Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies

Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment.
Advances in therapeutic strategies for Leber’s hereditary optic neuropathy

Introduction: Leber’s hereditary optic neuropathy (LHON) is a rare mitochondrial disease which preferentially affects the optic nerve. A genetic defect in the mitochondrial DNA encoding complex I of the respiratory chain underlies this genetic disorder. Patients typically present with subacute vision loss in one eye followed by the loss of vision in the second eye approximately 6 weeks later, ultimately leading to blindness. Areas covered: In this review, we discuss failed and active therapies as well as the future of clinical trials in LHON. A review of the literature was performed and articles were identified using PubMed. The search terms LHON and treatment were used. These publications were paired to the clinical trials listed on the clinicaltrials.gov website. Expert opinion: Several therapies have been tested to treat LHON; however, so far, no double-blind placebo-controlled clinical trial has been successful in the treatment of LHON. Avoidance of triggers which generate reactive oxygen species and treatment with idebenone is the best currently available therapy for LHON.
Utilizing wavelet deep learning network to classify different states of task-fMRI for verifying activation regions

Abstract Purpose: We propose a convolutional neural network (CNN) based on wavelet for verifying the activation regions decided with statistical analysis. Because the functional magnetic resonance imaging (fMRI) data contains lots of noises, it is difficult to get the data of blood-oxygen-level dependent (BOLD) signal directly for intervention testing like animal studies. So it is difficult to effectively verify these activation regions. Based on the rapid development of deep learning technology. Materials and methods: We select the task fMRI data of presenting food and nonfood pictures to volunteer subjects from open public data, whose website is https://www.openfmri. org/dataset/ds000157/. Firstly, the brain activation regions are obtained by utilizing the method of statistical analysis. Then the spatial coordinates are acquired from the activation regions by checking the atlas table. The P-value of the activation regions are less 0.05. The activation regions are the most responsive to perceive the differences of BOLD in the brain between the two states, presenting food and nonfood pictures. We select the part task fMRI data of from the activation regions, for preparing the training and validation samples. Then we design a deep leaning network based on wavelet to classify the task fMRI data between food and nonfood. Results and conclusions: The classification accuracy is 80.23%. However, when we select the spatial coordinates of other inactivation regions, the classification accuracy is only 60%. The differences of classification accuracy between the activation regions and the inactivation regions prove that the activation regions selected with statistical analysis method are accurate and effective. The two methods of deep learning and statistical analysis can be cross-validated for the study of human being brain.
Probing thermostability of detergent-solubilized CB2 receptor by parallel G protein–activation and ligand-binding assays

G protein–coupled receptors (GPCRs) comprise a large class of integral membrane proteins involved in the regulation of a broad spectrum of physiological processes and are a major target for pharmaceutical drug development. Structural studies can help advance the rational design of novel specific pharmaceuticals that target GPCRs, but such studies require expression of significant quantities of these proteins in pure, homogenous, and sufficiently stable form. An essential precursor for these structural studies is an assessment of protein stability under experimental conditions. Here we report that solubilization of a GPCR, type II cannabinoid receptor CB2, in a Façade detergent enables radioligand thermostability assessments of this receptor with low background from nonspecific interactions with lipophilic cannabinoid ligand. Furthermore, this detergent is compatible with a [35S]GTPγS radionucleotide exchange assay measuring guanine exchange factor activity that can be applied after heat treatment to further assess receptor thermostability. We demonstrate that both assays can be utilized to determine differences in CB2 thermostability caused by mutations, detergent composition, and the presence of stabilizing ligands. We report that a constitutively active CB2 variant has higher thermostability than the WT receptor, a result that differs from a previous thermostability assessment of the analogous CB1 mutation. We conclude that both ligand-binding and activity-based assays under optimized detergent conditions can support selection of thermostable variants of experimentally demanding GPCRs.
Impact of a new inhaler management policy on the hospitalised patient

