bluuebunny/crossref_metadata_2025_split huggingface dataset:
Homotopy type-theoretic interpretations of constructive set theories
Authors: Gallozzi Cesare 
Published: November 2019

AbstractWe introduce a family of (k, h)-interpretations for 2 ≤ k ≤ ∞ and 1 ≤ h ≤ ∞ of constructive set theory into type theory, in which sets and formulas are interpreted as types of homotopy level k and h, respectively. Depending on the values of the parameters k and h, we are able to interpret different theories, like Aczel’s CZF and Myhill’s CST. We also define a proposition-as-hproposition interpretation in the context of logic-enriched type theories. The rest of the paper is devoted to characterising and analysing the interpretations considered. The formulas valid in the prop-as-hprop interpretation are characterised in terms of the axiom of unique choice. We also analyse the interpretations of CST into homotopy type theory, providing a comparative analysis with Aczel’s interpretation. This is done by formulating in a logic-enriched type theory the key principles used in the proofs of the two interpretations. Finally, we characterise a class of sentences valid in the (k, ∞)-interpretations in terms of the ΠΣ axiom of choice.
Feet of Clay? How to Review Political Science Papers that Make Use of the Work of Historians
Authors: Møller Jørgen 
Published: November 2019

ABSTRACTPolitical scientists increasingly enlist the work of historians but they often treat this work in a nonchalant or superficial way, which makes their evidentiary record questionable. It follows that we need to check the validity of the interpretation of historians’ work in review processes. This article argues that enlisting historians as reviewers is not the answer. Instead, it proposes four simple criteria that can be used to flag situations in which the use of historians’ work as empirical evidence is unconvincing. The general purpose of the article is to increase awareness about what is at stake when political scientists base empirical analysis on evidence gathered by historians.
Analysis of Text-Analysis Syllabi: Building a Text-Analysis Syllabus Using Scaling
Authors: Fréchet Nadjim , Savoie Justin , Dufresne Yannick 
Published: November 2019

ABSTRACTIn the last decade, text-analytic methods have become a fundamental element of a political researcher’s toolkit. Today, text analysis is taught in most major universities; many have entire courses dedicated to the topic. This article offers a systematic review of 45 syllabi of text-analysis courses around the world. From these syllabi, we extracted data that allowed us to rank canonical sources and discuss the variety of software used in teaching. Furthermore, we argue that our empirical method for building a text-analysis syllabus could easily be extended to syllabi for other courses. For instance, scholars can use our technique to introduce their graduate students to the field of systematic reviews while improving the quality of their syllabi.
Quizalofop-p-ethyl application in water-seeded coenzyme A carboxylase–inhibiting herbicide-resistant rice with different flood systems
Authors: Webster Eric P. , Teló Gustavo M. , Rustom Samer Y. , McKnight Benjamin M. , Blouin David C. 
Published: November 2019

AbstractA field study was conducted during the 2016 and 2017 crop seasons at the LSU AgCenter H. Rouse Caffey Rice Research Station to evaluate weed control and rice yield after quizalofop-p-ethyl applications in water-seeded coenzyme A carboxylase (ACCase)–resistant ‘PVLO1’ long-grain rice production utilizing different flood systems, application timings, and quizalofop rates. The initial application of quizalofop was applied at five timings beginning when ‘PVLO1’ rice was at the coleoptile stage (PEG) through the one- to two-tiller stage. A total quizalofop rate of 240 g ai ha–1 was split into two applications: 97 followed by 143 g ha–1 or 120 followed by 120 g ai ha–1 in both pinpoint and delayed flood water-seeded management systems. A second quizalofop application was applied 14 d after initial treatment (DAIT). At 14 DAIT, a reduction in control of barnyardgrass and red rice was observed by delaying the initial quizalofop application to the two- to four-tiller stage compared with rice treated at earlier growth stages. At 42 DAIT, control of barnyardgrass was 94% to 96%, and red rice was 98% following the second application of quizalofop, regardless of initial application timing. Rice treated with quizalofop at the PEG and two- and three-leaf stage resulted in a rice height of 104 cm at harvest compared with 96 to 100 cm when the initial application of quizalofop was delayed to later growth stages. Applying the initial application of quizalofop to rice at the PEG timing in the pinpoint or the delayed flood system resulted in a total gross value per hectare of $450 and $590, respectively. Within each flood system, delaying the initial application of quizalofop to the one- to two-tiller stage resulted in a gross per-hectare value reduction of $100 ha-1 in the pinpoint flood and $110 ha-1 in the delayed flood.
Regional variation in endovascular treatment rate and in-hospital	mortality of abdominal aortic aneurysms in Germany
Authors: Trenner Matthias , Salvermoser Michael , Reutersberg Benedikt , Busch Albert , Schmid Volker , Eckstein Hans-Henning , Kuehnl Andreas 
Published: November 2019

