bluuebunny/crossref_metadata_2025 huggingface dataset:
Worldwide decline of IVF birth rates and its probable causes
Authors: Gleicher N , Kushnir V A , Barad D H
Published: June 2019

With steadily improving pregnancy and live birth rates, IVF over approximately the first two and a half decades evolved into a highly successful treatment for female and male infertility, reaching peak live birth rates by 2001–2002. Plateauing rates, thereafter, actually started declining in most regions of the world. We here report worldwide IVF live birth rates between 2004 and 2016, defined as live births per fresh IVF/ICSI cycle started, and how the introduction of certain practice add-ons in timing was associated with changes in these live birth rates. We also attempted to define how rapid worldwide ‘industrialization’ (transition from a private practice model to an investor-driven industry) and ‘commoditization’ in IVF practice (primary competitive emphasis on revenue rather than IVF outcomes) affected IVF outcomes. The data presented here are based on published regional registry data from governments and/or specialty societies, covering the USA, Canada, the UK, Australia/New Zealand (combined), Latin America (as a block) and Japan. Changes in live birth rates were associated with introduction of new IVF practices, including mild stimulation, elective single embryo transfer (eSET), PGS (now renamed preimplantation genetic testing for aneuploidy), all-freeze cycles and embryo banking. Profound negative associations were observed with mild stimulation, extended embryo culture to blastocyst and eSET in Japan, Australia/New Zealand and Canada but to milder degrees also elsewhere. Effects of ‘industrialization’ suggested rising utilization of add-ons (‘commoditization’), increased IVF costs, reduced live birth rates and poorer patient satisfaction. Over the past decade and a half, IVF, therefore, has increasingly disappointed outcome expectations. Remarkably, neither the profession nor the public have paid attention to this development which, therefore, also has gone unexplained. It now urgently calls for evidence-based explanations.
Enforcing constitutional conventions
Authors: Ahmed Farrah , Albert Richard , Perry Adam
Published: June 2019

In an earlier article, we disproved the three claims central to the dominant view in the study of constitutional conventions: that there is a shared “Commonwealth approach” to constitutional conventions; that Commonwealth courts will recognize and employ conventions but never enforce them; and that conventions are sharply distinguishable from rules of law. We drew from Canada, India, and the United Kingdom to demonstrate that Commonwealth courts have recognized, employed, and indeed also enforced conventions. In this article, we turn from the descriptive to the normative, arguing, again in contrast with the dominant view, that Commonwealth courts sometimes should enforce conventions. We argue that courts should act as executors of the will and judgment of constitutional actors, and limit themselves to enforcing only power-shifting conventions: conventions which transfer power from those who have legal power to those who can legitimately wield it. In playing this role, judges uphold the legitimate allocation of power—legitimate, not according to judges but according to constitutional actors themselves.
Poly-ℤ Group Actions on Kirchberg Algebras I
Authors: Izumi Masaki , Matui Hiroki
Published: June 2019

Toward the complete classification of poly-${\mathbb{Z}}$ group actions on Kirchberg algebras, we prove several fundamental theorems that are used in the classification. In addition, as an application of them, we classify outer actions of poly-${\mathbb{Z}}$ groups of Hirsch length not greater than three on unital Kirchberg algebras up to $KK$-trivial cocycle conjugacy.
Test collections for electronic health record-based clinical information retrieval
Authors: Wang Yanshan , Wen Andrew , Liu Sijia , Hersh William , Bedrick Steven , Liu Hongfang
Published: June 2019

Objectives

To create test collections for evaluating clinical information retrieval (IR) systems and advancing clinical IR research.

Materials and Methods

Electronic health record (EHR) data, including structured and free-text data, from 45 000 patients who are a part of the Mayo Clinic Biobank cohort was retrieved from the clinical data warehouse. The clinical IR system indexed a total of 42 million free-text EHR documents. The search queries consisted of 56 topics developed through a collaboration between Mayo Clinic and Oregon Health & Science University. We described the creation of test collections, including a to-be-evaluated document pool using five retrieval models, and human assessment guidelines. We analyzed the relevance judgment results in terms of human agreement and time spent, and results of three levels of relevance, and reported performance of five retrieval models.

Results

The two judges had a moderate overall agreement with a Kappa value of 0.49, spent a consistent amount of time judging the relevance, and were able to identify easy and difficult topics. The conventional retrieval model performed best on most topics while a concept-based retrieval model had better performance on the topics requiring conceptual level retrieval.

Discussion

IR can provide an alternate approach to leveraging clinical narratives for patient information discovery as it is less dependent on semantics. Our study showed the feasibility of test collections along with a few challenges.

