bluuebunny/crossref_metadata_2025_split huggingface dataset:
The complete chloroplast genome of Gleditsia sinensis and Gleditsia japonica: genome organization, comparative analysis, and development of taxon specific DNA mini-barcodes
Authors: Tan Wei , Gao Han , Jiang Weiling , Zhang Huanyu , Yu Xiaolei , Liu Erwei , Tian Xiaoxuan 
Published: October 2020

AbstractChloroplast genomes have been widely considered an informative and valuable resource for molecular marker development and phylogenetic reconstruction in plant species. This study evaluated the complete chloroplast genomes of the traditional Chinese medicine Gleditsia sinensis and G. japonica, an adulterant of the former. The complete chloroplast genomes of G. sinensis and G. japonica were found to be of sizes 163,175 bp and 162,391 bp, respectively. A total of 111 genes were identified in each chloroplast genome, including 77 coding sequences, 30 tRNA, and 4 rRNA genes. Comparative analysis demonstrated that the chloroplast genomes of these two species were highly conserved in genome size, GC contents, and gene organization. Additionally, nucleotide diversity analysis of the two chloroplast genomes revealed that the two short regions of ycf1b were highly diverse, and could be treated as mini-barcode candidate regions. The mini-barcode of primers ZJ818F-1038R was proven to precisely discriminate between these two species and reflect their biomass ratio accurately. Overall, the findings of our study will shed light on the genetic evolution and guide species identification of G. sinensis and G. japonica.
Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis
Authors: Walker Sidney P. , Barrett Maurice , Hogan Glenn , Flores Bueso Yensi , Claesson Marcus J. , Tangney Mark 
Published: October 2020

AbstractThe targeted sequencing of the 16S rRNA gene is one of the most frequently employed techniques in the field of microbial ecology, with the bacterial communities of a wide variety of niches in the human body have been characterised in this way. This is performed by targeting one or more hypervariable (V) regions within the 16S rRNA gene in order to produce an amplicon suitable in size for next generation sequencing. To date, all technical research has focused on the ability of different V regions to accurately resolve the composition of bacterial communities. We present here an underreported artefact associated with 16S rRNA gene sequencing, namely the off-target amplification of human DNA. By analysing 16S rRNA gene sequencing data from a selection of human sites we highlighted samples susceptible to this off-target amplification when using the popular primer pair targeting the V3–V4 region of the gene. The most severely affected sample type identified (breast tumour samples) were then re-analysed using the V1–V2 primer set, showing considerable reduction in off target amplification. Our data indicate that human biopsy samples should preferably be amplified using primers targeting the V1–V2 region. It is shown here that these primers result in on average 80% less human genome aligning reads, allowing for more statistically significant analysis of the bacterial communities residing in these samples.
Evidence of cortical thickness reduction and disconnection in high myopia
Authors: Wu Ya-Jun , Wu Na , Huang Xin , Rao Jie , Yan Li , Shi Ling , Huang Hui , Li Si-Yu , Zhou Fu-Qing , Wu Xiao-Rong 
Published: October 2020

AbstractHigh myopia (HM) is associated with impaired long-distance vision. accumulating evidences reported that abnormal visual experience leads to dysfunction in brain activity in HM even corrected. However, whether the long-term of abnormal visual experience lead to neuroanatomical changes remain unknown, the aim at this study is to investigate the alternation of cortical surface thickness in HM patients. 82 patients with HM (HM groups), 57 healthy controls (HC groups) were recruited. All participants underwent high-resolution T1 and resting-state functional magnetic resonance imaging (MRI) scans. The cortical thickness analysis was preformed to investigate the neuroanatomical changes in HM patients using computational anatomy toolbox (CAT 12) toolbox. Compare with HCs, HM patients showed decreased the cortical surface thickness in the left middle occipital gyrus (MOG), left inferior parietal lobule (IPL), right inferior temporal gyrus (ITG), right precuneus, right primary visual area 1 (V1), right superior temporal gyrus (STG), right superior parietal lobule (SPL), right occipital pole, and right the primary motor cortex (M1), and increased to the parietal operculum (OP4) (P < 0.01, FWE-corrected), the mean cortical thickness of right orbitofrontal cortex (OFC), right dorsolateral prefrontal cortex (DLPFC) and right subcallosal cortex showed negatively correlation between clinical variables (axis length (ALM), the average macular thickness (AMT), keratometer (KER) 1, KER2, the mean KER, the mean macular fovea thickness (MFK), the refractive diopter) in HM patients. Our result mainly provided an evidence of cortical thickness reduction and disconnection in visual center and visual processing area, and cortical thickness increase in left multimodal integration region in HM patients. This may provide important significance of the study of the neural mechanism of HM.
Fokker–Planck dynamics of the El Niño-Southern Oscillation
Authors: An Soon-Il , Kim Soong-Ki , Timmermann Axel 
Published: October 2020

