gebhart/patrepeval huggingface dataset:
Automatic 3D lesion segmentation on breast ultrasound images (2013)

Automatically acquired and reconstructed 3D breast ultrasound images allow radiologists to detect and evaluate breast lesions in 3D. However, assessing potential cancers in 3D ultrasound can be difficult and time consuming. In this study, we evaluate a 3D lesion segmentation method, which we had previously developed for breast CT, and investigate its robustness on lesions on 3D breast ultrasound images. Our dataset includes 98 3D breast ultrasound images obtained on an ABUS system from 55 patients containing 64 cancers. Cancers depicted on 54 US images had been clinically interpreted as negative on screening mammography and 44 had been clinically visible on mammography. All were from women with breast density BI-RADS 3 or 4. Tumor centers and margins were indicated and outlined by radiologists. Initial RGI-eroded contours were automatically calculated and served as input to the active contour segmentation algorithm yielding the final lesion contour. Tumor segmentation was evaluated by determining the overlap ratio (OR) between computer-determined and manually-drawn outlines. Resulting average overlap ratios on coronal, transverse, and sagittal views were 0.60 &plusmn; 0.17, 0.57 &plusmn; 0.18, and 0.58 &plusmn; 0.17, respectively. All OR values were significantly higher the 0.4, which is deemed “acceptable”. Within the groups of mammogram-negative and mammogram-positive cancers, the overlap ratios were 0.63 &plusmn; 0.17 and 0.56 &plusmn; 0.16, respectively, on the coronal views; with similar results on the other views. The segmentation performance was not found to be correlated to tumor size. Results indicate robustness of the 3D lesion segmentation technique in multi-modality 3D breast imaging.
Effects of sputtering technique on quaternary sputtered Cu(In,Ga)Se2films (2014)

While Cu(In,Ga)Se<sub>2</sub> (CIGS) has established itself as the thin film photovoltaic material of choice with current record efficiencies in excess of 20%, current high-efficiency laboratory-scale fabrication techniques, such as multi-stage evaporation, are ill suited to mass production. Quaternary-sputtering is a promising alternative technique for CIGS deposition, where a single sputtering target made from CIGS itself in the desired stoichiometry is used as the sole deposition source. Devices made using this technique do not require any additional post deposition selenium treatment and have demonstrated peak efficiency in our laboratory in excess of 10%, showing the potential of quaternary sputtering. In an effort to reduce deposition times, we have fabricated films using pulsed DC sputtering, which substantially reduces the substrate time-at-temperature during absorber formation. DC-sputtered films are observed to have reduced surface roughness and different internal morphology from RF-sputtered films, but show increased crystallographic alignment along the (112) plane. DC-sputtered CIGS is thickness-limited to less than 600 nm due to excessive target damage and exhibits power conversion efficiencies of 5-6%.
A new approach to design of directional couplers (2012)

The paper introduces a fundamentally new approach to a classical problem of design of coupled line directional couplers. It is applicable mainly to short couplers of weak coupling. Unlike the classical approach, the new one does not require the coupler outputs to be well matched and the even and odd mode velocities in the coupled line segment to be equal. Instead, high directivity is obtained by a proper choice of impedances terminating the output ports and shunt impedance between those ports. Examples show exceptionally good results for waveguide and microstrip couplers.
Development and application of methods for analysis of fungal glycosphingolipid structure and functional interactions (2007)

