Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation

Significance Evolution of organismal complexity and species diversity depends on the emergence of novel gene functions. Nevertheless, evolution rarely produces novelties from scratch but works on the weak promiscuous preexisting activities or appears by genomic tinkering. We provide evidence of how rearrangement of conserved regulatory blocks can act as a driving force for gene cooption and evolution of novel developmental mechanisms at the base of important ecological adaptations. We gain insight into a crucial system for segregation of neuronal progenitors within the hindbrain: the evolutionary origin of the actomyosin-dependent cell-sorting mechanism, with rac3b as a main effector. We unveil that the rac3b/rfng/sgca regulatory cluster—specifically expressed at boundaries—emerged by establishment of novel long-range cis-regulatory interactions, allowing the evolution of a backup regulatory mechanism for cell segregation. Developmental programs often rely on parallel morphogenetic mechanisms that guarantee precise tissue architecture. While redundancy constitutes an obvious selective advantage, little is known on how novel morphogenetic mechanisms emerge during evolution. In zebrafish, rhombomeric boundaries behave as an elastic barrier, preventing cell intermingling between adjacent compartments. Here, we identify the fundamental role of the small-GTPase Rac3b in actomyosin cable assembly at hindbrain boundaries. We show that the novel rac3b/rfng/sgca regulatory cluster, which is specifically expressed at the boundaries, emerged in the Ostariophysi superorder by chromosomal rearrangement that generated new cis-regulatory interactions. By combining 4C-seq, ATAC-seq, transgenesis, and CRISPR-induced deletions, we characterized this regulatory domain, identifying hindbrain boundary-specific cis-regulatory elements. Our results suggest that the capacity of boundaries to act as an elastic mesh for segregating rhombomeric cells evolved by cooption of critical genes to a novel regulatory block, refining the mechanisms for hindbrain segmentation.
Biology and Etiology of Young-Onset Breast Cancers among Premenopausal African American Women: Results from the AMBER Consortium

Background: African American (AA) women have higher incidence of aggressive, young-onset (<40 years) breast cancers. Young- and older-onset disease may have distinct tumor biologies and etiologies; however, studies investigating age differences among AA women have been rare and generally underpowered. Methods: We examined tumor characteristics and breast cancer risk factors associated with premenopausal young (<40) vs. older (≥40) AA women's breast cancer in the African American Breast Cancer Epidemiology and Risk Consortium (2,008 cases and 5,144 controls). Unconditional logistic regression models assessed heterogeneity of tumor biology and risk factor associations by age, overall, and by estrogen receptor status. Results: Premenopausal AA women <40 years had higher frequency of poorer-prognosis tumor characteristics compared with older women, including negative estrogen and progesterone receptor status, triple-negative subtype, higher grade, higher stage, and larger tumors. Adiposity (i.e., waist-to-hip ratio) and family history of breast cancer were more strongly associated with young-onset disease [case–control OR = 1.46, 95% confidence interval (CI) = 1.04–2.05; OR = 3.10, 95% CI = 2.08–4.63, respectively] compared with older-onset disease (OR = 1.11, 95% CI = 0.91–1.35; OR = 1.57, 95% CI = 1.26–1.94). Breastfeeding showed a slight inverse risk association among young women (OR = 0.70, 95% CI = 0.43–1.16). Oral contraceptive use was associated with increased risk regardless of age. Considering various cutoff points for young age (<40, <45, <50), age-related heterogeneity was greatest when <40 was used. Conclusions: Among premenopausal AA women, diagnosis before age 40 is associated with more aggressive breast tumor biology and some etiologic differences. Impact: Modifiable risk factors including breastfeeding, adiposity, and oral contraceptive use may be important targets for mitigating harms of young-onset breast cancer. Cancer Epidemiol Biomarkers Prev; 26(12); 1722–9. ©2017 AACR.
An R2R-DAC-Based Architecture for Equalization-Equipped Voltage-Mode PAM-4 Wireline Transmitter Design

