bluuebunny/crossref_metadata_2025_split huggingface dataset:
Health Insurance Portability and Accountability Act Noncompliance in Patient Photograph Management in Plastic Surgery
Authors: Lam Jonathan S. , Simpson Benjamin K. , Lau Frank H. 
Published: January 2019

Background
Today, plastic surgeons have largely transitioned to digital photography. This shift has introduced new risks to daily workflows, notably data theft and Health Insurance Portability and Accountability Act (HIPAA) violations.

Methods
We performed a national survey of digital photograph management patterns among members of the American Society of Plastic Surgery and trainees in Accreditation Council for Graduate Medical Education–accredited plastic surgery programs.

Results
Our findings showed that attendings preferred the use of stand-alone digital cameras (91.4%), whereas trainees preferred the use of smartphones (96.1%) for capturing patient photographs. The rate of noncompliance was nearly identical; 82.8% of attendings were HIPAA noncompliant when using stand-alone digital cameras compared with 90.2% of trainees using smartphones. Both groups also breached HIPAA rules when using other photographic management modalities.

Conclusions
This is the first study to quantify the prevalence of noncompliance with regard to an entire digital photograph management workflow. These findings were consistent with previous studies that reported that younger physicians tend to embrace newer technologies, whereas older attendings are more reluctant. The findings also suggest that HIPAA noncompliance in digital photograph security and management is a significant problem within the plastic surgery community.
Referrals of Plastic Surgery Patients to Integrative Medicine Centers
Authors: Ruan Qing Zhao , Chen Austin D. , Tobias Adam M. , Fukudome Eugene Y. , Lin Samuel J. , Lee Bernard T. , Singhal Dhruv 
Published: January 2019

Background
Integrative medicine (IM) centers are becoming more established nationwide and provide an expansive range of therapeutic services. Given the high prevalence of IM usage among plastic surgery patients, we sought to define referrals rates to IM centers by plastic surgeons to investigate (1) the role of IM in the continuous care process of plastic surgery patients and (2) whether IM centers are being effectively utilized.

Methods
Institutions with plastic surgery residency programs were identified using the American Medical Association's Fellowship and Residency Electronic Interactive Database Access System in January 2017. Data on the presence of a named IM center, director/administrator contact information, and types of therapeutic services offered were extracted. The total number of IM services at these centers was summed and tabulated for preliminary analyses. A survey questionnaire was sent to the center to ascertain referral patterns in February 2017.

Results
Of 96 institutions with plastic and reconstructive surgery residency programs in North America, 49 (51%) provide IM services, and 24 (25%) have affiliated named IM centers of which we attained a survey response from 13 (54.5%). Of these centers, 10 (76.9%) evaluate more than 50 patients per week. Patient referrals to these centers were primarily from the department of medicine (73.8%) as opposed to surgery (13.1%) (P < 0.0001). An average of 0.77% of surgical referrals, or 0.077% of all referrals, arose from plastic and reconstructive surgery.

Conclusions
Plastic surgeons appear to infrequently refer patients to IM centers. Given the high prevalence of IM usage among our patient population, IM centers are an underutilized adjunct in the care of our patients. Further study into specific IM services that may benefit our patients would be helpful in increasing IM utilization in our field.
Peripapillary Vessel Density Measured by Optical Coherence Tomography Angiography in Idiopathic Intracranial Hypertension
Authors: Tüntaş Bilen Feyza , Atilla Huban 
Published: January 2019

Background:
Although alterations in the peripapillary retinal nerve fiber layer (RNFL) in patients with idiopathic intracranial hypertension (IIH) have been characterized using optical coherence tomography (OCT), there are little data regarding the peripapillary vasculature in this patient population. Our aim was to evaluate findings of OCT angiography (OCT-A) in the peripapillary region in addition to the RNFL measurements on OCT in patients with IIH.

Methods:
Thirty-eight eyes of 19 patients with IIH and 42 eyes of 21 healthy controls were enrolled in our study. Papilledema was graded according to the Frisen scale. Peripapillary RNFL and vessel density were evaluated with OCT and OCT-A, respectively.

Results:
RNFL thickness was found to be increased with OCT, but this was statistically significant only in the inferior location in IIH patients when compared with the control group. There was a significant decrease in mean peripapillary vessel density measured with OCT-A in IIH patients with papilledema when compared with the control group (P < 0.05).

