bluuebunny/crossref_metadata_2025_split huggingface dataset:
Advanced achalasia: good candidate for peroral endoscopic myotomy
Authors: Qiu Shaotian , Chai Ningli , Zhai Yaqi , Wang Xiangyao , Wang Yan , Linghu Enqiang 
Published: October 2020

SUMMARY
Peroral endoscopic myotomy (POEM) has been increasingly accepted as the first-line treatment of achalasia. However, laparoscopic Heller myotomy or esophagectomy still remains as the mainstay treatment for advanced achalasia featured with megaesophagus and/or sigmoid-shaped esophagus. Although the efficacy of POEM for advanced achalasia with sigmoid-shaped esophagus has been described, little is known about the role of POEM for patients with megaesophagus. The aim of our study is to evaluate the efficacy and safety of POEM for advanced achalasia with megaesophagus. Patients who received initial examinations and underwent POEM in our hospital from June 2013 to December 2018 were identified and data were retrospectively analyzed. The advanced achalasia was defined as megaesophagus with a diameter of ≥6 cm. The primary outcome was clinical success. The secondary outcomes were technical success and adverse events. A total of 112 patients (50 females, 44.6%) were included with a mean age of 44.8 years. The median symptom duration was 6.5 years (IQR:3.0–13.0 years). Modified POEM techniques were used in 27.7% (31/112) of patients. Technical success rate was 99.1% (112/113) per procedure. Clinical success was seen in 93.1% patients with median Eckardt score decreasing from 8.0 to 1.0 (P &lt; 0.001) during a median 31.0 months of follow-up. The mean LES pressure decreased from 29.5 mmHg to 14.2 mmHg after POEM (P &lt; 0.05). Procedure-related adverse events occurred in 8.9% patients. Reflux disease was observed postoperatively in 26.7% of patients. POEM is also indicated for patients with advanced achalasia with a favorable safety and efficacy.
Reflection and transmission coefficient approximations for P, S1 and S2 waves in triclinic media
Authors: Jin Song , Stovas Alexey 
Published: October 2020

SUMMARY
The conventional assumptions, in most published approximations of the reflection and transmission (R/T) coefficients of plane waves at a plane interface between two anisotropic half-spaces, confine their applications to weakly anisotropic and/or weak contrast models. We consider the horizontal interface enclosed by two triclinic half-spaces to approximate the R/T coefficients normalized by the vertical energy flux. The homogeneous background medium can be anisotropic with arbitrary symmetry to better simulate the strongly anisotropic media. The second-order approximations are proposed to accommodate the strong contrast interface. We also consider an isotropic background medium under the weak anisotropy assumption. The obtained approximations can be applied to P, S1 and S2 waves, except for the transmission coefficients between the S1 and S2 waves. The S-wave transmission coefficients are insensitive to the model parameter contrasts and predominately rely on the S-wave polarization directions in the half-spaces above and below the interface. The proposed approximations are tested numerically.
Lower Rates of Colorectal Cancer in Patients With Inflammatory Bowel Disease Using Anti-TNF Therapy
Authors: Alkhayyat Motasem , Abureesh Mohammad , Gill Arshpal , Khoudari George , Abou Saleh Mohannad , Mansoor Emad , Regueiro Miguel 
Published: October 2020

Abstract

Background
Chronic inflammation is a key factor for the development of colorectal cancer (CRC) among patients with inflammatory bowel disease (IBD). Despite the increased use of biologic agents in patients with IBD, their impact on colorectal carcinogenesis remains unclear. With the use of a large database, we sought to describe the effect of biologics on CRC among patients with IBD.

Methods
We evaluated a multicenter database (Explorys) consisting of electronic medical records from several U.S. hospitals between 1999 and 2020. A cohort of patients with a diagnosis of IBD was identified. We performed a multivariate analysis to adjust for multiple factors including medical and surgical therapies.

