bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections
Authors: Gupta Anuj , Styczynski Mark P. , Galinski Mary R. , Voit Eberhard O. , Fonseca Luis L. 
Published: September 2021

AbstractPlasmodium knowlesi,a model malaria parasite, is responsible for a significant portion of zoonotic malaria cases in Southeast Asia and must be controlled to avoid disease severity and fatalities. However, little is known about the host-parasite interactions and molecular mechanisms in play during the course ofP. knowlesimalaria infections, which also may be relevant acrossPlasmodiumspecies. Here we contrastP. knowlesisporozoite-initiated infections inMacaca mulattaandMacaca fascicularisusing whole blood RNA-sequencing and transcriptomic analysis. These macaque hosts are evolutionarily close, yet malaria-naïveM. mulattawill succumb to blood-stage infection without treatment, whereas malaria-naïveM. fasciculariscontrols parasitemia without treatment. This comparative analysis reveals transcriptomic differences as early as the liver phase of infection, in the form of signaling pathways that are activated inM. fascicularis, but notM. mulatta. Additionally, while most immune responses are initially similar during the acute stage of the blood infection, significant differences arise subsequently. The observed differences point to prolonged inflammation and anti-inflammatory effects of IL10 inM. mulatta, whileM. fascicularisundergoes a transcriptional makeover towards cell proliferation, consistent with its recovery. Together, these findings suggest that timely detection ofP. knowlesiinM. fascicularis, coupled with control of inflammation while initiating the replenishment of key cell populations, helps contain the infection. Overall, this study points to specific genes and pathways that could be investigated as a basis for new drug targets that support recovery from acute malaria.
Vm-related extracellular potentials observed in red blood cells
Authors: Hughes Michael Pycraft , Kruchek Emily J. , Beale Andrew D. , Kitcatt Stephen J. , Qureshi Sara , Trott Zachary P. , Charbonnel Oriane , Agbaje Paul A. , Henslee Erin A. , Dorey Robert A. , Lewis Rebecca , Labeed Fatima H. 
Published: September 2021

AbstractEven in nonexcitable cells, the membrane potential Vm is fundamental to cell function, with roles from ion channel regulation, development, to cancer metastasis. Vm arises from transmembrane ion concentration gradients; standard models assume homogeneous extracellular and intracellular ion concentrations, and that Vm only exists across the cell membrane and has no significance beyond it. Using red blood cells, we show that this is incorrect, or at least incomplete; Vm is detectable beyond the cell surface, and modulating Vm produces quantifiable and consistent changes in extracellular potential. Evidence strongly suggests this is due to capacitive coupling between Vm and the electrical double layer, rather than molecular transporters. We show that modulating Vm changes the extracellular ion composition, mimicking the behaviour if voltage-gated ion channels in non-excitable channels. We also observed Vm-synchronised circadian rhythms in extracellular potential, with significant implications for cell–cell interactions and cardiovascular disease.
Revealing semantic and emotional structure of suicide notes with cognitive network science
Authors: Teixeira Andreia Sofia , Talaga Szymon , Swanson Trevor James , Stella Massimo 
Published: September 2021

AbstractUnderstanding how people who commit suicide perceive their cognitive states and emotions represents an important open scientific challenge. We build upon cognitive network science, psycholinguistics and semantic frame theory to introduce a network representation of suicidal ideation as expressed in multiple suicide notes. By reconstructing the knowledge structure of such notes, we reveal interconnections between the ideas and emotional states of people who committed suicide through an analysis of emotional balance motivated by structural balance theory, semantic prominence and emotional profiling. Our results indicate that connections between positively- and negatively-valenced terms give rise to a degree of balance that is significantly higher than in a null model where the affective structure is randomized and in a linguistic baseline model capturing mind-wandering in absence of suicidal ideation. We show that suicide notes are affectively compartmentalized such that positive concepts tend to cluster together and dominate the overall network structure. Notably, this positive clustering diverges from perceptions of self, which are found to be dominated by negative, sad conceptual associations in analyses based on subject-verb-object relationships and emotional profiling. A key positive concept is “love”, which integrates information relating the self to others and is semantically prominent across suicide notes. The emotions constituting the semantic frame of “love” combine joy and trust with anticipation and sadness, which can be linked to psychological theories of meaning-making as well as narrative psychology. Our results open new ways for understanding the structure of genuine suicide notes and may be used to inform future research on suicide prevention.
Indirect assessment of biomass accumulation in a wastewater-based Chlorella vulgaris photobioreactor by pH variation
Authors: Otim Francesca Nyega , Chen I-Ru , Otim Ochan 
Published: September 2021

