bluuebunny/crossref_metadata_2025 huggingface dataset:
How Rational and Competitive Is the Market for Mutual Funds?*
Authors: Leippold Markus , Rueegg Roger
Published: June 2019

To explore the rationality and competitiveness of the mutual fund industry, we analyze the alpha of active and index mutual funds from a global sample of more than 60,000 equity and fixed income funds and test the null hypothesis that alphas to investors are zero. We distinguish between institutional and retail investors since there are significant differences in management fees, economies of scale, and information asymmetries between these two groups. Using a new robust statistical test, we cannot reject our null hypothesis for the majority of investment categories. We find that the average active fund has less exposure to traditional risk factors, but higher sensitivity to alternative risk premia. Fund persistence and the impact of size and fees add further support to our conclusion that the mutual fund industry is highly competitive, except for US domestic funds. This set of funds is excessively overfunded compared with other fund categories.
Cardiovascular Disease-Related Serum Proteins in Workers Occupationally Exposed to Polycyclic Aromatic Hydrocarbons
Authors: Alhamdow Ayman , Lindh Christian , Albin Maria , Gustavsson Per , Tinnerberg Håkan , Broberg Karin
Published: June 2019

Chimney sweeps have higher incidence and mortality of cardiovascular disease (CVD), likely related to their exposure to polycyclic aromatic hydrocarbons (PAH). In order to identify underlying mechanisms of PAH-related CVD, we here investigated whether PAH exposure was associated with levels of putative CVD-related proteins in serum among currently working chimney sweeps. We enrolled 116 chimney sweeps and 125 unexposed controls, all nonsmoking male workers from Sweden. We measured monohydroxylated PAH metabolites in urine by liquid chromatography coupled to tandem mass spectrometry and a panel of 85 proteins in serum using proximity extension assay. Linear regression analysis adjusted for age and body mass index showed that 25 proteins were differentially expressed between chimney sweeps and the controls (p < .05, adjusted for false discovery rate). Of the 25 proteins, follistatin (FS), prointerleukin-16 (IL-16), and heat shock protein beta-1 (HSP 27) showed positive associations with the monohydroxylated metabolites of PAH in a dose-response manner (p < .05). Pathway and gene ontology analyses demonstrated that the differentially expressed proteins were mainly involved in inflammatory response and immunological functions, such as leukocyte migration, cell movement of leukocytes, and adhesion of immune cells. In conclusion, we found a number of putative CVD-related proteins differentially expressed, between PAH-exposed and unexposed individuals, and mainly involved in inflammation and immune function. Our data warrant protective measures to reduce PAH exposure and longitudinal investigations of the protein profile in chimney sweeps and other occupational groups exposed to PAH.
Short-time xylem tension relaxation prevents vessel refilling and alleviates cryo-fixation artifacts in diffuse-porous Carpinus tschonoskii and Cercidiphyllum japonicum
Authors: Ogasa Mayumi Y , Yazaki Kenichi , Utsumi Yasuhiro , Miki Naoko H , Fukuda Kenji
Published: June 2019

Xylem tension relaxation is an important procedure that closely resembles the in vivo xylem water distribution when measuring conductivity or observing water distribution of plant tissue samples by cryo-scanning electron microscopy (cryo-SEM). Recent studies have shown that partial xylem embolism occurs when samples under tension are cut under water and that gas-filled vessels are refilled during tension relaxation. Furthermore, the frequency of gas-filled vessels has been reported to increase in samples without tension relaxation before cryo-fixation by liquid nitrogen, particularly in samples with significant tension. Here, we examined the effect of tension relaxation on these artifacts in Carpinus tschonoskii and Cercidiphyllum japonicum using magnetic resonance imaging. We observed that xylem embolism rarely occurs in bench-dried samples cut under water. In both species, a small portion of the xylem was refilled within ~1 h after tension relaxation. Cryo-SEM observations revealed that short-time (<1 h) xylem tension relaxation decreases the frequency of gas-filled vessels in samples frozen after xylem tension relaxation regardless of the water potential compared with that in samples frozen without rehydration in both species. Therefore, short-time tension relaxation is necessary to retain xylem water distribution during sample preparation against artifacts.
Metabolic and physiological analyses reveal that Populus cathayana males adopt an energy-saving strategy to cope with phosphorus deficiency
Authors: Zhang Sheng , Tang Duoteng , Korpelainen Helena , Li Chunyang
Published: June 2019

