bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of different strategies on high thrombus burden in patients with ST-segment elevation myocardial infarction undergoing primary percutaneous coronary catheterization
Authors: Xiao Yuyang , Fu Xianghua , Wang Yanbo , Fan Yanming , Wu Yanqiang , Wang Wenlu , Zhang Qian 
Published: April 2019

Objective
This study aimed at evaluating efficacy and safety of thrombus aspiration and intracoronary-targeted thrombolysis on coronary thrombus burden in ST-elevation myocardial infarction (STEMI) patients undergoing primary percutaneous catheterization, comparing their effects on myocardial perfusion through index of microcirculatory resistance (IMR) and single-photon emission computed tomography (SPECT).

Participants and methods
From January 2017 to January 2018, STEMI patients with high thrombus burden undergoing primary catheterization were enrolled and randomly assigned to receiving thrombus aspiration (TA group) or intracoronary thrombolysis (IT group). IMR, SPECT, and other conventional measurements were adopted to assess myocardial perfusion. Major adverse cardiovascular events (MACEs) and complications were recorded over a 90-day follow-up and a 12-month follow-up after the procedure.

Results
The study consisted of 38 patients in the IT group and 33 in the TA group. After recanalization, thrombus burden score, corrected thrombolysis in myocardial infarction (TIMI) frame count, the proportion of TIMI myocardial perfusion 3 grade, and IMR in the IT group were significantly better than those of the TA group (P<0.05). During the 90-day follow-up, no difference was observed in cardiac function and MACEs. During the 12-month follow-up, there were significant differences in infarct size of SPECT (18.56±8.56 vs. 22.67±7.66, P=0.046), left ventricular ejection fraction of echocardiography (58.13±5.92 vs. 55.17±5.68, P=0.043), and the composite MACEs between the two groups (P=0.034).

Conclusion
Thrombus aspiration and intracoronary-targeted thrombolysis are effective and safe strategies in managing high coronary thrombus burden in STEMI patients. Compared with aspiration, intracoronary-targeted thrombolysis is more beneficial in improving myocardial microcirculation perfusion.
Trochanteric Fractures in Young Children
Authors: Harding Richard John , Moideen Abdul Nazeer , Carpenter Eleanor Clare , Thomas Daniel Phillip , Hemmadi Sandeep 
Published: April 2019

Background
Isolated avulsion fractures of the greater and lesser trochanter are usually seen in adolescents prior to the fusion of the apophysis. Greater trochanter fractures in adults have a high incidence of intertrochanteric extension1, 2 and lesser trochanter fractures are regarded as a pathognomonic sign of metastatic disease. These fractures are very rare among children.

Methods
We report five cases of trochanteric fractures in children of less than two years of age three of which were unrecognized initially in the accident and emergency department.

Results
Early and complete recovery ensued following immobilization and symptomatic treatment. Surgical intervention was not required.

Conclusions
There needs to be a high index of suspicion to diagnose these fractures in children and plain radiographs need to be carefully examined when assessing a limping child. Our experience shows when correctly diagnosed these injuries can be treated successfully with supportive treatment and no need for surgical intervention.

Level of Evidence
IV Case series.
Resting blood pressure modulates chest pain intensity in patients with acute myocardial infarction
Authors: Granot Michal , Dagul Pnina , Aronson Doron 
Published: April 2019

Abstract

Introduction and Objectives:
Animal models and human studies show that resting blood pressure (BP) is inversely associated with pain sensitivity. The phenomenon of “hypertension-associated hypoalgesia” was proposed as a possible explanation for the intervariability in pain perception. Given that a portion of patients with acute myocardial infarction (AMI) do not experience significant pain, we used the model of severe cardiac ischemia to explore whether BP affects the intensity of chest pain.

Methods:
Patients with AMI admitted to the cardiac intensive care unit with coronary catheterization-proven completely occluded coronary artery were included (n = 67). Resting BP at admission and 5 days after AMI was obtained. Participants reported chest pain intensity and underwent psychophysical evaluation including pain ratings for pressure, heat, and pinprick stimuli as well as temporal summation and conditioned pain modulation paradigms.

