Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray analysis reveals that lncRNA PWRN1-209 promotes human bone marrow mesenchymal stem cell osteogenic differentiation on microtopography titanium surface in vitro.

Sandblasted, large-grit, and acid-etched (SLA) titanium (Ti) with microtopography is currently one of the most widely used implant materials to accelerate osseointegration. Numerous long noncoding RNAs (lncRNAs) have been involved in bone remodeling, with their role in osseointegration, and the underlying mechanisms remain largely unclear. Here, microarrays of human bone marrow mesenchymal stem cells (hBMSCs) were used to identify differentially expressed lncRNAs during early cell differentiation stages (0-7 days) on SLA Ti and polished Ti surfaces. The function of lncRNAs in the osteogenic differentiation of hBMSCs was identified by RNA silencing and overexpression assays. RT-PCR and Western blot were used to detect RNA and protein expression. Alkaline phosphatase (ALP) protein activity was tested by ALP staining. Altogether, 4112 differentially expressed lncRNAs were identified from day 0 to day 7 on SLA Ti with a novel lncRNA, Prader-willi region non-coding RNA 1-209 (PWRN1-209) upregulated. We then proved that PWRN1-209 promoted osteogenic differentiation in hBMSCs by genetic tools. The upregulation of PWRN1-209 was further confirmed to be related to the surface topography of Ti by comparing SLA Ti and polished Ti. Interestingly, this trend seems to have a certain correlation with the mRNA expression level of integrins (α2, αV, β1, β2) and the phosphorylation of focal adhesion kinase (FAK). Taken together, the lncRNA PWRN1-209 was upregulated by the SLA microtopography Ti surface, which may regulate osteogenic differentiation of hBMSCs through integrin-FAK-ALP signaling. Our results provide new insights into the relationship between surface topography and osseointergration.
Snorkeling As an Alternative to Depletion Electrofishing for Assessing Cutthroat Trout and Brown Trout in Stream Pools

ABSTRACT We compared abundance and length structure estimates of cutthroat trout (Oncorhynchus clarki) and brown trout (Salmo trutta) of 15 cm total length or greater obtained by snorkeling in stream pools with estimates obtained by depletion electrofishing. We sampled 12 pools in each of two streams formed by large springs in the Salt River Valley of western Wyoming. Snorkeling counts provided a relatively accurate index of depletion electrofishing estimates of abundance of cutthroat trout, but not brown trout. Linear regression analysis showed that snorkeling counts were significantly related to depletion electrofishing estimates for both cutthroat trout (P < 0.001) and brown trout (P = 0.002), but the coefficient of determination for brown trout (r2 = 0.33) was low compared to cutthroat trout (r2 = 0.95). Frequencies of fish in three length classes observed by snorkeling and depletion electrofishing were close to being significantly different for cutthroat trout (P = 0.066) and substantially different for brown trout (P= 0.005). Snorkeling frequently failed to observe fish in the shortest length class (15–29 cm total length) of both cutthroat trout and brown trout.
A note on the interpretation of tree‐based regression models

Tree‐based models are a popular tool for predicting a response given a set of explanatory variables when the regression function is characterized by a certain degree of complexity. Sometimes, they are also used to identify important variables and for variable selection. We show that if the generating model contains chains of direct and indirect effects, then the typical variable importance measures suggest selecting as important mainly the background variables, which have a strong indirect effect, disregarding the variables that directly influence the response. This is attributable mainly to the variable choice in the first steps of the algorithm selecting the splitting variable and to the greedy nature of such search. This pitfall could be relevant when using tree‐based algorithms for understanding the underlying generating process, for population segmentation and for causal inference.
High-Throughput Image-Based Aggresome Quantification

Aggresomes are subcellular perinuclear structures where misfolded proteins accumulate by retrograde transport on microtubules. Different methods are available to monitor aggresome formation, but they are often laborious, time-consuming, and not quantitative. Proteostat is a red fluorescent molecular rotor dye, which becomes brightly fluorescent when it binds to protein aggregates. As this reagent was previously validated to detect aggresomes, we have miniaturized its use in 384-well plates and developed a method for high-throughput imaging and quantification of aggresomes. Two different image analysis methods, including one with machine learning, were evaluated. They lead to similar robust data to quantify cells having aggresome, with satisfactory Z′ factor values and reproducible EC50 values for compounds known to induce aggresome formation, like proteasome inhibitors. We demonstrated the relevance of this phenotypic assay by screening a chemical library of 1280 compounds to find aggresome modulators. We obtained hits that present similarities in their structural and physicochemical properties. Interestingly, some of them were previously described to modulate autophagy, which could explain their effect on aggresome structures. In summary, we have optimized and validated the Proteostat detection reagent to easily measure aggresome formation in a miniaturized, automated, quantitative, and high-content assay. This assay can be used at low, middle, or high throughput to quantify changes in aggresome formation that could help in the understanding of chemical compound activity in pathologies such as protein misfolding disorders or cancer.
The human brain processes hierarchical structures of meter and harmony differently: Evidence from musicians and nonmusicians.

