bluuebunny/crossref_metadata_2025 huggingface dataset:
A Retrospective Review of Physician-related Patient Complaints from a Tertiary Pediatric Hospital
Authors: Chaulk David , Krueger Carsten , Stang Antonia S.
Published: June 2019

Background:

Trends in patient concerns can identify systematic problems in health care delivery that may not be detected when addressing individual concerns. It can be difficult identifying trends without using a standardized taxonomy. The study objectives were to describe patient complaints from a tertiary care pediatric hospital and categorize them using a standardized complaint taxonomy.

Methods:

Physician-based patient complaints were compiled from April 2011 to May 2014 from a tertiary pediatric hospital. These complaints were coded independently by 2 reviewers using the Reader taxonomy, a published standardized taxonomy. Complaints were placed into 3 domains: clinical, management, and relationships then organized into categories. Inter-rater reliability for domain classification between the 2 reviewers was calculated using Cohen’s unweighted κ.

Results:

Eighty-seven patient complaints were identified, representing approximately 1 per 10,000 physician–patient encounters. Half (48/87) were related to care in the emergency department. When adjusted for volume, pediatric hospital medicine had the highest number of complaints, with 12.1 per 10,000 encounters. The majority of patient complaints, 66% (57/87), were of the clinical domain (κ = 0.61). Sixty percent (52/87) were in the relationship domain (κ = 0.68), and 16% (14/87) were in the management domain (κ = 0.65).

Conclusions:

We found a low overall complaint rate. Our results indicate that interventions to improve patient experience should initially be targeted at emergency and hospital medicine on the clinical and relationship domains. The inter-rater reliability of the Reader taxonomy was moderate with implications for processing patient complaints at a hospital level.
Quality Improvement Initiative for Assessing Allografts after Lung Transplantation
Authors: Hayes Don , Nicholson Kerri L. , Miller Rebecca , Nance Ashley E. , Kirkby Stephen E. , Parker William , Baker Peter B.
Published: June 2019

Introduction:

The histologic evaluation of lung allografts after transbronchial biopsy (TBBx) is a key component of the clinical care of lung transplant recipients. With established guidelines on diagnosing allograft rejection, no specific recommendations exist on timeliness to reaching a diagnosis and initiating therapy. A quality improvement initiative focused on 3 key stages of achieving a prompt diagnosis of acute cellular rejection including tissue processing, interpretation, and notification to the treating transplant pulmonologist was initiated to minimize time to treatment onset.

Methods:

We completed a single-center cohort study on all surveillance and clinically indicated TBBx from September 2006 to March 2018. The rapid tissue processing, interpretation, and notification system was instituted in March 2011 with data before this date serving as baseline.

Results:

We enrolled 28 patients who underwent 210 TBBx (1 excluded due to unknown notification date). Thirty-eight TBBx were included at baseline before implementation of the rapid tissue processing and communication system; 171 were included after implementation. Median time to notification following the change was 0 days (interquartile range, 0–1) compared with 1 day (interquartile range, 1–1) before the change (P < 0.001). After the change, same-day notification increased, with 110 (64%) TBBx resulting in same-day notification compared with 0 before (P < 0.001). We initiated treatment of acute cellular rejection on the day of diagnosis for the entire cohort.

Conclusions:

This quality improvement initiative resulted in more efficient analysis of TBBx of allografts in lung transplant recipients and faster communication of results to the clinical team.
Reducing the Cranial CT Rate for Pediatric Minor Head Trauma at Three Community Hospitals
Authors: Smith Alla , Gruskin Karen , Monuteaux Michael C. , Stack Anne M. , Sundberg Melissa , Yim Ramy , Seneski Annie , Becker Theresa
Published: June 2019

Objective:

Efforts to reduce the rate of computerized cranial tomography (CT) in pediatric patients with minor head trauma (MHT) have focused on academic medical centers. However, community hospitals deliver the majority of pediatric emergency care. We aimed to reduce cranial CT utilization in patients presenting with MHT at 3 community hospital emergency departments (EDs).

Methods:

Multidisciplinary stakeholder teams at each site oversaw the quality improvement effort, which included education about an evidence-based guideline for MHT and individual provider feedback on CT rates. Given the variation in hospital structure, we tailored the specifics of the intervention to each site. We used statistical process control methodology to measure CT rates over time. The primary balancing measure was returned to the ED within 72 hours with clinically important traumatic brain injury.

Results:

We included 3,215 pediatric ED visits for MHT: 1,253 in the baseline period and 1,962 in the intervention period. The CT rate dropped from 18% in the baseline period to 13% in the intervention period, a 28% relative reduction. Pediatric providers saw 72% of the intervention period encounters and drove this reduction. There was no increase in the number of children who returned to their local ED within 72 hours with clinically important traumatic brain injury.

Conclusions:

We safely reduced the proportion of children with MHT who received a cranial CT through a multicenter community ED quality improvement initiative. We did not see an increase in missed clinically important traumatic brain injury.
Implementing Standardized Screening for Adverse Childhood Experiences in a Pediatric Resident Continuity Clinic
Authors: Marsicek Sarah M. , Morrison John M. , Manikonda Neha , O’Halleran Michael , Spoehr-Labutta Zach , Brinn Melissa
Published: June 2019

Introduction:

Exposure to adversity in childhood has been shown to impact the development of children and increase their risk of poor early childhood mental health and chronic medical conditions in young children, and developing chronic diseases, mental health disorders, and substance abuse disorders as adults. The recognition of adverse childhood experiences (ACEs) and provision of behavioral-based interventions can help children build resilience. We implemented a screening method to help providers better assess patients’ exposure to adversity. Our goal was to increase the screening for ACEs utilizing a standardized ACEs screening tool from 0% to 80% of children presenting for annual well-child visits within 1 year.

