bluuebunny/crossref_metadata_2025 huggingface dataset:
The Association of Lifetime and Deployment-Acquired Traumatic Brain Injury With Postdeployment Binge and Heavy Drinking
Authors: Adams Rachel Sayko , Campbell-Sills Laura , Stein Murray B. , Sun Xiaoying , Larson Mary Jo , Kessler Ronald C. , Ursano Robert J. , Jain Sonia , Corrigan John D.
Published: July 2019

Objective:

To investigate associations of lifetime traumatic brain injury (LT-TBI) prior to an index deployment, and/or deployment-acquired TBI (DA-TBI), with postdeployment binge and heavy drinking.

Setting:

Soldiers from 3 Brigade Combat Teams deployed to Afghanistan in 2012.

Participants:

A total of 4645 soldiers who participated in the Army STARRS Pre/Post Deployment Study and completed 4 assessments: T0 (1-2 months predeployment), T1 (upon return to United States), T2 (3 months postdeployment), and T3 (9 months postdeployment).

Design:

Prospective, longitudinal study controlling for baseline binge drinking.

Main Measures:

Self-reported past month binge drinking (5+ alcoholic beverages on the same day) and past month heavy drinking (binge drinking at least weekly) at T2 and T3.

Results:

In total, 34.3% screened positive for LT-TBI, and 19.2% screened positive for DA-TBI. At T2 only, LT-TBI, but not DA-TBI, was associated with increased odds of binge drinking (adjusted odds ratio [AOR] = 1.39, 95% confidence interval [CI]: 1.20-1.60, P < .001) and heavy drinking (AOR = 1.28, 95% CI: 1.09-1.49, P = .007). Among the subgroup with LT-TBI, also having DA-TBI was associated with increased risk of heavy drinking at T3 (AOR = 1.42, 95% CI: 1.03-1.95, P = .047).

Conclusion:

Routine screening for LT-TBI may help target efforts to prevent alcohol misuse among military members.
Diagnostic and Treatment Trends in Children With Kawasaki Disease in the United States, 2006–2015
Authors: Dominguez Samuel R. , Birkholz Meghan , Anderson Marsha S. , Heizer Heather , Jone Pei-Ni , Glode Mary P. , Todd James K.
Published: July 2019

Objective:

To evaluate variations in treatment practice and compliance with national guidelines for the diagnostic evaluation of children with Kawasaki disease (KD).

Study Design:

We used the Pediatric Hospital Information System database to analyze demographic, laboratory and treatment data from patients admitted with KD between January 1, 2006, and December 31, 2015.

Results:

During the study period, 12,089 children with KD were diagnosed. Nearly all patients had a complete blood cell count, erythrocyte sedimentation rate, and C-reactive protein ordered. Fewer patients had alanine aminotransferase (48.6%) or a urinalysis (75.3%). A small percentage of children had abdominal imaging (11.5%), neck imaging (5.9%), and lumbar punctures (4.5%), and 36.0% of patients received antibiotic therapy. Obtaining echocardiograms pretreatment and the use of steroids and infliximab significantly increased over the study period (P < 0.001). For patients who failed initial intravenous immunoglobulin (IVIG) monotherapy, 82.0% received a second dose of IVIG, 7.7% received steroids, 6.5% received infliximab, and 3.9% received combination therapy. Patients receiving infliximab or steroids as second therapy had a higher response rate than those who received only a second IVIG dose (87.9% versus 83.0% versus 73.3%, P < 0.001).

Conclusions:

KD remains a challenging diagnosis. Opportunities exist for earlier use of echocardiograms in the evaluation of children with potential KD. Significant variations in practice exist surrounding second-line therapy. Our data suggest superiority of second-line therapy use of infliximab or steroids over IVIG in terms of reducing need for additional therapies. Prospective, controlled studies are needed to confirm this finding.
Candida tropicalis Thyroiditis Presenting With Thyroid Storm in a Pediatric Patient With Acute Lymphocytic Leukemia
Authors: Niles Denver , Boguniewicz Juri , Shakeel Omar , Margolin Judith , Chelius Daniel , Gupta Meenal , Paul David , King Katherine Y. , McNeil J. Chase
Published: July 2019

Suppurative thyroiditis is uncommon in the pediatric population and particularly rare to be caused by fungi. We present a case of Candida tropicalis thyroiditis in an adolescent male with acute lymphocytic leukemia that led to disseminated candidiasis, thyroid storm and eventual total thyroidectomy for source control.
Dermorphin [D-Arg2, Lys4] (1-4) amide inhibits below-level heat hypersensitivity in mice after contusive thoracic spinal cord injury
Authors: Liu Shuguang , Huang Qian , He Shaoqiu , Chen Zhiyong , Gao Xinyan , Ma Danxu , Duan Wanru , Ford Neil , Yang Fei , Chen Xueming , Raja Srinivasa N. , Hao Dingjun , Guan Yun
Published: July 2019

