Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of depth information on multiple-object tracking in three dimensions: A probabilistic perspective

Many daily situations require us to track multiple objects and people. This ability has traditionally been investigated in observers tracking objects in a plane. This simplification of reality does not address how observers track objects when targets move in three dimensions. Here, we study how observers track multiple objects in 2D and 3D while manipulating the average speed of the objects and the average distance between them. We show that performance declines as speed increases and distance decreases and that overall tracking accuracy is always higher in 3D than in 2D. The effects of distance and dimensionality interact to produce a more than additive improvement in performance during tracking in 3D compared to 2D. We propose an ideal observer model that uses the object dynamics and noisy observations to track the objects. This model provides a good fit to the data and explains the key findings of our experiment as originating from improved inference of object identity by adding the depth dimension.
EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec. ugent.be/explora-web/.
BES1 and BZR1 Redundantly Promote Phloem and Xylem Differentiation

Vascular development is a good model for studying cell differentiation in plants. Two conductive tissues, the xylem and phloem, are derived from common stem cells known as procambial/cambial cells. Glycogen synthase kinase 3 proteins (GSK3s) play crucial roles in maintaining procambial/cambial cells by suppressing their differentiation into xylem or phloem cells. We previously designed an in vitro culture system for analyzing vascular cell differentiation named VISUAL (Vascular cell Induction culture System Using Arabidopsis Leaves). Using this system, we found that the transcription factor BRI1-EMS-SUPPRESSOR 1 (BES1) functions as a downstream target of GSK3s during xylem differentiation. However, the function of BES1 in vascular development remains largely unknown. Here, we found that, in addition to xylem differentiation, BES1 positively regulates phloem differentiation downstream of GSK3s. Transcriptome analysis using VISUAL confirmed that BES1 promotes bi-directional differentiation of procambial cells into xylem and phloem cells. Genetic analysis of loss-of-function mutants newly generated using the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) system revealed that BRASSINAZOLE RESISTANT 1 (BZR1), the closest homolog of BES1, functions in vascular development redundantly with BES1. Notably, BZR1 has a weaker impact on vascular cell differentiation than BES1, suggesting that they contribute differentially to this process. In conclusion, our findings indicate that BES1 and BZR1 are key regulators of both xylem and phloem cell differentiation from vascular stem cells.
Memory for Important Item-Location Associations in Younger and Older Adults

Older adults typically experience memory impairments for verbal and visuospatial episodic information, which are most pronounced for associative information. Although some age-related verbal memory deficits may be reduced by selectively focusing on high-value item information, the binding of items to locations in visuospatial memory involves different processes that are impaired in older adults. In the current study, we examined whether age-related impairment in visuospatial binding could be alleviated by strategic focus on important information and whether varying study time and presentation formats would affect such selectivity. We also used novel spatial resolutions analysis to examine participants’ gist-based visuospatial memory with respect to information importance. Younger and older adults were presented with items worth different point values in a visuospatial display, either sequentially (Experiment 1) or simultaneously (Experiment 2). When items were presented sequentially, participants became more selective with task experience, but when items were presented simultaneously, selectivity was maintained throughout the task. These patterns were also observed when encoding time was reduced for younger adults. Although older adults successfully engaged in value-based memory strategies, age-related visuospatial memory deficits were still present, even for high-value information, consistent with the associative deficit hypothesis. However, under some conditions, older adults showed reduced spatial relocation errors for high-value item-location associations. The results suggest that strategic control can be used when binding information in visuospatial memory, and that both younger and older adults can benefit by focusing on high-value items and their locations, despite associative memory deficits present in old age.
Did Medicare Part D Reduce Mortality?

We investigate the implementation of Medicare Part D and estimate that this prescription drug benefit program reduced elderly mortality by 2.2% annually. This was driven primarily by a reduction in cardiovascular mortality, the leading cause of death for the elderly. There was no effect on deaths due to cancer, a condition whose drug treatments are covered under Medicare Part B. We validate these results by demonstrating that the changes in drug utilization following the implementation of Medicare Part D match the mortality patterns we observe. We calculate that the value of the mortality reduction is equal to $5 billion per year.
Proteome profiling of extracellular vesicles captured with the affinity peptide Vn96: comparison of Laemmli and TRIzol© protein-extraction methods