Methods:

We implemented a screening tool to determine a child’s exposure to ACEs within our general pediatrics clinic. A variety of interventions, including resident, faculty, and staff-focused educational lectures, simulation, and process changes were performed to increase screening. Also, we surveyed resident physicians and faculty about their experiences with ACEs screening.

Results:

Over 1 year, we screened 1,206 patients for exposure to ACEs and increased screening from 0% to 60%. Provider comfort with discussing abuse with patients and familiarity with resources for children exposed to ACEs did not change significantly.

Conclusions:

Patients can successfully be screened in a resident-led, general pediatric clinic using a standardized ACEs screening tool. Such an approach can successfully identify patients with high-risk ACE scores. Additionally, education on and implementation of the tool may improve provider comfort with screening for ACEs.
Prevention of Pressure Ulcers in a Pediatric Cardiac Intensive Care Unit
Authors: Simsic Janet M. , Dolan Kevin , Howitz Sarah , Peters Stephanie , Gajarski Robert
Published: June 2019

Background:

Pressure ulcer (PU) is an injury to skin or underlying tissue as a result of pressure or pressure with shear stress. We classify PUs by the level of tissue injury: stage I–IV, unstageable, suspected deep tissue injury. This quality project was aimed to reduce the incidence of PUs > stage II in the cardiothoracic intensive care unit.

Methods:

We reviewed PUs > stage II from March 2010 to December 2017. Interventions included: PU bundle (April 2010, revised January 2013); multidisciplinary huddles for PUs > stage II (October 2011); multidisciplinary weekly skin rounds (March 2010, revised August 2012); unit specific workgroup (October 2012); caregiver input form (December 2012). The PU bundle included diaper barrier cream, pulse oximeter probe rotation, turning schedule, pressure reduction surfaces, heel pressure release, head of the bed elevation.

Results:

Between 2010 and 2014, PUs decreased from 15.7 events per 1,000 patient days to a new baseline of 2.9 events per 1,000 patient days. We have sustained this rate for 3 years. PUs related to immobility decreased from 35 in 2010–2011 to 4 in 2016–2017. PU related to medical devices decreased from 34 in 2010–2011 to 15 in 2016–2017.

Conclusions:

Institution of PU bundle, multidisciplinary weekly skin rounds, and huddles for PUs > stage II reduced PUs related to immobility, allowed for earlier identification of stage II PUs and reduced stage III PUs. Challenges remain in reducing PUs related to medical devices. Importantly, we sustained this improvement over the past 3 years.
Operating Room Codes Redefined: A Highly Reliable Model Integrating the Core Hospital Code Team
Authors: Caruso Thomas J. , Rama Asheen , Knight Lynda J. , Gonzales Ralph , Munshey Farrukh , Darling Curtis , Chen Michael , Sharek Paul J.
Published: June 2019

Introduction:

Typically, multidisciplinary teams manage cardiac arrests occurring outside of the operating room (OR). This approach results in reduced morbidity. However, arrests that occur in the OR are usually managed by OR personnel alone, missing the benefits of out-of-OR hospital code teams. At our institution, there were multiple pathways to activate codes, each having different respondents, depending on time and day of the week. This improvement initiative aimed to create a reliable intraoperative emergency response system with standardized respondents and predefined roles.

Methods:

A multidisciplinary improvement team led this project at an academic pediatric hospital in California. After simulations performed in the OR (in situ), the team identified a valuable key driver—a consistent activation process that initiated standard respondents, 24 hours a day, 7 days a week. By utilizing core hospital code members routinely available outside of the OR during days, nights, and weekends, respondents were identified to augment OR personnel. Code roles were preassigned. After education, we conducted in situ simulations that included the perioperative and out-of-OR code team members. We administered a knowledge assessment to perioperative staff.

Results:

The knowledge assessment for perioperative staff (n = 52) had an average score of 96%. Review of subsequent OR codes reflects an improved initiation process and management.

Conclusions:

The process for activating the emergency response system and roles for intraoperative code respondents were standardized to ensure a predictable code response, regardless of time or day of the week. Ongoing simulations with perioperative personnel continue to optimize the process.
Putative novel cps loci in a large global collection of pneumococci
Authors: van Tonder Andries J. , Gladstone Rebecca A. , Lo Stephanie W. , Nahm Moon H. , du Plessis Mignon , Cornick Jennifer , Kwambana-Adams Brenda , Madhi Shabir A. , Hawkins Paulina A. , Benisty Rachel , Dagan Ron , Everett Dean , Antonio Martin , Klugman Keith P. , von Gottberg Anne , Breiman Robert F. , McGee Lesley , Bentley Stephen D. ,   The Global Pneumococcal Sequencing Consortium
Published: June 2019

