gebhart/patrepeval huggingface dataset:
Seven Patients with Plasma Cell Granuloma (Inflammatory Pseudotumor) of the Lung, Including Two with Intrabronchial Growth: An Immunohistochemical and Electron Microscopic Study. (1992)

Seven patients (mean age, 50.7 +/- 20.4 years; range 21-77) with plasma cell granuloma (PCG) of the lung are reported. Cough and sputum were the most common presenting symptoms, followed by fever. Elevated erythrocyte sedimentation rate and serum C-reactive protein levels were found in all patients tested. Radiologically, five cases presented as solitary, well-circumscribed masses and two as ill-defined, pneumonia-like densities. One showed focal calcification. No predilection of occurrence was observed in either lobe of the lung. Histologically, the lesions consisted of a proliferation of mature plasma cells and reticulo-endothelial cells supported by a stroma of granulation tissue, with varying degrees of myxoid change or collagenization. Angioinvasion within the lesion was observed in 4 of the 7 cases. Immunohistochemical staining revealed the IgG-predominant polyclonal nature of the plasma cells, indicating a reactive inflammatory process rather than a neoplastic one. Electron microscopy confirmed the benign nature of the plasma cells with fibroblast and myofibroblast proliferation admixed with that of other inflammatory cells.
Alsterpaullone, a novel cyclin‐dependent kinase inhibitor, induces apoptosis by activation of caspase‐9 due to perturbation in mitochondrial membrane potential (2003)

The majority of human neoplasms have aberrations in the retinoblastoma pathway due to hyperactivation of cyclin-dependent kinases (CDK). Based on this observation, novel small molecules, such as flavopiridol and UCN-01, are being developed and are currently being tested in the clinic. Efforts to develop CDK modulators led us to the discovery of a novel class of CDK inhibitors, the paullones [Cancer Res 1999;59:2566]. Initial studies demonstrated that paullones inhibit CDKs in vitro, thereby blocking cell-cycle progression. However, the exact mechanism for the antiproliferative effects of paullones was never explored. In this report, we demonstrate for the first time that the most potent paullone, alsterpaullone (Alp), induced apoptosis and promoted loss in clonogenicity in the Jurkat cell line. Alp caused early activation of both caspase-8 and -9, leading to cleavage of caspase-3 and poly(ADP-ribose) polymerase (PARP). Moreover, apoptosis by Alp was not associated with loss in anti-apoptotic proteins such as XIAP or BCL-XL. Pre-incubation with cell-permeable inhibitors z-Asp(OMe)-Glu(OMe)-Val-Asp(Ome)-fluoromethylketone and benzyloxycarbonyl-Val-Ala-Asp (OMe)-fluoromethylketone (ZVAD) blocked Alp-induced apoptosis. Moreover, the general caspase inhibitor ZVAD blocked the cleavage and activation of most caspases tested except caspase-9. Studies of mitochondrial membrane potential also demonstrated that Alp is able to disrupt mitochondrial potential in the presence of ZVAD, suggesting that the activation of caspase-9 by Alp follows mitochondrial perturbation. Pre-incubation of Jurkat cells with ZVAD did not prevent the depletion of cyclin D3, loss of CDK, or cell-cycle arrest by Alp. In summary, these experiments suggest that Alp activates caspase-9 via mitochondrial perturbation. Active caspase-9 cleaves and activates caspase-8 and caspase-3, leading to apoptosis. In the presence of the general caspase inhibitor ZVAD, the cell-cycle effects of Alp are unaltered while apoptosis is blocked, suggesting that the CDK effects of Alp are not sufficient for Alp-induced apoptosis. Additional studies with paullones are warranted to further characterize their preclinical effects and to explore their potential use in the clinical setting.
Fast Categorisation of Articulated Human Motion (2010)

Visual categorisation of human motion in video clips has been an active field of research in recent years. However, most published methods either analyse an entire video and assign it a single category label, or use relatively large look-ahead to classify each frame. Contrary to these strategies, the human visual system proves that simple categories can be recognised almost instantaneously. Here we present a system for categorisation from very short sequences (“snippets”) of 1–10 frames, and systematically evaluate it on several data sets. It turns out that even local shape and optic flow for a single frame are enough to achieve ˜80-90% correct classification, and snippets of 5-7 frames (0.2-0.3 seconds of video) yield results on par with the ones state-of-the-art methods obtain on entire video sequences.
Agglomeration Simulation of Chain-like Inclusions in Molten Steel Based on Fractal Cluster-Cluster Agglomeration Model (2007)