This brief presents a wireline transmitter architecture, enabling multilevel signaling with feedforward equalization (FFE) in voltage-mode. A compact R2R-DAC-based front end is proposed and analyzed in terms of its speed, power consumption, and linearity. A voltage-mode PAM-4 transmitter with 2-tap FFE utilizing the proposed architecture is implemented in the 65-nm CMOS technology. It achieves a data rate of 34 Gb/s and an energy efficiency of 2.7 mW/Gb/s.
Analysis of the Microbial Community in an Acidic Hollow-Fiber Membrane Biofilm Reactor (Hf-MBfR) Used for the Biological Conversion of Carbon Dioxide to Methane

Hydrogenotrophic methanogens can use gaseous substrates, such as H2 and CO2, in CH4 production. H2 gas is used to reduce CO2. We have successfully operated a hollow-fiber membrane biofilm reactor (Hf-MBfR) for stable and continuous CH4 production from CO2 and H2. CO2 and H2 were diffused into the culture medium through the membrane without bubble formation in the Hf-MBfR, which was operated at pH 4.5–5.5 over 70 days. Focusing on the presence of hydrogenotrophic methanogens, we analyzed the structure of the microbial community in the reactor. Denaturing gradient gel electrophoresis (DGGE) was conducted with bacterial and archaeal 16S rDNA primers. Real-time qPCR was used to track changes in the community composition of methanogens over the course of operation. Finally, the microbial community and its diversity at the time of maximum CH4 production were analyzed by pyrosequencing methods. Genus Methanobacterium, related to hydrogenotrophic methanogens, dominated the microbial community, but acetate consumption by bacteria, such as unclassified Clostridium sp. , restricted the development of acetoclastic methanogens in the acidic CH4 production process. The results show that acidic operation of a CH4 production reactor without any pH adjustment inhibited acetogenic growth and enriched the hydrogenotrophic methanogens, decreasing the growth of acetoclastic methanogens.
Risk factors associated with self-reported injury history in female youth soccer players

ABSTRACT Background: studies that investigate risk factors for musculoskeletal injuries in female youth athletes are limited, especially related to training attributes and position status. Objective: to determine risk factors including training attributes and position status for a self-reported musculoskeletal injury history in female youth soccer players. Methods: we conducted a cross-sectional study of young female soccer players (mean age: 13.6 ± 2.3 years). we asked about their history of musculoskeletal injuries using an electronic questionnaire. the proportion of young female soccer players with and without a history of soccer-related musculoskeletal injuries were compared based on physical characteristics, training attributes, position status (single vs. multiple), lower extremity strength, and joint laxity. a binary logistic regression analysis was used to generate, and adjusted odds ratios adjusted for potential co-variates (aor). a 95% confidence interval (95%ci) that did not cross one or p < 0.05 were considered statistically significant. Results: a total of 160 young female soccer players (mean age: 13.6 ± 2.3 years) participated in the study. an independent association was found between prior musculoskeletal injuries and older ages (aor: 1.60, 95%ci: 1.17, 2.20, p = 0.004), higher weight (aor: 1.10, 95%ci: 1.01, 1.20, p = 0.026), and greater bmi (aor: 1.43, 95%ci: 1.07, 1.90, p = 0.014). Conclusions: musculoskeletal injuries were associated with age, weight, and bmi in female youth players. the current study indicates that maintaining proper body composition may be beneficial to reduce musculoskeletal injuries among female youth soccer players.
The Gulf Coast Health Alliance: Health Risks Related to the Macondo Spill (GC-HARMS) Study: Self-Reported Health Effects

