bluuebunny/crossref_metadata_2025_split huggingface dataset:
Confirmed forecasts for the expansion of the COVID-19 epidemic in the largest Brazilian City
Authors: Celaschi Sergio 
Published: February 2021

AbstractObjectiveA SEIR compartmental model was previously selected to estimate future outcomes to the dynamics of the Covid-19 epidemic breakout in Brazil.MethodCompartments for individuals vaccinated, and prevalent SARS-Cov-2 variants were not included. A time-dependent incidence weight on the reproductive basic number accounted for Non Pharmaceutical Interventions (NPI). A first series of published data from March 1st to May 8, 2020 was used to adjust all model parameters aiming to forecast one year of evolutionary outbreak. The cohort study was set as a city population-based analysis.AnalysisThe population-based sample, 25,366 during the study period, was the number of confirmed cases on exposed individuals. The analysis was applied to predict the consequences of holding for posterior NPI releases, and indicates the appearance of a second wave starting last quarter of 2020.FindingsBy March 1st2021, the number of confirmed cases was predicted to reach 0.47Million (0.24-0.78), and fatalities would account for 21 thousand (12-33), 5 to 95% CRI. A second series of data published from May 9, 2020 to March 1st, 2021 confirms the forecasts previously reported for the evolution of infected people and fatalities.NoveltyBy March 1st 2021, the number of confirmed cases reached 527,710 (12% bellow predicted average of accumulated cases), and fatalities accounted for 18,769 (10% above the accumulated average of estimated fatalities). After March 1st, new peaks on reported numbers of daily new infected and new fatalities appeared as a combined result to the appearance of the prevalent SARS-CoV-2 P1 variant, and the increased number of vaccinated individuals.
Avian influenza A viruses reassort and diversify differently in mallards and mammals
Authors: Ganti Ketaki , Bagga Anish , DaSilva Juliana , Shepard Samuel S. , Barnes John R. , Shriner Susan , Koelle Katia , Lowen Anice C. 
Published: February 2021

AbstractReassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian IAV within their natural host (mallards) and a mammalian model system (guinea pigs). Animals were co-inoculated with A/wildbird/California/187718-36/2008 (H3N8) and A/mallard/Colorado/P66F1-5/2008 (H4N6) viruses. Longitudinal samples were collected from the cloaca of mallards or the nasal tract of guinea pigs and viral genetic exchange was monitored by genotyping clonal isolates from these samples. Relative to those in guinea pigs, viral populations in mallards showed higher frequencies of reassortant genotypes and were characterized by higher genotype richness and diversity. In line with these observations, analysis of pairwise segment combinations revealed lower linkage disequilibrium in mallards as compared to guinea pigs. No clear longitudinal patterns in richness, diversity or linkage disequilibrium were present in either host. Our results reveal mallards to be a highly permissive host for IAV reassortment and suggest that reduced viral mixing limits avian IAV reassortment in a mammalian host.
Using Adaptive Psychophysics to Identify the Neural Network Reset Time in Sub-second Interval Timing
Authors: Sadibolova Renata , Sun Stella , Terhune Devin B. 
Published: February 2021

