bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cellinker: a platform of ligand–receptor interactions for intercellular communication analysis
Authors: Zhang Yang , Liu Tianyuan , Wang Jing , Zou Bohao , Li Le , Yao Linhui , Chen Kechen , Ning Lin , Wu Bingyi , Zhao Xiaoyang , Wang Dong 
Published: January 2021

Abstract

Motivation
Ligand–receptor (L–R) interactions mediate cell adhesion, recognition and communication and play essential roles in physiological and pathological signaling. With the rapid development of single-cell RNA sequencing (scRNA-seq) technologies, systematically decoding the intercellular communication network involving L–R interactions has become a focus of research. Therefore, construction of a comprehensive, high-confidence and well-organized resource to retrieve L–R interactions in order to study the functional effects of cell–cell communications would be of great value.

Results
In this study, we developed Cellinker, a platform of literature-supported L–R interactions that play roles in cell–cell communication. We aimed to provide a useful platform for studies on cell–cell communication mediated by L–R interactions. The current version of Cellinker documents over 3700 human and 3200 mouse L–R protein–protein interactions (PPIs) and embeds a practical and convenient webserver with which researchers can decode intercellular communications based on scRNA-seq data. And over 400 endogenous small molecule (sMOL) related L–R interactions were collected as well. Moreover, to help with research on coronavirus (CoV) infection, Cellinker collects information on 16L–R PPIs involved in CoV–human interactions (including 12L–R PPIs involved in SARS-CoV-2 infection). In summary, Cellinker provides a user-friendly interface for querying, browsing and visualizing L–R interactions as well as a practical and convenient web tool for inferring intercellular communications based on scRNA-seq data. We believe this platform could promote intercellular communication research and accelerate the development of related algorithms for scRNA-seq studies.

Availability and implementation
Cellinker is available at http://www.rna-society.org/cellinker/

Supplementary information
Supplementary data are available at Bioinformatics online.
Survival after antireflux surgery versus medication in patients with reflux oesophagitis or Barrett’s oesophagus: multinational cohort study
Authors: Yanes M , Santoni G , Maret-Ouda J , Ness-Jensen E , Färkkilä M , Lynge E , Pukkala E , Romundstad P , Tryggvadóttir L , -Chelpin M von Euler , Lagergren J 
Published: January 2021

Abstract

Background
The aim was to examine the hypothesis that antireflux surgery with fundoplication improves long-term survival compared with antireflux medication in patients with reflux oesophagitis or Barrett’s oesophagus.

Method
Individuals aged between 18 and 70 years with reflux oesophagitis or Barrett’s oesophagus (intestinal metaplasia) documented from in-hospital and specialized outpatient care were selected from national patient registries in Denmark, Finland, Iceland, and Sweden from 1980 to 2014. The study investigated all-cause mortality and disease-specific mortality, comparing patients who had undergone open or laparoscopic antireflux surgery with fundoplication versus those using antireflux medication. Multivariable Cox regression analysis was used to estimate hazard ratios (HRs) with 95 per cent confidence intervals for all-cause mortality and disease-specific mortality, adjusted for sex, age, calendar period, country, and co-morbidity.

Results
Some 240 226 patients with reflux oesophagitis or Barrett’s oesophagus were included, of whom 33 904 (14.1 per cent) underwent antireflux surgery. The risk of all-cause mortality was lower after antireflux surgery than with use of medication (HR 0.61, 95 per cent c.i. 0.58 to 0.63), and lower after laparoscopic (HR 0.56, 0.52 to 0.60) than open (HR 0.80, 0.70 to 0.91) surgery. After antireflux surgery, mortality was decreased from cardiovascular disease (HR 0.58, 0.55 to 0.61), respiratory disease (HR 0.62, 0.57 to 0.66), laryngeal or pharyngeal cancer (HR 0.35, 0.19 to 0.65), and lung cancer (HR 0.67, 0.58 to 0.80), but not from oesophageal cancer (HR 1.05, 0.87 to 1.28), compared with medication, The decreased mortality rates generally remained over time.

Conclusion
In patients with reflux oesophagitis or Barrett’s oesophagus, antireflux surgery is associated with lower mortality from all causes, cardiovascular disease, respiratory disease, laryngeal or pharyngeal cancer, and lung cancer, but not from oesophageal cancer, compared with antireflux medication.
Sudden cardiac death after implantation of a cardiac resynchronization therapy pacemaker: a case report illustrating that not always less is more
Authors: Vollmann Dirk , Hansen Claudius , Hunold Peter , Lüthje Lars 
Published: January 2021

Abstract

Background
Cardiac resynchronization therapy (CRT) improves symptoms and survival in selected patients with systolic heart failure and ventricular conduction delay. In subjects without prior life-threatening ventricular arrhythmia, clinicians have to select between implanting a CRT pacemaker (CRT-P) or a more complex device with additional defibrillator capability (CRT-D). This individual decision can be challenging in light of the available evidence and the potential risks and benefits.

