Miracle-dz/UniFAR-FTUs huggingface dataset:
The assignment of chemokine‐chemokine receptor pairs: TARC and MIP‐1β are not ligands for human CC‐chemokine receptor 8

Identification of chemokine receptors and their associated ligands is crucial to the understanding of most immune reactions. Three human chemokines [I‐309, thymus and activation‐regulated chemokine (TARC) and macrophage inflammatory protein‐1β (MIP‐1β)] have been reported to be ligands for CC‐chemokine receptor 8 (CCR8). In this report, we present evidence that TARC and MIP‐1β did not bind to or induce chemotaxis through CCR8 on a stable transfected cell line (1D‐21) and did not bind to CCR8 on in vitro differentiated human CD4+ Th2 cell cultures. Also, I‐309‐dependent calcium mobilization in 1D‐21 cells and in Th2 cells was desensitized by I‐309 but not by MIP‐1β or TARC. These results provide strong evidence that, at physiologically relevant concentrations, I‐309 is the only known human ligand for CCR8. These data also provide a framework for suggesting minimum requirements for the assignment of chemokine receptor‐ligand pairs.
Using Lidar Data to Analyse Sinkhole Characteristics Relevant for Understory Vegetation under Forest Cover—Case Study of a High Karst Area in the Dinaric Mountains

In this article, we investigate the potential for detection and characterization of sinkholes under dense forest cover by using airborne laser scanning data. Laser pulse returns from the ground provide important data for the estimation of digital elevation model (DEM), which can be used for further processing. The main objectives of this study were to map and determine the geomorphometric characteristics of a large number of sinkholes and to investigate the correlations between geomorphology and vegetation in areas with such characteristics. The selected study area has very low anthropogenic influences and is particularly suitable for studying undisturbed karst sinkholes. The information extracted from this study regarding the shapes and depths of sinkholes show significant directionality for both orientation of sinkholes and their distribution over the area. Furthermore, significant differences in vegetation diversity and composition occur inside and outside the sinkholes, which indicates their presence has important ecological impacts.
Larval Starvation to Satiation: Influence of Nutrient Regime on the Success of Acanthaster planci

High density populations of the crown-of-thorns seastar, Acanthaster planci, are a major contributor to the decline of coral reefs, however the causes behind periodic outbreaks of this species are not understood. The enhanced nutrients hypothesis posits that pulses of enhanced larval food in eutrophic waters facilitate metamorphic success with a flow-on effect for population growth. The larval resilience hypothesis suggests that A. planci larvae naturally thrive in tropical oligotrophic waters. Both hypotheses remain to be tested empirically. We raised A. planci larvae in a range of food regimes from starvation (no food) to satiation (excess food). Algal cell concentration and chlorophyll levels were used to reflect phytoplankton conditions in nature for oligotrophic waters (0-100 cells ml-1; 0-0.01 μg chl a L-1), natural background levels of nutrients on the Great Barrier Reef (GBR) (1,000-10,000 cells ml-1; 0.1-1.0 μg chl a L-1), and enhanced eutrophic conditions following runoff events (100,000 cells ml-1; 10 μg chl a L-1). We determine how these food levels affected larval growth and survival, and the metamorphic link between larval experience and juvenile quality (size) in experiments where food ration per larvae was carefully controlled. Phytoplankton levels of 1 μg chl a L-1, close to background levels for some reefs on the GBR and following flood events, were optimal for larval success. Development was less successful above and below this food treatment. Enhanced larval performance at 1 μg chl a L-1 provides empirical support for the enhanced nutrients hypothesis, but up to a limit, and emphasizes the need for appropriate mitigation strategies to reduce eutrophication and the consequent risk of A. planci outbreaks.
Hierarchical Clustering of Breast Cancer Methylomes Revealed Differentially Methylated and Expressed Breast Cancer Genes

