Miracle-dz/UniFAR-FTUs huggingface dataset:
OCTN2-targeted nanoparticles for oral delivery of paclitaxel: differential impact of the polyethylene glycol linker size on drug delivery in vitro, in situ, and in vivo

Abstract Targeted nanocarriers have shown great promise in drug delivery because of optimized drug behavior and improved therapeutic efficacy. How to improve the targeting efficiency of nanocarriers for the maximum possible drug delivery is a critical issue. Here we developed L-carnitine-conjugated nanoparticles targeting the carnitine transporter OCTN2 on enterocytes for improved oral absorption. As a variable, we introduced various lengths of the polyethylene glycol linker (0, 500, 1000, and 2000) between the nanoparticle surface and the ligand (CNP, C5NP, C10NP and C20NP) to improve the ligand flexibility, and consequently for more efficient interaction with the transporter, to enhance the oral delivery of the cargo load into cells. An increased absorption was observed in cellular uptake in vitro and in intestinal perfusion assay in situ when the polyethylene glycol was introduced to link L-carnitine to the nanoparticles; the highest absorption was achieved with C10NP. In contrast, the linker decreased the absorption efficiency in vivo. As the presence or absence of the mucus layer was the primary difference between in vitro/in situ versus in vivo, the presence of this layer was the likely reason for this differential effect. In summary, the size of the polyethylene glycol linker improved the absorption in vitro and in situ, but interfered with the absorption in vivo. Even though this strategy of increasing the ligand flexibility with the variable size of the polyethylene glycol failed to increase oral absorption in vivo, this approach is likely to be useful for enhanced cellular uptake following intravenous administration of the nanocarriers.
Generating Stable Knockout Zebrafish Lines by Deleting Large Chromosomal Fragments Using Multiple gRNAs

The CRISPR (clustered regularly interspaced short palindromic repeats) and Cas9 (CRISPR associated protein 9) system has been successfully adopted as a versatile genetic tool for functional manipulations, due to its convenience and effectiveness. Genetics lesions induced by single guide RNA (gRNA) are usually small indel (insertion-deletion) DNA mutations. The impact of this type of CRISPR-induced DNA mutation on the coded mRNA transcription processing and protein translation can be complex. Unexpected or unknown transcripts, generated through alternative splicing, may impede the generation of successful loss-of-function mutants. To create null or null-like loss-of-function mutant zebrafish, we employed simultaneous multiple gRNA injection into single-cell stage embryos. We demonstrated that DNA composed of multiple exons, up to 78kb in length, can be deleted in the smarca2 gene locus. Additionally, two different genes (rnf185 and rnf215) were successfully mutated in F1 fish with multiple exon deletions using this multiplex gRNA injection strategy. We expect this approach will be useful for knock-out studies in zebrafish and other vertebrate organisms, especially when the phenotype of a single gRNA-induced mutant is not clear.
Environmental Toxicology and Chemistry

We describe 2 artificial stream experiments that exposed aquatic insect communities to zinc (Zn), copper (Cu), and cadmium (year 2014) and to Zn, Cu, and nickel (year 2015). The testing strategy was to concurrently expose insect communities to single metals and mixtures. Single‐metal tests were repeated to evaluate the reproducibility of the methods and year‐to‐year variability. Metals were strongly accumulated in sediments, periphyton, and insect (caddisfly) tissues, with the highest concentrations occurring in periphyton. Sensitive mayflies declined in metal treatments, and effect concentrations could be predicted effectively from metal concentrations in either periphyton or water. Most responses were similar in the replicated tests, but median effect concentration values for the mayfly Rhithrogena sp. varied 20‐fold between the tests, emphasizing the difficulty comparing sensitivities across studies and the value of repeated testing. Relative to the single‐ metal responses, the toxicity of the mixtures was either approximately additive or less than additive when calculated as the product of individual responses (response addition). However, even less‐than‐additive relative responses were sometimes greater than responses to similar concentrations tested singly. The ternary mixtures resulted in mayfly declines at concentrations that caused no declines in the concurrent single‐metal tests. When updating species‐sensitivity distributions (SSDs) with these results, the mayfly responses were among the most sensitive 10th percentile of available data for all 4 metals, refuting older literature placing mayflies in the insensitive portion of metal SSDs. Testing translocated aquatic insect communities in 30‐d artificial streams is an efficient approach to generate multiple species effect values under quasi‐natural conditions that are relevant to natural streams. Environ Toxicol Chem 2020;39:812–833. Published 2020 Wiley Periodicals, Inc.
Bariatric Surgery Rapidly Decreases Cardiac Dietary Fatty Acid Partitioning and Hepatic Insulin Resistance Through Increased Intra-abdominal Adipose Tissue Storage and Reduced Spillover in Type 2 Diabetes

