bluuebunny/crossref_metadata_2025 huggingface dataset:
Cefoxitin Prophylaxis During Pediatric Cardiac Surgery: Retrospective Exploration of Postoperative Trough Levels
Authors: Ricci Zaccaria , Benegni Simona , Cies Jeffrey J. , Marinari Eleonora , Haiberger Roberta , Garisto Cristiana , Cairoli Sara , Di Chiara Luca , Goffredo Bianca
Published: August 2018

Background:

This study aimed to explore inter-individual variability of cefoxitin trough levels, predictors of serum cefoxitin concentration and the probability of target attainment of drug levels above 4 mg/L after pediatric cardiac surgery.

Methods:

Retrospective study on children scheduled for elective cardiac surgery and having cefoxitin trough levels available up to 24 hours postsurgery.

Results:

Overall, 68 children (9 neonates, 34 infants, 15 children below or equal to 10 years old and 10 patients above this age) were included. Of these, 16 surgeries were performed off cardiopulmonary bypass and 52 were performed on cardiopulmonary bypass. The free cefoxitin concentrations showed a median (interquartile range) concentration of 1.7 (0.6–4.2) mg/L. The range of cefoxitin concentrations showed a 150-fold and 340-fold variability at cardiac intensive care unit admission and after 24 hours, respectively. The pharmacodynamics (PD) targets of free cefoxitin at 100% of the dosing interval, considering Eucast breakpoints for Methicillin Sensitive Staphylococcus Aureus (4 mg/L) and E.Coli (8 mg/L), were obtained in 28% and 16% of patients, respectively. Patient weight (odds ratio, 0.7; 95% confidence interval, 0.62–0.92; P = 0.006) and serum creatinine concentrations (odds ratio, 25; 95% confidence interval, 18–36; P = 0.004) showed a significant relationship with the PD targets.

Conclusions:

Cefoxitin trough concentrations vary significantly in the first 24 hours after pediatric cardiac surgery. Both serum creatinine and body weight showed independent associations with cefoxitin concentration. The PD target was not obtained in the vast majority of the explored population, regardless of the target bacteria.
Minimum Duration of Antibiotic Treatment Based on Blood Culture in Rule Out Neonatal Sepsis
Authors: Ur Rehman Durrani Naveed , Rochow Niels , Alghamdi Jameel , Pelc Anna , Fusch Christoph , Dutta Sourabh
Published: August 2018

Background:

Neonatologists usually wait 48 hours for blood culture results before deciding to discontinue antibiotics. The objective of the study was to analyze time to positive blood culture in rule out sepsis and estimate the minimum duration of antibiotics.

Methods:

Retrospective analysis of blood culture at the Neonatal Intensive Care Unit, McMaster Children’s Hospital (January 2004 to December 2013) using BacT/Alert® 3D microbial system was conducted. We calculated average time taken for blood culture samples to emit a positive signal and compared it between Gram-positive and Gram-negative organisms. Kaplan-Meier curves for time to detect positive culture were generated. A Cox proportional hazard regression model with the outcome variable “time to detect positive blood culture” and predictor variables “early-onset sepsis (EOS) versus late-onset sepsis (LOS)”, “Gram-positive versus Gram-negative” and “definite versus possible pathogen versus contaminant” was generated.

Results:

Of 7,480 blood cultures performed in 9,254 neonates, 885 samples grew microorganisms. 845 culture reports from 627 neonates were analyzed. Definite or opportunistic pathogens caused 815 (96%) infections (54 EOS and 791 LOS) and the rest were contaminants. Gram-negative organisms grew significantly faster than Gram-positive (P < 0.001). Cultures from EOS were positive significantly earlier than LOS (P = 0.032). Gram-negative status was an independent predictor of early detection of a positive culture (hazard ratio 3.5 [95% CI, 2.7–4.5] P < 0.001).

Conclusion:

The probability of positive blood culture beyond 24 hours for a Gram-negative organism is small. Empiric antimicrobial treatment can be reduced after 24 hours to target only Gram-positive organisms in LOS and can be stopped in EOS unless clinical or laboratory parameters strongly suggest sepsis.
Examining the Technical Adequacy of the Ages & Stages Questionnaires: INVENTORY
Authors: Clifford Jantina , Chen Ching-I , Xie Huichao , Chen Chieh-Yu , Murphy Kimberly , Ascetta Kate , Frantz Rebecca , Hansen Sarah
Published: August 2018

Although many children live in healthy, supportive environments, far too many are exposed to or experience biological and/or psychosocial risk factors (e.g., infectious diseases, maternal depression). To evaluate the effectiveness of early childhood programs that are established to support these vulnerable children, funding agencies and nongovernmental organizations are increasing their focus on the development and implementation of interventions aimed at supporting the development of infants and toddlers and need a means for evaluating the effectiveness of the programs. However, there is a lack of psychometrically sound, easy-to-administer, change-sensitive measurement tools to assess the developmental outcomes of children from birth to 3 years. The Ages & Stages Questionnaires: INVENTORY (ASQ:I) is a new measure that was designed to meet this need. The ASQ:I is a continuous measure that was developed by combining items from the Ages & Stages Questionnaires. The ASQ:I is intended to be used for evaluating and monitoring the development of children from 1 to 36 months of age using naturalistic methods that incorporate and capitalize on parent participation. This study presents preliminary evidence for the technical adequacy of the ASQ:I.
A cross-sectional study investigating frequency and features of definitely diagnosed diabetic painful polyneuropathy
Authors: Truini Andrea , Spallone Vincenza , Morganti Roberto , Tamburin Stefano , Zanette Giampietro , Schenone Angelo , De Michelis Chiara , Tugnoli Valeria , Simioni Valentina , Manganelli Fiore , Dubbioso Raffaele , Lauria Giuseppe , Lombardi Raffaella , Jann Stefano , De Toni Franceschini Luisa , Tesfaye Solomon , Fiorelli Marco , Spagnoli Alessandra , Cruccu Giorgio ,   On behalf of the Neuropathic Pain Special Interest Group of the Italian Society of Neurology
Published: August 2018

