gebhart/patrepeval huggingface dataset:
Effects of respiratory motion on dose uniformity with a charged particle scanning method (1992)

A three-dimensional spot-scanning technique for radiotherapy with protons is being developed at the Paul Scherrer Institute. As part of the effort to optimize the design and ensure clinically useful dose distributions, a computer simulation of the dose deposition in the presence of respiratory motion was performed. Preliminary experiments have characterized the proton beam and the scanning procedure. Using these parameters, the computer program calculated the dose within a uniform volume of water in the presence of respiratory motion. Respiration amplitude, respiration period, respiration direction, number of fractions, size and position of the beamspots and rescanning multiplicity were systematically varied and the effect on the dose distribution determined. The dose uniformity is very dependent on the direction of the respiration relative to the three independent beam scanning directions. The dose uniformity decreases with increasing respiration amplitude, but has little response to changes in respiration frequency. Rescanning the volume, such as with fractionation, improves the dose uniformity roughly as the square root of the number of fractions. Broad, Gaussian beams result in better dose uniformity than narrow, sharply delineated ones, but produce slower dose fall-off at the edges of the scanned volume. Results of this work are being incorporated into the design of the system.
Automatic programming of a time-optimal robot controller and an analog electrical circuit to implement the robot controller by means of genetic programming (2002)

Genetic programming is an automatic programming technique that evolves computer programs to solve, or approximately solve, problems. This paper presents two examples in which genetic programming creates a computer program for controlling a robot so that the robot moves to a specified destination point in minimal time. In the first approach, genetic programming evolves a computer program composed of ordinary arithmetic operations and conditional operations to implement a time-optimal control strategy. In the second approach, genetic programming evolves the design of an analog electrical circuit consisting of transistors, diodes, resistors, and power supplies to implement a near-optimal control strategy.
Abstract LB-209: Neuroblastoma is biphasic with classical neuro-epithelial cells and chemoresistant mesenchymal cells controlled by PRRX1-NOTCH signaling (2015)

Abstract Most high stage neuroblastoma initially respond to chemotherapy, but ultimately relapse as therapy-resistant tumor. The mechanisms driving relapse and resistance remain elusive. We observed that new neuroblastoma cell lines cultured in defined medium always include two phenotypically divergent cell types. Whole genome sequencing showed that both types were genetically identical. One cell type has a neuro-epithelial (NE) phenotype and expresses all classical and diagnostically used neuroblastoma markers. The other type has a mesenchymal (MES) character, lacks all neuroblastoma markers and is highly motile. MES cells are more chemo-resistant in vitro as compared to NE cells. Immunohistochemistry (IHC) of primary neuroblastoma detected a small fraction of MES cells in most tumors. However, MES cells were strongly enriched in surgically removed post-chemotherapy samples. Moreover, neuroblastoma patients that had been tumor-free for several years but relapsed, also showed a strong accumulation of MES type cells in their relapses as compared to the primary tumors. As these data suggest a major role for this new neuroblastoma cell type in development of therapy-resistant relapses, we analyzed their key regulatory pathways. In multiple cell line models, the homeobox gene PRRX1 was identified as a master regulator that converted the NE phenotype in a MES phenotype. PRRX1 concomitantly induced a chemo-resistant phenotype in vitro. PRRX1 activated a cascade of MEK, NOTCH and PDGFRβ signaling. Also NOTCH was able to induce the mesenchymal phenotype, as well as chemo-resistance. Analysis of the PRRX1-induced downstream signaling pathway identified several drugable key-players, like MEK and PDGFRβ. Targeting them with small-molecule inhibitors specifically killed MES cells in vitro. Our data suggest that neuroblastoma is a bi-phasic tumor. MES and NE cells have very different characteristics, but can transdifferentiate into each other. MES cells strongly accumulate after chemo-therapy and in relapses. They may survive classical therapy and seed relapses, that ultimately become heterogeneous again. Targeted elimination of MES cells with small molecule inhibitors shows how cells with a potential key role in relapse development are amenable to therapy. Note: This abstract was not presented at the meeting. Citation Format: Tim van Groningen, Natalia E. Nowakowska, Nurdan Akogul, Marloes Broekmans, Johannes Bras, Jan Booij, Marli E. Ebus, Jan J. Molenaar, Ellen M. Westerhout, Mohamed Hamdi, Peter van Sluis, Jan Koster, Bart A. Westerman, Godelieve A. Tytgat, Rogier Versteeg, Johan van Nes. Neuroblastoma is biphasic with classical neuro-epithelial cells and chemoresistant mesenchymal cells controlled by PRRX1-NOTCH signaling. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-209. doi:10.1158/1538-7445.AM2015-LB-209
DNA fingerprinting of glioma cell lines and considerations on similarity measurements (2012)

