gebhart/patrepeval huggingface dataset:
Hybrid clustering for microarray image analysis combining intensity and shape features (2004)

The new method presents a successful hybrid microarray image analysis solution. It incorporates both shape and histogram features and is specifically adapted to deal with typical microarray image characteristics. As a consequence of the filtering step pixels are divided into three groups, namely foreground, background and deletions. This allows a separate treatment of artifacts and their elimination from the further analysis.
Fabrication of Small Caliber Stent-grafts Using Electrospinning and Balloon Expandable Bare Metal Stents (2016)

Stent-grafts are widely used for the treatment of various conditions such as aortic lesions, aneurysms, emboli due to coronary intervention procedures and perforations in vasculature. Such stent-grafts are manufactured by covering a stent with a polymer membrane. An ideal stent-graft should have a biocompatible stent covered by a porous, thromboresistant, and biocompatible polymer membrane which mimics the extracellular matrix thereby promoting injury site healing. The goal of this protocol is to manufacture a small caliber stent-graft by encapsulating a balloon expandable stent within two layers of electrospun polyurethane nanofibers. Electrospinning of polyurethane has been shown to assist in healing by mimicking native extracellular matrix, thereby promoting endothelialization. Electrospinning polyurethane nanofibers on a slowly rotating mandrel enabled us to precisely control the thickness of the nanofibrous membrane, which is essential to achieve a small caliber balloon expandable stent-graft. Mechanical validation by crimping and expansion of the stent-graft has shown that the nanofibrous polyurethane membrane is sufficiently flexible to crimp and expand while staying patent without showing any signs of tearing or delamination. Furthermore, stent-grafts fabricated using the methods described here are capable of being implanted using a coronary intervention procedure using standard size guide catheters.
A diallel analysis of a maize donor population response to in vivo maternal haploid induction: II. Haploid male fertility (2020)

Abstract Doubled haploid (DH) lines are used in maize ( Zea mays L.) breeding to accelerate the breeding cycle and create homogenous inbred lines in as little as two seasons. These pure inbred lines allow breeders to quickly evaluate new cross combinations. There are two important steps in creating DH lines: (a) generation and selection of haploid progeny, and (b) genome doubling to create fertile, diploid inbreds. Colchicine is widely used to artificially double genomes in haploid plants, which is hazardous, expensive, and time consuming. In this study, three public inbred lines—A427, A637, and NK778—were found to have substantial haploid male fertility (HMF). A six‐parent full diallel between these three HMF lines and three non‐HMF lines was created and HMF was scored. Diallel analysis revealed significant general combining ability (GCA) estimates of up to 17% for HMF, as well as significant specific combining ability (SCA) effects of up to 25%. No significant reciprocal effects were found. Haploid male fertility is promising to be incorporated into elite maize breeding programs to potentially overcome the need of using colchicine treatments for genome doubling. Colchicine aided doubling success rates varying from almost 0 to 30%. Haploid male fertility has an advantage over artificial genome doubling, in terms of both increased success rates and decreased costs for DH line production.
Generation of intense pulsed ion beams (1974)

An electrostatic vacuum triode is described in which it is possible to efficiently produce intense ion beams in the energy range around 100 keV for short times (∼50 nsec). In experiments to date, results have shown excellent agreement with predicted behavior. Equivalent proton currents of almost 500 A have been obtained at a peak energy in excess of 100 keV. The triode can easily be adapted to existing electron beam facilities.
Estimation of Rice Growth Parameters Based on Linear Mixed-Effect Model Using Multispectral Images from Fixed-Wing Unmanned Aerial Vehicles (2019)