Opioid use for chronic pain is limited by severe central adverse effects. We examined whether activating mu-opioid receptors (MORs) in the peripheral nervous system attenuates spinal cord injury (SCI) pain-like behavior in mice. We produced a contusive SCI at the T10 vertebral level and examined motor and sensory dysfunction for 6 weeks. At 6 weeks, we tested the effect of subcutaneous (s.c.) injection of dermorphin [D-Arg2, Lys4] (1-4) amide (DALDA), a peripherally acting MOR-preferring agonist, on mechanical and heat hypersensitivity. Basso mouse scale score was significantly decreased after SCI, and mice showed hypersensitivity to mechanical and heat stimulation at the hind paw beginning at 2 weeks, as indicated by increased paw withdrawal frequency to mechanical stimulation and decreased paw withdrawal latency to heat stimulation. In wild-type SCI mice, DALDA (1 mg/kg, s.c.) attenuated heat but not mechanical hypersensitivity. The effect was blocked by pretreatment with an intraperitoneal injection of methylnaltrexone (5 mg/kg), a peripherally restricted opioid receptor antagonist, and was also diminished in Pirt-MOR conditional knockout mice. DALDA did not adversely affect exploratory activity or induced preference to drug treatment in SCI mice. In vivo calcium imaging showed that DALDA (1, 10 mg/kg, s.c.) inhibited responses of small dorsal root ganglion neurons to noxious heat stimulation in Pirt-GCaMP6s mice after SCI. Western blot analysis showed upregulation of MOR in the lumbar spinal cord and sciatic nerves at 6 weeks after SCI. Our findings suggest that peripherally acting MOR agonist may inhibit heat hypersensitivity below the injury level with minimal adverse effects.
Comparing the Barriers and Facilitators of Heart Failure Management as Perceived by Patients, Caregivers, and Clinical Providers
Authors: Trivedi Ranak B. , Slightam Cindie , Nevedal Andrea , Guetterman Timothy C. , Fan Vincent S. , Nelson Karin M. , Rosland Ann-Marie , Heidenreich Paul A. , Timko Christine , Asch Steven M. , Piette John D.
Published: July 2019

Background:

Heart failure (HF) management requires the participation of patients, their significant others, and clinical providers. Each group may face barriers to HF management that may be unique or may overlap.

Objective:

The aim of this study was to compare the barriers and facilitators of HF management as perceived by patients, significant others, and clinical providers.

Methods:

Participants were recruited from a Veterans Health Administration facility. Eligible patients had a diagnosis of HF (ICD9 code 428.XX), 1 or more HF-related visit in the previous year, and a significant other who was their primary caregiver. Significant others were adults with no history of cognitive impairments caring for patients with HF. Providers were eligible if they cared for patients with HF. All participants completed semistructured interviews designed to elicit barriers to managing HF and strategies that they used to overcome these barriers. Interviews were transcribed and analyzed using latent thematic analysis, and recruitment continued until thematic saturation was attained.

Results:

A total of 17 couples and 12 providers were recruited. All 3 groups identified poor communication as a key barrier to HF management, including communication between patients and their significant other, between couples and providers, and providers with each other. Significant others noted that the lack of direct communication with clinical providers hindered their efforts to care for the patient. All 3 groups emphasized the importance of family members in optimizing adherence to HF self-management recommendations.

Conclusions:

Providers, patients, and significant others all play important and distinct roles in the management of HF. Tools to enhance communication and collaboration for all 3 and supporting the needs of significant others are missing components of current HF care.
Factors Influencing Cardiovascular Risk Factors and Health Perception Among Kentuckians Living in Appalachia
Authors: Abraham Cilgy M. , Kelly Sarah , Wantland Dean , Chung Misook L. , Mudd-Martin Gia , Biddle Martha J. , Moser Debra K.
Published: July 2019

Background:

Cardiovascular disease (CVD) and risk factors for CVD are prevalent among Appalachians from Kentucky. Appalachian men and women have high rates of engagement in unhealthy behaviors and poor physical health measures that increase their risk for CVD.

Objective:

In this study, the relationship among gender, CVD risk factors, and health perception in Appalachians from Kentucky was explored.

Methods:

This cross-sectional secondary analysis is from a randomized controlled trial on CVD health in rural Kentucky. To assess gender differences in smoking history, χ
2 was used. Independent t tests compared the mean between participants 50 years or younger and those older than 50 years with differences in body mass index (BMI), waist circumference, systolic and diastolic blood pressure, hemoglobin A1C, total cholesterol, and physical activity. A multivariate linear regression analysis assessed variables predicting the outcome of health perception.

Results:

Most participants had a mean BMI of 33 kg/m2 and 94.3% of men used smokeless tobacco compared to 5.7% of the women. Differences existed between gender and current, ever, or never smoked (P < .001). Women had higher total cholesterol levels but men had higher waist circumference. Participants older than 50 years had higher engagement in physical activity than did those 50 years or younger. Higher BMI and hemoglobin A1C level were significant predictors of worse health perception (P ≤ .05). For every unit increase in the physical activity scale, there was a 0.2-unit improvement in health perception (P ≤ .001).

