bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concordance Between Rapid On-Site Evaluation and Final Cytologic Diagnosis in Patients Undergoing Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for Non-Small Cell Lung Cancer Staging
Authors: Caupena Cristina , Esteban Lluis , Jaen Angels , Barreiro Bienvenido , Albero Raquel , Perez-Ochoa Francisco , Pontes De Souza Patricia , Gibert Oriol , Ferrer Carme , Forcada Pilar , García Federico , Tarroch Xavier , Sanz-Santos José 
Published: August 2019

Abstract

Objectives
In patients with lung cancer undergoing mediastinal staging through endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA), decisions are based on rapid on-site evaluation (ROSE) findings. We aimed to analyze the concordance rate between ROSE diagnosis and final diagnosis.

Methods
A prospective study was carried out in patients undergoing EBUS-TBNA for lung cancer staging. Diagnosis concordance was defined as cases where lymph nodes (LNs) presented the same diagnosis in ROSE and final diagnosis. Determinants of concordance were analyzed.

Results
Sixty-four patients were included and 637 LNs sampled. ROSE diagnosis was concordant with final diagnosis in 612 (96.1%) LNs and nonconcordant in 25 (3.9%). Differences in the concordance rate were found between pathologists, ROSE diagnoses, presence of cell block, number of passes, and number of slides. The staging status was changed between ROSE and the final diagnosis in three (4.6%) patients.

Conclusions
ROSE diagnosis has a high concordance with the final diagnosis.
Genome-phenome explorer (GePhEx): a tool for the visualization and interpretation of phenotypic relationships supported by genetic evidence
Authors: Farré Xavier , Spataro Nino , Haziza Frederic , Rambla Jordi , Navarro Arcadi 
Published: August 2019

Abstract

Motivation
Association studies based on SNP arrays and Next Generation Sequencing technologies have enabled the discovery of thousands of genetic loci related to human diseases. Nevertheless, their biological interpretation is still elusive, and their medical applications limited. Recently, various tools have been developed to help bridging the gap between genomes and phenomes. To our knowledge, however none of these tools allows users to retrieve the phenotype-wide list of genetic variants that may be linked to a given disease or to visually explore the joint genetic architecture of different pathologies.

Results
We present the Genome-Phenome Explorer (GePhEx), a web-tool easing the visual exploration of phenotypic relationships supported by genetic evidences. GePhEx is primarily based on the thorough analysis of linkage disequilibrium between disease-associated variants and also considers relationships based on genes, pathways or drug-targets, leveraging on publicly available variant-disease associations to detect potential relationships between diseases. We demonstrate that GePhEx does retrieve well-known relationships as well as novel ones, and that, thus, it might help shedding light on the patho-physiological mechanisms underlying complex diseases. To this end, we investigate the potential relationship between schizophrenia and lung cancer, first detected using GePhEx and provide further evidence supporting a functional link between them.

Availability and implementation
GePhEx is available at: https://gephex.ega-archive.org/.

Supplementary information
Supplementary data are available at Bioinformatics online.
An Autoimmune Protocol Diet Improves Patient-Reported Quality of Life in Inflammatory Bowel Disease
Authors: Chandrasekaran Anita , Groven Shauna , Lewis James D , Levy Susan S , Diamant Caroline , Singh Emily , Konijeti Gauree Gupta 
Published: August 2019

Abstract

Background
Prior studies suggest dietary modification may improve clinical response or remission rates in patients with inflammatory bowel disease (IBD). Our aim was to examine whether an autoimmune protocol diet improves quality of life in patients with active Crohn disease (CD) and ulcerative colitis (UC).

Methods
We conducted an uncontrolled clinical trial of the autoimmune protocol diet in adult patients with active IBD (Harvey–Bradshaw Index ≥ 5 for CD or partial Mayo score ≥ 3 for UC, and erosions/ulcers on endoscopy and/or elevated fecal calprotectin). The dietary intervention consisted of a 6-week elimination phase, followed by a 5-week maintenance phase. Short Inflammatory Bowel Disease Questionnaire (SIBDQ) was completed at baseline, and weeks 3, 6, 9, and 11.

