bluuebunny/crossref_metadata_2025 huggingface dataset:
Marburg virus survivor immune responses are Th1 skewed with limited neutralizing antibody responses
Authors: Stonier Spencer W. , Herbert Andrew S. , Kuehne Ana I. , Sobarzo Ariel , Habibulin Polina , Dahan Chen V. Abramovitch , James Rebekah M. , Egesa Moses , Cose Stephen , Lutwama Julius Julian , Lobel Leslie , Dye John M.
Published: July 2017

Until recently, immune responses in filovirus survivors remained poorly understood. Early studies revealed IgM and IgG responses to infection with various filoviruses, but recent outbreaks have greatly expanded our understanding of filovirus immune responses. Immune responses in survivors of Ebola virus (EBOV) and Sudan virus (SUDV) infections have provided the most insight, with T cell responses as well as detailed antibody responses having been characterized. Immune responses to Marburg virus (MARV), however, remain almost entirely uncharacterized. We report that immune responses in MARV survivors share characteristics with EBOV and SUDV infections but have some distinct differences. MARV survivors developed multivariate CD4+ T cell responses but limited CD8+ T cell responses, more in keeping with SUDV survivors than EBOV survivors. In stark contrast to SUDV survivors, rare neutralizing antibody responses in MARV survivors diminished rapidly after the outbreak. These results warrant serious consideration for any vaccine or therapeutic that seeks to be broadly protective, as different filoviruses may require different immune responses to achieve immunity.
Fixed points in convex cones
Authors: Monod Nicolas
Published: July 2017

We propose a fixed-point property for group actions on cones in topological vector spaces. In the special case of equicontinuous representations, we prove that this property always holds; this statement extends the classical Ryll-Nardzewski theorem for Banach spaces. When restricting to cones that are locally compact in the weak topology, we prove that the property holds for all distal actions, thus extending the general Ryll-Nardzewski theorem for all locally convex spaces.

Returning to arbitrary actions, the proposed fixed-point property becomes a group property, considerably stronger than amenability. Equivalent formulations are established and a number of closure properties are proved for the class of groups with the fixed-point property for cones.
Direct interaction of the Golgi V-ATPase a-subunit isoform with PI(4)P drives localization of Golgi V-ATPases in yeast
Authors: Banerjee Subhrajit , Kane Patricia M.
Published: July 2017

Luminal pH and phosphoinositide content are fundamental features of organelle identity. Vacuolar H+-ATPases (V-ATPases) drive organelle acidification in all eukaryotes, and membrane-bound a-subunit isoforms of the V-ATPase are implicated in organelle-specific targeting and regulation. Earlier work demonstrated that the endolysosomal lipid PI(3,5)P2activates V-ATPases containing the vacuolar a-subunit isoform in Saccharomyces cerevisiae. Here we demonstrate that PI(4)P, the predominant Golgi phosphatidylinositol (PI) species, directly interacts with the cytosolic amino terminal (NT) domain of the yeast Golgi V-ATPase a-isoform Stv1. Lysine-84 of Stv1NT is essential for interaction with PI(4)P in vitro and in vivo, and interaction with PI(4)P is required for efficient localization of Stv1-containing V-ATPases. The cytosolic NT domain of the human V-ATPase a2 isoform specifically interacts with PI(4)P in vitro, consistent with its Golgi localization and function. We propose that NT domains of Voa-subunit isoforms interact specifically with PI lipids in their organelles of residence. These interactions can transmit organelle-specific targeting or regulation information to V-ATPases.
A recurrence-based approach for validating structural variation using long-read sequencing technology
Authors: Zhao Xuefang , Weber Alexandra M. , Mills Ryan E.
Published: July 2017

Although numerous algorithms have been developed to identify structural variations (SVs) in genomic sequences, there is a dearth of approaches that can be used to evaluate their results. This is significant as the accurate identification of structural variation is still an outstanding but important problem in genomics. The emergence of new sequencing technologies that generate longer sequence reads can, in theory, provide direct evidence for all types of SVs regardless of the length of the region through which it spans. However, current efforts to use these data in this manner require the use of large computational resources to assemble these sequences as well as visual inspection of each region. Here we present VaPoR, a highly efficient algorithm that autonomously validates large SV sets using long-read sequencing data. We assessed the performance of VaPoR on SVs in both simulated and real genomes and report a high-fidelity rate for overall accuracy across different levels of sequence depths. We show that VaPoR can interrogate a much larger range of SVs while still matching existing methods in terms of false positive validations and providing additional features considering breakpoint precision and predicted genotype. We further show that VaPoR can run quickly and efficiency without requiring a large processing or assembly pipeline. VaPoR provides a long read–based validation approach for genomic SVs that requires relatively low read depth and computing resources and thus will provide utility with targeted or low-pass sequencing coverage for accurate SV assessment. The VaPoR Software is available at: https://github.com/mills-lab/vapor.
Comparative Effectiveness of Surgical Treatments for Pediatric Hydrocephalus
Authors: Pan I-Wen , Harris Dominic A , Luerssen Thomas G , Lam Sandi K
Published: July 2017

BACKGROUND

Pediatric hydrocephalus represents a high health care burden in the United States (US). Surgery is the mainstay of treatment.

