gebhart/patrepeval huggingface dataset:
Industrial high‐performance liquid chromatography purification of docosahexaenoic acid ethyl ester and docosapentaenoic acid ethyl ester from single‐cell oil (1997)

Abstract The use of polyunsaturated fatty acids (PUFA) as medicine or in functional diets requires high purity. An industrial purification method for PUFA from Schizochytrium sp. SR21 oil was investigated. This oil contains fewer unwanted components than fish oils. Docosahexaenoic acid and docosapentaenoic acid ethyl esters (DHA‐E and DPA‐E) were prepared by treatment of this oil with ethanol and 1 N potassium hydroxide in hexane. DHA‐E and DPA‐E were purified by an industrial high‐performance liquid chromatography (HPLC) plant. The separation plant consists of two columns (400 mm i.d., 1,000 mml) with temperature‐controlled water jackets and double‐plunger (four heads) injection and eluent pumps. This plant was computer‐controlled and equipped with an explosion‐prevention system. The packed material was octadecylsilica (reverse‐phase ODS), and the eluent was methyl alcohol/water (98:2). DHA‐E and DPA‐E from single‐cell oil were highly purified by this industrial HPLC method in a one‐step process. The DHA‐E and DPA‐E obtained were better than 99% purity.
Programmable RNA recognition using a CRISPR-associated Argonaute (2018)

Argonaute proteins (Agos) are present in all domains of life. Although the physiological function of eukaryotic Agos in regulating gene expression is well documented, the biological roles of many of their prokaryotic counterparts remain enigmatic. In some bacteria, Agos are associated with CRISPR (clustered regularly interspaced short palindromic repeats) loci and use noncanonical 5'-hydroxylated guide RNAs (gRNAs) for nucleic acid targeting. Here we show that using 5-bromo-2'-deoxyuridine (BrdU) as the 5' nucleotide of gRNAs stabilizes in vitro reconstituted CRISPR-associated <i>Marinitoga piezophila</i> Argonaute-gRNA complexes (MpAgo RNPs) and significantly improves their specificity and affinity for RNA targets. Using reconstituted MpAgo RNPs with 5'-BrdU-modified gRNAs, we mapped the seed region of the gRNA and identified the nucleotides of the gRNA that play the most significant role in targeting specificity. We also show that these MpAgo RNPs can be programmed to distinguish between substrates that differ by a single nucleotide, using permutations at the sixth and seventh positions in the gRNA. Using these specificity features, we employed MpAgo RNPs to detect specific adenosine-to-inosine-edited RNAs in a complex mixture. These findings broaden our mechanistic understanding of the interactions of Argonautes with guide and substrate RNAs, and demonstrate that MpAgo RNPs with 5'-BrdU-modified gRNAs can be used as a highly specific RNA-targeting platform to probe RNA biology.
Design and Demonstration of Micro-Mirrors and Lenses for Low Loss and Low Cost Single-Mode Fiber Coupling in 3D Glass Photonic Interposers (2016)

This paper presents the first demonstration of a novel fiber coupling structure that enables low-loss and low-cost fiber coupling in an ultra-miniaturized 3D glass photonic interposer. The novel 3D coupling structure consists of a tapered optical waveguide with an integrated lensed turning mirror on one end and a cylindrical lens on the other end, in a 150 ìm glass substrate. The lens waveguide and turning mirror provide coupling loss of
The multipass amplifier: Theory and numerical analysis (1980)

Theoretical and numerical analysis of the multipass amplifier illustrates its flexibility in applications ranging from efficient high-power pulse amplification to short-pulse generation with great amplitude and pulse-width stability.
Voxel-based dose prediction with multi-patient atlas selection for automated radiotherapy treatment planning (2016)

