Miracle-dz/UniFAR-FTUs huggingface dataset:
Exogenous Auxin Induces Transverse Microtubule Arrays Through TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX Receptors1

Exogenous auxin triggers transverse patterning of cortical microtubule arrays through the TIR1/AFB receptor pathway. Auxin plays a central role in controlling plant cell growth and morphogenesis. Application of auxin to light-grown seedlings elicits both axial growth and transverse patterning of the cortical microtubule cytoskeleton in hypocotyl cells. Microtubules respond to exogenous auxin within 5 min, although repatterning of the array does not initiate until 30 min after application and is complete by 2 h. To examine the requirements for auxin-induced microtubule array patterning, we used an Arabidopsis (Arabidopsis thaliana) double auxin f-box (afb) receptor mutant, afb4-8 afb5-5, that responds to conventional auxin (indole-3-acetic acid) but has a strongly diminished response to the auxin analog, picloram. We show that 5 µm picloram induces immediate changes to microtubule density and later transverse microtubule patterning in wild-type plants, but does not cause microtubule array reorganization in the afb4-8 afb5-5 mutant. Additionally, a dominant mutant (axr2-1) for the auxin coreceptor AUXIN RESPONSIVE2 (AXR2) was strongly suppressed for auxin-induced microtubule array reorganization, providing additional evidence that auxin functions through a transcriptional pathway for transverse patterning. We observed that brassinosteroid application mimicked the auxin response, showing both early and late microtubule array effects, and induced transverse patterning in the axr2-1 mutant. Application of auxin to the brassinosteroid synthesis mutant, diminuto1, induced transverse array patterning but did not produce significant axial growth. Thus, exogenous auxin induces transverse microtubule patterning through the TRANSPORT INHIBITOR 1/AUXIN F-BOX (TIR1/AFB) transcriptional pathway and can act independently of brassinosteroids.
Trends and Disparities in Self-Reported and Measured Osteoporosis among US Adults, 2007–2014

(1) Background: Studies examining osteoporosis trends among US adults by different socioeconomic status (SES) are limited. The prevalence of self-reported osteoporosis in the US is rarely reported. (2) Methods: Data from the National Health and Nutritional Examination Survey (NHANES) between 2007–2008 and 2013–2014 cycles were analyzed. Age-adjusted prevalence of self-reported and that of measured osteoporosis were calculated overall and by sex, race/ethnicity, education attainment, and SES. (3) Results: The prevalence of self-reported osteoporosis was higher than that of measured osteoporosis in all three survey cycles for women, and in 2007–2008 and 2009–2010 for men. Participants with high school/GED or higher educational attainment had an increased prevalence of measured osteoporosis during the study period. Among all SES groups, participants with low family income (PIR < 1.3) had the highest prevalence of measured osteoporosis, and the prevalence increased from 49.3 per 1000 population to 71.8 per 1000 population during the study period. (4) Conclusions: The prevalence of self-reported osteoporosis was higher than that of measured osteoporosis in US adults between 2007 and 2014. The age-adjusted prevalence of measured osteoporosis increased in participants with the educational attainment of high school/GED or above, and individuals with low family income.
Reproductive autonomy and pregnancy decision-making among young Ghanaian women

ABSTRACT Decision-making regarding the outcome of a pregnancy may include participation of the woman herself, her sexual partner, parents, family, and/or community. This paper examines who had the most say in the outcome of young Ghanaian women’s last pregnancy and whether this correlated with her level of reproductive autonomy (RA). We analysed cross-sectional data from 380 previously pregnant young women in urban Ghana. We measured communication and decision-making RA using modified scales ranging from 3 (low RA) to 12 (high RA). We tested unadjusted associations between the RA sub-scales and who made the pregnancy decision (self, partner, both together, or someone else) and used multinomial regression models to understand these associations when controlling for sociodemographic, reproductive history, and social context variables. In final models, a one-point increase in decision-making RA was associated with an adjusted relative risk ratio of 0.79 (95% CI: 0.66–0.93; p = 0.006) of partner having the most say as compared to the woman having the most say. The communication RA scale was not associated. Programmes that increase RA may be effective in increasing women’s rights to execute decisions about reproductive health and outcomes. Future research should explore this notion and the role of pregnancy disclosure in this relationship.
Copy Number Variation of the CADM2 Gene and Its Association with Growth Traits in Yak