Conclusion

The conventional test collections for evaluating the IR system show potential for successfully evaluating clinical IR systems with a few challenges to be investigated.
Novel High-Throughput Quantitation of Potent hERG Blocker Dofetilide in Human Plasma by Liquid Chromatography Tandem Mass Spectrometry: Application in a Phase 1 ECG Biomarker Validation Study
Authors: Matta Murali K , Narayanasamy Suresh , Vicente Jose , Zusterzeel Robbert , Patel Vikram , Strauss David G
Published: June 2019

The authors developed a novel, sensitive high-throughput ultra-performance liquid chromatography-tandem mass spectrometric method for the determination of dofetilide in human plasma. To compensate for the matrix effect, a deuterated internal standard was used. The method employed a very low sample volume (50 μL) of plasma for sample processing by using simple protein precipitation extraction in a 96-well plate. The extracted samples were chromatographed on an Acquity BEH C18 column (2.1 × 100 mm, 1.7 μm) and eluted in a gradient manner at a flow rate of 0.5 mL/min for 2 min using 5 mM ammonium formate (0.1% formic acid) and methanol. The calibration curve was linear from 25 to 2,500 pg/mL with a correlation coefficient (r2) ≥ 0.99 (0.9969–0.9980; n = 3). The developed method was validated as per the current United States Food and Drug Administration’s guidance for industry on ‘Bioanalytical Method Validation’. The multiple reaction–monitoring mode was employed for quantitation of dofetilide with m/z 442.2/198.2 and dofetilide d4 with m/z 446.2/198.2. The validated method was used for evaluation of dofetilide concentration in the Comprehensive in vitro Proarrhythmia Assay phase 1 electrocardiogramic biomarker validation study.
Beyond BRCA: Review of Hereditary Syndromes Predisposing to Breast Cancer
Authors: Nguyen Jonathan V , Thomas Martha H
Published: June 2019

The majority of our hereditary breast cancer genes incur not only an increased risk for breast cancer but for other malignancies as well. Knowing whether an individual carries a pathogenic variant in a hereditary breast cancer gene can affect not only screening for the patient but for his or her family members as well. Identifying and appropriately testing individuals via multigene panels allows for risk reduction and early surveillance in at-risk individuals. Radiologists can serve as first-line identifiers of women who are at risk of having an inherited predisposition to breast cancer because they are interacting with all women receiving routine screening mammograms, and collecting family history suggestive of the presence of a mutation. We outline here the 11 genes associated with high breast cancer risk discussed in the National Comprehensive Cancer Network Genetic/Familial High-Risk: Breast and Ovarian (version 3.2019) as having additional breast cancer screening recommendations outside of annual mammography to serve as a guide for breast cancer screening and risk reduction, as well as recommendations for surveillance of nonbreast cancers.
Considerations for Insect Learning in Integrated Pest Management
Authors: Little Catherine M , Chapman Thomas W , Hillier N Kirk
Published: June 2019

The past 100 yr have seen dramatic philosophical shifts in our approach to controlling or managing pest species. The introduction of integrated pest management in the 1970s resulted in the incorporation of biological and behavioral approaches to preserve ecosystems and reduce reliance on synthetic chemical pesticides. Increased understanding of the local ecosystem, including its structure and the biology of its species, can improve efficacy of integrated pest management strategies. Pest management strategies incorporating insect learning paradigms to control insect pests or to use insects to control other pests can mediate risk to nontarget insects, including pollinators. Although our understanding of insect learning is in its early stages, efforts to integrate insect learning into pest management strategies have been promising. Due to considerable differences in cognitive abilities among insect species, a case-by-case assessment is needed for each potential application of insect learning within a pest management strategy.
Loss of hnRNP A1 in murine skeletal muscle exacerbates high-fat diet-induced onset of insulin resistance and hepatic steatosis
Authors: Zhao Mingxia , Shen Lihong , Ouyang Zijun , Li Manru , Deng Guoliang , Yang Chenxi , Zheng Wei , Kong Lingdong , Wu Xuefeng , Wu Xudong , Guo Wenjie , Yin Ye , Xu Qiang , Sun Yang
Published: June 2019

Impairment of glucose (Glu) uptake and storage by skeletal muscle is a prime risk factor for the development of metabolic diseases. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is a highly abundant RNA-binding protein that has been implicated in diverse cellular functions. The aim of this study was to investigate the function of hnRNP A1 on muscle tissue insulin sensitivity and systemic Glu homeostasis. Our results showed that conditional deletion of hnRNP A1 in the muscle gave rise to a severe insulin resistance phenotype in mice fed a high-fat diet (HFD). Conditional knockout mice fed a HFD showed exacerbated obesity, insulin resistance, and hepatic steatosis. In vitro interference of hnRNP A1 in C2C12 myotubes impaired insulin signal transduction and inhibited Glu uptake, whereas hnRNP A1 overexpression in C2C12 myotubes protected against insulin resistance induced by supraphysiological concentrations of insulin. The expression and stability of glycogen synthase (gys1) mRNA were also decreased in the absence of hnRNP A1. Mechanistically, hnRNP A1 interacted with gys1 and stabilized its mRNA, thereby promoting glycogen synthesis and maintaining the insulin sensitivity in muscle tissue. Taken together, our findings are the first to show that reduced expression of hnRNP A1 in skeletal muscle affects the metabolic properties and systemic insulin sensitivity by inhibiting glycogen synthesis.
The Medico-Legal ‘Making’ of ‘The Transgender Child’
Authors: Brunskell-Evans Heather
Published: June 2019