Results
The final cohort included 6 UC and 9 CD participants. Mean SIBDQ score improved significantly from baseline (46.5) to weeks 3 (54.0, P = 0.02), 6 (53.3, P = 0.02), 9 (62.0, P = 0.03), and 11 (60.5, P = 0.05). Among participants completing all 5 surveys, mean SIBDQ increased from 46.5 to 61.5 by week 11 (P = 0.03). By week 3, participants experienced significant improvements in bowel movement frequency (36%, P = 0.04), stress (28%, P = 0.01), and ability to perform leisure/sport activities (29%, P = 0.02). Effects were not significantly different between CD and UC participants.

Conclusions
Dietary modification can improve quality of life as early as week 3 in patients with active IBD. Larger randomized controlled trials are needed to examine dietary interventions in IBD.
Strategies and Tools to Embrace Prevention with Upstream Programs: A Novel Pilot Program for Enhancing Social and Emotional Protective Factors in Middle School Students
Authors: Knight M Amaris , Haboush-Deloye Amanda , Goldberg Pamela M , Grob Kelly 
Published: August 2019

AbstractSocial–emotional learning (SEL) programs can be considered upstream, or primary prevention, because they focus on providing students with the life skills necessary to navigate situations and relationships from which problem behaviors may arise to prevent a crisis situation. Strategies & Tools to Embrace Prevention with Upstream Programs (SEL@MS, formerly known as STEP UP) is a comprehensive SEL curriculum for middle school students aimed at promoting universal prevention strategies for healthy populations. SEL@MS enhances protective factors against negative behaviors by reinforcing multilevel approaches to strengthening community, interpersonal, and individual attributes with lesson plans that can be integrated into school curricula. This quasi-experimental pilot study was conducted over the course of two years with 59 middle school students assigned to either the intervention (n = 27) or control (n = 32) group. Analyses demonstrated significant improvements among students in the intervention group in self-regulation, responsibility, social competence, and empathy. Results of this study suggest that SEL@MS is a promising approach to enhance social and emotional protective factors that, when fostered over time, have the potential to improve overall mental health.
Acute coronary syndrome registry enrolment status: differences in patient characteristics and outcomes and implications for registry data use (ANZACS-QI 36)
Authors: Earle Nikki J , Kerr Andrew J , Legget Malcolm , Wu Billy P , Doughty Robert N , Poppe Katrina K 
Published: August 2019

Abstract

Aims
Clinical registry-derived data are widely used to represent patient populations. In New Zealand (NZ), a national registry—the All New Zealand Acute Coronary Syndrome Quality Improvement (ANZACS-QI) registry—aims to include all patients undergoing coronary angiography; other acute coronary syndrome (ACS) patients are also registered but without complete capture. This study compares national hospitalization data of all first-time ACS admissions in NZ with patients in the ANZACS-QI registry, to investigate the use of clinical registry-derived data in research and in assessing clinical care.

Methods and results
Patients admitted with first-time ACS in the NZ National Hospitalisation Dataset between 1 January 2015 and 31 December 2016 were included. Clinical characteristics and time to 12-month clinical outcomes were compared between patients captured and not-captured in the registry. A total of 16 569 patients were admitted with first-time ACS, median age 69 years, 61% male; 60% (n = 9918) were enrolled in ANZACS-QI. Registry-captured patients were younger, more often male, and with a lower comorbidity burden than non-captured patients. Overall, 16% patients died within 12 months, 15% experienced a non-fatal cardiovascular (CV) readmission, and 28% either died or were readmitted. Patients not captured in the registry were more than twice as likely to have experienced death or a non-fatal CV readmission within 12 months as captured patients.

Conclusions
First-time ACS patients captured in the ANZACS-QI registry had very different clinical characteristics and outcomes than those not captured. Cardiovascular registry-derived data are dependent on registry design and may not be representative of the wider patient population; this must be considered when using registry-derived data.
Scandcleft randomized trials of primary surgery for unilateral cleft lip and palate. Dental arch relationships in 8 year-olds
Authors: Heliövaara Arja , Skaare Pål , Küseler Annelise , Shaw William , Mølsted Kirsten , Karsten Agneta , Marcusson Agneta , Brinck Eli , Rizell Sara , Sæle Paul , Najar Chalien Midia , Bellardie Haydn , Mooney Jeanette , Eyres Phil , Semb Gunvor 
Published: August 2019

Summary

Background and trial design
The Scandcleft intercentre study evaluates the outcomes of four surgical protocols for treatment of children with unilateral cleft lip and palate (UCLP). Originally 10 cleft centres in Denmark, Finland, Norway, Sweden, and the UK participated in a set of three randomized trials of primary surgery. Three groups of centres (Trials 1, 2, and 3) tested their traditional local surgical protocols (Arms B, C, and D) against a common protocol (Arm A).