Simple Summary Cell adhesion molecule 2 (CADM2), also known as synaptic cell adhesion molecule 2 (SYNCAM2), is the mediator of synaptic signals enriched in the brain. Overlaps between copy number variation (CNV) regions in CADM2 and quantitative trait loci (QTL) related to body weight have been clarified in a previous study. In this study, two loci were amplified in the CADM2 gene (CNV1: 235,915 bp, exon 1 and partial intron 1; CNV2: 60,430 bp, intron 9) to explore the relationship between CNV types in the CADM2 gene and growth traits in 350 Ashidan yaks. Association analysis illustrated that no significant effect was found on growth traits in CNV1. However, the CNV2 mutation had a significant effect on body weight at the sixth month (p < 0.05). Individuals with the gain-type copy number variation CNV2 were significantly superior to those with loss- or normal-type in terms of body weight (p < 0.05). In summary, this study confirmed that CADM2-CNVs affect growth traits in yaks, and may be candidate genes for successful yak breeding and genetics projects. Abstract Copy number variation (CNV) is currently accepted as a common source of genetic variation. It is reported that CNVs may influence the resistance to disease and complex economic traits, such as residual feed intake, muscle formation, and fat deposition in livestock. Cell adhesion molecule 2 (CADM2) is expressed widely in the brain and adipose tissue and can regulate body weight through the central nervous system. Growth traits are important economic traits for animal selection. In this study, we aimed to explore the effect of CADM2 gene copy number variants on yak growth traits. Here, two CNVs in the CADM2 gene were investigated using the quantitative polymerase chain reaction (qPCR), and the association of the CNVs with growth traits in yak was analyzed using statistical methods by SPSS software. Differences were considered significant if the p value was < 0.05. Statistical analysis indicated significant association of CADM2-CNV2 with the body weight of the Chinese Ashidan yak. A significant effect of CNV2 (p < 0.05) was found on body weight at 6 months. In CNV2, the gain-type copy number variation exhibited greater performance than the other variants, with greater body weight observed at 6 months (p < 0.05). To the best of our knowledge, this is the first attempt to investigate the function of CADM2-CNVs and their association with growth traits in animals. This may be a useful candidate marker in marker-assisted selection of yaks.
Structure–Function Analysis Reveals the Singularity of Plant Mitochondrial DNA Replication Components: A Mosaic and Redundant System

Plants are sessile organisms, and their DNA is particularly exposed to damaging agents. The integrity of plant mitochondrial and plastid genomes is necessary for cell survival. During evolution, plants have evolved mechanisms to replicate their mitochondrial genomes while minimizing the effects of DNA damaging agents. The recombinogenic character of plant mitochondrial DNA, absence of defined origins of replication, and its linear structure suggest that mitochondrial DNA replication is achieved by a recombination-dependent replication mechanism. Here, I review the mitochondrial proteins possibly involved in mitochondrial DNA replication from a structural point of view. A revision of these proteins supports the idea that mitochondrial DNA replication could be replicated by several processes. The analysis indicates that DNA replication in plant mitochondria could be achieved by a recombination-dependent replication mechanism, but also by a replisome in which primers are synthesized by three different enzymes: Mitochondrial RNA polymerase, Primase-Helicase, and Primase-Polymerase. The recombination-dependent replication model and primers synthesized by the Primase-Polymerase may be responsible for the presence of genomic rearrangements in plant mitochondria.
Effects of particle diameter and magnetocrystalline anisotropy on magnetic relaxation and magnetic particle imaging performance of magnetic nanoparticles

