gebhart/patrepeval huggingface dataset:
Land Treatment of Petroleum Hydrocarbon-Based Drill Cuttings: Pilot Scale Field Study (1992)

Abstract A pilot scale feasibility study was initiated to evaluate the feasibility of landfarming diesel mud residues in southeastern Oklahoma. Results indicated that land application of diesel residues is an environmentally acceptable disposal method. In a plot with an initial oil and grease (O&amp;G) loading rate of 7.6%, the O&amp;G content decreased by 89.5% during the 209-day study interval. Addition of nutrients enhanced degradation rates and reduced O&amp;G levels below the 1% phytotoxic threshold. An O&amp;G loading rate of 5.8% resulted in no measurable hydrocarbon migration in the soil profile. BTEX levels in leachate samples did not exceed drinking water standards. Total metals measured in the zone of incorporation did not exceed guidelines for limiting constituents. Seed germination studies suggested that landfarming operations could be revegetated within 180 days.
Temperature-Dependent Regulation of Upstream Open Reading Frame Translation in S. Cerevisiae (2019)

Abstract Background Translation of an mRNA in eukaryotes starts at AUG in most cases. Near-cognate codons (NCCs) such as UUG, ACG and AUU are also used as start sites at low levels in S. cerevisiae . Initiation from NCCs or AUGs in the 5’-untranslated regions (UTRs) of mRNAs can lead to translation of upstream open reading frames (uORFs) that might regulate expression of the main ORF (mORF). Although there is some circumstantial evidence that the translation of uORFs can be affected by environmental conditions, little is known about how it is affected by changes in growth temperature. Results Using reporter assays, we found that changes in growth temperature can affect translation from NCC start sites in yeast cells, suggesting the possibility that gene expression could be regulated by temperature by altering use of different uORF start codons. Using ribosome profiling, we provide evidence that growth temperature regulates the efficiency of translation of nearly 200 uORFs in S. cerevisiae . Of these uORFs, most that start with an AUG codon have increased translational efficiency at 37 °C relative to 30 °C and decreased efficiency at 20 °C. For translationally regulated uORFs starting with NCCs, we did not observe a general trend for the direction of regulation as a function of temperature, suggesting mRNA-specific features can determine the mode of temperature-dependent regulation. Consistent with this conclusion, the position of the uORFs in the 5’-leader relative to the 5’-cap and the start codon of the main ORF correlates with the direction of temperature-dependent regulation of uORF translation. We have identified several novel cases in which changes in uORF translation are inversely correlated with changes in the translational efficiency of the downstream main ORF. Our data suggest that translation of these mRNAs is subject to temperature-dependent, uORF-mediated regulation. Conclusions Overall, our data suggest that alterations in the translation of specific uORFs by temperature can regulate gene expression in S. cerevisiae .
Interactions between higher-order aberrations and sphero-cylinder refraction (2006)

Purpose To investigate how the presence of higher–order wavefront errors such as combinations of trefoil (along 30°), vertical coma, and spherical aberration influence the optimal sphero–cylindrical correction of the eye. Methods A total of 25 artificial test wavefronts, subdivided in to 5 different combinations of trefoil, coma, and spherical aberration and 5 levels of total higher–order root mean square errors (HO–RMS), were created for a 5 mm pupil zone. Four of the wavefront combinations contained coma, trefoil and spherical aberration of various signs with total HO–RMS levels between 0.1 and 0.5 microns. The other wavefront type contained only spherical aberration with HO–RMS levels also between 0.1 and 0.5 microns. Refractive power maps were created from the wavefronts and fitted with 2,025 different sphero–cylindrical combinations. For each sphero–cylinder the visual Strehl ratio based on the modulation transfer function (VSMTF) was calculated (i.e. ratio of the volumes under the MTF and the diffraction limited MTF). Retinal images and refractive power histograms were calculated for the refractive power maps corresponding to the peak of the VSMTF. Wavefronts from 3 real keratoconic eyes were also used for the analysis. Results The retinal image quality (VSMTF) for wavefronts consisting of vertical coma, trefoil (along 30°) and spherical aberration, could be improved with sphero–cylinders of various magnitudes and directions (i.e. positive or negative sphere and with–the–rule or against–the rule cylinder). For example the combination of positive trefoil (Z(3,–3) = +0.325 microns), negative vertical coma (Z(3,–1) = –0.325 microns) and negative spherical aberration (Z(4,0) = –0.2 microns, i.e. total HO–RMS = 0.5 microns) was optimized with positive sphere and against–the–rule cylinder (+0.875/–0.625x90°). As expected, spherical aberration alone changed the best focal plane thereby affecting the best sphere. A clinically significant level of sphero–cylinder corrections (i.e. 0.25 D) was reached when HO–RMS levels were between 0.2 and 0.3 microns. For the keratoconic eyes, higher–order aberrations also influenced the optimal sphero–cylinder required to produce the best retinal image. Conclusions The combination of the three higher–order aberrations trefoil, coma, and spherical aberration, at levels that are often encountered in aberrated eyes, influence sphero–cylindrical refraction. These findings have implications for the understanding of optimal subjective and objective sphero–cylinder refraction results.
A Survey of Robust Control in Both Frequency Domain and Time Domain (2014)

