bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of X-rays on CO emission from high-z galaxies
Authors: Vallini L , Tielens A G G M , Pallottini A , Gallerani S , Gruppioni C , Carniani S , Pozzi F , Talia M 
Published: October 2019

ABSTRACT
We study the impact of active galactic nuclei (AGNs) on the CO spectral line energy distribution (SLED) of high-z galaxies. In particular, we want to assess if the CO SLED can be used as a probe of AGN activity. To this purpose, we develop a semi-analytical model that takes into account the radiative transfer and the clumpy structure of giant molecular clouds where the CO lines are excited, their distribution in the galaxy disc, and the torus obscuration of the AGN radiation. We study the joint effect on the CO SLED excitation of (i) the X-ray luminosity from the AGNs (LX), (ii) the size of the molecular disc, (iii) the inclination angle (Ω) of the torus with respect to the molecular disc, and (iv) the Giant Molecular Cloud (GMC) mean density. We also discuss the possibility of an enhanced cosmic ray ionization rate (CRIR). We find that the X-ray-dominated region (XDR) generated by the AGNs in every case enhances the CO SLED for J > 5, with increasing excitation of high-J CO lines for increasing X-ray luminosity. Because high-z galaxies are compact, the XDR typically encloses the whole disc, thus its effect can be more important with respect to lower redshift objects. The impact of the XDR can be disentangled from an enhanced CRIR either if $L_\mathrm{ X}\,\gt\, 10^{44} \rm \, erg\, s^{-1}$, or if Ω ≥ 60°. We finally provide predictions on the CO(7–6)/[C ii] and CO(17–16)/[C ii] ratios as a function of LX, which can be relevant for ALMA follow-up of galaxies and quasars previously detected in [C ii].
ProCarbDB: a database of carbohydrate-binding proteins
Authors: Copoiu Liviu , Torres Pedro H M , Ascher David B , Blundell Tom L , Malhotra Sony 
Published: October 2019

Abstract
Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein–carbohydrate interfaces. In order to better understand protein–carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 3D X-ray crystal structures of protein–carbohydrate complexes. In ProCarbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein–carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.
Transcriptome visualization and data availability at the Saccharomyces Genome Database
Authors: Ng Patrick C , Wong Edith D , MacPherson Kevin A , Aleksander Suzi , Argasinska Joanna , Dunn Barbara , Nash Robert S , Skrzypek Marek S , Gondwe Felix , Jha Sagar , Karra Kalpana , Weng Shuai , Miyasato Stuart , Simison Matt , Engel Stacia R , Cherry J Michael 
Published: October 2019

Abstract
The Saccharomyces Genome Database (SGD; www.yeastgenome.org) maintains the official annotation of all genes in the Saccharomyces cerevisiae reference genome and aims to elucidate the function of these genes and their products by integrating manually curated experimental data. Technological advances have allowed researchers to profile RNA expression and identify transcripts at high resolution. These data can be configured in web-based genome browser applications for display to the general public. Accordingly, SGD has incorporated published transcript isoform data in our instance of JBrowse, a genome visualization platform. This resource will help clarify S. cerevisiae biological processes by furthering studies of transcriptional regulation, untranslated regions, genome engineering, and expression quantification in S. cerevisiae.
Controlling aggregation of cholesterol-modified DNA nanostructures
Authors: Ohmann Alexander , Göpfrich Kerstin , Joshi Himanshu , Thompson Rebecca F , Sobota Diana , Ranson Neil A , Aksimentiev Aleksei , Keyser Ulrich F 
Published: October 2019

AbstractDNA nanotechnology allows for the design of programmable DNA-built nanodevices which controllably interact with biological membranes and even mimic the function of natural membrane proteins. Hydrophobic modifications, covalently linked to the DNA, are essential for targeted interfacing of DNA nanostructures with lipid membranes. However, these hydrophobic tags typically induce undesired aggregation eliminating structural control, the primary advantage of DNA nanotechnology. Here, we study the aggregation of cholesterol-modified DNA nanostructures using a combined approach of non-denaturing polyacrylamide gel electrophoresis, dynamic light scattering, confocal microscopy and atomistic molecular dynamics simulations. We show that the aggregation of cholesterol-tagged ssDNA is sequence-dependent, while for assembled DNA constructs, the number and position of the cholesterol tags are the dominating factors. Molecular dynamics simulations of cholesterol-modified ssDNA reveal that the nucleotides wrap around the hydrophobic moiety, shielding it from the environment. Utilizing this behavior, we demonstrate experimentally that the aggregation of cholesterol-modified DNA nanostructures can be controlled by the length of ssDNA overhangs positioned adjacent to the cholesterol. Our easy-to-implement method for tuning cholesterol-mediated aggregation allows for increased control and a closer structure–function relationship of membrane-interfacing DNA constructs — a fundamental prerequisite for employing DNA nanodevices in research and biomedicine.
PhenoModifier: a genetic modifier database for elucidating the genetic basis of human phenotypic variation
Authors: Sun Hong , Guo Yangfan , Lan Xiaoping , Jia Jia , Cai Xiaoshu , Zhang Guoqing , Xie Jingjing , Liang Qian , Li Yixue , Yu Guangjun 
Published: October 2019