This cross-sectional multicentre study aimed at investigating frequency and features of painful diabetic polyneuropathy. We consecutively enrolled 816 patients attending hospital diabetic outpatient clinics. We first definitely diagnosed diabetic polyneuropathy and pure small-fibre polyneuropathy using clinical examination, nerve conduction study, and skin biopsy or quantitative sensory testing. Adhering to widely agreed criteria, we then identified neuropathic pain and diagnosed painful polyneuropathy using a combined approach of clinical examination and diagnostic tests. Of the 816 patients, 36% had a diabetic polyneuropathy associated with male sex, age, and diabetes severity; 2.5% of patients had a pure small-fibre polyneuropathy, unrelated to demographic variables and diabetes severity. Of the 816 patients, 115 (13%) suffered from a painful polyneuropathy, with female sex as the only risk factor for suffering from painful polyneuropathy. In this large study, providing a definite diagnosis of diabetic polyneuropathy and pure small-fibre polyneuropathy, we show the frequency of painful polyneuropathy and demonstrate that this difficult-to-treat complication is more common in women than in men.
Response to BRAF/MEK Inhibition After Progression With BRAF Inhibition in a Patient With Anaplastic Pleomorphic Xanthoastrocytoma
Authors: Hussain Faiz , Horbinski Craig M. , Chmura Steven J. , Yamini Bakhtiar , Lukas Rimas V.
Published: August 2018

Pleomorphic xanthoastrocytoma (PXA) is a rare primary central nervous system tumor which frequently harbors mutations in BRAF. Anaplastic PXA follow a more aggressive course than their nonanaplastic counterparts. We present the case of an anaplastic PXA initially treated with the BRAF inhibitor vemurafenib. After progression of disease the MEK inhibitor trametinib was added to the regimen leading to radiographic improvement. The rationale for combined BRAF and MEK inhibition in PXA is reviewed.
Ocular Syphilis and Human Immunodeficiency Virus Coinfection Among Syphilis Patients in North Carolina, 2014–2016
Authors: Cope Anna B. , Mobley Victoria L. , Oliver Sara E. , Larson Mara , Dzialowy Nicole , Maxwell Jason , Rinsky Jessica L. , Peterman Thomas A. , Fleischauer Aaron , Samoff Erika
Published: August 2018

Background

Ocular syphilis (OS) has been associated with human immunodeficiency virus (HIV) coinfection previously. We compared demographic and clinical characteristics of syphilis patients with and without HIV to identify risk factors for developing OS.

Methods

We reviewed all syphilis cases (early and late) reported to the North Carolina Division of Public Health during 2014 to 2016 and categorized HIV status (positive, negative, unknown) and OS status based on report of ocular symptoms with no other defined etiology. We estimated prevalence ratios (PR) and 95% confidence intervals (CI) for OS by HIV status. Among syphilis patients with HIV, we compared viral loads and CD4 cell counts by OS status. We compared symptom resolution by HIV status for a subset of OS patients.

Results

Among 7123 confirmed syphilis cases, 2846 (39.9%) were living with HIV, 109 (1.5%) had OS, and 59 (0.8%) had both. Ocular syphilis was more prevalent in syphilis patients with HIV compared to HIV-negative/unknown-status patients (PR, 1.8; 95% CI, 1.2–2.6). Compared with other patients with HIV, the prevalence of OS was higher in patients with viral loads greater than 200 copies/mL (1.7; 1.0–2.8) and in patients with a CD4 count of 200 cells/mL or less (PR, 2.3; 95% CI, 1.3–4.2). Among 11 patients with severe OS, 9 (81.8%) were HIV-positive. Among 39 interviewed OS patients, OS symptom resolution was similar for HIV-positive (70.0%) and HIV-negative/unknown-status (68.4%) patients.

Conclusions

Syphilis patients with HIV were nearly twice as likely to report OS symptoms as were patients without documented HIV. Human immunodeficiency virus–related immunodeficiency possibly increases the risk of OS development in co-infected patients.
Utilization and Abandonment of Low Vision Devices Prescribed on a Mobile Clinic
Authors: Gobeille Micaela R. , Malkin Alexis G. , Jamara Richard , Ross Nicole C.
Published: August 2018

SIGNIFICANCE

Device utilization and abandonment for patients seen on a mobile clinic are explored. Findings are informative for resource allocation in a novel low vision rehabilitation (LVR) delivery model. This study also explores the relationships between device abandonment and LVR patient-reported functional outcomes.