AbstractThe asymmetric nature of the El Niño-Southern Oscillation (ENSO) is explored by using a probabilistic model (PROM) for ENSO. Based on a Fokker–Planck Equation (FPE), PROM describes the dynamics of a nonlinear stochastic ENSO recharge oscillator model for eastern equatorial Pacific temperature anomalies and equatorial Pacific basin-averaged thermocline depth changes. Eigen analyses of PROM provide new insights into the stationary and oscillatory solutions of the stochastic dynamical system. The first probabilistic eigenmode represents a stationary mode, which exhibits the asymmetric features of ENSO, in case deterministic nonlinearities or multiplicative noises are included. The second mode is linked to the oscillatory nature of ENSO and represents a cyclic asymmetric probability distribution, which emerges from the key dynamical processes. Other eigenmodes are associated with the temporal evolution of higher order statistical moments of the ENSO system. The model solutions demonstrate that the deterministic nonlinearity plays a stronger role in establishing the observed asymmetry of ENSO as compared to the multiplicative stochastic part.
Utilizing conductivity of seawater for bioelectric measurement of fish
Authors: Saiki Tsunemasa , Takizawa Yukako , Miyahara Kazutaka , Arima Masakazu 
Published: October 2020

AbstractTo manage health conditions of farmed fish and other living creatures, a simple method to measure bioelectric signals of the creatures in seawater is expected. A novel method to measure bioelectric signals by utilizing the conductivity of seawater surrounding the entire body of a fish is proposed. As for the proposed method, a needle-type internal electrode is inserted into the fish’s muscle at a certain measurement point, and an external electrode is sunk in seawater. The internal electrode is isolated from the seawater by virtue of being inserted in the fish. Bioelectric signals generated between the external and internal electrodes are then measured. By sharing the external electrode with the internal electrode, it is possible to measure bioelectric signals with half the number of bioelectrodes used by conventional methods. To demonstrate the practicality of the proposed method, two internal electrodes were inserted into different parts (above the gills and near the tail) of three fish (Parajulis poecilepterus, ca. 20 cm fork length) kept in a tank. The proposed method obtained reliable bioelectric signals corresponding to electrocardiograms (ECGs) and electromyograms (EMGs) from each part of the individual fish.
Polystyrene adsorbents: rapid and efficient surrogate for dialysis in membrane protein purification
Authors: Palanirajan Santosh Kumar , Govindasamy Punitha , Gummadi Sathyanarayana N. 
Published: October 2020

AbstractMembrane protein purification is a laborious, expensive, and protracted process involving detergents for its extraction. Purifying functionally active form of membrane protein in sufficient quantity is a major bottleneck in establishing its structure and understanding the functional mechanism. Although overexpression of the membrane proteins has been achieved by recombinant DNA technology, a majority of the protein remains insoluble as inclusion bodies, which is extracted by detergents. Detergent removal is essential for retaining protein structure, function, and subsequent purification techniques. In this study, we have proposed a new approach for detergent removal from the solubilized extract of a recombinant membrane protein: human phospholipid scramblase 3 (hPLSCR3). N-lauryl sarcosine (NLS) has been established as an effective detergent to extract the functionally active recombinant 6X-his- hPLSCR3 from the inclusion bodies. NLS removal before affinity-based purification is essential as the detergent interferes with the matrix binding. Detergent removal by adsorption onto hydrophobic polystyrene beads has been methodically studied and established that the current approach was 10 times faster than the conventional dialysis method. The study established the potency of polystyrene-based beads as a convenient, efficient, and alternate tool to dialysis in detergent removal without significantly altering the structure and function of the membrane protein.
FUBP1 and FUBP2 enforce distinct epigenetic setpoints for MYC expression in primary single murine cells
Authors: Zheng Ying , Dubois Wendy , Benham Craig , Batchelor Eric , Levens David 
Published: October 2020

