Miracle-dz/UniFAR-FTUs huggingface dataset:
Maximum Entropy Approach in Dynamic Contrast-Enhanced Magnetic Resonance Imaging

Summary Background: In the estimation of physiological kinetic parameters from Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI) data, the determination of the arterial input function (AIF) plays a key role. Objectives: This paper proposes a Bayesian method to estimate the physiological parameters of DCE-MRI along with the AIF in situations, where no measurement of the AIF is available. Methods: In the proposed algorithm, the maximum entropy method (MEM) is combined with the maximum a posterior approach (MAP). To this end, MEM is used to specify a prior probability distribution of the unknown AIF. The ability of this method to estimate the AIF is validated using the Kullback-Leibler divergence. Subsequently, the kinetic parameters can be estimated with MAP. The proposed algorithm is evaluated with a data set from a breast cancer MRI study. Results: The application shows that the AIF can reliably be determined from the DCE-MRI data using MEM. Kinetic parameters can be estimated subsequently. Conclusions: The maximum entropy method is a powerful tool to reconstructing images from many types of data. This method is useful for generating the probability distribution based on given information. The proposed method gives an alternative way to assess the input function from the existing data. The proposed method allows a good fit of the data and therefore a better estimation of the kinetic parameters. In the end, this allows for a more reliable use of DCE-MRI.
Single-pixel interior filling function approach for detecting and correcting errors in particle tracking

Significance Researchers in many areas of science and engineering gather imaging data consisting of a set of pixel intensities. Quantitative analyses of such data often rely on estimating the positions of objects (e.g., single-particle tracking), and many of the algorithms used promise subpixel precision and accuracy. Here, we introduce a method that can reveal biases in such tracking algorithms and correct the associated errors. An advantage of the method is that it uses only the output of the tracking algorithm without needing knowledge of how it works. We illustrate how the method can solve common problems in single-particle tracking. Under some circumstances the method can even outperform the precision limit to which most algorithms are compared. We present a general method for detecting and correcting biases in the outputs of particle-tracking experiments. Our approach is based on the histogram of estimated positions within pixels, which we term the single-pixel interior filling function (SPIFF). We use the deviation of the SPIFF from a uniform distribution to test the veracity of tracking analyses from different algorithms. Unbiased SPIFFs correspond to uniform pixel filling, whereas biased ones exhibit pixel locking, in which the estimated particle positions concentrate toward the centers of pixels. Although pixel locking is a well-known phenomenon, we go beyond existing methods to show how the SPIFF can be used to correct errors. The key is that the SPIFF aggregates statistical information from many single-particle images and localizations that are gathered over time or across an ensemble, and this information augments the single-particle data. We explicitly consider two cases that give rise to significant errors in estimated particle locations: undersampling the point spread function due to small emitter size and intensity overlap of proximal objects. In these situations, we show how errors in positions can be corrected essentially completely with little added computational cost. Additional situations and applications to experimental data are explored in SI Appendix. In the presence of experimental-like shot noise, the precision of the SPIFF-based correction achieves (and can even exceed) the unbiased Cramér–Rao lower bound. We expect the SPIFF approach to be useful in a wide range of localization applications, including single-molecule imaging and particle tracking, in fields ranging from biology to materials science to astronomy.
Comprehensive Reference Ranges for Hematology and Clinical Chemistry Laboratory Parameters Derived from Normal Nigerian Adults

