gebhart/patrepeval huggingface dataset:
Application of molecular markers to wheat breeding in Canada (2013)

Abstract Marker‐assisted breeding provides an opportunity for wheat breeders to introgress/pyramid genes of interest into breeding lines and to identify genes and/or quantitative trait loci in germplasm to be used as parents. Molecular markers were deployed to assist selection for disease resistance, agronomic and quality traits in several wheat cultivars released for commercial cultivation in C anada. Marker‐assisted breeding is routinely used in most wheat breeding programmes for rust resistance (leaf, stem and stripe rust), orange wheat blossom midge resistance, high grain protein concentration, Fusarium head blight and common bunt resistance. Markers are being used selectively within breeding programmes to target traits that relate to market class or regional adaptation. For example, marker‐assisted breeding for low lipoxygenase activity and low grain cadmium is being performed in durum breeding programmes and for enhancing stem solidness in programmes targeting resistance to the wheat stem sawfly. Markers are also being utilized for ergot resistance in durum wheat. Increased gluten strength is being selected with a marker for the overexpression of the B x7 high‐molecular‐weight glutenin subunit. Marker‐assisted breeding is also being used to pyramid resistance genes against a group of stem rust races related to TTKS ( U g99), a disease that poses a serious threat to global wheat production. Development of tightly linked diagnostic markers and high‐throughput genotyping with SNP markers will result in more effective molecular wheat breeding in the near future and will open the door to genomic selection.
Three-dimensional photonic crystals by large-area membrane stacking (2012)

We designed and analyzed a "mesh-stack" three-dimensional photonic crystal of a 12.4% bandgap with a dielectric constant ratio of 12 : 1. The mesh-stack consists of four offset identical square-lattice air-hole patterned membranes in each vertical period that is equal to the in-plane period of the square lattice. This design is fully compatible with the membrane-stacking fabrication method, which is based on alignment and stacking of large-area single-crystal membranes containing engineered defects. A bandgap greater than 10% is preserved as long as the membranes are subjected to in-plane misalignment less than 3% of the square period. By introducing a linear defect with a nonsymmorphic symmetry into the mesh-stack, we achieved a single-mode waveguide over a wide bandwidth.
Lignin content in natural Populus variants affects sugar release (2011)

The primary obstacle to producing renewable fuels from lignocellulosic biomass is a plant's recalcitrance to releasing sugars bound in the cell wall. From a sample set of wood cores representing 1,100 individual undomesticated Populus trichocarpa trees, 47 extreme phenotypes were selected across measured lignin content and ratio of syringyl and guaiacyl units (S/G ratio). This subset was tested for total sugar release through enzymatic hydrolysis alone as well as through combined hot-water pretreatment and enzymatic hydrolysis using a high-throughput screening method. The total amount of glucan and xylan released varied widely among samples, with total sugar yields of up to 92% of the theoretical maximum. A strong negative correlation between sugar release and lignin content was only found for pretreated samples with an S/G ratio < 2.0. For higher S/G ratios, sugar release was generally higher, and the negative influence of lignin was less pronounced. When examined separately, only glucose release was correlated with lignin content and S/G ratio in this manner, whereas xylose release depended on the S/G ratio alone. For enzymatic hydrolysis without pretreatment, sugar release increased significantly with decreasing lignin content below 20%, irrespective of the S/G ratio. Furthermore, certain samples featuring average lignin content and S/G ratios exhibited exceptional sugar release. These facts suggest that factors beyond lignin and S/G ratio influence recalcitrance to sugar release and point to a critical need for deeper understanding of cell-wall structure before plants can be rationally engineered for reduced recalcitrance and efficient biofuels production.
Geschichte von Mergentheim (2022)

Schönhuth, Ottmar Friedrich Heinrich: Chronik der vormaligen Deutschordens-Stadt Mergentheim. Aus urkundlichen Quellen hrsg., Bad Mergentheim: Thom, 1857. 94 Seiten. Neue umgearb. Ausg.
Stretchable Si Logic Devices with Graphene Interconnects (2015)

