Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of the Submergence Tolerance QTL Come Quick Drowning1 (CQD1) in Arabidopsis thaliana

Global climate change is predicted to increase water precipitation fluctuations and lead to localized prolonged floods in agricultural fields and natural plant communities. Thus, understanding the genetic basis of submergence tolerance is crucial in order to improve plant survival under these conditions. In this study, we performed a quantitative trait locus (QTL) analysis in Arabidopsis to identify novel candidate genes for increased submergence tolerance by using Kas-1 and Col (gl1) parental accessions and their derived recombinant inbred lines (RILs). We measured survival after submergence in dark for a 13-day period and used median lethal time, LT50 values for the QTL analysis. A major QTL, the Come Quick, Drowning (CQD1) locus, was detected in 2 independent experiments on the lower arm of chromosome 5 involved in higher submergence tolerance in the parental accession Kas-1. For fine-mapping, we then constructed near isogenic lines (NILs) by backcrossing the CQD1 QTL region. We also analyzed QTL regions related to size, leaf number, flowering, or survival in darkness and none of the QTL related to these traits overlapped with CQD1. The submergence tolerance QTL, CQD1, region detected in this study includes genes that have potential to be novel candidates effecting submergence tolerance such as trehalose-6-phosphate phosphatase and respiratory burst oxidase protein D. Gene expression and functional analysis for these genes under submergence would reveal the significance of these novel candidates and provide new perspectives for understanding genetic basis of submergence tolerance.
Optimal aeroacoustic shape design using approximation modeling

Reduction of noise generated by turbulent flow past a trailing edge continues to pose a challenge in many aeronautical and naval applications. Aeroacoustics problems related to such applications necessitate the use of large-eddy simulation (LES) or direct numerical simulation in order to capture a wide range of turbulence scales which are the source of broadband noise. Much previous work has focused on development of accurate computational methods for the prediction of trailing-edge noise. For instance, aeroacoustic calculations of the flow over a model airfoil trailing edge using LES and aeroacoustic theory have been presented by Wang & Moin (2000) and were shown to agree well with experiments. To make the simulations more cost-effective, Wang & Moin (2002) successfully employed wall models in the trailing-edge flow LES, resulting in a drastic reduction in computational cost with minimal degradation of the flow solutions. With the recent progress in simulation capabilities, the focus can now move from noise prediction to noise control. The goal of the present work is to apply shape optimization and control theory to the trailing-edge flow previously studied, in order to minimize aerodynamic noise. In this work approximation modeling techniques are applied for shape optimization, resulting in significant noise reduction in several cases.
Non-neoplastic Renal Diseases are Often Unrecognized in Adult Tumor Nephrectomy Specimens: A Review of 246 Cases

The pathologic evaluation of tumor nephrectomy specimens focuses on the diagnosis, grading, and staging of the neoplasm. The presence of coincidental non-neoplastic diseases in these specimens may have significant implications for patient outcomes. The purpose of this study is to determine the spectrum of non-neoplastic disease processes that may be overlooked in tumor nephrectomies, and to ascertain the extent to which surgical pathologists are trained to recognize these lesions. We reviewed the hematoxylin and eosin-stained slides of 246 adult tumor nephrectomy specimens with an emphasis on the non-neoplastic renal parenchyma. Further analysis of cases with pathologic alterations included special stains and direct immunofluorescence microscopy. The surgical pathology reports were reviewed to determine whether the non-neoplastic lesions were originally identified. We also surveyed United States pathology residency programs to determine how many require training in medical renal pathology. Forty-one cases (16.7%) had alterations, such as diffuse and/or nodular mesangial sclerosis, mesangial hypercellularity, or glomerular basement membrane thickening that warranted further study. After further work-up and clinical correlation, the pathologic changes in 24 cases were categorized as follows: diabetic nephropathy (19 cases) of which one demonstrated atheroembolic disease, thrombotic microangiopathy (3 cases), sickle cell nephropathy (1 case), and focal segmental glomerulosclerosis (1 case). Twenty-one (88%) of these diagnoses were not identified at initial pathologic evaluation. Only 35 of 98 pathology residency programs that responded to our survey require any formal training in medical renal pathology. Although accurate pathologic evaluation of renal neoplasms remains essential, surgical pathologists should be aware that coincidental non-neoplastic renal diseases are common, often not recognized, and may have important implications for patient care. Further consideration should be given to the training requirements of pathology residents and the guidelines for evaluation of nephrectomy specimens to avoid missing non-neoplastic renal lesions.
Correlated expression patterns of microRNA genes with age‐dependent behavioural changes in honeybee

