gebhart/patrepeval huggingface dataset:
Simulation of organ-specific patient effective dose due to secondary neutrons in proton radiation treatment (2005)

Cancer patients undergoing radiation treatment are exposed to high doses to the target (tumour), intermediate doses to adjacent tissues and low doses from scattered radiation to all parts of the body. In the case of proton therapy, secondary neutrons generated in the accelerator head and inside the patient reach many areas in the patient body. Due to the improved efficacy of management of cancer patients, the number of long term survivors post-radiation treatment is increasing substantially. This results in concern about the risk of radiation-induced cancer appearing at late post-treatment times. This paper presents a case study to determine the effective dose from secondary neutrons in patients undergoing proton treatment. A whole-body patient model, VIP-Man, was employed as the patient model. The geometry dataset generated from studies made on VIP-Man was implemented into the GEANT4 Monte Carlo code. Two proton treatment plans for tumours in the lung and paranasal sinus were simulated. The organ doses and ICRP-60 radiation and tissue weighting factors were used to calculate the effective dose. Results show whole body effective doses for the two proton plans of 0.162 Sv and 0.0266 Sv, respectively, to which the major contributor is due to neutrons from the proton treatment nozzle. There is a substantial difference among organs depending on the treatment site.
Dynamic Resource Allocation Using Virtual Machines for Cloud Computing Environment (2012)

Cloud computing allows business customers to scale up and down their resource usage based on needs. Many of the touted gains in the cloud model come from resource multiplexing through virtualization technology. In this paper, we present a system that uses virtualization technology to allocate data center resources dynamically based on application demands and support green computing by optimizing the number of servers in use. We introduce the concept of "skewness” to measure the unevenness in the multidimensional resource utilization of a server. By minimizing skewness, we can combine different types of workloads nicely and improve the overall utilization of server resources. We develop a set of heuristics that prevent overload in the system effectively while saving energy used. Trace driven simulation and experiment results demonstrate that our algorithm achieves good performance.
Commercial Fibrin Sealants Are Not Equivalent in a Rabbit Liver-Resection Model Which Quantitatively Evaluates Hemostasis and Formation of Adhesions (2005)

A rabbit partial liver resection model was used to determine the hemostatic effectiveness of a new fibrin sealant. Persistent bleeding, with a mean bleeding time of 372 s and blood loss of 18 ml, from a resected lobe of the liver was achieved after rabbits in the untreated control group had been infused continuously with unfractionated heparin over 20 min with 0.2 IU/ml at a rate of 1 ml/min. Spraying the resected surface with the new fibrin sealant, Quixil, reduced bleeding to < 1 ml and the post-resection bleeding times was 25 s. Bleeding time, blood loss and the volume of sealant used in the rabbit model were inversely correlated with the thrombin concentration in the sealant. In direct comparisons with Tissucol and Beriplast, Quixil was associated with the shortest bleeding times, the lowest volume of sealant used and the lowest score of abdominal adhesions.
A Case of Low-grade Papillary Adenocarcinoma of the Nasopharynx (2005)

Low-grade nasopharyngeal papillary adenocarcinoma is a very rare nasopharyngeal, surface epithelium-derived malignant tumor characterized with adenocarcinomatous differentiation and an indolent biological behavior. We report a case of 36-year old female presenting a papillary adenocarcinoma of the nasopharynx. The tumor was of a 0.5 cm sized exophytic mass located on the nasopharyngeal mucosa near the posterior choanal septum. Because of the histologic similarities with thyroid papillary carcinoma, it was necessary to rule out metastasis from thyroid by immunohistochemical staining for thyroglobulin. Surgical excision was done via transpalatal approach; mass was removed with a clear resection margin
Explicit Compensator Performance Constraints for Control of Lightly Damped Plants (1992)

Explicit constraints on the compensator are derived which provide specified levels of closed loop tracking and disturbance rejection performance. In the case of lightly damped plants, simple geometric descriptions of compensator constraints are obtained. An example of the application of these constraints in active vibration isolation is provided.
Pushing Point Cloud Compression to the Edge (2022)

