Miracle-dz/UniFAR-FTUs huggingface dataset:
Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems

Significance Bacteria and other organisms make extensive use of signaling molecules that are derived from ribonucleotides or their derivatives. Previously, five riboswitch classes had been discovered that sense the four RNA-derived signaling molecules: c-di-GMP, c-di-AMP, c-AMP-GMP, and ZTP. We now report the discovery and biochemical validation of bacterial riboswitches for the widespread alarmone guanosine tetraphosphate (ppGpp), which signals metabolic and physiological adaptations to starvation. These findings expand the number of natural partnerships between riboswitches and ribonucleotide-like signaling molecules, and provide RNA-based sensors for detecting ppGpp production in cells. Riboswitches are noncoding portions of certain mRNAs that bind metabolite, coenzyme, signaling molecule, or inorganic ion ligands and regulate gene expression. Most known riboswitches sense derivatives of RNA monomers. This bias in ligand chemical composition is consistent with the hypothesis that widespread riboswitch classes first emerged during the RNA World, which is proposed to have existed before proteins were present. Here we report the discovery and biochemical validation of a natural riboswitch class that selectively binds guanosine tetraphosphate (ppGpp), a widespread signaling molecule and bacterial “alarmone” derived from the ribonucleotide GTP. Riboswitches for ppGpp are predicted to regulate genes involved in branched-chain amino acid biosynthesis and transport, as well as other gene classes that previously had not been implicated to be part of its signaling network. This newfound riboswitch–alarmone partnership supports the hypothesis that prominent RNA World signaling pathways have been retained by modern cells to control key biological processes.
Couple Reports on Intimate Partner Violence and their Health Impact: Evidence From a Population-Based Survey in Japan

Recent studies have shown that couples’ reports of intimate partner violence (IPV) are not necessarily consistent. This study investigated the associations between patterns of partner victimization and perpetration reports and health and perceived wellbeing. Using household survey data from a probabilistic urban sample of adults aged 25 to 50 years and their partners, we identified 1,467 heterosexual pairs who completed the modified Japanese version of the Conflict Tactics Scale 2 Short Form. We classified responses into four categories: congruent report of no IPV, incongruent respondent victimization report, incongruent partner perpetration report, and congruent report of IPV. We used analysis of covariance to compare physical and mental health (measured by the SF-8 Health Survey Questionnaire) and life satisfaction among the four groups. The results showed that 22.4% of respondents were involved in IPV, and approximately 75% of them had incongruent reports. Compared with congruent reports of no IPV, respondents with an incongruent victimization report and an incongruent partner perpetration report scored significantly lower on physical health (−0.96, p = .03 and −1.16, p = .04, respectively). Those with an incongruent victimization report and congruent report of IPV had lower mental health scores (−2.32, p = .00 and −2.21, p = .00, respectively) and lower life satisfaction (−0.32, p = .00 and −0.21, p = .01, respectively). The results indicated that the respondent’s victimization report was associated with worse mental health regardless of their partner’s perpetration report, and physical health was worse only in cases with incongruent reports. Cases with a partner perpetration report but no respondent victimization report showed worse physical health but no negative effects on mental health and perceived wellbeing. These results indicate that research and practice regarding IPV should consider both partners’ experiences of violence when assessing the impact of health and wellbeing on victims.
Effects of probiotic supplementation on performance traits, bone mineralization, cecal microbial composition, cytokines and corticosterone in laying hens.

Recent researches have showed that probiotics promote bone health in humans and rodents. The objective of this study was to determine if probiotics have the similar effects in laying hens. Ninety-six 60-week-old White Leghorn hens were assigned to four-hen cages based on their BW. The cages were randomly assigned to 1 of 4 treatments: a layer diet mixed with a commercial probiotic product (containing Enterococcus faecium, Pediococcus acidilactici, Bifidobacterium animalis and Lactobacillus reuteri) at 0, 0.5, 1.0 or 2.0 g/kg feed (Control, 0.5×, 1.0× and 2.0×) for 7 weeks. Cecal Bifidobacterium spp. counts were higher in all probiotic groups (P0.05). In addition, the plasma concentrations of cytokines (interleukin-1β, interleukin-6, interleukin-10, interferon-γ and tumor necrosis factor-α) and corticosterone as well as the levels of heterophil to lymphocyte ratio were similar between the 2.0× group and the control group (P>0.05). In line with these findings, no differences of cecal tonsil mRNA expressions of interleukin-1β, interleukin-6 and lipopolysaccharide-induced tumor necrosis factor-α factor were detected between these two groups (P>0.05). These results suggest that immune cytokines and corticosterone may not involve in the probiotic-induced improvement of eggshell quality and bone mineralization in laying hens. In conclusion, the dietary probiotic supplementation altered cecal microbiota composition, resulting in reduced shell-less egg production and improved bone mineralization in laying hens; and the dietary dose of the probiotic up to 2.0× did not cause negative stress reactions in laying hens.
Identification of MC1R SNPs and their Association with Plumage Colors in Asian Duck