The hive‐living honeybees (Apis mellifera) show age‐dependent behavioural changes; young bees usually nurse the broods in the colony and the older bees engage in foraging activities. These developmentally regulated behavioural changes were previously shown to be correlated with genome‐wide transcriptional changes in the honeybee brain. The indigenous small regulatory RNA molecules, known as microRNAs (miRNAs), are potent regulators of gene expression and also are developmentally regulated. Thus, we wanted to study if there might be correlation of differential expression of miRNA genes in the brain with age‐dependent behavioural changes of the bees. We determined expression patterns of a set (n= 20) of predicted miRNA genes, by quantitative real‐time PCR assays, in the brains of young and old bees that were engaged in nursing or foraging activities in the colony, respectively. Our data show correlated up‐regulation of miRNA‐124, miRNA‐14, miRNA‐276, miRNA‐13b, let‐7 and miRNA‐13a in the young nurse bees. miRNA‐12, miRNA‐9, miRNA‐219, miRNA‐210, miRNA‐263, miRNA‐92 and miRNA‐283 showed correlated expression patterns in the old forager bees. The modular changes of miRNA genes in the young nurse and old forager bees suggest possible roles of miRNAs in age‐dependent behavioural changes in bees. The correlated expression of intronic miRNA genes and their host genes as well as of miRNA genes physically clustered in the genome are also observed.
Tooth serration morphologies in the genus Machimosaurus (Crocodylomorpha, Thalattosuchia) from the Late Jurassic of Europe

Machimosaurus was a large-bodied durophagous/chelonivorous genus of teleosaurid crocodylomorph that lived in shallow marine and brackish ecosystems during the Late Jurassic. Among teleosaurids, Machimosaurus and its sister taxon ‘Steneosaurus’ obtusidens are characterized by having foreshortened rostra, proportionally enlarged supratemporal fenestrae and blunt teeth with numerous apicobasal ridges and a shorter anastomosed ridged pattern in the apical region. A recent study on ‘S. ’ obtusidens dentition found both true denticles and false serrations (enamel ridges which contact the carinae). Here, we comprehensively describe and figure the dentition of Machimosaurus, and find that Machimosaurus buffetauti and Machimosaurus hugii have four types of serration or serration-like structures, including both denticles and false denticles on the carinae. The denticles are irregularly shaped and are not always discrete units, whereas the false denticles caused by the interaction between the superficial enamel ridges and the carinae are restricted to the apical region. Peculiarly, the most ‘denticle-like’ structures are discrete, bulbous units on the apicobasal and apical anastomosed ridges of M. hugii. These ‘pseudo-denticles’ have never, to our knowledge, previously been reported among crocodylomorphs, and their precise function is unclear. They may have increased the surface area of the apical region and/or strengthened the enamel, both of which would have been advantageous for a durophagous taxon feeding on hard objects such as turtles.
Genome size scaling through phenotype space.

