bluuebunny/crossref_metadata_2025_split huggingface dataset:
ORTHOSKIM: In silico sequence capture from genomic and transcriptomic libraries for phylogenomic and barcoding applications
Authors: Pouchon Charles , Boyer Frédéric , Roquet Cristina , Denoeud France , Chave Jérome , Coissac Eric , Alsos Inger Greve ,   The PhyloAlps Consortium,   The PhyloNorway Consortium, Lavergne Sébastien 
Published: January 2022

AbstractLow‐coverage whole genome shotgun sequencing (or genome skimming) has emerged as a cost‐effective method for acquiring genomic data in nonmodel organisms. This method provides sequence information on chloroplast genome (cpDNA), mitochondrial genome (mtDNA) and nuclear ribosomal regions (rDNA), which are over‐represented within cells. However, numerous bioinformatic challenges remain to accurately and rapidly obtain such data in organisms with complex genomic structures and rearrangements, in particular for mtDNA in plants or for cpDNA in some plant families. Here we introduce the pipeline ORTHOSKIM, which performs in silico capture of targeted sequences from genomic and transcriptomic libraries without assembling whole organelle genomes. ORTHOSKIM proceeds in three steps: (i) global sequence assembly, (ii) mapping against reference sequences and (iii) target sequence extraction; importantly it also includes a range of quality control tests. Different modes are implemented to capture both coding and noncoding regions of cpDNA, mtDNA and rDNA sequences, along with predefined nuclear sequences (e.g., ultraconserved elements) or collections of single‐copy orthologue genes. Moreover, aligned DNA matrices are produced for phylogenetic reconstructions, by performing multiple alignments of the captured sequences. While ORTHOSKIM is suitable for any eukaryote, a case study is presented here, using 114 genome‐skimming libraries and four RNA sequencing libraries obtained for two plant families, Primulaceae and Ericaceae, the latter being a well‐known problematic family for cpDNA assemblies. ORTHOSKIM recovered with high success rates cpDNA, mtDNA and rDNA sequences, well suited to accurately infer evolutionary relationships within these families. ORTHOSKIM is released under a GPL‐3 licence and is available at: https://github.com/cpouchon/ORTHOSKIM.
Metastatic pulmonary nodule after a seventeen‐year disease‐free interval resected through thoracoscopic subsegmentectomy: A case report
Authors: Uchida Tsuyoshi , Matsubara Hirochika , Sato Daisuke , Onuki Yuichiro , Nakajima Hiroyuki 
Published: January 2022

AbstractThe lung is the most common site of metastasis in patients with renal cell carcinoma (RCC). Metastatic RCCs, even those classified as stage I, can recur after >10 years. Therefore, it is critical to completely resect metastatic nodules. Here, we report the case of a 74‐year‐old man who underwent a nephrectomy for RCC and was diagnosed with lung metastasis 17 years later. The metastatic nodule was resected through complete thoracoscopic subsegmentectomy. He had previously undergone partial nephrectomy for clear cell renal carcinoma pT1bN0M0. During his annual follow‐up, a computed tomography scan revealed a pulmonary nodule. The intraoperative frozen section revealed a metastatic clear cell RCC. Thus, additional lobectomy was not performed. The postoperative course was uneventful with no complications. This case demonstrates that even early stage metastatic clear cell renal carcinoma can recur after over 17 years. Thoracoscopic segmentectomy is less invasive and can preserve pulmonary function.
How materialism shapes the effectiveness of financial literacy messages: A cross‐cultural perspective
Authors: Khenfer Jamel 
Published: January 2022

AbstractThis cross‐cultural experiment (N = 1000) shows that messages designed to promote financial literacy are differently effective among US and Arab consumers depending on the salience of materialistic thoughts at the time of exposure. Among US consumers, financial literacy messages increased savings intention by heightening the importance of saving when materialistic thoughts were salient but had no impact otherwise. This is consistent with existing research that has largely focused on WEIRD countries (Western, Educated, Industrial, Rich, Democratic; Henrich et al., 2010). However, among Arab consumers (data collected in the United Arab Emirates), we found that financial optimism was a key construct to explain savings behaviors. Specifically, our results show that financial literacy messages lower levels of financial optimism and, thus, increase savings intention at baseline levels. When materialistic thoughts are salient, our results suggest that Arab consumers prefer spending in the presence of financial literacy messages because having materialistic thoughts heightens financial optimism when one is assured that acquiring financial knowledge and skills guarantees one's financial success.
Making a podcast: Reflecting on creating a place‐based podcast
Authors: Scriven Richard 
Published: January 2022

