gebhart/patrepeval huggingface dataset:
Genetic characterization and curation of diploid A-genome wheat species (2022)

A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, β, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.
Constraints from rocks in the Taiwan orogen on crustal stress levels and rheology (2012)

Taiwan's Hsüehshan range experienced penetrative coaxial deformation within and near the brittle‐plastic transition between ∼6.5 and 3 Ma. This recent and short‐lasting deformation in an active, well‐studied orogen makes it an ideal natural laboratory for studying crustal rheology. Recrystallized grain size piezometry in quartz and Ti‐in‐quartz thermobarometry yield peak differential stresses of ∼200 MPa at 250–300°C that taper off to ∼80 MPa at ∼350°C and ∼14 MPa at ∼400–500°C. Stress results do not vary with lithology: recrystallized quartz veins in slates and metasiltstones yield equivalent stresses as recrystallized grains in quartzites. A minimum strain rate of 2.9 × 10 −15 s −1 associated with this deformation is calculated by dividing a strain measurement (axial strain ∼0.3) in a strongly deformed quartzite by the available 3.5 m.y. deformation interval. We estimate a maximum strain rate of 7.0 × 10 −14 s −1 by distributing the geodetic convergence rate throughout a region homogeneously deformed under horizontal compression. These stress, strain rate and temperature estimates are consistent with the predictions of widely applied dislocation creep flow laws for quartzite. The samples record stress levels at the brittle‐plastic transition, indicating a coefficient of friction ( μ ) of 0.37 in the upper crust consistent with results based on critical taper. Integrated crustal strength of the Hsüehshan range amounts to 1.7 × 10 12 N/m based on our analysis, consistent with potential energy constraints based on topography. Other strength profiles are considered, however high crustal stresses (&gt;300 MPa) conflict with our analysis. The study supports the use of the recrystallized grain size piezometer in quartz as a quick and inexpensive method for resolving stress histories in greenschist facies rocks. For consistency with the independent constraints presented here, we find it accurate to within +20%/−40%, significantly better than previously recognized.
Directional antennas improve the link-connectivity of interference limited ad hoc networks (2015)

We study wireless ad hoc networks in the absence of any channel contention or transmit power control and ask how antenna directivity affects network connectivity in the interference limited regime. We answer this question by deriving closed-form expressions for the outage probability, capacity and mean node degree of the network using tools from stochastic geometry. These novel results provide valuable insights for the design of future ad hoc networks. Significantly, our results suggest that the more directional the interfering transmitters are, the less detrimental are the effects of interference to individual links. We validate our analytical results through computer simulations.
Phase I Study of Hepatic Arterial Melphalan Infusion and Hepatic Venous Hemofiltration Using Percutaneously Placed Catheters in Patients With Unresectable Hepatic Malignancies (2005)

Delivery of melphalan via this system is feasible, with limited, manageable toxicity and evidence of substantial antitumor activity; 3 mg/kg is the maximum safe tolerated dose of melphalan administered via this technique.
Effects of time‐division multiplexing of two‐pump wavelengths on a counter‐pumped Raman‐fiber amplifier (2004)

Abstract We demonstrate the impacts of the time‐division multiplexing (TDM) technique on a two‐pump wavelength Raman‐fiber amplifier. Modulation frequency is critical in this pumping technique, which can create temporal gain variations at low frequencies. The effective noise figure also degrades when utilizing this pumping scheme due to the arising of amplified spontaneous emission. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 42: 238–239, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20263
Extruder system for high-throughput/steady-state hydrogen ice supply and application for pellet fueling of reactor-scale fusion experiments (1998)

Pellet injection systems for the next-generation fusion devices, such as the proposed International Thermonuclear Experimental Reactor (ITER), will require feed systems capable of providing a continuous supply of hydrogen ice at high throughputs. A straightforward concept in which multiple extruder units operate in tandem has been under development at the Oak Ridge National Laboratory. A prototype with three large-volume extruder units has been fabricated and tested in the laboratory. In experiments, it was found that each extruder could provide volumetric ice flow rates of up to ∼1.3 cm3/s (for ∼10 s), which is sufficient for fueling fusion reactors at the gigawatt power level. With the three extruders of the prototype operating in sequence, a steady rate of ∼0.33 cm3/s was maintained for a duration of 1 h. Even steady-state rates approaching the full ITER design value (∼1 cm3/s) may be feasible with the prototype. However, additional extruder units (1–3) would facilitate operations at the higher throughputs and reduce the duty cycle of each unit. The prototype can easily accommodate steady-state pellet fueling of present large tokamaks or other near-term plasma experiments.
Polarimetric modeling and parameter estimation with applications to remote sensing (1995)

