Miracle-dz/UniFAR-FTUs huggingface dataset:
Goldmine integrates information placing genomic ranges into meaningful biological contexts

Bioinformatic analysis often produces large sets of genomic ranges that can be difficult to interpret in the absence of genomic context. Goldmine annotates genomic ranges from any source with gene model and feature contexts to facilitate global descriptions and candidate loci discovery. We demonstrate the value of genomic context by using Goldmine to elucidate context dynamics in transcription factor binding and to reveal differentially methylated regions (DMRs) with context-specific functional correlations. The open source R package and documentation for Goldmine are available at http://jeffbhasin.github. io/goldmine.
Lemur Tyrosine Kinase 2, a novel target in prostate cancer therapy

Progression from early forms of prostate cancer to castration-resistant disease is associated with an increase in signal transduction activity. The majority of castration-resistance cancers persist in the expression of the androgen receptor (AR), as well as androgen-dependent genes. The AR is regulated not only by it associated steroid hormone, but also by manifold regulatory and signaling molecules, including several kinases. We undertook evaluation of the role of Lemur Tyrosine Kinase 2 (LMTK2) in modulating AR activity, as several Genome Wide Association Studies (GWAS) have shown a marked association of LMTK2 activity with the development of prostate cancer. We confirm that not only is LMTK2 mRNA reduced in prostate cancer tissue, but also LMTK2 protein levels are markedly diminished. Knockdown of LMTK2 protein in prostate cell lines greatly increased the transcription of androgen-responsive genes. In addition, LMTK2 knockdown led to an increase in prostate cancer stem cell populations in LNCaP cells, indicative of increased tumorogenicity. Using multiple approaches, we also demonstrate that LMTK2 interacts with the AR, thus putting LMTK2 as a component of a signaling complex modulating AR activity. Our finding that LMTK2 is a negative regulator of AR activity defines a novel cellular pathway for activation of AR-responsive genes in castrate resistant-prostate cancer. Moreover, pharmacologic manipulation of LMTK2 activity will provide a novel therapeutic target for more effective treatments for patients with castrate-resistant prostate cancer.
The use of personalized biomarkers and liquid biopsies to monitor treatment response and disease recurrence in locally advanced rectal cancer after neoadjuvant chemoradiation

Neoadjuvant chemoradiotherapy (nCRT) followed by surgery is the mainstay treatment for locally advanced rectal cancer. Variable degrees of tumor regression are observed after nCRT and alternative treatment strategies, including close surveillance without immediate surgery, have been investigated to spare patients with complete tumor regression from potentially adverse outcomes of radical surgery. However, clinical and radiological assessment of response does not allow accurate identification of patients with complete response. In addition, surveillance for recurrence is similarly important for these patients, as early detection of recurrence allows salvage resections and adjuvant interventions. We report the use of liquid biopsies and personalized biomarkers for monitoring treatment response to nCRT and detecting residual disease and recurrence in patients with rectal cancer. We sequenced the whole-genome of four rectal tumors to identify patient-specific chromosomal rearrangements that were used to monitor circulating tumor DNA (ctDNA) in liquid biopsies collected at diagnosis and during nCRT and follow-up. We compared ctDNA levels to clinical, radiological and pathological response to nCRT. Our results indicate that personalized biomarkers and liquid biopsies may not be sensitive for the detection of microscopic residual disease. However, it can be efficiently used to monitor treatment response to nCRT and detect disease recurrence, preceding increases in CEA levels and radiological diagnosis. Similar good results were observed when assessing tumor response to systemic therapy and disease progression. Our study supports the use of personalized biomarkers and liquid biopsies to tailor the management of rectal cancer patients, however, replication in a larger cohort is necessary to introduce this strategy into clinical practice.
Optimized selection of three major EGFR-TKIs in advanced EGFR-positive non-small cell lung cancer: a network metaanalysis