The dynamic magnetization of immobilized spherical single-domain magnetic nanoparticles (MNPs) with uniaxial or cubic magnetocrystalline anisotropy was studied computationally by executing simulations based on the Landau–Lifshitz–Gilbert (LLG) equation. For situations when a static magnetic field was suddenly applied and then removed, the effects of particle diameter and anisotropy (considering both type of symmetry and characteristic energy) on the characteristic magnetic relaxation time were studied parametrically. The results, for both anisotropy symmetries, show that when a static magnetic field is suddenly turned on or off the MNPs undergo a successive two-step or combined one-step relaxation. Whether a MNP relaxes with one or two steps when the field is turned on is determined by the competition between the energy of the applied magnetic field, the magnetic anisotropy energy, and thermal energy. When the applied magnetic field is suddenly turned off, our results show good agreement with theoretical predictions for the cases of and , where represents the magnetic anisotropy energy barrier, is the Boltzmann constant and represents the absolute temperature. For the case of an applied alternating magnetic field (AMF) that is typical of magnetic particle imaging (MPI) applications, the effects of particle diameter and anisotropy symmetry were studied in terms of time-domain magnetization dynamics, dynamic hysteresis loops, harmonic spectra, and x-space point spread functions (PSFs). Results illustrate that the type of magnetocrystalline anisotropy (uniaxial versus cubic) has a significant effect on the MPI performance of the nanoparticles. These computational studies provide insight into the role of particle diameter and magnetic anisotropy on the performance of MNPs for applications in magnetorelaxometry and MPI.
Personal Factors, Internet Characteristics, and Environmental Factors Contributing to Adolescent Internet Addiction: A Public Health Perspective

Individual characteristics, family- and school-related variables, and environmental variables have equal importance in understanding Internet addiction. Most previous studies on Internet addiction have focused on individual factors; those that considered environmental influence typically only examined the proximal environment. Effective prevention and intervention of Internet addiction require a framework that integrates individual- and environmental-level factors. This study examined the relationships between personal factors, family/school factors, perceived Internet characteristics, and environmental variables as they contribute to Internet addiction among adolescents based on the public health model. A representative sample of 1628 junior high school students from 56 regions in Seoul and Gyeonggi-do participated in the study via questionnaires with the cooperation of the Ministry of Health and Welfare and the district office of education. The study analyzed psychological factors, family cohesion, attitudes toward academic activities, Internet characteristics, accessibility to PC cafés, and exposure to Internet game advertising. About 6% of the adolescents were categorized as being in the severely addicted group. Between-group comparisons showed that the addicted group had started using the Internet earlier; had higher levels of depression, compulsivity, and aggressiveness as well as lower family cohesion; and reported higher accessibility to PC cafés and exposure to Internet game advertising. Multiple logistic regression indicated that for adolescents, environmental factors had a greater influence than family or school-related factors. Policy implications for prevention and intervention are discussed.
Transcription Factor Networks in Leaves of Cichorium endivia: New Insights into the Relationship between Photosynthesis and Leaf Development

Cichorium endivia is a leafy crop closely related to Lactuca sativa that comprises two major botanical varieties characterized by a high degree of intraspecific morphological variation: var. latifolium with broad leaves (escarole) and var. crispum with narrow crisp curly leaves (endive). To investigate the relationship between leaf morphology and photosynthetic activity, escaroles and endives were used as a crop model due to the striking morphological diversity of their leaves. We constructed a leaf database for transcription factors (TFs) and photosynthesis-related genes from a refined C. endivia transcriptome and used RNA-seq transcriptomic data from leaves of four commercial endive and escarole cultivars to explore transcription factor regulatory networks. Cluster and gene co-expression network (GCN) analyses identified two main anticorrelated modules that control photosynthesis. Analysis of the GCN network topological properties identified known and novel hub genes controlling photosynthesis, and candidate developmental genes at the boundaries between shape and function. Differential expression analysis between broad and curly leaves suggested three novel TFs putatively involved in leaf shape diversity. Physiological analysis of the photosynthesis properties and gene expression studies on broad and curly leaves provided new insights into the relationship between leaf shape and function.
Major vault protein plays important roles in viral infection