Dioecious trees have evolved sex-specific adaptation strategies to cope with inorganic phosphorus (Pi) limitation. Yet, little is known about the effects of Pi limitation on plant metabolism, particularly in dioecious woody plants. To identify potential gender-specific metabolites appearing in response to Pi limitation in poplars, we studied the metabolic and ionomic responses in the roots and leaves of Populus cathayana Rehd males and females exposed to a 60-day period of Pi deficiency. Besides significant decreases in phosphorus contents in both Pi-deficient roots and leaves, the calcium level decreased significantly and the sulfur content increased significantly in Pi-deficient male roots, while the zinc and ferrum contents increased significantly in Pi-deficient female roots. Inorganic P deficiency caused a smaller change in the abscisic acid content, but a significant increase in the jasmonic acid content was detected in both leaves and roots. Salicylic acid significantly decreased under Pi deficiency in male leaves and female roots. Changes were found in phospholipids and phosphorylated metabolites (e.g., fructose-6-phosphate, glycerol-3-phosphate, glucose-6-phosphate, phosphoric acid and inositol-1-phosphate) in roots and leaves. Both P. cathayana males and females relied on inorganic pyrophosphate-dependent but not on Pi-dependent glycolysis under Pi-deficient conditions. Sex-specific metabolites in leaves were primarily in the category of primary metabolites (e.g., amino acids), while in roots primarily in the category of secondary metabolites (e.g., organic acids) and sugars. The metabolome analysis revealed that sexually different pathways occurred mainly in amino acid metabolism, and the tissue-related differences were in the shikimate pathway and glycolysis. We observed changes in carbon flow, reduced root biomass and increased amino acid contents in P. cathayana males but not in females, which indicated that males have adopted an energy-saving strategy to adapt to Pi deficiency. Thus, this study provides new insights into sex-specific metabolic responses to Pi deficiency.
Prevalence and Outcome of Preterm Births in the National Referral Hospital in Bhutan: An Observational Study
Authors: Pradhan Dinesh , Nishizawa Yoriko , Chhetri Hari P
Published: June 2019

Introduction

Preterm birth-related complications are the leading cause of under-5 mortality globally. Bhutan does not have a reliable preterm birth rate or data regarding outcome of preterm babies.

Aim

To determine the preterm birth rate at the Jigme Dorji Wangchuck National Referral Hospital (JDWNRH) in Thimphu, Bhutan, and assess their outcomes.

Methods

All live preterm births at JDWNRH from 1 January 2017 to 31 December 2017 were followed from birth till hospital discharge. Maternal demographic data, pregnancy details and delivery details were collected. Morbidity and mortality information as well as discharge outcome were collected on babies admitted to neonatal intensive care unit (NICU).

Results

Preterm birth rate among live births was 6.4%. Most mothers were younger than 30 years, housewives and had secondary education. Pregnancy registration rate and adequacy of antenatal visits were high. Most preterm births were singleton and the predominant mode of delivery was cesarean section. More than half of the births were initiated spontaneously, and the male:female ratio was 1.2:1. Most babies were late preterm and low birth weight. Half of them required NICU admission. Overall mortality rate was 11% and 21.6% for admitted preterm neonates. Preterm small-for-gestational-age neonates, and those born after provider-initiated preterm birth had significantly increased risk of mortality. Most preterm neonates were discharged without complications. The rate of extrauterine growth restriction was high.

Conclusion

This is the first study on the prevalence of preterm births and their outcomes in the largest tertiary-care hospital in Bhutan.
Catastrophic health care expenditure due to septic shock and dengue shock in Vietnam
Authors: McBride Angela , Thuy Duong B , Chau Nguyen V Vinh , Thwaites C Louise , Turner Hugo C , Hao Nguyen V
Published: June 2019

Background

The cost of treatment for infectious shock in intensive care in Vietnam is unknown.

Methods

We prospectively investigated hospital bills for adults treated for septic and dengue shock in Vietnam and calculated the proportion who faced catastrophic health care expenditures.

Results

The median hospital bills were US$617 for septic shock (n=100) and US$57 for dengue shock (n=88). Catastrophic payments were incurred by 47% (47/100) and 13% (11/88) of patients with septic shock and dengue shock, respectively, and 56% (25/45) and 84% (5/6) fatal cases of septic shock and dengue shock respectively.

Conclusions

Further advocacy is required to moderate insurance co-payments for costly critical care interventions.
Repeated administration of synthetic cathinone 3,4-methylenedioxypyrovalerone persistently increases impulsive choice in rats
Authors: Hyatt William S. , Berquist Michael D. , Chitre Neha M. , Russell Lauren N. , Rice Kenner C. , Murnane Kevin S. , Fantegrossi William E.
Published: June 2019

3,4-Methylenedioxypyrovalerone (MDPV) is a selective catecholamine reuptake inhibitor abused for its psychostimulant properties. This study examined if MDPV administration alters impulsive choice measured by delay discounting in rats. Three groups of rats were tested in daily delay discounting sessions to determine the effects of acute cocaine (1.0–30.0 mg/kg), MDPV (0.1–3.0 mg/kg), or saline on mean adjusted delay (MAD). Dose-dependent decreases in MAD were elicited only by acute MDPV, which also suppressed operant responding at the highest dose. Next, rats received post-session injections (30.0 mg/kg cocaine, 3.0 mg/kg MDPV, or saline) every other day for a total of 10 injections. MAD increased during saline treatment, did not change during cocaine treatment, and was reduced during MDPV treatment. In dose-effect re-determinations, no acute drug effects on MAD were observed, but compared to the initial dose-effect determination, MDPV suppressed operant responding in more animals, with zero animals completing trials at the highest dose. All saline and MDPV-treated subjects were sacrificed, and striatal and cortical dopamine levels were quantified by HPLC. These studies indicate that administration of MDPV may increase impulsive choice acutely and persistently. These proimpulsive effects are possibly mediated by increases in striatal dopamine turnover.
Role of Ancillary Procedures in Facial Rejuvenation
Authors: Rohrich Rod. J. , Mohan Raja
Published: June 2019

Face-lift techniques have evolved beyond the concept of lifting and now include incorporating superficial and deep filling of facial fat compartments to address volume deflation and aging. In addition to traditional face-lift methods involving the excision and tightening of skin and the underlying soft tissues, the following ancillary procedures have become paramount in achieving an optimal result: blending the lid-cheek junction; chin augmentation; lobule augmentation; hand rejuvenation; perioral rejuvenation; chemical peels; and laser resurfacing. We presented a summary of these integral techniques.
Vertical Augmentation Mastopexy with Implant Isolation and Tension Management
Authors: Hubbard Thomas J.
Published: June 2019

Background:

The increasingly popular vertical method of mastopexy is less commonly the technique of choice in augmentation mastopexy possibly due to concerns raised in the literature. The purpose of this report is to evaluate safety and satisfaction of the author’s variation of the vertical method in this combination surgery. It includes unique tension management steps and total implant isolation from cut parenchyma.