Thirty years ago, the transgender child would have made no sense to the general public, nor to young people. Today, children and adolescents declare themselves transgender, the National Health Service diagnoses ‘gender dysphoria’, and laws and policy are developed which uphold young people’s ‘choice’ to transition and to authorize stages at which medical intervention is permissible and desirable. The figure of the ‘transgender child’ presumed by medicine and law is not a naturally occurring category of person external to medical diagnosis and legal protection. Medicine and law construct the ‘transgender child’ rather than that the ‘transgender child’ exists independently of medico-legal discourse. The ethical issue of whether the child and young person can ‘consent’ to social and medical transition goes beyond legal assessment of whether a person under16 years has the mental capacity to consent, understand to what s/he is consenting, and can express independent wishes. It shifts to examination of the recent making of ‘the transgender child’ through the complex of power/knowledge/ethics of medicine and the law of which the child can have no knowledge but within which its own desires are both constrained and incited.
Magnetic inhibition of convection in O-star envelopes
Authors: MacDonald James , Petit Véronique
Published: June 2019

It has been suggested that the absence of macroturbulence in the atmosphere of NGC 1624−2 is due its strong magnetic field (the strongest known for a massive O star) suppressing convection in its outer layers, removing the mechanism thought responsible for the observed macroturbulence in stars with lower field strengths. Here, we develop and apply a criterion for a uniform magnetic field to suppress convection in stellar envelopes in which radiation pressure is a significant contributor to hydrostatic balance. We find upper mass limits of ∼55 and ∼30 M⊙ for magnetic suppression to be possible in zero-age main-sequence and terminal-age main-sequence stars, respectively. For evolved stars, magnetic suppression of convection can significantly alter the stars’ evolution. For NGC 1624−2, we find that a polar dipole strength of 16.5 ± 5.9 kG is required to suppress convection, in good agreement with the value ∼20 kG measured by spectropolarimetry.
SIRT7 mediates L1 elements transcriptional repression and their association with the nuclear lamina
Authors: Vazquez Berta N , Thackray Joshua K , Simonet Nicolas G , Chahar Sanjay , Kane-Goldsmith Noriko , Newkirk Simon J , Lee Suman , Xing Jinchuan , Verzi Michael P , An Wenfeng , Vaquero Alejandro , Tischfield Jay A , Serrano Lourdes
Published: June 2019

Long interspersed elements-1 (LINE-1, L1) are retrotransposons that hold the capacity of self-propagation in the genome with potential mutagenic outcomes. How somatic cells restrict L1 activity and how this process becomes dysfunctional during aging and in cancer cells is poorly understood. L1s are enriched at lamin-associated domains, heterochromatic regions of the nuclear periphery. Whether this association is necessary for their repression has been elusive. Here we show that the sirtuin family member SIRT7 participates in the epigenetic transcriptional repression of L1 genome-wide in both mouse and human cells. SIRT7 depletion leads to increased L1 expression and retrotransposition. Mechanistically, we identify a novel interplay between SIRT7 and Lamin A/C in L1 repression. Our results demonstrate that SIRT7-mediated H3K18 deacetylation regulates L1 expression and promotes L1 association with elements of the nuclear lamina. The failure of such activity might contribute to the observed genome instability and compromised viability in SIRT7 knockout mice. Overall, our results reveal a novel function of SIRT7 on chromatin organization by mediating the anchoring of L1 to the nuclear envelope, and a new functional link of the nuclear lamina with transcriptional repression.
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
Authors: Tarbell Evan D , Liu Tao
Published: June 2019

ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without considering the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human ATAC-seq datasets. We find that single-end sequenced or size-selected ATAC-seq datasets result in a loss of sensitivity compared to paired-end datasets without size-selection.
SMARTer single cell total RNA sequencing
Authors: Verboom Karen , Everaert Celine , Bolduc Nathalie , Livak Kenneth J , Yigit Nurten , Rombaut Dries , Anckaert Jasper , Lee Simon , Venø Morten T , Kjems Jørgen , Speleman Frank , Mestdagh Pieter , Vandesompele Jo
Published: June 2019

Single cell RNA sequencing methods have been increasingly used to understand cellular heterogeneity. Nevertheless, most of these methods suffer from one or more limitations, such as focusing only on polyadenylated RNA, sequencing of only the 3′ end of the transcript, an exuberant fraction of reads mapping to ribosomal RNA, and the unstranded nature of the sequencing data. Here, we developed a novel single cell strand-specific total RNA library preparation method addressing all the aforementioned shortcomings. Our method was validated on a microfluidics system using three different cancer cell lines undergoing a chemical or genetic perturbation and on two other cancer cell lines sorted in microplates. We demonstrate that our total RNA-seq method detects an equal or higher number of genes compared to classic polyA[+] RNA-seq, including novel and non-polyadenylated genes. The obtained RNA expression patterns also recapitulate the expected biological signal. Inherent to total RNA-seq, our method is also able to detect circular RNAs. Taken together, SMARTer single cell total RNA sequencing is very well suited for any single cell sequencing experiment in which transcript level information is needed beyond polyadenylated genes.
Banks’ Balance Sheets and Liquidation Values: Evidence from Real Estate Collateral
Authors: Ramcharan Rodney
Published: June 2019

