Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of Bioengineered Organ Using Biological Acellular Rat Liver Scaffold and Hepatocytes

ABSTRACT The increasing demand for organs for transplantation necessitates the development of substitutes to meet the structural and physiological functions. Tissue decellularization and recellularization aids in retaining the three-dimensional integrity, biochemical composition, tissue ultra-structure, and mechanical behavior, which makes them functionally suitable for organ transplantation. Herein, we attempted to rebuild functional liver grafts in small animal model (Wistar rat) with a potential of translation. A soft approach was adopted using 0.1% SDS (Sodium Dodecyl Sulfate) for decellularization and primary hepatocytes were used as a potential cell source for recellularization. The decellularization process was evaluated and confirmed using histology, DNA content, ultra-structure analysis. The resultant scaffold was re-seeded with the rat hepatocytes and their biocompatibility was assessed by its metabolic functions and gene expression. The structural components of the Extracellular matrix (ECM) (Laminins, Collagen type I, Reticulins) were conserved and the liver cell-specific proteins like CK-18, alpha-fetoprotein, albumin were expressed in the recellularized scaffold. The functionality and metabolic activity of the repopulated scaffold were evident from the albumin and urea production. Expression of Cytokeratin-19 (CK-19), Glucose 6-Phosphatase (G6P), Albumin, Gamma Glutamyl Transferase (GGT) genes has distinctly confirmed the translational signals after the repopulation process. Our study clearly elucidates that the native extracellular matrix of rat liver can be utilized as a scaffold for effective recellularization for whole organ regeneration.
TaxIt: An iterative computational pipeline for untargeted strain-level identification using MS/MS spectra from pathogenic single-organism samples.

Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to non-iterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt.
To be ionized or not to be ionized: the vital role of physicochemical properties of galbanic acid derivatives in AChE assay

Abstract Alzheimer’s disease is a progressive neurodegenerative disorder and patients suffer from memory loss, a decline in language skill and impairment in other cognitive functions. In the cholinergic hypothesis, dysfunction of cholinergic neurons especially in the hippocampus and cerebral cortex contributes to cognitive decline in patients. So agents that enhance acetylcholine concentration could improve cognitive function. AChEIs are among the most studied anti-Alzheimer agents. Galbanic acid as a natural compound with a sesquiterpene coumarin scaffold is a weak inhibitor of AChE. In the present contribution, we discussed the impact of carboxylic group ionization on inhibitory effects. We performed in vitro and in silico studies on galbanic acid, methyl and ethyl galbanates as AChE inhibitors. The order of inhibitory effect on AChE was obtained as ethyl galbanate ∼ methyl galbanate > galbanic acid. Our study highlights the important role of the physicochemical properties of natural lead compounds in each specific assay. Communicated by Ramaswamy H. Sarma
Endurance Exercise in Seniors: Tonic, Toxin or Neither?

INTRODUCTION Cardiac adaptation to sustained exercise in the athletes is established. However, exercise-associated effect on the cardiac function of the elderly has to be elucidated. The aim of this study was to analyze left (LV) and right ventricular (RV) characteristics at different levels of chronic exercise in the senior heart. MATERIAL AND METHODS We studied 178 participants in the World Senior Games (mean age 68±8yrs, 86 were men; 48%). Three groups were defined based on the type and intensity of sports: low, moderate and high intensity level. Exclusion criteria were coronary artery disease, atrial fibrillation, valvular heart disease or uncontrolled hypertension. LV and RV size and function were evaluated with an echocardiogram. RESULTS LV trans-mitral inflow deceleration time decreased in parallel to the intensity of chronic exercise: 242±54ms in low, 221±52 ms in moderate and 215±58 ms in high intensity level, p = 0.03. Left atrial volume index (LAVI) was larger in high intensity group, p=0.001. The LAVI remained significantly larger when adjusting for age, gender, heart rate, hypertension and diabetes (p=0.002). LV and RV sizes were larger in the high intensity group. LV ejection fraction and RV systolic function evaluated by tissue Doppler velocity, atrioventricular plane displacement and strain did not differ between groups. CONCLUSION LV diastolic filling is not only preserved, but may also be enhanced in long term, top-level senior athletes. Moreover, LV and RV systolic function remains unchanged at different levels of exercise. This supports the beneficial effects of endurance exercise participation in senior hearts.
Effect of gamma irradiation on the lipid peroxidation in chicken, lamb and buffalo meat during chilled storage