PURPOSE

This prospective cohort study investigated low vision device utilization and abandonment in a novel mobile clinic delivery model.

METHODS

A device abandonment questionnaire was administered by telephone 3 months and 1 year after mobile clinic LVR. Participants (n = 65) had previously met the U.S. definition of legal blindness and were prescribed a total of 154 devices at their low vision consultative visits. Trends in device utilization and correlations with clinical and demographic participant characteristics, as well as functional outcomes as assessed by Massof Activity Inventory, are explored.

RESULTS

An average of 2.6 device recommendations were made per participant. Digital magnification, optical magnifiers, and filters were most frequently recommended. At 3 months, 29% of participants abandoned at least one device, although only 17% of received devices were abandoned. There was no significant difference in the number of devices used, abandoned, or not received at 3 months versus 1 year after LVR. Devices prescribed for reading goals were most frequently used and least often abandoned, whereas glare control and distance magnification devices were more frequently abandoned. Neither patient characteristics nor Massof Activity Inventory change score was predictive of device abandonment. There was no significant difference in the odds of device abandonment in comparison with a previous study that assessed academic outpatient LVR clinics using the same questionnaire.

CONCLUSIONS

Although more device recommendations are given per patient on the mobile clinic, there is no significant difference in device abandonment for patients seen on the mobile clinic versus other outpatient LVR delivery models.
Fittle: A Novel Braille Toy
Authors: Jain Tania , Christy Beula , Das Anthony Vipin , Bhaumik Debanshu , Satgunam PremNandhini
Published: August 2018

SIGNIFICANCE

Toys for children with visual impairment and blindness are very limited. We have developed a three-dimensional (3D)–printed Braille puzzle with a potential for educational use.

PURPOSE

This article describes the development of a novel Braille toy using 3D printing technology that potentially could be used for teaching Braille for children with blindness and/or profound visual impairment.

METHODS

Fittle is a 3D-printed puzzle with embossed Braille letters. Upon correct fitting of the puzzle, one not only can spell the Braille word but also would be able to feel the contour of the representative object that the word denotes. A smartphone application (Sound of Fittle) was developed to be used in conjunction with Fittle. A pilot testing was done on participants with vision impairment. Time taken to solve the puzzle and/or identify the Braille letters was calculated. Three Fittle puzzles were tested. Instructions to solve the puzzle were given only after the first attempt.

RESULTS

Seven participants (one adult and six children) were recruited. The mean time taken for the first attempt was longer (4.5 minutes), and upon instructions, the time taken to solve the puzzle was reduced on an average by a factor of 2.5. All the subjects were able to fit and read the embossed Braille in the Fittle.

CONCLUSIONS

Fittle is a novel Braille toy made using 3D printing technology. Fittle can potentially be used as an educational toy. The Sound of Fittle application gives the experiential sound for the associated word. The designs for the Fittle and the application are made available as open source on the Internet. Anyone with an access to a 3D printer can print, produce, and use the Fittle for free. With instructions, an individual can quickly learn to solve and play with the puzzle.
Epistemological Trends in the Literature on Mobile Devices, Mobile Learning, and Learners with Visual Impairments
Authors: Hayhoe Simon
Published: August 2018

This study is significant because learning with mobile devices is increasing as a method of educating and training learners with visual impairments, but evaluation of its method is rare. In addition, the epistemological model used in this study is designed to improve future research designs. This article reviews the literature on the use of mobile devices by learners with visual impairments in a variety of learning environments. The study's three objectives are to pursue avenues of research in m-learning and visual impairment, stimulate debate on the nature and role of mobile technologies in the education of learners with visual impairments, and develop a debate on the best use of technologies in m-learning. The study uses an epistemological model of visual impairment as an instrument to critically analyze different ontologies and paradigms of research. The epistemological model is also analyzed as an analytical instrument. The study identifies three academic paradigms in this field: (1) conceptual, (2) design and user testing, (3) m-learning in situ. The study also finds these three paradigms ontologize visual impairment in different ways, meaning that there is little cohesion in research and practice. The study finds that research on the development and use of technologies by learners with visual impairments is restricted by a lack of cohesion in theory and practice. This lack of cohesion is thought to be largely due to the immature nature of this topic as a field of study.
Recommendations on RBC Transfusion in Critically Ill Children With Acute Brain Injury From the Pediatric Critical Care Transfusion and Anemia Expertise Initiative
Authors: Tasker Robert C. , Turgeon Alexis F. , Spinella Philip C.
Published: August 2018

Objectives:

To present the recommendations and supporting literature for RBC transfusions in critically ill children with acute brain injury developed by the Pediatric Critical Care Transfusion and Anemia Expertise Initiative.

Design:

Consensus conference series of international, multidisciplinary experts in RBC transfusion management of critically ill children.

Methods:

The panel of 38 experts developed evidence-based, and when evidence was lacking, expert-based clinical recommendations as well as research priorities for RBC transfusions in critically ill children. The acute brain injury subgroup included three experts. Electronic searches were conducted using PubMed, EMBASE, and Cochrane Library databases from 1980 to May 2017. Agreement was obtained using the Research and Development/UCLA Appropriateness Method. Results were summarized using the Grading of Recommendations Assessment, Development, and Evaluation method.