Conclusions:
In patients with IIH, there was a decrease in peripapillary vessel density measured by OCT-A, and this decrease may be a consequence of the swelling of axons in the peripapillary retina due to papilledema. However, autoregulatory vascular mechanisms may also play a role in decreased peripapillary vessel density.
Dispersive and effective properties of two-dimensional periodic media
Authors: Godin Yuri A. , Vainberg Boris 
Published: January 2019

We consider transverse propagation of electromagnetic waves through a two-dimensional composite material containing a periodic rectangular array of circular cylinders. Propagation of waves is described by the Helmholtz equation with the continuity conditions for the tangential components of the electric and magnetic fields on the boundaries of the cylinders. We assume that the cell size is small compared with the wavelength, but large compared with the radius
a
of the inclusions. Explicit formulae are obtained for asymptotic expansion of the solution of the problem in terms of the dimensionless magnitude
q
of the wavevector and radius
a
. This leads to explicit formulae for the effective dielectric tensor and the dispersion relation with the rigorously justified error of order
O
((
q
2
+
a
2
)
5/2
).
BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactions
Authors: Chicco Davide , Bi Haixin Sarah , Reimand Jüri , Hoffman Michael M. 
Published: January 2019

AbstractTransforming data from genome-scale assays into knowledge of affected molecular functions and pathways is a key challenge in biomedical research. Using vocabularies of functional terms and databases annotating genes with these terms, pathway enrichment methods can identify terms enriched in a gene list. With data that can refer to intergenic regions, however, one must first connect the regions to the terms, which are usually annotated only to genes. To make these connections, existing pathway enrichment approaches apply unwarranted assumptions such as annotating non-coding regions with the terms from adjacent genes. We developed a computational method that instead links genomic regions to annotations using data on long-range chromatin interactions. Our method, Biological Enrichment of Hidden Sequence Targets (BEHST), finds Gene Ontology (GO) terms enriched in genomic regions more precisely and accurately than existing methods. We demonstrate BEHST’s ability to retrieve more pertinent and less ambiguous GO terms associated with results ofin vivomouse enhancer screens or enhancer RNA assays for multiple tissue types. BEHST will accelerate the discovery of affected pathways mediated through long-range interactions that explain non-coding hits in genome-wide association study (GWAS) or genome editing screens. BEHST is free software with a command-line interface for Linux or macOS and a web interface (http://behst.hoffmanlab.org/).
Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data
Authors: Lei Haoyun , Lyu Bochuan , Gertz E. Michael , Schäffer Alejandro A. , Shi Xulian , Wu Kui , Li Guibo , Xu Liqin , Hou Yong , Dean Michael , Schwartz Russell 
Published: January 2019

AbstractCharacterizing intratumor heterogeneity (ITH) is crucial to understanding cancer development, but it is hampered by limits of available data sources. Bulk DNA sequencing is the most common technology to assess ITH, but mixes many genetically distinct cells in each sample, which must then be computationally deconvolved. Single-cell sequencing (SCS) is a promising alternative, but its limitations — e.g., high noise, difficulty scaling to large populations, technical artifacts, and large data sets — have so far made it impractical for studying cohorts of sufficient size to identify statistically robust features of tumor evolution. We have developed strategies for deconvolution and tumor phylogenetics combining limited amounts of bulk and single-cell data to gain some advantages of single-cell resolution with much lower cost, with specific focus on deconvolving genomic copy number data. We developed a mixed membership model for clonal deconvolution via non-negative matrix factorization (NMF) balancing deconvolution quality with similarity to single-cell samples via an associated efficient coordinate descent algorithm. We then improve on that algorithm by integrating deconvolution with clonal phylogeny inference, using a mixed integer linear programming (MILP) model to incorporate a minimum evolution phylogenetic tree cost in the problem objective. We demonstrate the effectiveness of these methods on semi-simulated data of known ground truth, showing improved deconvolution accuracy relative to bulk data alone.
Quality of life and satisfaction of users of total tissue-supported and implant-supported prostheses in the municipality of Macapá, Brazil
Authors: Paraguassu Éber Coelho , de Cardenas Anneli Celis Mercedes 
Published: January 2019

AbstractDespite the high number of total edentulism cases in Brazil, no studies have yet examined the characteristics of people with edentulism in Amapá. Therefore, the objective of this study was to evaluate and compared the satisfaction and quality of life of edentulous users of total tissue-supported and total implant-supported prostheses in Macapá, Amapá, Brazil. Two hundred ninety-nine users of total tissue-supported prostheses and 48 users of total implant-supported prostheses were surveyed using two questionnaires: The Oral Health Impact Profile-14Br and a visual analog scale of satisfaction. The means and standard deviations were used to characterize the quantitative variables and absolute and relative frequencies were used to characterize the qualitative variables as well as certain quantitative variables. When evaluating users’ satisfaction according to the type of prosthesis, we found that users of implant-supported prostheses were 100% satisfied with both upper and lower prostheses. By contrast, among users of tissue-supported prostheses, 90% reported being satisfied with the upper prosthesis, while 56% demonstrated some dissatisfaction with the lower removable prosthesis. All users of implant-supported prostheses reported good quality of life; by contrast, only 5% of users of tissue-supported prostheses reported good quality of life, while 73% reported a reasonable quality of life and 22% a poor quality of life. To our knowledge, this is the first study on this topic in Amapá. The study results are clinically relevant for accurately determining the quality of life of these prosthesis users.
Mature sperm small RNA profile in the sparrow: implications for transgenerational effects of age on fitness
Authors: Matsushima Wayo , Brink Kristiana , Schroeder Julia , Miska Eric A. , Gapp Katharina 
Published: January 2019