As Point Clouds (PCs) gain popularity in processing millions of data points for 3D rendering in many applications, efficient data compression becomes a critical issue. This is because compression is the primary bottleneck in minimizing the latency and energy consumption of existing PC pipelines. Data compression becomes even more critical as PC processing is pushed to edge devices with limited compute and power budgets. In this paper, we propose and evaluate two complementary schemes, intra-frame compression and inter-frame compression, to speed up the PC compression, without losing much quality or compression efficiency. Unlike existing techniques that use sequential algorithms, our first design, intra-frame compression, exploits parallelism for boosting the performance of both geometry and attribute compression. The proposed parallelism brings around $43.7 \times$ performance improvement and 96.6% energy savings at a cost of $1.01 \times$ larger compressed data size. To further improve the compression efficiency, our second scheme, inter-frame compression, considers the temporal similarity among the video frames and reuses the attribute data from the previous frame for the current frame. We implement our designs on an NVIDIA Jetson AGX Xavier edge GPU board. Experimental results with six videos show that the combined compression schemes provide $34.0 \times$ speedup compared to a state-of-the-art scheme, with minimal impact on quality and compression ratio.
Multi-Modal Tracking of Interacting Targets Using Gaussian Approximations (2001)

We introduce a modular tracker architecture that combines the advantages of several simple and rapidly performing tracking algorithms. Robust tracking is facilitated by framerate or near-frame-rate processing. A Kalman filter is used to integrate tracking results across detection modules and over time. Processing regions are smoothly localized by weighting with a Gaussian that is dimensioned according to the target sizes and uncertainties estimated by the Kalman filter. From this Gaussian mask, Gaussian approximations of known nearby targets are subtracted to allow individual tracking of interacting targets, that can be merged and split based on Mahalanobis distances and a robust version of connected components. The result is an adaptive tracker that can robustly track at video frame rates several targets, each of which corresponds to one or more individual objects. Its performance degrades gracefully with increased system load.
Is the FAA slow growth approach to certification of composite and bonded structures feasible (2017)

This paper addresses on the problem of the growth of impact damage/delaminations in composite airframes. The focus of the paper is on the FAA slow growth approach to aircraft certification. It is shown that whilst significant progress has been made there are still a range of questions that need to be addressed and a need for test data that characterize the fatigue threshold and residual strength surfaces associated with impact damage/delamination damage.
Clinical Trial of Exercise for Shoulder Pain in Chronic Spinal Injury (2006)

A selective 8-week home exercise program is effective in reducing pain and improving function and satisfaction in this population of wheelchair users.
Oxidation Resistance of Ti–Si–N and Ti–Al–Si–N Films Deposited by Reactive Sputtering Using Alloy Targets (2011)

Ti–Si–N and Ti–Al–Si–N films, which possess high hardness due to the formation of a nanocomposite structure in the films, were deposited by reactive magnetron sputtering using alloy targets and then postannealed in air at temperatures ranging from 300 to 800 °C. The hardness of both the films decreased significantly as postannealing temperature increased. However, the hardness of Ti–Al–Si–N films postannealed up to 500 °C remained at more than 30 GPa, which was significantly higher than that of the Ti–Si–N films after the post annealings. Electron probe microanalyses and X-ray photoelectron spectroscopy revealed that Al2O3 phases were formed in the postannealed Ti–Al–Si–N films. Transmission electron microscopy with energy-dispersive X-ray analysis showed that the Al2O3 layer of the postannealed Ti–Al–Si–N films was formed 40 nm below the surface, whereas the depth of the TiO2–SiO2 layer of the postannealed Ti–Si–N films was 100 nm from the surface. These results indicate that Al2O3 phases existed at the surface of the Ti–Al–Si–N films and prevented the oxidation of the interior of the films during postannealing at high temperatures in air.
Electron tunneling and ab initio calculations related to the one-electron oxidation of NAD(P)H bound to catalase (1995)