ABSTRACT Sample amount is often a limiting factor for multi-parametric analyses that encompass at least three areas of ‘-omics’ research: genomics, transcriptomics and proteomics. Limited sample amounts are also an important consideration when these multi-parametric analyses are performed on extracellular vesicles (EVs), as the amount of EVs (and EV cargo) that can be isolated is often very low. It is well understood that a monophasic solution of phenol and guanidine isothiocyanate (i.e. TRIzol©) can simultaneously isolate DNA, RNA and proteins from biological samples; however, it is most commonly used for the extraction of RNA. Validation of this reagent for the isolation of multiple classes of biological molecules from EVs would provide a widely applicable method for performing multi-parametric analyses of EV material. In this report, we describe a comparison of proteins identified from EVs processed with either TRIzol© or the conventional Laemmli buffer protein-extraction reagents. EVs were isolated from 3 mL of cell-culture supernatant derived from MCF-10A, MCF-7 and MDA-MB-231 cells using the Vn96 EV capture technology. For the TRIzol© extraction protocol, proteins were precipitated with acetone from the organic phase and then re-solubilized in a mixture of 8M urea, 0.2% SDS and 1 M Tris-HCl pH 6.8, followed by dilution in 5× loading buffer prior to fractionation with 1D SDS-PAGE. NanoLC-MS/MS of the trypsin-digested proteins was used to generate proteomic profiles from EV protein samples extracted with each method. Of the identified proteins, 57.7%, 69.2% and 57.0% were common to both extraction methods for EVs from MCF-10A, MCF-7 and MDA-MB-231, respectively. Our results suggest that TRIzol© extraction of proteins from EVs has significant equivalence to the traditional Laemmli method. The advantage of using TRIzol© reagent is the ability to accumulate multi-parametric data (e.g., RNA and protein profiles) on the same limited EV sample while minimizing sample preparation and processing time.
Effects of feeding different proportions of silver leaf desmodium (Desmodium uncinatum) with banana (Musa paradisiaca) leaf on nutrient utilization in Horro sheep fed a basal diet of natural grass hay

Objective The objective was to evaluate feed intake, digestibility, body weight change and carcass characteristics of sheep fed a basal diet of hay supplemented with banana leaves and silver leaf desmodium. Methods Thirty yearling lambs with an average initial body weight of 15.85±1.6 kg were grouped into six blocks of five rams in each block. The treatments were: hay alone (T1), hay+ 100% banana leaf (T2), hay+67% banana leaf+33% desmodium leaf (T3), hay+33% banana leaf+67% desmodium leaf (T4), andhay+100% desmodium leaf (T5). Three hundred grams of treatment diets were offered daily on as fed basis. The feeding and digestibility trials lasted for 84 and 7 days, respectively, followed by carcass evaluation. Results The total dry matter (DM) intake for T3, T4, and T5 were greater (p<0.05) than those fed T1 and T2 diets. The lowest (p<0.05) organic matter (OM) intake was recorded in rams reared on T1 diet. The total crude protein (CP) intake was in the following order: T5> T4>T3>T2>T1. Ram lambs receiving supplementary diets had higher (p<0.05) DM, OM, CP, neutral detergent fiber and acid detergent fiber digestibility compared with the control diet. The empty body weight and slaughter weight was highest (p<0.05) in rams receiving T3, T4, and T5 diets. The average daily gain and feed conversion efficiency was highest (p< 0.05) in rams receiving the supplementary diets. The dressing percentage on the basis of hot carcass weight linearly increased with increasing levels of desmodium. Rams reared on supplementary diet had higher (p<0.05) rib eye area compared with the control diet. Conclusion In conclusion, when banana leaf is used as a supplement to poor quality grass, better body weight gain was obtained when fed in combination with desmodium.
EPS‐LASSO: test for high‐dimensional regression under extreme phenotype sampling of continuous traits