Develops and analyzes two parametric models in which electromagnetic plane waves carrying polarimetric information are received. The first model considers estimation of the polarimetric response of a surface by measuring the reflections of actively generated waves. The second considers estimation of the polarization of passively generated waves. Both models have applications to remote sensing. The authors propose a natural parametrization of the distribution of the received signal. Using the Cramer-Rao bound, they characterize the best possible accuracy of unbiased estimators of these parameters. Simple estimators are given. Both models are fitted into a common framework and compared.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Development and validation of the Axiom®Apple480K SNP genotyping array (2016)

Cultivated apple (Malus × domestica Borkh.) is one of the most important fruit crops in temperate regions, and has great economic and cultural value. The apple genome is highly heterozygous and has undergone a recent duplication which, combined with a rapid linkage disequilibrium decay, makes it difficult to perform genome-wide association (GWA) studies. Single nucleotide polymorphism arrays offer highly multiplexed assays at a relatively low cost per data point and can be a valid tool for the identification of the markers associated with traits of interest. Here, we describe the development and validation of a 487K SNP Affymetrix Axiom(®) genotyping array for apple and discuss its potential applications. The array has been built from the high-depth resequencing of 63 different cultivars covering most of the genetic diversity in cultivated apple. The SNPs were chosen by applying a focal points approach to enrich genic regions, but also to reach a uniform coverage of non-genic regions. A total of 1324 apple accessions, including the 92 progenies of two mapping populations, have been genotyped with the Axiom(®) Apple480K to assess the effectiveness of the array. A large majority of SNPs (359 994 or 74%) fell in the stringent class of poly high resolution polymorphisms. We also devised a filtering procedure to identify a subset of 275K very robust markers that can be safely used for germplasm surveys in apple. The Axiom(®) Apple480K has now been commercially released both for public and proprietary use and will likely be a reference tool for GWA studies in apple.
Self-Learning Cruise Control Using Kernel-Based Least Squares Policy Iteration (2013)

This paper presents a novel learning-based cruise controller for autonomous land vehicles (ALVs) with unknown dynamics and external disturbances. The learning controller consists of a time-varying proportional-integral (PI) module and an actor-critic learning control module with kernel machines. The learning objective for the cruise control is to make the vehicle's longitudinal velocity follow a smoothed spline-based speed profile with the smallest possible errors. The parameters in the PI module are adaptively tuned based on the vehicle's state and the action policy of the learning control module. Based on the state transition data of the vehicle controlled by various initial policies, the action policy of the learning control module is optimized by kernel-based least squares policy iteration (KLSPI) in an offline way. The effectiveness of the proposed controller was tested on an ALV platform during long-distance driving in urban traffic and autonomous driving on off-road terrain. The experimental results of the cruise control show that the learning control method can realize data-driven controller design and optimization based on KLSPI and that the controller's performance is adaptive to different road conditions.
A distinct 5′ flanking var gene region regulates Plasmodium falciparum variant erythrocyte surface antigen expression in placental malaria (2002)

The Plasmodium falciparum multigene var family codes for approximately 50 variant adhesive proteins expressed in a mutually exclusive manner at the surface of infected red blood cells (iRBCs). Switching expression of var genes can lead to fundamental changes in the adhesive and antigenic properties of iRBCs. For example, a specific phenotypic switch in adhesion from CD36 to chondroitin sulphate A (CSA) is associated with malaria pathogenesis in pregnant women. The factors and DNA elements that control the expression of a particular member of the var gene family during gestational malaria remains enigmatic. Here, we report that the subtelomeric FCR3 varCSA is expressed under the control of a unique DNA element of 1.8 kb, whereas the other members of the var multigene family are flanked by common regulatory elements. The 5' varCSA-type element is conserved as a single copy in laboratory strains and clinical isolates from Brazil and West Africa and contains two distinct repetitive elements of 150 bp and 60 bp respectively. The 5' varCSA-type sequence tags a var gene in the 3D7 genome that is homologous to the FCR3 varCSA gene. A recombinant DBL gamma domain of this var gene showed specific binding to CSA. This subtelomeric varCSA gene is transcribed in the opposite sense when compared with the usual orientation of telomere-adjacent var genes. This unique arrangement might explain why the varCSA gene is relatively conserved in genetically distinct parasites despite being located in a highly recombinogenic chromosome compartment. The 5' untranslated region (UTR) of the varCSA-type sequence is also transcribed in placental isolates that bind to CSA, illustrating an important role for the unique 5' varCSA-type sequence in the regulation of var genes involved in malaria pathogenesis in pregnant women. However, this promoter is not always found to be transcribing var genes selected for expression of products that bind to CSA in vitro. Our work identifies a sequence tag for the identification of varCSA genes in placental isolates for the first time.
P.38: Estimate of the Distribution of Contrast Ratio in Optically Compensated In‐Plane‐Switching‐Mode Using Response Surface Method (2013)

