bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALK and ROS1 rearrangement tested by ARMS‐PCR in non‐small‐cell lung cancer patients via cytology specimens: The experience of Shanghai Pulmonary Hospital
Authors: Cao Ziyang , Wu Wei , Zhang Wei , Li Zhixin , Gao Caixia , Huang Yan , Zhang Liping 
Published: March 2020

AbstractBackgroundCytology specimens are the main samples used for the diagnosis of advanced lung cancer. The objective of our study was to assess anaplastic lymphoma kinase (ALK) and c‐ros oncogene 1 receptor tyrosine kinase (ROS1) genes by an amplification refractory mutation system (ARMS)‐polymerase chain reaction (PCR) using cytology specimens and to then evaluate the mutation frequency of ALK and ROS1 in non‐small‐cell lung cancer (NSCLC) patients.MethodsA large cohort that consisted of 8180 NSCLC patients who were genetically tested using cytology samples or formalin‐fixed and paraffin‐embedded (FFPE) samples (tumor tissue or biopsy) from January 2015 to December 2018 were screened. The gene rearrangement ratio and clinical characteristics of the two sample groups were analyzed by SPSS software.ResultsIn our hospital, cytology specimens are the main resource used for gene testing in NSCLC. In most cases, an abundant quantity of nucleic acid was extracted from the residual liquid‐based cell pellet for testing the ALK and ROS1 genes. In certain cases, when the residual cell pellet was insufficient for the gene testing, the cell block and liquid‐based cell smear served as alternative options. In addition, we retrospectively analyzed our previous data, and the mutation ratio of the ALK/ROS1 rearrangements obtained by using the cytology samples (4.98%/1.80%) and the FFPE samples (6.06%/1.62%) was almost the same (P‐value = .09/.634).ConclusionsThis study demonstrated that AMRS‐PCR method can effectively identify ALK and ROS1 gene rearrangements and cytology specimens might be an excellent source for routine molecular testing in patients with advanced NSCLC.
Parallel, targeted analysis of environmental samples via high‐throughput quantitative PCR
Authors: Wilcox Taylor M. , McKelvey Kevin S. , Young Michael K. , Engkjer Cory , Lance Richard F. , Lahr Andrew , Eby Lisa A. , Schwartz Michael K. 
Published: March 2020

AbstractWhen analyzing environmental samples for DNA from multiple taxa, researchers must usually decide between iterative analyses with single‐taxon assays—which are reliable and sensitive, but also laborious to apply—and approaches such as metabarcoding that can simultaneously target multiple species, but which are less sensitive for detection across taxa. Here, we test an intermediate approach that allows efficient, parallel assessment of taxon‐specific qPCR assays via high‐throughput quantitative PCR (HT‐qPCR). Based on an assessment of over 500 environmental samples, we found that sensitivity and specificity of our HT‐qPCR approach were similar (concordance 0.900–1.000) to values achieved through single‐species qPCR in six out of seven assays tested. Thus, HT‐qPCR may provide analyses of similar quality as single‐species qPCR analyses for environmental DNA, but at a lower cost per taxon. We see this approach as being a valuable addition to the eDNA sampling toolbox, particularly for situations where reliable inferences are needed for a defined suite of rare invasive or imperiled taxa.
Racial differences in takotsubo cardiomyopathy outcomes in a large nationwide sample
Authors: Zaghlol Raja , Dey Amit K. , Desale Sameer , Barac Ana 
Published: March 2020

