bluuebunny/crossref_metadata_2025 huggingface dataset:
Obesity, Second Stage Duration, and Labor Outcomes in Nulliparous Women
Authors: Frolova Antonina I. , Raghuraman Nandini , Stout Molly J. , Tuuli Methodius G. , Macones George A. , Cahill Alison G.
Published: September 2019

Objective This study aimed to estimate second stage duration and its effects on labor outcomes in obese versus nonobese nulliparous women.

Study Design This was a secondary analysis of a cohort of nulliparous women who presented for labor at term and reached complete cervical dilation. Adjusted relative risks (aRR) were used to estimate the association between obesity and second stage characteristics, composite neonatal morbidity, and composite maternal morbidity. Effect modification of prolonged second stage on the association between obesity and morbidity was assessed by including an interaction term in the regression model.

Results Compared with nonobese, obese women were more likely to have a prolonged second stage (aRR: 1.48, 95% CI: 1.18–1.85 for ≥3 hours; aRR: 1.65, 95% CI: 1.18–2.30 for ≥4 hours). Obesity was associated with a higher rate of second stage cesarean (aRR: 1.78, 95% CI: 1.34–2.34) and cesarean delivery for fetal distress (aRR: 2.67, 95% CI: 1.18–3.58). Obesity was also associated with increased rates of neonatal (aRR: 1.38, 95% CI: 1.05–1.80), but not maternal morbidity (aRR: 1.06, 95% CI: 0.90–1.25). Neonatal morbidity risk was not modified by prolonged second stage.

Conclusion Obesity is associated with increased risk of neonatal morbidity, which is not modified by prolonged second stage of labor.
The Association between Maternal Race and Ethnicity and Risk Factors for Primary Cesarean Delivery in Nulliparous Women
Authors: Stark Elisabeth L. , Grobman William A. , Miller Emily S.
Published: September 2019

Objective To understand whether maternal, perinatal, and systems-level factors can be identified to explain racial/ethnic disparities in cesarean delivery rates.

Study Design This retrospective cohort study included nulliparous women with singleton gestations who delivered at a tertiary care center from 2015 to 2017. Maternal, perinatal, and systems-level factors were compared by race/ethnicity. Multilevel multivariable logistic regression was used to identify whether race/ethnicity was independently associated with cesarean. Effect modification was evaluated using interaction terms. Bivariable analyses and multinomial logistic regression were used to determine differences in indication for cesarean.

Results Of 9,865 eligible women, 2,126 (21.5%) delivered via cesarean. The frequency of cesarean was lowest in non-Hispanic white women (19.2%) and highest in non-Hispanic black women (28.2%; p < 0.001). Accounting for factors associated with cesarean delivery did not lessen the odds of cesarean associated with non-Hispanic black race (aOR: 1.58, 95% CI: 1.31–1.91). Compared with non-Hispanic white women, non-Hispanic black women were more likely to undergo cesarean for nonreassuring fetal status (aOR: 2.73, 95% CI: 2.06–3.61).

Conclusion Examined maternal, perinatal, and systems-level risk factors for cesarean delivery did not explain the racial/ethnic disparities observed in cesarean delivery rates. Increased cesarean delivery for nonreassuring fetal status contributed substantially to this disparity.
Risk of Stillbirth after Antepartum Hospitalization for Hypertensive Diseases of Pregnancy
Authors: Wen Timothy , Breslin Noelle , Overton Eve E. , Turitz Amy L. , D'Alton Mary E. , Attenello Frank , Mack William J. , Friedman Alexander M.
Published: September 2019

Objective To determine if women with an antepartum admission for hypertensive diseases of pregnancy (HDP) were at increased risk for stillbirth.

Study Design This study utilized the 2010 to 2014 Nationwide Readmissions Database. Antepartum admissions with HDP were identified and linked to subsequent delivery hospitalizations. Delivery hospitalizations with HDP without a preceding antepartum HDP admission were also identified. Risk for stillbirth, abruption, or both was compared between these two groups.

Results An estimated 382,621 deliveries with an HDP diagnosis were identified of which 14,857 (3.9%) had a preceding antepartum admission for HDP. Stillbirth occurred in 7.8 per 1,000 delivery hospitalizations complicated by HDP with risk higher with a preceding HDP antepartum admission in both unadjusted (1.1 vs. 0.8%, risk ratios [RR] 1.46, 95% confidence interval [CI] 1.24–1.70) and adjusted (adjusted risk ratios [aRR] 1.24, 95% CI 1.06, 1.46) analyses. Abruption occurred in 19.6 per 1,000 delivery hospitalizations complicated by HDP with risk higher with a preceding HDP antepartum admission in both unadjusted (2.5 vs. 1.9%, RR 1.30, 95% CI 1.17–1.44) and adjusted (aRR 1.24, 95% CI 1.11, 1.37) analyses. Risk for combined abruption and stillbirth did not differ significantly.