Conclusion:

Appalachians from Kentucky have many CVD risk factors. Minimal engagement in preventative measures against CVD can worsen patient outcomes.
Screening Versus Brief Domain-specific Tests to Assess Long-term Postoperative Cognitive Dysfunction After Concomitant Aortic Valve Replacement and Coronary Artery Bypass Grafting
Authors: Pérez-Belmonte Luis M. , Florido-Santiago Mercedes , Osuna-Sánchez Julio , Barbancho Miguel A. , Millán-Gómez Mercedes , Jímenez-Navarro Manuel F. , Bernal-López M. Rosa , Gómez-Huelgas Ricardo , Lara José P.
Published: July 2019

Background

Although postoperative cognitive dysfunction is a relevant complication after surgery, assessment for the condition is not routine in clinical practice.

Objective

The aim of this study was to compare the use of screening versus brief domain-specific cognitive tests in assessing long-term cognitive dysfunction after concomitant aortic valve replacement and coronary artery bypass grafting.

Methods

In this observational prospective study, we evaluated 70 patients preoperatively and after 1, 6, and 12 months using 2 screening tests (Mini-Mental State Examination and Clock Drawing Test) and 2 brief domain-specific cognitive tests (Trail Making Test to evaluate attention and executive function, and Semantic and Phonological Tests to evaluate verbal fluency).

Results

The brief domain-specific cognitive tests detected significant postoperative worsening in performances (up to 19% on the Trail Making Test and 15.4% on verbal fluency tests at 6 months). Postoperative mild attention/executive dysfunction or inferior normal performance was detected with the maximums being seen at 6 months (44.6%, P < .001). Performances on screening tests did not significantly change during the study period.

Conclusions

A brief domain-specific cognitive evaluation could be routinely implemented in perioperative care practice to detect postoperative cognitive dysfunction.
Comprehensive vibrational dynamics of half-open fluid-filled shells
Authors: Lendermann Markus , Koh Jin Ming , Tan Joel Shi Quan , Cheong Kang Hao
Published: July 2019

Fluid-filled shells are near-ubiquitous in natural and engineered structures—a familiar example is that of glass harps comprising partially filled wineglasses or glass bowls, whose acoustic properties are readily noticeable. Existing theories modelling the mechanical properties of such systems under vibrational load either vastly simplify shell geometry and oscillatory modal shapes to admit analytical solutions or rely on finite-element black-box computations for general cases, the former yielding poor accuracy and the latter offering limited tractability and physical insight. In the present study, we derive a theoretical framework encompassing elastic shell deformation with structural and viscous dissipation, accommodating arbitrary axisymmetric shell geometries and fluid levels; reductions to closed-form solutions under specific assumptions are shown to be possible. The theory is extensively verified against a range of geometries, fluid levels and fluid viscosities in experiments; an extension of the model encompassing additional solid objects within the fluid-filled shell is also considered and verified. The presented theoretical advance in describing vibrational response is relevant in performance evaluation for engineered structures and quality validation in manufacturing.
Quantifying magic for multi-qubit operations
Authors: Seddon James R. , Campbell Earl T.
Published: July 2019

The development of a framework for quantifying ‘non-stabilizerness’ of quantum operations is motivated by the magic state model of fault-tolerant quantum computation and by the need to estimate classical simulation cost for noisy intermediate-scale quantum (NISQ) devices. The robustness of magic was recently proposed as a well-behaved magic monotone for multi-qubit states and quantifies the simulation overhead of circuits composed of Clifford + Tgates, or circuits using other gates from the Clifford hierarchy. Here we present a general theory of the ‘non-stabilizerness’ of quantum operations rather than states, which are useful for classical simulation of more general circuits. We introduce two magic monotones, called channel robustness and magic capacity, which are well-defined for generaln-qubit channels and treat all stabilizer-preserving CPTP maps as free operations. We present two complementary Monte Carlo-type classical simulation algorithms with sample complexity given by these quantities and provide examples of channels where the complexity of our algorithms is exponentially better than previously known simulators. We present additional techniques that ease the difficulty of calculating our monotones for special classes of channels.
Character displacement of a learned behaviour and its implications for ecological speciation
Authors: Porter Cody K. , Benkman Craig W.
Published: July 2019

Cultural evolution may accelerate population divergence and speciation, though most support for this hypothesis is restricted to scenarios of allopatric speciation driven by random cultural drift. By contrast, the role of cultural evolution in non-allopatric speciation (i.e. speciation with gene flow) has received much less attention. One clade in which cultural evolution may have figured prominently in speciation with gene flow includes the conifer-seed-eating finches in the red crossbill (Loxia curvirostra) complex. Here we focus on Cassia crossbills (Loxiasinesciuris; an ecotype recently split taxonomically from red crossbills) that learn social contact calls from their parents. Previous work found that individuals modify their calls throughout life such that they become increasingly divergent from a closely related, sympatric red crossbill ecotype. This open-ended modification of calls could lead to character displacement if it causes population-level divergence in call structure that, in turn, reduces (maladaptive) heterospecific flocking. Heterospecific flocking is maladaptive because crossbills use public information from flockmates to assess resource quality, and feeding rates are depressed when flockmates differ in their ability to exploit a shared resource (i.e. when flockmates are heterospecifics). We confirm the predictions of character displacement by documenting substantial population-level divergence in Cassia crossbill call structure over just two decades and by using field experiments to demonstrate that Cassia and red crossbills differentially respond to these evolved differences in call structure, reducing heterospecific flock formation. Moreover, because crossbills choose mates from within flocks, a reduction in heterospecific flocking should increase assortative mating and may have been critical for speciation of Cassia crossbills in the face of ongoing gene flow in as few as 5000 years. Our results provide evidence for a largely neglected yet potentially widespread mechanism by which reproductive isolation can evolve between sympatric lineages as a byproduct of adaptive cultural evolution.
Male black widows parasitize mate-searching effort of rivals to find females faster
Authors: Scott Catherine E. , McCann Sean , Andrade Maydianne C. B.
Published: July 2019