An audit using an adherence monitor device (adherence = time and technique) of hospitalised patients identified that 16% of patients overused on their inhalers, 21% of doses were not administered and 40% of doses were taken incorrectly. Hence a need to change practice to improve patient safety as well as patient and staff awareness regarding inhaler administration and technique was identified. A practice change with the introduction of a new Inhaler Management Policy was developed. This included inhaler education for all staff involved in inhaler administration, supervision of inhaler technique and administration for all patients, a change in the storage of inhalers and updated nursing documentation. A prospective, observational study was performed following the implementation of this policy. Four key components of the policy were monitored; inhaler storage, patient knowledge, nursing knowledge, and nursing documentation. An audit tool based on the NHS Metrics Assurance framework was devised to monitor the impact of the new policy. Seventeen wards were included in the study. Monthly audits were performed and results relayed back to the wards with appropriate action plans. Six months after implementation there was a 90-100% improvement in inhaler storage on 15 wards as well as a 90-100% improvement in patients and nurses knowledge regarding inhaler technique on all 17 wards and 7 wards demonstrated a 90-100% improvement in nursing documentation. In conclusion, a change in practice regarding inhaler management with the introduction of a new inhaler management policy for patients whilst in hospital has improved the safety of inhaler administration and knowledge of inhaler technique for both patients and staff.
Methyl Salicylate Increases Attraction and Function of Beneficial Arthropods in Cranberries

Methyl salicylate (MeSA) is an herbivore-induced plant volatile (HIPV) known to attract the natural enemies of herbivores in agro-ecosystems; however, whether this attraction leads to an increase in natural enemy functioning, i.e., predation, remains largely unknown. Here, we monitored for 2 years (2011–2012) the response of herbivores and natural enemies to MeSA lures (PredaLure) by using sticky and pitfall traps in cranberry bogs. In addition, European corn borer, Ostrinia nubilalis, egg masses were used to determine whether natural enemy attraction to MeSA leads to higher predation. In both years, MeSA increased adult hoverfly captures on sticky traps and augmented predation of O. nubilalis eggs. However, MeSA also attracted more phytophagous thrips and, in 2012, more plant bugs (Miridae) to sticky traps. Furthermore, we used surveillance cameras to record the identity of natural enemies attracted to MeSA and measure their predation rate. Video recordings showed that MeSA lures increase visitation by adult lady beetles, adult hoverflies, and predatory mites to sentinel eggs, and predation of these eggs doubled compared to no-lure controls. Our data indicate that MeSA lures increase predator attraction, resulting in increased predation; thus, we provide evidence that attraction to HIPVs can increase natural enemy functioning in an agro-ecosystem.
A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes

Abstract Modifications at the 5′-end of RNAs play a pivotal role in determining their fate. In eukaryotes, the DXO/Rai1 family of enzymes removes numerous 5′-end RNA modifications, thereby regulating RNA turnover. Mouse DXO catalyzes the elimination of incomplete 5′-end caps (including pyrophosphate) and the non-canonical NAD+ cap on mRNAs, and possesses distributive 5′-3′ exoribonuclease activity toward 5′-monophosphate (5′-PO4) RNA. Here, we demonstrate that DXO also catalyzes the hydrolysis of RNAs bearing a 5′-hydroxyl group (5′-OH RNA). The crystal structure of DXO in complex with a 5′-OH RNA substrate mimic at 2.0 Å resolution provides elegant insight into the molecular mechanism of this activity. More importantly, the structure predicts that DXO first removes a dinucleotide from 5′-OH RNA. Our nuclease assays confirm this prediction and demonstrate that this 5′-hydroxyl dinucleotide hydrolase (HDH) activity for DXO is higher than the subsequent 5′-3′ exoribonuclease activity for selected substrates. Fission yeast Rai1 also has HDH activity although it does not have 5′-3′ exonuclease activity, and the Rat1-Rai1 complex can completely degrade 5′-OH RNA. An Arabidopsis DXO1 variant is active toward 5′-OH RNA but prefers 5′-PO4 RNA. Collectively, these studies demonstrate the diverse activities of DXO/Rai1 and expands the collection of RNA substrates that can undergo 5′-3′ mediated decay.
A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies

Abstract Unwanted experimental/biological variation and technical error are frequently encountered in current metabolomics, which requires the employment of normalization methods for removing undesired data fluctuations. To ensure the ‘thorough’ removal of unwanted variations, the collective consideration of multiple criteria (‘intragroup variation’, ‘marker stability’ and ‘classification capability’) was essential. However, due to the limited number of available normalization methods, it is extremely challenging to discover the appropriate one that can meet all these criteria. Herein, a novel approach was proposed to discover the normalization strategies that are consistently well performing (CWP) under all criteria. Based on various benchmarks, all normalization methods popular in current metabolomics were ‘first’ discovered to be non-CWP. ‘Then’, 21 new strategies that combined the ‘sample’-based method with the ‘metabolite’-based one were found to be CWP. ‘Finally’, a variety of currently available methods (such as cubic splines, range scaling, level scaling, EigenMS, cyclic loess and mean) were identified to be CWP when combining with other normalization. In conclusion, this study not only discovered several strategies that performed consistently well under all criteria, but also proposed a novel approach that could ensure the identification of CWP strategies for future biological problems.
Percutaneous Endoscopic Lumbar Discectomy for Lumbar Disc Herniation with Modic Changes via a Transforaminal Approach: A Retrospective Study.