The Deepwater Horizon (DWH) explosion in 2010 is the largest oil spill (Macondo) in U.S. history. We focused on gaining an understanding of the physical health and mental health effects attributable to the Macondo oil spill. This is a report of a cross-sectional cohort study (wave 1) to establish ‘baseline’ findings and meant to provide descriptive information to be used for a multi-wave, longitudinal study. Gulf Coast Health Alliance: health Risks related to the Macondo Spill (GC-HARMS) uses a Community-Based Participatory Research approach, thus including multi-disciplinary, multi-institutional academic partners and representatives of three communities impacted by the spill. Three research sites were selected for human sampling along the Gulf of Mexico coast including two from Mississippi and one from Louisiana, with Galveston, Texas, serving as a comparison site, given that it was not directly impacted by the spill. One hundred participants were selected from each community, representing adults, seniors and children, with approximately equal numbers of males and females in each group. Participants completed initial assessments including completion of a ‘baseline’ survey and, rigorous physical assessments. Results from wave 1 data collection reported herein reveal changes in self-reported physical health and mental health status following the oil spill, disparities in access to healthcare, and associations between mental health and emotional conditions related to displacement/unemployment. Few environmental health studies have been conducted in communities impacted by significant oil spills. Results imply potential prolonged effects on mental health and community vulnerability.
One-Pot Enzymatic Production of Lignin-Composites

A novel and efficient one-pot system for green production of artificial lignin bio-composites has been developed. Monolignols such as sinapyl (SA) and coniferyl (CA) alcohols were linked together with caffeic acid (CafAc) affording a polymeric network similar with natural lignin. The interaction of the dissolved SA/CA with CafAc already bound on a solid support (SC2/SC6-CafAc) allowed the attachment of the polymeric product direct on the support surface (SC2/SC6-CafAc-L1 and SC2/SC6-CafAc-L2, from CA and SA, respectively). Accordingly, this procedure offers the advantage of a simultaneous polymer production and deposition. Chemically, oxi-copolymerization of phenolic derivatives (SA/CA and CAfAc) was performed with H2O2 as oxidation reagent using peroxidase enzyme (2-1B mutant of versatile peroxidase from Pleurotus eryngii) as catalyst. The system performance reached a maximum of conversion for SA and CA of 71.1 and 49.8%, respectively. The conversion is affected by the system polarity as resulted from the addition of a co-solvent (e.g., MeOH, EtOH, or THF). The chemical structure, morphology, and properties of the bio-composites surface were investigated using different techniques, e.g., FTIR, TPD-NH3, TGA, contact angle, and SEM. Thus, it was demonstrated that the SA monolignol favored bio-composites with a dense polymeric surface, high acidity, and low hydrophobicity, while CA allowed the production of thinner polymeric layers with high hydrophobicity.
Direct Interactions Between Gli3, Wnt8b, and Fgfs Underlie Patterning of the Dorsal Telencephalon

Abstract A key step in the development of the cerebral cortex is a patterning process, which subdivides the telencephalon into several molecularly distinct domains and is critical for cortical arealization. This process is dependent on a complex network of interactions between signaling molecules of the Fgf and Wnt gene families and the Gli3 transcription factor gene, but a better knowledge of the molecular basis of the interplay between these factors is required to gain a deeper understanding of the genetic circuitry underlying telencephalic patterning. Using DNA‐binding and reporter gene assays, we here investigate the possibility that Gli3 and these signaling molecules interact by directly regulating each other's expression. We show that Fgf signaling is required for Wnt8b enhancer activity in the cortical hem, whereas Wnt/&bgr;‐catenin signaling represses Fgf17 forebrain enhancer activity. In contrast, Fgf and Wnt/&bgr;‐catenin signaling cooperate to regulate Gli3 expression. Taken together, these findings indicate that mutual interactions between Gli3, Wnt8b, and Fgf17 are crucial elements of the balance between these factors thereby conferring robustness to the patterning process. Hence, our study provides a framework for understanding the genetic circuitry underlying telencephalic patterning and how defects in this process can affect the formation of cortical areas.
Minimally Invasive Versus Open Esophageal Resection: Three-year Follow-up of the Previously Reported Randomized Controlled Trial the TIME Trial