Automating the radiotherapy treatment planning process is a technically challenging problem. The majority of automated approaches have focused on customizing and inferring dose volume objectives to be used in plan optimization. In this work we outline a multi-patient atlas-based dose prediction approach that learns to predict the dose-per-voxel for a novel patient directly from the computed tomography planning scan without the requirement of specifying any objectives. Our method learns to automatically select the most effective atlases for a novel patient, and then map the dose from those atlases onto the novel patient. We extend our previous work to include a conditional random field for the optimization of a joint distribution prior that matches the complementary goals of an accurately spatially distributed dose distribution while still adhering to the desired dose volume histograms. The resulting distribution can then be used for inverse-planning with a new spatial dose objective, or to create typical dose volume objectives for the canonical optimization pipeline. We investigated six treatment sites (633 patients for training and 113 patients for testing) and evaluated the mean absolute difference in all DVHs for the clinical and predicted dose distribution. The results on average are favorable in comparison to our previous approach (1.91 versus 2.57). Comparing our method with and without atlas-selection further validates that atlas-selection improved dose prediction on average in whole breast (0.64 versus 1.59), prostate (2.13 versus 4.07), and rectum (1.46 versus 3.29) while it is less important in breast cavity (0.79 versus 0.92) and lung (1.33 versus 1.27) for which there is high conformity and minimal dose shaping. In CNS brain, atlas-selection has the potential to be impactful (3.65 versus 5.09), but selecting the ideal atlas is the most challenging.
Vitamin A, carotenoids, and retinoids (1986)

One promising area of current research in chemoprevention is the possibility that micronutrients, including vitamin A analogues, may decrease cancer incidence. The term "vitamin A" refers either to retinol (preformed vitamin A) and its synthetic analogues, or to certain carotenoids (provitamin A), which are converted to retinol in the body, as needed. Retinol and the other retinoids are integrally involved in cell growth and differentiation, which may affect carcinogenesis. Such a role has been supported by a large number of in vitro and animal experiments. Data from studies among humans are sparse, in part because most dietary studies have been conducted in populations in which the vast majority of vitamin A intake is actually beta-carotene and other carotenoids, found in carrots and other vegetables and fruits. Although the carotenoids do not have the hormone-like properties of retinol, they do have a potent antioxidant effect and could thus reduce cancer risk by preventing tissue damage due to oxidation. This possibility is supported by data from a large number of observational epidemiologic studies, most of which have consistently found an inverse relation between consumption of carotene-rich vegetables and cancer risk. However, the only direct way to determine whether carotenoids have a beneficial effect is through large, carefully conducted randomized trials. Several such studies are currently underway and should provide sound evidence on which future medical policy and practice can be based.
Reverse Thermal Gelation of Aliphatically Modified Biodegradable Triblock Copolymers (2006)

A simple aliphatic modification demonstrated how to turn a water-soluble biodegradable triblock copolymer synthesized from PEG, L-lactide, and epsilon-caprolactone into a thermoreversible polymer of which aqueous solution underwent a sol-to-gel phase transition upon a mild temperature rise. Thermogelling behavior of the aliphatically modified polymer was dependent on the degree of aliphatic modification and polymer concentration. When the polymer solutions were subcutaneously injected into rats, immediate depot formation has been observed. The polymeric gel depots have lasted for two weeks in vivo. This aliphatically modified thermogelling polymer can find applications in drug delivery.
Novel Approach to Integration of Numerical Modeling and Field Observations for Deep Excavations (2006)

Precedent and observation of performance are an essential part of the design and construction process in geotechnical engineering. For deep urban excavations designers rely on empirical data to estimate potential deformations and impact on surrounding structures. Numerical simulations are also employed to estimate induced ground deformations. Significant resources are dedicated to monitor construction activities and control induced ground deformations. While engineers are able to learn from observations, numerical simulations have been unable to fully benefit from information gained at a given site or prior excavation case histories in the same area. A novel analysis method, self-learning in engineering simulations (SelfSim), is introduced to integrate precedent into numerical simulations. SelfSim is an inverse analysis technique that combines finite element method, biologically inspired material models, and field measurements. SelfSim extracts relevant constitutive soil information from field measurements of excavation response such as lateral wall deformations and surface settlement. The resulting soil model, used in a numerical analysis, provides correct ground deformations and can be used in estimating deformations of similar excavations. The soil model can continuously evolve using additional field information. SelfSim is demonstrated using two excavation case histories in Boston and Chicago.
Analyst E: Shear Wave Velocity Profile Determined from the UTexas1 Surface Wave Dataset (2014)

