gebhart/patrepeval huggingface dataset:
Development and Validation of SNP and InDel Markers for Pod-Shattering Tolerance in Soybean (2022)

Pod-shattering causes a significant yield loss in many soybean cultivars. Shattering-tolerant cultivars provide the most effective approach to minimizing this loss. We developed molecular markers for pod-shattering and validated them in soybeans with diverse genetic backgrounds. The genes <i>Glyma.16g141200</i>, <i>Glyma.16g141500</i>, and <i>Glyma.16g076600</i>, identified in our previous study by quantitative trait locus (QTL) mapping and whole-genome resequencing, were selected for marker development. The whole-genome resequencing of three parental lines (one shattering-tolerant and two shattering-susceptible) identified single nucleotide polymorphism (SNP) and/or insertion/deletion (InDel) regions within or near the selected genes. Two SNPs and one InDel were converted to Kompetitive Allele-Specific PCR (KASP) and InDel markers, respectively. The accuracy of the markers was examined in the two recombinant inbred line populations used for the QTL mapping, as well as the 120 varieties and elite lines, through allelic discrimination and phenotyping by the oven-drying method. Both types of markers successfully discriminated the pod shattering-tolerant and shattering-susceptible genotypes. The prediction accuracy, which was as high as 90.9% for the RILs and was 100% for the varieties and elite lines, also supported the accuracy and usefulness of these markers. Thus, the markers can be used effectively for genetic and genomic studies and the marker-assisted selection for pod-shattering tolerance in soybean.
Size of the embryoid body influences chondrogenesis of mouse embryonic stem cells (2008)

For applications in tissue engineering and regenerative medicine, embryonic stem cells (ESCs) are commonly pre-differentiated in the form of embryoid bodies (EBs). The uncontrolled cell differentiation in EBs results in a highly heterogeneous cell population, an unfavourable condition for therapeutic development. The purpose of this study was to determine an optimal size of EBs for chondrogenic differentiation. EBs were produced in suspension culture with mouse ESCs (ES-D3 GL). The 5-day-old EBs were sorted under a microscope by diameter: small EBs (S-EBs, < 100 microm), medium EBs (M-EBs, 100-150 microm) and large EBs (L-EBs, > 150 microm). The three sizes of EBs were cultured separately for 3 weeks in chondrogenic medium. Type II collagen and aggrecan gene expression was significantly upregulated in the S-EBs, when compared with the M-EBs and L-EBs (p < 0.05 and p < 0.001, respectively). Proteoglycans produced by the cells derived from S-EBs were > 50% of the other two groups. In addition, both Oct4 and Sox2 were expressed more in S-EBs than in M-EBs and L-EBs. Type X collagen expression was relatively increased in L-EBs. Slight shifts toward haematopoietic and endothelial differentiation were seen in the L- and M-EBs. In summary, the size of EBs has implications on ESC differentiation. Cells derived from S-EBs have a greater chondrogenic potential than those from M-EBs and L-EBs. The size of EBs can be a parameter utilized to optimize ESC differentiation for tissue engineering.
Trials and Tribulations of Viscoelastic-Based Determination of Fibrinogen Concentration (2019)

Acquired fibrinogen deficiency is a major determinant of severe bleeding in different clinical conditions, including cardiac surgery, trauma, postpartum hemorrhage, liver surgery, and transplantation. The existing guidelines recommend to supplement fibrinogen in patients with severe bleeding when the fibrinogen concentration is <1.5 g/L. Viscoelastic tests (VETs) provide a fast determination of the fibrinogen contribution to clot firmness and allow prompt treatment of acquired fibrinogen deficiency. However, different VET devices are presently available on the market, based on different technologies and different activators and platelet inhibitors. The available tests are the functional fibrinogen (FF, thromboelastography), the fibrinogen contribution to clot firmness (fibrinogen determination [FIBTEM], thromboelastometry), and the fibrinogen contribution to clot strength (FCS, sonorheometry). All these tests have a moderate to very good correlation with the Clauss fibrinogen assays; however, when comparing VET-based fibrinogen contribution to clot firmness with Clauss fibrinogen concentration, strong differences occur within the same test under different conditions and between different tests. The most widely studied test is the thromboelastometric FIBTEM; the best predictor of a Clauss fibrinogen <1.5 g/L is placed at a maximum clot firmness around 8 mm of amplitude. Fewer data are available for thromboelastographic FF, but the correspondent value is in the range of 12 mm. Overall, due to an incomplete inhibition of platelet contribution, FF overestimates the fibrinogen contribution with respect to FIBTEM. Data on sonorheometry FCS are limited and conflicting. When addressing the correlation between different tests, it is good in general, but no fixed conversion factors can be proposed, due to a considerable dispersion of the experimental points. In conclusion, VET-based fibrinogen tests are certainly powerful tools that are presently suggested by the existing guidelines; however, when using them for clinical decision-making, users should consider the possible sources of bias, which include the different level of platelet inhibition, the role of platelet count and function, the possible different degrees of blood activation with tissue factor, the important role of factor XIII in stabilizing the fibrin clot, and others.
Strategy for Good Dispersion of Well‐Defined Tetrapods in Semiconducting Polymer Matrices (2014)