Reduced storage of dietary fatty acids (DFAs) in abdominal adipose tissues with enhanced cardiac partitioning has been shown in subjects with type 2 diabetes (T2D) and prediabetes. We measured DFA metabolism and organ partitioning using positron emission tomography with oral and intravenous long-chain fatty acid and glucose tracers during a standard liquid meal in 12 obese subjects with T2D before and 8–12 days after bariatric surgery (sleeve gastrectomy or sleeve gastrectomy and biliopancreatic diversion with duodenal switch). Bariatric surgery reduced cardiac DFA uptake from a median (standard uptake value [SUV]) 1.75 (interquartile range 1.39–2.57) before to 1.09 (1.04–1.53) after surgery (P = 0.01) and systemic DFA spillover from 56.7 mmol before to 24.7 mmol over 6 h after meal intake after surgery (P = 0.01), with a significant increase in intra-abdominal adipose tissue DFA uptake from 0.15 (0.04–0.31] before to 0.49 (0.20–0.59) SUV after surgery (P = 0.008). Hepatic insulin resistance was significantly reduced in close association with increased DFA storage in intra-abdominal adipose tissues (r = −0.79, P = 0.05) and reduced DFA spillover (r = 0.76, P = 0.01). We conclude that bariatric surgery in subjects with T2D rapidly reduces cardiac DFA partitioning and hepatic insulin resistance at least in part through increased intra-abdominal DFA storage and reduced spillover.
Rapid Detection of Genes Encoding Extended-Spectrum Beta-Lactamase and Carbapenemase in Clinical Escherichia coli Isolates with eazyplex SuperBug CRE System.

Objectives: This study evaluated the diagnostic performance of the eazyplex® SuperBug CRE (eSBCRE) system, based on a loop-mediated isothermal amplification (LAMP), for the detection of the most common extended-spectrum beta-lactamases (ESBL) and carbapenemase genes in 140 clinical isolates of Escherichia coli. Materials and Methods: ESBL (blaCTX-M-1group and blaCTX-M-9group) and carbapenemase (blaKPC, blaVIM, blaNDM, blaOXA-48, and blaOXA-181) genes were detected using the eSBCRE test and compared with the results obtained by PCR, real-time PCR, and phenotypic methods. Results: Concordant results of 100% between PCR/real-time PCR and eSBCRE assays were observed. Two of 140 E. coli isolates were positive for both ESBL and carbapenemase genes according to eSBCRE, PCR, and real-time PCR assays, whereas they were negative in double-disk synergy test. Of 16 E. coli isolates suspected of producing carbapenemase, 9 were positive for 48-oxacillinases (OXA-48) by 30 μg temocillin test, whereas the blaOXA-48 was found only in 1 E. coli isolate by all molecular methods. Maximum threshold time values (minutes:seconds) in the eSBCRE test were 6:00, 11:15, 11:00, and 9:00 for the blaCTX-M-1group, blaCTX-M-9group, blaVIM, and blaOXA-48 genes, respectively. Conclusions: The eSBCRE test based on LAMP method is a reliable, easy-to-use, and timesaving molecular system, which can be successfully used in the routine diagnostic for the rapid detection of the most common ESBL and carbapenemase genes among clinical E. coli isolates.
Transcriptional memory inherited from donor cells is a developmental defect of bovine cloned embryos