The pneumococcus produces a polysaccharide capsule, encoded by the cps locus, that provides protection against phagocytosis and determines serotype. Nearly 100 serotypes have been identified with new serotypes still being discovered, especially in previously understudied regions. Here we present an analysis of the cps loci of more than 18  000 genomes from the Global Pneumococcal Sequencing (GPS) project with the aim of identifying novel cps loci with the potential to produce previously unrecognized capsule structures. Serotypes were assigned using whole genome sequence data and 66 of the approximately 100 known serotypes were included in the final dataset. Closer examination of each serotype’s sequences identified nine putative novel cps loci (9X, 11X, 16X, 18X1, 18X2, 18X3, 29X, 33X and 36X) found in ~2.6  % of the genomes. The large number and global distribution of GPS genomes provided an unprecedented opportunity to identify novel cps loci and consider their phylogenetic and geographical distribution. Nine putative novel cps loci were identified and examples of each will undergo subsequent structural and immunological analysis.
Learning to evoke complex motor outputs with spatiotemporal neurostimulation using a hierarchical and adaptive optimization algorithm
Authors: Laferriere Samuel , Bonizzato Marco , Dancause Numa , Lajoie Guillaume
Published: June 2019

The development of neurostimulation techniques to evoke motor patterns is an active area of research. It serves as a crucial experimental tool to probe computation in neural circuits, and it has applications in neuroprostheses used to aid recovery of function after stroke or injury. There are two important challenges when designing algorithms to unveil and control neurostimulation-to-motor mappings, thereby linking spatiotemporal patterns of neural stimulation to muscle activation: (1) the exploration of motor maps needs to be fast and efficient (exhaustive search is to be avoided for clinical and experimental reasons) (2) online learning needs to be flexible enough to track ongoing changes in these maps. We propose a stimulation search algorithm to address these issues, and demonstrate its efficacy with experiments in non-human primate models. Our solution is a novel iterative process using Bayesian Optimization via Gaussian Processes on increasingly complex signal spaces. We show that our algorithm can successfully and rapidly learn mappings between complex stimulation patterns and evoked muscle activation patterns, where standard approaches fail. Importantly, we uncover nonlinear circuit-level computations in M1 that would not have been possible to identify using conventional mapping techniques.
Transcranial Pulse Stimulation with Ultrasound in Alzheimer’s disease – A new navigated focal brain therapy
Authors: Beisteiner R. , Matt E. , Fan C. , Baldysiak H. , Schönfeld M. , Philippi Novak T. , Amini A. , Aslan T. , Reinecke R. , Lehrner J. , Weber A. , Reime U. , Goldenstedt C. , Marlinghaus E. , Hallett M. , Lohse-Busch H.
Published: June 2019

Ultrasound-based brain stimulation techniques offer an exciting potential to modulate the human brain in a highly focal and precisely targeted manner. However, for clinical applications the current techniques have to be further developed. We introduce a new ultrasound stimulation technique, based on single ultrashort ultrasound pulses (transcranial pulse stimulation, TPS) and describe a first navigable clinical TPS system. Feasibility, safety and preliminary (uncontrolled) efficacy data in Alzheimer’s disease (AD) are provided. Simulation data,in vitromeasurements with rat and human skulls/brains and clinical data in 35 AD patients were acquired in a multicentric setting (including CERAD scores and functional MRI). Preclinical results show large safety margins and patient results show high treatment tolerability. Neuropsychological scores improved significantly when tested immediately as well as 1 and 3 months after stimulation and fMRI data displayed significant connectivity increases within the memory network. The results encourage broad neuroscientific application and translation of the new method to clinical therapy and randomized sham-controlled studies.
Arabidopsis Proteome and the Mass Spectral Assay Library
Authors: Zhang Huoming , Liu Pei , Guo Tiannan , Zhao Huayan , Bensaddek Dalila , Aebersold Ruedi , Xiong Liming
Published: June 2019

Arabidopsis is an important model organism and the first plant with its genome sequenced. Knowledge from studying this species has either direct or indirect applications to agriculture and human health. Quantitative proteomics by data-independent acquisition (SWATH/DIA-MS) was recently developed and considered as a high-throughput targetedlike approach for accurate proteome quantitation. In this approach, a high-quality and comprehensive library is a prerequisite. Here, we generated a protein expression atlas of 10 organs of Arabidopsis and created a library consisting of 15,514 protein groups, 187,265 unique peptide sequences, and 278,278 precursors. The identified protein groups correspond to ~56.5% of the predicted proteome. Further proteogenomics analysis identified 28 novel proteins. We subsequently applied DIA-mass spectrometry using this library to quantify the effect of abscisic acid on Arabidopsis. We were able to recover 8,793 protein groups with 1,787 of them being differentially expressed which includes 65 proteins known to respond to abscisic acid stress. Mass spectrometry data are available via ProteomeXchange with identifier PXD012710 for data-dependent acquisition and PXD014032 for DIA analyses.
Investigating Affective and Motor Improvements with Dance in Parkinson’s Disease
Authors: Ciantar Sarah R. , Bearss Karolina A. , Levkov Gabriella , Bar Rachel J. , DeSouza Joseph F.X.
Published: June 2019

Background

Research has supported the notion that dance alleviates motor symptoms for people with Parkinson’s disease (PD) illustrated by observed improvements in gait, balance, and quality of life. However, what remains unclear is whether engaging in weekly dance classes also positively influences nonmotor symptoms of PD, such as affect regulation (mood).

