Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthesis and Characterization of Anti-HER2 Antibody Conjugated CdSe/CdZnS Quantum Dots for Fluorescence Imaging of Breast Cancer Cells

The early detection of HER2 (human epidermal growth factor receptor 2) status in breast cancer patients is very important for the effective implementation of anti-HER2 antibody therapy. Recently, HER2 detections using antibody conjugated quantum dots (QDs) have attracted much attention. QDs are a new class of fluorescent materials that have superior properties such as high brightness, high resistance to photo-bleaching, and multi-colored emission by a single-light source excitation. In this study, we synthesized three types of anti-HER2 antibody conjugated QDs (HER2Ab-QDs) using different coupling agents (EDC/sulfo-NHS, iminothiolane/sulfo-SMCC, and sulfo-SMCC). As water-soluble QDs for the conjugation of antibody, we used glutathione coated CdSe/CdZnS QDs (GSH-QDs) with fluorescence quantum yields of 0.23∼0.39 in aqueous solution. Dispersibility, hydrodynamic size, and apparent molecular weights of the GSH-QDs and HER2Ab-QDs were characterized by using dynamic light scattering, fluorescence correlation spectroscopy, atomic force microscope, and size-exclusion HPLC. Fluorescence imaging of HER2 overexpressing cells (KPL-4 human breast cancer cell line) was performed by using HER2Ab-QDs as fluorescent probes. We found that the HER2Ab-QD prepared by using SMCC coupling with partially reduced antibody is a most effective probe for the detection of HER2 expression in KPL-4 cells. We have also studied the size dependency of HER2Ab-QDs (with green, orange, and red emission) on the fluorescence image of KPL-4 cells.
Mapping of quantitative trait loci associated with size, shape, and parr mark traits using first and second generation backcrosses between European and North American Atlantic salmon (<i>Salmo salar</i>)

1 Mapping of quantitative trait loci associated with size, shape, and parr mark traits using 1 first and second generation backcrosses between European and North American Atlantic 2 salmon (Salmo salar). 3 4 Stephanie Pedersen, Lei Liu, Brian Glebe, Steven Leadbeater, Sigbjørn Lien, and Elizabeth 5 G. Boulding 6 7 Department of Integrative Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1 8 Department of Fisheries and Oceans Canada, St. Andrews Biological Station, St. Andrews, NB, 9 Canada, E5B 2L9 10 Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, 11 Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, N-1432 Ås, 12 Norway 13 4 Present address: School of Marine Sciences, Ningbo University, 818 Fenghua Road, Ningbo 14 315211, China 15 16 *Corresponding author: Tel. : +1 (519) 824-4120 extension: 54961; fax: +1 (519) 767-1656; E17 mail address: boulding@uoguelph.ca 18 19 Running title: Mapping of QTL in TransAtlantic Salmon Crosses 20 21 Word count: 6552 without abstract or references 22
Optimizing streaming graph partitioning via a heuristic greedy method and caching strategy

ABSTRACT Graph partitioning is an important method for accelerating large distributed graph computation. Streaming graph partitioning is more efficient than offline partitioning, and it has been developed continuously in the application of graph partitioning in recent years. In this work, we first introduce a heuristic greedy streaming partitioning method and show that it outperforms the state-of-the-art streaming partitioning methods, leading to exact balance and fewer cut edges. Second, we propose a cache structure for streaming partitioning, called an adjacent edge structure, which can improve the partition efficiency several times on a single commodity type computer without affecting the partition quality. Regardless as to whether the memory capacity is limited (local cache) or not (global cache), our strategy can also improve the partition quality by restreaming partitioning. Taking linear weight greedy streaming algorithm as an example, the experimental results on 19 real-world graphs show that the average partitioning time of the new method is 4.9 times faster than that of the original method, which proves the effectiveness and superiority of the cache structure mentioned in this paper.
University of Dundee A genome wide association scan for ( 1 , 3 ; 1 , 4 )-- glucan content in the grain of contemporary 2-row Spring and Winter barleys