Oncogenic transformation of normal cells often involves epigenetic alterations, including histone modification and DNA methylation. We conducted whole-genome bisulfite sequencing to determine the DNA methylomes of normal breast, fibroadenoma, invasive ductal carcinomas and MCF7. The emergence, disappearance, expansion and contraction of kilobase-sized hypomethylated regions (HMRs) and the hypomethylation of the megabase-sized partially methylated domains (PMDs) are the major forms of methylation changes observed in breast tumor samples. Hierarchical clustering of HMR revealed tumor-specific hypermethylated clusters and differential methylated enhancers specific to normal or breast cancer cell lines. Joint analysis of gene expression and DNA methylation data of normal breast and breast cancer cells identified differentially methylated and expressed genes associated with breast and/or ovarian cancers in cancer-specific HMR clusters. Furthermore, aberrant patterns of X-chromosome inactivation (XCI) was found in breast cancer cell lines as well as breast tumor samples in the TCGA BRCA (breast invasive carcinoma) dataset. They were characterized with differentially hypermethylated XIST promoter, reduced expression of XIST, and over-expression of hypomethylated X-linked genes. High expressions of these genes were significantly associated with lower survival rates in breast cancer patients. Comprehensive analysis of the normal and breast tumor methylomes suggests selective targeting of DNA methylation changes during breast cancer progression. The weak causal relationship between DNA methylation and gene expression observed in this study is evident of more complex role of DNA methylation in the regulation of gene expression in human epigenetics that deserves further investigation.
Mind the Gap: Genetic Manipulation of Basicranial Growth within Synchondroses Modulates Calvarial and Facial Shape in Mice through Epigenetic Interactions

Phenotypic integration patterns in the mammalian skull have long been a focus of intense interest as a result of their suspected influence on the trajectory of hominid evolution. Here we test the hypothesis that perturbation of cartilage growth, which directly affects only the chondrocranium during development, will produce coordinated shape changes in the adult calvarium and face regardless of mechanism. Using two murine models of cartilage undergrowth that target two very different mechanisms, we show that strong reduction in cartilage growth produces a short, wide, and more flexed cranial base. This in turn produces a short, wide face in both models. Cranial base and face are already correlated early in ontogeny, and the relationship between these modules gains structure through postnatal growth and development. These results provide further evidence that there exist physical interactions between developing parts of the phenotype that produce variation at a distance from the actual locus upon which a particular selective pressure is acting. Phenotypic changes observed over the course of evolution may not all require adaptationist explanations; rather, it is likely that a substantial portion of observed phenotypic variation over the history of a clade is not directly adaptive but rather a secondary consequence of some local response to selection.
Association of Blood Lead Levels with Methylenetetrahydrofolate Reductase Polymorphisms among Chinese Pregnant Women in Wuhan City

Background Pregnancy is an important stimulus of bone lead release. Elevated blood lead levels (BLLs) may cause adverse pregnancy outcomes for mothers and harmful lead effects on fetuses. However, the reports about maternal BLL changes during pregnancy are conflicting to some extent. This article is to explore the variations in BLLs among pregnant women. The relationships of BLLs with methylenetetrahydrofolate reductase (MTHFR) gene C677T, A1298C, and G1793A polymorphisms, which are associated with bone resorption, were also studied. A total of 973 women, including 234, 249, and 248 women in their first, second, and third trimesters, respectively, and 242 non-pregnant women, were recruited at the Wuhan Women and Children Medical Health Center. Methods BLLs were determined using a graphite furnace atomic absorption spectrometer. Single-nucleotide polymorphisms of MTHFR were identified with the TaqMan probe method. Results The geometric mean (geometric standard deviation) of BLLs was 16.2 (1.78) μg/L for all participants. All the studied MTHFR alleles were in Hardy-Weinberg equilibrium. Multiple-linear regression analysis revealed the following results. Among the pregnant women, those that carried MTHFR 677CC (i.e. wild-genotype homozygote) and 1298CC (i.e. mutant-genotype homozygote) exhibited higher BLLs than those that carried 677CT/TT (standardized β = 0.074, P = 0.042) and 1298AC/AA (standardized β = 0.077, P = 0.035) when other covariates (e.g., age, no. of children, education and income, etc.) were adjusted. The BLLs of pregnant women consistently decreased during the pregnancy and these levels positively correlated with BMI (standard β = 0.086–0.096, P<0.05). Conclusions The 1298CC mutant-type homozygote in the MTHFR gene is a risk factor for high BLLs among low-level environmental lead-exposed Chinese pregnant women, whose BLLs consistently decreased during gestation.
Variation in Pollen-Donor Composition among Pollinators in an Entomophilous Tree Species, Castanea crenata, Revealed by Single-Pollen Genotyping

