Miracle-dz/UniFAR-FTUs huggingface dataset:
Depressive Symptoms Are Not Associated with Leukocyte Telomere Length: Findings from the Nova Scotia Health Survey (NSHS95), a Population-Based Study

Background Premature shortening of leukocyte telomere length has been proposed as a novel mechanism by which depression may confer increased risk of adverse cardiovascular events. Prior studies demonstrating associations of depression and depressive symptoms with shorter leukocyte telomere length were small, included selected psychiatric outpatients, were based on convenience samples, and/or adjusted for a limited number of possible confounding factors. Methods and Findings We examined the associations of depressive symptoms, probable depressive disorder, and specific depressive symptom clusters, as assessed by the Center for Epidemiological Studies—Depression (CES-D) scale, with leukocyte telomere length, measured by using a real-time PCR method, in 2,225 apparently healthy participants from the 1995 Nova Scotia Health Survey population-based study. The mean age was 48.2±18.9 years; 49.9% of participants were female; and the mean CES-D score was 7.4±7.9. The mean telomere length was 5,301±587 base pairs. In an unadjusted model, depressive symptoms were significantly associated with longer leukocyte telomere length (B = 27.6 base pairs per standard deviation increase in CES-D, 95% confidence interval [CI] = 3.1–52.1, p = 0.027). This association was no longer significant after adjustment for age and sex (B = 9.5, 95% CI = −14.6–33.6, p = 0.44) or after further adjustment for body mass index, Framingham risk score and previous history of ischemic heart disease (all p's≥0.37). Neither probable depressive disorder nor specific depressive symptom clusters were independently associated with leukocyte telomere length. Conclusions Concurrent depressive symptoms were not associated with leukocyte telomere length in a large, representative, population-based study.
Potential for bispecific T-cell engagers: role of blinatumomab in acute lymphoblastic leukemia

Patients with relapsed/refractory (R/R) B-precursor acute lymphoblastic leukemia (ALL) and patients whose minimal residual disease persists during treatment have a poor leukemia-free survival. Despite improvements in front-line therapy, the outcome in these patients remains poor, especially after relapse. As there are no standard chemotherapeutic regimens for the treatment of patients with R/R B-precursor ALL, T-cell-based therapeutic approaches have recently come to the forefront in ALL therapy. Recently, monoclonal antibodies have been developed to target specific antigens expressed in B-lineage blast cells. In this setting, CD19 is of great interest as this antigen is expressed in B-lineage cells. Therefore, it has been selected as the target antigen for blinatumomab, a new bi-specific T-cell engager antibody. This sophisticated antibody binds sites for both CD19 and CD3, leading to T-cell proliferation and activation and B-cell apoptosis. Owing to its short serum half-life, blinatumomab has been administrated by continuous intravenous infusion with a favorable safety profile. The most significant toxicities were central nervous system events and the cytokine release syndrome. This new therapeutic approach using blinatumomab has been shown to be effective in patients with positive minimal residual disease and in patients with R/R B-precursor ALL leading to a recent approval by the US Food and Drug Administration after an accelerated review process. This review focuses on the profile of blinatumomab and its efficacy and safety.
Dopamine Transporter Genetic Variants and Pesticides in Parkinson’s Disease

