bluuebunny/crossref_metadata_2025_split huggingface dataset:
Soluble angiotensin-converting enzyme 2 is transiently elevated in COVID-19 and correlates with specific inflammatory and endothelial markers
Authors: Lundström Annika , Ziegler Louise , Havervall Sebastian , Rudberg Ann-Sofie , von Meijenfeldt Fien , Lisman Ton , Mackman Nigel , Sandén Per , Thålin Charlotte 
Published: March 2021

AbstractRationaleAngiotensin-converting enzyme 2 (ACE2) is the main entry receptor of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but how SARS-CoV-2 interactions with ACE2 influences the renin-angiotensin system (RAS) in Coronavirus disease 2019 (COVID-19) is unknown.ObjectiveTo measure circulating ACE2 and ACE levels in COVID-19 patients and investigate association with risk factors, outcome and inflammatory markers.Methods and resultsSoluble ACE2 (sACE2) and sACE concentrations were measured by ELISA in plasma samples from 114 hospital-treated COVID-19 patients and 10 healthy controls. Follow-up samples after four months were available for 58/114 patients. Von Willebrand factor (VWF), factor VIII (fVIII), D-dimer, interleukin 6 (IL-6), tumor necrosis factor α and plasminogen activator inhibitor 1 (PAI-1) had previously been determined. Levels of sACE2 were higher in COVID-19 patients than in healthy controls, median 5.0 (interquartile range 2.8-11.8) ng/ml versus 1.4 (1.1-1.6) ng/ml, p < 0.0001. sACE2 was higher in men than women, but were not affected by other risk factors for severe COVID-19. sACE 2 decreased to 2.3 (1.6-3.9) ng/ml at follow-up, p < 0.0001, but remained higher than in healthy controls, p=0.012. Follow-up sACE2 levels were higher with increasing age, BMI, total number of comorbidities, for patients with diabetes and patients on RAS-inhibition. sACE was marginally lower during COVID-19 compared with at follow-up, 57 (45-70) ng/ml versus 72 (52-87) ng/ml, p=0.008. Levels of sACE2 and sACE did not differ depending on survival or disease severity (care level, respiratory support). sACE2 during COVID-19 correlated with VWF, fVIII and D-dimer, while sACE correlated with IL-6, TNFα and PAI-1.ConclusionssACE2 was transiently elevated in COVID-19, likely due to increased shedding from infected cells. sACE2 and sACE during COVID-19 differed distinctly in their correlations with markers of inflammation and endothelial dysfunction, suggesting release from different cell types and/or vascular beds.
Factors associated with severe sepsis in diarrheal adults and their outcome at an urban hospital, Bangladesh: A retrospective analysis
Authors: Sarmin Monira , Begum Monjory , Islam Farhana , Afroze Farzana , Shahrin Lubaba , zaman Sharifuz , Alam Tahmina , Bin Shahid Abu Sadat Mohammad Sayeem , Ahmed Tahmeed , Chisti Mohammod Jobayer 
Published: March 2021

AbstractBackgroundClinical features of sepsis and severe diarrhea often overlap and create a dilemma among the clinicians. To describe factors associated with severe sepsis in diarrheal adults and their outcomes to understand their interplay as clinical features of sepsis and severe diarrhea often overlap.Methods and resultsWe used this retrospective chart analysis employing a case-control design to study critically ill diarrheal adults aged ≥ 18 years treated in ICU Dhaka hospital, icddr,b between January 2011 to December 2015. Diarrheal adults with a diagnosis of severe sepsis were cases and an equal number of randomly selected non-septic patients were the controls. Of 8,863 in-patient adults, 350 fulfilled the criteria of cases. Cases died significantly more (9% vs 3%, p=0.002) than controls. 69% of the cases progressed to septic shock. In logistic regression analysis, steroid intake, ileus, acute kidney injury, metabolic acidosis, and hypocalcemia were significantly associated with severe sepsis in diarrheal adults (all, p<0.05). 12% of cases (40/335) had bacteremia. Streptococcus pneumoniae [9 (22.5%)] was the single most common pathogen and gram-negatives [27 (67.5%)] were prevailing as a group.ConclusionDiarrheal adults who had ileus, AKI, metabolic acidosis, hypocalcemia, and also took steroids were prone to have severe sepsis. Strikingly, gram-negatives were the predominant bacteria among the diarrheal adults having severe sepsis.
V3 Interneurons are Active and Recruit Spinal Motor Neurons DuringIn VivoFictive Swimming in Larval Zebrafish
Authors: Wiggin Timothy D. , Montgomery Jacob E. , Brunick Amanda J. , Peck Jack H. , Masino Mark A. 
Published: March 2021