Methods:

A retrospective analysis was done of 105 consecutive patients treated with the author’s method over an 8 year 6 month period. Clinical outcomes were examined, and a Breast-Q survey and Spear’s 2004 survey were mailed to all patients who agreed to it by phone.

Results:

There were no hematomas or delayed healing but one pulmonary embolus treated as an outpatient and one infection appearing 6 weeks postoperatively. There were only 3 grade 3 or 4 capsular contractures. Sixty-seven patients consented to the survey and 36 were returned. With Breast-Q, there was a mean score of 82.78 for outcome satisfaction and 75.94 for satisfaction with breasts. Spear’s survey confirmed high satisfaction with 90.9% indicating that they were satisfied or extremely satisfied. Comparison with Spear’s own surgical results did not reach statistical significance.

Conclusions:

The author’s specific adaptation of vertical augmentation mastopexy appears to be very safe and successfully addresses a variety of healing, tension, and exposure concerns mentioned in the literature. Implant isolation may decrease capsular contracture rate. Both Breast-Q survey and Spear’s more specific survey indicate high patient satisfaction.
Use of Acellular Dermal Matrix to Prevent Recurrence of Radioulnar Heterotopic Ossification
Authors: Gould Daniel J. , Rahgozar Paymon , Nagengast Eric S. , Kulber David A.
Published: June 2019

Radioulnar heterotopic ossification is a rare occurrence found in approximately 2% of all forearm injuries. Treatment is complicated by relatively high recurrence rates. Strategies to decrease recurrence have included the range of motion exercises and the interposition of inert or autogenous barriers. We report on the interposition of human acellular dermal matrix (ADM) for the treatment of distal radioulnar synostosis. We report a novel technique for the treatment of distal radioulnar heterotopic ossification. After resection, ADM in a cigar-shaped construct is interposed between the radius and ulna. Patients are followed clinically and radiographically. Two female patients were treated. Both patients had significant improvement in the range of motion in supination and pronation of the affected wrist postoperatively with an average follow-up of 36 months. There were no postoperative complications. Neither patient had recurrent disease. We describe the successful treatment of 2 patients with distal radioulnar heterotopic ossification with the use of human ADM. The ADM provides a barrier between the radius and ulna to prevent the recurrent formation of heterotopic ossification. ADM usage results in no donor site morbidity and is theoretically more resistant to infection when compared with nonbiologic barriers such as silicone and Integra. This technique is a simple, safe, and effective way to treat and prevent the recurrence of radioulnar heterotopic ossification.
Smartphone-based Gonio-Imaging: A Novel Addition to Glaucoma Screening Tools
Authors: Kumar Nilesh , Francesco Bandello , Sharma Ashish
Published: June 2019

Gonioscopy is one of the most difficult skill acquired by ophthalmologists. It is one of the key components of glaucoma diagnosis and management. Smartphone based imaging solutions have revolutionised the imaging in ophthalmology by virtue of their ease of use and portability. Authors hereby describe a smartphone based gonioimaging technique with a 4-mirror goniolens, which can detect the gross findings in anterior chamber angle, and thus can be utilised as screening tool for glaucoma.
Diabetic Ketoacidosis Management in the Emergency Department: Implementation of a Protocol to Reduce Variability and Improve Safety
Authors: Griffey Richard T. , Schneider Ryan M. , Malone Nora , Peterson Charlie , McCammon Craig
Published: June 2019

Emergency departments (EDs) are the primary venue for diagnosis and initiation of treatment of diabetic ketoacidosis (DKA). Typically managed in an intensive care unit (ICU), in many medical centers, limited ICU bed availability necessitates DKA-extended ED management until sufficient improvement for admission to a non-ICU bed. Although DKA treatment is well established, coordinating safe and effective extended care in a busy ED is complex. Recurrent problems in this high-risk transition of care led us to improvement efforts. We studied the impact of a standardizing ED DKA management in two phases: rollout of a DKA pathway in our computerized order entry system followed by audit and feedback. We evaluated adherence, clinical process, operational, and safety measures following these interventions. Adherence to the pathway was initially slow, improving significantly after audit and feedback. We observed mixed improvements in clinical processes, no changes in operational metrics (as expected), and reductions in variability for several measures. There were no deteriorations and improvements in measures of safety, and a reduction in the number of adverse event reports in the postimplementation periods.
A Quality Improvement Approach to External Infliximab Infusions in Pediatric Inflammatory Bowel Disease
Authors: Gupta Shivani R. , Crandall Wallace V. , Donegan Amy , Johnson Marci , Drobnic Barbara , Oates Melanie , Boyle Brendan , Maltz Ross M. , Dotson Jennifer L.
Published: June 2019

Objectives:

We used a quality improvement (QI) approach to improve access and reduce barriers to care by increasing the number of external infliximab infusions at our pediatric inflammatory bowel disease center.