Background: (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed above recommended threshold levels. This leads to diametrically opposed quality requirements for different applications as low levels of (1,3;1,4)-β-glucan are required for brewing and distilling and high levels for positive impacts on human health. Results: We quantified grain (1,3;1,4)-β-glucan content in a collection of 399 2-row Spring-type, and 204 2-row Winter-type elite barley cultivars originating mainly from north western Europe. We combined these data with genotypic information derived using a 9 K Illumina iSelect SNP platform and subsequently carried out a Genome Wide Association Scan (GWAS). Statistical analysis accounting for residual genetic structure within the germplasm collection allowed us to identify significant associations between molecular markers and the phenotypic data. By anchoring the regions that contain these associations to the barley genome assembly we catalogued genes underlying the associations. Based on gene annotations and transcript abundance data we identified candidate genes. Conclusions: We show that a region of the genome on chromosome 2 containing a cluster of CELLULOSE SYNTHASE-LIKE (Csl) genes, including CslF3, CslF4, CslF8, CslF10, CslF12 and CslH, as well as a region on chromosome 1H containing CslF9, are associated with the phenotype in this germplasm. We also observed that several regions identified by GWAS contain glycoside hydrolases that are possibly involved in (1,3;1,4)-β-glucan breakdown, together with other genes that might participate in (1,3;1,4)-β-glucan synthesis, re-modelling or regulation. This analysis provides new opportunities for understanding the genes related to the regulation of (1,3;1,4)-β-glucan content in cereal grains.
Environmental monitoring of the St.Petersburg region using ERS data (AO2. No 109)

The work has been dedicated to some preliminary results of the Project ESA A02. No. 109 Pilot Demonstrations of Environmental Information Retrieval from the ERS Sensors for Monitoring of the St.Petersburg Region. This is a multi-disciplinary research project with a wide scientific scope. Besides, it is a part of a long-term program - The St.Petersburg Region's Environment Monitoring System Development.
Rationale and development of image-guided intensity-modulated radiotherapy postprostatectomy: the present standard of care?

: The indications for post-prostatectomy radiotherapy have evolved over the last decade, although the optimal timing, dose, and target volume remain to be well defined. The target volume is susceptible to anatomical variations with its borders interfacing with the rectum and bladder. Image-guided intensity-modulated radiotherapy has become the gold standard for radical prostate radiotherapy. Here we review the current evidence for image-guided techniques with intensity-modulated radiotherapy to the prostate bed and describe current strategies to reduce or account for interfraction and intrafraction motion.
A Direct Discontinuous Galerkin Method with Interface Correction for the Compressible Navier-Stokes Equations on Unstructured Grids

Since the original DDG method has been introduced by Liu et al. [8] in 2009, a variety of DDG type methods have been proposed and further developed. In this paper, we further investigate and develop a new DDG method with interface correction (DDG (IC)) as the discretization of viscous and heat fluxes for the compressible Navier-Stokes equations on unstructured grids. Compared to the original DDG method, the newly developed DDG (IC) method demonstrates its superior in delivering the optimal order of accuracy under demanding situations. Strategies in extension and application of this newly developed DDG (IC) method for solving the compressible Navier-Stokes equations and special treatments designed for handling boundary viscous fluxes are presented and examined in this work. The performance of the new DDG method with interface correction is carefully evaluated and assessed through a number of typical test cases. Numerical experiments show that the new DDG method with interface correction can achieve the optimal order of accuracy on both uniform structured grids and nonuniform unstructured grids, which clearly indicates its potential for further applications of real engineering practices. AMS subject classifications: 65M60, 76N15
Launching Global Health: The Caribbean Odyssey of the Rockefeller Foundation