Results:
Patients with lower systolic BP (≤120 mm Hg) vs higher (≥140 mm Hg) reported higher chest pain scores at symptom onset (82.3 vs 61.7, P = 0.048) and during peak AMI (82.8 vs 57.5, P = 0.019). Higher pain ratings in response to pinprick stimulus were associated with lower BP at admission (analysis of variance P = 0.036). Patients with hypertension demonstrated lower pain sensitivity in response to pressure stimulation (531.7 ± 158.9 kPa/s vs 429.1 ± 197.4). No significant associations were observed between BP and the other assessed psychophysical measures.

Conclusion:
Study findings reinforce the phenomenon of hypertension-associated hypoalgesia through characterization of the association between BP and clinical pain experiences at onset and during AMI in a model of acute clinical pain.
A New Face Subunit Transplant Model in Mice, Containing Skin, Mandible, and Oral Mucosa for Future Face Vascularized Composite Allotransplantation Studies
Authors: Cardona Esteban , Wang Aline Yen Ling , Loh Charles Yuen Yung , Chuang Sheng-Hao , Lee Chin-Ming , ALDeek Nidal , Lin Cheng-Hung , Wei Fu-Chan 
Published: April 2019

Background:
In immunologic research, mice have advantages over other animals, such as low costs, easy handling, suitable life cycle, and adequate laboratory resources. However, vascularized composite allotransplantation surgery using mice is not popular, partly because of technical difficulties and high mortality rates. The authors’ goal was to demonstrate a face transplantation model in mice that includes skin, mandible, and oral mucosa.

Methods:
The authors developed a new syngeneic face transplantation model composed of skin, mandible, teeth, and oral mucosa in C57BL/6 mice. The following assessment included measuring the length of the right incisor on the transplanted mandibles, computed tomographic scan in one mouse for mandibular structure evaluation, and histologic examination of different tissue samples in another mouse for viability evaluation.

Results:
The authors performed five consecutive transplantations. The donor vessels were the common carotid artery (approximately equal to 0.4 mm) and the anterior facial vein (approximately equal to 0.2 mm), and the recipients were the common carotid artery and the posterior facial vein (approximately equal to 0.4 mm). The mean operative time was 80 minutes for the donor and 123 minutes for the recipient. There were neither flap failures nor animal deaths. The follow-up was 6 months. The right incisor of the transplant grew at different rates in all cases. Histologic samples showed viability in all tissues, including mandibular bone marrow. Computed tomography demonstrated normal structure of the transplanted bone.

Conclusion:
The authors’ syngeneic partial face transplantation model in mice, which included skin, oral mucosa, and mandible with teeth, should be useful for future face allotransplantation research, as the myriad of tissues it provides, of different immunomodulatory functions, is similar to that in the clinical scenario.
Lysosomal cystine mobilization shapes the response of mTORC1 and tissue growth to fasting
Authors: Jouandin Patrick , Marelja Zvonimir , Parkhitko Andrey A , Dambowsky Miriam , Asara John M , Nemazanyy Ivan , Dibble Christian C. , Simons Matias , Perrimon Norbert 
Published: April 2019

AbstractAdaptation to nutrient scarcity involves an orchestrated response of metabolic and signaling pathways to maintain homeostasis. We provide evidence that lysosomal export of cystine coordinates remobilization of internal nutrient stores with reactivation of the growth regulator TORC1 signaling upon fasting in theDrosophilafat body. Mechanistically, cystine is reduced to cysteine and metabolized to acetyl-CoA by consuming lipids. In turn, acetyl-CoA retains carbons from alternative amino acids in the form of TCA cycle intermediates, thereby restricting amino acids availability, notably aspartate. This process limits TORC1 reactivation to maintain autophagy and allows animals to cope with starvation periods. We propose that cysteine metabolism mediates a communication between lysosomes and mitochondria to maintain the balance between nutrient supply and consumption under starvation, highlighting how changes in diet divert the fate of an amino acid into a growth suppressive program.One Sentence SummaryLysosomal cysteine recycling is a metabolic break that maintains autophagy upon starvation through coenzyme A synthesis.
Random burst sensing of neurotransmitters
Authors: Montague P. Read , Lohrenz Terry , White Jason , Moran Rosalyn J , Kishida Kenneth T. 
Published: April 2019

