Miracle-dz/UniFAR-FTUs huggingface dataset:
Folded gastrulation and T48 drive the evolution of coordinated mesoderm internalization in flies

Gastrulation constitutes a fundamental yet diverse morphogenetic process of metazoan development. Modes of gastrulation range from stochastic translocation of individual cells to coordinated infolding of an epithelial sheet. How such morphogenetic differences are genetically encoded and whether they have provided specific developmental advantages is unclear. Here we identify two genes, folded gastrulation and t48, which in the evolution of fly gastrulation acted as a likely switch from an ingression of individual cells to the invagination of the blastoderm epithelium. Both genes are expressed and required for mesoderm invagination in the fruit fly Drosophila melanogaster but do not appear during mesoderm ingression of the midge Chironomus riparius. We demonstrate that early expression of either or both of these genes in C.riparius is sufficient to invoke mesoderm invagination similar to D.melanogaster. The possible genetic simplicity and a measurable increase in developmental robustness might explain repeated evolution of similar transitions in animal gastrulation. DOI: http://dx.doi. org/10.7554/eLife.18318. 001
Response of larval Xenopus laevis to atrazine: Assessment of growth, metamorphosis, and gonadal and laryngeal morphology

Larval Xenopus laevis were exposed to one of four concentrations of atrazine (0, 1, 10, or 25 μg/L, 11 replicate tanks per treatment, 60–65 larvae per replicate) dissolved in an artificial pond water (frog embryo teratogenesis assay‐Xenopus [FETAX]) medium beginning 48 h after hatching until the completion of metamorphosis. Separate groups of larvae (six replicate tanks per treatment, 60–65 larvae per replicate) were exposed to estradiol (100 μg/L), dihydrotestosterone (100 μg/L), or ethanol vehicle control dissolved in FETAX medium. None of the treatments affected posthatch mortality, larval growth, or metamorphosis. There were no treatment effects on sex ratios except for estradiol, which produced a greater percentage of female offspring. Exposure to either estradiol or 25 μg atrazine/L increased the incidence of intersex animals based on assessment of gonadal morphology. Atrazine did not reduce the size of the laryngeal dilator muscle, a sexually dimorphic muscle in this species. We conclude that environmentally relevant concentrations of atrazine do not influence metamorphosis or sex ratios and do not inhibit sexually dimorphic larynx growth in X. laevis. The incidence of atrazine‐induced intersex animals was small (<5%) and occurred only at the greatest concentration of atrazine tested, a concentration that is rarely observed in surface waters in the United States.
Factors Associated With Suboptimal Colorectal Cancer Screening in US Immigrants

Background: Our objectives were to: (1) compare colorectal cancer screening (CRCS) among US born citizens (USBs), naturalized citizens (NACs), and noncitizens (NOCs) and (2) evaluate clinical factors and potential barriers associated with CRCS in these populations. Methods: Screening-eligible patients were identified from the 2007 California Health Interview Survey. Up-to-date CRCS was defined as a fecal occult blood test within 1 year, a sigmoidoscopy within 5 years, or a colonoscopy within 10 years. Using logistic regression, we determined the effects of immigrant status on CRCS. Stratified analyses based on location of residence, health insurance status, and English proficiency were conducted. Results: A total of 30,434 average-risk adults aged 50 years or older completed the survey. Only 67% of USBs, 61% of NACs, and 46% of NOCs underwent CRCS. Advanced age, male sex, high-income earners, nonsmokers, and those who were married or visited their physicians frequently were more likely to receive CRCS (all P<0.05). Compared with USBs, both NACs and NOCs showed decreased odds of CRCS (odds ratio 0.88, 95% confidence interval, 0.74-1.06 and odds ratio 0.68, 95% confidence interval, 0.53-0.88, respectively; P=0.011). Stratified analyses revealed that the associations between immigrants and decreased CRCS were more prominent for those who lived in rural areas, lacked insurance, or were not English proficient. Conclusions: CRCS remains suboptimal, especially in new US immigrants. Improving health care access and mitigating language barriers may minimize this disparity.
Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles

Understanding the phylogenetic position of crown turtles (Testudines) among amniotes has been a source of particular contention. Recent morphological analyses suggest that turtles are sister to all other reptiles, whereas the vast majority of gene sequence analyses support turtles as being inside Diapsida, and usually as sister to crown Archosauria (birds and crocodilians). Previously, a study using microRNAs (miRNAs) placed turtles inside diapsids, but as sister to lepidosaurs (lizards and Sphenodon) rather than archosaurs. Here, we test this hypothesis with an expanded miRNA presence/absence dataset, and employ more rigorous criteria for miRNA annotation. Significantly, we find no support for a turtle + lepidosaur sister‐relationship; instead, we recover strong support for turtles sharing a more recent common ancestor with archosaurs. We further test this result by analyzing a super‐alignment of precursor miRNA sequences for every miRNA inferred to have been present in the most recent common ancestor of tetrapods. This analysis yields a topology that is fully congruent with our presence/absence analysis; our results are therefore in accordance with most gene sequence studies, providing strong, consilient molecular evidence from diverse independent datasets regarding the phylogenetic position of turtles.
Transient TTP in childhood

Thrombotic thrombocytopenic purpura (TTP) is a type of microangiopathic hemolytic anemia that is uncommon in childhood. Adults with TTP have a high mortality rate unless they are treated with plasma exchange. There are few reports of children with acquired idiopathic TTP, and most of those children received some form of treatment. We describe a child with acquired idiopathic TTP who had severe thrombocytopenia and anemia that resolved over several months without the use of any medications. This case suggests that some children with acquired idiopathic TTP might be safely observed without ill effects. Pediatr Blood Cancer 2009;52:424–426. © 2008 Wiley‐Liss, Inc.
Associations Between Reasons for Living and Diminished Suicide Intent Among African-American Female Suicide Attempters

Abstract African-American women are at high risk for suicide ideation and suicide attempts and use emergency psychiatric services at disproportionately high rates relative to men and other ethnic groups. However, suicide death rates are low for this population. Cultural variables in the African-American community may promote resilience and prevent fatal suicidal behavior among African-American women. The present study evaluated self-reported reasons for living as a protective factor against suicidal intent and suicide attempt lethality in a sample of African-American female suicide attempters (n = 150). Regression analyses revealed that reasons for living were negatively associated with suicidal intent, even after controlling for spiritual well-being and symptoms of depression. These results indicate that the ability to generate and contemplate reasons for valuing life may serve as a protective characteristic against life-threatening suicidal behavior among African-American women. Implications for research and clinical practice are further discussed.
Fault injection acceleration by architectural importance sampling

Radiation-induced soft errors are major reliability concerns in advanced technology nodes. The de facto approach for evaluation of the soft error vulnerability is to perform a costly fault injection campaign. Due to the long residency of some errors in system states, the error has to be traced for even millions of cycles. However, only a very small portion of injected errors leads to the failure. This means that many simulation cycles are wasted as they contribute to no failure due to various masking effects. In this paper, we present an importance sampling technique based on Architecturally Correct Execution (ACE) analysis to identify the non-vulnerable time intervals in memory arrays and avoid unnecessary fault injections to speedup the soft error vulnerability evaluation process without sacrificing the accuracy. Our analysis reveals that this approach significantly expedites our architecture-level fault injection technique (on average by 13X).
Using 0.45% saline solution and a modified dosing regimen for infusing N‐acetylcysteine in children with paracetamol poisoning

Introduction: N‐acetylcysteine (NAC) administration is recommended to all patients judged to be at risk of developing hepatotoxicity following paracetamol overdose. However, it has been shown that standard i.v. dosing can cause symptomatic hyponatraemia in children. We describe a case series using 0.45% NaCl plus 5% dextrose for infusing i.v. NAC in children with paracetamol poisoning.
by Vaccination Spontaneous Priming and Efficient Boosting Melanoma-Specific T Cell Responses: and Differentiation of Human A Novel Approach to Characterize Clonality