OBJECTIVE

To perform a comparative effectiveness analysis for endoscopic third ventriculostomy (ETV) and cerebrospinal fluid shunt placement in pediatric hydrocephalus patients in the US using a large administrative claims database through the application of propensity scores matching.

METHODS

The MarketScan® database (Truven Health Analytics, Atlanta, Georgia) 2003 to 2011 was used. Patients 19 yr or younger at first occurrence of ETV or shunt during the study period were included. The study outcome, surgery failure, was defined as further surgical treatment for hydrocephalus subsequent to initial ETV or shunt procedure. Age, etiology of hydrocephalus, and history of shunt were used to create matched samples for the ETV and shunt cohorts. Kaplan–Meier survival curves, stratified log-rank test, and Cox proportional-hazard models were used to analyze samples.

RESULTS

There were 3231 eligible cases (478 ETV; 2753 shunt). Propensity scores matching produced 455 balanced pairs. For matched samples, 326 of 455 (72%) pairs were concordant, while 129 pairs were discordant in surgery outcomes within 3 mo. Among discordant pairs, ETV patients were more likely to experience surgery failure compared to patients receiving shunt (relative risk = 1.4, P value = .011). Furthermore, patients’ age < 1 yr had lower ETV success rates than those with shunt (P value = .009). No similar pattern was found in patients’ age ≥ 1 yr.

CONCLUSION

There was no significant effect on time to failure between patients undergoing ETV and shunt, except in infants’ age <1 yr.
Fusarium oxysporum f. sp. mori, a New Forma Specialis Causing Fusarium Wilt of Blackberry
Authors: Pastrana A. M. , Kirkpatrick S. C. , Kong M. , Broome J. C. , Gordon T. R.
Published: July 2017

Fusarium oxysporum has recently been identified as the cause of a wilt disease affecting blackberry in California and Mexico. Thirty-six isolates of F. oxysporum obtained from symptomatic blackberry plants in California and Mexico were comprised of nine distinct somatic compatibility groups (SCGs). Phylogenetic analysis of a concatenated data set, consisting of sequences of the translation elongation factor 1-α and β-tubulin genes and the intergenic spacer of the ribosomal DNA, identified nine three-locus sequence types, each of which corresponded to an SCG. Six SCGs were present only in California, two only in Mexico, and one in both California and Mexico. An isolate associated with the most common SCG in California was tested for pathogenicity on blueberry, raspberry, strawberry, and lettuce. All blueberry, raspberry, and lettuce plants that were inoculated remained healthy, but two of the five strawberry cultivars tested developed symptoms. The three strawberry cultivars that were resistant to the blackberry pathogen were also resistant to F. oxysporum f. sp. fragariae, the cause of Fusarium wilt of strawberry. We propose to designate strains of F. oxysporum that are pathogenic to blackberry as Fusarium oxysporum f. sp. mori forma specialis nov.
Effects of Wound Size, Amount of Sap, and Number of Blighted Nuts on Infection of Pistachio Organs by Neofusicoccum mediterraneum
Authors: Moral J. , Ahimera N. , Felts D. G. , Morgan D. P. , Michailides T. J.
Published: July 2017

Laboratory and field studies were conducted to determine the effects of wounding of nut exocarp, susceptibility period after wounding, and sap nut on infection of pistachio nut by Neofusicoccum mediterraneum, the main causal agent of panicle and shoot blight of pistachio. Under controlled conditions and in the field, detached nuts were inoculated with a conidial suspension 30 min before or after wounding. In addition, a 30-µl drop of pistachio sap was placed on the surface of noninjured nuts 30 min before or after they were wounded and then inoculated. Wounding increased the disease severity under both controlled and field conditions. The addition of sap increased the susceptibility of nuts under controlled conditions but not in the field, possibly due to dried sap blocking the pathogen infection. When nuts of Kerman, Kalehghouchi, and Golden Hills pistachio were wounded and inoculated at different time periods after wounding; the nuts of the three cultivars were highly susceptible to pathogen infection during at least the first 24 h after wounding. Under field conditions, there was not a clear effect of increasing the number of inoculated nuts per panicle or the inoculation position (basal or apical) in killing (blight) of the panicle. Conversely, inoculations conducted with mycelial plugs resulted in higher disease, increased the proportion of dead panicles, and resulted in faster symptom expression than inoculations conducted with a conidial suspension. To determine the temporal infection pattern, leaves and panicles were regularly collected from different orchards from 2004 to 2007 and the pathogen was isolated on medium. Important differences in latent infection were detected between years and orchards, with nut and rachis being, in general, the tissues most susceptible to infection. Results of this study help in better understanding the dynamic of infection and colonization of pistachio by N. mediterraneum.
Pupillometry-guided Intraoperative Remifentanil Administration versus Standard Practice Influences Opioid Use
Authors: Sabourdin Nada , Barrois Jérôme , Louvet Nicolas , Rigouzzo Agnès , Guye Marie-Laurence , Dadure Christophe , Constant Isabelle
Published: July 2017

Background

Pupillometry has shown promising results for assessing nociception in anesthetized patients. However, its benefits in clinical practice are not demonstrated. The aim of this prospective randomized study was to evaluate the impact of intraoperative pupillometry monitoring on perioperative opioid consumption in major gynecologic surgery.

