Miracle-dz/UniFAR-FTUs huggingface dataset:
Error‐free recombination in sugarcane mediated by only 30 nucleotides of homology and CRISPR/Cas9 induced DNA breaks or Cre‐recombinase

Precision genome editing by homology directed repair has tremendous potential for crop improvement. This study describes in planta homologous recombination mediated by CRISPR/Cas9 induced DNA double strand break in proximity to a single short (∼30 nt) homology arm. The efficiency of CRISPR/Cas9‐mediated recombination between two loxP sites was compared with Cre (Cyclization recombination enzyme) and codon‐optimized Cre‐mediated site‐specific recombination in sugarcane. A transgenic locus was generated with a selectable nptII coding sequence with terminator between two loxP sites located downstream of a constitutive promoter and acting as transcription block for the downstream promoter‐less gusA coding sequence with terminator. Recombination between the two loxP sites resulted in deletion of the transcription block and restored gus activity. This transgenic locus provided an efficient screen for identification of recombination events in sugarcane callus following biolistic delivery of Cre, codon‐optimized Cre, or the combination of sgRNA and Cas9 targeting the 5′ loxP site. The Cre codon optimized for sugarcane displayed the highest efficiency in mediating the recombination that restored gus activity followed by cre and CRISPR/Cas9. Remarkably the short region of homology of the loxP site cleaved by Cas9 (30 nt)‐mediated error‐free recombination in all 21 events from three different experiments that were analyzed by Sanger sequencing consistent with homology directed repair. These findings will inform rational design of strategies for precision genome editing in plants.
Comparison of Different Natural Sorbents for Removing CO2 from Combustion Gases, as Studied in a Bench-Scale Fluidized Bed

The reaction of CO2 with porous particles of CaO in CaO(cr)+CO2(g) → CaCO3(cr) was studied, along with its reverse reaction, for chicken eggshells, mussel shells, and limestone. Reaction I is a promising way of removing CO2, e.g., from the exhaust of a power station, so that a pure stream of CO2 can subsequently be produced for sequestration by calcining (roasting) the solid CaCO3 from reaction I. The reverse of reaction I regenerates the sorbent, which can thus be used cyclically. The forward and reverse steps of reaction I were investigated using a small electrically heated bed of sand at ∼750 °C, fluidized by N2. Typically, a sample (∼2 g) of cleaned calcareous material (sieved to ∼600 μm) was added to the hot bed, and the CO2 produced was measured, while the material was fully calcined. Next, enough CO2 was added to the fluidizing N2 to raise [CO2] to above the value for equilibrium; thus, the CaO was carbonated. This forward step of reaction I is shown to exhibit an apparent final conversion, the car.
Fracture mapping of complex intra-articular calcaneal fractures

Background Intra-articular calcaneal fracture remains challenging to manage. Computed tomography and fracture mapping are useful for the diagnosis and treatment of calcaneal fractures. The aim of the present study was to characterize calcaneal fracture patterns using fracture mapping. Methods Sixty-two calcaneal fractures were retrospectively included in the study. For each case, the fracture was simulated reduction manually. The fracture lines and zones of comminution were graphically superimposed onto an intact calcaneal template to identify fracture patterns. Major fracture lines and comminution were assessed by focusing on the posterior joint facet, medial wall, lateral wall, sustentaculum tali, and anterior process. Results The fracture lines were mostly concentrated on the area anterior to the posterior joint facet and extended medially. The longitudinal lines ran posteriorly from the angle of Gissane, and separated the sustentaculum tali and medial wall from the calcaneal tuberosity. In the lateral wall, the fracture lines extended posteriorly with some branches to the bottom of the calcaneus. No fracture lines passed through the sustentaculum tali. Fracture lines of the posterior tuberosity and anterior process were rare. Conclusions Calcaneal fracture lines follow characteristic patterns, which are closely related to the bone structure and fracture mechanism. These fracture patterns will aid clinicians choose surgical approach and fixations in the treatment of calcaneal fractures.
Manganese-Based Catalysts for the Catalytic Remediation of Phenolic Acids by Ozone