Results are presented from analysis of active and passive (ambient) surface wave data (data set UTexas1) collected in Christchurch, New Zealand. This data set was made available to several analysts as part of a study of inter-analyst variability in shear wave velocity (VS) profile determination. In this analysis, dispersion curves were developed from active-source surface wave data and from the vertical component of ambient noise measurements using f-k beamforming methods. A representative average experimental dispersion curve for the site was created from the ambient measurements supplemented by the dispersion data from the active-source hammer measurements. A final shear wave velocity profile was developed to a depth of 500 m at this site.
SODIUM SILICATE GLASS AS AN INORGANIC BINDER IN FOUNDRY INDUSTRY (2001)

Mixtures of sand, sodium silicate, some additives such as iron oxide, pitch or sugar and an ester can form a temporary mould . Sodium silicate is used in foundries to bind sand grains by means of anappropriateacid, either directly such as CO2, or indirectly with an organic ester, which hydrolyzes and subsequently gels the silicate sand mass . A gel network is prepared by acidifying concentrated sodium silicate (3 .3 ratio of SiO2 :Na2O) solution. Sodium silicate solution, under acidic conditions is polymerized to silica and acts as an inorganic binder. In other word, lowering the pH of an alkali silicate solution below about 10.9 causes the polymerization to occur, thus leading to high molecular weight aggregates of hydrated silica. The produced hydrated silica namely silica gel is responsible for giving the necessary strength to the mould. Concentration of the sodium silicate solution is adjusted to 55%(wlw) in water. The viscosity of this solution is adjusted on 500 cp by addition of sugar in an amount of 1 .0—2 .0% based on weight of sodium silicate . The sugar or pitch is used as a thickening agent, to concentrate the binder solution at a desirable limit Sodium silicate solution as an inorganic binder is of particular importance mainly because, the necessary time for curing the silicate is low, and it is environmentally extremely beneficial.
On Natural Motion Processing using Inertial Motion Capture and Deep Learning (2020)

Human motion collected in real-world environments without instruction from researchers - or natural motion - is an understudied area of the field of motion capture that could increase the efficacy of assistive devices such as exoskeletons, robotics, and prosthetics. With this goal in mind, a natural motion dataset is presented in this thesis alongside algorithms for analyzing human motion. The dataset contains more than 36 hours of inertial motion capture data collected while the 16 participants went about their lives. The participants were not instructed on what actions to perform and interacted freely with real-world environments such as a home improvement store and a college campus. We apply our dataset in two experiments. The first is a study into how manual material handlers lift and bend at work, and what postures they tend to use and why. Workers rarely used symmetric squats and infrequently used symmetric stoops typically studied in lab settings. Instead, they used a variety of different postures that have not been well-characterized such as one-legged lifting and split-legged lifting. The second experiment is a study of how to infer human motion using limited information. We present methods for inferring human motion from sparse sensors using Transformers and Seq2Seq models. We found that Transformers perform better than Seq2Seq models in producing upper-body and full-body motion, but that each model can accurately infer human motion for a variety of postures like sitting, standing, kneeling, and bending given sparse sensor data.
A Compiler Approach for Exploiting Partial SIMD Parallelism (2016)