Background: To answer which epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) is the best choice for advanced non-small cell lung cancer (NSCLC) EGFR mutants. Results: 16 phase III randomized trials involving 2962 advanced NSCLC EGFR mutants were enrolled. Multiple treatment comparisons showed different EGFR-TKIs shared equivalent curative effect in terms of all outcome measures among the overall, chemo-naïve and previously treated patients. Rank probabilities showed that erlotinib and afatinib had potentially better efficacy compared with gefitinib in both of the overall and chemo-naïve patients. Potentially survival benefit of erlotinib was also observed in previously treated patients compared with gefitinib. Additionally, EGFR-TKI showed numerically greater survival benefit in 19 Del compared with chemotherapy, while it was opposite in 21 L858R. Furthermore, afatinib, erlotinib and gefitinib had high, moderate and low risk of rash & diarrhea, respectively, while the occurrence of elevated liver transaminase was more common in gefitinib. Methods: Data of objective response rate (ORR), disease control rate (DCR), progression-free survival (PFS), overall survival (OS) and adverse events were extracted from included studies. Efficacy and toxicity of all included treatments were integrated by network meta-analyses. Conclusion: Our study indicated a high efficacy-high toxicity pattern of afatinib, a high efficacy-moderate toxicity pattern of erlotinib and a medium efficacy-moderate toxicity pattern of gefitinib. Recommended EGFR-TKI should be suggested according to patients' tolerability and therapeutic efficacy in clinical practice. Moreover, the treatment for advanced EGFR-positive NSCLC might be different between 19 Del and 21 L858R.
The Determination Coliforms and E. coli in Drinking Water of Van and Province

Bu calisma Van ve yoresindeki icme ve dogal kaynak sularinin koliform grubu ve Escherichia coli yonunden incelenmesi amaciyla yapildi. Bu amacla 24 dogal kaynak ve 176 sebeke suyu olmak uzere degisik yerlerden toplam 200 su ornegi toplandi. Koliform bakteri ve E. coli’nin aranmasinda membran filtrasyon teknigi kullanildi. Degisik kaynaklardan toplanan icme suyu orneklerinde % 17.5 koliform ve %10 E. coli bulundu. Sonuc olarak; incelenen icme suyu orneklerinde E. coli’nin bulunmasinin halk sagligi acisindan potansiyel bir saglik tehlikesi olusturabilecegi kanaatine varildi
Management of obesity, insulin resistance and type 2 diabetes in children: consensus and controversy

: Childhood obesity has become a national and international epidemic. The prevalence and incidence of type 2 diabetes in youth have been increasing, and type 2 diabetes is one of the most challenging complications of obesity in childhood. Comprehensive lifestyle interventions that include attention to dietary change, increased physical activity and behavior change appear to be required for the successful treatment of pediatric obesity. In particular, aspects of behavioral interventions that have been identified as contributing to effectiveness have included intensity, parent/family participation, addressing healthy dietary change, promoting physical activity, and involving behavioral management principles such as goal setting. A multidisciplinary team approach is required for successful management of type 2 diabetes in youth as well. As with many therapies in pediatrics, clinical trials and support for treatments of obesity and type 2 diabetes in youth lag behind adult data. Pediatric recommendations may be extrapolated from adult data and are often based on consensus guidelines. Type 2 diabetes in children is most commonly managed with lifestyle modification and medications, metformin and/or insulin, the only medications currently approved for use in children. However, many opportunities exist for ongoing research to clarify optimal management for obesity and type 2 diabetes in youth.
Structure-based analysis of the ultraspiracle protein and docking studies of putative ligands

The ultraspiracle protein (USP) is the insect ortholog of the mammalian retinoid X receptor (RXR). Fundamental questions concern the functional role of USP as the heterodimerization partner of insect nuclear receptors such as the ecdysone receptor. The crystallographic structures of the ligand binding domain of USPs of Heliothis virescens and Drosophila melanogaster solved recently show that helix 12 is locked in an antagonist conformation raising the question whether USPs could adopt an agonist conformation as observed in RXRα. In order to investigate this hypothesis, a homology model for USP is proposed that allows a structural analysis of the agonist conformation of helix 12 based on the sequence comparison with RXR. For USP, one of the main issues concerns its function and in particular whether its activity is ligand independent or not. The x-ray structures strongly suggest that USP can bind ligands. Putative ligands have therefore been docked in the USP homology model. Juvenile hormones and juvenile hormone analogs were chosen as target ligands for the docking study. The interaction between the ligand and the receptor are examined in terms of the pocket shape as well as in terms of the chemical nature of the residues lining the ligand binding cavity.
Urban land cover classification using polarimetric SAR interferometry