BACKGROUND AND AIMS Early observations that genome size was positively correlated with cell size formed the basis of hypothesized consequences of genome size variation at higher phenotypic scales. This scaling was supported by several studies showing a positive relationship between genome size and seed mass, and various metrics of growth and leaf morphology. However, many of these studies were undertaken with limited species sets, and often performed within a single genus. Here we seek to generalize the relationship between genome size and the phenotype by examining eight phenotypic traits using large cross-species comparisons involving diverse assemblages of angiosperm and gymnosperm species. These analyses are presented in order of increasing scale (roughly equating to the number of cells required to produce a particular phenotypic trait), following the order of: cell size (guard cell and epidermal), stomatal density, seed mass, leaf mass per unit area (LMA), wood density, photosynthetic rate and finally maximum plant height. SCOPE The results show that genome size is a strong predictor of phenotypic traits at the cellular level (guard cell length and epidermal cell area had significant positive relationships with genome size). Stomatal density decreased with increasing genome size, but this did not lead to decreased photosynthetic rate. At higher phenotypic scales, the predictive power of genome size generally diminishes (genome size had weak predictive power for both LMA and seed mass), except in the interesting case of maximum plant height (tree species tend to have small genomes). There was no relationship with wood density. The general observation that species with larger genome size have larger seed mass was supported; however, species with small genome size can also have large seed masses. All of these analyses involved robust comparative methods that incorporate the phylogenetic relationships of species. CONCLUSIONS Genome size correlations are quite strong at the cellular level but decrease in predictive power with increasing phenotypic scale. Our hope is that these results may lead to new mechanistic hypotheses about why genome size scaling exists at the cellular level, and why nucleotypic consequences diminish at higher phenotypic scales.
Impacts of some environmentally relevant parameters on the sorption of polycyclic aromatic hydrocarbons to aqueous suspensions of fullerene

The wide application of engineered carbon nanomaterials (CNMs), such as fullerene (C60), inevitably will result in their introduction into the aqueous environment. It is likely CNMs will associate with abundant natural organic matter (NOM) and engineered surfactants to form stable aqueous suspensions through various environmental processes. The present study reveals that sorption of polycyclic aromatic hydrocarbons (PAHs) to fullerene resulted in a remarkable decline of freely dissolved PAH concentrations. For the three PAHs studied (phenanthrene, fluoranthene, and chrysene) with log KOW in the range of 4.56 to 5.81, the measured sorption coefficients to aqueous suspensions of fullerene (log KC60 = 4.71–5.48) were close to that of dissolved organic carbon (DOC) from Aldrich humic acid (log KDOC = 4.48–5.91). Aqueous suspensions of fullerene were stable for a wide range of pH (3.0–11.0) and salinity conditions (0–25 mM NaCl), and the pH and salinity had minor effects on the sorption of PAHs to aqueous suspensions of fullerene. The addition of humic acids (5 mg/L DOC) to the fullerene (5 mg/L) suspensions resulted in an additional reduction of freely dissolved PAH concentrations. The high PAH sorption coefficients to suspended fullerene suggest that the release of fullerene to the aquatic environment might affect PAH fate and exposures.
Multi-Stage Multi-Task Learning with Reduced Rank

Multi-task learning (MTL) seeks to improve the generalization performance by sharing information among multiple tasks. Many existing MTL approaches aim to learn the low-rank structure on the weight matrix, which stores the model parameters of all tasks, to achieve task sharing, and as a consequence the trace norm regularization is widely used in the MTL literature. A major limitation of these approaches based on trace norm regularization is that all the singular values of the weight matrix are penalized simultaneously, leading to impaired estimation on recovering the larger singular values in the weight matrix. To address the issue, we propose a Reduced rAnk MUlti-Stage multi-tAsk learning (RAMUSA) method based on the recently proposed capped norms. Different from existing trace-norm-based MTL approaches which minimize the sum of all the singular values, the RAMUSA method uses a capped trace norm regularizer to minimize only the singular values smaller than some threshold. Due to the non-convexity of the capped trace norm, we develop a simple but well guaranteed multi-stage algorithm to learn the weight matrix iteratively. We theoretically prove that the estimation error at each stage in the proposed algorithm shrinks and finally achieves a lower upper-bound as the number of stages becomes large enough. Empirical studies on synthetic and real-world datasets demonstrate the effectiveness of the RAMUSA method in comparison with the state-of-the-art methods.
Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language

This article presents a measure of semantic similarity in an IS-A taxonomy based on the notion of shared information content. Experimental evaluation against a benchmark set of human similarity judgments demonstrates that the measure performs better than the traditional edge-counting approach. The article presents algorithms that take advantage of taxonomic similarity in resolving syntactic and semantic ambiguity, along with experimental results demonstrating their effectiveness.
Polarization of What? A Model of Elections with Endogenous Valence