Stretchable integrated circuits consisting of ultrathin Si transistors connected by multilayer graphene are demonstrated. Graphene interconnects act as an effective countervailing component to maintain the electrical performance of Si integrated circuits against external strain. Concentration of the applied strain on the graphene interconnect parts can stably protect the Si active devices against applied strains over 10%.
Bifurcation route to chaos for a ferroresonant circuit using an electromagnetic transients program (1996)

The ferroresonant behaviour of a nonlinear power system circuit is examined using the diagnostic tools of deterministic chaos. An electromagnetic-transients simulation program is used to retain the component nature of the system and allow metering as for a real system. The information from state space trajectories, Poincaré maps and bifurcation diagrams is compared to that normally available from time and frequency domain analyses. They reveal the global behaviour of the system and the particular points of behavioural change.
Functional analysis of DM64, an antimyotoxic protein with immunoglobulin‐like structure from Didelphis marsupialis serum (2002)

Bothrops snake venoms are known to induce local tissue damage such as hemorrhage and myonecrosis. The opossum Didelphis marsupialis is resistant to these snake venoms and has natural venom inhibitors in its plasma. The aim of this work was to clone and study the chemical, physicochemical and biological properties of DM64, an antimyotoxic protein from opossum serum. DM64 is an acidic protein showing 15% glycosylation and with a molecular mass of 63 659 Da when analysed by MALDI-TOF MS. It was cloned and the amino acid sequence was found to be homologous to DM43, a metalloproteinase inhibitor from D. marsupialis serum, and to human alpha1B-glycoprotein, indicating the presence of five immunoglobulin-like domains. DM64 neutralized both the in vivo myotoxicity and the in vitro cytotoxicity of myotoxins I (mt-I/Asp49) and II (mt-II/Lys49) from Bothrops asper venom. The inhibitor formed noncovalent complexes with both toxins, but did not inhibit the PLA2 activity of mt-I. Accordingly, DM64 did not neutralize the anticoagulant effect of mt-I nor its intracerebroventricular lethality, effects that depend on its enzymatic activity, and which demonstrate the dissociation between the catalytic and toxic activities of this Asp49 myotoxic PLA2. Furthermore, despite its similarity with metalloproteinase inhibitors, DM64 presented no antihemorrhagic activity against Bothrops jararaca or Bothrops asper crude venoms, and did not inhibit the fibrinogenolytic activity of jararhagin or bothrolysin. This is the first report of a myotoxin inhibitor with an immunoglobulin-like structure isolated and characterized from animal blood.
Compositional dependence of the absorption edge and dark currents in Ge1−x−ySixSny/Ge(100) photodetectors grown via ultra-low-temperature epitaxy of Ge4H10, Si4H10, and SnD4 (2012)

Lattice-matched Ge1−x−ySixSny (x ≤ 0.2, y ≤ 0.05) alloys were deposited defect-free on Ge(001) substrates via low-temperature (330–290 °C) reactions of Ge4H10, Si4H10 and SnD4 hydrides, and used to fabricate pin photodetectors. The growth is carried out under gas-source molecular beam epitaxy conditions in a specially designed single-wafer reactor. Optical responsivity measurements reveal absorption edges between 0.88 eV and 0.98 eV, which are used to determine the compositional dependence of the direct band gap. A study of the I-V characteristics of the diodes shows that the dark current is very weakly correlated with the number of Si-Sn bonds in the alloy.
Lymph-Node-Targeted Immune Activation by Engineered Block Copolymer Amphiphiles–TLR7/8 Agonist Conjugates (2018)

Small molecule immuno-modulators such as agonists of Toll-like receptors (TLRs) are attractive compounds to stimulate innate immune cells toward potent antiviral and antitumor responses. However, small molecules rapidly enter the systemic circulation and cause "wasted inflammation". Hence, synthetic strategies to confine their radius of action to lymphoid tissue are of great relevance, to both enhance their efficacy and concomitantly limit toxicity. Here, we demonstrate that covalent conjugation of a small molecule TLR7/8 agonist immunomodulatory to a micelle-forming amphiphilic block copolymer greatly alters the pharmacokinetic profile, resulting in highly efficient lymphatic delivery. Moreover, we designed amphiphilic block copolymers in such a way to form thermodynamically stable micelles through π-π stacking between aromatic moieties, and we engineered the block copolymers to undergo an irreversible amphiphilic to hydrophilic transition in response to the acidic endosomal pH.
Cost-Effectiveness of Autologous Hematopoietic Stem Cell Transplantation for Elderly Patients with Multiple Myeloma using the Surveillance, Epidemiology, and End Results–Medicare Database (2020)