Studies on the effects of transcriptional memory on clone reprogramming in mammals are limited. In the present study, we observed higher levels of active histone H3 lysine 4 trimethylation (H3K4me3 and 5‐hydroxymethylcytosine) and repressive (5‐methylcytosine) epigenetic modifications in bovine early cloned embryos than in in vitro fertilized embryos. We hypothesized that aberrant epigenetic modification may result in transcriptional disorders in bovine somatic cell nuclear transfer (SCNT) embryos. RNA sequencing results confirmed that both abnormal transcriptional silencing and transcriptional activation are involved in bovine SCNT reprogramming. The cloned embryos exhibited excessive transcription in RNA processing‐ and translation‐related genes as well as transcriptional defects in reproduction‐related genes whose transcriptional profiles were similar to those in donor cells. These results demonstrated the existence of active and silent memory genes inherited from donor cells in early bovine SCNT embryos. Further, H3K4me3‐specific demethylase 5B (KDM5B) mRNA was injected into the reconstructed embryos to reduce the increased H3K4me3 modification. KDM5B overexpression not only reduced the transcriptional level of active memory genes, but also promoted the expression of silent memory genes; in particular, it rescued the expression of multiple development‐related genes. These results showed that transcriptional memory acts as a reprogramming barrier and KDM5B improves SCNT reprogramming via bidirectional regulation effects on transcriptional memory genes in bovines.
Candidate genes identified by whole-exome sequencing in preeclampsia families: insights into functional annotation and in-silico prediction of deleterious variants.

REFERENCES 1. Kuwabara M, Chintaluru Y, Kanbay M, Niwa K, Hisatome I, AndresHernando A, et al. Fasting blood glucose is predictive of hypertension in a general Japanese population. J Hypertens 2020; 38:167–174. 2. Shi W, Zhou Y, Sun Y, Wang H. Could fasting blood glucose predict hypertension: findings from a low-resource community. J Hypertens 2020; 38:369–371. 3. Tatsumi Y, Morimoto A, Asayama K, Sonoda N, Miyamatsu N, Ohno Y, et al. Fasting blood glucose predicts incidence of hypertension independent of HbA1c levels and insulin resistance in middle-aged Japanese: the Saku study. Am J Hypertens 2019; doi: 10.1093/ajh/hpz123 [Epub ahead of print]. 4. Kuwabara M, Hisatome I. The relationship between fasting blood glucose and hypertension. Am J Hypertens 2019; doi: 10.1093/ajh/ hpz147. [Epub ahead of print].
Myopathy reversion in mice after restauration of mitochondrial complex I

Myopathies are common manifestations of mitochondrial diseases. To investigate whether gene replacement can be used as an effective strategy to treat or cure mitochondrial myopathies, we have generated a complex I conditional knockout mouse model lacking NDUFS3 subunit in skeletal muscle. NDUFS3 protein levels were undetectable in muscle of 15‐day‐old smKO mice, and myopathy symptoms could be detected by 2 months of age, worsening over time. rAAV9‐Ndufs3 delivered systemically into 15‐ to 18‐day‐old mice effectively restored NDUFS3 levels in skeletal muscle, precluding the development of the myopathy. To test the ability of rAAV9‐mediated gene replacement to revert muscle function after disease onset, we also treated post‐symptomatic, 2‐month‐old mice. The injected mice showed a remarkable improvement of the mitochondrial myopathy and biochemical parameters, which remained for the duration of the study. Our results showed that muscle pathology could be reversed after restoring complex I, which was absent for more than 2 months. These findings have far‐reaching implications for the ability of muscle to tolerate a mitochondrial defect and for the treatment of mitochondrial myopathies.
JIB.tools 2.0 – A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

Abstract JIB.tools 2.0 is a new approach to more closely embed the curation process in the publication process. This website hosts the tools, software applications, databases and workflow systems published in the Journal of Integrative Bioinformatics (JIB). As soon as a new tool-related publication is published in JIB, the tool is posted to JIB.tools and can afterwards be easily transferred to bio.tools, a large information repository of software tools, databases and services for bioinformatics and the life sciences. In this way, an easily-accessible list of tools is provided which were published in JIB a well as status information regarding the underlying service. With newer registries like bio.tools providing these information on a bigger scale, JIB.tools 2.0 closes the gap between journal publications and registry publication. (Reference: https://jib.tools).
Epidemiology of podoconiosis in Ethiopia: a systematic review and meta-analysis protocol