Motivation: Extreme phenotype sampling (EPS) is a broadly‐used design to identify candidate genetic factors contributing to the variation of quantitative traits. By enriching the signals in extreme phenotypic samples, EPS can boost the association power compared to random sampling. Most existing statistical methods for EPS examine the genetic factors individually, despite many quantitative traits have multiple genetic factors underlying their variation. It is desirable to model the joint effects of genetic factors, which may increase the power and identify novel quantitative trait loci under EPS. The joint analysis of genetic data in high‐dimensional situations requires specialized techniques, e.g. the least absolute shrinkage and selection operator (LASSO). Although there are extensive research and application related to LASSO, the statistical inference and testing for the sparse model under EPS remain unknown. Results: We propose a novel sparse model (EPS‐LASSO) with hypothesis test for high‐dimensional regression under EPS based on a decorrelated score function. The comprehensive simulation shows EPS‐LASSO outperforms existing methods with stable type I error and FDR control. EPS‐LASSO can provide a consistent power for both low‐ and high‐dimensional situations compared with the other methods dealing with high‐dimensional situations. The power of EPS‐LASSO is close to other low‐dimensional methods when the causal effect sizes are small and is superior when the effects are large. Applying EPS‐LASSO to a transcriptome‐wide gene expression study for obesity reveals 10 significant body mass index associated genes. Our results indicate that EPS‐LASSO is an effective method for EPS data analysis, which can account for correlated predictors. Availability and implementation: The source code is available at https://github.com/xu1912/EPSLASSO. Supplementary information: Supplementary data are available at Bioinformatics online.
Outer Membrane Permeability of Cyanobacterium Synechocystis sp. Strain PCC 6803: Studies of Passive Diffusion of Small Organic Nutrients Reveal the Absence of Classical Porins and Intrinsically Low Permeability

ABSTRACT The outer membrane of heterotrophic Gram-negative bacteria plays the role of a selective permeability barrier that prevents the influx of toxic compounds while allowing the nonspecific passage of small hydrophilic nutrients through porin channels. Compared with heterotrophic Gram-negative bacteria, the outer membrane properties of cyanobacteria, which are Gram-negative photoautotrophs, are not clearly understood. In this study, using small carbohydrates, amino acids, and inorganic ions as permeation probes, we determined the outer membrane permeability of Synechocystis sp. strain PCC 6803 in intact cells and in proteoliposomes reconstituted with outer membrane proteins. The permeability of this cyanobacterium was >20-fold lower than that of Escherichia coli. The predominant outer membrane proteins Slr1841, Slr1908, and Slr0042 were not permeable to organic nutrients and allowed only the passage of inorganic ions. Only the less abundant outer membrane protein Slr1270, a homolog of the E. coli export channel TolC, was permeable to organic solutes. The activity of Slr1270 as a channel was verified in a recombinant Slr1270-producing E. coli outer membrane. The lack of putative porins and the low outer membrane permeability appear to suit the cyanobacterial autotrophic lifestyle; the highly impermeable outer membrane would be advantageous to cellular survival by protecting the cell from toxic compounds, especially when the cellular physiology is not dependent on the uptake of organic nutrients. IMPORTANCE Because the outer membrane of Gram-negative bacteria affects the flux rates for various substances into and out of the cell, its permeability is closely associated with cellular physiology. The outer membrane properties of cyanobacteria, which are photoautotrophic Gram-negative bacteria, are not clearly understood. Here, we examined the outer membrane of Synechocystis sp. strain PCC 6803. We revealed that it is relatively permeable to inorganic ions but is markedly less permeable to organic nutrients, with >20-fold lower permeability than the outer membrane of Escherichia coli. Such permeability appears to fit the cyanobacterial lifestyle, in which the diffusion pathway for inorganic solutes may suffice to sustain the autotrophic physiology, illustrating a link between outer membrane permeability and the cellular lifestyle.
ESMO International Consortium Study on the availability, out-of-pocket costs and accessibility of antineoplastic medicines in countries outside of Europe

