Miracle-dz/UniFAR-FTUs huggingface dataset:
Preferences for group dominance track and mediate the effects of macro-level social inequality and violence across societies

Significance Individuals differ in the degree to which they endorse group-based hierarchies in which some social groups dominate others. Much research demonstrates that among individuals this preference robustly predicts ideologies and behaviors enhancing and sustaining social hierarchies (e.g., racism, sexism, and prejudice). Combining aggregate archival data from 27 countries (n = 41,824) and multilevel data from 30 US states (n = 4,613) with macro-level indicators, we demonstrate that the degree of structural inequality, social instability, and violence in different countries and US states is reflected in their populations’ minds in the form of support of group-based hegemony. This support, in turn, increases individual endorsement of ideologies and behaviors that ultimately sustain group-based inequality, such as the ethnic persecution of immigrants. Whether and how societal structures shape individual psychology is a foundational question of the social sciences. Combining insights from evolutionary biology, economy, and the political and psychological sciences, we identify a central psychological process that functions to sustain group-based hierarchies in human societies. In study 1, we demonstrate that macrolevel structural inequality, impaired population outcomes, socio-political instability, and the risk of violence are reflected in the endorsement of group hegemony at the aggregate population level across 27 countries (n = 41,824): The greater the national inequality, the greater is the endorsement of between-group hierarchy within the population. Using multilevel analyses in study 2, we demonstrate that these psychological group-dominance motives mediate the effects of macrolevel functioning on individual-level attitudes and behaviors. Specifically, across 30 US states (n = 4,613), macrolevel inequality and violence were associated with greater individual-level support of group hegemony. Crucially, this individual-level support, rather than cultural-societal norms, was in turn uniquely associated with greater racism, sexism, welfare opposition, and even willingness to enforce group hegemony violently by participating in ethnic persecution of subordinate out-groups. These findings suggest that societal inequality is reflected in people’s minds as dominance motives that underpin ideologies and actions that ultimately sustain group-based hierarchy.
Differential Response of Fish Assemblages to Coral Reef-Based Seaweed Farming

As the global demand for seaweed-derived products drives the expansion of seaweed farming onto shallow coral ecosystems, the effects of farms on fish assemblages remain largely unexplored. Shallow coral reefs provide food and shelter for highly diverse fish assemblages but are increasingly modified by anthropogenic activities. We hypothesized that the introduction of seaweed farms into degraded shallow coral reefs had potential to generate ecological benefits for fish by adding structural complexity and a possible food source. We conducted 210 transects at 14 locations, with sampling stratified across seaweed farms and sites adjacent to and distant from farms. At a seascape scale, locations were classified by their level of exposure to human disturbance. We compared sites where (1) marine protected areas (MPAs) were established, (2) neither MPAs nor blast fishing was present (hence “unprotected”), and (3) blast fishing occurred. We observed 80,186 fish representing 148 species from 38 families. The negative effects of seaweed farms on fish assemblages appeared stronger in the absence of blast fishing and were strongest when MPAs were present, likely reflecting the positive influence of the MPAs on fish within them. Species differentiating fish assemblages with respect to seaweed farming and disturbance were typically small but also included two key target species. The propensity for seaweed farms to increase fish diversity, abundance, and biomass is limited and may reduce MPA benefits. We suggest that careful consideration be given to the placement of seaweed farms relative to MPAs.
Parallel Faster-X Evolution of Gene Expression and Protein Sequences in Drosophila: Beyond Differences in Expression Properties and Protein Interactions

