Miracle-dz/UniFAR-FTUs huggingface dataset:
Forest Entomology Intra-Annual Variation in Responses by Flying Southern Pine Beetles (Coleoptera: Curculionidae: Scolytinae) to Pheromone Component endo-Brevicomin

The southern pine beetle Dendroctonus frontalis Zimmermann (Coleoptera: Curculionidae: Scolytinae) is attracted to an aggregation pheromone that includes the multifunctional pheromone component endobrevicomin. The effect of endo-brevicomin on attractive lures varies from strong enhancement to reduction of beetle attraction depending upon release rate, lure component spacing, and proximity of beetle infestations. Anecdotal observations have further suggested that the effects of endo-brevicomin vary during the year. We investigated this possibility under nonoutbreak conditions in southwestern Mississippi where for two-and-a-half years we monitored traps baited with frontalin and the host odor alpha-pinene either (a) alone, or with an endobrevicomin release device either (b) located directly on the trap, or (c) displaced 6 m away. The endo-brevicomin devices in our tests increased D. frontalis catches during all times of year, and 6 m displacement of the endobrevicomin release device from the trap did not significantly alter responses except during the spring flight peak when displacement increased catches. Our data suggest that flying D. frontalis have a stronger tendency to avoid the immediate proximity of a release point of endo-brevicomin during their springtime dispersal flight when catches are greatest. Catches of Thanasimus dubius (F.) (Coleoptera: Cleridae), a major predator of D. frontalis, were not altered by endo-brevicomin, and ratios of D. frontalis to T. dubius changed over the course of the year. We discuss the possible effects of intra-annual variation in D. frontalis response to endo-brevicomin both on beetle attack behavior and use of endo-brevicomin as a lure adjuvant in D. frontalis population monitoring.
Impact of iron-fortified foods on Hb concentration in children (<10 years): a systematic review and meta-analysis of randomized controlled trials

Abstract Objective To combine evidence from randomized controlled trials to assess the effect of Fe-fortified foods on mean Hb concentration in children (<10 years). Design We conducted a meta-analysis of randomized, controlled, Fe-fortified feeding trials that evaluated Hb concentration. The weighted mean difference was calculated for net changes in Hb by using random-effects models. Meta-regression and covariate analyses were performed to explore the influence of confounders on the net pooled effect. Setting Trials were identified through a systematic search of PubMed, the Cochrane Library and secondary references. Subjects Eighteen studies covering 5142 participants were identified. The duration of feeding of fortified foods ranged from 6 to 12 months in these studies. Results Eighteen studies were included and evaluated in the meta-analysis. The overall pooled estimate of Hb concentration showed a significant increase in the fortification group compared with the control group (weighted mean difference = 5·09 g/l; 95 % CI 3·23, 6·95 g/l; I 2 = 90 %, τ 2 = 18·37, P < 0·0001). Meta-regression analysis indicated that duration of feeding was positively related to the effect size (regression coefficient = 0·368; 95 % CI 0·005, 0·731; P < 0·05). The net pooled effect size after removing the confounders was 4·74 (95 % CI 3·08, 6·40) g/l. Conclusions We observed an association between intake of Fe-fortified foods and Hb concentration in children aged <10 years. Fe-fortified foods could be an effective strategy for reducing Fe-deficiency anaemia in children.
KymoAnalyzer: a software tool for the quantitative analysis of intracellular transport in neurons

In axons, proper localization of proteins, vesicles, organelles, and other cargoes is accomplished by the highly regulated coordination of kinesins and dyneins, molecular motors that bind to cargoes and translocate them along microtubule (MT) tracks. Impairment of axonal transport is implicated in the pathogenesis of multiple neurodegenerative disorders including Alzheimer's and Huntington's diseases. To understand how MT‐based cargo motility is regulated and to delineate its role in neurodegeneration, it is critical to analyze the detailed dynamics of moving cargoes inside axons. Here, we present KymoAnalyzer, a software tool that facilitates the robust analysis of axonal transport from time‐lapse live‐imaging sequences. KymoAnalyzer is an open‐source software that automatically classifies particle trajectories and systematically calculates velocities, run lengths, pauses, and a wealth of other parameters that are characteristic of motor‐based transport. We anticipate that laboratories will easily use this package to unveil previously uncovered intracellular transport details of individually‐moving cargoes inside neurons.
High-Resolution HLA-A Typing in Normal Iranian Population

