Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered expression of β-galactosidase-1-like protein 3 (Glb1l3) in the retinal pigment epithelium (RPE)-specific 65-kDa protein knock-out mouse model of Leber’s congenital amaurosis

Purpose In this study, we investigated the expression of the gene encoding β-galactosidase (Glb)-1-like protein 3 (Glb1l3), a member of the glycosyl hydrolase 35 family, during retinal degeneration in the retinal pigment epithelium (RPE)-specific 65-kDa protein knockout (Rpe65−/−) mouse model of Leber congenital amaurosis (LCA). Additionally, we assessed the expression of the other members of this protein family, including β-galactosidase-1 (Glb1), β-galactosidase-1-like (Glb1l), and β-galactosidase-1-like protein 2 (Glb1l2). Methods The structural features of Glb1l3 were assessed using bioinformatic tools. mRNA expression of Glb-related genes was investigated by oligonucleotide microarray, real-time PCR, and reverse transcription (RT) -PCR. The localized expression of Glb1l3 was assessed by combined in situ hybridization and immunohistochemistry. Results Glb1l3 was the only Glb-related member strongly downregulated in Rpe65−/− retinas before the onset and during progression of the disease. Glb1l3 mRNA was only expressed in the retinal layers and the RPE/choroid. The other Glb-related genes were ubiquitously expressed in different ocular tissues, including the cornea and lens. In the healthy retina, expression of Glb1l3 was strongly induced during postnatal retinal development; age-related increased expression persisted during adulthood and aging. Conclusions These data highlight early-onset downregulation of Glb1l3 in Rpe65-related disease. They further indicate that impaired expression of Glb1l3 is mostly due to the absence of the chromophore 11-cis retinal, suggesting that Rpe65 deficiency may have many metabolic consequences in the underlying neuroretina.
Random Constraint Satisfaction Problems

Random instances of constraint satisfaction problems such as k-SAT provide challenging benchmarks. If there are m constraints over n variables there is typically a large range of densities r=m/n where solutions are known to exist with probability close to one due to non-constructive arguments. However, no algorithms are known to find solutions efficiently with a non-vanishing probability at even much lower densities. This fact appears to be related to a phase transition in the set of all solutions. The goal of this extended abstract is to provide a perspective on this phenomenon, and on the computational challenge that it poses.
Measuring the evolutionary rate of protein–protein interaction

Despite our extensive knowledge about the rate of protein sequence evolution for thousands of genes in hundreds of species, the corresponding rate of protein function evolution is virtually unknown, especially at the genomic scale. This lack of knowledge is primarily because of the huge diversity in protein function and the consequent difficulty in gauging and comparing rates of protein function evolution. Nevertheless, most proteins function through interacting with other proteins, and protein–protein interaction (PPI) can be tested by standard assays. Thus, the rate of protein function evolution may be measured by the rate of PPI evolution. Here, we experimentally examine 87 potential interactions between Kluyveromyces waltii proteins, whose one to one orthologs in the related budding yeast Saccharomyces cerevisiae have been reported to interact. Combining our results with available data from other eukaryotes, we estimate that the evolutionary rate of protein interaction is (2.6 ± 1.6) × 10−10 per PPI per year, which is three orders of magnitude lower than the rate of protein sequence evolution measured by the number of amino acid substitutions per protein per year. The extremely slow evolution of protein molecular function may account for the remarkable conservation of life at molecular and cellular levels and allow for studying the mechanistic basis of human disease in much simpler organisms.
Diversity Gain and Coding Performance of OST-CPM System in Spatially Correlated Channels