AbstractState dependent network models of sub-second interval timing propose that duration is encoded in states of neuronal populations that need to reset prior to a novel timing operation in order to maintain optimal timing performance. Previous research has shown that the approximate boundary of this reset interval can be inferred by varying the interstimulus interval between two to-be-timed intervals. However, the estimated boundary of this reset interval is broad (250-500ms) and remains underspecified with implications for the characteristics of state dependent network dynamics subserving interval timing. Here we probed the interval specificity of this reset boundary by manipulating the interstimulus interval between standard and comparison intervals in two sub-second auditory duration discrimination tasks (100 and 200ms) and a control (pitch) discrimination task using adaptive psychophysics. We found that discrimination thresholds improved with the introduction of a 333ms interstimulus interval relative to a 250ms interstimulus interval in both duration discrimination tasks, but not in the control task. This effect corroborates previous findings of a breakpoint in the discrimination performance for sub-second stimulus interval pairs as a function of an incremental interstimulus delay but more precisely localizes the minimal interstimulus delay range. These results suggest that state dependent networks subserving sub-second timing require approximately 250-333ms for the network to reset in order to maintain optimal interval timing.New & NoteworthyThe state-dependent-network model considers interval timing as an intrinsic ability of neuronal populations to track the temporal evolution of their collective state. However, the time-dependent nature of neuronal properties imposes constraints on a maximum encodable interval and on the processing of intervals that are presented before the network resets to its baseline state. Investigating temporal discrimination thresholds as a function of variable inter-stimulus-intervals, we showed that the network reset time is between 250 and 333ms.
On the application of BERT models for nanopore methylation detection
Authors: Zhang Yao-zhong , Hatakeyama Sera , Yamaguchi Kiyoshi , Furukawa Yoichi , Miyano Satoru , Yamaguchi Rui , Imoto Seiya 
Published: February 2021

AbstractMotivationDNA methylation is a common epigenetic modification, which is widely associated with various biological processes, such as gene expression, aging, and disease. Nanopore sequencing provides a promising methylation detection approach through monitoring abnormal signal shifts for detecting modified bases in target motif regions. Recently, model-based approaches, especially those with deep learning models, have achieved significant performance improvements on nanopore methylation detection. In this work, we explore using bidirectional encoder representations from transformers (BERT) for doing the task, which can provide non-recurrent neural structures for fast parallel computation.ResultsWe find original BERT architecture does not work as well as the bidirectional recurrent neural network (biRNN) on the nanopore methylation prediction task. Through further analysis, we observe recurrent patterns of positional-signal-shift in the context window surrounding target 5-methylcytosine (5mC) and N6-methyladenine (6mA) motifs. We propose a refined BERT with relative position representation and center hidden units concatenation, which takes account of task-specific characters into modeling. We perform systematic evaluations in-sample and cross-sample. The experiment results show that the refined BERT model can achieve competitive or even better results than the state-of-the-art biRNN model, while the model inference speed is about 6x faster. Besides, on the cross-sample evaluation of datasets from the different research groups, BERT models demonstrate a good generalization performance.AvailabilityThe source code and data are available athttps://github.com/yaozhong/methBERTContactyaozhong@ims.u-tokyo.ac.jp
Modeling features of addiction with an oral oxycodone self-administration paradigm
Authors: Murphy Caitlin A. , Chang Yu-Hsuan , Pareta Rajesh , Li Jun-Nan , Slivicki Richard A. , Earnest Tom , Tooley Jessica , Abiraman Kavitha , Vachez Yvan M. , Gereau Robert W. , Copits Bryan A. , Kravitz Alexxai V. , Creed Meaghan C. 
Published: February 2021

AbstractPrescription opioid use is an initiating factor driving the current opioid epidemic. There are several challenges with modeling prescription opioid addiction. First, prescription opioids such as oxycodone are orally self-administered and have different pharmacokinetics and dynamics than morphine or fentanyl. This oral route of administration determines the pharmacokinetic profile, which is critical for establishing reliable drug-reinforcement associations in animals. Moreover, the pattern of intake and environment in which addictive drugs are self-administered intake are critical determinants of the levels of drug intake, sensitization and relapse behavior. This is an important consideration with prescription opioid use, which is characterized by continuous drug access in familiar environments. Thus, to model features of prescription opioid use and the transition to abuse, we present an oral oxycodone self-administration paradigm that is administered in the home cage. Mice voluntarily self-administer oxycodone in this paradigm without any taste modification such as sweeteners, and exhibit preference for oxycodone, escalation of intake, physical signs of dependence, reinstatement of seeking after withdrawal, and a subset of animals demonstrate drug taking that is resistant to aversive consequences. This model could be useful for studying the neurobiological substrates specifically relevant to prescription opioid abuse.
Finger somatotopy is preserved after tetraplegia but deteriorates over time
Authors: Kikkert Sanne , Pfyffer Dario , Verling Michaela , Freund Patrick , Wenderoth Nicole 
Published: February 2021