Methods

After receiving ethics committee approval and written consent of patients, American Society of Anesthesiologists status I to II women undergoing gynecologic surgery were included in this single-blinded, prospective, parallel-arm randomized study. General anesthesia was standardized with propofol–remifentanil target-controlled infusion. Patients were randomly assigned into two groups. In the pupillometry group, remifentanil administration was guided by pupillary diameter changes. In the standard group, remifentanil administration was left to the discretion of the anesthesiologist. The primary outcome was intraoperative remifentanil consumption.

Results

Fifty-five patients were analyzed. Remifentanil consumption was markedly decreased in the pupillometry group (3.8 [3.4 to 4.8 µg · kg–1 · h–1] vs. 7.9 µg · kg–1 · h–1 [6.5 to 9.0 µg · kg–1 · h–1] in the standard group; difference = 4.2 µg · kg–1 · h–1 [95% CI, 3.0 to 5.3 µg · kg–1 · h–1]; P < 0.001). Cumulative 0- to 12-h morphine consumption was reduced in the pupillometry group (two-way repeated measures ANOVA 0.3 ± 0.1 vs. 0.4 ± 0.2 mg/kg; P = 0.048). A telephone survey 3 months after surgery revealed that 15 of 29 patients in the standard group still experienced procedure-related pain versus 3 of 23 in the pupillometry group (chi-square P = 0.037). No adverse events associated with pupillometry were observed during the study.

Conclusions

The use of pupillometry to guide intraoperative analgesia reduced intraoperative remifentanil consumption and postoperative morphine requirements. The possible consequences of decreasing intraoperative remifentanil in terms of chronic pain require further investigation.
Formula Feeding as a Risk Factor for Attention-Deficit/Hyperactivity Disorder: Is Bisphenol A Exposure a Smoking Gun?
Authors: Adesman Andrew , Soled Derek , Rosen Lisa
Published: July 2017

Objective:

Breastfeeding during infancy is associated with a lower risk of attention-deficit/hyperactivity disorder (ADHD). Although this is presumably due to breast milk's nutritional advantages, formula-fed infants have, until recently, also been exposed to bisphenol A (BPA), a neurotoxic chemical previously used to manufacture baby bottles and formula cans. Our goal was to examine the association between formula feeding and preschool ADHD in 2 comparable, serial cohorts of preschool children who differ in BPA exposure during infancy.

Methods:

Cross-sectional analysis of the 2007 and 2011/12 National Survey of Children's Health (NSCH). Logistic regression was used to model preschool ADHD diagnoses as a function of breastfeeding, adjusting for 12 possible confounding variables using a propensity score.

Results:

In the 2007 data set (weighted n = 9,644,405), formula-fed subjects had a 5-fold increased odds of ADHD compared with breastfed subjects (adjusted odds ratio [aOR]: 5.58, 95% confidence interval [CI], 2.16–14.41). In the 2011/12 data set (n = 9,732,865), there was no significant association between formula feeding and later ADHD (aOR: 1.05, 95% CI, 0.42–2.64). This is despite an increase in the prevalence of preschool ADHD in 2011 (0.88%) compared with 2007 (0.40%) (Rao-Scott χ2, p < .0075).

Conclusion:

Compared with breastfed infants, ADHD was more common among formula-fed infants in the 2007 but not the 2011/12 sample, where exposure to BPA was markedly reduced. These findings suggest that the reduced prevalence of ADHD among breastfed infants may not be due to the nutritional benefits of breast milk, but rather early exposure to BPA, a neurotoxic chemical previously found in infant formula.
Preclinical Development of EBI-005: An IL-1 Receptor-1 Inhibitor for the Topical Ocular Treatment of Ocular Surface Inflammatory Diseases
Authors: Kovalchin Joseph , King Bracken , Masci Allyson , Hopkins Elizabeth , Fry Jeremy , Hou Jay , Li Christian , Tenneson Kelly , Weber Steve , Wolfe Gary , Collins Kathy , Furfine Eric S.
Published: July 2017

Objective:

Topical interleukin (IL)-1 receptor (R)1 blockade is therapeutically active in reducing signs and symptoms of dry eye disease. Herein, we describe in vitro and in vivo nonclinical Investigational New Drug (IND)-enabling studies of EBI-005, a novel protein chimera of IL-1β and IL-1 receptor antagonist (IL-1Ra or anakinra) that potently binds IL-1R1 and blocks signaling. These studies provide an assessment of receptor affinity, drug bioavailability, immunogenic response, safety, and tolerability in mice and rabbits.

Methods:

In vitro and in silico along with Good Laboratory Practices (GLP) and non-GLP in vivo studies in mice and rabbits assessed the topical ocular and systemic immunogenicity and toxicology of EBI-005. Animals were treated with EBI-005 once daily subcutaneously or four times daily by topical ocular administration for up to 6 weeks (with 2-week recovery phase).