Manganese-based catalysts supported on Al2O3, TiO2, ZrO2 and CeO2 were tested for the catalytic ozonation of a simulated wastewater involving phenolic acids. Comparing the Mn-Ce catalysts preparation method, wetness impregnation and co-precipitation, the last one showed to be more active. Moreover, the increase of Mn/Ce molar proportion from 22/78 to 70/30 increased the ozonation efficiency. The catalysts stability in terms of Mn leaching, carbon adsorption and effluent biodegradability was evaluated. Mn-Ce-O (70/30) CP shows to be the most suitable catalyst to improve phenolic wastewaters catalytic remediation by ozone.
Comparing long-term outcomes between endoscopic submucosal dissection (ESD) and endoscopic mucosal resection (EMR) for type II esophagogastric junction neoplasm

Background Endoscopic submucosal dissection (ESD) and endoscopic mucosal resection (EMR) are used to remove esophagogastric junction (EGJ) neoplasm. This study aimed to compare feasibility, safety, and effectiveness between ESD and EMR to help endoscopists choose treatment methods. Methods A total of 130 patients with EGJ neoplasm underwent endoscopic resection, including 52 patients with EMR and 78 patients with ESD. Cap-assisted EMR (EMRC) was performed with typical sequences. Larger lesions required removal in multiple pieces (i.e., piecemeal EMR). The ESD procedures were included that marking the periphery of the lesion, submucosa injected, circumferentially cutting and submucosal dissection. Resection time, adverse events, en bloc resection rate, R0 resection rate and recurrence rate were compared between the two groups. Results There were no significant differences in demographic characteristics or histopathological features between the two groups. Resection time was longer in the ESD group than in the EMR group (64.4±33.9 vs. 22.1±8.0 minutes; P<0.01). Adverse events were more common in the ESD group than in the EMR group (16.7% vs. 3.8%; P=0.03), including bleeding (7.7% vs. 3.8%), perforation (5.1% vs. 0%) and stenosis (5.1% vs. 0%). The en bloc resection rate and R0 resection rate were much higher in the ESD group than in the EMR group (98.7% and 92.3% vs. 23.1% and 23.1%, respectively; P<0.01). The 5-year overall survival rate and disease-free survival rate were 100% vs. 92.0% and 100% vs. 90.1% between the ESD and EMR groups, respectively (P=0.01 and P=0.01). The 5-year cancer-specific survival rate was 100% vs. 96.0% between the ESD and EMR groups (P=0.08). The recurrence rate was lower in the ESD group than in the EMR group (0% vs. 9.6%; P=0.01). Conclusions ESD is an acceptable first-line endoscopic treatment for type II EGJ neoplasm, however, it is time-consuming and has a higher rate of adverse events. Furthermore, EMR is a safe and alternative technique, particularly when EMR could achieve en bloc resection.
9.0% efficient Cu2ZnSn(S,Se)4 solar cells from selenized nanoparticle inks

Thin‐film solar cells using Cu2ZnSn(S,Se)4 absorber materials continue to attract increasing attention. The synthesis of kesterite Cu2ZnSnS4 nanoparticles by a modified method of hot injection is explained. Characterization of the nanoparticles by energy dispersive X‐ray spectroscopy, X‐ray diffraction, Raman, and transmission electron microscopy is presented and discussed. When suspended in an ink, coated, and processed into a device, the nanoparticles obtained by this synthesis achieve a total area (active area) efficiency of 9.0% (9.8%) using AM 1.5 illumination and light soaking. This improvement over the previous efficiency of 7.2% is attributed to the modified synthesis approach, as well as fine‐tuned conditions for selenizing the coated nanoparticles into a dense absorber layer. Copyright © 2014 John Wiley & Sons, Ltd.
Highly successful production of viable mice derived from vitrified germinal vesicle oocytes

The vitrification of immature germinal vesicle (GV) oocytes is an important way to preserve genetic resources and female fertility. However, it is well known that cryopreserved GV oocytes have very poor developmental ability and that further improvement in this technique is needed. We previously reported the successful vitrification of matured mouse oocytes with enclosed cumulus cells using the calcium-free vitrification solution supplemented with ethylene glycol (EG) by the minimal volume cooling (MVC) method. In this study, we investigated whether our method is applicable to the vitrification of mouse oocytes at the GV stage (GV oocytes). Following maturation and fertilization in vitro, vitrified GV oocytes showed high survival (94.3 ± 2.0%) and maturation (94.3 ± 2.1%) rates. Although the fertilization and blastocyst rates of vitrified oocytes (fertilization: 46.6 ± 4.9% and blastocyst: 46.6 ± 3.0%) were significantly lower than those of fresh oocytes (fertilization: 73.0 ± 7.1% and blastocyst: 71.6 ± 8.0%) (P < 0.01), there were no differences in the ability to develop to term between fresh oocytes (50.0 ± 8.4%) and vitrified oocytes (37.5 ± 4.6%) (P > 0.05). In conclusion, we here show, for the first time, the efficient production of live mice derived from vitrified GV oocytes.
Heart rate fluctuation predicts mortality in critically ill patients in the intensive care unit: a retrospective cohort study