ABSTRACTSurvival for vertebrate animals is dependent on the ability to successfully find food, locate a mate, and avoid predation. Each of these behaviors requires motor control, which is set by a combination of kinematic properties. For example, the frequency and amplitude of motor output combine in a multiplicative manner to determine features of locomotion such as distance traveled, speed, force (thrust), and vigor. Although there is a good understanding of how different populations of excitatory spinal interneurons establish locomotor frequency, there is a less thorough mechanistic understanding for how locomotor amplitude is established. Recent evidence indicates that locomotor amplitude is regulated in part by a subset of functionally and morphologically distinct V2a excitatory spinal interneurons (type II, non-bursting) in larval and adult zebrafish. Here we provide direct evidence, for the first time, that most V3 interneurons (V3-INs), which are a developmentally and genetically defined population of ventromedial glutamatergic spinal neurons, are active during fictive swimming. We also show that elimination of the spinal V3-IN population reduces the proportion of active MNs during fictive swimming but does not alter the range of locomotor frequencies produced. These data are consistent with V3-INs providing excitatory drive to spinal motor neurons and contributing to the production of locomotor amplitude, but not frequency, during swimming in larval zebrafish.SIGNIFICANCE STATEMENTCurrently, there is a limited understanding about the cellular and spinal network properties that produce locomotor amplitude, defined as limb displacement in limbed animals or tail-bend in non-limbed animals during locomotion. Here we show, directly for the first time in a vertebrate, that V3 interneurons (V3-INs) in zebrafish larvae are active duringin vivofictive locomotion, and that targeted ablation of the spinal V3-IN population reduces the proportion of active motoneurons during fictive swimming. Importantly, ablation of V3-INs does not affect locomotor frequency (speed), which clarifies their role in motor control rather than rhythm generation. Thus, we propose that the V3-IN population is a source of excitation in the vertebrate locomotor neural circuitry that regulates locomotor amplitude independently of speed.
Pro-inflammatory alveolar macrophages associated with allograft dysfunction after lung transplantation
Authors: Moshkelgosha Sajad , Wilson Gavin , Duong Allen , Andrews Tallulah , Berra Gregory , Renaud-Picard Benjamin , Keshavjee Shaf , Martinu Tereza , MacParland Sonya , Yeung Jonathan , Juvet Stephen 
Published: March 2021

AbstractPurposeLung transplant (LT) recipients experience episodes of immune-mediated acute lung allograft dysfunction (ALAD). We have applied single-cell RNA sequencing (scRNAseq) to bronchoalveolar lavage (BAL) cells of stable and ALAD patients to determine key cellular elements in dysfunctional lung allografts. Our particular focus here is on studying alveolar macrophages (AMs) as scRNAseq enables us to elucidate their heterogeneity and possible association with ALAD where our knowledge from cytometry-based assays is very limited.MethodsFresh bronchoalveolar lavage (BAL) cells from 6 LT patients, 3 with stable lung function (3044 ± 1519 cells) and 3 undergoing an episode of ALAD (2593 ± 904 cells) were used for scRNAseq. R Bioconductor and Seurat were used to perform QC, dimensionality reduction, annotation, pathway analysis, and trajectory. Donor and recipient deconvolution was performed using single nucleotide variations.ResultsOur data revealed that AMs are highly heterogeneous (12 transcriptionally distinct subsets in stable). We identified two AM subsets uniquely represented in ALAD. Based on pathway analysis and the top differentially expressed genes in BAL we annotated them as pro-inflammatory interferon-stimulated genes (ISG) and metallothioneins-mediated inflammatory (MT). Pseudotime analysis suggested that ISG AMs represent an earlier stage of differentiation which may suggest them as monocyte drive macrophages. Our functional analysis on an independent set of BAL samples shows that ALAD samples have significantly higher expression of CXCL10, a marker of ISG AM, as we as higher secretion of pro-inflammatory cytokines. Single nucleotide variation calling algorithm has allowed us to identify macrophages of donor origin and demonstrated that donor AMs are lost with time post-transplant.ConclusionUsing scRNAseq, we observed AMs heterogeneity and identified specific subsets that may be associated with allograft dysfunction. Further exploration with scRNAseq will shed light on LT immunobiology and the role of AMs in allograft injury and dysfunction.
In situ community dynamics influences the temperature- and light- dependent succession of seasonal phytoplankton
Authors: Tragin Margot , Lambert Stefan , Lozano Jean-Claude , Bouget François-Yves 
Published: March 2021