This survey paper reviews robust control problems in both frequency domain and time domain. Robust control is focused on model uncertainties such as modeling error, system parameter variations, and disturbances. Robust control design problems are discussed according to parameter uncertainty, polytopic uncertainty, and norm-bounded uncertainty. Nowadays, robust control theory is combined with various control theory such as model predictive control, adaptive control, intelligent control, and time delay control.
Adaptive Analytical MMA with time-varying MIMO channels and diversity in interception context (2009)

This paper deals with blind source separation (BSS) with time-varying MIMO (Multiple Input Multiple Output) channels in interception and diversity context (Alamouti code). A new algorithm based on an adaptive AnalyticalMultiModulus Algorithm (MMA) is proposed and called adaptive-AMMA. An analytical method, which converges quickly, is necessary with time varying channels. Performances obtained with adaptive-AMMA are better than adaptive-ACMA (Analytical Constant Modulus Algorithm) and simple MMA for time-varying channels. In addition, this proposed method has done jointly source separation and carrier phase recovery contrary to the adaptive-ACMA. After separation by BSS, the Alamouti code synchronization is found again and then an exploitation of the Alamouti diversity is proposed to raise sources order indetermination inherent with BSS.
Hyp3rArmor: reducing web application exposure to automated attacks (2016)

Web applications (webapps) are subjected constantly to automated, opportunistic attacks from autonomous robots (bots) engaged in reconnaissance to discover victims that may be vulnerable to specific exploits. This is a typical behavior found in botnet recruitment, worm propagation, largescale fingerprinting and vulnerability scanners. Most anti-bot techniques are deployed at the application layer, thus leaving the network stack of the webapp’s server exposed. In this paper we present a mechanism called Hyp3rArmor, that addresses this vulnerability by minimizing the webapp’s attack surface exposed to automated opportunistic attackers, for JavaScriptenabled web browser clients. Our solution uses port knocking to eliminate the webapp’s visible network footprint. Clients of the webapp are directed to a visible static web server to obtain JavaScript that authenticates the client to the webapp server (using port knocking) before making any requests to the webapp. Our implementation of Hyp3rArmor, which is compatible with all webapp architectures, has been deployed and used to defend single and multi-page websites on the Internet for 114 days. During this time period the static web server observed 964 attempted attacks that were deflected from the webapp, which was only accessed by authenticated clients. Our evaluation shows that in most cases client-side overheads were negligible and that server-side overheads were minimal. Hyp3rArmor is ideal for critical systems and legacy applications that must be accessible on the Internet. Additionally Hyp3rArmor is composable with other security tools, adding an additional layer to a defense in depth approach.
Ionothermal Synthesis of Sulfidobismuth spiro‐Dicubane Cations (2021)