AbstractPhysiologically, MYC levels must be precisely set to faithfully amplify the transcriptome, but in cancer MYC is quantitatively misregulated. Here, we study the variation of MYC amongst single primary cells (B-cells and murine embryonic fibroblasts, MEFs) for the repercussions of variable cellular MYC-levels and setpoints. Because FUBPs have been proposed to be molecular “cruise controls” that constrain MYC expression, their role in determining basal or activated MYC-levels was also examined. Growing cells remember low and high-MYC setpoints through multiple cell divisions and are limited by the same expression ceiling even after modest MYC-activation. High MYC MEFs are enriched for mRNAs regulating inflammation and immunity. After strong stimulation, many cells break through the ceiling and intensify MYC expression. Lacking FUBPs, unstimulated MEFs express levels otherwise attained only with stimulation and sponsor MYC chromatin changes, revealed by chromatin marks. Thus, the FUBPs enforce epigenetic setpoints that restrict MYC expression.
Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy
Authors: Cho Hyunjin , Choi Yuri , Min Kyungjin , Son Jung Bae , Park Hyojin , Lee Hyung Ho , Kim Seokhee 
Published: October 2020

AbstractRising antibiotic resistance urgently begs for novel targets and strategies for antibiotic discovery. Here, we report that over-activation of the periplasmic DegP protease, a member of the highly conserved HtrA family, can be a viable strategy for antibiotic development. We demonstrate that tripodal peptidyl compounds that mimic DegP-activating lipoprotein variants allosterically activate DegP and inhibit the growth of an Escherichia coli strain with a permeable outer membrane in a DegP-dependent fashion. Interestingly, these compounds inhibit bacterial growth at a temperature at which DegP is not essential for cell viability, mainly by over-proteolysis of newly synthesized proteins. Co-crystal structures show that the peptidyl arms of the compounds bind to the substrate-binding sites of DegP. Overall, our results represent an intriguing example of killing bacteria by activating a non-essential enzyme, and thus expand the scope of antibiotic targets beyond the traditional essential proteins or pathways.
Unbiased description of magnetic polarons in a Mott insulator
Authors: Blomquist Emil , Carlström Johan 
Published: October 2020

AbstractPolarons are among the most elementary quasiparticles of interacting quantum matter, consisting of a charge carrier dressed by an excited background. In Mott insulators, they take the form of a dopant surrounded by a distorted spin-background. Despite the fundamental importance of polarons for the electronic structure of strongly correlated systems, access to their internal structure was only recently realized in experiments, while controllable theoretical results are still lacking due to the sign problem. Here we report unbiased high-precision data obtained from worm-algorithm Monte Carlo that reveal the real-space structure of a polaron in the t-J model deep inside the region where the sign problem becomes significant. These results are directly comparable to recent quantum gas microscopy experiments, but give access to significantly lower temperatures.
Efficiency of Percutaneous Stent Angioplasty in Renal Artery Stenosis – 15 Years of Experience at a Single Center
Authors: Guerreiro Helena , Avanesov Maxim , Dinnies Stefanie , Sehner Susanne , Schön Gerhard , Wenzel Ulrich , Adam Gerhard , Ittrich Harald , Regier Marc 
Published: October 2020

