gebhart/patrepeval huggingface dataset:
Chromosome‐level <i>Thlaspi arvense</i> genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates (2022)

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
Alcohols as Latent Coupling Fragments for Metallaphotoredox Catalysis: sp<sup>3</sup>–sp<sup>2</sup> Cross-Coupling of Oxalates with Aryl Halides (2016)

Alkyl oxalates, prepared from their corresponding alcohols, are engaged for the first time as carbon radical fragments in metallaphotoredox catalysis. In this report, we demonstrate that alcohols, native organic functional groups, can be readily activated with simple oxalyl chloride to become radical precursors in a net redox-neutral C<sub>sp<sup>3</sup></sub>-C<sub>sp<sup>2</sup></sub> cross-coupling with a broad range of aryl halides. This alcohol-activation coupling is successfully applied to the functionalization of a naturally occurring steroid and the expedient synthesis of a medicinally relevant drug lead.
Plasma clearance, tissue distribution and metabolism of hyaluronic acid injected intravenously in the rabbit (1981)

The plasma clearance, tissue distribution and metabolism of hyaluronic acid were studied with a high average molecular weight [3H]acetyl-labelled hyaluronic acid synthesized in synovial cell cultures. After intravenous injection in the rabbit the label disappeared from the plasma with a half-life of 2.5--4.5 min, which corresponds to a normal hyaluronic acid clearance of approx. 10 mg/day per kg body weight. Injection of unlabelled hyaluronic acid 15 min after the tracer failed to reverse its absorption. Clearance of labelled polymer was retarded by prior injection of excess unlabelled hyaluronic acid. The maximum clearance capacity was estimated in these circumstances to be about 30 mg/day per kg body wt. The injected material was concentrated in the liver and spleen. As much as 88% of the label was absorbed by the liver, where it was found almost entirely in non-parenchymal cells. Degradation was rapid and complete, since volatile material, presumably 3H2O, appeared in the plasma within 20 min. Undegraded [3H]hyaluronic acid, small labelled residues and 3H2O were detected in the liver, but there was little evidence of intermediate oligosaccharides. No metabolite except 3H2O was recognized in plasma or urine. Two-thirds of the radioactivity was retained in the body water 24 h later, and small amounts were found in liver lipids. Radioactivity did not decline in the spleen as rapidly as in the liver. The upper molecular weight limit for renal excretion was about 25 000. Renal excretion played a negligible part in clearance. It is concluded that hyaluronic acid is removed from the plasma and degraded quickly by an efficient extrarenal system with a high reserve capacity, sited mainly in the liver.
3D modeling from outcrop data in a salt tectonic context: Example from the Inceyol minibasin, Sivas Basin, Turkey (2016)

Abstract We have developed a 3D modeling strategy of the encased minibasin of Inceyol in Sivas (Turkey). The challenge lies in the combination of sparse outcrop data and the complex interpretive geometry of geologic structures that come from salt tectonics. We have succeeded in modeling the convoluted salt surface using an explicit indirect surface patch construction method followed by a manual mesh improvement. Then, we modeled the minibasin sediments with an implicit approach. The result highlighted the remarkable geometry of the convoluted salt horizon and its associated minibasin by extending in 3D the geologist’s interpretive 2D sections. This case study proved that building complex geometries is feasible with the existing tools and a good expertise in the various geomodeling techniques. Our work also underlined the need for new methods to ease the modeling of such tectonic features from sparse data. We have developed a 3D view of the model thanks to WebGL technology, as well as downloadable data to constitute a reference case study.
Next generation intermediate representations for binary code analysis (2018)

