bluuebunny/crossref_metadata_2025_split huggingface dataset:
The HARPS search for southern extra-solar planets
Authors: Unger N. , Ségransan D. , Queloz D. , Udry S. , Lovis C. , Mordasini C. , Ahrer E. , Benz W. , Bouchy F. , Delisle J.-B. , Díaz R. F. , Dumusque X. , Lo Curto G. , Marmier M. , Mayor M. , Pepe F. , Santos N. C. , Stalport M. , Alonso R. , Collier Cameron A. , Deleuil M. , Figueira P. , Gillon M. , Moutou C. , Pollacco D. , Pompei E. 
Published: October 2021

Context.We present precise radial-velocity measurements of five solar-type stars observed with the HARPS Echelle spectrograph mounted on the 3.6-m telescope in La Silla (ESO, Chile). With a time span of more than 10 yr and a fairly dense sampling, the survey is sensitive to low mass planets down to super-Earths on orbital periods up to 100 days.Aims.Our goal was to search for planetary companions around the stars HD 39194, HD 93385, HD 96700, HD 154088, and HD 189567 and use Bayesian model comparison to make an informed choice on the number of planets present in the systems based on the radial velocity observations. These findings will contribute to the pool of known exoplanets and better constrain their orbital parameters.Methods.A first analysis was performed using the Data & Analysis Center for Exoplanets online tools to assess the activity level of the star and the potential planetary content of each system. We then used Bayesian model comparison on all targets to get a robust estimate on the number of planets per star. We did this using the nested sampling algorithm POLYCHORD. For some targets, we also compared different noise models to disentangle planetary signatures from stellar activity. Lastly, we ran an efficient Markov chain Monte Carlo algorithm for each target to get reliable estimates for the planets’ orbital parameters.Results.We identify 12 planets within several multiplanet systems. These planets are all in the super-Earth and sub-Neptune mass regime with minimum masses ranging between 4 and 13M⊕and orbital periods between 5 and 103 days. Three of these planets are new, namely HD 93385 b, HD 96700 c, and HD 189567 c.
Lithium on the lower red giant branch of five Galactic globular clusters
Authors: Aguilera-Gómez C. , Monaco L. , Mucciarelli A. , Salaris M. , Villanova S. , Pancino E. 
Published: October 2021

Context. Lithium is one of the few elements produced during Big Bang nucleosynthesis in the early universe. Moreover, its fragility makes it useful as a proxy for stellar environmental conditions. As such, the lithium abundance in old systems is at the core of various astrophysical investigations.
Aims. Stars on the lower red giant branch are key to studies of globular clusters where main sequence stars are too faint to be observed. We use these stars to analyze the initial Li content of the clusters and compare it to cosmological predictions, to measure spreads in Li between different stellar populations, and to study signs of extra depletion in these giants.
Methods. We used the GIRAFFE spectra to measure the lithium and sodium abundances of lower red giant branch stars in five globular clusters. These cover an extensive range in metallicity, from [Fe/H] ∼ −0.7 to [Fe/H] ∼ −2.3 dex.
Results. We find that the lithium abundance in these lower red giant branch stars forms a plateau, with values from A(Li)NLTE = 0.84 to 1.03 dex, showing no clear correlation with metallicity. When using stellar evolutionary models to calculate the primordial abundance of these clusters, we recover values of A(Li)NLTE = 2.1 − 2.3 dex, consistent with the constant value observed in warm metal-poor halo stars, namely the Spite plateau. Additionally, we find no difference in the lithium abundance of first and second population stars in each cluster. We also report the discovery of a Li-rich giant in the cluster NGC 3201, with A(Li)NLTE = 1.63 ± 0.18 dex, where the enrichment mechanism is probably pollution from external sources.
Eine innerbetriebliche Leistungsverrechnung in der Notaufnahme als wirtschaftlicher Erfolgsfaktor?
Authors: Warnholz Jannik , Hoffmann Felix 
Published: October 2021