We connect three characteristics of political candidates: their preferences, their platforms, and their valence. To do so, we define and study three types of elite polarization: preference polarization, valence polarization, and platform polarization. In our model, policy is represented as a position in a unidimensional space; candidates are policy motivated; valence is represented as a dimension orthogonal to policy; and candidates can increase their valence by paying a cost. We find that candidates will in general not converge to one another in the policy dimension or in the valence dimension. A candidate’s preferences are positively, but not perfectly, correlated with her platform. Strikingly, under some circumstances, candidates’ platforms will diverge when their preferences converge. And there is an unfortunate trade-off regarding candidates’ attributes: they will display high valence or low polarization, but not both. One of our empirical predictions is a positive correlation between campaign spendi.
Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110

The spliceosome cycle consists of assembly, catalysis, and recycling phases. Recycling of postspliceosomal U4 and U6 small nuclear ribonucleoproteins (snRNPs) requires p110/SART3, a general splicing factor. In this article, we report that the zebrafish earl grey (egy) mutation maps in the p110 gene and results in a phenotype characterized by thymus hypoplasia, other organ-specific defects, and death by 7 to 8 days postfertilization. U4/U6 snRNPs were disrupted in egy mutant embryos, demonstrating the importance of p110 for U4/U6 snRNP recycling in vivo. Surprisingly, expression profiling of the egy mutant revealed an extensive network of coordinately up-regulated components of the spliceosome cycle, providing a mechanism compensating for the recycling defect. Together, our data demonstrate that a mutation in a general splicing factor can lead to distinct defects in organ development and cause disease.
Histological type-specific prognostic factors of cervical small cell neuroendocrine carcinoma, adenocarcinoma, and squamous cell carcinoma

Background The study aimed to determine the prognostic impact of clinical and pathological factors on survival among patients with small cell neuroendocrine carcinoma (SNEC), adenocarcinoma (ADC), and squamous cell carcinoma (SCC). Methods Eligible participants were all patients with histologically confirmed cervical cancer treated at Chiang Mai University Hospital between 1995 and 2011. We included all patients with SNEC and randomly enrolled patients with ADC and SCC. We used competing-risk regression analysis to examine the risk of cancer-related death by histological type. Results We included 130 (6.2%) women with SNEC, 346 (16.4%) with ADC, and 1,632 (77.4%) with SCC. Age >60 years (hazard ratio [HR] 4.9, 95% confidence interval [CI] 2.0–12.0) and lymph node involvement (HR 3.0, 95% CI 1.2–7.4) were prognostic factors among surgically-treated patients with SNEC. Deeper stromal invasion (HR 3.6, 95% CI 1.6–8.3) was a prognostic factor in patients with SCC. In patients with advanced SNEC, age >60 years had a strong prognostic impact (HR 2.6, 95% CI 1.0–6.5) while the International Federation of Gynecology and Obstetrics stages III and IV were prognostic factors for patients with advanced stage ADC (HR 2.9, 95% CI 2.0–4.4 and HR 4.5, 95% CI 2.6–7.9, respectively) and SCC (HR 1.7, 95% CI 1.4–2.0 and HR 3.7, 95% CI 2.8–4.9, respectively) compared with the International Federation of Gynecology and Obstetrics stage IIB. Conclusion Clinical and pathological prognostic factors in cervical cancer differed according to histological type. Taking the important prognostic factors for each histological type into consideration may be beneficial for tailored treatment and follow-up planning.
SecGraph: A Uniform and Open-source Evaluation System for Graph Data Anonymization and De-anonymization