Results:

EBI-005 has 500 times higher affinity than anakinra to IL-1R1. Predictive immunogenicity testing suggested that EBI-005 is not more immunogenic. Systemic bioavailability of EBI-005 is low (1.4% in mice and 0.2% in rabbits) after topical ocular administration. EBI-005 penetrated into the anterior ocular tissues within 15 min of topical ocular administration. However, it is low or undetectable after 4 hr and does not form a depot after repeated topical ocular administration. EBI-005 was safe and well tolerated, and exposure to drug was maintained despite an antidrug antibody response after systemic administration, based on IND-enabling toxicology and safety pharmacology studies.

Conclusions:

Ocular doses of EBI-005 at 50 mg/mL in mice and rabbits totaling 0.15 mg/eye in mice and 1.5 mg/eye in rabbits, administered 4 times daily, did not produce adverse effects, and demonstrated excellent bioavailability in target tissues with low systemic exposure. In addition, immunogenic response to the drug did not cause adverse effects or diminish the drug's activity in most cases. The results support drug administration of the highest anticipated human clinical study dose of a 20 mg/mL solution (40 μL 3 times daily in each eye).
Increase in intracranial pressure by application of a rigid cervical collar: a pilot study in healthy volunteers
Authors: Maissan Iscander M. , Ketelaars Rein , Vlottes Boris , Hoeks Sanne E. , den Hartog Dennis , Stolker Robert J.
Published: July 2017

Objectives

Rigid cervical collars are known to increase intracranial pressure (ICP) in severe traumatic brain injury (TBI). Cerebral blood flow might decrease according to the Kellie Monroe doctrine. For this reason, the use of the collar in patients with severe TBI has been abandoned from several trauma protocols in the Netherlands. There is no evidence on the effect of a rigid collar on ICP in patients with mild or moderate TBI or indeed patients with no TBI. As a first step we tested the effect in healthy volunteers with normal ICPs and intact autoregulation of the brain.

Methods

In this prospective blinded cross-over study, we evaluated the effect of application of a rigid cervical collar in 45 healthy volunteers by measuring their optical nerve sheath diameter (ONSD) by transocular sonography. Sonographic measurement of the ONSD behind the eye is an indirect noninvasive method to estimate ICP and pressure changes.

Results

We included 22 male and 23 female volunteers. In total 360 ONSD measurements were performed in these 45 volunteers. Application of a collar resulted in a significant increase in ONSD in both the left (β=0.06, 95% confidence interval: 0.05–0.07, P<0.001) and the right eye (β=0.01, 95% confidence interval: 0.00–0.02, P=0.027)

Conclusion

Application of a rigid cervical collar significantly increases the ONSD in healthy volunteers with intact cerebral autoregulation. This suggests that ICP may increase after application of a collar. In healthy volunteers, this seems to be of minor importance. On the basis of our findings the effect of a collar on ONSD and ICP in patients with mild and moderate TBI needs to be determined.
Rising Incidence of Paediatric Inflammatory Bowel Disease in Canterbury, New Zealand, 1996–2015
Authors: Lopez Robert N. , Appleton Laura , Gearry Richard B. , Day Andrew S.
Published: July 2017

Background:

The incidence of paediatric inflammatory bowel disease (IBD) around the world is increasing. Canterbury, New Zealand, has one of the highest Crohn disease (CD) incidence rates published. The present study aimed to document the incidence of paediatric IBD in Canterbury between 1996 and 2015.

Methods:

All patients diagnosed with IBD in Canterbury, while younger than 16 years, between January 1, 1996 and December 31, 2015 were identified. Demographic and disease phenotypic details were collected and entered into a secure database. Age‐specific population data for Canterbury were obtained and annual incidence rates were then calculated.

Results:

The mean annual incidence rate over the 20‐year period was 7.18/100,000 (95% confidence interval 5.55–8.81) children. There was a 4‐fold increase in the incidence of paediatric IBD in Canterbury between 1996 and 2015. The ratio of CD to ulcerative colitis (UC) diagnosed was 8.4:1. Disease phenotype of CD and UC, based on the Paris classification, were comparable with other studies.

Conclusions:

The incidence of paediatric IBD in Canterbury has increased dramatically during the last 2 decades. Some of the observed incidence rates are among the highest documented anywhere in the world. The preponderance of CD over UC in the present study is the highest published.
Complementary and Alternative Medicine Use and Symptom Burden in Women Undergoing Chemotherapy for Breast Cancer in Malaysia
Authors: Chui Ping Lei , Abdullah Khatijah Lim , Wong Li Ping , Taib Nur Aishah
Published: July 2017

Background:

Complementary and alternative medicine (CAM) is commonly used for cancer- and chemotherapy-related symptoms. Nurses are likely to encounter many CAM users in their practice.

Objective:

The aims of this study were to assess CAM use and examine the symptom burden of CAM and non-CAM users among patients with breast cancer who are undergoing chemotherapy.

Methods:

A CAM use questionnaire and the Side-Effect Burden Scale were administered to 546 patients. Complementary and alternative medicine use was categorized as mind-body practices (MBPs), natural products (NPs), or traditional medicine (TM).