Existing vectorization techniques are ineffective for loops that exhibit little loop-level parallelism but some limited superword-level parallelism (SLP). We show that effectively vectorizing such loops requires partial vector operations to be executed correctly and efficiently, where the degree of partial SIMD parallelism is smaller than the SIMD datapath width. We present a simple yet effective SLP compiler technique called P aver (PArtial VEctorizeR), formulated and implemented in LLVM as a generalization of the traditional SLP algorithm, to optimize such partially vectorizable loops. The key idea is to maximize SIMD utilization by widening vector instructions used while minimizing the overheads caused by memory access, packing/unpacking, and/or masking operations, without introducing new memory errors or new numeric exceptions. For a set of 9 C/C++/Fortran applications with partial SIMD parallelism, P aver achieves significantly better kernel and whole-program speedups than LLVM on both Intel’s AVX and ARM’s NEON.
TLR7 Is Involved in Sequence-Specific Sensing of Single-Stranded RNAs in Human Macrophages (2008)

Human TLR7 and 8 (hTLR7/8) have been implicated in the sequence-dependent detection of RNA oligonucleotides in immune cells. Although hTLR7 sequence-specific sensing of short RNAs has been inferred from studies of murine TLR7, this has yet to be established for hTLR7. We found that different short ssRNA sequences selectively induced either TNF-alpha or IFN-alpha in human PBMCs. The sequence-specific TNF-alpha response to ssRNAs observed in PBMCs could be replicated in activated human macrophage-like (THP-1) cells pretreated with IFN-gamma. Surprisingly, suppression of hTLR7 expression by RNA interference in this model reduced sensing of all immunostimulatory ssRNAs tested. Modulation of the relative expression ratio of hTLR7 to hTLR8 in THP-1 cells correlated with differential sensing of immunostimulatory sequences. Furthermore, the sequence-specific IFN-alpha induction profile in human PBMCs was accurately modeled by a sequence-specific activation of murine TLR7 in mouse macrophages. Thus, we demonstrate for the first time that hTLR7 is involved in sequence-specific sensing of ssRNAs. We establish a novel cell model for the prediction of TNF-alpha induction by short RNAs in human macrophages. Our results suggest that differential sequence-specific sensing of RNA oligonucleotides between human and mouse macrophages is due to the modulation of TLR7 sensing by human TLR8.
Recent Trends in Field-Effect Transistors-Based Immunosensors (2016)

Immunosensors are analytical platforms that detect specific antigen-antibody interactions and play an important role in a wide range of applications in biomedical clinical diagnosis, food safety, and monitoring contaminants in the environment. Field-effect transistors (FET) immunosensors have been developed as promising alternatives to conventional immunoassays, which require complicated processes and long-time data acquisition. The electrical signal of FET-based immunosensors is generated as a result of the antigen-antibody conjugation. FET biosensors present real-time and rapid response, require small sample volume, and exhibit higher sensitivity and selectivity. This review brings an overview on the recent literature of FET-based immunosensors, highlighting a diversity of nanomaterials modified with specific receptors as immunosensing platforms for the ultrasensitive detection of various biomolecules.
What we can learn from a tadpole about ciliopathies and airway diseases: Using systems biology in <i>Xenopus</i> to study cilia and mucociliary epithelia (2017)

Over the past years, the Xenopus embryo has emerged as an incredibly useful model organism for studying the formation and function of cilia and ciliated epithelia in vivo. This has led to a variety of findings elucidating the molecular mechanisms of ciliated cell specification, basal body biogenesis, cilia assembly, and ciliary motility. These findings also revealed the deep functional conservation of signaling, transcriptional, post-transcriptional, and protein networks employed in the formation and function of vertebrate ciliated cells. Therefore, Xenopus research can contribute crucial insights not only into developmental and cell biology, but also into the molecular mechanisms underlying cilia related diseases (ciliopathies) as well as diseases affecting the ciliated epithelium of the respiratory tract in humans (e.g., chronic lung diseases). Additionally, systems biology approaches including transcriptomics, genomics, and proteomics have been rapidly adapted for use in Xenopus, and broaden the applications for current and future translational biomedical research. This review aims to present the advantages of using Xenopus for cilia research, highlight some of the evolutionarily conserved key concepts and mechanisms of ciliated cell biology that were elucidated using the Xenopus model, and describe the potential for Xenopus research to address unresolved questions regarding the molecular mechanisms of ciliopathies and airway diseases.
A survey of physical education support services in Montana high schools (2015)