In the past decade, the number of autologous hematopoietic stem cell transplants (Auto HSCT) for older patients with multiple myeloma (MM) has increased dramatically, as has the cost of transplantation. The cost-effectiveness of this modality in patients over age 65 is unclear. Using the Surveillance, Epidemiology, and End ResultseMedicare database to create a propensity-score matched sample of patients over age 65 between 2000 and 2007, we compared the survival and cost for those who received Auto HSCT to those who did not undergo transplantation but survived at least 6 months after diagnosis, and we calculated an incremental cost-effectiveness ratio (ICER). Two hundred seventy patients underwent transplantation. Median overall survival from diagnosis in those who underwent transplantation was significantly longer than in patients who did not (58 months versus 37 months, P < .001). For patients living longer than 2 years, the median monthly cost during the first year was significantly different, but the middle and last year of life costs were similar. The median cost of the first 100 days after transplantation was $60,000 (range, $37,000 to $85,000). The resultant ICER was $72,852 per life-year gained. Survival after transplantation was comparable to that in those who underwent transplantation patients under 65 years and significantly longer than older patients who did not undergo transplantation. With an ICER less than $100,000/life-year gained, Auto HSCT is cost-effective when compared with nontransplantation care in the era of novel agents and should be considered, where clinically indicated, for patients over the age of 65.
PHS with inert blocking groups for DUV negative resist (1997)

The synthesis, characterization, and lithographic evaluation of a polyhydroxystyrene (PHS) modified with isopropyloxycarbonate groups is described. The inert blocking group is attached to the hydroxyl sites on PHS resin to slow the dissolution rate and make the resin useful in resists designed for 0.263 N TMAH developers. A negative tone resist (CGR-IP) that is formulated with the modified polymer is compatible with the industry standard 0.263 N TMAH developer and is capable of resolving 0.22 micrometer L/S features and 0.14 micrometer isolated lines on a 0.50 NA imaging system. Reaction with PHS resin occurs primarily at the phenolic sites as shown by carbon-13 NMR and 10% protection is sufficient to lower the dissolution rate to an acceptable level so that there is less than 50 angstrom film loss in exposed areas. The blocking group described here is not acid labile and reaming intact after the resist film is baked at 150 degrees Celsius.
Free‐breathing whole‐heart coronary MR angiography on a clinical scanner in four minutes (2006)

The employed 32-receive channel technology enabled a robust trade-off among SNR, spatial resolution, and scan time. In this study the most robust results were obtained using the smallest possible SENSE factors for a given voxel size and scan time.
Feasibility exploration of NVM based I-cache through MSHR enhancements (2014)

SRAM based memory systems are plagued by a number of problems like sub-threshold leakage and susceptibility to read/write failure with dynamic voltage scaling schemes or low supply voltage. Non-Volatile Memory (NVM) technologies are being explored extensively nowadays to replace the conventional SRAM memories even for level 1 (L1) caches. These NVMs like Spin Torque Transfer RAM (STT-MRAM), Resistive-RAM (ReRAM) and Phase Change RAM (PRAM) are less hindered by leakage problems with technology scaling and consume lesser area. However, simple replacement of SRAM by NVMs is not a viable option due to their write related issues. The main focus of this paper is the exploration of write delay and write energy issues in a NVM based L1 Instruction cache (I-cache) for an ARM like single core system. We propose a NVM I-cache and extend its MSHR (Miss Status Handling Register) functionality to address the NVMs write related issues. According to our simulations, appropriate tuning of selective architecture parameters can reduce the performance penalty introduced by the NVM (~45%) to extremely tolerable levels (~1%) and show energy gains up to 35%. Furthermore, on configuring our modified NVM based system to occupy area comparable to the original SRAM-based configuration, it outperforms the SRAM baseline and leads to even more energy savings.
Magnetic nanoparticle hyperthermia: predictive model for temperature distribution (2013)