AbstractTemperature and light play a crucial role in regulating phytoplankton blooms in the Ocean. To assess the importance of these two parameters experimentally, microcosms were conducted on seven picoplankton communities (<3 μm) sampled in December, March, June and September 2015 and 2016 in the North Western Mediterranean Sea. Each community was exposed to 4 realistic seasonal conditions (December, March, June and September). Metabarcoding was used to investigate the eukaryotic diversity in the 56 microcosms experiments in parallel to high-frequency monitoring of environmental diversity in the sea. The three major lineages identified were the Stramenopiles, Alveolata and Archaeplastida. Overall, the five-day incubations were not sufficient to reshape the initial microbial communities completely. The microcosm outcome was strongly influenced by the dynamics of phytoplankton starting communities. In pre-bloom conditions, phytoplanktonic species were the most sensitive to temperature and light conditions. During a bloom, species belonging to diatoms or Chlorodendrophyceae usually did not respond to light and temperature in microcosms and continued to bloom independently of the applied seasonal condition. Together, these results suggest that light and temperature seasonal conditions play a crucial role in regulating phytoplankton dynamics in pre-bloom conditions and biotic interactions may be preponderant in bloom and post-bloom conditions.
Towards a standardization of non-symbolic numerical experiments: GeNEsIS, a flexible and user-friendly tool to generate controlled stimuli
Authors: Zanon Mirko , Potrich Davide , Bortot Maria , Vallortigara Giorgio 
Published: March 2021

AbstractSeveral studies have suggested that vertebrate and invertebrate species may possess anumber sense, i.e. an ability to process in a non-symbolic and non-verbal way the numerousness of a set of items. However, this hypothesis has been challenged by the presence of other non-numerical continuous physical variables, that vary along with numerosity (e.g. any change in the number of visual physical elements in a set naturally involves a related change in visual features such as area, density, contour length and convex hull of the stimulus). It is therefore necessary to control and manipulate the continuous physical information when investigating the ability of humans and other animals to perceive numerousness. During decades of research, different methods have been implemented in order to address this issue, which has implications for experiments replicability and inter-species comparisons, since no general standardized procedure is currently being used. Here we present the “Generation of Numerical Elements Images Software” (GeNEsIS) for the creation of non-symbolic numerical arrays in a standardized and user-friendly environment. The main aim of this tool would be to provide researchers in the field of numerical cognition with a manageable and precise instrument to produce visual numerical arrays controlled for all the continuous variables; additionally, we implemented the possibility to actively guide stimuli presentation during habituation/dishabituation and dual-choice comparison tasks used in human and comparative research.
PyADM1: a Python implementation of Anaerobic Digestion Model No. 1
Authors: Sadrimajd P. , Mannion P. , Howley E. , Lens P. N. L. 
Published: March 2021

AbstractAnaerobic Digestion (AD) is a waste treatment technology widely used for wastewater and solid waste treatment, with the advantage of being a source of renewable energy in the form of biogas. Anaerobic digestion model number 1 (ADM1) is the most common mathematical model available for AD modelling. Commercial software implementations of ADM1 are available but have limited flexibility and availability due to the closed sources and licensing fees. Python is the fastest growing programming language and is open source freely available. Python implementation of ADM1 makes this AD model available to the mass user base of the Python ecosystem and it’s libraries. The open easy to use implementation in PyADM1 makes it more accessible and provides possibilities for flexible direct use of the model linked to other software, e.g. machine learning libraries or Linux operating system on embedded hardware.
LncRNA analyses reveal increased levels of non-coding centromeric transcripts in hepatocellular carcinoma
Authors: Necsulea Anamaria , Veber Philippe , Boldanova Tuyana , Ng Charlotte K Y , Wieland Stefan , Heim Markus H 
Published: March 2021