Viral replication and related protein expression inside the host cells, and host antiviral immune responses can lead to the occurrence of diverse diseases. With the outbreak of viral infection, a large number of newly diagnosed and died patients infected with various viruses are still reported every year. Viral infection has already been one of the major global public health issues and lead to huge economic and social burdens. Studying of viral pathogenesis is a very important way to find methods for prevention, diagnosis, and cure of viral infection; more evidence has confirmed that major vault protein (MVP) is closely associated with viral infection and pathogenesis, and this review is intended to provide a broad relationship between viruses and MVP to stimulate the interest of related researchers.
Prognostic and Predictive Value of Microsatellite Instability, Inflammatory Reaction and PD-L1 in Gastric Cancer Patients Treated with Either Adjuvant 5-FU/LV or Sequential FOLFIRI Followed by Cisplatin and Docetaxel: A Translational Analysis from the ITACA-S Trial.

BACKGROUND Patients with high microsatellite instability (MSI) gastric cancer (GC) show improved survival and no benefit or harm from adjuvant and/or perioperative chemotherapy. The role of immune microenvironment in GC is largely unknown. MATERIALS AND METHODS In the present study, 256 tumor tissue blocks were centrally collected from patients enrolled in ITACA-S, a randomized adjuvant trial of 5-FU/LV versus sequential FOLFIRI and cisplatin-docetaxel. MSI status was assessed by multiplex PCR, inflammatory reaction by H&E morphological assessment, and programmed death-ligand 1 (PD-L1) expression by immunohistochemistry. RESULTS Overall, 9% patients had MSI-high tumors, 23% had high inflammatory reaction, 11% had tumor PD-L1 ≥ 1%, and 11% had stromal PD-L1 ≥ 1%. A significant association with disease-free survival (DFS) and overall survival (OS) was found for MSI-high (hazard ratio [HR], 0.43; p = .02; HR, 0.40; p = .02) and high inflammatory reaction (HR, 0.55; p = .010; HR, 0.53; p = .008) but not for PD-L1. At multivariable analysis, only MSI showed an independent association with both DFS (p = .02) and OS (p = .01), whereas inflammatory reaction showed an independent association only with OS (p = .04). Patients with tumor PD-L1 ≥ 1% had a significantly longer DFS in sequential chemotherapy than in than 5-FU/LV arm (interaction p = .04) and a trend for OS (interaction p = .12). CONCLUSION Our data suggest that MSI status could be a useful prognostic biomarker in patients with radically resected stage II-III GC and should be used as stratification factor in future trials. Tumor PD-L1 ≥ 1% should be further investigated as a potential predictor of benefit from intensive chemotherapy. IMPLICATIONS FOR PRACTICE In this post hoc analysis of patients with radically resected gastric cancer randomized to an intensive sequential chemotherapy regimen versus 5-FU/LV monotherapy as adjuvant treatment in the ITACA-S trial, MSI-high status was independently associated with better disease-free survival and overall survival (OS) and inflammatory reaction was independently associated with better OS. Moreover, tumor PD-L1 expression ≥1% was associated with greater benefit from intensive sequential chemotherapy compared with 5-fluorouracil plus leucovorin (5-FU/LV), whereas PD-L1 expression <1% was not, conditioning a statistically significant interaction between such biomarker and treatment arms. The meta-analysis of individual patients' data from available studies could yield data on the role of MSI status that could inform clinical decisions.
Comparative Analysis of the YABBY Gene Family of Bienertia sinuspersici, a Single-Cell C4 Plant