Objective: The aim of this study was to investigate 3-year survival following a randomized controlled trial comparing minimally invasive with open esophagectomy in patients with esophageal cancer. Background: Research on minimally invasive esophagectomy (MIE) has shown faster postoperative recovery and a marked decrease in pulmonary complications. Debate is ongoing as to whether the procedure is equivalent to open resection regarding oncologic outcomes. The study is a follow-up study of the TIME-trial (traditional invasive vs minimally invasive esophagectomy, a multicenter, randomized trial). Methods: Between June 2009 and March 2011, patients with a resectable intrathoracic esophageal carcinoma, including the gastroesophageal junction tumors (Siewert I), were randomized between open and MI esophagectomy with curative intent. Primary outcome was 3-year disease-free survival. Secondary outcomes include overall survival, lymph node yield, short-term morbidity, mortality, complications, radicality, local recurrence, and metastasis. Analysis was by intention-to-treat. This trial is registered with the Netherlands Trial Register, NTR TC 2452. Both trial protocol and short-term results have been published previously. Results: One hundred fifteen patients were included from 5 European hospitals and randomly assigned to open (n = 56) or MI esophagectomy (n = 59). Combined overall 3-year survival was 40.4% (SD 7.7%) in the open group versus 50.5% (SD 8%) in the minimally invasive group (P = 0.207). The hazard ratio (HR) is 0.883 (0.540 to 1.441) for MIE compared with open surgery. Disease-free 3-year survival was 35.9% (SD 6.8%) in the open versus 40.2% (SD 6.9%) in the MI group [HR 0.691 (0.389 to 1.239). Conclusions: The study presented here depicted no differences in disease-free and overall 3-year survival for open and MI esophagectomy. These results, together with short-term results, further support the use of minimally invasive surgical techniques in the treatment of esophageal cancer.
Infrared and Visible Image Fusion Based on Different Constraints in the Non-Subsampled Shearlet Transform Domain

There are many artificial parameters when fuse infrared and visible images, to overcome the lack of detail in the fusion image because of the artifacts, a novel fusion algorithm for infrared and visible images that is based on different constraints in non-subsampled shearlet transform (NSST) domain is proposed. There are high bands and low bands of images that are decomposed by the NSST. After analyzing the characters of the bands, fusing the high level bands by the gradient constraint, the fused image can obtain more details; fusing the low bands by the constraint of saliency in the images, the targets are more salient. Before the inverse NSST, the Nash equilibrium is used to update the coefficient. The fused images and the quantitative results demonstrate that our method is more effective in reserving details and highlighting the targets when compared with other state-of-the-art methods.
Palatal wound healing using a xenogeneic collagen matrix - histological outcomes of a randomized controlled clinical trial.

AIM The aim of this study was to test whether or not a collagen matrix can improve early wound healing compared to spontaneous healing based on histological and immunohistologic analyses. METHODS In 20 volunteers, 6 mm punch biopsies were harvested at the palate. A xenogeneic collagen matrix (XCM) was sutured in one site; the other one was left untreated (control). Biopsies with a diameter of 8 mm were subsequently obtained at 4, 8, 15 and 29 days and histological and immunohistologic analyses were performed. RESULTS At day 4, wound bed keratinization amounted to 12.4 ± 7.5% (control) and 18.0 ± 10.2% (XCM). This increased up to day 8 (19.7 ± 25.5% control; 29.1 ± 8.0% XCM) and reached complete keratinization at day 15 in both groups. The quantitative analyses of the superficial compartment measured an increase in the amount of granulation tissue (32-88% control; 14-41% XCM) from day 4 to day 8. Angiogenesis was first detected at 8 days. At day 29, the amount of connective tissue in all compartments reached values similar to the native tissue at baseline. CONCLUSIONS The application of a XCM as a wound dressing on palatal wounds might be beneficial in the early stages of wound healing. Further research with a larger sample size is needed to confirm these results.
Comparing the Pearson and Spearman correlation coefficients across distributions and sample sizes: A tutorial using simulations and empirical data.