Purpose To determine the therapeutic efficiency of percutaneous revascularization in renal artery stenosis (RAS), as well as the role of comprehensive factors such as patient selection and degree of artery stenosis, on clinical outcome.
Methods and Materials 101 patients with hemodynamically relevant RAS underwent percutaneous angioplasty (PTA). 65.7 % were male (mean age: 64 years; range: 18–84). The clinical data was retrospectively analyzed. The serum creatinine (Cr), glomerular filtration rate (GFR), and blood pressure (BP) levels pre- and postprocedural, between 6 months and 1 year, were retrospectively collected and statistically analyzed.
Results Follow-up data was available in 34 (33.7 %) and 28 patients (27.7 %) for Cr and MAP, respectively. A significant drop in mean arterial pressure (MAP) was observed on follow-up (mean –5.27 mmHg). Higher baseline Cr and MAP values showed a more pronounced drop in the follow-up (Cr: p 0.002; difference to baseline –0.25 mg/dL, 95 %CI:–0.36, –0.07 and BP p < 0.001; diff. to baseline –0.72 mmHg; 95 %CI: –1.4, –0.40). There was no association between comorbidities, gender, and degree of stenosis with renal and BP outcome. No significant improvement in renal function was observed on follow-up (mean Cr drop: –0.015 mg/dL). The age group 51–60 years showed a significant improvement in BP (p 0.030; diff. to baseline –19.2 mmHg; 95 %CI: –34, –4.3). There was a slight reduction in antihypertensive medication following angioplasty (0.2 fewer). Minor complications were recorded in five procedures (4.9 %).
Conclusion Percutaneous renal artery revascularization in the presence of atherosclerotic RAS is a safe procedure associated with a significant drop in post-procedural BP. No significant improvement in renal function was observed. Further prospective studies focused on patient selection are necessary.
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Citation Format
Review of Type III Endoleaks
Authors: Stoecker Jordan B. , Glaser Julia D. 
Published: October 2020

AbstractEndoleak remains a significant challenge to endovascular aneurysm repair, particularly as evolving techniques and devices have allowed treatment of increasingly complex aneurysm anatomy with increasing number of device components. Intervention is recommended for both type I and III endoleaks due to their risk of rupture, and endovascular techniques are the favored modality with placement of a bridging endograft over the endoleak defect. Conversion to open surgical repair remains the definitive option in cases where less invasive methods have failed or are precluded. In this article, the authors review evidence on the etiology, incidence, diagnosis, and current techniques for type III endoleak management.
Surveillance Imaging following Endovascular Aneurysm Repair: State of the Art
Authors: Kim Stephanie H. , Litt Harold I. 
Published: October 2020

AbstractEndovascular aneurysmal repair (EVAR) has become a prominent modality for the treatment of abdominal aortic aneurysm. Surveillance imaging is important for the detection of device-related complications, which include endoleak, structural abnormalities, and infection. Currently used modalities include ultrasound, X-ray, computed tomography, magnetic resonance imaging, and angiography. Understanding the advantages and drawbacks of each modality, as well available guidelines, can guide selection of the appropriate technique for individual patients. We review complications following EVAR and advances in surveillance imaging modalities.
The Association of Cesarean Skin Incision Length and Postoperative Wound Complications
Authors: Subramaniam Akila , Jauk Victoria , Saade George , Boggess Kim , Longo Sheri , Clark Erin A.S. , Esplin Sean , Cleary Kirsten , Wapner Ron , Letson Kellett , Owens Michelle Y. , Blackwell Sean , Szychowski Jeff M. , Andrews William W. , Tita Alan T. 
Published: October 2020

Objective This study was aimed to evaluate the relationship between cesarean skin incision length and wound complications.
Study Design Planned secondary analysis of a multicenter double-blind randomized trial of adjunctive azithromycin versus placebo (in addition to standard cefazolin) in women ≥24 weeks undergoing cesarean delivery during labor or ≥4 hours after membrane rupture. Skin incision length (cm) was measured just prior to skin closure. The primary outcome was a composite of wound complications (wound infection, separation, seroma, hematoma, or dehiscence) up to 6 weeks of postpartum. Individual components of the composite were examined as secondary outcomes. Outcomes were compared between groups defined by the lowest (≤25th), middle (25–75th) and highest (>75th) incision length quartiles. Logistic regression was used to adjust for potential confounding variables.
Results Of the 2,013 women enrolled in the primary trial, 1,916 had recorded incision lengths and were included in this secondary analysis. The overall rate of composite wound complications was 7.8%. Median incision length was 15.0 cm (interquartile range: 14.0–16.5) with the lowest quartile defined as ≤14, middle as >14 to ≤16.5, and highest as >16.5 cm. Mean BMI, parity, use of staples, and duration of surgery differed significantly between the three incision length groups. In unadjusted analysis, the longest incision lengths were associated with an increased risk of the wound composite and wound infections (odds ratio [OR] = 2.27, 95% confidence interval [CI]: 1.43–3.60 and OR = 2.30, 95% CI: 1.27–4.15, respectively) compared with the shortest incision lengths. However, after multivariable adjustments, these associations were nullified. Additional analyses considering incision length as a continuous variable and using 10th/90th percentile cut-offs still did not suggest any associations with outcomes.
Conclusion Increasing skin incision length is not independently associated with an increased risk of postoperative wound complications.
Key Points
Self-Reported Effectiveness of e-Learning Classes during COVID-19 Pandemic: A Nation-Wide Survey of Pakistani Undergraduate Dentistry Students
Authors: Sarwar Huma , Akhtar Hira , Naeem Meshal Muhammad , Khan Javeria Ali , Waraich Khadija , Shabbir Sumaiya , Hasan Arshad , Khurshid Zohaib 
Published: October 2020

