Miracle-dz/UniFAR-FTUs huggingface dataset:
Cell type discovery using single-cell transcriptomics: implications for ontological representation

Abstract Cells are fundamental function units of multicellular organisms, with different cell types playing distinct physiological roles in the body. The recent advent of single-cell transcriptional profiling using RNA sequencing is producing ‘big data’, enabling the identification of novel human cell types at an unprecedented rate. In this review, we summarize recent work characterizing cell types in the human central nervous and immune systems using single-cell and single-nuclei RNA sequencing, and discuss the implications that these discoveries are having on the representation of cell types in the reference Cell Ontology (CL). We propose a method, based on random forest machine learning, for identifying sets of necessary and sufficient marker genes, which can be used to assemble consistent and reproducible cell type definitions for incorporation into the CL. The representation of defined cell type classes and their relationships in the CL using this strategy will make the cell type classes being identified by high-throughput/high-content technologies findable, accessible, interoperable and reusable (FAIR), allowing the CL to serve as a reference knowledgebase of information about the role that distinct cellular phenotypes play in human health and disease.
Preclinical Studies of Stem Cell Therapy for Heart Disease

As part of the TACTICS (Transnational Alliance for Regenerative Therapies in Cardiovascular Syndromes) series to enhance regenerative medicine, here, we discuss the role of preclinical studies designed to advance stem cell therapies for cardiovascular disease. The quality of this research has improved over the past 10 to 15 years and overall indicates that cell therapy promotes cardiac repair. However, many issues remain, including inability to provide complete cardiac recovery. Recent studies question the need for intact cells suggesting that harnessing what the cells release is the solution. Our contribution describes important breakthroughs and current directions in a cell-based approach to alleviating cardiovascular disease.
Metabolic control analysis of insulin-stimulated glucose disposal in rat skeletal muscle.

Metabolic control analysis was used to calculate the distributed control of insulin-stimulated skeletal muscle glucose disposal in awake rats. Three separate hyperinsulinemic infusion protocols were performed: 1) protocol I was a euglycemic (∼6 mM)-hyperinsulinemic (10 mU ⋅ kg-1 ⋅ min-1) clamp, 2) protocol II was a hyperglycemic (∼11 mM)-hyperinsulinemic (10 mU ⋅ kg-1 ⋅ min-1) clamp, and 3) protocol III was a euglycemic (∼6 mM)-hyperinsulinemic (10 mU ⋅ kg-1 ⋅ min-1)-lipid/heparin (increased plasma free fatty acid) clamp. [1-13C]glucose was administered in all three protocols for a 3-h period, during which time [1-13C]glucose label incorporation into [1-13C]glycogen, [3-13C]lactate, and [3-13C]alanine was detected in the hindlimb of awake rats via13C-NMR. Combined steady-state and kinetic data were used to calculate rates of glycogen synthesis and glycolysis. Additionally, glucose 6-phosphate (G-6- P) was measured in the hindlimb muscles with the use of in vivo31P-NMR during the three infusion protocols. The clamped glucose infusion rates were 31.6 ± 2.9, 49.7 ± 1.0, and 24.0 ± 1.5 mg ⋅ kg-1 ⋅ min-1at 120 min in protocols I- III, respectively. Rates of glycolysis were 62.1 ± 10.3, 71.6 ± 11.8, and 19.5 ± 3.6 nmol ⋅ g-1 ⋅ min-1and rates of glycogen synthesis were 125 ± 15, 224 ± 23, and 104 ± 17 nmol ⋅ g-1 ⋅ min-1in protocols I- III, respectively. Insulin-stimulated G-6- Pconcentrations were 217 ± 8, 265 ± 12, and 251 ± 9 nmol/g in protocols I- III, respectively. A top-down approach to metabolic control analysis was used to calculate the distributed control among glucose transport/phosphorylation [GLUT-4/hexokinase (HK)], glycogen synthesis, and glycolysis from the metabolic flux and G-6- P data. The calculated values for the control coefficients ( C) of these three metabolic steps ([Formula: see text]= 0.55 ± 0.10,[Formula: see text]= 0.30 ± 0.06, and[Formula: see text] = 0.15 ± 0.02; where J is glucose disposal flux, and glycogen syn is glycogen synthesis) indicate that there is shared control of glucose disposal and that glucose transport/phosphorylation is responsible for the majority of control of insulin-stimulated glucose disposal in skeletal muscle.
Neuronal nitric oxide synthase modulates rat renal microvascular function.