The Pearson product–moment correlation coefficient (rp) and the Spearman rank correlation coefficient (rs) are widely used in psychological research. We compare rp and rs on 3 criteria: variability, bias with respect to the population value, and robustness to an outlier. Using simulations across low (N = 5) to high (N = 1,000) sample sizes we show that, for normally distributed variables, rp and rs have similar expected values but rs is more variable, especially when the correlation is strong. However, when the variables have high kurtosis, rp is more variable than rs. Next, we conducted a sampling study of a psychometric dataset featuring symmetrically distributed data with light tails, and of 2 Likert-type survey datasets, 1 with light-tailed and the other with heavy-tailed distributions. Consistent with the simulations, rp had lower variability than rs in the psychometric dataset. In the survey datasets with heavy-tailed variables in particular, rs had lower variability than rp, and often corresponded more accurately to the population Pearson correlation coefficient (Rp) than rp did. The simulations and the sampling studies showed that variability in terms of standard deviations can be reduced by about 20% by choosing rs instead of rp. In comparison, increasing the sample size by a factor of 2 results in a 41% reduction of the standard deviations of rs and rp. In conclusion, rp is suitable for light-tailed distributions, whereas rs is preferable when variables feature heavy-tailed distributions or when outliers are present, as is often the case in psychological research.
Behavioral Economics of Cigarette Purchase Tasks: Within-Subject Comparison of Real, Potentially Real, and Hypothetical Cigarettes.

INTRODUCTION Hypothetical rewards are commonly used in studies of laboratory-based tobacco demand. However, behavioral economic demand procedures require confirmation that the behavior elicited from real and hypothetical reward types are equivalent, and that results attained from these procedures are comparable to other accepted tasks, such as the hypothetical purchase task. METHODS Nineteen smokers were asked to purchase 1 week's worth of cigarettes that they would consume over the following week either at one price that incrementally increased across four weekly sessions ("real" sessions) or four prices in a single session ("potentially real" session), one of which was randomly chosen to be actualized. At each session, participants also completed a hypothetical cigarette purchase task. After each week, participants reported the number of cigarettes they actually smoked. RESULTS Demand was found to be equivalent under both the real and potentially real reward conditions but statistically different from the demand captured in the hypothetical purchase task. However, the amounts purchased at specific prices in the hypothetical purchase task were significantly correlated with the amount purchased at comparable prices in the other two tasks (except for the highest price examined in both tasks of $1.00 per cigarette). Number of cigarettes consumed that were obtained outside of the study was correlated with study cigarette price. CONCLUSIONS Combined, these results suggest that purchasing behavior during potentially real sessions (1) was not functionally different from real sessions, (2) imposes fewer costs to the experimenter, and (3) has high levels of both internal and external validity.
Transcription profiling of peripheral B cells in antibody‐positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature

B cells play a key role in the pathogenesis of primary Sjögren's syndrome (pSS). The aim of this study was to analyse the transcriptome of CD19+ B cells from patients with pSS and healthy controls to decipher the B cell–specific contribution to pSS. RNA from purified CD19+ B cells from 12 anti‐SSA antibody‐positive untreated female patients with pSS and 20 healthy blood donors was subjected to whole transcriptome sequencing. A false discovery rate corrected significance threshold of α < 0.05 was applied to define differential gene expression. As validation, gene expression in B cells from 17 patients with pSS and 16 healthy controls was analysed using a targeted gene panel. RNA‐sequencing identified 4047 differentially expressed autosomal genes in pSS B cells. Upregulated expression of type I and type II interferon (IFN)‐induced genes was observed, establishing an IFN signature in pSS B cells. Among the top upregulated and validated genes were CX3CR1, encoding the fractalkine receptor involved in regulation of B‐cell malignancies, CCL5/RANTES and CCR1. Increased expression of several members of the TNF superfamily was also identified; TNFSF4/Ox40L, TNFSF10/TRAIL, TNFSF13B/BAFF, TNFRSF17/BCMA as well as S100A8 and −A9/calprotectin, TLR7, STAT1 and STAT2. Among genes with downregulated expression in pSS B cells were SOCS1 and SOCS3, CD70 and TNFAIP3/A20. We conclude that B cells from patients with anti‐SSA antibody‐positive pSS display immune activation with upregulated expression of chemokines, chemokine receptors and a prominent type I and type II IFN signature, while suppressors of cytokine signalling are downregulated. This adds insight into the autoimmune process and suggests potential targets for future functional studies.