Objectives
To evaluate dental arch relationships at age 8 years after four different protocols of primary surgery for UCLP. These results are secondary outcomes of the overall trial.

Methods
Study models of 411 children (270 boys, 141 girls) with non-syndromic UCLP at a mean age of 8.1 (range 7.0–10.0) years were available. Dental arch relationships were analysed using the GOSLON Yardstick by a blinded panel of 11 orthodontists. To assess reliability, Kappa statistics were calculated. The trials were tested statistically with t-tests.

Results
Comparisons within each trial showed no statistically significant differences in the mean 8-year index scores or their distributions between the common protocol and the local team protocol. The mean index scores were Trial 1: Arm A 3.03, Arm B 2.82, Trial 2: Arm A 2.78, Arm C 2.64, and Trial 3: Arm A 3.06, Arm D 3.08. Comparisons between the trials detected a significantly (P < 0.005) better mean index score Trial 2 Arm C than in Trial 3 Arm D. The intra- and inter-rater reliabilities were acceptable.

Conclusion
The results of these three trials do not provide evidence that one surgical protocol is better than the others.

Trial registration
ISRCTN29932826
Determinants of left atrium thrombi in scheduled cardioversion: an ENSURE-AF study analysis
Authors: Merino Jose L , Lip Gregory Y H , Heidbuchel Hein , Cohen Aron-Ariel , De Caterina Raffaele , de Groot Joris R , Ezekowitz Michael D , Le Heuzey Jean-Yves , Themistoclakis Sakis , Jin James , Melino Michael , Winters Shannon M , Merkely Béla , Goette Andreas 
Published: August 2019

Abstract

Aims
ENSURE-AF (NCT 02072434) was the largest prospective randomized clinical trial of anticoagulation for cardioversion in atrial fibrillation (AF), which also provides the largest prospective dataset for transoesophageal echocardiography (TOE) prior to cardioversion. This ancillary analysis investigated determinants of TOE-detected left atrium thrombi (LAT) in patients scheduled for electrical cardioversion (ECV).

Methods and results
The ENSURE-AF multicentre PROBE evaluation trial compared edoxaban 60 mg once daily (QD) with enoxaparin/warfarin in 2199 subjects undergoing ECV of non-valvular AF. Patients were stratified by the use of TOE, anticoagulant experience, and selected edoxaban dose. Electrical cardioversion was cancelled or deferred when TOEdetected LAT. In total, 1183 subjects were stratified to the TOE arm and LAT was reported in 91 (8.2%). In univariate analysis, age ≥75 years (26.4% vs. 16.9%, P = 0.0308), lower weight (86.5 ± 15.0 vs. 90.7 ± 18.0 kg, P = 0.0309), lower creatinine clearance (80.1 ± 30.6 vs. 93.2 ± 33.9 mL/min, P = 0.0007), heart failure (59.3% vs. 43.0%, P = 0.0029), and diuretic treatment (53.9% vs. 40.1%, P = 0.0141) were more prevalent in the LAT group. Non-significant trends were seen for higher mean CHA2DS2-VASc score (3.0 ± 1.41 vs. 2.7 ± 1.48, P = 0.0571) and more prevalent anticoagulation use prior to enrolment (60.4% vs. 50.3%, P = 0.0795) in the LAT group. In logistic regression analysis, age (P = 0.0202) and heart failure (P = 0.0064) were independently associated with LAT.