The accurate estimation of aboveground biomass (AGB) and leaf area index (LAI) is critical to characterize crop growth status and predict grain yield. Unmanned aerial vehicle (UAV) -based remote sensing has attracted significant interest due to its high flexibility and easiness of operation. The mixed effect model introduced in this study can capture secondary factors that cannot be captured by standard empirical relationships. The objective of this study was to explore the potential benefit of using a linear mixed-effect (LME) model and multispectral images from a fixed-wing UAV to estimate both AGB and LAI of rice. Field experiments were conducted over two consecutive years (2017–2018), that involved different N rates, planting patterns and rice cultivars. Images were collected by a compact multispectral camera mounted on a fixed-wing UAV during key rice growth stages. LME, simple regression (SR), artificial neural networks (ANN) and random forests (RF) models were developed relating growth parameters (AGB and LAI) to spectral information. Cultivar (C), growth stage (S) and planting pattern (P) were selected as candidates of random effects for the LME models due to their significant effects on rice growth. Compared to other regression models (SR, ANN and RF), the LME model improved the AGB estimation accuracy for all stage groups to varying degrees: the R2 increased by 0.14–0.35 and the RMSE decreased by 0.88–1.80 t ha−1 for the whole season, the R2 increased by 0.07–0.15 and the RMSE decreased by 0.31–0.61 t ha−1 for pre-heading stages and the R2 increased by 0.21–0.53 and the RMSE decreased by 0.72–1.52 t ha−1 for post-heading stages. Further analysis suggested that the LME model also successfully predicted within the groups when the number of groups was suitable. More importantly, depending on the availability of C, S, P or combinations thereof, mixed effects could lead to an outperformance of baseline retrieval methods (SR, ANN or RF) due to the inclusion of secondary effects. Satisfactory results were also obtained for the LAI estimation while the superiority of the LME model was not as significant as that for AGB estimation. This study demonstrates that the LME model could accurately estimate rice AGB and LAI and fixed-wing UAVs are promising for the monitoring of the crop growth status over large-scale farmland.
Alternative Splicing as a Therapeutic Target for Human Diseases (2009)

The majority of eukaryotic genes undergo alternative splicing, an evolutionarily conserved phenomenon, to generate functionally diverse protein isoforms from a single transcript. The fact that defective pre-mRNA splicing can generate non-functional and often toxic proteins with catastrophic effects, accurate removal of introns and joining of exons is vital for cell homeostasis. Thus, molecular tools that could either silence a disease-causing gene or regulate its expression in trans will find many therapeutic applications. Here we present two RNA-based approaches, namely RNAi and theophylline-responsive riboswitch that can regulate gene expression by loss-of-function and modulation of splicing, respectively. These strategies are likely to continue to play an integral role in studying gene function and drug discovery.
Correlation Between Perpendicular Anisotropy and Magnetoresistance in Magnetic Tunnel Junctions (2010)

The perpendicular magnetic anisotropy (PMA) of Pt/CoFe(B)/MgO bottom electrodes and the tunnel magnetoresistance (TMR) of CoFeB-based magnetic tunnel junctions (MTJ) have been analyzed as a function of Mg thickness for naturally oxidized barriers. Low PMA and TMR values are found for over-oxidized (small MgO thickness) and under-oxidized (large MgO thickness) barriers. When CoFe is used as bottom electrode, a strong correlation is observed between TMR and PMA variation as a function of MgO thickness with maxima in both quantities occurring for an MgO thickness around 1.2 nm. On the contrary, for CoFeB bottom electrodes, the sensitivity of PMA to MgO thickness is completely lost, as a probable consequence of boron diffusion towards the MgO interface.
Complement components, proteolysis‑related, and cell communication‑related proteins detected in urine proteomics are associated with IgA nephropathy (2014)

We demonstrated that urine proteomics is a promising tool for diagnosing and monitoring patients with IgAN.
Noninterferometric phase-contrast images obtained with incoherent x-ray sources (2011)

We report on what are believed to be the first full-scale images obtained with the coded aperture concept, which uses conventional x-ray sources without the need to collimate/aperture their output. We discuss the differences in the underpinning physical principles with respect to other methods, and explain why these might lead to a more efficient use of the source. In particular, we discuss how the evaluation of the first imaging system provided promising indications on the method's potential to detect details invisible to conventional absorption methods, use an increased average x-ray energy, and reduce exposure times-all important aspects with regards to real-world implementations.
Propane/Propylene Separation by Simulated Moving Bed I. Adsorption of Propane, Propylene and Isobutane in Pellets of 13X Zeolite (2007)