A lot of binary code analysis tools do not work directly with machine instructions, instead relying on an intermediate representation from the binary code. In this paper, we first analyze problems in binary code analysis that benefit from such an IR and construct a list of requirements that an IR suitable for solving these problems must meet. Generally speaking, a universal binary analysis platform requires two principal components. The first component is a retargetable instruction decoder that utilizes external specifications for describing target instruction sets. External specifications facilitate maintainability and allow for quickly adding support for new instruction sets. We analyze some of the more common ISAs, including those used in microcontrollers, and from that produce a list of requirements for a retargetable decoder. We then survey existing multi-ISA decoders and propose our vision of a more generic approach, based on a multi-layered directed acyclic graph describing the decoding process in universal terms. The second component of an analysis platform is the actual architecture-neutral IR. In this paper we describe such existing IRs, and propose Pivot 2, an IR that is low-level enough to be easily constructed from decoded machine instructions, and at the same time is also easy to analyze. The main features of Pivot 2 are explicit side effects, SSA variables, a simpler alternative to phi-functions, and an extensible elementary operation set at the core. The IR also supports machines that have multiple memory address spaces. Finally, we propose a way to tie the decoder and the IR together to fit them to most binary code analysis tasks through abstract interpretation on top of the IR. The proposed scheme takes into account various aspects of target architectures that are overlooked in many other works, including pipeline specifics (handling of delay slots, hardware loop support, etc.), exception and interrupt management, and a generic address space model where accesses may have arbitrary side effects due to memory-mapped devices or other non-trivial behavior of the memory system.
Screening for Gastric Cancer (2023)

Gastric cancer remains one of the most lethal types of cancer.When examining the global distribution of gastric cancer, the highest incidences are observed in South-East Asia, as well as in China and Japan [1].Histologically, most gastric cancers are adenocarcinomas.Known risk factors are H. pylori infection, chronic gastritis, tobacco use and heavy alcohol consumption.A small percentage of gastric cancers occur hereditary.The TNM-classification is used for gastric cancer staging.Imaging methods, blood tests with tumor markers, and gastroscopy with biopsies are employed for detection, diagnosis, grading and staging.Treatment options include operation, chemotherapy, immunotherapy and radiotherapy.There are non-invasive methods (such as H. pylori serology and plasminogen tests), invasive methods (endoscopy), and radiological methods (upper gastrointestinal series with barium, photofluorography) to screen for gastric cancer.Screening programs are most useful for countries with high incidence of gastric cancer, where the technical and economic conditions exist at the same time.That applies to most countries in East Asia, for instance for South Korea, and of course also for Japan and increasingly for China, where the overall costs are in a favorable relationship to the benefits [2].In countries with lower incidence of gastric cancer, non-invasive screening programs are discussed controversially, although endoscopy is readily available almost everywhere, has few complications and is affordable for most health systems.In Europe and the United States gastric cancer screening programs and recommendations regarding screening are in place in some but by far not in all countries [3].
Tobramycin Affinity Tag Purification of Spliceosomes (2004)

The ability to isolate native ribonucleoprotein (RNP) particles is of fundamental importance in the study of processes such as pre-messenger RNA (mRNA) processing and translation. We have developed an RNA affinity tag that allows the large-scale preparation of native spliceosomes in a solid-phase assembly scheme. A tobramycin-binding aptamer cotranscriptionally added to the 3' end of the pre-mRNA is used to bind the pre-mRNA to tobramycin immobilized on a matrix. Incubation of the pre-mRNA thus immobilized allows the assembly of spliceosomes, which can be released from the matrix under native conditions by competition with tobramycin. Further density-gradient centrifugation affords highly purified spliceosomes suitable for the characterization of associated proteins by mass spectrometry as well as for studies using biochemical and biophysical methods. Although the method was developed for the preparation of spliceosomes, it is likewise applicable to the preparation of other RNP particles.
Development and evaluation of a practical method to measure the Depth of Interaction function for a single side readout PET detector (2016)