Glioma cell lines are an important tool for research in basic and translational neuro-oncology. Documentation of their genetic identity has become a requirement for scientific journals and grant applications to exclude cross-contamination and misidentification that lead to misinterpretation of results. Here, we report the standard 16 marker short tandem repeat (STR) DNA fingerprints for a panel of 39 widely used glioma cell lines as reference. Comparison of the fingerprints among themselves and with the large DSMZ database comprising 9 marker STRs for 2278 cell lines uncovered 3 misidentified cell lines and confirmed previously known cross-contaminations. Furthermore, 2 glioma cell lines exhibited identity scores of 0.8, which is proposed as the cutoff for detecting cross-contamination. Additional characteristics, comprising lack of a B-raf mutation in one line and a similarity score of 1 with the original tumor tissue in the other, excluded a cross-contamination. Subsequent simulation procedures suggested that, when using DNA fingerprints comprising only 9 STR markers, the commonly used similarity score of 0.8 is not sufficiently stringent to unambiguously differentiate the origin. DNA fingerprints are confounded by frequent genetic alterations in cancer cell lines, particularly loss of heterozygosity, that reduce the informativeness of STR markers and, thereby, the overall power for distinction. The similarity score depends on the number of markers measured; thus, more markers or additional cell line characteristics, such as information on specific mutations, may be necessary to clarify the origin.
A Concise Route to 2-Amino-3-aryl-3H-benzofurans and their Use as Precursors to 3-Aryl-3H-benzofuran-2-one and 1H-Benzofuro[2,3-b]pyridin-2-one Derivatives (2004)

A concise approach to 2-amino-3-aryl-3H-benzofurans based on the Michael addition of NaCN onto in situ generated substituted o-quinone methides has been developed. Straightforward access to 3-aryl-3H-benzofuran-2-ones was achieved upon acidic hydrolysis whereas N-Boc-protected 2-amino-3-aryl-3H-benzofurans underwent smooth intramolecular cyclisation to give 1H-benzofuro[2,3-b]pyridin-2-one derivatives.
A qualitative and quantitative comparison of the fat in human, feline and canine kidneys. (1977)

While xanthogranulomatous pyelonephritis in humans tends to be rich in birefringent fat, this variety cannot be demonstrated microscopically in the feline morphological counterpart of the condition, which is, however, rich in readily stainable fat. Since normal feline kidney is rich in such lipid, a qualitative and quantitative comparison of the lipid in human, feline and canine kidney was carried out in an attempt to throw further light on the possible origin of the birefringent fat in the human disease. No significant difference could be found in the amount of cholesterol in the 3 species. Despite its visual prominence in feline kidneys, human kidney was richer in neutral fat and the percentage of total lipid formed by cholesterol was greater in humans than in the other species. The results suggested that cases of xanthogranulomatous pyelonephritis may occur in those kidneys unusually rich in cholesterol.
Distance Dependence of Electronic Coupling through Trans Alkyl Chains:  Effects of Electron Correlation (1998)

