Miracle-dz/UniFAR-FTUs huggingface dataset:
The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival

Asna1, also known as TRC40, is implicated in the delivery of tail-anchored (TA) proteins into the endoplasmic reticulum (ER), in vesicle-mediated transport, and in chaperoning unfolded proteins during oxidative stress/ATP depletion. Here, we show that Asna1 inactivation in pancreatic progenitor cells leads to redistribution of the Golgi TA SNARE proteins syntaxin 5 and syntaxin 6, Golgi fragmentation, and accumulation of cytosolic p62+ puncta. Asna1−/− multipotent progenitor cells (MPCs) selectively activate integrated stress response signaling and undergo apoptosis, thereby disrupting endocrine and acinar cell differentiation, resulting in pancreatic agenesis. Rescue experiments implicate the Asna1 ATPase activity and a CXXC di-cysteine motif in ensuring Golgi integrity, syntaxin 5 localization and MPC survival. Ex vivo inhibition of retrograde transport reproduces the perturbed Golgi morphology, and syntaxin 5 and syntaxin 6 expression, whereas modulation of p53 activity, using PFT-α and Nutlin-3, prevents or reproduces apoptosis in Asna1-deficient and wild-type MPCs, respectively. These findings support a role for the Asna1 ATPase activity in ensuring the survival of pancreatic MPCs, possibly by counteracting p53-mediated apoptosis. Summary: Conditional inactivation of Asna1/TRC40 in pancreatic progenitor cells results in pancreatic agenesis resulting from pancreatic progenitor cell apoptosis, thus revealing a crucial role for Asna1/TRC40 in pancreatic progenitor cell survival.
Dose response effect of rutin a dietary antioxidant on alcohol‐induced prooxidant and antioxidant imbalance – a histopathologic study

The present study was designed to investigate the effect of rutin on ethanol‐induced hepatotoxicity in a dose‐dependent manner in rats. Male albino rats were divided into six groups. Group 1 rats served as control and group 2 rats received rutin 100 mg/kg body weight. Hepatotoxicity was induced in groups 3–6 rats (20% ethanol) for 60 days. In addition, groups 4–6 rats received rutin at doses of 25, 50, 100 mg/kg body weight, respectively for the last 30 days of the experiment. We observed a significant increase in the activities of liver marker enzymes, serum amino transferases, alkaline phosphatase, γ‐glutamyl transpeptidase the levels of thiobarbituric acid reactive substances, conjugated dienes, lipid hydroperoxides, and a decrease in the activities of superoxide dismutase (SOD), catalase (CAT), glutathione and its related enzymes, vitamins C and E when compared to ethanol‐fed rats. Rutin supplementation along with ethanol significantly decreased the levels of liver marker enzymes, lipid peroxidation and significantly elevated the activities of liver SOD, CAT, GSH, glutathione peroxidase, vitamins C and E when compared to untreated ethanol supplemented rats. Among the three doses, 100 mg/kg body weight of rutin was found to exert a more pronounced hepatoprotective effect against ethanol‐induced toxicity. Our results were also confirmed by the histopathologic observations.
Numerical Bifurcation Analysis of Homoclinic Orbits Embedded in One-Dimensional Manifolds of Maps

We describe new methods for initializing the computation of homoclinic orbits for maps in a state space with arbitrary dimension and for detecting their bifurcations. The initialization methods build on known and improved methods for computing one-dimensional stable and unstable manifolds. The methods are implemented in MatContM, a freely available toolbox in Matlab for numerical analysis of bifurcations of fixed points, periodic orbits, and connecting orbits of smooth nonlinear maps. The bifurcation analysis of homoclinic connections under variation of one parameter is based on continuation methods and allows us to detect all known codimension 1 and 2 bifurcations in three-dimensional (3D) maps, including tangencies and generalized tangencies. MatContM provides a graphical user interface, enabling interactive control for all computations. As the prime new feature, we discuss an algorithm for initializing connecting orbits in the important special case where either the stable or unstable manifold is one-dimensional, allowing us to compute all homoclinic orbits to saddle points in 3D maps. We illustrate this algorithm in the study of the adaptive control map, a 3D map introduced in 1991 by Frouzakis, Adomaitis, and Kevrekidis, to obtain a rather complete bifurcation diagram of the resonance horn in a 1:5 Neimark-Sacker bifurcation point, revealing new features.
Cohort of birth modifies the association between FTO genotype and BMI