This paper finds that declining bank equity or liquidity reduces liquidation values of bank-owned real estate and accelerates the pace of asset sales. Buyers of these assets earn significant returns for providing liquidity to banks, as prices tend to rebound sharply after sales by illiquid banks. Lower liquidation values also depress the prices of nearby real estate transactions. Policy interventions, such as equity injections and central bank asset purchases, increase liquidation values by providing institutions with the balance sheet capacity to slow asset sales. This evidence suggests that balance sheet adjustments at financial institutions can explain real asset price dynamics.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
Subcellular Targets of Zinc Oxide Nanoparticles During the Aging Process: Role of Cross-talk Between Mitochondrial Dysfunction and Endoplasmic Reticulum Stress in the Genotoxic Response
Authors: Wang Meimei , Wang Juan , Liu Yun , Wang Jingjing , Nie Yaguang , Si Bo , Liu Ying , Wang Xue , Chen Shaopeng , Hei Tom K , Wu Lijun , Zhao Guoping , Xu An
Published: June 2019

Zinc oxide nanoparticles (ZnO NPs) are being produced abundantly and applied increasingly in various fields. The special physicochemical characteristics of ZnO NPs make them incline to undergo physicochemical transformation over time (aging), which modify their bioavailability and toxicity. However, the subcellular targets and the underlying molecular mechanisms involved in the genotoxicity induced by ZnO NPs during aging process are still unknown. This study found that the acute cytotoxic effects of fresh ZnO NPs was largely regulated by mitochondria-dependent apoptosis, which the level of cleaved Caspase-3 and mitochondria damage were significantly higher than that of 60-day-aged ZnO NPs. In contrast, aged ZnO NPs induced more reactive oxygen species (ROS) production and endoplasmic reticulum (ER) stress marker protein (BIP/GRP78) expression and their genotoxicity could be dramatically suppressed by either ROS scavengers (dimethyl sulfoxide, catalase, and sodium azide) or ER stress inhibitor (4-phenylbutyrate). Using mitochondrial-DNA deficient (ρ0) AL cells, we further found that ER stress induced by aged ZnO NPs was triggered by ROS generated from mitochondria, which eventually mediated the genotoxicity of aged NPs. Our data provided novel information on better understanding the contribution of subcellular targets to the genotoxic response of ZnO NPs during the aging process.
Functional outcome and muscle wasting in adults with tetanus
Authors: Trung Truong N , Duoc Nguyen V T , Nhat Le T H , Yen Lam M , Hao Nguyen V , Truong Nguyen T , Duong Ha T H , Thuy Duong B , Phong Nguyen T , Tan Le V , Puthucheary Zudin A , Thwaites C Louise
Published: June 2019

Background

In many countries, in-hospital survival from tetanus is increasing, but long-term outcome is unknown. In high-income settings, critical illness is associated with muscle wasting and poor functional outcome, but there are few data from resource-limited settings. In this study we aimed to assess muscle wasting and long-term functional outcome in adults with tetanus.

Methods

In a prospective observational study involving 80 adults with tetanus, sequential rectus femoris ultrasound measurements were made at admission, 7 days, 14 days and hospital discharge. Functional outcome was assessed at hospital discharge using the Timed Up and Go test, Clinical Frailty Score, Barthel Index and RAND 36-item Short Form Health Survey (SF-36) and 3 and 6 months after discharge using the SF-36 and Barthel Index.

Results

Significant muscle wasting occurred between hospital admission and discharge (p<0.01), particularly in severe disease, where a median 23.49% (interquartile range 10.01–26.07) reduction in rectus femoris cross-sectional area occurred in those with severe (Ablett grades 3 and 4) disease. Muscle mass at discharge was related to objective and subjective measures of physical and emotional function at discharge and 3 and 6 months after discharge. In patients >70 y of age, functional recovery at 6 months was reduced compared with younger patients. Hospital-acquired infection and age were risk factors for muscle wasting.

Conclusions

Significant muscle wasting during hospitalization occurred in patients with tetanus, the extent of which correlates with functional outcome.
Within-host infectious disease models accommodating cellular coinfection, with an application to influenza†
Authors: Koelle Katia , Farrell Alex P , Brooke Christopher B , Ke Ruian
Published: June 2019

Within-host models are useful tools for understanding the processes regulating viral load dynamics. While existing models have considered a wide range of within-host processes, at their core these models have shown remarkable structural similarity. Specifically, the structure of these models generally consider target cells to be either uninfected or infected, with the possibility of accommodating further resolution (e.g. cells that are in an eclipse phase). Recent findings, however, indicate that cellular coinfection is the norm rather than the exception for many viral infectious diseases, and that cells with high multiplicity of infection are present over at least some duration of an infection. The reality of these cellular coinfection dynamics is not accommodated in current within-host models although it may be critical for understanding within-host dynamics. This is particularly the case if multiplicity of infection impacts infected cell phenotypes such as their death rate and their viral production rates. Here, we present a new class of within-host disease models that allow for cellular coinfection in a scalable manner by retaining the low-dimensionality that is a desirable feature of many current within-host models. The models we propose adopt the general structure of epidemiological ‘macroparasite’ models that allow hosts to be variably infected by parasites such as nematodes and host phenotypes to flexibly depend on parasite burden. Specifically, our within-host models consider target cells as ‘hosts’ and viral particles as ‘macroparasites’, and allow viral output and infected cell lifespans, among other phenotypes, to depend on a cell’s multiplicity of infection. We show with an application to influenza that these models can be statistically fit to viral load and other within-host data, and demonstrate using model selection approaches that they have the ability to outperform traditional within-host viral dynamic models. Important in vivo quantities such as the mean multiplicity of cellular infection and time-evolving reassortant frequencies can also be quantified in a straightforward manner once these macroparasite models have been parameterized. The within-host model structure we develop here provides a mathematical way forward to address questions related to the roles of cellular coinfection, collective viral interactions, and viral complementation in within-host viral dynamics and evolution.
Efferocytosis perpetuates substance accumulation inside macrophage populations
Authors: Ford Hugh Z. , Zeboudj Lynda , Purvis Gareth S. D. , ten Bokum Annemieke , Zarebski Alexander E. , Bull Joshua A. , Byrne Helen M. , Myerscough Mary R. , Greaves David R.
Published: June 2019