The Chernoff bound on Pair-Wise Error Probability (PWEP) performance of orthogonal space-time coded CPM (OST-CPM) systems is investigated, for two transmit antennas, over spatially correlated channels. Approximate Chernoff bound for high Signal-to-Noise Ratio (SNR) is derived to evaluate the diversity gain and coding performance in correlated channels. The achievable diversity gain of this system decreases due to the signal correlation between the antennas. Simulation results show that the error performance over a correlated channel is degraded when the correlation coefficient increases. And the penalty on the code performance increases a lot in fully correlated channels. It can also be seen that the diversity gain decreases when the channel is fully correlated, which matches well with the theoretical analysis. The upper bounds can be looser when diversity order decreases.
Computer simulations aimed at structure prediction of supersecondary motifs in proteins

It is well established that protein structures are more conserved than protein sequences. One‐third of all known protein structures can be classified into ten protein folds, which themselves are composed mainly of α‐helical hairpin, β hairpin, and βαβ supersecondary structural elements. In this study, we explore the ability of a recent Monte Carlo–based procedure to generate the 3D structures of eight polypeptides that correspond to units of supersecondary structure and three‐stranded antiparallel beta sheet. Starting from extended or misfolded compact conformations, all Monte Carlo simulations show significant success in predicting the native topology using a simplified chain representation and an energy model optimized on other structures. Preliminary results on model peptides from nucleotide binding proteins suggest that this simple protein folding model can help clarify the relation between sequence and topology. Proteins 2001;45:159–166. © 2001 Wiley‐Liss, Inc.
Invariant object description with inverse pyramid based on the truncated modified discrete Mellin-Fourier transform

In this paper is offered one new algorithm for global description of pre-segmented objects in a halftone image. The new algorithm has relatively low computational complexity than the famous Mellin-Fourier transform and permits multi-layer access which enhances the search by content in indexed image databases. The new algorithm is based on the previously developed methods of the inverse pyramid decomposition and of the truncated modified discrete Mellin-Fourier transform, which are combined here.
Inhibition of Heme Oxygenase-1 Partially Reverses the Arsenite-Mediated Decrease of CYP1A1, CYP1A2, CYP3A23, and CYP3A2 Catalytic Activity in Isolated Rat Hepatocytes

Heme oxygenase (HO-1), the rate-limiting enzyme in the physiological breakdown of heme, is ubiquitous, and its expression can be increased by arsenite [As(III)], and similar other stimuli that induce cellular oxidative stress. Interestingly, it has been shown that the As(III)-induced HO-1 is inversely correlated with a decrease in cytochromes P450 (P450s) activity; however, the direct role for HO-1 in the inhibition of P450 enzymes remains unknown. Our results showed that As(III) at a concentration of 5 μM decreased the constitutive and inducible expression of CYP1A1, CYP1A2, CYP3A23, and CYP3A2 at the mRNA, protein, and catalytic activity levels. Moreover, As(III) decreased the nuclear accumulation of aryl hydrocarbon receptor (AhR) and pregnane X receptor without increasing their degradation. As(III) also increased the binding of cytosolic AhR to heat shock protein 90 and hepatitis B virus X-associated protein 2. In the presence of 2,3,7,8-tetrachlorodibenzo-p-dioxin as an inducer for CYP1A and rifampin as an inducer for CYP3A, As(III) decreased the enzymatic activity of the four P450s more than it decreased their mRNA or protein expression levels. It is noteworthy that treatment with the competitive HO-1 inhibitor, tin-mesoporphyrin, or supplementing external heme partially reversed the As(III)-mediated decrease in activities of the four P450s. In conclusion, the current study provides the first evidence that As(III) decreases CYP1A1, CYP1A2, CYP3A23, and CYP3A2 expression in freshly isolated rat primary hepatocytes. Furthermore, inhibiting the As(III)-mediated induction of HO-1 partially restores the enzymatic activity of these P450s that was initially decreased by As(III), confirming the direct role of HO-1 in the inhibition of P450s.
A Parent’s Worst Nightmare: Grief, Families, and the Death of a Child

