gebhart/patrepeval huggingface dataset:
Genetic Alterations and Personalized Medicine in Melanoma: Progress and Future Prospects (2014)

High-throughput sequencing technologies are providing new insights into the genetic alterations involved in melanomagenesis. It appears likely that most genetic events important in the pathogenesis of melanoma will be discovered over the next few years. Genetic analysis is also increasingly being used to direct patient care. In parallel with the discovery of new genes and the elucidation of molecular pathways important in the development of melanoma, therapies targeting these pathways are becoming available. In other words, the age of personalized medicine has arrived, characterized by molecular profiling of melanoma to identify the relevant genetic alterations and the abnormal signaling mechanisms involved, followed by selection of optimal, individualized therapies. In this review, we summarize the key genetic alterations in melanoma and the development of targeted agents against melanomas bearing specific mutations. These developments in melanoma serve as a model for the implementation of personalized medicine for patients with all cancers.
Visual representation of construction progress monitoring metrics on time-lapse photographs (2007)

Low cost progress data collection technique for construction project using time-lapse photography or real-time videotaping can provide a wealth of spatial and temporal information for progress data collection. The benefits of using photographs would be maximized if the progress deviations between planned and actual (as-built) performance are visually shown on these photographs. The importance of such visual representation of construction progress is well understood when the participation of diverse parties with different levels of expertise (from owners to subcontractors) is considered. Current formats of monitoring reports (e.g. textual progress reports, progress graphs or charts) may not properly and quickly communicate progress situations and would make understanding of progress situation difficult. Current methods of monitoring require manual data collection and extensive data extraction from construction documents making progress monitoring a time-consuming process and distracts managers from the important task of decision making. As an effort to address this issue, a visual representation of construction progress is proposed that aims to picture the progress situation on time-lapse photographs (representing actual progress), superimpose the planned progress (obtained from the 4D as-planned model), and provide the clear comparison in an augmented reality environment between as-planned and as-built progress. A series of visualization techniques (e.g. colour and colour gradient) is developed to communicate and visualize detected discrepancies and progress performance metrics. Schedule deviations, construction sequence, budget distribution and earned value analysis metrics (cost performance and schedule performance indexes) are also visualized. These techniques if automated could accurately and quickly communicate progress situation on photographs and provides a powerful tool for prompt progress control decision making.
Holographic SAR Tomography 3-D Reconstruction Based on Iterative Adaptive Approach and Generalized Likelihood Ratio Test (2020)

Holographic synthetic aperture radar (HoloSAR) tomography is an attractive imaging mode that can retrieve the 3-D scattering information of the observed scene over 360° azimuth angle variation. To improve the resolution and reduce the sidelobes in elevation, the HoloSAR imaging mode requires many passes in elevation, thus decreasing its feasibility. In this article, an imaging method based on iterative adaptive approach (IAA) and generalized likelihood ratio test (GLRT) is proposed for the HoloSAR with limited elevation passes to achieve super-resolution reconstruction in elevation. For the elevation reconstruction in each range-azimuth cell, the proposed method first adopts the nonparametric IAA to retrieve the elevation profile with improved resolution and suppressed sidelobes. Then, to obtain sparse elevation estimates, the GLRT is used as a model order selection tool to automatically recognize the most likely number of scatterers and obtain the reflectivities of the detected scatterers inside one range-azimuth cell. The proposed method is a super-resolving method. It does not require averaging in range and azimuth, thus it can maintain the range-azimuth resolution. In addition, the proposed method is a user parameter-free method, so it does not need the fine-tuning of any hyperparameters. The super-resolution power and the estimation accuracy of the proposed method are evaluated using the simulated data, and the validity and feasibility of the proposed method are verified by the HoloSAR real data processing results.
Bacterial bioinformatics: pathogenesis and the genome. (2002)

As the number of completed microbial genome sequences continues to grow, there is a pressing need for the exploitation of this wealth of data through a synergistic interaction between the well-established science of bacteriology and the emergent discipline of bioinformatics. Antibiotic resistance and pathogenicity in virulent bacteria has become an increasing problem, with even the strongest drugs useless against some species, such as multi-drug resistant Enterococcus faecium and Mycobacterium tuberculosis. The global spread of Human Immunodeficiency Virus (HIV) and Acquired Immune Deficiency Syndrome (AIDS) has contributed to the re-emergence of tuberculosis and the threat from new and emergent diseases. To address these problems, bacterial pathogenicity requires redefinition as Koch's postulates become obsolete. This review discusses how the use of bacterial genomic information, and the in silico tools available at present, may aid in determining the definition of a current pathogen. The combination of both fields should provide a rapid and efficient way of assisting in the future development of antimicrobial therapies.
Improving deep learning model performance under parametric constraints for materials informatics applications (2023)

