Miracle-dz/UniFAR-FTUs huggingface dataset:
Selection of Reliable Reference Genes for Analysis of Gene Expression in Spinal Cord during Rat Postnatal Development and after Injury

In order to obtain unbiased results of target gene expression, selection of the most appropriate reference gene (RG) remains a key precondition. However, an experimental study focused on the validation of stably expressed RGs in the rat spinal cord (SC) during development or after spinal cord injury (SCI) is missing. In our study, we tested the stability of the expression of nine selected RGs in rat SC tissue during normal development (postnatal days 1–43, adulthood) and after minimal (mSCI) and contusion (cSCI) spinal cord injury. The following RGs were tested: common housekeeping genes of basal cell metabolism (Gapdh, Hprt1, Mapk6) and protein translation (Rpl29, Eef1a1, Eif2b2), as well as newly designed RGs (Gpatch1, Gorasp1, Cds2) selected according to the RefGenes tool of GeneVestigator. The stability of RGs was assessed by geNorm, NormFinder, and BestKeeper. All three applets favored Gapdh and Eef1a1 as the most stable genes in SC during development. In both models of SCI, Eif2b2 displayed the highest stability of expression, followed by Gapdh and Gorasp1/Hprt1 in cSCI, and Gapdh and Eef1a1 in the mSCI experiments. To verify our results, selected RGs were employed for normalization of the expression of genes with a clear biological context in the SC—Gfap and Slc1a3/Glast during postnatal development and Aif1/Iba1 and Cd68/Ed1 after SCI.
Bioaccumulation of Cadmium Affects Development, Mating Behavior, and Fecundity in the Asian Corn Borer, Ostrinia furnacalis

Heavy metal pollution is becoming an increasingly serious problem in agricultural ecosystems. Heavy metals such as cadmium (Cd) accumulate in the food chain and may lead to detrimental effects on the physiological functions of living organisms, including herbivorous insects. One such example is the Asian Corn Borer, Ostrinia furnacalis (Lepidoptera: Pyralidae). However, how Cd can affect the development and reproduction of O. furnacalis is largely unknown. In this study, we exposed larvae of O. furnacalis to a diet containing Cd and investigated the effects of Cd on the development, mating behavior, and fecundity of the insect. We showed that Cd accumulates in the larvae and inhibits development by extending larval and pupal duration and decreasing the survival rate. The excretion of Cd through multiple routes during the larval and pupal stages resulted in low levels of residual Cd in the adult insects, which were not fed with Cd. However, the mating behavior and fecundity of these insects were significantly affected, compared to control insects. This suggests that the bioaccumulation of heavy metals such as Cd has long lasting and detrimental effects on O. furnacalis over the entire life cycle, affecting fecundity, even when specimens are only exposed at an early life stage.
Influence of the Design Solutions of Extruder Screw Mixing Tip on Selected Properties of Wheat Bran-Polyethylene Biocomposite

The study investigated the impact of the extruder screw design solution—the intensive mixing tip used—on the course of the extrusion process and the properties of the obtained biocomposite extrudate. A lignocellulosic wheat bran biocomposite based on a low-density polyethylene matrix was extruded. Three mixing tips of the screw were used interchangeably: apineapple tip, a cut rings tip, and a Maddock tip. The experimental tests carried out included the production of an extrudate with a mass content of bran altered within the range from 10% to 50%. Processing properties such as the melt flow rate (MFR) and mass flow rate of the extruded biocomposite were determined. Selected physical, mechanical, and structural properties of the biocomposite extrudate obtained with the use of the three tested mixing tips at five bran contents were tested.
Marine Toxins Detection by Biosensors Based on Aptamers

