bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Use of Cryopreserved Ultra-thick Human Amniotic Membrane for Management of Anophthalmic Socket Contracture
Authors: Slentz Dane H. , Nelson Christine C. 
Published: November 2018

Purpose:
To describe the use of cryopreserved ultra-thick human amniotic membrane for management of anophthalmic socket contracture.

Methods:
A chart review was performed to identify patients undergoing fornix reconstruction with cryopreserved ultra-thick human amniotic membrane for management of anophthalmic socket contracture. Patient demographics, disease etiology, and data regarding postoperative prosthesis fit and complications were collected.

Results:
The technique is described in 3 female patients with anophthalmic socket contracture who underwent fornix reconstruction using cryopreserved ultra-thick human amniotic membrane. All patients had excellent prosthesis fit at final follow up (range, 10–14 months). There were no clinically significant complications and no reoperations were performed. One pyogenic granuloma developed and was excised without affecting ocular prosthesis fit.

Conclusions:
Cryopreserved ultra-thick human amniotic membrane is easy to use, well tolerated, and produces good outcomes for management of anophthalmic socket contracture.
Assessing Clinical Utility of Cerebral Oximetry Monitoring During Pediatric Scoliosis Surgery
Authors: Mukuno Kaela , Vacchiano Charles , Funk Emily , Morgan Brett 
Published: November 2018

Introduction
High-quality evidence indicates that active cerebral oximetry monitoring during surgery improves patient outcomes in populations at risk for hemodynamic instability. This project piloted the use of a near-infrared spectroscopy (NIRS) monitor in a pediatric surgical population with similar risk factors. Controlled hypotension is an anesthetic technique used to minimize blood loss during pediatric spinal surgery for scoliosis correction. Consensus for safe blood pressure thresholds does not exist, and cerebral oxygenation may be impeded during this anesthetic technique.

Methods
Fifteen pediatric patients scheduled for posterior spinal fusion and scoliosis correction received intraoperative NIRS monitoring. Regional cerebral oxygen saturation (rSO2) and blood pressure data were collected. Possible relationships between mean arterial pressure and rSO2 were also explored. Anesthesia provider feedback regarding device use was obtained via a voluntary survey.

Results
Twenty-four cerebral desaturation events (CDEs) were recorded among four patients (27%) involved in the project. The median CDE duration, nadir rSO2, and percent change from baseline was 3.38 minutes, 69%, and 22.5%, respectively (Interquartile ranges = 8.69, 22, and 22.99). There was no relationship between mean cerebral rSO2 and mean arterial pressure (rs
(25) = −0.194, p = .353).

Discussion
The results support the continued use of NIRS monitoring during pediatric scoliosis surgery. Analysis of individual CDEs reveals that some patients may incur more prolonged and significant CDEs. In addition, cerebral desaturations are difficult to predict using solely blood pressure parameters. Device ease of use, availability, and a high perception of clinical utility among anesthesia providers support adoption of the monitor in this setting.
Shared Decision Making About Starting Anti‐TNFs
Authors: Michel Hilary K. , Noll Robert B. , Siripong Nalyn , Kim Sandra C. , Lipstein Ellen A. 
Published: November 2018

ABSTRACTShared decision making (SDM) is central to patient‐centered medicine and has the potential to improve outcomes for pediatric patients with inflammatory bowel diseases. We surveyed specialists about their use of SDM in the decision to start a tumor necrosis factor‐α inhibitor in pediatric patients. Results were compared between those who reported using SDM and those who did not. Of 209 respondents, 157 (75%) reported using SDM. Physician/practice characteristics were similar between users and nonusers. There were no statistically significant differences between groups in the components deemed important to the decision‐making process nor the number of barriers or facilitators to SDM. Exploratory analyses suggested that physicians using SDM were more accepting of adolescent involvement in the decision‐making process. Our results question the effectiveness of using reported barriers and facilitators to guide interventions to improve use of SDM, and suggest further work is needed to understand the adolescent role in decision making.
Interest of Youth Living With HIV in Long-Acting Antiretrovirals
Authors: Weld Ethel D. , Rana Md Sohel , Dallas Ronald H. , Camacho-Gonzalez Andres F. , Ryscavage Patrick , Gaur Aditya H. , Chakraborty Rana , Swindells Susan , Flexner Charles , Agwu Allison L. 
Published: November 2018

Objectives:
This study's primary objective was to characterize attitudes to long-acting antiretrovirals (LAARV), among youth aged 13–24 years living with perinatally acquired HIV and nonperinatally acquired HIV. Secondary objectives included: assessing whether those with detectable HIV RNA PCR viral load had higher enthusiasm for LAARV compared to those with suppressed viral load, and examining characteristics associated with LAARV enthusiasm.