AbstractWe introduce a random sensing approach to neurotransmitter detection that provides concurrent, co-localized detection of dopamine, serotonin, norepinephrine and pH. The approach generates high quality out-of-sample predictions at 10 milliseconds per estimate. Similar high-quality estimates result when the data are down-sampled suggesting that even more dramatic speedups are possible. The method also works using electrophysiological probes in routine use in clinical preparations thus transforming these and similar electrodes into ultra-fast sources of multi-transmitter information.
The disease progression and molecular defense response in Chenopodium quinoa infected with Peronospora variabilis, the causal agent of quinoa downy mildew
Authors: Rollano-Peñaloza Oscar M. , Palma-Encinas Valeria , Widell Susanne , Rasmusson Allan G. , Mollinedo Patricia 
Published: April 2019

AbstractThe downy mildew disease, caused by the biotrophic oomycete Peronospora variabilis, is the largest environmental threat to quinoa (Chenopodium quinoa Willd.) cultivation in the Andean highlands. However, so far no molecular information on the quinoa-Peronospora interaction has been reported. Here, we have developed tools to study the downy mildew disease in quinoa at gene expression level. Living P. variabilis could be isolated and maintained in the presence of a fungicide, allowing the characterization of downy mildew disease progression in two differently susceptible quinoa cultivars under controlled conditions. Quinoa gene expression changes induced by P. variabilis were analysed by qRT-PCR for quinoa homologues of Arabidopsis thaliana pathogen-associated genes. Overall, we observed a slower disease progression and higher tolerance in the quinoa cultivar Kurmi than in the cultivar Maniquena Real. We also observed that quinoa orthologs of A. thaliana genes involved in the salicylic acid defense response pathway (AtCAT2 and AtEP3) did not have changes in its gene expression. In contrast, quinoa orthologs of A. thaliana gene markers of the induction of the jasmonic acid response pathway (AtWRKY33 and AtHSP90) were significantly induced in plants infected with P. variabilis. These genes could be used as defense response markers to select quinoa cultivars that are more tolerant to P. variabilis infection.
The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response
Authors: Finkel Omri M. , Salas-González Isai , Castrillo Gabriel , Spaepen Stijn , Law Theresa F. , Lima Teixeira Paulo José Pereira , Jones Corbin D. , Dangl Jeffery L. 
Published: April 2019

AbstractPhosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms – the plant microbiota – are exposed to direct influence by the soil’s phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrationsper sethan bacteria, and less depended on the soil community composition.Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genusBurkholderiais specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence ofBurkholderiafrom the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant’s P starvation.
The meaning of the Michaelis-Menten constant: Kmdescribes a steady-state
Authors: Canela Enric I. , Navarro Gemma , Beltrán José Luis , Franco Rafael 
Published: April 2019

AbstractOften, in vitro or in vivo enzyme-mediated catalytic events occur far from equilibrium and, therefore, substrate affinity measured as the inverse of ES ⇄ E+S dissociation equilibrium constant (Kd) has a doubtful physiological meaning; in practice it is almost impossible to determineKd(except using stopped-flow or other sophisticated methodologies). The Michaelis-Menten constant (Km), the concentration of substrate ([S]) providing half of enzyme maximal activity, is not the (Kd). In the simple E+S ⇄ ES → E+P or in more complex models describing S conversion into P,Kmmust be considered the constant defining the steady state at any substrate concentration. Enzyme kinetics is based on initial rate determination, i.e. in the linear part of the S to P conversion when the concentration of [ES] remains constant while steady state occurs. We also show that Systems Biology issues such as the time required to respond to a system perturbation, is more dependent onk1, the kinetic constant defining substrateenzyme association, than onKm. WhereasKmis instrumental for biochemical basic and applied approaches, in any physiological condition, an important parameter to be considered is the substrate association rate (k1).
Loss-of-function tolerance of enhancers in the human genome
Authors: Xu Duo , Gokcumen Omer , Khurana Ekta 
Published: April 2019