Case summary
A 76-year-old male with non-ischaemic cardiomyopathy, heart failure New York Heart Association Class III, left bundle branch block (QRS duration 185 ms) and a left ventricular ejection fraction of 30% despite optimal medical therapy was indicated for CRT. In light of the patient characteristics and clinical condition, a CRT-P device was implanted. No complication occurred, and the patient was discharged after an appropriate device function was confirmed. Despite the clinical improvement, he died suddenly without prior symptoms approximately 2 months thereafter. Post-mortem device interrogation provided no evidence for device malfunction and confirmed sudden cardiac death (SCD) due to spontaneous ventricular fibrillation.

Discussion
Patients indicated for CRT often have overlapping internal cardioverter defibrillator indication for the primary prevention of SCD. By weighing individual risks and potential benefits, clinicians have to decide whether to implant a CRT-P (less is more) or a more complex and costly CRT-D device. Despite careful consideration of patient characteristics and clinical conditions, however, SCD can occur in subjects categorized as low risk and implanted with a CRT-P. More data from randomized clinical trials are needed to better support physicians in the often challenging process of selecting the most appropriate device for CRT.
Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism
Authors: Zajac Natalia , Zoller Stefan , Seppälä Katri , Moi David , Dessimoz Christophe , Jokela Jukka , Hartikainen Hanna , Glover Natasha 
Published: January 2021

Abstract
Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host–parasite adaptation.
Pan-Arctic suitable habitat model for Greenland halibut
Authors: Vihtakari Mikko , Hordoir Robinson , Treble Margaret , Bryan Meaghan D , Elvarsson Bjarki , Nogueira Adriana , Hallfredsson Elvar H , Christiansen Jørgen Schou , Albert Ole Thomas 
Published: January 2021

Abstract
Deep-sea marine fishes support important fisheries but estimates of their distributions are often incomplete as the data behind them may reflect fishing practices, access rights, or political boundaries, rather than actual geographic distributions. We use a simple suitable habitat model based on bottom depth, temperature, and salinity to estimate the potential distribution of Greenland halibut (Reinhardtius hippoglossoides). A large presence-only dataset is examined using multivariate kernel densities to define environmental envelopes, which we link to spatial distribution using a pan-Arctic oceanographic model. Occurrences generally fit the model well, although there were gaps in the predicted circum-Arctic distribution likely due to limited survey activity in many of the ice-covered seas around the Arctic Ocean. Bottom temperature and depth were major factors defining model fit to observations, but other factors, such as ecosystem interactions and larval drift could also influence distribution. Model predictions can be tested by increasing sampling effort in poorly explored regions and by studying the connectivity of putative populations. While abundances of Greenland halibut in the High Arctic are currently low, some areas are predicted to be suitable habitat for this species, suggesting that on-going sea-ice melt may lead to fisheries expansion into new areas.
Low antileishmanial drug exposure in HIV-positive visceral leishmaniasis patients on antiretrovirals: an Ethiopian cohort study
Authors: Kip Anke E , Blesson Séverine , Alves Fabiana , Wasunna Monique , Kimutai Robert , Menza Peninah , Mengesha Bewketu , Beijnen Jos H , Hailu Asrat , Diro Ermias , Dorlo Thomas P C 
Published: January 2021

Abstract

Background
Despite high HIV co-infection prevalence in Ethiopian visceral leishmaniasis (VL) patients, the adequacy of antileishmanial drug exposure in this population and effect of HIV-VL co-morbidity on pharmacokinetics of antileishmanial and antiretroviral (ARV) drugs is still unknown.

Methods
HIV-VL co-infected patients received the recommended liposomal amphotericin B (LAmB) monotherapy (total dose 40 mg/kg over 24 days) or combination therapy of LAmB (total dose 30 mg/kg over 11 days) plus 28 days 100 mg/day miltefosine, with possibility to extend treatment for another cycle. Miltefosine, total amphotericin B and ARV concentrations were determined in dried blood spots or plasma using LC–MS/MS.

Results
Median (IQR) amphotericin B Cmax on Day 1 was 24.6 μg/mL (17.0–34.9 μg/mL), which increased to 40.9 (25.4–53.1) and 33.2 (29.0–46.6) μg/mL on the last day of combination and monotherapy, respectively. Day 28 miltefosine concentration was 18.7 (15.4–22.5) μg/mL. Miltefosine exposure correlated with amphotericin B accumulation. ARV concentrations were generally stable during antileishmanial treatment, although efavirenz Cmin was below the 1 μg/mL therapeutic target for many patients.