The morphology or dispersion control in inorganic/organic hybrid systems is studied, which consist of monodisperse CdSe tetrapods (TPs) with grafted semiconducting block copolymers with excess polymers of the same type. Tetrapod arm-length and amount of polymer loading are varied in order to find the ideal morphology for hybrid solar cells. Additionally, polymers without anchor groups are mixed with the TPs to study the effect of such anchor groups on the hybrid morphology. A numerical model is developed and Monte Carlo simulations to study the basis of compatibility or dispersibility of TPs in polymer matrices are performed. The simulations show that bare TPs tend to form clusters in the matrix of excess polymers. The clustering is significantly reduced after grafting polymer chains to the TPs, which is confirmed experimentally. Transmission electron microscopy reveals that the block copolymer-TP mixtures ("hybrids") show much better film qualities and TP distributions within the films when compared with the homopolymer-TP mixtures ("blends"), representing massive aggregations and cracks in the films. This grafting-to approach for the modification of TPs significantly improves the dispersion of the TPs in matrices of "excess" polymers up to the arm length of 100 nm.
À-la-carte Prompt Tuning (APT): Combining Distinct Data Via Composable Prompting (2023)

We introduce À-la-carte Prompt Tuning (APT), a transformer-based scheme to tune prompts on distinct data so that they can be arbitrarily composed at inference time. The individual prompts can be trained in isolation, possibly on different devices, at different times, and on different distributions or domains. Furthermore each prompt only contains information about the subset of data it was exposed to during training. During inference, models can be assembled based on arbitrary selections of data sources, which we call "à-la-carte learning". À-la-carte learning enables constructing bespoke models specific to each user's individual access rights and preferences. We can add or remove information from the model by simply adding or removing the corresponding prompts without retraining from scratch. We demonstrate that à-la-carte built models achieve accuracy within $5\%$ of models trained on the union of the respective sources, with comparable cost in terms of training and inference time. For the continual learning benchmarks Split CIFAR-100 and CORe50, we achieve state-of-the-art performance.
Bacterial Microbiota Profiling in Gastritis without Helicobacter pylori Infection or Non-Steroidal Anti-Inflammatory Drug Use (2009)

Recent 16S ribosomal RNA gene (rRNA) molecular profiling of the stomach mucosa revealed a surprising complexity of microbiota. Helicobacter pylori infection and non-steroidal anti-inflammatory drug (NSAID) use are two main contributors to gastritis and peptic ulcer. However, little is known about the association between other members of the stomach microbiota and gastric diseases. In this study, cloning and sequencing of the 16S rRNA was used to profile the stomach microbiota from normal and gastritis patients. One hundred and thirty three phylotypes from eight bacterial phyla were identified. The stomach microbiota was found to be closely adhered to the mucosa. Eleven Streptococcus phylotypes were successfully cultivated from the biopsies. One to two genera represented a majority of clones within any of the identified phyla. We further developed two real-time quantitative PCR assays to quantify the relative abundance of the Firmicutes phylum and the Streptococcus genus. Significantly higher abundance of the Firmicutes phylum and the Streptococcus genus within the Firmicutes phylum was observed in patients with antral gastritis, compared with normal controls. This study suggests that the genus taxon level can largely represent much higher taxa such as the phylum. The clinical relevance and the mechanism underlying the altered microbiota composition in gastritis require further functional studies.
Compiler-Based Approach for Exploiting Scratch-Pad in Presence of Irregular Array Access (2005)

Scratch-pad memory is becoming an important fixture in embedded multimedia systems. It is significantly more efficient than the cache, in performance and power, and has the added advantage of better timing-predictability. Current techniques for the management of the scratch-pad are quite mature in the case of arrays accessed in a regular fashion, i.e. inside nested-loop by index expressions which are affine functions of the loop-iterators. Many multimedia codes, however, also use arrays as subscripted variables in the index expression of other arrays, thereby making the access pattern irregular. Existing techniques fail in such cases, bringing down the performance. In this paper, we extend the framework that exists today, to the case of irregular access. We provide a clear and precise compiler-based technique for analyzing irregular array-access, and efficiently mapping such arrays to the scratch-pad. On the average, 20% reduction in energy consumption, for a set of realistic applications, was achieved using our methods.
Development of a Pilot-Plant Process for a Nevirapine Analogue HIV NNRT Inhibitor (2008)