AbstractPrevious studies have surveyed the potential impact of loss-of-function (LoF) variants and identified LoF-tolerant protein-coding genes. However, the tolerance of human genomes to losing enhancers has not yet been evaluated. Here we present the catalog of LoF-tolerant enhancers using structural variants from whole-genome sequences. Using a conservative approach, we estimate that each individual human genome possesses at least 28 LoF-tolerant enhancers on average. We assessed the properties of LoF-tolerant enhancers in a unified regulatory network constructed by integrating tissue-specific enhancers and gene-gene interactions. We find that LoF-tolerant enhancers are more tissue-specific and regulate fewer and more dispensable genes. They are enriched in immune-related cells while LoF-intolerant enhancers are enriched in kidney and brain/neuronal stem cells. We developed a supervised learning approach to predict the LoF-tolerance of enhancers, which achieved an AUROC of 96%. We predict 5,677 more enhancers would be likely tolerant to LoF and 75 enhancers that would be highly LoF-intolerant. Our predictions are supported by known set of disease enhancers and novel deletions from PacBio sequencing. The LoF-tolerance scores provided here will serve as an important reference for disease studies.
Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER) Workflow for Research and Clinical Brain PET Applications
Authors: Raman Fabio , Grandhi Sameera , Murchison Charles F. , Kennedy Richard E. , Landau Susan , Roberson Erik D. , McConathy Jonathan ,   Alzheimer’s Disease Neuroimaging Initiative
Published: April 2019

ABSTRACTObjectiveThere is a need for tools enabling efficient evaluation of amyloid- and tau-PET images suited for both clinical and research settings. The purpose of this study was to assess and validate a semi-automated imaging workflow, called Biomarker Localization, Analysis, Visualization, Extraction, and Registration (BLAzER). We tested BLAzER using two different segmentation platforms, FreeSurfer (FS) and Neuroreader (NR), for regional brain PET quantification in images from participants in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) dataset.Methods127 amyloid-PET and 55 tau-PET studies along with corresponding volumetric MRI were obtained from ADNI. The BLAzER workflow utilizes segmentation of MR images by FS or NR, then visualizes and quantifies regional brain PET data using FDA-cleared software (MIM), enabling quality control to ensure optimal registration and detect segmentation errors.ResultsBLAzER analysis required only ∼5 min plus segmentation time. BLAzER using FS segmentation showed strong agreement with ADNI for global amyloid-PET standardized uptake value ratios (SUVRs) (r = 0.9922, p < 0.001) and regional tau-PET SUVRs across all Braak staging regions (r > 0.97, p < 0.001) with high inter-operator reproducibility for both (ICC > 0.97) and nearly identical dichotomization as amyloid-positive or -negative (2 discrepant cases out of 127). Comparing FS vs. NR segmentation with BLAzER, the global SUVRs were strongly correlated for global amyloid-PET (r = 0.9841, p < 0.001), but were systematically higher (4% on average) with NR, likely due to more inclusion of white matter, which has high florbetapir binding.ConclusionsBLAzER provides an efficient workflow for regional brain PET quantification. FDA-cleared components and the ability to visualize registration reduce barriers between research and clinical applications.
Host sex and genotype modify the gut microbiome response to helminth infection
Authors: Ling Fei , Steinel Natalie , Weber Jesse , Ma Lei , Smith Chris , Correa Decio , Zhu Bin , Bolnick Daniel , Wang Gaoxue 
Published: April 2019