Background Research suggests that independent and joint effects of genetic variability in the dopamine transporter (DAT) locus and pesticides may influence Parkinson’s disease (PD) risk. Materials Methods: In 324 incident PD patients and 334 population controls from our rural California case–control study, we genotyped rs2652510, rs2550956 (for the DAT 5′ clades), and the 3′ variable number of tandem repeats (VNTR). Using geographic information system methods, we determined residential exposure to agricultural maneb and paraquat applications. We also collected occupational pesticide use data. Employing logistic regression, we calculated odds ratios (ORs) for clade diplotypes, VNTR genotype, and number of susceptibility (A clade and 9-repeat) alleles and assessed susceptibility allele–pesticide interactions. Results PD risk was increased separately in DAT A clade diplotype carriers [AA vs. BB: OR = 1.66; 95% confidence interval (CI), 1.08–2.57] and 3′ VNTR 9/9 carriers (9/9 vs. 10/10: OR = 1.8; 95% CI, 0.96–3.57), and our data suggest a gene dosing effect. Importantly, high exposure to paraquat and maneb in carriers of one susceptibility allele increased PD risk 3-fold (OR = 2.99; 95% CI, 0.88–10.2), and in carriers of two or more alleles more than 4-fold (OR = 4.53; 95% CI, 1.70–12.1). We obtained similar results for occupational pesticide measures. Discussion Using two independent pesticide measures, we a) replicated previously reported gene–environment interactions between DAT genetic variants and occupational pesticide exposure in men and b) overcame previous limitations of nonspecific pesticide measures and potential recall bias by employing state records and computer models to estimate residential pesticide exposure. Conclusion Our results suggest that DAT genetic variability and pesticide exposure interact to increase PD risk.
A Randomized Controlled Trial of Multicomponent Exercise in Older Adults with Mild Cognitive Impairment

Background To examine the effect of multicomponent exercise program on memory function in older adults with mild cognitive impairment (MCI), and identify biomarkers associated with improvement of cognitive functions. Methodology/Principal Findings Subjects were 100 older adults (mean age, 75 years) with MCI. The subjects were classified to an amnestic MCI group (n = 50) with neuroimaging measures, and other MCI group (n = 50) before the randomization. Subjects in each group were randomized to either a multicomponent exercise or an education control group using a ratio of 1∶1. The exercise group exercised for 90 min/d, 2 d/wk, 40 times for 6 months. The exercise program was conducted under multitask conditions to stimulate attention and memory. The control group attended two education classes. A repeated-measures ANOVA revealed that no group × time interactions on the cognitive tests and brain atrophy in MCI patients. A sub-analysis of amnestic MCI patients for group × time interactions revealed that the exercise group exhibited significantly better Mini-Mental State Examination (p = .04) and logical memory scores (p = .04), and reducing whole brain cortical atrophy (p<.05) compared to the control group. Low total cholesterol levels before the intervention were associated with an improvement of logical memory scores (p<.05), and a higher level of brain-derived neurotrophic factor was significantly related to improved ADAS-cog scores (p<.05). Conclusions/Significance The results suggested that an exercise intervention is beneficial for improving logical memory and maintaining general cognitive function and reducing whole brain cortical atrophy in older adults with amnestic MCI. Low total cholesterol and higher brain-derived neurotrophic factor may predict improvement of cognitive functions in older adults with MCI. Further studies are required to determine the positive effects of exercise on cognitive function in older adults with MCI. Trial Registration UMIN-CTR UMIN000003662 ctr.cgi? function = brows&action = brows&type = summary&recptno = R000004436&language = J.
Registration based retargeted image quality assessment

In recent years, a large number of image retargeting methods have been proposed. Measuring their relative quality is of significant importance, and there is still room for improvement in the effectiveness of objective retargeted image quality assessment (RIQA) metrics. In this paper, we propose a registration based RIQA metric. First, we propose to calculate the flow map using an image registration method which involves SURF point matching and halfway domain optimization. Using the computed flow map and the source image, we propose an LGI metric which contains three factors: 1) local similarity which assesses the local aspect ratio change, edge directional similarity and flow smoothness; 2) global distortion which measures the appearance change of salient objects; 3) salient information loss. Comparing with other six metrics, our LGI metric correlates the best with subjective rankings on the RetargetMe dataset.
Generalizing Swendsen–Wang for Image Analysis