Bi<sub>2</sub> S<sub>3</sub> was dissolved in the presence of NaCl in the ionic liquid [BMIm]Cl ⋅ 4AlCl<sub>3</sub> (BMIm=1-n-butyl-3-methylimidazolium) through annealing the mixture at 180 °C. Upon cooling to room temperature, orange, air-sensitive crystals of Na(Bi<sub>7</sub> S<sub>8</sub> )[S(AlCl<sub>3</sub> )<sub>3</sub> ]<sub>2</sub> [AlCl<sub>4</sub> ]<sub>2</sub> (1) precipitated. X-ray diffraction on single-crystals of 1 revealed a triclinic crystal structure that contains (Bi<sub>7</sub> S<sub>8</sub> )<sup>5+</sup> spiro-dicubanes, [S(AlCl<sub>3</sub> )<sub>3</sub> ]<sup>2-</sup> tetrahedra triples, isolated [AlCl<sub>4</sub> ]<sup>-</sup> tetrahedra, and sodium cations.
Estudo da dissolução de polieletrólitos em água pura e em meios de força iônica moderada (1999)

O processo de dissolução de polieletrólitos em pó foi monitorado pela passagem da amostra através de um filtro em linha, um detector de espalhamento de luz multi-ângulo, um refratômetro e um viscosímetro capilar. Quando os polieletrólitos foram dissolvidos em soluções de força iônica moderada, o seu comportamento de dissolução foi similar ao de polímeros neutros. No entanto, quando dissolvidos em água pura, uma pequena população de agregados surgiu no início do processo de dissolução. A conformação dos agregados evoluiu desde uma distribuição gaussiana esféricamente simétrica de densidade de massa até estruturas similares a novelos aleatórios, contendo diversas cadeias. Ao final do processo de dissolução, as cadeias de polieletrólito se encontravam rígidas, distendidas e bem dispersas.
Thrombopoietin induces tyrosine phosphorylation of Stat3 and Stat5 in human blood platelets (1996)

Thrombopoietin is known to be essential for megakaryocytopoiesis and thrombopoiesis. Recently, we and others have shown that thrombopoietin induces rapid tyrosine phosphorylation of Jak2 and other proteins in human platelets and BaF3 cells, genetically engineered to express c-Mpl, a receptor for thrombopoietin. The Jak family of tyrosine kinases are known to mediate some of the effects of cytokines or hematopoietic growth factors by recruitment and tyrosine phosphorylation of a variety of Stat (signal transducers and activators of transcription) proteins. Hence, we have investigated whether Stat proteins are present in platelets and, if so, whether they become tyrosine phosphorylated in response to thrombopoietin. We immunologically identified Stat1, Stat2, Stat3, and Stat5 in human platelet lysates. Thrombopoietin induced tyrosine phosphorylation of Stat3 and Stat5 in these cells. Thrombopoietin also induced tyrosine phosphorylation of Stat3 and Stat5 in FDCP-2 cells genetically engineered to constitutively express human c-Mpl. Thus, our data indicate that Stat3 and Stat5 may be involved in signal transduction after ligand binding to c-Mpl and that this event may have a role in megakaryopoiesis/thrombopoiesis or possibly a mature platelet function such as aggregation.
A Study on Blistering Resistance of Coated Paper (2001)

We reported that we developed the air permeability tester with which we could measure the acceleration of the air permeability (AAP) of coated paper under high temperatures and high pressures during a short time.And we found that AAP was more strongly related to the blistering tendency of coated paper.In this paper, we used various commercial A 2 web offset coated papers, and studied on the blistering resistance.Then we found that the internal bond of coated paper and AAP that had a direction from base paper to coating layer, was strongly related to the blistering tendency.So.the result indicated that the direction of the air permeability from base paper to coating layer was important to understand the blistering phenomenon.
A radiation-hard AGC stabilized SOS crystal oscillator (1990)

A 12 MHz crystal oscillator/divider fabricated in silicon on sapphire (SOS) is presented. The chip incorporates a significant analog component, as an automatic gain control (AGC) loop is used to minimize the influence of changing transistor parameters due to radiation. The design tackles the problems associated with realizing analog circuitry in a floating substrate technology and the use of circuit techniques to achieve radiation hardness. A simple system-level modeling method is used to predict the oscillator start-up and AGC loop stability. The measured stability is around 0.1 p.p.m./V; circuits are still functional at more than 50 Mrad (Si) and show frequency deviations of typically 8 p.p.m. from nominal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Downregulation of microRNA-29c is associated with hypermethylation of tumor-related genes and disease outcome in cutaneous melanoma (2011)