AbstractAlthough podcasts have become a popular medium since the early 2000s, geographers' use of the format as a research and dissemination method is underdeveloped. This paper examines how audio podcasts can be deployed as geographical processes to explore place and convey spatial themes in an impactful and innovative inclusive manner. Using the case study of a short series produced to consider the role of a river in the life of a region, I show how field recordings, interviews, and historical sources can be woven together to examine a place in an evocative and accessible manner. Podcasting is a research and communication tool, which can dovetail with existing approaches, with the potential to understand different environments in new ways, let community voices speak for themselves, and reach broader audiences. The paper argues that podcasts present new opportunities to consider how we appreciate and use sound to tell the story of places in participative and evocative ways.
Perceived threat and support for right‐wing ideology in Finland
Authors: Nshom Elvis 
Published: January 2022

AbstractSupport for right‐wing ideology is on the rise in Finland and has been for the past decade. Using the intergroup threat theory, this study investigates the extent to which support for right‐wing ideology in Finland is explained by the perception of threat from immigrants. According to the intergroup threat theory, immigrants can be perceived as a realistic threat and a symbolic threat. Another aim of this study is to understand how differently the types of threats explain support for right‐wing ideology in Finland. With a sample of 604 participants, results showed that while controlling for age, gender, education and religiosity, perceived threat was a significant predictor of support for right‐wing ideology. However, when considered individually without the effect of other factors, it was revealed that symbolic threat was a stronger predictor of support for right‐wing ideology in Finland when compared to realistic threat.
Wealth into voice: Political behavior of private entrepreneurs in the Chinese People's Political Consultative Conference (2008–2012)
Authors: Yu Bin , Zhang Yang 
Published: January 2022

AbstractThis article explores the political behavior of private entrepreneur delegates (PEDs) in the Chinese People's Political Consultative Conference (CPPCC). Drawing evidence from a data set consisting of personal background and behavioral information for 2295 members of the 11th CPPCC (2008‐12), we probe into the behavioral patterns of 178 PEDs in the proposal process. Our findings reveal that PEDs' participation demonstrates more economic rather than political aspirations, which suggests that a major motivation of their participation is enhancing economic well‐being rather than initiating political changes. Party affiliation is associated with the PEDs' engagement in the proposal process, possibly through two mechanisms. In the pre‐selection mechanism, PEDs' with different political ideologies and preferences tend to be assimilated into different party backgrounds before becoming a delegate, hence different participation patterns. In the resource mobilization mechanism, party backgrounds may influence their capacity to effectively participate in the proposal process due to the resources provided by their party organizations.
Pharmacological profile of ALKS 7119, an investigational compound evaluated for the treatment of neuropsychiatric disorders, in healthy volunteers
Authors: Dijkstra Francis M. , Zuiker Rob G. J. A. , Siebenga Pieter S. , Leigh‐Pemberton Richard A. , Sun Lei , Manthis Joan D. , de Kam Marieke L. , Lin Richard , von Moltke Lisa L. , Rezendes David , van Gerven Joop M. A. 
Published: January 2022