Conclusion
Elective ECV is commonly cancelled or deferred due to TOE-detected LAT in patients with non-valvular AF. Age ≥75 years and heart failure were associated with the presence of LAT.
Viruses of fungi and oomycetes in the soil environment
Authors: Sutela Suvi , Poimala Anna , Vainio Eeva J 
Published: August 2019

ABSTRACTSoils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
Aerobic catabolism of sterols by microorganisms: key enzymes that open the 3-ketosteroid nucleus
Authors: Kreit Joseph 
Published: August 2019

ABSTRACT
Aerobic degradation of the sterol tetracyclic nucleus by microorganisms comprises the catabolism of A/B-rings, followed by that of C/D-rings. B-ring rupture at the C9,10-position is a key step involving 3-ketosteroid Δ1-dehydrogenase (KstD) and 3-ketosteroid 9α-hydroxylase (KstH). Their activities lead to the aromatization of C4,5-en-containing A-ring causing the rupture of B-ring. C4,5α-hydrogenated 3-ketosteroid could be produced by the growing microorganism containing a 5α-reductase. In this case, the microorganism synthesizes, in addition to KstD and KstH, a 3-ketosteroid Δ4-(5α)-dehydrogenase (Kst4D) in order to produce the A-ring aromatization, and consequently B-ring rupture. KstD and Kst4D are FAD-dependent oxidoreductases. KstH is composed of a reductase and a monooxygenase. This last component is the catalytic unit; it contains a Rieske-[2Fe-2S] center with a non-haem mononuclear iron in the active site. Published data regarding these enzymes are reviewed.
Non-intubated subxiphoid uniportal video-assisted thoracoscopic thymectomy
Authors: Liu Zhengcheng , Yang Rusong , Sun Yang 
Published: August 2019

Abstract
This report describes a non-intubated, subxiphoid, uniportal approach to video-assisted thoracoscopic thymectomy. A laryngeal mask was used as a safety precaution for ventilatory management, and thymectomy was accomplished through a single transverse incision below the lower edge of the xiphoid. Patients were uneventfully discharged with fast recovery. This novel surgical approach may merge the potential benefits of a subxiphoid incision for treatment of anterior mediastinum lesion and adoption of a non-intubated anaesthesia protocol.
Barriers to Deprescribing
Authors: Gupta Swapnil , Miller Rebecca , Cahill John D. 
Published: August 2019

Abstract
This chapter identifies the possible barriers to deprescribing, and presents suggestions for strategies to overcome them. Although deprescribing has the potential to streamline medication regimens, minimize side effects, cut costs, improve patient adherence, and strengthen the relationship between the patient and the prescribing professional, barriers may originate from the patient, physician, and/or the institution, both local and the larger medical institution. Barriers related to prescriber-related factors such as the physician’s illusion and fear of litigation, are discussed. Potential patient- and environment-related barriers are also discussed, including sociocultural factors which may emerge in the process of initiating a course of deprescribing. Included in this chapter is a discussion of the possibility of relapse, colloquially defined, and the patient’s and provider’s fears for rehospitalization. Possible strategies for overcoming each of these barriers are discussed.
The Process of Deprescribing
Authors: Gupta Swapnil , Miller Rebecca , Cahill John D. 
Published: August 2019

Abstract
Deprescribing of psychotropic medications introduces additional complexities related to the specific context of psychiatric disorders and their cultural meaning. This chapter expands on the process of deprescribing as it relates specifically to psychiatry, taking the five essential steps of deprescribing in general medicine and elaborating on them for use in psychiatry. These include a detailed decision-making process, psychoeducation of both the patient and friends or family, and close monitoring and adaptation during medication reduction. Given the current absence of guidelines in this area, documentation is a key element of the process and is discussed in this chapter. Included are suggested templates to support accurate documentation, including the decision-making process, the patient’s response to medication changes, medication lists with their indications, and the appearance and management of withdrawal symptoms and/or relapse.
Deprescribing Antipsychotic Medications
Authors: Gupta Swapnil , Miller Rebecca , Cahill John D. 
Published: August 2019