Background In plants, reproductive success is largely determined by the composition of pollen (i.e., self-pollen and outcross-pollen from near and distant pollen-donors) transported as a result of pollinator foraging behavior (e.g., pollen carryover). However, little evidence is available on how and to what extent the pollen carryover affects the pollen-donor composition and on which insect taxa are effective outcross-pollen transporters under field conditions. In this study, we explored roles of foraging behavior of insect pollinators on pollen-donor composition and subsequent reproductive success in a woody plant. Methods We performed paternity analyses based on microsatellite genotyping of individual pollen grains found on diurnal pollinators (i.e., bumblebee, small bee, fly, small beetle, and honeybee) visiting Castanea crenata trees. Results The outcross-pollen rate was highest in bumblebees (66%), followed by small bees (35%), flies (31%), and small beetles (18%). The effective number of pollen donors, representing pollen carryover, was greater in bumblebees (9.71) than in flies (3.40), small bees (3.32), and small beetles (3.06). The high percentages of pollen from outside the plot on bumblebees (65.4%) and flies (71.2%) compared to small bees (35.3%) and small beetles (13.5%) demonstrated their longer pollen dispersal distances. Conclusions All of the diurnal insects carried outcross-pollen grains for long distances via pollen carryover. This fact suggests that a wide range of insect taxa are potential outcross-pollen transporters for the self-incompatible C. crenata.
Is Ground Cover Vegetation an Effective Biological Control Enhancement Strategy against Olive Pests?

Ground cover vegetation is often added or allowed to generate to promote conservation biological control, especially in perennial crops. Nevertheless, there is inconsistent evidence of its effectiveness, with studies reporting positive, nil or negative effects on pest control. This might arise from differences between studies at the local scale (e.g. orchard management and land use history), the landscape context (e.g. presence of patches of natural or semi-natural vegetation near the focal orchard), or regional factors, particularly climate in the year of the study. Here we present the findings from a long-term regional monitoring program conducted on four pest species (Bactrocera oleae, Prays oleae, Euphyllura olivina, Saissetia oleae) in 2,528 olive groves in Andalusia (Spain) from 2006 to 2012. Generalized linear mixed effect models were used to analyze the effect of ground cover on different response variables related to pest abundance, while accounting for variability at the local, landscape and regional scales. There were small and inconsistent effects of ground cover on the abundance of pests whilst local, landscape and regional variability explained a large proportion of the variability in pest response variables. This highlights the importance of local and landscape-related variables in biological control and the potential effects that might emerge from their interaction with practices, such as groundcover vegetation, implemented to promote natural enemy activity. The study points to perennial vegetation close to the focal crop as a promising alternative strategy for conservation biological control that should receive more attention.
Genetic Diversity of Mycobacterium tuberculosis from Guadalajara, Mexico and Identification of a Rare Multidrug Resistant Beijing Genotype