Results
There were a total of 62,007,510 patients in the database between 1999 and 2020. Amongst those, 225,090 (0.36%) individuals had Crohn’s disease and 188,420 (0.30%) had ulcerative colitis. After adjusting for confounding factors using multivariate analysis, patients with IBD were more likely to develop CRC. Among the IBD cohort, patients treated with anti-TNF agents were less likely to develop CRC; patients with Crohn’s disease: odds ratio, 0.69; 95% confidence interval, 0.66-0.73; P &lt; 0.0001 vs patients with ulcerative colitis: odds ratio, 0.78; 95% confidence interval, 0.73-0.83; P &lt; 0.0001.

Conclusions
Patients with IBD who were treated with anti-tumor necrosis factor agents were less likely to develop CRC. Prospective studies are needed to evaluate whether anti-tumor necrosis factor drugs provide a chemoprotective effect in patients with IBD by inflammation control and mucosal healing.
Therapeutic Drug Monitoring of Tumor Necrosis Factor Antagonists in Crohn Disease: A Theoretical Construct to Apply Pharmacokinetics and Guidelines to Clinical Practice
Authors: Vande Casteele Niels , Feagan Brian G , Wolf Douglas C , Pop Anca , Yassine Mohamed , Horst Sara N , Ritter Timothy E , Sandborn William J 
Published: October 2020

Abstract
Therapeutic drug monitoring (TDM) is the measurement of drug and antidrug antibody concentrations in individuals to guide treatment decisions. In patients with Crohn disease (CD), TDM, used either reactively or proactively, is emerging as a valuable tool for optimization of tumor necrosis factor (TNF) antagonist therapy. Reactive TDM is carried out in response to treatment failure, whereas proactive TDM involves the periodic monitoring of patients responding to TNF antagonist therapy to allow treatment optimization. In patients with CD, most of the available data for TDM relate to the first-to-market TNF antagonist infliximab and, to a lesser extent, to adalimumab and certolizumab pegol. Several gastroenterology associations, including the American Gastroenterology Association, have endorsed the use of reactive TDM in patients with active CD. However, fewer recommendations currently exist for the use of proactive TDM, although several new prospective randomized controlled trials evaluating proactive TDM strategies have been published. In this review, the current evidence for reactive and proactive TDM is discussed, and a proactive treatment algorithm for certolizumab pegol based on previously published threshold concentrations is proposed.
National Estimates of Financial Hardship From Medical Bills and Cost-related Medication Nonadherence in Patients With Inflammatory Bowel Diseases in the United States
Authors: Nguyen Nghia H , Khera Rohan , Dulai Parambir S , Boland Brigid S , Ohno-Machado Lucila , Sandborn William J , Singh Siddharth 
Published: October 2020

Abstract

Background
Inflammatory bowel diseases (IBDs) are associated with substantial health care needs. We estimated the national burden and patterns of financial toxicity and its association with unplanned health care utilization in adults with IBD in the United States.

Methods
Using the National Health Interview survey (2015), we identified individuals with self-reported IBD and assessed national estimates of financial toxicity across domains of financial hardship due to medical bills, cost-related medication nonadherence (CRN) and adoption of cost-reducing strategies, personal and health-related financial distress (worry about expenses), and health care affordability. We also evaluated the association of financial toxicity with emergency department (ED) utilization.

Results
Of the estimated 3.1 million adults with IBD in the United States, 23% reported financial hardships due to medical bills, 16% of patients reported CRN, and 31% reported cost-reducing behaviors. Approximately 62% of patients reported personal and/or health-related financial distress, and 10% of patients deemed health care unaffordable. Prevalence of financial toxicity was substantial even in participants with higher education, with private insurance, and belonging to middle/high-income families, highlighting underinsurance. Inflammatory bowel disease was associated with 1.6 to 2.6 times higher odds of financial toxicity across domains compared with patients without IBD. Presence of any marker of financial toxicity was associated with higher ED utilization.