Objectives

To examine depressive symptoms of participants in a dance program for people with PD, and to extend previous findings on the topics for motor symptoms.

Methods

People with PD (n=23) and age-matched healthy controls (n=11) between the ages of 58-75 (M=67.91, SD=5.43) participated in a weekly Dance for PD® class. Nonmotor symptoms of PD were assessed using the Geriatric Depression Scale (GDS), administered at three time points over the 1st year of a newly-developed dance program. The Berg Balance Scale (BBS) and the Timed Up and Go (TUG) were also administered at three time points to assess motor function.

Results

Longitudinal mixed methods analysis showed significant improvements in GDS scores, when examining effects of the dance class over the time, with a significant main effect of time (p < 0.01) and condition: pre/post dance class (p < 0.025). Significant improvements were also observed across the motor tests of BBS (p < 0.001) and TUG (p < 0.001) measurements.

Conclusion

Our findings suggest dance can facilitate positive improvements in both motor and mood related symptoms of PD. These findings show important nonmotor effects of dance as an adjunct treatment for mood that may reduce the burden of this disease.
Longitudinal, Multiparametric MRI Assessment of repetitive mild TBI in rats
Authors: Khan Ahmad Raza , Hansen Brian , Iversen Nina K. , Olesen Jonas L. , Angoa-Perez Mariana , Kuhn Donald M. , Østergaard Leif , Jespersen Sune N.
Published: June 2019

Repetitive mild traumatic brain injury (mTBI) has long term health effects and may result in the development of neurodegenerative or neuropsychiatric disorders. Histology shows axonal and dendritic beading, synaptic atrophy, vasodilation and gliosis occuring within hours/days post-mTBI. However, current neuroimaging techniques are unable to detect the early effects of repetitive mTBI. Consequently, mTBI brain scans are normal appearing and inconclusive. Hence, neuroimaging markers capable of detecting subtle microstructural and functional alterations are needed. We present results from longitudinal, multiparametric magnetic resonance imaging (MRI) assessment of repetitive mTBI in rats. We employ advanced in-vivo diffusion MRI (dMRI) to probe brain microstructural alterations, perfusion MRI to assess cerebral blood flow (CBF), close to the injury site, and proton MR spectroscopy to assess metabolic alterations in the ipsilateral cerebral cortex. High resolution anatomical scans were also acquired. In agreement with clinical observations, anatomical scans of rats were normal appearing even after repeated mTBI. Throughout, significance is regarded as p<0.05 post false discovery rate correction. dMRI revealed significant microstructural remodelling in ipsilateral hippocampus (reduced radial kurtosis), may be due to axonal/dendritic beading, demyelination, synaptic atrophy and edema. Consistent with prior reports of reduced cell/fiber density in mTBI, we find significantly increased mean diffusivity in ipsilateral corpus callosum. We also find significantly decreased glutathione (GSH) and increased total Choline (tCho) following second and third mTBI (vs baseline), also reported in clinical mTBI cohorts. Reduced GSH suggests oxidative stress and increase in tCho indicate cell damage/repair. CBF did not change significantly, however, high variability in CBF following the second and third mTBI suggest increased variability in CBF likely due to tissue hypoxia and oxidative stress. Oxidative stress may affect capillary blood flow by disturbing pericyte capillary contraction. Around 40% of pericytes retract after mTBI causing pericyte depletion and white matter dysfunction as suggested by dMRI findings. Multiparametric MRI detects meaningful mTBI-induced alterations otherwise undetectable with conventional MRI. Similar strategies may provide useful information to aid diagnosis of human mTBI.
RobustClone: A robust PCA method of tumor clone and evolution inference from single-cell sequencing data
Authors: Chen Ziwei , Gong Fuzhou , Ma Liang , Wan Lin
Published: June 2019

Single-cell sequencing (SCS) data provide unprecedented insights into intratumoral heterogeneity. With SCS, we can better characterize clonal genotypes and build phylogenetic relationships of tumor cells/clones. However, high technical errors bring much noise into the genetic data, thus limiting the application of evolutionary tools in the large reservoir. To recover the low-dimensional subspace of tumor subpopulations from error-prone SCS data in the presence of corrupted and/or missing elements, we developed an efficient computational framework, termed RobustClone, to recover the true genotypes of subclones based on the low-rank matrix factorization method of extended robust principal component analysis (RPCA) and reconstruct the subclonal evolutionary tree. RobustClone is a model-free method, fast and scalable to large-scale datasets. We conducted a set of systematic evaluations on simulated datasets and demonstrated that RobustClone outperforms state-of-the-art methods, both in accuracy and efficiency. We further validated RobustClone on 2 single-cell SNV and 2 single-cell CNV datasets and demonstrated that RobustClone could recover genotype matrix and infer the subclonal evolution tree accurately under various scenarios. In particular, RobustClone revealed the spatial progression patterns of subclonal evolution on the large-scale 10X Genomics scCNV breast cancer dataset. RobustClone software is available at https://github.com/ucasdp/RobustClone.
Serum-free culture system for spontaneous human mesenchymal stem cell spheroids formation
Authors: Dong Guoyi , Wang Shengpeng , Ge Yuping , Deng Qiuting , Cao Qi , Wang Quanlei , Shang Zhouchun , OuYang Wenjie , Li Jing , Liu Chao , Tang Jie , Zhao Weihua , Gu Ying
Published: June 2019