BACKGROUND The surgical selection for patients with lumbar disc herniation (LDH) with Modic changes (MCs) is still contentious. Percutaneous endoscopic lumbar discectomy via a transforaminal approach (TF-PELD) as a representative minimally invasive spine surgery technique for LDH has been standardized. However, its efficacy has not been thoroughly described in the patients with LDH with MCs. OBJECTIVES The goal of this study was to assess the clinical outcomes of TF-PELD in the treatment of LDH and MCs. STUDY DESIGN Retrospective study. SETTING Inpatient surgery center. METHODS From January 2015 to December 2016, 276 patients with LDH showing normal or MCs signals in their bone marrow in our hospital were enrolled in this retrospective study. All patients suffered low back and leg pain because of LDH and underwent the TF-PELD procedure. Clinical outcomes were assessed according to the Visual Analog Scale (VAS) for back pain and leg pain, Oswestry Disability Index (ODI) for functional status assessment, and modified MacNab criteria for patient satisfaction. RESULTS A total of 182 patients showed normal intensity, 44 patients showed Modic type 1 signals, and 50 patients showed Modic type 2 signals before surgery. The postoperative VAS and ODI scores were significantly improved compared with those preoperatively among the groups. In the Modic type 1 and 2 signals groups, however, the postoperative VAS scores for back pain and ODI scores showed an upward trend with the follow-up time extending. The recurrence rates were 4.4%, 9.1%, and 8.0% in the normal, Modic type 1 and 2 signals groups, respectively. The recurrence rates and satisfaction rates showed no significant difference among the groups at the final follow-up. LIMITATIONS This study has a small sample size and the follow-up period was too short. There is no comparison with other therapeutic options such as fusion surgery or the lack of any other treatment. CONCLUSIONS TF-PELD is an option for treatment of patients with LDH even if the patients show MCs. However, the postoperative back pain and functional status have the trend of deterioration with the time extending in patients with MCs, especially in the Modic type 1 signals. KEY WORDS Modic changes, Modic type 1, Modic type 2, transforaminal percutaneous endoscopic lumbar discectomy, lumbar disc herniation, back pain, recurrence, complication.
Evolution of high tooth replacement rates in theropod dinosaurs

Tooth replacement rate is an important contributor to feeding ecology for polyphyodont animals. Dinosaurs exhibit a wide range of tooth replacement rates, mirroring their diverse craniofacial specializations, but little is known about broad-scale allometric or evolutionary patterns within the group. In the current broad but sparse dinosaurian sample, only three non-avian theropod tooth replacement rates have been estimated. We estimated tooth formation and replacement rates in three additional non-avian theropod dinosaurs, the derived latest Cretaceous abelisaurid Majungasaurus and the more generalized Late Jurassic Allosaurus and Ceratosaurus. We created the largest dental histological and CT dataset for any theropod dinosaur, sectioning and scanning over a dozen toothed elements of Majungasaurus and several additional elements from the other two genera. Using this large sample, we created models of tooth formation time that allow for theropod replacement rates to be estimated non-destructively. In contrast to previous results for theropods, we found high tooth replacement rates in all three genera, with Allosaurus and Ceratosaurus rates of ~100 days and 56 days for Majungasaurus. The latter rate is on par with those of derived herbivorous dinosaurs including some neosauropods, hadrosaurids, and ceratopsians. This elevated rate may be a response to high rates of tooth wear in Majungasaurus. Within Dinosauria, there is no relationship between body mass and tooth replacement rate and no trends in replacement rate over time. Rather, tooth replacement rate is clade-specific, with elevated rates in abelisaurids and diplodocoids and lower rates in coelurosaurs.
Genome size and endopolyploidy evolution across the moss phylogeny.