The pilot-plant synthesis of nevirapine analogue 1 is described. The compound was prepared in eight steps from substituted pyridine raw materials and 4-hydroxyquinoline. The key transformation involves a novel one-pot conversion of an arylhalide to arylacetic acid under palladium catalysis, followed by regioselective reduction via in situ generated BH3/THF to the arylethanol intermediate 2. All stages were carried out on 10−150-kg scale.
ChemInform Abstract: Preparation and Evaluation of Diarylalkynes as Antitumor Agents. (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
A Set Theoretic Framework for Watermarking and Its Application to Semifragile Tamper Detection (2006)

We introduce a set theoretic framework for watermarking. Multiple requirements, such as watermark embedding strength, imperceptibility, robustness to benign signal processing, and fragility under malicious attacks are described as constraint sets and a watermarked image is determined as a feasible solution satisfying these constraints. We illustrate that several constraints can be formulated as convex sets and develop a watermarking algorithm based on the method of projections onto convex sets. The framework allows flexible incorporation of different constraints, including embedding strength requirements for multiple watermarks that share the same spatial context and different imperceptibility requirements based on frequency-weighted error and local texture perceptual models. We illustrate the effectiveness of the framework by designing a hierarchical semifragile watermark that is tolerant to mild compression, allows tamper localization, and is fragile under aggressive compression. Using a quad-tree representation, a spatial resolution hierarchy is established on the image and a watermark is embedded corresponding to each node of the hierarchy. The spatial hierarchy of watermarks provides a graceful tradeoff between robustness and localization under mild JPEG compression, where watermarks at coarser levels demonstrate progressively higher immunity to JPEG compression. Under aggressive compression, watermarks at all hierarchy levels vanish, indicating a lack of trust in the image data. The constraints implicitly partition watermark power in the resolution hierarchy as well as among image regions based on robustness and invisibility requirements. Experimental results illustrate the flexibility and effectiveness of the method
<title>Multiobjective genetic optimization of diagnostic classifiers used in the computerized detection of mass lesions in mammography</title> (2000)

We have recently proposed and developed a multiobjective approach to training classification systems. In this approach, the objectives, i.e., the sensitivity and specificity, of a classifier are simultaneously optimized, resulting in a series of solutions that are equivalent in the absence of any a priori knowledge regarding the relative merits of the two objectives. These solutions form a receiver operating characteristic (ROC) curve that is, theoretically, the best possible ROC curve that can be obtained using the given classifier and given training dataset. We have applied this technique to the optimization of classifiers for the computerized detection of mass lesions in digitized mammograms. Comparisons will be made between the results obtained using the multiobjective approach and results obtained using more conventional approaches. We employed a database of 60 consecutive, non-palpable mass lesion cases. Features relating to the geometry, intensity, and gradients of the images were calculated for each visible lesion and for many false detections. Using a conventionally trained linear classifier we were able to achieve an A<SUB>z</SUB> of 0.84 while the multiobjective approach to training a linear classifier yielded an A<SUB>z</SUB> of 0.87 in the task of distinguishing between true lesions and false detections. Using a multiobjective approach to train a rule-based classifier with 5 thresholding rules resulted in an A<SUB>z</SUB> of 0.88 in the task of distinguishing between true lesions and false detections.
A Process for Developing Additively Manufactured Interposers for Use in Printed Circuit Boards (2022)

Additive manufacturing has seen much growth in the past few years due to many advantages it provides. Although much progress has been made in the field so far, there is still more optimization that needs to be done before it can be used for mass production. Utilizing the strengths of both manufacturing methods, a hybrid approach is discussed in this paper. An additively manufactured interposer is placed inside of a traditionally manufactured printed circuit board (PCB). The interposer connects the board to circuit components via conformally printed interconnects. Due to the low-loss characteristics of the interposer material in the X-Band, they can be used in multi-stack boards with RF components.
Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses (2021)

Abstract The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo . Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses and thus its promise as an agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses, but also uncovered a new antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine. One sentence summary A monoclonal antibody that neutralizes or binds all sarbecoviruses tested and represents a reproducible antibody class.
Recent Progress on Micro-holographic Data (2011)

Advances in micro-holographic materials and systems are presented. New materials show improved index change (10x) and sensitivity (100x) at &gt;3x lower intensity vs. previously reported. Experimental results supporting single-sided optical drive concept is presented.
20 kV 4H-SiC N-IGBTs (2014)