Results:

We identified 386 CAM users (70.7%) in this study. The CAM users reported a higher marginal mean total symptom burden score (40.39 ± 2.6) than non-CAM users (36.93 ± 3.21), although this difference was not statistically significant (P = .09). Triple-modality (MBP-NP-TM) CAM users had a significantly higher marginal mean total symptom burden score (47.44 ± 4.12) than single-modality (MBP) users (34.09 ± 4.43). The risk of having a high total symptom burden score was 12.9-fold higher among the MBP-NP-TM users than among the MBP users.

Conclusions:

Complementary and alternative medicine use is common among Malaysian patients who are undergoing chemotherapy for breast cancer. However, CAM and non-CAM users reported similar symptom burdens, although single-modality use of MBP is likely associated with a lower symptom burden.

Implications for Practice:

Nurses should keep abreast of current developments and trends in CAM use. Understanding CAM use and the related symptom burden will allow nurses to initiate open discussion and guide their patients in seeking additional information or referrals for a particular therapy.
Clinical Application of a Transurethral Holmium Laser Excision of Exposed Polypropylene Mesh at Lower Urinary Tract: Single Surgeon Experience With Long-term Follow-up
Authors: Lee Chan Ho , Ku Ja Yoon , Lee Kyoung , Lee Jeong Zoo , Shin Dong Gil
Published: July 2017

Purpose

The aim of this study was to evaluate the clinical application of a transurethral holmium laser excision of exposed polypropylene mesh as an effective minimally invasive surgical approach in patients with lower urinary tract mesh erosion following the transvaginal placement of polypropylene mesh.

Methods

A retrospective analysis was conducted on the data of 22 patients with exposed polypropylene mesh in the lower urinary tract that was managed using the transurethral holmium laser technique. The patients were divided into 2 groups based on the type of mesh surgery: a midurethral sling (MUS) group (n = 18) and a pelvic organ prolapse (POP) group (n = 4). The surgical outcomes were compared.

Results

The mean time follow-up after the first surgery was 23.2 months, and 14 patients (64%) reported symptomatic improvement. During outpatient follow-up, eroded residual mesh and failed re-epithelialization were discovered in 6 patients. The recurrence rates in the MUS and POP groups after the first surgery were 22% and 50%, respectively. The recurrence-free periods of each group were 30.5 versus 13.5 months, respectively. Whereas 5 patients had successful epithelialization of the surgical wound following the second endoscopic surgery, 1 patient in the POP group required a third endoscopic surgery because of persistent mesh erosion.

Conclusions

The excision of exposed polypropylene mesh using a transurethral holmium laser following MUS appears to be a feasible option because of potentially low rates of complication and recurrent stress incontinence. However, minimally invasive approach using holmium laser may not be as successful for mesh erosion after transvaginal mesh repair for POP.
California scrub-jays reduce visual cues available to potential pilferers by matching food colour to caching substrate
Authors: Kelley Laura A. , Clayton Nicola S.
Published: July 2017

Some animals hide food to consume later; however, these caches are susceptible to theft by conspecifics and heterospecifics. Caching animals can use protective strategies to minimize sensory cues available to potential pilferers, such as caching in shaded areas and in quiet substrate. Background matching (where object patterning matches the visual background) is commonly seen in prey animals to reduce conspicuousness, and caching animals may also use this tactic to hide caches, for example, by hiding coloured food in a similar coloured substrate. We tested whether California scrub-jays (
Aphelocoma californica
) camouflage their food in this way by offering them caching substrates that either matched or did not match the colour of food available for caching. We also determined whether this caching behaviour was sensitive to social context by allowing the birds to cache when a conspecific potential pilferer could be both heard and seen (acoustic and visual cues present), or unseen (acoustic cues only). When caching events could be both heard and seen by a potential pilferer, birds cached randomly in matching and non-matching substrates. However, they preferentially hid food in the substrate that matched the food colour when only acoustic cues were present. This is a novel cache protection strategy that also appears to be sensitive to social context. We conclude that studies of cache protection strategies should consider the perceptual capabilities of the cacher and potential pilferers.
Stiffness distribution in insect cuticle: a continuous or a discontinuous profile?
Authors: Rajabi H. , Jafarpour M. , Darvizeh A. , Dirks J.-H. , Gorb S. N.
Published: July 2017

Insect cuticle is a biological composite with a high degree of complexity in terms of both architecture and material composition. Given the complex morphology of many insect body parts, finite-element (FE) models play an important role in the analysis and interpretation of biomechanical measurements, taken by either macroscopic or nanoscopic techniques. Many previous studies show that the interpretation of nanoindentation measurements of this layered composite material is very challenging. To develop accurate FE models, it is of particular interest to understand more about the variations in the stiffness through the thickness of the cuticle. Considering the difficulties of making direct measurements, in this study, we use the FE method to analyse previously published data and address this issue numerically. For this purpose, sets of continuous or discontinuous stiffness profiles through the thickness of the cuticle were mathematically described. The obtained profiles were assigned to models developed based on the cuticle of three insect species with different geometries and layer configurations. The models were then used to simulate the mechanical behaviour of insect cuticles subjected to nanoindentation experiments. Our results show that FE models with discontinuous exponential stiffness gradients along their thickness were able to predict the stress and deformation states in insect cuticle very well. Our results further suggest that, for more accurate measurements and interpretation of nanoindentation test data, the ratio of the indentation depth to cuticle thickness should be limited to 7% rather than the traditional ‘10% rule’. The results of this study thus might be useful to provide a deeper insight into the biomechanical consequences of the distinct material distribution in insect cuticle and also to form a basis for more realistic modelling of this complex natural composite.
Identifying hybridization and admixture using SNPs: application of the DArTseq platform in phylogeographic research on vertebrates
Authors: Melville Jane , Haines Margaret L. , Boysen Katja , Hodkinson Luke , Kilian Andrzej , Smith Date Katie L. , Potvin Dominique A. , Parris Kirsten M.
Published: July 2017