Abstract Background The availability and affordability of safe, effective, high-quality, affordable anticancer therapies are a core requirement for effective national cancer control plans. Method Online survey based on a previously validated approach. The aims of the study were to evaluate (i) the availability on national formulary of licensed antineoplastic medicines across the globe, (ii) patient out-of-pocket costs for the medications, (iii) the actual availability of the medication for a patient with a valid prescription, (iv) information relating to possible factors adversely impacting the availability of antineoplastic agents and (v) the impact of the country’s level of economic development on these parameters. A total of 304 field reporters from 97 countries were invited to participate. The preliminary set of data was posted on the ESMO website for open peer review and amendments have been incorporated into the final report. Results Surveys were submitted by 135 reporters from 63 countries and additional peer-review data were submitted by 54 reporters from 19 countries. There are substantial differences in the formulary availability, out-of-pocket costs and actual availability for many anticancer medicines. The most substantial issues are in lower-middle- and low-income countries. Even among medications on the WHO Model List of Essential Medicines (EML) the discrepancies are profound and these relate to high out-of-pocket costs (in low-middle-income countries 32.0% of EML medicines are available only at full cost and 5.2% are not available at all, and for low-income countries, the corresponding figures are even worse at 57.7% and 8.3%, respectively). Conclusions There is wide global variation in formulary availability, out-of-pocket expenditures and actual availability for most licensed anticancer medicines. Low- and low-middle-income countries have significant lack of availability and high out-of-pocket expenditures for cancer medicines on the WHO EML, with much less availability of new, more expensive targeted agents compared with high-income countries.
Addressing Oncofertility Needs: Views of Female Cancer Patients in Fertility Preservation

A total of 41 questionnaires were returned from 64 respondents who consented to receive a questionnaire through the mail. Almost all valued the opportunity to receive consultation to address their fertility concerns and discuss fertility preservation options. Psychological stress, time pressure, and costs were identified as main factors affecting respondents’ decision to proceed with in-vitro fertilization to cryopreserve oocytes or embryos. About one third indicated that the discussion of fertility matters was initiated by themselves, their friends, and families rather than their health care providers. The findings have identified several major barriers encountered by female cancer patients when seeking fertility preservation services.
Depressive symptoms and workplace-violence-related risk factors among otorhinolaryngology nurses and physicians in Northern China: a cross-sectional study

Objectives Workplace violence is relatively frequent among medical professionals who work in otorhinolaryngology units. This phenomenon reduces the quality of provided medical care and increases the incidence of depressive symptoms among physicians and nurses, seriously affecting their job satisfaction and work efficiency with a negative attitude towards providing treatment. Few existing studies have assessed workplace-violence-related factors associated with depressive symptoms among otorhinolaryngology physicians and nurses. Methods We conducted a cross-sectional study in grade A tertiary hospitals of Heilongjiang province in Northern China, to evaluate the occurrence and level of depressive symptoms among otorhinolaryngology physicians and nurses and to analyse the relationship between them and workplace-violence-related risk factors and demographic variables. Results Of all our participating professionals, (379 otorhinolaryngologists and 273 nurses), 57.2% were found to have depressive symptoms, whereas, of the respondents who had suffered from physical violence, 71.25% had depressive symptoms. Professionals with less than 1 year of experience, as well as professionals who more frequently worked alone, were more likely to suffer from depressive symptoms than their colleagues. Conclusions This research addresses an emerging issue of clinical practice, and its results differ from those of previous studies; specifically, it indicates that the frequency of depressive symptoms among otorhinolaryngology physicians and nurses may be influenced by physical violence, the number of coworkers they have for more than half of their working hours and other workplace-violence-related factors. To reduce the depressive symptoms caused by workplace violence and improve the quality of medical services, medical institutions should implement effective measures to prevent the occurrence of physical violence, strengthen team cooperation ability and increase peer support.
Traumatic injuries and persistent opioid use in the USA: findings from a nationally representative survey

Background Although opioid abuse is a rising epidemic in the USA, there are no studies to date on the incidence of persistent opioid use following injuries. Therefore, the aims of this study are: (1) to examine the incidence of persistent opioid use among a nationally representative sample of injured and non-injured populations; (2) to evaluate whether an injury is an independent predictor of persistent opioid use. Method Data from the Medical Expenditure Panel Survey were pooled (years 2009–2012). Adults were followed for about 2 years, during which they were surveyed about injury status and opioid use every 4–5 months. To determine whether injuries are associated with persistent opioid use, weighted multiple logistic regressions were constructed. Results While 2.3 million injured individuals received any opioid during the follow-up, 371 170 (15.6%) individuals became persistent opioid users (defined as opioid use across multiple time points). In a multiple logistic regression analysis adjusting for sociodemographic characteristics and self-reported health, those who sustained injuries were 1.4 times (95% CI 1.1 to 1.9) more likely to report persistent opioid use than those without injuries. Conclusions We found injuries to be significantly associated with persistent opioid use in a nationally representative sample. Further investment in injury prevention may facilitate reduction of persistent opioid use and, thus, improve population health and reduce health expenditures.