Significance Our finding of a significant gene-by-birth-cohort interaction adds a previously unidentified dimension to gene-by-environment interaction research, suggesting that global changes in the environment over time can modify the penetrance of genetic risk factors for diverse phenotypes. This result also suggests that presence (or absence) of a genotype–phenotype correlation may depend on the period of time study subjects were born in, or the historical moment researchers conduct their investigations. A substantial body of research has explored the relative roles of genetic and environmental factors on phenotype expression in humans. Recent research has also sought to identify gene–environment (or g-by-e) interactions, with mixed success. One potential reason for these mixed results may relate to the fact that genetic effects might be modified by changes in the environment over time. For example, the noted rise of obesity in the United States in the latter part of the 20th century might reflect an interaction between genetic variation and changing environmental conditions that together affect the penetrance of genetic influences. To evaluate this hypothesis, we use longitudinal data from the Framingham Heart Study collected over 30 y from a geographically relatively localized sample to test whether the well-documented association between the rs993609 variant of the FTO (fat mass and obesity associated) gene and body mass index (BMI) varies across birth cohorts, time period, and the lifecycle. Such cohort and period effects integrate many potential environmental factors, and this gene-by-environment analysis examines interactions with both time-varying contemporaneous and historical environmental influences. Using constrained linear age–period–cohort models that include family controls, we find that there is a robust relationship between birth cohort and the genotype–phenotype correlation between the FTO risk allele and BMI, with an observed inflection point for those born after 1942. These results suggest genetic influences on complex traits like obesity can vary over time, presumably because of global environmental changes that modify allelic penetrance.
Multi-talker background and semantic priming effect

The reported studies have aimed to investigate whether informational masking in a multi-talker background relies on semantic interference between the background and target using an adapted semantic priming paradigm. In 3 experiments, participants were required to perform a lexical decision task on a target item embedded in backgrounds composed of 1–4 voices. These voices were Semantically Consistent (SC) voices (i.e., pronouncing words sharing semantic features with the target) or Semantically Inconsistent (SI) voices (i.e., pronouncing words semantically unrelated to each other and to the target). In the first experiment, backgrounds consisted of 1 or 2 SC voices. One and 2 SI voices were added in Experiments 2 and 3, respectively. The results showed a semantic priming effect only in the conditions where the number of SC voices was greater than the number of SI voices, suggesting that semantic priming depended on prime intelligibility and strategic processes. However, even if backgrounds were composed of 3 or 4 voices, reducing intelligibility, participants were able to recognize words from these backgrounds, although no semantic priming effect on the targets was observed. Overall this finding suggests that informational masking can occur at a semantic level if intelligibility is sufficient. Based on the Effortfulness Hypothesis, we also suggest that when there is an increased difficulty in extracting target signals (caused by a relatively high number of voices in the background), more cognitive resources were allocated to formal processes (i.e., acoustic and phonological), leading to a decrease in available resources for deeper semantic processing of background words, therefore preventing semantic priming from occurring.
Comparison of polymerase chain reaction and histopathology for the detection of Helicobacter pylori in gastric biopsies