Summary: Background: Abdominal aortic aneurysms (AAA) can be treated by either open surgery (OAR) or endovascular aortic repair (EVAR). The aim of this study was to analyze regional variations in application of (EVAR) and in-hospital mortality after intact AAA (iAAA) repair. Methods: Using data provided by the German Federal Statistical Office, a nationwide analysis for 2012 to 2014 was conducted. Patients with a diagnosis of iAAA (I71.4) and corresponding procedure codes for OAR (5-384.5/7) or EVAR (5-38a.1) were included. Odds ratios (ORs) for use of EVAR (proportion of EVAR among total EVAR + OAR cases) and mortality were calculated for all regions in Germany. ORs for EVAR use were adjusted for age, sex, and risk (Elixhauser score). ORs for mortality were additionally adjusted for type of procedure (OAR/EVAR). Results: Finally, 31,757 procedures for iAAA were included. Median age of all patients was 73 years (interquartile range 67–78 years) and 87.1 % were male. The mean proportion of EVAR procedures was 72.6 %; however, the application of EVAR for repair of iAAA varied widely depending on region. The lowest unadjusted regional rate of EVAR use was 48.8 %, while the highest was 92.5 %. After adjustment, the lowest regional OR for EVAR use (compared to the nationwide mean) was 0.23 (95 % confidence interval [0.15–0.36]), the highest 5.93 [1.79–19.65]. Overall in-hospital mortality was 2.9 % (OAR 6.2 %; EVAR 1.7 %). The adjusted regional OR for mortality ranged from 0.31 [0.07–1.42] to 4.98 [2.08–11.93]. Conclusions: This study reveals variations in use of EVAR and in-hospital mortality for iAAA treatment in Germany. This may imply that selection of treatment might not only be influenced by patient characteristics, but also by regional location. These results need to be taken into account when discussing centralization of AAA treatment in Germany.
Seryl tRNA synthetase cooperates with POT1 to regulate telomere length and cellular senescence
Authors: Li Yingxi , Li Xiyang , Cao Mei , Jiang Yuke , Yan Jie , Liu Ze , Yang Rongcun , Chen Xu , Sun Peiqing , Xiang Rong , Wang Longlong , Shi Yi 
Published: November 2019

AbstractDeregulated telomere length is a causative factor in many physiological and pathological processes, including aging and cancer. Many studies focusing on telomeres have revealed important roles for cooperation between the Shelterin protein complex and telomerase in maintaining telomere length. However, it remains largely unknown whether and how aging-related stresses, such as deregulated protein homeostasis, impact telomere length. Here, we explored the possible roles of aminoacyl tRNA synthetases (AARSs), key enzymes catalyzing the first reactions in protein synthesis, in regulating telomere length and aging. We selected seryl tRNA synthetase (SerRS) since our previous studies discovered expanded functions of SerRS in the nucleus in addition to its canonical cytoplasmic role in protein synthesis. In this study, we revealed that overexpression of SerRS promoted cellular senescence and inhibited the growth of cervical tumor xenografts in mice by triggering the senescence of tumor cells. In the nucleus, SerRS directly bound to telomeric DNA repeats and tethered more POT1 proteins to telomeres through a direct interaction between the UNE-S domain of SerRS and the OB1 domain of POT1. We further demonstrated that SerRS-induced enrichment of POT1 prevented the recruitment of telomerase to telomeres, resulting in progressive telomere shortening. Our data suggested a possible molecular link between protein synthesis and telomere length control, the deregulation of which may be associated with aging and cancer.
Tumor-suppressive function and mechanism of HOXB13 in right-sided colon cancer
Authors: Xie Binbin , Bai Bingjun , Xu Yuzi , Liu Yunlong , Lv Yiming , Gao Xing , Wu Fei , Fang Zhipeng , Lou Ying , Pan Hongming , Han Weidong 
Published: November 2019