Methods:
A cross-sectional survey of 303 youth living with HIV (YHIV) followed at 4 pediatric/adolescent HIV clinics in the United States was performed to determine interest in LAARV, using a modified survey instrument previously used in adults. Interest in LAARV across groups was compared. Poisson regression with robust variance was used to determine the impact of various characteristics on interest in LAARV.

Findings:
Overall, 88% of YHIV reported probable or definite willingness to use LAARV. The enthusiasm level was similar between youth with perinatally acquired HIV and nonperinatally acquired HIV (P = 0.93). Youth with HIV viral load >1000 copies per milliliter had significantly higher interest than youth with suppressed viral load [prevalence ratio 1.12 (95% confidence interval: 1.03 to 1.20); P = 0.005]. Female youth participants who had had past experience with implantable contraceptive methods had a significantly higher interest in LAARV (100% vs. 85.5%; P = 0.002). Proportion of respondents endorsing definite willingness to use was significantly higher with decreased injection frequency compared with increased injection frequency.

Interpretation:
YHIV at 4 urban US pediatric/adolescent HIV clinics had high levels of enthusiasm for LAARV. LAARV should be given high priority as a potentially viable treatment option to improve clinical outcomes in YHIV.
Comparison of Unilateral With Bilateral Metal Stenting for Malignant Hilar Biliary Obstruction
Authors: Teng Fei , Xian Yu-Tao , Lin Jia , Li Yu , Wu An-Le 
Published: November 2018

Purpose:
The main purpose of this study was to compare the clinical effectiveness between unilateral and bilateral metal stenting for malignant hilar biliary obstruction (MHBO).

Methods:
From January 2012 to October 2017, consecutive patients with MHBO underwent unilateral or bilateral stent insertion at our center. Technical and clinical success, stent patency, and survival were compared between these 2 groups.

Results:
A total of 110 patients with MHBO were included in this study. Technical successful rates of unilateral and bilateral stenting were 93.1% (54/58) and 90.4% (47/52), respectively (P=0.864). Clinical successful rates of unilateral and bilateral stenting were 96.4% (53/55) and 97.9% (46/47), respectively (P=1.000). There was no significant difference in stent patency period (unilateral, 182 d; bilateral, 198 d; P=0.999) and survival (unilateral, 189 d; bilateral, 199 d; P=0.867) between 2 groups.

Conclusions:
Unilateral and bilateral metal stenting had similar clinical effectiveness and long-term outcomes in patients with MHBO.
Genetic predisposition to hypouricemia on whole-exome sequencing analysis and its utilities in primary screening purposes
Authors: Cha Do Hyeon , Gee Heon Yung , Cachau Raul , Choi Jong Mun , Park Daeui , Jee Sun Ha , Ryu Seungho , Kim Kyeong Kyu , Winkler Cheryl A. , Cho Sung Kweon 
Published: November 2018

AbstractDifferentiating between inherited renal hypouricemia and transient hypouricemia is challenging. Here, we aimed to describe the genetic predisposition of hypouricemia patients using whole-exome sequencing (WES) and assess the feasibility for genetic diagnosis in primary screening. WES was performed for the discovery of diagnostic markers in discovery cohorts (N=31). Two known genetic markers SLC22A12 c.774G>A (p.Trp258*) and SLC22A12 c.269G>A (p.Arg90His) were identified, We genotyped for the 2 SLC22A12 SNPs among screened 50 hypouricemia subjects for the replication cohorts; 47 carried known SLC22A12 markers; three unexplained hypouricemic cases were analyzed by using WES. We used 46 healthy internal controls for the variant discovery. Four novel variants of SLC22A12, c.408C>A (p.Asn136Lys), c.674C>A (p.Thr225Lys), c.851G>A (p.Arg284Gln), and c.1285G>A (p.Glu429Lys), and one novel variant of SLC2A9, c. 376A>G (p.Met155Val), were identified. After filtering out known genes (SLC22A12 and SLC2A9), the p.Arg78His variant in ASB12 was overlapped in two unexplained conditions. This is the first attempt to investigate the effectiveness of integrating exome sequencing and genotype into the clinical care for hypouricemia and determine the value of genetic diagnostic screening for hypouricemia in the clinical setting. Screening of just two SNPs (p.Trp258* and p.Arg90His) identified 87.7% (71/81) of patients with hypouricemia. Early identification and intervention of hypouricemia is feasible using genetic screening to prevent acute kidney injury, especially for soldiers and athletics.
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings
Authors: Kulmanov Maxat , Kafkas Senay , Karwath Andreas , Malic Alexander , Gkoutos Georgios V , Dumontier Michel , Hoehndorf Robert 
Published: November 2018

