gebhart/patrepeval huggingface dataset:
Screening freshness of seafood by measuring trimethylamine (TMA) levels using helium-plasma ionization mass spectrometry (HePI-MS) (2019)

Abstract Background Trimethylamine (TMA) is a marker used for monitoring the quality of seafood because it is the primary component of the “fishy” odor. Methods The levels of TMA in seafood samples were directly measured by helium-plasma ionization mass spectrometry (HePI-MS). Each sample was directly exposed to the HePI source, and the intensity of the m/z 60 signal for protonated TMA was monitored by a selected-ion-recording (SIR) protocol. Using a set of TMA-spiked water standards, the TMA levels in seafood samples were quantified. Results The signal intensity of the m/z 60 ion from shrimp samples maintained at room temperature for 2 days can be attenuated to baseline levels by adding lime juice. The amounts of TMA in samples of salmon and shrimp recovered from some sushi preparations, and in squid samples, were found to be 0.24 μ g, 0.16 μ g, and 17.2 μg per gram, respectively. Conclusions HePI-MS is an efficient technique to screen and monitor the TMA content and assess the quality of seafood.
Pirprofen in the Treatment of Sports Injuries (1989)

Patients with sports injuries were treated with pirprofen, a non-steroidal anti-inflammatory drug, in two separate studies. In the single centre study, 39 athletes were treated with 1000 mg/day pirprofen for 2 weeks. In the multicentre study, a further 80 athletes were treated with a variable dosage (600-1200 mg/day) until the disappearance of symptoms, but for no longer than 2 weeks. Efficacy was considered excellent or good in 99/119 (83%) of the patients treated. The clinical variables of pain and mobility significantly (P less than 0.05) improved after 1 week of treatment. Tolerability was satisfactory, the main side-effects involving the gastro-intestinal tract.
Inout Secure DB: Maximizing Security for Data INside and OUTside the Database (2019)

As cloud services are becoming an alternative for IT infrastructures in many organizations, guarantees of
data privacy become a priority. This article presents a secure database system that takes privacy as a design principle.
The proposed system offers improved privacy guarantees for data in primary and secondary memory as well as for data
that is served to users as results of SQL queries. Data in working memory is protected using Intel’s SGX platform for
trusted execution, while data in secondary memory uses network coding for secure storage. SGX provides hardware-
based processing privacy offering protection for a wide range of sophisticated attacks. Network coding provides inter
and intra-cloud privacy for stored data (by means of a storage provided by Chocolate Cloud). For privacy of data served
to the outside world, we propose a flexible role-based access control mechanism that anonymizes data at query-time.
We have implemented a modular, multi-service architecture that is well suited to the advantages and limitations of the
SGX platform. We present the architecture of the system, its components and performance evaluation.
RNAi Therapeutics and Applications of MicroRNAs in Cancer Treatment (2013)

RNA interference-based therapies are proving to be powerful tools for combating various diseases, including cancer. Scientists are researching the development of safe and efficient systems for the delivery of small RNA molecules, which are extremely fragile in serum, to target organs and cells in the human body. A dozen pre-clinical and clinical trials have been under way over the past few years involving biodegradable nanoparticles, lipids, chemical modification and conjugation. On the other hand, microRNAs, which control the balance of cellular biological processes, have been studied as attractive therapeutic targets in cancer treatment. In this review, we provide an overview of RNA interference-based therapeutics in clinical trials and discuss the latest technology for the systemic delivery of nucleic acid drugs. Furthermore, we focus on dysregulated microRNAs in human cancer, which have progressed in pre-clinical trials as therapeutic targets, and describe a wide range of strategies to control the expression levels of endogenous microRNAs. Further development of RNA interference technologies and progression of clinical trials will contribute to the achievement of practical applications of nucleic acid drugs.
The combination of electron capture dissociation and fixed charge derivatization increases sequence coverage for <i>O</i>-glycosylated and <i>O</i>-phosphorylated peptides (2007)

