gebhart/patrepeval huggingface dataset:
Syntaxin Requirement for Ca<sup>2+</sup>-Triggered Exocytosis in Neurons and Endocrine Cells Demonstrated with an Engineered Neurotoxin (2011)

Botulinum neurotoxins cleave synaptic SNAREs and block exocytosis, demonstrating that these proteins function in neurosecretion. However, the function of the SNARE syntaxin remains less clear because no neurotoxin cleaves it selectively. Starting with a botulinum neurotoxin that cleaves both syntaxin and SNAP-25, we engineered a version that retains activity against syntaxin but spares SNAP-25. These mutants block synaptic release in neurons and norepinephrine release in neuroendocrine cells, thus establishing an essential role for syntaxin in Ca2+-triggered exocytosis. These mutants can generate syntaxin-free cells as a useful experimental system for research and may lead to pharmaceuticals that target syntaxin selectively.
A multi-omic cohort as a reference point for promoting a healthy human gut microbiome (2019)

Abstract More than a decade of gut microbiome studies have a common goal for human health. As most of the disease studies sample the elderly or the middle-aged, a reference cohort for young individuals has been lacking. It is also not clear what other omics data need to be measured to better understand the gut microbiome. Here we present high-depth metagenomic shotgun sequencing data for the fecal microbiome together with other omics data in a cohort of 2,183 adults, and observe a number of vitamins, hormones, amino acids and trace elements to correlate with the gut microbiome and cluster with T cell receptors. Associations with physical fitness, sleeping habits and dairy consumption are identified in this large multi-omic cohort. Many of the associations are validated in an additional cohort of 1,404 individuals. Our comprehensive data are poised to advise future study designs to better understand and manage our gut microbiome both in population and in mechanistic investigations.
Formation of Ion Irradiation Induced Small-Scale Defects on Graphite Surfaces (1996)

We use molecular dynamics simulations and ab initio calculations to study the structures and formation probabilities of isolated surface defects produced by ion irradiation of (1000) graphite. We improve the conventionally used Tersoff potential [J. Tersoff, Phys. Rev. Lett. 61, 2879 (1988)] to realistically describe interlayer forces in graphite and high-energy processes in carbon. We identify three defect structures which correspond to experimentally observed hillocks on graphite surfaces, and examine their formation at different implantation energies.
PSCR: a coherence protocol for eliminating passive sharing in shared-bus shared-memory multiprocessors (1999)

In high-performance general-purpose workstations and servers, the workload can be typically constituted of both sequential and parallel applications. Shared-bus shared-memory multiprocessor can be used to speed-up the execution of such workload. In this environment, the scheduler takes care of the load balancing by allocating a ready process on the first available processor, thus producing process migration. Process migration and the persistence of private data into different caches produce an undesired sharing, named passive sharing. The copies due to passive sharing produce useless coherence traffic on the bus and coping with such a problem may represent a challenging design problem for these machines. Many protocols use smart solutions to limit the overhead to maintain coherence among shared copies. None of these studies treats passive-sharing directly, although some indirect effect is present while dealing with the other kinds of sharing. Affinity scheduling can alleviate this problem, but this technique does not adapt to all load conditions, especially when the effects of migration are massive. We present a simple coherence protocol that eliminates passive sharing using information from the compiler that is normally available in operating system kernels. We evaluate the performance of this protocol and compare it against other solutions proposed in the literature by means of enhanced trace-driven simulation. We evaluate the complexity in terms of the number of protocol states, additional bus lines, and required software support. Our protocol further limits the coherence-maintaining overhead by using information about access patterns to shared data exhibited in parallel applications.
IL-10 and IL-10 Receptor Mutations in Very Early Onset Inflammatory Bowel Disease (2017)