The melanocortin 1 receptor (MC1R) gene is a candidate functional gene that controls the pigment production in melanocytes. The aim of this study was to identify polymorphisms and investigate the effect of the MC1R gene on plumage coloration in duck breeds, including Korean native ducks. Initially, 34 individuals from seven duck breeds were sequenced, obtaining 12 polymorphisms. Five single nucleotide polymorphisms (SNPs) in the coding region were non-synonymous, with mutations corresponding to amino acid changes. Among these, four SNPs were genotyped using polymerase chain reaction-restriction fragment length polymorphism method in 264 individuals from same seven duck breeds. Fisher's exact test was conducted to identify possible relationships between the MC1R gene polymorphisms and plumage color variations. Four non-synonymous SNPs, c.52A>G (p.Lys18Glu), and c.376 A>G (p.Ile126Val), c.409G>A (p.Ala137Thr) and c.649C>T (p.Arg217Cys), were associated with the two deduced genotypes (i.e., E/E and e+ /e+) based on plumage color phenotypes. In addition, we reconstructed MC1R gene haplotypes, where the haplotype AAGC showed its highest frequency in Nageswari duck breed, which presents an extended black phenotype. Our results indicate that the identified polymorphisms by this study can be used to explore associations with plumage color variations in Asian duck breeds.
Ecosystem heterogeneity and diversity mitigate Amazon forest resilience to frequent extreme droughts.

The impact of increases in drought frequency on the Amazon forest's composition, structure and functioning remain uncertain. We used a process- and individual-based ecosystem model (ED2) to quantify the forest's vulnerability to increased drought recurrence. We generated meteorologically realistic, drier-than-observed rainfall scenarios for two Amazon forest sites, Paracou (wetter) and Tapajós (drier), to evaluate the impacts of more frequent droughts on forest biomass, structure and composition. The wet site was insensitive to the tested scenarios, whereas at the dry site biomass declined when average rainfall reduction exceeded 15%, due to high mortality of large-sized evergreen trees. Biomass losses persisted when year-long drought recurrence was shorter than 2-7 yr, depending upon soil texture and leaf phenology. From the site-level scenario results, we developed regionally applicable metrics to quantify the Amazon forest's climatological proximity to rainfall regimes likely to cause biomass loss > 20% in 50 yr according to ED2 predictions. Nearly 25% (1.8 million km2 ) of the Amazon forests could experience frequent droughts and biomass loss if mean annual rainfall or interannual variability changed by 2σ. At least 10% of the high-emission climate projections (CMIP5/RCP8.5 models) predict critically dry regimes over 25% of the Amazon forest area by 2100.
Sluggish Cognitive Tempo Predicts Academic Fluency, Beyond Contributions of Core Academic Skills, Attention, and Motor Speed

Objective: Sluggish Cognitive Tempo (SCT) is a distinct behavioral phenotype characterized by such symptoms as being slow to complete tasks, appearing drowsy or sleepy, and lacking initiative. Subcomponents of SCT appear differentially associated with inattention symptoms and child outcomes. Much of the work in this area has examined associations between SCT symptoms and ratings of behavior; few studies have examined associations with child performance. Method: We examined associations between SCT and timed reading and math skills in 247 referred youth (M age = 11.55, range = 6-20; 67.6% male), controlling for the untimed academic skills, inattention, and graphomotor speed. Results: SCT consistently predicted timed academic fluency, after controlling for other component skills, for both reading (SCT ΔR2 = .039, p = .001) and math (ΔR2 = .049, p = .001). Conclusion: Results provide initial evidence for the unique association of SCT with timed academic performance. Understanding associations of SCT with actual child performance may allow for greater specificity in targeting interventions to address speed of performance.
Targeted therapies in squamous cell carcinoma of the head and neck

Head and neck cancer is a challenging disease that is expected to account for greater than 500,000 new cases worldwide in 2008. Toxicity has impeded advances in chemotherapy and radiation for head and neck cancer, and the prognosis for patients with recurrent and/or metastatic disease remains poor. Over the past decade, clinical research in head and neck cancer has focused on improving the efficacy of current multimodal approaches by targeting cellular pathways associated with carcinogenesis. Blocking the epidermal growth factor receptor (EGFR) and the vascular endothelial growth factor receptor (VEGFR) have emerged as primary strategies that account for the success of current targeted therapies in cancer. Recent studies with cetuximab, a monoclonal antibody inhibitor of the EGFR, have demonstrated survival benefits across the range of treatment settings in advanced head and neck cancer, and it is the only targeted therapy approved for use in this malignancy. In this review, the authors present the current development status of targeted therapies, focusing on those that have potential to impact the management of head and neck cancer in the near‐term future. Trials are ongoing in all stages of disease and with a variety of modalities and agents, and those trials should provide critical insight into the best way to use these agents to improve patient outcomes. Cancer 2009. © 2009 American Cancer Society.
Learning and Processing Abstract Words and Concepts: Insights From Typical and Atypical Development