Based on the fractal cluster-cluster agglomeration (CCA) model, two-dimensional simulations of cluster aggregation process have been carried out by varying initial particle number, particle size and sticking probability between clusters. Particle size and amount of seed particles have small effects on the shape of clusters. Actual alumina clusters observed in tundish show the chain-like appearance and are very similar to the simulated agglomerated clusters with high sticking probability. The agglomeration process of alumina chain-like clusters around immersion nozzle in the tundish and RH process are plausibly controlled by the random collision process with high sticking probability values.
Development of a robot arm controlled by force sensors as a walking aid for elderly (1998)

This paper presents a prototype development of a robot arm to assist walking of elderly people. For effective use in Japanese houses, a robot arm mounted on a rail was designed. Force sensors were used to provide an easy-to-use interface. Thresholds of forces were determined to detect the user's intention to walk as well as for safety considerations. Applying a step by step motion, the arm could follow the rhythmical walking of the subject. We examined an interface method using force sensors and concluded that it can detect the user's motion at the beginning of a walk.
Genotypic subtyping of the HIV-1 polymerase gene in 30 naåve patients from Thailand. (2001)

To investigate the subtype classification of the circulating virus strains among infected Thai patients with human immunodeficiency virus type 1 (HIV-1). A random population of patients who were HIV-1 antibody positive after two independent screening assays was selected. HIV RNA from plasma samples was reverse-transcribed and amplified with specific primers that annealed to conserve regions of the HIV-1 pol gene. Amplified products were sequenced directly by using an automated sequencer. The sequencing products represent about 1.2 kb of the pol gene from each patient and they were phylogenetically analyzed and compared to the corresponding pol sequences of the published HIV-1 sequences of known genotypes. Genotype E was found in 25 of 30 patients (83.3%), and 5 patients (16.7%) were HIV-1 genotype B. The result confirmed that HIV-1 subtype E is still predominant in Thailand. Genotype B is found frequently, but there have been no examples of genotype A. In concordance with the serotypic assay, which was previously reported using the V3-peptide enzyme immunoassay (V3-PEIA), the genotypic assay of subtype E was high, at 80% and 83.3% in serotyping and genotyping, respectively. These findings of two subtypes with low heterogeneity indicate that Thailand may be a desirable site for evaluating candidate HIV-1 antiretroviral drugs and vaccines. The mixture of subtype E and B' strains also offers the opportunity to study phenotypic differences between the two subtypes.
Generation of intense 25-fs, 290-nm seed pulses for the terawatt-class ultraviolet solid-state laser system (2003)

Summary form only given. We have successfully demonstrated the generation of 15-/spl mu/J, 25-fs pulses at 290 nm with high peak-power at 1 kHz repetition rate. These ultrashort pulses will be very suitable to be used as the seed pulses of TW Ce:LiCaAlF/sub 6/ (Ce:LiCAF) laser system that is expected to become a new source for generation of coherent XUV light.
Somatic mosaicism and common genetic variation contribute to the risk of very-early-onset inflammatory bowel disease (2020)

Very-early-onset inflammatory bowel disease (VEO-IBD) is a heterogeneous phenotype associated with a spectrum of rare Mendelian disorders. Here, we perform whole-exome-sequencing and genome-wide genotyping in 145 patients (median age-at-diagnosis of 3.5 years), in whom no Mendelian disorders were clinically suspected. In five patients we detect a primary immunodeficiency or enteropathy, with clinical consequences (XIAP, CYBA, SH2D1A, PCSK1). We also present a case study of a VEO-IBD patient with a mosaic de novo, pathogenic allele in CYBB. The mutation is present in ~70% of phagocytes and sufficient to result in defective bacterial handling but not life-threatening infections. Finally, we show that VEO-IBD patients have, on average, higher IBD polygenic risk scores than population controls (99 patients and 18,780 controls; P < 4 × 10<sup>-10</sup>), and replicate this finding in an independent cohort of VEO-IBD cases and controls (117 patients and 2,603 controls; P < 5 × 10<sup>-10</sup>). This discovery indicates that a polygenic component operates in VEO-IBD pathogenesis.
DNA Binding Mechanism of O6-Alkylguanine-DNA Alkyltransferase:  Stoichiometry and Effects of DNA Base Composition and Secondary Structure on Complex Stability (1996)