Electron capture dissociation (ECD) has become an alternative method to collision-activated dissociation (CAD) to avoid gas-phase cleavage of post-translational modifications carried by side chains from the peptide backbone. Nonetheless, as illustrated herein by the study of O-glycosylated and O-phosphorylated peptides, the extent of ECD fragmentations may be insufficient to cover the entire peptide sequence and to localize accurately these modifications. The present work demonstrates that the derivatization of peptides at their N-terminus by a phosphonium group improves dramatically and systematically the sequence coverage deduced from the ECD spectrum for both O-glycosylated and O-phosphorylated peptides compared with their native counterparts. The exclusive presence of N-terminal fragments (c-type ions) in the ECD spectra of doubly charged molecular cations simplifies peptide sequence interpretation. Thus, the combination of ECD and fixed charge derivatization appears as an efficient analytical tool for the extensive sequencing of peptides bearing labile groups.
Improved stomatal opening enhances photosynthetic rate and biomass production in fluctuating light (2020)

It has been reported that stomatal conductance often limits the steady-state photosynthetic rate. On the other hand, the stomatal limitation of photosynthesis in fluctuating light remains largely unknown, although in nature light fluctuates due to changes in sun position, cloud cover, and the overshadowing canopy. In this study, we analysed three mutant lines of Arabidopsis with increased stomatal conductance to examine to what extent stomatal opening limits photosynthesis in fluctuating light. The slac1 (slow anion channel-associated 1) and ost1 (open stomata 1) mutants with stay-open stomata, and the PATROL1 (proton ATPase translocation control 1) overexpression line with faster stomatal opening responses exhibited higher photosynthetic rates and plant growth in fluctuating light than the wild-type, whereas these four lines showed similar photosynthetic rates and plant growth in constant light. The slac1 and ost1 mutants tended to keep their stomata open in fluctuating light, resulting in lower water-use efficiency (WUE) than the wild-type. However, the PATROL1 overexpression line closed stomata when needed and opened stomata immediately upon irradiation, resulting in similar WUE to the wild-type. The present study clearly shows that there is room to optimize stomatal responses, leading to greater photosynthesis and biomass accumulation in fluctuating light in nature.
Trusted Geolocation-Aware Data Placement in Infrastructure Clouds (2014)

Data geolocation in the cloud is becoming an increasingly pressing problem, aggravated by incompatible legislation in different jurisdictions and compliance requirements of data owners. In this work we present a mechanism allowing cloud users to control the geographical location of their data, stored or processed in plaintext on the premises of Infrastructure-as-a Service cloud providers. We use trusted computing principles and remote attestation to establish platform state. We enable cloud users to confine plaintext data exclusively to the jurisdictions they specify, by sealing decryption keys used to obtain plaintext data to the combination of cloud host geolocation and platform state. We provide a detailed description of the implementation as well as performance measurements on an open source cloud infrastructure platform using commodity hardware.
Application Of Fourier Techniques In CT Detector Alignment (1989)

The application of DFT and FFT techniques provides a simpler detector alignment procedure in a fourth generation computed tomography system. A single scan of a circularly symmetric object can be used to provide the alignment data for this technique. Due to the symmetry involved, filtered autoconvolution employing an FFT technique similar to that used in CT reconstruction generates the locus of the perceived detector positions (known as the alignment curve). The fundamental components of this curve are seperated using a DFT to generate the actual detector alignment correction values. Applying these Fourier techniques to the CT alignment problem has simplified the calibration procedure necessary. Other applications having accurate positioning requirements may also benefit from these techniques.
Nitinol Surface Modification in Gentle Conditions By in Situ Generated Diazonium Salt (2013)

Abstract not Available.
Fast Particle Filters For Multi-Rate Sensors (2007)

Publication in the conference proceedings of EUSIPCO, Poznan, Poland, 2007
Three scenarios of ranking inconsistencies involving search tasks (2016)