Magnetic nanoparticle (mNP) hyperthermia is a promising adjuvant cancer therapy. mNP's are delivered intravenously or directly into a tumor, and excited by applying an alternating magnetic field (AMF). The mNP's are, in many cases, sequestered by cells and packed into endosomes. The proximity of the mNP's has a strong influence on their ability to heat due to inter-particle magnetic interaction effects. This is an important point to take into account when modeling the mNP's. Generally, more mNP heating can be achieved using higher magnetic field strengths. The factor which limits the maximum field strength applied to clinically relevant volumes of tissue is the heating caused by eddy currents, which are induced in the noncancerous tissue. A coupled electromagnetic and thermal model has been developed to predict dynamic thermal distributions during AMF treatment. The EM model is based on the method of auxiliary sources and the thermal modeling is based on the Pennes bioheat equation. The results of our phantom study are used to validate the model which takes into account nanoparticle heating, interaction effects, particle spatial distribution, particle size distribution, EM field distribution, and eddy current generation in a controlled environment. Preliminary <i>in vivo</i> data for model validation are also presented. Once fully developed and validated, the model will have applications in experimental design, AMF coil design, and treatment planning.
Abstract 2120: Platinum-based cancer chemotherapeutics inhibit STAT signaling by blocking the SH2 domain. (2013)

Abstract Platinum-based drugs form the corner stone of many treatment schedules in cancer. Their main mechanism of actions is the covalent binding to DNA, leading to the formation of platinum-DNA adducts and thereby inducing apoptosis. Recently, other so called off-target effects of these drugs have been described. These include the induction of immunogenic cell death and the downregulation of inhibitory molecule Programmed Death-Ligand 2 by inactivation of signaling molecule/transcription factor STAT6, a member of the Signal Transducer and Activator of Transcription (STAT) protein family. STAT proteins play crucial roles in the pathogenesis and progression of cancer and much research is being conducted to identify inhibitors of STAT signaling for use in cancer treatment. Here, we investigated the potential of platinum-based chemotherapeutics to inhibit STAT signaling. We found that treatment of tumor cells of various origins with platinum drugs inhibit the activation of STAT proteins and leads to loss of cytokine-induced and constitutive STAT protein phosphorylation. Concurrently, a decrease of STAT protein nuclear accumulation was evident by confocal microscopy analysis. This resulted in a downregulation of STAT-regulated tumorigenic genes such as Bcl-xL, MCL-1, VEGF and survivin. Non-STAT target genes were not affected. Analysis of the known STAT inactivation pathways showed that these were not activated nor enhanced by treatment with platinum drugs. Finally, using a biochemical alphascreen-based assay, we demonstrated that platinum compounds directly interact with STAT proteins and inhibit binding to the SH2 domain. These findings provide novel insight into the mechanism of action of platinum drugs and show for the first time that these clinically used compounds directly affect important cellular signaling pathways. These results indicate that part of the efficacy of these drugs may be derived from their inhibition of STAT signaling and they provide important leads for the development of novel innovative treatment schedules in cancer that exploit the STAT-inhibiting effect of platinum drugs, for example by potentiating targeted therapies or immunotherapy. Citation Format: W. Joost Lesterhuis, Stanleyson V. Hato, Carl G. Figdor, Susumu Takahashi, Cornelis J.A. Punt, Akira Asai, I. Jolanda M. De Vries. Platinum-based cancer chemotherapeutics inhibit STAT signaling by blocking the SH2 domain. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2120. doi:10.1158/1538-7445.AM2013-2120
Low-complexity HOG for efficient video saliency (2015)

In this paper, we propose a low-complexity histogram of oriented gradients (HOG) implementation for efficient video saliency framework. After showing how original HOG calculations present significant computation bottleneck for visual understanding pipes, we present the optimized HOG flow and algorithm for video saliency framework, which can reduce computational requirements without losing algorithmic performance. Furthermore, simplification for light-weight computations and data-reusable scanning for optimal memory usage are explained for improving system efficiency. Based on our testing and analysis, the proposed HOG implementation optimizes computational complexity and performance while maintaining the video saliency algorithm capability.
Coreceptor Tropism in Human Immunodeficiency Virus Type 1 Subtype D: High Prevalence of CXCR4 Tropism and Heterogeneous Composition of Viral Populations (2007)