Very early onset inflammatory bowel disease (VEO-IBD) is a unique disease entity with a complex genetic susceptibility in affected patients. Next-generation gene sequencing techniques have revealed various monogenetic mutations contributing to the pathogenesis of VEO-IBD, including interleukin 10 (IL-10) and IL-10 receptor (IL-10R) mutations. In this article, we reviewed the features of and effective therapeutic options for VEO-IBD with IL-10 and/or IL-10R mutations. The IL-10 signal pathway inhibits the release of several key cytokines and thereby has a significant anti-inflammatory effect in the gastrointestinal tract. Mutations of the genes encoding IL-10 and/or IL-10R have been detected in VEO-IBD patients among myriad populations throughout the world. VEO-IBD patients with IL-10 or IL-10R mutations often present with repeated bouts of bloody diarrhea, marked weight loss, growth retardation, and recurrent perianal problems, including abscesses, fistulas, and significant fissures. Moreover, some patients may have folliculitis and present with pulmonary infections. While the therapeutic efficacy of immunosuppressants is typically poor in these patients, allogeneic hematopoietic stem cell transplantation (HSCT) has been reported to improve symptoms significantly. However, the long-term prognosis of VEO-IBD patients with IL-10 or IL-10R gene mutations treated with HSCT requires further exploration to verify the efficacy and safety of this treatment. We concluded that clinicians should recognize the clinical phenotype of VEO-IBD, as mutational analysis of the IL-10 pathway can support the diagnosis and prompt early treatment of this complicated disease.
Zero-energy pinning of topologically trivial bound states in multiband semiconductor-superconductor nanowires (2019)

Recent tunneling conductance measurements on semiconductor-superconductor nanowires find zero-bias peaks to be ubiquitous across wide ranges of chemical potential and Zeeman energy J. Chen et al., Phys. Rev. Lett. 123, 107703 (2019). Motivated by this, we demonstrate that topologically trivial Andreev abound states (ABSs) pinned near zero energy are produced rather generically in inhomogeneous systems with multiband occupancy in the presence of interband coupling. We first investigate the interband coupling mechanism responsible for the pinning within a multiband one-dimensional toy model, then we confirm the findings using a three-dimensional Schr\"odinger-Poisson approach that incorporates the geometric and electrostatic details of the actual device. Our analysis shows that level repulsion generated by interband coupling can lead to a rather spectacular pinning of the lowest-energy mode near zero energy in systems (or regions) characterized by very short length scales ($\ensuremath{\sim}100\phantom{\rule{0.28em}{0ex}}\mathrm{nm}$). We show that level repulsion between the lowest-energy levels can mimic the gap opening feature (simultaneous with the emergence of a near-zero-energy mode) predicted to occur in Majorana hybrid systems. We also demonstrate that nearly zero-bias differential conductance features exhibiting particle-hole asymmetry are due to the presence of (topologically trivial) ABSs pinned near zero energy by level repulsion, not to Majorana zero modes, quasi-Majoranas, or any other low-energy mode that involves (partially) separated Majorana bound states. Our findings demonstrate the importance of understanding in detail multiband physics and electrostatic effects in the context of the ongoing search for Majorana modes in semiconductor-superconductor heterostructures.
Deep learning methods for automated detection of new multiple sclerosis lesions in longitudinal magnetic resonance images (2020)

This thesis is focused on developing novel and fully automated methods for the detection of new multiple sclerosis (MS) lesions in\n\n\t\t\t\t longitudinal brain magnetic resonance imaging (MRI). First, we proposed a fully automated logistic regression-based framework for\n\n\t\t\t\t the detection and segmentation of new T2-w lesions. The framework was based on intensity subtraction and deformation field (DF).\n\n\t\t\t\t Second, we proposed a fully convolutional neural network (FCNN) approach to detect new T2-w lesions in longitudinal brain MR\n\n\t\t\t\t images. The model was trained end-to-end and simultaneously learned both the DFs and the new T2-w lesions. Finally, we\n\n\t\t\t\t proposed a deep learning-based approach for MS lesion synthesis to improve the lesion detection and segmentation performance\n\n\t\t\t\t in both cross-sectional and longitudinal analysis
Chitosan Films Doped with Gold Nanorods as Laser‐Activatable Hybrid Bioadhesives (2010)