AbstractAimsTakotsubo cardiomyopathy (TC) is characterized by transient ventricular impairment, often preceded by emotional or physical stress. Racial differences affect the outcomes of several cardiovascular conditions; however, the effect of race on TC remains unknown. This investigation aims to assess the effect of race on in‐hospital outcomes of TC in a large national sample.Methods and resultsWe conducted a US‐wide analysis of TC hospitalizations from 2006 to 2014 by querying the National Inpatient Sample database for the International Classification of Diseases‐ninth Revision TC code, characteristics, and inpatient outcomes. Patients with a primary diagnosis of acute coronary syndrome were excluded to reduce selection bias. Caucasians were compared with African Americans (AA) for differences in baseline characteristics and in‐hospital outcomes. Multivariate regression models were created to adjust for potential confounders. Of 97 650 TC patients, 83 807 (86.9%) were women, 89 624 (91.8%) identified as Caucasians, and 8026 (8.2%) as AA. The annual number of TC hospitalizations increased significantly from 2006 to 2014 in both races (from 335 to 21 265 annual cases, P < 0.001). In‐hospital mortality initially increased (1–2% in 2006 to 5–6% in 2009, P < 0.001) and subsequently remained relatively stable around 5–7% with no significant difference between races. In unadjusted analysis, AA had more cardiac arrests [304 (3.8%) vs. 2569 (2.9%), P = 0.04], invasive mechanical ventilation [1671 (20.8%) vs. 15 897 (17.7%), P = 0.002], tracheostomies [242 (3%) vs. 1600 (1.8%), P = 0.001], acute kidney injuries [1765 (22%) vs. 14 608 (16.3%), P < 0.0001], and longer hospital stays [4.5 (3.2–4.8) vs. 3.8 (3.7–3.9) days, P < 0.0001] compared with Caucasians. After the adjustment for differences in age, gender, comorbidities (using the enhanced Charlson comorbidity index), hospital location/teaching status, and socio‐economic factors, all differences were significantly attenuated or eliminated. Additionally, the adjusted risk was lower in AA compared with Caucasians, for cardiogenic shock [odds ratio (OR) 0.61 (0.47–0.78), P < 0.0001], mechanical ventilation [OR 0.8 (0.70–0.92), P = 0.002] and intraaortic balloon pump insertion [OR 0.63 (0.41–0.99), P = 0.04].ConclusionsOur investigation is the first large US‐wide analysis studying racial variations in TC outcomes. AA overall have more in‐hospital complications; however, the differences are driven by racial disparities in demographics, comorbidities, and socio‐economic factors.
mGluR5 receptor availability is associated with lower levels of negative symptoms and better cognition in male patients with chronic schizophrenia
Authors: Régio Brambilla Cláudia , Veselinović Tanja , Rajkumar Ravichandran , Mauler Jörg , Orth Linda , Ruch Andrej , Ramkiran Shukti , Heekeren Karsten , Kawohl Wolfram , Wyss Christine , Kops Elena Rota , Scheins Jürgen , Tellmann Lutz , Boers Frank , Neumaier Bernd , Ermert Johannes , Herzog Hans , Langen Karl‐Josef , Jon Shah N. , Lerche Christoph , Neuner Irene 
Published: March 2020

AbstractConsistent findings postulate disturbed glutamatergic function (more specifically a hypofunction of the ionotropic NMDA receptors) as an important pathophysiologic mechanism in schizophrenia. However, the role of the metabotropic glutamatergic receptors type 5 (mGluR5) in this disease remains unclear. In this study, we investigated their significance (using [11C]ABP688) for psychopathology and cognition in male patients with chronic schizophrenia and healthy controls. In the patient group, lower mGluR5 binding potential (BPND) values in the left temporal cortex and caudate were associated with higher general symptom levels (negative and depressive symptoms), lower levels of global functioning and worse cognitive performance. At the same time, in both groups, mGluR5 BPND were significantly lower in smokers (F[27,1] = 15.500; p = .001), but without significant differences between the groups. Our findings provide support for the concept that the impaired function of mGluR5 underlies the symptoms of schizophrenia. They further supply a new perspective on the complex relationship between tobacco addiction and schizophrenia by identifying glutamatergic neurotransmission—in particularly mGluR5—as a possible connection to a shared vulnerability.
Sensitive and selective determination of 4‐nitrophenol in water and food using modified polyethyleneimine‐capped carbon dots
Authors: Zhai Hui‐Yun , Xiao Wen‐Li , Li Yan , Li Rong‐Zhen , Liu Hua‐Ji , Yu Li‐Ping 
Published: March 2020