Modern machine learning (ML) and deep learning (DL) techniques using high-dimensional data representations have helped accelerate the materials discovery process by efficiently detecting hidden patterns in existing datasets and linking input representations to output properties for a better understanding of the scientific phenomenon. While a deep neural network comprised of fully connected layers has been widely used for materials property prediction, simply creating a deeper model with a large number of layers often faces with vanishing gradient problem, causing a degradation in the performance, thereby limiting usage. In this paper, we study and propose architectural principles to address the question of improving the performance of model training and inference under fixed parametric constraints. Here, we present a general deep-learning framework based on branched residual learning (BRNet) with fully connected layers that can work with any numerical vector-based representation as input to build accurate models to predict materials properties. We perform model training for materials properties using numerical vectors representing different composition-based attributes of the respective materials and compare the performance of the proposed models against traditional ML and existing DL architectures. We find that the proposed models are significantly more accurate than the ML/DL models for all data sizes by using different composition-based attributes as input. Further, branched learning requires fewer parameters and results in faster model training due to better convergence during the training phase than existing neural networks, thereby efficiently building accurate models for predicting materials properties.
Structural elucidation of the 3-deoxy-D-manno-octulosonic acid containing meningococcal 29-e capsular polysaccharide antigen using carbon-13 nuclear magnetic resonance (1978)

The capsular polysaccharide antigen from Neisseria meningitidis serogroup 29-e contains equimolar quantities of 2-acetamido-2-deoxy-D-galactose and 3-deoxy-D-manno-octulosonic acid (KDO), the latter of which is rarely found in biopolymers other than lipopolysaccharides. Carbon-13 nuclear mangetic resonance in conjunction with other chemical data indicated that the polysaccharide is composed of an alternating sequence of these two residues, the linkages being at C-3 of galactosamine and C-7 of KDO in the alpha-D and beta-D configuration, respectively. The native 29-e polysaccharide is O-acetylated, the O-acetyl groups being located at C-4 and C-5 of the KDO residues. Assignments of signals in the 13C nuclear magnetic resonance spectrum of the 29-e polysaccharide were made by consideration of those in the spectra of the monomer models, which necessitated the first recorded syntheses of methyl-alpha- and beta-D-3-deoxy-manno-octulopyranosonic acid. Like the methyl alpha- and beta-D-ketosides of sialic acid (Na+ salts), the equivalent methyl alpha- and beta-D-ketosides of KDO exhibit large chemical shift differences in the exocyclic C-8 position dependent on anomeric configuration. This can again be attributed to hydrogen bonding between the axial carboxylate group of the methyl beta-D anomer of KDO (C1 conformation) and the primary hydroxyl group at C-8. This phenomenon is also exhibited by the beta-D-linked KDO units of the 29-e polysaccharide.
Teratogenic Actions of Thermally-stressed Culinary Oils in Rats (2002)

Lipid oxidation products (LOPs), generated in culinary oils during episodes of thermal stressing can give rise to cellular damage. The aims of this study were to determine whether orally-administered, LOP-containing thermally-stressed safflower oil exerts teratogenic actions in rats, and whether this effect could be prevented by co-administration of alpha-tocopherol (alpha-TOH). Safflower oil was heated for a period of 20 min according to standard frying practices and stored at -20 degrees C under N2. Four experimental groups of pregnant Wistar rats were employed; two received 0.30 ml of pre-heated oil (HO), one of which was also supplemented with 150 mg of alpha-TOH (HOE), and two served as controls, one treated with the non-heated oil (O) and the other without any treatment (C). The oil was administered daily by gavage from day 1 of pregnancy to day 11.5, when the animals were killed and the embryos examined. LOPs and alpha-TOH were determined both in the heated and non-heated oils. The percentage of embryo malformations and reabsorptions were determined in the above four experimental groups. Heating the oil substantially increased its concentration of LOPs and decreased its alpha-TOH content. The percentage of embryo malformations in the HO group was 21.73%, compared with 5.6 and 7% in the O and C groups, respectively. Supplementation of the pre-heated oil with alpha-TOH was found to decrease the percentage of malformations to 7%. The results obtained from these investigations indicate that LOPs detectable at millimolar levels in the heated cooking oils administered (e.g. saturated and alpha,beta-unsaturated aldehydes, and/or their conjugated hydroperoxydiene precursors) exert potent teratogenic actions in experimental animals which are at least partially circumventable by co-administration of the chain-breaking antioxidant alpha-TOH. Plausible mechanisms for these processes and their health relevance to humans regarding diet and methods of frying/cooking are discussed.
Leg Lengthening With a Motorized Nail in Adolescents (2008)

Level IV Therapeutic study.
208-LB: Plasma Lipidomics Reveals Sex-Specific Associations with? Brown Adipose Tissue in Asian Children (2023)