In human immunodeficiency virus type 1 (HIV-1) subtype B, CXCR4 coreceptor use ranges from approximately 20% in early infection to approximately 50% in advanced disease. Coreceptor use by non-subtype B HIV is less well characterized. We studied coreceptor tropism of subtype A and D HIV-1 collected from 68 pregnant, antiretroviral drug-naive Ugandan women (HIVNET 012 trial). None of 33 subtype A or 10 A/D-recombinant viruses used the CXCR4 coreceptor. In contrast, nine (36%) of 25 subtype D viruses used both CXCR4 and CCR5 coreceptors. Clonal analyses of the nine subtype D samples with dual or mixed tropism revealed heterogeneous viral populations comprised of X4-, R5-, and dual-tropic HIV-1 variants. In five of the six samples with dual-tropic strains, V3 loop sequences of dual-tropic clones were identical to those of cocirculating R5-tropic clones, indicating the presence of CXCR4 tropism determinants outside of the V3 loop. These dual-tropic variants with R5-tropic-like V3 loops, which we designated "dual-R," use CCR5 much more efficiently than CXCR4, in contrast to dual-tropic clones with X4-tropic-like V3 loops ("dual-X"). These observations have implications for pathogenesis and treatment of subtype D-infected individuals, for the association between V3 sequence and coreceptor tropism phenotype, and for understanding potential mechanisms of evolution from exclusive CCR5 use to efficient CXCR4 use by subtype D HIV-1.
Computational and Experimental Study of Colloidal Stability of CuPc Aqueous Dispersions (2011)

Dispersions of copper phthalocyanine (CuPc) pigments are commonly used in digital printing. Their colloidal stability is essential for fulfilling desirable shelf life and achieving good printing performance. In order to understand the role of electrostatic and van der Waals forces in their stability, a combined computational and experimental study has been performed to investigate the stability of the CuPc aqueous dispersions.The Hamaker constant was calculated with a novel combination of an ab initio and an empirical methodology (J. Chem. Theory Comput., 2010, 6 (2), pp 491&#x2013;498) to address the van der Waals attractions between the pigment particles. The calculated Hamaker constant was then employed in the DLVO (Derjaguin-Landau-Verwey-Overbeek) equation for dispersion stability simulation. The predictions allow comparisons with experimental colloidal stability study of CuPc aqueous dispersions (Langmuir, 2010, 26 (10), pp 6995&#x2013;7006)). The effect of a nonionic surfactant on the dispersion stability of CuPc particles was taken into consideration. The experimental dispersion stability ratio (W) was determined from dynamic light scattering (DLS) data and based on the Rayleigh-Debye-Gans (RDG) scattering theory. The adsorption isotherms show that the adsorption density increases with increasing equilibrium concentration of surfactant up to the cmc, and then reaches a plateau. Desorption tests were conducted to determine the reversibility or irreversibility of adsorption. Preliminary results suggest that a portion of the surfactant adsorbs irreversibly. The comparisons reveal that electrostatic forces play a significant role in the dispersion stabilization.
Adaptive sequential Monte Carlo for multiple changepoint analysis (2016)

Process monitoring and control requires detection of structural changes in a data stream in real time. This article introduces an efficient sequential Monte Carlo algorithm designed for learning unknown changepoints in continuous time. The method is intuitively simple: new changepoints for the latest window of data are proposed by conditioning only on data observed since the most recent estimated changepoint, as these observations carry most of the information about the current state of the process. The proposed method shows improved performance over the current state of the art. Another advantage of the proposed algorithm is that it can be made adaptive, varying the number of particles according to the apparent local complexity of the target changepoint probability distribution. This saves valuable computing time when changes in the changepoint distribution are negligible, and enables re-balancing of the importance weights of existing particles when a significant change in the target distribution is encountered. The plain and adaptive versions of the method are illustrated using the canonical continuous time changepoint problem of inferring the intensity of an inhomogeneous Poisson process, although the method is generally applicable to any changepoint problem. Performance is demonstrated using both conjugate and non-conjugate Bayesian models for the intensity. Appendices to the article are available online, illustrating the method on other models and applications.