The processing of temporal structure has been widely investigated, but evidence on how the brain processes temporal and nontemporal structures simultaneously is sparse. Using event-related potentials (ERPs), we examined how the brain responds to temporal (metric) and nontemporal (harmonic) structures in music simultaneously, and whether these processes are impacted by musical expertise. Fifteen musicians and 15 nonmusicians rated the degree of completeness of musical sequences with or without violations in metric or harmonic structures. In the single violation conditions, the ERP results showed that both musicians and nonmusicians exhibited an early right anterior negativity (ERAN) as well as an N5 to temporal violations ("when"), and only an N5-like response to nontemporal violations ("what"), which were consistent with the behavioral results. In the double violation condition, however, only the ERP results, but not the behavioral results, revealed a significant interaction between temporal and nontemporal violations at a later integrative stage, as manifested by an enlarged N5 effect compared to the single violation conditions. These findings provide the first evidence that the human brain uses different neural mechanisms in processing metric and harmonic structures in music, which may shed light on how the brain generates predictions for "what" and "when" events in the natural environment.
Electrogastrography for psychophysiological research: Practical considerations, analysis pipeline, and normative data in a large sample

Abstract Electrogastrography (EGG) is the noninvasive electrophysiological technique used to record gastric electrical activity by means of cutaneous electrodes placed on the abdomen. EGG has been so far mostly used in clinical studies in gastroenterology, but it represents an attractive method to study brain‐viscera interactions in psychophysiology. Compared to the literature on electrocardiography for instance, where practical recommendations and normative data are abundant, the literature on EGG in humans remains scarce. The aim of this article is threefold. First, we review the existing literature on the physiological basis of the EGG, pathways of brain‐stomach interactions, and experimental findings in the cognitive neuroscience and psychophysiology literature. We then describe practical issues faced when recording the EGG in young healthy participants, from data acquisition to data analysis, and propose a semi‐automated analysis pipeline together with associated MATLAB code. The analysis pipeline aims at identifying a regular rhythm that can be safely attributed to the stomach, through multiple steps. Finally, we apply these recording and analysis procedures in a large sample (N = 117) of healthy young adult male and female participants in a moderate (<5 hr) to prolonged (>10 hr) fasting state to establish the normative distribution of several EGG parameters. Our results are overall congruent with the clinical gastroenterology literature, but suggest using an electrode coverage extending to lower abdominal locations than current clinical guidelines. Our results indicate a marginal difference in EGG peak frequency between male and female participants, and that the gastric rhythm becomes more irregular after prolonged fasting.
Patterns of Wood Duck Nest Temperatures during Egg-Laying and Incubation

We studied the thermal environment of Wood Duck (Aix sponsa) nests in southeastern British Columbia. Mean daily nest temperatures (T N ) were correlated with maximum daily air temperatures. T N increased as the egg-laying period advanced among both successful and unsuccessful nests, although T N was lower among unsuccessful nests. Hens began spending nights on nests when there were as few as four eggs in clutches. T N and the precision of nest thermoregulation increased among successful nests as the incubation period advanced, although there was a great deal of variation between days and nests. Length of the incubation period was not correlated with clutch size, nor with mean overall nest temperature during incubation, but was correlated with the variance of T N 's during incubation.
Using IPM-CPR as a Management Program for Apple Orchards

Abstract We have demonstrated how management of key orchard pests including the insect invasive species Halyomorpha halys (Stål) (Hemiptera: Pentatomidae) can be accomplished using a systems-level approach termed IPM-CPR (Integrated Pest Management-Crop Perimeter Restructuring) in apple. We conducted on-farm comparisons of IPM-CPR to standard management program for managing H. halys, Cydia pomonella (L.) (Lepidoptera: Tortricidae), Grapholita molesta (Busck) (Lepidoptera: Tortricidae), and Lygus lineolaris Palisot de Beauvois (Hemiptera: Miridae) in commercial apple orchards in 2014, 2016, and 2017 in New Jersey, Maryland, and Virginia. The presence and abundance of key pests and fruit injury at harvest were used as a measure of success of the program. We compared the amount of insecticide applied for each management program. In majority of instances, there were no differences in the IPM-CPR and the standard management program in terms of H. halys numbers in baited pyramid traps and stink bug injury at harvest. Damage from C. pomonella and G. molesta in the IPM-CPR treatment was significantly lower than the standard management program in 2014 and 2017. Amount of active ingredient used was on average 62.1% lower in the IPM-CPR treatment compared with standard management program. Despite a reduction in insecticide use, there were minimal impacts on beneficial insects. Overall, IPM-CPR in apples successfully managed key orchard pests, including H. halys, and used significantly less insecticide than a standard insecticide-based management program and could be adopted as a systems-level approach for pest population reduction.
A Subset of p23 Localized on Secretory Granules in Pancreatic β-cells