AbstractThe search for new biomarkers and drug targets for hepatocellular carcinoma (HCC) has spurred an interest in long non-coding RNAs (lncRNAs), often proposed as oncogenes or tumor suppressors. Furthermore, lncRNA expression patterns can bring insights into the global de-regulation of cellular machineries in tumors. Here, we examine lncRNAs in a large HCC cohort, comprising RNA-seq data from paired tumor and adjacent tissue biopsies from 114 patients. We find that numerous lncRNAs are differentially expressed between tumors and adjacent tissues and between tumor progression stages. Although we find strong differential expression for most lncRNAs previously associated with HCC, the expression patterns of several prominent HCC-associated lncRNAs disagree with their previously proposed roles. We examine the genomic characteristics of HCC-expressed lncRNAs and reveal an enrichment for repetitive elements among the lncRNAs with the strongest expression increases in advanced-stage tumors. This enrichment is particularly striking for lncRNAs that overlap with satellite repeats, a major component of centromeres. Consistently, we find increased non-coding RNA transcription from centromeres in tumors, in the majority of patients, suggesting that aberrant centromere activation takes place in HCC.
Experimental tests of functional molecular regeneration via a standard framework for coordinating synthetic cell building
Authors: Wei Eric , Endy Drew 
Published: March 2021

AbstractThe construction of synthetic cells from lifeless ensembles of molecules is expected to require integration of hundreds of genetically-encoded functions whose collective capacities enable self-reproduction in simple environments. To date the regenerative capacities of various life-essential functions tend to be evaluated on an ad hoc basis, with only a handful of functions tested at once and only successful results typically reported. Here, we develop a framework for systematically evaluating the capacity of a system to remake itself. Using the cell-free Protein synthesis Using Recombinant Elements (PURE) as a model system we apply our framework to evaluate the capacity of PURE, whose composition is completely known, to remake 36 life-essential functions. We find that only 23 of the components can be well tested and that only 19 of the 23 can be remade by the system itself; translation release factors remade by PURE are not fully functional. From both a qualitative and quantitative perspective PURE alone cannot remake PURE. We represent our findings via a standard visual form we call the Pureiodic Table that serves as a tool for tracking which life-essential functions can work together in remaking one another and what functions remain to be remade. We curate and represent all available data to create an expanded Pureiodic Table in support of collective coordination among ongoing but independent synthetic cell building efforts. The history of science and technology teaches us that how we organize ourselves will impact how we organize our cells, and vice versa.
Modulation of tactile feedback for the execution of dexterous movement
Authors: Conner James M. , Bohannon Andrew , Igarashi Masakazu , Taniguchi James , Baltar Nicholas , Azim Eiman 
Published: March 2021

AbstractWhile dexterity relies on the constant transmission of sensory information, unchecked feedback can be disruptive to behavior. Yet how somatosensory feedback from the hands is regulated as it first enters the brain, and whether this modulation exerts any influence on movement, remain unclear. Leveraging molecular-genetic access in mice, we find that tactile afferents from the hand recruit neurons in the brainstem cuneate nucleus whose activity is modulated by distinct classes of local inhibitory neurons. Selective manipulation of these inhibitory circuits can suppress or enhance the transmission of tactile information, affecting behaviors that rely on movement of the hands. Investigating whether these local circuits are subject to top-down control, we identify distinct descending cortical pathways that innervate cuneate in a complementary pattern. Somatosensory cortical neurons target the core tactile region of cuneate, while a large rostral cortical population drives feed-forward inhibition of tactile transmission through an inhibitory shell. These findings identify a circuit basis for tactile feedback modulation, enabling the effective execution of dexterous movement.
Detection of ESKAPE pathogens andClostridioides difficilein Simulated Skin Transmission Events with Metagenomic and Metatranscriptomic Sequencing
Authors: Ternus Krista L. , Keplinger Nicolette C. , Kappell Anthony D. , Godbold Gene D. , Palsikar Veena , Acevedo Carlos A. , Weber Katharina L. , LeSassier Danielle S. , Schulte Kathleen Q. , Westfall Nicole M. , Hewitt F. Curtis 
Published: March 2021