Methods:

Using an iterative QI strategy, pediatric patients ≥12 years of age with inflammatory bowel disease were offered the opportunity to receive infliximab infusions at home/an external infusion center. They were required to first have >5 infusions at the hospital without any significant infusion reactions. Data were collected and tracked monthly using P‐charts. Comparisons between control chart centerlines were analyzed using the Fisher exact test.

Results:

Fifty‐four patients received external infusions, 87% had Crohn disease, 63% boys, average age 17.6 ± 2.9 years, and 89% with private insurance. From September 2016 to January 2018, the percentage of eligible patients receiving external infusions was approximately 7%, increasing to approximately 30% by January 2018. A centerline shift, representing a statistically significant change, occurred in October 2016 and June 2017 (P < 0.001). No serious safety concerns have occurred.

Conclusions:

Through a multidisciplinary team of stakeholders using QI strategies, we now offer external infusion service options to all appropriate patients as routine practice. Home infusions are a viable option to reduce barriers to care, and our patients did not experience any safety events.
Paying Attention to Speech: The Role of Cognitive Capacity and Acquired Experience
Authors: Lambez Bar , Agmon Galit , Har-Shai Paz , Rassovsky Yuri , Golumbic Elana Zion
Published: June 2019

Managing attention in multi-speaker environments is a challenging feat that is critical for human performance. However, why some people are better than others in allocating attention appropriately, remains highly unknown. Here we investigated the contribution of two factors – Cognitive Capacity and Acquired Experience – to performance on two different types of Attention task: Selective Attention to one speaker and Distributed Attention among multiple concurrent speakers. We compared performance across three groups: Individuals with low (n=20) and high cognitive capacity (n=26), and Aircraft Pilots (n=25), who have gained extensive experience on both Selective and Distributed attention to speech through their training and profession. Results indicate that both types of Attention benefit from higher Cognitive Capacity, suggesting reliance on common capacity-limited resources. However, only Selective Attention was further improved in the Pilots, pointing to its flexible and trainable nature, whereas Distributed Attention seems to suffer from more fixed and hard-wired processing-bottlenecks.
Influence of genetic polymorphism on transcriptional enhancer activity in the malaria vector Anopheles coluzzii
Authors: Nardini Luisa , Holm Inge , Pain Adrien , Bischoff Emmanuel , Gohl Daryl M , Zongo Soumanaba , Guelbeogo Wamdaogo M. , Sagnon N’Fale , Vernick Kenneth D , Riehle Michelle M
Published: June 2019

Enhancers are cis-regulatory elements that control most of the developmental and spatial gene expression in eukaryotes. Genetic variation of enhancer sequences is known to influence phenotypes, but the effect of enhancer variation upon enhancer functional activity and downstream phenotypes has barely been examined in any species. In the African malaria vector, Anopheles coluzzii, we identified a pilot set of candidate enhancers in the proximity of genes relevant for immunity, insecticide resistance, and development. The candidate enhancers were functionally validated using luciferase reporter assays, and their activity was found to be essentially independent of their physical orientation, a typical property of enhancers. All of the enhancer intervals segregated genetically polymorphic alleles, which displayed significantly different levels of functional activity, and inactive null alleles were also observed. Deletion mutagenesis and functional testing revealed a modular structure of positive and negative regulatory elements within the tested enhancers. The enhancer alleles carry genetic polymorphisms that also segregate in wild A. coluzzii populations in West Africa, indicating that enhancer variants with likely phenotypic consequences are frequent in nature. These results demonstrate the feasibility of screening for naturally polymorphic A. coluzzii enhancers that underlie important aspects of malaria transmission and vector biology.
PI4K2β constrains non-canonical Wnt-PCP signalling and is localised by PAR-1 (MARK2/3) phosphorylation
Authors: Tsang S. M. , Cheng William , Li Jingjing , Green Jeremy B. A.
Published: June 2019

Canonical Wnt signalling is critically important in embryonic cell-type specification and cancer, while non-canonical Wnt signalling is primarily implicated in physical morphogenesis, especially planar cell polarity (PCP). Both are modulated by the polarity kinase PAR-1 (MARK2/3). PAR-1 phosphorylates the Wnt transducer Dishevelled, but there is evidence that it exerts control through other targets. Here we describe an in vitro screen for new targets of PAR-1 in which we identified phosphatidyl-inositol-4-kinase-2-beta (PI4K2β) as a substrate. Perturbation phenotypes and reporter assays in vivo show that PI4K2β inhibits both canonical and non-canonical Wnt pathways, in contrast to PI4K2α, which promotes canonical but does not affect non-canonical signalling. We show that PI4K2β acts in Wnt-responding tissue, not in Wnt production or secretion. Subcellularly, PI4K2β is cortically enriched, unlike PI4K2α, and is basolateral in polarised cells. Mutation of the PAR-1 phosphorylation site of PI4K2β mis-localises it and the endogenous core PCP protein, Vangl2. Our results reveal that PAR-1 interacts with the vertebrate PCP signalling pathway via PI4K2β.
The soil microbial community alters patterns of selection on flowering time and fitness related traits in Ipomoea purpurea
Authors: Chaney Lindsay , Baucom Regina S.
Published: June 2019

Premise of the study

Plant flowering time plays an important role in plant fitness and thus evolutionary processes. Soil microbial communities are diverse and have a large impact, both positive and negative, on the host plant. However, owing to few available studies, how the soil microbial community may influence the evolutionary response of plant populations is not well understood. Here we sought to uncover if below-ground microbial communities act as an agent of selection on flowering and growth traits in the common morning glory, Ipomoea purpurea.