This study was performed to determine the influence of neuronal nitric oxide synthase (nNOS) on renal arteriolar tone under conditions of normal, interrupted, and increased volume delivery to the macula densa segment and on the microvascular responses to angiotensin II (ANG II). Experiments were performed in vitro on afferent (21.2 ± 0.2 μm) and efferent (18.5 ± 0.2 μm) arterioles of kidneys harvested from male Sprague-Dawley rats, using the blood-perfused juxtamedullary nephron technique. Superfusion with the specific nNOS inhibitor, S-methyl-l-thiocitrulline (l-SMTC), decreased afferent and efferent arteriolar diameters, and these decreases in arteriolar diameters were prevented by interruption of distal volume delivery by papillectomy. When 10 mM acetazolamide was added to the blood perfusate to increase volume delivery to the macula densa segment, afferent arteriolar vasoconstrictor responses tol-SMTC were enhanced, but this effect was again completely prevented after papillectomy. In contrast, the arteriolar diameter responses to the nonselective NOS inhibitor, N ω-nitro-l-arginine (l-NNA) were only attenuated by papillectomy.l-SMTC (10 μM) enhanced the efferent arteriolar vasoconstrictor response to ANG II but did not alter the afferent arteriolar vasoconstrictor responsiveness to ANG II. In contrast, l-NNA (100 μM) enhanced both afferent and efferent arteriolar vasoconstrictor responses to ANG II. These results indicate that the modulating influence of nNOS on afferent arteriolar tone of juxtamedullary nephrons is dependent on distal tubular fluid flow. Furthermore, nNOS exerts a differential modulatory action on the juxtamedullary microvasculature by enhancing efferent, but not afferent, arteriolar responsiveness to ANG II.
Deep Unsupervised Saliency Detection: A Multiple Noisy Labeling Perspective

The success of current deep saliency detection methods heavily depends on the availability of large-scale supervision in the form of per-pixel labeling. Such supervision, while labor-intensive and not always possible, tends to hinder the generalization ability of the learned models. By contrast, traditional handcrafted features based unsupervised saliency detection methods, even though have been surpassed by the deep supervised methods, are generally dataset-independent and could be applied in the wild. This raises a natural question that "Is it possible to learn saliency maps without using labeled data while improving the generalization ability? ". To this end, we present a novel perspective to unsupervised saliency detection through learning from multiple noisy labeling generated by "weak" and "noisy" unsupervised handcrafted saliency methods. Our end-to-end deep learning framework for unsupervised saliency detection consists of a latent saliency prediction module and a noise modeling module that work collaboratively and are optimized jointly. Explicit noise modeling enables us to deal with noisy saliency maps in a probabilistic way. Extensive experimental results on various benchmarking datasets show that our model not only outperforms all the unsupervised saliency methods with a large margin but also achieves comparable performance with the recent state-of-the-art supervised deep saliency methods.
Calcium influx and intracellular stores in angiotensin II stimulation of normal and hyperplastic pituitary cells.

In rat pituitary cells from estrogen-induced hyperplasia, angiotensin II (ANG II) does not evoke a clear spike elevation of intracellular Ca2+concentration ([Ca2+]i) but induces a plateau increase. The present work was undertaken to establish whether this difference was related to a differential participation of intracellular and/or plasma membrane Ca2+ channels. We first tested the effect of 10 nM ANG II on [Ca2+]iin the absence of extracellular Ca2+ in cells depolarized with 25 mM K+ or in the presence of blockers of L-type voltage-sensitive Ca2+ channels (VSCC). These treatments did not alter spike elevation in [Ca2+]iin controls but reduced plateau levels in hyperplastic cells. Intracellular Ca2+ stores were similar in both groups, as assessed by thapsigargin treatment, but this drug abolished spike increase in controls and scarcely modified plateau levels in hyperplastic cells. Finally, inositol trisphosphate (InsP3) production in response to ANG II was significantly higher in control cells. We conclude that the observed plateau rise in hyperplastic cells results mainly from Ca2+ influx through VSCC. In contrast, in control cells, the ANG II-induced spike increase in [Ca2+]iresults from mobilization of Ca2+from thapsigargin-sensitive internal channels, activated by higher inositol 1,4,5-trisphosphate generation.
Short- and long-term enalapril affect renal medullary hemodynamics in the spontaneously hypertensive rat.