Mate-searching success is a critical precursor to mating, but there is a dearth of research on traits and tactics that confer a competitive advantage in finding potential mates. Theory and available empirical evidence suggest that males locate mates using mate-attraction signals produced by receptive females (personal information) and avoid inadvertently produced cues from rival males (social information) that indicate a female has probably already mated. Here, we show that western black widow males use both kinds of information to find females efficiently, parasitizing the searching effort of rivals in a way that guarantees competition over mating after reaching a female's web. This tactic may be adaptive because female receptivity is transient, and we show that (i) mate searching is risky (88% mortality) and (ii) a strongly male-biased operational sex ratio (from 1.2 : 1 to more than 10 : 1) makes competition inevitable. Males with access to rivals' silk trails moved at higher speeds than those with only personal information, and located females even when personal information was unreliable or absent. We show that following rivals can increase the potential for sexual selection on females as well as males and argue it may be more widespread in nature than is currently realized.
Fox Insight Collects Online, Longitudinal Patient-Reported Outcomes and Genetic Data on Parkinson’s disease
Authors: Smolensky Luba , Amondikar Ninad , Crawford Karen , Neu Scott , Kopil Catherine M. , Daeschler Margaret , Riley Lindsey ,   23andMe Research Team, Brown Ethan , Toga Arthur W. , Tanner Caroline
Published: July 2019

Fox Insight is an online, longitudinal health study of people with and without Parkinson’s disease with targeted enrollment set to at least 125,000 individuals. Fox Insight data is a rich data set facilitating discovery, validation, and reproducibility in Parkinson’s disease research. The dataset is generated through routine longitudinal assessments (health and medical questionnaires evaluated at regular cycles), one-time questionnaires about environmental exposure and healthcare preferences, and genetic data collection.

Qualified Researchers can explore, analyze, and download patient-reported outcomes (PROs) data and Parkinson’s disease-related genetic variants at https://foxden.michaeljfox.org. The full Fox Insight genetic data set, including approximately 600,000 single nucleotide polymorphisms (SNPs), can be requested separately with institutional review and are described outside of this data descriptor.

Fox Insight is sponsored by The Michael J. Fox Foundation for Parkinson’s Research.
Reversal of ageing- and injury-induced vision loss by Tet-dependent epigenetic reprogramming
Authors: Lu Yuancheng , Krishnan Anitha , Brommer Benedikt , Tian Xiao , Meer Margarita , Vera Daniel L. , Wang Chen , Zeng Qiurui , Yu Doudou , Bonkowski Michael S. , Yang Jae-Hyun , Hoffmann Emma M. , Zhou Songlin , Korobkina Ekaterina , Davidsohn Noah , Schultz Michael B. , Chwalek Karolina , Rajman Luis A. , Church George M. , Hochedlinger Konrad , Gladyshev Vadim N. , Horvath Steve , Gregory-Ksander Meredith S. , Ksander Bruce R. , He Zhigang , Sinclair David A.
Published: July 2019

Ageing is a degenerative process leading to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise, which disrupts youthful gene expression patterns that are required for cells to function optimally and recover from damage1–3. Changes to DNA methylation patterns over time form the basis of an ‘ageing clock’4, 5, but whether old individuals retain information to reset the clock and, if so, whether this would improve tissue function is not known. Of all the tissues in the body, the central nervous system (CNS) is one of the first to lose regenerative capacity6, 7. Using the eye as a model tissue, we show that expression of Oct4, Sox2, and Klf4 genes (OSK) in mice resets youthful gene expression patterns and the DNA methylation age of retinal ganglion cells, promotes axon regeneration after optic nerve crush injury, and restores vision in a mouse model of glaucoma and in normal old mice. This process, which we call recovery of information via epigenetic reprogramming or REVIVER, requires the DNA demethylases Tet1 and Tet2, indicating that DNA methylation patterns don’t just indicate age, they participate in ageing. Thus, old tissues retain a faithful record of youthful epigenetic information that can be accessed for functional age reversal.
Super-resolution microscopy unveils FIP200-scaffolded, cup-shaped organization of mammalian autophagic initiation machinery
Authors: Kenny Samuel J , Chen Xuyan (Shirley) , Ge Liang , Xu Ke
Published: July 2019