AimsALKS 7119 is a novel compound with in vitro affinity highest for the SERT, and for μ receptor, α1A‐adrenoceptor, α1B‐adrenoceptor, NMDA receptor and sigma non‐opioid intracellular receptor 1. This first‐in‐human study evaluated safety and PK/PD effects of single ascending doses (SAD) of ALKS 7119 in healthy males and compared effects with neurotransmitter modulators with partially overlapping targets.MethodsIn 10 cohorts (n = 10 subjects each), PK, safety and PD (NeuroCart tests, measuring neurophysiologic effects [pupillometry, pharmaco‐EEG (pEEG)], visuomotor coordination, alertness, [sustained] attention [saccadic peak velocity, adaptive tracking], subjective drug effects [VAS Bowdle and VAS Bond and Lader] and postural stability [body sway]) were evaluated. Neuroendocrine effects (cortisol, prolactin, growth hormone) were measured. Data were analysed over the 12‐hour post‐dose period using mixed‐effects model for repeated measure (MMRM) with baseline as covariate.ResultsALKS 7119 demonstrated linear PK and was generally well tolerated. QTcF interval increases of 30–60 ms compared to baseline were observed with ALKS 7119 doses of ≥50 mg without related adverse events. Significant increases in left and right pupil/iris ratio were observed at dose levels ≥50 mg (estimate of difference [95% CI], P‐value) (0.04 [0.01; 0.07], P < .01) and (0.06 [0.03; 0.09], P = .01), respectively. From dose levels ≥50 mg significant increases (% change) of serum cortisol (51.7 [8.4; 112.3], P = .02) and prolactin (77.9 [34.2; 135.8], P < .01) were observed.ConclusionIn line with ALKS 7119’s in vitro pharmacological profile, the clinical profile observed in this study is most comparable to SERT inhibition.
Design and Analysis of Two-Phase Studies with Multivariate Longitudinal Data
Authors: Di Gravio Chiara , Tao Ran , Schildcrout Jonathan S. 
Published: January 2022

Abstract
Two-phase studies are crucial when outcome and covariate data are available in a first-phase sample (e.g., a cohort study), but costs associated with retrospective ascertainment of a novel exposure limit the size of the second-phase sample, in whom the exposure is collected. For longitudinal outcomes, one class of two-phase studies stratifies subjects based on an outcome vector summary (e.g., an average or a slope over time) and oversamples subjects in the extreme value strata while undersampling subjects in the medium-value stratum. Based on the choice of the summary, two-phase studies for longitudinal data can increase efficiency of time-varying and/or time-fixed exposure parameter estimates. In this manuscript, we extend efficient, two-phase study designs to multivariate longitudinal continuous outcomes, and we detail two analysis approaches. The first approach is a multiple imputation analysis that combines complete data from subjects selected for phase two with the incomplete data from those not selected. The second approach is a conditional maximum likelihood analysis that is intended for applications where only data from subjects selected for phase two are available. Importantly, we show that both approaches can be applied to secondary analyses of previously conducted two-phase studies. We examine finite sample operating characteristics of the two approaches and use the Lung Health Study (Connett et al. (1993), Controlled Clinical Trials, 14, 3S–19S) to examine genetic associations with lung function decline over time.
Information theory approaches to improve glioma diagnostic workflows in surgical neuropathology
Authors: Cevik Lokman , Landrove Marilyn Vazquez , Aslan Mehmet Tahir , Khammad Vasilii , Garagorry Guerra Francisco Jose , Cabello‐Izquierdo Yolanda , Wang Wesley , Zhao Jing , Becker Aline Paixao , Czeisler Catherine , Rendeiro Anne Costa , Véras Lucas Luis Sousa , Zanon Maicon Fernando , Reis Rui Manuel , Matsushita Marcus de Medeiros , Ozduman Koray , Pamir M. Necmettin , Ersen Danyeli Ayca , Pearce Thomas , Felicella Michelle , Eschbacher Jennifer , Arakaki Naomi , Martinetto Horacio , Parwani Anil , Thomas Diana L. , Otero José Javier 
Published: January 2022

AbstractAimsResource‐strained healthcare ecosystems often struggle with the adoption of the World Health Organization (WHO) recommendations for the classification of central nervous system (CNS) tumors. The generation of robust clinical diagnostic aids and the advancement of simple solutions to inform investment strategies in surgical neuropathology would improve patient care in these settings.MethodsWe used simple information theory calculations on a brain cancer simulation model and real‐world data sets to compare contributions of clinical, histologic, immunohistochemical, and molecular information. An image noise assay was generated to compare the efficiencies of different image segmentation methods in H&E and Olig2 stained images obtained from digital slides. An auto‐adjustable image analysis workflow was generated and compared with neuropathologists for p53 positivity quantification. Finally, the density of extracted features of the nuclei, p53 positivity quantification, and combined ATRX/age feature was used to generate a predictive model for 1p/19q codeletion in IDH‐mutant tumors.ResultsInformation theory calculations can be performed on open access platforms and provide significant insight into linear and nonlinear associations between diagnostic biomarkers. Age, p53, and ATRX status have significant information for the diagnosis of IDH‐mutant tumors. The predictive models may facilitate the reduction of false‐positive 1p/19q codeletion by fluorescence in situ hybridization (FISH) testing.ConclusionsWe posit that this approach provides an improvement on the cIMPACT‐NOW workflow recommendations for IDH‐mutant tumors and a framework for future resource and testing allocation.
A framework for understanding the relation between spoken language input and outcomes for children with cochlear implants
Authors: Houston Derek M. 
Published: January 2022