Our previous work on assessment of digital breast tomosynthesis (DBT) image quality revealed inconsistencies in ranking the reconstruction algorithms’ performances for a location-known-exactly (LKE) detection and a location-unknown searching task. Such results made us wonder that ranking inconsistencies may not be rare phenomena at all. In this work, we conducted a small literature review that involved three publications (He, Samuelson, Zeng and Sahiner SPIE 2016; Park, Kupinski, Clarkson and Barrett, IPMI 2003 and JOSA 2005). These publications compared the LKE and search performance for a variety of observers using the AUC value as the performance criterion (human observers, CHOs for detection, scanning CHOs for search, and the Markov Chain Monte Carlo ideal observer for detection and search). We categorized the experimental findings into three types of ranking inconsistencies: 1) Ranking inconsistencies in LKE and search tasks; 2) human/ideal observer ranking inconsistencies; and 3) LKE/search ranking inconsistencies in the presence of signal variability. The empirical evidence presented in this work suggested that ranking inconsistencies for imaging systems existed, but these inconsistencies often do not draw enough attention in the literature.
Choroidal Neovascular Membrane Formation and Retinochoroidopathy in a Patient with Systemic Langerhans Cell Histiocytosis: A Case Report and Review of the Literature (2012)

We report a case of bilateral atrophic retinochoroidopathy with choroidal neovascular membrane (CNVM) formation in a patient with systemic Langerhans cell histiocytosis (LCH). A 35-year-old female, diagnosed with LCH at the age of 3, experienced an episode of acute vision loss in her right eye. Visual acuity was counting fingers. Dilated fundus exam and fluorescein angiography revealed the presence of CNVM along with bilateral widespread areas of chorioretinal atrophy. The patient underwent removal of CNVM with excellent postoperative visual acuity (20/25); however, indolent progression of her disease led to gradual deterioration of visual acuity (20/80 in the right eye and 20/320 in the left). This case shows that in contrast to previous reports, intraocular involvement of LCH does not need to be dramatic and clinically evident but it can acquire a chronic degenerative form. This report aims to raise awareness among ophthalmologists concerning the potential intraocular sequelae of LCH.
[P1–260]: A COMPUTATIONAL MONTE‐CARLO SIMULATION STRATEGY TO COMPARE THE ONSET OF DIFFERENT BIOMARKER AND COGNITIVE CHANGES (2017)

Longitudinal data can be used to clarify the temporal sequence of biomarker and cognitive changes associated with Alzheimer's disease (AD). Here, we capitalizing on longitudinal data from the AD Neuroimaging Initiative (ADNI) and mixed effect modeling to introduce the use of a Computational Monte-Carlo Simulation (CMCS) method to compare the onset of different AD-related biomarker and cognitive changes. We sought to characterize and compare the onset of progressive hippocampus volume (VHC) and Mini-Mental State Examination (MMSE) declines in 129 persons with mild cognitive impairment (MCI) who progressed to probable AD dementia and 253 persons with MCI who remained stage during the same time frame. The CMCS method was used in the following way to test the hypothesis that the onset of VHC decline is x-years earlier than MMSE decline in subsequent progressors versus non-progressors: It 1) simulated each person's longitudinal data with mixed effect model using the perspective fixed effect parameters, characterized random effect parameters and residual error, and accounted for a variance as high as 200%; 2) fitted the mixed effect model to simulated data to characterize respective ages at onset of progressive VHC and MMSE decline in the progressors; 3) computed the difference between these ages of onset; 4) repeated the process N times; and 5) computed type-I error of finding based on the percentage of times that VHCdecline preceded MMSE decline by a given number of years. VHC and MMSE declines in progressors diverged from non-progressors 6.7 and 3.5 years before progression to probable AD dementia, respectively. Out of 500 simulations, VHCfailed to decline earlier than MMSE scores 0 times (p<0.002); at least one year earlier 4 times (p=0.008); at least 2 years earlier 23 times (p=0.045), and at least 3 years earlier 85 times (p=0.17). Findings remained significant with variances as high as 200%. The CMCS method can be used to compare the temporal sequence of different AD biomarker and cognitive changes.
INSULIN ATTENUATES THE SYSTEMIC INFLAMMATORY RESPONSE DURING ENDOTOXEMIA (2004)