AbstractAlgae bloom in coastal waters is partly supported by residual nutrients in treated wastewater (WW) released from coastally located treatment plants. In response, a Chlorella vulgaris-based photobioreactor was recently proposed for lowering nutrient levels in WW prior to release. However, the solution requires maintaining biomass accumulation to within a photobioreactor capacity for optimum operation. For high density Chlorella vulgaris suspensions, this is easily done by monitoring turbidity increase, a property directly related to biomass accumulation. For low density suspensions however, direct turbidity measurement would require a cumbersome process of concentrating large volumes of Chlorella vulgaris suspensions. Here, we demonstrate that by measuring pH of the suspensions, turbidity (T) can be estimated indirectly by the following wastewater-dependent expression: pH = aT + pH0, hence avoiding the need to concentrate large volumes. The term pH0 is the initial pH of the suspensions and a, a wastewater-dependent constant, can be computed independently from a = − 0.0061*pH0 + 0.052. In the event %WW is unknown, the following wastewater-independent Gaussian expression can be used to estimate T: pH = 8.71*exp(− [(T − 250)2]/[2*1.26E05]). These three equations should offer an avenue for monitoring the turbidity of dilute Chlorella vulgaris suspensions in large, stagnant municipal Chlorella vulgaris-based wastewater treatment system via pH measurements.
Evaluation of JATSdecoder as an automated text extraction tool for statistical results in scientific reports
Authors: Böschen Ingmar 
Published: September 2021

AbstractThe extraction of statistical results in scientific reports is beneficial for checking studies on plausibility and reliability. The R packageJATSdecodersupports the application of text mining approaches to scientific reports. Its functionget.stats()extracts all reported statistical results from text and recomputespvalues for most standard test results. The output can be reduced to results with checkable or computablepvalues only. In this article,get.stats()’s ability to extract, recompute and check statistical results is compared to that ofstatcheck, which is an already established tool. A manually coded data set, containing the number of statistically significant results in 49 articles, serves as an initial indicator forget.stats()’s andstatcheck’s differing detection rates for statistical results. Further 13,531 PDF files by 10 mayor psychological journals, 18,744 XML documents byFrontiers of Psychologyand 23,730 articles related to psychological research and published byPLoS Oneare scanned for statistical results with both algorithms.get.stats()almost replicates the manually extracted number of significant results in 49 PDF articles.get.stats()outperforms thestatcheckfunctions in identifying statistical results in every included journal and input format. Furthermore, the raw results extracted byget.stats()increasestatcheck’s detection rate.JATSdecoder’s functionget.stats()is a highly general and reliable tool to extract statistical results from text. It copes with a wide range of textual representations of statistical standard results and recomputespvalues for two- and one-sided tests. It facilitates manual and automated checks on consistency and completeness of the reported results within a manuscript.
Capacity differences in working memory based on resting state brain networks
Authors: Osaka Mariko , Kaneda Mizuki , Azuma Miyuki , Yaoi Ken , Shimokawa Tetsuya , Osaka Naoyuki 
Published: September 2021

AbstractHerein, we compared the connectivity of resting-state networks between participants with high and low working memory capacity groups. Brain network connectivity was assessed under both resting and working memory task conditions. Task scans comprised dual-task (reading sentences while memorizing target words) and single-task (reading sentences) conditions. The low capacity group showed relatively stronger connectivity during resting-state in most brain regions, and the high capacity group showed a stronger connectivity between the medial prefrontal and posterior parietal cortices. During task performance, the dorsal attention and salience networks were relatively strongly connected in the high capacity group. In the comparison between dual- and single-task conditions, increased coupling between the anterior cingulate cortex and other attentional control-related areas were noted in the high capacity group. These findings suggest that working memory differences are related with network connectivity variations in attentional control-associated regions during both resting and task performance conditions.
Collagen fibers provide guidance cues for capillary regrowth during regenerative angiogenesis in zebrafish
Authors: Senk Anita , Djonov Valentin 
Published: September 2021