AbstractHazardous 4‐nitrophenol (4‐NP) has created serious threats to humans and the environment; therefore, it is highly desirable to develop a facile and practical method for the monitoring of 4‐NP in environment and food. Here, a fluorescence method based on modified polyethyleneimine‐capped carbon dots (mPEI‐CDs) was developed for sensitive and selective determination of 4‐NP in water, fruit, and vegetable samples. First, highly fluorescent mPEI‐CDs (quantum yield about 40.3%) were easily synthesized via a one‐step hydrothermal method by using novel acetic anhydride modified polyethyleneimine (mPEI) and citric acid as precursors. Compared to the unmodified PEI‐CDs, the acetic anhydride mPEI‐CDs exhibited excellent fluorescent stability in a wider pH range of 4.0–9.0. Under pH 8.0, a selective determination of 4‐NP was achieved based on the inner filter effect (IFE) mechanism. After optimization, good linear relationships between fluorescence intensity function (F0‐F)/F0 and the concentration of 4‐NP were obtained in ranges of 0.5–10 and 10–100 μM, respectively, while efficiently avoiding the interferences from two other nitrophenol isomers, possible coexisting metal cations and anions in samples. Finally, the proposed approach was successfully applied for the determination of 4‐NP in water, honey, strawberry, and tomato samples.
Quantitative MRCP Imaging: Accuracy, Repeatability, Reproducibility, and Cohort‐Derived Normative Ranges
Authors: Goldfinger Marc H. , Ridgway Gerard R. , Ferreira Carlos , Langford Caitlin R. , Cheng Lin , Kazimianec Arina , Borghetto Andrea , Wright Thomas G. , Woodward Gary , Hassanali Neelam , Nicholls Rowan C. , Simpson Hayley , Waddell Tom , Vikal Siddarth , Mavar Marija , Rymell Soubera , Wigley Ioan , Jacobs Jaco , Kelly Matt , Banerjee Rajarshi , Brady J. Michael 
Published: March 2020

BackgroundMagnetic resonance cholangiopancreatography (MRCP) is an important tool for noninvasive imaging of biliary disease, however, its assessment is currently subjective, resulting in the need for objective biomarkers.PurposeTo investigate the accuracy, scan/rescan repeatability, and cross‐scanner reproducibility of a novel quantitative MRCP tool on phantoms and in vivo. Additionally, to report normative ranges derived from the healthy cohort for duct measurements and tree‐level summary metrics.Study TypeProspective.Phantoms/SubjectsPhantoms: two bespoke designs, one with varying tube‐width, curvature, and orientation, and one exhibiting a complex structure based on a real biliary tree.SubjectsTwenty healthy volunteers, 10 patients with biliary disease, and 10 with nonbiliary liver disease.Sequence/Field StrengthMRCP data were acquired using heavily T2‐weighted 3D multishot fast/turbo spin echo acquisitions at 1.5T and 3T.AssessmentDigital instances of the phantoms were synthesized with varying resolution and signal‐to‐noise ratio. Physical 3D‐printed phantoms were scanned across six scanners (two field strengths for each of three manufacturers). Human subjects were imaged on four scanners (two fieldstrengths for each of two manufacturers).Statistical TestsBland–Altman analysis and repeatability coefficient (RC).ResultsAccuracy of the diameter measurement approximated the scanning resolution, with 95% limits of agreement (LoA) from –1.1 to 1.0 mm. Excellent phantom repeatability was observed, with LoA from –0.4 to 0.4 mm. Good reproducibility was observed across the six scanners for both phantoms, with a range of LoA from –1.1 to 0.5 mm. Inter‐ and intraobserver agreement was high. Quantitative MRCP detected strictures and dilatations in the phantom with 76.6% and 85.9% sensitivity and 100% specificity in both. Patients and healthy volunteers exhibited significant differences in metrics including common bile duct (CBD) maximum diameter (7.6 mm vs. 5.2 mm P = 0.002), and overall biliary tree volume 12.36 mL vs. 4.61 mL, P = 0.0026).Data ConclusionThe results indicate that quantitative MRCP provides accurate, repeatable, and reproducible measurements capable of objectively assessing cholangiopathic change.Evidence Level: 1Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;52:807–820.
Spatial and Temporal Distribution of a Multiple Gear Fishing Fleet Exploiting the Caribbean Sea and North Brazil Shelf Large Marine Ecosystems
Authors: Laurent Singh Carolina Mercedes , Aguiar-Santos Jamerson , Gondim Ferreira Efrem Jorge , Evaristo Eucaris del Carmen , Freitas Carlos Edwar de Carvalho 
Published: March 2020