AbstractMammalian sperm RNA has recently received a lot of interest due to its involvement in epigenetic germline inheritance. Studies of epigenetic germline inheritance have shown that environmental exposures can induce effects in the offspring without altering the DNA sequence of germ cells. Most mechanistic studies were conducted in laboratory rodents and C.elegans while observational studies confirm the phenotypic phenomenon in wild populations of humans and other species including birds. Prominently, paternal age in house sparrows affects offspring fitness, yet the mechanism is unknown. This study provides a first reference of house sparrow sperm small RNA as an attempt to uncover their role in the transmission of the effects of paternal age on the offspring. In this small scale pilot, we found no statistically significant differences between miRNA and tRNA fragments in aged and prime sparrow sperm. These results indicate a role of other epigenetic information carriers, such as distinct RNA classes, RNA modifications, DNA methylation and retained histones, and a clear necessity of future studies in wild populations.
Retapamulin-assisted ribosome profiling reveals the alternative bacterial proteome
Authors: Meydan Sezen , Marks James , Klepacki Dorota , Sharma Virag , Baranov Pavel V. , Firth Andrew E. , Margus Tōnu , Kefi Amira , Vázquez-Laslop Nora , Mankin Alexander S. 
Published: January 2019

SUMMARYThe use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes but, strikingly, it also revealed putative internal start sites in a number ofEscherichia coligenes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at an internal in-frame and out-of-frame start sites, can be functionally important and contribute to the ‘alternative’ bacterial proteome. The internal start sites my also play regulatory roles in gene expression.
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords
Authors: Gur Tamer 
Published: January 2019

AbstractDue to their nature, bioinformatics datasets are often closely related to each other. For this reason, search, mapping and visualization of these relations are often performed manual or programmatically via identifiers or special keywords such as gene symbols. Although various tools exist for these situations, the growing volume of bioinformatics datasets, emerging new software tools and approaches motivates new solutions. To provide a new tool for these current cases, I present the Biobtree bioinformatics tool. Biobtree effectively fetches and indexes identifiers and special keywords with their related identifiers from supported datasets, optionally with user pre-defined datasets and provides a web interface, web services and direct B+ tree data structure–based single uniform database output. Biobtree can handle billions of identifiers and runs via a single executable file with no installation and dependency required. It also aims to provide a relatively small codebase for easy maintenance, addition of new features and extension to larger datasets. Biobtree is available to download at https://www.github.com/tamerh/biobtree.
Dean flow assisted single cell and bead encapsulation for high performance single cell expression profiling
Authors: Li Luoquan , Wu Ping , Luo Zhaofeng , Wang Lei , Ding Weiping , Wu Tao , Chen Jinyu , He Jinlong , He Yi , Wang Heran , Chen Ying , Li Guibo , Li Zida , He Liqun 
Published: January 2019

AbstractSingle-cell RNA sequencing examines the transcriptome of individual cells and reveals the inter-cell transcription heterogeneity, playing a critical role in both scientific research and clinical applications. Recently, droplet microfluidics-based platform for expression profiling has been shown as a powerful tool to capture of the transcriptional information on single cell level. Despite the breakthrough this platform brought about, it required the simultaneous encapsulation of single cell and single barcoded bead, the incidence of which was very low. Suboptimal capturing efficiency limited the throughput of the Drop-seq platform. In this work, we leveraged the advance in inertial microfluidics-based cell sorting and designed a microfluidic chip for high efficiency cell-bead co-encapsulation, increasing the capturing rate by more than four folds. Specifically, we adopted spiral and serpentine channels and ordered cells/beads before the encapsulation region. We characterized the effect of cell concentration on the capturing rate and achieved a cell-bead co-capturing rate up to 3%. We tested this platform by co-encapsulating barcoded beads and human-mouse cell mixtures. The sequencing data distinguished the majority of human and mice expressions, with the doublet rate being as low as 5.8%, indicating that the simultaneous capturing of two or more cells in one droplet was minimal even when using high cell concentration. This chip design showed great potential in improving the efficiency for future single cell expression profiling.
TheDrosophilaERG channelseizureplays a role in the neuronal homeostatic stress response
Authors: Hill Alexis S. , Jain Poorva , Ben-Shahar Yehuda 
Published: January 2019