Next-generation sequencing (NGS) approaches are increasingly being used to generate multi-locus data for phylogeographic and evolutionary genetics research. We detail the applicability of a restriction enzyme-mediated genome complexity reduction approach with subsequent NGS (DArTseq) in vertebrate study systems at different evolutionary and geographical scales. We present two case studies using SNP data from the DArTseq molecular marker platform. First, we used DArTseq in a large phylogeographic study of the agamid lizardCtenophorus caudicinctus, including 91 individuals and spanning the geographical range of this species across arid Australia. A low-density DArTseq assay resulted in 28 960 SNPs, with low density referring to a comparably reduced set of identified and sequenced markers as a cost-effective approach. Second, we applied this approach to an evolutionary genetics study of a classic frog hybrid zone (Litoria ewingii–Litoria paraewingi) across 93 individuals, which resulted in 48 117 and 67 060 SNPs for a low- and high-density assay, respectively. We provide a docker-based workflow to facilitate data preparation and analysis, then analyse SNP data using multiple methods including Bayesian model-based clustering and conditional likelihood approaches. Based on comparison of results from the DArTseq platform and traditional molecular approaches, we conclude that DArTseq can be used successfully in vertebrates and will be of particular interest to researchers working at the interface between population genetics and phylogenetics, exploring species boundaries, gene exchange and hybridization.
Robust extraction of quantitative structural information from high-variance histological images of livers from necropsied Soay sheep
Authors: Caudron Q. , Garnier R. , Pilkington J. G. , Watt K. A. , Hansen C. , Grenfell B. T. , Aboellail T. , Graham A. L.
Published: July 2017

Quantitative information is essential to the empirical analysis of biological systems. In many such systems, spatial relations between anatomical structures is of interest, making imaging a valuable data acquisition tool. However, image data can be difficult to analyse quantitatively. Many image processing algorithms are highly sensitive to variations in the image, limiting their current application to fields where sample and image quality may be very high. Here, we develop robust image processing algorithms for extracting structural information from a dataset of high-variance histological images of inflamed liver tissue obtained during necropsies of wild Soay sheep. We demonstrate that features of the data can be measured in a fully automated manner, providing quantitative information which can be readily used in statistical analysis. We show that these methods provide measures that correlate well with a manual, expert operator-led analysis of the same images, that they provide advantages in terms of sampling a wider range of information and that information can be extracted far more quickly than in manual analysis.
Lessons and recommendations from three decades as an NSF REU Site: A call for systems-based assessment
Authors: McDevitt Andrew L. , Patel Manisha V. , Ellison Aaron M.
Published: July 2017

NSF’s Research Experiences for Undergraduates (REU) program supports thousands of undergraduate researchers annually. REU sites operate independently with regards to their research mission and structure, leading to a complex educational milieu distinct from traditional classrooms and labs. Overall, REU sites are perceived as providing highly formative experiences for developing researchers. However, given improved assessment practices over REU’s three decades, best practices for student learning and evaluation of long-term impacts remain limited. To address this limitation, we recommend the use of systems-based theoretical frameworks when studying REU programs. We outline how one such framework, cultural-historical activity theory (CHAT), could inform the collection of assessment data. Among other strengths, CHAT guides collection of quantitative and qualitative information that can help characterize REU programs in an educationally meaningful context. Adoption of CHAT and similar approaches by REU Sites could improve dialogue among programs, encourage collaborations, and improve evidence-based practices.
Engineered CRISPR-Cas9 system enables noiseless, fine-tuned and multiplexed repression of bacterial genes
Authors: Vigouroux Antoine , Oldewurtel Enno , Cui Lun , Teeffelen Sven van , Bikard David
Published: July 2017

Over the past few years, tools that make use of the Cas9 nuclease have led to many breakthroughs, including in the control of gene expression. The catalytically dead variant of Cas9 known as dCas9 can be guided by small RNAs to block transcription of target genes, in a strategy also known as CRISPRi. Here, we reveal that the level of complementarity between the guide RNA and the target controls the rate at which dCas9 successfully blocks the RNA polymerase. We use this mechanism to precisely and robustly reduce gene expression by defined relative amounts. We demonstrate broad applicability of this method to the study of genetic regulation and cellular physiology. First, we characterize feedback strength of a model auto-repressor. Second, we study the impact of copy-number variations of cell-wall synthesizing enzymes on cell morphology. Finally, we demonstrate that this system can be multiplexed to obtain any combination of fractional repression of two genes.
Defining the synaptic mechanisms that tune CA3-CA1 reactivation during sharp-wave ripples
Authors: Malerba Paola , Jones Matt W. , Bazhenov Maxim A.
Published: July 2017