AbstractThe microbial community can be altered by direct/indirect interactions with parasites infecting host. Direct interactions can arise from physical/chemical contact with the parasite. Indirect interactions can involve parasite-induced changes in host immunity. If so, this would represent a case of genetic polymorphism in one species controlling an ecological interaction between other species. Here, we report a test of this expectation: we experimentally exposed Gasterosteus aculeatus to their naturally co-evolved parasite, Schistocephalus solidus. The host microbiome differed in response to parasite exposure, and between infected and uninfected fish. The microbial response to infection differed between host sexes, and also varied between variants at autosomal quantitative trait loci (QTL). These results indicate that host genotype regulates the indirect effect of infection on a vertebrate gut microbiome. Our results also raise the possibility that this sex-bias may be related to sex-specific microbial responses to the presence (or, absence) of helminthes. Therefore, helminth-based therapeutics as possible treatments for inflammatory bowel diseases might need to take account of these interactions, potentially requiring therapies tailored to host sex or genotype.
Network science inspires novel tree shape statistics
Authors: Chindelevitch Leonid , Hayati Maryam , Poon Art F. Y. , Colijn Caroline 
Published: April 2019

1AbstractThe shape of phylogenetic trees can be used to gain evolutionary insights. A tree’s shape specifies the connectivity of a tree, while its branch lengths reflect either the time or genetic distance between branching events; well-known measures of tree shape include the Colless and Sackin imbalance, which describe the asymmetry of a tree. In other contexts, network science has become an important paradigm for describing structural features of networks and using them to understand complex systems, ranging from protein interactions to social systems. Network science is thus a potential source of many novel ways to characterize tree shape, as trees are also networks. Here, we tailor tools from network science, including diameter, average path length, and betweenness, closeness, and eigenvector centrality, to summarize phylogenetic tree shapes. We thereby propose tree shape summaries that are complementary to both asymmetry and the frequencies of small configurations. These new statistics can be computed in linear time and scale well to describe the shapes of large trees. We apply these statistics, alongside some conventional tree statistics, to phylogenetic trees from three very different viruses (HIV, dengue fever and measles), from the same virus in different epidemiological scenarios (influenza A and HIV) and from simulation models known to produce trees with different shapes. Using mutual information and supervised learning algorithms, we find that the statistics adapted from network science perform as well as or better than conventional statistics. We describe their distributions and prove some basic results about their extreme values in a tree. We conclude that network science-based tree shape summaries are a promising addition to the toolkit of tree shape features. All our shape summaries, as well as functions to select the most discriminating ones for two sets of trees, are freely available as an R package athttp://github.com/Leonardini/treeCentrality.
VARUS: Sampling Complementary RNA Reads from the Sequence Read Archive
Authors: Stanke Mario , Bruhn Willy , Becker Felix , Hoff Katharina 
Published: April 2019

AbstractVast amounts of next generation sequencing RNA data has been deposited in archives, accompanying very diverse original studies. The data is readily available also for other purposes such as genome annotation or transcriptome assembly. However, selecting a subset of available experiments, sequencing runs and reads for this purpose is a nontrivial task and complicated by the inhomogeneity of the data.This article presents the software VARUS that selects, downloads and aligns reads from NCBI’s Sequence Read Archive, given only the species’ binomial name and genome. VARUS automatically chooses runs from among all archived runs to randomly select subsets of reads. The objective of its online algorithm is to cover a large number of transcripts adequately when network bandwidth and computing resources are limited. For most tested species VARUS achieved both a higher sensitivity and specificity with a lower number of downloaded reads than when runs were manually selected. At the example of twelve eukaryotic genomes, we show that RNA-Seq that was sampled with VARUS is well-suited for fully-automatic genome annotation with BRAKER.With VARUS, genome annotation can be automatized to the extent that not even the selection and quality control of RNA-Seq has to be done manually. This introduces the possibility to have fully automatized genome annotation loops over potentially many species without incurring a loss of accuracy over a manually supervised annotation process.