Methods

We performed a controlled greenhouse experiment in which genetic lines of I. purpurea were planted into either sterilized soils, or soils that were sterilized and re-inoculated with the microbial community from original field soil. This allowed us to directly test the influence of alterations to the microbial community on plant growth, flowering, and fitness, as well as assess patterns of selection in both soil microbial environments.

Results

We found that a more complex soil microbial community resulted in larger plants that produced more flowers. Selection strongly favored earlier flowering when plants were grown in the complex microbial environment than compared to sterilized soil. Additionally, we uncovered a pattern of negative correlational selection on growth rate and flowering time, indicating that selection favored different combinations of growth and flowering traits in the simplified versus complex soil community.

Conclusions

Together these results suggest the soil microbial community is a selective agent on flowering time and ultimately that soil microbial community influences important plant evolutionary processes.
JARA: ‘Just Another Red-List Assessment’
Authors: Winker Henning , Pacoureau Nathan , Sherley Richard B.
Published: June 2019

Identifying species at risk of extinction is necessary to prioritise conservation efforts. The International Union for Conservation of Nature’s (IUCN) Red List of Threatened Species is the global standard for quantifying extinction risk, with many species categorised according to population reduction thresholds. We introduce the Bayesian state-space framework ‘JARA’ (Just Another Red-List Assessment). Designed as decision-support tool, JARA allows both process error and uncertainty to be incorporated into IUCN Red List assessments under criterion A. JARA is implemented via an R package that is designed to be easy to use, rapid and widely applicable, so conservation practitioners can apply it to their own count or relative abundance data. JARA outputs display easy to interpret graphics of the posterior probability of the population trend against the corresponding IUCN Red List categories, as well as additional graphics to describe the timeseries and model diagnostics. We illustrate JARA using three real-world examples: (1) relative abundance indices for two elasmobranchs, Yellowspotted SkateLeucoraja wallaceiand Whitespot SmoothhoundMustelus palumbes; (2) a comparison of standardized abundance indices for Atlantic Blue MarlinMakaira nigricansand (3) absolute abundance data for Cape GannetsMorus capensis. Finally, using a simulation experiment, we demonstrate how JARA provides greater accuracy than two approaches commonly used to assigning a Red List Status under criterion A. Tools like JARA can help further standardise Red List evaluations, increasing objectivity and lowering the risk of misclassification, with substantial benefits for global conservation efforts.
A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification
Authors: Wyman Dana , Balderrama-Gutierrez Gabriela , Reese Fairlie , Jiang Shan , Rahmanian Sorena , Forner Stefania , Matheos Dina , Zeng Weihua , Williams Brian , Trout Diane , England Whitney , Chu Shu-Hui , Spitale Robert C. , Tenner Andrea J. , Wold Barbara J. , Mortazavi Ali
Published: June 2019

Alternative splicing is widely acknowledged to be a crucial regulator of gene expression and is a key contributor to both normal developmental processes and disease states. While cost-effective and accurate for quantification, short-read RNA-seq lacks the ability to resolve full-length transcript isoforms despite increasingly sophisticated computational methods. Long-read sequencing platforms such as Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) bypass the transcript reconstruction challenges of short reads. Here we introduce TALON, the ENCODE4 pipeline for platform-independent analysis of long-read transcriptomes. We apply TALON to the GM12878 cell line and show that while both PacBio and ONT technologies perform well at full-transcript discovery and quantification, each displayed distinct technical artifacts. We further apply TALON to mouse hippocampus and cortex transcriptomes and find that 422 genes found in these regions have more reads associated with novel isoforms than with annotated ones. We demonstrate that TALON is a capable of tracking both known and novel transcript models as well as their expression levels across datasets for both simple studies and in larger projects. These properties will enable TALON users to move beyond the limitations of short-read data to perform isoform discovery and quantification in a uniform manner on existing and future long-read platforms.
Cell cycle oscillators underlying orderly proteolysis of E2F8
Authors: Wasserman Danit , Nachum Sapir , Cohen Meital , Enrico Taylor P , Noach-Hirsh Meirav , Parasol Jasmin , Zomer-Polak Sarit , Auerbach Naomi , Sheinberger-Chorni Evelin , Nevenzal Hadas , Levi-Dadon Nofar , Wang Xianxi , Lahmi Roxane , Michaely Efrat , Gerber Doron , Emanuele Michael J. , Tzur Amit
Published: June 2019