Marine toxins cause great harm to human health through seafood, therefore, it is urgent to exploit new marine toxins detection methods with the merits of high sensitivity and specificity, low detection limit, convenience, and high efficiency. Aptasensors have emerged to replace classical detection methods for marine toxins detection. The rapid development of molecular biological approaches, sequencing technology, material science, electronics and chemical science boost the preparation and application of aptasensors. Taken together, the aptamer-based biosensors would be the best candidate for detection of the marine toxins with the merits of high sensitivity and specificity, convenience, time-saving, relatively low cost, extremely low detection limit, and high throughput, which have reduced the detection limit of marine toxins from nM to fM. This article reviews the detection of marine toxins by aptamer-based biosensors, as well as the selection approach for the systematic evolution of ligands by exponential enrichment (SELEX), the aptamer sequences. Moreover, the newest aptasensors and the future prospective are also discussed, which would provide thereotical basis for the future development of marine toxins detection by aptasensors.
GTP Binding Is Necessary for the Activation of a Toxic Mutant Isoform of the Essential GTPase ObgE

Even though the Obg protein is essential for bacterial viability, the cellular functions of this universally conserved GTPase remain enigmatic. Moreover, the influence of GTP and GDP binding on the activity of this protein is largely unknown. Previously, we identified a mutant isoform of ObgE (the Obg protein of Escherichia coli) that triggers cell death. In this research we explore the biochemical requirements for the toxic effect of this mutant ObgE* isoform, using cell death as a readily accessible read-out for protein activity. Both the absence of the N-terminal domain and a decreased GTP binding affinity neutralize ObgE*-mediated toxicity. Moreover, a deletion in the region that connects the N-terminal domain to the G domain likewise abolishes toxicity. Taken together, these data indicate that GTP binding by ObgE* triggers a conformational change that is transmitted to the N-terminal domain to confer toxicity. We therefore conclude that ObgE*–GTP, but not ObgE*–GDP, is the active form of ObgE* that is detrimental to cell viability. Based on these data, we speculate that also for wild-type ObgE, GTP binding triggers conformational changes that affect the N-terminal domain and thereby control ObgE function.
Lycium Barbarum Exerts Protection against Glaucoma-Like Injury Via Inhibition of MMP-9 Signaling In Vitro

Background The phytochemical ingredients of berries have been used in the treatment of various bodily ailments; while their roles in preventing the severity of glaucoma are poorly understood. Hence, the present study was framed to investigate whether ethanolic extracts of Lycium barbarum exerts protection against the onset of glaucoma using cultured PC12 neuronal cells by modulating the expression of extracellular matrix proteins. Material/Methods In order to develop glaucoma like condition in cells, cultured PC12 cells were subjected to 50 and 100 mmHg hydrostatic pressure for 24 hours. The pressure exposed cells were analyzed for the expression of glaucoma markers such as ANGPTL7 and the expressions of extracellular matrix proteins in the presence and absence of L. barbarum, matrix metalloproteinase (MMP)-9 inhibitor, and latanoprost, a current drug for the treatment of glaucoma. Results PC12 cells exposed to hydrostatic pressures (50 and 100 mmHg) increased the expression of glaucoma marker, ANGPTL7. Moreover, results have demonstrated the significant changes in the expression of MMP-2, MMP-9, collagen I, and TGF-β at the gene level. In contrast, cells pretreated with L. barbarum extracts showed reduced expression of ANGPTL7 and extracellular matrix proteins compared to control. Furthermore, to elucidate the role of MMP-9 in the onset of glaucoma, cells were silenced using MMP-9 inhibitor along with L. barbarum demonstrated a significant reduction in the glaucoma marker ANGPTL7 while improving the expression of caveolin-1 expression in cells subjected to pressure. Conclusions The extract of L. barbarum protects the cells from intraocular pressure by activating caveolin-1 dependent pathway via inhibition of MMP-9 expression.
Proteomics Analysis of Early Developmental Stages of Zebrafish Embryos