Autophagy is an essential physiological process by which eukaryotic cells degrade and recycle cellular materials. Although the biochemical hierarchies of the mammalian autophagy pathway have been identified, questions remain regarding the sequence, subcellular location, and structural requirements of autophagosome formation. Here, we characterize the structural organization of key components of the mammalian autophagic initiation machinery at ∼20 nm spatial resolution via three-color, three-dimensional super-resolution fluorescence microscopy. We thus show that upon cell starvation, FIP200, a large structural protein of the ULK1 complex with no direct yeast homolog, scaffolds the formation of cup-like structures located at SEC12-enriched remodeled ER-exit sites prior to LC3 lipidation. This cup scaffold, then, provides a structural asymmetry to enforce the directional recruitment of downstream components, including the Atg12-Atg5-Atg16 complex, WIPI2, and LC3, to the cup inside. Moreover, we provide evidence that the early autophagic machinery is recruited in its entirety to these cup structures prior to LC3 lipidation, and gradually disperses and dissociates on the outer face of the phagophore membrane during elongation. We thus shed new light on the physical process of mammalian autophagic initiation and development at the nanometer-scale.
Can Orthopaedics become the Gold Standard for Reproducibility? A Roadmap to Success
Authors: Fladie Ian A. , Evans Sheridan , Checketts Jake , Tritz Daniel , Norris Brent , Vassar Matt
Published: July 2019

Background

Scientific research is replete with poor accessibility to data, materials, and protocol, which limits the reproducibility of a study. Transparency with regard to materials, protocols, and raw data sets enhances reproducibility by providing the critical information necessary to verify, replicate, and resynthesize research findings. The extent to which transparency and reproducibility exist in the field of orthopaedics is unclear. In our study, we aimed to evaluate transparency and reproducibility-related characteristics of randomly sampled publications in orthopaedic journals.

Methods

We used the National Library of Medicine catalog to identify English language and MEDLINE-indexed orthopaedic journals. From the 74 journals meeting our inclusion criteria, we randomly sampled 300 publications using a refined PubMed search that were published between January 1, 2014, and December 31, 2018. Two investigators were trained for data extraction and analysis. Both investigators were blinded and independently extracted data from the 300 studies.

Results

Our initial search yielded 68,102 publications, from which we drew a random sample of 300 publications. Of these 300 publications, 286 were screened for empirical data and 14 were inaccessible. For analysis purposes, we excluded publications without empirical data. Of the 182 with empirical data, 13 studies (7.1%) included a data availability statement, 9 (4.9%) reported materials were available, none (0.0%) provided analysis scripts, 2 (1.1%) provided access to the protocol used, 5 (2.7%) were preregistered, and only 2 (1.1%) provided a statement about being a replicated study.

Conclusions

Components necessary for reproducibility are lacking in orthopaedic surgery journals. The vast majority of publications did not provide data or material availability statements, protocols, or analysis scripts, and had no preregistration statements. Intervention is needed to improve reproducibility in the field of orthopaedics. The current state of reproducibility in orthopaedic surgery could be improved by combined efforts from funding agencies, authors, peer reviewers, and journals alike.

Level of Evidence

N/A
Induction of long-term allogeneic cell acceptance and formation of immune privileged tissue in immunocompetent hosts
Authors: Harding Jeffrey , Vintersten-Nagy Kristina , Shutova Maria , Yang Huijuan , Tang Jean Kit , Massumi Mohammad , Izaidfar Mohammad , Izadifar Zohreh , Zhang Puzheng , Li ChengJin , Nagy Andras
Published: July 2019

A vast number of diseases could be treated with therapeutic cells derived from pluripotent stem cells (PSCs). However, cell products that come from non-autologous sources can be immune rejected by the recipient’s immune system. Here, we show that forced expression of eight immunomodulatory transgenes, includingCcl21, Pdl1, Fasl, Serpinb9, H2-M3, Cd47, Cd200, andMfge8, allows mouse embryonic stem cells (mESCs) and their derivatives to escape immune rejection in fully immunocompetent, allogeneic recipients. Despite no genetic alterations to major histocompatibility complex (MHC) genes, immune-modified C57BL/6 mESCs could generate long-term, allogeneic tissues in inbred FVB/N, C3H, and BALB/c, as well as outbred CD-1 recipients. Due to the tandem incorporation of our safe-cell suicide system, which allows tight and drug-inducible control over proliferationin vivo, these allotolerated cells can generate safe and dormant ectopic tissues in the host. We show that these ectopic tissues maintain high expression of all eight immunomodulatory transgenes and are immune-privileged sites that can host and protect unmodified mouse and human cells from rejection in allogeneic and xenogeneic settings, respectively. If translated to human clinical settings, we envision the development of a single pluripotent cell line that can be used to generate allo-tolerated, off-the-shelf cell products to serve all humankind, as well as immune-privileged ectopic tissues to host and immune-protect any kind of therapeutic cell product.
The endoplasmic reticulum-associated mRNA-binding proteins ERBP1 and ERBP2 interact in bloodstream-formTrypanosoma brucei
Authors: Bajak Kathrin , Leiss Kevin , Clayton Christine , Erben Esteban
Published: July 2019