Using data from a Venezuelan cohort of 1,948 adults, the gastric detection of Helicobacter pylori (H. pylori) by polymerase chain reaction (PCR) of the vacA gene in 1 antral biopsy was compared to the detection of H. pylori by histopathology (hematoxylin–eosin and Giemsa staining) in 5 biopsies (antrum and corpus). Overall, H. pylori was detected in 85% and 95% of the subjects by PCR and histopathology, respectively. When results were analyzed by severity of precancerous lesions, PCR on 1 biopsy detected the bacteria less often than histopathology on 5 biopsies in subjects with normal gastric mucosa and non‐atrophic gastritis. However, in subjects with the most severe lesions (intestinal metaplasia type III and dysplasia), PCR on 1 biopsy detected H. pylori as often as histopathology on 5 biopsies, and significantly more often than histopathology on a single biopsy. In conclusion, these findings confirm that histopathology on 5 biopsies is an accurate tool for H. pylori detection in most subjects, compared to the PCR method on 1 biopsy. Nevertheless, the elevated sensitivity of PCR for detecting the bacteria in advanced precancerous lesions, and the possibility to use PCR to distinguish between cagA‐positive and cagA‐negative strains, makes the PCR technique especially useful in studies of stomach cancer.
Tripartite ATP-Independent Periplasmic (TRAP) Transporters and Tripartite Tricarboxylate Transporters (TTT): From Uptake to Pathogenicity

The ability to efficiently scavenge nutrients in the host is essential for the viability of any pathogen. All catabolic pathways must begin with the transport of substrate from the environment through the cytoplasmic membrane, a role executed by membrane transporters. Although several classes of cytoplasmic membrane transporters are described, high-affinity uptake of substrates occurs through Solute Binding-Protein (SBP) dependent systems. Three families of SBP dependant transporters are known; the primary ATP-binding cassette (ABC) transporters, and the secondary Tripartite ATP-independent periplasmic (TRAP) transporters and Tripartite Tricarboxylate Transporters (TTT). Far less well understood than the ABC family, the TRAP transporters are found to be abundant among bacteria from marine environments, and the TTT transporters are the most abundant family of proteins in many species of β-proteobacteria. In this review, recent knowledge about these families is covered, with emphasis on their physiological and structural mechanisms, relating to several examples of relevant uptake systems in pathogenicity and colonization, using the SiaPQM sialic acid uptake system from Haemophilus influenzae and the TctCBA citrate uptake system of Salmonella typhimurium as the prototypes for the TRAP and TTT transporters, respectively. High-throughput analysis of SBPs has recently expanded considerably the range of putative substrates known for TRAP transporters, while the repertoire for the TTT family has yet to be fully explored but both types of systems most commonly transport carboxylates. Specialized spectroscopic techniques and site-directed mutagenesis have enriched our knowledge of the way TRAP binding proteins capture their substrate, while structural comparisons show conserved regions for substrate coordination in both families. Genomic and protein sequence analyses show TTT SBP genes are strikingly overrepresented in some bacteria, especially in the β-proteobacteria and some α-proteobacteria. The reasons for this are not clear but might be related to a role for these proteins in signaling rather than transport.
Vortex disruption by magnetohydrodynamic feedback

In an electrically conducting fluid, vortices stretch out a weak, large-scale magnetic field to form strong current sheets on their edges. Associated with these current sheets are magnetic stresses, which are subsequently released through reconnection, leading to vortex disruption, and possibly even destruction. This disruption phenomenon is investigated here in the context of two-dimensional, homogeneous, incompressible magnetohydrodynamics. We derive a simple order of magnitude estimate for the magnetic stresses—and thus the degree of disruption—that depends on the strength of the background magnetic field (measured by the parameter M, a ratio between the Alfven speed and a typical flow speed) and on the magnetic diffusivity (measured by the magnetic Reynolds number Rm). The resulting estimate suggests that significant disruption occurs when M²Rm=O(1). To test our prediction, we analyze direct numerical simulations of vortices generated by the breakup of unstable shear flows with an initially weak background magnetic field. Using the Okubo-Weiss vortex coherence criterion, we introduce a vortex disruption measure, and show that it is consistent with our predicted scaling, for vortices generated by instabilities of both a shear layer and a jet.
Comparison of the Patient Health Questionnaire and the Older Adult Health and Mood Questionnaire for self-reported depressive symptoms after spinal cord injury.