Electronic coupling between CH2 π donor/acceptor groups at the termini of trans alkyl chains [H2C−(CH2)n-2−CH2, n = 4−16] was investigated using Hartree−Fock (HF) theory, second-order Moller−Plesset perturbation theory (MP2), and density functional theory (DFT). For each method the couplings in the ions were calculated in two ways: (1) the difference in donor/acceptor orbital energies [Koopmans' theorem (KT)] and (2) the difference between the ground state and first excited state energy of the ions (ΔE). The distance dependence of the coupling in anions was found to be independent of the method used, indicating that electron correlation has little effect. In contrast, the distance dependence of the couplings in cations was very dependent on the method used. For cations, couplings from ΔDFT calculations have a weak distance dependence (β < 0.4) similar to that found previously for KT couplings from HF (β ∼ 0.4), while couplings from KT(DFT) and ΔMP2 calculations have a stronger distance dependence (β ∼ 0.6−0.7) similar to that found previously from ΔHF calculations. When energetics are examined, it appears that the weak distance dependence for some of the methods may arise from small energy differences between the donor/acceptor levels and the energies of the filled orbitals. This was confirmed by calculations on a series of trans alkyls with different donor/acceptor groups (NH2, SiH2, PH2). The couplings for the anions have a stronger distance dependence (β ∼ 0.6−0.7) in all of the methods. Finally, it is found that the inclusion of diffuse functions in the basis set does not introduce problems for the calculation of anion couplings by density functional theory, in contrast to ab initio molecular orbital calculations where erratic results are obtained.
Assessment of contrast‐enhanced computed tomography for imaging of cartilage during fracture healing (2012)

Assessment of the early stages of fracture healing via X-rays and computed tomography is limited by the low radio-opacity of cartilage. We validated a method of contrast-enhanced computed tomography (CECT) for non-destructive identification of cartilage within a healing fracture callus. Closed, stabilized fractures in femora of C57BL/6 mice were harvested on post-operative day 9.5 and imaged ex vivo with micro-computed tomography (µCT) before and after incubation in a cationic contrast agent that preferentially accumulates in cartilage due to the high concentration of sulfated glycosaminoglycans in the tissue. Co-registration of the pre- and post-incubation images, followed by image subtraction, enabled two- and three-dimensional delineation of mineralized tissue, soft callus, and cartilage. The areas of cartilage and callus identified with CECT were compared to those identified with the gold-standard method of histomorphometry. No difference was found between the areas of cartilage measured by the two methods (p = 0.999). Callus area measured by CECT was smaller than, but strongly predictive of (R(2) = 0.80, p < 0.001), the corresponding histomorphometric measurements. CECT also enabled qualitative identification of mineralized cartilage. These findings indicate that the CECT method provides accurate, quantitative, and non-destructive visualization of the shape and composition of the fracture callus, even during the early stages of repair when little mineralized tissue is present. The non-destructive nature of this method would allow subsequent analyses, such as mechanical testing, to be performed on the callus, thus enabling higher-throughput, comprehensive investigations of bone healing.
The spectroscopic properties of the lipodepsipeptide, syringomycin E (1992)

The spectroscopic properties of syringomycin E, an antibiotic lipodepsinonapeptide associated with pathological states in plants, have been investigated by uv absorbance and CD spectroscopies, and by the synthesis of relevant model compounds. Initial studies [E. Vaillo, A. Ballio, P. L. Luisi, and R. M. Thomas (1990) in Peptides 1990, Giralt, E. & Andreu, D., Eds., Escom Scientific, Leiden, Netherlands] suggested that a significant contribution to the spectra was due to the presence of a zdehydroaminobutyric acid residue in the amino acid sequence. The model peptides N-Boc-L-Phe-delta zAbu-OMe and its analogue, N-Boc-L-Phe-L-Thr-OMe, lacking the unsaturated bond, were synthesized using standard solution chemistry, and a detailed investigation was made in which the spectra of the models and that of syringotoxin (an antibiotic closely related to syringomycin E but without a Phe residue) were compared with those of syringomycin E under a variety of solvent conditions. The uv absorbance spectra of both N-Boc-L-Phe-delta zAbu-OMe and syringomycin E clearly showed the presence of the unsaturated residue while the CD spectra were complex, environmentally sensitive, and contained contributions from both the delta zAbu and Phe residues. In the course of these studies extinction coefficients were obtained for syringomycin E and its dipeptide model. The origins of the uv and CD spectra are discussed in detail, and a comparison is made with the spectra of other, similar lipopeptide antibiotics. Finally, a structural model for syringomycin is proposed in which the changes induced in the spectrum by alterations in the solvent environment are accommodated.
Ultrasound Versus Digitally Directed Prostatic Needle Biopsy (1986)