Abstract
This chapter discusses some of reasons for considering a deprescribing intervention with neuroleptic medications, including clear instances such as irrational antipsychotic polypharmacy and off-label use, as well as other situations driven by stakeholder pressures or medical comorbidity. The indefinite prescription of antipsychotic medications for psychotic disorders such as schizophrenia is commonly considered a recommended practice, although some uncertainty remains. The confidence of treatment recommendations also hinges on the accuracy of diagnoses—syndromes and classifications which typically evolve over time. This chapter describes a collaborative process of decision-making about the long-term use of antipsychotic medications as many patients wishing to attempt to decrease or discontinue these medications may do so without support of the prescriber, risking harm. The ability of current data to identify which patients may need long-term medication management versus those who may not is lacking. Considering the potential serious neurological and metabolic side effects of these medications, a patient’s preferences versus risks must be carefully weighed. Nonpharmacological interventions that may support the reduction of antipsychotic medications (but should not yet be presented as validated alternatives, alone) include psychoeducation, strategies for early identification and management of relapse, cognitive behavioral therapy for psychosis, and open dialogue are reviewed. The process is illustrated by case examples at the end of the chapter.
A multiwavelength study of a massive, active galaxy at z ∼ 2: coupling the kinematics of the ionized and molecular gas
Authors: Loiacono Federica , Talia Margherita , Fraternali Filippo , Cimatti Andrea , Di Teodoro Enrico M , Caminha Gabriel B 
Published: August 2019

ABSTRACTWe report a multiwavelength study of the massive ($M_{\star } \gtrsim 10^{11} \rm {M}_{\odot }$), z ∼ 2 star-forming galaxy GMASS 0953, which hosts an obscured AGN. We combined near-infrared observations of the GNIRS, SINFONI and KMOS spectrographs to study the kinematics of the [O  iii] λ5007 and H α emission lines. Our analysis shows that GMASS 0953 may host an ionized disc extending up to 13 kpc, which rotates at a velocity of $V_{\rm {ion}} = 203^{+17}_{-20}$  km s−1 at the outermost radius. Evidence of rotation on a smaller scale (R ∼ 1 kpc) arises from the CO(J = 6–5) line. The central velocity $V_{\rm {CO}} = 320^{+ 92}_{-53}$  km s−1 traced by the molecular gas is higher than Vion, suggesting that the galaxy harbours a multiphase disc with a rotation curve that peaks in the very central regions. The galaxy appears well located on the z = 0 baryonic Tully–Fisher relation. We also discuss the possibility that the [O  iii] λ5007 and H α velocity gradients are due to a galactic-scale wind. Besides, we found evidence of an AGN-driven outflow traced by a broad blueshifted wing affecting the [O  iii] λ5007 line, which presents a velocity offset Δv = −535 ± 152  km s−1 from the systemic velocity. Because of the short depletion time-scale (τdep ∼ 108 yr) due to gas ejection and gas consumption by star formation activity, GMASS 0953 may likely evolve into a passive galaxy. However, the role of the AGN in depleting the gas reservoir of the galaxy is quite unclear because of the uncertainties affecting the outflow rate.
Are the planetary orbital effects of the solar dark matter wake detectable?
Authors: Iorio Lorenzo 
Published: August 2019

ABSTRACT
Recently, there has been some discussion in the literature about the effects of the anisotropy in the spatial density of dark matter in the Solar neighbourhood arising from the motion of the Sun through the Galactic halo. In particular, questions have been asked about the orbital motions of the Solar system’s planets and whether these motions can be effectively constrained by the radiotechnical observations collected by Cassini. I show that the semilatus rectum p, the eccentricity e, the inclination I, the longitude of the ascending node Ω, the longitude of perihelion ϖ, and the mean anomaly at epoch η of a test particle of a restricted two-body system affected by the gravity of a dark matter wake undergo secular rates of change. In the case of Saturn, they are completely negligible, being at the order of ≃0.1 millimetres per century and ≃0.05–2 nanoarcseconds per century: the current (formal) accuracy level in constraining any anomalous orbital precessions is of the order of ≃0.002–2 milliarcseconds per century for Saturn. I also numerically simulate the Earth–Saturn range signature Δρ(t) arising from the dark matter wake over the same time span (2004–2017) as covered by the Cassini data record. I find that it is as low as ${\simeq}0.1{-}0.2\, \mathrm{m}$, while the existing range residuals, computed by astronomers without modelling any dark matter wake effect, are of the order of ${\simeq}$ 30 m. The local dark matter density ϱDM would need to be larger than the currently accepted value of $\varrho _\mathrm{DM}=0.018\, \mathrm{M}_\odot \, \mathrm{pc}^{-3}$ by a factor of 2.5 × 106 in order to induce a geocentric Kronian range signature large enough to make it discernible in the present-day residuals.