Brown adipose tissue (BAT) plays a crucial role in lipid metabolism. Activated BAT oxidizes fatty acids from triglycerides in lipid droplets during thermogenesis, increasing energy expenditure. The lipidomic profile of BAT has been primarily studied in animals but little in humans. We sought to identify the plasma lipidomic profile associated with BAT in a thermoneutral condition in 6-year-old children (n=134) in the Growing Up in Singapore Towards healthy Outcomes (GUSTO) cohort. LC-MS/MS-based quantification of 480 lipids was performed on plasma samples; %BAT was quantified based on fat-signal-fractions of water-fat-MRI. Associations between plasma lipids and the child's %BAT were investigated using multivariate regression analysis adjusting for sex, ethnicity, and BMI. Sex stratification was applied to investigate the sex-specific lipid signatures of %BAT among the 68 boys and 66 girls. The inverse association between %BAT and BMI was stronger in boys (R2 =0.28) than in girls (R2 =0.07). More lipid signatures of %BAT were observed in boys compared to girls; of 63 unique lipid species significantly associated with %BAT, 12 were associated in both genders, 50 in boys and 11 in girls. In boys, lipid species representing triacylglycerol, cholesteryl ester, acylcarnitine, sphingomyelin, ceramide, hexosylceramides and lysophosphatidylcholine classes showed negative associations with %BAT, whereas several phosphatidylethanolamine lipids displayed positive association with %BAT. In girls, opposite trends in effect sizes (R=-0.44) were, however, observed; several lipids in acylcarnitine, diacylglycerol and sphingolipid classes presented positive association with %BAT, while phosphatidylethanolamine lipids showed negative associations with %BAT. These unique associations between plasma lipid species and BAT in a sex-specific manner provide insights into the different potential lipidomic pathways involved in BAT energy metabolism. Disclosure M. Tint: None. M. Fortier: None. K. Godfrey: Other Relationship; See box. M. Wenk: None. J. Eriksson: None. L. Chen: None. N. Kothandaraman: None. M. K. Leow: None. B. Kn: None. F. Yap: None. Y. Lee: None. E. H. Tham: None. Y. Chong: None. Funding Open Fund Large-Collaborative Grant (000504)
Endonasal Frontal Sinusotomy in Surgical Management of Chronic Sinusitis: A Critical Evaluation (1997)

Frontal sinusotomy was performed on 110 patients undergoing routine endoscopic endonasal ethmoidectomy and the minimum diameter of the frontal sinus neo-ostium was determined intraoperatively. A total of 82 patients could be subjected to follow-up and redetermination of the neo-ostium diameter 13 months later. A postoperative CT was scheduled in 62 cases. The average minimum diameter of the frontal sinus neo-ostium, measured intraoperatively, was 5.6 mm (0-11 mm). After completion of wound healing, 81% of the frontal sinuses could be explored by probing or even inspected by rigid endoscopy. The average minimum diameter of the neo-ostia determined postoperatively was 3.5 mm (0-11 mm). Patients exhibiting aspirin sensitivity or diffuse nasal polyposis showed a more pronounced scarred constriction of the frontal sinus access compared to other cases. Neo-ostia exceeding 5 mm intraoperatively were preserved with a considerably higher percentage than those with diameters of less than 5 mm. Radiologically, the fenestrated frontal sinuses frequently showed continued or even increasing mucosal congestion. No conclusive relationship was found to exist between such post-operative clouding and frontal sinus accessibility (endoscopy and/or probing) or patient complaints. The investigations confirm the safety and reliability of frontal sinusotomy in surgical management of chronic paranasal sinusitis. The mucosa of the frontal sinus often reacts to surgery in the form of persistent or even newly developing mucosal swelling to which a specific pathophysiological significance cannot always be attributed.
Indole-Diterpene Biosynthetic Capability ofEpichloeEndophytes as Predicted byltmGene Analysis (2009)

Bioprotective alkaloids produced by Epichloë and closely related asexual Neotyphodium fungal endophytes protect their grass hosts from insect and mammalian herbivory. One class of these compounds, known for antimammalian toxicity, is the indole-diterpenes. The LTM locus of Neotyphodium lolii (Lp19) and Epichloë festuce (Fl1), required for the biosynthesis of the indole-diterpene lolitrem, consists of 10 ltm genes. We have used PCR and Southern analysis to screen a broad taxonomic range of 44 endophyte isolates to determine why indole-diterpenes are present in so few endophyte-grass associations in comparison to that of the other bioprotective alkaloids, which are more widespread among the endophtyes. All 10 ltm genes were present in only three epichloë endophytes. A predominance of the asexual Neotyphodium spp. examined contained 8 of the 10 ltm genes, with only one N. lolii containing the entire LTM locus and the ability to produce lolitrems. Liquid chromatography-tandem mass spectrometry profiles of indole-diterpenes from a subset of endophyte-infected perennial ryegrass showed that endophytes that contained functional genes present in ltm clusters 1 and 2 were capable of producing simple indole-diterpenes such as paspaline, 13-desoxypaxilline, and terpendoles, compounds predicted to be precursors of lolitrem B. Analysis of toxin biosynthesis genes by PCR now enables a diagnostic method to screen endophytes for both beneficial and detrimental alkaloids and can be used as a resource for screening isolates required for forage improvement.
Optimal sizing of permanent magnet synchronous machine for a given profile for hybrid application (2014)