Markov chain Monte Carlo (MCMC) methods have been used in many fields (physics, chemistry, biology, and computer science) for simulation, inference, and optimization. In many applications, Markov chains are simulated for sampling from target probabilities π(X) defined on graphs G. The graph vertices represent elements of the system, the edges represent spatial relationships, while X is a vector of variables on the vertices which often take discrete values called labels or colors. Designing efficient Markov chains is a challenging task when the variables are strongly coupled. Because of this, methods such as the single-site Gibbs sampler often experience suboptimal performance. A well-celebrated algorithm, the Swendsen–Wang (SW) method, can address the coupling problem. It clusters the vertices as connected components after turning off some edges probabilistically, and changes the color of one cluster as a whole. It is known to mix rapidly under certain conditions. Unfortunately, the SW method has limited applicability and slows down in the presence of “external fields;” for example, likelihoods in Bayesian inference. In this article, we present a general cluster algorithm that extends the SW algorithm to general Bayesian inference on graphs. We focus on image analysis problems where the graph sizes are in the order of 103–106 with small connectivity. The edge probabilities for clustering are computed using discriminative probabilities from data. We design versions of the algorithm to work on multi grid and multilevel graphs, and present applications to two typical problems in image analysis, namely image segmentation and motion analysis. In our experiments, the algorithm is at least two orders of magnitude faster (in CPU time) than the single-site Gibbs sampler.
Tumor Texture Analysis in 18F-FDG PET: Relationships Between Texture Parameters, Histogram Indices, Standardized Uptake Values, Metabolic Volumes, and Total Lesion Glycolysis

Texture indices are of growing interest for tumor characterization in 18F-FDG PET. Yet, on the basis of results published in the literature so far, it is unclear which indices should be used, what they represent, and how they relate to conventional indices such as standardized uptake values (SUVs), metabolic volume (MV), and total lesion glycolysis (TLG). We investigated in detail 31 texture indices, 5 first-order statistics (histogram indices) derived from the gray-level histogram of the tumor region, and their relationship with SUV, MV, and TLG in 3 different tumor types. Methods: Three patient groups corresponding to 3 cancer types at baseline were studied independently: patients with metastatic colorectal cancer (72 lesions), non–small cell lung cancer (24 lesions), and breast cancer (54 lesions). Thirty-one texture indices were studied in addition to SUVs, MV, and TLG, and 5 indices extracted from histogram analysis were also investigated. The relationships between indices were studied as well as the robustness of the various texture indices with respect to the parameters involved in the calculation method (sampling schemes and tumor volume of interest). Results: Regardless of the patient group, many indices were highly correlated (Pearson correlation coefficient |r| ≥ 0.80), making it desirable to focus on only a few uncorrelated indices. Three histogram indices were highly correlated with SUVs (|r| ≥ 0.84). Four texture indices were highly correlated with MV, and none was highly correlated with SUVs (|r| ≤ 0.55). The resampling formula used to calculate texture indices had a substantial impact, and resampling using at least 32 discrete values should be used for texture indices calculation. The texture indices change as a function of the segmentation method was higher than that of peak and maximum SUVs but less than mean SUV for 5 texture indices and was larger than that of MV for 14 texture indices and for the 5 histogram indices. All these results were extremely consistent across the 3 tumor types and explained many of the observations reported in the literature so far. Conclusion: None of the histogram indices and only 17 of 31 texture indices were robust with respect to the tumor-segmentation method. An appropriate resampling formula with at least 32 gray levels should be used to avoid introducing a misleading relationship between texture indices and SUV. Some texture indices are highly correlated or strongly correlate with MV whatever the tumor type. Such correlation should be accounted for when interpreting the usefulness of texture indices for tumor characterization, which might call for systematic multivariate analyses.
In vivo organization of the FtsZ‐ring by ZapA and ZapB revealed by quantitative super‐resolution microscopy