Conclusions
One in 4 adults with IBD experiences financial hardship due to medical bills, and 1 in 6 adults reports cost-related medication nonadherence. These financial determinates of health—especially underinsurance—have important implications in the context of value-based care.
Prevalence of MDR organism (MDRO) carriage in children and their household members in Siem Reap Province, Cambodia
Authors: Singh Shweta R , Mao Bunsoth , Evdokimov Konstantin , Tan Pisey , Leab Phana , Ong Rick , Vonthanak Saphonn , Tam Clarence C , Hsu Li Yang , Turner Paul 
Published: October 2020

AbstractBackgroundThe rising incidence of infections caused by MDR organisms (MDROs) poses a significant public health threat. However, little has been reported regarding community MDRO carriage in low- and middle-income countries.MethodsWe conducted a cross-sectional study in Siem Reap, Cambodia comparing hospital-associated households, in which an index child (age: 2–14 years) had been hospitalized for at least 48 h in the preceding 2–4 weeks, with matched community households on the same street, in which no other child had a recent history of hospitalization. Participants were interviewed using a survey questionnaire and tested for carriage of MRSA, ESBL-producing Enterobacterales (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) by culture followed by antibiotic susceptibility testing. We used logistic regression analysis to analyse associations between collected variables and MDRO carriage.ResultsForty-two pairs of households including 376 participants with 376 nasal swabs and 290 stool specimens were included in final analysis. MRSA was isolated from 26 specimens (6.9%). ESBL-producing Escherichia coli was detected in 269 specimens (92.8%) whereas ESBL-producing Klebsiella pneumoniae was isolated from 128 specimens (44.1%), of which 123 (42.4%) were co-colonized with ESBL-producing E. coli. Six (2.1%) specimens tested positive for CPE (4 E. coli and 2 K. pneumoniae). The prevalence ratios for MRSA, ESBL-producing E. coli and ESBL-producing K. pneumoniae carriage did not differ significantly in hospital-associated households and hospitalized children compared with their counterparts.ConclusionsThe high prevalence of ESBL-E across both household types suggests that MDRO reservoirs are common in the community. Ongoing genomic analyses will help to understand the epidemiology and course of MDRO spread.
A review ofTriops granarius(Lucas, 1864)sensu lato(Notostraca: Triopsidae) of southern Africa and Madagascar, with comments on the group
Authors: Rogers D Christopher , Schwentner Martin , Dalu Tatenda , Wasserman Ryan J 
Published: October 2020

AbstractWe review the current knowledge surrounding the Triops granarius morphological species group globally, and present a revision of the southern African T. granarius forms based on collections from southern Africa and Madagascar. We also provide comparisons with other material of T. granarius from outside this region. We revise the morphological descriptions of T. numidicus (Grube, 1865) and T. namaquensis (Richters, 1886) using modern standards, and resurrect T. sakalavus Nobili, 1905 from synonymy, using both morphological and molecular techniques. Morphological definitions focus primarily on the form of the apical portion of the thoracopod II endite. Differential diagnoses are presented for the three species, including characters that separate them from the other members with similar morphology. Furthermore, we treat T. dybowskii (Braem, 1893), T. orientalis (Tiwari, 1951), and T. mavliensis (Tiwari, 1951), which had been recently resurrected, as species inquirenda.
Structured Plurality Reconsidered
Authors: Grimau Berta 
Published: October 2020

AbstractIn this article, I address the question of the semantic analysis of structured plurals, that is, expressions like these children and those children, which seem to refer to pluralities of individuals divided into groups. In the first half of the article, I describe a variety of structured plural expressions and predicates they can combine with and I point out the difficulties faced by two extant approaches to the semantics of plurals: inflationary and cover-based semantics. In the second half of the article, I propose an alternative account which combines elements from both of them. The main novelty of my proposal is that, by capitalising on the background operation of certain pragmatic principles, it correctly formalises the fact that some interpretations of ambiguous sentences involving structured plurality are more accessible than others.
Uncovering two phases of early intercontinental COVID-19 transmission dynamics
Authors: Yang Jing , Li Juan , Lai Shengjie , Ruktanonchai Corrine W , Xing Weijia , Carioli Alessandra , Wang Peihan , Ruktanonchai Nick W , Li Ruiyun , Floyd Jessica R , Wang Liang , Bi Yuhai , Shi Weifeng , Tatem Andrew J 
Published: October 2020

Abstract

Background
The COVID-19 pandemic has posed an ongoing global crisis, but how the virus spread across the world remains poorly understood. This is of vital importance for informing current and future pandemic response strategies.

