermined. In this study, we further refined this locus to identify a single candidate gene, by fine mapping using microsatellite markers and association studies using high-density single nucleotide polymorphisms (SNP).&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Six multigenerational families with five or more affected members were chosen for fine-mapping the 6q linkage region using microsatellite markers. For association mapping, we genotyped 24 6q-linked cases and 72 unrelated noncancer controls from the Genetic Epidemiology of Lung Cancer Consortium resources using the Affymetrix 500K chipset. Significant associations were validated in two independent familial lung cancer populations: 226 familial lung cases and 313 controls from the Genetic Epidemiology of Lung Cancer Consortium, and 154 familial cases and 325 controls from Mayo Clinic. Each familial case was chosen from one high-risk lung cancer family that has three or more affected members.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; A region-wide scan across 6q23-25 found significant association between lung cancer susceptibility and three single nucleotide polymorphisms in the first intron of the &lt;i&gt;RGS17&lt;/i&gt; gene. This association was further confirmed in two independent familial lung cancer populations. By quantitative real-time PCR analysis of matched tumor and normal human tissues, we found that &lt;i&gt;RGS17&lt;/i&gt; transcript accumulation is highly and consistently increased in sporadic lung cancers. Human lung tumor cell proliferation and tumorigenesis in nude mice are inhibited upon knockdown of &lt;i&gt;RGS17&lt;/i&gt; levels.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusion:&lt;/b&gt;&lt;i&gt;RGS17&lt;/i&gt; is a major candidate for the familial lung cancer susceptibility locus on chromosome 6q23-25.&lt;/p&gt;&lt;/div&gt;
Approaches to the design of HIV protease inhibitors with improved resistance profiles (2008)

Several theories on how to design HIV protease inhibitors with improved resistance profiles have been proposed during the review period. The general concepts that are incorporated into most design strategies include maximizing the interactions with the backbone and conserved side chains of the enzyme while minimizing inhibitor size and maintaining conformational flexibility to allow for modified binding modes.
Front Cover Advanced Engineering Materials 1‐2/2013 (2013)

These days nanotechnology start-ups are emerging with increasing frequency in almost every country around the globe, indicating that attitudes towards entrepreneurship are undergoing a significant change. Innovation in nanotechnology often springs from ideas birthed in universities yet the mindset of stakeholders towards entrepreneurship in our seats of knowledge is vastly underappreciated. In this article the challenges faced by academics and students are explored when confronted with the collision between fundamental research in the pursuit of knowledge and applied research directed at the creation of inventions, intellectual property, companies, jobs, products and wealth. For details see the article by Ozin et al. on page 8.
A novel EPID design for enhanced contrast and detective quantum efficiency (2016)

Beams-eye-view imaging applications such as real-time soft-tissue motion estimation are hindered by the inherently low image contrast of electronic portal imaging devices (EPID) currently available for clinical use. We introduce and characterize a novel EPID design that provides substantially increased detective quantum efficiency (DQE), contrast-to-noise ratio (CNR) and sensitivity without degradation in spatial resolution. The prototype design features a stack of four conventional EPID layers combined with low noise integrated readout electronics. Each layer consists of a copper plate, a scintillator ([Formula: see text]) and a photodiode/TFT-switch (aSi:H). We characterize the prototype's signal response to a 6 MV photon beam in terms of modulation transfer function (MTF), DQE and CNR. The presampled MTF is estimated using a slanted slit technique, the DQE is calculated from measured normalized noise power spectra (nNPS) and the MTF and CNR is estimated using a Las Vegas contrast phantom. The prototype has been designed and built to be interchangeable with the current clinical EPID on the Varian TrueBeam platform (AS-1200) in terms of size and data output specifications. Performance evaluation is conducted in absolute values as well as in relative terms using the Varian AS-1200 EPID as a reference detector. A fivefold increase of DQE(0) to about 6.7% was observed by using the four-layered design versus the AS-1200 reference detector. No substantial differences are observed between each layer's individual MTF and the one for all four layers operating combined indicating that defocusing due to beam divergence is negligible. Also, using four layers instead of one increases the signal to noise ratio by a factor of 1.7.
Modeling biomembranes. (2005)

Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles.
Reprogramming mouse embryonic fibroblasts using different systems (2015)

This protocol describes 4 methods to reprogram MEFs into iPSCs: the pMXs-based retroviral 4-factor, the polycistronic lentiviral 4-factor, the doxycycline inducible 4-factor secondary, and the iCD1 medium based Sox2+Oct4 2-factor systems.
Placental Growth Factor Regulates Cardiac Adaptation and Hypertrophy Through a Paracrine Mechanism (2011)

PGF is a secreted factor that supports hypertrophy and cardiac function during pressure overload by affecting endothelial cells and fibroblasts that in turn stimulate and support the myocytes through additional paracrine factors.
Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study (2016)

Gender is a previously unrecognized factor influencing DM1 clinical profile and severity of the disease, with worse socio-economic consequences of the disease and higher morbidity and mortality in males. Gender should be considered in the design of both stratified medical management and clinical trials.
Digital signal processing for short haul optical data communication systems (2015)

Digital Signal processing is going on spreading from long reach systems to short reach systems. Especially Discrete Multi-Tone is an attractive technology for short reach optical transmission systems. In this paper we review this technology.
Fully automated longitudinal segmentation of new or enlarged multiple sclerosis lesions using 3D convolutional neural networks (2020)

The quantification of new or enlarged lesions from follow-up MRI scans is an important surrogate of clinical disease activity in patients with multiple sclerosis (MS). Not only is manual segmentation time consuming, but inter-rater variability is high. Currently, only a few fully automated methods are available. We address this gap in the field by employing a 3D convolutional neural network (CNN) with encoder-decoder architecture for fully automatic longitudinal lesion segmentation. Input data consist of two fluid attenuated inversion recovery (FLAIR) images (baseline and follow-up) per patient. Each image is entered into the encoder and the feature maps are concatenated and then fed into the decoder. The output is a 3D mask indicating new or enlarged lesions (compared to the baseline scan). The proposed method was trained on 1809 single point and 1444 longitudinal patient data sets and then validated on 185 independent longitudinal data sets from two different scanners. From the two validation data sets, manual segmentations were available from three experienced raters, respectively. The performance of the proposed method was compared to the open source Lesion Segmentation Toolbox (LST), which is a current state-of-art longitudinal lesion segmentation method. The mean lesion-wise inter-rater sensitivity was 62%, while the mean inter-rater number of false positive (FP) findings was 0.41 lesions per case. The two validated algorithms showed a mean sensitivity of 60% (CNN), 46% (LST) and a mean FP of 0.48 (CNN), 1.86 (LST) per case. Sensitivity and number of FP were not significantly different (p < 0.05) between the CNN and manual raters. New or enlarged lesions counted by the CNN algorithm appeared to be comparable with manual expert ratings. The proposed algorithm seems to outperform currently available approaches, particularly LST. The high inter-rater variability in case of manual segmentation indicates the complexity of identifying new or enlarged lesions. An automated CNN-based approach can quickly provide an independent and deterministic assessment of new or enlarged lesions from baseline to follow-up scans with acceptable reliability.