Determining the genetic diversity of M. tuberculosis strains allows identification of the distinct Mycobacterium tuberculosis genotypes responsible for tuberculosis in different regions. Several studies have reported the genetic diversity of M. tuberculosis strains in Mexico, but little information is available from the state of Jalisco. Therefore, the aim of this study was to determine the genetic diversity of Mycobacterium tuberculosis clinical isolates from Western Mexico. Sixty-eight M. tuberculosis isolates were tested for susceptibility to first-line drugs using manual Mycobacteria Growth Indicator Tube method and genotyped using spoligotyping and IS6110-restriction fragment length polymorphism (RFLP) pattern analyses. Forty-seven (69.1%) isolates were grouped into 10 clusters and 21 isolates displayed single patterns by spoligotyping. Three of the 21 single patterns corresponded to orphan patterns in the SITVITWEB database, and 1 new type that contained 2 isolates was created. The most prevalent lineages were T (38.2%), Haarlem (17.7%), LAM (17.7%), X (7.4%), S (5.9%), EAI (1.5%) and Beijing (1.5%). Six (12.8%) of the clustered isolates were MDR, and type 406 of the Beijing family was among the MDR isolates. Seventeen (26.2%) isolates were grouped into 8 clusters and 48 isolates displayed single patterns by IS6110-RFLP. Combination of IS6110-RFLP and spoligotyping reduced the clustering rate to 20.0%. The results show that T, Haarlem, and LAM are predominant lineages among clinical isolates of M. tuberculosis in Guadalajara, Mexico. Clustering rates indicated low transmission of MDR strains. We detected a rare Beijing genotype, SIT406, which was a highly resistant strain. This is the first report of this Beijing genotype in Latin America.
Balance and Frustration in Signed Networks under Different Contexts

Frustration index is a key measure for analysing signed networks that has been underused due to its computational complexity. We use an optimisation-based method to analyse frustration as a global structural property of signed networks under different contexts. We provide exact numerical results on social and biological signed networks as well as networks of formal alliances and antagonisms between countries and financial portfolio networks. Molecular graphs of carbon and spin glass models are among other networks that we consider to discuss context-dependent interpretations of the frustration index. The findings unify the applications of a graph-theoretical measure in understanding signed networks. Highlights: - Models involving signed networks in 6 different disciplines are analysed - An optimisation model is used for a wide range of computational experiments - Values of the frustration index in large graphs are computed exactly and efficiently - Applications of signed network balance and frustration are unified
Early Life-History Consequences of Growth-Hormone Transgenesis in Rainbow Trout Reared in Stream Ecosystem Mesocosms

There is persistent commercial interest in the use of growth modified fishes for shortening production cycles and increasing overall food production, but there is concern over the potential impact that transgenic fishes might have if ever released into nature. To explore the ecological consequences of transgenic fish, we performed two experiments in which the early growth and survival of growth-hormone transgenic rainbow trout (Oncorhynchus mykiss) were assessed in naturalized stream mesocosms that either contained predators or were predator-free. We paid special attention to the survival bottleneck that occurs during the early life-history of salmonids, and conducted experiments at two age classes (first-feeding fry and 60 days post-first-feeding) that lie on either side of the bottleneck. In the late summer, the first-feeding transgenic trout could not match the growth potential of their wild-type siblings when reared in a hydrodynamically complex and oligotrophic environment, irrespective of predation pressure. Furthermore, overall survival of transgenic fry was lower than in wild-type (transgenic = 30% without predators, 8% with predators; wild-type = 81% without predators, 31% with predators). In the experiment with 60-day old fry, we explored the effects of the transgene in different genetic backgrounds (wild versus domesticated). We found no difference in overwinter survival but significantly higher growth by transgenic trout, irrespective of genetic background. We conclude that the high mortality of GH-transgenic trout during first-feeding reflects an inability to sustain the basic metabolic requirements necessary for life in complex, stream environments. However, when older, GH-transgenic fish display a competitive advantage over wild-type fry, and show greater growth and equal survival as wild-type. These results demonstrate how developmental age and time of year can influence the response of genotypes to environmental conditions. We therefore urge caution when extrapolating the results of GH-transgenesis risk assessment studies across multiple life-history or developmental stages.
Assessing the Effects of Multiple Stressors on the Recruitment of Fruit Harvested Trees in a Tropical Dry Forest, Western Ghats, India

