Miracle-dz/UniFAR-FTUs huggingface dataset:
Parvulin (Par14), a Peptidyl-Prolyl cis-trans Isomerase, Is a Novel rRNA Processing Factor That Evolved in the Metazoan Lineage

Although parvulin (Par14/eukaryotic parvulin homolog), a peptidyl-prolyl cis-trans isomerase, is found associated with the preribosomal ribonucleoprotein (pre-rRNP) complexes, its roles in ribosome biogenesis remain undetermined. In this study, we describe a comprehensive proteomics analysis of the Par14-associated pre-rRNP complexes using LC-MS/MS and a knockdown analysis of Par14. Together with our previous results, we finally identified 115 protein components of the complexes, including 39 ribosomal proteins and 54 potential trans-acting factors whose yeast homologs are found in the pre-rRNP complexes formed at various stages of ribosome biogenesis. We give evidence that, although Par14 exists in both the phosphorylated and unphosphorylated forms in the cell, only the latter form is associated with the pre-40 S and pre-60 S ribosomal complexes. We also show that Par14 co-localizes with the nucleolar protein B23 during the interphase and in the spindle apparatus during mitosis and that actinomycin D treatment results in the exclusion of Par14 from the nucleolus. Finally we demonstrate that knockdown of Par14 mRNA decelerates the processing of pre-rRNA to 18 and 28 S rRNAs. We propose that Par14 is a component of the pre-rRNA complexes and functions as an rRNA processing factor in ribosome biogenesis. As the amino acid sequence of Par14 including that in the amino-terminal pre-rRNP binding region is conserved only in metazoan homologs, we suggest that its roles in ribosome biogenesis have evolved in the metazoan lineage.
Accuracy of short‐term sea ice drift forecasts using a coupled ice‐ocean model

Abstract Arctic sea ice drift forecasts of 6 h–9 days for the summer of 2014 are generated using the Marginal Ice Zone Modeling and Assimilation System (MIZMAS); the model is driven by 6 h atmospheric forecasts from the Climate Forecast System (CFSv2). Forecast ice drift speed is compared to drifting buoys and other observational platforms. Forecast positions are compared with actual positions 24 h–8 days since forecast. Forecast results are further compared to those from the forecasts generated using an ice velocity climatology driven by multiyear integrations of the same model. The results are presented in the context of scheduling the acquisition of high‐resolution images that need to follow buoys or scientific research platforms. RMS errors for ice speed are on the order of 5 km/d for 24–48 h since forecast using the sea ice model compared with 9 km/d using climatology. Predicted buoy position RMS errors are 6.3 km for 24 h and 14 km for 72 h since forecast. Model biases in ice speed and direction can be reduced by adjusting the air drag coefficient and water turning angle, but the adjustments do not affect verification statistics. This suggests that improved atmospheric forecast forcing may further reduce the forecast errors. The model remains skillful for 8 days. Using the forecast model increases the probability of tracking a target drifting in sea ice with a 10 km × 10 km image from 60 to 95% for a 24 h forecast and from 27 to 73% for a 48 h forecast.
A Nonsense Mutation in FAM161A Is a Recurrent Founder Allele in Dutch and Belgian Individuals With Autosomal Recessive Retinitis Pigmentosa.