Fungal lectins from the mushrooms Polyporus squamosus and Coprinus cinereus have an affinity for beta-galactosides, with extended binding sites for the non-reducing terminal trisaccharide sequence NeuAcalpha2→6Galbeta1→4Glc/GlcNAc, and substituted beta-galactosides resembling mammalian blood group determinants, respectively. In considering the possibility that glycosylinositol phosphorylceramides (GIPCs) could be endogenous ligands of such fungal lectins, structural characterization of glycosphingolipids (GSLs) from the fruiting bodies of these mushrooms was performed. The extraction, isolation and purification of the lipids, and their subsequent characterization by nuclear magnetic resonance (NMR), mass spectrometry (MS) and gas chromatography-mass spectrometry (GC-MS) was performed. One monohexosylceramide (CMH) and three major GIPCs were identified from P. squamosus. The GIPCs were identified as Manalpha1→2Ins-P-Cer (Ps-1), Galbeta1→6Manalpha1→21ns-P-Cer (Ps-2) and Manalpha1→3Fucalpha1→2Galalpha1→6Galbeta1→6Manalpha1→21ns-P-Cer (Ps-5). Of these GSLs, Ps-2 could be a potential ligand for P. squamosus lectin. From C. cinereus, three components were identified as typical fungal Manalpha1→21ns-P-Cer incorporating unusually short chained ceramides not previously reported in other basidiomycetes. In addition, preliminary studies towards development of high throughput methods for glycosphingolipidome analysis were performed. These studies explored (i) the use of MSn for disassembly of permethylated glycosylinositols (GIs) and (ii) the construction of GSL-based glycan microarrays. MS n analysis of GIs efficiently provided useful information on linkage and sequence. An essential step in microarray development involved the enzymatic release of the hydroxyl fatty acyl of the ceramide moiety of selected fungal GIPCs with sphingolipid N-deacylase (SCDase). Derivatives were generated from the reaction of the resulting free amino group with N-reactive F-tag (N-[4-(1 H,1H,2H,2H perfluorodecyl)benzyloxycarbonyloxyl]succinimide (F17-Cbz-OSu, C22H14F17NO 5), and with a linker assembled from succinimidyl-[(N-maleimidopropionamido)diethyleneglycol] ester (NHS-PEO2-maleimide) and 2-mercaptoethylamine (2-MEA). The derivatives were immobilized via fluorous-flourous affinity, and by amide bond formation on N-hydroxysuccinimide-activated micro-glass slides, respectively. Preliminary evaluation of their use in assaying protein-carbohydrate binding interactions was carried out. The potential utility of this methodology for designing microarrays that incorporate both mammalian and fungal GSLs for serodiagnosis is discussed.
Physical Cell ID Detection Probability Using Synchronization Signals of NB-IoT Radio Interface in 28-GHz Band (2020)

This paper presents the physical-layer cell identity (PCID) detection probability using the narrowband primary synchronization signal (NPSS) and narrowband secondary synchronization signal (NSSS) based on the narrowband Internet-of-Things (NB-IoT) radio interface considering frequency offset and the maximum Doppler frequency in the 28-GHz band. Simulation results show that autocorrelation based NPSS detection achieves almost the same PCID detection probability as that for cross-correlation based NPSS detection using frequency offset estimation and compensation before the NPSS received timing detection, while the former achieves a lower level of computational complexity than the latter. We also show that when using autocorrelation based NPSS detection, the loss in the PCID detection probability at the carrier frequency of f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> = 28 GHz compared to that for f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">c</sub> = 3.5 GHz is only approximately 5% at the average received SNR of 0 dB when the frequency error of a temperature compensated crystal oscillator of a set of user equipment (UE) is 20 ppm. Therefore, we conclude that the multiplexing schemes and sequences of NPSS and NSSS based on the NB-IoT radio interface associated with autocorrelation based NPSS detection will be applicable to the 28-GHz frequency spectra.
[Four cases of airway obstruction successfully treated by airway stenting]. (2012)

We report 4 cases of malignant airway obstruction treated by airway stenting. Three cases were caused by esophageal cancer and the fourth case by malignant lymphoma. Two patients with esophageal cancer received chemoradiotherapy after airway stenting and survived for 24 months and 54 months, respectively (without cancer recurrence). One patient with esophageal cancer died of airway bleeding 2 months after stent placement. The malignant lymphoma patient was treated by cyclophosphamide+doxorubicin+vincristine+prednisolone(CHOP) with rituximab. Airway obstruction due to malignancy is an urgent oncological situation that should be treated immediately. Airway stenting shows a marked and immediate improvement in dyspnea. Consequently, the induction of chemoradiotherapy or chemotherapy is possible. Two patients were successfully treated by chemoradiotherapy, of which 1 survived for more than 4 years without any evidence of cancer recurrence. Additional chemoradiotherapy for patients who receive esophageal stenting is controversial because of the high frequency of adverse events. However, chemoradiotherapy after airway stenting may demonstrate acceptable anti-cancer effects with fewer adverse events. Airway stenting was an effective treatment for airway obstruction, and additional treatment is essential for longer survival.
Effect of channel thickness, electrolyte ions, and dissolved oxygen on the performance of organic electrochemical transistors (2015)