Abstract
An industrial multigear fishing fleet from Venezuela emerged in 2009 as a governmental strategy to reduce the impact of industrial trawling on the Venezuelan coast of the North Brazil Shelf Large Marine Ecosystem. The current study aimed to examine the spatial–temporal distribution of fishing effort and the catch levels obtained by the Venezuelan industrial multigear fishing fleet during the period 2015–2018. Fishing gear types employed by this fleet in order of preference were as follows: bottom longline (target sea catfishes [family Ariidae]), trap (target snappers [family Lutjanidae]), pelagic longline (target tunas [family Scombridae]), hand line (target mackerels [family Scombridae]), and shark longline (target sea catfishes and sharks [families Carcharhinidae, Squalidae, Sphyrnidae, Ginglymostomatidae, Alopiidae, and Triakidae]). The kernel intensity estimator determined that the main fishing area was the North Brazil Shelf (comprising 95% of the total fishing sets). Fishing effort (fishing sets per trip) distribution may be associated with oceanic fronts present in the region. A change in the dynamics of the fleet were recorded, with an increase in the use of bottom longlines, along with a decrease in the use of traps, possibly due to overfishing of resources caught by traps. The analyses of covariance showed a linear and positive relationship between the catch and fishing effort but with significant changes over the study period for traps and bottom longlines, since in the years where the fishing effort of traps was lower there were greater catches by unit of effort, and vice versa for bottom longlines, where lower catches by unit effort were obtained in years with greater effort.
Aromatic L‐Amino Acid Decarboxylase Gene Therapy Enhances Levodopa Response in Parkinson's Disease
Authors: Nutt John G. , Curtze Carolin , Hiller Amie , Anderson Shannon , Larson Paul S. , Van Laar Amber D. , Richardson R. Mark , Thompson Marin E. , Sedkov Alexander , Leinonen Mika , Ravina Bernard , Bankiewicz Krystof S. , Christine Chadwick W. 
Published: March 2020