This is an in-depth look at the Rockefeller Foundation's earliest ventures in international health. From the Rockefeller Foundation to the Bill and Melinda Gates Foundation, U.S. philanthropies have played a leading role in the evolution of international health. "Launching Global Health" is about the Rockefeller Foundation's very first initiative abroad. The foundation's flagship, the International Health Board, made its first call in British Guiana in March 1914 to experiment with its new 'American Method' for the treatment of hookworm disease. Within months the agency was involved in ambitious hookworm programs in six Central American and Caribbean sites, its directors self-consciously choosing to test-run the prototype for their global project in the nearest and clearest domain of American imperial influence. This book examines the nature and evolution of those hookworm campaigns in British Guiana, Costa Rica, Trinidad, and Guatemala, as well as relevant evidence from Nicaragua and Panama. The study takes into account the late 19th-century backdrop and considers events through to about 1930 when most of the International Health Board hookworm campaigns had evolved into public health projects of a different nature.
On the robustness of tropospheric adjustment in CMIP5 models

Effective radiative forcing associated with the tropospheric adjustment (TA) caused by atmospheric CO2 quadrupling (4×CO2) is quantified using fixed sea surface temperature experiments in CMIP5 models. Several features of TA in the tropics, partly related to weakening of the hydrological cycle, are found robust among the models: warming and drying of the free troposphere, near‐surface moistening, strengthened stability in the lower troposphere, reduction in total cloud amount and shortwave cloud radiative effect (SWcld) over oceans. A positive SWcldchange prevailing in the tropical subsidence regime gives rise to large uncertainty in total effective radiative forcing, and is regulated quantitatively by changes in relative humidity (RH) that measure cloud decrease in the lower troposphere. A robust tropospheric warming primarily explains the RH decrease in the lower troposphere, but the change in specific humidity is largely model‐dependent, which contributes to the inter‐model spread of TA.
Stochastic Discount Factor Approach to International Risk-Sharing:A Robustness Check of the Bilateral Setting

This paper presents a robustness check of the stochastic discount factor approach to international (bilateral) risk-sharing given in Brandt, Cochrane, and Santa-Clara (2006). We demonstrate two main inherent limitations of the bilateral SDF approach to international risk-sharing. First, the discount factors are not uniquely determined in the bilateral framework and crucially depend on the partner country included in the calculations. Second, the deviations between the discount factors obtained in this way (the imprecision in the measurement of marginal utility growth) are larger for countries whose stock market excess return shocks are relatively less important. In order to account for some of these criticisms, we extend the bilateral into a three-country setting. Although the trilateral framework demonstrates that the (final) results for the international risk-sharing index are quite robust to the number of countries used in their calculation, it does not resolve the inherent incoherence found in the bilateral SDF approach.
MODEL BASED WHEAT YIELD ESTIMATION IN THE PUNJAB, PAKISTAN