We investigated the device characteristics of organic electrochemical transistors based on thin films of poly(3,4-ethylenedioxythiophene) doped with poly(styrene-sulfonate). We employed various channel thicknesses and two different electrolytes: the micelle forming surfactant cetyltrimethyl ammonium bromide (CTAB) and NaCl. The highest ON/OFF ratios were achieved at low film thicknesses using CTAB as the electrolyte. Cyclic voltammetry suggests that a redox reaction between oxygen dissolved in the electrolytes and PEDOT:PSS leads to low ON/OFF ratios when NaCl is used as the electrolyte. Electrochemical impedance spectroscopy reveals that doping/dedoping of the channel becomes slower at high film thickness and in the presence of bulky ions.
Methane Catalytic Pyrolysis by Microwave and Thermal Heating over Carbon Nanotube-Supported Catalysts: Productivity, Kinetics, and Energy Efficiency (2022)

Methane catalytic pyrolysis, which is the reaction to produce hydrogen and carbon without emitting CO2, represents an approach for decarbonization using natural gas as an energy resource. The endothermic pyrolysis reaction was carried out under two heating scenarios: convective thermal heating and microwave-driven irradiative heating. The pyrolysis reaction was conducted at 550–600 °C over carbon nanotube (CNT)-supported Ni–Pd and Ni–Cu catalysts. On both catalysts, an enhanced methane conversion rate was observed under microwave irradiation. The enhanced catalytic activity was hypothetically caused by the presence of free electrons in the carbon atoms within the CNT that enabled the CNT support to absorb microwave energy effectively and to be heated efficiently by microwave. The microwave catalytic pyrolysis has shown improvement in kinetics, where the apparent activation energy dropped from 45.5 kJ/mol under conventional convective heating to 24.8 kJ/mol under microwave irradiation. When the methane conversion rate is increased by 37%, the microwave power consumption only changed by 10.8%. The research demonstrated the potential of transforming natural gas into clean hydrogen and value-added carbon in a more energy-efficient way. Process simulation and techno-economic analysis showed that potentially hydrogen minimum selling price of about $1/kg H2 could be achieved.
Cofactor-Independent Pinacolase Directs Non-Diels-Alderase Biogenesis of the Brevianamides (2019)

&lt;p&gt;Fungal bicyclo[2.2.2]diazaoctane indole alkaloids demonstrate intriguing structures and a wide spectrum of biological activities. Although biomimetic total syntheses have been completed for representative compounds of this structural family, the details of their biogenesis have remained largely uncharacterized. Among them, Brevianamide A represents the most basic form within this class bearing a dioxopiperazine core structure and a rare 3-&lt;i&gt;spiro&lt;/i&gt;-&lt;i&gt;psi&lt;/i&gt;-indoxyl skeleton. Here, we identified the Brevianamide A biosynthetic gene cluster from &lt;i&gt;Penicillium brevicompacticum&lt;/i&gt; NRRL 864 and fully elucidated the metabolic pathway by targeted gene disruption, heterologous expression, precursor incorporation studies, and &lt;i&gt;in vitro&lt;/i&gt; biochemical analysis. In particular, we determined that BvnE is a cofactor-independent isomerase that is essential for selective production of Brevianamide A. Based on a high resolution crystal structure of BvnE, molecular modeling, mutational analysis, and computational studies provided new mechanistic insights into the diastereoselective formation of the 3-&lt;i&gt;spiro&lt;/i&gt;-&lt;i&gt;psi&lt;/i&gt;-indoxyl moiety in Brevianamide A. This occurs through a biocatalyst controlled semi-Pinacol rearrangement and a subsequent spontaneous intramolecular [4+2] &lt;i&gt;hetero&lt;/i&gt;-Diels-Alder cycloaddition.&lt;/p&gt;
Structures of benzonitrile dimer radical cation and the protonated dimer: Observation of hydronium ion core solvated by benzonitrile molecules (2019)