In small animal and organ dedicated PET scanners, the knowledge of depth of interaction (DOI) of the gamma ray along the main axis of the scintillator is a fundamental information in order to avoid parallax error and to achieve high performances in terms of spatial resolution. Recently we developed a new method to obtain the DOI function for a single side readout PET module, recirculating the scintillation light in the matrix by means of a mirror placed on top of the module. In a complete PET scanner, periodical DOI calibrations have to be performed to prevent time dependent miscalibrations and performance degradations. The current DOI calibration relies on a coincidence system between the module and an external scintillator to provide a priori the DOI information and it is clearly not feasible in a real system without unpractical disassemblies of the scanner. In this paper we develop instead a fast and precise calibration method based on uniform irradiation of the scintillators. Three irradiation modalities are presented, in particular one where the source is placed on top of the module, one with the source placed on one side of the module and one that exploits the internal radioactivity of the scintillator. The three different procedures are evaluated and the calibration method is validated by comparing the information provided by the coincidence setup.
Broadband optical detection of ultrasound by optical sideband stripping with a confocal Fabry–Perot (1989)

A method which allows broadband optical detection of ultrasound with large étendue from a scattering surface is presented. The wave scattered by the surface interferes with a reference wave which is derived from the scattered wave after stripping it from its optical sidebands by a confocal resonator. Simple implementation by a confocal Fabry–Perot used in reflection is explained and demonstrated experimentally.
Localization of glutamate receptors in dorsal horn of rat spinal cord (1998)

Immunocytochemical localization of metabotropic glutamate receptors (mGluRs) and ionotropic glutamate receptors (NMDA-type: NMDAR1 and NMDAR2A-C; AMPA-type: GluR1-4) was performed on sections of rat dorsal horn. Immunoreactivity for mGluR1 alpha was detected in laminae I-III of the dorsal horn, whilst mGluR2/3 immunoreactivity was detected primarily in lamina III. Immunoreactivity for NMDAR1, GluR1, GluR2, GluR2/3, GluR4 and GluR5/6/7 was strongly localized in neuronal elements of laminae I-III. Immunoreactivity for NMDAR2B was localized in laminae I-III. No mGluR5, NMDAR2A and NMDAR2C immunoreactivity was detected. In addition, immunoreactivity for receptors was found to co-localize with immunoreactivity for glutamate in the dorsal horn. The present results indicate that glutamate receptors are differentially localized in neuronal elements of dorsal horn where receptor-neurotransmitter interaction takes place.
Blunt traumatic injury in the Arab Middle Eastern populations (2014)

In the Arab Middle East, population-based studies on the incidence, mechanism of injury, prevention and outcome of BTI are not well-documented. Therefore, region-specific BTI studies would strengthen surveillance to better understand the burden of these injuries in the region.
Dropping Out of High School: Assessing the Relationship between Supportive Messages from Family and Educational Attainment (2011)

The purpose of this study is to assess the potential impact of various aspects of supportive messages from parents/primary caregivers on the decision to stay in or drop out of high school. Specifically, the relationships between the number, valence, and helpfulness of the messages, as well as type of support and message framing with educational achievement were investigated. Eighty respondents completed in-depth interviews about their experiences in high school. Ordinal regression was used to assess the relationships posited in the three research questions. Limitations and directions for future research are discussed.
Medicinal Flowers. XXX. Eight New Glycosides, Everlastosides F-M, from the Flowers of Helichrysum arenarium (2009)

Eight new glycosides, everlastosides F (1), G (2), H (3), I (4), J (5), K (6), L (7), and M (8), were isolated from the methanolic extract of the flowers of Helichrysum arenarium. Their structures were elucidated on the basis of chemical and physicochemical evidence.
Securing Cryptographic Keys in the Cloud: A Survey (2016)

Public cloud users are increasingly interested in securing their data and network traffic by using outsourced encryption or decryption services (cryptography as a service). However, many concerns have been raised about trusting the outsourced service's memory with sensitive information like the user's cryptographic keys. This survey reviews techniques for securing data owners' cryptographic keys in a public cloud, preserving them from any inquisitive actions on the part of cotenants (fellow data owners, domain administrators, or other third parties) and the cloud provider itself. The aim is to provide readers with a comparative in-depth analysis of available techniques and point to open research problems.
Construction of Small RNA cDNA Libraries for Deep Sequencing (2010)