In both cells and animals, cannibalism can transfer harmful substances from the consumed to the consumer. Macrophages are immune cells that consume their own dead via a process called cannibalistic efferocytosis. Macrophages that contain harmful substances are found at sites of chronic inflammation, yet the role of cannibalism in this context remains unexplored. Here we take mathematical and experimental approaches to study the relationship between cannibalistic efferocytosis and substance accumulation in macrophages. Through mathematical modelling, we deduce that substances which transfer between individuals through cannibalism will concentrate inside the population via a coalescence process. This prediction was confirmed for macrophage populations inside a closed system. We used image analysis of whole slide photomicrographs to measure both latex microbead and neutral lipid accumulation inside murine bone marrow-derived macrophages (10
4
–

10

5

 
cells

) following their stimulation into an inflammatory state
ex vivo
. While the total number of phagocytosed beads remained constant, cell death reduced cell numbers and efferocytosis concentrated the beads among the surviving macrophages. As lipids are also conserved during efferocytosis, these cells accumulated lipid derived from the membranes of dead and consumed macrophages (becoming macrophage foam cells). Consequently, enhanced macrophage cell death increased the rate and extent of foam cell formation. Our results demonstrate that cannibalistic efferocytosis perpetuates exogenous (e.g. beads) and endogenous (e.g. lipids) substance accumulation inside macrophage populations. As such, cannibalism has similar detrimental consequences in both cells and animals.
Effects of major vein blockage and aquaporin inhibition on leaf hydraulics and stomatal conductance
Authors: Harayama Hisanori , Kitao Mitsutoshi , Agathokleous Evgenios , Ishida Atsushi
Published: June 2019

The density and architecture of leaf veins determine the network and efficiency of water transport within laminae and resultant leaf gas exchange and vary widely among plant species. Leaf hydraulic conductance (
K
leaf
) can be regulated by vein architecture in conjunction with the water channel protein aquaporin. However, our understanding of how leaf veins and aquaporins affect leaf hydraulics and stomatal conductance (
g
s
) remains poor. By inducing blockage of the major veins and inhibition of aquaporin activity using HgCl
2
, we examined the effects of major veins and aquaporins on
K
leaf
and
g
s
in species with different venation types. A vine species, with thick first-order veins and low vein density, displayed a rapidly declined
g
s
with high leaf water potential in response to vein blockage and a greatly reduced
K
leaf
and
g
s
in response to aquaporin inhibition, suggesting that leaf aquaporins are involved in isohydric/anisohydric stomatal behaviour. Across species, the decline in
K
leaf
and
g
s
due to aquaporin inhibition increased linearly with decreasing major vein density, possibly indicating that a trade-off function between vein architecture (apoplastic pathway) and aquaporin activity (cell-to-cell pathway) affects leaf hydraulics.
From spikes to intercellular waves: tuning intercellular Ca2+signaling dynamics modulates organ size control
Authors: Soundarrajan Dharsan K. , Huizar Francisco J. , Paravitorghabeh Ramezan , Robinett Trent , Zartman Jeremiah J.
Published: June 2019

Information flow within and between cells depends in part on calcium (Ca2+) signaling dynamics. However, the biophysical mechanisms that govern emergent patterns of Ca2+signaling dynamics at the organ level remain elusive. Recent experimental studies in developingDrosophilawing imaginal discs demonstrate the emergence of four distinct patterns of Ca2+activity: Ca2+spikes, intercellular Ca2+transients, tissue-level Ca2+waves, and a global “fluttering” state. Here, we used a combination of computational modeling and experimental approaches to identify two different populations of cells within tissues that are connected by gap junctional proteins. We term these two subpopulations “initiator cells” defined by elevated levels of Phospholipase C (PLC) activity and “standby cells,” which exhibit baseline activity. We found that the strength of hormonal stimulation and extent of gap junctional communication jointly determine the predominate class of Ca2+signaling activity. Further, single-cell Ca2+spikes are stimulated by insulin, while intercellular Ca2+waves depend on Gαq activity. Our computational model successfully recapitulates how the dynamics of Ca2+transients varies during organ growth. Phenotypic analysis of perturbations to Gαq and insulin signaling support an integrated model of cytoplasmic Ca2+as a dynamic reporter of overall tissue growth. Further, we show that perturbations to Ca2+signaling tune the final size of organs. This work provides a platform to further study how organ size regulation emerges from the crosstalk between biochemical growth signals and heterogeneous cell signaling states.