AbstractBackgroundAs Parkinson's disease progresses, levodopa treatment loses efficacy, partly through the loss of the endogenous dopamine‐synthesizing enzyme L‐amino acid decarboxylase (AADC). In the phase I PD‐1101 study, putaminal administration of VY‐AADC01, an investigational adeno‐associated virus serotype‐2 vector for delivery of the AADC gene in patients with advanced Parkinson's disease, was well tolerated, improved motor function, and reduced antiparkinsonian medication requirements.ObjectivesThis substudy aimed to determine whether the timing and magnitude of motor response to intravenous levodopa changed in PD‐1101 patients after VY‐AADC01 administration.MethodsParticipants received 2‐hour threshold (0.6 mg/kg/h) and suprathreshold (1.2 mg/kg/h) levodopa infusions on each of 2 days, both before and approximately 6 months after VY‐AADC01. Infusion order was randomized and double blinded. Unified Parkinson's Disease Rating Scale motor scores, finger‐tapping speeds, and dyskinesia rating scores were assessed every 30 minutes for 1 hour before and ≥3 hours after start of levodopa infusion.ResultsOf 15 PD‐1101 patients, 13 participated in the substudy. Unified Parkinson's Disease Rating Scale motor score area under the curve responses to threshold and suprathreshold levodopa infusions increased by 168% and 67%, respectively, after VY‐AADC01; finger‐tapping speeds improved by 162% and 113%, and dyskinesia scores increased by 208% and 72%, respectively, after VY‐AADC01. Adverse events (mild/moderate severity) were reported in 5 participants during levodopa infusions pre–VY‐AADC01 and 2 participants post–VY‐AADC01 administration.ConclusionsVY‐AADC01 improved motor responses to intravenous levodopa given under controlled conditions. These data and findings from the parent study support further clinical development of AADC gene therapy for people with Parkinson's disease. © 2020 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Concept of Unburning Ratio and Combustion Modeling of ZPP and BKNO3 in Pyroshock‐Reduced Separation Nut
Authors: Woo Jeongmin , Cha Seung‐Won , Kim Gyubin , Kim Jeong Ho , Roh Tae‐Seong , Cho Jin Yeon , Jang Seung‐Gyo , Lee Hyo‐Nam , Yang Hee Won 
Published: March 2020

AbstractAlthough BKNO3 ignited by ZPP is commonly used as an explosive charge for many pyrotechnics, only a limited number of modeling studies can be found in the literature. Thus, recently proposed governing equations for combustion modeling of ZPP are supplemented to simulate the combustion of the BKNO3 with ZPP. The combustion model was independently validated using CBT results with fixed volume chambers of various sizes. In this process, the concept of the unburning ratio was introduced to correlate the combustion modeling with actual phenomena. The term “unburned” means that some fraction of explosive charge turns into non‐reactive solid rather than into combustion products. The model was then coupled with the equations of motion for the internal moving parts of a pyroshock‐reduced separation nut. Tests with prototype were performed to validate the coupled model. For accurate verification, the pressure of the expansion chamber and annular chamber and the displacement of the bolt were measured and compared. All measurements are in good agreement with the analysis results obtained from the coupled model. The results validated the generality of the modeling approach for the simulation of the pyroshock‐reduced separation nut.
Generalized multiple dependent state optimal control charts under ranked set sampling for monitoring process mean
Authors: Nawaz Tahir , Raza Muhammad Ali , Han Dong 
Published: March 2020

AbstractThis paper proposes two optimal control charts by using the generalized multiple dependent state (GMDS) plan to monitor the process mean. These charts make advantageous use of the ranked set sampling schemes and integrate them with the GMDS plan to improve the shift detection ability of the Shewhart‐type control charts. The proposed control charts have two pairs of control limits, inner and outer, which enables them to consider the current and previous sample information while making a decision about the process state. The run‐length profiles of the proposed charts are obtained through extensive Monte Carlo simulations. The individual and overall mean shift detection abilities of the proposed charts are compared with various competing control charts by using out‐of‐control average run length (
) and the average extra quadratic loss (
) as performance metrics. The comparison establishes the complete dominance of the proposed charting strategy. In the end, the practical implementation of the proposed charts is demonstrated by using a real data set related to the cement manufacturing industry.
Assessment of Foliar Uptake and Accumulation of Airborne Polyaromatic Hydrocarbons Under Laboratory Conditions
Authors: Teke Gábor , Hubai Katalin , Diósi Dorina , Kováts Nora 
Published: March 2020