Abstract The separation of propane‐propylene mixture is the most energy consuming operation in the petrochemical industry. Various studies have been investigated to relieve the cryogenic distillation ordinarily used for this separation, and the adsorption technology appeared to be a promising option. Considering the encouraging results obtained by cyclic adsorption processes and notably by pressure swing adsorption, the simulated moving bed (SMB) has been suggested as a new and competitive alternative. The keystone of a SMB for a gas mixture separation is the choice of an adequate and pertinent adsorbent‐desorbent couple. In this work, isobutane has been tested as a potential desorbent over 13X zeolite. A gravimetric method has been used to measure the adsorption equilibrium isotherms of propylene, propane, and isobutane on 13X zeolite pellets over a temperature range from 333 K to 393 K and pressure up to 160 kPa. Experimental adsorption equilibrium isotherms were correlated with the Toth model. The 13X zeolite shows an intermediate loading capacity for isobutane at low pressures. Equilibrium capacities for propylene, propane, and isobutane at 373 K and 110 kPa were 2.12, 1.61, and 1.53 mol/kg, respectively. The heats of adsorption at zero coverage for propylene, propane, and isobutane were found to be 42.4, 36.9, 41.6 kJ/mol, respectively. Breakthrough curves of pure components were measured at 373 K and 150 kPa with different initial conditions (adsorbent bed saturated with nitrogen or isobutane). Experimental breakthrough curves were well‐predicted by an exhaustive mathematical model taking into account the energy balance in the three phases (gas, solid, and wall column). Multi‐component fixed bed adsorption experiments allowed us to observe that isobutane could displace an adsorbed propane/propylene mixture from the 13X zeolite and itself was fairly easily displaced from the adsorbent by this same mixture. These results confirmed the assumption that isobutane is a good desorbent for the adsorptive separation of C3H6/C3H8 mixture by a simulated moving bed.
Biological Markers for Non–Small Cell Lung Cancer Patient Selection for Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor Therapy (2006)

The selection of patients for tumor-specific therapies using molecular/biological properties of the patient's tumor has been a long tradition in breast cancer (e.g., estrogen receptor, progesterone receptor, and HER-2/ neu ) but has not been widely accepted in lung cancer therapy selection ([1][1
Mechanical enhancement of a tissue-engineered scaffold for bone regeneration (2014)

With over 600,000 patients suffering from bone deficiencies annually in the United States, bone regeneration has come to the forefront of medical research. Current repair treatments utilize autografts (transplanting a patient's own bone from one site to another) and allografts (tissue donated from a cadaver) to treat extensive bone fractures. Although the autograft is the benchmark treatment, both autografts and allografts have their drawbacks such as donor site morbidity and disease transmission, respectively. As a result, alternative treatment methods including tissue-engineered solutions are being explored to potentially circumvent these disadvantages. The Musculoskeletal Tissue Regeneration laboratory has previously created a composite trabecular and cortical biomimetic synthetic bone scaffold, which mimics the architecture of native bone. However, the compressive strength of the current cortical scaffold does not match that of native bone. This study specifically focuses on the incorporation of sintered hydroxyapatite (HAP) columns to enhance the mechanical properties of these scaffolds, particularly under compressive loads. The integration of mechanically enhanced HAP columns serves as a promising step towards developing one of the first biomimetic bone scaffolds that exhibits the mechanical properties of native bone, while simultaneously promoting osteoblastic and vascular differentiation.
X-ray attenuation models to account for beam hardening in computed tomography (2020)

We introduce a beam-hardening correction method for lab-based X-ray computed tomography (CT) by modifying existing iterative tomographic reconstruction algorithms. Our method simplifies the standard Alvarez-Macovski X-ray attenuation model [Phys. Med. Biol.21, 733 (1976)] and is compatible with conventional (i.e., single-spectrum) CT scans. The sole modification involves a polychromatic projection operation, which is equivalent to applying a weighting that more closely matches the attenuation of polychromatic X-rays. Practicality is a priority, so we only require information about the X-ray spectrum and some constants relating to material properties. No other changes to the experimental setup or the iterative algorithms are necessary. Using reconstructions of simulations and several large experimental datasets, we show that this method is able to remove or reduce cupping, streaking, and other artefacts from X-ray beam hardening and improve the self-consistency of projected attenuation in CT. When the assumptions made in the simplifications are valid, the reconstructed tomogram can even be quantitative.
Creation of Lipid Partitions by Deposition of Amphipathic Viral Peptides (2007)