AbstractFollowing spinal cord injury (SCI), the motor output flow to the limb(s) and sensory input to the brain is largely lost. While attempted movements with the paralysed and sensory deprived body part can still evoke signals in the sensorimotor system, this task-related “net” brain activity of SCI patients differs substantially from healthy controls. Such reorganised and/or altered activity is thought to reflect abnormal processing. It is however possible that this altered ‘net’ sensorimotor activity in SCI patients conceals preserved somatotopically-specific representations of the paralysed and sensory deprived body parts that could be exploited in a functionally meaningful manner (e.g. via neuroprosthetics).In this cross-sectional study, we investigated whether a functional connection between the periphery and the brain is necessary to maintain somatosensory representations. We used functional MRI and an (attempted) finger movement task to characterise the somatotopic hand layout in the primary somatosensory cortex and structural MRI to assess spared spinal tissue bridges. We tested 14 tetraplegic SCI patients (mean age ± s.e.m.=55 ± 3.6; 1 female) who differed in terms of lesion completeness, retained sensorimotor functioning, and time since injury, as well as 18 healthy control participants (mean age ± s.e.m.=56 ± 3.6 years; 1 female).Our results revealed somatotopically organised representations of patients’ hands in which neighbouring clusters showed selectivity for neighbouring fingers in contralateral S1, qualitatively similar to those observed in healthy controls. To quantify whether these representations were normal in tetraplegic SCI patients we correlated each participant’s intricate representational distance pattern across all fingers (revealed using representational similarity analysis) with a canonical inter-finger distance pattern obtained from an independent sample. The resulting hand representation typicality scores were not significantly different between patients and controls. This was even true when considering two individual patients with no sensory hand functioning, no hand motor functioning, and no spared spinal tissue bridges. However, a correlational analysis revealed that over years since SCI the hand representation typicality in primary somatosensory cortex deteriorates.We show that somatosensory representations can be maintained for several years following SCI even in the absence of perhiperhal inputs. Such preserved cortical hand representations could therefore be exploited in a functionally meaningful way by rehabilitation approaches that attempt to establish new functional connections between the hand and the brain after an SCI (e.g. through neuroprosthetics). However, time since injury may critically influence the somatotopic representations of SCI patients and might thereby impact the success of such rehabilitation approaches.
Maternal obesity programs white and brown adipose tissue transcriptome and lipidome in offspring in a sex-dependent manner
Authors: Savva Christina , Helguero Luisa A. , González-Granillo Marcela , Melo Tânia , Couto Daniela , Buyandelger Byambajav , Gustafsson Sonja , Liu Jianping , Domingues Maria Rosário , Li Xidan , Korach-André Marion 
Published: February 2021

SUMMARYThe prevalence of overweight and obesity among children has drastically increased during the last decades and maternal obesity has been demonstrated as one of the ultimate factors. Nutrition-stimulated transgenerational epigenetic regulation of key metabolic genes is fundamental to the developmental origins of the metabolic syndrome. Fetal nutrition may differently influence female and male offspring. In this work, we investigated the sex-dependent programming of maternal obesity in visceral, subcutaneous and brown adipose tissues of offspring using magnetic resonance imaging and spectroscopy and a lipidomic approach combined with a Smart-Seq2 differential sequencing analysis. We show that the triglyceride profile varies between adipose depots, sexes and maternal diet. Our results demonstrate for the first time that a sex-dependent gene programming exists in visceral, subcutaneous and brown adipose tissues. Maternal obesity differentially programs gene expression in adipose depots of female and male offspring, which may contribute to the sex-dependent metabolic complications later in life.Graphical abstract
Tiara: Deep learning-based classification system for eukaryotic sequences
Authors: Karlicki Michał , Antonowicz Stanisław , Karnkowska Anna 
Published: February 2021