Despite major progress in T lymphocyte analysis in melanoma patients, TCR repertoire selection and kinetics in response to tumor Ags remain largely unexplored. In this study, using a novel ex vivo molecular-based approach at the single-cell level, we identiﬁed a single, naturally primed T cell clone that dominated the human CD8 (cid:1) T cell response to the Melan-A/MART-1 Ag. The dominant clone expressed a high-avidity TCR to cognate tumor Ag, efﬁciently killed tumor cells, and prevailed in the differentiated effector-memory T lymphocyte compartment. TCR sequencing also revealed that this particular clone arose at least 1 year before vaccination, displayed long-term persistence, and efﬁcient homing to metastases. Remarkably, during concomitant vaccination over 3.5 years, the frequency of the pre-existing clone progressively increased, reaching up to 2.5% of the circulating CD8 pool while its effector functions were enhanced. In parallel, the disease stabilized, but subsequently progressed with loss of Melan-A expression by melanoma cells. Collectively, combined ex vivo analysis of T cell differentiation and clonality revealed for the ﬁrst time a strong expansion of a tumor Ag-speciﬁc human T cell clone, comparable to protective virus-speciﬁc T cells. The observed successful boosting by peptide vaccination support further development of immunotherapy by including strategies to overcome immune escape.
Response of Soil Properties and Microbial Communities to Agriculture: Implications for Primary Productivity and Soil Health Indicators

Agricultural intensification is placing tremendous pressure on the soil’s capacity to maintain its functions leading to large-scale ecosystem degradation and loss of productivity in the long term. Therefore, there is an urgent need to find early indicators of soil health degradation in response to agricultural management. In recent years, major advances in soil meta-genomic and spatial studies on microbial communities and community-level molecular characteristics can now be exploited as ‘biomarker’ indicators of ecosystem processes for monitoring and managing sustainable soil health under global change. However, a continental scale, cross biome approach assessing soil microbial communities and their functional potential to identify the unifying principles governing the susceptibility of soil biodiversity to land conversion is lacking. We conducted a meta-analysis from a dataset generated from 102 peer-reviewed publications as well as unpublished data to explore how properties directly linked to soil nutritional health (total C and N; C:N ratio), primary productivity (NPP) and microbial diversity and composition (relative abundance of major bacterial phyla determined by next generation sequencing techniques) are affected in response to agricultural management across the main biomes of Earth (arid, continental, temperate and tropical). In our analysis, we found strong statistical trends in the relative abundance of several bacterial phyla in agricultural (e.g., Actinobacteria and Chloroflexi) and natural (Acidobacteria, Proteobacteria, and Cyanobacteria) systems across all regions and these trends correlated well with many soil properties. However, main effects of agriculture on soil properties and productivity were biome-dependent. Our meta-analysis provides evidence on the predictable nature of the microbial community responses to vegetation type. This knowledge can be exploited in future for developing a new set of indicators for primary productivity and soil health.
Association of Vascular Endothelial Growth Factor (VEGF) and VEGF Receptor Gene Polymorphisms with Coronary Artery Lesions of Kawasaki Disease