AbstractSpoken language outcomes after cochlear implantation are highly variable. Some variance can be attributed to individual characteristics. Research with typically hearing children suggests that the amount of language directed to children may also play a role. However, several moderating factors may complicate the association between language input and language outcomes in children with cochlear implants. In this article, I present a conceptual framework that posits that the association between total language input directed to children and language outcomes is moderated by factors that influence what is accessible, attended to, and coordinated with the child. The framework also posits that children with cochlear implants exhibit more variability on those moderating factors, which explains why the relation between language input and language outcomes may be more complex even if language input is more important for successful language outcomes in this population.
Radiation-induced subacute cutaneous lupus erythematosus
Authors: De Caux Deborah , Kelly Áine , Pearce Julian , Natkunarajah Janakan 
Published: January 2022

AbstractWe present an unusual case of radiation-induced subacute cutaneous lupus erythematosus (SCLE) occurring in a patient with non-Hodgkin lymphoma. Dermatologists should be aware of the ability of low-dose radiation treatment to induce a first presentation or flare of SCLE, with the possibility of extension of disease outside of the radiation field.
Proton pump inhibitor use and risk of depression and anxiety in children: nationwide cohort study
Authors: Wang Yun‐Han , Wintzell Viktor , Ludvigsson Jonas F. , Svanström Henrik , Pasternak Björn 
Published: January 2022

AbstractAlthough some data have linked proton pump inhibitor (PPI) use to risk of depression and anxiety, there are no studies investigating this safety issue in children. This study investigated the association between PPI use and risk of depression and anxiety in children. We conducted a nationwide register‐based cohort study in Sweden, July 1, 2007, to December 31, 2016. Following matching on age and propensity score, we included 29,320 pairs of PPI initiators and noninitiators among children aged 7–17 years old. The primary analysis examined the risk of incident depression and anxiety, a composite outcome defined as a diagnosis of depression, anxiety, or a prescription for an antidepressant. Children who initiated PPI use had higher hazards for risk of depression and anxiety compared with noninitiators (hazard ratios [HRs], 2.61; 95% confidence interval [CI], 2.32–2.94). In analyses of the timing of depression and anxiety onset after PPI initiation, the HRs were 3.71 (95% CI, 2.17–6.34) for 1–30 days, 3.47 (95% CI, 2.33–5.18) for 31–90 days, 2.71 (2.04–3.60) for 91–180 days, 2.52 (2.00–3.16) for 181–365 days, and 2.34 (1.94–2.82) for 366–730 days. Significant associations were observed across all age groups. The magnitude of the association increased with longer duration of PPI use (p for trend < 0.0001). The association was consistent through all sensitivity analyses, including high‐dimensional propensity score matching (HR, 2.31, 95% CI, 2.05–2.61). PPI use was associated with increased risk of depression and anxiety in children. Further investigation is warranted to confirm or refute this potential association.
Inhibition of 11β‐Hydroxysteroid dehydrogenase‐1 with AZD4017 in patients with nonalcoholic steatohepatitis or nonalcoholic fatty liver disease: A randomized, double‐blind, placebo‐controlled, phase II study
Authors: Yadav Yogesh , Dunagan Kelly , Khot Rachita , Venkatesh Sudhakar K. , Port John , Galderisi Alfonso , Cobelli Claudio , Wegner Craig , Basu Ananda , Carter Rickey , Basu Rita 
Published: January 2022