Long-term angiotensin-converting enzyme (ACE) inhibition in the spontaneously hypertensive rat (SHR) resets pressure natriuresis and shifts the relationship between renal arterial pressure (RAP) and renal interstitial hydrostatic pressure (RIHP) to lower levels of arterial pressure. These effects persist after withdrawal of treatment. The purpose of this study was to determine the effect of short- and long-term ACE inhibition on medullary blood flow (MBF). Enalapril (25 mg ⋅ kg-1 ⋅ day-1in drinking water) was given to male SHR from 4 to 14 wk of age. Four weeks after stopping treatment, we measured MBF over a wide range of RAP using laser-Doppler flowmetry in anesthetized rats. Additional rats, either untreated or previously treated for 10 wk, received 3-day enalapril treatment just before the experiment. MAP (mmHg ± SE) was 178 ± 6 ( n = 8), 134 ± 6 ( n = 8), 138 ± 5 ( n = 9), and 111 ± 6 mmHg ( n = 9) for the untreated, 3 day, 10 wk, and 10 wk + 3 day groups, respectively. Total renal blood flow for the groups receiving 3-day treatment was significantly higher when compared with that in rats with an intact renin-angiotensin system. Three-day treatment had no effect on the relationship between RAP and RIHP, whereas that in rats receiving 10-wk treatment was shifted to lower levels of RAP by ∼30 mmHg. Both 10-wk and 3-day treatment independently increased the slope of the RAP versus MBF relationship at values of RAP > 100 mmHg. The slopes in perfusion units/mmHg were 0.12 ± 0.01 ( n = 8), 0.26 ± 0.01 ( n = 8), 0.27 ± 0.01 ( n = 9), and 0.30 ± 0.02 ( n = 9) for the untreated, 3 day, 10 wk, and 10 wk + 3 day groups, respectively. These results indicate that the effect of short-term and the persistent effect of long-term enalapril alter renal medullary hemodynamics in a way that may contribute to the resetting of the pressure-natriuresis relationship in treated rats.
Distinct human α(1,3)-fucosyltransferases drive Lewis-X/sialyl Lewis-X assembly in human cells

In humans, six α(1,3)-fucosyltransferases (α(1,3)-FTs: FT3/FT4/FT5/FT6/FT7/FT9) reportedly fucosylate terminal lactosaminyl glycans yielding Lewis-X (LeX; CD15) and/or sialyl Lewis-X (sLeX; CD15s), structures that play key functions in cell migration, development, and immunity. Prior studies analyzing α(1,3)-FT specificities utilized either purified and/or recombinant enzymes to modify synthetic substrates under nonphysiological reaction conditions or molecular biology approaches wherein α(1,3)-FTs were expressed in mammalian cell lines, notably excluding investigations using primary human cells. Accordingly, although significant insights into α(1,3)-FT catalytic properties have been obtained, uncertainty persists regarding their human LeX/sLeX biosynthetic range across various glycoconjugates. Here, we undertook a comprehensive evaluation of the lactosaminyl product specificities of intracellularly expressed α(1,3)-FTs using a clinically relevant primary human cell type, mesenchymal stem cells. Cells were transfected with modified mRNA encoding each human α(1,3)-FT, and the resultant α(1,3)-fucosylated lactosaminyl glycoconjugates were analyzed using a combination of flow cytometry and MS. The data show that biosynthesis of sLeX is driven by FTs-3, -5, -6, and -7, with FT6 and FT7 having highest potency. FT4 and FT9 dominantly biosynthesize LeX, and, among all FTs, FT6 holds a unique capacity in creating sLeX and LeX determinants across protein and lipid glycoconjugates. Surprisingly, FT4 does not generate sLeX on glycolipids, and neither FT4, FT6, nor FT9 synthesizes the internally fucosylated sialyllactosamine VIM-2 (CD65s). These results unveil the relevant human lactosaminyl glycans created by human α(1,3)-FTs, providing novel insights on how these isoenzymes stereoselectively shape biosynthesis of vital glycoconjugates, thereby biochemically programming human cell migration and tuning human immunologic and developmental processes.
A miniature mechanical apparatus and test protocol for bending and crushing tests in wood preservation research