Abstract We propose to use the Response Surface Method for estimation of contras ratio. This method makes it possible to estimate the contrast ratio easily and quickly even in the optically compensated In‐Plane‐Switching‐Mode panel which has many optical axes. Additionally, using combination Response Surface Method and Monte Carlo Method, the distribution of contrast ratio can be calculated. This approach is quite useful for prediction of contrast ratio in mass production. Furthermore, utilizing the interactions between design factors, the distribution of contrast ratio can be reduced.
Rely-guarantee bound analysis of parameterized concurrent shared-memory programs (2021)

Abstract We present a thread-modular proof method for complexity and resource bound analysis of concurrent, shared-memory programs. To this end, we lift Jones’ rely-guarantee reasoning to assumptions and commitments capable of expressing bounds. The compositionality (thread-modularity) of this framework allows us to reason about parameterized programs, i.e., programs that execute arbitrarily many concurrent threads. We automate reasoning in our logic by reducing bound analysis of concurrent programs to the sequential case. As an application, we automatically infer time complexity for a family of fine-grained concurrent algorithms, lock-free data structures , to our knowledge for the first time.
Initial Genetic Characterization of the 1918 “Spanish” Influenza Virus (1997)

The "Spanish" influenza pandemic killed at least 20 million people in 1918-1919, making it the worst infectious pandemic in history. Understanding the origins of the 1918 virus and the basis for its exceptional virulence may aid in the prediction of future influenza pandemics. RNA from a victim of the 1918 pandemic was isolated from a formalin-fixed, paraffin-embedded, lung tissue sample. Nine fragments of viral RNA were sequenced from the coding regions of hemagglutinin, neuraminidase, nucleoprotein, matrix protein 1, and matrix protein 2. The sequences are consistent with a novel H1N1 influenza A virus that belongs to the subgroup of strains that infect humans and swine, not the avian subgroup.
High-temperature toughening in ternary medium-entropy (Ta1/3Ti1/3Zr1/3)C carbide consolidated using spark-plasma sintering (2020)

We report for the first time the effect of temperature on the mechanical properties of (Ta1/3Ti1/3Zr1/3)C carbide. Flexural strength and fracture toughness were investigated using the three-point bending technique in argon. Using commercially available carbide powders with an equimolar ratio and performing spark plasma consolidation at 1973°C, we obtained a bulk single-phase medium-entropy carbide ceramic with the lattice parameter a= 4.458 Å. The flexural strength and fracture toughness at room temperature reached on average 700 MPa and 3.2 MPa m1/2, respectively. At 1800°C, local decomposition of the medium-entropy carbide took place as a structure with a local chemical gradient was observed after high-temperature tests, which increased fracture toughness by 30% (to 4.4 MPa m1/2).
Spectral decomposition of susceptibility artifacts for spectral‐spatial radiofrequency pulse design (2012)

Susceptibility induced signal loss is a limitation in gradient echo functional MRI. The through-plane artifact in axial slices is particularly problematic due to the inferior position of air cavities in the brain. Spectral-spatial radiofrequency pulses have recently been shown to reduce signal loss in a single excitation. The pulses were successfully demonstrated assuming a linear relationship between susceptibility gradient and frequency, however, the exact frequency and spatial distribution of the susceptibility gradient in the brain is unknown. We present a spiral spectroscopic imaging sequence with a time-shifted radiofrequency pulse that can spectrally decompose the through-plane susceptibility gradient for spectral-spatial radiofrequency pulse design. Maps of the through-plane susceptibility gradient as a function of frequency were generated for the human brain at 3T. We found that the linear relationship holds well for the whole brain with an optimal slope of -1.0 μT/m/Hz.
Coaxing HESC to form Oocyte-Like Structures by Co-Culture with Testicular Extract and Hormones (2011)