AbstractRecent developments in machine learning have lead to a rise of large number of methods for extracting features from structured data. The features are represented as a vectors and may encode for some semantic aspects of data. They can be used in a machine learning models for different tasks or to compute similarities between the entities of the data. SPARQL is a query language for structured data originally developed for querying Resource Description Framework (RDF) data. It has been in use for over a decade as a standardized NoSQL query language. Many different tools have been developed to enable data sharing with SPARQL. For example, SPARQL endpoints make your data interoperable and available to the world. SPARQL queries can be executed across multiple endpoints. We have developed a Vec2SPARQL, which is a general framework for integrating structured data and their vector space representations. Vec2SPARQL allows jointly querying vector functions such as computing similarities (cosine, correlations) or classifications with machine learning models within a single SPARQL query. We demonstrate applications of our approach for biomedical and clinical use cases. Our source code is freely available athttps://github.com/bio-ontology-research-group/vec2sparqland we make a Vec2SPARQL endpoint available athttp://sparql.bio2vec.net/.
Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)
Authors: Brown Bradley , Atallah Christian , McLaughlin James Alastair , Misirli Göksel , Goñi-Moreno Ángel , Roehner Nicholas , Skelton David James , Bartley Bryan , Beal Jacob , Poh Chueh Loo , Ofiteru Irina Dana , Wipat Anil 
Published: November 2018

AbstractSynthetic biology aims to improve the development of biological systems and in-crease their reproducibility through the use of engineering principles, such as stan-dardisation and modularisation. It is important that these systems can be represented and shared in a standard way to ensure they are easily understood, reproduced, and utilised by other researchers. The Synthetic Biology Open Language (SBOL) is a data standard for sharing biological designs and information about their implementation and characterisation. Thus far, this standard has been used to represent designs in homogeneous systems, where the same design is implemented in every cell. In recent years there has been increasing interest in multicellular systems, where biological designs are split across multiple cells to optimise the system behaviour and function. Here we show how the SBOL standard can be used to represent such multicellular systems, and hence how researchers can better share designs with the community.
LeafCutter vs. MAJIQ and comparing software in the fast moving field of genomics
Authors: Vaquero-Garcia Jorge , Norton Scott , Barash Yoseph 
Published: November 2018

AbstractIn a recent publication, Li et al. introduced LeafCutter, a new method for detecting and quantifying differential splicing of RNA from RNASeq data. In this work, Li et al. first compared LeafCutter to existing methods, then used it for a study of splicing variations and sQTL analysis from a large set of GTEx samples. While the study was elaborate and comprehensive, we want to highlight several issues with the comparative analysis performed by Li et al. We argue these issues created an inaccurate and misleading representation of other tools, namely MAJIQ and rMATS. More broadly, we believe the points we raise regarding the comparative analysis by Li et al. are representative of general issues we all, as authors, editors, and reviewers, are faced with and must address in the current times of fast paced genomics and computational research.
Rationalizing Translation Elongation by Reinforcement Learning
Authors: Hu Hailin , Liu Xianggen , Xiao An , Song Sen , Zeng Jianyang 
Published: November 2018