AbstractRight-sided colon cancer (RCC) and left-sided colon cancer (LCC) differ in their clinical and molecular features. An investigation of differentially expressed genes (DEGs) between RCC and LCC could contribute to targeted therapy for colon cancer, especially RCC, which has a poor prognosis. Here, we identified HOXB13, which was significantly less expressed in RCC than in LCC and associated with prognosis in RCC, by using 5 datasets from the Gene Expression Omnibus (GEO). Tissue sample analysis showed that HOXB13 was differentially expressed between normal and only RCC tumor tissues. HOXB13 inhibited colon cancer cell proliferation and induced apoptosis both in vitro and in vivo. Furthermore, we found that HOXB13 might be regulated by DNMT3B and suppress C-myc expression to exert antitumor effects via β-catenin/TCF4 signals in RCC. In conclusion, the current study is the first to demonstrate that HOXB13 has a tumor-suppressive effect in RCC. High expression levels of HOXB13 are associated with prolonged overall survival in patients with RCC. The DNMT3B-HOXB13-C-myc signaling axis might be a molecular target for the treatment of RCC.
Origin of Ising magnetism in Ca3Co2O6 unveiled by orbital imaging
Authors: Leedahl Brett , Sundermann Martin , Amorese Andrea , Severing Andrea , Gretarsson Hlynur , Zhang Lunyong , Komarek Alexander C. , Maignan Antoine , Haverkort Maurits W. , Tjeng Liu Hao 
Published: November 2019

AbstractThe one-dimensional cobaltate Ca$${}_{3}$$3Co$${}_{2}$$2O$${}_{6}$$6 is an intriguing material having an unconventional magnetic structure, displaying quantum tunneling phenomena in its magnetization. Using a newly developed experimental method, $$s$$s-core-level non-resonant inelastic x-ray scattering ($$s$$s-NIXS), we were able to image the atomic Co $$3d$$3d orbital that is responsible for the Ising magnetism in this system. We can directly observe that corrections to the commonly accepted ideal prismatic trigonal crystal field scheme occur in Ca$${}_{3}$$3Co$${}_{2}$$2O$${}_{6}$$6, and it is the complex $${d}_{2}$$d2 orbital occupied by the sixth electron at the high-spin Co$${}_{\,\text{trig}\,}^{3+}$$trig3+ ($${d}^{6}$$d6) sites that generates the Ising-like behavior. The ability to directly relate the orbital occupation with the local crystal structure is essential to model the magnetic properties of this system.
A high-throughput screen identifies that CDK7 activates glucose consumption in lung cancer cells
Authors: Ghezzi Chiara , Wong Alicia , Chen Bao Ying , Ribalet Bernard , Damoiseaux Robert , Clark Peter M. 
Published: November 2019

AbstractElevated glucose consumption is fundamental to cancer, but selectively targeting this pathway is challenging. We develop a high-throughput assay for measuring glucose consumption and use it to screen non-small-cell lung cancer cell lines against bioactive small molecules. We identify Milciclib that blocks glucose consumption in H460 and H1975, but not in HCC827 or A549 cells, by decreasing SLC2A1 (GLUT1) mRNA and protein levels and by inhibiting glucose transport. Milciclib blocks glucose consumption by targeting cyclin-dependent kinase 7 (CDK7) similar to other CDK7 inhibitors including THZ1 and LDC4297. Enhanced PIK3CA signaling leads to CDK7 phosphorylation, which promotes RNA Polymerase II phosphorylation and transcription. Milciclib, THZ1, and LDC4297 lead to a reduction in RNA Polymerase II phosphorylation on the SLC2A1 promoter. These data indicate that our high-throughput assay can identify compounds that regulate glucose consumption and that CDK7 is a key regulator of glucose consumption in cells with an activated PI3K pathway.
Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation
Authors: Subramanian Ayshwarya , Sidhom Eriene-Heidi , Emani Maheswarareddy , Vernon Katherine , Sahakian Nareh , Zhou Yiming , Kost-Alimova Maria , Slyper Michal , Waldman Julia , Dionne Danielle , Nguyen Lan T. , Weins Astrid , Marshall Jamie L. , Rosenblatt-Rosen Orit , Regev Aviv , Greka Anna 
Published: November 2019

