gebhart/patrepeval huggingface dataset:
Determinants of the 3' splice site for self-splicing of the Tetrahymena pre-rRNA. (1988)

Tetrahymena preribosomal RNA undergoes self-splicing in vitro. The structural components involved in recognition of the 5' splice site have been identified, but the mechanism by which the 3' splice site is recognized is not established. To identify some components of 3'splice site recognition, we have generated mutations near the 3' splice site and determined their effects on self-splicing. Alteration of the 3'-terminal guanosine of the intervening sequence (IVS), a conserved nucleotide in group I IVSs, almost eliminated 3' splice site activity; the IVS-3' exon splicing intermediate accumulated, and exon ligation was extremely slow. These mutations do not result in recruitment of cryptic 3' splice sites, in contrast to mutations that affect the 5' splice site. Alteration of the cytidine preceding the 3'-terminal guanosine or of the first two nucleotides of the 3' exon had similar but less severe effects on exon ligation. Most of the mutants showed some reduction (less than threefold) in GTP addition at the 5' splice site. A mutation that placed a new guanosine residue just upstream from the 3'-terminal guanosine misspliced to produce ligated exons with one extra nucleotide between the 5' and 3' exons. We conclude that multiple nucleotides, located both at the 3' end of the IVS and in the 3' exon, are required for 3' splice site recognition.
Simultaneous GBR and Implant Placement with Resorbable Membranes in the Rehabilitation of Partially Edentulous and Horizontally Atrophic Dental Arches: A Retrospective Study on 97 Implants with a 3- to 7-Year Follow-up (2022)

This retrospective study evaluates the clinical and radiographic outcomes of simultaneous guided bone regeneration (GBR) and implant placement procedures in the rehabilitation of partially edentulous and horizontally atrophic dental arches using resorbable membranes. A total of 49 patients were included, and 97 implants were placed. Patients were followed up for 3 to 7 years after loading. The data indicate that GBR with simultaneous implant placement and resorbable membranes can be a good clinical choice, and the data suggest that it could be better to horizontally reconstruct no more than 3 mm of bone in order to reduce the number of complications and to obtain stable results. However, this technique remains difficult and requires expert surgeons.
Postoperative Respiratory Complications in SARS-CoV-2 Positive Pediatric Patients Across 20 United States Hospitals: A Cohort Study (2022)

Iii, Respiratory complications.
A Discussion on the Properties of Physically Unclonable Functions (2010)

The increasing interest in physically unclonable functions or PUFs and in PUF-based security applications desires a concrete and as formal as possible description of what a PUF is and which properties can be naturally expected. However, the wide and growing variety of different PUF and PUF-like proposals makes such a formalization attempt a nontrivial task. In this work we provide a starting point by developing a concrete, though still informal, description of the minimal requirements a construction needs to meet in order to be called a PUF. Additionally, this study gives an insight into attainable and/or desirable PUF properties and reveals some interesting research directions for future investigation.
Calibrating dynamic pedestrian route choice with an Extended Range Telepresence System (2011)

In this contribution we present the results of a pilot study in which an Extended Range Telepresence System is used to calibrate parameters of a pedestrian model for simulation. The parameters control a model element that is intended to make simulated agents walk in the direction of the estimated smallest remaining travel time. We use this to, first, show that that an Extended Range Telepresence System can serve for such a task in general and second to actually find simulation parameters that yield realistic results.
New Approximate Methods of Dielectric Measurement in the Centimeter Wave Region I (1953)

In the previous paper, starting from Maxwell's equations in the wave guide system and taking into consideration the conditions at the boundaries between the sample and the air columns, we introduced the fundamental equation for the dielectric measurement and from this equation, we derived several new methods of measurement, one of which especially was simpler in practical calculation than any method proposed by other researchers.In the present paper, we introduce the form of fundamental equation which is convenient to Make approximation and show the simplest methd out of the various methods which can be obtained by approximation from that equation for low loss sample.This method is also simple in procedure and calculation of mesurement, compared with the approximate methods reported up to the present.Furthermore, we describe the experiments which have been performed on two low loss samples and shown a good agreement with the theory.
GEANT4 simulation of NSECT for detection of iron overload in the liver (2008)