Zebrafish is a well-recognized organism for investigating vertebrate development and human diseases. However, the data on zebrafish proteome are scarce, particularly during embryogenesis. This is mostly due to the overwhelming abundance of egg yolk proteins, which tend to mask the detectable presence of less abundant proteins. We developed an efficient procedure to reduce the amount of yolk in zebrafish early embryos to improve the Liquid chromatography–tandem mass spectrometry (LC–MS)-based shotgun proteomics analysis. We demonstrated that the deyolking procedure resulted in a greater number of proteins being identified. This protocol resulted in approximately 2-fold increase in the number of proteins identified in deyolked samples at cleavage stages, and the number of identified proteins increased greatly by 3–4 times compared to non-deyolked samples in both oblong and bud stages. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed a high number of functional proteins differentially accumulated in the deyolked versus non-deyolked samples. The most prominent enrichments after the deyolking procedure included processes, functions, and components related to cellular organization, cell cycle, control of replication and translation, and mitochondrial functions. This deyolking procedure improves both qualitative and quantitative proteome analyses and provides an innovative tool in molecular embryogenesis of polylecithal animals, such as fish, amphibians, reptiles, or birds.
Gait Asymmetry Post-Stroke: Determining Valid and Reliable Methods Using a Single Accelerometer Located on the Trunk

Asymmetry is a cardinal symptom of gait post-stroke that is targeted during rehabilitation. Technological developments have allowed accelerometers to be a feasible tool to provide digital gait variables. Many acceleration-derived variables are proposed to measure gait asymmetry. Despite a need for accurate calculation, no consensus exists for what is the most valid and reliable variable. Using an instrumented walkway (GaitRite) as the reference standard, this study compared the validity and reliability of multiple acceleration-derived asymmetry variables. Twenty-five post-stroke participants performed repeated walks over GaitRite whilst wearing a tri-axial accelerometer (Axivity AX3) on their lower back, on two occasions, one week apart. Harmonic ratio, autocorrelation, gait symmetry index, phase plots, acceleration, and jerk root mean square were calculated from the acceleration signals. Test–retest reliability was calculated, and concurrent validity was estimated by comparison with GaitRite. The strongest concurrent validity was obtained from step regularity from the vertical signal, which also recorded excellent test–retest reliability (Spearman’s rank correlation coefficients (rho) = 0.87 and Intraclass correlation coefficient (ICC21) = 0.98, respectively). Future research should test the responsiveness of this and other step asymmetry variables to quantify change during recovery and the effect of rehabilitative interventions for consideration as digital biomarkers to quantify gait asymmetry.
Circular RNA NF1-419 enhances autophagy to ameliorate senile dementia by binding Dynamin-1 and Adaptor protein 2 B1 in AD-like mice

Recent studies have demonstrated circular RNAs (circRNAs) to be widely expressed and to have important physiological functions. However, the expression, regulation, and function of circRNAs in neuroglial cells are unknown. Herein, we characterized the expression, regulation, and function of circRNAs in astrocytes. Astrocyte circRNAs were identified by computational analysis of newborn SD rat primary astrocytes cultured with 20 g/L D-galactose. In this manner, 7376 circRNAs were identified, among which most circRNAs (5754) were derived from annot_exons, whereas 27 were antisense, 853 were exon/intron, 329 were intergenic, 41 were intronic, and 372 were one exon. Among these, circNF1-419 was demonstrated to regulate autophagy, in over-expressing circNF1-419 transfected astrocytes, through the PI3K-I/Akt-AMPK-mTOR and PI3K-I/Akt-mTOR signaling pathways. An adenovirus associated virus packaging system (virus titer 1 ×1012), over-expressing circNF1-419 and injected into mouse cerebral cortex, showed autophagy enhancing activity by binding the proteins Dynamin-1 and Adaptor protein 2 B1 (AP2B1). This binding regulated aging markers (p21, p35/25, and p16) and inflammatory factors (TNF-α and NF-κB), and reduced the expression of Alzheimer’s disease marker proteins (Tau, p-Tau, Aβ1-42, and APOE), which delayed senile dementia. Transcriptome analysis of the brain showed that circNF1-419 improved other signaling pathways, especially those related to the synapses of SAMP8 mice. These findings provide novel insights into circNF1-419 and its potential usefulness for the diagnosis and treatment of dementia by regulating Dynamin-1 and AP2B1 mediated autophagy.
Recurrent transmural tracheal schwannoma resected by video-assisted thoracoscopic window resection