Results:

Transfusion and Anemia Expertise Initiative Consensus Conference experts developed and agreed upon two clinical and two research recommendations focused on RBC transfusion in the critically ill child with acute brain injury. Recommendations include consideration of RBC transfusion for a hemoglobin concentration between 7 and 10 g/dL in patients with acute brain injury and do not support the use of brain tissue Po
2 monitoring to guide RBC transfusion decisions. Research is needed to better understand transfusion thresholds and brain tissue monitoring for pediatric patients with acute brain injury.

Conclusions:

The Transfusion and Anemia Expertise Initiative Consensus Conference developed pediatric-specific clinical and research recommendations regarding RBC transfusion in the critically ill child with acute brain injury. Although agreement among experts was very strong, the available pediatric evidence was extremely limited with major gaps in the literature.
Ultrasound Combined With Microbubbles Increase the Delivery of Doxorubicin by Reducing the Interstitial Fluid Pressure
Authors: Xiao Nina , Liu Jianhua , Liao Lianlian , Sun Jimei , Jin Wenhui , Shu Xian
Published: August 2018

The aims of this study were to determine the change of interstitial fluid pressure (IFP) after therapy using pulsed low-frequency ultrasound combined with microbubbles and to determine the change of doxorubicin penetration in VX2 tumor. In this study, all 48 tumor-bearing rabbits were divided randomly into 6 groups (n = 8 per group). These 6 groups include doxorubicin therapy together with ultrasound combined with microbubble treatment group (Ad-US-MB treatment group), US-MB treatment group, US treatment group, MB treatment group, doxorubicin treatment group (Ad treatment group), and blank control group. The animals were intravenously injected with doxorubicin hydrochloride, and then the tumors of the animals were disposed by low-intensity ultrasound and mirobubbles for 10 minutes. The IFP of tumor tissues in rabbits was detected before and after intervention. Rabbits in each group were sacrificed immediately after treatment. The concentration and the distribution of doxorubicin were detected. The tumor IFP was significantly lower than that before treatment in the Ad-US-MB treatment and US-MB treatment groups (P = 0.01, P = 0.013). Ultrasound combined with microbubble increased the concentration of doxorubicin in the sample of the Ad-US-MB treatment group compared with the Ad treatment group (P < 0.05). In immunofluorescent staining section, high concentrations of doxorubicin were observed mainly around the blood vessels, and some were even discovered at a farther area in the Ad-US-MB treatment group. The pulsed low-frequency ultrasound combined with the microbubbles enhances the vascular clearance of particles into the tumor interstitium by reducing IFP.
Gray Scale Ultrasound, Color Doppler Ultrasound, and Contrast-Enhanced Ultrasound in Renal Parenchymal Diseases
Authors: Quaia Emilio , Correas Jean Michel , Mehta Maithili , Murchison John T. , Gennari Antonio Giulio , van Beek Edwin J.R.
Published: August 2018

Ultrasound (US), which may be combination of gray scale and spectral Doppler US, color and power Doppler US, with or without microbubble contrast agents, is usually the first imaging modality to be used in renal parenchymal diseases. The most typical appearance of diffuse renal parenchymal diseases on gray scale US is an increased renal cortical echogenicity and increased or reduced corticomedullary differentiation. Spectral Doppler analysis of intrarenal flows may reveal an increase in intrarenal resistive index value greater than 0.70 in native kidneys, and greater than 0.8 in renal transplants. Gray scale US and spectral Doppler US do not exhibit high specificity and sensitivity because different renal parenchymal diseases often display the same US appearance, whereas the same renal parenchymal disease may present different appearances on US according to disease stage. Consequently, correlation of the US pattern with patient's history and clinical background is essential for a correct characterization.
Course Review
Authors: Berner Juan Enrique , Kyriazidis Ioannis
Published: August 2018

Dermoscopy is a physical examination technique that combines the use of illumination and magnification, provided by a handheld device, to scrutinize skin lesions. Its use increases the diagnostic accuracy for the trained operator, providing more information for making better decisions for the management of skin cancer. The “International Dermoscopy Course for Plastic Surgeons” aims to train plastic surgery trainees and consultants in the use of this technique. This 1-day, lecture-based course is held 4 times a year in the city of Oxford, United Kingdom, at a cost of £250 (US $340). This article intends to provide a review of this course.
Molecular dating of the emergence of anaerobic rumen fungi and the impact of laterally acquired genes
Authors: Wang Yan , Youssef Noha , Couger M.B. , Hanafy Radwa , Elshahed Mostafa , Stajich Jason E.
Published: August 2018