Introduction Podoconiosis is a non-filarial swelling of the lower extremity endemic in tropical regions, North America and India. The aetiology and pathophysiology of the disease remain unknown. We propose conducting a systematic review and meta-analysis to evaluate the burden and risk factors of podoconiosis in Ethiopia reported in studies from 2009 to 2019. Methods and analysis We will search the following electronic databases: PubMed (MEDLINE), EMBASE, Hinari, Cumulative Index to Nursing and Allied Health Literature, ISI (Web of Science) and Google Scholar. Medical subject headings will be used to extensively search relevant literature on electronic databases using related keywords such as epidemiology or prevalence, magnitude or burden, podoconiosis, and Ethiopia. Grey literature and manual search will also be performed to retrieve unindexed research articles. Two reviewers will screen all retrieved articles, conduct data extraction and then critically appraise all identified studies. We will analyse data using STATA V.14 statistical software. We will demonstrate pooled estimates of podoconiosis and associated factors with effect size and 95% CI. The presence of heterogeneity among studies will be examined by forest plot as well as the I2 heterogeneity test. Potential causes of heterogeneity will be explored by carrying out sensitivity and subgroup analyses. The presence of publication bias will also be examined by observing funnel plots and objectively by Egger’s regression test. If the funnel plot is asymmetric and/or Egger’s test was found to be statistically significant (p<0.05), the trim and fill (Duval and Tweedie’s) analysis will be performed. Ethics and dissemination The study will use publicly available data and will not identify the authors of the publication by name. In light of these and as has been indicated, research ethics clearance is not required for evidence syntheses in such reviews. The results of this study will be published in a peer-reviewed journal and presented at national and international conferences. PROSPERO registration number CRD42019127459.
Extending the sequences of HLA class I alleles without full‐length genomic coverage using single molecule real‐time DNA sequencing

The assignment of an HLA allele name to a sequence requires a comparison between the generated target sequence and a reference sequence on the IPD‐IMGT/HLA database. Absence of a full‐length reference sequence can result in the inability of HLA typing software to accurately compare and assign the sequence. We sequenced the most frequently seen HLA class I alleles on the Anthony Nolan register present in the database with only a partial genomic sequence, with the aim of increasing the number of complete reference sequences. We successfully extended 95 full‐length HLA class I sequences and identified 13 novel variants. Increasing the number of full‐length HLA class I reference sequences in the database has aided accuracy of HLA analysis tools for all histocompatibility and immunogenetics laboratories.
Revisiting the Blood Supply of the Rectus Femoris

Background Rectus femoris necrosis is a rare but severe complication after anterolateral thigh flap (ALTF) harvesting. It has been previously reported that the blood supply of the rectus femoris (RF) often arises from the same source artery as the ALTF; however, precise descriptions of the relationship remain limited. This article revisits the blood supply of the RF based on computed tomography angiography (CTA) and analyzes the possible influence of the blood supply on the RF during ALTF harvesting. Methods Between December 2017 and June 2018, CTA images of the bilateral lower extremities of 25 patients were studied. The RF length, number, and diameter of branches at the entry point into muscle, location, and overall branch vessel origins were recorded. Results The average ± SD RF length was 384.73 ± 19.28 mm. There were 170 branches (mean ± SD, 3.4 ± 0.96 branches per thigh), mainly arising from the lateral circumflex femoral artery. The average ± SD diameter was 1.90 ± 0.51 mm. The first branch was located at 1/5 of the proximal site of the RF, and 91% of all branches were located above the midpoint. The RF vascularity can be classified into 2 types: type 1 (36% of sides) has branches that arise from a single artery (descending lateral circumflex femoral artery or femoral artery), whereas type 2 (64% of sides) has branches at the 1/5 proximal and 4/5 distal parts, which arise from different arteries. Conclusions Preoperative CTA can provide anatomic information about the RF's nutrient vessel(s) and helps to optimize ALTF design.
Optimization of extraction of total trans-resveratrol from peanut seeds and its determination by HPLC.