Kinetoplastids rely heavily on post-transcriptional mechanisms for control of gene expression, and on RNA-binding proteins that regulate mRNA splicing, translation and decay.Trypanosoma bruceiERBP1 (Tb927.10.14150) and ERBP2 (Tb927.9.9550) were previously identified as mRNA binding proteins that lack canonical RNA-binding domains. We here show that ERBP1 is associated with the endoplasmic reticulum, like ERBP2, and that the two proteins interactin vivo. Loss of ERBP1 from bloodstream-formT. bruceiinitially resulted in a growth defect but proliferation was restored after more prolonged cultivation. Results from a pull-down of tagged ERBP1 suggest that it preferentially binds to ribosomal protein mRNAs. The ERBP1 sequence resembles that ofSaccharomyces cerevisiaeBfr1, which also localises to the endoplasmic reticulum and binds to ribosomal protein mRNAs. However, unlike Bfr1, ERBP1 does not bind to mRNAs encoding secreted proteins, and it is also not recruited to stress granules after starvation.
Developmental Genome-Wide DNA Methylation Asymmetry Between Mouse Placenta and Embryo
Authors: Legault LM , Doiron K , Lemieux A , Caron M , Chan D , Lopes FL , Bourque G , Sinnett D , McGraw S
Published: July 2019

In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, thede novomethyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principalde novomethyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.
Rapid resistance to pesticide control is predicted to evolve in an invasive fish
Authors: Christie Mark R. , Sepúlveda Maria S. , Dunlop Erin S.
Published: July 2019

Xenobiotic resistance is commonly found in species with short generation times such as bacteria, annual plants, and insects. Nevertheless, the fundamental evolutionary principles that govern the spread of resistance alleles hold true for species with longer generation times. One such example could occur with sea lamprey (Petromyzon marinus), a parasitic invasive species in the Laurentian Great Lakes that decimated native fish populations prior to its control with the pesticide 3-trifluoromethyl-4-nitrophenol (TFM). Since the 1950s, tributaries have been treated annually with TFM, where treatments effectively remove most, but not all, larval sea lamprey. We developed an eco-genetic model of sea lamprey to examine factors affecting the evolution of resistance and found that resistance alleles rapidly rise to fixation after 40-80 years of treatment, despite the species’ relatively long generation time (4-7 years). The absence of natal homing allows resistant individuals to spread quickly throughout the entire system, but also makes the early detection of resistance challenging. High costs of resistance and density independent reproduction can delay, but not prevent, the onset of resistance. These results illustrate that sea lamprey have the potential to evolve resistance to their primary control agent in the near future, highlighting the urgent need for alternative controls.
Probabilistic index models for testing differential expression in single cell RNA sequencing data
Authors: Assefa Alemu Takele , Vandesompele Jo , Thas Olivier
Published: July 2019

Single-cell RNA sequencing (scRNA-seq) technologies profile gene expression patterns in individual cells. It is often of interest to test for differential expression (DE) between conditions, e.g. treatment vs control or between cell types. Simulation studies have shown that non-parametric tests, such as the Wilcoxon-rank sum test, can robustly detect significant DE, with better performance than many parametric tools specifically developed for scRNA-seq data analysis. However, these rank tests cannot be used for complex experimental designs involving multiple groups, multiple factors and confounding variables. Further, rank based tests do not provide an interpretable measure of the effect size. We propose a semi-parametric approach based on probabilistic index models (PIM) that form a flexible class of models that generalize classical rank tests. Our method does not rely on strong distributional assumptions and it allows accounting for confounding factors. Moreover, it allows for the estimation of the effect size in terms of a probabilistic index. Real data analysis demonstrate that PIM is capable of identifying biologically meaningful DE. Our simulation studies also show that DE tests succeed well in controlling the false discovery rate at its nominal level, while maintaining good sensitivity as compared to competing methods.
Evaluating the burstlet theory of inspiratory rhythm and pattern generation
Authors: Kallurkar Prajkta S. , Grover Cameron , Picardo Maria Cristina D. , Del Negro Christopher A.
Published: July 2019

The preBötzinger complex (preBötC) generates the rhythm and rudimentary motor pattern for inspiratory breathing movements. Here, we test ‘burstlet’ theory (Kam, Worrell, Janczewski, et al. 2013), which posits that low amplitude burstlets, subthreshold from the standpoint of inspiratory bursts, reflect the fundamental oscillator of the preBötC. In turn, a discrete suprathreshold process transforms burstlets into full amplitude inspiratory bursts that drive motor output, measurable via hypoglossal nerve (XII) dischargein vitro. We recap observations by Kam & Feldman: field recordings from preBötC demonstrate bursts and concurrent XII motor output intermingled with lower amplitude burstlets that do not produce XII motor output. Manipulations of excitability affect the relative prevalence of bursts and burstlets and modulate their frequency. Whole-cell and photonic recordings of preBötC neurons suggest that burstlets involve inconstant subsets of rhythmogenic interneurons. We conclude that discrete rhythm- and pattern-generating mechanisms coexist in the preBötC and that burstlets reflect its fundamental rhythmogenic nature.
Low-dose Perampanel rescues cortical gamma dysregulation associated with parvalbumin interneuron GluA2 upregulation in epileptic Syngap1+/- mice
Authors: Sullivan Brennan J. , Ammanuel Simon , Kipnis Pavel A. , Araki Yoichi , Huganir Richard L. , Kadam Shilpa D.
Published: July 2019