Neutron stimulated emission computed tomography (NSECT) is being proposed as a non-invasive technique to diagnose iron overload in humans. It uses inelastic scatter interactions between incident neutrons and iron nuclei to stimulate gamma-ray emission from iron. Tomographic detection of the emitted gamma-rays yields information about the concentration and spatial distribution of iron in the liver. Early proof-of-concept experiments have shown that NSECT has the potential to quantify clinical quantities of liver iron overload through single-position spectroscopy. However, a tomography application for patient diagnosis has never been tested. This work uses a Monte-Carlo simulation of a tomographic NSECT system to investigate the feasibility of imaging the spatial distribution of liver iron through tomography. A simulation of an NSECT system has been designed in GEANT4 and used to tomographically scan a simulated human liver phantom with high-concentration iron lesions. Images are reconstructed with the MLEM algorithm and analyzed for pixel values within iron regions to determine the statistical significance of detection. Analysis results indicate that a wet iron concentration of 3 mg/g can be detected in surrounding liver tissue with p-value &le; 0.0001 for neutron exposure corresponding to a radiation dose of 0.72 mSv. The research performed here demonstrates that NSECT has the ability to image clinically relevant distributions of iron through tomographic scanning.
Free-space MEMS tunable optical filter on [110] silicon (2006)

Tunable optical filters (TOFs) are key components in optical communication WDM networks. In this paper we have successfully demonstrated two-Bragg mirror Fabry-Perot MEMS tunable optical filter fabrication by a combination of KOH and deep reactive ion etching in (110) silicon
Economic evaluation of water loss saving due to the biological control of water hyacinth at New Year’s Dam, Eastern Cape province, South Africa (2016)

Water hyacinth Eichhornia crassipes is considered the most damaging aquatic weed in the world. However, few studies have quantified the impact of this weed economically and ecologically, and even fewer studies have quantified the benefits of its control. This paper focuses on water loss saving as the benefit derived from biological control of this plant between 1990 and 2013 at New Year’s Dam, Alicedale, Eastern Cape, South Africa. Estimates of water loss due to evapotranspiration from water hyacinth vary significantly; therefore, the study used three different rates, high, medium and low. A conservative raw agriculture value of R 0.26 per m3 was used to calculate the benefits derived by the water saved. The present benefit and cost values were determined using 10% and 5% discount rates. The benefit/cost ratio at the low evapotranspiration rate was less than one, implying that biological control was not economically viable but, at the higher evapotranspiration rates, the return justified the costs of biological control. However, at the marginal value product of water, the inclusion of the costs of damage to infrastructure, or the adverse effects of water hyacinth on biodiversity, would justify the use of biological control, even at the low transpiration rate.
Strong expression of TGF-beta in human host tissues around subcutaneous Dirofilaria repens (2010)

Dirofilaria repens and other Dirofilaria species are widely distributed parasitic nematodes of carnivores, which occasionally are transmitted to men, causing subcutaneous nodules. In humans, it usually occurs only as single male or female filariae without production of microfilariae. The non-productive living or dead Dirofilaria worms in subcutaneous biopsies from 15 human patients permitted us to study the role of the pleiotropic and immunoregulatory cytokine transforming growth factor beta (TGF-beta) independent from the influence of microfilariae. Antiserum against latent TGF-beta 1 was used for an immunohistological examination. In the infiltrates around female and male filariae, there occurred strongly TGF-beta-positive macrophages, mast cells, endothelial cells, fibrocytes, and giant cells adjacent to dead worms. In one nodule, secondary lymph follicles were observed with clearly TGF-beta-positive B cells in the mantle zone and weakly positive macrophages and B cells in the germinal centre. A network of CD35-positive follicular dendritic cells was observed in the germinal centre. All Dirofilaria contained Wolbachia endobacteria, which probably had attracted the numerous TGF-beta-negative neutrophils near to the worm. Wolbachia were phagocytosed by neutrophils adjacent to dead filariae. Macrophages and lymphocytes expressed the MHC class II molecule HLA-DR in small accumulations of immune cells in the outer zone of the infiltrate and the mantle zone and germinal centre of secondary lymph follicles. It is concluded that single non-productive Dirofilaria worms elicit a strong expression of TGF-beta. This result is in accordance with observations on Onchocerca volvulus from patients with the hyporeactive (generalised) form.
Additive effect of VIP or isoproterenol on forskolin-stimulated cyclic AMP accumulation in rat prostatic epithelial cells. (1986)