A miniature mechanical test apparatus for determining the modulus of elasticity and crushing strength of small wood specimens has been developed. This apparatus provides a sensitive method for laboratory studies to measure both soft-rot and basidiomycete decay in wood test samples. Test results show that progressive soft-rot attack can be accurately measured by changes in modulus of elasticity. Tests on use of the apparatus to monitor the amount of basidiomycete decay in soil block tests are underway.
Interactive Book Reading to Accelerate Word Learning by Kindergarten Children With Specific Language Impairment: Identifying Adequate Progress and Successful Learning Patterns.

Purpose The goal of this study was to provide guidance to clinicians on early benchmarks of successful word learning in an interactive book reading treatment and to examine how encoding and memory evolution during treatment contribute to word learning outcomes by kindergarten children with specific language impairment (SLI). Method Twenty-seven kindergarten children with SLI participated in a preliminary clinical trial using interactive book reading to teach 30 new words. Word learning was assessed at 4 points during treatment through a picture naming test. Results The results indicate that the following performance during treatment was cause for concern, indicating a need to modify the treatment: naming 0-1 treated words correctly at Naming Test 1; naming 0-2 treated words correctly at Naming Test 2; naming 0-3 treated words correctly at Naming Test 3. In addition, the results showed that encoding was the primary limiting factor in word learning, but rmemory evolution also contributed (albeit to a lesser degree) to word learning success. Conclusion Case illustrations demonstrate how a clinician's understanding of a child's word learning strengths and weaknesses develop over the course of treatment, substantiating the importance of regular data collection and clinical decision-making to ensure the best possible outcomes for each individual child.
Gender differences in clinical registration trials: is there a real problem?

Aims Several studies have reported the under‐representation of women in clinical trials, thereby challenging the external validity of the benefit/risk assessments of launched drugs. Our aim was to determine the extent to which women have been included in clinical trials used for drug registration and to analyse the fraction of women participating in phases I, II and III. Methods We conducted cross‐sectional, structured research into publicly available registration dossiers of Food and Drug Administration (FDA)‐approved drugs that are prescribed frequently. Furthermore, we analysed compounds with high hepatic clearance and a known gender‐related difference in drug response. In a sensitivity analysis, we compared figures with US disease prevalence data. Results For 38 of the initial 137 drugs (28%), sufficient data were reported and publicly available. For these drugs, 185 479 trial participants were included, of whom 47% were female and 44% were male; gender was not reported for 9% of participants. However, the number of female participants varied with the phase of the trial, with 22% females in phase I trials vs. 48% and 49%, respectively, in phase II and III trials. When compared with US disease prevalence data, 10 drugs (26%) had a greater than 20% difference between the proportion of females affected with the disease compared with representation in clinical trials. Conclusions From these publicly available data, there was no evidence of any systematic under‐representation of women in clinical trials.
Application of Silver Nanostructures Synthesized by Cold Atmospheric Pressure Plasma for Inactivation of Bacterial Phytopathogens from the Genera Dickeya and Pectobacterium

Pectinolytic bacteria are responsible for significant economic losses by causing diseases on numerous plants. New methods are required to control and limit their spread. One possibility is the application of silver nanoparticles (AgNPs) that exhibit well-established antibacterial properties. Here, we synthesized AgNPs, stabilized by pectins (PEC) or sodium dodecyl sulphate (SDS), using a direct current atmospheric pressure glow discharge (dc-APGD) generated in an open-to-air and continuous-flow reaction-discharge system. Characterization of the PEC-AgNPs and SDS-AgNPs with UV/Vis absorption spectroscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, and selected area electron diffraction revealed the production of spherical, well dispersed, and face cubic centered crystalline AgNPs, with average sizes of 9.33 ± 3.37 nm and 28.3 ± 11.7 nm, respectively. Attenuated total reflection-Fourier transformation infrared spectroscopy supported the functionalization of the nanostructures by PEC and SDS. Antibacterial activity of the AgNPs was tested against Dickeya spp. and Pectobacterium spp. strains. Both PEC-AgNPs and SDS-AgNPs displayed bactericidal activity against all of the tested isolates, with minimum inhibitory concentrations of 5.5 mg∙L−1 and 0.75–3 mg∙L−1, respectively. The collected results suggest that the dc-APGD reaction-discharge system can be applied for the production of defined AgNPs with strong antibacterial properties, which may be further applied in plant disease management.
Comparison of Tentative Radiographic Working Length with and without grid Versus Electronic Apex Locator