Background Interpretation of laboratory test results with appropriate diagnostic accuracy requires reference or cutoff values. This study is a comprehensive determination of reference values for hematology and clinical chemistry in apparently healthy voluntary non-remunerated blood donors and pregnant women. Methods and findings Consented clients were clinically screened and counseled before testing for HIV, Hepatitis B, Hepatitis C and Syphilis. Standard national blood donors’ questionnaire was administered to consented blood donors. Blood from qualified volunteers was used for measurement of complete hematology and chemistry parameters. Blood samples were analyzed from a total of 383 participants, 124 (32.4%) males, 125 (32.6%) non-pregnant females and 134 pregnant females (35.2%) with a mean age of 31 years. Our results showed that the red blood cells count (RBC), Hemoglobin (HB) and Hematocrit (HCT) had significant gender difference (p = 0.000) but not for total white blood count (p>0.05) which was only significantly higher in pregnant verses non-pregnant women (p = 0.000). Hemoglobin and Hematocrit values were lower in pregnancy (P = 0.000). Platelets were significantly higher in females than men (p = 0.001) but lower in pregnant women (p = 0.001) with marked difference in gestational period. For clinical chemistry parameters, there was no significant difference for sodium, potassium and chloride (p>0.05) but gender difference exists for Bicarbonate (HCO3), Urea nitrogen, Creatinine as well as the lipids (p<0.05). Total bilirubin was significantly higher in males than females (p = 0.000). Significant differences exist for all chemistry parameters between pregnant and non-pregnant women in this study (p<0.05), except Amylase and total cholesterol (p>0.05). Conclusions Hematological and Clinical Chemistry reference ranges established in this study showed significant gender differences. Pregnant women also differed from non-pregnant females and during pregnancy. This is the first of such comprehensive study to establish reference values among adult Nigerians and difference observed underscore the need to establish reference values for different populations.
Grouping methods for estimating the prevalences of rare traits from complex survey data that preserve confidentiality of respondents

Originally, 2‐stage group testing was developed for efficiently screening individuals for a disease. In response to the HIV/AIDS epidemic, 1‐stage group testing was adopted for estimating prevalences of a single or multiple traits from testing groups of size q, so individuals were not tested. This paper extends the methodology of 1‐stage group testing to surveys with sample weighted complex multistage‐cluster designs. Sample weighted‐generalized estimating equations are used to estimate the prevalences of categorical traits while accounting for the error rates inherent in the tests. Two difficulties arise when using group testing in complex samples: (1) How does one weight the results of the test on each group as the sample weights will differ among observations in the same group. Furthermore, if the sample weights are related to positivity of the diagnostic test, then group‐level weighting is needed to reduce bias in the prevalence estimation; (2) How does one form groups that will allow accurate estimation of the standard errors of prevalence estimates under multistage‐cluster sampling allowing for intracluster correlation of the test results. We study 5 different grouping methods to address the weighting and cluster sampling aspects of complex designed samples. Finite sample properties of the estimators of prevalences, variances, and confidence interval coverage for these grouping methods are studied using simulations. National Health and Nutrition Examination Survey data are used to illustrate the methods.
Structural stress responses and degradation of dictyosomes in algae analysed by TEM and FIB‐SEM tomography

Stress‐induced physiological deficiencies in cells are reflected in structural, morphological and functional reactions of organelles. Although numerous investigations have focused on chloroplasts and mitochondria as main targets of different stressors in plant cells, there is insufficient information on the plant Golgi apparatus as stress sensor. By using the advantages of field emission scanning electron microscopy tomography in combination with classical ultrathin sectioning and transmission electron microscopic analyses, we provide structural evidence for common stress responses of the large and highly stable dictyosomes in the algal model system Micrasterias. Stress is induced by different metals such as manganese and lead, by starvation in 9 weeks of darkness or by inhibiting photosynthesis or glycolysis and by disturbing ionic homeostasis via KCl. For the first time a stress‐induced degradation pathway of dictyosomes is described that does not follow “classical” autophagy but occurs by disintegration of cisternae into single membrane balls that seem to be finally absorbed by the endoplasmic reticulum (ER). Comparison of the morphological features that accompany dictyosomal degradation in Micrasterias to similar reactions observed during the same stress application in Nitella indicates an ubiquitous degradation process at least in algae. As the algae investigated belong to the closest relatives of higher land plants these results may also be relevant for understanding dictyosomal stress and degradation responses in the latter phylogenetic group. In addition, this study shows that two‐dimensional transmission electron microscopy is insufficient for elucidating complex processes such as organelle degradation, and that information from three‐dimensional reconstructions as provided by field emission scanning electron microscopy tomography is absolutely required for a comprehensive understanding of the phenomenon.
Long-Range Gene Flow and the Effects of Climatic and Ecological Factors on Genetic Structuring in a Large, Solitary Carnivore: The Eurasian Lynx