Biocompatible chitosan/gold nanorods films are fabricated and tested as laser-activatable adhesives. When exposed to near-infrared laser light the nanoparticles carry out efficient photothermal conversion, which activates the polar groups of chitosan strands and mediates functional adhesion with a biological tissue. This technology may enable a number of key applications in medicine including tissue repair, wound dressing and drug delivery. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Vitamin C and isovitamin C derived chemistry. 3. Chiral butenolides via efficient 2,3-didehydroxylations of L-gulono-, D-mannono-, and D-ribono-1,4-lactones (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVitamin C and isovitamin C derived chemistry. 3. Chiral butenolides via efficient 2,3-didehydroxylations of L-gulono-, D-mannono-, and D-ribono-1,4-lactonesJozef A. J. M. Vekemans, Gabriel A. M. Franken, Cornelis W. M. Dapperens, Erik F. Godefroi, and Gordon J. F. ChittendenCite this: J. Org. Chem. 1988, 53, 3, 627–633Publication Date (Print):February 1, 1988Publication History Published online1 May 2002Published inissue 1 February 1988https://pubs.acs.org/doi/10.1021/jo00238a028https://doi.org/10.1021/jo00238a028research-articleACS PublicationsRequest reuse permissionsArticle Views732Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Antiepileptic drugs for neuropathic pain and fibromyalgia - an overview of Cochrane reviews (2013)

Clinical trial evidence supported the use of only gabapentin and pregabalin in some neuropathic pain conditions (painful diabetic neuropathy, postherpetic neuralgia, and central neuropathic pain) and fibromyalgia. Only a minority of people achieved acceptably good pain relief with either drug, but it is known that quality of life and function improved markedly with the outcome of at least 50% pain intensity reduction. For other antiepileptic drugs there was no evidence, insufficient evidence, or evidence of a lack of effect; this included carbamazepine. Evidence from clinical practice and experience is that some patients can achieve good results with antiepileptics other than gabapentin or pregabalin.There is no firm evidence to answer the important pragmatic questions about which patients should have which drug, and in which order the drugs should be used. There is a clinical effectiveness research agenda to provide evidence about strategies rather than interventions, to produce the overall best results in a population, in the shortest time, and at the lowest cost to healthcare providers.
Secure Evaluation of Private Linear Branching Programs with Medical Applications. (2009)

Abstract. Diagnostic and classification algorithms play an important role in data analysis, with applications in areas such as health care, fault diagnostics, or benchmarking. Branching programs (BP) is a popular representation model for describing the underlying classification/diagnostics algorithms. Typical application scenarios involve a client who provides data and a service provider (server) whose diagnostic program is run on client’s data. Both parties need to keep their inputs private. We present new, more efficient privacy-protecting protocols for remote evaluation of such classification/diagnostic programs. In addition to efficiency improvements, we generalize previous solutions – we securely evaluate private linear branching programs (LBP), a useful generalization of BP that we introduce. We show practicality of our solutions: we apply our protocols to the privacy-preserving classification of medical ElectroCardioGram (ECG) signals and present implementation results. Finally, we discover and fix a subtle security weakness of the most recent remote diagnostic proposal, which allowed malicious clients to learn partial information about the program. 1
CRISPR targeting of MEIOTIC-TOPOISOMERASE VIB-dCas9 to a recombination hotspot is insufficient to increase crossover frequency in Arabidopsis (2021)