Zusammenfassung
Zielsetzung Das Ziel dieser Studie war es, zu untersuchen, in welchem Ausmaß sich die finanziellen Verluste durch ambulante Notfallversorgungen in der Notaufnahme mittels der Verrechnung innerbetrieblicher Aufnahmeleistungen der Notaufnahme gegenfinanzieren lassen und wie sich dies auf die Gesamtwirtschaftlichkeit einer Notaufnahme auswirkt.
Methodik Die Auswertung erfolgte durch eine simulierte innerbetrieblichen Leistungsverrechnung am Beispiel einer Notaufnahme eines Akutkrankenhauses in Norddeutschland. Hierzu wurden verschiedene Kosten- und Erlösgrößen ambulanter Notfallbehandlungen des Jahres 2019 ausgewertet und simulierten innerbetrieblichen Erlösen auf kosten- sowie marktpreisorientierter Basis gegenübergestellt.
Ergebnisse Die Auswertung konnte aufzeigen, dass die marktpreisorientierte Leistungsverrechnung auf Grundlage der verwendeten Kosten- und Erlösgrößen die ambulanten Verluste um 40 Prozent senken konnte. Der kostenorientierten Verrechnung gelang eine simulierte Kompensation von 75 Prozent.
Schlussfolgerung Basierend auf den Ergebnissen zeigte sich, dass die innerbetriebliche Leistungsverrechnung eine sinnvolle Möglichkeit darstellt, Verluste auf Abteilungsebene der Notaufnahme zu minimieren. Geeigneter erscheint die Verwendung eines kostenorientierten Ansatzes, da Umsetzbarkeit und Effektivität in Bezug auf die verwendete Methodik überwogen. Dennoch konnte kein positives Gesamtwirtschaftsergebnis erreicht werden. Hierzu empfiehlt sich die Verwendung weiterer
erlösgenerierender Instrumente, wie die vollstationäre Abrechnung einzelner Fälle in bettenführenden Einheiten der Notaufnahme sowie eine langfristige gesundheitspolitische Patientensteuerung.
Dissolved organic carbon from the forest floor with different decomposition rates in a rainforest in south-eastern Brazil
Authors: Miranda Felipe Soter de Mariz e , Avelar André de Souza 
Published: October 2021

Dissolved organic carbon (DOC) fluxes between environmental compartments are an important component of the global carbon balance and pedoecological processes. Tropical forests are the world’s most productive ecosystems and the forest floor is the main DOC-source in these environments. This study aimed to compare DOC concentrations under the forest floor with different litter-decomposition rates. Four study plots were established along a hillslope profile where heterogeneity was observed in previous studies: drainage divide (DRD); upper-hillslope (UHS); lower-hillslope (LHS); and valley bottom (VLB). Inversely proportional to the decomposition rates, the litter storage in this profile was as follows: DRD > UHS ≅ LHS > VLB. The bulk precipitation was a DOC source statistically similar to canopy-washing, and DOC concentrations in throughfall were statistically similar among the hillslope positions. There was some dilution effect in the inter-event modulation, mainly in throughfall and associated with the rainfall maximum intensity. The DOC concentrations under the forest floor were related in a non-linear manner with the litter storage: thin stocks in VLB showed lower DOC concentrations, but the thicker stocks in DRD did not materialise in the highest concentrations; the litter storage in UHS and LHS showed higher DOC-concentrations as a result of a balance between maintaining the DOC-source and making new soluble byproducts available that favoured the DOC-release to water.
Trained innate immunity, long-lasting epigenetic modulation, and skewed myelopoiesis by heme
Authors: Jentho Elisa , Ruiz-Moreno Cristian , Novakovic Boris , Kourtzelis Ioannis , Megchelenbrink Wout. L. , Martins Rui , Chavakis Triantafyllos , Soares Miguel P. , Kalafati Lydia , Guerra Joel , Roestel Franziska , Bohm Peter , Godmann Maren , Grinenko Tatyana , Eugster Anne , Beretta Martina , Joosten Leo A. B. , Netea Mihai G. , Bauer Michael , Stunnenberg Hendrik G. , Weis Sebastian 
Published: October 2021