Abstract
From clinical observations to large-scale sequencing studies, the phenotypic impact of genetic modifiers is evident. To better understand the full spectrum of the genetic contribution to human disease, concerted efforts are needed to construct a useful modifier resource for interpreting the information from sequencing data. Here, we present the PhenoModifier (https://www.biosino.org/PhenoModifier), a manually curated database that provides a comprehensive overview of human genetic modifiers. By manually curating over ten thousand published articles, 3078 records of modifier information were entered into the current version of PhenoModifier, related to 288 different disorders, 2126 genetic modifier variants and 843 distinct modifier genes. To help users probe further into the mechanism of their interested modifier genes, we extended the yeast genetic interaction data and yeast quantitative trait loci to the human and we also integrated GWAS data into the PhenoModifier to assist users in evaluating all possible phenotypes associated with a modifier allele. As the first comprehensive resource of human genetic modifiers, PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation. The portal has a broad scientific and clinical scope, spanning activities relevant to variant interpretation for research purposes as well as clinical decision making.
CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database
Authors: Alcock Brian P , Raphenya Amogelang R , Lau Tammy T Y , Tsang Kara K , Bouchard Mégane , Edalatmand Arman , Huynh William , Nguyen Anna-Lisa V , Cheng Annie A , Liu Sihan , Min Sally Y , Miroshnichenko Anatoly , Tran Hiu-Ki , Werfalli Rafik E , Nasir Jalees A , Oloni Martins , Speicher David J , Florescu Alexandra , Singh Bhavya , Faltyn Mateusz , Hernandez-Koutoucheva Anastasia , Sharma Arjun N , Bordeleau Emily , Pawlowski Andrew C , Zubyk Haley L , Dooley Damion , Griffiths Emma , Maguire Finlay , Winsor Geoff L , Beiko Robert G , Brinkman Fiona S L , Hsiao William W L , Domselaar Gary V , McArthur Andrew G 
Published: October 2019

Abstract
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
Individual Responsibilities in Partial Compliance: Skilled Health Worker Emigration from Under-Served Regions
Authors: Yuksekdag Yusuf 
Published: October 2019

AbstractOne of the ways to address the effects of skilled worker emigration is to restrict the movement of skilled workers. However, even if skilled workers have responsibilities to assist their compatriots, what if other parties, such as affluent countries or source country governments, do not fulfil their fair share of responsibilities? This discussion raises an interesting problem about how to think of individual responsibilities under partial compliance where other agents (including affluent countries, developing states, or other individuals) do not fulfil their fair share of responsibilities. What is fair to expect from them? Taking health worker emigration as a case in point, I discuss whether the individual health workers’ fair share of responsibilities to address basic health care needs decreases or increases when the other parties do not fulfil their share. First, I review the responsibilities that different stakeholders may hold. Second, I argue that there are strong reasons against increasing or decreasing health workers’ fair share of responsibilities in a situation of partial compliance. I also argue that it is unfair for non-complier states to enforce health workers to fulfil their fair share or take up the slack.
Repeat Cooled Radiofrequency Ablation Is Beneficial for Chronic Posterior Sacroiliac Joint Pain
Authors: Kurklinsky Svetlana , Boone M Katherine , Candler Shawn A , Schwab Adam , Ghazi Salim 
Published: October 2019

AbstractObjectiveThis study aimed to investigate the effectiveness of repeat cooled radiofrequency ablation (CRFA) in chronic posterior sacroiliac joint (SIJ) pain.DesignThe electronic records of 41 adult patients who had successful CRFA were reviewed for duration of pain relief and utilization of medical care for six months before and after each CRFA procedure.SettingAcademic, tertiary medical center.PatientsForty-one adult patients who had CRFA for chronic posterior SIJ pain.ResultsA repeat ipsilateral CRFA ablation procedure provided 9.0 months of pain relief compared with 5.5 months after the first CRFA procedure (P = 0.0378). The total number of medical treatments decreased after the first CRFA procedure (from 343 to 201). The medical cost decreased by 51.0% after the first CRFA and by 70.4% after the repeated CRFA procedure.ConclusionsUsing repeated nonsurgical, minimally invasive approach, CRFA relieves chronic posterior SIJ pain and reduces patients’ utilization of medical services.
Justifying Alexander Pope’s Unjustifiable Rhymes
Authors: Tomalin Marcus 
Published: October 2019