AbstractMotivationWith a large number of metagenomic datasets becoming available, the eukaryotic metagenomics emerged as a new challenge. The proper classification of eukaryotic nuclear and organellar genomes is an essential step towards the better understanding of eukaryotic diversity.ResultsWe developed Tiara, a deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data sets. Its two-step classification process enables the classification of nuclear and organellar eukaryotic fractions and subsequently divides organellar sequences to plastidial and mitochondrial. Using test dataset, we have shown that Tiara performs similarly to EukRep for prokaryotes classification and outperformed it for eukaryotes classification with lower calculation time. Tiara is also the only available tool correctly classifying organellar sequences.Availability and implementationTiara is implemented in python 3.8, available athttps://github.com/ibe-uw/tiaraand tested on Unix-based systems. It is released under an open-source MIT license and documentation is available athttps://ibe-uw.github.io/tiara. Version 1.0.1 of Tiara has been used for all benchmarks.
RNF43 inhibits WNT5A driven signaling and suppresses melanoma invasion
Authors: Radaszkiewicz Tomasz , Nosková Michaela , Gömöryová Kristína , Vondálová Blanářová Olga , Radaszkiewicz Katarzyna Anna , Picková Markéta , Víchová Ráchel , Gybel’ Tomáš , Kaiser Karol , Demková Lucia , Kučerová Lucia , Potěšil David , Zdráhal Zbyněk , Souček Karel , Bryja Vítězslav 
Published: February 2021

AbstractRNF43 is a E3 ubiquitin ligase and known negative regulator of WNT/β-catenin signaling. We demonstrate that RNF43 is also regulator of noncanonical WNT5A-induced signaling in human cells. Analysis of the RNF43 interactome using BioID and immunoprecipitation showed that RNF43 can interact with the core receptor complex components dedicated to the noncanonical Wnt pathway such as ROR1, ROR2, VANGL1 and VANGL2. RNF43 triggers VANGL2 ubiquitination and proteasomal degradation and clathrin-dependent internalization of ROR1 receptor. This activity of RNF43 is physiologically relevant and blocks pro-metastatic WNT5A signaling in melanoma. RNF43 inhibits responses to WNT5A, which results in the suppression of invasive properties of melanoma cells. Furthermore, RNF43 prevented WNT5A-assisted development of resistance to BRAF V600E inhibitor. In line with these findings,RNF43expression decreases during melanoma progression and RNF43-low patients have worse prognosis. We conclude that RNF43 is a newly discovered negative regulator of WNT5A-mediated biological responses that desensitizes cells to WNT5A.
Wavelength-dependent effects of artificial light at night on phytoplankton growth and community structure
Authors: Diamantopoulou Christina , Christoforou Eleni , Dominoni Davide M. , Kaiserli Eirini , Czyzewski Jakub , Mirzai Nosrat , Spatharis Sofie 
Published: February 2021

AbstractArtificial light at night (ALAN) is increasingly recognised as a disruptive form of environmental pollution, impacting many physiological and behavioural processes that may scale up to population and community-level effects. Mounting evidence from animal studies show that the severity and type of the impact depends on the wavelength and intensity of ALAN. This knowledge has been instrumental for informing policy-making and planning for wildlife-friendly illumination. However, most of this evidence comes from terrestrial habitats, while research testing alternative wavelength illumination in marine environments is lagging behind. In this study we investigated the effect of such alternative ALAN colours on marine primary producers. Specifically, we tested the effect of green, red, and natural white LED illumination at night, compared to a dark control, on the growth of a green microalgae as well as the biomass, diversity and composition of a phytoplankton assemblage. Our findings show that green ALAN boosted chlorophyll production at the exponential growth stage, resulting in higher biomass production in the green algaeTetraselmis suesica.All ALAN wavelengths affected the biomass and diversity of the assemblage with the red and green ALAN having the stronger effects, leading to higher overall abundance and selective dominance of specific diatom species compared to white ALAN and the dark control.SynthesisOur work indicates that the wavelength of artificial light sources in marine areas should be carefully considered in management and conservation plans. In particular, green and red light should be used with caution in coastal areas, where there might be a need to strike a balance between the strong effects of green and red light on marine primary producers with the benefit they bring to other organisms.
C1q binding to surface-bound IgG is stabilized by C1r2s2proteases
Authors: Zwarthoff Seline A. , Widmer Kevin , Kuipers Annemarie , Strasser Jürgen , Ruyken Maartje , Aerts Piet C. , de Haas Carla J.C. , Ugurlar Deniz , Vidarsson Gestur , Van Strijp Jos A. G. , Gros Piet , Parren Paul W.H.I. , van Kessel Kok P.M. , Preiner Johannes , Beurskens Frank J. , Schuurman Janine , Ricklin Daniel , Rooijakkers Suzan H.M. 
Published: February 2021