Human mesenchymal stem cells (hMSCs) are widely used in clinical research because of their multipotential, immunomodulatory, and reparative properties. Previous studies determined that hMSC spheroids from three-dimensional (3D) culture possess higher therapeutic efficacy than conventional hMSCs from monolayer (2D) culture. To date, various 3D culture methods have been developed to form hMSC spheroids, but most of them used culture medium containing fetal bovine serum (FBS), which is not suitable for further clinical use. Here, we demonstrate that dissociated single MSCs seeded in induced pluripotent stems medium (MiPS), adhere loosely to the dish and spontaneously migrate to form spheroids during day 3 to day 6. Through component deletion screening and complementation experiments, the knockout serum replacement (KSR) was identified as necessary and sufficient for hMSC spheroid formation. Transcriptome analysis showed that the overall expression profiles were highly similar between 2D culture with FBS and KSR derived spheroids. Interestingly, genes related to inflammatory response, immune response, and angiogenesis were up-regulated in spheroids at day 6, and qPCR results further validated the increased expression level of related genes, including STC1, CCL7, HGF, IL24, and TGFB3. When spheroids were re-plated in normal FBS medium, cells formed a typical spindle-shaped morphology, and FACS results showed that the recovered cells retained MSC-specific surface markers, such as CD73, CD90, and CD105. In summary, we developed a practical and convenient method to generate hMSC spheroids for clinical research and therapy.
The genomic basis of evolved virus resistance is dependent on environmental resources
Authors: Roberts Katherine , Meaden Sean , Sharpe Stephen , Kay Suzanne , Doyle Toby , Wilson Drew , Bartlett Lewis J. , Paterson Steve , Boots Mike
Published: June 2019

Parasites impose strong selection on their hosts, but the level of resistance evolved may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource mediated selection are rare, particularly in non-model organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and associated trade-offs, in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole genome sequencing we identify putative mechanisms of resistance that depend on the nutritional environment during selection. We find that the evolution of resistance is specific to diet, with adaptation to a low nutrition diet constraining resistance when challenged with the pathogen on a high nutrition diet. Resistance in a low nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development. Whole genome resequencing of the host shows that resistance mechanisms are highly polygenic and suggests evidence for trade-offs at the genetic level. Critically when populations evolve in high resource conditions, resistance is linked to metabolic and immune pathways, however it is more closely associated with cytoskeleton organisation when selected under low nutrition. Our results emphasise the importance of resources on the evolution of resistance.
Conformational flexibility of GRASP protein and its constituent PDZ subdomains reveals structural basis of its promiscuous interactome
Authors: Mendes Luis Felipe S. , Batista Mariana R. B. , Judge Peter J. , Watts Anthony , Redfield Christina , Costa-Filho Antonio J.
Published: June 2019

The Golgi complex is a central component of the secretory pathway, responsible for several critical cellular functions in eukaryotes. The complex is organized by the Golgi matrix, which includes the Golgi Reassembly and Stacking Proteins (GRASPs), which participate in cisternae stacking and lateral linkage in vertebrates. GRASPs also have critical roles in other processes, with an unusual ability to interact with several different protein binding partners. The conserved N-terminus of the GRASP family includes two PDZ domains. Previous crystallographic studies of orthologues suggest that PDZ1 and PDZ2 have similar conformations and secondary structure content, however PDZ1 alone mediates nearly all the interactions between GRASPs and their binding partners. In this work, NMR, Synchrotron-Radiation Circular Dichroism and Molecular Dynamics were used to examine the structure, flexibility and stability of the two constituent PDZ domains. GRASP PDZs are structured in an unusual β3α1β4β5α2β6β1β2 secondary structural arrangement and NMR data indicates that the PDZ1 binding pocket is formed by a stable β2-strand and a more flexible and unstable α2-helix, suggesting an explanation for the higher PDZ1 promiscuity. The conformational free energy profiles of the two PDZ domains were calculated using Molecular Dynamics simulations. The data suggest that, after binding, the protein partner significantly reduces the conformational space that GRASPs can access by stabilizing one particular conformation, in a partner-dependent fashion. The structural flexibility of PDZ1, modulated by PDZ2, and the coupled, coordinated movement between the two PDZs enable GRASPs to interact with multiple partners, allowing them to function as promiscuous, multitasking proteins.

Significance Statement

Golgi Reassembly and Stacking Proteins (GRASPs) play pivotal roles in the maintenance of Golgi structure as well as in unconventional protein secretion. Their broad network of interactions is mainly sustained by the two-PDZ domains located in the N-terminal portion of the protein. The asymmetry of the PDZ domains in terms of number and diversity of interacting partners has been long recognized, but the molecular determinants of that asymmetry remains largely unknown. The biophysical data presented here provide a firm basis for understanding why PDZ1 behaves differently to PDZ2 in solution, despite their similar 3D structures. Furthermore, we propose that PDZ2 assist ligand binding to PDZ1, by means of conformational stabilization.
Sperm quality parameters are increased and asymmetric in house mouse hybrids
Authors: Martincová Iva , Ďureje Ľudovít , Baird Stuart J. E. , Piálek Jaroslav
Published: June 2019