Resveratrol, a stilbene phytoalexin in plants, is believed to benefit human health. In this study, an optimized enzyme-assisted method was developed to extract the total content of trans-resveratrol (free or combined with glucose) in peanut seeds, followed by detection using high-performance liquid chromatography. The extraction process was optimized by Box-Behnken design and response surface methodology. The optimized enzyme concentration, digestion time, pH, and temperature were 3.02 g/L, 57.06 min, 5.88, and 51.05°C, respectively. Validation tests indicated that the experimental yield of trans-resveratrol was 0.183 ± 0.007 µg/g with a relative standard deviation of 3.87% (n = 5) under the optimal condition, which was closely agreed with the predicted value (0.182 µg/g). The recoveries obtained from the spiked samples were varied from 89.4 to 103.9%. Therefore, this study will provide a useful method for quantification of total trans-resveratrol in peanut seeds.
Osteoclasts Derive Predominantly from Bone Marrow–Resident CX3CR1+ Precursor Cells in Homeostasis, whereas Circulating CX3CR1+ Cells Contribute to Osteoclast Development during Fracture Repair

Key Points OCP express CX3CR1 and, in unperturbed conditions, differentiate into osteoclasts. The contribution of circulating CX3CR1+ OCP to OC development is low during homeostasis. Mature OC can originate from circulating CX3CR1+ cells during fracture repair. Osteoclasts (OC) originate from either bone marrow (BM)–resident or circulating myeloid OC progenitors (OCP) expressing the receptor CX3CR1. Multiple lines of evidence argue that OCP in homeostasis and inflammation differ. We investigated the relative contributions of BM-resident and circulating OCP to osteoclastogenesis during homeostasis and fracture repair. Using CX3CR1-EGFP/TRAP tdTomato mice, we found CX3CR1 expression in mononuclear cells, but not in multinucleated TRAP+ OC. However, CX3CR1-expressing cells generated TRAP+ OC on bone within 5 d in CX3CR1CreERT2/Ai14 tdTomato reporter mice. To define the role that circulating cells play in osteoclastogenesis during homeostasis, we parabiosed TRAP tdTomato mice (CD45.2) on a C57BL/6 background with wild-type (WT) mice (CD45.1). Flow cytometry (CD45.1/45.2) demonstrated abundant blood cell mixing between parabionts after 2 wk. At 4 wk, there were numerous tdTomato+ OC in the femurs of TRAP tdTomato mice but almost none in WT mice. Similarly, cultured BM stimulated to form OC demonstrated multiple fluorescent OC in cell cultures from TRAP tdTomato mice, but not from WT mice. Finally, flow cytometry confirmed low-level engraftment of BM cells between parabionts but significant engraftment in the spleens. In contrast, during fracture repair, we found that circulating CX3CR1+ cells migrated to bone, lost expression of CX3CR1, and became OC. These data demonstrate that OCP, but not mature OC, express CX3CR1 during both homeostasis and fracture repair. We conclude that, in homeostasis mature OC derive predominantly from BM-resident OCP, whereas during fracture repair, circulating CX3CR1+ cells can become OC.
ROCK2 inhibition enhances the thermogenic program in white and brown fat tissue in mice

The RhoA/ROCK‐mediated actin cytoskeleton dynamics have been implicated in adipogenesis. The two ROCK isoforms, ROCK1 and ROCK2, are highly homologous. The contribution of ROCK2 to adipogenesis in vivo has not been elucidated. The present study aimed at the in vivo and in vitro roles of ROCK2 in the regulation of adipogenesis and the development of obesity. We performed molecular, histological, and metabolic analyses in ROCK2+/− and ROCK2+/KD mouse models, the latter harboring an allele with a kinase‐dead (KD) mutation. Both ROCK2+/− and ROCK2+/KD mouse models showed a lean body mass phenotype during aging, associated with increased amounts of beige cells in subcutaneous white adipose tissue (sWAT) and increased thermogenic gene expression in all fat depots. ROCK2+/− mice on a high‐fat diet showed increased energy expenditure accompanying by reduced obesity, and improved insulin sensitivity. In vitro differentiated ROCK2+/− stromal‐vascular (SV) cells revealed increased beige adipogenesis associated with increased thermogenic gene expressions. Treatment with a selective ROCK2 inhibitor, KD025, to inhibit ROCK2 activity in differentiated SV cells reproduced the pro‐beige phenotype of ROCK2+/− SV cells. In conclusion, ROCK2 activity‐mediated actin cytoskeleton dynamics contribute to the inhibition of beige adipogenesis in WAT, and also promotes age‐related and diet‐induced fat mass gain and insulin resistance.