Significance
During infection, extracellular “labile” heme, released from damaged red blood or parenchymal cells, acts as prototypical alarmin stimulating myeloid cells. A characteristic hallmark of myeloid cell activation is the development of trained immunity, specified as long-lasting adaptations based on transcriptional and epigenetic modifications. In vivo, this is maintained by the rerouting of hematopoiesis. We found that heme is a previously unrecognized trained immunity inducer promoting resistance to bacterial infection in mice. This goes along with extensive long-lasting epigenetic memory in hematopoietic stem cells provoking drastic changes in the transcription factor–binding landscape of myeloid progenitor cells. Given the critical role of heme during infections, we propose that trained immunity is a more general component of innate immunity than previously suggested.
Days of our ‘quarantined’ lives
Authors: Aslan Erhan 
Published: October 2021

Abstract
During the early stages of the COVID-19 pandemic, many users around the world exploited internet memes as a
digital source of humour to cope with the negative psychological effects of quarantining. Drawing on multimodal discourse analysis, this study investigates a set of COVID-19 internet memes to explore the quarantine activities and routines to understand ordinary people’s mindsets, anxieties and emotional
narratives surrounding self-isolation as well as the pragmatically generated humorous meanings relying on verbal and visual components of memes. The findings revealed that quarantine humour is centred around themes including quarantine day comparisons focusing on the perceived effects of home quarantines on physical and mental well-being, quarantine routines, and physical appearance	predictions at the end of quarantine. Intertextuality was a productive resource establishing connections between quarantine practices and popular texts. In addition, humorous meanings were created through anomalous juxtapositions of different texts and
incongruity resolution is largely dependent on the combined meanings of verbal and visual components.
Understanding handouts in candidate selection: Challenging party authority in Malawi
Authors: Chiweza Asiyati Lorraine , Kayuni Happy , Muriaas Ragnhild Louise 
Published: October 2021

Abstract
This article discusses the purposes and drivers of handouts in party primaries in Malawi. We argue that existing explanations of handouts are incomplete because they are developed to identify dynamics in presidential or legislative elections. Rules of national elections are constitutionally protected, and their fairness is monitored by both local and international observers. In contrast, rules guiding candidate selection in parties are less institutionalized, and, in some contexts, such as Malawi, a secret ballot cannot be taken for granted. This underlines the need for empirical studies of the logic of handouts at the candidate selection stage to study how differences in institutional context affect the strategic choices behind engaging in the practice. We demonstrate why such an analysis needs to be informed by an in-depth knowledge about the party organizations in which the candidate selection process itself takes place. Through qualitative interviews with members of selectorates and party primary contestants, we find that the institutional environment affects the propensity to use handouts. Mechanisms such as leadership interventions and the opportunity to stand as independent candidates make primary outcomes less final. This reduces the authority of local party organizations to control candidate selection and appropriates the use of patrimonial strategies.
Prognostic and predictive value of a metabolic risk score model in breast cancer: an immunogenomic landscape analysis
Authors: Su Dongqing , Wang Shiyuan , Xi Qilemuge , Lin Lin , Lu Qianzi , Yu Yao , Xiong Yuqiang , Wei Haodong , Liang Pengfei , Lv Yingli , Zuo Yongchun , Yang Lei 
Published: October 2021

AbstractBreast cancer is a kind of malignant tumor that occurs in breast tissue, which is the most common cancer in women. Cellular metabolism is a critical determinant of the viability and function of cancer cells in tumor microenvironment. In this study, based on the gene expression profile of metabolism-related genes, the prognostic value of 20 metabolic pathways in patients with breast cancer was identified. A universal risk stratification signature that relies on 20 metabolic pathways was established and validated in training cohort, two testing cohorts and The Cancer Genome Atlas pan cancer cohort. Then, the relationship between metabolic risk score subtype, prognosis, immune infiltration level, cancer genotypes and their impact on therapeutic benefit were characterized. Results demonstrated that the patients with the low metabolic risk score subtype displayed good prognosis, high level of immune infiltration and exhibited a favorable response to neoadjuvant chemotherapy and immunotherapy. Taken together, the work presented in this study may deepen the understanding of metabolic hallmarks of breast cancer, and may provide some valuable information for personalized therapies in patients with breast cancer.
Calling small variants using universality with Bayes-factor-adjusted odds ratios
Authors: Zhao Xiaofei , Hu Allison C , Wang Sizhen , Wang Xiaoyue 
Published: October 2021