Population genetics models predict that the X (or Z) chromosome will evolve at faster rates than the autosomes in XY (or ZW) systems. Studies of molecular evolution using large datasets in multiple species have provided evidence supporting this faster-X effect in protein-coding sequences and, more recently, in transcriptomes. However, X-linked and autosomal genes differ significantly in important properties besides hemizygosity in males, including gene expression levels, tissue specificity in gene expression, and the number of interactions in which they are involved (i.e., protein-protein or DNA-protein interactions). Most important, these properties are known to correlate with rates of evolution, which raises the question of whether differences between the X chromosome and autosomes in gene properties, rather than hemizygosity, are sufficient to explain faster-X evolution. Here I investigate this possibility using whole genome sequences and transcriptomes of Drosophila yakuba and D. santomea and show that this is not the case. Additional factors are needed to account for faster-X evolution of both gene expression and protein-coding sequences beyond differences in gene properties, likely a higher incidence of positive selection in combination with the accumulation of weakly deleterious mutations.
Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins

HIV type 1 (HIV-1) is characterized by its rapid genetic evolution, leading to challenges in anti-HIV therapy. However, the sequence variations in HIV-1 proteins are not randomly distributed due to a combination of functional constraints and genetic drift. In this study, we examined patterns of sequence variability for evidence of linked sequence changes (termed as coevolution or covariation) in 15 HIV-1 proteins. It shows that the percentage of charged residues in the coevolving residues is significantly higher than that in all the HIV-1 proteins. Most of the coevolving residues are spatially proximal in the protein structures and tend to form relatively compact and independent units in the tertiary structures, termed as “protein sectors”. These protein sectors are closely associated with anti-HIV drug resistance, T cell epitopes, and antibody binding sites. Finally, we explored candidate peptide inhibitors based on the protein sectors. Our results can establish an association between the coevolving residues and molecular functions of HIV-1 proteins, and then provide us with valuable knowledge of pathology of HIV-1 and therapeutics development.
Laser-induced photo-thermal strain imaging

Vulnerable plaque is the one of the leading causes of cardiovascular disease occurrence. However, conventional intravascular imaging techniques suffer from difficulty in finding vulnerable plaque due to limitation such as lack of physiological information, imaging depth, and depth sensitivity. Therefore, new techniques are needed to help determine the vulnerability of plaque, Thermal strain imaging (TSI) is an imaging technique based on ultrasound (US) wave propagation speed that varies with temperature of medium. During temperature increase, strain occurs in the medium and its variation tendency is depending on the type of tissue, which makes it possible to use for tissue differentiation. Here, we demonstrate laser-induced photo-thermal strain imaging (pTSI) to differentiate tissue using an intravascular ultrasound (IVUS) catheter and a 1210-nm continuous-wave laser for heating lipids intensively. During heating, consecutive US images were obtained from a custom-made phantom made of porcine fat and gelatin. A cross correlation-based speckle-tracking algorithm was then applied to calculate the strain of US images. In the strain images, the positive strain produced in lipids (porcine fat) was clearly differentiated from water-bearing tissue (gelatin). This result shows that laser-induced pTSI could be a new method to distinguish lipids in the plaque and can help to differentiate vulnerability of plaque.
Fetal Surgery for Myelomeningocele: A Systematic Review and Meta-Analysis of Outcomes in Fetoscopic versus Open Repair

Background/Objectives: The Management of Myelomeningocele (MMC) Study (MOMS) showed that prenatal repair of MMC resulted in improved neurological outcomes but was associated with high rates of obstetrical complications. This study compares outcomes of open and fetoscopic MMC repair. Data Sources: PubMed and Embase studies reporting outcomes of fetal MMC repair published since the completion of the MOMS. Results: We analyzed 11 studies and found no difference in mortality or the rate of shunt placement for hydrocephalus. Percutaneous fetoscopic repair was associated with higher rates of premature rupture of membranes (91 vs. 36%, p < 0.01) and preterm birth (96 vs. 81%, p = 0.04) compared to open repair, whereas fetoscopic repair via maternal laparotomy reduced preterm birth. The rate of dehiscence and leakage from the MMC repair site was higher after both types of fetoscopic surgery (30 vs. 7%, p < 0.01), while the rate of uterine dehiscence was higher after open repair (11 vs. 0%, p < 0.01). Discussion: Fetoscopic repair is a promising alternative to open fetal MMC repair with a lower risk of uterine dehiscence; however, fetoscopic techniques should be optimized to overcome the high rate of dehiscence and leakage at the MMC repair site. A fetoscopic approach via maternal laparotomy reduces the risk of preterm birth.
A Genome-Wide Association Study for Clinical Mastitis in First Parity US Holstein Cows Using Single-Step Approach and Genomic Matrix Re-Weighting Procedure