At this paper, from high resolution airborne E-SAR PolinSAR data and its statistical characteristics, Urban area land cover unsupervised classification method using polarimetric, coherence and interferometric phase differentials was proposed, and what is the role of interferometric phase differential for identification and classification of the target with vertical structure was investigated; and the potential and validation of PolinSAR data for urban area land cover identification and classification was demonstrated. The preliminary result indicates that the good classification result has been obtained, and the inclusion of interferometric phase differential significantly improved the building or man-made target identification and classification.
Machine Learning Distinguishes Neurosurgical Skill Levels in a Virtual Reality Tumor Resection Task

Background: Virtual reality simulators and machine learning have the potential to augment understanding, assessment and training of psychomotor performance in neurosurgery residents. Objective: This study outlines the first application of machine learning to distinguish"skilled"and"novice"psychomotor performance during a virtual reality neurosurgical task. Methods: Twenty-three neurosurgeons and senior neurosurgery residents comprising the"skilled"group and 92 junior neurosurgery residents and medical students the"novice"group. The task involved removing a series of virtual brain tumors without causing injury to surrounding tissue. Over 100 features were extracted and 68 selected using t-test analysis. These features were provided to 4 classifiers: K-Nearest Neighbors, Parzen Window, Support Vector Machine, and Fuzzy K-Nearest Neighbors. Equal Error Rate was used to assess classifier performance. Results: Ratios of train set size to test set size from 10% to 90% and 5 to 30 features, chosen by the forward feature selection algorithm, were employed. A working point of 50% train to test set size ratio and 15 features resulted in an equal error rates as low as 8.3% using the Fuzzy K-Nearest Neighbors classifier. Conclusion: Machine learning may be one component helping realign the traditional apprenticeship educational paradigm to a more objective model based on proven performance standards. Keywords: Artificial intelligence, Classifiers, Machine learning, Neurosurgery skill assessment, Surgical education, Tumor resection, Virtual reality simulation
Targets, methods, and sites for assessing the in-flight spatial resolution of electro-optical data products

The spatial resolution of a digital, electro-optical remote sensing imaging system or product is an important image quality characteristic that helps determine the utility of an imaging source. Although spatial resolution is often described by a single image quality parameter, the ground sample distance, there are several other parameters that affect image sharpness and need to be considered. These other parameters are associated with the point-spread function, signal-to-noise ratio, and dynamic range of the image product. This review paper covers the various approaches to in-flight measurement of spatial resolution parameters, including ground sample distance, point spread function, optical transfer function, modulation transfer function, far field response, and edge response and their significance, as well as target types and methods to determine these spatial resolution parameters. To this end, the paper lists and describes various targets found across the world, as well as astronomical ones. These targets are appropriate for evaluating a wide range of image scale products. For high spatial resolution imaging systems, the types of targets range from engineered fixed and deployable targets to agricultural and urban features, allowing almost any site to be used for determining spatial resolution. Independent, comprehensive image product evaluation sites that are currently in use in the US and Europe are also described.
Evaluating Institutional Arrangements to Support Watershed-scale Cumulative Effects Assessment in the Grand River Watershed, Canada

ii ACKNOWLEDGEMENTS . iii DEDICATIONS . iv TABLE OF CONTENTS . v LIST OF APPENDICES . viii LIST OF TABLES. ix LIST OF FIGURES . x LIST OF ABBREVIATIONS . xi CHAPTER 1: INTRODUCTION . 1 1.1 Impetus for the study . 1 1.2 The watershed as a regional basis for cumulative effects assessment . 4 1.3 Integrated water resources management frameworks and supporting science . 5 1.4 Institutional arrangements to support W-CEA . 7 1.5 Thesis organization and research products . 8 CHAPTER 2: LITERATURE REVIEW . 10 2.
Determination of the surface geostrophic velocity field from satellite altimetry