Author Summary

Calcium (Ca2+) is a universal second messenger that regulates a myriad of cellular processes such as cell division, cell proliferation and apoptosis. Multiple patterns of Ca2+signaling including single cell spikes, multicellular Ca2+transients, large-scale Ca2+waves, and global “fluttering” have been observed in epithelial systems during organ development. Key molecular players and biophysical mechanisms involved in formation of these patterns during organ development are not well understood. In this work, we developed a generalized multicellular model of Ca2+that captures all the key categories of Ca2+activity as a function of key hormonal signals. Integration of model predictions and experiments reveals two subclasses of cell populations and demonstrates that Ca2+signaling activity at the organ scale is defined by a general decrease in gap junction communication as organ growth. Our experiments also reveal that a “goldilocks zone” of optimal Ca2+activity is required to achieve optimal growth at the organ level.
Pneumococcal Colonisation is an Asymptomatic Event in Healthy Adults using an Experimental Human Colonisation Model
Authors: Trimble Ashleigh , Connor Victoria , Robinson Ryan E , Hancock Carole A , Wang Duolao , Gordon Stephen B , Ferreira Daniela M , Wright Angela D , Collins Andrea M
Published: June 2019

Introduction

Pneumococcal colonisation is regarded as a pre-requisite for developing pneumococcal disease. In children previous studies have reported colonisation to be a symptomatic event and described a relationship between symptom severity/frequency and colonisation density. The evidence for this in adults is lacking in the literature. This study uses an experimental human pneumococcal challenge model to explore whether pneumococcal colonisation (or co-colonisation with a respiratory virus) is a symptomatic event in healthy adults.

Methods

Healthy volunteers aged 18-50 were recruited and inoculated intra-nasally with either Streptococcus pneumoniae (serotypes 6B, 23F) or saline as a control. Respiratory viral swabs were obtained prior to inoculation. Nasal and non-nasal symptoms were then assessed using a modified Likert score between 1 (no symptoms) to 7 (cannot function). The rate of symptoms reported between groups was compared and a correlation analysis performed.

Results

Data from 54 participants were analysed. 46 were inoculated with S. pneumoniae (29 with 6B, 17 with 23F) and 8 received saline. In total, 14 became experimentally colonised (30.4%), all of which were inoculated with 6B serotype. There was no statistically significant difference in nasal (p= 0.45) or non-nasal symptoms (p=0.28) between the pneumococcal inoculation group and the saline group. There was no direct correlation between colonisation density and symptom severity in those who were colonised. In the 22% (12/52) who were co-colonised with pneumococcus and respiratory viruses there was no statistical difference in either nasal or non-nasal symptoms (virus positive p=0.74 and virus negative p=1.0).

Conclusion

Pneumococcal colonisation is asymptomatic in healthy adults, regardless of bacterial density or viral co-colonisation.
Preconditioning cathodal transcranial direct current stimulation facilitates the neuroplastic effect of subsequent anodal transcranial direct current stimulation applied during cycling in young adults
Authors: Pourmajidian Maryam , Lauber Benedikt , Sidhu Simranjit K
Published: June 2019

The study aimed to examine the effect of a priming cathodal transcranial direct current stimulation (ctDCS) before subsequent anodal-tDCS (atDCS) was applied during low workload cycling exercise on the corticospinal responses in young healthy individuals. Eleven young subjects participated in two sessions receiving either priming ctDCS or sham stimulation, followed by atDCS while cycling (i.e. ctDCS-atDCS, sham-atDCS) at 1.2 times their body weight (84 ± 20 W) in a counterbalanced double-blind design. Corticospinal excitability was measured with motor evoked potentials (MEPs) elicited via transcranial magnetic stimulation with the intensity set to produce an MEP amplitude of 1 mV in a resting hand muscle at baseline (PRE), following priming tDCS (POST-PRIMING) and post atDCS combined with cycling exercise (POST-TEST). There was a significant interaction between time and intervention (P < 0.01) on MEPs. MEPs increased from PRE (1.0 ± 0.06 mV) to POST-TEST (1.3 ± 0.06 mV) during ctDCS-atDCS (P < 0.001) but did not change across time during sham-atDCS (1.0 ± 0.06 mV, P > 0.7). Furthermore, MEPs were higher in ctDCS-atDCS compared to sham-atDCS (P < 0.01) at both POST-PRIMING (ctDCS-atDCS: 1.1 ± 0.06, sham-atDCS: 1.0 ± 0.06) and POST-TEST (ctDCS-atDCS: 1.3 ± 0.06, sham-atDCS: 1.0 ± 0.06). These outcomes demonstrate that cathodal tDCS priming can enhance corticospinal excitability following anodal tDCS applied in combination with cycling exercise. The findings have implications for the application of tDCS in combination with cycling exercise in rehabilitation and sporting contexts.
Simplified high-throughput methods for deep proteome analysis on the timsTOF Pro
Authors: Sandow Jarrod J , Infusini Giuseppe , Dagley Laura F , Larsen Rune , Webb Andrew I
Published: June 2019