In most bacterial cells, cell division is dependent on the polymerization of the FtsZ protein to form a ring‐like structure (Z‐ring) at the midcell. Despite its essential role, the molecular architecture of the Z‐ring remains elusive. In this work we examine the roles of two FtsZ‐associated proteins, ZapA and ZapB, in the assembly dynamics and structure of the Z‐ring in Escherichia coli cells. In cells deleted of zapA or zapB, we observed abnormal septa and highly dynamic FtsZ structures. While details of these FtsZ structures are difficult to discern under conventional fluorescence microscopy, single‐molecule‐based super‐resolution imaging method Photoactivated Localization Microscopy (PALM) reveals that these FtsZ structures arise from disordered arrangements of FtsZ clusters. Quantitative analysis finds these clusters are larger and comprise more molecules than a single FtsZ protofilament, and likely represent a distinct polymeric species that is inherent to the assembly pathway of the Z‐ring. Furthermore, we find these clusters are not due to the loss of ZapB–MatP interaction in ΔzapA and ΔzapB cells. Our results suggest that the main function of ZapA and ZapB in vivo may not be to promote the association of individual protofilaments but to align FtsZ clusters that consist of multiple FtsZ protofilaments.
COMBINATORIAL RICCI FLOWS ON SURFACES

We show that the analogue of Hamilton’s Ricci flow in the combinatorial setting produces solutions which converge exponentially fast to Thurston’s circle packing on surfaces. As a consequence, a new proof of Thurston’s existence of circle packing theorem is obtained. As another consequence, Ricci flow suggests a new algorithm to find circle packings.
Data Fusion by Kernel Combination for Behavioral Data

Technological advances have radically changed the collection of behavioral data in animals. Modern tools complement, or even replace human observations in some labs. Also, behavior manifests itself in many different and complex ways, so behavioral scientists have developed a strategy of subjecting the animals to multiple observation systems, for longer periods of time, in order to get as much information as possible. Methodologically, the sample size (i.e. the number of animals) should be balanced from a statistical and an animal welfare point of view. Efficient statistical methods are therefore required to combine and analyze data from different types of experiments, while using a minimum number of animals. In this article, we present a generic framework that enables such a combination of diverse behavioral data.
Homogeneous Esterification Mechanism of Bagasse Modified with Phthalic Anhydride in Ionic Liquid, Part 3: Structural Transformation of Lignins

The phthalation of bagasse was investigated comparatively with the three main isolated components in 1-allyl-3-methylidazium chloride (AmimCl) to reveal the reaction behavior of bagasse. In the first two parts, the detailed changes of cellulosic and hemicellulosic components in bagasse were elucidated during phthalation. In Part 3, the phthalation of lignins was performed in AmimCl with various ratios of phthalic anhydride/lignins from 10 to 50 mmol/g. The phthalation degree ranged from 41.1% to 68.8% for the phthalated lignins. The aliphatic hydroxyls of lignins were more easily phthalated than the phenolic hydroxyls as revealed by 31P nuclear magnetic resonance (NMR) analysis. Fourier transform infrared spectroscopy (FT-IR) and two dimensional (2D) heteronuclear single quantum correlation (HSQC) confirmed the attachment of phthaloyl group onto lignins. Severe degradation of lignin macromolecules was found at high ratios of phthalic anhydride/lignins (30 to 50 mmol/g) by gel permeation chromatography (GPC) analysis. These results provide a detailed understanding of reaction behaviors of lignins during bagasse phthalation, which are beneficial to prepare composites based on phthalated lignocellulose with better properties.
Demographic Processes Influencing Population Viability of the Iowa Pleistocene Snail (Discus Macclintocki)