AbstractTranslation elongation plays a crucial role in multiple aspects of protein biogenesis. In this study, we develop a novel deep reinforcement learning based framework, named RiboRL, to model the distributions of ribosomes on transcripts. In particular, RiboRL employs a policy network (PolicyNet) to perform a context-dependent feature selection to facilitate the prediction of ribosome density. Extensive tests demonstrate that RiboRL can outperform other state-of-the-art methods in predicting ribosome densities. We also show that the reinforcement learning based strategy can generate more informative features for the prediction task when compared to other commonly used attribution methods in deep learning. Moreover, the in-depth analyses and a case study also indicate the potential applications of the RiboRL framework in generating meaningful biological insights regarding translation elongation dynamics. These results have established RiboRL as a useful computational tool to facilitate the studies of the underlying mechanisms of translational regulation.
An Efficient, Scalable and Exact Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
Authors: Almodaresi Fatemeh , Pandey Prashant , Ferdman Michael , Johnson Rob , Patro Rob 
Published: November 2018

AbstractThe colored de Bruijn graph (cdbg) and its variants have become an important combinatorial structure used in numerous areas in genomics, such as population-level variation detection in metagenomic samples, large scale sequence search, and cdbg-based reference sequence indices. As samples or genomes are added to the cdbg, the color information comes to dominate the space required to represent this data structure.In this paper, we show how to represent the color information efficiently by adopting a hierarchical encoding that exploits correlations among color classes — patterns of color occurrence — present in the de Bruijn graph (dbg). A major challenge in deriving an efficient encoding of the color information that takes advantage of such correlations is determining which color classes are close to each other in the high-dimensional space of possible color patterns. We demonstrate that the dbg itself can be used as an efficient mechanism to search for approximate nearest neighbors in this space. While our approach reduces the encoding size of the color information even for relatively small cdbgs (hundreds of experiments), the gains are particularly consequential as the number of potential colors (i.e. samples or references) grows to thousands of experiments.We apply this encoding in the context of two different applications; the implicit cdbg used for a large-scale sequence search index, Mantis, as well as the encoding of color information used in population-level variation detection by tools such as Vari and Rainbowfish. Our results show significant improvements in the overall size and scalability of representation of the color information. In our experiment on 10,000 samples, we achieved more than 11× better compression compared to RRR.
Effects of BMP-2 on neovascularization during large bone defect regeneration
Authors: Pearson HB , Mason DE , Kegelman CD , Zhao L , Dawahare JH , Kacena MA , Boerckel JD 
Published: November 2018

AbstractInsufficient blood vessel supply is a primary limiting factor for regenerative approaches to large bone defect repair. Recombinant BMP-2 delivery induces robust bone formation and has been observed to enhance neovascularization, but whether the angiogenic effects of BMP-2 are due to direct endothelial cell stimulation or to indirect paracrine signaling remains unclear. Here, we evaluated the effects of BMP-2 delivery on vascularized bone regeneration and tested whether BMP-2 induces neovascularization directly or indirectly. We found that delivery of BMP-2 (5 μg) enhanced both bone formation and neovascularization in critically sized (8 mm) rat femoral bone defects; however, BMP-2 did not directly stimulate angiogenesisin vitro. In contrast, conditioned medium from both mesenchymal progenitor cells and osteoblasts induced angiogenesisin vitro, suggesting a paracrine mechanism of BMP-2 action. Consistent with this inference, co-delivery of BMP-2 with endothelial colony forming cells (ECFCs) to a heterotopic site, distant from the bone marrow niche, induced ossification but had no effect on neovascularization. Taken together, these data suggest that BMP-2 induces neovascularization during bone regeneration primarily through paracrine activation of osteoprogenitor cells.
Gene regulation inference from single-cell RNA-seq data with linear differential equations and velocity inference
Authors: Aubin-Frankowski Pierre-Cyril , Vert Jean-Philippe 
Published: November 2018

AbstractSingle-cell RNA sequencing (scRNA-seq) offers new possibilities to infer gene regulation networks (GRN) for biological processes involving a notion of time, such as cell differentiation or cell cycles. It also raises many challenges due to the destructive measurements inherent to the technology. In this work we propose a new method named GRISLI for de novo GRN inference from scRNA-seq data. GRISLI infers a velocity vector field in the space of scRNA-seq data from profiles of individual data, and models the dynamics of cell trajectories with a linear ordinary differential equation to reconstruct the underlying GRN with a sparse regression procedure. We show on real data that GRISLI outperforms a recently proposed state-of-the-art method for GRN reconstruction from scRNA-seq data.
Ultrasound functional neuroimaging reveals propagation of task-related brain activity in behaving primates
Authors: Dizeux Alexandre , Gesnik Marc , Ahnine Harry , Blaize Kevin , Arcizet Fabrice , Picaud Serge , Sahel José-Alain , Deffieux Thomas , Pouget Pierre , Tanter Mickael 
Published: November 2018