Jeschke, M G; Klein, D; Rensing, H; Tracey, K J; Bolder, U; Einspanier, R Author Information
Numerical Studies of Reacting Flows over Flat Walls with Fuel Injection. (Part 1, Velocity Anomaly and Hydrodynamic Instability). (1998)

A computational study is performed on a chemically reacting laminar boundary layer over a porous horizontal wall with a diffusion flame. The generation of counter-rotating vortices along the flame sheet is observed. Our attention is focused on i)local acceleration, which induces an anomaly in the velocity distributions across the flat plate boundary layer, and ii)the origin of hydrodynamic instability, which may disturb and wrinkle the flame downstream. Results show that when reaction exothermicity is taken into account in the numerical simulation, both the aerodynamic structures and the mass transfer of the chemical species change significantly, especially in the region near the front edge of the burner. Counter-rotating vortices are generated along the flame sheet and are expected to induce hydrodynamic instability. A high pressure zone in front of the leading flame edge and local acceleration are numerically simulated in agreement with experimental observation. Buoyancy plays a negligible role in the behavior of flow and combustion in regions upstream of the burner.
Optimizing Patient Positioning and Understanding Radiofrequency Energy in Gynecologic Surgery (2010)

Safety in the operating room environment should be a priority for every surgeon. Two areas where safety can often be overlooked and taken for granted are patient positioning and electrosurgical use. Understanding neuroanatomical relationships can help the surgeon optimally position patients and minimize the incidence of postoperative neuropathy while maintaining functional and unobstructed access to the patient and surgical field. Given the widespread use of radiofrequency devices in daily surgical practice, a working knowledge of the principles of electrosurgery is vital to the gynecologic surgeon. Although electrothermal injuries are rare, they can be devastating when unrecognized and poorly understood. Advances in the safety and efficacy of these instruments will continue to aid in decreasing the risks associated with electrosurgery.
Magnetic ground state of a thin-film element (2000)

By means of three-dimensional numerical calculations we studied possible micromagnetic configurations in a rectangular Permalloy-like thin-film element. The parameters were chosen to be compatible with the so-called micromagnetic standard problem 1. We demonstrate that for these parameters a diamond domain pattern is the lowest energy state that replaces cross-tie patterns favorable in larger elements. Only at smaller sizes does the originally envisaged Landau pattern form the ground state. The transition to high-remanence structures (or what would be comparable to a "single-domain" state) is found for lateral sizes that are an order of magnitude smaller than the benchmark parameters. The transitions among the different domain patterns become plausible in view of the energy of symmetric Neel walls in extended thin films. The features of the high-remanence structures can be derived from the principle of uniform charge distribution.
The A-factor-binding protein of Streptomyces griseus negatively controls streptomycin production and sporulation (1990)

A-factor, 2-(6'-methylheptanoyl)-3R-hydroxymethyl-4-butanolide, is an autoregulator essential for streptomycin production and sporulation in Streptomyces griseus. S. griseus 2247 that requires no A-factor for streptomycin production or sporulation was found to have a defect in the A-factor-binding protein. This observation implied that the A-factor-binding protein in the absence of A-factor repressed the expression of both phenotypes in the wild-type strain. Screening among mutagenized S. griseus colonies for strains producing streptomycin and sporulating in the absence of A-factor yielded three mutants that were also deficient in the A-factor-binding protein. Reversal of the defect in the A-factor-binding protein of these mutants led to the simultaneous loss of streptomycin production and sporulation. These data suggested that the A-factor-binding protein played a role in repressing both streptomycin production and sporulation and that the binding of A-factor to the protein released its repression. Mutants deficient in the A-factor-binding protein began to produce streptomycin and sporulate at an earlier stage of growth than did the wild-type strain. These mutants produced approximately 10 times more streptomycin than did the parental strain. These findings are consistent with the idea that the intracellular concentration of A-factor determines the timing of derepression of the gene(s) whose expression is repressed by the A-factor-binding protein.
Epimerization and desaturation by carbapenem synthase (CarC). A hybrid DFT study (2006)