rief is the most universal of human experi ences; it is also one of the least under stood. Layered in this argu ment is the complex reality that, although we expect to bury and grieve loved ones in our lives, we never antici pate that our chil dren should die before us. The death of a child brings both the loss of a past and a future. I contend that those of us working in the health care system are obligated to under stand this human phenom enon in order to be able to effectively support chil dren and fami lies, as well as our peers and ourselves. This applies equally those of us that work throughout this system as child life workers, nurses, social workers, or members of any of the other professions that come into the “stop in the tracks” expe ri ence of the priv i lege of being alongside chil dren who are dying and fami lies who have to let them go. Current Under stand ings of Grief Grief, as an expe ri ence of mystery (Attig, 1996; Klass, Silverman, & Nickman, 1996) that “pervades our human condi tion” (Attig, 1996, p. 15), has prompted the call to under stand, define, predict, and ulti mately erad i cate it. Within this call, there has been a distinct evolu tion of thinking of grief as a process of energy with drawal involved in the psychic process of releasing -
The regulation of dendritic arbor development and plasticity by glutamatergic synaptic input: a review of the synaptotrophic hypothesis

The synaptotropic hypothesis, which states that synaptic inputs control the elaboration of dendritic (and axonal) arbors was articulated by Vaughn in 1989. Today the role of synaptic inputs in controlling neuronal structural development remains an area of intense research activity. Several recent studies have applied modern molecular genetic, imaging and electrophysiological methods to this question and now provide strong evidence that maturation of excitatory synaptic inputs is required for the development of neuronal structure in the intact brain. Here we critically review data concerning the hypothesis with the expectation that understanding the circumstances when the data do and do not support the hypothesis will be most valuable. The synaptotrophic hypothesis contributes at both conceptual and mechanistic levels to our understanding of how relatively minor changes in levels or function of synaptic proteins may have profound effects on circuit development and plasticity.
The Working Class Promise: A Communicative Account of Mobility-Based Ambivalences

In-depth interviews with 62 people with working class ties (blue-collar workers and adult sons and daughters of blue-collar workers) reveal a social construction of working class that imbues it with four core, positively valenced values: strong work ethic, provider orientation, the dignity of all work and workers, and humility. This constellation of values is communicated through a ubiquitous macrolevel discourse—which I coin the Working Class Promise—that elevates working class to the highest position in the social class hierarchy and fosters a strong commitment to maintain a working class value system and identity. However, this social construction is only a partial social construction. That is, these individuals do not question material, socioeconomic-based delineations of class boundaries (e.g., income, education level, occupational prestige). Consequently, their acceptance of structural class boundaries, combined with their high regard of working class values, positions social classes in ways that make the goals of the American Dream (i.e., class mobility) and the Working Class Promise (i.e., class maintenance) paradoxical. I argue that the paradox of social mobility that results from this partial social construction is the root of mobility-based ambivalences.
The effectiveness of acupuncture on the sleep quality of elderly with dementia: a within-subjects trial

Purpose Elderly with dementia are often afflicted with sleep problems. Recent studies have suggested that acupuncture may be a feasible alternative to traditional sleep medicine for treating sleep disturbance. This study investigated the effectiveness of acupuncture on sleep quality of elderly with dementia. Patients and methods Nineteen elders with dementia were followed through a control period and an acupuncture treatment period, each lasting 6 weeks. Outcome measures were subjects’ sleep quality and cognitive function. Sleep parameters were recorded by wrist actigraphy. Cognitive function was assessed by the Alzheimer’s Disease Assessment Scale – Cognitive (ADAS-Cog). Pretests and posttests were conducted immediately before and after the control and treatment periods. Changes in the outcome measures between control and treatment periods were compared. Results Wilcoxon signed rank tests revealed that the subjects gained significantly more resting time and total sleep time in the treatment period than in the control period (P < 0.05). A nonsignificant trend for improvement in sleep efficiency was observed. Improvement in cognitive function was not statistically significant. A total of 86% of the subjects completed the treatment regime. Conclusion Results reveal that acupuncture was effective in improving some domains of sleep quality of elderly with dementia, and the subjects showed acceptance towards the intervention. Strengths and limitations of the present study as well as suggestions for further studies were considered.
Maximum correntropy unscented filter