Conclusion In this analysis, prior antenatal hospitalization was associated with increased risk for stillbirth among women with HDP.
Drug-Induced Thrombocytopenia: Mechanisms and Laboratory Diagnostics
Authors: Danese Elisa , Montagnana Martina , Favaloro Emmanuel J. , Lippi Giuseppe
Published: September 2019

Thrombocytopenia is a condition characterized by a decreased number of platelets in peripheral blood, which can be caused by a myriad of both congenital and acquired disorders. Drug-induced thrombocytopenia (DIT) deserves a special focus since its cumulative incidence can be as high as 10 cases per million population per year, with a prevalence of approximately 25% in critically ill patients. This condition is usually suspected following identification of an acute and severe decrease in platelet count, with values usually < 50 ×109/L, thus potentially exposing patients to an increased risk of developing spontaneous hemorrhages. Conversely, however, some drug-related thrombocytopenias are instead (and perhaps counterintuitively) associated with increased thrombosis risk. Although a vast number of drugs have been implicated in DIT, the underlying pathogenetic mechanisms are essentially bifold, encompassing reduced platelet production due to bone marrow suppression (thus insufficient maturation or inefficient expansion of megakaryocytes, impaired release of platelets, or accelerated platelet apoptosis) or accelerated clearance of platelets from the circulation. This second form of DIT can be sustained by nonimmune, immune-mediated, or autoimmune mechanisms. An early and accurate diagnosis of DIT, which is crucial for reversing an otherwise unfavorable clinical outcome, is essentially based on the complete blood cell count, blood smear analysis, and performance of specific functional or immunochemical tests aimed at demonstrating the presence of antiplatelet antibodies.
Surgery in Traumatic Injury and Perioperative Considerations
Authors: Curry Nicola , Brohi Karim
Published: September 2019

A severely injured patient presents several unique challenges to an admitting trauma team. Not only must the extent of the patient's injuries, particularly those that are life-threatening, be determined within minutes of hospital arrival, but also the trauma team needs to be able to assess whether the patient is bleeding and/or has an attendant coagulopathy. Early management of trauma patients is dictated by the presence (or absence) of significant bleeding. Standard definitive surgical procedures can be conducted in hemodynamically stable patients, but those in hemorrhagic shock should be treated according to damage control resuscitation (DCR) principles. DCR is a practice that has evolved over the last two to three decades, combining limited surgical techniques, which provide early hemorrhage control, and balanced transfusion resuscitation strategies, which mitigate (and ideally) treat trauma-induced coagulopathy (TIC). This review describes the contemporary perioperative management of trauma patients who have significant bleeding and/or TIC and sets out the evidence around the current approach for hemostatic resuscitation in these patients.
Using Artificial Intelligence to Manage Thrombosis Research, Diagnosis, and Clinical Management
Authors: Mishra Aastha , Ashraf Mohammad Zahid
Published: September 2019

Thrombosis development in either arterial or venous system remains a major cause of death and disability worldwide. This poorly controlled in vivo clotting could result in many severe complications including myocardial infarction, venous thromboembolism, stroke, and cerebral venous thrombosis, to name a few. These conditions are collectively known as thromboembolic disorders (TEDs). Appropriate understanding of TEDs is challenging, as they are multifactorial and involve several and often different risk factors. Hence, it requires a collective effort and data from numerous research studies to fully comprehend molecular mechanisms for prediction, prevention, treatment, and overall management of these conditions. To accomplish this arduous feat, a comprehensive approach is required that can compile thousands of available experimental data and transform these into more applicable and purposeful findings. Thus, large datasets could be utilized to generate models that could be predictive of how an individual would respond when subjected to any kind of additional risk factors or surgery, hospitalization, etc., or in the presence of some susceptible genetic variations. Artificial intelligence-based methods harness the capabilities of computer software to imitate human behaviors such as language translation, visual perception, and, most importantly, decision making. These emerging tools, if appropriately explored, might assist in processing of large data and tackle the complexities of identifying novel or interesting pathways that could otherwise be hidden due to their enormity. This narrative review attempts to compile the applications of various subfields of artificial intelligence and machine learning in the context of thrombosis research to date. It further reflects on the potential of artificial intelligence in transforming enormous research data into translational application in the form of predictive computational models.
The Erosive Potential of Some Flavoured Waters
Authors: Rees Jeremy , Loyn Theresa , Hunter Lindsay , Sadaghiani Leili , Gilmour Alan
Published: September 2019

Objectives: To assess the erosive potential of a number of readily available flavoured waters in the laboratory.

Methods: The erosive potential was assessed by measuring the pH, neutralisable acidity and ability to erode enamel. These were compared to an orange juice positive control.

Results: The pH of the flavoured waters ranged from 2.64-3.24 with their neutralisable acidity ranging from 4.16-16.30 mls of 0.1M NaOH. The amount of enamel removed following 1-hour immersion in the drinks ranged from 1.18-6.86 microns. In comparison, the orange juice control had a pH of 3.68, a neutralisable acidity of 19.68 mls of 0.1 M NaOH and removed 3.24 microns of enamel.

Results: The pH of the flavoured waters ranged from 2.64-3.24 with their neutralisable acidity ranging from 4.16-16.30 mls of 0.1M NaOH. The amount of enamel removed following 1-hour immersion in the drinks ranged from 1.18-6.86 microns. In comparison, the orange juice control had a pH of 3.68, a neutralisable acidity of 19.68 mls of 0.1 M NaOH and removed 3.24 microns of enamel.
Fluoride Levels of Human Plasma and Breast Milk
Authors: Şener Yağmur , Tosun Gül , Kahvecioğlu Firdevs , Gökalp Alparslan , Koç Hasan
Published: September 2019

Objectives: The aim of this study was to determine the fluoride levels in breast milk and plasma of lactating mothers who regularly consumed drinking water with low levels of fluoride.