O6-Alkylguanine-DNA alkyltransferase (AGT) is an important cellular defense against the mutagenic effects of DNA alkylating agents. In humans this defense can contribute to the ability of some tumors to resist the effects of chemotherapeutic agents that act through DNA alkylation. We report here studies that characterize the interaction of AGT with DNA. We show that although AGT sediments as a monomer in the absence of DNA, it binds cooperatively to single stranded deoxyribonucleotides. The stoichiometries of complexes formed with 16-, 30-, and 80-base oligodeoxyribonucleotides are 3.8 +/- 0.3, 5.3 +/- 0.2, and 8.9 +/- 0.2, respectively; the binding density decreasing from approximately 4 nt/monomer to approximately 9 nt/monomer as DNA length increases over this range. Binding competition assays show that DNA affinities depend only weakly on base composition or secondary structure, although in general G + C-rich sequences are bound with greater affinity than are A + T-rich ones and single-stranded DNA is bound with greater affinity than duplex forms. These results suggest mechanisms by which AGT may search for alkylated sites and interact with them to effect DNA repair.
Expression of Vitreoscilla haemoglobin in hybrid aspen (Populus tremula × tremuloides) (2003)

We describe the first ever expression of Vitreoscilla haemoglobin (VHb) in an economically important boreal woody plant hybrid aspen (Populus tremula x tremuloides). VHb has mainly been expressed in biotechnologically important unicellular organisms of both prokaryotic and eukaryotic origin. VHb expression, in this study, was analysed under different greenhouse cultivation conditions and under elevated UV-B illumination. Microscope analyses of leaves grown under optimized conditions revealed significant differences both in cell structure and size when the transgenic VHb lines were compared with the control lines. VHb lines displayed a higher relative volume of mitochondria and a significantly enhanced accumulation of starch in chloroplasts, all of which pointed towards changes in cellular energy production. Under elevated UV-B illumination, the differences between VHb lines became evident. Some specific VHb lines had elevated levels of total flavonoids, individual quercetin, kaempferol- and myricetin-derivatives relative to controls and other transgenic lines. This observation may reflect the availability of extra energy resources for secondary metabolite production and possibly an enhanced protection ability of these transgenic lines against UV-B illumination. Thus, all these findings point to changes in the energy metabolism of VHb lines. In the cultivation conditions tested this observation did not, however, result in a general improvement of elongation growth.
Self-tuning process monitoring system for process-based product (1998)

The hidden qualities of a product are often revealed in the process. Subsurface material damage, surface cracks, and unusual burr formation can occur during a poorly controlled machining process. Standard post process inspection is costly and may not reveal these conditions. However, by monitoring the proper process parameters, these conditions are readily detectable without incurring the cost of post process inspection. In addition, many unforeseen process anomalies may be detected using an advanced process monitoring system. This work created a process monitoring system for milling machines which mapped the forces, power, vibration, and acoustic emissions generated during a cutting cycle onto a 3D model of the part being machined. The hyperpoint overlay can be analyzed and visualized with VRML (Virtual Reality Modeling Language). Once the Process Monitoring System is deployed, detailed inspection may be significantly reduced or eliminated. The project deployed a Pro-Engineer to VRML model conversion routine, advanced visualization interface, tool path transformation with mesh generation routine, hyperpoint overlay routine, stable sensor array, sensor calibration routine, and machine calibration methodology. The technology created in this project can help validate production of WR (War Reserve) components by generating process signatures for products, processes, and lot runs. The signatures of each product can be compared across all products made within and across lot runs to determine if the processes that produced the product are consistently providing superior quality. Furthermore, the qualities of the processes are visibly apparent, since the part model is overlaid with process data. The system was evaluated on three different part productions.
The Control of Reproduction in Farmed Fish (1993)

To raise fish successfully in captivity a producer often needs to control and manipulate fish reproduction. A variety of technologies is available to encourage species that do not breed naturally in captivity to alter the timing of reproduction for year-round production, to choose the sex of fish grown and even to prevent sexual maturation for improved fish growth.
Colloid Chemistry of Silica (1994)