Proteins on the membrane of secretory granules (SGs) involved in their biogenesis and exocytosis are poorly characterized compared with those of synaptic vesicle in neurons. Thus the secretory granule membrane was prepared from a mouse pancreatic β-cell line MIN6 by subcellular fractionation, and protein constituents were analyzed by microscale two-dimensional liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Using this proteomics approach, one of the p24 family proteins, p23, was unexpectedly found in the granule fraction, although p24 proteins are generally regarded as functioning in the early secretory pathways between the endoplasmic reticulum and the Golgi apparatus. We further showed that p23 is expressed at high levels in endocrine cells. Furthermore, immunocytochemical analyses of pancreatic β-cells at the light and electron microscopic levels demonstrated that a significant amount of p23 is localized on the insulin granule membrane, although it is most intensely concentrated at the cis-Golgi compartment as previously shown in non-endocrine cells. These findings suggest that a fraction of p23 enters post-Golgi compartments and may function in the biogenesis and/or quality control of SGs.
Pathogens of peritoneal dialysis peritonitis: Trends from a single-center experience over 15 years

Background Concerns are increasing about the emergence of pathogens with antibiotic resistance in peritoneal dialysis (PD) peritonitis. We investigated the current pathogen trends and risk factors in PD peritonitis. Methods We conducted a retrospective study analyzing data from 643 patients who maintained PD over 3 months between January 2001 and December 2015. The isolated pathogens from PD peritonitis were compared between period A (2001-2008) and period B (2009-2015). Results Among 643 PD patients, 252 patients experienced one or more episodes of PD peritonitis (total 308 episodes) during the median follow-up of 66 months. In both periods, gram-positive bacteria were the dominant pathogens (22.2% vs. 53.8%, P < 0.01). Gram-negative bacteria showed an increasing tendency in period B, but without statistical significance (17.0% vs. 23.7%, P = 0.15). The culture-negative rate was improved from 57% in period A to 18% in period B (P < 0.01). There was no increase in the prevalence of resistant pathogens such as methicillin-resistant Staphylococcus epidermidis (MRSE), Staphylococcus aureus (MRSA) and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli between periods A and B. Preserved residual renal function was associated with a lower risk of PD peritonitis (odds ratio, 0.53; 95% confidence interval, 0.31-0.88; P = 0.01). Conclusion Over the past two decades, the pathogens of PD peritonitis have not significantly changed in Korea. Gram-positive organisms remained dominant, with S. epidermidis being the most common pathogen. Resistant bacteria such as MRSE, MRSA, ESBL-producing Gram-negative bacilli did not increase, but should be monitored.
Follicle-Stimulating Hormone Induction of Ley dig Cell Maturation

The effects of FSH on the testes of immature hypophysectomized rats were investigated by comparing functional changes in Leydig cells with changes in their number and morphological appearance. Rats were treated twice daily for 7 days with 0.5 ml saline vehicle, 10 μg rat FSH, or 20 ng ovine LH (an equivalent amount of LH known to contaminate the FSH preparation). FSH treatment caused a significant increase in testis weight and stimulated more advanced spermatogenic activity compared to saline or LH treatment. Morphometric analysis of glutaraldehyde perfusion-fixed testes showed no significant increase in Leydig cell number after LH treatment [saline, 4.63 ± 0.14 million cells; LH, 6.38 ± 0.55 million (mean ± SE)], but a significant (P < 0.001) increase after FSH treatment (11.55 ± 0.79 million). FSH, but not LH or saline, treatment resulted in Leydig cell hypertrophy and ultrastructural features identical to those of adult Leydig cells, these changes being reflected by enhanced hCG- and LHRH agonist-stimu.
Comparison of crown cover estimates for woody vegetation in arid rangelands