Background: Human leukocyte antigen (HLA) gene is a highly polymorphic region. HLA typing is required to match patients and donors for transplantation; therefore, development of HLA registries is necessary for finding HLA match donors. HLA system is highly informative, and numerous studies have been conducted on HLA allele distribution in different populations. Methods: In this study, 100 unrelated Iranian individuals were typed for HLA-A locus using sequence-based typing method. Samples were subjected to the PCR, followed by Sanger sequencing and software analysis. Results: A*02:01 (13%) and A*24:02 (12%) were the two most frequent alleles, while A*01:14, A*02:05, A*02:11, A*02:34, A*02:50, A*11:04, A*23:02, A*24:34, A*25:01, A*26:09, A*26:43, A*29:67, A*30:54, A*31:02, A*31:66, A*32:03, A*32:04, A*33:03, and A*66:15 alleles had the least frequencies (1%). Conclusion: This is the first report of HLA-A allele level typing in a randomized population of Iran and can be useful for development of national registries of HLA-typed volunteer marrow donors and local cord blood banks.
Bruceantin inhibits multiple myeloma cancer stem cell proliferation

ABSTRACT Multiple myeloma (MM) continues to claim the lives of a majority of patients. MM cancer stem cells (CSCs) have been demonstrated to sustain tumor growth. Due to their ability to self-renew and to express detoxifying enzymes and efflux transporters, MM-CSCs are rendered highly resistant to conventional therapies. Therefore, managing MM-CSCs characteristics could have profound clinical implications. Bruceantin (BCT) is a natural product previously demonstrated to inhibit the growth of MM in RPMI 8226 cells-inoculated mouse xenograft models, and to cause regression in already established tumors. The objectives of the present study were to test the inhibitory effects of BCT on MM-CSCs growth derived from a human primary tumor, and to explore a mechanism of action underlying these effects. BCT exhibited potent antiproliferative activity in MM-CSCs starting at 25 nM. BCT induced cell cycle arrest, cell death and apoptosis in MM-CSCs as well as inhibited cell migration and angiogenesis in vitro. Using a qPCR screen, it was found that the gene expression of a number of Notch pathway members was altered. Pretreatment of MM-CSCs with the γ-secretase inhibitor RO4929097, a Notch pathway inhibitor, reversed BCT-induced effects on MM-CSCs proliferation. In this study, BCT was shown to be an effective agent in controlling the proliferation, viability and migration of MM-CSCs as well as angiogenesis in vitro. The effect on MM-CSCs proliferation may be mediated by the Notch pathway. These results warrant further investigation of BCT in a broader set of human-derived MM-CSCs and with in vivo models representative of MM.
Transfusion‐related immunomodulation: review of the literature and implications for pediatric critical illness

Transfusion‐related immunomodulation (TRIM) in the intensive care unit (ICU) is difficult to define and likely represents a complicated set of physiologic responses to transfusion, including both proinflammatory and immunosuppressive effects. Similarly, the immunologic response to critical illness in both adults and children is highly complex and is characterized by both acute inflammation and acquired immune suppression. How transfusion may contribute to or perpetuate these phenotypes in the ICU is poorly understood, despite the fact that transfusion is common in critically ill patients. Both hyperinflammation and severe immune suppression are associated with poor outcomes from critical illness, underscoring the need to understand potential immunologic consequences of blood product transfusion. In this review we outline the dynamic immunologic response to critical illness, provide clinical evidence in support of immunomodulatory effects of blood product transfusion, review preclinical and translational studies to date of TRIM, and provide insight into future research directions.
Pre‐drill Groundwater Geochemistry in the Karoo Basin, South Africa