The emergence and expression of the YABBY gene family (YGF) coincided with the evolution of leaves in seed plants, and was integral to the early evidence of lamina followed by reproductive development. YGF contains six subclasses, i.e., CRC, INO, FIL, YAB2, YAB3, and YAB5. This study aims to extract the genome sequences of the YGF in Bienertia sinuspersici, an important model plant for single-cell C4 (SCC4), non-Kranz photosynthesis. A comparative genomic analysis was undertaken with Vitis vinefera, Arabidopsis thaliana, Brassica rapa, and Chenopodium quinoa. Six copies of YGF were present in B. sinuspersici and A. thaliana with a single copy of each YGF subgroup. V. vinefera possessed seven copies of YGF with duplicates in FIL and YAB2 subgroups, but no YAB3. B. rapa and C. quinoa after whole genome duplication contained additional copies of YGF. The gene structure and conserved motifs were analyzed among the YGF. In addition, the relative quantification of YGF was analyzed in the leaves, reproductive developmental stages such as the bud, and the pre-anthesis and anthesis stages in B. sinuspersici, A. thaliana, and B. rapa. CRC and INO possessed conserved floral-specific expression. Temporal and perpetual changes in the expression of YGF orthologs were observed in the leaves and reproductive developmental stages. The results of this study provide an overview of YGF evolution, copy number, and its differential expression in B. sinuspersici. Further studies are required to shed light on the roles of YABBY genes in the evolution of SCC4 plants and their distinct physiologies.
Complex Diffractive Optical Elements Stored in Photopolymers

We study the recording of complex diffractive elements, such as achromatic lenses, fork gratings or axicons. Using a 3-D diffusion model, previously validated, we are able to predict the behavior of photopolymer during recording. The experimental recording of these complex elements is possible thanks to a new generation spatial light modulator capable of generating periodic and aperiodic profiles. Both experimental and theoretical are analyzed and compared. The results show not only the good response of theoretical model to predict the behavior of the materials, but also the viability of photopolymers to store these kind of elements.
Reproducible phenotype alteration due to prolonged cooling of the pupae of Polyommatus icarus butterflies

The phenotypic changes induced by prolonged cooling (2–12 weeks at 5 °C in the dark) of freshly formed Polyommatus icarus pupae were investigated. Cooling halted the imaginal development of pupae collected shortly after transformation from the larval stage. After cooling, the pupae were allowed to continue their developmental cycle. The wings of the eclosed specimens were investigated by optical microscopy, scanning and cross-sectional transmission electron microscopy, UV-VIS spectroscopy and microspectroscopy. The eclosed adults presented phenotypic alterations that reproduced results that we published previously for smaller groups of individuals remarkably well; these changes included i) a linear increase in the magnitude of quantified deviation from normal ventral wing patterns with increasing cooling time; ii) slight alteration of the blue coloration of males; and iii) an increasing number of blue scales on the dorsal wing surface of females with increasing cooling time. Several independent factors, including disordering of regular scale rows in males, the number of blue scales in females, eclosion probability and the probability of defect-free eclosion, showed that the cooling time can be divided into three periods: 0–4 weeks, 4–8 weeks, and 8–12 weeks, each of which is characterized by specific changes. The shift from brown female scales to first blue scales with a female-specific shape and then to blue scales with a male-specific shape with longer cooling times suggests slow decomposition of a substance governing scale formation.
The AKT isoforms 1 and 2 drive B cell fate decisions during the germinal center response

B cell–intrinsic AKT1/2 are essential for germinal center formation, antibody production and affinity maturation, and plasma cell differentiation. The PI3K pathway is integral for the germinal center (GC) response. However, the contribution of protein kinase B (AKT) as a PI3K effector in GC B cells remains unknown. Here, we show that mice lacking the AKT1 and AKT2 isoforms in B cells failed to form GCs, which undermined affinity maturation and antibody production in response to immunization. Upon B-cell receptor stimulation, AKT1/2–deficient B cells showed poor survival, reduced proliferation, and impaired mitochondrial and metabolic fitness, which collectively halted GC development. By comparison, Foxo1T24A mutant, which cannot be inactivated by AKT1/2 phosphorylation and is sequestered in the nucleus, significantly enhanced antibody class switch recombination via induction of activation-induced cytidine deaminase (AID) expression. By contrast, repression of FOXO1 activity by AKT1/2 promoted IRF4-driven plasma cell differentiation. Last, we show that T-cell help via CD40, but not enforced expression of Bcl2, rescued the defective GC response in AKT1/2–deficient animals by restoring proliferative expansion and energy production. Overall, our study provides mechanistic insights into the key role of AKT and downstream pathways on B cell fate decisions during the GC response.