Due to their high mobility, large terrestrial predators are potentially capable of maintaining high connectivity, and therefore low genetic differentiation among populations. However, previous molecular studies have provided contradictory findings in relation to this. To elucidate patterns of genetic structure in large carnivores, we studied the genetic variability of the Eurasian lynx, Lynx lynx throughout north-eastern Europe using microsatellite, mitochondrial DNA control region and Y chromosome-linked markers. Using SAMOVA we found analogous patterns of genetic structure based on both mtDNA and microsatellites, which coincided with a relatively little evidence for male-biased dispersal. No polymorphism for the cytochrome b and ATP6 mtDNA genes and Y chromosome-linked markers were found. Lynx inhabiting a large area encompassing Finland, the Baltic countries and western Russia formed a single genetic unit, while some marginal populations were clearly divergent from others. The existence of a migration corridor was suggested to correspond with distribution of continuous forest cover. The lowest variability (in both markers) was found in lynx from Norway and Białowieża Primeval Forest (BPF), which coincided with a recent demographic bottleneck (Norway) or high habitat fragmentation (BPF). The Carpathian population, being monomorphic for the control region, showed relatively high microsatellite diversity, suggesting the effect of a past bottleneck (e.g. during Last Glacial Maximum) on its present genetic composition. Genetic structuring for the mtDNA control region was best explained by latitude and snow cover depth. Microsatellite structuring correlated with the lynx's main prey, especially the proportion of red deer (Cervus elaphus) in its diet. Eurasian lynx are capable of maintaining panmictic populations across eastern Europe unless they are severely limited by habitat continuity or a reduction in numbers. Different correlations of mtDNA and microsatellite population divergence patterns with climatic and ecological factors may suggest separate selective pressures acting on males and females in this solitary carnivore.
Arousal vs. Relaxation: A Comparison of the Neurophysiological and Cognitive Correlates of Vajrayana and Theravada Meditative Practices

Based on evidence of parasympathetic activation, early studies defined meditation as a relaxation response. Later research attempted to categorize meditation as either involving focused or distributed attentional systems. Neither of these hypotheses received strong empirical support, and most of the studies investigated Theravada style meditative practices. In this study, we compared neurophysiological (EEG, EKG) and cognitive correlates of meditative practices that are thought to utilize either focused or distributed attention, from both Theravada and Vajrayana traditions. The results of Study 1 show that both focused (Shamatha) and distributed (Vipassana) attention meditations of the Theravada tradition produced enhanced parasympathetic activation indicative of a relaxation response. In contrast, both focused (Deity) and distributed (Rig-pa) meditations of the Vajrayana tradition produced sympathetic activation, indicative of arousal. Additionally, the results of Study 2 demonstrated an immediate dramatic increase in performance on cognitive tasks following only Vajrayana styles of meditation, indicating enhanced phasic alertness due to arousal. Furthermore, our EEG results showed qualitatively different patterns of activation between Theravada and Vajrayana meditations, albeit highly similar activity between meditations within the same tradition. In conclusion, consistent with Tibetan scriptures that described Shamatha and Vipassana techniques as those that calm and relax the mind, and Vajrayana techniques as those that require ‘an awake quality’ of the mind, we show that Theravada and Vajrayana meditations are based on different neurophysiological mechanisms, which give rise to either a relaxation or arousal response. Hence, it may be more appropriate to categorize meditations in terms of relaxation vs. arousal, whereas classification methods that rely on the focused vs. distributed attention dichotomy may need to be reexamined.
CYR61/CCN1 Regulates Sclerostin Levels and Bone Maintenance