Recent advances in mass spectrometry technology have seen remarkable increases in proteomic sequencing speed, while improvements to dynamic range have remained limited. An exemplar of this is the new timsTOF Pro instrument, which thanks to its trapped ion mobility, pushes effective fragmentation rates beyond 100Hz and provides accurate CCS values as well as impressive sensitivity. Established data dependent methodologies underutilize these advances by relying on long analytical columns and extended LC gradients to achieve comprehensive proteome coverage from biological samples. Here we describe the implementation of methods for short packed emitter columns that fully utilize instrument speed and CCS values by combining rapid generation of deep peptide libraries with enhanced matching of single shot data dependent sample analysis. Impressively, with only a 17 minute separation gradient (50 samples per day), the combination of high performance chromatography and CCS enhanced library based matching resulted in an average of 5,931 protein identifications within individual samples, and 7,244 proteins cumulatively across replicates from HeLa cell tryptic digests. Additionally, an ultra-high throughput setup utilizing 5 min gradients (180 samples per day) yielded an average of 3,666 protein identifications within individual samples and 4,659 proteins cumulatively across replicates. These workflows are simple to implement on available technology and do not require complex software solutions or custom-made consumables to achieve high throughput and deep proteome analysis from biological samples.
CAMIO for deletion analysis of endogenous DNA sequences in multicellular organisms
Authors: Chen Hui-Min , Marques Jorge Garcia , Sugino Ken , Wei Dingjun , Miyares Rosa Linda , Lee Tzumin
Published: June 2019

The genome is the blueprint for an organism. Interrogating the genome, especially locating critical cis-regulatory elements, requires deletion analysis. This is conventionally performed using synthetic constructs, making it cumbersome and non-physiological. Thus, we createdCas9-mediatedArrayedMutagenesis of IndividualOffspring (CAMIO) to achieve high-throughput analysis of native DNA. CAMIO utilizes CRISPR that is spatially restricted to generate independent deletions. Controlled by recombination, a single guide RNA is stochastically chosen from a set targeting a specific DNA region. Combining two sets increases variability, leading to either indels at 1-2 target sites or inter-target deletions. Cas9 restriction to male germ cells elicits autonomous double-strand-break repair, consequently creating offspring with diverse mutations. Thus, from a single population cross, we can obtain a deletion matrix covering a large expanse of DNA at both coarse and fine resolution. We demonstrate the ease and power of CAMIO by mapping 5’UTR sequences crucial forchinmo’spost-transcriptional regulation.
Zebrafish Dscaml1 is Essential for Retinal Patterning and Function of Oculomotor Subcircuits
Authors: Ma Manxiu , Ramirez Alexandro D. , Wang Tong , Roberts Rachel L. , Harmon Katherine E. , Schoppik David , Sharma Avirale , Kuang Christopher , Goei Stephanie L. , Gagnon James A. , Zimmerman Steve , Tsai Shengdar Q. , Reyon Deepak , Joung J. Keith , Aksay Emre R. F. , Schier Alexander F. , Pan Y. Albert
Published: June 2019

Down Syndrome Cell Adhesion Molecules (dscam and dscaml1) are essential regulators of neural circuit assembly, but their roles in vertebrate neural circuit function are still mostly unexplored. We investigated the role of dscaml1 in the zebrafish oculomotor system, where behavior, circuit function, and neuronal activity can be precisely quantified. Loss of zebrafish dscaml1 resulted in deficits in retinal patterning and light adaptation, consistent with its known roles in mammals. Oculomotor analyses showed that mutants have abnormal gaze stabilization, impaired fixation, disconjugation, and faster fatigue. Notably, the saccade and fatigue phenotypes in dscaml1 mutants are reminiscent of human ocular motor apraxia, for which no animal model exists. Two-photon calcium imaging showed that loss of dscaml1 leads to impairment in the saccadic premotor pathway but not the pretectum-vestibular premotor pathway, indicating a subcircuit requirement for dscaml1. Together, we show that dscaml1 has both broad and specific roles in oculomotor circuit function, providing a new animal model to investigate the development of premotor pathways and their associated human ocular disorders.
Caenorhabditis elegansExhibits Positive Gravitaxis
Authors: Chen Wei-Long , Ko Hungtang , Chuang Han-Sheng , Bau Haim H. , Raizen David
Published: June 2019

Whether or not the micro swimmerCaenorhabditis eleganssenses and respond to gravity is unknown. We find thatC. elegansaligns its swimming direction with that of the gravity vector (positive gravitaxis). When placed in an aqueous solution that is denser than the animals, they still orient downwards, indicating that non-uniform mass distribution and/or hydrodynamic effects are not responsible for animal’s downward orientation. Paralyzed worms and worms with globally disrupted sensory cilia do not change orientation as they settle in solution, indicating that gravitaxis is an active behavior that requires gravisensation. Other types of sensory driven orientation behaviors cannot explain our observed downward orientation. Like other neural behaviors, the ability to respond to gravity declines with age. Our study establishes gravitaxis in the micro swimmerC. elegansand suggests thatC. eleganscan be used as a genetically tractable system to study molecular and neural mechanisms of gravity sensing and orientation.