Background To evaluate the association between heart rate (HR) fluctuation and mortality in critically ill patients in the intensive care unit (ICU). Methods A total of 27,814 patients were enrolled from the Medical Information Mart for Intensive Care database and were divided into 3 groups: low HR fluctuation [<25 beats per minute (bpm)], control (25–34 bpm), and high HR fluctuation (≥35 bpm), based on the initial 24-hour HR fluctuation (calculated as the maximum HR minus minimum HR). Multivariate Cox regression and restricted cubic spline models were used. Results Compared to the control group, higher risk of 28-day and 1-year mortality remained significant in an adjusted model, with hazard ratios of 1.210 [95% confidence interval (CI), 1.103–1.327] and 1.150 (95% CI, 1.078–1.227), respectively, in the high HR fluctuation group, as well as hazard ratios of 1.130 (95% CI, 1.035–1.232) and 1.087 (95% CI, 1.022–1.157), respectively, in the low HR fluctuation group. Restricted cubic splines showed a U-type curve, with the lowest risk of mortality at an HR fluctuation of 30 bpm. Conclusions This retrospective cohort study revealed that both high and low HR fluctuation correlated with increased mortality in critically ill ICU patients, providing new insights for optimizing HR control strategies.
Effects of menopausal hormone therapy on erythrocyte n-3 and n-6 PUFA concentrations in the Women's Health Initiative randomized trial.

BACKGROUND The factors other than dietary intake that determine tissue concentrations of EPA and DHA remain obscure. Prior studies suggested that, in women, endogenous estrogen may accelerate synthesis of DHA from ɑ-linolenic acid (ALA), but the effects of exogenous estrogen on RBC n-3 (ɷ-3) PUFA concentrations are unknown. OBJECTIVE We tested the hypothesis that menopausal hormone therapy (HT) would increase RBC n-3 PUFA concentrations. METHODS Postmenopausal women (ages 50-79 y) were assigned to HT or placebo in the Women's Health Initiative (WHI) randomized trial. The present analyses included a subset of 1170 women (ages 65-79 y) who had RBC PUFA concentrations measured at baseline and at 1 y as participants in the WHI Memory Study. HT included conjugated equine estrogens (E) alone for women without a uterus (n = 560) and E plus medroxyprogesterone acetate (P) for those with an intact uterus (n = 610). RBC n-3 and n-6 (ɷ-6) PUFAs were quantified. RESULTS Effects of E alone and E+P on PUFA profiles were similar and were thus combined in the analyses. Relative to the changes in the placebo group after 1 y of HT, docosapentaenoic acid (DPA; n-3) concentrations decreased by 10% (95% CI: 7.3%, 12.5%), whereas DHA increased by 11% (95% CI: 7.4%, 13.9%) in the HT group. Like DHA, DPA n-6 increased by 13% from baseline (95% CI: 10.0%, 20.3%), whereas linoleic acid decreased by 2.0% (95% CI: 1.0%, 4.1%; P values at least <0.01 for all). EPA and arachidonic acid concentrations were unchanged. CONCLUSIONS HT increased RBC concentrations of the terminal n-3 and n-6 PUFAs (DHA and DPA n-6). These findings are consistent with an estrogen-induced increase in DHA and DPA n-6 synthesis, which is consistent with an upregulation of fatty acid elongases and/or desaturases in the PUFA synthetic pathway. The clinical implications of these changes require further study. The Women's Health Initiative Memory Study is registered at clinicaltrials.gov as NCT00685009. Note that the data presented here were not planned as part of the original trial, and therefore are to be considered exploratory.
Profiles of differentially expressed long noncoding RNAs and messenger RNAs in the myocardium of septic mice