Models for NAD(P)H le- oxidation in bovine catalase were studied using Hartree-Fock ab initio calculations, along with information taken from the published X-ray structure of the enzyme. Geometries and energies of ground states and transition states were calculated at the 6-31G* level for N-methyl-1,4-dihydropyridine and N-methyl-1,4-dihydronicotinamide undergoing the pathway (i) le- oxidation to yield the radical cation, (ii) general-base-catalyzed (hydroxide and/or imidazole) deprotonation of the radical cation to yield the neutral radical, and (iii) le- oxidation of the neutral radical to the N-methylpyridinium or N-methylnicotinamide cation. Barrier heights for deprotonation of the radical cation intermediates were calculated to be 7-11 kcal/mol. Kinetic isotope effects were calculated for general-base-catalyzed deprotonation of the N-methyl-1,4-dihydropyridine radical cation and the 4,4-dideuterio species and found to be kH/kD2 = 5.38 (hydroxide) or 3.64 (imidazole), in qualitative agreement with published experimental isotope effects for the analogous deprotonation of N-methyl-1,10-dihydroacridan or the N-methyl-1,10-dideuterioacridan radical cation. In the calculated transition state for imidazole deprotonation of the N-methyl-1,4-dihydronicotinamide radical cation, an unusual short contact was calculated and interpreted as a hydrogen bond (2.35 A) between the amide oxygen and the hydrogen attached to C2 of imidazole. Similar hydrogen bonds were also observed and calculated at the 3-21G and 6-31G* levels between His234 of catalase and the amide oxygen of bound NAD(P)H and complexes of N,N'-dimethyl-1,4-dihydronicotinamide or cis-N-methylformamide with N-methylimidazole. Comparison of these results to the X-ray structure of bovine catalase allows for further interpretation of the possible roles of the imidazole bases His234 and His304 and the hydrogen-bonded contacts in the NAD(P)H binding site. Electron tunneling pathways between NAD(P)H and the iron protoporphyrin IX (PP-IX) axial tyrosinate ligand Tyr357 in molecular dynamics and X-ray crystal structures of bovine catalase were calculated using PATHWAYS II (version 2.01). The pathways which were calculated included those involving the amino acid residue Tyr214, which is near the NAD(P)H binding site. Coupling involving Tyr357 was not particularly efficient; however, strong coupling between Tyr214 and iron-protoporphyrin IX was observed. These pathways may be important if electron transfer is stepwise; i.e., Tyr214 oxidized first, followed by NAD(P)H.
An Assertional Characterization of Serializability (1989)

Serializability is usually defined operationally in terms of sequences of operations. This paper gives another definition of serializability-in terms of sequences of states. It also shows how this definition can be used to prove correctness of solutions to the concurrency control problem.
Nucleotide and deduced amino acid sequence of aMycobacterium leprae12K protein (1990)

Journal Article Nucleotide and deduced amino acid sequence of a Mycobacterium leprae 12K protein Get access Rudy A. Hartskeerl, Rudy A. Hartskeerl N.H.Swellengrebel Laboratory of Tropical Hygiene, Royal Tropical InstituteMeibergdreef 39, 1105 Amsterdam AZ, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Linda F.E.M. Stabel, Linda F.E.M. Stabel N.H.Swellengrebel Laboratory of Tropical Hygiene, Royal Tropical InstituteMeibergdreef 39, 1105 Amsterdam AZ, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Caroline J. Hermans, Caroline J. Hermans N.H.Swellengrebel Laboratory of Tropical Hygiene, Royal Tropical InstituteMeibergdreef 39, 1105 Amsterdam AZ, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Paul R. Klatser, Paul R. Klatser N.H.Swellengrebel Laboratory of Tropical Hygiene, Royal Tropical InstituteMeibergdreef 39, 1105 Amsterdam AZ, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Jelle E.R. Thole Jelle E.R. Thole N.H.Swellengrebel Laboratory of Tropical Hygiene, Royal Tropical InstituteMeibergdreef 39, 1105 Amsterdam AZ, The Netherlands Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 5, 11 March 1990, Page 1294, https://doi.org/10.1093/nar/18.5.1294 Published: 11 March 1990 Article history Received: 29 January 1990 Published: 11 March 1990
Medical Students' Exposure to Bloodborne Pathogens in the Operating Room: 15 Years Later (2008)