CYR61/CCN1 is a matricellular protein that resides in the extracellular matrix, but serves regulatory rather than structural roles. CYR61/CCN1 is found in mineralized tissues and has been shown to influence bone healing in vivo and osteogenic differentiation in vitro. In this study we generated Cyr61 bone‐specific knockout mice to examine the physiological role of CYR61/CCN1 in bone development and maintenance in vivo. Extensive analysis of Cyr61 conditional knockout mice showed a significant decrease in both trabecular and cortical bone mass as compared to WT littermates. Our data suggest that CYR61/CCN1 exerts its effects on mature osteoblast/osteocyte function to modulate bone mass. Specifically, changes were observed in osteocyte/osteoblast expression of RankL, VegfA, and Sost. The increase in RankL expression was correlated with a significant increase in osteoclast number; decreased VegfA expression was correlated with a significant decrease in bone vasculature; increased Sost expression was associated with decreased Wnt signaling, as revealed by decreased Axin2 expression and increased adiposity in the bone marrow. Although the decreased number of vascular elements in bone likely contributes to the low bone mass phenotype in Cyr61 conditional knockout mice, this cannot explain the observed increase in osteoclasts and the decrease in Wnt signaling. We conducted in vitro assays using UMR‐106 osteosarcoma cells to explore the role CYR61/CCN1 plays in modulating Sost mRNA and protein expression in osteocytes and osteoblasts. Overexpression of CYR61/CCN1 can suppress Sost expression in both control and Cyr61 knockout cells, and blocking Sost with siRNA can rescue Wnt responsiveness in Cyr61 knockout cells in vitro. Overall, our data suggest that CYR61/CCN1 modulates mature osteoblast and osteocyte function to regulate bone mass through angiogenic effects as well as by modulating Wnt signaling, at least in part through the Wnt antagonist Sost. © 2018 American Society for Bone and Mineral Research.
Metabolic dysregulation accelerates injury‐induced joint degeneration, driven by local inflammation; an in vivo rat study

Evidence is growing for the existence of an obesity‐related phenotype of osteoarthritis in which low‐grade inflammation and a disturbed metabolic profile play a role. The contribution of an obesity‐induced metabolic dysbalance to the progression of the features of osteoarthritis upon mechanically induced cartilage damage was studied in a rat in vivo model. Forty Wistar rats were randomly allocated 1:1 to a standard diet or a high‐fat diet. After 12 weeks, in 14 out of 20 rats in each group, cartilage was mechanically damaged in the right knee joint. The remaining six animals in each group served as controls. After a subsequent 12 weeks, serum was collected for metabolic state, subchondral bone changes assessed by μCT imaging, osteoarthritis severity determined by histology, and macrophage presence assessed by CD68 staining. The high‐fat diet increased statistically all relevant metabolic parameters, resulting in a dysmetabolic state and subsequent synovial inflammation, whereas cartilage degeneration was hardly influenced. The high‐fat condition in combination with mechanical cartilage damage resulted in a clear statistically significant progression of the osteoarthritic features, with increased synovitis and multiple large osteophytes. Both the synovium and osteophytes contained numerous CD68 positive cells. It is concluded that a metabolic dysbalance due to a high‐fat diet increases joint inflammation without cartilage degeneration. The dysmetabolic state clearly accelerates progression of osteoarthritis upon surgically induced cartilage damage supported by inflammatory responses as demonstrated by histology and increased CD68 expressing cells localized on the synovial membrane and osteophytes. © 2017 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:881–890, 2018.
What Parents and Their Gay and Bisexual Sons Say About HIV Prevention

Despite ongoing prevention efforts, young gay and bisexual men (YGBM) accounted for more than three fourths of all recent HIV infections. Furthermore, they continue to engage in high-risk sexual behaviors at alarming rates. Nowadays, families are beginning to emerge as important resources for these youth. However, the viewpoints of YGBM and their families are largely missing from HIV prevention research and intervention development. To address this gap, we solicited the opinions of YGBM and their parents as to why YGBM engage in unsafe sex and what might be done to help them avoid HIV. Participants discussed youth’s sense of invulnerability, sexual arousal, parental disapproval, and lack of societal acceptance as contributors to unsafe sex. Participants called for gay-sensitive sex education and community programming as well as increased societal acceptance. Overall, respondents recommended interpersonal and structural-level interventions that emphasized the importance of reducing stigma as a key component of HIV prevention.
Iterative Metallic Artifact Reduction for In-Plane Gonadal Shielding During Computed Tomographic Venography of Young Males