The effects of forskolin alone or in combination with vasoactive intestinal peptide (VIP) and the beta-adrenergic agonist isoproterenol on cyclic AMP accumulation in epithelial cells of rat ventral prostate were examined. Forskolin stimulated cyclic AMP in a time- and temperature-dependent manner. At 15 degrees C, forskolin behaved as a highly potent and relatively efficient stimulatory agent. The combination of forskolin with maximal doses of VIP or isoproterenol were purely additive. These results suggest that forskolin might act directly upon the catalytic subunit of adenylate cyclase in this particular class of cells.
H2 permeation through N117 and its consumption by IrOx in PEM water electrolyzers (2019)

It is considered that the oxidation activity of Ir based anodes on H2 permeating the polymer electrolyte membrane (PEM) in PEM water electrolyzers (WE) is poor, resulting in high H2-in-O2 contents at idle or dynamic operating conditions, especially with asymmetric pressure. In the present work, the dependence of H2 permeation on cathode pressure was quantified by the pressure drop method. H2 consumption was detected by chronoamperometry at potentials preceding water splitting. The addition of N2 in the anode outlet gas allowed the on-line monitoring of the mixture composition during idle PEMWE operation by a thermal conductivity sensor. It is found that H2 is effectively consumed with IrOx oxyhydroxide anodes at low current densities, with 75% conversion of the zero-current permeation at cathode pressure of 5 bar and 60 °C. Hence, both H2-in-O2 content and lowest current density at which the H2-in-O2 flammability limit is not exceeded decrease by more than 50%. Current density corrections accounting for H2 consumption and mass transport potential corrections accounting for the enhancement of H2 permeation with current density were implemented. The resulting Tafel slope values suggest that the rate determining step of the oxygen evolution reaction with IrOx oxyhydroxides is a chemical step.
CKD-MBD新しい話題 (2) ; FGF23とKlotho (2018)

CKD-MBDに関わる因子のうちで, 最も生命予後と関係の深い因子である, リンの調整系が判明したのは最近のことである. fibroblast growth factor 23 (FGF23) は骨細胞より分泌されるが, KlothoとFGF受容体の複合体に結合すると, 近位尿細管でのナトリウム-リン共輸送体 (NaPi-Ⅱ) の発現が抑制され, リンの再吸収が低下する. また, 活性型ビタミンD [1,25(OH)2D] 産生を抑制し, 腸管からのリン再吸収を抑制する. KlothoはCKDの早期から発現が低下し始めるが, 動物実験などから腎保護作用を有することが確かめられている. FGF23もCKD早期から上昇を認めるが, 透析患者のみならず, 保存期CKD患者の予後とも関係が深い. また, FGF23は予後予測因子というだけでなく, 予後不良因子として, FGF23自体が左室肥大をきたすことも指摘されており, そのメカニズムも解明されつつある. さらには, 肥大心自体もFGF23を産生することが判明している.
Model‐Based Energy Efficiency Optimization of a Low‐Temperature Adsorption Dryer (2011)

Abstract Low‐temperature drying is important for heat‐sensitive products, but at these temperatures conventional convective dryers have low energy efficiencies. To overcome this challenge, an energy efficiency optimization procedure is applied to a zeolite adsorption dryer subject to product quality. The procedure finds a trade‐off between the improved drying capacity due to dehumidification and energy expenditure due to regeneration while incorporating product drying properties. By optimizing the regeneration air inlet temperature, drying air, adsorbent, and regeneration air flow rates as well as sensible and latent heat recovery from the regenerator exhausts, the energy efficiency is improved by up to 45 % compared to the state‐of‐the‐art. The high mass transfer effect of high temperatures is utilized in the regenerator to boost dehumidification while isolating the heat‐sensitive dried product from the quality‐degrading effect.
High-Risk Coronary Plaque at Coronary CT Angiography Is Associated with Nonalcoholic Fatty Liver Disease, Independent of Coronary Plaque and Stenosis Burden: Results from the ROMICAT II Trial (2014)

NAFLD is associated with advanced high-risk coronary plaque, independent of traditional cardiovascular risk factors and the extent and severity of coronary artery disease.
ANTIFERTILITY PROPERTIES OF BOVINE PINEAL EXTRACTS: REDUCTION OF OVULATION AND PRE-OVULATORY LUTEINIZING HORMONE IN THE RAT (1977)