Methods
We performed two independent analyses, travel network-based epidemiological modelling and Bayesian phylogeographic inference, to investigate the intercontinental spread of COVID-19.

Results
Both approaches revealed two distinct phases of COVID-19 spread by the end of March 2020. In the first phase, COVID-19 largely circulated in China during mid-to-late January 2020 and was interrupted by containment measures in China. In the second and predominant phase extending from late February to mid-March, unrestricted movements between countries outside of China facilitated intercontinental spread, with Europe as a major source. Phylogenetic analyses also revealed that the dominant strains circulating in the USA were introduced from Europe. However, stringent restrictions on international travel across the world since late March have substantially reduced intercontinental transmission.

Conclusions
Our analyses highlight that heterogeneities in international travel have shaped the spatiotemporal characteristics of the pandemic. Unrestricted travel caused a large number of COVID-19 exportations from Europe to other continents between late February and mid-March, which facilitated the COVID-19 pandemic. Targeted restrictions on international travel from countries with widespread community transmission, together with improved capacity in testing, genetic sequencing and contact tracing, can inform timely strategies for mitigating and containing ongoing and future waves of COVID-19 pandemic.
Discovery and follow-up of ASASSN-19dj: an X-ray and UV luminous TDE in an extreme post-starburst galaxy
Authors: Hinkle Jason T , Holoien T W-S , Auchettl K , Shappee B J , Neustadt J M M , Payne A V , Brown J S , Kochanek C S , Stanek K Z , Graham M J , Tucker M A , Do A , Anderson J P , Bose S , Chen P , Coulter D A , Dimitriadis G , Dong Subo , Foley R J , Huber M E , Hung T , Kilpatrick C D , Pignata G , Piro A L , Rojas-Bravo C , Siebert M R , Stalder B , Thompson Todd A , Tonry J L , Vallely P J , Wisniewski J P 
Published: October 2020

ABSTRACT
We present observations of ASASSN-19dj, a nearby tidal disruption event (TDE) discovered in the post-starburst galaxy KUG 0810+227 by the All-Sky Automated Survey for Supernovae (ASAS-SN) at a distance of d ≃ 98 Mpc. We observed ASASSN-19dj from −21 to 392 d relative to peak ultraviolet (UV)/optical emission using high-cadence, multiwavelength spectroscopy and photometry. From the ASAS-SN g-band data, we determine that the TDE began to brighten on 2019 February 6.8 and for the first 16 d the rise was consistent with a flux ∝t2 power law. ASASSN-19dj peaked in the UV/optical on 2019 March 6.5 (MJD = 58548.5) at a bolometric luminosity of L = (6.2 ± 0.2) × 1044 erg s−1. Initially remaining roughly constant in X-rays and slowly fading in the UV/optical, the X-ray flux increased by over an order of magnitude ∼225 d after peak, resulting from the expansion of the X-ray emitting region. The late-time X-ray emission is well fitted by a blackbody with an effective radius of ∼1 × 1012 cm and a temperature of ∼6 × 105 K. The X-ray hardness ratio becomes softer after brightening and then returns to a harder state as the X-rays fade. Analysis of Catalina Real-Time Transient Survey images reveals a nuclear outburst roughly 14.5 yr earlier with a smooth decline and a luminosity of LV ≥ 1.4 × 1043 erg s−1, although the nature of the flare is unknown. ASASSN-19dj occurred in the most extreme post-starburst galaxy yet to host a TDE, with Lick HδA = 7.67 ± 0.17 Å.
Inevitable imprints of patchy reionization on the cosmic microwave background anisotropy
Authors: Paul Sourabh , Mukherjee Suvodip , Choudhury Tirthankar Roy 
Published: October 2020