AbstractHuman iPSC-derived kidney organoids have the potential to revolutionize discovery, but assessing their consistency and reproducibility across iPSC lines, and reducing the generation of off-target cells remain an open challenge. Here, we profile four human iPSC lines for a total of 450,118 single cells to show how organoid composition and development are comparable to human fetal and adult kidneys. Although cell classes are largely reproducible across time points, protocols, and replicates, we detect variability in cell proportions between different iPSC lines, largely due to off-target cells. To address this, we analyze organoids transplanted under the mouse kidney capsule and find diminished off-target cells. Our work shows how single cell RNA-seq (scRNA-seq) can score organoids for reproducibility, faithfulness and quality, that kidney organoids derived from different iPSC lines are comparable surrogates for human kidney, and that transplantation enhances their formation by diminishing off-target cells.
Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression
Authors: Montaldo Nicola P. , Bordin Diana L. , Brambilla Alessandro , Rösinger Marcel , Fordyce Martin Sarah L. , Bjørås Karine Øian , Bradamante Stefano , Aas Per Arne , Furrer Antonia , Olsen Lene C. , Kunath Nicolas , Otterlei Marit , Sætrom Pål , Bjørås Magnar , Samson Leona D. , van Loon Barbara 
Published: November 2019

AbstractBase excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3′end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression.
A psychophysical measurement on subjective well-being and air pollution
Authors: Li Yuan , Guan Dabo , Yu Yanni , Westland Stephen , Wang Daoping , Meng Jing , Wang Xuejun , He Kebin , Tao Shu 
Published: November 2019

AbstractAlthough the physical effects of air pollution on humans are well documented, there may be even greater impacts on the emotional state and health. Surveys have traditionally been used to explore the impact of air pollution on people’s subjective well-being (SWB). However, the survey techniques usually take long periods to properly match the air pollution characteristics from monitoring stations to each respondent’s SWB at both disaggregated spatial and temporal levels. Here, we used air pollution data to simulate fixed-scene images and psychophysical process to examine the impact from only air pollution on SWB. Findings suggest that under the atmospheric conditions in Beijing, negative emotions occur when PM2.5 (particulate matter with a diameter less than 2.5 µm) increases to approximately 150 AQI (air quality index). The British observers have a stronger negative response under severe air pollution compared with Chinese observers. People from different social groups appear to have different sensitivities to SWB when air quality index exceeds approximately 200 AQI.
Suppression of FOXM1 activities and breast cancer growth in vitro and in vivo by a new class of compounds
Authors: Ziegler Yvonne , Laws Mary J. , Sanabria Guillen Valeria , Kim Sung Hoon , Dey Parama , Smith Brandi P. , Gong Ping , Bindman Noah , Zhao Yuechao , Carlson Kathryn , Yasuda Mayuri A. , Singh Divya , Li Zhong , El-Ashry Dorraya , Madak-Erdogan Zeynep , Katzenellenbogen John A. , Katzenellenbogen Benita S. 
Published: November 2019

AbstractThe transcription factor FOXM1 is upregulated and overexpressed in aggressive, therapy-resistant forms of hormone receptor-positive and triple negative breast cancers, and is associated with less good patient survival. FOXM1 signaling is also a key driver in many other cancers. Here, we identify a new class of compounds effective in suppressing FOXM1 activity in breast cancers, and displaying good potency for antitumor efficacy. The compounds bind directly to FOXM1 and alter its proteolytic sensitivity, reduce the cellular level of FOXM1 protein by a proteasome- dependent process, and suppress breast cancer cell proliferation and cell cycle progression and increase apoptosis. RNA-seq and gene set enrichment analyses indicate that the compounds decrease expression of FOXM1-regulated genes and suppress gene ontologies under FOXM1 regulation. Several compounds have favorable pharmacokinetic properties and show good tumor suppression in preclinical breast tumor models. These compounds may be suitable for further clinical evaluation in targeting aggressive breast cancers driven by FOXM1.
Angle-dependent magnetoresistance and its implications for Lifshitz transition in W2As3
Authors: Wang Jialu , Yang Haiyang , Ding Linchao , You Wei , Xi Chuanying , Cheng Jie , Shi Zhixiang , Cao Chao , Luo Yongkang , Zhu Zengwei , Dai Jianhui , Tian Mingliang , Li Yuke 
Published: November 2019