Abstract
Drawing upon recent research into historical phonology, this article re-examines the prosodic structure of Alexander Pope’s verse. The underlying purpose is to demonstrate that the widespread tendency to hear Pope’s poetry with a modern ear can lead to literary-critical interpretations that are alarmingly brittle. By contrast, a willingness to undertake some kind of pronunciation-related auditory archaeology can reveal phonological patterns that would otherwise remain hidden—and an awareness of these patterns can transform our appreciation of his intricate couplet art. A task of this kind necessarily involves a careful reading of prominent contemporaneous dictionaries, grammar textbooks, and orthoepic works, as well as recent revisionist studies of eighteenth-century English phonology. As an initial case study, the central discussion in this article will focus predominantly on two words: &lt;war&gt; and &lt;gods&gt;. Jonathan Swift accused Pope of deploying too many ‘unjustifiable rhymes’ for these words in his Iliad, and seeking to understand this critique leads to an exploration of how Pope structured his poetry using subtle phonological correspondences which frequently occur at locations other than the tenth syllable in his couplets.
What every PA needs to know about anorectal pain
Authors: Hubbard Yasmine , Rizzolo Denise 
Published: October 2019

ABSTRACT
Anorectal pain is common but often misdiagnosed, and patients may suffer in silence if they are too uncomfortable discussing the topic with their healthcare provider. This article reviews rectal anatomy and the signs and symptoms of several common anorectal conditions and how to manage them.
Recognizing abdominal wall endometriosis
Authors: Huber Marisa , Grosel John , Showen Chad 
Published: October 2019

ABSTRACT
Abdominal wall endometriosis is ectopic endometrial tissue in the abdominal wall. Consider this condition in any woman presenting with chronic abdominal pain and a surgical history significant for exposure of the abdominal cavity to the endometrial canal. The diagnosis can be suspected with accurate history taking and a thorough physical examination. In patients with suspected abdominal wall endometriosis, MRI is the imaging study of choice and complete surgical resection is the treatment of choice.
Can propranolol prevent progression of melanoma?
Authors: Kao Jason , Luu Brent 
Published: October 2019

ABSTRACT
The worldwide incidence of melanoma has risen rapidly in the past 50 years and is a considerable public health burden in the United States, with significant financial implications. Studies have demonstrated the potential anticarcinogenic effects of antihypertensive agents, specifically beta-blockers, in patients with prostate cancer, breast cancer, and lately cutaneous malignant melanoma. This article explores the empirical clinical evidence of propranolol's anticarcinogenic effects on melanoma and the chemoprotective mechanisms of beta-blockers and other agents that have been used to modify melanoma progression.
STEMI in a patient with mirror-image dextrocardia
Authors: Harris K. Yvonne , Umar Mohamad 
Published: October 2019

ABSTRACT
ST-segment elevation myocardial infarction (STEMI) is a potentially life-threatening diagnosis that cannot be missed on ECG interpretation. However, ECG interpretation may not be straightforward in patients with dextrocardia. This case report discusses the presentation of a patient with situs inversus with dextrocardia who was found to have an acute inferior MI, and how this anatomical change results in an atypical ECG and clinical presentation.
Clinical Validation of a Dried Blood Spot Assay for 8 Antihypertensive Drugs and 4 Active Metabolites
Authors: Peeters Laura E. J. , Feyz Lida , Hameli Edon , Zwart Tom , Bahmany Soma , Daemen Joost , van Gelder Teun , Versmissen Jorie , Koch Birgit C. P. 
Published: October 2019

Background:Drug nonadherence is one of the major challenges faced by resistant hypertension patients, and identification of this problem is needed for optimizing pharmacotherapy. Dried blood spot (DBS) sampling is a minimally invasive method designed to detect and determine the degree of nonadherence. In this study, a DBS method for qualifying 8 antihypertensive drugs (AHDs) and 4 active metabolites was developed and validated using ultra high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS).Method:The DBS assay was validated analytically and clinically, in accordance with FDA requirements. Analytical validation was accomplished using UHPLC-MS/MS. For clinical validation, paired peak and trough levels of DBS and plasma samples were simultaneously collected and comparatively analyzed using Deming regression and Bland–Altman analyses. All concentrations below the set lower limit were excluded. Deming regression analysis was used to predict comparison bias between the collected plasma and DBS samples, with DBS concentrations corrected accordingly.Results:The UHPLC-MS/MS method for simultaneously measuring 8 AHDs and their metabolites in DBS, was successfully validated. With Deming regression no bias was observed in N = 1; constant bias was seen in N = 6 and proportional bias in N = 11 of the AHDs and metabolites. After correction for bias, only one metabolite (canrenone) met the 20% acceptance limit for quantification, after Bland–Altman analyses. In addition, amlodipine, valsartan, and [enalaprilate] met the 25% acceptance limit.Conclusions:A novel DBS assay for simultaneously qualifying and quantifying 8 AHDs and their metabolites, has been successfully developed and validated. The DBS assay is therefore a suitable method to detect drug nonadherence. However, with the exception of canrenone, the interchangeable use of plasma and DBS sampling to interpret drug quantities should be avoided.
Nontraumatic Orbital Subperiosteal Hematoma in a Case of Bernard-Soulier Syndrome With Bilateral Pansinusitis
Authors: Ali Abdullah A. , Alsafran Hend E. , Alomairah Hamad A. , Almazdi Abdulaziz A. , Behbehani, ABopth Raed S. 
Published: October 2019