Chicken, lamb and buffalo meat were subjected to low-dose gamma irradiation (2.5 kGy) and stored at 0-3C. Lipid peroxidation in terms of thiobarbituric acid (TBA) number and carbonyl content were monitored during storage. While irradiated meat showed slight increase in TBA number and carbonyl content on storage as compared to nonirradiated meat, this did not affect the sensory qualities of meat. Free fatty acid content decreased markedly on irradiation. Irradiated meats were microbiologically safe and sensorily acceptable up to 4 weeks in the nonfrozen state (0-3C) while nonirradiated meat had a shelf-life of less than 2 weeks.
Intracellular calcium leak lowers glucose storage in human muscle, promoting hyperglycemia and diabetes

Most glucose is processed in muscle, for energy or glycogen stores. Malignant Hyperthermia Susceptibility (MHS) exemplifies muscle conditions that increase [Ca2+]cytosol. 42% of MHS patients have hyperglycemia. We show that phosphorylated glycogen phosphorylase (GPa), glycogen synthase (GSa) – respectively activated and inactivated by phosphorylation – and their Ca2+-dependent kinase (PhK), are elevated in microsomal extracts from MHS patients’ muscle. Glycogen and glucose transporter GLUT4 are decreased. [Ca2+]cytosol, increased to MHS levels, promoted GP phosphorylation. Imaging at ~100 nm resolution located GPa at sarcoplasmic reticulum (SR) junctional cisternae, and apo-GP at Z disk. MHS muscle therefore has a wide-ranging alteration in glucose metabolism: high [Ca2+]cytosol activates PhK, which inhibits GS, activates GP and moves it toward the SR, favoring glycogenolysis. The alterations probably cause these patients’ hyperglycemia. For basic studies, MHS emerges as a variable stressor, which forces glucose pathways from the normal to the diseased range, thereby exposing novel metabolic links.
Zwitterionic Polymer Coating Suppresses Microglial Encapsulation to Neural Implants In Vitro and In Vivo

For brain computer interfaces (BCI), the immune response to implanted electrodes is a major biological cause of device failure. Bioactive coatings such as neural adhesion molecule L1 have been shown to improve the biocompatibility, but are difficult to handle or produce in batches. Here, a synthetic zwitterionic polymer coating, poly(sulfobetaine methacrylate) (PSBMA) is developed for neural implants with the goal of reducing the inflammatory host response. In tests in vitro, the zwitterionic coating inhibits protein adsorption and the attachment of fibroblasts and microglia, and remains stable for at least 4 weeks. In vivo two‐photon microscopy on CX3CR1‐GFP mice shows that the zwitterionic coating significantly suppresses the microglial encapsulation of neural microelectrodes over a 6 h observation period. Furthermore, the lower microglial encapsulation on zwitterionic polymer‐coated microelectrodes is revealed to originate from a reduction in the size but not the number of microglial end feet. This work provides a facile method for coating neural implants with zwitterionic polymers and illustrates the initial interaction between microglia and coated surface at high temporal and spatial resolution.
Identification of the membrane receptor for the complement fragment C3d by means of a monoclonal antibody