AbstractAlthough well investigated, the importance of collagen fibers in supporting angiogenesis is not well understood. In this study, we demonstrate that extracellular collagen fibers provide guidance cues for endothelial cell migration during regenerative angiogenesis in the caudal zebrafish fin. Inhibition of collagen cross-linking by β-Aminopropionitrile results in a 70% shorter regeneration area with 50% reduced vessel growth and disintegrated collagen fibers. The disrupted collagen scaffold impedes endothelial cell migration and induces formation of abnormal angioma-like blood vessels. Treatment of the Fli//colRN zebrafish line with the prodrug Nifurpirinol, which selectively damages the active collagen-producing 1α2 cells, reduced the regeneration area and vascular growth by 50% with wider, but less inter-connected, capillary segments. The regenerated area contained larger vessels partially covered by endothelial cells embedded in atypical extracellular matrix containing cell debris and apoptotic bodies, macrophages and granulocytes. Similar experiments performed in early embryonic zebrafish suggested that collagens are important also during embryonic angiogenesis. In vitro assays revealed that collagen I allows for the most efficient endothelial cell migration, followed by collagen IV relative to the complete absence of exogenous matrix support. Our data demonstrates severe vascular defects and restricted fin regeneration when collagens are impaired. Collagen I therefore, provides support and guidance for endothelial cell migration while collagen IV is responsible for proper lumen formation and vascular integrity.
Identification of new reference genes with stable expression patterns for gene expression studies using human cancer and normal cell lines
Authors: Rácz Gergely Attila , Nagy Nikolett , Tóvári József , Apáti Ágota , Vértessy Beáta G. 
Published: September 2021

AbstractReverse transcription—quantitative real-time PCR (RT-qPCR) is a ubiquitously used method in biological research, however, finding appropriate reference genes for normalization is challenging. We aimed to identify genes characterized with low expression variability among human cancer and normal cell lines. For this purpose, we investigated the expression of 12 candidate reference genes in 13 widely used human cancer cell lines (HeLa, MCF-7, A-549, K-562, HL-60(TB), HT-29, MDA-MB-231, HCT 116, U-937, SH-SY5Y, U-251MG, MOLT-4 and RPMI-8226) and, in addition, 7 normal cell lines (HEK293, MRC-5, HUVEC/TERT2, HMEC, HFF-1, HUES 9, XCL-1). In our set of genes, we included SNW1 and CNOT4 as novel candidate reference genes based on the RNA HPA cell line gene data from The Human Protein Atlas. HNRNPL and PCBP1 were also included along with the „classical” reference genes ACTB, GAPDH, IPO8, PPIA, PUM1, RPL30, TBP and UBC. Results were evaluated using GeNorm, NormFiner, BestKeeper and the Comparative ΔCt methods. In conclusion, we propose IPO8, PUM1, HNRNPL, SNW1 and CNOT4 as stable reference genes for comparing gene expression between different cell lines. CNOT4 was also the most stable gene upon serum starvation.
Pharmacological modulation of fish-induced depth selection in D. magna: the role of cholinergic and GABAergic signalling
Authors: Bedrossiantz Juliette , Fuertes Inmaculada , Raldua Demetrio , Barata Carlos 
Published: September 2021

