Miracle-dz/UniFAR-FTUs huggingface dataset:
Arabidopsis ROCK1 transports UDP-GlcNAc/UDP-GalNAc and regulates ER protein quality control and cytokinin activity

Significance Nucleotide sugars are donor substrates for the formation of glycan modifications, which are important for the function of many macromolecules such as proteins and lipids. Although most of the glycosylation reactions occur in the endoplasmic reticulum (ER) and Golgi of eukaryotic cells, nucleotide sugar activation occurs in the cytosol and specific transporters must carry these molecules across the membrane. We identified REPRESSOR OF CYTOKININ DEFICIENCY 1 (ROCK1) as an ER-localized transporter of UDP-GlcNAc and UDP-GalNAc in plants. In contrast to animals, nothing is known about the function of the two respective sugar residues in the plant ER. We demonstrate that ROCK1-mediated transport plays a role in the ER-associated protein quality control and loss of ROCK1 enhances cytokinin responses by suppressing the activity of cytokinin-degrading CKX proteins. The formation of glycoconjugates depends on nucleotide sugars, which serve as donor substrates for glycosyltransferases in the lumen of Golgi vesicles and the endoplasmic reticulum (ER). Import of nucleotide sugars from the cytosol is an important prerequisite for these reactions and is mediated by nucleotide sugar transporters. Here, we report the identification of REPRESSOR OF CYTOKININ DEFICIENCY 1 (ROCK1, At5g65000) as an ER-localized facilitator of UDP-N-acetylglucosamine (UDP-GlcNAc) and UDP-N-acetylgalactosamine (UDP-GalNAc) transport in Arabidopsis thaliana. Mutant alleles of ROCK1 suppress phenotypes inferred by a reduced concentration of the plant hormone cytokinin. This suppression is caused by the loss of activity of cytokinin-degrading enzymes, cytokinin oxidases/dehydrogenases (CKXs). Cytokinin plays an essential role in regulating shoot apical meristem (SAM) activity and shoot architecture. We show that rock1 enhances SAM activity and organ formation rate, demonstrating an important role of ROCK1 in regulating the cytokinin signal in the meristematic cells through modulating activity of CKX proteins. Intriguingly, genetic and molecular analysis indicated that N-glycosylation of CKX1 was not affected by the lack of ROCK1-mediated supply of UDP-GlcNAc. In contrast, we show that CKX1 stability is regulated in a proteasome-dependent manner and that ROCK1 regulates the CKX1 level. The increased unfolded protein response in rock1 plants and suppression of phenotypes caused by the defective brassinosteroid receptor bri1-9 strongly suggest that the ROCK1 activity is an important part of the ER quality control system, which determines the fate of aberrant proteins in the secretory pathway.
Executive control training from middle childhood to adolescence

Executive functions (EFs) include a number of higher-level cognitive control abilities, such as cognitive flexibility, inhibition, and working memory, which are instrumental in supporting action control and the flexible adaptation changing environments. These control functions are supported by the prefrontal cortex and therefore develop rapidly across childhood and mature well into late adolescence. Given that executive control is a strong predictor for various life outcomes, such as academic achievement, socioeconomic status, and physical health, numerous training interventions have been designed to improve executive functioning across the lifespan, many of them targeting children and adolescents. Despite the increasing popularity of these trainings, their results are neither robust nor consistent, and the transferability of training-induced performance improvements to untrained tasks seems to be limited. In this review, we provide a selective overview of the developmental literature on process-based cognitive interventions by discussing (1) the concept and the development of EFs and their neural underpinnings, (2) the effects of different types of executive control training in normally developing children and adolescents, (3) individual differences in training-related performance gains as well as (4) the potential of cognitive training interventions for the application in clinical and educational contexts. Based on recent findings, we consider how transfer of process-based executive control trainings may be supported and how interventions may be tailored to the needs of specific age groups or populations.
Cnidarian microRNAs frequently regulate targets by cleavage

In bilaterians, which comprise most of extant animals, microRNAs (miRNAs) regulate the majority of messenger RNAs (mRNAs) via base-pairing of a short sequence (the miRNA “seed”) to the target, subsequently promoting translational inhibition and transcript instability. In plants, many miRNAs guide endonucleolytic cleavage of highly complementary targets. Because little is known about miRNA function in nonbilaterian animals, we investigated the repertoire and biological activity of miRNAs in the sea anemone Nematostella vectensis, a representative of Cnidaria, the sister phylum of Bilateria. Our work uncovers scores of novel miRNAs in Nematostella, increasing the total miRNA gene count to 87. Yet only a handful are conserved in corals and hydras, suggesting that microRNA gene turnover in Cnidaria greatly exceeds that of other metazoan groups. We further show that Nematostella miRNAs frequently direct the cleavage of their mRNA targets via nearly perfect complementarity. This mode of action resembles that of small interfering RNAs (siRNAs) and plant miRNAs. It appears to be common in Cnidaria, as several of the miRNA target sites are conserved among distantly related anemone species, and we also detected miRNA-directed cleavage in Hydra. Unlike in bilaterians, Nematostella miRNAs are commonly coexpressed with their target transcripts. In light of these findings, we propose that post-transcriptional regulation by miRNAs functions differently in Cnidaria and Bilateria. The similar, siRNA-like mode of action of miRNAs in Cnidaria and plants suggests that this may be an ancestral state.
Aggressive behaviors among demented nursing home residents in Japan