Significance Statement

Understanding how animals respond to gravity is not only of fundamental scientific interest, but has clinical relevance, given the prevalence of postural instability in aged individuals. Determining whetherC. elegansresponds to gravity is important for mechanistic studies of gravity sensing in an experimentally tractable animal, for a better understanding of nematode ecology and evolution, and for studying biological effects of microgravity. Our experiments, which indicate thatC. eleganssenses and responds to gravity, set the stage for mechanistic studies on molecular mechanisms of gravity sensing.
Adaptive and Innate Immune Cell Responses in Tendons and Lymph Nodes After Tendon Injury and Repair
Authors: Noah Andrew C , Li Thomas M , Martinez Leandro M , Wada Susumu , Swanson Jacob B , Disser Nathaniel P , Sugg Kristoffer B , Rodeo Scott A , Lu Theresa T , Mendias Christopher L
Published: June 2019

Tendon injuries are a common clinical condition with limited treatment options. The cellular components of the innate system, such as neutrophils and macrophages, have been well studied in tendon injuries. However the adaptive immune system, comprised of specialized lymphocytes, plays an important role in orchestrating the healing of numerous tissues but less is known about these cells in tendon healing. To gain a greater understanding of the biological processes that regulate tendon healing, we sought to determine how the cellular components of the adaptive and innate immune system respond to a tendon injury using two-month old male mice. We determined that the lymphatic vasculature is present in the epitenon and superficial regions of Achilles tendons. We then created an acute Achilles tenotomy followed by repair, and collected tendons and draining lymph nodes one, two, and four weeks after injury. Using flow cytometry and histology, after tendon injury we observed a robust adaptive immune cell response that followed an initial innate immune cell response. There was an accumulation of monocytes, neutrophils, and macrophages one week after injury that declined thereafter. Dendritic cells and CD4+ T cells peaked two weeks after injury, while B cells and CD8+ T cells progressively increased over time. In parallel, immune cells of the draining popliteal lymph node demonstrated a similarly coordinated response to the injury. These results suggest that there is an adaptive immune response to tendon injury and adaptive immune cells may play a role in regulating tendon healing.
GenAPI: a tool for gene absence-presence identification in fragmented bacterial genome sequences
Authors: Gabrielaite Migle , Marvig Rasmus L.
Published: June 2019

Bacterial gene loss and acquisition is a well-known phenomenon which contributes to bacterial adaptation through changes in important phenotypes such as virulence, antibiotic resistance and metabolic capability. While advances in DNA sequencing have accelerated our ability to generate short-read genome sequencing to disentangle phenotypic changes caused by gene loss and acquisition, the short-read genome sequencing often results in fragmented genome assemblies as a basis for identification of gene loss and acquisition events. However, sensitive and precise determination of gene content change for fragmented genome assemblies remain challenging as analysis needs to account for cases when only a fragment of the gene is assembled or when the gene assembly is split in more than one contig.

We developed GenAPI, a command-line tool that is designed to compare the gene content of bacterial genomes for which only fragmented genome assemblies are available. GenAPI, unlike other available tools of similar purpose, accounts for genome assembly imperfections and aims to compensate for them. We tested the performance of GenAPI on three different datasets to show that GenAPI has high sensitivity while it maintains precision when dealing with partly assembled genes in both simulated and real datasets. Furthermore, we compared and evaluated the performance of GenAPI with six popular tools for gene presence-absence identification. While we find that the compared tools have the same precision and recall rates when analyzing complete genome sequences, GenAPI performs better than the other tools on fragmented genome assemblies.
Silver nanoparticle induced oxidative stress augments anticancer gut bacterial metabolites production
Authors: Bhalla Prerna , Rengaswamy Raghunathan , Karunagaran Devarajan , Suraishkumar G. K. , Sahoo Swagatika
Published: June 2019

Colorectal cancer (CRC) is the fourth leading cause of mortality, world-wide. Gut bacterial dysbiosis being one of the major causes of CRC onset. Gut microbiota produced metabolites, e.g. folate and butyrate play crucial roles in cancer progression and treatment, and thus, need to be considered for effective CRC management. A potential cancer therapy, i.e., use of silver nanoparticles (AgNPs), imparts cytotoxic effects by inducing high intracellular reactive oxygen species (ROS) levels. However, the simultaneous interactions of AgNPs with gut microbiota to aid CRC treatment has not been reported thus far. Therefore, in this study, variation of intracellular ROS concentrations, in Enterococcus durans (E. durans), a representative gut microbe, was studied in the presence of low AgNP concentrations (25 ppm). Increases were observed in intracellular hydroxyl radical and extracellular folic acid concentrations by 48% and 52%, respectively, at the 9thhour of microbial growth. To gain a systems level understanding of ROS metabolism in E. durans, genome scale metabolic network reconstruction and modeling was adopted. In silico modeling reconfirmed the critical association between ROS and folate metabolism. Further, amino acids, energy metabolites, nucleotides, and butyrate were found to be important key players. Consequently, the anticancer effect of folic acid was experimentally studied on HCT116 (i.e., colon cancer cell line), wherein, its viability was reduced to 79% via folate present in the supernatants from AgNP treated E. durans cultures. Thus, we suggest that the inter-relationship between gut bacteria and AgNP-based cancer treatment can be used to design robust and effective cancer therapies.