Abstract Rationale: Primary schwannoma is extremely rare in the trachea, and its optimal treatment has not yet been established. Previous literature have indicated that traditional resection by thoracotomy is an effective surgical procedure but with huge trauma, and endoscopic excision is a minimally invasive surgical method but with possibility of recurrence. Window resection was usually utilized for selected patients with trachea invasion by thyroid carcinoma, but video-assisted thoracoscopic window resection for trachea schwannoma has not been reported previously. Patient concerns: A 23-year-old woman was admitted to hospital due to dyspnea, coughing and wheezing that had persisted for 2 months with aggravation for 1 week. Diagnoses: Chest computed tomography (CT) scan revealed a well-circumscribed soft-tissue mass located on the right lateral posterior wall of the trachea. Bronchofibroscopy (BFS) showed a whitish, smooth and round mass with a wide base in the trachea. Immunohistochemical staining demonstrated cells labeled with Vim (+), S-100 (+), SOX-10 (+), SMA (–), CK (–). Histopathological examinations showed that the mass was a schwannoma. Interventions: The tumor was nearly completely excised via BFS, but relapsed 2 times at 12 days and 3 weeks after endoscopic resection. Finally, the patient underwent video-assisted thoracoscopic window resection of trachea. Outcomes: The patient recovered rapidly and no recurrence was observed over 6 months of follow-up. Lessons: The treatment of tracheal schwannoma depends on the characteristics of tumor and the condition of patient. Surgical resection is a preferred alternative for sessile or transmural tumors and recurrence after endoscopic excision. Tracheal window resection by video-assisted thoracoscopy is beneficial for some appropriate patients with a small and sessile tumor.
Benzodiazepine and unhealthy alcohol use among adult outpatients.

OBJECTIVES Concomitant excessive alcohol consumption and benzodiazepine use is associated with adverse health outcomes. We examined associations of unhealthy alcohol use and other patient characteristics with benzodiazepine use. STUDY DESIGN A cross-sectional analysis of 2,089,525 Kaiser Permanente of Northern California outpatients screened for unhealthy alcohol use in primary care between November 1, 2014, and December 31, 2016. METHODS We fit multivariable generalized linear models to estimate the associations between unhealthy alcohol use and benzodiazepine dispensation and, among patients who were dispensed a benzodiazepine, mean doses (in mean lorazepam-equivalent daily doses [LEDDs]) and prescription durations. We controlled for patient sex, age, race/ethnicity, estimated household income, Charlson Comorbidity Index (CCI) score, anxiety disorder, alcohol use disorder, insomnia, musculoskeletal pain, and epilepsy. RESULTS In the 12 months centered around (6 months before and 6 months after) the first alcohol-screening visit, 7.5% of patients used benzodiazepines. The following characteristics were independently associated with higher rates of benzodiazepine use, higher LEDD, and longer prescription duration: older age, white race/ethnicity, lower estimated household income, higher CCI score, and the presence of an anxiety disorder, insomnia, musculoskeletal pain, or epilepsy. Women and patients with an alcohol use disorder or unhealthy alcohol use, compared with men and patients with low-risk drinking or abstinence, were more likely to use a benzodiazepine; however, their LEDDs were lower and their prescription durations were shorter. CONCLUSIONS Benzodiazepine use in primary care was associated with older age, female sex, white race/ethnicity, lower socioeconomic status, and unhealthy alcohol use. These findings may be applied to develop policies and interventions to promote judicious benzodiazepine use.
Molecular Biomarkers and Influential Factors of Denitrification in a Full-Scale Biological Nitrogen Removal Plant