During an 8-month period 55 patients with suspected but unproved prostatic carcinoma were entered randomly into a study designed to evaluate the effectiveness of ultrasound-directed transperineal needle biopsy of the prostate. Each patient was biopsied with and without ultrasound assistance; the method used first was determined randomly. Of the 15 patients diagnosed as having adenocarcinoma only 9 were proved by conventional transperineal biopsy, whereas ultrasound-guided biopsy was accurate in all 15 patients (p less than 0.005). Transrectal ultrasound guidance significantly improves the yield of transperineal needle biopsy when it is performed for suspected malignancy.
Effect of Surgery First Orthognathic Approach on the Temporomandibular Joint (2018)

Surgery first approach is an innovative orthognathic procedure and, by undergoing surgery first approach, patients with pre-existing TMJ dysfunction may experience a significant improvement or even resolution of the TMDs signs and symptoms.
Trajectory Tracking Control of Heterogenous UGV-MMS system (2021)

A new control strategy is presented for trajectory tracking of heterogeneous Unmanned Ground Vehicle (UGV)-Mobile Manipulators (MMS) system in this paper. The heterogenous UGV-MMS system is comprised of the UGV and the MMS. The main innovation of this paper is that the situation that the manipulator compensates the dynamic interactions produced by the UGV is considered, while the UGV doesn't compensate the dynamic interactions produced by the manipulator. In this situation, we do low calculation and the tracking precision is excellent. Firstly, a kinematic and dynamic controller is designed for the UGV to ensure the UGV to track the desired trajectory. Secondly, a control law based on the sliding mode control is designed for the manipulator to track the desired trajectory. Finally, the Lyapunov function approach and the simualtion results in MATLAB are used to demonstrate the effectiveness and feasibility of the proposed control approach of both the UGV and the manipulator.
Low-Cost High-Tech Robotics for Ambient Assisted Living: From Experiments to a Methodology (2015)

Abstract Aging of the population in developed countries is an important challenge to overcome. Robots have a role to play to offer solutions to old and dependent persons and also to their families and carers. We investigated low-cost high-tech robotics in order to offer affordable mobile robots that could be used in the context of ambient assisted living (AAL). We used a bottom–up approach and tried different technical solutions in order to propose an efficient prototype. Results of this experimental work are presented in the first part of this paper. From the different experiments we carried out, we felt the need to use a top–down approach that could be used to develop such robots and also any system that requires the use of mechanical, electronic, and software components. In the second part of this paper, we present the X-methodology and try to show its use in our AAL context.
Recursive erosion, dilation, opening, and closing transforms (1995)

A new group of recursive morphological transforms on the discrete space Z(2) are discussed. The set of transforms include the recursive erosion transform (RET), the recursive dilation transform (RDT), the recursive opening transform (ROT), and the recursive closing transform (RCT), The transforms are able to compute in constant time per pixel erosions, dilations, openings, and closings with all sized structuring elements simultaneously. They offer a solution to some vision tasks that need to perform a morphological operation but where the size of the structuring element has to be determined after a morphological examination of the content of the image. The computational complexities of the transforms show that the recursive erosion and dilation transform can be done in N+2 operations per pixel, where N is the number of pixels in the base structuring element. The recursive opening and closing transform can be done in 14N operations per pixel based on experimental results.
Segmenting spoken language utterances into clauses for semantic classification (2004)

Robust spoken language understanding in large-scale conversational dialog applications is usually performed by classification of the user utterances into one or many semantic classes. The features used for classification are sensitive to variations caused by artifacts of spoken language, such as edits, repairs and other dysfluencies. Furthermore, the performance of these classifiers typically degrades when the user's utterance contains multiple semantic classes. In this paper, we present a semantic classification technique that first automatically removes dysfluencies and segments the user's utterance into clauses and then classifies the utterance based on the classification of the clauses. We show that this preprocessing improves the semantic classification accuracy for utterances and significantly decreases the amount of training data needed for a given classification accuracy level.
Programmable Bio-NanoChip Technology for the Diagnosis of Cardiovascular Disease at the Point of Care (2012)