This study investigates the frequency of aggressive behaviors in a sample of elderly nursing home residents with dementia in Japan. Behavioral data were collected on 391 residents using the Cohen‐Mansfield Agitation Inventory (CMAI). Data were also gathered on residents' age, sex, and ability to perform self‐care. Another scale was used to code the degree of resistance that each resident manifested during bathing, toileting, dressing and eating. In addition, qualitative data were collected from caregivers regarding their main caregiving problems with dementia residents. Findings show that 45.4% of the sample manifested aggressive behavior during the 2‐week study period. Men were significantly more likely to manifest physically aggressive behavior, but there was no gender difference for verbal aggression. Age had no relationship to aggressive behavior. Residents who were most dependent in self‐care had significantly higher frequencies of aggressive behaviors. Caregivers reported that most aggressive behavior took place during personal care. The majority of caregivers identified verbal agitation rather than physical aggression as their main caregiving problem. This study represents the first time that the CMAI has been translated and used in Japan and the first time empirical data has been collected on the behavior of dementia patients in Japanese nursing homes. Copyright © 2000 John Wiley & Sons, Ltd.
The Effects Of Song Singing On Improvements In Affective Intonation Of People With Traumatic Brain Injury

This study examined the effects of a song-singing program on the affective speaking intonation of traumatically brain-injured people who presented with monotonal voices. Four subjects received 15 sessions of music therapy comprising the singing of three subject-preferred songs. The variables of: speaking fundamental frequency, standardised variability and slope, pitch range, pitch-matching accuracy and mood were analysed pre and post-session. The audio data was analysed using Multi-speech with real-time pitch module. A key phrase selected from songs used in the subjects' sessions was also analysed to determine pitch-matching accuracy and later compared with the intervals in the pitch-matching exercise. The visual analogue mood scales were assessed as per standardised procedure. Results suggest that long-term improvements in affective intonation are evident, especially in fundamental frequency, however the response direction and degree of change are idiosyncratic. Immediate treatment effects (pre/post-session differences) were in the direction contrary to that expected (negative). Fatigue is suggested as one explanation for this result, particularly as fatigue was reported in the visual analogue mood scale. Vocal range improved over time in all four subjects and was positively correlated with all three intonation components, particularly the standardised variability score. High variability in responses was evident in the interval tasks. The mood scale responses were also variable, and interpretations of therapy effects on mood should be treated with caution. Negative correlations (that opposite to expected) were found between the mood scales and intonation variables suggesting that as subjects reported becoming more emotional, they became more monotonal, had flatter slope measures and a lower fundamental frequency. Subjects sang intervals more accurately when they were in a song than when presented in isolation.
Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis.

The ability to accurately predict gene function based on gene sequence is an important tool in many areas of biological research. Such predictions have become particularly important in the genomics age in which numerous gene sequences are generated with little or no accompanying experimentally determined functional information. Almost all functional prediction methods rely on the identification, characterization, and quantification of sequence similarity between the gene of interest and genes for which functional information is available. Because sequence is the prime determining factor of function, sequence similarity is taken to imply similarity of function. There is no doubt that this assumption is valid in most cases. However, sequence similarity does not ensure identical functions, and it is common for groups of genes that are similar in sequence to have diverse (although usually related) functions. Therefore, the identification of sequence similarity is frequently not enough to assign a predicted function to an uncharacterized gene; one must have a method of choosing among similar genes with different functions. In such cases, most functional prediction methods assign likely functions by quantifying the levels of similarity among genes. I suggest that functional predictions can be greatly improved by focusing on how the genes became similar in sequence (i.e., evolution) rather than on the sequence similarity itself. It is well established that many aspects of comparative biology can benefit from evolutionary studies (Felsenstein 1985), and comparative molecular biology is no exception (e.g., Altschul et al. 1989; Goldman et al. 1996). In this commentary, I discuss the use of evolutionary information in the prediction of gene function. To appreciate the potential of a phylogenomic approach to the prediction of gene function, it is necessary to first discuss how gene sequence is commonly used to predict gene function and some general features about gene evolution.
EQUIVALENCES OF REAL SUBMANIFOLDS IN COMPLEX SPACE