Phospholipid vesicles exhibit a natural characteristic to fuse and reform into a continuous single bilayer membrane on hydrophilic solid substrates such as glass, mica, and silica. The resulting solid-supported bilayer mimics physiological tendencies such as lipid flip-flop and lateral mobility. The lateral mobility of fluorescently labeled lipids fused into solid-supported bilayers is found to change upon deposition on the membrane surface of an amphipathic alpha-helical peptide (AH) derived from the hepatitis C virus (HCV) NS5A protein. The binding of the AH peptide to a phospholipid bilayer, with the helical axis parallel to the bilayer, leads to immobilization of the bilayer. We used AFM to better understand the mechanistic details of this specific interaction, and determined that the diminished fluidity of the bilayer is due to membrane thinning. Utilizing this specific interaction between AH peptides and lipid molecules, we demonstrate a novel process for the creation of lipid partition by employing AH peptides as agents to immobilize lipid molecules, thus creating a patterned solid support with partition-defined areas of freely mobile lipid bilayers. This architecture could have a wide range of applications in novel sensing, biotechnology, high-throughput screening, and biomimetic strategies.
A Truncated Plasminogen Activator Inhibitor-1 Protein Blocks the Availability of Heparin-binding Vascular Endothelial Growth Factor A Isoforms (2002)

We have made deletions of the porcine plasminogen activator inhibitor-1 (PAI-1) gene to obtain recombinant truncated PAI-1 proteins to examine functions of the PAI-1 isoforms. We previously reported that one recombinant truncated protein, rPAI-1(23), induces the formation of angiostatin by cleaving plasmin. The rPAI-1(23) protein is also able to bind urokinase plasminogen activator and plasminogen and then reduce the amount of plasmin that is formed. We have now prepared three different truncated rPAI-1 proteins and demonstrate that PAI-1 conformations control the release of heparin-binding vascular endothelial growth factor (VEGF) isoforms. The rPAI-1(23) isoform can regulate the functional activity of heparan sulfate-binding VEGF-A isoforms by blocking the activation of VEGF from heparan sulfate. The rPAI-1(23) conformation induced extensive apoptosis in cultured endothelial cells and thus reduced the number of proliferating cells. The rPAI-1(23) isoform inhibited migration of VEGF-stimulated sprouting from chick aortic rings by 65%, thus displaying a role in anti-angiogenic mechanisms. This insight into anti-angiogenic functions related to PAI-1 conformational changes could provide potential intervention points in angiogenesis associated with atherosclerotic plaques and cancer.
On-Plate Desalting and SALDI-MS Analysis of Peptides with Hydrophobic Silicate Nanofilms on a Gold Substrate (2010)

We report the use of silicate nanofilms for on-plate desalting and subsequently direct laser desorption/ionization-mass spectrometric (LDI-MS) analysis of peptides. A hydrophobic octadecyltrichlorosilane (OTS) monolayer is formed on a calcinated nanofilm on a gold substrate to facilitate sample deposition and interaction with the surface that allows effective removal of MS-incompatible contaminants such as salts and surfactants by simple on-plate washing while the peptides are retained on the spot. By elimination of interferences from matrix-related ions and contaminants, sensitivity of MS analysis has been enhanced over ca. 20 times, leading to improved detection of peptides at the low-femtomolar level. A high recovery rate of the peptides is obtained by using relatively rough nanofilms, which are prepared through a modified layer-by-layer deposition/calcination process. The performance of the films has been investigated with peptide samples in the presence of high salts (NaCl and sodium acetate) and urea. Compared to matrix-assisted laser desorption/ionization analysis with CHCA matrix, LDI with on-plate desalting offers marked improvement for analysis of peptides due to low background ions and reduction of sample complexity. Additionally, selective capture of the hydrophobic components of a protein can be achieved, providing a highly useful strategy for specific peptide enrichment. LDI with on-plate desalting approach has also been successfully applied to peptide analysis from protein digests.
A versatile snap chip for high-density sub-nanoliter chip-to-chip reagent transfer (2015)