Reports have shown that murine embryonic stem cells (mESC) can differentiate into primordial germ cells (PGC) and then to early gametes (oocytes and sperm) that after fertilization form blastocysts. Preliminary studies indicated that hESC also have the potential to differentiate into germ cells. Currently, there are no reports on directed differentiation of hESCs into oocytes. Here, we investigated the effects of human fetal testicular extracts (HFTE) and hormones i.e. follicle-stimulating hormone (FSH), human chorionic gonadotropin (hCG) to coax hESC to differentiate into oocytes. The embryoid bodies (EBs) derived from hESC formed ovarian-like structures (OLS) after treatment with HFTE for 7 days and with hormones (FSH + hCG) for 20-30 days. OLS exhibited typical oocyte-like spherical shape of variable sizes and some with zona pellucida-like covering RT-PCR, immunological fluorescence staining and flow cytometry analyses showed that these structures are positive for specific germ cell and oocyte markers such as OCT4, SCP3, C-KIT and DDX4, STELLA, FIGLA, GDF9, NANOGFSHR, ZP1, ZP2 and ZP3. Quantitative RT-PCR analysis showed that FSHR, GDF9 and FIGLA were up-regulated during OLS differentiation from EB in a time-dependent manner. These results demonstrated that hESC have the ability to differentiate into ovarian structures. This study thus provides an in vitro model to study germ-cell formation from hESC and these germ cells may generate a potential source of oocytes for therapeutic cloning.
XML Metadata Services (2006)

As the Service Oriented Architecture (SOA) principles have gained importance, an emerging need has appeared for methodologies to locate desired services that provide access to their capability descriptions. These services must typically be assembled into short-term service collections that, together with code execution services, are combined into a meta-application to perform a particular task. To address metadata requirements of these problems, we introduce XML Metadata Services to manage both stateless and stateful (transient) metadata. We leverage the two widely used web service standards: Universal Description, Discovery, and Integration (UDDI) and Web Services Context (WS-Context) in our design. We describe our approach and experiences when designing semantics"" for XML Metadata Services. We report results from a prototype of the system that is applied to mobile environment for optimizing Web Service communications.""
A comparative performance evaluation of MAC protocols for underwater sensor networks (2008)

A propagation-delay-aware MAC protocol, based on carrier sensing multiple access, is proposed. The design aims at maximizing the bandwidth utilization by keeping track of neighboring transmissions to avoid collisions, thus enabling interleaved packet transmission between different pairs of users. The performance is compared to several representative MAC protocols: the standard and slotted ALOHA, and three protocols designed specifically for the underwater acoustic environment, APCAP [1], DACAP [2] and T-Lohi [3]. Simulation results identify network settings (traffic load, node density, single/multi-hop topologies) in which each protocol offers the best performance.
On the synthesis and microstructure analysis of high performance MnBi (2016)

Highly anisotropic MnBi powder with over 90 wt% low-temperature phase can be prepared using conventional arc-melting and 2 hour-low energy ball milling (BM) followed by magnetic separation. After proper alignment, the purified Mn55Bi45(Mn45Bi55) powder show remarkable magnetic properties: mass remanence of 71(65) Am2/kg and coercivity of 1.23(1.18) T at 300 K. The nominal maximum energy product of 120 kJ/m3 is achieved in the purified 2h-BM Mn55Bi45 powder, close to theoretical value of 140.8 kJ/m3. The Mn55Bi45(Mn45Bi55) bulk magnets show the highest volume remanence of 0.68(0.57) T at 300 K, while they were consolidated at 573(523) K by a pressure of 200 MPa for 5 minutes using hot-compaction method. In addition to the observed grain size, the coercivity of the hot-compacted samples at 300 K was found to be strongly related to the amount of metallic Mn and Bi residue at the grain-boundary. Our study proves that the magnetic properties of the Mn45Bi55 bulk magnets are stable up to 500 K, and the nominal (BH)max values are still above 40 kJ/m3 at 500 K showing the potential ability for high-temperature applications.
Preparation and Properties of One-Dimensional Metals in Dielectric Matrices. (1973)

The aim of this research was to prepare monocrystals of several compounds possessing metallic chains which are one-dimensionally or two-dimensionally constrained and evaluate their electronic properties. Such structures have been suggested to be possible models for high temperature superconductors. One-dimensional platinum complexes, and channel complexes of iodine and polysulfur nitrides were grown. Two-dimensional intercalation complexes and polymerization of monomeric Lewis bases were prepared. The superconducting critical temperature was determined by measuring ac magnetic susceptibility as a function of temperature. (Author)
Tissue microarrays compared with whole sections and biochemical analyses. A subgroup analysis of DBCG 82 b&c. (2008)

IHC stainings for ER, PgR, and HER2 showed a substantial agreement between a single 1mm TMA core and the corresponding whole section, between central and peripheral cores, and between cores from two different paraffin blocks from the same tumor. In addition, a fine agreement was found for ER and PgR between IHC stainings of TMA cores and biochemical analyses. Divergence between IHC and biochemical analyses was predominantly due to the chosen thresholds. IHC staining of one 1mm core from each tumor revealed a significant independent prognostic value of PgR and HER2 on overall survival. In conclusion, IHC stainings for ER, PgR, and HER2 of just a single 1mm TMA core seems to be sufficient, as no significant heterogeneity was noticed.