PURPOSE To identify mutations in FAM161A underlying autosomal recessive retinitis pigmentosa (arRP) in the Dutch and Belgian populations and to investigate whether common FAM161A-associated phenotypic features could be identified. METHODS Homozygosity mapping, amplification-refractory mutation system (ARMS) analysis, and Sanger sequencing were performed to identify mutations in FAM161A. Microsatellite and SNP markers were genotyped for haplotype analysis. Patients with biallelic mutations underwent detailed ophthalmologic examinations, including measuring best-corrected visual acuity, extensive fundus photography with reflectance and autofluorescence imaging, and optical coherence tomography. RESULTS Homozygosity mapping in 230 Dutch individuals with suspected arRP yielded five individuals with a homozygous region harboring FAM161A. Sanger sequencing revealed a homozygous nonsense mutation (c.1309A>T; p.[Arg437*]) in one individual. Subsequent ARMS analysis and Sanger sequencing in Dutch and Belgian arRP patients resulted in the identification of seven additional individuals carrying the p.(Arg437*) mutation, either homozygously or compound heterozygously with another mutation. Haplotype analysis identified a shared haplotype block of 409 kb surrounding the p.(Arg437*) mutation in all patients, suggesting a founder effect. Although the age of onset was variable among patients, all eight developed pronounced outer retinal loss with severe visual field defects and a bull's eye-like maculopathy, followed by loss of central vision within 2 decades after the initial diagnosis in five subjects. CONCLUSIONS A founder mutation in FAM161A p.(Arg437*) underlies approximately 2% of arRP cases in the Dutch and Belgian populations. The age of onset of the retinal dystrophy appears variable, but progression can be steep, with almost complete loss of central vision later in life.
Non-linear impulsive dynamical systems. Part I: Stability and dissipativity

In this paper we develop Lyapunov and invariant set stability theorems for non-linear impulsive dynamical systems. Furthermore, we generalize dissipativity theory to non-linear dynamical systems with impulsive effects. Specifically, the classical concepts of system storage functions and supply rates are extended to impulsive dynamical systems providing a generalized hybrid system energy interpretation in terms of stored energy, dissipated energy over the continuous-time system dynamics and dissipated energy over the resetting instants. Furthermore, extended Kalman‐Yakubovich‐Popov conditions in terms of the impulsive system dynamics characterizing dissipativeness via system storage functions are derived. Finally, the framework is specialized to passive and non-expansive impulsive systems to provide a generalization of the classical notions of passivity and non-expansivity for non-linear impulsive systems. These results are used in the second part of this paper to develop extensions of the small gain and positivity theorems for feedback impulsive systems as well as to develop optimal hybrid feedback controllers.
Reply to letter: Transcranial magnetic stimulation for Parkinson's disease

With great interest, we read the article by Kojovic and colleagues. Surprisingly, the group results of their patients with Parkinson’s disease (PD) showed little change in any of the parameters over 12 months, whereas at the individual level, the investigators found that asymmetry in clinical motor symptoms was reflected in asymmetry of plasticity and inhibition. Although we agree with Kojovic and colleagues that within-subject comparisons seem to be more useful diagnostic fingerprints of disease than between-group comparisons, there seem to be two logical explanations for their finding that no group-level differences were found in clinical or electrophysiological measures between treated and untreated patients or between early and late treated patients. First, we understand that owing to ethical and practical reasons, their follow-up study has methodological shortcomings (i.e., not a randomized study, the dose and kinds of drug use are not controlled for, and so on), but we do not understand why the investigators did not control for gender (e.g., 9 male patients vs. 3 female patients) in their clinical sample (see Table 1, on page 1099). From the literature, it is known that important differences in brain asymmetry exist between males and females, with male brains being more asymmetric than female brains. Moreover, sex is known to be an important factor in PD. Sex differences in PD (i.e., a greater prevalence and earlier age of onset in men) are determined, largely, by biological sex differences in the nigrostriatal dopaminergic system. In short, sex seems to have significantly affected their (nonsignificant) group results. Second, there is a wide variance in mean age over the 12 patients (ranging from 34 to 71 years old; see also Table 1, on page 1099). Age was found to be a significant factor in brain asymmetry. Brain asymmetry was found to decrease with age in the precentral gyrus, optic radiation, and angular gyrus, whereas asymmetry was found to increase significantly with age in the inferior frontal gyrus, anterior cingulate, anterior insula, parahippocampal gyrus, retrosplenial, coronal radiate, cortex, and knee region of the internal capsule. Therefore, this factor should have been better controlled for and seems to be an additional explanation for the nonsignificant group-level results.
Compositional Semantics using Feature-Based Models from WordNet