Bovine pineal glands were extracted with acetic acid and partially purified on Sephadex G-25. Three fractions, F3, F4 and F5, were each administered to cycling female rats for 4, 2 or 1 day prior to ovulation to determine their effects on fertility, ovulation and the pro-oestrous surge of luteinizing hormone (LH). The incidence of pregnancy and the mean number of foetuses were reduced in animals after treatment with F3 or F4 but not in those treated with F5. Each of the F3 and F4 fractions significantly reduced the mean number of ova shed and the pre-ovulatory concentration of serum LH. The F5 fraction caused a moderate reduction of the pro-oestrous rise of serum LY but had no significant effect on ovulation. The data suggest that fertility in rats can be reduced by more than one substance of low molecular weight present in bovine pineal extracts through a modifying effect on LH secretion and subsequent ovulation.
Spiral Disk Assembly for HSCCC: Column Design and Basic Studies on Chromatographic Resolution and Stationary Phase Retention (2003)

Abstract A set of four separation disks equipped with spiral channel(s) was designed for our type‐J high speed countercurrent chromatography (J‐HSCCC) centrifuge to improve retention of the stationary phase of polar solvent systems. Four different spiral disks were tested: two had a single spiral channel with different depths and the other two had four spiral channels connected in series to provide a greater spiral pitch. Performance of each disk was tested in terms of chromatographic resolution and/or stationary phase retention using three different two‐phase solvent systems, including 1‐butanol/acetic acid/water (4:1:5, v/v/v) for dipeptide separation; 12.5% (w/w) polyethylene glycol (PEG) 1000–12.5% (w/w) dibasic potassium phosphate for protein separation; and 4% (w/w) PEG8000–5% (w/w) dextran T500 in 10 mM dibasic sodium phosphate for determination of stationary phase retention. The results show that the spiral column retains a satisfactory amount of stationary phase for all solvent systems, even at a relatively high mobile phase flow rate where the spiral pitch plays a significant role. Separation of dipeptides with the butanol solvent system was possible using 10 mL/min flow rate of the mobile phase and 4‐spiral‐disks with their greater spiral pitch. In protein separations with the PEG–phosphate system, the single‐spiral disks yielded the best separation using the upper phase in tail‐to‐head elution mode at 1 mL/min, while the 4‐spiral disks show higher retention of the stationary phase. The retention of the PEG–dextran system is improved in the 4‐spiral disks, which exceed 60% at a flow rate of 0.5 mL/min. Various parameters, which affect the performance of the spiral disk separation column are discussed.
A Case Study in Meta-Simulation Design and Performance Analysis for Large-Scale Networks (2005)

Simulation and emulation techniques are fundamental to aid the process of large-scale protocol design and network operations. However, the results from these techniques are often view with a great deal of skepticism from the networking community. Criticisms come in two flavors: (i) the study presents isolated and potentially random feature interactions, and (ii) the parameters used in the study may not be representative of real-world conditions. In this paper, we explore both issues by applying large-scale experiment design and black-box optimization techniques to analyze convergence of network routes in the open shortest path first protocol over a realistic network topology. By using these techniques, we show that: (i) the needed number of simulation experiments can be reduced by an order of magnitude compared to traditional full-factorial experiment design (FFED) approach, (ii) unnecessary parameters can easily be eliminated, and (iii) rapid understanding of key parameter interactions can be achieved.
Case Studies Illustrating a Science and Risk-Based Approach to Ensuring Drug Quality When Using Enzymes in the Manufacture of Active Pharmaceuticals Ingredients for Oral Dosage Form (2016)