Abstract The coordinated delivery of minute amounts of different reagents is important for microfluidics and microarrays, but is dependent on advanced equipment such as microarrayers. Previously, we developed the snap chip for the direct transfer of reagents, thus realizing fluidic operations by only manipulating microscope slides. However, owing to the misalignment between arrays spotted on different slides, millimeter spacing was needed between spots and the array density was limited. In this work, we have developed a novel double transfer method and have transferred 625 spots cm −2 , corresponding to >10000 spots for a standard microscope slide. A user-friendly snapping system was manufactured to make liquid handling straightforward. Misalignment, which for direct transfer ranged from 150–250 μm, was reduced to <40 μm for double transfer. The snap chip was used to quantify 50 proteins in 16 samples simultaneously, yielding limits of detection in the pg/mL range for 35 proteins. The versatility of the snap chip is illustrated with a 4-plex homogenous enzyme inhibition assay analyzing 128 conditions with precise timing. The versatility and high density of the snap chip with double transfer allows for the development of high throughput reagent transfer protocols compatible with a variety of applications.
Novel scalable synthesis of highly conducting and robust PEDOT paper for a high performance flexible solid supercapacitor (2015)

A scalable method to produce flexible PEDOT/cellulose paper by surfactant-free interfacial polymerization is developed and its application is demonstrated for a flexible solid-state supercapacitor.
Opportunistic Channel Estimation for Implicit 802.11af MU-MIMO. (2016)

Multi-User MIMO (MU-MIMO) linear channel coding can greatly increase wireless system capacity when Stations (STAs) have fewer antennas than the Access Point (AP), but it comes at the cost of significant Channel State Information (CSI) estimation overhead. Previous work has suggested that 802.11af MU-MIMO systems might benefit from long channel coherence time, extending the useful duration of CSI. In this paper, we propose and analyze an opportunistic channel sounding policy that avoids sounding overhead in wireless channels by gathering implicit CSI opportunistically. This policy not only avoids CSI overhead, but also has the potential to enable efficient interoperability of multi-user APs with legacy single-stream STAs. To investigate the performance of this new policy, we implement a new mobile channel sounding framework on a custom 802.11af Software-Defined Radio (SDR) system designed for UHF-band experimentation and evaluate channel sounding performance in indoor and outdoor environments under various mobility modes. Additional protocol analysis shows that in UHF channels with sufficient channel coherence time, an opportunistic channel sounding policy offers significant protocol optimization while improving the scalability of next-generation MU-MIMO systems.
A novel DNA-binding motif in the nuclear matrix attachment DNA-binding protein SATB1. (1994)

The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a sequence context-specific binding protein that binds in the minor groove, making virtually no contact with the DNA bases. The SATB1 binding sites consist of a special AT-rich sequence context in which one strand is well-mixed A's, T's, and C's, excluding G's (ATC sequences), which is typically found in clusters within different MARs. To determine the extent of conservation of the SATB1 gene among different species, we cloned a mouse homolog of the human STAB1 cDNA from a cDNA expression library of the mouse thymus, the tissue in which this protein is predominantly expressed. This mouse cDNA encodes a 764-amino-acid protein with a 98% homology in amino acid sequence to the human SATB1 originally cloned from testis. To characterize the DNA binding domain of this novel class of protein, we used the mouse SATB1 cDNA and delineated a 150-amino-acid polypeptide as the binding domain. This region confers full DNA binding activity, recognizes the specific sequence context, and makes direct contact with DNA at the same nucleotides as the whole protein. This DNA binding domain contains a novel DNA binding motif: when no more than 21 amino acids at either the N- or C-terminal end of the binding domain are deleted, the majority of the DNA binding activity is lost. The concomitant presence of both terminal sequences is mandatory for binding. These two terminal regions consist of hydrophilic amino acids and share homologous sequences that are different from those of any known DNA binding motifs. We propose that the DNA binding region of SATB1 extends its two terminal regions toward DNA to make direct contact with DNA.