The purpose of this study was to survey the support services in physical education in small Montana high schools.Specifically this study attempted to identify: (1) what facilities were being used for physical education, (2) methods for organizing students into physical education classes, (3) budget for physical education programs, (4) supplies and equipment used for physical education programs, (5) support of administration toward physical education.This study was delimited to high schools in Montana holding membership in the Montana High School Association for the 1976-1977 school year.It was further delimited by the enrollment of one hundred and fifty students or less per school.Questionnaires were sent to 92 physical education instructors in Montana high schools.The questionnaire was completed and returned by 66 instructors, each representing one high school.Participation of physical education instructors in Montana for this study totaled 71.4 percent.A questionnaire was designed and developed by the investigator to collect data needed for this study.Results from the questionnaire support the following conclusions: (1) the majority of the physical education instructors were young in age and had only a few years of teaching experience, (2) facilities in most schools supported activities such as track, football, basketball, softball, and baseball, (3) only a small number of schools had facilities for individual and leisure time activities, (4) most common method of organizing students into physical education classes was by the year in school, (5) budgets for the majority of the schools was between zero and two thousand dollars, (6) equipment for gymnastics was found in only a small number of schools, (7) the majority of schools have equipment that support team activities, (8) supplies for individual or recreation type activities such as dance, archery, shuffleboard, horseshoes, wrestling, golf, handball, squash, and swimming were not found in most schools, (9) the majority of the physical education instructors felt that the support of the administration toward physical education was average, above average, or excellent.
Development and qualification of a mechanical-optical interface for parallel optics links (2015)

As parallel optics applications continue to expand, there remains a need for an effective coupling interface between the board-level active components and the passive components of the network. While mid-board level photonic turn connectors are available, coupling interfaces are generally not available outside of proprietary solutions. Development of a general mechanical-optical coupling interface opens the door for broader parallel optics implementation. An interface for use between the optical transmitter and the photonic turn connector is introduced. The interface is a monolithic injection molded component with an array of collimating lenses to couple efficiently with common VCSEL/PD designs. The component has precise epoxy control features to manage epoxy bond-line thickness and strength. Suitable UV and thermal epoxies have been qualified for effective die bond placement of the component in the VCSEL/PD environment. Environmental and mechanical performance of the component to industry-standard qualification requirements are reviewed, and tensile force testing and durability results validate the mechanical characteristics of the interface.
Relationship between reduced heart rate variability and insulin resistance, serum cystatin C in type 2 diabetes patients (2019)

Objective
To investigate the relationship between heart rate variability and insulin resistance (IR), serum cystatin C (Cys-C) in patients with type 2 diabetes mellitus (T2DM).


Methods
A total of 95 T2DM patients hospitalized in the Department of Endocrinology of the First Affiliated Hospital of Zhengzhou University from January 2014 to August 2018 were selected. According to the standard deviation (SDNN) of RR interval of all sinus beats in dynamic electrocardiogram, the patients were divided into normal heart rate variability group (n=56) and reduced heart rate variability group (n=39). The levels of serum Cys-C, fasting insulin and fasting blood glucose were observed and the level of insulin resistance index (HOMA-IR) was calculated.


Results
The HOMA-IR and serum Cys-C levels in patients with reduced heart rate variability were higher than those in patients with normal heart rate variability (P<0.01). After correcting the duration of diabetes mellitus, partial correlation analysis showed that HOMA-IR and Cys-C were negatively correlated with SDNN (P<0.05).


Conclusions
Reduced heart rate variability in type 2 diabetes mellitus is closely correlated with insulin resistance and serum Cys-C levels, suggesting that the high levels of Cys-C and insulin resistance are correlated with diabetic cardiac autonomic neuropathy.


Key words: 
Type 2 diabetic mellitus; Heart rate variability; Insulin resistance; Cystatin C; Cardiac autonomic neuropathy