OBJECTIVE To directly compare estimates of potential depressive disorders and clinically significant depressive symptoms using the Patient Health Questionnaire-9 (PHQ-9) and Older Adult Health and Mood Questionnaire (OAHMQ) among participants with spinal cord injury (SCI). RESEARCH DESIGN 727 participants from a hospital in the Southeastern United States were administered the PHQ-9 and OAHMQ during a follow-up survey. We compared the rates of depressive disorders using cutoff scores and diagnostic criteria for each instrument. No independent psychiatric diagnostic interviews were conducted. RESULTS The PHQ-9 and OAHMQ were significantly correlated (r = .78), and both were correlated with satisfaction with life (r = -.48, -.54). Using recommended diagnostic scoring procedures, 10.7% of participants met the diagnostic criteria for major depressive disorder with the PHQ-9; 9.3% met the criteria for major depression based on PHQ-9 > or = 10; and 19.7% based on PHQ-9 > or = 15. Using the OAHMQ, 19.7% reported probable major depression and 44.5% clinically significant symptomatology. CONCLUSIONS The measures were highly correlated overall. However, the estimated prevalence of depressive disorders varied substantially between the 2 instruments. These estimates were comparable to those previously reported for each instrument (i.e., higher rates with the OAHMQ). Therefore, differing estimates of depressive disorders reported in the literature using these instruments were largely attributable to the instruments themselves.
Early temperamental fearfulness and the developmental trajectory of error‐related brain activity

The error-related negativity (ERN) is a negative deflection in the event-related potential waveform that occurs when an individual makes a mistake, and an increased ERN has been proposed as a biomarker for anxiety. However, previous work suggests that fearful children are characterized by a smaller ERN. We have proposed that this may reflect the changing phenomenology of anxiety across development. In the current study, we investigate this possibility using a longitudinal within-subject design. In 271 children, we completed observational measures of fear when the children were 3 years old, and then measured the ERN when the children were 6 and 9 years old. Fearful children were characterized by a decreased ERN when they were 6-year-old; by age 9, the same children who were fearful at age 3 had increased ERNs-a pattern that closely resembles that of anxious adolescents and adults.
Moisture sorption isotherms for paper and paperboard in food chain conditions

The moisture content of paper and paper‐based packaging materials affects packaging function and integrity. For perishable food products it is especially important to understand the moisture sorption properties of paper based materials in high humidity, and the frozen to ambient temperature conditions experienced during storage and distribution. This paper reviews the published moisture sorption isotherm data for paper and paper based materials and the reasons for the differences in measured behaviour of different materials. Particular focus is made on the availability and prediction of the moisture sorption isotherm in the high relative humidity region. Copyright © 2006 John Wiley & Sons, Ltd.
Complete Chloroplast Genomes of Papaver rhoeas and Papaver orientale: Molecular Structures, Comparative Analysis, and Phylogenetic Analysis

Papaver rhoeas L. and P. orientale L. , which belong to the family Papaveraceae, are used as ornamental and medicinal plants. The chloroplast genome has been used for molecular markers, evolutionary biology, and barcoding identification. In this study, the complete chloroplast genome sequences of P. rhoeas and P. orientale are reported. Results show that the complete chloroplast genomes of P. rhoeas and P. orientale have typical quadripartite structures, which are comprised of circular 152,905 and 152,799-bp-long molecules, respectively. A total of 130 genes were identified in each genome, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Sequence divergence analysis of four species from Papaveraceae indicated that the most divergent regions are found in the non-coding spacers with minimal differences among three Papaver species. These differences include the ycf1 gene and intergenic regions, such as rpoB-trnC, trnD-trnT, petA-psbJ, psbE-petL, and ccsA-ndhD. These regions are hypervariable regions, which can be used as specific DNA barcodes. This finding suggested that the chloroplast genome could be used as a powerful tool to resolve the phylogenetic positions and relationships of Papaveraceae. These results offer valuable information for future research in the identification of Papaver species and will benefit further investigations of these species.
Continuum damage mechanics application in low-cycle thermal fatigue