Enhanced production of unconventional hydrocarbons in the United States has driven interest in natural gas development globally, but simultaneously raised concerns regarding water quantity and quality impacts associated with hydrocarbon extraction. We conducted a pre‐development assessment of groundwater geochemistry in the critically water‐restricted Karoo Basin, South Africa. Twenty‐two springs and groundwater samples were analyzed for major dissolved ions, trace elements, water stable isotopes, strontium and boron isotopes, hydrocarbons and helium composition. The data revealed three end‐members: a deep, saline groundwater with a sodium‐chloride composition, an old, deep freshwater with a sodium‐bicarbonate‐chloride composition and a shallow, calcium‐bicarbonate freshwater. In a few cases, we identified direct mixing of the deep saline water and shallow groundwater. Stable water isotopes indicate that the shallow groundwater was controlled by evaporation in arid conditions, while the saline waters were diluted by apparently fossil meteoric water originated under wetter climatic conditions. These geochemical and isotopic data, in combination with elevated helium levels, suggest that exogenous fluids are the source of the saline groundwater and originated from remnant seawater prior to dilution by old meteoric water combined with further modification by water‐rock interactions. Samples with elevated methane concentrations (>14 ccSTP/kg) were strongly associated with the sodium‐chloride water located near dolerite intrusions, which likely provide a preferential pathway for vertical migration of deeply sourced hydrocarbon‐rich saline waters to the surface. This pre‐drill evaluation indicates that the natural migration of methane‐ and salt‐rich waters provides a source of geogenic contamination to shallow aquifers prior to shale gas development in the Karoo Basin.
Three‐dimensional genome architecture in health and disease

More than a decade of massive DNA sequencing efforts have generated a large body of genomic, transcriptomic and epigenomic information that has provided a more and more detailed view of the functional elements and transactions within the human genome. Considerable efforts have also focused on linking these elements with one another by mapping their interactions and by establishing 3‐dimensional (3D) genomic landscapes in various cell and tissue types. In parallel, multiple studies have associated genomic deletions, duplications and other rearrangements with human pathologies. In this review, we explore recent progresses that have allowed connecting disease‐causing alterations with perturbations of the 3D genome organization.
Temporomandibular Joint Disorders’ Impact on Pain, Function, and Disability

The aim of this study was to determine the association between more advanced stages of temporomandibular joint (TMJ) intra-articular disorders (“TMJ intra-articular status”), representing a transition from normal joint structure to TMJ disc displacement with and without reduction (DDwR and DDwoR) to degenerative joint disease (DJD), and patient-reported outcomes of jaw pain, function, and disability (“TMD impact”). This cross-sectional study included 614 cases from the RDC/TMD Validation Project with at least one temporomandibular disorder (TMD) diagnosis. TMJ intra-articular status was determined by 3 blinded, calibrated radiologists using magnetic resonance imaging and computed tomography as one of normal joint structure, DDwR, DDwoR, or DJD, representing the subject’s most advanced TMJ diagnosis. TMD impact was conceptualized as a latent variable consisting of 1) pain intensity (Characteristic Pain Index from the Graded Chronic Pain Scale [GCPS]), 2) jaw function (Jaw Functional Limitation Scale), and 3) disability (Disability Points from GCPS). A structural equation model estimated the association of TMJ intra-articular status with the latent measure TMD impact as a correlation coefficient in all TMD cases (n = 614) and in cases with a TMD pain diagnosis (n = 500). The correlations between TMJ intra-articular status and TMD impact were 0.05 (95% confidence interval [CI], −0.04 to 0.13) for all TMD cases and 0.07 (95% CI, −0.04 to 0.17) for cases with a pain diagnosis, which are neither statistically significant nor clinically relevant. Conceptualizing worsening of TMJ intra-articular disorders as 4 stages and characterizing impact from TMD as a composite of jaw pain, function, and disability, this cross-sectional study found no clinically significant association. Models of TMJ intra-articular status other than ours (normal structure → DDwR → DDwoR → DJD) should be explored.
Double Minimum Variance Beamforming Method to Enhance Photoacoustic Imaging