The B2 antigen characterized by means of a monoclonal antibody (14) is a 140,000 Mr protein expressed only in certain stages of the differentiation of lymphocytes of the B lineage. Here we examine the relationship between B2 and the membrane complement receptor type 2 (CR2) for the complement fragment C3d (11, 12), which is also associated only with B cells. Both phenotypic markers are distributed in a similar manner among B cell malignancies and, as shown here, among established cell lines. A polypeptide with binding affinity for C3d was isolated from the membrane of B2-positive cells, i.e., tonsil lymphocytes and Raji cells. We found that this C3d-binding protein not only had the same Mr and isoelectric point (pI) as the B2 antigen, but that it was recognized by the monoclonal antibody to B2. However, anti- B2 does not mask the ligand-binding site of CR2 since it does not prevent the interaction of the purified 140,000 Mr polypeptide with immobilized C3d. Rosette formation between tonsil lymphocytes and erythrocyte intermediates bearing C3d was specifically inhibited by anti-B2. In the case of Raji cells, rosette formation was strongly inhibited only when the lymphocytes were sequentially treated with anti- B2 and with a polyclonal antibody against mouse Ig. In short, B2 and CR2 have a similar distribution among normal and malignant cells, have the same Mr and pI under denaturing conditions, and react with a single monoclonal antibody. We conclude that B2 is identical to CR2.
Ramps remain a barrier to safe wheelchair user transit bus ingress/egress

Abstract Background: Wheelchair users (WCUs) often rely on ramps for access to transit buses. Previous studies indicate WCUs have difficulty using ramps for bus ingress/egress and many transportation-related incidents occur on ramps. However, experiences of WCU ramp usage during ingress/egress have not been fully described. Methods: Cross-sectional, internet-based survey of WCUs who ride transit buses was conducted. The participants were queried on frequency of bus usage, difficulty and incidents involving ramps, and factors contributing to difficulty and incidents. Wheelchair characteristics, primary condition, and whether participants received travel training were also captured. Chi-square was used to describe relationships between wheelchair type and frequency of difficulties and incidents, and odd ratios were used to determine likelihood of the incidents. Results: The majority (55.7%) of 384 participants reported using public transportation ≥ 1 per week. Seventy-eight percent of WCUs had ≥ 1 ramp incident over the past 3 years, with an increased likelihood of incidents occurring during ingress (OR = 1.53; CI 1.21–1.86). Of those who had an incident, 22% were injured or had damage to their wheelchair. Over 60% of those who had an incident identified steep ramp slope as being the contributing factor. Steep ramp slope, exterior ramp thresholds and wet surfaces were the most common contributing factors to difficulty using ramps. Conclusion: This is the first large-scale US study enabling WCUs to describe their experiences using transit bus ramps. Despite ADA guidelines, steep ramps remain the primary factor contributing to incidents and difficulty when using ramps to access transit buses. Implications for rehabilitation The discrepancy between ADA maximum allowable ramp slopes for the built environment and transit buses may require an increased level of effort that is a barrier to transportation accessibility for some wheelchair users. Wheelchair users who access transit buses should be made aware of, and trained, to navigate ramp configurations found in the environment. We suggest rehabilitation therapists provide skills training specific to navigating transit bus ramp slopes that may be steeper and narrower than building ramps.
Identification of blood pressure reflecting personalized traits using bilateral photoplethysmography