ABSTRACT Understanding the importance of variable local population abundance and the limited potential for dispersal and genetic exchange is crucial for the conservation of many species with limited geographic distribution and specialized habitat requirements. Because of rareity, it is often difficult to study the relative importance of variation in recruitment and survival and their net effect on population growth. We designed a survey of natural populations of endangered Iowa Pleistocene snails (Discus macclintocki) using the robust mark-recapture design to estimate population size and vital rates. A dense population remained stationary throughout the 6-y study whereas vital rates fluctuated substantially in two much smaller populations. In the smaller populations rates of growth varied from sharply increasing to sharply decreasing among years, and changes in estimated recruitment were the primary vital rate influencing these fluctuations. Snails were highly sedentary and sampling at random locations showed that the populations were highly subdivided within a site. Fluctuations in demographic rates and patchy distribution may provide the basis for substantially different rates of genetic change within and among sites. Although in the short-term, fluctuations in recruitment of these snails may influence local dynamics most substantially, long-term threats of habitat loss or climatic change will likely affect survival of adults and persistence of the populations.
Relational query coprocessing on graphics processors

Graphics processors (GPUs) have recently emerged as powerful coprocessors for general purpose computation. Compared with commodity CPUs, GPUs have an order of magnitude higher computation power as well as memory bandwidth. Moreover, new-generation GPUs allow writes to random memory locations, provide efficient interprocessor communication through on-chip local memory, and support a general purpose parallel programming model. Nevertheless, many of the GPU features are specialized for graphics processing, including the massively multithreaded architecture, the Single-Instruction-Multiple-Data processing style, and the execution model of a single application at a time. Additionally, GPUs rely on a bus of limited bandwidth to transfer data to and from the CPU, do not allow dynamic memory allocation from GPU kernels, and have little hardware support for write conflicts. Therefore, a careful design and implementation is required to utilize the GPU for coprocessing database queries. In this article, we present our design, implementation, and evaluation of an in-memory relational query coprocessing system, GDB, on the GPU. Taking advantage of the GPU hardware features, we design a set of highly optimized data-parallel primitives such as split and sort, and use these primitives to implement common relational query processing algorithms. Our algorithms utilize the high parallelism as well as the high memory bandwidth of the GPU, and use parallel computation and memory optimizations to effectively reduce memory stalls. Furthermore, we propose coprocessing techniques that take into account both the computation resources and the GPU-CPU data transfer cost so that each operator in a query can utilize suitable processors—the CPU, the GPU, or both—for an optimized overall performance. We have evaluated our GDB system on a machine with an Intel quad-core CPU and an NVIDIA GeForce 8800 GTX GPU. Our workloads include microbenchmark queries on memory-resident data as well as TPC-H queries that involve complex data types and multiple query operators on data sets larger than the GPU memory. Our results show that our GPU-based algorithms are 2--27x faster than their optimized CPU-based counterparts on in-memory data. Moreover, the performance of our coprocessing scheme is similar to, or better than, both the GPU-only and the CPU-only schemes.
Marine carbonate system evolution during the EPOCA Arctic pelagic ecosystem experiment in the context of simulated Arctic ocean acidification

Abstract. A major, potential stressor of marine systems is the changing water chemistry following increasing seawater carbon dioxide concentration (CO2), commonly termed ocean acidification. In order to understand how an Arctic pelagic ecosystem may respond to future CO2, a deliberate ocean acidification and nutrient perturbation study was undertaken in an Arctic fjord. The initial setting and evolution of seawater carbonate chemistry were investigated. Additions of carbon dioxide resulted in a wide range of ocean acidification scenarios. This study documents the changes to the CO2 system throughout the study following net biological consumption and gas exchange with the atmosphere. In light of the common practice of extrapolating results to cover regions away from experimental conditions, a modelling study was also performed to assess the representativeness, in the context of the simulated present and future carbonate system, of the experimental study region to both the near and wider Arctic region. The mesocosm experiment represented the range of simulated marine carbonate system for the coming century and beyond (pCO2 to 1420 μatm) and thus extrapolations may be appropriate to ecosystems exhibiting similar levels of CO2 system drivers. However, as the regional ocean acidification was very heterogenous and did not follow changes in atmospheric CO2, care should be taken in extrapolating the mesocosm response to other regions based on atmospheric CO2 scenarios.