The anaerobic gut fungi (AGF) or Neocallimastigomycota inhabit the rumen and alimentary tract of herbivorous mammals, where they play an important role in the degradation of plant fiber. Comparative genomic and phylogenomic analysis of the AGF has long been hampered by their fastidious growth pattern as well as their large and AT-biased genomes. We sequenced 21 AGF transcriptomes and combined them with 5 available genome sequences of AGF taxa to explore their evolutionary relationships, time their divergence, and characterize patterns of gene gain/loss associated with their evolution. We estimate that the most recent common ancestor of the AGF diverged 66 (±10) million years ago, a timeframe that coincides with the evolution of grasses (Poaceae), as well as the mammalian transition from insectivory to herbivory. The concordance of these independently estimated ages of AGF evolution, grasses evolution, and mammalian transition to herbivory suggest that AGF have been important in shaping the success of mammalian herbivory transition by improving the efficiency of energy acquisition from recalcitrant plant materials. Comparative genomics identified multiple lineage-specific genes and protein domains in the AGF, two of which were acquired from an animal host (galectin) and rumen gut bacteria (carbohydrate-binding domain) via horizontal gene transfer (HGT). Four of the bacterial derived “Cthe_2159” genes in AGF genomes also encode eukaryotic Pfam domains (“Atrophin-1”, “eIF-3_zeta”, “Nop14”, and “TPH”) indicating possible gene fusion events after the acquisition of “Cthe_2159” domain. A third AGF domain, plant-like polysaccharide lyase N-terminal domain (“Rhamnogal_lyase”), represents the first report from fungi that potentially aids AGF to degrade pectin. Analysis of genomic and transcriptomic sequences confirmed the presence and expression of these lineage-specific genes in nearly all AGF clades supporting the hypothesis that these laterally acquired and novel genes in fungi are likely functional. These genetic elements may contribute to the exceptional abilities of AGF to degrade plant biomass and enable metabolism of the rumen microbes and animal hosts.
Integrin α6β4 recognition of a linear motif of bullous pemphigoid antigen BP230 controls its recruitment to hemidesmosomes
Authors: Manso José A , Gómez-Hernández Maria , Carabias Arturo , Alonso-García Noelia , García-Rubio Inés , Kreft Maaike , Sonnenberg Arnoud , de Pereda José M
Published: August 2018

Mechanical stability of epithelia requires firm attachment to the basement membrane via hemidesmosomes. Dysfunction of hemidesmosomal proteins causes severe skin blistering diseases. Two plakins, plectin and BP230 (BPAG1e), link the integrin α6β4 to intermediate filaments in epidermal hemidesmosomes. Here, we show that a linear sequence within the isoform-specific N-terminal region of BP230 binds to the third and fourth FnIII domains of β4. The crystal structure of the complex and mutagenesis analysis revealed that BP230 binds between the two domains of β4. BP230 induces closing of the two FnIII domains that are looked in place by an inter-domain ionic clasp required for binding. Disruption of the BP230-β4 interface prevents the recruitment of BP230 to hemidesmosomes in human keratinocytes, revealing a key role of the BP230-β4 interaction for hemidesmosome assembly. Phosphomimetic substitutions in β4 and BP230 disrupt binding. Our study provides insights into the molecular mechanisms of hemidesmosome architecture and regulation.
What we (don’t) know about global plant diversity
Authors: Cornwell William K. , Pearse William D. , Dalrymple Rhiannon L. , Zanne Amy
Published: August 2018

Rationale

The era of big biodiversity data has led to rapid, exciting advances in theoretical and applied biological, ecological and conservation sciences. While large genetic, geographic and trait databases are available, these are neither complete nor random samples of the globe. Biases in species absence in these databases create problems, reducing our inferential and predictive power.

Methods

We performed a comprehensive examination of the taxonomic and spatial sampling in the most complete current databases for plant genes, locations, and traits.

Results

Only 17.7% of the world’s described land plants feature in all three databases, meaning that more than 82% of plant biodiversity lacks representation in at least one database. Species coverage is highest for location data and lowest for genetic data. Bryophytes and orchids stand out taxonomically and the equatorial region stands out spatially as poorly represented in all databases.

Conclusion

We have highlighted a number of clades and regions about which we know little functionally, spatially and genetically, on which we should set research targets. The scientific community should recognize and reward the significant value, both for biodiversity science and conservation, of filling in these gaps in our knowledge of the plant tree of life.
Organization of state transitions in the resting-state human cerebral cortex
Authors: Kang Jiyoung , Pae Chongwon , Park Hae-Jeong
Published: August 2018

The resting-state brain is often considered a nonlinear dynamic system transitioning among multiple coexisting stable states. Despite the increasing number of studies on the multistability of the brain system, the processes of state transitions have rarely been systematically explored. Thus, we investigated the state transition processes of the human cerebral cortex system at rest by introducing a graph-theoretic analysis of the state transition network. The energy landscape analysis of brain state occurrences, estimated using the pairwise maximum entropy model for resting-state fMRI data, identified multiple local minima, some of which mediate multi-step transitions toward the global minimum. The state transition among local minima is clustered into two groups according to state transition rates and most inter-group state transitions were mediated by a hub transition state. The distance to the hub transition state determined the path length of the inter-group transition. The cortical system appeared to have redundancy in inter-group transitions when the hub transition state was removed. Such a hub-like organization of transition processes disappeared when the connectivity of the cortical system was altered from the resting-state configuration. In summary, the resting-state cerebral cortex has a well-organized architecture of state transitions among stable states, when evaluated by nonlinear systematic approach.
Cytotoxic Profiling of Annotated and Diverse Chemical Libraries Using Quantitative High-Throughput Screening
Authors: Lee Olivia W. , Austin Shelley , Gamma Madison , Cheff Dorian M. , Lee Tobie D. , Wilson Kelli M. , Johnson Joseph , Travers Jameson , Braisted John C. , Guha Rajarshi , Klumpp-Thomas Carleen , Shen Min , Hall Matthew D.
Published: August 2018