One of the common algorithms used to reconstruct photoacoustic (PA) images is the non-adaptive Delay-and-Sum (DAS) beamformer. However, the quality of the reconstructed PA images obtained by DAS is not satisfying due to its high level of sidelobes and wide mainlobe. In contrast, adaptive beamformers, such as minimum variance (MV), result in an improved image compared to DAS. In this paper, a novel beamforming method, called Double MV (D-MV) is proposed to enhance the image quality compared to the MV. It is shown that there is a summation procedure between the weighted subarrays in the output of the MV beamformer. This summation can be interpreted as the non-adaptive DAS beamformer. It is proposed to replace the existing DAS with the MV algorithm to reduce the contribution of the off-axis signals caused by the DAS beamformer between the weighted subarrays. The numerical results show that the proposed technique improves the full-width-half-maximum (FWHM) and signal-to-noise ratio (SNR) for about 28.83 \mu m and 4.8 dB in average, respectively, compared to MV beamformer. Also, quantitative evaluation of the experimental results indicates that the proposed D-MV leads to 0.15 mm and 1.96 dB improvement in FWHM and SNR, in comparison with MV beamformer.
MRI‐based prostate cancer detection with high‐level representation and hierarchical classification

Purpose: Extracting the high‐level feature representation by using deep neural networks for detection of prostate cancer, and then based on high‐level feature representation constructing hierarchical classification to refine the detection results. Methods: High‐level feature representation is first learned by a deep learning network, where multiparametric MR images are used as the input data. Then, based on the learned high‐level features, a hierarchical classification method is developed, where multiple random forest classifiers are iteratively constructed to refine the detection results of prostate cancer. Results: The experiments were carried on 21 real patient subjects, and the proposed method achieves an averaged section‐based evaluation (SBE) of 89.90%, an averaged sensitivity of 91.51%, and an averaged specificity of 88.47%. Conclusions: The high‐level features learned from our proposed method can achieve better performance than the conventional handcrafted features (e.g., LBP and Haar‐like features) in detecting prostate cancer regions, also the context features obtained from the proposed hierarchical classification approach are effective in refining cancer detection result.
The effect of seasonal heat stress on rigor development and the incidence of pale, exudative turkey meat.

Heat stress is one of the prominent ante-mortem stressors that elicits pale, soft, and exudative meat characteristics in stress-susceptible pigs. Industry reports of exudative turkey meat increase in the early summer with the onset of prolonged high temperatures. To study the effect of seasonal heat exposure on turkeys, 122 17-wk-old Nicholas tom turkeys were subjected in January either to growth temperatures of 16/24 C (night/day) (control) or to elevated temperatures of 32/38 C (night/day) (heat-stressed, HS). Turkeys were processed at 21 wk of age in a manner simulating commercial conditions. Pectoralis muscle samples were taken at 15 min (prechill), 2 h (postchill), and 24 h and analyzed for R-value, pH, and color. At 2 h, the remaining intact Pectoralis muscle was harvested, aged on ice for 23 h, and analyzed for drip loss and cook loss. Percentage mortality and carcass weights were not significantly different between treatments. By 15 min post-mortem, the HS birds exhibited a faster pH decline and had higher R-values that persisted through 24 h. The HS birds were also paler in color and exhibited increased drip loss and cook loss when compared to controls; however, expressible moisture was not different between treatments. In addition, the HS birds had a higher frequency of abnormal birds than controls when birds were grouped as normal (L* < 53) or abnormal (L* > 53).
Assessing gaps in cholesterol treatment guidelines for primary prevention of cardiovascular disease based on available randomised clinical trial evidence: The Rotterdam Study