This article describes a method to build semantic representations of composite expressions in a compositional way by using WordNet relations to represent the meaning of words. The meaning of a target word is modelled as a vector in which its semantically related words are assigned weights according to both the type of the relationship and the distance to the target word. Word vectors are compositionally combined by syntactic dependencies. Each syntactic dependency triggers two complementary compositional functions: the named head function and dependent function. The experiments show that the proposed compositional method outperforms the state-of-the-art for both intransitive subject-verb and transitive subject-verb-object constructions.
mRNA Expression of VEGF and Its Receptors in Fallopian Tubes of Women with Ectopic Pregnancies

Background Establishment of viable pregnancy requires embryo implantation and placentation. Ectopic pregnancy (EP) is a pregnancy complication which occurs when an embryo implants outside of the uterine cavity, most often in a fallopian tube. On the other hand, an important aspect of successful implantation is angiogenesis. Vascular endothelial growth factor (VEGF) is a potent angiogenic factor responsible for vascular development that acts through its receptors, VEGF receptor 1 (VEGFR1) and VEGFR2. This study aims to investigate mRNA expression of VEGF and its receptors in fallopian tubes of women who have EP compared with fallopian tubes of pseudo-pregnant women. We hypothesize that expression of VEGF and its receptors in human fallopian tubes may change during EP. Materials and Methods This was a case-control study. The case group consisted of women who underwent salpingectomy because of EP. The control group consisted of women with normal fallopian tubes that underwent hysterectomy. Prior to tubal sampling, each control subject received an injection of human chorionic gonadotropin (hCG) to produce a state of pseudo-pregnancy. Fallopian tubes from both groups were procured. We investigated VEGF, VEGFR1 and VEGFR2 mRNA expressions in different sections of these tubes (infundibulum, ampulla and isthmus) by reverse transcription polymerase chain reaction (RT-PCR) and quantitative PCR (Q-PCR). Results RT-PCR showed expressions of these genes in all sections of the fallopian tubes in both groups. Q-PCR analysis revealed that expressions of VEGF, VEGFR1 and VEGFR2 were lower in all sections of the fallopian tubes from the case group compared to the controls. Only VEGFR2 had higher expression in the ampulla of the case group. Conclusion Decreased expressions of VEGF, VEGFR1 and VEGFR2 in the EP group may have a role in the pathogenesis of embryo implantation in fallopian tubes.
Can Adults With Autism Spectrum Disorders Infer What Happened to Someone From Their Emotional Response?

Can adults with autism spectrum disorders (ASD) infer what happened to someone from their emotional response? Millikan has argued that in everyday life, others' emotions are most commonly used to work out the antecedents of behavior, an ability termed retrodictive mindreading. As those with ASD show difficulties interpreting others' emotions, we predicted that these individuals would have difficulty with retrodictive mindreading. Sixteen adults with high‐functioning autism or Asperger's syndrome and 19 typically developing adults viewed 21 video clips of people reacting to one of three gifts (chocolate, monopoly money, or a homemade novelty) and then inferred what gift the recipient received and the emotion expressed by that person. Participants' eye movements were recorded while they viewed the videos. Results showed that participants with ASD were only less accurate when inferring who received a chocolate or homemade gift. This difficulty was not due to lack of understanding what emotions were appropriate in response to each gift, as both groups gave consistent gift and emotion inferences significantly above chance (genuine positive for chocolate and feigned positive for homemade). Those with ASD did not look significantly less to the eyes of faces in the videos, and looking to the eyes did not correlate with accuracy on the task. These results suggest that those with ASD are less accurate when retrodicting events involving recognition of genuine and feigned positive emotions, and challenge claims that lack of attention to the eyes causes emotion recognition difficulties in ASD. Autism Res 2014, 7: 112–123. © 2013 International Society for Autism Research, Wiley Periodicals, Inc.
Innervation of Anulus Tears: An Experimental Animal Study