The apical termination of obturation is the most important factor influencing the success of root canal treatment (RCT). Working length (WL) is the key element in achieving this. Aim: The aim of this study is to compare and evaluate the preoperative estimated WL with conventional radiograph and with grid radiograph, with reference to electronic apex locator (EAL) in single-rooted teeth. Settings and Design: Thirty permanent anterior teeth with complete root formation indicated for RCT were included in this study. Materials and Methods: Conventional radiograph (Group 1) and conventional radiograph with external grid (Group 2) were made before access opening. WL with EAL (Group 3) was determined after access opening. Statistical Analysis: The statistical package for the social sciences (SPSS) version 16.0 (SPSS Inc., Chicago, IL, USA) was used to compare the WLs of three groups, and the statistical significance was considered to be P ≤ 0.05. ANOVA, post hoc test were made to measure the intergroup comparison, and Pearson correlation values were obtained. Results and Conclusion: The results of the study showed a higher correlation between grid WL and apex locator WL than conventional WL and apex locator WL. Preoperative metrics with radiographic grid along with the apex locator is a better measuring tool compared to the conventional radiographic WL in a single-rooted tooth.
Route and Type of Formulation Administered Influences the Absorption and Disposition of Vitamin B12 Levels in Serum

The administration of biological compounds that optimize health benefits is an ever-evolving therapeutic goal. Pharmaceutical and other adjunctive biological compounds have been administered via many different routes in order to produce a systemic pharmacological effect. The article summarizes the findings from an Australian comparative study in adults administered vitamin B12 through different oral delivery platforms. A total of 16 subjects (9 males, 7 females) voluntarily partook in a comparative clinical study of five different vitamin B12 formulations across a six-month period, completing 474 person-hours of cumulative contribution, that was equivalent to an n = 60 participation. A nanoparticle delivered vitamin B12 through a NanoCelle platform was observed to be significantly (p < 0.05) better absorbed than all other dose equivalent platforms (i.e., tablets, emulsions, or liposomes) from baseline to 1, 3, and 6 h of the study period. The nanoparticle platform delivered vitamin B12 demonstrated an enhanced and significant absorption profile as exemplified by rapid systemic detection (i.e., 1 h from baseline) when administered to the oro-buccal mucosa with no reports of any adverse events of toxicity. The nanoparticle formulation of methylcobalamin (1000 µg/dose in 0.3 mL volume) showed bioequivalence only with a chewable-dissolvable tablet that administered a five times higher dose of methylcobalamin (5000 µg) per tablet. This study has demonstrated that an active metabolite embedded in a functional biomaterial (NanoCelle) may constitute a drug delivery method that can better access the circulatory system.
Regulation of the depth of surface liquid in bovine trachea.

The luminal surface of airways is lined by a thin film of airway surface liquid (ASL). Physiological regulation of the depth of ASL has not been reported previously. In this paper, we have used low-temperature scanning electron microscopy of rapidly frozen specimens of bovine tracheal epithelium to demonstrate alterations in the depth of ASL in response to the cholinergic agonist methacholine. We first established that methacholine selectively stimulated airway glands, with maximal secretion at ∼2 min and a return to baseline within ∼5 min. A 2-min exposure to methacholine increased the depth of ASL from 23 to 78 μm. Thereafter, depth decreased linearly with time, reaching 32 μm at 30 min. The initial increase in depth was blocked by bumetanide, an inhibitor of active chloride secretion, whereas the slow decline back to baseline was inhibited by amiloride, a blocker of active sodium absorption. We conclude that the methacholine-induced changes in ASL depth reflect transient gland secretion followed by liquid absorption across the surface epithelium.