AbstractAnimal behaviour is closely related to individual fitness, which allows animals to choose suitable mates or avoid predation. The central nervous system regulates many aspects of animal behaviour responses. Therefore, behavioural responses can be especially sensitive to compounds with a neurodevelopmental or neurofunctional mode of action. Phototactic behavioural changes against fish in the freshwater crustacean Daphnia magna have been the subject of many ecological investigations. The aim of this study was to identify which neurotransmitter systems modulate phototactic behaviour to fish kairomones. We used a positive phototactic D. magna clone (P132,85) that shows marked negative phototactism after exposure to fish kairomones. Treatments included up to 16 known agonists and antagonists of the serotonergic, cholinergic, dopaminergic, histaminergic, glutamatergic and GABAergic systems. It was hypothesized that many neurological signalling pathways may modulate D. magna phototactic behaviour to fish kairomones. A new custom-designed device with vertically oriented chambers was used, and changes in the preferred areas (bottom, middle, and upper areas) were analysed using groups of animals after 24 h of exposure to the selected substance(s). The results indicated that agonists of the muscarinic acetylcholine and GABAA receptors and their equi-effective mixture ameliorated the negative phototactic response to fish kairomones, whereas antagonists and their mixtures increased the negative phototactism to fish kairomones. Interestingly, inhibition of the muscarinic acetylcholine receptor abolished positive phototaxis, thus inducing the phototactic response to fish kairomones. Analysis of the profile of neurotransmitters and their related metabolites showed that the D. magna behavioural responses induced by fish depend on changes in the levels of acetylcholine, dopamine and GABA.
Quantitative modeling of the impact of facemasks and associated leakage on the airborne transmission of SARS-CoV-2
Authors: Schmitt Jean , Wang Jing 
Published: September 2021

AbstractThe ongoing worldwide outbreak of COVID-19 has set personal protective equipment in the spotlight. A significant number of countries impose the use of facemasks in public spaces and encourage it in the private sphere. Even in countries where relatively high vaccination rates are achieved at present, breakthrough infections have been frequently reported and usage of facemasks in certain settings has been recommended again. Alternative solutions, including community masks fabricated using various materials, such as cotton or jersey, have emerged alongside facemasks following long-established standards (e.g., EN 149, EN 14683). In the present work, we present a computational model to calculate the ability of different types of facemasks to reduce the exposure to virus-laden respiratory particles, with a focus on the relative importance of the filtration properties and the fitting on the wearer’s face. The model considers the facemask and the associated leakage, the transport of respiratory particles and their accumulation around the emitter, as well as the fraction of the inhaled particles deposited in the respiratory system. Different levels of leakages are considered to represent the diversity of fittings likely to be found among a population of non-trained users. The leakage prevails over the filtration performance of a facemask in determining the exposure level, and the ability of a face protection to limit leakages needs to be taken into account to accurately estimate the provided protection. Filtering facepieces (FFP) provide a better protection efficiency than surgical and community masks due to their higher filtration efficiency and their ability to provide a better fit and thus reduce the leakages. However, an improperly-fitted FFP mask loses a critical fraction of its protection efficiency, which may drop below the protection level provided by properly-worn surgical and community masks.
The value of gut microbiota to predict feed efficiency and growth of rabbits under different feeding regimes
Authors: Velasco-Galilea María , Piles Miriam , Ramayo-Caldas Yuliaxis , Sánchez Juan P. 
Published: September 2021

AbstractGut microbiota plays an important role in nutrient absorption and could impact rabbit feed efficiency. This study aims at investigating such impact by evaluating the value added by microbial information for predicting individual growth and cage phenotypes related to feed efficiency. The dataset comprised individual average daily gain and cage-average daily feed intake from 425 meat rabbits, in which cecal microbiota was assessed, and their cage mates. Despite microbiota was not measured in all animals, consideration of pedigree relationships with mixed models allowed the study of cage-average traits. The inclusion of microbial information into certain mixed models increased their predictive ability up to 20% and 46% for cage-average feed efficiency and individual growth traits, respectively. These gains were associated with large microbiability estimates and with reductions in the heritability estimates. However, large microbiabililty estimates were also obtained with certain models but without any improvement in their predictive ability. A large proportion of OTUs seems to be responsible for the prediction improvement in growth and feed efficiency traits, although specific OTUs taxonomically assigned to 5 different phyla have a higher weight. Rabbit growth and feed efficiency are influenced by host cecal microbiota, thus considering microbial information in models improves the prediction of these complex phenotypes.
Socioeconomic differences in handgrip strength and its association with measures of intrinsic capacity among older adults in six middle-income countries
Authors: Arokiasamy P. , Selvamani Y. , Jotheeswaran A. T. , Sadana Ritu 
Published: September 2021