E2F8 is a transcriptional repressor that antagonizes the canonical cell cycle transcription factor E2F1. Despite the importance of this atypical E2F family member in cell cycle, apoptosis and cancer, we lack a complete description of the mechanisms that control its dynamics. To address this question, we developed a complementary set of static and dynamic cell-free systems of human origin, which recapitulate inter-mitotic and G1 phases, and a full transition from pro-metaphase to G1. This revealed an interlocking molecular switch controlling E2F8 degradation at mitotic exit, involving dephosphorylation of Cdk1 sites in E2F8 and the activation of APC/CCdh1, but not APC/CCdc20. Further, we revealed a differential stability of E2F8, accounting for its accumulation in late G1 while APC/CCdh1 is still active and suggesting a key role for APC/C in controlling G1-S transcription. Finally, we identified SCF-Cyclin F as the ubiquitin ligase controlling E2F8 in G2-phase. Altogether, our data provide new insights into the regulation of E2F8 throughout the cell cycle, illuminating an extensive coordination between phosphorylation, ubiquitination and transcription in promoting orderly cell cycle progression.
Rapid single-step affinity purification of HA-tagged mitochondria from Arabidopsis thaliana
Authors: Kuhnert Franziska , Stefanski Anja , Overbeck Nina , Stühler Kai , Weber Andreas P.M.
Published: June 2019

Photosynthesis in plant cells would not be possible without the supportive role of mitochondria. However, isolation of mitochondria from plant cells, for physiological and biochemical analyses, is a lengthy and tedious process. Established isolation protocols require multiple centrifugation steps and substantial amounts of starting material. To overcome these limitations, we tagged mitochondria in Arabidopsis thaliana with a triple haemagglutinin-tag for rapid purification via a single affinity purification step. This protocol yields a substantial quantity of highly pure mitochondria from 1 g of Arabidopsis seedlings. The purified mitochondria were suitable for enzyme activity analyses and yielded sufficient amounts of proteins for deep proteomic profiling. We applied this method for the proteomic analysis of the Arabidopsis bou-2 mutant deficient in the mitochondrial glutamate transporter À bout de souffle (BOU) and identified 27 differentially expressed mitochondrial proteins compared with transgenic Col-0 controls. Our work also sets the stage for the development of advanced mitochondria isolation protocols for distinct cell types.

One-sentence summary

Affinity-tagging of mitochondria in plant cells with a triple hemagglutinin-tag enables single-step affinity purification of mitochondria in less than 20 min.
Robust Normalization of Luciferase Reporter Data
Authors: Repele Andrea , Manu
Published: June 2019

Transient Luciferase reporter assays are widely used in the study of gene regulation and intracellular cell signaling. In order to control for sample-to-sample variation in luminescence arising from variability in transfection efficiency and other sources, an internal control reporter is co-transfected with the experimental reporter. The luminescence of the experimental reporter is normalized against the control by taking the ratio of the two. Here we show that this method of normalization, “ratiometric”, performs poorly when the transfection efficiency is low and leads to biased estimates of relative activity. We propose an alternative methodology based on linear regression that is much better suited for the normalization of reporter data, especially when transfection efficiency is low. We compare the ratiometric method against three regression methods on both simulated and empirical data. Our results suggest that robust errors-in-variables (REIV) regression performs the best in normalizing Luciferase reporter data. We have made the R code for Luciferase data normalization using REIV available on GitHub.
Bone marrow adipose tissue is a unique adipose subtype with distinct roles in systemic glucose homeostasis
Authors: Suchacki Karla J. , Tavares Adriana A.S. , Mattiucci Domenico , Scheller Erica L. , Papanastasiou Giorgos , Gray Calum , Sinton Matthew C. , Ramage Lynne E. , McDougald Wendy A. , Lovdel Andrea , Sulston Richard J. , Thomas Benjamin J. , Nicholson Bonnie M. , Drake Amanda J. , Alcaide-Corral Carlos J. , Said Diana , Poloni Antonella , Cinti Saverio , MacPherson Gavin J. , Dweck Marc R. , Andrews Jack P.M. , Williams Michelle C. , Wallace Robert J. , van Beek Edwin J.R. , MacDougald Ormond A. , Morton Nicholas M. , Stimson Roland H. , Cawthorn William P.
Published: June 2019

Bone marrow adipose tissue (BMAT) represents >10% of total adipose mass, yet unlike white or brown adipose tissues (WAT or BAT), its role in systemic metabolism remains unclear. Using transcriptomics, we reveal that BMAT is molecularly distinct to WAT but is not enriched for brown or beige adipocyte markers. Instead, pathway analysis indicated altered glucose metabolism and decreased insulin responsiveness in BMAT. We therefore tested these functions in mice and humans using positron emission tomography–computed tomography (PET/CT) with18F-fluorodeoxyglucose, including establishing a new method for BMAT identification from clinical CT scans. This revealed that BMAT resists insulin- and cold-stimulated glucose uptake and is thus functionally distinct to WAT and BAT. However, BMAT displayed greater basal glucose uptake than axial bones or subcutaneous WAT, underscoring its potential to influence systemic glucose homeostasis. These PET/CT studies are the first to characterise BMAT functionin vivoand identify BMAT as a distinct, major subtype of adipose tissue.

HIGHLIGHTS

Bone marrow adipose tissue (BMAT) is molecularly distinct to other adipose subtypes.

BMAT is less insulin responsive than WAT and, unlike BAT, is not cold-responsive.

Human BMAT has greater basal glucose uptake than axial bone or subcutaneous WAT.