Methods: One hundred twenty five healthy mothers aged between 20-30 years old who had given birth within 5-7 days were included in the study. Besides being otherwise healthy, the primary selection criteria stipulated the absence of fluoride supplement consumption one month before delivery. Approximately 5 ml breast milk and 5 ml blood samples were obtained from each participating mother at a hospital setting, where the mothers were scheduled for a regular hospital diet. The blood samples were centrifuged in fluoride-free heparinized polyethylene tubes and stored at -18oC until measurements were made. Breast milk samples were directly refrigerated as with blood samples until measurements. The fluoride concentrations of milk and blood samples were assessed using an ion-selective fluoride electrode combined with an ion analyzer.

Results: The fluoride levels of the plasma and breast milk samples were measured as 0.017±0.011 ppm and 0.006±0.002 ppm, respectively. The fluoride concentration of plasma was significantly higher than that of breast milk (P<.01). Correlation analysis revealed a significant relation between the groups (P<.01).

Conclusion: A limited level of fluoride transmission from plasma to breast milk was detected. Nevertheless, a significant correlation between the fluoride concentrations of breast milk and plasma was evident. (Eur J Dent 2007;1:21-24)
Apical Leakage of Different Gutta-Percha Techniques: Thermafil, Js Quick-Fill, Soft Core, Microseal, System B and Lateral Condensation with a Computerized Fluid Filtration Meter
Authors: Gençoğlu Nimet , Oruçoğlu Hasan , Helvacıoğlu Dilek
Published: September 2019

Objectives: To investigate apical leakage of roots filled with 6 different gutta-percha techniques; Thermafil, JS Quick-Fill, Soft Core, Microseal, System B and lateral condensation using a new computerized filtration meter.

Methods: Materials and Methods: 60 extracted single rooted teeth were used. Coronal part of each tooth was removed and the root canals were prepared with step-back technique. The roots were randomly divided into six groups of 10 teeth, filled by one of the obturation technique and Kerr sealer. The teeth were kept in 100% humidity for 2 years. After this period, apical parts of roots (10±0.05 mm) were attached to computerized fluid filtration meter. Apical leakage quantity was determined as μl.cmH2O-1.min-1.

Results: Statistical analysis indicated that Thermafil, Soft Core, Quick-Fill and System B techniques showed lower leakage than Microseal and lateral condensation (P>.05). However, statistically no difference was found among the core techniques and no difference was found between microseal and lateral condensation techniques (P>.05).

Conclusions: Thermafil, Soft Core,Quick-Fill and System B techniques showed lower leakage than Microseal and lateral condensation. In addition, this new computerized fluid filtration meter allowed quantitative measurement of leakage easily. (Eur J Dent 2007;2:97-103)
An Industrial Dental-Erosion by Chromic Acid: A Case Report
Authors: Dülgergil Ç Türksel , Erdemir Ebru Olgun , Ercan Ertuğrul , Erdemir Ali
Published: September 2019

A case of uncommon occupational dental erosion was reported in an individual who had worked in the war industry for twenty years. This occupation involved daily, at least 8 hours, inhalation of chromic acid being used for cleaning of barrel of cannons. The erosion manifested as dental sensitivity with excessive cervical erosion even with pulpal exposure in certain teeth. Moreover, due to the adverse effect of the chemical against to gingival and/or periodontal tissues, the lesions were extremely harmful with respect to the exposed root-cementum. After proper periodontal therapy, cervical lesions were treated conservatively with a compomer based restorative material without cavity preparation. Although today it is not common due to the well-controlled working conditions, occupational combined dental and medical problems via airborne fumes and/or elements can be seen at workers in chemical factories. A cumulative biohazardous effect is generally seen as not only medical but also dental disorders. (Eur J Dent 2007;2:119-122)
The Prevalence of Carotid Artery Calcification on the Panoramic Radiographs in Cappadocia Region Population
Authors: Sisman Yildiray , Ertas Elif Tarim , Gokce Cumali , Menku Ahmed , Ulker Mustafa , Akgunlu Faruk
Published: September 2019

Objectives: The aim of this study is to determine retrospectively the presence of carotid artery calcifications (CACs) detected on panoramic radiographs (PRs) in a group of Turkish population. Further, the relationships between CACs and gender, life style, and medical history were evaluated.

Methods:During the years 2004 to 2006, a random sample of 1282 PRs was collected from patients older than 40 years who were being treated by the School of Dentistry, Erciyes University. Of these 1282 PRs, 750 PRs were included in this study. Medical data was collected from the archival records of the dental school.

Results: About 38 (5.06%) CACs were found on the PRs of 12 (4.5%) males and 26 (5.4%) females. The CAC prevalence was not significantly different between the males and females (P=0.583). These calcifications were unilateral in 26 (68.4%) and bilateral in 12 (31.6%) subjects. Of those in the positive group, there were 12 subjects (31.58%) with hyperlipidemia, 12 subjects (31.58%) with hypertension, 7 subjects (18.4%) with diabetes mellitus, 6 subjects (15.8%) with cardiovascular disease, and 6 subjects (15.8%) with smoking history.