BACKGROUND AND AIMS Compared to other plant lineages, bryophytes have very small genomes with little variation across species, and high levels of endopolyploid nuclei. This study is the first analysis of moss genome evolution over a broad taxonomic sampling using phylogenetic comparative methods. We aim to determine whether genome size evolution is unidirectional as well as examine whether genome size and endopolyploidy are correlated in mosses. METHODS Genome size and endoreduplication index (EI) estimates were newly generated using flow cytometry from moss samples collected in Canada. Phylogenetic relationships between moss species were reconstructed using GenBank sequence data and maximum likelihood methods. Additional 1C-values were compiled from the literature and genome size and EI were mapped onto the phylogeny to reconstruct ancestral character states, test for phylogenetic signal, and perform phylogenetic independent contrasts. KEY RESULTS Genome size and EI were obtained for over 50 moss taxa. New genome size estimates are reported for 33 moss species and new EIs are reported for 20 species. In combination with data from the literature, genome sizes were mapped onto a phylogeny for 173 moss species with this analysis indicating that genome size evolution in mosses does not appear to be unidirectional. Significant phylogenetic signal was detected for genome size when evaluated across the phylogeny, whereas phylogenetic signal was not detected for EI. Genome size and EI were not found to be significantly correlated when using phylogenetically corrected values. CONCLUSIONS Significant phylogenetic signal indicates closely related mosses have more similar genome sizes and EI values. This study supports that DNA content in mosses is defined by small genomes that are highly endopolyploid, suggesting strong selective pressure to maintain these features. Further research is needed to understand the functional significance of DNA content evolution in mosses.
The emergence of subgenotype ON‐1 of Human orthopneumovirus type A in Riyadh, Saudi Arabia: A new episode of the virus epidemiological dynamic

Lower respiratory tract infections caused by Human orthopneumovirus are still a threat to the pediatric population worldwide. To date, the molecular epidemiology of the virus in Saudi Arabia has not been adequately charted. In this study, a total of 205 nasopharyngeal aspirate samples were collected from hospitalized children with lower respiratory tract symptoms during the winter seasons of 2014/15 and 2015/16. Human orthopneumovirus was detected in 89 (43.4%) samples, of which 56 (27.3%) were positive for type A and 33 (16.1%) were positive for type B viruses. The fragment that spans the two hypervariable regions (HVR1 and HVR2) of the G gene of Human orthopneumovirus A was amplified and sequenced. Sequence and phylogenetic analyses have revealed a genotype shift from NA1 to ON‐1, which was prevalent during the winter seasons of 2007/08 and 2008/09. Based on the intergenotypic p‐distance values, ON‐1 was reclassified as a subgenotype of the most predominant genotype GA2. Three conserved N‐glycosylation sites were observed in the HVR2 of Saudi ON‐1 strains. The presence of a 23 amino acid duplicated region in ON‐1 strains resulted in a higher number of O‐glycosylation sites as compared to other genotypes. The data presented in this report outlined the replacement of NA1 and NA2 subgenotypes in Saudi Arabia with ON‐1 within 7 to 8 years. The continuous evolution of Human orthopneumovirus through point mutations and nucleotide duplication may explain its ability to cause recurrent infections.
Aneurysm inside meningioma: an unusual association

Abstract The association of a meningioma and intratumoral aneurysm is extremely rare. The coexistence of both lesions may cause difficulties in diagnosis and treatment. We present the case of a 65 y.o. woman with a left temporal meningioma and an intralesional ruptured aneurysm of a terminal branch of the middle cerebral artery whose parental vessel fed the tumor. The tumor and the embedded aneurysm were removed safely with improvement of her symptoms.
Synthesis of Amino Acid–Naphthoquinones and In Vitro Studies on Cervical and Breast Cell Lines

We performed an extensive analysis about the reaction conditions of the 1,4-Michael addition of amino acids to 1,4-naphthoquinone and substitution to 2,3-dichloronaphthoquinone, and a complete evaluation of stoichiometry, use of different bases, and the pH influence was performed. We were able to show that microwave-assisted synthesis is the best method for the synthesis of naphthoquinone–amino acid and chloride–naphthoquinone–amino acid derivatives with 79–91% and 78–91% yields, respectively. The cyclic voltammetry profiles showed that both series of naphthoquinone–amino acid derivatives mainly display one quasi-reversible redox reaction process. Interestingly, it was shown that naphthoquinone derivatives possess a selective antitumorigenic activity against cervix cancer cell lines and chloride–naphthoquinone–amino acid derivatives against breast cancer cell lines. Furthermore, the newly synthetized compounds with asparagine–naphthoquinones (3e and 4e) inhibited ~85% of SiHa cell proliferation. These results show promising compounds for specific cervical and breast cancer treatment.