Abstract
Objectives The main aim of this study was to determine the undergraduate dental students’ self-reported effectiveness of online classes offered by various dental institutes of Pakistan.
Materials and Methods A cross-sectional study was conducted using an online survey. A pretested and validated questionnaire comprising of 31 questions was circulated among dental students. The study participants were inquired about the perceived level of accessibility of resources and the effectiveness of online teaching. The data was analyzed using SPSS version 24. Mann–Whitney U test and Kruskal–Wallis test were used for statistical analysis at p ≤0.05.
Results A total of 1,207 students from all over Pakistan responded. The majority of students was dissatisfied with the institutional learning management system and quality of learning resources available. Students were also dissatisfied with the level of training of teachers for online lectures. The worst rating was reported for questions related to the effectiveness of online classes (average rating: 3.83 and 3.781/5). First-year students reported poor interaction with teachers (p < 0.001) and strongly disagreed with the effectiveness of online classes (mean rating: 4.14 ± 0.935).
Conclusions The results from the present survey showed that dental students of Pakistan unanimously voiced dissatisfaction toward various elements of online teaching sessions. Findings from this survey will aid the academic institutes to establish proficient learning platforms focused on improving students` learning experience.
Role of Ultrahigh Frequency Ultrasound in Evaluating Experimental Flaps
Authors: Morarasu Stefan , Ghetu Nicolae , Coman Corneliu George , Morarasu Bianca Codrina , Boicu Daniel , Spiridon Irene Alexandra , Gardikiotis Ioannis , Danciu Mihai , Pieptu Dragos 
Published: October 2020

Abstract
Background Experimental flap follow-up needs faster, safer, and less invasive techniques that can be easily correlated to clinical procedures. For this reason, we aimed to test the role of ultrahigh frequency ultrasound in follow-up of flap viability. Further on, we aimed to analyze if the chimeric groin flap can be mobilized in a sandwiched position without affecting its vascular supply by twisting its pedicle.
Methods A total of 12 male Wistar rats, split into three groups, were used. Group A (n = 4) had the chimeric groin flap repositioned in a sandwich position on the anterior abdominal wall and underwent ultrahigh frequency ultrasound follow-up at days 10 and 14. Group B (n = 4) also had the flaps sandwiched, however, at day 14 the vascularity of flaps was proven by infusion of nontargeted ultrasound contrast agents, after which flaps were sent for histological analysis. Group C (C1 n = 2, C2 n = 2) was the control group. In C1 the chimeric groin flap was harvested and sent for histology on day 0, acting as a histological benchmark of flap viability, and in C2 the chimeric groin flap was re-sutured in its anatomical position and after 14 days, flaps were harvested and sent for histological analysis, acting as a direct control for Group B.
Results Ultrasound showed constant vascular flow in both adipose and skin flaps in the sandwiched position. Microbubble study showed diffuse perfusion within flaps. Ultrasound measurements of flow velocity, flap volume, and percentage of vascularity showed a decrease in flap volume and increase in vascularity over 14 days. Histology showed similar viability in both groups.
Conclusion Ultrahigh frequency ultrasound may be a valuable tool for postoperative flap assessment, while the chimeric flap can be moved freely in a sandwich position making it suitable for adding tissue substitutes within its components.