Spermatogenesis is a tuned cascade of processes producing sperm; impairment of any phase of this process can affect fitness of males. The level of impairment can be pronounced in hybrids between genetically divergent populations. To explore the effect of hybridization on sperm quality we produced F1 hybrids from 29 wild derived strains of two house mouse subspecies,M. m. musculusandM. m. domesticus, which diverged 0.5 MY ago. The measured sperm quality traits did not significantly differ between intrasubspecific crosses. Effects of intersubspecific hybridization were dependent on sperm trait and cross direction. The proportion of sperm head abnormalities was increased in F1 intersubspecific hybrids. The frequency of dissociated sperm heads was increased in theM. m. musculus×M. m. domesticus(♀×♂) F1 but decreased inM. m. domesticus×M. m. musculus(♀×♂) F1 hybrids, with the difference in medians being more than 180%. We deduce that the dissociated sperm heads trait is associated with the X chromosome and modulated by interaction with the Y chromosome; nevertheless, the high proportion of unexplained variance (55.46 %) suggests the presence of polymorphic autosomal interactions. The reported differences in sperm quality between cross types may be highly relevant to male fitness in zones of secondary contact between the two subspecies. The cross direction asymmetry in frequency of dissociated sperm heads should favour theM. m. musculusY chromosome. This is consistent with the spread of theM. m. musculusY chromosome in nature across the hybrid zone between these two subspecies.
Uncyclized xanthommatin is a key ommochrome intermediate in invertebrate coloration
Authors: Figon Florent , Munsch Thibaut , Croix Cécile , Viaud-Massuard Marie-Claude , Lanoue Arnaud , Casas Jérôme
Published: June 2019

Ommochromes are widespread pigments that mediate multiple functions in invertebrates. The two main families of ommochromes are ommatins and ommins, which both originate from the kynurenine pathway but differ in their backbone, thereby in their coloration and function. Despite its broad significance, how the structural diversity of ommochromes arisesin vivohas remained an open question since their first description. In this study, we combined organic synthesis, analytical chemistry and organelle purification to address this issue. From a set of synthesized ommatins, we derived a fragmentation pattern that helped elucidating the structure of new ommochromes. We identified uncyclized xanthommatin as the elusive biological intermediate that links the kynurenine pathway to the ommatin pathway within ommochromasomes, the ommochrome-producing organelles. Due to its unique structure, we propose that uncyclized xanthommatin functions as a key branching metabolite in the biosynthesis and structural diversification of ommatins and ommins, from insects to cephalopods.
Molecular and cellular determinants of motor asymmetry in zebrafish
Authors: Horstick Eric J. , Bayleyen Yared , Burgess Harold A.
Published: June 2019

Asymmetries in motor behavior, such as human hand preference, are observed throughout bilateria. However, neural substrates and developmental signaling pathways that impose underlying functional lateralization on a broadly symmetric nervous system are unknown. Here we report that in the absence of over-riding visual information, zebrafish larvae show intrinsic lateralized motor behavior that is mediated by a cluster of 60 posterior tuberculum (PT) neurons in the forebrain. PT neurons impose motor bias via a projection through the epithalamic commissure to the habenula. Acquisition of left/right identity is disrupted by heterozygous mutations inmosaic eyesandmindbomb, genes that regulate Notch signaling. These results define the neuronal substrate for motor asymmetry in a vertebrate and support the idea that developmental pathways that establish visceral asymmetries also govern acquisition of left/right identity.
The P387 Thrombospondin-4 Variant Promotes Accumulation of Macrophages in Atherosclerotic Lesions
Authors: Muppala Santoshi , Rahman Mohammed Tanjimur , Krukovets Irene , Verbovetskiy Dmitriy , Pluskota Elzbieta , Fleischman Aaron , Vince D. Geoffrey , Plow Edward F. , Stenina-Adognravi Olga
Published: June 2019

Aims

Thrombopspondin-4 (TSP4) is a pro-angiogenic protein that has been implicated in tissue remodeling and local vascular inflammation. TSP4 and, in particular, its SNP variant, P387 TSP4, have been associated with cardiovascular disease.

Macrophages are central to initiation and resolution of inflammation and development of atherosclerotic lesions, but the effects of the P387 TSP4 on macrophages remain essentially unknown. We examined the effects of the P387 TSP4 variant on macrophages in cell culture andin vivoin a murine model of atherosclerosis. Further, the levels and distributions of the twoTSP4 variants were assessed in human atherosclerotic arteries.

Methods and Results

InApoE−/−/P387-TSP4 knock-in mice, atherosclerotic lesions accumulated more macrophages than lesions bearing A387 TSP4. The levels of inflammatory markers were increased in lesions ofApoE−/−/P387-TSP4 knock-in mice compared toApoE−/−mice. Lesions in human arteries from individuals carrying the P387 variant had higher levels of TSP4 and higher macrophage accumulation. P387 TSP4 was more active in supporting adhesion of cultured human and mouse macrophages in experiments using recombinant TSP4 variants and in cells derived from P387-TSP4 knock-in mice.

Conclusions

TSP4 supports the adhesion of macrophages and their accumulation in atherosclerotic lesions. P387 TSP4 is more active in supporting these pro-inflammatory events in the vascular wall, which may contribute to the increased association of P387 TSP4 with cardiovascular disease.