AbstractNeuronal physiology is particularly sensitive to acute stressors that affect excitability, many of which can trigger seizures and epilepsies. Although intrinsic neuronal homeostasis plays an important role in maintaining overall nervous system robustness and its resistance to stressors, the specific genetic and molecular mechanisms that underlie these processes are not well understood. Here we used a reverse genetic approach inDrosophilato test the hypothesis that specific voltage-gated ion channels contribute to neuronal homeostasis, robustness, and stress resistance. We found that the activity of the voltage-gated potassium channelseizure (sei), an ortholog of the mammalian ERG channel family, is essential for protecting flies from acute heat-induced seizures. Althoughseiis broadly expressed in the nervous system, our data indicate that its impact on the organismal robustness to acute environmental stress is primarily mediated via its action in excitatory neurons, the octopaminergic system, as well as glia. Furthermore, our studies suggest that human mutations in the human ERG channel (hERG), which have been primarily implicated in the cardiac Long QT Syndrome (LQTS), may also contribute to the high incidence of seizures in LQTS patients via a cardiovascular-independent neurogenic pathway.Author SummaryNeurons are extremely sensitive to diverse environmental stressors, including rapid changes in the ambient temperature. To buffer stress, all animals have evolved diverse physiological mechanisms to protect neuronal activity from acute and chronic stressors, and failures of these safeguards often lead to hyperexcitability, episodic seizures, and chronic epilepsy. Although seizures and related syndromes are common, their underlying molecular and genetic factors, and their interactions with environmental triggers, remain mostly unknown. Here, we show that in the fruit fly, mutations in the ERG voltage-gated potassium channelseizure (sei), an ortholog of the human hERG channel that has been previously implicated in the cardiac Long-QT syndrome, could also increase seizure susceptibility. We demonstrate that in addition to its cardiac expression, theseichannel is broadly expressed in the nervous system, specifically localized to axonal projections, and is specifically required in excitatory and modulatory neurons, as well as non-neuronal glia for maintaining organismal resistance to heat-induced seizures. Thus, our work suggests that the previously reported increase in seizure susceptibility in individuals with mutations in hERG are likely directly related to its neuronal action, independent of its cardiac function.
High-quality genome assembly and high-density genetic map of asparagus bean
Authors: Xia Qiuju , Zhang Ru , Ni Xuemei , Pan Lei , Wang Yangzi , Dong Xiao , Gao Yun , Zhang Zhe , Kui Ling , Li Yong , Wang Wen , Yang Huanming , Chen Chanyou , Miao Jianhua , Chen Wei , Dong Yang 
Published: January 2019

AbstractAsparagus bean (Vigna. unguiculata ssp. sesquipedialis), known for its very long and tender green pods, is an important vegetable crop broadly grown in the developing countries. Despite its agricultural and economic values, asparagus bean does not have a high-quality genome assembly for breeding novel agronomic traits. In this study, we reported a high-quality 632.8 Mb assembly of asparagus bean based on the whole genome shotgun sequencing strategy. We also generated a high-density linkage map for asparagus bean, which helped anchor 94.42% of the scaffolds into 11 pseudo-chromosomes. A total of 42,609 protein-coding genes and 3,579 non-protein-coding genes were predicted from the assembly. Taken together, these genomic resources of asparagus bean will facilitate the investigation of economically valuable traits in a variety of legume species, so that the cultivation of these plants would help combat the protein and energy malnutrition in the developing world.
The organization of leukotriene biosynthesis on the nuclear envelope revealed by single molecule localization microscopy and computational analyses
Authors: Schmider Angela B. , Vaught Melissa , Bauer Nicholas C. , Elliott Hunter L. , Godin Matthew D. , Ellis Giorgianna E. , Nigrovic Peter , Soberman Roy J. 
Published: January 2019

AbstractThe initial steps in the synthesis of leukotrienes are the translocation of 5-lipoxygenase (5-LO) to the nuclear envelope and its subsequent association with its scaffold protein 5-lipoxygenase-activating protein (FLAP). A major gap in our understanding of this process is the knowledge of how the organization of 5-LO and FLAP on the nuclear envelope regulates leukotriene synthesis. We combined single molecule localization microscopy with Clus-DoC cluster analysis, and also a novel unbiased cluster analysis to analyze changes in the relationships between 5-LO and FLAP in response to activation of RBL-2H3 cells to generate leukotriene C4. We identified the time-dependent reorganization of both 5-LO and FLAP into higher-order assemblies or clusters in response to cell activation via the IgE receptor. Clus-DoC analysis identified a subset of these clusters with a high degree of interaction between 5-LO and FLAP that specifically correlates with the time course of LTC4synthesis, strongly suggesting their role in the initiation of leukotriene biosynthesis.