We establish a PET/CT method for BMAT localisation and functional analysisin vivo.
Functions of ventral visual cortex after bilateral hippocampal loss
Authors: Kim Jiye G. , Gregory Emma , Landau Barbara , McCloskey Michael , Turk-Browne Nicholas B. , Kastner Sabine
Published: June 2019

Repeated stimuli elicit attenuated responses in visual cortex relative to novel stimuli. This adaptation phenomenon can be considered a form of rapid learning and a signature of perceptual memory. Adaptation occurs not only when a stimulus is repeated immediately, but also when there is a lag in terms of time and other intervening stimuli before the repetition. But how does the visual system keep track of which stimuli are repeated, especially after long delays and many intervening stimuli? We hypothesized that the hippocampus supports long-lag adaptation, given that it learns from single experiences, maintains information over delays, and sends feedback to visual cortex. We tested this hypothesis with fMRI in an amnesic patient, LSJ, who has encephalitic damage to the medial temporal lobe resulting in complete bilateral hippocampal loss. We measured adaptation at varying time lags between repetitions in functionally localized visual areas that were intact in LSJ. We observed that these areas track information over a few minutes even when the hippocampus is unavailable. Indeed, LSJ and controls were identical when attention was directed away from the repeating stimuli: adaptation occurred for lags up to three minutes, but not six minutes. However, when attention was directed toward stimuli, controls now showed an adaptation effect at six minutes but LSJ did not. These findings suggest that visual cortex can support one-shot perceptual memories lasting for several minutes but that the hippocampus is necessary for adaptation in visual cortex after longer delays when stimuli are task-relevant.
Mitochondrial DNA Copy Number (mtDNA-CN) Can Influence Mortality and Cardiovascular Disease via Methylation of Nuclear DNA CpGs
Authors: Castellani Christina A. , Longchamps Ryan J. , Sumpter Jason A. , Newcomb Charles E. , Lane John A. , Grove Megan L. , Bressler Jan , Brody Jennifer A. , Floyd James S. , Bartz Traci M. , Taylor Kent D. , Wang Penglong , Tin Adrienne , Coresh Josef , Pankow James S. , Fornage Myriam , Guallar Eliseo , O’Rourke Brian , Pankratz Nathan , Liu Chunyu , Levy Daniel , Sotoodehnia Nona , Boerwinkle Eric , Arking Dan E.
Published: June 2019

Background

Mitochondrial DNA copy number (mtDNA-CN) has been associated with a variety of aging-related diseases, including all-cause mortality. However, the mechanism by which mtDNA-CN influences disease is not currently understood. One such mechanism may be through regulation of nuclear gene expression via the modification of nuclear DNA (nDNA) methylation.

Methods

To investigate this hypothesis, we assessed the relationship between mtDNA-CN and nDNA methylation in 2,507 African American (AA) and European American (EA) participants from the Atherosclerosis Risk in Communities (ARIC) study. To validate our findings we assayed an additional 2,528 participants from the Cardiovascular Health Study (CHS) (N=533) and Framingham Heart Study (FHS) (N=1,995). We further assessed the effect of experimental modification of mtDNA-CN through knockout of TFAM, a regulator of mtDNA replication, via CRISPR-Cas9.

Results

Thirty-four independent CpGs were associated with mtDNA-CN at genome-wide significance (P<5×10-8). Meta-analysis across all cohorts identified six mtDNA-CN associated CpGs at genome-wide significance (P<5×10-8). Additionally, over half of these CpGs were associated with phenotypes known to be associated with mtDNA-CN, including coronary heart disease, cardiovascular disease, and mortality. Experimental modification of mtDNA-CN demonstrated that modulation of mtDNA-CN directly drives changes in nDNA methylation and gene expression of specific CpGs and nearby transcripts. Strikingly, the ‘neuroactive ligand receptor interaction’ KEGG pathway was found to be highly overrepresented in the ARIC cohort (P= 5.24×10-12), as well as the TFAM knockout methylation (P=4.41×10-4) and expression (P=4.30×10-4) studies.

Conclusions

These results demonstrate that changes in mtDNA-CN influence nDNA methylation at specific loci and result in differential expression of specific genes that may impact human health and disease via altered cell signaling.
Do African savanna elephants (Loxodonta africana) eat crops because they crave micronutrients?
Authors: Vogel Susanne Marieke , de Boer Willem Frederik , Masake Moses , Songhurst Anna Catherine , McCulloch Graham , Stronza Amanda , Henley Michelle Deborah , Coulson Tim
Published: June 2019

Elephants can cause negative consequences for both themselves and for humans by consuming agricultural crops. It is unclear whether savanna elephant crop consumption is merely opportunistic behaviour or related to insufficient quality of natural forage. We analysed the role of vegetation quality on elephant crop consumption. We focused on the role of micronutrients, as natural elephant diets are thought to be insufficient in elements such as sodium and phosporus, which can influence their foraging decisions.

For 12 months across four seasons we collected elephant feeding trail data along with tree, grass and crop samples. We investigated how the quality and availability of these items influenced elephant dietary choices across months and seasons. Subsequently, we compared levels of fibre, digestible energy, dry matter intake, and micronutrients, together with secondary compounds (tannins) across the three vegetation groups. As elephants do not make dietary choices based on one component, we also analysed the nutrient balance of food items with right-angle mixture models.

The levels of phosphorus, magnesium and dry matter intake corresponded to foraging preference. Compared to trees and grasses, crops contained significantly higher amounts of digestible energy content, dry matter intake, nitrogen, phosphorus, calcium and magnesium. PCA results showed that crops differed in phosphorus and magnesium levels. The right-angle mixture models indicated that except for one tree species, all food items elephants consumed were relatively deficient in phosphorus.