Loss-of-function SYNGAP1 mutations cause a neurodevelopmental disorder characterized by intellectual disability and epilepsy. SYNGAP1 is a Ras-GTPase-activating protein that underlies the formation and experience-dependent regulation of postsynaptic densities. The mechanisms that contribute to this proposed monogenic cause of intellectual disability and epilepsy remain unresolved. Here, we establish the phenotype of the epileptogenesis in a Syngap1+/- mouse model using 24h video electroencephalogram/electromyogram (vEEG/EMG) recordings at advancing ages. A progressive worsening of clinically-similar seizure phenotypes, interictal spike frequency, sleep dysfunction, and hyperactivity was identified in Syngap1+/- mice. Interictal spikes emerged predominantly during NREM in 24h vEEG of Syngap1+/- mice. Myoclonic seizures occurred at behavioral-state transitions both in Syngap1+/- mice and during an overnight EEG from a child with SYNGAP1 haploinsufficiency. In Syngap1+/- mice, EEG spectral power analyses identified a significant loss of cortical gamma homeostasis during behavioral-state transitions from NREM to Wake and NREM to REM. The loss of gamma homeostasis was associated with a region- and location-specific significant increase of GluA2 AMPA receptor subunit expression in the somas of parvalbumin-positive (PV+) interneurons. Acute dosing with Perampanel, an FDA approved AMPA antagonist significantly rescued cortical gamma homeostasis, identifying a novel mechanism implicating Ca2+ impermeable AMPARs on PV+ interneurons underlying circuit dysfunction in SYNGAP1 haploinsufficiency.
Role of a kinesin motor in cancer cell mechanics
Authors: Mandal Kalpana , Pogoda Katarzyna , Nandi Satabdi , Mathieu Samuel , Kasri Amal , Radvanyi François , Goud Bruno , Janmey Paul A , Manneville Jean-Baptiste
Published: July 2019

Molecular motors play important roles in force generation, migration and intracellular trafficking. Changes in specific motor activities are altered in numerous diseases. KIF20A, a motor protein of the kinesin-6 family, is overexpressed in bladder cancer, and KIF20A levels correlate negatively with the clinical outcome. We report here a new role for the KIF20A kinesin motor protein in intracellular mechanics. Using optical tweezers to probe intracellular mechanics and surface AFM to probe cortical mechanics, we first confirm that bladder cells soften with increasing cancer grade. We then show that inhibiting KIF20A makes the intracellular environment softer for both high and low grade bladder cancer cells. Upon inhibition of KIF20A cortical stiffness also decreases in lower grade cells, while it surprisingly increases in higher grade malignant cells. Changes in cortical stiffness correlate with the interaction of KIF20A with myosin IIA. Moreover, KIF20A negatively regulates bladder cancer cell motility irrespective of the underlying substrate stiffness. Our results reveal a central role for a microtubule motor in cell mechanics and migration in the context of bladder cancer.
Highly reduced genomes of protist endosymbionts show evolutionary convergence
Authors: George Emma E. , Husnik Filip , Tashyreva Daria , Prokopchuk Galina , Horák Aleš , Kwong Waldan K. , Lukeš Julius , Keeling Patrick J.
Published: July 2019

Genome evolution in bacterial endosymbionts is notoriously extreme: the combined effects of strong genetic drift and unique selective pressures result in highly reduced genomes with distinctive adaptations to hosts [1–4]. These processes are mostly known from animal endosymbionts, where nutritional endosymbioses represent the best-studied systems. However, eukaryotic microbes, or protists, also harbor diverse bacterial endosymbionts, but their genome reduction and functional relationships with their more diverse hosts are largely unexplored [5–7]. We sequenced the genomes of four bacterial endosymbionts from three species of diplonemids, poorly-studied but abundant and diverse heterotrophic protists [8–10]. The endosymbionts come from two intracellular families from different orders, Rickettsiaceae and Holosporaceae, that have invaded diplonemids multiple times, and their genomes have converged on an extremely small size (605–632 kbp), similar gene content (e.g., metabolite transporters and secretion systems), and reduced metabolic potential (e.g., loss of energy metabolism). These characteristics are generally found in both families, but the diplonemid endosymbionts have evolved greater extremes in parallel. Their modified type VI secretion systems are likely involved in the manipulation of host metabolism (e.g., interactions with host mitochondria) or defense against bacterial infections, although their similar effector/immunity proteins may also allow for co-occurring Holosporaceae species in one diplonemid host. Finally, modified cellular machinery like ATP synthase without oxidative phosphorylation and reduced flagella present in both diplonemid endosymbionts and nutritional animal endosymbionts indicates that intracellular mechanisms have converged in bacterial endosymbionts with various functions and from different eukaryotic hosts across the tree of life.
Choice of host cell line is essential for the functional glycosylation of the fragment crystallizable (Fc) region of human IgG1 inhibitors of influenza B viruses
Authors: Blundell Patricia A. , Lu Dongli , Dell Anne , Haslam Stuart M. , Pleass Richard J.
Published: July 2019