Background Sepsis is the primary cause of mortality in the intensive care unit (ICU), mainly due to sepsis-induced dysfunction of essential organs such as the heart and lungs. This study investigated the myocardium’s epigenetic characterization from septic mice to identify potential treatment targets for septic myocardial dysfunction. Methods Cecal ligation and puncture (CLP) was used to induce sepsis in male C57BL/6 mice. Hearts were collected 24 h after surgery to determine the expression profiles of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray. To validate the reliability of microarray results, we randomly chose six differentially expressed lncRNAs for qRT-PCR. Functional mapping of differentially expressed mRNAs was annotated with gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses; lncRNA-mRNA co-expression network was constructed to reveal connections between lncRNAs and mRNAs. Results Microarray analysis indicated that 1,568 lncRNAs and 2,166 mRNAs were differentially expressed in the myocardium from septic mice, which was further confirmed by qRT-PCR. KEGG pathway analysis showed that numerous differentially expressed mRNAs were relevant to tumor necrosis factor (TNF) and phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathways. Moreover, according to the lncRNA-mRNA co-expression network constructed by the above six lncRNAs and their interacting mRNAs, the co-expression network profiles had 57 network nodes and 134 connections, including 76 positive interactions and 58 negative interactions. Conclusions In mouse hearts, sepsis resulted in differential expression of lncRNAs and mRNAs related to TNF and PI3K-Akt signaling pathways, suggesting that lncRNAs and their interacting mRNAs may participate in the pathogenesis of septic myocardial dysfunction by regulating TNF and PI3K-Akt signaling pathways.
Y-chromosome loss is frequent in male renal tumors

Background Loss of the Y-chromosome is a common event in different tumor types but its prevalence and clinical relevance in renal cell tumors is still not understood. Methods It was the aim of this study to estimate the frequency and clinical relevance of Y-loss in kidney neoplasms. A cohort of 1,252 male renal tumors was analyzed in a tissue microarray format by fluorescence in-situ hybridization (FISH). Results Y-loss was found in 47% of tumors. The frequency of this alteration varied markedly between kidney tumor subtypes. Y-loss was most prevalent in papillary renal cell carcinoma (RCC) (77%) followed by chromophobe RCC (60%), oncocytoma (51%), clear cell RCC (39%) and clear cell (tubulo)papillary RCC (19%). Y-loss was linked to higher patient age and smaller tumor size at diagnosis. Mean age (95% CI) was 65 (64–66) years in patients with Y-loss in their tumor compared to 60 (58–61) years in patients without Y-loss (P<0.0001). Significant correlations between Y-loss and tumor phenotype were found only for papillary carcinomas (P=0.002), especially for type 1 (P=0.03). Conclusions Y-loss is present in different histologic subtypes of renal neoplasm. The highest frequency is in papillary RCC, where it may represent a potentially relevant prognostic biomarker suggesting favorable disease outcome.
Incident cerebral microbleeds and hypertension defined by the 2017 ACC/AHA Guidelines

Background The cut-off for hypertension was lowered to blood pressure (BP) over 130/80 mmHg in the 2017 American College of Cardiology/American Heart Association (ACC/AHA) guideline. Whether the new definition of hypertension remains a potent risk factor of cerebral microbleeds (CMBs) is uncertain. We aimed to analyze the relationship between the new definition of hypertension and incident CMBs in a 7-year longitudinal community study. Methods This study is a sub-study of the Shanghai Aging Study (SAS). A total of 317 participants without stroke or dementia were included at baseline (2009–2011), and were invited to repeated clinical examinations and cerebral magnetic resonance imaging (MRI) at follow-up (2016–2018). CMBs at baseline and follow-up were evaluated on T2*-weighted gradient recalled echo (GRE) and susceptibility-weighted angiography (SWAN) sequence of MRI. We classified baseline BP into four categories: normal BP, elevated systolic BP, stage 1 hypertension and stage 2 hypertension according to the ACC/AHA guideline. We assessed the associations between BP categories and incident CMBs by generalized linear models. Results A total of 159 participants (median age, 67 years) completed follow–up examinations with a mean interval of 6.9 years. Both stage 1 and stage 2 hypertension at baseline were significantly related with a higher risk of incident CMBs (IRR 2.77, 95% CI, 1.11–6.91, P=0.028; IRR 3.04, 95% CI, 1.29–7.16, P=0.011, respectively), indicating dose-response effects across BP categories. Participants with ≥5 incident CMBs or incident CMBs in the deep locations all had baseline stage 1 and 2 hypertension. Conclusions Participants with baseline stage 1 and stage 2 hypertension had a significantly higher risk of incident CMBs in this 7-year longitudinal community cohort.
Predictors of Fibrotic and Bone Tissue Formation With 3-D Reconstructions of Post-implantation Human Temporal Bones