AbstractComplement is an important effector mechanism for antibody-mediated clearance of infections and tumor cells. Upon binding to target cells, the antibody’s constant (Fc) domain recruits complement component C1 to initiate a proteolytic cascade that generates lytic pores and stimulates phagocytosis. The C1 complex (C1qr2s2) consists of the large recognition protein C1q and a heterotetramer of proteases C1r and C1s (C1r2s2). While interactions between C1 and IgG-Fc’s are believed to be mediated by the globular heads of C1q, we here find that C1r2s2proteases affect the capacity of C1q to form an avid complex with surface-bound IgG molecules (on various DNP-coated surfaces and pathogenicStaphylococcus aureus). The extent to which C1r2s2contribute to C1q-IgG stability strongly differs between human IgG subclasses. Using antibody engineering of monoclonal IgG we reveal that hexamer-enhancing mutations improve C1q-IgG stability, both in absence and presence of C1r2s2. In addition, hexamer-enhanced IgGs targetingS. aureusmediate improved complement-dependent phagocytosis by human neutrophils. Altogether, these molecular insights into complement binding to surface-bound IgGs could be important for optimal design of antibody therapies.
The desert green algaeChlorella ohadiithrives at excessively high light intensities by exceptionally enhancing the mechanisms that protect photosynthesis from photoinhibition
Authors: Levin Guy , Kulikovsky Sharon , Liveanu Varda , Eichenbaum Benjamin , Meir Ayala , Isaacson Tal , Tadmor Yaakov , Adir Noam , Schuster Gadi 
Published: February 2021

AbstractAlthough light is the driving force of photosynthesis, excessive light can be harmful. One of the main processes that limits photosynthesis is photoinhibition, the process of light-induced photodamage. When the absorbed light exceeds the amount that is dissipated by photosynthetic electron flow and other processes, damaging radicals are formed that mostly inactivate photosystem II (PSII). Damaged PSII must be replaced by a newly repaired complex in order to preserve full photosynthetic activity.Chlorella ohadiiis a green micro-alga, isolated from biological desert soil crusts, that thrives under extreme high light and is highly resistant to photoinhibition. Therefore,C. ohadiiis an ideal model for studying the molecular mechanisms underlying protection against photoinhibition. Comparison of the thylakoids ofC. ohadiicells that were grown under low light versus extreme high light intensities, found that the alga employs all three known photoinhibition protection mechanisms:i)massive reduction of the PSII antenna size;ii)accumulation of protective carotenoids; andiii)very rapid repair of photo-damaged reaction center proteins. This work elucidated the molecular mechanisms of photoinhibition resistance in one of the most light-tolerant photosynthetic organisms and shows how photoinhibition protection mechanisms evolved to marginal conditions, enabling photosynthesis-dependent life in severe habitats.One Sentence HighlightAnalysis of the photosynthetic properties of a desert algae that thrives at extreme high light intensities revealed protection from photoinhibition driven by the remarkable enhancement of three protection mechanisms.