The combined results of these analyses suggest a phosphorus deficiency in elephant diet in northern Botswana. Crops, with their high absolute phosphorus levels and dry matter intake, provide an alternative source of phosphorus to reduce the deficiency. This may explain the high intensity of crop consumption in the wet season in our study area. A potential mitigation measure against elephant crop consumption might be to provide supplementary phosphorus sources.
Estrogen induces mammary ductal dysplasia
Authors: Itou Junji , Takahashi Rei , Sasanuma Hiroyuki , Tsuda Masataka , Morimoto Suguru , Matsumoto Yoshiaki , Ishii Tomoko , Sato Fumiaki , Takeda Shunichi , Toi Masakazu
Published: June 2019

Mammary ductal dysplasia is a phenotype observed in precancerous lesions and early-stage breast cancer. However, the mechanism of dysplasia formation remains elusive. Here we show, by establishing a novel dysplasia model system, that estrogen, a female hormone, has the potential to cause mammary ductal dysplasia. We injected estradiol (E2), the most active form of estrogen, daily into scid mice with a defect in nonhomologous end joining repair and observed dysplasia formation with cell proliferation at day 30. Moreover, we found that isoflavones inhibited E2-induced dysplasia formation. Our dysplasia model system provides insight into the mechanistic understanding of breast tumorigenesis, and the development of breast cancer prevention.
Calretinin positive neurons form an excitatory amplifier network in the spinal cord dorsal horn
Authors: Smith KM , Browne TJ , Davis O , Coyle A , Boyle KA , Watanabe M , Dickinson SA , Iredale JA , Gradwell MA , Jobling P , Callister RJ , Dayas CV , Hughes DI , Graham BA
Published: June 2019

The passage of nociceptive information is relayed through the spinal cord dorsal horn, a critical area in sensory processing. The neuronal circuits in this region that underpin sensory perception must be clarified to better understand how dysfunction can lead to pathological pain. This study used an optogenetic approach to selectively activate neurons that contain the calcium-binding protein calretinin (CR). We show that CR+ interneurons form an interconnected network that can initiate and sustain enhanced excitatory signaling, and directly relays signals to lamina I projection neurons. In vivo photoactivation of CR+ interneurons resulted in a significant nocifensive behavior that was morphine sensitive and cause a conditioned place aversion. Furthermore, halorhodopsin-mediated inhibition of CR+ interneurons elevated sensory thresholds. These results suggest that neuronal circuits in the superficial dorsal horn that involve excitatory CR+ neurons are important for the generation and amplification of pain, and identify these interneurons as a future analgesic target.
KCND3 is a novel susceptibility locus for early repolarization
Authors: Teumer Alexander , Trenkwalder Teresa , Kessler Thorsten , Jamshidi Yalda , van den Berg Marten E. , Kaess Bernhard , Nelson Christopher P. , Bastiaenen Rachel , De Bortoli Marzia , Rossini Alessandra , Deisenhofer Isabel , Stark Klaus , Assa Solmaz , Braund Peter S. , Cabrera Claudia , Dominiczak Anna F. , Gögele Martin , Hall Leanne M. , Ikram M. Arfan , Kavousi Maryam , Lackner Karl J. ,   Lifelines Cohort Study, Müller Christian , Münzel Thomas , Nauck Matthias , Padmanabhan Sandosh , Pfeiffer Norbert , Spector Tim D. , Uitterlinden Andre G. , Verweij Niek , Völker Uwe , Warren Helen R. , Zafar Mobeen , Felix Stephan B. , Kors Jan A. , Snieder Harold , Munroe Patricia B. , Pattaro Cristian , Fuchsberger Christian , Schmidt Georg , Nolte Ilja M. , Schunkert Heribert , Pramstaller Peter , Wild Philipp S. , van der Harst Pim , Stricker Bruno H. , Schnabel Renate B. , Samani Nilesh J. , Hengstenberg Christian , Dörr Marcus , Behr Elijah R. , Reinhard Wibke
Published: June 2019

The presence of an early repolarization pattern (ERP) on the surface electrocardiogram (ECG) is associated with risk of ventricular fibrillation and sudden cardiac death. Family studies have shown that ERP is a highly heritable trait but molecular genetic determinants are unknown. We assessed the ERP in 12-lead ECGs of 39,456 individuals and conducted a two-stage meta-analysis of genome-wide association studies (GWAS). In the discovery phase, we included 2,181 cases and 23,641 controls from eight European ancestry studies and identified 19 genome-wide significant (p<5E-8) variants in the KCND3 (potassium voltage gated channel subfamily D member 3) gene with a p-value of 4.6E-10. Replication of two loci in four additional studies including 1,124 cases and 12,510 controls confirmed the association at the KCND3 gene locus with a pooled odds ratio of 0.82, p=7.7E-12 (rs1545300 minor allele T). A subsequent GWAS meta-analysis combining all samples did not reveal additional loci. The lead SNP of the discovery stage (rs12090194) was in strong linkage disequilibrium with rs1545300 (r2=0.96, D’=1). Summary statistics based conditional analysis did not reveal any secondary signals. Co-localization analyses indicate causal effects of KCND3 gene expression levels on ERP in both the left ventricle of the heart and in tibial artery.

In this study we identified for the first time a genome-wide significant association of a genetic variant with ERP. Our findings of a locus in the KCND3 gene not only provide insights into the genetic determinants but also into the pathophysiological mechanism of ERP, revealing a promising candidate for functional studies.