BACKGROUND: Blood pressure (BP) is currently diagnosed by cuff-based devices, which are inconvenient and provide discontinuous measurements. Photoplethysmography (PPG)-based cuffless techniques have recently been used to accurately estimate both systolic BP (SBP) and diastolic BP (DBP). However, it is difficult to use these SBP and DBP estimations to reflect the personalized traits in the peripheral vascular condition; thus, their accuracy is limited. OBJECTIVE: The purpose of this study is to describe a technique that can be distinguished simply among three BP categories (normotensive, prehypertensive, and hypertensive) and reflect individual traits using PPG only. METHODS: We measured BP over 120 s using the fingers of 105 subjects. The PPG waveforms varied in size and amplitude over time. Therefore, normalization for uniform features for individual traits was done after the extracted waveforms were divided into multiple windows. The feature is determined by the lowest amplitude in the waveform within each divided window. The features have been applied to distinguish three BP categories using the first-eigenvector (1-EV) and second-eigenvector (2-EV) in linear discriminant analysis. RESULTS: The best decision boundary for each BP category was estimated using 1-EV (-0.02 to +0.02) and 2-EV (>+0.02) in the hypertensive category, 1-EV (< 0) and 2-EV (⩽+0.02) in the prehypertensive category, and 1-EV (⩾-0.02) and 2-EV (⩽+0.02) in the normotensive category. The overlap range with 1-EV (-0.02 to 0) and 2-EV (⩽+0.02) in particular accurately reflected individual traits. CONCLUSION: Discrimination among the three BP categories reflecting individual traits was successfully achieved using PPG. This method could improve limitations of cuff-based techniques.
The prevalence of verocytotoxin-producingEscherichia coli(VTEC) andE. coliO157:H7 in beef in Sweden determined by PCR assays and an immuno-magnetic separation (IMS) method

Abstract The number of cases of enterohaemorrhagic Escherichia coli (EHEC) in Sweden has increased dramatically since 1995, but no source of the infections has been identified. The prevalence of verocytotoxin-producing E. coli (VTEC), including E. coli O157:H7 in imported and domestic raw beef in Sweden, was determined by PCR assays and immuno-magnetic separation (IMS, Dynal). VTEC was detected by a multiplex PCR directed at sequences on the vt1 and vt2 genes, and the prevalence of E. coli O157:H7 was estimated by the IMS assay and a SZ-PCR which detects E. coli O157:H7 (and some strains of O157:NM, O55:H7 and O55:NM). VTEC was detected in 15.055% (57/368) and 1.051% (6/543) of the imported and domestic beef samples, respectively, by the multiplex PCR. E. coli O 157:H7 was detected in 0.053% and 2.054% of the imported beef samples by the IMS and SZ-PCR assays, respectively. In domestic beef E. coli O157:H7 was not detected by either method, indicating that the occurrence in Swedish beef was less than 0.056% with a 95% certainty. The overall prevalence of VTEC was estimated to be 4.050%, by adjusting for the relative proportion of imported and domestic beef in Sweden and, similarly, the overall prevalence of E. coli O157:H7 was 0.0506% (IMS) or 0.055% (SZ-PCR). We propose that a useful strategy to analyse a large number of food samples for VTEC and E. coli O157:H7 is an initial screening of samples using the multiplex VT-PCR in conjunction with enrichment and buoyant density centrifugation, followed by further analyses on the fraction of VT-positive samples using either the IMS method or SZ-PCR.
Larachelus morla, gen. et sp. nov., A New Member of the Little-Known European Early Cretaceous Record of Stem Cryptodiran Turtles

ABSTRACT A relatively diverse record of European Early Cretaceous pan-cryptodiran turtles has been revealed from the analysis of new specimens and from a review of previously defined taxa. However, knowledge about many of these taxa remains relatively limited. We erect the new taxon, Larachelus morla, gen. et sp. nov., on the basis of a shell from the late Hauterivian—early Barremian of the Iberian Range (Spain). The comparative study of this taxon with the continental European Cretaceous pan-cryptodiran representatives and cladistic analyses reveal L. morla to be a member of the little-known European Early Cretaceous stem Cryptodira. Stem cryptodirans have been recognized from the Early Cretaceous of several continents. The study of L. morla not only confirms the presence of this group in the Early Cretaceous of Europe, it also provides new insights into the European evolution of Pan-Cryptodira. This finding reveals greater diversity in European Early Cretaceous continental pan-cryptodires, highlighting its Hauterivian—Aptian record. This diversity is particularly relevant in the Iberian Range, where several clades of turtles whose coexistence has not been recognized in the Lower Cretaceous of any other region are identified: paracryptodiran members, stem cryptodiran turtles, and representatives of several lineages of the crown group Cryptodira. This very high diversity of continental taxa shows a wide range of morphological diversity that could be related to adaptation to different ecological niches.
Attentional biases in depression: Relation to disorder severity, rumination, and anhedonia.