AbstractThe application of next-generation sequencing in research and particularly in clinical routine requires highly accurate variant calling. Here we describe UVC, a method for calling small variants of germline or somatic origin. By unifying opposite assumptions with sublation, we discovered the following two empirical laws to improve variant calling: allele fraction at high sequencing depth is inversely proportional to the cubic root of variant-calling error rate, and odds ratios adjusted with Bayes factors can model various sequencing biases. UVC outperformed other variant callers on the GIAB germline truth sets, 192 scenarios of in silico mixtures simulating 192 combinations of tumor/normal sequencing depths and tumor/normal purities, the GIAB somatic truth sets derived from physical mixture, and the SEQC2 somatic reference sets derived from the breast-cancer cell-line HCC1395. UVC achieved 100% concordance with the manual review conducted by multiple independent researchers on a Qiagen 71-gene-panel dataset derived from 16 patients with colon adenoma. UVC outperformed other unique molecular identifier (UMI)-aware variant callers on the datasets used for publishing these variant callers. Performance was measured with sensitivity-specificity trade off for called variants. The improved variant calls generated by UVC from previously published UMI-based sequencing data provided additional insight about DNA damage repair. UVC is open-sourced under the BSD 3-Clause license at https://github.com/genetronhealth/uvc and quay.io/genetronhealth/gcc-6-3-0-uvc-0-6-0-441a694
HPODNets: deep graph convolutional networks for predicting human protein–phenotype associations
Authors: Liu Lizhi , Mamitsuka Hiroshi , Zhu Shanfeng 
Published: October 2021

Abstract

Motivation
Deciphering the relationship between human genes/proteins and abnormal phenotypes is of great importance in the prevention, diagnosis and treatment against diseases. The Human Phenotype Ontology (HPO) is a standardized vocabulary that describes the phenotype abnormalities encountered in human disorders. However, the current HPO annotations are still incomplete. Thus, it is necessary to computationally predict human protein–phenotype associations. In terms of current, cutting-edge computational methods for annotating proteins (such as functional annotation), three important features are (i) multiple network input, (ii) semi-supervised learning and (iii) deep graph convolutional network (GCN), whereas there are no methods with all these features for predicting HPO annotations of human protein.

Results
We develop HPODNets with all above three features for predicting human protein–phenotype associations. HPODNets adopts a deep GCN with eight layers which allows to capture high-order topological information from multiple interaction networks. Empirical results with both cross-validation and temporal validation demonstrate that HPODNets outperforms seven competing state-of-the-art methods for protein function prediction. HPODNets with the architecture of deep GCNs is confirmed to be effective for predicting HPO annotations of human protein and, more generally, node label ranking problem with multiple biomolecular networks input in bioinformatics.

Availability and implementation
https://github.com/liulizhi1996/HPODNets.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effects of the availability of floral resources and neighboring plants on nectar robbery in a specialized pollination system
Authors: Almeida Júlia Mendonça , Missagia Caio César Corrêa , Alves Maria Alice Santos 
Published: October 2021

AbstractMany plants pollinated by nectar-foraging animals have to maintain a balance between legitimate visitor attraction strategies and mechanisms that minimize illegitimate visits. This study investigated how floral display and neighboring species composition influences nectar robbing by hummingbirds in the tropical ornithophilous herb Heliconia spathocircinata. We tested the role of inflorescence display, flower abundance, and neighboring species in the reduction of nectar robbing in H. spathocircinata. Our results indicate that nectar robbing hummingbird activity was higher in moderately large inflorescence displays and that the frequency of nectar robbing in H. spathocircinata decreases with increased flower abundance and the presence of neighboring plant species. Neighboring non-ornithophilous plants decreased the frequency of nectar robbing in H. spathocircinata flowers to a greater extent than ornithophilous ones. These results suggest that nectar robbing hummingbirds are attracted to similar conditions that attract legitimate visitors and that spatial aggregation and mixed-species displays may represent a mechanism to dilute nectar robbing effects at an individual level.
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses
Authors: Khan Taimoor , Khan Abbas , Wei Dong-Qing 
Published: October 2021