Clinical mastitis (CM) is one of the health disorders with large impacts on dairy farming profitability and animal welfare. The objective of this study was to perform a genome-wide association study (GWAS) for CM in first-lactation Holstein. Producer-recorded mastitis event information for 103,585 first-lactation cows were used, together with genotype information on 1,361 bulls from the Illumina BovineSNP50 BeadChip. Single-step genomic-BLUP methodology was used to incorporate genomic data into a threshold-liability model. Association analysis confirmed that CM follows a highly polygenic mode of inheritance. However, 10-adjacent-SNP windows showed that regions on chromosomes 2, 14 and 20 have impacts on genetic variation for CM. Some of the genes located on chromosome 14 (LY6K, LY6D, LYNX1, LYPD2, SLURP1, PSCA) are part of the lymphocyte-antigen-6 complex (LY6) known for its neutrophil regulation function linked to the major histocompatibility complex. Other genes on chromosome 2 were also involved in regulating immune response (IFIH1, LY75, and DPP4), or are themselves regulated in the presence of specific pathogens (ITGB6, NR4A2). Other genes annotated on chromosome 20 are involved in mammary gland metabolism (GHR, OXCT1), antibody production and phagocytosis of bacterial cells (C6, C7, C9, C1QTNF3), tumor suppression (DAB2), involution of mammary epithelium (OSMR) and cytokine regulation (PRLR). DAVID enrichment analysis revealed 5 KEGG pathways. The JAK-STAT signaling pathway (cell proliferation and apoptosis) and the ‘Cytokine-cytokine receptor interaction’ (cytokine and interleukines response to infectious agents) are co-regulated and linked to the ‘ABC transporters’ pathway also found here. Gene network analysis performed using GeneMania revealed a co-expression network where 665 interactions existed among 145 of the genes reported above. Clinical mastitis is a complex trait and the different genes regulating immune response are known to be pathogen-specific. Despite the lack of information in this study, candidate QTL for CM were identified in the US Holstein population.
An LS-Decomposition Approach for Robust Data Recovery in Wireless Sensor Networks

Wireless sensor networks are widely adopted in military, civilian and commercial applications, which fuels an exponential explosion of sensory data. However, a major challenge to deploy effective sensing systems is the presence of {\em massive missing entries, measurement noise, and anomaly readings}. Existing works assume that sensory data matrices have low-rank structures. This does not hold in reality due to anomaly readings, causing serious performance degradation. In this paper, we introduce an {\em LS-Decomposition} approach for robust sensory data recovery, which decomposes a corrupted data matrix as the superposition of a low-rank matrix and a sparse anomaly matrix. First, we prove that LS-Decomposition solves a convex program with bounded approximation error. Second, using data sets from the IntelLab, GreenOrbs, and NBDC-CTD projects, we find that sensory data matrices contain anomaly readings. Third, we propose an accelerated proximal gradient algorithm and prove that it approximates the optimal solution with convergence rate $O(1/k^2)$ ($k$ is the number of iterations). Evaluations on real data sets show that our scheme achieves recovery error $\leq 5\%$ for sampling rate $\geq 50\%$ and almost exact recovery for sampling rate $\geq 60\%$, while state-of-the-art methods have error $10\% \sim 15\%$ at sampling rate $90\%$.
Genetic Structure Analysis of Spirometra erinaceieuropaei Isolates from Central and Southern China