The paper describes two plausible hypotheses concerning the learning of abstract words and concepts. According to a first hypothesis, children would learn abstract words by extracting co-occurrences among words in linguistic input, using, for example, mechanisms as described by models of Distributional Semantics. According to a second hypothesis, children would exploit the fact that abstract words tend to have more emotional associations than concrete words to infer that they refer to internal/mental states. Each hypothesis makes specific predictions with regards to when and which abstract words are more likely to be learned; also they make different predictions concerning the impact of developmental disorders. We start by providing a review of work characterizing how abstract words and concepts are learned in development, especially between the ages of 6 and 12. Second, we review some work from our group that tests the two hypotheses above. This work investigates typically developing (TD) children and children with atypical development (developmental language disorders [DLD] and autism spectrum disorder [ASD] with and without language deficits). We conclude that the use of strategies based on emotional information, or on co-occurrences in language, may play a role at different developmental stages.
A Computationally More Efficient and More Accurate Stepwise Approach for Correcting for Sampling Error and Measurement Error

ABSTRACT Over the last decade or two, multilevel structural equation modeling (ML-SEM) has become a prominent modeling approach in the social sciences because it allows researchers to correct for sampling and measurement errors and thus to estimate the effects of Level 2 (L2) constructs without bias. Because the latent variable modeling software Mplus uses maximum likelihood (ML) by default, many researchers in the social sciences have applied ML to obtain estimates of L2 regression coefficients. However, one drawback of ML is that covariance matrices of the predictor variables at L2 tend to be degenerate, and thus, estimates of L2 regression coefficients tend to be rather inaccurate when sample sizes are small. In this article, I show how an approach for stabilizing covariance matrices at L2 can be used to obtain more accurate estimates of L2 regression coefficients. A simulation study is conducted to compare the proposed approach with ML, and I illustrate its application with an example from organizational research.
Analysis of Switching Transients during Energization in Large Offshore Wind Farms

In order to study switching transients in an offshore wind farm (OWF) collector system, we employ modeling methods of the main components in OWFs, including vacuum circuit breakers (VCBs), submarine cables, and wind turbine transformers (WTTs). In particular, a high frequency (HF) VCB model that reflects the prestrike characteristics of VCBs was developed. Moreover, a simplified experimental system of an OWF electric collection system was set up to verify the developed models, and a typical OWF medium voltage (MV) cable collection system was built in PSCAD/EMTDC based on the developed models. Finally, we investigated the influences of both the initial closing phase angle of VCBs and typical system operation scenarios on the amplitude and steepness of transient overvoltages (TOVs) at the high-voltage side of WTTs.
Idiosyncratic Risk and Earnings Noncommonality

The seminal Campbell et al. (2001) paper showing that idiosyncratic risk has increased considerably in recent years has spawned a large number of articles to explain the phenomenon. In this paper, we propose growing earnings noncommonality as a possible source of the increasing idiosyncratic volatility. The empirical results of this research validate this proposition. Our conclusions stand the test of several robustness checks which show that market power and innovativeness previously considered in literature as sources of increased idiosyncratic volatility are not significant in the presence of earnings noncommonality. The findings of this research will be useful for analysts and investors involved in asset pricing.
Building an End-to-End Spatial-Temporal Convolutional Network for Video Super-Resolution

We propose an end-to-end deep network for video super-resolution. Our network is composed of a spatial component that encodes intra-frame visual patterns, a temporal component that discovers inter-frame relations, and a reconstruction component that aggregates information to predict details. We make the spatial component deep, so that it can better leverage spatial redundancies for rebuilding high-frequency structures. We organize the temporal component in a bidirectional and multi-scale fashion, to better capture how frames change across time. The effectiveness of the proposed approach is highlighted on two datasets, where we observe substantial improvements relative to the state of the arts.
The relationship between employment and health and health care among working-age adults with and without disabilities in the United States