In this article, a fatigue model for low-cycle thermal fatigue formulated in a continuum damage mechanics framework is presented. The model is based on a unified damage law presented by Lemaitre for low-cycle fatigue, which has been extended to low-cycle thermal fatigue. The temperature dependencies of material parameters are considered in the damage evolution integration to take the non-isothermal condition of loading into account. This model considers the stress triaxiality and non-linearity of damage evolution, and it is developed to a fatigue damage accumulation rule in which the load sequence effect is also included. The stabilized structural response under thermomechanical loading motivates the use of uncoupled analysis approach making the model a fast tool suitable for design purposes in the costly and time-consuming field of thermomechanical fatigue life assessment. To demonstrate the capability and ease of use of this model for real industrial applications, the low-cycle thermal fatigue life of a stainless steel engine exhaust manifold which is in an early stage of design is assessed.
Repeat Renal Biopsy in Lupus Nephritis: A Change in Histological Pattern Is Common

Background: The role of longitudinal change in sequential renal biopsies of lupus nephritis (LN) patient remains elusive. Methods: Clinical and pathological documents of 156 LN patients with repeat renal biopsies (412 times) were collected from a database. Results: The percent of transformation of the biopsy class from reference biopsies to repeat biopsies was 75%. For the reference biopsies that showed pure proliferative, pure membranous, and mixed nephritis, the histological pattern in the repeat biopsies changed in 57.8, 50.0, and 60.4%, respectively. As compared to reference biopsy, repeat biopsy had a higher degree of tubulointerstitial scarring (p < 0.001), chronicity index (p < 0.001) and serum creatinine (p < 0.001). In addition, baseline serum creatinine was significantly lower (p = 0.004), and the time lapse between the two biopsies was significantly longer (p < 0.001) amongst patients who had a change in the histological pattern upon repeat renal biopsy than those whose histological pattern remained the same. Conclusion: The present study suggests that a change in the histological class of LN is common in systemic lupus erythematosus patients with lupus flare, and the histology during disease flare could not be predicted by baseline clinical, biochemical, or pathological parameters. Our results indicate that when there is lupus flare with renal involvement, repeat renal biopsy is often necessary to guide the treatment.
Luminal B breast cancer: patterns of recurrence and clinical outcome

In recent years, most studies on breast cancer relapse and metastasis have focused on non-luminal breast cancers (including the basal-like and HER-2 subtypes) because of their poor prognosis. However, the luminal B subtype is more common, but this type has not been investigated as thoroughly. In the current study, we collected data on 258 patients with luminal-B breast cancer patients with recurrence and metastasis served as the observation group, and 189 patients with non-luminal breast cancer during the same period served as the control group. This study aimed to investigate the pattern of recurrence and clinical outcome after follow-up treatment for luminal B breast cancer. We found a higher proportion of local recurrence and single bone metastasis in patients with luminal B breast cancer than in patients in the non-luminal groups. The risk of recurrence and metastasis in patients with luminal B breast cancer during a 2- to 5-year period and after 5 years was still present, but the risk in patients with non-luminal breast cancers had obviously decreased during the same period. Patients with luminal B breast cancer with recurrence or/and metastasis had a better prognosis after reasonable treatment. The recurrence patterns and clinical outcomes of patients with luminal B breast cancer according to HER2 status were also different, to some degree. These results are of potential clinical relevance especially for the monitoring of clinical prognosis and targeted therapy intervention for luminal B breast cancer.