ABSTRACTIn recent decades, neuroimaging has played an invaluable role in improving the fundamental understanding of the brain. At the macro scale, neuroimaging modalities such as MRI, EEG, and MEG, exploit a wide field of view to explore the brain as a global network of interacting regions. However, this comes at the price of either limited spatiotemporal resolution or limited sensitivity. At the micro scale, electrophysiology is used to explore the dynamic aspects of neuronal activity with a very high temporal resolution. However, this modality requires a statistical averaging of several tens of single task responses. A large-scale neuroimaging modality of sufficient spatial and temporal resolution and sensitivity to study brain region activation dynamically would open new territories of possibility in neuroscienceWe show that neurofunctional ultrasound imaging (fUS) is both able to assess brain activation during single cognitive tasks within superficial and deeper areas of the frontal cortex areas, and image the directional propagation of information within and between these regions. Equipped with an fUS device, two macaque rhesus monkeys were instructed before a stimulus appeared to rest (fixation) or to look towards (saccade) or away (antisaccade) from a stimulus. Our results identified an abrupt transient change in activity for all acquisitions in the supplementary eye field (SEF) when the animals were required to change a rule regarding the task cued by a stimulus. Simultaneous imaging in the anterior cingulate cortex and SEF revealed a time delay in the directional functional connectivity of 0.27 ± 0.07 s and 0.9 ± 0.2 s for animals S and Y, respectively. These results provide initial evidence that recording cerebral hemodynamics over large brain areas at a high spatiotemporal resolution and sensitivity with neurofunctional ultrasound can reveal instantaneous monitoring of endogenous brain signals and behavior.
Data-Independent Acquisition Mass Spectrometry to Localize Phosphosites
Authors: Li Qing-Run , Wang Shi-Sheng , Zhu Hong-Wen , Xia Fang-Ying , Roepstorff Peter , Wu Jia-Rui , Zeng Rong 
Published: November 2018

AbstractIn conventional data-dependent acquisition (DDA) mode used for phosphoproteome analysis by mass spectrometry, a considerable number of phosphosites are localized ambiguously. We found that data-independent acquisition (DIA) method could localize phosphosite accurately and confidently due to its acquisition nature of repeated and unbiased mode. Here, we present a robust and promising DIA workflow for modification sites determination. Through dedicated collection and analyses of site-determining ions following their chromatographic profilings, phosphosites could be assigned or rectified unambiguously.
Axonal localization of the Fragile X family of RNA binding proteins is conserved across mammals
Authors: Shepard Katherine A. , Korsak Lulu I T. , Akins Michael R. 
Published: November 2018

AbstractSpatial segregation of proteins to neuronal axons arises in part from local translation of select mRNAs that are first transported into axons in ribonucleoprotein particles (RNPs), complexes containing mRNAs and RNA binding proteins. Understanding the importance of local translation for a particular circuit requires not only identifying axonal RNPs and their mRNA cargoes, but also whether these RNPs are broadly conserved or restricted to only a few species. Fragile X granules (FXGs) are axonal RNPs containing the Fragile X related family of RNA binding proteins along with ribosomes and specific mRNAs. FXGs were previously identified in mouse, rat, and human brains in a conserved subset of neuronal circuits but with species-dependent developmental profiles. Here we asked whether FXGs are a broadly conserved feature of the mammalian brain and sought to better understand the species-dependent developmental expression pattern. We found FXGs in a conserved subset of neurons and circuits in the brains of every examined species that together include mammalian taxa separated by up to 160 million years of divergent evolution. A developmental analysis of rodents revealed that FXG expression in frontal cortex and olfactory bulb followed consistent patterns in all species examined. In contrast, FXGs in hippocampal mossy fibers showed an increase in abundance across development for most species except for guinea pigs and members of the Mus genus, animals that navigate particularly small home ranges in the wild. The widespread conservation of FXGs suggests that axonal translation is an ancient, conserved mechanism for regulating the proteome of mammalian axons.