In time yield estimation of a crop is essential for the economy of a country.It is also important for planners to have an accurate and precise estimate of a crop and this especially important when the crop is insufficient to meet the demand of the country.As among all the crops, wheat is the most important staple food of Pakistan, so the most of government agricultural polices are wheat oriented.Pakistan faced a very serious shortage of wheat and in the late 2007 and this created a serious challenge to law and order. The prime objective of this research is to build a statistical model in a scientific way, using all available ground information, so that a good and reliable estimate of wheat crop can be achieved at least two months prior to the arrival of actual production of the crop.Also a comprehensive descriptive study has been conducted regarding the wheat production in the Punjab taking various dimensions of explanatory variables. In the detailed descriptive study, impact of irrigated / un-irrigated areas, sowing time, fertilizers, pesticides spray, seed quantity, number of water (number of turns same amount of water is supplied to one acre of wheat on different times during the whole growing season of the crop), number of plough, number of level (number of turns ground level of the field is smoothened for even distribution of water throughout the field and for moisture conservation) , seasonal rainfall, seasonal humidity level, maximum / minimum average temperature of the season and also different combination of these variables on the quantity of yield of the crop has been examined, which has revealed many folded dimensions. A new methodology titled as ‘Weighted Rainfalls’ is created to develop a stronger relationship between yield of wheat and seasonal rainfalls because rainfalls of different months of Rabi season have varying impact on the final yield of wheat, which leads to the need of weighted rainfalls.The concept of weighted rainfalls verified very effective in estimation of wheat production through the statistical model.Different criteria like MSE, AIC and SIC for competing models have also supported that estimates of wheat using weighted rainfalls concept are better than the estimates using total rainfalls of the season. After the development of the model, its validity has been examined through different confirmation runs.All validity runs also have supported that the developed model is working properly and can be used as general wheat’s model for its projection in any year.This concept can be easily extended for other crops using weighted rainfall pattern for that crop.As, this study is based on the sample data taken from the whole province, so a method of unequal probability sampling using more than one measure of sizes has also been proposed for the sake of an improvement in the sample selection of villages giving priorities to more than one parameter of interest. Obviously a suitable sample of villages having a reasonable representation of all the major surveyed crops of the province will ultimately give a good estimate of a crop.
Design and in-vitro/in-vivo evaluation in colon cancer cells of targeted oxaliplatin liposomes to epidermal growth factor receptor by conjugation of different ligands

The colorectal cancer (CRC) is one of the main cancers diagnosed in the first world. Oxaliplatin is currently in the first therapeutic line for metastatic CRC treatment. This drug presents a good tolerability and low toxicity in patients. However, it shows a high and irreversible binding to erythrocytes and plasma proteins leading to a low free drug. This active fraction is rapidly cleared from plasma by covalent binding to tissues and renal elimination. These characteristics provide a low antitumor efficacy to oxaliplatin in monotherapy. On the other hand, nanotechnology is a strategy that has proved to modulate the pharmacokinetic properties of several encapsulated drugs. In this field, liposomes, considered as a biocompatible particle system with low toxicity and dynamism, allow the encapsulation of different types of agents, including platinum derivatives. In the last few years advanced strategies in these kind of carriers have been applied. One of them consist in the coupling of several ligands on the surface of the liposome to target specific receptors or antigens expressed in the tumor cell. In this way, the Epidermal Growth Factor Receptor (EGFr) implicated in the cellular proliferation process, is one of the receptor over-expressed in CRC. To inhibit its activity, several approaches with biomolecules like monoclonal antibodies (mAb) are currently used in clinic. Cetuximab is a mAb combined with other chemotherapeutic drugs, as oxaliplatin in CRC treatment. Therefore, the aim of the work was the development of EGFr targeted oxaliplatin liposomes using Cetuximab or its Fab? fragment as specific ligands. Based on that objective, several types of lipids and methods were evaluated to finally select the Film method and the lipid composition HSCP:CH:DSPE-PEG2000, to develop oxaliplatin liposomes with adequate particle size, efficiency of encapsulation and stability in in-vitro studies. In addition, the in-vivo experiments showed a greater antitumor efficacy for liposomes than for the free oxaliplatin. In the second step, this liposomal formulation was conjugated with Cetuximab and Fab? using the conventional method for the coupling. The cell uptake of these targeted formulations in EGFr positive cell lines was higher than for non-targeted liposomes. The role of the receptor was evaluated by a pre-treatment with Cetuximab which caused its inhibition. In fact, the uptake was dramatically decreased, supporting the targeted receptor of these formulations. According to these results, the targeted formulations were able to reduce statistically the tumor growth of an EGFr positive cell line inoculated in mice, in comparison with non-targeted liposomes or the free drug. Between targeted liposomes, the greater efficacy was observed for Fab? -formulation. In conclusion, EGFr targeted liposomes of oxaliplatin seem to be a promising strategy to improve the free drug activity.
Texture-based Probability Mapping in cardiac LGE images: A novel automatic assessment of myocardial injury following revascularized STEMI.