A 1 cm x 1 cm 4H-SiC N-IGBT exhibited a blocking voltage of 20.7 kV with a leakage current of 140 μA, which represents the highest blocking voltage reported from a semiconductor power switching device to this date. The device used a 160 μm thick drift layer and a 1 μm thick Field-Stop buffer layer, and showed a V F of 6.4 V at an I C of 20 A, and a differential R on,sp of 28 mΩ-cm 2 . Switching measurements with a supply voltage of 8 kV were performed, and a turn-off time of 1.1 μs and turn-off losses of 10.9 mJ were measured at 25°C, for a 8.4 mm x 8.4 mm device with 140 μm drift layer and 2 μm F-S buffer layer. The turn-off losses were reduced by approximately 50% by using a 5 μm F-S buffer layer. A 55 kW, 1.7 kV to 7 kV boost converter operating at 5 kHz was demonstrated using the 4H-SiC N-IGBT, and an efficiency value of 97.8% was reported.
A 1.6Gb/s CMOS LVDS transmitter with a programmable pre-emphasis system (2014)

A 12 parallel low voltage differential signaling (LVDS) transmitter fabricated in 0.13 μm CMOS is presented. Each LVDS channel can operate over 1.6 Gb/s and includes a programmable pre-emphasis circuit designed to reduce the data-dependent jitter (DDJ) caused by different lengths of PCB traces. Experimental results of the fabricated LVDS confirm the correct operation of the programmable pre-equalization circuit. The power consumption and area per channel is less than 20 mW and 0.084 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , respectively.
Fecal calprotectin levels and serological responses to microbial antigens among children and adolescents with inflammatory bowel disease (2008)

Increased levels of serological responses to microbial antigens (ASCA, I2, and OmpW) and fecal calprotectin are evident in both CD and UC patients. The combination of these markers provides valuable, noninvasive tools for the diagnosis of IBD.
Mathematical modeling of diurnal patterns of carbon allocation to shoot and root in Arabidopsis thaliana (2019)

We developed a mathematical model to simulate dynamics of central carbon metabolism over complete diurnal cycles for leaves of <i>Arabidopsis thaliana</i> exposed to either normal (120 µmol m<sup>-2</sup> s<sup>-1</sup>) or high light intensities (1200 µmol m<sup>-</sup> <sup>2</sup> s<sup>-1</sup>). The main objective was to obtain a high-resolution time series for metabolite dynamics as well as for shoot structural carbon formation (compounds with long residence time) and assimilate export of aerial organs to the sink tissue. Model development comprised a stepwise increment of complexity to finally approach the <i>in vivo</i> situation. The correct allocation of assimilates to either sink export or shoot structural carbon formation was a central goal of model development. Diurnal gain of structural carbon was calculated based on the daily increment in total photosynthetic carbon fixation, and this was the only parameter for structural carbon formation implemented in the model. Simulations of the dynamics of central metabolite pools revealed that shoot structural carbon formation occurred solely during the light phase but not during the night. The model allowed simulation of shoot structural carbon formation as a function of central leaf carbon metabolism under different environmental conditions without structural modifications. Model simulations were performed for the accession Landsberg <i>erecta</i> (Ler) and its hexokinase null-mutant <i>gin2-1</i>. This mutant displays a slow growth phenotype especially at increasing light intensities. Comparison of simulations revealed that the retarded shoot growth in the mutant resulted from an increased assimilate transport to sink organs. Due to its central function in sucrose cycling and sugar signaling, our findings suggest an important role of hexokinase-1 for carbon allocation to either shoot growth or assimilate export.
Hybridization analysis of three chloramphenicol resistance determinants from Clostridium perfringens and Clostridium difficile (1989)

The chloramphenicol resistance determinant from a nonconjugative strain of Clostridium perfringens was cloned and shown to be expressed in Escherichia coli. Subcloning and deletion analysis localized the resistance gene, catQ, to within a 1.25-kilobase (kb) partial Sau3A fragment. The catQ gene contained internal HindII, HaeIII, and DraI restriction sites and was distinct from the catP gene, which was originally cloned (L. J. Abraham, A. J. Wales, and J. I. Rood Plasmid 14:37-46, 1985) from the conjugative C. perfringens R plasmid, pIP401. Hybridization studies were carried out with a 0.35-kb DraI-P fragment of pJIR260 as an internal catQ-specific probe and a 0.38-kb EcoRV-HinfI fragment of pJIR62 as an internal catP-specific gene probe. The results showed that the catP and catQ genes were not similar and that neither probe hybridized with cat genes from other bacterial genera. However, the catP gene was similar to the cloned catD gene from Clostridium difficile. Comparative studies with both catP and catD probes showed that these genes had significant restriction identity. We therefore suggest that these genes were derived from a common source.