Abstract Purpose: To better understand the relationship between employment and health and health care for people with disabilities in the United States (US). Methods: We pooled US Medical Expenditure Panel Survey (2004–2010) data to examine health status, and access to health care among working-age adults, comparing people with physical disabilities or multiple disabilities to people without disabilities, based on their employment status. Logistic regression and least squares regression were conducted, controlling for sociodemographics, health insurance (when not the outcome), multiple chronic conditions, and need for assistance. Results: Employment was inversely related to access to care, insurance, and obesity. Yet, people with disabilities employed in the past year reported better general and mental health than their peers with the same disabilities who were not employed. Those who were employed were more likely to have delayed/forgone necessary care, across disability groups. Part-time employment, especially for people with multiple limitations, was associated with better health and health care outcomes than full-time employment. Conclusion: Findings highlight the importance of addressing employment-related causes of delayed or foregone receipt of necessary care (e.g., flex-time for attending appointments) that exist for all workers, especially those with physical or multiple disabilities. Implications for rehabilitation These findings demonstrate that rehabilitation professionals who are seeking to support employment for persons with physical limitations need to ensure that overall health concerns are adequately addressed, both for those seeking employment and for those who are currently employed. Assisting clients in prioritizing health equally with employment can ensure that both areas receive sufficient attention. Engaging with employers to develop innovative practices to improve health, health behaviors and access to care for employees with disabilities can decrease turnover, increase productivity, and ensure longer job tenure.
The effects of condensed tannins from Desmodium intortum and Calliandra calothyrsus on protein and carbohydrate digestion in sheep and goats

A factorial experiment was conducted to study the effects of condensed tannins (CT) from the tropical legumes Desmodium intorturn and Calliandra calothyrsus on the digestion and utilization of protein and carbohydrate in sheep and goats. CT-free Centrusema pubescens was also fed for comparison with the CT legumes, and each legume was included (300 g/kg DM) in a basal diet of pangola grass (Digitmia decumbens). Pangola grass alone was used as a control diet. There were no significant (P>0.05) differences between sheep and goats for the efficiency of digestion of N (0.574, SE 0.013), organic matter (OM; 0.519, SE 0.010), neutral-detergent fibre (NDF; 0.524, SE 0.011) and acid-detergent fibre (ADF; 0.407, SE 0.016). Diets containing desmodium and calliandra were digested less well in the rumen (64 and 62% of total OM digested) when compared with the pangola and centrosema diets (74 and 73% of total OM digested in rumen). There was an apparent net gain of 30% in ADF across the digestive tract of sheep and goats given calliandra, and this gain was ascribed to the formation of ‘artifact’ fibre as a result of fibre-tannin interaction. Overall, inclusion of legume at 300 g/kg in the diet significantly increased (P>0.05) the concentration of acetic acid and decreased butyric acid concentration in the rumen fluid of sheep and goats. Significantly higher proportions of dietary N apparently reached the abomasum of animals given the diets containing desmodium (50%) and calliandra (56%) when compared with animals given the centrosema and pangola diets (35%). Sheep and goats given the CT diets also had higher excretions of faecal N. This increment of faecal N (14%) did not affect post-rumen N digestion (P>0.05) since animals given CT diets absorbed more N (19%) per kg total OM digested than those given the control diets. It was concluded that whilst the low levels of CT provided in desmodium (1.0%) and calliandra (2.3%) diets protected dietary protein from degradation in the rumen, there were no overall beneficial or detrimental effects of CT in these diets for sheep or goats. A method was developed to categorize CT into fractions representative of their forms (free, protein-bound, and fibre-bound) during the digestion process. A quantitative model of CT metabolism during passage through the digestive tract was developed from the measured exchanges of CT between free, protein-bound and fibre-bound pools in the rumen and lower digestive tract. CT interchange mainly occurred in the reticulo-rumen of both animal species. Desmodium and calliandra free CT showed net losses of 68 and 78% in the rumen respectively and 57 and 68% of the fibre-bound CT was lost in the same site for sheep and goats respectively. However, protein-bound CT increased across the rumen by 73 and 56% for both animal species. Post-rumen losses of the total CT abomasal flow were 86 and 83% (free CT) for sheep and goats respectively, 70 and 66% (protein-bound CT), whilst 28% loss of fibre-bound CT occurred in sheep and goats respectively.
Data-mining the Foundational Patents of Photovoltaic Materials: An application of Patent Citation Spectroscopy

We apply Patent Citation Spectroscopy (PCS)--originally developed as Reference Publication Year Spectroscopy for studying landmarks and milestones in scientific literature--to patent literature classified into the nine Y-subclasses of the Cooperative Patent Classification (CPC) that describe material photovoltaic technologies. For this study we extended the routine with the option to use the advanced search queries at PatentsView. On the basis of two normalizations of the longitudinal distribution of the publication years of the patents cited by the retrieved patents, the routine (at this http URL) provides a best guess of the foundational patent for the subject specified in the string. In five of the nine cases, we found corroborating evidence for the foundational character of the patent indicated by the routine.