Three denitrifying bacteria, Paracoccus spp. , Thauera spp. , Pseudomonas-like spp. , and two functional genes, nitrate reductase (narG and napA), were studied as potential biomarkers for total nitrogen removal. These bacterial genera and the functional genes showed significant negative correlations with total nitrogen in the effluent (TNeff). Thauera spp. had the highest correlation (r = −0.793, p < 0.001) with TNeff, and narG-like and napA genes also showed significant correlations (r = −0.663 and −0.643, respectively), suggesting functional genes have equal validity to 16S rRNA genes in monitoring denitrification performance. The most explanatory variables were a combination of constituents, with temperature emerging as the most important in Pearson’s correlation and redundancy analysis. Thauera spp. had the highest correlation with temperature (r = 0.739) followed closely by Paracoccus spp. (r = 0.705). Denitrification was also significantly affected by pH (r = 0.369), solids retention time (r = −0.377), total nitrogenin (r = 0.635), and organic matter in the influent (biochemical oxygen demand and chemical oxygen demand; r = 0.320 and 0.522, respectively). Our data verified that major denitrifiers’ 16S rRNA genes and nitrate reductase genes were better biomarkers than the biomass concentration, and any of the biomarkers could track denitrification in real time.
Surrounding Tissue Response to Surface-Treated Zirconia Implants

Yttria-stabilized tetragonal zirconia polycrystals (Y-TZP), which are partially stabilized zirconia, have been used for fabricating dental implants. This study investigated the soft tissue attachment, the collagen fiber orientation to zirconia at different surface conditions, and the bone response using implantation experiments in animals. The zirconia implant surfaces were treated with ultraviolet irradiation (UV), a combination of large-grit sandblasting and hydrofluoric acid etching (blastedHF), and a combination of blastedHF and UV (blastedHF+UV). The surface treated with blastedHF and blastedHF+UV appeared rough and hydrophilic. The surface treated with blastedHF+UV appeared to be superhydrophilic. Subsequently, tapered cylindrical zirconia implants were placed in the alveolar sockets of the maxillary molars of rats. The bone-to-implant contact ratio of blastedHF and blastedHF+UV implants was significantly higher than that of the non-treated controls and UV-treated implants. The four different surface-treated zirconia implants demonstrated tight soft tissue attachments. Perpendicularly oriented collagen fibers towards zirconia implants were more prominent in blastedHF and blastedHF+UV implants compared to the controls and UV-treated implants. The area of the soft tissue attachment was the greatest with the perpendicularly oriented collagen fibers of blastedHF+UV-treated implants. In conclusion, blastedHF+UV treatment could be beneficial for ensuring greater soft-tissue attachment for zirconia implants.
Total triterpenes from the fruits of Chaenomeles speciosa (Sweet) Nakai protects against indomethacin‐induced gastric mucosal injury: involvement of TFF1‐mediated EGF/EGFR and apoptotic pathways

Our previous studies indicated that the triterpenes from the fruits of Chaenomeles speciosa (Sweet) Nakai (TCS) owned effectively therapeutic effects on gastric ulcer patients and animals, but its mechanisms have not been fully understood. The current study was to further investigate its protective effect on indomethacin (IND)‐damaged RGM‐1 cells and rats, as well as its mechanisms involved.
Summary of Revisions: Standards of Medical Care in Diabetes—2020

The field of diabetes care is rapidly changing as new research, technology, and treatments that can improve the health and well-being of people with diabetes continue to emerge. With annual updates since 1989, the American Diabetes Association (ADA) has long been a leader in producing guidelines that capture the most current state of the field. Although levels of evidence for several recommendations have been updated, these changes are not outlined below where the clinical recommendation has remained the same. That is, changes in evidence level from, for example, E to C are not noted below. The 2020 Standards of Care contains, in addition to many minor changes that clarify recommendations or reflect new evidence, the following more substantive revisions.