Cell-based phenotypic screening is a commonly used approach to discover biological pathways, novel drug targets, chemical probes and high-quality hit-to-lead molecules. Many hits identified from high-throughput screening campaigns are ruled out through a series of follow-up potency, selectivity/specificity, and cytotoxicity assays. Prioritization of molecules with little or no cytotoxicity for downstream evaluation can influence the future direction of projects, so cytotoxicity profiling of screening libraries at an early stage is essential for increasing the likelihood of candidate success. In this study, we assessed cell-based cytotoxicity of nearly 10,000 compounds in NCATS annotated libraries, and over 100,000 compounds in a diversity library, against four ‘normal’ cell lines (HEK 293, NIH 3T3, CRL-7250 and HaCat) and one cancer cell line (KB 3-1, a HeLa subline). This large-scale library profiling was analyzed for overall screening outcomes, hit rates, pan-activity and selectivity. For the annotated library, we also examined the primary targets and mechanistic pathways regularly associated with cell death. To our knowledge, this is the first study to use high-throughput screening to profile a large screening collection (>100,000 compounds) for cytotoxicity in both normal and cancer cell lines. The results generated here constitutes a valuable resource for the scientific community and provides insight on the extent of cytotoxic compounds in screening libraries, identifying and avoiding compounds with cytotoxicity during high-throughput screening campaigns.
A least microenvironmental uncertainty principle (LEUP) as a generative model of collective cell migration mechanisms
Authors: Barua Arnab , Nava-Sedeño Josue M. , Hatzikirou Haralampos
Published: August 2018

Collective migration is commonly observed in groups of migrating cells, in the form of swarms or aggregates. Mechanistic models have proven very useful in understanding collective cell migration. Such models, either explicitly consider the forces involved in the interaction and movement of individuals or phenomenologically define rules which mimic the observed behavior of cells. However, mechanisms leading to collective migration are varied and specific to the type of cells involved. Additionally, the precise and complete dynamics of many important chemomechanical factors influencing cell movement, from signalling pathways to substrate sensing, are typically either too complex or largely unknown. The question is how to make quantitative/qualitative predictions of collective behavior without exact mechanistic knowledge. Here we propose the least microenvironmental uncertainty principle (LEUP) that serves as a generative model of collective migration without incorporation of full mechanistic details. Interestingly we show that the famous Vicsek model is a special case of LEUP. Finally, as a proof of concept, we apply the LEUP to quantitatively study ofthe collective behavior of spherical Serratia marcescens bacteria, where the underlying migration mechanisms remain elusive.
Human-like NSG mouse glycoproteins sialylation pattern changes the phenotype of human lymphocytes and sensitivity to HIV-1 infection
Authors: Dagur Raghubendra Singh , Woods Amanda Branch , Mathews Saumi , Joshi Poonam S. , Quadros Rolen M. , Harms Donald W. , Cheng Yan , Miles Shana M , Pirruccello Samuel J. , Gurumurthy Channabasavaiah B. , Gorantla Santhi , Poluektova Larisa Y.
Published: August 2018

Background

The use of immunodeficient mice transplanted with human hematopoietic stem cells is an accepted approach to study human-specific infectious diseases, like HIV-1, and to investigate multiple aspects of human immune system development. However, mouse and human are different in sialylation patterns of proteins due to evolutionary mutations of the CMP-N-acetylneuraminic acid hydroxylase (CMAH) gene that prevent formation of N-glycolylneuraminic acid from N-acetylneuraminic acid. How changes of mouse glycoproteins chemistry will affect phenotype and function of transplanted human hematopoietic stem cells and mature human immune cells in the course of HIV-1 infection is not known.

Results

We mutated mouseCMAHon the most widely human cells transplantation strain NOD/scid-IL2Rγc-/-(NSG) mouse background using the CRISPR/Cas9 system. The new strain provides a better environment for human immune cells. Transplantation of human hematopoietic stem cells leads to broad B cells repertoire, higher sensitivity to HIV-1 infection, and enhanced proliferation of transplanted peripheral blood lymphocytes. The mice showed low effects on the clearance of human immunoglobulins and enhanced transduction efficiency of recombinant adeno-associated viral vector rAAV2/DJ8.

Conclusion

NSG-cmah-/-mice expand the mouse models suitable for human cells transplantation and this new model has advantages in generating a human B cell repertoire. This strain is suitable to study different aspects of the human immune system development, might provide advantages in patient-derived tissue and cell transplantation, and could allow studies of viral vectors and infectious agents that are sensitive to human-like sialylation of mouse glycoproteins.
Anti-microRNA screen uncovers miR-17 family within miR-17~92 cluster as the primary driver of kidney cyst growth
Authors: Yheskel Matanel , Lakhia Ronak , Flaten Andrea , Patel Vishal
Published: August 2018