Conclusions
This study demonstrates that antileishmanial drug exposure was low in this cohort of HIV co-infected VL patients. Amphotericin B Cmax was 2-fold lower than previously observed in non-VL patients. Miltefosine exposure in HIV-VL co-infected patients was 35% lower compared with adult VL patients in Eastern Africa, only partially explained by a 19% lower dose, possibly warranting a dose adjustment. Adequate drug exposure in these HIV-VL co-infected patients is especially important given the high proportion of relapses.
Magnetogenesis around the first galaxies: the impact of different field seeding processes on galaxy formation
Authors: Garaldi Enrico , Pakmor Rüdiger , Springel Volker 
Published: January 2021

ABSTRACT
We study the evolution of magnetic fields generated by charge segregation ahead of ionization fronts during the Epoch of Reionization, and their effects on galaxy formation. We compare this magnetic seeding process with the Biermann battery, injection from supernovae, and an imposed seed field at redshift z ≳ 127. Using a suite of self-consistent cosmological and zoom-in simulations based on the Auriga galaxy-formation model, we determine that all mechanisms produce galactic magnetic fields that equally affect galaxy formation, and are nearly indistinguishable at z ≲ 1.5. The former is compatible with observed values, while the latter is correlated with the gas metallicity below a seed-dependent redshift. Low-density gas and haloes below a seed-dependent mass threshold retain memory of the initial magnetic field. We produce synthetic Faraday rotation measure maps, showing that they have the potential to constrain the seeding process, although current observations are not yet sensitive enough. Our results imply that the ad-hoc assumption of a primordial seed field – widely used in galaxy formation simulations but of uncertain physical origin – can be replaced by physically motivated mechanisms for magnetogenesis with negligible impact on galactic properties. Additionally, magnetic fields generated ahead of ionization fronts appear very similar but weaker than those produced by the Biermann battery. Hence, in a realistic scenario where both mechanisms are active, the former will be negligible compared to the latter. Finally, our results highlight that the high-redshift Universe is a fruitful testing ground for our understanding of magnetic fields generation.
Red noise and pulsations in evolved massive stars
Authors: Nazé Yaël , Rauw Gregor , Gosset Eric 
Published: January 2021

ABSTRACT
We examine high-cadence space photometry taken by the Transiting Exoplanet Survey Satellite (TESS) of a sample of evolved massive stars: 26 Wolf–Rayet stars (WRs) and eight luminous blue variables (LBVs) or candidate LBVs. To avoid confusion problems, only stars without bright Gaia neighbours and without evidence of bound companions are considered. This leads to a clean sample, the variability properties of which should truly reflect the properties of the WR and LBV classes. Red noise is detected in all cases and its fitting reveals characteristics very similar to those found for OB stars. Coherent variability is also detected for 20 per cent of the WR sample. Most detections occur at moderately high frequency (3–14 d−1), hence they are most probably linked to pulsational activity. This work doubles the number of WRs known to exhibit high-frequency signals.
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
Authors: Elosua-Bayes Marc , Nieto Paula , Mereu Elisabetta , Gut Ivo , Heyn Holger 
Published: January 2021

Abstract
Spatially resolved gene expression profiles are key to understand tissue organization and function. However, spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots). Simulating varying reference quantities and qualities, we confirmed high prediction accuracy also with shallowly sequenced or small-sized scRNA-seq reference datasets. SPOTlight deconvolution of the mouse brain correctly mapped subtle neuronal cell states of the cortical layers and the defined architecture of the hippocampus. In human pancreatic cancer, we successfully segmented patient sections and further fine-mapped normal and neoplastic cell states. Trained on an external single-cell pancreatic tumor references, we further charted the localization of clinical-relevant and tumor-specific immune cell states, an illustrative example of its flexible application spectrum and future potential in digital pathology.
Long non-coding RNAs in brain tumors
Authors: Katsushima Keisuke , Jallo George , Eberhart Charles G , Perera Ranjan J 
Published: January 2021

Abstract
Long non-coding RNAs (lncRNAs) have been found to be central players in the epigenetic, transcriptional and post-transcriptional regulation of gene expression. There is an accumulation of evidence on newly discovered lncRNAs, their molecular interactions and their roles in the development and progression of human brain tumors. LncRNAs can have either tumor suppressive or oncogenic functions in different brain cancers, making them attractive therapeutic targets and biomarkers for personalized therapy and precision diagnostics. Here, we summarize the current state of knowledge of the lncRNAs that have been implicated in brain cancer pathogenesis, particularly in gliomas and medulloblastomas. We discuss their epigenetic regulation as well as the prospects of using lncRNAs as diagnostic biomarkers and therapeutic targets in patients with brain tumors.
Gram-Negative Ventriculostomy-Associated Infections Predict Shunt Dependency in Stroke Diagnoses and Other Brain Injuries
Authors: Unda Santiago R , Mousa Hamad , Labagnara Kevin , Birnbaum Jessie , de Silva Neranjan , Wong Megan , Scoco Aleka N , Haranhalli Neil , Altschul David J 
Published: January 2021

Abstract

BACKGROUND
Several predictors have been studied for shunt dependency after stroke and other brain injuries. However, little is known about the association between ventriculostomy-associated infections (VAIs) and impaired cerebrospinal fluid (CSF) outflow. Moreover, gram-negative (GN) VAIs induce a potent neuroinflammatory process and are clinically challenging to treat.