ABSTRACT The unscented transformation (UT) is an efficient method to solve the state estimation problem for a non-linear dynamic system, utilising a derivative-free higher-order approximation by approximating a Gaussian distribution rather than approximating a non-linear function. Applying the UT to a Kalman filter type estimator leads to the well-known unscented Kalman filter (UKF). Although the UKF works very well in Gaussian noises, its performance may deteriorate significantly when the noises are non-Gaussian, especially when the system is disturbed by some heavy-tailed impulsive noises. To improve the robustness of the UKF against impulsive noises, a new filter for non-linear systems is proposed in this work, namely the maximum correntropy unscented filter (MCUF). In MCUF, the UT is applied to obtain the prior estimates of the state and covariance matrix, and a robust statistical linearisation regression based on the maximum correntropy criterion is then used to obtain the posterior estimates of the state and covariance matrix. The satisfying performance of the new algorithm is confirmed by two illustrative examples.
Preliminary in vitro evaluation of Carisolv as a root canal irrigant.

AIM To test the null hypothesis that Carisolv is no better than PBS in removing organic debris from uninstrumented root canals. METHODOLOGY The pulps of two uniform groups of 36 immature, sheep mandibular incisors were grossly removed with barbed broaches immediately prior to the study. Roots in group 1 were irrigated with phosphate buffered saline (PBS), strong sodium hypochlorite (4.5%) or Carisolv without ultrasonic agitation, whilst in group 2 the same irrigants were activated with ultrasound. Canal walls were exposed to irrigants for 10, 20 or 30 min at 37 degree C. In group 2, ultrasound was applied for 30 s at 2, 5 and 7 min within each 10 min incubation period. After washing irrigants free and immersion in fixative, all teeth were split longitudinally, critical point dried and sputter coated for SEM analysis. SEM photomicrographs were recorded of representative areas in the coronal, middle and apical canal thirds and debris scored by a single assessor against a five-point scale. Intraobserver reliability was assessed by Cohens kappa scores and debris scores analysed by the non-parametric Kruskal-Wallis test at P < 0.05. RESULTS Sodium hypochlorite was significantly better than Carisolv and PBS in cleaning root canals (P < 0.0001), whether or not ultrasound was applied. Carisolv was shown to clean canals better than PBS, again whether or not ultrasound was applied (P = 0.01). Both incubation time and ultrasound enhanced the action of Carisolv (P < 0.001) whilst the activity of PBS was not significantly improved by exposure time or the application of ultrasound. Kappa scores of 0.90-0.95 indicated excellent consistency in debris scoring. CONCLUSIONS Within the limitations of this preliminary study (i). Carisolv cleaned root canals better than PBS and shows promise as an adjunct to root canal preparation; (ii). the action of Carisolv was enhanced by incubation times beyond 20 min whether or not ultrasound was applied; (iii). sodium hypochlorite solution remains the gold standard endodontic irrigant, provided that it is used with care and is contained in the canal system.
Pixel and spatial mechanisms of color constancy

Color constancy remains an important subject of research on color standards, computer imaging, and human color vision. There are many different theories and algorithms that interpret and predict constancy. This paper analyzes three different approaches that are frequently discussed separately in the literature: pixel-based colorimetric standards of appearance; computer imaging calculations of an object's reflectance; and calculation of appearance using spatial comparisons. This paper compares and contrasts these approaches. Further, it reviews experiments that measure appearance in color constancy in a variety of situations. A pivotal tool in analyzing models of constancy is the correlation of object's reflectance with appearance. Each approach has different interpretation of this correlation. Using measurements of constancy with particular attention to reflectance, illumination, and appearance helps us to see the successes and limitations of each constancy approach.
Modelling the Interplay of Multiple Cues in Prosodic Focus Marking