We show that for any real-analytic submanifold M in CN there is a proper real-analytic subvariety V ⊂ M such that for any p ∈ M \ V , any real- analytic submanifold Min CN , and any p� ∈ M � , the germs (M, p) and (M � ,p � ) of the submanifolds M and Mat p and prespectively are formally equivalent if and only if they are biholomorphically equivalent. As an ap- plication, for p ∈ M \ V , the problem of biholomorphic equivalence of the germs (M, p) and (M � ,p � ) is reduced to that of solving a system of polyno- mial equations. More general results for k-equivalences are also stated and proved.
Detection of the onset of upper-limb movements based on the combined analysis of changes in the sensorimotor rhythms and slow cortical potentials

Objective. Characterizing the intention to move by means of electroencephalographic activity can be used in rehabilitation protocols with patients’ cortical activity taking an active role during the intervention. In such applications, the reliability of the intention estimation is critical both in terms of specificity ‘number of misclassifications’ and temporal accuracy. Here, a detector of the onset of voluntary upper-limb reaching movements based on the cortical rhythms and the slow cortical potentials is proposed. The improvement in detections due to the combination of these two cortical patterns is also studied. Approach. Upper-limb movements and cortical activity were recorded in healthy subjects and stroke patients performing self-paced reaching movements. A logistic regression combined the output of two classifiers: (i) a naïve Bayes classifier trained to detect the event-related desynchronization preceding the movement onset and (ii) a matched filter detecting the bereitschaftspotential. The proposed detector was compared with the detectors by using each one of these cortical patterns separately. In addition, differences between the patients and healthy subjects were analysed. Main results. On average, 74.5 ± 13.8% and 82.2 ± 10.4% of the movements were detected with 1.32 ± 0.87 and 1.50 ± 1.09 false detections generated per minute in the healthy subjects and the patients, respectively. A significantly better performance was achieved by the combined detector (as compared to the detectors of the two cortical patterns separately) in terms of true detections (p = 0.099) and false positives (p = 0.0083). Significance. A rationale is provided for combining information from cortical rhythms and slow cortical potentials to detect the onsets of voluntary upper-limb movements. It is demonstrated that the two cortical processes supply complementary information that can be summed up to boost the performance of the detector. Successful results have been also obtained with stroke patients, which supports the use of the proposed system in brain–computer interface applications with this group of patients.
Extraction of photoplethysmographic waveform variability by lowpass filtering

Cardiovascular variability is known to provide useful physiological information about autonomic function and peripheral vascular tone. Previous studies have used systolic values (peaks) or diastolic values (troughs) in the photoplethysmographic signal (PPG) to represent the variability in the finger pulse waveform. However, the feature detection process is error prone and often requires manual correction which is time consuming. The current study has proposed the lowpass filtering method as an alternative means to extract the variability signal. The similarities between the lowpass filtered spectrum and the spectra produced by other representation methods were assessed quantitatively via the computation of normalized cross-correlations. Results showed that the lowpass filtered signal produced a variability spectrum which was nearly identical to that of the pulse waveform mean value (correlation = 0.996), and was highly correlated with the trough and the peak variability spectra (correlation > 0.9). Compared with feature extraction methods, the lowpass filtering method is much simpler and computationally efficient to implement. In addition, the lowpass filtering method can be applied in conjunction with signal decomposition techniques such as principal component analysis (PCA) to better quantify sympathetic change
Effects of the Degree of Deacetylation on the Physicochemical Properties and Schwann Cell Affinity of Chitosan Films

Chitosan is a potential material for the preparation of nerve repair conduits. In order to find a better chitosan for the application in peripheral nerve regeneration, the effects of the degree of deacetylation (DD) on the physicochemical properties and Schwann cell affinity of chitosan films have been evaluated. Six kinds of chitosan samples with similar molecular weight, but various DD in a range from 70.1 to 95.6% were prepared from one stock chitosan material and fabricated into films. X-ray diffraction analysis showed that there were more crystalline regions in the higher DD chitosan films. Swelling and mechanical property measurements revealed that the swelling index of chitosan films decreased and their elastic modulus and tensile strength increased with the increase in DD. The adsorption amount of fibronectin and laminin on chitosan films was measured by means of enzyme-linked immunosorbent assay (ELISA). Culture of adult rat Schwann cells on the films showed that the chitosan films with higher DD provided better substrata for Schwann cell spreading and proliferation. In conclusion, DD of chitosan plays an important role in their physicochemical properties and affinity with Schwann cells. The results suggest that chitosan with a DD higher than 90% is considered as a promising material for application in peripheral nerve regeneration.
WT1 modulates apoptosis by transcriptionally upregulating the bcl‐2 proto‐oncogene