Hypermethylation of the promoter region of tumor-related genes (TRGs) has been shown to silence gene expression during melanoma progression, whereas microRNA-29(miR-29) has been found to downregulate DNA methyltransferases DNMT3A and DNMT3B which were shown as essential to the methylation of TRGs. We hypothesized that the expression level of miR-29 is associated to TRG methylation status and may have prognostic utility in melanoma. AJCC stage I-IV cutaneous melanoma paraffin-embedded archival tissue (PEAT) specimens (n=149) were assessed. Expression of miR-29 isoforms a, b, and c were analyzed by reverse-transcription quantitative real-time polymerase chain reaction(RT-qPCR). Expression of DNMT3A and DNMT3B was assessed by immunohistochemistry(IHC) on defined clinically annotated tissue microarrays (TMA) of AJCC stage III melanoma lymph node metastases. Promoter region CpG island methylation status of RASSF1A, TFPI-2, RAR-β, SOCS, GATA4 and genomic repeat sequence MINT17 and MINT31 were previously evaluated in melanoma tissues. Only miR-29c isoform expression was correlated to advancing AJCC stages in melanoma. miR-29c expression was significantly downregulated in AJCC stage IV melanoma tumors compared to primary melanomas. Hypermethylation status of TRGs and non-coding MINT loci in different stages of melanoma showed an inverse association with miR-29c expression. Overall, an increase in miR-29c expression inversely correlated to both DNMT3A and DNMT3B protein expression in melanomas. Expression of DNMT3B and miR-29c were significantly (p=0.004 and p=0.002, respectively) associated with overall survival(OS) in AJCC stage III melanoma patients by multivariate analysis. The studies demonstrated that both miR-29c and DNMT3B have significant roles in melanoma progression, and may be useful epigenetic biomarkers for disease outcome.
Opioid Peptidomimetics: Leads for the Design of Bioavailable Mixed Efficacy μ Opioid Receptor (MOR) Agonist/δ Opioid Receptor (DOR) Antagonist Ligands (2013)

We have previously described opioid peptidomimetic, 1, employing a tetrahydroquinoline scaffold and modeled on a series of cyclic tetrapeptide opioid agonists. We have recently described modifications to these peptides that confer a μ opioid receptor (MOR) agonist, δ opioid receptor (DOR) antagonist profile, which has been shown to reduce the development of tolerance to the analgesic actions of MOR agonists. Several such bifunctional ligands have been reported, but none has been demonstrated to cross the blood-brain barrier. Here we describe the transfer of structural features that evoked MOR agonist/DOR antagonist behavior in the cyclic peptides to the tetrahydroquinoline scaffold and show that the resulting peptidomimetics maintain the desired pharmacological profile. Further, the 4R diastereomer of 1 was fully efficacious and approximately equipotent to morphine in the mouse warm water tail withdrawal assay following intraperitoneal administration and thus a promising lead for the development of opioid analgesics with reduced tolerance.
The Chemistry of Peroxynitrite: Involvement of an ET Process in the Radical Nitration of Unsaturated and Aromatic Systems (2001)