Focus marking is an important function of prosody in many languages. While many phonological accounts concentrate on fundamental frequency (F 0 ), studies have established several additional cues to information structure. However, the relationship between these cues is rarely investigated. We simultaneously analyzed five prosodic cues to focus—F 0 range, word duration, intensity, voice quality, the location of the F 0 maximum, and the occurrence of pauses—in a set of 947 simple Subject Verb Object (SVO) sentences uttered by 17 native speakers of Finnish. Using random forest and generalized additive mixed modelling, we investigated the systematicity of prosodic focus marking, the importance of each cue as a predictor, and their functional shape. Results indicated a highly consistent differentiation between narrow focus and givenness, marked by at least F 0 range, word duration, intensity, and the location of the F 0 maximum, with F 0 range being the most important predictor. No cue had a linear relationship with focus condition. To account for the simultaneous significance of several predictors, we argue that these findings support treating multiple prosodic cues to focus in Finnish as correlates of prosodic phrasing. Thus, we suggest that prosodic phrasing, having multiple functions, is also marked with multiple cues to enhance communicative efficiency.
What can i do around here? Deep functional scene understanding for cognitive robots

For robots that have the capability to interact with the physical environment through their end effectors, understanding the surrounding scenes is not merely a task of image classification or object recognition. To perform actual tasks, it is critical for the robot to have a functional understanding of the visual scene. Here, we address the problem of localization and recognition of functional areas in an arbitrary indoor scene, formulated as a two-stage deep learning based detection pipeline. A new scene functionality testing-bed, which is compiled from two publicly available indoor scene datasets, is used for evaluation. Our method is evaluated quantitatively on the new dataset, demonstrating the ability to perform efficient recognition of functional areas from arbitrary indoor scenes. We also demonstrate that our detection model can be generalized to novel indoor scenes by cross validating it with images from two different datasets.
A Bipolar Model of Groupthink

Group processes among individuals united in a group sometimes take the figure of group-think, with paranoid and omnipotent imaginations. However, from a psychodynamic frame of reference, and in consequence with Klein's "position theory, " we postulated a depressive groupthink mode because work teams sometimes behave in a depressed manner We assumed that a group might be predisposed to take up either a depressive or a paranoid groupthink position. In this study, we operationalized five important symptoms that distinguish a depressive and an omnipotent version of groupthink The instrument was applied to two different psychiatric teams. We found that it was possible to differentiate between different modes of groupthink. The results suggest that Janis 's concept of groupthink might be seen as too one-sided, not renderingfull justice to different regressive movements in a work team.
Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans

Mangroves are among the most diverse and productive coastal ecosystems in the tropical and subtropical regions. Environmental conditions particular to this biome make mangroves hotspots for microbial diversity, and the resident microbial communities play essential roles in maintenance of the ecosystem. Recently, there has been increasing interest to understand the composition and contribution of microorganisms in mangroves. In the present study, we have analyzed the diversity and distribution of archaea in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. The extraction of DNA from sediment samples and the direct application of 16S rRNA gene amplicon sequencing resulted in approximately 142 Mb of data from three distinct mangrove areas (Godkhali, Bonnie camp, and Dhulibhashani). The taxonomic analysis revealed the dominance of phyla Euryarchaeota and Thaumarchaeota (Marine Group I) within our dataset. The distribution of different archaeal taxa and respective statistical analysis (SIMPER, NMDS) revealed a clear community shift along the sampling stations. The sampling stations (Godkhali and Bonnie camp) with history of higher hydrocarbon/oil pollution showed different archaeal community pattern (dominated by haloarchaea) compared to station (Dhulibhashani) with nearly pristine environment (dominated by methanogens). It is indicated that sediment archaeal community patterns were influenced by environmental conditions.