Three methods for estimating crown cover of woody vegetation were compared, in three mapped field sites and one theoretical map of randomly distributed individuals, by computer simulated sampling. The effect of plant size on the performance of the methods was investigated by varying the size of individuals in the theoretical map. Using the line-intercept and point-sampling techniques according to standard procedures, the net crown cover of a species is estimated and overlapping areas are not recognized. The variable plot or Bitterlich gauge technique estimates the total crown cover of individuals, and areas of overlap are thus recorded more than once. Consequently, Bitterlich gauge estimates will always be greater whenever individuals intermingle or overtop one another. Line-intercept and point-sampling techniques produced highly variable estimates when plants were small, but were not prone to greater variability when plant distribution departed from randomness. The Bitterlich gauge estimates were no more variable with small than with large plants, but were affected by the degree of plant aggregation. The problem is overcome by selecting a sample point spacing and a half-angle for the gauge that optimizes plant counting. The advantages of the variable plot method over the other two are discussed in terms of speed and operator differences, and it is recommended as a monitoring technique for woody vegetation in arid rangelands.
DNA content in Tradescantia

There is a wide variation in the nuclear DNA content and chromosome size between the species belonging to the T. crassifolia and T. virginiana alliances (all the species but one are native to Central and North America). Also the DNA content per genome decreases when the ploidy level increases within the same specific polyploid complex with three ploidy levels (2x, 4x, and 6x). In contrast, no variation was found in the DNA content per genome between different ploidy levels in the T. fluminensis alliance (all the species are native to South America) where they range from 6x to 22x. Since all the species described here are perennials with various life forms, it was possible to analyze the relationship between the DNA content and their vegetative adaptation to the environment. The more specialized species (geophytes and hemicryptophytes) have a higher amount of DNA than the chamaephytes adapted to live in relatively more mesic regions. In the species living in Central and North America there is a positive co.
Immediate versus wait-and-gradual discontinuation in antipsychotic switching: A meta-analysis

Introduction: In two previous meta-analyses of randomized controlled trials (RCTs) examining antipsychotic switching strategies in patients with schizophrenia, we showed no significant differences in any clinical outcomes between immediate versus gradual and gradual versus wait-and-gradual discontinuation of the pre-switch antipsychotic. In this report, we compared immediate versus wait-and-gradual antipsychotic discontinuation. Methods: We identified five RCTs examining immediate versus wait-and-gradual discontinuation of the pre-switch antipsychotic in antipsychotic switching involving patients with schizophrenia. However, no data were available from one RCT. The following clinical outcome data were extracted and meta-analyzed: study discontinuation, psychopathology, extrapyramidal symptoms, and treatment-emergent adverse events that were reported in two or more of the studies. Results: The meta-analysis included four RCTs involving 351 patients (n=175 for immediate and n=176 for wait-and-gradual antipsychotic discontinuation). A significant difference was found in study discontinuation due to all causes (n=4, n=351, risk ratio=1.58, 95% confidence interval 1.15–2.17, p=0.005, I2=0%) between the immediate and wait-and-gradual antipsychotic discontinuation groups, while there was no significant difference in any other clinical outcomes. The group difference in study discontinuation due to all causes remained significant for the studies adopting immediate antipsychotic initiation but not for the studies switching to ziprasidone. Conclusion: Findings suggest that wait-and-gradual antipsychotic discontinuation may be preferable when a more cautious antipsychotic switch is needed. However, further long-term, double-blind RCTs are needed to confirm the present findings.
Mycorrhizal associations of Salix repens L. communities in succession of dune ecosystems. I. Above-ground and below-ground views of ectomycorrhizal fungi in relation to soil chemistry

The diversity of ectomycorrhizal (EcM) communities in 16 stands of Salix repens L. growing under a variety of environmental conditions was studied by repeated sampling of EcM sporocarps and ectomycorrhizas, to assess the possible correspondence between above- and below-ground views of fungal taxa. Above- and below-ground views were also related to soil chemistry. Sporocarps of 78 taxa of EcM fungi belonging to 12 genera were found. The majority of the species found, especially those of the Cortinariaceae, were host-specific for Salicaceae. Canonical correspondence analysis (CCA) based on fungal species showed that only pH and the concentration of available phosphorus significantly contributed to the variation explained. CCA based on fungal genera indicated that pH and moisture significantly contributed to the variation explained. Fifteen different EcM morphotypes were recognized and morphotype composition was different on two sampling dates. CCA based on morphotype composition yielded different results depending on sampling date. The numbers of EcM sporocarps and root tips were not correlated (on either sampling date). Diversity above ground (species and genus) was also not correlated with morphotype diversity below ground on either sampling date. Therefore, neither diversity nor abundance of above-ground EcM fungi can be used to assess below-ground EcM diversity or abundance. Lack of correlation in below-ground parameters on different sampling dates indicates substantial variation. Causes for temporal variation are discussed. The importance of investigating both above- and below-ground variability in EcM communities is stressed.