Study Design. A prospective immunohistological study in an animal model. Objective. To identify and describe the phenotype of neoinnervation in experimental anular tears. Summary of Background Data. Controversy surrounds neoinnervation of degenerate discs which has been proposed as the anatomic basis for discogenic pain. Ablation of neoinnervation has been postulated as the theoretical basis for the claimed successes of procedures such as intradiscal electrotherapy. The animal model of disc degeneration previously developed in our research center provides an opportunity to investigate the innervation of anular tears in an extensively characterized lesion. Methods. A surgical anular tear was created in 5 lumbar discs in 11 sheep which were killed at 1, 2, 3, and 12 months. Each spine was x-rayed and divided into motion segments for histologic analysis. Serial sections through the tear were immunostained for protein gene product 9.5, tyrosine hydroxylase, and calcitonin gene receptor protein. Results. Neoinnervation of the periphery of the anular tear was observed. Ingrowing nerves penetrated marginally deeper than the normal anular innervation but no nerves were identified in the inner anulus or nucleus. A minority of the new axons were calcitonin gene receptor protein or tyrosine hydroxylase positive. Conclusion. The anulus tears in this model are innervated only peripherally to a depth only marginally greater than that of the normal anulus.
Bacterial interactions and successions during plaque development.

Studies from the 1960s indicated that increased microbial diversity and a succession in the predominant bacterial species in plaque correlate with the appearance of gingival inflammation and the development of periodontal disease. In the past few years, molecular characterization of the microflora found in various sites of the oral cavity of different subjects has detected around 700 bacterial species or phylotypes (1, 63, 93). Some of these species are considered commensal and a positive feature of our healthy microflora, while others are considered pathogenic. The colonization of pathogenic bacteria is probably dependent upon the interaction of pathogens and commensal organisms. The clinical relevance and periodontal microbial ecology of these bacteria have been presented in an outstanding, comprehensive review (101). The discussion in the present article centers on interactions among bacterial species and how these interactions contribute to the development of plaque and ultimately to the formation of periodontopathogenic communities. Interactions among human oral bacteria are integral to the development of plaque. From the early stages of colonization to the formation of mature supragingival and subgingival plaque, a diverse array of bacterial species colonizes into densely populated communities. Interactions among different bacterial cell types are proposed to drive the maturation of plaque. These interactions occur at several levels, including physical contact, metabolic exchange, small-signal-molecule-mediated communication and exchange of genetic material. A principal feature of human oral bacteria is their ability to interact by coaggregation with other oral bacteria (48). Coaggregation is defined as the specific cell-to-cell recognition that occurs between genetically distinct cell types. Each cell type bears on its surface one or more types of coaggregation mediator, which are called adhesins and receptors (described below). The adhesins and receptors confer a particular set of coaggregation properties. Coaggregation partnerships are central to the development of biodiversity in supragingival and subgingival plaque. Coaggregations effect changes in populations, from low diversity in initial communities of supragingival plaque to high diversity in subgingival plaque. This article will provide an overview of the physical and metabolic interactions that occur among the oral microflora in the context of plaque development.
Overtaking vehicle detection using a spatio-temporal CRF

Overtaking vehicle detection is vital for road safety, as the dangerous behavior of that vehicle may affect the safety of ego-vehicle and the time is not enough for the driver to attend and react. Therefore, it is one of the key components of the Advanced Driver Assistance Systems. Mostly, traditional methods only use local information, appearance or motion. In this paper, we build a novel CRF model to make use of the interaction between local regions, and the motion features from multiple scales as well. The whole model is based on the low-level optical flows. In order to increase the robustness to the noise in the flow, we divided the motion field into small blocks, and learned Mixture of Probabilistic Principle Analysis models for the common motion patterns of the background. Moreover, we also adopted an online scheme for updating the parameters. Results of testing on the real road images demonstrated the capability of the proposed algorithm.
Reliability of Categorical Loudness Scaling and Its Relation to Threshold