We analyzed the genetic polymorphisms of vascular endothelial growth factor (VEGF) and its receptors [Fms-related tyrosine kinase-1, kinase insert domain receptor (KDR)] in Japanese patients with Kawasaki disease (KD) and normal control subjects to examine whether these genes would contribute to the KD occurrence and/or the development of coronary artery lesion (CAL) in KD. We found that the frequency of G allele of VEGF g. −634 G>C single-nucleotide polymorphism in the promoter region was significantly higher in KD patients with CAL than in those without CAL (p = 0.012) or control subjects (p = 0.021) because of a significantly higher frequency of the GG genotype in KD patients with CAL. In addition, the frequency of the A1 allele with 11 AC repeats of KDR g. +4422(AC)11–14 dinucleotide repeat polymorphism in intron 2 was significantly higher in KD patients with CAL than in those without CAL (p = 0.013) or control subjects (p = 0.040) as a result of a significantly higher frequency of the A1A1 genotype in KD with CAL patients. The multivariate analysis of clinical features and genotypes of the two polymorphisms showed that the A1A1 genotype of KDR g. +4422(AC)11–14 polymorphism was an independent risk factor for the development of CAL with the highest odds ratio among several clinical parameters (odds ratio 6.76; 95% confidence interval 1.05–43.48). Dual luciferase assay demonstrated that the A1 allele with KDR g. +4422(AC)11 repeats showed a weaker silencer function than the A2 allele with 12 AC repeats. These findings suggested that VEGF and its receptor, KDR, genes contributed to the development of CAL in KD patients.
Effectiveness of Contrasting Approaches to Response-Contingent Learning Among Children With Significant Developmental Delays and Disabilities

Findings from a randomized controlled design study of an ability-based versus needs-based approach to response-contingent learning among children with significant developmental delays and disabilities who did not use instrumental behavior to produce reinforcing consequences are reported. The ability-based intervention and needs-based intervention differed in terms of how child behavior was identified and used to elicit reinforcing consequences as part of response-contingent learning games implemented by the children’s parents. For the ability-based group, behavior that children were capable of producing, but did not yet use intentionally, was identified and used to elicit reinforcing consequences. For the needs-based group, behavior children did not yet produce, but were expected to learn, was identified through a developmental assessment and used to elicit reinforcing consequences. Results showed that the children in the ability-based group had more learning opportunities, acquired more response-contingent behavior, and demonstrated more efficient learning compared with children in the needs-based group.
Increased mortality in narcolepsy.

OBJECTIVE To evaluate the mortality rate in patients with narcolepsy. DESIGN Data were derived from a large database representative of the US population, which contains anonymized patient-linked longitudinal claims for 173 million individuals. SETTING Symphony Health Solutions (SHS) Source Lx, an anonymized longitudinal patient dataset. PATIENTS/PARTICIPANTS All records of patients registered in the SHS database between 2008 and 2010. INTERVENTIONS None. MEASUREMENTS AND RESULTS Identification of patients with narcolepsy was based on ≥ 1 medical claim with the diagnosis of narcolepsy (ICD-9 347.xx) from 2002 to 2012. Dates of death were acquired from the Social Security Administration via a third party; the third party information was encrypted in the same manner as the claims data such that anonymity is ensured prior to receipt by SHS. Annual all-cause mortality rates for 2008, 2009, and 2010 were calculated retrospectively for patients with narcolepsy and patients without narcolepsy in the database, and standardized mortality ratios (SMR) were calculated. Mortality rates were also compared with the general US population (Centers for Disease Control data). SMRs of the narcolepsy population were consistent over the 3-year period and showed an approximate 1.5-fold excess mortality relative to those without narcolepsy. The narcolepsy population had consistently higher mortality rates relative to those without narcolepsy across all age groups, stratified by age decile, from 25-34 years to 75+ years of age. The SMR for females with narcolepsy was lower than for males with narcolepsy. CONCLUSIONS Narcolepsy was associated with approximately 1.5-fold excess mortality relative to those without narcolepsy. While the cause of this increased mortality is unknown, these findings warrant further investigation.
Work-family balance: The 3-way interaction effect of role demands, collectivism value and ethnicity

Work and family are experienced somewhat differently across culture. This paper examines whether the relationship between role-demands and work-family balance (WFB) experience across ethnicity is influenced by the groups’ collectivism value. A total of 324 female teachers were sampled. Using a hierarchical regression analysis, some support was found that the collectivism value do moderate the role demands-WFB relationship. Moreover, evidence was found that, to some extent, the collectivism moderating influence does vary among the different ethnic groups.
Growth Factors in Proliferative Diabetic Retinopathy