Conclusions: This study has the highest CACs prevalence in comparison to the other studies. Therefore, dentists caring for subjects with dental problems should carefully evaluate their PRs for the evidence of CACs, and refer them for medical evaluation as indicated. So, incidental findings could provide life-saving information. (Eur J Dent 2007;1:132-138)
Influence of Diamond Sono-Abrasion, Air-Abrasion and Er:YAG Laser Irradiation on Bonding of Different Adhesive Systems to Dentin
Authors: de Oliveira Marcelo Tavares , de Freitas Patrícia Moreira , Eduardo Carlos de Paula , Ambrosano Glaucia Maria Bovi , Giannini Marcelo
Published: September 2019

Objectives: Different surface treatments may affect bonding performance of adhesive systems to dentin. This study evaluated the influence of different methods of surface treatment on adhesion of bonding agents to dentin.

Methods: TDentin surfaces abraded with #600-grit SiC paper were used as control. Three methods of surface treatment (sono-abrasion, air-abrasion and Er:YAG laser irradiation) were used under specific parameters. Four adhesive systems (Tyrian, Clearfil SE Bond, Unifil Bond and Single Bond) were applied to treated surfaces, according to the manufacturers’ instructions. Composite blocks were built on bonded surfaces, then restored teeth were vertically and serially sectioned to obtain bonded slices for interfacial micromorphologic analysis or to produce beam specimens for μ-TBS bond test. Data were analyzed with two-way ANOVA and Tukey test at a significance level of 5%.

Results: The results indicated that the preparation of dentin with sono-abrasion or laser did not affect the bond strength, while the preparation of dentin with SiC paper and air-abrasion influenced the bond strength for some systems. A clear difference of the preparation of dentin surfaces and formation of hybrid layer and resin tags were noted.

Conclusions: Bonding effectiveness of both the etch-and-rinse and the self-etch adhesives can be influenced by different methods of dentin preparation. (Eur J Dent 2007;1:158-166)
Reattachment of Coronal Fragment Using Fiber-Reinforced Post: A Case Report
Authors: ZORBA Yahya Orcun , ÖZCAN Erdal
Published: September 2019

Coronal fractures of permanent dentition are the most frequent type of dental injury. If the original tooth fragment is retained following fracture, the natural tooth structures can be reattached using adhesive protocols. The development and use of fiber-reinforced composite root canal posts make possible of the reattachment of the crown esthetically. This case report presents a clinical technique to reattachment maxillary lateral incisor tooth after trauma using direct fiber-reinforced post systems. At the 1-year follow-up, a slightly marginal discoloration, but no recurrent decay or composite clefts were detected and the resultant appearance was acceptable to the patient. (Eur J Dent 2007;1:174-178)
Multiple Hereditary Osteochondromatosis: A Case Report
Authors: Küçükesmen Çiğdem , Özen Buğra , Akçam Mustafa
Published: September 2019

Objectives: Common carious lesions owing to vomiting are not widespread in children. In this case, we aimed to report an 11-years-old male patient with common carious lesions due to repeated vomitings, chewing and eating difficulty and retarded growth with Multiple Hereditary Osteochondromatosis (MHO).

Case Report: An 11-years-old boy was referred to Department of Pediatric Dentistry in Faculty of Dentistry because of eating difficulty owing to common carious lesions. It was seen that the patient growth was generally retarded in extra-oral examination. Some exostoses were also present on the extremities. It was learned that he was previously diagnosed as MHO in Faculty of Medicine. Nausea and vomiting have been commonly occurring after taking of Didronat. Chewing and eating difficulty and inadequate nutrition were present because of bad oral hygiene, carious lesions and remained roots. Growth was negatively affected by malnutrition and MHO.

Results: Diet recommendations were given and oral hygiene behaviors were rearranged. Preventive, surgical, restorative and prosthetical dental applications were applied for dental treatments. (Eur J Dent 2007;1:183-187)
Effect of Mouthrinse Containing Propolis on Oral Microorganisms and Human Gingival Fibroblasts
Authors: Özan Fatih , Sümer Zeynep , Polat Zübeyde Akın , Er Kürşat , Özan Ülkü , Değer Orhan
Published: September 2019

Objectives: The aim of this study was to compare the effects of four different mouthrinse containing propolis solutions and mouthrinse containing 0.2% chlorhexidine (CHX) on oral microorganisms and human gingival fibroblasts.

Methods: Four different solutions of propolis were prepared and propylene glycol and alcohol were used as solvents for each propolis sample. Mouthrinse containing propolis was prepared at four different concentrations as 10%, 5%, 2.5% and 1%. Besides, CHX was used as control group. The antibacterial effects of five solutions on oral microorganisms were tested and their cytotoxic effects on human gingival fibroblasts were evaluated by agar diffusion test.

Results: At this concentrations effectiveness of mouthrinse containing propolis samples on oral microorganisms were not found as effective as CHX. On the contrary, samples found less cytotoxic on human gingival fibroblasts than CHX.