Silicon dioxide is the main component of the crust of the earth. Combined with the oxides of magnesium, aluminum, calcium, and iron, it forms the silicate minerals in our rocks and soil. Over millions of years silicon dioxide, or silica, has been separated from the original silicate rocks by the action of water to appear as quartz. In a few places it was deposited in the amorphous form as opal. Our English word silica has a very broad connotation: it includes silicon dioxide in all its crystalline, amorphous, soluble, or chemically combined forms in which the silicon atom is surrounded by four or six oxygen atoms. This definitely excludes all the organosilicon compounds made by man in which carbon atoms have been linked directly to silicon atoms—commonly referred to as "silicones", which do not occur in nature. Silica is soluble enough in water to play important roles in many forms of life. It forms the skeletons of diatoms, the earliest form of life that absorbed sunlight and began to release oxygen into the atmosphere. Many plants use silica to stiffen stems and form needles on the surface for protection. As animals developed, the role of silica became less obvious. But each one of us contains about half a gram of silica, without which our bones could not have been formed, and probably also not our brains. Silica has played a key role since the beginning of civilization, first in flint for tools and weapons and in clay and sand for pottery. The high strength and durability of Roman cement 2000 years ago is now known to be due to the use of a special volcanic ash that is an almost pure form of amorphous colloidal silica. Today there is active research on the use of the somewhat similar silica fume from electric furnaces to make a super-strong Portland cement. Our present technology would be very different without the silica for the catalysts of our oil refineries, for the molds for casting the superalloys in our jet engines, for modern glass and ceramics, electronic microcircuits, quartz crystals, and fiber optics. — Ralph K. Iler, Alexander Memorial Lecture, Australia, 1989. Reprinted with permission from Chemistry in Australia (October 1986, p 355).
Frequent induction of mammary carcinomas following neu oncogene transfer into in situ mammary epithelial cells of susceptible and resistant rat strains. (1991)

Varying results have been reported on the role of neu oncogene in mammary carcinogenesis. In order to further address this issue, the activated neu oncogene was introduced into mammary epithelial cells in situ of both mammary carcinoma-susceptible Wistar Furth and resistant Copenhagen rats by infusing replication-defective recombinant retroviruses carrying the neu oncogene into the mammary gland lumen. At the highest virus titer tested, very high numbers of mammary carcinomas developed within 2 weeks in all exposed glands in both rat strains. When the virus titer was reduced, however, individual tumors occurred with varying latencies. In addition, not all of the neu-infected mammary cells progressed to form mammary carcinomas. These results suggest that while neu is a potent mammary transforming gene, either other events in addition to neu expression may be required for full malignant transformation or not all mammary ductal epithelial cells are able to be neoplastically transformed.
Spectrophotometric and spectrofluorimetric studies of novel heterocyclic Schiff base dyes (2013)

Novel heterocyclic Schiff base dyes were prepared by the reaction of salicylaldehyde/2-Hydroxy-1-naphthaldehyde with different heterocyclic amines. Results of the newly synthesized compounds established by FT-IR, 1H-NMR, 13C-NMR and GC–MS spectroscopic experiments were consistent with their chemical structures. Resulted heterocyclic Schiff base dyes were found to be pure from data obtained by the elemental analysis. In addition, spectrophotometric and spectrofluorimetric studies showed that these dyes were good absorbent and fluorescent. Fluorescence polarity study data revealed that some of these compounds were sensitive to the polarity of the microenvironment provided by different solvents. Time-based fluorescence steady-state measurements also showed that these heterocyclic Schiff base dyes have high photostability against photobleaching.
Inter‐ and intra‐scanner variability of icobrain DM automated brain volumetry software on three different MRI systems (2021)