AbstractUrban horticulture and community gardening have become more and more popular in the past years, however, the risk of bioaccumulation of atmospheric polyaromatic hydrocarbons (PAHs) in vegetables grown in polluted areas cannot be neglected. In our study, the No. 227 OECD GUIDELINE FOR THE TESTING OF CHEMICALS: Terrestrial Plant Test: Vegetative Vigour Test was followed to assess foliar uptake of PAHs from aqueous extract of an urban aerosol. Using lettuce (Lactuca sativa) as a test organism, significant accumulation was experienced. The highest bioconcentration factors (BCFs) were experienced for naphthalene and for anthracene, pyrene and fluoranthene showed the lowest bioaccumulation potential. BCF of each PAH showed strong correlation with molecular weight. The standard protocol defined by the Guideline made it possible to assess bioaccumulation pattern under controlled laboratory conditions.
Gross–Pitaevskii Limit of a Homogeneous Bose Gas at Positive Temperature
Authors: Deuchert Andreas , Seiringer Robert 
Published: March 2020

AbstractWe consider a dilute, homogeneous Bose gas at positive temperature. The system is investigated in the Gross–Pitaevskii limit, where the scattering lengthais so small that the interaction energy is of the same order of magnitude as the spectral gap of the Laplacian, and for temperatures that are comparable to the critical temperature of the ideal gas. We show that the difference between the specific free energy of the interacting system and the one of the ideal gas is to leading order given by$$4 \pi a \left( 2 \varrho ^2 - \varrho _0^2 \right) $$4πa2ϱ2-ϱ02. Here$$\varrho $$ϱdenotes the density of the system and$$\varrho _0$$ϱ0is the expected condensate density of the ideal gas. Additionally, we show that the one-particle density matrix of any approximate minimizer of the Gibbs free energy functional is to leading order given by the one of the ideal gas. This in particular proves Bose–Einstein condensation with critical temperature given by the one of the ideal gas to leading order. One key ingredient of our proof is a novel use of the Gibbs variational principle that goes hand in hand with the c-number substitution.
Prevalence of hyperfunctioning thyroid nodules among those in need of fine needle aspiration cytology according to ATA 2015, EU-TIRADS, and ACR-TIRADS
Authors: Noto Benjamin , Eveslage Maria , Pixberg Michaela , Gonzalez Carvalho José Manuel , Schäfers Michael , Riemann Burkhard , Kies Peter 
Published: March 2020

Abstract
Purpose
Given the large number of patients with thyroid nodules, improvement of the specificity of current ultrasound-based thyroid nodule classification systems (ATA, EU-TIRADS, and ACR-TIRADS) is warranted to reduce the number of diagnostic thyroidectomies. Thyroid scintigraphy has been shown to demonstrate hyperfunctional nodules, associated with a low malignancy risk, in euthyroid patients. However, it is not known if thyroid scintigraphy could improve specificity of current classification systems. The aim of this study, therefore, was to determine the frequency of hyperfunctional nodules among those nodules in need of fine needle aspiration cytology (FNA) according to current classification systems and to test if nodule functional status is associated with sonographic features.

Methods
Five hundred sixty-six euthyroid patients (TSH 0.55–4.20 μU/ml) presenting for thyroid nodule workup including thyroid sonography and scintigraphy at our department between 09/2013 and 02/2018 were included in this retrospective study. All nodules > 10 mm were classified according to ATA, EU-TIRADS, and ACR-TIRADS and correlated to their functional status as assessed by 99mTc-pertechnetate scintigraphy.

Results
Ultrasound detected 1029 thyroid nodules ≥ 10 mm, including 545 nodules ≥ 15 mm. Prevalence of hyperfunctional nodules among those with recommendation for FNA according to ATA 2015, EU-TIRADS, and ACR-TIRADS was 6.4%, 6.9%, and 6.5% for nodules ≥ 10 mm and 7.2%, 7.6%, and 7.5% only considering nodules ≥ 15 mm. No sonographic feature was correlated to hyperfunctionality of nodules.

Conclusion
In euthyroid patients, thyroid scintigraphy demonstrates hyperfunctionality, which cannot be predicted by ultrasound, in up to 6.9% of nodules in need of FNA according to ultrasound-based classifications. Given the known low risk of malignancy in hyperfunctional nodules, thyroid scintigraphy can lower the frequency of fine needle aspirations and—potentially—the frequency of diagnostic hemithyroidectomies in euthyroid patients.