Since the phenomenon of small RNA-mediated gene silencing was first described over 15 years ago (Lee et al. Cell 75:843-854, 1993; Wightman et al. Cell 75:855-862, 1993), it has become evident that a variety of endogenous small RNAs play an important role in establishing and maintaining cell lineages. MicroRNAs (miRNAs), in particular, have been shown to exert regulatory control over the development and function of the many specialized cells that comprise the mammalian immune system (Baltimore et al. Nat Immunol 9:839-845, 2008; Kanellopoulous and Monticelli Semin Cancer Biol 18:79-88, 2008; Xiao and Rajewsky Cell 136:26-36, 2009). The advent of next generation sequencers provides an important tool for profiling the small RNA transcriptome of many diverse cell types. Compared to traditional Sanger sequencing, next generation sequencing machines can process millions of sequence reads in parallel, generating megabases of data within just a few days. The generation of small RNA libraries for sequencing is relatively straightforward and involves the ligation of platform-specific adapter sequences to small RNAs, followed by reverse transcription of the ligated species and PCR amplification. While other hybridization-based techniques are available for profiling well-characterized small RNAs, high-throughput sequencing remains the most powerful method for discovering novel small RNAs and posttranscriptional editing.
Tantalum‐Based Encapsulants For Thermal Annealing of GaAs (1991)

During thermal annealing of there is a tendency for arsenic to evaporate. This process can have deleterious consequences and must be controlled during annealing by encapsulants. We survey conducting electrically, sputtered tantalum‐based encapsulants as capping materials for thermal annealing of in the temperature range 550–900°C. Conducting capping layers have the advantage that they can be integrated in a contact metallization scheme. The backscattering spectrometry results show that Ta is not an effective cap. Evaporation through can be detected after annealing at 700°C. Amorphous was a good cap up to 800°C, and amorphous up to 850°C. Thus, while the effectiveness of Ta‐based caps was improved significantly by the addition of either nitrogen or silicon alone, the best results were obtained for caps containing both Si and N.
Increasing the capacity in real WDM network requirements: dispersion management and wide-band flat-gain optical amplifiers in Nx10 Gb/s transmission systems (2002)

In this presentation, we will study the system design aspects of high-capacity, large wavelength span, and long distance transmission links based on conventional single-mode fiber. A particular attention will be brought to the dispersion map architecture. Indeed, a careful design of this map in terms of choice, position, and length of the dispersion-compensating fiber will reveal it to be a critical parameter for a reliable transmission in view of the interplay between the accumulated chromatic dispersion and the nonlinear effects. We will show that limitations brought by modulational instability and the accumulated dispersion per amplifier span rule out the propagation of the channels in a predominantly-positive total dispersion regime.
Polycarbonate Resins: Synthesis and Thermogravimetric Analysis (1991)

Abstract Resins from diphenols with an aromatic ring as side group, phosgene, and a triphenol as crosslinking agent were synthesized under phase transfer conditions. The resins obtained with a phase transfer catalyst showed higher thermal stability than those obtained without catalyst. The function of the catalyst is to transport triphenol from the aqueous phase to the organic phase. The thermal stability of the resins was related to the structure and the content of triphenol. It was found that resins derived from diphenol I exhibited higher thermal stability as the content of triphenol increased. On the other hand, when diphenol II was used, the thermal stability decreased as the content of triphenol increased, due to steric hindrance of the methyl group on the side ring. Also, a resin from the triphenol alone was synthesized in the same conditions. The kinetic parameters of the decomposition process were determined for all resins.
Blood pressure and calf muscle oxygen extraction during plantar flexion exercise in peripheral artery disease (2017)