The recent discovery of benzonitrile (C<sub>6</sub>H<sub>5</sub>CN), one of the simplest nitrogen-bearing polar aromatic molecules, in the interstellar medium motivates structural characterization of the benzonitrile-containing molecular ions as potential precursors for nitrogen-containing complex organics in space. Herein, we present mass-selected ion mobility measurements combined with density functional theory (DFT) calculations to reveal, for the first time, the structures of the benzonitrile dimer radical cation, the protonated dimer, and the protonated hydrated small clusters in the gas phase. The measured collision cross sections of the investigated ions in helium are in excellent agreement with the calculated values of the lowest energy DFT structures. Unlike the dimer radical cations of nonpolar aromatic molecules which adopt parallel sandwich configurations, the (C<sub>6</sub>H<sub>5</sub>CN)<sub>2</sub> <sup>·+</sup> displays a symmetrically planar geometry with a double hydrogen bond formed between the nitrogen and hydrogen atoms. The protonated dimer has the structure of a proton-bound dimer (C<sub>6</sub>H<sub>5</sub>CNH<sup>+</sup>NCC<sub>6</sub>H<sub>5</sub>) where the bridging proton connects the nitrogen atoms in the two benzonitrile molecules resulting in a calculated collision cross section of 101.1 Å<sup>2</sup> in excellent agreement with the measured value of 103.3 Å<sup>2</sup>. The structure of the hydrated protonated trimer consists of a hydronium ion core solvated by three benzonitrile molecules. By locating the proton on the lower proton affinity water molecule, the resulting hydronium ion can be fully solvated by forming three ionic hydrogen bonds with the benzonitrile molecules. These unique structural motifs could be useful for the molecular design and recognition involving charged aromatic systems and also for the search of nitrogen-containing complex organics in space.
Standard Imaging Planes in Cardiac MR Imaging (2015)

Abstract The purpose of this chapter is to provide step-by-step protocols for acquiring common cardiac magnetic resonance (MR) imaging planes. The workflow diagrams presented are not complete in that each represents only one example of a pathway that can be followed to facilitate consistent cardiac examinations. However, they do promote both consistent visualization of the most clinically relevant cardiac anatomy and completion of the cardiac examination in a practical time frame for the patient and imaging department alike.
Evaluation of natural colorants and their application on citrus fruit as alternatives to Citrus Red No. 2. (2019)

Warm field temperatures can often result in poor peel color of some citrus varieties, especially early in the harvest season. Under these conditions, Florida oranges, temples, tangelos, and K-Early citrus fruit are allowed to be treated with Citrus Red No.2 dye (CR2) to help produce a more acceptable peel color.Unfortunately, CR2, the commercial colorant used in Florida, has been listed as a group 2B carcinogen by the European Union (EU) and the International Agency for Research on Cancer (IARC). Although not likely dangerous at levels used on citrus, and on a part of the fruit that is not ingested, there is a negative health perception, and thus, a need for natural or food grade alternative colorants to replace CR2 for use on citrus. This research demonstrated that three out of five oil-soluble natural red/orange colorants resulted in peel colors somewhat similar to the industry standard CR2. These three (annatto extract, paprika extract, and paprika oleoresin) were selected for further in vivo studies. The stability of the natural colorants along with CR2 was evaluated by applying them on test papers and then on fresh ‘Hamlin’ oranges. All natural colorants were found to be easily oxidized and faded when applied on test papers. However, coating the colored surfaces with carnauba wax apparently inhibited oxidation and the subsequent discoloration of the surface. When applying the natural colorants to ‘Hamlin’ oranges before waxing, the treatments retained the improved color after storage in the dark at 5 °C, simulating cold storage. However, only annatto extract maintained a stable color when subsequently stored in a simulated market condition, at 23 °C exposed to 300 lx of standard fluorescent white light.
Measurement error analysis in the determination of microwave dielectric properties using cavity reflection method (1996)

Abstract Using the cavity reflection method for the determination of the resonant frequency and the Q-value of a dielectric resonator, the effect of test cavity dimensions on the measured results was examined. Samples of different permittivities and sizes were measured in six different test cavities. A reduction of measured Q-value and a shift of resonance frequency towards higher values when analyzing a TE01δ dielectric resonator mode positioned below the TM010 test cavity mode was noticed. For measurements above the TM010 mode reliable identification of the TE01δ mode was obtained by previous calculation of the test cavity modes. For this purpose a simple empirical calculation procedure was developed which allows calculation of the resonant frequencies of test cavities with dielectrics inserted. The error of the calculation for TM010 and TE111 modes is lower than ±1%, and slightly higher for other modes.
Genetic Heterogeneity of Adrenocorticotropin (ACTH) Resistance Syndromes: Identification of a Novel Mutation of the ACTH Receptor Gene in Hereditary Glucocorticoid Deficiency (1998)