Conclusions: Standardized preparations of propolis can be used as a mouthrinse at appropriate concentrations. To obtain a standardized chemical composition, advanced researches are needed. (Eur J Dent 2007;1:195-201)
The Effect of Tobacco Smoking on Gingival Crevicular Fluid Volume
Authors: Üstün Kemal , Ö. Alptekin Nilgün
Published: September 2019

Objectives: The negative effects of smoking on periodontal health are well known. But the mechanism is not clear yet. The aim of the present study is to investigate the effects of smoking on gingival crevicular fluid (GCF) volume

Methods: The study included 26 age and gender matched periodontally healthy males. Half of the participants were smokers and the others were non-smokers. After periodontal measures were taken GCF samples were collected from 4 teeth of the subjects. The GCF volume was measured with an electronical device

Results: The mean plaque index (PI) and gingival crevicular fluid (GCF) volumes were significantly lower in non-smokers (P=.019 and P=.027, respectively). The other parameters did not show significant differences

Conclusions: Smoking significantly increased GCF volume compared to non-smoking subjects. This may contribute to the negative effects of smoking on periodontal tissues. (Eur J Dent 2007;1:236- 239)
Intrinsically undamped plasmon modes in narrow electron bands
Authors: Lewandowski Cyprian , Levitov Leonid
Published: September 2019

Significance

We argue that moiré graphene provides an opportunity to realize plasmons not subject to Landau damping. Eliminating damping is central for the ongoing quest for low-loss plasmons and dissipationless light–matter coupling. “Lifting the curse” of Landau dissipation is a surprising behavior originating from plasmon modes extending far above the narrow-band particle–hole continuum into the forbidden energy gap, where they decouple from particle–hole excitations. While our findings apply broadly to all narrow electron bands with an energy gap above the flat band, these effects are particularly prominent in moiré graphene because of uniquely strong electron interactions in this material. The intrinsically undamped plasmons feature enhanced optical coherence and spatial interference, directly testable by state-of-the-art near-field techniques.
Identification of the characteristic components in walnut and anti-inflammatory effect of glansreginin A as an indicator for quality evaluation
Authors: Haramiishi Rie , Okuyama Satoshi , Yoshimura Morio , Nakajima Mitsunari , Furukawa Yoshiko , Ito Hideyuki , Amakura Yoshiaki
Published: September 2019

Walnut is a nutritious food material, but only a few studies have been conducted on the mechanisms of its functions and the technique for quality evaluation. Therefore, we analyzed the components in aqueous methanol extract of walnut, and characterized 30 components, including three new compounds, glansreginin C, ellagic acid 4-O-(3′-O-galloyl)-β-D-xyloside, and platycaryanin A methyl ester. We analyzed the extracts of other nuts using HPLC and clarified that a characteristic peak corresponding to glansreginin A was mainly observed in walnut. These results suggested that glansreginin A might be an indicator component of the quality of walnut. We then examined whether glansreginin A has neuroprotective effect, using lipopolysaccharide (LPS)-induced inflammatory model mice. The results revealed that oral administration of glansreginin A prevented LPS-induced abnormal behavior and LPS-induced hyper-activation of microglia in the hippocampus. These results suggested that glansreginin A has the ability to exert neuroprotective effect via anti-inflammation in the brain.
Large scale production of lacto-N-biose I, a building block of type I human milk oligosaccharides, using sugar phosphorylases
Authors: Nishimoto Mamoru
Published: September 2019

Human milk oligosaccharides (HMOs) have drawn attention for their contribution to the explosive bifidobacterial growth in the intestines of neonates. We found that bifidobacteria can efficiently metabolize lacto-N-biose I (LNB), the major building blocks of HMOs, and we have developed a method to synthesize LNB by applying this system. We produced LNB on a kilogram scale by the method. This proved that, among the enterobacteria, only bifidobacteria can assimilate LNB, and provided the data that supported the explosive growth of bifidobacteria in neonates. Furthermore, we were also able to reveal the structure of LNB crystal and the low stability for heating at neutral pH, which has not been clarified so far. In this paper, using bifidobacteria and LNB as examples, I describe the research on oligosaccharide synthesis that was conducted by utilizing a sugar metabolism.

Abbreviations: LNB: lacto-N-biose I; GNB: galacto-N-biose; HMOs: human milk oligosaccharides; GLNBP: GNB/LNB phosphorylase; NahK: N-acetylhexosamine 1-kinase; GalT: UDP-glucose-hexose-1-phosphate uridylyltransferase; GalE: UDP-glucose 4-epimerase; SP: sucrose phosphorylase.
Circulating extracellular vesicle content reveals de novo DNA methyltransferase expression as a molecular method to predict septic shock
Authors: Dakhlallah Duaa A. , Wisler Jon , Gencheva Marieta , Brown Candice M. , Leatherman Erin R. , Singh Kanhaiya , Brundage Kathy , Karsies Todd , Dakhlallah Ahmad , Witwer Kenneth W. , Sen Chandan K. , Eubank Timothy D. , Marsh Clay B.
Published: September 2019