Abstract During meiosis, homologous chromosomes pair and recombine, which can result in reciprocal crossovers that increase genetic diversity. Crossovers are unevenly distributed along eukaryote chromosomes and show repression in heterochromatin and the centromeres. Within the chromosome arms crossovers are often concentrated in hotspots, which are typically in the kilobase range. The uneven distribution of crossovers along chromosomes, together with their low number per meiosis, creates a limitation during crop breeding, where recombination can be beneficial. Therefore, targeting crossovers to specific genome locations has the potential to accelerate crop improvement. In plants, meiotic crossovers are initiated by DNA double strand breaks (DSBs) that are catalysed by SPO11 complexes, which consist of two catalytic (SPO11-1 and SPO11-2) and two non-catalytic subunits (MTOPVIB). We used the model plant Arabidopsis thaliana to target a dCas9-MTOPVIB fusion protein to the 3a crossover hotspot via CRISPR. We observed that this was insufficient to significantly change meiotic crossover frequency or pattern within 3a . We discuss the implications of our findings for targeting meiotic recombination within plant genomes.
Functionalized Single-Walled Carbon Nanotube-Based Fuel Cell Benchmarked Against US DOE 2017 Technical Targets (2013)

Chemically modified single-walled carbon nanotubes (SWNTs) with varying degrees of functionalization were utilized for the fabrication of SWNT thin film catalyst support layers (CSLs) in polymer electrolyte membrane fuel cells (PEMFCs), which were suitable for benchmarking against the US DOE 2017 targets. Use of the optimum level of SWNT -COOH functionality allowed the construction of a prototype SWNT-based PEMFC with total Pt loading of 0.06 mg(Pt)/cm²--well below the value of 0.125 mg(Pt)/cm² set as the US DOE 2017 technical target for total Pt group metals (PGM) loading. This prototype PEMFC also approaches the technical target for the total Pt content per kW of power (<0.125 g(PGM)/kW) at cell potential 0.65 V: a value of 0.15 g(Pt)/kW was achieved at 80°C/22 psig testing conditions, which was further reduced to 0.12 g(Pt)/kW at 35 psig back pressure.
Characterization of the Reaction between Sialic Acid (N-Acetylneuraminic Acid) and Hydrogen Peroxide (2007)

In a previous report, we had demonstrated the antioxidant activity of the sialic acid N-acetylneuraminic acid (Neu5Ac, NANA). This activity can counteract the cytotoxicity of hydrogen peroxide (H2O2), and the antitoxicity is a result of a direct chemical reaction, whereby NANA reduces H2O2 in the culture media. The influence of the potential of hydrogen (pH) and temperature in this reaction was investigated. The reaction velocity is remarkably less at low pH and/or low temperature, but it increases with these parameters. Furthermore, the reaction product generated in the slow reaction under acidic conditions (pH 3.1) was analyzed. We detected 4-(acetylamino)-2,4-dideoxy-D-glycero-D-galacto-octonic acid (ADOA) as the decarboxylation product of NANA; this is the same product we previously obtained in a faster reaction at neutral pH (pH 7.5). Furthermore, ADOA was generated not only from the reaction with the NANA monomer but also from that with alpha(2-->8) homodimer of NANA (DP2). Thus, it can be considered that the reaction between NANA and H2O2 can occur under various pH conditions and for NANA residues in a glycochain.
Model-based Deep Reinforcement Learning for Dynamic Portfolio Optimization (2019)

Dynamic portfolio optimization is the process of sequentially allocating wealth to a collection of assets in some consecutive trading periods, based on investors' return-risk profile. Automating this process with machine learning remains a challenging problem. Here, we design a deep reinforcement learning (RL) architecture with an autonomous trading agent such that, investment decisions and actions are made periodically, based on a global objective, with autonomy. In particular, without relying on a purely model-free RL agent, we train our trading agent using a novel RL architecture consisting of an infused prediction module (IPM), a generative adversarial data augmentation module (DAM) and a behavior cloning module (BCM). Our model-based approach works with both on-policy or off-policy RL algorithms. We further design the back-testing and execution engine which interact with the RL agent in real time. Using historical {\em real} financial market data, we simulate trading with practical constraints, and demonstrate that our proposed model is robust, profitable and risk-sensitive, as compared to baseline trading strategies and model-free RL agents from prior work.
Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. (1993)