Abstract
The recent viral outbreaks and the current pandemic situation urges us to timely address any emerging viral infections by designing therapeutic strategies. Multi-omics and therapeutic data are of great interest to develop early remedial interventions. This work provides a therapeutic data platform (Mammarenavirus (MMV)-db) for pathogenic mammarenaviruses with potential catastrophic effects on human health around the world. The database integrates vaccinomics and RNA-based therapeutics data for seven human pathogenic MMVs associated with severe viral hemorrhagic fever and lethality in humans. Protein-specific cytotoxic T lymphocytes, B lymphocytes, helper T-cell and interferon-inducing epitopes were mapped using a cluster of immune-omics-based algorithms and tools for the seven human pathogenic viral species. Furthermore, the physiochemical and antigenic properties were also explored to guide protein-specific multi-epitope subunit vaccine for each species. Moreover, highly efficacious RNAs (small Interfering RNA (siRNA), microRNA and single guide RNA (sgRNA)) after extensive genome-based analysis with therapeutic relevance were explored. All the therapeutic RNAs were further classified and listed on the basis of predicted higher efficacy. The online platform (http://www.mmvdb.dqweilab-sjtu.com/index.php) contains easily accessible data sets and vaccine designs with potential utility in further computational and experimental work. Conclusively, the current study provides a baseline data platform to secure better future therapeutic interventions against the hemorrhagic fever causing mammarenaviruses.
Database URL: http://www.mmvdb.dqweilab-sjtu.com/index.php
Prognostic value of depressed cardiac index after STEMI: a phase-contrast magnetic resonance study
Authors: Schwaiger Johannes P , Reinstadler Sebastian J , Holzknecht Magdalena , Tiller Christina , Reindl Martin , Begle Jana , Lechner Ivan , Lamina Claudia , Mayr Agnes , Graziadei Ivo , Bauer Axel , Metzler Bernhard , Klug Gert 
Published: October 2021

AbstractAims An invasively measured cardiac index (CI) of ≤2.2 L/min/m2 is one of the strongest prognostic indicators after ST-elevation myocardial infarction (STEMI), however, knowledge is mainly based on invasive evaluations performed in the pre-stent era. Velocity-encoded phase-contrast cardiac magnetic resonance (PC-CMR) allows non-invasive determination of CI.Methods and results In this prospective study, CMR was performed in 406 stable and contemporarily revascularized patients a median of 3 days after STEMI. Forward stroke volume was assessed at the level of the ascending aorta by PC-CMR. Left ventricular ejection fraction (LVEF) and global longitudinal strain (GLS) were determined by cine CMR. Major adverse cardiac events (MACE) were defined as the composite of death, myocardial infarction, or hospitalization for heart failure. Median CI was 2.52 L/min/m2 and 27% of patients had ≤2.2 L/min/m2. Median LVEF was 53% and median GLS was −12.2%. During a median follow-up of 14.2 [95% confidence interval (95% CI) 13.6–14.7] months, 41 patients (10.1%) experienced a MACE. A depressed CI was significantly associated with MACE after adjustment for LVEF, GLS, Thrombolysis in Myocardial Infarction (TIMI) risk score, and infarct size [hazard ratio = 3.15 (95% CI 1.53–6.47); P = 0.002] and led to significant discrimination improvement [net reclassification improvement 0.61 (95% CI 0.25–0.97); P &lt; 0.001].Conclusions A CI of 2.2 L/min/m2 or less as measured by PC-CMR was present in 27% of clinically stable patients after STEMI and strongly and independently predicted medium-term MACE. The prognostic value of a depressed CI was superior and incremental to LVEF, GLS, TIMI risk score, and infarct size.