AbstractAimTo evaluate whether short‐term treatment with a selective 11β‐Hydroxysteroid dehydrogenase‐1 (11β‐HSD1) inhibitor, AZD4017, would block hepatic cortisol production and thereby decrease hepatic fat in patients with nonalcoholic fatty liver disease (NAFLD)/nonalcoholic steatohepatitis (NASH), with or without type 2 diabetes (T2D).Materials and MethodsThis was a randomized, double‐blind, placebo‐controlled, phase 2 study conducted at two sites. Key inclusion criteria were the presence of NAFLD or NASH on magnetic resonance imaging (MRI) or recent biopsy positive for NASH. Enrolled patients were randomly assigned (1:1) to AZD4017 or placebo for 12 weeks. Primary outcomes were between‐group differences in mean change from baseline to week 12 in liver fat fraction (LFF) and conversion of 13C cortisone to 13C cortisol in the liver.ResultsA total of 93 patients were randomized; 85 patients completed treatment. The mean (standard deviation [SD]) change in LFF was −0.667 (5.246) and 0.139 (4.323) in the AZD4017 and placebo groups (P = 0.441). For patients with NASH and T2D, the mean (SD) change in LFF was significantly improved in the AZD4017 versus the placebo group (−1.087 [5.374] vs. 1.675 [3.318]; P = 0.033). Conversion of 13C cortisone to 13C cortisol was blocked in all patients in the AZD4017 group. There were no significant between‐group differences (AZD4017 vs. placebo) in changes in fibrosis, weight, levels of liver enzymes or lipids, or insulin sensitivity.ConclusionAlthough the study did not meet one of the primary outcomes, AZD4017 blocked the conversion of 13C cortisone to 13C cortisol in the liver in all patients who received the drug. In patients with NASH and T2D, AZD4017 improved liver steatosis versus placebo.
Combination therapy with pioglitazone/exenatide/metformin reduces the prevalence of hepatic fibrosis and steatosis: The efficacy and durability of initial combination therapy for type 2 diabetes (EDICT)
Authors: Lavynenko Olga , Abdul‐Ghani Muhammad , Alatrach Mariam , Puckett Curtiss , Adams John , Abdelgani Siham , Alkhouri Naim , Triplitt Curtis , Clarke Geoffrey D. , Vasquez Juan A. , Li Jinqi , Cersosimo Eugenio , Gastaldelli Amalia , DeFronzo Ralph A. 
Published: January 2022

AbstractAimTo compare the efficacy of triple therapy (metformin/exenatide/pioglitazone) versus stepwise conventional therapy (metformin → glipizide → glargine insulin) on liver fat content and hepatic fibrosis in newly diagnosed, drug‐naïve patients with type 2 diabetes.MethodsSixty‐eight patients completed the 6‐year follow‐up and had an end‐of‐study (EOS) FibroScan to provide measures of steatosis (controlled attenuation parameter [CAP] in dB/m) and fibrosis (liver stiffness measurement [LSM] in kPa); 59 had magnetic resonance imaging‐proton density fat fraction (MRI‐PDFF) to measure liver fat.ResultsAt EOS, HbA1c was 6.8% and 6.0% in triple and conventional therapy groups, respectively (P = .0006). Twenty‐seven of 39 subjects (69%) receiving conventional therapy had grade 2/3 steatosis (CAP, FibroScan) versus nine of 29 (31%) in triple therapy (P = .0003). Ten of 39 (26%) subjects receiving conventional therapy had stage 3/4 fibrosis (LSM) versus two of 29 (7%) in triple therapy (P = .04). Conventional therapy subjects had more liver fat (MRI‐PDFF) than triple therapy (12.9% vs. 8.8%, P = .03). The severity of steatosis (CAP) (r = 0.42, P < .001) and fibrosis (LSM) (r = −0.48, P < .001) correlated inversely with the Matsuda Index of insulin sensitivity, but not with percentage body fat. Aspartate aminotransferase (AST) to Platelet Ratio Index (APRI), non‐alcoholic fatty liver disease fibrosis score (NFS), plasma AST, and alanine aminotransferase (ALT) all decreased significantly with triple therapy, but only the decrease in plasma AST and ALT correlated with the severity of steatosis and fibrosis at EOS.ConclusionsAt EOS, subjects with type 2 diabetes treated with triple therapy had less hepatic steatosis and fibrosis versus conventional therapy; the severity of hepatic steatosis and fibrosis were both strongly and inversely correlated with insulin resistance; and changes in liver fibrosis scores (APRI, NFS, Fibrosis‐4, and AST/ALT ratio) have limited value in predicting response to therapy.