Background Sparganosis caused by invasion of the plerocercoid larvae (spargana) of Spirometra erinaceieuropaei have increased in recent years in China. However, the population genetic structure regarding this parasite is still unclear. In this study, we used the sequences of two mitochondrial genes cytochrome b (cytb) and cytochrome c oxidase subunit I (cox1) to analyze genetic variation and phylogeographic structure of the S. erinaceieuropaei populations. Methodology/Principal Findings A total of 88 S. erinaceieuropaei isolates were collected from naturally infected frogs in 14 geographical locations of China. The complete cytb and cox1 genes of each sample was amplified and sequenced. Total 61 haplotypes were found in these 88 concatenated sequences. Each sampled population and the total population have high haplotype diversity (Hd), accompanied by very low nucleotide diversity (Pi). Phylogenetic analyses of haplotypes revealed two distinct clades (HeN+HuN+GZ-AS clade and GX+HN+GZ-GY clade) corresponding two sub-networks yielded by the median-joining network. Pairwise F ST values supported great genetic differentiation between S. erinaceieuropaei populations. Both negative Fu’s F S value of neutrality tests and unimodal curve of mismatch distribution analyses supported demographic population expansion in the HeN+HuN+GZ-AS clade. The BEAST analysis showed that the divergence time between the two clades took place in the early Pleistocene (1.16 Myr), and by Bayesian skyline plot (BSP) an expansion occurred after about 0.3 Myr ago. Conclusions S. erinaceieuropaei from central and southern China has significant phylogeographic structure, and climatic oscillations during glacial periods in the Quaternary may affect the demography and diversification of this species.
MR elastography of liver tumors: preliminary results.

OBJECTIVE The purpose of this study was to evaluate the potential value of MR elastography (MRE) in the characterization of solid liver tumors. MATERIALS AND METHODS Forty-four liver tumors (14 metastatic lesions, 12 hepatocellular carcinomas, nine hemangiomas, five cholangiocarcinomas, three cases of focal nodular hyperplasia, and one hepatic adenoma) were evaluated with MRE. MRE was performed with a 1.5-T system with a modified phase-contrast gradient-echo sequence to collect axial wave images sensitized along the through-plane motion direction. The tumors were identified on T2- and T1-weighted and gadolinium-enhanced T1-weighted images, and the MRE images were obtained through the tumor. A stiffness map (elastogram) was generated in an automated process consisting of an inversion algorithm. The mean shear stiffness of the tumor was calculated with a manually specified region of interest over the tumor in the stiffness map. The stiffness value of tumor-free hepatic parenchyma was calculated. Statistical analysis was performed on the stiffness values for differentiation of normal liver, fibrotic liver, benign tumors, and malignant tumors. RESULTS Malignant liver tumors had significantly greater mean shear stiffness than benign tumors (10.1 kPa vs 2.7 kPa, p < 0.001), fibrotic liver (10.1 kPa vs 5.9 kPa, p < 0.001), and normal liver (10.1 kPa vs 2.3 kPa, p < 0.001). Fibrotic livers had stiffness values overlapping both the benign and the malignant tumors. A cutoff value of 5 kPa accurately differentiated malignant tumors from benign tumors and normal liver parenchyma in this preliminary investigation. CONCLUSION MR elastography is a promising noninvasive technique for assessing solid liver tumors. Use of MRE may lead to new quantitative tissue characterization parameters for differentiating benign and malignant liver tumors.
Risk of Hepatocellular Cancer in HCV Patients Treated With Direct-Acting Antiviral Agents.