During non-REM sleep, memory consolidation is driven by a dialogue between hippocampus and cortex involving the reactivation of specific neural activity sequences (‘replay’). In the hippocampus, replay occurs during sharp-wave ripples (SWRs), short bouts of excitatory activity in area CA3 which induce high frequency oscillations in the inhibitory interneurons of area CA1. Despite growing evidence for the functional importance of replay, its neural mechanisms remain poorly understood. Here, we develop a novel theoretical model of hippocampal spiking during SWRs. In our model, noise-induced activation of CA3 pyramidal cells triggered an excitatory cascade capable of inducing local ripple events in CA1. Ripples occurred stochastically, with Schaffer Collaterals driving their coordination, so that localized sharp waves in CA3 produced consistently localized CA1 ripples. In agreement with experimental data, the majority of pyramidal cells in the model showed low reactivation probabilities across SWRs. We found, however, that a subpopulation of pyramidal cells had high reactivation probabilities, which derived from fine-tuning of the network connectivity. In particular, the excitatory inputs along synaptic pathway(s) converging onto cells and cell pairs controlled emergent single cell and cell pair reactivation, with inhibitory inputs and intrinsic cell excitability playing differential roles in CA3 vs. CA1. Our model predicts (1) that the hippocampal network structure driving the emergence of SWR is also able to generate and modulate reactivation, (2) inhibition plays a particularly prominent role in CA3 reactivation and (3) CA1 sequence reactivation is reliant on CA3-CA1 interactions rather than an intrinsic CA1 process.
Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection
Authors: Bertram Jason , Masel Joanna
Published: July 2017

The long-running debate about the role of selection in maintaining genetic variation has been given new impetus by the discovery of hundreds of seasonally oscillating polymorphisms in wildDrosophila,possibly stabilized by an alternating summer-winter selection regime. Historically there has been skepticism about the potential of temporal variation to balance polymorphism, because selection must be strong to have a meaningful stabilizing effect — unless dominance also varies over time (“reversal of dominance”). Here we develop a simplified model of seasonally variable selection that simultaneously incorporates four different stabilizing mechanisms, including two genetic mechanisms (“cumulative overdominance” and reversal of dominance), as well as ecological “storage” (“protection from selection” and boom-bust demography). We use our model to compare the stabilizing effects of these mechanisms. Although reversal of dominance has by far the greatest stabilizing effect, we argue that the three other mechanisms could also stabilize polymorphism under plausible conditions, particularly when all three are present. With many loci subject to diminishing returns epistasis, reversal of dominance stabilizes many alleles of small effect. This makes the combination of the other three mechanisms, which are incapable of stabilizing small effect alleles, a better candidate for stabilizing the detectable frequency oscillations of large effect alleles.
A global synthesis of phenological responses to climate change
Authors: Cohen Jeremy M. , Lajeunesse Marc J. , Rohr Jason R.
Published: July 2017

Phenology, or the timing of seasonal activities, is shifting with climate change, resulting in disruptions to the timing of migration and breeding and in emerging asynchronies between interacting species1-5. Recent syntheses have concluded that trophic level1, latitude6, and how phenological responses are measured7are key to determining the strength of phenological responses to climate change. However, despite these insights, researchers still lack a comprehensive framework that can predict responses to climate change globally and across diverse taxa. For example, little is known about whether phenological shifts are driven by different climatic factors across regions or which ecologically important species characteristics (e.g., body size) predict the strength of phenological responses. Here, we address these questions by synthesizing hundreds of published time series of animal phenology from across the planet. We find that temperature drives phenological responses at mid-latitudes, but precipitation is more important at lower latitudes, likely because these climate factors often drive seasonality in each of these regions. Body size is also negatively associated with the strength of phenological shift, suggesting emerging asynchronies between interacting species that differ in size, such as hosts and ectoparasites and predators and prey. Finally, although there are many compelling biological explanations for spring phenological delays, some examples of delays are associated with short annual records prone to sampling error. As climate change intensifies, our findings arm biologists with predictions concerning which climatic variables and organismal traits drive phenological shifts.
Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils
Authors: Kaminsky Rachel , Morales Sergio E.
Published: July 2017

Conditionally rare taxa (CRT) are thought to greatly impact microbial community turnover across many environments, but little is known about their role in soils. Here, we investigate the contribution of CRT to whole community variation over space and time in a series of geographically distinct soils dedicated to three agricultural practices of differing intensities and sampled over a full seasonal cycle. We demonstrate that soil CRT do not account for observed total community changes, but that these rare taxa can be modified by spatiotemporal filters.
Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing
Authors: Anvar Seyed Yahya , Allard Guy , Tseng Elizabeth , Sheynkman Gloria , de Klerk Eleonora , Vermaat Martijn , Yin Raymund H. , Johansson Hans E. , Ariyurek Yavuz , den Dunnen Johan T. , Turner Stephen W. , 't Hoen Peter A.C.
Published: July 2017