Abbreviations

BSA, bovine serum albumin; DMSO, dimethyl sulfoxide; ECM, extracellular matrix;Thbs4−/−, thrombospondin-4 gene knock-out; WT, wild type; P387-TSP4 KI, P387TSP4knock-in mice; OCT, Optimum Cutting Temperature; vWF, von Willebrand factor; α-SMA, alpha-smooth muscle actin; Egr2, Early Growth Response 2; PBS, Phosphate Buffer saline; DMEM, Dulbecco’s Modified Eagle Medium.
Kinetic mechanism of human mitochondrial RNase P
Authors: Liu Xin , Wu Nancy , Shanmuganathan Aranganathan , Klemm Bradley P. , Howard Michael J. , Lim Wan Hsin , Koutmos Markos , Fierke Carol A.
Published: June 2019

A first step in processing mitochondrial precursor tRNA (pre-tRNA) is cleavage of the 5’ leader catalyzed by ribonuclease P (RNase P). Human mitochondrial RNase P (mtRNase P) is composed of three protein subunits: mitochondrial RNase P protein (MRPP) 1, 2 and 3. Even though MRPP3 is the metallonuclease subunit responsible for catalysis, cleavage is observed only in the presence of the MRPP1/2 subcomplex. To understand the functional role of MRPP1/2, we reconstituted human mitochondrial RNase P in vitro and performed kinetic and thermodynamic analyses. MRPP1/2 significantly enhances both the catalytic activity and the apparent substrate affinity of mtRNase P. Additionally, pull-down and binding data demonstrate synergy between binding pre-tRNA and formation of a catalytically active MRPP1/2/3 complex. These data suggest that conformational changes in the MRPP1/2-pre-tRNA complex lead to protein-protein or protein-RNA interactions that increase both MRPP3 recognition and cleavage efficiency. This work presents the first kinetic model for human mtRNase P, providing a fundamental framework for the function of MRPP1/2 for recognition and processing of pre-tRNA.
Disrupting ß-catenin dependent Wnt signaling activates an invasive gene program predictive of colon cancer progression
Authors: Chen George T. , Tifrea Delia F. , Murad Rabi , Lyou Yung , Mortazavi Ali , Edwards Robert A. , Waterman Marian L.
Published: June 2019

The recent classification of colon cancer into molecular subtypes revealed that patients with the poorest prognosis harbor tumors with the lowest levels of Wnt signaling. This is contrary to the long-standing understanding that overactive Wnt signaling promotes tumor progression from early initiation stages through to the later stages including invasion and metastasis. Here, we lower the levels of Wnt signaling in colon cancer via interference with two different steps in the pathway that lie upstream or downstream of the effector protein ß-catenin. We find that these Wnt-reduced cancer cells exhibit a more aggressive disease phenotype, including increased mobility in vitro and localized invasion in an orthotopic mouse model. RNA sequencing reveals that interference with Wnt signaling leads to an upregulation of gene programs that favor cell migration and invasion. We identify a set of upregulated genes common among the Wnt perturbations and find that elevated expression of these genes is strongly predictive of poor patient outcomes in early-invasive colon cancer. These genes may have clinical applications as patient biomarkers or new drug targets to be used in concert with existing therapies.

One Sentence Summary

Low Wnt Signaling Leads to Invasive Tumor Phenotypes in Colorectal Cancer.
Levodopa Responsiveness Subtypes of Freezing of Gait: Results Using a Levodopa Challenge
Authors: McKay J. Lucas , Goldstein Felicia C. , Sommerfeld Barbara , Bernhard Douglas , Perez Parra Sahyli , Factor Stewart A.
Published: June 2019

Objective

To demonstrate that levodopa-unresponsive freezing of gait (ONOFF-FOG), which is a disabling untreatable feature of Parkinson’s disease (PD), is distinct from responsive/OFF only FOG (OFF-FOG) and potentially has a distinct pathophysiology.

Methods

Fifty-five PD patients completed levodopa challenges after >12 hours OFF with supratherapeutic doses to classify them as NOFOG, OFF-FOG or ONOFF-FOG. Serum levodopa levels ensured threshold levels were met. An “ON” response was defined as ≥20% improvement in MDS-UPDRS-III score. Main outcome measure was MDS-UPDRS-III based on clinical exam, timed-up-and-go tests and 360° turns.

Results

45 patients exhibited an “ON” response to the challenge. Levodopa-equivalent-dose was 142±56% of patients’ typical morning doses. Patients could be classified as: 19 ONOFF-FOG, 11 OFF-FOG, 15 NOFOG. The ONOFF-FOG group exhibited significantly higher NFOG-Q, MDS-UPDRS-II/III scores compared to the OFF-FOG group. MDS-UPDRS-III total varied significantly across medication response states (P<0.01) and groups (P=0.03). Among MDS-UPDRS-III subdomains, significant effects of group (highest in ONOFF-FOG group) were identified for measures of lower extremities and gait. Linear mixed models revealed a highly significant association between serum levodopa level and MDS-UPDRS-III score that did not vary across the groups. There was a highly significant group interaction effect on the association between serum levodopa level with MDS-UPDRS-III item 11 “Freezing of Gait” (P<0.001).