Hypothesis: Years of implantation, surgical insertion approach, and electrode length will impact the volume of new tissue formation secondary to cochlear implantation. Background: New tissue formation, fibrosis, and osteoneogenesis after cochlear implantation have been implicated in increasing impedance and affecting performance of the cochlear implant. Methods: 3-D reconstructions of 15 archival human temporal bones from patients with a history of cochlear implantation (CI) were generated from H&E histopathologic slides to study factors which affect volume of tissue formation. Results: Years of implantation was a predictor of osteoneogenesis (r = 0.638, p-value = 0.011) and total new tissue formation (r = 0.588, p-value = 0.021), however not of fibrosis (r = 0.235, p-value = 0.399). Median total tissue formation differed between cochleostomy and round window insertions, 25.98 and 10.34%, respectively (Mann–Whitney U = 7, p = 0.018). No correlations were found between electrode length or angular insertion depth and total new tissue (p = 0.192, p = 0.35), osteoneogenesis (p = 0.193, p = 0.27), and fibrosis (p = 0.498, p = 0.83), respectively. However, the type II error for electrode length and angular insertion depth ranged from 0.73 to 0.90, largely due to small numbers of the shorter electrodes. Conclusions: With numbers of cochlear implant recipients increasing worldwide, an understanding of how to minimize intracochlear changes from implantation is important. The present study demonstrates that increasing years of implantation and inserting electrodes via a cochleostomy compared with a round window approach are associated with significantly greater degree of new tissue volume formation. While previous studies have demonstrated increased intracochlear damage in the setting of translocation with longer electrodes, length, and angular insertion depth of CI electrodes were not associated with increased tissue formation.
Review of Neuropsychological and Electrophysiological Correlates of Callous-unemotional Traits in Children: Implications for EEG Neurofeedback Intervention

Conduct disorder is a significant psychiatric disorder of childhood and adolescence. The Diagnostic and Statistical Manual of Mental Disorders, fifth version (DSM-5), added the limited prosocial specifier to identify those individuals who exhibit a more severe pattern of behavior characterized by a callous and unemotional (CU) interpersonal style across multiple settings and relationships. This review has attempted to summarize the relevant research focusing on the significance of CU interpersonal style in the development of psychopathy. The primary focus was on the electrophysiological and neuropsychological correlates of CU traits and their implication on the treatment protocol using neurofeedback training for children with such traits. The source of the literature search was PubMed, which majorly uses the MEDLINE database. The keywords used included CU traits, conduct disorder, child psychopathy, empathy, electrophysiology, criminal behavior, neuropsychology, neurofeedback training, and so on. Studies from the last 15 years were considered for the review. This review revealed that children with conduct disorder and high-CU traits with a combination of reactive and proactive aggression are more likely to develop psychopathy. Evidence suggests that these children have distinct forms of electrophysiological and neuropsychological correlates. However, research in this area is still not conclusive as they yield variation in findings. Studies on the efficacy of neurofeedback training on reducing symptoms such as impulsivity, hostility, and psychopathy indicate that neurofeedback training can be a promising treatment alternative for children with severe conduct disorder.
A novel machine learning approach (svmSomatic) to distinguish somatic and germline mutations using next-generation sequencing data

Somatic mutations are a large category of genetic variations, which play an essential role in tumorigenesis. Detection of somatic single nucleotide variants (SNVs) could facilitate downstream analysis of tumorigenesis. Many computational methods have been developed to detect SNVs, but most require normal matched samples to differentiate somatic SNVs from the normal state, which can be difficult to obtain. Therefore, developing new approaches for detecting somatic SNVs without matched samples are crucial. In this work, we detected somatic mutations from individual tumor samples based on a novel machine learning approach, svmSomatic, using next-generation sequencing (NGS) data. In addition, as somatic SNV detection can be impacted by multiple mutations, with germline mutations and co-occurrence of copy number variations (CNVs) common in organisms, we used the novel approach to distinguish somatic and germline mutations based on the NGS data from individual tumor samples. In summary, svmSomatic: (1) considers the influence of CNV co-occurrence in detecting somatic mutations; and (2) trains a support vector machine algorithm to distinguish between somatic and germline mutations, without requiring normal matched samples. We further tested and compared svmSomatic with other common methods. Results showed that svmSomatic performance, as measured by F1-score, was significantly better than that of others using both simulation and real NGS data.