The multifaceted control of gene expression requires tight coordination of regulatory mechanisms at transcriptional and post-transcriptional level. Here, we studied the interdependence of transcription, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells, we found 2,700 genes with interdependent alternative transcription, splicing and polyadenylation events, both in proximal and distant parts of mRNA molecules. The analysis of three human primary tissues revealed similar patterns of interdependency between transcription and mRNA processing events. We predict thousands of novel Open Reading Frames from the sequence of full-length mRNAs and obtained evidence for their translation by shotgun proteomics. The mapping database rescued 358 previously unassigned peptides and improved the assignment of others. By recognizing sample-specific amino-acid changes and novel splicing patterns, full-length mRNA sequencing improved proteogenomics analysis of MCF-7 cells. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a basis to reveal largely unresolved mechanisms that coordinate transcription and mRNA processing.
Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Authors: Haghverdi Laleh , Lun Aaron T. L. , Morgan Michael D. , Marioni John C.
Published: July 2017

The presence of batch effects is a well-known problem in experimental data analysis, and single- cell RNA sequencing (scRNA-seq) is no exception. Large-scale scRNA-seq projects that generate data from different laboratories and at different times are rife with batch effects that can fatally compromise integration and interpretation of the data. In such cases, computational batch correction is critical for eliminating uninteresting technical factors and obtaining valid biological conclusions. However, existing methods assume that the composition of cell populations are either known or the same across batches. Here, we present a new strategy for batch correction based on the detection of mutual nearest neighbours in the high-dimensional expression space. Our approach does not rely on pre-defined or equal population compositions across batches, only requiring that a subset of the population be shared between batches. We demonstrate the superiority of our approach over existing methods on a range of simulated and real scRNA-seq data sets. We also show how our method can be applied to integrate scRNA-seq data from two separate studies of early embryonic development.
Wikipedia as a gateway to biomedical research: The relative distribution and use of citations in the English Wikipedia
Authors: Maggio Lauren A. , Willinsky John M. , Steinberg Ryan M. , Mietchen Daniel , Wass Joseph L. , Dong Ting
Published: July 2017

Wikipedia is a gateway to knowledge. However, the extent to which this gateway ends at Wikipedia or continues via supporting citations is unknown. Wikipedia’s gateway functionality has implications for information design and education, notably in medicine. This study aims to establish benchmarks for the relative distribution and referral (click) rate of citations—as indicated by presence of a Digital Object Identifier (DOI)—from Wikipedia, with a focus on medical citations.

DOIs referred from the English Wikipedia in August 2016 were obtained from Crossref.org. Next, based on a DOI’s presence on a WikiProject Medicine page, all DOIs in Wikipedia were categorized as medical (WP:MED) or non-medical (non-WP:MED). Using this categorization, referred DOIs were classified as WP:MED, non-WP:MED, or BOTH, meaning the DOI may have been referred from either category. Data were analyzed using descriptive and inferential statistics.

Out of 5.2 million Wikipedia pages, 4.42% (n=229,857) included at least one DOI. 68,870 were identified as WP:MED, with 22.14% (n=15,250) featuring one or more DOIs. WP:MED pages featured on average 8.88 DOI citations per page, whereas non-WP:MED pages had on average 4.28 DOI citations. For DOIs only on WP:MED pages, a DOI was referred every 2,283 pageviews and for non-WP-MED pages every 2,467 pageviews. DOIs from BOTH pages accounted for 12% (n=58,475) of referrals, making determining a referral rate for BOTH impossible.

While these results cannot provide evidence of greater citation referral from WP:MED than non-WP:MED, they do provide benchmarks to assess strategies for changing referral patterns. These changes might include editors adopting new methods for designing and presenting citations or the introduction of teaching strategies that address the value of consulting citations as a tool for extending learning.
Cellular reductase activity in uncultivatedThiomargarita spp. assayed using a redox-sensitive dye
Authors: Bailey Jake V. , Flood Beverly E. , Ricci Elizabeth , Delherbe Nathalie
Published: July 2017

The largest known bacteria,Thiomargarita spp.,have yet to be isolated in pure culture, but their large size allows for individual cells to be followed in time course experiments, or to be individually sorted for ‘omics-based investigations. Here we report a novel application of a tetrazolium-based dye that measures the flux of reductase production from catabolic pathways to investigate the metabolic activity of individual cells ofThiomargaritaspp. When coupled to microscopy, staining of the cells with a tetrazolium-formazan dye allows for metabolic responses inThiomargaritaspp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity ofThiomargaritaspp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox-dye-based assay suggests thatThiomargaritais the most metabolically versatile under anoxic conditions where it appears to express cellular reductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H2, and H2S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate, and likely acetate, citrate, and H2S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H2S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies ofCa.Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular reductase response of bacteria attached to the exteriors ofThiomargaritaalso supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts.

IMPORTANCE

The metabolic potentials of many microorganisms that cannot be grown in the laboratory are known only from genomic data. Genomes ofThiomargaritaspp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolisms with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity ofThiomargaritaobserved in recently produced genomes. Finding new cultivation- independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.