AbstractLifshitz transition represents a sudden reconstruction of Fermi surface structure, giving rise to anomalies in electronic properties of materials. Such a transition does not necessarily rely on symmetry-breaking and thus is topological. It holds a key to understand the origin of many exotic quantum phenomena, for example, the mechanism of extremely large magnetoresistance (MR) in topological Dirac/Weyl semimetals. Here, we report studies of the angle-dependent MR (ADMR) and the thermoelectric effect in W2As3 single crystal. The compound shows a large unsaturated MR (of about 7000% at 4.2 K and 53 T). The most striking finding is that the ADMR significantly deforms from the horizontal dumbbell-like shape above 40 K to the vertical lotus-like pattern below 30 K. The window of 30–40 K also corresponds substantial changes in Hall effect, thermopower and Nernst coefficient, implying an abrupt change of Fermi surface topology. Such a temperature-induced Lifshitz transition results in a compensation of electron-hole transport and the large MR as well. We thus suggest that the similar method can be applicable in detecting a Fermi-surface change of a variety of quantum states when a direct Fermi-surface measurement is not possible.
Peptide-based vaccine successfully induces protective immunity against canine visceral leishmaniasis
Authors: Petitdidier Elodie , Pagniez Julie , Pissarra Joana , Holzmuller Philippe , Papierok Gérard , Vincendeau Philippe , Lemesre Jean-Loup , Bras-Gonçalves Rachel 
Published: November 2019

AbstractDogs are the main reservoir of zoonotic visceral leishmaniasis. Vaccination is a promising approach to help control leishmaniasis and to interrupt transmission of theLeishmaniaparasite. The promastigote surface antigen (PSA) is a highly immunogenic component ofLeishmaniaexcretory/secretory products. A vaccine based on three peptides derived from the carboxy-terminal part ofLeishmania amazonensisPSA and conserved amongLeishmaniaspecies, formulated with QA-21 as adjuvant, was tested on naive Beagle dogs in a preclinical trial. Four months after the full course of vaccination, dogs were experimentally infected withLeishmania infantumpromastigotes. Immunization of dogs with peptide-based vaccine conferred immunity against experimental infection withL. infantum. Evidence for macrophage nitric oxide production and anti-leishmanial activity associated with IFN-γ production by lymphocytes was only found in the vaccinated group. An increase in specific IgG2 antibodies was also measured in vaccinated dogs from 2 months after immunization. Additionally, after challenge withL. infantum, the parasite burden was significantly lower in vaccinated dogs than in the control group. These data strongly suggest that this peptide-based vaccine candidate generated cross-protection against zoonotic leishmaniasis by inducing a Th1-type immune response associated with production of specific IgG2 antibodies. This preclinical trial including a peptide-based vaccine against leishmaniasis clearly demonstrates effective protection in a natural host. This approach deserves further investigation to enhance the immunogenicity of the peptides and to consider the possible engineering of a vaccine targeting severalLeishmaniaspecies.
A manually denoised audio-visual movie watching fMRI dataset for the studyforrest project
Authors: Liu Xingyu , Zhen Zonglei , Yang Anmin , Bai Haohao , Liu Jia 
Published: November 2019

AbstractThe data presented here are related to the studyforrest project that uses the movie ‘Forrest Gump’ to map brain functions in a real-life context using functional magnetic resonance imaging (fMRI). However, neural-related fMRI signals are often small and confounded by various noise sources (i.e., artifacts) that makes searching for the signals induced by specific cognitive processes significantly challenging. To make neural-related signals stand out from the noise, the audio-visual movie watching fMRI dataset from the project was denoised by a combination of spatial independent component analysis and manual identification of signals or noise. Here, both the denoised data and the labeled decomposed components are shared to facilitate further study. Compared with the original data, the denoised data showed a substantial improvement in the temporal signal-to-noise ratio and provided a higher sensitivity in subsequent analyses such as in an inter-subject correlation analysis.