We compared the rates of exposure to blood in the operating room among third-year medical students during 2005-2006 with the rates reported in a study completed at the same institution during 1990-1991. The number of medical students exposed to blood decreased from 66 (68%) of 97 students during 1990-1991 to 8 (11%) of 75 students during 2005-2006 (P<.001).
Surge in regulatory cells does not prevent onset of hyperglycemia in NOD mice (2013)

Immune profiling of non-obese diabetic (NOD) is a widely employed tool to assess the mechanisms of inflammatory insulitis. Our analysis of the female NOD colony revealed similar distribution of lymphoid lineages to wild type mice, and at various ages of prediabetic and diabetic mice. The profiles of mesenteric and pancreatic lymph nodes differ and often change reciprocally due to directed migration of T cells towards the site of inflammation. Significant events in our colony include early decline in CD4(+)CD25(+)CD62L(+) Treg, accompanied by gradual increase in CD4(+)CD25(+)FoxP3(+) Treg in peripheral lymphoid organs and pancreatic infiltrates. Impressively, aged euglycemic mice display significant transient rise in CD4(+)CD25(-)FoxP3(+) Treg in the thymus, pancreas and draining lymph nodes. A significant difference was superior viability of effector and suppressor cells from new onset diabetics in the presence of high interleukin-2 (IL-2) concentrations in vitro as compared to cells of prediabetic mice. Overall, we found no correlation between FoxP3(+) Treg in the pancreatic lymph nodes and the inflammatory scores of individual NOD mice. CD25(-)FoxP3(+) Treg are markedly increased in the pancreatic infiltrates in late stages of inflammation, possibly an effort to counteract destructive insulitis. Considering extensive evidence that Treg in aged NOD mice are functionally sufficient, quantitative profiling evolves as an unreliable tool to assess mechanism and causes of inflammation under baseline conditions. Immune profiles are modulated by thymic output, cell migration, shedding of markers, proliferation, survival and in-situ evolution of regulatory cells.
Study of thermo-sensitive gel-forming properties of sucrose stearates (2010)

Sucrose esters (SEs) are biodegradable surfactants that can be manufactured in various hydrophilic-lipophilic balances (HLB), through the use of different fatty acids. They are used in foods, and in industries, such as the cosmetics, detergents and pharmaceutical industries. In aqueous media, they can form gels, which can exert effects on the various industrial processes. The modern pharmaceutical industry is currently displaying an increasing preference for biomaterials and environmentally sensitive gels, and in particular thermosensitive gels. By virtue of the non-toxic, biodegradable and gel-forming properties of SEs, they are promising materials with which to form thermosensitive delivery systems.
In this study, the gelling properties of some sucrose stearates were investigated by rheological measurements, and compared with each other. The effects of the gel-forming SEs on model drug (paracetamol) release were evaluated through in vitro drug release studies. The rheological results indicated that the sucrose stearates with lower HLB values have higher gel strengths than those of the more hydrophilic sucrose stearates. The gelling of the SEs is concentration- and temperature-dependent, and this gelling behaviour is responsible for the great effect of sucrose stearates on drug release.
Inferring translational heterogeneity from Saccharomyces cerevisiae ribosome profiling (2021)