Abstract Background Magnetic Resonance Imaging (MRI) has become part of clinical routine for diagnosis of neurodegenerative brain disorders. Acquisitions are performed at multiple centers, using multiple imaging systems and is therefore subjected to intra‐ and inter‐scanner variability. Detailed analysis of brain volumetry differences between MRI systems and scan‐rescan acquisitions can provide useful information to correct for different MRI scanner effects in future multi‐center longitudinal studies. Method The study population (n=10) consisted of five cognitively healthy controls and five patients belonging to different stages of the AD continuum. Subjects underwent brain MRI acquisitions on three different MRI systems with harmonized scan parameters: Philips Achieva dStream 1.5T, Philips Ingenia 3T and GE Discovery MR750w 3T. Sequences were harmonized by keeping acquisition parameters similar (Table 1). To test intra‐scanner variability, each participant underwent two subsequent MRI scans (between‐scan repositioning time 3‐5 minutes) per imaging system, repeated on three different MRI systems within two hours to test inter‐scanner variability. A total of 60 MRI scans were acquired for downstream comparative analysis. Brain volumes, including whole brain, (cortical) gray matter, hippocampal volumes, lateral ventricles, frontal, temporal and parietal cortices were computed with ico brain dm (v5.0). Coefficients of variation (CV), absolute volume differences (AVD), Dice similarity coefficients (DSC) and intraclass correlation coefficients (ICC) were computed to assess within‐ and between‐scanner agreement. Result The intra‐scanner CVs over all volumes were 0.948% for Discovery MR750w, 1.050% for Achieva and 1.152% for Ingenia. The inter‐scanner CVs were 3.016% for all‐scanner comparisons, 2.044% for Ingenia vs. Achieva, 3.191% for Achieva vs. GE and 3.326% for Ingenia vs. GE. The AVDs and ICCs were in line with the CV values. The intra‐scanner DSCs (mean±SD) over all volumes were 0.917±0.011 for Discovery MR750w, 0.917±0.010 for Achieva and 0.917±0.015 for Ingenia. The inter‐scanner DSCs were 0.898±0.017 for all‐scanner comparisons, 0.912±0.012 for Ingenia vs. Achieva, 0.888±0.013 for Achieva vs. Discovery MR750w and 0.893±0.015 for Ingenia vs. Discovery MR750w (Table 2, 3, Figure 1). Conclusion The variability results show an excellent agreement (CV&lt;2%) for within‐scanner and a good agreement (CV&lt;5%) for between‐scanner comparisons in terms of clinical relevance, indicating that MRI acquisition harmonization is beneficial for automated MRI volumetry software.
Efforts Directed Toward the Synthesis of Colchicine: Application of Palladium‐Catalyzed Siloxane Cross‐Coupling Methodology. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
The computational complexity of high-dimensional correlation search (2002)

There is a growing awareness that the popular support metric (often used to guide search in market-basket analysis) is not appropriate for use in every association mining application. Support measures only the co-occurrence frequency of a set of events when determining which patterns to report back to the user. It incorporates no rigorous statistical notion of surprise or interest, and many of the patterns deemed interesting by the support metric are uninteresting to the user. However, a positive aspect of support is that search using support is very efficient. The question addresses in the paper is: can we retain this efficiency if we move beyond support, and to other more rigorous metrics? We consider the computational implications of incorporating simple expectation into the data mining task. It turns out that many variations on the problem which incorporate more rigorous tests of dependence (or independence) result in NP-hard problem definitions.
A novel mutation at position +12 in the intron following Exon 10 of the tau gene in familial frontotemporal dementia (FTD‐Kumamoto) (2000)

Exonic and intronic mutations in the tau gene cause familial frontotemporal dementia and parkinsonism linked to chromosome 17. Here, we describe a new mutation, consisting of a C-to-T transition at position +12 of the intron following exon 10 of the tau gene in the Kumamoto pedigree, showing frontotemporal dementia. The mutation caused a marked reduction in melting temperature of the tau exon 10–splicing regulatory element RNA and a large increase in exon 10–containing transcripts. Brain tissue from affected individuals showed an abnormal preponderance of exon 10–containing transcripts that was reflected at the protein level by an overproduction of tau isoforms with four microtubule-binding repeats. Immunostaining revealed the presence of tau aggregates in degenerating neurons and glial cells. Isolated tau filaments had a twisted ribbon-like morphology and were made of hyperphosphorylated four-repeat tau isoforms. The additional mutation located close to the splice-donor site of the intron following exon 10 of the tau gene supports the view that intronic mutations exercize their pathogenic effect by destabilizing RNA secondary structure. Ann Neurol 2000;47:422–429.