In eukaryotes, initiation of mRNA synthesis is a multistep process that is carried out by RNA polymerase II and auxiliary factors that are commonly referred to as basal or general factors. In this study accurate initiation of transcription was reconstituted with purified, Escherichia coil-synthesized TFIIB, TBP (the TATA box-binding polypeptide of the TFIID complex), and the 30-kD subunit of TFIIF (also known as RAP30), along with purified, native RNA polymerase II from Drosophila embryos, calf thymus, or HeLa cells. This minimal set of factors was able to transcribe a subset of the promoters tested. The addition of both subunits of TFIIE and the 74-kD subunit of TFIIF increased the efficiency of transcription by a factor of 2 to 4. In contrast, the inclusion of a crude TFIID fraction from Drosophila embryos in place of recombinant TBP resulted in a strong dependence on TFIIE. By gel mobility-shift analysis, TFIIB, TBP, RAP30, and polymerase were able to assemble into DB and DBPolF30 complexes with transcriptionally competent (wild type or initiator mutant), but not with transcriptionally inactive (TATA and TATA/initiator mutant), versions of the Drosophila Adh promoter. Thus, it appears that RNA polymerase II is able to initiate transcription subsequent to assembly of the DBPolF30 complex, which is a minitranscription complex that represents the central core of the RNA polymerase II transcriptional machinery.
Access control policies enforcement in a cloud environment: Openstack (2015)

Cloud computing has become a widely used paradigm in many IT domains such as e-health. It offers several advantages to the users, e.g. elasticity, flexibility and the rapid sharing of a huge set of digital data. However, many security and privacy concerns still pose significant challenges. In particular, the most identified problem is how to enforce the user's security policy in the access control of the outsourced data. In fact, cloud environments does not provide facilities to support high level defined security policies. For instance, the swift storage component of openstack supports only fine grained access control to execute a specific action on a specific defined object. In this paper, we designed and implemented a middleware to provide high level security policies while using such swift fine grained primitives. An e-health collaborative application dedicated for remote diagnosis is used to illustrate the suggested approach.
Speech coding, reconstruction and recognition using acoustics and electromagnetic waves (2023)

The use of EM radiation in conjunction with simultaneously recorded acoustic speech information enables a complete mathematical coding of acoustic speech. The methods include the forming of a feature vector for each pitch period of voiced speech and the forming of feature vectors for each time frame of unvoiced, as well as for combined voiced and unvoiced speech. The methods include how to deconvolve the speech excitation function from the acoustic speech output to describe the transfer function each time frame. The formation of feature vectors defining all acoustic speech units over well defined time frames can be used for purposes of speech coding, speech compression, speaker identification, language-of-speech identification, speech recognition, speech synthesis, speech translation, speech telephony, and speech teaching.
High-Quality Metal Oxide Core/Shell Nanowire Arrays on Conductive Substrates for Electrochemical Energy Storage (2012)

The high performance of a pseudocapacitor electrode relies largely on a scrupulous design of nanoarchitectures and smart hybridization of bespoke active materials. We present a powerful two-step solution-based method for the fabrication of transition metal oxide core/shell nanostructure arrays on various conductive substrates. Demonstrated examples include Co(3)O(4) or ZnO nanowire core and NiO nanoflake shells with a hierarchical and porous morphology. The "oriented attachment" and "self-assembly" crystal growth mechanisms are proposed to explain the formation of the NiO nanoflake shell. Supercapacitor electrodes based on the Co(3)O(4)/NiO nanowire arrays on 3D macroporous nickel foam are thoroughly characterized. The electrodes exhibit a high specific capacitance of 853 F/g at 2 A/g after 6000 cycles and an excellent cycling stability, owing to the unique porous core/shell nanowire array architecture, and a rational combination of two electrochemically active materials. Our growth approach offers a new technique for the design and synthesis of transition metal oxide or hydroxide hierarchical nanoarrays that are promising for electrochemical energy storage, catalysis, and gas sensing applications.