Autosomal dominant polycystic kidney disease (ADPKD) is the leading genetic cause of renal failure. We have recently shown that inhibiting miR-17~92 is a potential novel therapeutic approach for ADPKD. However, miR-17~92 is a polycistronic cluster that encodes microRNAs (miRNAs) belonging to the miR-17, miR-18, miR-19 and miR-25 families, and the relative pathogenic contribution of these miRNA families to ADPKD progression is unknown. Here we performed an in vivo anti-miR screen to identify the miRNA drug targets within the miR-17~92 miRNA cluster. We designed anti-miRs to individually inhibit miR-17, miR-18, miR-19 or miR-25 families in an orthologous ADPKD model. Treatment with anti-miRs against the miR-17 family reduced cyst proliferation, kidney-weight-to-body-weight ratio and cyst index. In contrast, treatment with anti-miRs against the miR-18, 19, or 25 families did not affect cyst growth. Anti-miR-17 treatment recapitulated the gene expression pattern observed after miR-17~92 genetic deletion and was associated with upregulation of mitochondrial metabolism, suppression of the mTOR pathway, induction of autophagy, and inhibition of cyst-associated inflammation. Our results argue against functional cooperation between the various miR-17~92 cluster families in promoting cyst growth, and instead point to miR-17 family is the primary therapeutic target for ADPKD.
Extreme variation in rates of evolution in the plastid Clp protease complex
Authors: Williams Alissa M. , Friso Giulia , van Wijk Klaas J. , Sloan Daniel B.
Published: August 2018

Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. TheclpP1gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history ofclpP1molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g., loss of introns and RNA-editing sites) within seed plants. AlthoughclpP1is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely the case. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genusSilene, which has highly elevated and heterogeneous rates ofclpP1evolution. We confirmed thatclpP1is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergentSilenespecies. Additionally, there is a tight correlation between amino-acid substitution rates inclpP1and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting ongoing selection on interactions within this complex.
Wnt/Fgf crosstalk is required for the specification of tracheal basal progenitor cells
Authors: Hou Zhili , Wu Qi , Sun Xin , Chen Huaiyong , Li Yu , Zhang Yongchun , Mori Munemasa , Yang Ying , Jiang Ming , Que Jianwen
Published: August 2018

Basal progenitor cells are critical for the establishment and maintenance of the tracheal epithelium. However, it remains unclear how these progenitor cells are specified during foregut development. Here, we found that ablation of the Wnt chaperon protein Gpr177 (also known as Wntless) in the epithelium causes significant reduction in the numbers of basal progenitor cells accompanied by cartilage loss inShh-Cre;Gpr177loxp/loxpmutants. Consistent with the association between cartilage and basal cell development, Nkx2.1+p63+basal cells are co-present with cartilage nodules inShh-Cre;Ctnnb1DM/loxpmutants which keep partial cell-cell adhesion but not the transcription regulation function of ß-catenin. More importantly, deletion ofCtnnb1in the mesenchyme leads to the loss of basal cells and cartilage concomitant with the reduced transcript levels of Fgf10 inDermo1-Cre;Ctnnb1loxp/loxpmutants. Furthermore, deletion ofFgf receptor 2(Fgfr2) in the epithelium also leads to significantly reduced numbers of basal cells, supporting the importance of the Wnt/Fgf crosstalk in early tracheal development.
Transcription Termination and Antitermination of Bacterial CRISPR Arrays
Authors: Stringer Anne M. , Baniulyte Gabriele , Lasek-Nesselquist Erica , Seed Kimberley D. , Wade Joseph T.
Published: August 2018

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences (“repeats”) interspersed with short, variable sequences (“spacers”). CRISPR arrays are transcribed and processed into individual CRISPR RNAs (crRNAs) that each include a single spacer, and direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho termination functionally limits the length of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of Rho termination in the evolution of bacterial CRISPR-Cas systems.
F-actin dynamics transform filopodial bridges into intercellular nanotubes capable of distant cell communication
Authors: Chang Minhyeok , Oh Jaeho , Doh Junsang , Lee Jong-Bong
Published: August 2018

A novel actin-based bridge connecting cells has been recognized as a new pathway for the distant transport of cytoplasmic components, viruses, or pathogenic substances between cells. However, it is not yet known how such a fine structure extends over several hundred micrometres and remains robust for several hours. Using optical fluorescence imaging methods, we found that random contact promotes the formation of filopodial bridges through N-cadherin interactions between filopodia, which are slender actin-rich plasma membrane protrusions. These filopodial bridges eventually evolve into a single actin-based bridge (intercellular nanotube) that connects two cells via an intermediate state that involves a helical structure. Surprisingly, the twisting of two filopodia is likely to result from the rotational motion of actin filaments inside the filopodia by myosin V. The accumulated torsion of the filopodia triggers the release of one of the paired filopodia, whose end is attached to the other cell body by an N-cadherin cluster. The resulting retraction of the filopodium by retrograde F-actin flow leaves a single bridge. The N-cadherin/catenin cluster is likely to form a synapse between the intercellular nanotube and the cell body. This study sheds light on the formation mechanism of the filopodial bridge-based intercellular nanotubes for long-distance communication between cells.
Dogs, but not wolves, lose their sensitivity towards novelty with age
Authors: Hansen Wheat Christina , van der Bijl Wouter , Temrin Hans
Published: August 2018