Extracellular vesicles (EVs) are mRNA‐containing cell fragments shed into circulation during pathophysiological events. DNA methyltransferases (DNMT1, DNMT3A, and DNMT3B) regulate gene expression by modifying DNA methylation and altering transcription. Sepsis is a systemic insult resulting in vascular dysfunction, which can lead to shock and death. We analysed plasma from ICU patients for circulating EV numbers, defined as particles isolated from 1 mL plasma at 21,000xg, and DNMTs mRNA content as prognostic markers of septic shock. Compared to plasma from critically ill patients with or without sepsis, plasma from septic shock patients contained more EVs per mL, expressed as total DNMTs mRNAs over 5 days, and more individual DNMT mRNAs at each day. A comparison of EV‐DNMT1 (maintenance methylation) with EV‐DNMT3A+DNMT3B (de novo methylation) expression correlated highly with severity, and EVs from septic shock patients carried more total DNMT mRNAs and more DNMT3A+DNMT3B mRNAs than control or sepsis EVs. Total plasma EVs also correlated with sepsis severity. EV‐DNMT mRNAs load, when coupled with total plasma EV number, may be a novel method to diagnose septic shock upon ICU admittance and offer opportunities to more precisely intervene with standard therapy or other targeted interventions to regulate EV release and/or specific DNMT activity.
Loss of myosin Vb promotes apical bulk endocytosis in neonatal enterocytes
Authors: Engevik Amy C. , Kaji Izumi , Postema Meagan M. , Faust James J. , Meyer Anne R. , Williams Janice A. , Fitz Gillian N. , Tyska Matthew J. , Wilson Jean M. , Goldenring James R.
Published: September 2019

In patients with inactivating mutations in myosin Vb (Myo5B), enterocytes show large inclusions lined by microvilli. The origin of inclusions in small-intestinal enterocytes in microvillus inclusion disease is currently unclear. We postulated that inclusions in Myo5b KO mouse enterocytes form through invagination of the apical brush border membrane. 70-kD FITC-dextran added apically to Myo5b KO intestinal explants accumulated in intracellular inclusions. Live imaging of Myo5b KO–derived enteroids confirmed the formation of inclusions from the apical membrane. Treatment of intestinal explants and enteroids with Dyngo resulted in accumulation of inclusions at the apical membrane. Inclusions in Myo5b KO enterocytes contained VAMP4 and Pacsin 2 (Syndapin 2). Myo5b;Pacsin 2 double-KO mice showed a significant decrease in inclusion formation. Our results suggest that apical bulk endocytosis in Myo5b KO enterocytes resembles activity-dependent bulk endocytosis, the primary mechanism for synaptic vesicle uptake during intense neuronal stimulation. Thus, apical bulk endocytosis mediates the formation of inclusions in neonatal Myo5b KO enterocytes.
Atomistic simulations on nanoimprinting of copper by aligned carbon nanotube arrays under a high-frequency mechanical vibration
Authors: Li Lili , Xia Zhenhai , Yang Yanqing , Yuan M N
Published: September 2019

Nanoimprinting behaviors of copper substrates and double-walled carbon nanotubes with interwall sp
3 bonds are investigated using molecular dynamics simulations. A high-frequency mechanical vibration with various amplitudes is applied on the carbon nanotube (CNT) mold and copper substrate in different directions. Results show that exciting mechanical resonances both on the CNT and substrate drastically decrease the maximum imprint force and interfacial friction up to 50% under certain amplitudes. Meanwhile, it is demonstrated that defects occur in the {111} plane in the copper substrate during nanoimprinting. For different CNT array densities, a higher grafting density needs more imprint force to transfer patterns. The maximum imprint force for a large range of CNT array densities can be reduced by vibrational perturbations, while reduction rates depend on the CNT grafting density. This work sheds deep insights into the nanoimprint process at the atomic level, suggesting that vibration perturbation is an effective approach for improving the nanoimprinting accuracy and preventing the fracture of nanopatterns.
Blind deconvolution in model-based iterative reconstruction for CT using a normalized sparsity measure
Authors: Hehn Lorenz , Tilley Steven , Pfeiffer Franz , Stayman J Webster
Published: September 2019

Model-based iterative reconstruction techniques for CT that include a description of the noise statistics and a physical forward model of the image formation process have proven to increase image quality for many applications. Specifically, including models of the system blur into the physical forward model and thus implicitly performing a deconvolution of the projections during tomographic reconstruction, could demonstrate distinct improvements, especially in terms of resolution. However, the results strongly rely on an exact characterization of all components contributing to the system blur. Such characterizations can be laborious and even a slight mismatch can diminish image quality significantly. Therefore, we introduce a novel objective function, which enables us to jointly estimate system blur parameters during tomographic reconstruction. Conventional objective functions are biased in terms of blur and can yield lowest cost to blurred reconstructions with low noise levels. A key feature of our objective function is a new normalized sparsity measure for CT based on total-variation regularization, constructed to be less biased in terms of blur. We outline a solving strategy for jointly recovering low-dimensional blur parameters during tomographic reconstruction. We perform an extensive simulation study, evaluating the performance of the regularization and the dependency of the different parts of the objective function on the blur parameters. Scenarios with different regularization strengths and system blurs are investigated, demonstrating that we can recover the blur parameter used for the simulations. The proposed strategy is validated and the dependency of the objective function with the number of iterations is analyzed. Finally, our approach is experimentally validated on test-bench data of a human wrist phantom, where the estimated blur parameter coincides well with visual inspection. Our findings are not restricted to attenuation-based CT and may facilitate the recovery of more complex imaging model parameters.
Contribution of rice variety renewal and agronomic innovations to yield improvement and greenhouse gas mitigation in China
Authors: Zhang Yi , Jiang Yu , Tai Amos P K , Feng Jinfei , Li Zhijie , Zhu Xiangcheng , Chen Jin , Zhang Jun , Song Zhenwei , Deng Aixing , Lal Rattan , Zhang Weijian
Published: September 2019