In this paper, we analyze and systematize the state-of-the-art graph data privacy and utility techniques. Specifically, we propose and develop SecGraph (available at [1]), a uniform and open-source Secure Graph data sharing/publishing system. In SecGraph, we systematically study, implement, and evaluate 11 graph data anonymization algorithms, 19 data utility metrics, and 15 modern Structure-based De-Anonymization (SDA) attacks. To the best of our knowledge, SecGraph is the first such system that enables data owners to anonymize data by state-of-the-art anonymization techniques, measure the data's utility, and evaluate the data's vulnerability against modern De-Anonymization (DA) attacks. In addition, SecGraph enables researchers to conduct fair analysis and evaluation of existing and newly developed anonymization/DA techniques. Leveraging SecGraph, we conduct extensive experiments to systematically evaluate the existing graph data anonymization and DA techniques. The results demonstrate that (i) most anonymization schemes can partially or conditionally preserve most graph utilities while losing some application utility; (ii) no DA attack is optimum in all scenarios. The DA performance depends on several factors, e.g., similarity between anonymized and auxiliary data, graph density, and DA heuristics; and (iii) all the state-of-the-art anonymization schemes are vulnerable to several or all of the modern SDA attacks. The degree of vulnerability of each anonymization scheme depends on how much and which data utility it preserves.
Domestic violence typologies: What value to practice?

Over the last few decades, understandings of the nature and causes of domestic violence have increased in sophistication. This has been influenced by, and led to, an influx of domestic violence typologies that have attempted to identify differences between groups of offenders and victims based on factors ranging from physiological reactions to specific stimuli through to historical experiences of violence and abuse. While this research has been of undeniable conceptual and theoretical value, its applicability to the day-to-day work of domestic violence practitioners is less clear. This study represents one of the first attempts to speak directly to professionals about how domestic violence typologies inform their everyday decision making and case practice.
The economic cost of obesity: the French situation.

OBJECTIVE To estimate the economic burden of obesity in France. DESIGN A prevalence-based approach identifying the costs incurred during a given year (1992) by obese subjects. MEASUREMENTS Direct costs (personal health care, hospital care, physician services, drugs) and indirect costs (lost output as a result of cessation or reduction of productivity caused by morbidity and mortality); economic benefits due to the reduced incidence of hip fractures. RESULTS The direct costs of obesity (BMI > or = 27) were 11.89 billion French Francs (FF), which corresponded to about 2% of the expenses of the French care system. Hypertension represented 33% of the total amount and cancer 2.5% of the direct cost of obesity. Indirect costs represented FF 0.6 billion. These are conservative estimates as far as all obesity-related diseases and all health care and indirect costs were not included due to missing information. CONCLUSION These results were remarkably similar to previous reports on the economic costs of obesity in other western countries (USA, Sweden, Netherlands, Australia) which concluded that the cost of obesity amounted to around 2% to 5% of the total cost of health care in industrialized societies.
Insulin resistant phenotype is associated with high serum leptin levels in offspring of patients with non-insulin-dependent diabetes mellitus.

OBJECTIVE To investigate whether there are differences in serum leptin levels between the offspring of non-insulin-dependent diabetes mellitus (NIDDM) patients representing different phenotypes of NIDDM, and furthermore to investigate the role of different fat tissue (subcutaneous fat area (SCFAT) and intra-abdominal fat area (IAFAT)) and insulin sensitivity on serum leptin levels. DESIGN Twenty non-diabetic offspring of NIDDM patients with insulin secretion deficient phenotype (IS-group), 18 non-diabetic offspring of NIDDM patients with insulin resistant phenotype (IR-group) and 14 healthy control subjects without a family history of diabetes were studied. METHODS Serum leptin levels were measured by RIA. SCFAT and IAFAT were measured by computed tomography. the total fat mass (TFM) by bioelectrical impedance and the whole body glucose uptake (WBGU) by the euglycemic hyperinsulinemic clamp technique. RESULTS Subjects of the control group (P = 0.003) and the IS-group (P<0.001) had lower serum leptin levels than subjects of the IR-group even after adjustment for gender (P<0.001). TFM (P = 0.009), fasting plasma insulin (P = 0.003) and for IAFAT (P<0.001). The differences weakened after adjustments for SCFAT (P = 0.028) or WBGU (P = 0.040) and disappeared after adjustment for both SCFAT and WBGU (P = 0.058). In the stepwise multiple regression analyses SCFAT. WBGU and gender explained 58% of the variation of serum leptin levels whereas IAFAT failed to be a significant determinant of serum leptin levels. CONCLUSIONS The higher serum leptin levels in the IR-group was markedly, but not solely, explained by lower rates of WBGU and higher SCFAT. SCFAT was shown to be a more important determinant of serum leptin levels than IAFAT among these study groups.