Orbital subperiosteal hemorrhages are usually due to trauma. However, nontraumatic subperiosteal hemorrhages have also been rarely reported. Here, the authors present a 13-year-old boy with Bernard-Soulier syndrome who presented with right orbital subperiosteal hemorrhage causing optic neuropathy which was surgically drained with full visual recovery.
The authors describe a case of rare coagulopathy (Bernard-Soulier syndrome) and pansinusitis presenting with nontraumatic subperiosteal hemorrhage.
Impression Methods for Custom Foot Orthoses—Comparing Semi–Weight-Bearing Foam and Non–Weight-Bearing Plaster Using a Kinematic Measurement of the Medial Longitudinal Arch
Authors: Balsdon Megan E.R. , Dombroski Colin E.A. , Bushey Kristen M. , Jenkyn Thomas R. 
Published: October 2019

ABSTRACT

INTRODUCTION
One of the goals for custom foot orthoses (CFOs) is to provide relief for pressure-sensitive areas and provide support to the joints of the foot for an optimal weight-bearing position. The most common CFO impression methods used by practitioners include plaster bandage, foam box, fiberglass, and laser-optical scanning, and are often compared by measuring foot molds created from those methods. The objective of this study is to compare the biomechanical effects of CFOs made from two common casting methods using skeletal kinematics.

MATERIALS AND METHODS
The medial longitudinal arch (MLA) angle was measured for 13 participants of different foot types: five pes planus, four pes cavus, and four normally arched. Four conditions were compared: barefoot, shod, and CFOs made from both semi-weight-bearing foam and non-weight-bearing plaster casting methods. The MLA angle was measured from three-dimensional bone models using biplane fluoroscopy images during midstance.

RESULTS
Foam (P = 0.02) and plaster (P = 0.01) cast foot orthoses were significantly different from the barefoot condition, and the shod condition was significantly different from both foam (P = 0.004) and plaster (P = 0.014) cast orthoses. No statistically significant differences were found when comparing the two casting methods: non-weight-bearing plaster and semi-weight-bearing foam (P = 0.170).

CONCLUSIONS
Clinicians favoring one particular style of casting can feel confident, for the patient set described, that either choice will produce similar biomechanical outcomes with respect to foot kinematics.
Bracing to Treat Dropped Head Syndrome in Cancer Patients: A Retrospective Review
Authors: Knowlton Sasha E. , Zheng Mimi , Diamond Yoni , Yakaboski Michelle , Ruppert Lisa M. 
Published: October 2019

ABSTRACT

Introduction
The objective of this study is to describe the use of postural bracing to treat dropped head syndrome (DHS) in cancer patients. The study design is a retrospective review over a 3-year period of cancer patients who presented to a cancer physiatry outpatient practice for treatment of DHS. Patients were individuals with a history of head and neck cancer, Hodgkin lymphoma, or other cancer with a diagnosis of DHS.

Materials and Methods
The treatment intervention was postural bracing with either a figure-of-eight orthosis with or without a lumbosacral orthosis or a thoracolumbosacral orthosis.

Results
Subjective, patient-reported improvements in pain, posture, and neck or back strength in addition to objective improvements in physical examination were made. Out of 41 patients initially evaluated for DHS who followed up in brace clinic, 61% reported a positive response to bracing with 17.1% reporting improvement in neck or back strength, 17.1% reporting improvement in pain, and 39% reporting improvement in posture.

Discussion
In this study, we present a successful alternative to treat DHS through the use of active bracing. The technique of active bracing in this population theoretically strengthens the weak muscles in head drop and improves head position. Maintenance of these achievements, although not directly studied in this project, must be performed through a regular home exercise and bracing program as patients likely have a tendency to weaken again given prior oncologic treatments.

Conclusions
Active postural bracing using a combination of a figure-of-eight brace with or without a lumbosacral orthosis or a thoracolumbosacral orthosis in conjunction with physical therapy can help improve the posture, pain, and neck and back strength of cancer patients with DHS.