Objective: To further examine the reliability of categorical loudness scaling (CLS) for individual loudness categories and for the slope of the CLS functions. And, to evaluate the relationship between CLS and audiometric threshold. Design: CLS functions were obtained in 74 subjects, 58 with hearing loss and 16 with normal hearing. CLS functions were measured at three frequencies (1, 2, and 4 kHz) in two separate sessions separated by as little as 1 wk and as much as 6 mo. Reliability of mean and median levels within each loudness category was assessed using SDs and correlation coefficients. Lines were fit to the CLS functions, and slopes of the lines were used to assess reliability and the relation between CLS and audiometric threshold. Results: Similar reliability for CLS measurements was observed in both normal-hearing and hearing-impaired subjects at all frequencies. Across both groups of subjects, correlations describing the reliability of mean stimulus level within category exceeded 0.92 at all frequencies. In addition, SDs of the mean stimulus-level difference between visits ranged from 6.6 to 7.8 dB, depending on frequency. The correlation between the slope of a straight line fitted to the entire CLS function and audiometric threshold collapsed across frequencies was 0.72. Two line segments were then fit to the CLS function: one segment was fit to the soft portion of the CLS function (categorical units ≤20) and the other segment to the loud portion (categorical unit >20). Slopes of the line fit to the entire CLS function and of the line fit to the soft portion of the CLS function were both reliable across sessions. The slope of the line fit to the soft portion increased as audiometric threshold increased, with the correlations greater than 0.86 at all frequencies. No relationship was observed between slope of the line fit to the loud portion of the CLS function and audiometric threshold. Iso-loudness contours were constructed from the CLS data and used to determine the gain that would be needed to produce “normal” loudness percepts for hearing-impaired individuals. Conclusions: Within-subject CLS measurements were reliable across sessions both for individual loudness categories and for slope of the CLS functions. In addition, the slope of the low-level portion of the CLS function varied in a predictable manner with audiometric threshold, with slope increasing as audiometric threshold increased. Finally, gain as a function of input level needed to provide loudness percepts for individuals with hearing loss equal to the loudness percepts of normal-hearing individuals can be estimated from audiometric threshold. This finding supports the assumption that audiometric threshold and response growth (loudness) are both determined by the same underlying cochlear mechanisms.
High-Fat Diet Induces Significant Metabolic Disorders in a Mouse Model of Polycystic Ovary Syndrome1

ABSTRACT Polycystic ovary syndrome (PCOS) is the most common female endocrinopathy associated with both reproductive and metabolic disorders. Dehydroepiandrosterone (DHEA) is currently used to induce a PCOS mouse model. High-fat diet (HFD) has been shown to cause obesity and infertility in female mice. The possible effect of an HFD on the phenotype of DHEA-induced PCOS mice is unknown. The aim of the present study was to investigate both reproductive and metabolic features of DHEA-induced PCOS mice fed a normal chow or a 60% HFD. Prepubertal C57BL/6 mice (age 25 days) on the normal chow or an HFD were injected (s.c.) daily with the vehicle sesame oil or DHEA for 20 consecutive days. At the end of the experiment, both reproductive and metabolic characteristics were assessed. Our data show that an HFD did not affect the reproductive phenotype of DHEA-treated mice. The treatment of HFD, however, caused significant metabolic alterations in DHEA-treated mice, including obesity, glucose intolerance, dyslipidemia, and pronounced liver steatosis. These findings suggest that HFD induces distinct metabolic features in DHEA-induced PCOS mice. The combined DHEA and HFD treatment may thus serve as a means of studying the mechanisms involved in metabolic derangements of this syndrome, particularly in the high prevalence of hepatic steatosis in women with PCOS.
Cross validation in LASSO and its acceleration

We investigate leave-one-out cross validation (CV) as a determinator of the weight of the penalty term in the least absolute shrinkage and selection operator (LASSO). First, on the basis of the message passing algorithm and a perturbative discussion assuming that the number of observations is sufficiently large, we provide simple formulas for approximately assessing two types of CV errors, which enable us to significantly reduce the necessary cost of computation. These formulas also provide a simple connection of the CV errors to the residual sums of squares between the reconstructed and the given measurements. Second, on the basis of this finding, we analytically evaluate the CV errors when the design matrix is given as a simple random matrix in the large size limit by using the replica method. Finally, these results are compared with those of numerical simulations on finite-size systems and are confirmed to be correct. We also apply the simple formulas of the first type of CV error to an actual dataset of the supernovae.