The harvest of non-timber forest products (NTFPs), together with other sources of anthropogenic disturbance, impact plant populations greatly. Despite this, conservation research on NTFPs typically focuses on harvest alone, ignoring possible confounding effects of other anthropogenic and ecological factors. Disentangling anthropogenic disturbances is critical in regions such as India’s Western Ghats, a biodiversity hotspot with high human density. Identifying strategies that permit both use and conservation of resources is essential to preserving biodiversity while meeting local needs. We assessed the effects of NTFP harvesting (fruit harvest from canopy and lopping of branches for fruit) in combination with other common anthropogenic disturbances (cattle grazing, fire frequency and distance from village), in order to identify which stressors have greater effects on recruitment of three tropical dry forest fruit tree species. Specifically, we assessed the structure of 54 populations of Phyllanthus emblica, P. indofischeri and Terminalia chebula spread across the Nilgiri Biosphere Reserve, Western Ghats to ask: (1) How are populations recruiting? and (2) What anthropogenic disturbance and environmental factors, specifically forest type and elevation, are the most important predictors of recruitment status? We combined participatory research with an information-theoretic model-averaging approach to determine which factors most affect population structure and recruitment status. Our models illustrate that for T. chebula, high fire frequency and high fruit harvest intensity decreased the proportion of saplings, while lopping branches or stems to obtain fruit increased it. For Phyllanthus spp, recruitment was significantly lower in plots with more frequent fire. Indices of recruitment of both species were significantly higher for plots in more open-canopy environments of savanna woodlands than in dry forests. Our research illustrates an approach for identifying which factors are most important in limiting recruitment of NTFP populations and other plant species that may be in decline, in order to design effective management strategies.
Relationship of Ocular Microcirculation, Measured by Laser Speckle Flowgraphy, and Silent Brain Infarction in Primary Aldosteronism

Purpose Recent studies have shown that the risk of cerebro- and cardiovascular events (CVEs) is higher in patients with primary aldosteronism (PA) than in those with essential hypertension (EH), and that silent brain infarction (SBI) is a risk factor and predictor of CVEs. Here, we evaluated the relationship between findings from laser speckle flowgraphy (LSFG), a recently introduced non-invasive means of measuring mean blur rate (MBR), an important biomarker of ocular blood flow, and the occurrence of SBI in patients with PA. Methods 87 PA patients without symptomatic cerebral events (mean 55.1 ± 11.2 years old, 48 male and 39 female) were enrolled in this study. We measured MBR in the optic nerve head (ONH) with LSFG and checked the occurrence of SBI with magnetic resonance imaging. We examined three MBR waveform variables: skew, blowout score (BOS) and blowout time (BOT). We also recorded clinical findings, including age, blood pressure, and plasma aldosterone concentration. Results PA patients with SBI (15 of 87 patients; 17%) were significantly older and had significantly lower BOT in the capillary area of the ONH than the patients without SBI (P = 0.02 and P = 0.03, respectively). Multiple logistic regression analysis revealed that age and BOT were independent factors for the presence of SBI in PA patients (OR, 1.15, 95% CI 1.01–1.38; P = .03 and OR, 0.73, 95% CI 0.45–0.99; P = .04, respectively). Conclusion PA patients with SBI were older and had lower MBR BOT than those without SBI. Our analysis showed that age was a risk factor for SBI, and that BOT was a protective factor, in patients with PA. This suggests that BOT, a non-invasive and objective biomarker, may be a useful predictor of SBI and form part of future PA evaluations and clinical decision-making.
Solving (most) of a set of quadratic equalities: Composite optimization for robust phase retrieval

We develop procedures, based on minimization of the composition $f(x) = h(c(x))$ of a convex function $h$ and smooth function $c$, for solving random collections of quadratic equalities, applying our methodology to phase retrieval problems. We show that the prox-linear algorithm we develop can solve phase retrieval problems—even with adversarially faulty measurements—with high probability as soon as the number of measurements $m$ is a constant factor larger than the dimension $n$ of the signal to be recovered. The algorithm requires essentially no tuning—it consists of solving a sequence of convex problems—and it is implementable without any particular assumptions on the measurements taken. We provide substantial experiments investigating our methods, indicating the practical effectiveness of the procedures and showing that they succeed with high probability as soon as $m / n \ge 2$ when the signal is real-valued.