Hereditary primary adrenal insufficiency syndromes due to ACTH resistance include hereditary glucocorticoid deficiency (HGD) and Allgrove's syndrome (AS). Patients with both conditions present in childhood with failure to thrive, weakness, and fatigue or adrenal crisis; patients with AS in addition have alacrima and achalasia (triple A syndrome). We studied four kindreds with HGD and four kindreds with AS for abnormalities of the ACTH receptor (ACTHR) gene. The ACTHR coding sequence in all AS kindreds and two HGD kindreds was normal. Analysis of the ACTHR gene of the proband in one of the HGD kindreds showed him to be homozygous for the previously described G221T transition causing a Ser74Ile substitution of the protein, which has been shown to inactivate the ACTHR in signal transduction. The proband in another HGD kindred was found to be a compound heterozygote with the G221T transition in one allele and a novel C818A transition in the other allele of ACTHR. The C818A transition caused the substitution of the highly conserved Pro273 by His in the receptor protein. In vitro expression of the mutated ACTHR in mouse melanoma M3 cells showed that at a medium ACTH concentration of 3 nM, cells transfected with the wild-type ACTHR produced twofold and threefold, respectively, of the amount of intracellular cAMP when compared to cells transfected with the ACTHR carrying the Pro273His and the Ser74Ile mutation, respectively, confirming that HGD in this kindred is caused by loss-of-function mutations of the ACTHR. These results showed that the genetic cause of the ACTH-resistant syndromes is heterogeneous.
Visible‐Light Photoresponsivity of a 4‐(Dimethylamino)azobenzene Unit Incorporated into Single‐Stranded DNA: Demonstration of a Large Spectral Change Accompanying Isomerization in DMSO and Detection of Rapid (Z)‐to‐(E) Isomerization in Aqueous Solution (2007)

In Scheme 1 on p. 1847 of the original article,1 the 4-(dimethylamino) groups of compounds 2–5 are missing; the correct Scheme 1 is shown here. Synthetic pathway for the phosphoramidite monomer 5. (a) p-Phenylenediamine, glacial acetic acid, benzene, 42 % yield. (b) 2,2-Bis(hydroxymethyl)propionic acid, 1-hydroxybenzotriazole, dicyclohexylcarbodiimide, DMF, 27 % yield. (c) 4,4′-Dimethoxytrityl chloride (DMTr), 4-(dimethylamino)pyridine, pyridine, CH2Cl2, 53 % yield. (d) 2-Cyanoethyl N,N,N′,N′-tetraisopropylphosphorodiamidite, 1H-tetrazole, acetonitrile, 36 % yield. The Editors
Bovine veneral vibriosis: cure of genital infection in females by systemic immunization (1975)

Cure of female cattle with venereal vibriosis by systemic immunization with killed Campylobacter fetus cells in incomplete Freund adjuvant was investigated. Heifers infected in the cervicovaginal area with a cloned population of C. fetus venerealis were vaccinated subcutaneously 14 and 24 days thereafter with the infecting strain in incomplete Freund adjuvant. Six of eight vaccinated heifers were free of infection 25 to 48 days postinfection. One of the cured animals had an intercurrent infection which precluded interpretation of a vaccine effect. All controls remained infected 48 to 51 days postinfection, when the experiment was terminated. In vaccinated animals, agglutination titers against whole cells of the infecting strain reached peaks varying from 1,280 to 20,480 in serum and from 20 to 5,120 in cervicovaginal mucus (CVM) within days 24 to 32 postinfection. No consistent relationship was noted between levels of whole cell antibodies in serum and those in CVM. Evidence for the occurrence of antigenic variation in the organism after vaccination was sought by comparing the agglutinability of the infecting strain and CVM isolates in serum and CVM extracts. Serum samples of most cured heifers agglutinated whole cells prepared from isolates of the respective heifers to the same extent as cells of the infecting strain. In the corresponding comparisons, those from noncured animals agglutinated isolates to lower titers. CVM extracts from one cured animals agglutinated isolates derived from the same or closely spaced CVM samples to titers comparable with those obtained with the infecting strain. In the remaining animals, CVM extracts which agglutinated the infecting strain produced lower or undetectable reactions with corresponding isolates. It is proposed that the elimination of infection is dependent upon opposing responses of host and parasite, of which the degree of antigenic alteration in the infecting strain and the rate of mobilization and the concentration of specific antibodies in the genital secretions are key factors.