Conclusions

ONOFF-FOG is a distinct subtype of FOG in PD, as opposed to OFF-FOG. This is an important step in demonstrating that FOG is not a single entity and, in turn, could lead to better understanding of pathophysiology and development of effective therapies.
Evolving neoantigen profiles in colorectal cancers with DNA repair defects
Authors: Rospo Giuseppe , Lorenzato Annalisa , Amirouchene-Angelozzi Nabil , Magrì Alessandro , Cancelliere Carlotta , Corti Giorgio , Negrino Carola , Amodio Vito , Montone Monica , Bartolini Alice , Barault Ludovic , Novara Luca , Isella Claudio , Medico Enzo , Bertotti Andrea , Trusolino Livio , Germano Giovanni , Nicolantonio Federica Di , Bardelli Alberto
Published: June 2019

Background

Neoantigens that arise as a consequence of tumour-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumour types, a high number of neoantigens is associated with patient response to immune therapies. The molecular processes governing the generation of neoantigens and their turnover in cancer cells are poorly understood. We exploited CRC as a model system to understand how alterations in DNA repair pathways modulate neoantigen profiles over time.

Methods

We performed Whole Exome Sequencing (WES) and RNA sequencing (RNAseq) in CRC cell lines,in vitroandvivo, and in CRC patient-derived xenografts (PDXs) to track longitudinally genomic profiles, clonal evolution, mutational signatures and predicted neoantigens.

Results

The majority of CRC models showed remarkably stable mutational and neoantigen profiles, however those carrying defects in DNA repair genes continuously diversified. Rapidly evolving and evolutionary stable CRCs displayed characteristic genomic signatures, and transcriptional profiles. Downregulation of molecules implicated in antigen presentation occurred selectively in highly mutated and rapidly-evolving CRC.

Conclusions

These results indicate that CRC carrying alterations in DNA repair pathways display dynamic neoantigen patterns that fluctuate over time. We define CRC subsets characterized by slow and fast evolvability and link this phenotype to downregulation of antigen-presenting cellular mechanisms. Longitudinal monitoring of the neoantigen landscape could be relevant in the context of precision medicine.
Children with Cerebral Palsy Return to Baseline Community Arm Movement after Constraint Induced Movement Therapy
Authors: Goodwin Brianna M. , Sabelhaus Emily K. , Pan Ying-Chun , Bjornson Kristie F. , Pham Kelly L. D. , Walker William O. , Steele Katherine M.
Published: June 2019

Importance

Constraint Induced Movement Therapy (CIMT) is a common treatment for children with unilateral cerebral palsy (CP). While clinic-based assessments have demonstrated improvements in arm function after CIMT, quantifying if these changes are translated and sustained outside of a clinic setting remains unclear.

Objective

Accelerometers were used to quantify arm movement for children with CP one week before, during, and 4+ weeks after CIMT and compared to typically-developing (TD) peers.

Design

Observational during CIMT

Setting

Clinical assessments and treatment occurred in a tertiary hospital and accelerometry data were collected in the community

Participants

7 children with CP (5m/2f, 7.4 ± 1.2 yrs) and 7 TD peers (2m/5f, 7.0 ± 2.3 yrs)

Intervention

30-hour CIMT protocol

Outcomes and Measures

The use ratio, magnitude ratio, and bilateral magnitude were calculated from the accelerometry data. Clinical measures were evaluated before and after CIMT and surveys were used to assess the feasibility of using accelerometers.

Results

Before CIMT, children with CP used their paretic arm less than their TD peers. During therapy, their frequency and magnitude of paretic arm use increased in the clinic and in daily life. After therapy, although clinical scores improved, children reverted to baseline accelerometry values. Additionally, children and parents in both cohorts had positive perceptions of wearing accelerometers.

Conclusions and Relevance

The lack of sustained improved accelerometry metrics following CIMT suggest therapy gains did not translate to increased movement outside the clinic. Additional therapy may be needed to help the transfer of skills to the community setting.

What this Article Adds

This study compares the movement of children with CP undergoing CIMT in the community setting with their typically developing peers. Additional interventions may be needed in combination with or following CIMT to sustain the benefits of the therapy outside of the clinic.
PROTEINATOR: Web-UI exploring repurposing hypotheses of PROTEIN InhibiTORs based on protein interactions
Authors: Tangadu Santhosh , Shankara Susmitha , Varanasi Bhaskaram V. , Athri Prashanth
Published: June 2019

PROTEINATOR is the first version of a staggered, multi-paradigm and extensible drug repurposing platform, focusing on a novel data analytic and integration strategy to find repurposing candidates that have potential to modulate targets through protein-protein interactions. The UI was created as an explorer to find ‘indirect’ drugs for a protein of interest. PROTEINATOR is developed as a web application that lets researchers search for alternate drugs for a protein of interest, based on the protein’s direct interaction with a another druggable protein. This unique tool provides researchers exploring specific implicated protein(s) (in the context of drug development), alternate, plausible routes to modulation by listing proteins that interact with the protein of interest that have reported inhibitors. It is a search engine to identify indirect drugs through connecting various databases, thus avoiding multiple steps and avoiding any manual errors. Using a representative set of databases, 112083 number of ‘indirect’ drug interactions are discovered that are potential modulators of proteins, detailed annotations of which are provided in the UI. PROTEINATOR is freely available athttp://www.proteinator.in.