[1] Presently available marine geoid models are not accurate enough to extract the mean surface circulation directly from satellite altimetry. A novel method for estimating the mean velocity field of major ocean current systems is derived from the free surface boundary condition. With a given quasi-geostrophic balance for the horizontal surface flow, a scaling analysis of this boundary condition indicates that although the vertical velocity w is mostly balanced by the local change of the free surface, ∂η′/∂t, useful information on the mean current (, ) is contained in a small ageostrophic departure (∂η′/∂t − w). Our method consists in the development of a simple algebraic equation with two unknowns (, ) and an adjustable parameter associated with ∂η′/∂t, assuming that the latter is proportional to (∂η′/∂t − w). Most interestingly, ∂η′/∂t and all other coefficients of the equation can be determined from altimetry. The altimeter data used is combined TOPEX/Poseidon-ERS gridded data, and the solution is obtained by least squares, minimizing the contribution from the time-variable part of the parameter and prescribing the zonal direction of the mean current. The method, which is found to be particularly useful for quasi-zonal high-energy current systems, has been validated against direct observations in the Gulf Stream and Southern Ocean. Comparisons with direct observations and Monte Carlo experiments suggest an overall solution error of about 10 cm s−1. Once calibrated against regional velocity statistics, this method will be able to determine from altimetry the mean or instantaneous surface velocity field down to the frontal scale, with a realism that has been inaccessible because of the geoid constraint.
Functional Endoscopic Sinus Surgery: The Messerklinger Technique

The technique of using fiber-optic instrumentation for sinus surgery is becoming more popular. By going through the nose, there are far fewer complications than when traditional open surgical techniques were used. The authors are respected in the field of otolaryngology and this reference manual should be useful to both trainees and practitioners.
ANTIGENIC ANALYSIS OF CERTAIN GROUP B ARTHROPOD- BORNE VIRUSES BY ANTIBODY ABSORPTION BY D. H. CLARKE, M.D

As a result of intensified studies during recent years, the number of known arthropod-borne (arbor) viruses has been greatly increased. One of the most valuable pieces of knowledge which has emerged from these studies is tha t many of these arbor viruses fall into dear ly defined antigenic groups (1). Although immunologic relationships between some of them had been previously shown, the introduction of the group concept by Casals (2, 3) clarified and systematized these relationships. While cross-neutralization and complement-fixation tests are also used in establishing group relationships, the technique of hemagglutination-inhibition (HI) has provided the best method for the demonstration of antigenic relationships between members of group B and, indeed, the extent of overlap observed by H I m y be so great as to resemble the situation that exists between various strains of type A influenza. As antigenic analysis by ant ibody absorption has proved fruitful in the s tudy of the latter viruses (4-6), it was decided to apply a similar approach to an analysis of the relationship among certain group B arbor viruses. The results of some of the studies are the subject of the present paper.
Assessment and management of nutrition in older people and its importance to health

: Nutrition is an important element of health in the older population and affects the aging process. The prevalence of malnutrition is increasing in this population and is associated with a decline in: functional status, impaired muscle function, decreased bone mass, immune dysfunction, anemia, reduced cognitive function, poor wound healing, delayed recovery from surgery, higher hospital readmission rates, and mortality. Older people often have reduced appetite and energy expenditure, which, coupled with a decline in biological and physiological functions such as reduced lean body mass, changes in cytokine and hormonal level, and changes in fluid electrolyte regulation, delay gastric emptying and diminish senses of smell and taste. In addition pathologic changes of aging such as chronic diseases and psychological illness all play a role in the complex etiology of malnutrition in older people. Nutritional assessment is important to identify and treat patients at risk, the Malnutrition Universal Screening Tool being commonly used in clinical practice. Management requires a holistic approach, and underlying causes such as chronic illness, depression, medication and social isolation must be treated. Patients with physical or cognitive impairment require special care and attention. Oral supplements or enteral feeding should be considered in patients at high risk or in patients unable to meet daily requirements.
The Stanford Microarray Database: data access and quality assessment tools