ABSTRACT
Reionization of the cosmic neutral hydrogen by the first stars in the Universe is an inhomogeneous process, which produces spatial fluctuations in free electron density. These fluctuations lead to observable signatures in cosmological probes like the cosmic microwave background (CMB). We explore the effect of the electron density fluctuations on CMB using photon-conserving seminumerical simulations of reionization named SCRIPT. We show that the amplitude of the kinematic Sunyaev–Zeldovich (kSZ) and the B-mode polarization signal depends on the patchiness in the spatial distribution of electrons along with the dependence on mid-point and extent of the reionization history. Motivated by this finding, we provide new scaling relations for the amplitude of kSZ and the B-mode polarization signal which can capture the effects arising from the mean optical depth, width of reionization, and spatial fluctuations in the electron density arising from patchy reionization. We show that the amplitude of the kSZ and the B-mode polarization signal exhibits different dependency on the width of reionization and the patchiness of reionization, and hence a joint study of these CMB probes will be able to break the degeneracy. By combining external data sets from 21-cm measurements, the degeneracy can be further lifted by directly exploring the sizes of the ionized regions.
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
Authors: Wacker Anna , Weigand Julia E , Akabayov Sabine R , Altincekic Nadide , Bains Jasleen Kaur , Banijamali Elnaz , Binas Oliver , Castillo-Martinez Jesus , Cetiner Erhan , Ceylan Betül , Chiu Liang-Yuan , Davila-Calderon Jesse , Dhamotharan Karthikeyan , Duchardt-Ferner Elke , Ferner Jan , Frydman Lucio , Fürtig Boris , Gallego José , Grün J Tassilo , Hacker Carolin , Haddad Christina , Hähnke Martin , Hengesbach Martin , Hiller Fabian , Hohmann Katharina F , Hymon Daniel , de Jesus Vanessa , Jonker Henry , Keller Heiko , Knezic Bozana , Landgraf Tom , Löhr Frank , Luo Le , Mertinkus Klara R , Muhs Christina , Novakovic Mihajlo , Oxenfarth Andreas , Palomino-Schätzlein Martina , Petzold Katja , Peter Stephen A , Pyper Dennis J , Qureshi Nusrat S , Riad Magdalena , Richter Christian , Saxena Krishna , Schamber Tatjana , Scherf Tali , Schlagnitweit Judith , Schlundt Andreas , Schnieders Robbin , Schwalbe Harald , Simba-Lahuasi Alvaro , Sreeramulu Sridhar , Stirnal Elke , Sudakov Alexey , Tants Jan-Niklas , Tolbert Blanton S , Vögele Jennifer , Weiß Lena , Wirmer-Bartoschek Julia , Wirtz Martin Maria A , Wöhnert Jens , Zetzsche Heidi 
Published: October 2020

AbstractThe current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5′ end, the ribosomal frameshift segment and the 3′-untranslated region (3′-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
TENET: gene network reconstruction using transfer entropy reveals key regulatory factors from single cell transcriptomic data
Authors: Kim Junil , T. Jakobsen Simon , Natarajan Kedar N , Won Kyoung-Jae 
Published: October 2020

AbstractAccurate prediction of gene regulatory rules is important towards understanding of cellular processes. Existing computational algorithms devised for bulk transcriptomics typically require a large number of time points to infer gene regulatory networks (GRNs), are applicable for a small number of genes and fail to detect potential causal relationships effectively. Here, we propose a novel approach ‘TENET’ to reconstruct GRNs from single cell RNA sequencing (scRNAseq) datasets. Employing transfer entropy (TE) to measure the amount of causal relationships between genes, TENET predicts large-scale gene regulatory cascades/relationships from scRNAseq data. TENET showed better performance than other GRN reconstructors, in identifying key regulators from public datasets. Specifically from scRNAseq, TENET identified key transcriptional factors in embryonic stem cells (ESCs) and during direct cardiomyocytes reprogramming, where other predictors failed. We further demonstrate that known target genes have significantly higher TE values, and TENET predicted higher TE genes were more influenced by the perturbation of their regulator. Using TENET, we identified and validated that Nme2 is a culture condition specific stem cell factor. These results indicate that TENET is uniquely capable of identifying key regulators from scRNAseq data.