Antibodies are glycoproteins that carry a conserved N-linked carbohydrate attached to the Fc, whose presence and fine structure profoundly impacts on theirin vivoimmunogenicity, pharmacokinetics and functional attributes. The host cell line used to produce IgG has a major impact on this glycosylation, as different systems express different glycosylation enzymes and transporters that contribute to the specificity and heterogeneity of the final IgG-Fc glycosylation profile. Here we compare two panels of glycan-adapted IgG1-Fc mutants expressed in either the HEK 293-F or CHO-K1 systems. We show that the types of N-linked glycans between matched pairs of Fc mutants vary significantly, and in particular with respect to sialylation. These cell line effects on glycosylation profoundly influence the ability of the engineered Fcs to interact with either human or pathogen receptors. For example, we describe Fc mutants that potently disrupted influenza B-mediated agglutination of human erythrocytes when expressed in CHO-K1 but not in HEK 293-F cells.
Genotyping Test Development and Genotyping Survey of Pakistani population of Holstein Friesian imported from Different Origins for A1/A2 SNP in Beta-casein Gene
Authors: Ali Waqas Rafique , Amin Imran , Asif Muhammad , Mansoor Shahid
Published: July 2019

Quality of milk is determined by multiple factors including microbial load, somatic cell score, content percentages and absence of adulterants. However, in term of genetics, milk quality can be linked with beta casein. Beta casein is a milk protein having genetic variants, one of which is believed to be linked with progression of many diseases including cardiovascular diseases, metabolic diseases and nervous disorders. As beta casein has genetic basis so milk quality can be elucidated by animal genotyping. But no such genotyping facility was available country wide for this purpose. Hence objective of this study is the development of diagnostic test using ARMS-PCR technology in Pakistan and genotyping of beta casein variants in Pakistani population of Holstein Friesian cattle. A total of 166 blood samples were collected from Holstein Friesian (imported from Holland, USA and Australia) and genotyped using ARMS-PCR. Validation of ARMS-PCR was confirmed by Sanger sequencing of beta casein gene from 78 animals. ARMS-PCR based test was then compared with parallel genotyping techniques in term of cost and time effectivity. Reproducibility of this test was tested and validation of this test was done by Sanger sequencing. This test is cost effective as well as time effective in compared to other techniques. Holstein Friesian originating from different countries have different percentages of beta casein variants. This test can be used routinely for genotyping of beta casein. In future there is a need to find out prevalence of beta casein variants of indigenous cattle as well as cross bred population of Pakistan and formulation of breeding policy, keeping in view health concerns of A1 genotype of β-casein.

Novelty Statement

In this study, a diagnostic test is developed to genotype beta casein variants in animal. This is the first report of its kind in Pakistan as before this report either sequencing or tedious and costly procedures were in use for genotyping of beta casein variants in Pakistan. Additionally, for the first time in Pakistan Holstein Friesian imported from Holland, United States and Australia were genotyped to elucidate their genotype status for beta casein polymorphism.
A preliminary study of the cytotoxicity of the protein extract of Chrysobalanus icaco L. and Eugenia astringens Cambess., commercialized in markets
Authors: Pedrete Thaís A. , Carmo Julianderson O.S. , Barreto Emiliano O. , Moreira Josino C.
Published: July 2019

The use of plants and their products for medical treatment is very common procedure in Brazil, especially for treatment of diabetes. In fact, several plants can demonstrate hypoglycemic effects in vitro assays. However, the use for human treatment requires the knowledge of their toxicological properties. The aim of this study was to evaluate the effect of protein extracts of Chrysobalanus icaco collected from natural habitats and of Eugenia astringens acquired from the market of Rio de Janeiro on the viability and migration of fibroblasts. E. astringens has a similar morphology as C. icaco and it is sold as Chrysobalanus in a popular market in Rio de Janeiro. Being a different plant, E. astringens expresses different proteins, and its protein extract has proved to possess higher toxic properties than C. icaco does. Cytotoxicity assays indicated that, as the protein extract concentration increases, fibroblast viability decreases. Only the E. astringens extract displayed cytotoxicity at all concentrations, in addition to reduced fibroblast migration. The results obtained in this study demonstrates that it’s necessary integrative policies for rational use of medicinal plants and their commercialization, since the current use of medicinal plants may be inadequate and it is of great importance for Public Health.
Spatially resolved transcriptomics reveals plant host responses to pathogens
Authors: Giolai Michael , Verweij Walter , Lister Ashleigh , Heavens Darren , Macaulay Iain , Clark Matthew D.
Published: July 2019

Background

Thorough understanding of complex model systems requires the characterisation of processes in different cell types of an organism. This can be achieved with high-throughput spatial transcriptomics at a large scale. However, for plant model systems this is still challenging as suitable transcriptomics methods are sparsely available. Here we present Grid-seq, an easy to adopt, micro-scale spatial-transcriptomics workflow that allows to study expression profiles across small areas of plant tissue at a fraction of the cost of existing sequencing-based methods.

Results

We compare the Grid-seq method with widely used library preparation methods (Illumina TruSeq). In spatial experiments we show that the Grid-seq method is sensitive enough to identify expression differences across a plant organ. We further assess the spatial transcriptome response of Arabidopsis thaliana leaves exposed to the bacterial molecule flagellin-22.

Conclusion

We show that our method can be used to identify known, rapidly flagellin-22 elicited genes, plant immune response pathways to bacterial attack and spatial expression patterns of genes associated with these pathways.