Background The purpose of this study was to determine how American College of Cardiology/American Heart Association (ACC/AHA) 2013 and European Society of Cardiology 2016 guidelines for the primary prevention of atherosclerotic cardiovascular disease (CVD) compare in reflecting the totality of accrued randomised clinical trial evidence for statin treatment at population level. Methods From 1997–2008, 7279 participants aged 45–75 years, free of atherosclerotic cardiovascular disease, from the population-based Rotterdam Study were included. For each participant, we compared eligibility for each one of 11 randomised clinical trials on statin use in primary prevention of CVD, with recommendations on lipid-lowering therapy from the ACC/AHA and European Society of Cardiology (ESC) guidelines. Atherosclerotic cardiovascular disease incidence and cardiovascular disease mortality rates were calculated. Results The proportion of participants eligible for each trial ranged from 0.4% for ALLHAT-LLT to 30.8% for MEGA. The likelihood of being recommended for lipid-lowering treatment was lowest for those eligible for low-to-intermediate risk RCTs (HOPE-3, MEGA, and JUPITER), and highest for high-risk individuals with diabetes (MRC/BHF HPS, CARDS, and ASPEN) or elderly PROSPER. Eligibility for an increasing number of randomised clinical trials correlated with a greater likelihood of being recommended lipid-lowering treatment by either guideline (p < 0.001 for both guidelines). Conclusion Compared to RCTs done in high risk populations, randomised clinical trials targeting low-to-intermediate risk populations are less well-reflected in the ACC/AHA, and even less so in the ESC guideline recommendations. Importantly, the low-to-intermediate risk population targeted by HOPE-3, the most recent randomised clinical trial in this field, is not well-captured by the current European prevention guidelines and should be specifically considered in future iterations of the guidelines.
Robust Watertight Manifold Surface Generation Method for ShapeNet Models

In this paper, we describe a robust algorithm for 2-Manifold generation of various kinds of ShapeNet Models. The input of our pipeline is a triangle mesh, with a set of vertices and triangular faces. The output of our pipeline is a 2-Manifold with vertices roughly uniformly distributed on the geometry surface. Our algorithm uses an octree to represent the original mesh, and construct the surface by isosurface extraction. Finally, we project the vertices to the original mesh to achieve high precision. As a result, our method can be adopted efficiently to all ShapeNet models with the guarantee of correct 2-Manifold topology.
Differential Expression of PCSK9 Modulates Infection, Inflammation, and Coagulation in a Murine Model of Sepsis

Introduction: Proprotein convertase subtilisin/kexin type 9 (PCSK9) targets lipoprotein receptors for degradation, thereby reducing hepatic lipid clearance. PCSK9 inhibition reduces mortality in septic mice, presumably through increased hepatic clearance of pathogen lipids due to increased lipoprotein receptor concentrations. However, PCSK9 overexpression in vivo has not been studied in sepsis. Therefore, this study aimed to evaluate the effects of differential PCSK9 expression on systemic infection, inflammation, and coagulation in sepsis. Methods: Wild-type, PCSK9 knockout (KO), and transgenic (Tg) mice that overexpress PCSK9 were subjected to sham surgery or cecal ligation and puncture (CLP). Bacterial loads were measured in lungs, peritoneal cavity fluid, and blood. Organ pathology was assessed in lungs, liver, and kidneys. Lung myeloperoxidase activity, and plasma concentrations of alanine aminotransferase (ALT), creatinine, cell-free DNA (cfDNA), protein C, thrombin–antithrombin (TAT) complexes, interleukin (IL)-6, and IL-10 were also measured 6 h postoperatively. Morbidity was assessed for 16 h following CLP. Results: Overexpression of PCSK9 in mice increased liver and kidney pathology, plasma IL-6, ALT, and TAT concentrations during sepsis, whereas PCSK9 KO mice exhibited reduced bacterial loads, lung and liver pathology, myeloperoxidase activity, plasma IL-10, and cfDNA during CLP-induced sepsis. All septic mice had reduced plasma levels of protein C, but the protein C ratio relative to normal was significantly decreased in PCSK9 Tg mice. Dyspnea, cyanosis, and overall grimace scores were greatest in septic mice overexpressing PCSK9, whereas PCSK9 KO mice retained core body temperature during sepsis. Conclusion: These findings demonstrate that PCSK9 deficiency confers protection against systemic bacterial dissemination, organ pathology, and tissue inflammation, particularly in the lungs and liver, while PCSK9 overexpression exacerbates multi-organ pathology as well as the hypercoagulable and pro-inflammatory states in early sepsis.