International audience
Optimal Frequency-Reuse Partitioning For Ubiquitous Coverage In Cellular Systems (2008)

Publication in the conference proceedings of EUSIPCO, Lausanne, Switzerland, 2008
Overexpression of gamma-Glutamyl Cyclotransferases 2;1 (CsGGCT2;1) Reduces Arsenic Toxicity and Accumulation in Camelina sativa (L.) (2023)

Environmental arsenic contamination adversely affects human health, and its accumulation diminishes food quality. Glutathione (GSH) is known to bind and detoxify arsenic and other toxic metals. GSH homeostasis in living cells is maintained via γ-glutamyl cycle. Previously, γ-glutamyl cyclotransferases ( GGCT s) have been shown to be involved in GSH degradation in plants and increasing tolerance to toxic metals. Here we characterized the GGCT2;1 homolog from Camelina sativa for its role in arsenic tolerance and accumulation. Overexpressing CsGGCT2;1 in Camelina resulted in strong tolerance to arsenite (AsIII). Compared to wild-type, overexpression (OE) lines had significantly higher shoot (2.6-3.5-fold) and root (7-10-fold) biomass on AsIII containing media and accumulated 40-60% less arsenic in root and shoot tissues. Further, OE lines had higher chlorophyll content, lower lipid peroxidation and oxidative stress. There was a small but nonsignificant increase in 5-oxoproline (5-OP) in OE lines and the upregulation of Oxoprolinase 1 ( OXP1 ) suggested accelerated conversion of 5-OP to glutamate, which is then utilized for GSH resynthesis for maintaining homeostasis. Overall, overexpression of GGCT2;1 and it homologs in Camelina and other crops will enable their cultivation on contaminated marginal lands to reduce As accumulation, addressing food safety issues as well as future food and biofuel needs.
Simulation input analysis: difficulties in simulating queues with Pareto service (2002)

M/G/1 queues, where G is a heavy-tailed distribution, have applications in Internet modeling and modeling for insurance claim risk. The Pareto distribution is a special heavy-tailed distribution called a power-tailed distribution, and has been found to serve as adequate models for many of these situations. However, to get the waiting time distribution, one must resort to numerical methods, e.g., simulation. Many difficulties arise in simulating queues with Pareto service and we investigate why this may be so. Even if we are willing to consider truncated Pareto service, there still can be problems in simulating if the truncation point (maximum service time possible) is too large.
A hybrid registration method for outdoor augmented reality (2002)

A registration method for outdoor wearable AR systems is described. Our approach is based on using a high precision gyroscope, which can measure 3DOF angle of head direction accurately, but with some drift error. We solved the drift problem with a vision-based drift compensation algorithm, which tracks natural features in the outdoor environment as landmarks from images captured by a camera on an HMD. The paper first describes the detail of the vision-based drift compensation method. Then, a calibration method for the orientation sensor is proposed. Finally, using results from an actual wearable AR system, a comparison of registration error with and without vision-based drift compensation demonstrates the feasibility of the proposed method.
Methanol as a hydrate inhibitor and hydrate activator (2018)

During their transport to processing plants, produced hydrocarbon streams are always accompanied by water appearing as a separate phase in contact with the hydrocarbons. Dramatic temperature and pressure changes during processing can lead to condensation of water and possibly hazardous formation of ice and hydrates. Historically, methanol has been the dominating chemical agent added to prevent the formation of solid water phases. In this work, the technique of molecular dynamics simulation has been utilized to investigate and illustrate the impact of methanol as a surfactant in a water-methane system. We have found that adding 5% of methanol boosted the diffusion of methane through the interface by more than 40% compared to the reference system. The amount of methane accumulated in the aqueous phase was also significantly higher. This effect will likely also result in a significant increase in homogeneous and heterogeneous hydrate formation in these regions in the case of the methanol-stimulated system, and thus necessitate the application of classical nucleation theory. In particular, our analysis emphasised the fact that several different hydrates may form in this scenario. In case of the homogeneous hydrate formation, there will theoretically exist an infinite number of hydrate phases corresponding to concentrations spanning the range between methane's solubility and its hydrate stability limit.