Objective The purpose of this study was to evaluate a gonadal shield (GS) and iterative metallic artifact reduction (IMAR) during computed tomography scans, regarding the image quality and radiation dose. Methods A phantom was imaged with and without a GS. Prospectively enrolled, young male patients underwent lower extremity computed tomography venography (precontrast imaging without the GS and postcontrast imaging with the GS). Radiation dose was measured each time, and the GS-applied images were reconstructed by weighted filtered back projection and IMAR. Results In the phantom study, image artifacts were significantly reduced by using IMAR (P = 0.031), whereas the GS reduced the radiation dose by 61.3%. In the clinical study (n = 29), IMAR mitigated artifacts from the GS, thus 96.6% of the IMAR image sets were clinically usable. Gonadal shielding reduced the radiation dose to the testes by 69.0%. Conclusions The GS in conjunction with IMAR significantly reduced the radiation dose to the testes while maintaining the image quality.
Spatial Niche Facilitates Clonal Reproduction in Seed Plants under Temporal Disturbance

The evolutionary origins and advantages of clonal reproduction relative to sexual reproduction have been discussed for several taxonomic groups. In particular, organisms with a sessile lifestyle are often exposed to spatial and temporal environmental fluctuations. Thus, clonal propagation may be advantageous in such fluctuating environments, for sessile species that can reproduce both sexually and clonally. Here we introduce the concept of niche to a lattice space that changes spatially and temporally, by incorporating the compatibility between the characteristics of a sessile clonal plant with its habitat into a spatially explicit individual-based model. We evaluate the impact of spatially and temporally heterogeneous environments on the evolution of reproductive strategies: the optimal balance between seed and clonal reproduction of a clonal plant. The spatial niche case with local habitats led to avoidance of specialization in reproductive strategy, whereas stable environments or intensive environmental change tended to result in specialization in either clonal or seed reproduction under neutral conditions. Furthermore, an increase in spatial niches made clonal reproduction advantageous, as a consequence of competition among several genets under disturbed conditions, because a ramet reached a favorable habitat through a rare long-distance dispersal event via seed production. Thus, the existence of spatial niches could explain the advantages of clonal propagation.
In Situ Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine

ABSTRACT Microbial biofilms and mineral precipitation commonly co-occur in engineered water systems, such as cooling towers and water purification systems, and both decrease process performance. Microbial biofilms are extremely challenging to control and eradicate. We previously showed that in situ biomineralization and the precipitation and deposition of abiotic particles occur simultaneously in biofilms under oversaturated conditions. Both processes could potentially alter the essential properties of biofilms, including susceptibility to biocides. However, the specific interactions between mineral formation and biofilm processes remain poorly understood. Here we show that the susceptibility of biofilms to chlorination depends specifically on internal transport processes mediated by biomineralization and the accumulation of abiotic mineral deposits. Using injections of the fluorescent tracer Cy5, we show that Pseudomonas aeruginosa biofilms are more permeable to solutes after in situ calcite biomineralization and are less permeable after the deposition of abiotically precipitated calcite particles. We further show that biofilms are more susceptible to chlorine killing after biomineralization and less susceptible after particle deposition. Based on these observations, we found a strong correlation between enhanced solute transport and chlorine killing in biofilms, indicating that biomineralization and particle deposition regulate biofilm susceptibility by altering biocide penetration into the biofilm. The distinct effects of in situ biomineralization and particle deposition on biocide killing highlight the importance of understanding the mechanisms and patterns of biomineralization and scale formation to achieve successful biofilm control.