Reactions of peroxynitrous acid, HPN, with styrene under acidic conditions lead to the oxime 1, the nitrate 2, benzaldehyde (3), and α-nitroacetophenone (4) in overall yields that depend strongly on the pH value and with a product distribution that depends on the dioxygen concentration. The results are rationalized by assuming that HPN undergoes acid-catalyzed decomposition to give nitrous anhydride, or its synthetic equivalent, which is responsible for the regioselective nitration of the styrene double bond by an ET process. The resulting β-nitrobenzyl radical 6 can, depending on the reaction conditions, undergo reversible coupling with nitric oxide to afford the nitroso derivative 7 and then the tautomeric oxime 1, or trapping by dioxygen, eventually leading to products 2, 3, and 4 through the intermediacy of the peroxynitrite derivative 8. Oxime 1 and nitrate 2 are also obtained by treating styrene with nitrous anhydride under protic conditions, the latter being produced in situ from nitric oxide/dioxygen. Similarly to styrene, 1,4-diphenylbutadiene (14) gives radicals 22 and 21 by competitive trapping at the side chain and at the aromatic ring. In turn, radicals 22 and 21 undergo β-fragmentation reactions or trapping by dioxygen with eventual formation of nitrates 16 and 17, cinnamic aldehyde (18), and the diol 15. Finally, the HPN-promoted reaction of p-cresol (27) leads to the 2-nitro derivative 28 through an initial electron-transfer process followed by in cage recombination of the resulting radical ion pair.
Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers (2013)

This study is the largest to examine composition of the lower respiratory tract microbiome in healthy individuals and the first to use the neutral model to compare the lung to the mouth. Specific bacteria appear in significantly higher abundance in the lungs than would be expected if they originated from the mouth, demonstrating that the lung microbiome does not derive entirely from the mouth. The mouth microbiome differs in nonsmokers and smokers, but lung communities were not significantly altered by smoking.
Protective Effects of Plasma Carotenoids on the Risk of Bladder Cancer (2006)

Our results show protective effects of carotenoids on bladder cancer. They suggest that bladder cancer may be a preventable disease through nutritional intervention, especially in smokers.
InDistill: Transferring Knowledge From Pruned Intermediate Layers (2023)

In this paper we introduce InDistill, a model compression approach that combines knowledge distillation and channel pruning in a unified framework for the transfer of the critical information flow paths from a heavyweight teacher to a lightweight student. Such information is typically collapsed in previous methods due to an encoding stage prior to distillation. By contrast, InDistill leverages a pruning operation applied to the teacher's intermediate layers reducing their width to the corresponding student layers' width. In that way, we force architectural alignment enabling the intermediate layers to be directly distilled without the need of an encoding stage. Additionally, a curriculum learning-based training scheme is adopted considering the distillation difficulty of each layer and the critical learning periods in which the information flow paths are created. The proposed method surpasses state-of-the-art performance on three standard benchmarks, i.e. CIFAR-10, CUB-200, and FashionMNIST by 3.08%, 14.27%, and 1% mAP, respectively, as well as on more challenging evaluation settings, i.e. ImageNet and CIFAR-100 by 1.97% and 5.65% mAP, respectively.
Recombination Events Shape the Genomic Evolution of Infectious Bronchitis Virus in Europe (2021)

Infectious bronchitis of chicken is a high morbidity and mortality viral disease affecting the poultry industry worldwide; therefore, a better understanding of this pathogen is of utmost importance. The primary aim of this study was to obtain a deeper insight into the genomic diversity of field infectious bronchitis virus (IBV) strains using phylogenetic and recombination analysis. We sequenced the genome of 20 randomly selected strains from seven European countries. After sequencing, we created a genome sequence data set that contained 36 European origin field isolates and 33 vaccine strains. When analyzing these 69 IBV genome sequences, we identified 215 recombination events highlighting that some strains had multiple recombination breaking points. Recombination hot spots were identified mostly in the regions coding for non-structural proteins, and multiple recombination hot spots were identified in the nsp2, nsp3, nsp8, and nsp12 coding regions. Recombination occurred among different IBV genotypes and involved both field and vaccine IBV strains. Ninety percent of field strains and nearly half of vaccine strains showed evidence of recombination. Despite the low number and the scattered geographical and temporal origin of whole-genome sequence data collected from European Gammacoronaviruses, this study underlines the importance of recombination as a major evolutionary mechanism of IBVs.
Mechanical Stability and Self-Recovery Property of Liquid Crystal Gel Films with Hydrogen-Bonding Interaction (2019)

In this study, we examined the mechanical durability and self-recovery characterization of liquid crystal gel films with lysine-based gelator. The results indicated that the structural destruction in liquid crystal gel films is attributed to dissociation among network structure. The cracked LC gel films can be recovered by formation of sol-sate films.
Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics (2023)

The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.