Biocatalysis is essentially the use of enzymes to perform chemical transformations on organic compounds and has been exploited for applications in various industries including food, fine chemicals, agrochemicals, and pharmaceuticals. Due to their selectivity and ability to operate under mild conditions, enzymes offer clear advantages for efficient sustainable manufacturing processes. Rapid development of enabling technologies including gene mining, molecular biology, biocatalyst evolution, and bioprocess engineering, has created opportunities to use biocatalysis more broadly for the manufacture of small molecule intermediates and APIs (active pharmaceutical ingredients). To facilitate the adoption of biocatalysis for API manufacture and address a perceived lack of regulatory clarity, several of the current authors published a science and risk based approach to ensuring patient safety and drug quality when using biocatalysis (Org. Process Res. Dev. 2012, 16, 1986−1993). Since this publication, consultation of multiple users and stakeholders in the biocatalysis community has expanded on key guidance and specific approaches, as well as providing real examples of regulatory review and approval in this article. Our ultimate goal as highlighted in this publication is to provide a clear path and knowledge base to enable a robust and sound science and risk-based approach for utilizing biocatalysis whenever appropriate for the manufacture of small molecule pharmaceuticals.
Microstructural Characterization Of The Pd-Ge Ohmic Contact On Gaas By Cross-Sectional Transmission Electron Microscopy (Tem) (1999)

Abstract In the last decade, Pd-Ge contact system emerged as the most promising replacement of the Au-Ni-Ge alloy, still used by most of today's GaAs technology. Its better electrical properties stem from the fact that contact formation is based on a series of solid state reactions without any melting of the metal thin films and the GaAs substrate taking place during annealing. Research studies by E.D. Marshall et al. (1) demonstrated that thermally stable contacts with low resistivities could be achieved by low temperature annealing of Pd and Ge thin films. Their studies also revealed that the excess Ge is regrown on top of the GaAs substrate by a solid state epitaxy mechanism. Typical TEM cross-sectional specimen preparation techniques limit the electron transparent area and make the global characterization of the contact difficult. In this study, we employed a focus ion beam (FEB) method as described by Bassile et al.(2), which allowed us to observe a minimum of 4 microns of the interface cross section in each of the specimens examined.
Mechanisms of transcriptional regulation by WT1 (Wilms’ tumour 1) (2014)

The WT1 (Wilms' tumour 1) gene encodes a zinc finger transcription factor and RNA-binding protein that direct the development of several organs and tissues. WT1 manifests both tumour suppressor and oncogenic activities, but the reasons behind these opposing functions are still not clear. As a transcriptional regulator, WT1 can either activate or repress numerous target genes resulting in disparate biological effects such as growth, differentiation and apoptosis. The complex nature of WT1 is exemplified by a plethora of isoforms, post-translational modifications and multiple binding partners. How WT1 achieves specificity to regulate a large number of target genes involved in diverse physiological processes is the focus of the present review. We discuss the wealth of the growing molecular information that defines our current understanding of the versatility and utility of WT1 as a master regulator of organ development, a tumour suppressor and an oncogene.
Study Of Sugarcane Bagasse Pretreatment With Sulfuric Acid As A Step Of Cellulose Obtaining (2012)

To produce sugar and ethanol, sugarcane processing generates several agricultural residues, being straw and bagasse is considered as the main among them. And what to do with this residues has been subject of many studies and experiences in an industry that, in recent years, highlighted by the ability to transform waste into valuable products such as electric power. Cellulose is the main component of these materials. It is the most common organic polymer and represents about 1.5 x 1012 tons of total production of biomass per year and is considered an almost inexhaustible source of raw material. Pretreatment with mineral acids is one of the most widely used as stage of cellulose extraction from lignocellulosic materials for solubilizing most of the hemicellulose content. This study had as goal to find the best reaction time of sugarcane bagasse pretreatment with sulfuric acid in order to minimize the losses of cellulose concomitantly with the highest possible removal of hemicellulose and lignin. It was found that the best time for this reaction was 40 minutes, in which it was reached a loss of hemicelluloses around 70% and lignin and cellulose, around 15%. Over this time, it was verified that the cellulose loss increased and there was no loss of lignin and hemicellulose.
A Divergent Hepatitis D-Like Agent in Birds (2018)

Hepatitis delta virus (HDV) is currently only found in humans and is a satellite virus that depends on hepatitis B virus (HBV) envelope proteins for assembly, release, and entry. Using meta-transcriptomics, we identified the genome of a novel HDV-like agent in ducks. Sequence analysis revealed secondary structures that were shared with HDV, including self-complementarity and ribozyme features. The predicted viral protein shares 32% amino acid similarity to the small delta antigen of HDV and comprises a divergent phylogenetic lineage. The discovery of an avian HDV-like agent has important implications for the understanding of the origins of HDV and sub-viral agents.