AbstractHandgrip strength, a measure of muscular strength is a powerful predictor of declines in intrinsic capacity, functional abilities, the onset of morbidity and mortality among older adults. This study documents socioeconomic (SES) differences in handgrip strength among older adults aged 50 years and over in six middle-income countries and investigates the association of handgrip strength with measures of intrinsic capacity—a composite of all the physical and mental capacities of an individual. Secondary data analysis of cross-sectional population-based data from six countries from the WHO’s Study on global AGEing and adult health (SAGE) Wave 1 were conducted. Three-level linear hierarchical models examine the association of demographic, socioeconomic status and multimorbidity variables with handgrip strength. Regression-based Relative Index of Inequality (RII) examines socioeconomic inequalities in handgrip strength; and multilevel linear and logistic hierarchical regression models document the association between handgrip strength and five domains of intrinsic capacity: locomotion, psychological, cognitive capacity, vitality and sensory. Wealth quintiles are positively associated with handgrip strength among men across all countries except South Africa while the differences by education were notable for China and India. Work and nutritional status are positively associated with handgrip strength. Our findings provide new evidence of robust association between handgrip strength and other measures of intrinsic capacity and confirms that handgrip strength is a single most important measure of capacity among older persons.
Application of FLIC model to predict adverse events onset in neuroendocrine tumors treated with PRRT
Authors: Scalorbi Federica , Argiroffi Giovanni , Baccini Michela , Gherardini Luca , Fuoco Valentina , Prinzi Natalie , Pusceddu Sara , Garanzini Enrico Matteo , Centonze Giovanni , Kirienko Margarita , Seregni Ettore , Milione Massimo , Maccauro Marco 
Published: September 2021

AbstractTo develop predictive models of side effect occurrence in GEPNET treated with PRRT. Metastatic GEPNETs patients treated in our centre with PRRT (177Lu-Oxodotreotide) from 2019 to 2020 were considered. Haematological, liver and renal toxicities were collected and graded according to CTCAE v5. Patients were grouped according with ECOG-PS, number of metastatic sites, previous treatment lines and therapies received before PRRT. A FLIC model with backward selection was used to detect the most relevant predictors. A subsampling approach was implemented to assess variable selection stability and model performance. Sixty-seven patients (31 males, 36 females, mean age 63) treated with PRRT were considered and followed up for 30 weeks from the beginning of the therapy. They were treated with PRRT as third or further lines in 34.3% of cases. All the patients showed at least one G1–G2, meanwhile G3–G5 were rare events. No renal G3–G4 were reported. Line of PRRT administration, age, gender and ECOG-PS were the main predictors of haematological, liver and renal CTCAE. The model performance, expressed by AUC, was > 65% for anaemia, creatinine and eGFR. The application of FLIC model can be useful to improve GEPNET decision-making, allowing clinicians to identify the better therapeutic sequence to avoid PRRT-related adverse events, on the basis of patient characteristics and previous treatment lines.
Cleaner fish are sensitive to what their partners can and cannot see
Authors: McAuliffe Katherine , Drayton Lindsey A. , Royka Amanda , Aellen Mélisande , Santos Laurie R. , Bshary Redouan 
Published: September 2021

AbstractMuch of human experience is informed by our ability to attribute mental states to others, a capacity known as theory of mind. While evidence for theory of mind in animals to date has largely been restricted to primates and other large-brained species, the use of ecologically-valid competitive contexts hints that ecological pressures for strategic deception may give rise to components of theory of mind abilities in distantly-related taxonomic groups. In line with this hypothesis, we show that cleaner wrasse (Labroides dimidiatus) exhibit theory of mind capacities akin to those observed in primates in the context of their cooperative cleaning mutualism. These results suggest that ecological pressures for strategic deception can drive human-like cognitive abilities even in very distantly related species.