Translation of mRNAs into proteins by the ribosome is the most important step of protein biosynthesis. Accordingly, translation is tightly controlled and heavily regulated to maintain cellular homeostasis. Ribosome profiling (Ribo-seq) has revolutionized the study of translation by revealing many of its underlying mechanisms. However, equally many aspects of translation remain mysterious, in part also due to persisting challenges in the interpretation of data obtained from Ribo-seq experiments. Here, we show that some of the variability observed in Ribo-seq data has biological origins and reflects programmed heterogeneity of translation. Through a comparative analysis of Ribo-seq data from Saccharomyces cerevisiae, we systematically identify short 3-codon sequences that are differentially translated (DT) across mRNAs, that is, identical sequences that are translated sometimes fast and sometimes slowly beyond what can be attributed to variability between experiments. Remarkably, the thus identified DT sequences link to mechanisms known to regulate translation elongation and are enriched in genes important for protein and organelle biosynthesis. Our results thus highlight examples of translational heterogeneity that are encoded in the genomic sequences and tuned to optimizing cellular homeostasis. More generally, our work highlights the power of Ribo-seq to understand the complexities of translation regulation.
Wide Temperature Range Operation of a 1.55-$\mu$m 40-Gb/s Electroabsorption Modulator Integrated DFB Laser for Very Short-Reach Applications (2009)

We present the uncooled operation of a 1.55- mum 40-Gb/s InGaAlAs electroabsorption modulator (EAM) integrated distributed-feedback (DFB) laser within a temperature range of 95degC (-15degC to 80degC ). To the best of our knowledge, this is the largest temperature range reported so far for such a 40-Gb/s EAM integrated DFB laser. We designed the EAM to operate at high speed by reducing the electrical parasitics, and we achieved a 3-dB frequency bandwidth of over 39 GHz for an EAM length of less than 150 mum. We demonstrated a 2-km single-mode fiber (SMF) transmission at 40-Gb/s over a wide temperature range of -15degC to 80degC by adjusting only the bias voltage to the EAM while keeping the modulation voltage swing constant at 2.0 V when the temperature changed. We achieved a dynamic extinction ratio of over 8.2 dB and a 2-km SMF transmission with a power penalty of less than 2 dB over a wide temperature range.
Integrating Correlation‐Based Feature Selection and Clustering for Improved Cardiovascular Disease Diagnosis (2018)

Based on the growing problem of heart diseases, their efficient diagnosis is of great importance to the modern world. Statistical inference is the tool that most physicians use for diagnosis, though in many cases it does not appear powerful enough. Clustering of patient instances allows finding out groups for which statistical models can be built more efficiently. However, the performance of such an approach depends on the features used as clustering attributes. In this paper, the methodology that consists of combining unsupervised feature selection and grouping to improve the performance of statistical analysis is considered. We assume that the set of attributes used in clustering and statistical analysis phases should be different and not correlated. Thus, the method consisting of selecting reversed correlated features as attributes of cluster analysis is considered. The proposed methodology has been verified by experiments done on three real datasets of cardiovascular cases. The obtained effects have been evaluated regarding the number of detected dependencies between parameters. Experiment results showed the advantage of the presented approach compared to other feature selection methods and without using clustering to support statistical inference.
Genomics of Aspergillus oryzae: Learning from the History of Koji Mold and Exploration of Its Future (2008)

At a time when the notion of microorganisms did not exist, our ancestors empirically established methods for the production of various fermentation foods: miso (bean curd seasoning) and shoyu (soy sauce), both of which have been widely used and are essential for Japanese cooking, and sake, a magical alcoholic drink consumed at a variety of ritual occasions, are typical examples. A filamentous fungus, Aspergillus oryzae, is the key organism in the production of all these traditional foods, and its solid-state cultivation (SSC) has been confirmed to be the secret for the high productivity of secretory hydrolases vital for the fermentation process. Indeed, our genome comparison and transcriptome analysis uncovered mechanisms for effective degradation of raw materials in SSC: the extracellular hydrolase genes that have been found only in the A. oryzae genome but not in A. fumigatus are highly induced during SSC but not in liquid cultivation. Also, the temperature reduction process empirically adopted in the traditional soy-sauce fermentation processes has been found to be important to keep strong expression of the A. oryzae-specific extracellular hydrolases. One of the prominent potentials of A. oryzae is that it has been successfully applied to effective degradation of biodegradable plastic. Both cutinase, responsible for the degradation of plastic, and hydrophobin, which recruits cutinase on the hydrophobic surface to enhance degradation, have been discovered in A. oryzae. Genomic analysis in concert with traditional knowledge and technology will continue to be powerful tools in the future exploration of A. oryzae.