Background: Scar size is critical to left ventricular (LV) remodeling and adverse outcomes following myocardial infarction (MI). Late Gadolinium-enhancement (LGE) in cardiac magnetic resonance imaging is the gold standard for assessing MI size. Texture-based probability mapping (TPM) is a novel machine learning-based analysis of LGE images. This proof-of-concept study investigates the potential clinical implications of temporal changes in TPM during the first year following an acute revascularized MI. Methods: 41 patients with first-time acute ST-elevation MI were included in this study. All patients had a single-vessel disease and were successfully revascularized by primary percutaneous coronary intervention. LGE images were obtained two days, one week, two months, and one year post-MI. MI size by TPM was compared with manual LGE-based MI calculation, LV remodeling, and biomarkers. Results: TPM showed a significant increase in infarct size from the second month through the first year (p<0.01). MI size estimated by TPM at all different time points demonstrated strong correlations with peak Troponin T levels. At one week, TPM assessment correlated positively with maximum C-reactive protein (r=0.54, p<0.01), and at two months, TPM positively correlated with N-Terminal Pro Brain Natriuretic Peptide. Conclusion: This proof-of-concept study suggests that TPM may provide additional information to conventional LGE-based MI analysis of scar formation, LV remodeling, and biomarkers following an acute revascularized MI.
Dose-Response Relationships between Physical Exercises and Mental Health during Early Adolescence: an Investigation of the Underlying Neural and Genetic Mechanisms from the ABCD Study

Adolescence is a critical developmental with increased vulnerability to mental disorders. While the positive impact of physical exercise on adult mental health is well-established, dose-response relationships and the underlying neural and genetic mechanisms in adolescents remain elusive. Leveraging data from >11,000 pre-adolescents (9-10 years, ABCD Study) we examined associations between seven different measures of exercise dosage across 15 exercises and psychopathology, and the roles of brain function and structure and psychiatric genetic risks. Five specific exercises (basketball, baseball/softball, soccer, football, and skiing) were associated with better mental health while the beneficial effects varied with exercise types, dosage measures and dimensions of psychopathology. Interestingly, more exercise does not always translate to better mental health whilst earlier initiation was consistently advantageous. Communication between attention and default-mode brain networks mediated the beneficial effect of playing football. Crucially, exercise mitigates the detrimental effects of psychiatric genetic risks on mental health. We offer a nuanced understanding of exercise effects on adolescent mental health to promote personalized exercise-based interventions in youth.
Childhood abuse and opioid prescription use in adulthood: Differences between non-Hispanic Whites and non-Hispanic Blacks in the United States

Despite the rapid rise in opioid prescription medication usage, little research has examined the role of early life adversity, such as childhood abuse, particularly in the context of race, in opioid prescription usage in adulthood. Guided by the life course perspective, the current study investigates whether experiencing childhood abuse increases the risk of opioid prescription use in adulthood and whether this association varies by race. Data were sourced from the second wave of the Midlife in the United States (MIDUS) study (2004–2005). The analytic sample consisted of two groups: non-Hispanic Whites (n = 714) and non-Hispanic Blacks (n = 151). Opioid prescription use was identified from the participants’ medication list using the MULTUM Lexicon Drug Database Classification System. Three types of childhood abuse—emotional, physical, and sexual—were assessed via summary scales derived from the Childhood Trauma Questionnaire. The results indicate a significant interaction between childhood physical abuse and race. Among non-Hispanic Whites, higher exposure to physical abuse during childhood was associated with greater odds of opioid prescription use in adulthood, even after adjusting for chronic pain, physical and mental health, and sociodemographic characteristics. However, the association between childhood physical abuse and opioid prescription use in adulthood was non-significant among non-Hispanic Black individuals. These findings underscore the long-term adverse health effects of physical abuse in childhood, particularly for non-Hispanic Whites, and suggest support for developing and implementing tailored intervention strategies.