1AbstractBackgroundAntimicrobial resistance is a significant global threat, posing major public health risks and economic costs to healthcare systems. Bacterial cultures are typically used to diagnose healthcare-acquired infections (HAI); however, culture-dependent methods provide limited presence/absence information and are not applicable to all pathogens. Next generation sequencing (NGS) has the capacity to detect a wide variety of pathogens, virulence elements, and antimicrobial resistance (AMR) signatures in healthcare settings without the need for culturing, but few research studies have explored how NGS could be used to detect viable human pathogen transmission events under different HAI-relevant scenarios.MethodsThe objective of this project was to assess the capability of NGS-based methods to detect the direct and indirect transmission of high priority healthcare-related pathogens. DNA was extracted and sequenced from a previously published study exploring pathogen transfer with simulated skin containing background microorganisms, which allowed for complementary culture and metagenomic analysis comparisons. RNA was also isolated from an additional set of samples to evaluate metatranscriptomic analysis methods at different concentrations.ResultsUsing various analysis methods and custom reference databases, both pathogenic and non-pathogenic members of the microbial community were taxonomically identified. Virulence and AMR genes known to reside within the community were also routinely detected. Ultimately, pathogen abundance within the overall microbial community played the largest role in successful taxonomic classification and gene identification.ConclusionsThese results illustrate the utility of metagenomic analysis in clinical settings or for epidemiological studies, but also highlight the limits associated with the detection and characterization of pathogens at low abundance in a microbial community.
Identification and characterization of novel plasma proteins in drug resistant HIV/AIDS patients by SWATH-MS
Authors: Barik Sushanta Kumar , Tripathy Srikanth Prasad , Bisht Deepa , Singh Praveen , Chakraborty Rahul , Chadar Monu Kumar , Patil Shripad A , Singh Tej Pal , Tandon Rekha , Jena Srikanta , Mohanty Keshar Kunja 
Published: March 2021

AbstractBackground and ObjectivesAcquired immunodeficiency syndrome is one of the most important diseases caused by human immunodeficiency virus. Understanding its molecular pathogenesis is essential to manage the disease at the population level. In this study, a quantitative analysis of plasma proteins was carried out in drug resistant and drug respondent patients using the SWATH-MS.MethodsSequential window acquisition of all theoretical mass spectra (SWATH-MS) is a prime technique to seek the key plasma proteins involved in virus replication and drug metabolism during therapy.ResultsIn total, 204 proteins were identified and quantified, 57 proteins were differentially expressed, 25 proteins were down regulated and 32 proteins were upregulated in drug resistant patients. Six proteins such as complement C4-A, immunoglobulin heavy variable 1-2, carboxylic ester hydrolase, fibulin-1, immunoglobulin lambda constant 7, secreted phosphoprotein 24 were statistically expressed in drug resistant patients compared to the drug respondent patients. Gene ontology study and protein-protein interaction networks were established in six statistically significant differentially expressed proteins of the drug resistant patients.Interpretation and ConclusionOur findings high lights the novel proteins that were differentially expressed in drug resistant patients. A label-free quantitative proteomics method for depleted human plasma samples by SWATH-MS that can be useful in plasma proteomics research in any biological system.
Canopy Volume as a Tool for Early Detection of Plant Drought and Fertilization Stress: Banana plant fine-phenotype
Authors: Brook Anna , Tal Yasmin , Markovich Oshry , Rybnikova Nataliya 
Published: March 2021

AbstractIrrigation and fertilization stress in plants are limitations for securing global food production. Sustainable agriculture is at the heart of global goals because threats of a rapidly growing population and climate changes are affecting agricultural productivity. Plant phenotyping is defined as evaluating plant traits. Traditionally, this measurement is performed manually but with advanced technology and analysis, these traits can be observed automatically and nondestructively. A high correlation between plant traits, growth, biomass, and final yield has been found. From the early stages of plant development, lack of irrigation and fertilization directly influence developing stages, thus the final crop yield is significantly reduced. In order to evaluate drought and fertilization stress, plant height, as a morphological trait, is the most common one used in precision-agriculture research. The present study shows that three-dimension volumetric approaches are more representative markers for alerting growers to the early stages of stress in young banana plants’ for fine-scale phenotyping. This research demonstrates two different group conditions: 1) Normal conditions; and 2) zero irrigation and zero fertilization. The statistical analysis results show a successfully distinguished early stress with the volumetric traits providing new insights on identifying the key phenotypes and growth stages influenced by drought stress.