Cardiovascular disease remains the leading cause of death in the world and continues to serve as the major contributor to healthcare costs. Likewise, there is an ever-increasing need and demand for novel and more efficient diagnostic tools for the early detection of cardiovascular disease, especially at the point-of-care (POC). This article reviews the programmable bio-nanochip (P-BNC) system, a new medical microdevice approach with the capacity to deliver both high performance and reduced cost. This fully integrated, total analysis system leverages microelectronic components, microfabrication techniques, and nanotechnology to noninvasively measure multiple cardiac biomarkers in complex fluids, such as saliva, while offering diagnostic accuracy equal to laboratory-confined reference methods. This article profiles the P-BNC approach, describes its performance in real-world testing of clinical samples, and summarizes new opportunities for medical microdevices in the field of cardiac diagnostics.
Discharge-pumped soft-x-ray laser in neon-like argon (1995)

Starting with the discovery of x-ray lasers in 1984, laser-created plasmas remained for almost a decade, the only medium in which large amplification of soft-x-ray radiation could be obtained. In this paper the recent first demonstration of large soft-x-ray amplification in a discharge-created plasma column, realized utilizing a fast capillary discharge to collisionally excite the 46.9 nm transition of Ne-like, Ar is reviewed. Results of the parametrization of the Ar IX discharge-pumped amplifier, the study of the dynamics of its plasma column, and the measurement of the time history of the laser pulse are reported. Prospects for laser operation at shorter wavelengths are also discussed.
510 Ginger, Paullinia Cupana, Muira Puama, and L-citrulline (COMP-4) as a Novel Natural Treatment for Severe Constipation (2019)

INTRODUCTION: Epidemiologic studies report that about 15% of adults and 30% of people older than 60 years suffer from constipation in the United States. The actual prevalence is likely greater as many people believe their bowel habits are normal and underreport symptoms of constipation. Moreover, most recent surveys assessing current medical management of constipation show that patients are dissatisfied and believe that conventional treatments, like laxatives and colonic stimulants, are suboptimal since they can cause explosive bowel movements which are difficult to control. COMP-4, a combination of ginger, Paullinia cupana, muira puama, and L-citrulline is a novel nutraceutical that has been shown to stimulate the production of nitric oxide and cGMP in smooth muscle cells resulting in smooth muscle relaxation and possibly increases intestinal secretion. In this study, we aim to demonstrate that treatment with COMP-4 is an effective treatment for severe constipation. METHODS: Seventeen patients with constipation were treated COMP-4 (2-4 capsules per day) for 2-4 weeks. Constipation was defined as two or more of the following: the sensation of incomplete evacuation, Bristol stool score 1-2 (hard, lumpy nut or sausage-shaped bowel movements), and straining during the majority of defecations. Patients were surveyed before and after the treatment regarding their approximate number of bowel movements per week, their typical Bristol stool score, the presence of abdominal pain, and the feeling of incomplete evacuation. Statistical analysis was performed using the Wilcoxon rank test with a P &lt; 0.05 considered significant. RESULTS: Following treatment with COMP-4, the average weekly number of stools significantly ( P &lt; 0.0001) increased from 2.7+/-0.68 to 7.3+/- 1.11 (Figure 1). Prior to COMP-4, 16/17 patients reported incomplete bowel evacuation during bowel movements. After COMP-4, 10/17 patients reported complete bowel evacuation. The mean Bristol Stool Score significantly ( P &lt; 0.0001) increased from 1.5+/- 0.15 to 3.4+/-0.29 with softer and more formed stools (Figure 2). Patients also experienced a significant ( P &lt; 0.0001) decrease in abdominal pain (Figure 3). CONCLUSION: The combination of ginger, Paulinia cupana, muira puama, and L-citrulline improves the frequency and consistency of stools and helps relieve symptoms of constipation. The nutraceutical may be a novel agent used to treat severe constipation not responding well to other conventional treatments.