The Wilms‘ tumor suppressor gene, WT1, encodes a zinc finger transcription factor that has been demonstrated to negatively regulate several growth factor and cognate receptor genes. However, inconsistent with its tumor suppressor function, WT1 has also been demonstrated to be required to inhibit programmed cell death in vitro and in vivo. Moreover, anaplastic Wilms’ tumors, which typically express wild‐type WT1, display extreme resistance to chemotherapeutic agents that kill tumor cells through the induction of apoptosis. Although p53 mutations in anaplastic Wilms‘ tumors have been associated with chemoresistance, this event is believed to occur late during tumor progression. Therefore, since dysregulated WT1 expression occurs relatively early in Wilms’ tumors, we hypothesized that WT1 was required to transcriptionally upregulate genes that provide a cell survival advantage to tumor cells. Here we demonstrate that sporadic Wilms' tumors coexpress WT1 and the anti‐apoptotic Bcl‐2 protein. Using rhabdoid cell lines overexpressing WT1, we show that WT1 activates the endogenous bcl‐2 gene through a transcriptional mechanism. Transient transfections and electromobility shift assays demonstrate that WT1 positively stimulates the bcl‐2 promoter through a direct interaction. Moreover, WT1 expressing cells displaying upregulated Bcl‐2 were found to be resistant to apoptosis induced by staurosporine, vincristine and doxorubicine. These data suggest that in certain cellular contexts, WT1 exhibits oncogenic potential through the transcriptional upregulation of anti‐apoptotic genes such as bcl‐2.
Using Linguistic Cues for the Automatic Recognition of Personality in Conversation and Text

It is well known that utterances convey a great deal of information about the speaker in addition to their semantic content. One such type of information consists of cues to the speaker's personality traits, the most fundamental dimension of variation between humans. Recent work explores the automatic detection of other types of pragmatic variation in text and conversation, such as emotion, deception, speaker charisma, dominance, point of view, subjectivity, opinion and sentiment. Personality affects these other aspects of linguistic production, and thus personality recognition may be useful for these tasks, in addition to many other potential applications. However, to date, there is little work on the automatic recognition of personality traits. This article reports experimental results for recognition of all Big Five personality traits, in both conversation and text, utilising both self and observer ratings of personality. While other work reports classification results, we experiment with classification, regression and ranking models. For each model, we analyse the effect of different feature sets on accuracy. Results show that for some traits, any type of statistical model performs significantly better than the baseline, but ranking models perform best overall. We also present an experiment suggesting that ranking models are more accurate than multi-class classifiers for modelling personality. In addition, recognition models trained on observed personality perform better than models trained using self-reports, and the optimal feature set depends on the personality trait. A qualitative analysis of the learned models confirms previous findings linking language and personality, while revealing many new linguistic markers.
A superlinear iteration method for calculation of finite length journal bearing's static equilibrium position

Solving the static equilibrium position is one of the most important parts of dynamic coefficients calculation and further coupled calculation of rotor system. The main contribution of this study is testing the superlinear iteration convergence method—twofold secant method, for the determination of the static equilibrium position of journal bearing with finite length. Essentially, the Reynolds equation for stable motion is solved by the finite difference method and the inner pressure is obtained by the successive over-relaxation iterative method reinforced by the compound Simpson quadrature formula. The accuracy and efficiency of the twofold secant method are higher in comparison with the secant method and dichotomy. The total number of iterative steps required for the twofold secant method are about one-third of the secant method and less than one-eighth of dichotomy for the same equilibrium position. The calculations for equilibrium position and pressure distribution for different bearing length, clearance and rotating speed were done. In the results, the eccentricity presents linear inverse proportional relationship to the attitude angle. The influence of the bearing length, clearance and bearing radius on the load-carrying capacity was also investigated. The results illustrate that larger bearing length, larger radius and smaller clearance are good for the load-carrying capacity of journal bearing. The application of the twofold secant method can greatly reduce the computational time for calculation of the dynamic coefficients and dynamic characteristics of rotor-bearing system with a journal bearing of finite length.
Abstract-to-publication ratio for papers presented at scientific meetings: a quality marker for UK emergency medicine research

Objectives: To determine the publication rate of abstracts presented by UK emergency physicians at major emergency medicine meetings, and to identify the site of publication of papers. Method: All abstracts presented to the annual scientific meetings of both the British Association of Emergency Medicine and the Faculty of Accident and Emergency Medicine between 2001 and 2002 were identified retrospectively from conference programmes. To identify whether the work relating to the abstract had been published in a peer-reviewed journal, the Medline database (Ovid interface) was searched using the first and last authors as well as key words from the abstract. Results: Of the 404 abstracts identified, 124 (30%) had been published as full articles. For abstracts presented in the oral sessions, 83 (57%) resulted in publication. A range of journals accepted papers for publication. Conclusion: The abstract-to-publication ratio for UK emergency medicine is lower than for other specialties, but broadly similar to emergency medicine in the US and Australia.