Peripheral artery disease (PAD) is an atherosclerotic vascular disease that affects 200 million people worldwide. Although PAD primarily affects large arteries, it is also associated with microvascular dysfunction, an exaggerated blood pressure (BP) response to exercise, and high cardiovascular mortality. We hypothesized that fatiguing plantar flexion exercise that evokes claudication elicits a greater reduction in skeletal muscle oxygenation (SmO<sub>2</sub>) and a higher rise in BP in PAD compared with age-matched healthy subjects, but low-intensity steady-state plantar flexion elicits similar responses between groups. In the first experiment, eight patients with PAD and eight healthy controls performed fatiguing plantar flexion exercise (from 0.5 to 7 kg for up to 14 min). In the second experiment, seven patients with PAD and seven healthy controls performed low-intensity plantar flexion exercise (2.0 kg for 14 min). BP, heart rate (HR), and SmO<sub>2</sub> were measured continuously using near-infrared spectroscopy (NIRS). SmO<sub>2</sub> is the ratio of oxygenated hemoglobin to total hemoglobin, expressed as a percent. At fatigue, patients with PAD had a greater increase in mean arterial BP (18 ± 2 vs. vs. 10 ± 2 mmHg, <i>P</i> = 0.029) and HR (14 ± 2 vs. 6 ± 2 beats/min, <i>P</i> = 0.033) and a greater reduction in SmO<sub>2</sub> (-54 ± 10 vs. -12 ± 4%, <i>P</i> = 0.001). However, both groups had similar physiological responses to low-intensity, nonpainful plantar flexion exercise. These data suggest that patients with PAD have altered oxygen uptake and/or utilization during fatiguing exercise coincident with an augmented BP response.<b>NEW & NOTEWORTHY</b> In this laboratory study, patients with peripheral artery disease performed plantar flexion exercise in the supine posture until symptoms of claudication occurred. Relative to age- and sex-matched healthy subjects we found that patients had a higher blood pressure response, a higher heart rate response, and a greater reduction in skeletal muscle oxygenation as determined by near-infrared spectroscopy. Our data suggest that muscle ischemia contributes to the augmented exercise pressor reflex in peripheral artery disease.
Earthward plasma sheet flows during substorm phases (2011)

[1] Magnetic reconnection in the Earth's magnetotail converts open magnetic flux to closed, producing fast flows in the plasma sheet. Earthward fast flows can thus be used as a proxy for energy and momentum transfer into the closed magnetosphere during the course of a substorm. Characteristics of flows observed before substorm onset can provide information on the role of the flows in substorm onset triggering as well as the sequence of substorm-related processes. We use 15 years of data obtained by Geotail, Cluster, and THEMIS to study statistically the distribution of earthward plasma sheet flows during substorms. Substorm phases are determined from time series of the AL index and the z-component of the interplanetary magnetic field. We find that the occurrence frequency of medium-speed (100 km/s 500 km/s) flows, on the other hand, does not clearly increase during the substorm growth phase. The increase at substorm onset is more gradual than for the medium-speed flows. The occurrence frequency of high-speed flows peaks at the beginning of substorm recovery. These results indicate that any effect of the flows on substorm onset triggering would be caused by medium rather than very high speed flows.
Improvement of Bio‐crude Oil Yield and Phosphorus Content by Hydrothermal Liquefaction Using Microalgae (2017)

Abstract Hydrothermal liquefaction (HTL) is a thermal depolymerization process used to convert wet biomass such as microalgae into bio‐crude oil. Four main products, gas, bio‐crude oil, an aqueous phase, and solid residue, are generated through HTL. In this study, various HTL conditions were investigated to enhance the phosphorus content in the aqueous phase as well as the yield of bio‐crude oil. Tetraselmis sp. was used as the microalgae feedstock, and the product yields according to catalyst type were explored. The phosphate ion (PO 4 3− ) content in the aqueous phase was significantly enhanced when acetic acid was added because of the effect of pH. In addition, it was found that both the bio‐crude oil yield and the ammonium ion content could be increased by recycling the post‐HTL aqueous phase, while the phosphate content was not.