The mechanism of the unusual epimerization and desaturation reactions catalyzed by carbapenem synthase was investigated using the hybrid density functional method B3LYP. Several different models have been used in the calculations to study five component reactions. Both protonated and deprotonated models for the substrate have been explored so that the effects of hydrogen bonds could be characterized. Besides the iron site, it is proposed that a some tyrosine residue, possibly Tyr67, is involved in the hydrogen abstraction step. The calculated energetics and barrier heights support this hypothesis, and are consistent with the known experimental data concerning CarC and other 2-oxoglutarate dependent dioxygenases.
A critique on decentralized finance from a social, political, and economic perspective (2023)

Throughout the ages, social change has largely been brought as a reaction against an establishing entity or idea. Communism, for instance, was a reaction against the industrial revolution that exacerbated the exploitative nature of capitalism. Contemporarily, we are living through perhaps one of the most critical turning points in finance that began as a reaction against the solipsistic nature of Wall Street bankers prior to the 2008 financial crisis. This new movement exists within the robust ecosystem of decentralized finance (DeFi). Throughout the past decade, innovation within DeFi has grown exponentially, such that literature on its social, political, and economic effects is yet to be well-understood. Thus, this research paper intends to deconstruct the underlying socio-economic systems surrounding DeFi in order to understand, analyze, and critique its fundamental values and assumptions. The primary philosophical concern is whether decentralized finance can be a suitable substitute to the current financial system via its notions of personal financial freedom.
Lynch syndrome founder mutations in families of Navajo and German-American heritage (2004)

9511 Background: Lynch syndrome is caused by mutations in mismatch repair (MMR) genes which confer extraordinarily high risk of colorectal cancer, endometrial, ovarian as well as lesser occurring cancer types. Carriers of these MMR mutations require genetic counseling, clinical surveillance, and targeted management. Methods: An MLH1 mutation among the Navajo consisted of a four basepair deletion beginning at the first nucleotide of codon 727. In Caucasians a deletion encompassing exons 1 - 6 of MSH2 occurred. To facilitate the diagnosis of these mutations, specific PCR-based tests were developed and used for large-scale screening of individuals at risk. An extensive genealogical and historical study was performed in search for a common origin of each mutation and its spread. Results: The MLH1 deletion mutation was found in members of six widely dispersed Navajo families in Arizona. To date, 386 individuals from these families have been identified to be at risk of whom 142 individuals have been tested with 56 harboring the mutation. The MSH2 deletion mutation was found in members of nine Caucasian families living in various parts of the U.S. To date 566 family members of the nine probands have been identified to be at risk and counseled; 137 of these have been tested, and 61 carry the mutation. Carriers of the mutation have already been identified in 14 states. Three of these families have been genealogically shown to descend from a German immigrant family that arrived in Pennsylvania in 1727. Conclusions: The postulated high frequency and continent-wide geographic distribution of these founder mutations beg the suggestion that until more is learned about their occurrences, the routine testing of individuals at risk for Lynch syndrome in the U.S. might include an assay for these mutations in the interest of early cancer detection and improved cancer control. No significant financial relationships to disclose.
Very late relapse in diffuse large B-cell lymphoma represents clonally related disease and is marked by germinal center cell features (2003)

Patients with diffuse large B-cell lymphoma (DLBCL) rarely show relapse after 4 years of complete remission (CR). In this study, we addressed the following questions: (1) Does late-relapsing DLBCL represent clonally related disease or a second malignancy; and (2) is there a characteristic biologic background? In 10 of 13 DLBCL patients with relapse after 4 to 17 years, a clonal relationship was established based on identical IgH-sequences and/or identical bcl2-IgH translocation. Most (77%) showed features of germinal center (GC) cells, as defined by expression of CD10, bcl-2, and bcl-6 protein and ongoing immunoglobulin heavy chain variable region (VH) hypermutation. A GC phenotype was seen in 8 (20%) of 38 control patients matched for age, stage, and (extra)nodal localization with relapse within 2.5 years (P =.005). In conclusion, we have found evidence that late-relapsing DLBCL represents truly clonally related disease episodes in most cases and that this clinical behavior may be related to the biologic features of GC cells.