China’s rice agriculture, a primary source of greenhouse gases (GHGs), has experienced great changes in the last five decades due to changes in dominant varieties and farming practices. However, the impacts of these changes on GHG emissions have not been comprehensively assessed. While most earlier studies focused on the GHG emissions per unit area, recent research indicated that the yield-scaled impact may better reflect the reality. Through integrating the results from a meta-analysis, two multi-site field experiments and an expert survey, we quantify the integrated impacts of different practices on both area- and yield-scaled GHG emissions in China. Results from the expert survey showed that rice planting area has shifted northwards, and alternate water-saving (WS) irrigation has been applied in nearly 78% of Chinese rice paddy areas in both the rice nursery stage and post-transplanting period over the past five decades. The changes of these practices and replacement of new rice varieties have increased China’s rice yield by 131%. During the same period, cropping system adjustment, variety replacement, and implementation of WS irrigation have reduced total GHG emissions by 7%, 31%, and 42%, respectively. Also, the major decrease in GWP occurred prior to the 2000s, and the decreasing trend continued in the post-2000s period but at a slower rate. Our results have some limitations as these estimates ignore a number of important variations and interactions among management factors as well as climatic and edaphic conditions. Still, our findings illustrate that it is possible to enhance rice productivity at reduced environmental costs through screening for low emission varieties and agronomic practices. Future innovations should ensure that rice farming progressively adapts to climate change, while continuing to reduce GHG emissions.
Islands for an Anxious Empire: Japan’s Pacific Island Mandate
Authors: Loo Tze M.
Published: September 2019

A century after the victorious Allied powers distributed their spoils of victory in 1919, the world still lives with the geopolitical consequences of the mandates system established by the League of Nations. The Covenant article authorizing the new imperial dispensation came cloaked in the old civilizationist discourse, entrusting sovereignty over “peoples not yet able to stand by themselves under the strenuous conditions of the modern world” to the “advanced nations” of Belgium, England, France, Japan, and South Africa. In this series of AHR “reflections” on the mandates, ten scholars of Europe, Africa, the Middle East, Asia, and the international order consider the consequences of the new geopolitical order birthed by World War I. How did the reshuffling of imperial power in the immediate postwar period configure long-term struggles over minority rights, decolonization, and the shape of nation-states when the colonial era finally came to a close? How did the alleged beneficiaries—more often the victims—of this “sacred trust” grasp their own fates in a world that simultaneously promised and denied them the possibility of self-determination? From Palestine, to Namibia, to Kurdistan, and beyond, the legacies of the mandatory moment remain pressing questions today.
Overexpression of PtHMGR enhances drought and salt tolerance of poplar
Authors: Wei Hui , Movahedi Ali , Xu Chen , Sun Weibo , Li Lingling , Wang Pu , Li Dawei , Zhuge Qiang
Published: September 2019

Background and Aims

Soil salinization and aridification are swiftly engulfing the limited land resources on which humans depend, restricting agricultural production. Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is important in the biosynthesis of terpenoids, which are involved in plant growth, development and responses to environmental stresses. This study aimed to provide guidance for producing salt- and drought-resistant poplar.

Methods

A protein expression system was used to obtain PtHMGR protein, and high-performance liquid chromatography was used to detect the activity of PtHMGR protein in vitro. In addition, a simplified version of the leaf infection method was used for transformation of ‘Nanlin895’ poplar (Populus×euramericana). qRT–PCR was used to identify expression levels of genes.

Key Results

PtHMGR catalysed a reaction involving HMG-CoA and NADPH to form mevalonate. Overexpression of PtHMGR in Populus × euramericana ‘Nanlin895’ improved drought and salinity tolerance. In the presence of NaCl and PEG6000, the rates of rooting and survival of PtHMGR-overexpressing poplars were higher than those of wild-type poplars. The transgenic lines also exhibited higher proline content and peroxidase and superoxide dismutase activities, and a lower malondialdehyde level under osmotic stress. In addition, the expression of genes related to reactive oxygen species (ROS) scavenging and formation was altered by osmotic stress. Moreover, the effect of osmotic stress on transcript levels of stress-related genes differed between the transgenic and wild-type poplars.

Conclusion

PtHMGR catalysed a reaction involving HMG-CoA and NADPH to form mevalonate in vitro. Overexpression of PtHMGR promoted root development, increased the expression of ROS scavenging-related genes, decreased the expression of ROS formation-related genes, and increased the activity of antioxidant enzymes in transgenic poplars, enhancing their tolerance of osmotic stress. In addition, overexpression of PtHMGR increased expression of the stress-related genes KIN1, COR15 and AAO3 and decreased that of ABI, MYB, MYC2 and RD22, enhancing the stress resistance of poplar.
Social Media’s Influence on Breast Augmentation
Authors: Zahedi Sanam , Hancock Ellen , Hameed Samee , Phillips Linda G , Moliver Clayton L
Published: September 2019

Background

The purpose of this study is to evaluate if and what social media use influences our patients’ decisions to undergo breast augmentation.

Objectives

A single-institution study was designed to evaluate women who underwent elective breast augmentation from 2017 to 2018.