Selection on behavioural traits holds a prominent role in the domestication of animals, with reductions in fear behaviour considered to be a key component. Specifically, there is a general assumption that domesticated species express reduced fear and reactivity towards novel stimuli compared to their ancestral species. However, very few studies have explicitly tested this proposed link between domestication and reduced fear responses. Of the limited number of studies experimentally addressing the alterations of fear during domestication, the majority have been done on canids. Previous work in foxes, wolves and dogs has led to the suggestion that decreased expression of fear in domesticated animals is linked to a domestication driven delay in the first onset of fearful behaviour during early ontogeny. Thus, wolves are expected to express exaggerated fearfulness earlier during ontogeny compared to dogs. However, while adult dogs are less fearful towards novelty than adult wolves and wolf-dog hybrids, consensus is lacking on when differences in fear expression arise in wolves and dogs. Here we present the first extended examination of fear development in hand-raised dogs and European grey wolves, using repeated novel object tests from six to 26 weeks of age. Contrary to expectations, we found no evidence in support of an increase in fearfulness in wolves with age or a delayed onset of fear response in dogs compared to wolves. Instead, we found that dogs strongly reduced their fear response in the period between six and 26 weeks of age, resulting in a significant species difference in fear expression towards novelty at 26 weeks. Critically, as wolves did not differ in their fear response towards novelty over time, the detected species difference was caused solely by a progressive reduced fear response in dogs. Our results thereby suggest that species differences in fear of novelty between wolves and dogs are not caused by a domestication driven shift in the first onset of fear response. Instead, we suggest that a loss of sensitivity towards novelty with age in dogs causes the difference in fear expression towards novelty in wolves and dogs.
ECM deposition is driven by caveolin1-dependent regulation of exosomal biogenesis and cargo sorting
Authors: Albacete-Albacete Lucas , Navarro-Lérida Inmaculada , Lopez Juan Antonio , Martín-Padura Inés , Astudillo Alma M. , Van-Der-Heyden Michael , Balsinde Jesús , Orend Gertraud , Vazquez Jesús , Ángel del Pozo Miguel
Published: August 2018

The composition and physical properties of the extracellular matrix (ECM) critically influence tumour cell behaviour, and ECM deposition and remodelling by stromal fibroblast populations is therefore pivotal for tumour progression. The molecular mechanisms by which stromal and tumour cell populations regulate ECM layering are poorly understood. Tumour-stroma interaction is critically dependent on cell-cell communication mediated by exosomes, small vesicles secreted by most cell types and generated within multivesicular bodies (MVBs). Here, we show that caveolin-1 (Cav1), an essential regulator of stromal remodelling and tumour cell fate, plays a central role in modulating both exosome biogenesis and exosomal protein cargo sorting through cholesterol-dependent mechanisms. Quantitative proteomics profiling revealed that a major share of Cav1-dependent exosomal cargoes are compsed of ECM proteins, one of the most important components being tenascin-C (TnC). Comparative functional assays demonstrated that Cav1 is required for fibroblast-derived exosomes to depose ECM and promote tumour cell invasiveness. Exosomes purified from Cav1WT cells, but not those from Cav1-null cells, were able to nucleate distant stromal niches in different organs in vivo. These findings suggest a key role for Cav1 as a cholesterol rheostat in MVBs, and seems to determine ECM deposition by eliciting ECM component sorting into specific exosome pools. These results, together with previous work, support a model in which Cav1 is a central regulatory hub for tumour-stroma interactions through a novel exosome-dependent ECM deposition mechanism.
Icariin induces MC3T3-E1 cell proliferation and differentiation via the BMP-2/Smads/Runx2 signal pathway
Authors: An Qing , Gou Bo , Ma Shaocheng , Goh En Lin , Liu GuoXiong , Sah Bikash Kumar , Cao Hong
Published: August 2018

Icariin, the main active ingredient of Epimedium, has played an important role in bone anabolism. However, the molecular mechanism for this effect was not convincingly reported yet. In this paper, the role of icariin on cell morphology, viability, cell cycling and the activity of alkaline phosphatase (ALP) were studied, and the molecular mechanism of icariin induced osteogenic effect was also investigated. Icariin with different concentrations (10, 20 and 40 ng/ml) was used to modify the pre-osteoblastic MC3T3-E1 cells for 48, 72 and 96 h, and the proliferation, morphology, and the cell cycle of the cells were evaluated by Cell Counting Kit-8 (CCK-8), microscopy and flow cytometry, respectively. Bone morphogenic protein-2 (BMP-2), bone morphogenic protein receptor-2 (BMPR-2), Smad4, Smadl/5/8 proteins expression levels were obtained by Western blotting and the expression levels of runt-related transcription factor 2 (Runx2) mRNA was examined by reverse transcription-polymerase chain reaction (RT-PCR). In this study, we found that icariin could promote the proliferation and differentiation of MC3T3-E1 cells in a dose - and time-dependent manner. Icariin could stimulate the expression of the BMP-2, BMPR-2, Smad4 and Smadl/5/8 proteins. Furthermore, icariin could upregulate the expression of Runx2 mRNA. These results showed that icariin played an important role in upregulating BMP-2 expression to activate the BMP-2/Smads/Runx2 signal pathway for increasing both the proliferation and differentiation of the MC3T3-E1 cells. However, the osteogenic effects of icariin can be suppressed by the BMP-2 antagonist (Noggin). In conclusion, we demonstrate that icariin is an osteoinductive factor that exerts its osteogenic effect by regulating the BMP-2/Smads/Runx2 signal pathway in MC3T3-E1 cells.