OBJECTIVE
To assess if GN-VAIs predict ventriculoperitoneal shunt (VPS) dependency.

METHODS
Retrospective analysis of postprocedure infection rates was performed in 586 patients with external ventricle drainage (EVD) placed on site between 2012 and 2018. We collected sex, age, stroke and nonstroke related, location of EVD placement, type of hospital, EVD duration, and EVD exchange.

RESULTS
Among 586 patients requiring an EVD, 55 developed a VAI. Most were caused by gram-positive (GP) pathogens (61.8%). A total of 120 patients required a conversion from EVD to VPS. Patients with VAIs had higher rates of VPS placement (49.09% vs 17.65%, P < .001), whereas patients with GN-VAIs had significantly higher rates of EVD conversion to VPS (77.78% vs 35.29%, P = .012) compared with GP-VAIs. The multivariate analysis showed that GN-VAIs were an independent predictor for shunt dependency (odds ratio = 12.896; 95% CI 3.407-48.82, P < .001). In receiver operating characteristics analysis, those less than 44.5 yr of age and more than 12 d of EVD duration were identified as the best cutoff values to discriminate the development of GN-VAI.

CONCLUSION
Patients who experience a GN VAI are in greater risk of impaired CSF outflow, thus requiring VPS placement.
Savanna on the Nile
Authors: Fuller Dorian Q. , Lucas Leilani 
Published: January 2021

AbstractThis paper provides an overview of changing agricultural systems from the Neolithic to the Post-Meroitic Period in the greater Nubian region. There remain major gaps in the archaeobotanical evidence, and larger samples collected by systematic sieving and flotation are few and far between. Gaps in our knowledge include the initial establishment of the summer, sub-Saharan cereal cultivation system, but other important trends are much clearer, such as the arrival of the classic Egyptian winter cereal cultivation system of Near Eastern origin in the Late Neolithic at least in Lower Nubia; the latter of which complemented established pastoral traditions providing for the emergent political economy. The northward spread of the summer savannah crop system during the first few centuries ce formed the basis for subsequent intensification through the adoption of the cattle-powered saqia. Diversification and intensification through an integration of the summer and winter crop systems along with the development of a cash crop industry facilitated the development of Meroitic state. These processes also may have played an important role in economic changes in the Late Meroitic to Post-Meroitic transition, including the devolution of the Meroitic state. In addition to representing a long-term frontier of overlapping agricultural systems, Nubia was a frontier in cooking traditions, a crossroads between a world of bread in the North and one of liquid preparations, porridges, and beers in the South.
Political Organizations and Participation
Authors: Vromen Ariadne , Vaughan Michael , Halpin Darren 
Published: January 2021

Abstract
This chapter introduces four core dimensions of contemporary research on political organizations and participation to argue that this is a vibrant area of research within the study of Australian politics. First, there has been a productive debate between traditional understandings of participation—underpinned by dutiful, government-centred norms—and research focused on the emergence of newer forms of participation characterized by individualization, project identities, and issue-based mobilizations. Together, these areas of research show how citizens’ involvement with politics has changed over time. Second, digital communication technologies have provided new avenues for political action and for research, compounding processes of individualization and personalization. Third, in pioneering research, Australian interest organizations have been found to play a central role in Australian political life, particularly as participation preferences shift to project- and issue-based advocacy. Finally, these intersecting processes of normative, technological, and organizational change are evident in the arrival of new hybrid campaigning organizations like GetUp.
Early Modern Forerunners of Terrorism in Europe
Authors: Dillinger Johannes 
Published: January 2021

Abstract
First, this chapter explores political violence in the late Middle Ages and the early modern era. Even though the term terrorism did not exist before the French Revolution, political phenomena that closely resembled various forms of modern-day terrorism have been known and feared since the fourteenth century. The late Middle Ages and the early modern period witnessed the assassinations of numerous princes. The authorities as well as the populace feared organized gangs of criminals in the pay of rival political or religious leaders. These gangs were said to attack the civilian population using arson and mass poisoning in order to destabilize whole states. The fear of the terrorist “state destroyer” was part and parcel of state building from its very beginning. Secondly, the chapter discusses nineteenth-century historiography about early modern political violence. Nineteenth-century historians refused to interpret early modern political crime as terrorism: they either denounced it as lacking any political concept or vindicated it as justifiable resistance.