Methods

Patients were contacted via validated, prompted telephone survey. Data regarding their demographic information and social media utilization pertaining to breast augmentation were collected after obtaining verbal consent.

Results

Inclusion criteria were met by 180 patients, of which 69% participated in the survey. Ninety-seven percent of the participants reported utilizing social media in general; the most common platforms were Facebook, Instagram, and the physician’s website. Millennials (97%) and Generation X (92%) utilized social media the most and none of the baby boomers. Sixty-four percent of participants reported utilizing some form of social media to research breast augmentation, with the most common resource being Instagram. When analyzing the impact of the social media resources utilized by the participants, Instagram was reported as the most impactful at 54%. Only 18% of participants were utilizing a physician’s social media account to research breast augmentation. Among the 50% of patients who utilized social media to compare their surgeon’s work with another physician’s, the majority (83%) were utilizing the physician’s website.

Conclusions

Social media influences patients’ education and decisions to undergo breast augmentation, with Instagram being the most impactful. This study evaluated the patient population to stay up to date on their social media utilization and resources of education prior to breast augmentation.
Interindividual spacing affects the finder’s share in ring-tailed coatis (Nasua nasua)
Authors: Hirsch Ben T , Malpass Erica , Di Blanco Yamil E
Published: September 2019

Social foraging models are often used to explain how group size can affect an individual’s food intake rate and foraging strategies. The proportion of food eaten before the arrival of conspecifics, the finder’s share, is hypothesized to play a major role in shaping group geometry, foraging strategy, and feeding competition. The variables that affect the finder’s share in ring-tailed coatis were tested using a series of food trials. The number of grapes in the food trials had a strong negative effect on the finder’s share and the probability that the finder was joined. The effect of group size on the finder’s share and foraging success was not straightforward and was mediated by sociospatial factors. The finder’s share increased when the time to arrival of the next individual was longer, the group was more spread out, and the finder was in the back of the group. Similarly, the total amount of food eaten at a trial was higher when more grapes were placed, arrival time was longer, and the number of joiners was smaller. Individuals at the front edge of the group found far more food trials, but foraging success was higher at the back of the group where there were fewer conspecifics to join them. This study highlights the importance of social spacing strategies and group geometry on animal foraging tactics and the costs and benefits of sociality.
bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data
Authors: Tang Wenhao , Bertaux François , Thomas Philipp , Stefanelli Claire , Saint Malika , Marguerat Samuel , Shahrezaei Vahid
Published: September 2019

Motivation

Normalization of single-cell RNA-sequencing (scRNA-seq) data is a prerequisite to their interpretation. The marked technical variability, high amounts of missing observations and batch effect typical of scRNA-seq datasets make this task particularly challenging. There is a need for an efficient and unified approach for normalization, imputation and batch effect correction.

Results

Here, we introduce bayNorm, a novel Bayesian approach for scaling and inference of scRNA-seq counts. The method’s likelihood function follows a binomial model of mRNA capture, while priors are estimated from expression values across cells using an empirical Bayes approach. We first validate our assumptions by showing this model can reproduce different statistics observed in real scRNA-seq data. We demonstrate using publicly available scRNA-seq datasets and simulated expression data that bayNorm allows robust imputation of missing values generating realistic transcript distributions that match single molecule fluorescence in situ hybridization measurements. Moreover, by using priors informed by dataset structures, bayNorm improves accuracy and sensitivity of differential expression analysis and reduces batch effect compared with other existing methods. Altogether, bayNorm provides an efficient, integrated solution for global scaling normalization, imputation and true count recovery of gene expression measurements from scRNA-seq data.

Availability and implementation

The R package ‘bayNorm’ is publishd on bioconductor at https://bioconductor.org/packages/release/bioc/html/bayNorm.html. The code for analyzing data in this article is available at https://github.com/WT215/bayNorm_papercode.

Supplementary information

Supplementary data are available at Bioinformatics online.
Historical allopatry and secondary contact or primary intergradation in the Puerto Rican crested anole, Anolis cristatellus, on Vieques Island in the Caribbean
Authors: Quach Quynh N , Reynolds R Graham , Revell Liam J
Published: September 2019

Recent work has revealed surprisingly deep mitochondrial genetic divergence in the lizard Anolis cristatellus among samples obtained from the small Caribbean island of Vieques. Here we sought to determine whether this had resulted from natural or anthropogenic causes, and (if the former) whether divergence occurred in a biogeographical context of allopatry followed by secondary contact, or via isolation-by-distance across the species’ historical range. We first estimated a mitochondrial gene tree for 379 samples and then genotyped 3407 single nucleotide polymorphic sites from 48 individuals using a modified genotyping-by-sequencing approach. We found that A. cristatellus samples from Vieques belong to two highly divergent mitochondrial subclades, but the geographical distribution of these haplogroups indicates that this pattern is probably natural in origin. Analysis of our single nucleotide polymorphic dataset revealed differentiation that is consistent with isolation-by-distance between the western and eastern ends of Vieques, suggesting that the overall pattern of divergence probably reflects primary intergradation with a mitochondrial break on the historical Puerto Rico Bank palaeo-island that happened to coincide with the present-day location of Vieques. Our findings help to underline the growing consensus that results from a single genetic marker can prove highly misleading in studies of historical population genetic structure.