Many growth factors are implicated in the pathogenesis of proliferative diabetic retinopathy. Alteration of growth factors and their receptors in diabetes has been shown in both experimental and clinical studies. Sustained hyperglycemia resulting from long-standing diabetes leads to several biochemical abnormalities that consequently result in retinal hypoxia. Retinal oxygenation state regulates various growth factors that promote angiogenesis in order to meet the oxygen demands of the tissue. However, unregulated expression of these growth factors and induction of complex cascades leading to augmentation of other proangiogenic factors, which may not be regulated by tissue oxygenation, leads to uncontrolled retinal neovascularization and blindness in diabetic patients.
User-Chosen Phrases in Interactive Query Formulation for Information Retrieval

The impact of using phrases as content representation for documents and for queries has generally been accepted as a desirable feature in information retrieval systems because phrases are generally regarded as being more content-bearing than their constituent words. This has been borne by experiments in which the impact of phrases on retrieval performance has usually been found to be positive. However, most of the experimental results reported have derived phrases from documents and from queries in a fully automatic way. While this is acceptable for document indexing it is less acceptable for query formulation which is increasingly heading towards being an iterative process with users investing time in browsing the term space to choose appropriate search terms. In this paper we report a series of experiments in which two users, one experienced and the other a novice, formulate their queries by browsing the term space in advance of issuing a retrieval request. For these users we analyse the relative contributions and the impact of single words and multi-word phrases as search terms, on overall retrieval performance. Our results have implications for how choosing phrases as search terms should be presented to novice and to experienced searchers.
FGF21 and Cardiac Physiopathology

The heart is not traditionally considered either a target or a site of fibroblast growth factor-21 (FGF21) production. However, recent findings indicate that FGF21 can act as a cardiomyokine; that is, it is produced by cardiac cells at significant levels and acts in an autocrine manner on the heart itself. The heart is sensitive to the effects of FGF21, both systemic and locally generated, owing to the expression in cardiomyocytes of β-Klotho, the key co-receptor known to confer specific responsiveness to FGF21 action. FGF21 has been demonstrated to protect against cardiac hypertrophy, cardiac inflammation, and oxidative stress. FGF21 expression in the heart is induced in response to cardiac insults, such as experimental cardiac hypertrophy and myocardial infarction in rodents, as well as in failing human hearts. Intracellular mechanisms involving PPARα and Sirt1 mediate transcriptional regulation of the FGF21 gene in response to exogenous stimuli. In humans, circulating FGF21 levels are elevated in coronary heart disease and atherosclerosis, and are associated with a higher risk of cardiovascular events in patients with type 2 diabetes. These findings provide new insights into the role of FGF21 in the heart and may offer potential therapeutic strategies for cardiac disease.
Effects of Hypoxia on Embryonic Development in Two Ambystoma and Two Rana Species

Oxygen available to amphibian embryos fluctuates widely and is often very low. We investigated the effects of oxygen partial pressure (1.3–16.9 kPa) on embryonic development and hatching of two salamander (Ambystoma) and two frog (Rana) species. In Ambystoma, chronic hypoxia resulted in slowed development, delayed hatching, and embryos that were less developed at the time of hatching. Although hypoxia was not lethal to embryos, temporary developmental abnormalities were observed in Ambystoma at oxygen partial pressures of 3.8 kPa and below. Posthatching survival decreased below 3.3 kPa. In Rana, hypoxia did not affect developmental rate, presumably because hatching occurs at a very early stage of development relative to Ambystoma. However, Rana embryos hatched sooner in hypoxia than in normoxia, resulting in less developed embryos at the time of hatching. The results suggest that embryonic hypoxia may negatively affect survival and fitness in these species.
Preserving Color in Neural Artistic Style Transfer

This note presents an extension to the neural artistic style transfer algorithm (Gatys et al.). The original algorithm transforms an image to have the style of another given image. For example, a photograph can be transformed to have the style of a famous painting. Here we address a potential shortcoming of the original method: the algorithm transfers the colors of the original painting, which can alter the appearance of the scene in undesirable ways. We describe simple linear methods for transferring style while preserving colors.