INTRODUCTION According to cognitive models of depression, selective attentional biases (ABs) for mood-congruent information are core vulnerability factors of depression maintenance. However, findings concerning the presence of these biases in depression are mixed. This study aims to clarify the presence of these ABs among individuals with clinical and subclinical depression. METHOD We compared three groups based on a semi-structured diagnostic interview and a depressive symptoms scale (BDI-II): 34 individuals with major depressive disorder (clinically depressed); 35 with a dysphoric mood but without the criteria of major depressive disorder (i.e., subclinically depressed), and 26 never been depressed individuals. We examined AB for sad and happy materials in three modified versions of the exogenous cueing task using scenes, facial expressions, and words. Brooding, anhedonia, and anxiety were also evaluated. RESULTS In contrast to our hypotheses, there were no ABs for negative or positive information, regardless of the task and the groups. Neither the association between AB toward negative information and brooding nor the one between AB away from positive stimuli and anhedonia was significant. Bayes factors analyses revealed that the present pattern of findings does not result from a lack of statistical power. DISCUSSION Our results raise questions about how common AB is in depression. From a theoretical point of view, because individuals with depression did not exhibit AB, our results also seemingly challenge the claim that AB figures prominently in the maintenance of depression. We believe the present null results to be particularly useful for future meta-research in the field.
RELATIVE SPECIES RICHNESS AND COMMUNITY COMPLETENESS: BIRDS AND URBANIZATION IN THE MID‐ATLANTIC STATES

The idea that local factors govern local richness has been dominant for years, but recent theoretical and empirical studies have stressed the influence of regional factors on local richness. Fewer species at a site could reflect not only the influence of local factors, but also a smaller regional pool. The possible dependency of local richness on the regional pool should be taken into account when addressing the influence of local factors on local richness. It is possible to account for this potential dependency by comparing relative species richness among sites, rather than species richness per se. We consider estimation of a metric permitting assessment of relative species richness in a typical situation in which not all species are detected during sampling sessions. In this situation, estimates of absolute or relative species richness need to account for variation in species detection probability if they are to be unbiased. We present a method to estimate relative species richness based on capture–recapture models. This approach involves definition of a species list from regional data, and estimation of the number of species in that list that are present at a site–year of interest. We use this approach to address the influence of urbanization on relative richness of avian communities in the Mid-Atlantic region of the United States. There is a negative relationship between relative richness and landscape variables describing the level of urban development. We believe that this metric should prove very useful for conservation and management purposes because it is based on an estimator of species richness that both accounts for potential variation in species detection probability and allows flexibility in the specification of a “reference community. ” This metric can be used to assess ecological integrity, the richness of the community of interest relative to that of the “original” community, or to assess change since some previous time in a community.
Parkin contributes to synaptic vesicle autophagy in Bassoon-deficient mice

Mechanisms regulating the turnover of synaptic vesicle (SV) proteins are not well understood. They are thought to require poly-ubiquitination and degradation through proteasome, endo-lysosomal or autophagy-related pathways. Bassoon was shown to negatively regulate presynaptic autophagy in part by scaffolding Atg5. Here, we show that increased autophagy in Bassoon knockout neurons depends on poly-ubiquitination and that the loss of Bassoon leads to elevated levels of ubiquitinated synaptic proteins per se. Our data show that Bassoon knockout neurons have a smaller SV pool size and a higher turnover rate as indicated by a younger pool of SV2. The E3 ligase Parkin is required for increased autophagy in Bassoon-deficient neurons as the knockdown of Parkin normalized autophagy and SV protein levels and rescued impaired SV recycling. These data indicate that Bassoon is a key regulator of SV proteostasis and that Parkin is a key E3 ligase in the autophagy-mediated clearance of SV proteins.