The Stanford Microarray Database (SMD; http://genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investigators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools to explore and analyze those data. SMD currently provides public access to data from 3500 microarrays, including data from 85 publications, and this total is increasing rapidly. In this article, we describe some of SMD's newer tools for accessing public data, assessing data quality and for data analysis.
Near-field motion of the Haiyuan fault zone in the northeastern margin of the Tibetan plateau derived from InSAR permanent scatterers analysis

Abstract The Haiyuan fault zone is a major discontinuity in the northeastern margin of the Tibetan plateau. A magnitude 8.5 earthquake occurred there in 1920. Both geological investigations and GPS measurements show that this fault zone is still highly active, with a slip rate of 3 to 10 mm / year , exhibiting a large range of variance in both space and time. We attempt to use the permanent scatterers interferometric (PSI) synthetic aperture radar technique to better detect the near-field motion of this fault zone. We process and analyze 38 scenes of ENVISAT/ASAR images from two neighboring descending orbits using the PSI method. The results show a remarkable velocity gradient of about 5 mm / year across the central segment of the fault zone and a rate of about 5 to 6 mm / year on its eastern segment. The motion senses are consistent with a left-lateral strike slip. The motion histories of most PS points show a stable linear variation trend in time series. In addition to these motion features that agree with those from geological, GPS and other observations, the dense PS analysis also reveals spatially continuous variations of crustal motion around the fault zone.
Geological significance of middle Cambrian trilobites from near Melba Flats, western Tasmania

In western Tasmania, near Melba Flats, a basalt within the Serpentine Hill Complex is overlain unconformably by Dundas Group sediments (Hodge Slate). About 32 m above the unconformity, a siltstone contains agnostoid and polymerid trilobites that indicate correlation with the middle Cambrian Ptychagnostus punctuosus Zone (Drumian Stage of unnamed Epoch 3 of the Cambrian). This provides an upper limit of about 505.2–504.5 Ma to the emplacement of ultramafic allochthons in western Tasmania. Other fossils present include dendroids, inarticulate brachiopods, hyolithids, helcionellids and sponges. The widespread agnostoid trilobite Ptychagnostus affinis (Brøgger 1878) and the holocephalinid trilobites Meneviella and Holocephalina are recorded for the first time in Tasmania.
Evaluation of ASTER GDEM using GPS benchmarks and SRTM in China

The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Global Digital Elevation Model (GDEM) has generated one of the most complete high-resolution digital topographic data sets of the world to date. The ASTER GDEM covers land surfaces between 83° N and 83° S at a spatial resolution of 1 arc-second (approximately 30 m at the equator). As an improvement over Shuttle Radar Topography Mission (SRTM) coverage, the ASTER GDEM will be a very useful product for many applications, such as relief analysis, hydrological studies, and radar interferometry. In this article, its absolute vertical accuracy in China was assessed at five study sites using ground control points (GCPs) from high-accuracy GPS benchmarks and also using a DEM-to-DEM comparison with the Consultative Group on International Agriculture Research Consortium for Spatial Information (CGIAR-CSI) SRTM DEM Version 4.1. It is demonstrated that the vertical accuracy of ASTER GDEM is 26 m (root mean square error (RMSE)) against GPS-GCPs, while for the SRTM DEM it is 23 m. Furthermore, height differences in the GDEM-SRTM comparison appear to be overestimated in the areas with a south or southwest aspect in the five study areas. To a certain extent, the error can be attributed to variations in heights due to land-cover effects and undefined inland waterbodies. But the ASTER GDEM needs further error-mitigating improvements to meet the expected accuracy specification. However, as for its unprecedented detail, it is believed that the ASTER GDEM offers a major alternative in accessibility to high-quality elevation data.