BACKGROUND AND AIMS The risk of hepatocellular cancer (HCC) after sustained virological response (SVR) with direct-acting antivirals (DAA) is unclear. Our aim was to examine the risk and determinants of HCC in patients cured with DAA. METHODS We conducted a retrospective cohort study of hepatitis C virus patients who were treated with DAA in any of the 129 Veterans Health Administration hospitals between January 1, 2015 and December 31, 2015. We calculated the annual incidence rates of HCC by SVR. We used Cox regression models to compare the risk of HCC in patients with vs those without SVR and to identify factors associated with incident HCC among patients with SVR. We reviewed a sample of HCC patients for tumor size and stage at diagnosis. RESULTS Among 22,500 patients treated with DAA (19,518 with SVR; 2982 without SVR), the mean (standard deviation) age was 61.6 (6.1) years, and 39.0% had cirrhosis. There were 271 new cases of HCC, including 183 in patients with SVR. Compared with patients without SVR, those with SVR had a significantly reduced risk of HCC (0.90 vs 3.45 HCC/100 person-years; adjusted hazard ratio, 0.28, 95% CI=0.22-0.36). Patients with cirrhosis had the highest annual incidence of HCC after SVR (1.82 vs 0.34/100 person-years in patients without cirrhosis; adjusted hazard ratio, 4.73. 95% CI, 3.34-6.68). Most (>44.8%) HCC were classified as stage I. Maximum size of the largest lesion was ≤5 cm in over 75% of cases. CONCLUSIONS Among patients treated with DAA, SVR was associated with a considerable reduction in the risk of HCC. We did not find any evidence to suggest that DAAs promote HCC. However, in patients with SVR, the absolute risk of HCC remained high in patients with established cirrhosis. These patients should be considered for ongoing HCC surveillance.
Protective effects of melatonin on the in vitro developmental competence of bovine oocytes.

The present study investigated the effects of melatonin on bovine oocyte maturation and subsequent embryonic development in vitro. Results showed that the nuclear and cytoplasmic maturation, characterized by first polar body extrusion, normal distribution of cortical granules and mitochondria, as well as increased mitochondrial membrane potential, were significantly improved in 10-9 mol/L melatonin-treated oocytes. Melatonin supplementation reduced intracellular reactive oxygen species level and enhanced glutathione production. Meanwhile, the presence of melatonin (10-9 mol/L) during oocyte maturation resulted in a decreased early apoptotic rate in oocytes. After in vitro fertilization, oocytes receiving melatonin supplementation exhibited a significantly higher blastocyst formation rate and yielded a markedly lower number of apoptotic cells. Mechanistic explorations showed that addition of 10-9 mol/L melatonin to in vitro maturation media significantly attenuated the transcript level of caspase-3, while the expressions of BCL-2, XIAP, CAT and HSP70 were significantly reinforced in the resultant embryos. Taken together, melatonin ameliorates bovine oocyte maturation potential, and the beneficial effects can affect subsequent embryonic development. The protective role of melatonin may be due to its anti-apoptotic and anti-oxidative activities.
Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.
Preventing Effect of L-Type Calcium Channel Blockade on Electrophysiological Alterations in Dentate Gyrus Granule Cells Induced by Entorhinal Amyloid Pathology

The entorhinal cortex (EC) is one of the earliest affected brain regions in Alzheimer’s disease (AD). EC-amyloid pathology induces synaptic failure in the dentate gyrus (DG) with resultant behavioral impairment, but there is little known about its impact on neuronal properties in the DG. It is believed that calcium dyshomeostasis plays a pivotal role in the etiology of AD. Here, the effect of the EC amyloid pathogenesis on cellular properties of DG granule cells and also possible neuroprotective role of L-type calcium channel blockers (CCBs), nimodipine and isradipine, were investigated. The amyloid beta (Aβ) 1–42 was injected bilaterally into the EC of male rats and one week later, electrophysiological properties of DG granule cells were assessed. Voltage clamp recording revealed appearance of giant sIPSC in combination with a decrease in sEPSC frequency which was partially reversed by CCBs in granule cells from Aβ treated rats. EC amyloid pathogenesis induced a significant reduction of input resistance (Rin) accompanied by a profound decreased excitability in the DG granule cells. However, daily administration of CCBs, isradipine or nimodipine (i.c.v. for 6 days), almost preserved the normal excitability against Aβ. In conclusion, lower tendency to fire AP along with reduced Rin suggest that DG granule cells might undergo an alteration in the membrane ion channel activities which finally lead to the behavioral deficits observed in animal models and patients with early-stage Alzheimer’s disease.