bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large metropolitan region
Authors: Emmenegger Marc , Cecco Elena De , Lamparter David , Jacquat Raphaël P. B. , Riou Julien , Menges Dominik , Ballouz Tala , Ebner Daniel , Schneider Mathias M. , Morales Itzel Condado , Doğançay Berre , Guo Jingjing , Wiedmer Anne , Domange Julie , Imeri Marigona , Moos Rita , Zografou Chryssa , Batkitar Leyla , Madrigal Lidia , Schneider Dezirae , Trevisan Chiara , Gonzalez-Guerra Andres , Carrella Alessandra , Dubach Irina L. , Xu Catherine K. , Meisl Georg , Kosmoliaptsis Vasilis , Malinauskas Tomas , Burgess-Brown Nicola , Owens Ray , Hatch Stephanie , Mongkolsapaya Juthathip , Screaton Gavin R. , Schubert Katharina , Huck John D. , Liu Feimei , Pojer Florence , Lau Kelvin , Hacker David , Probst-Müller Elsbeth , Cervia Carlo , Nilsson Jakob , Boyman Onur , Saleh Lanja , Spanaus Katharina , von Eckardstein Arnold , Schaer Dominik J. , Ban Nenad , Tsai Ching-Ju , Marino Jacopo , Schertler Gebhard F. X. , Ebert Nadine , Thiel Volker , Gottschalk Jochen , Frey Beat M. , Reimann Regina , Hornemann Simone , Ring Aaron M. , Knowles Tuomas P. J. , Puhan Milo A. , Althaus Christian L. , Xenarios Ioannis , Stuart David I. , Aguzzi Adriano 
Published: June 2020

AbstractEffective public-health measures and vaccination campaigns against SARS-CoV-2 require granular knowledge of population-level immune responses. We developed a Tripartite Automated Blood Immunoassay (TRABI) to assess the IgG response against the ectodomain and the receptor-binding domain of the spike protein as well as the nucleocapsid protein of SARS-CoV-2. We used TRABI for continuous seromonitoring of hospital patients and healthy blood donors (n=72’222) in the canton of Zurich from December 2019 to December 2020 (pre-vaccine period). Seroprevalence peaked in May 2020 and rose again in November 2020 in both cohorts. Validations of results included antibody diffusional sizing and Western Blotting. Using an extended Susceptible-Exposed-Infectious-Removed model, we found that antibodies waned with a half-life of 75 days, whereas the cumulative incidence rose from 2.3% in June 2020 to 12.2% in mid-December 2020 in the population of the canton of Zurich. A follow-up health survey indicated that about 10% of patients infected with wildtype SARS-CoV-2 sustained some symptoms at least twelve months post COVID-19 and up to the timepoint of survey participation. Crucially, we found no evidence for a difference in long-term complications between those whose infection was symptomatic and those with asymptomatic acute infection. The cohort of asymptomatic SARS-CoV-2- infected subjects represents a resource for the study of chronic and possibly unexpected sequelae.
Machine Learning Models for Diagnosis of Cushing’s Syndrome Using Retrospective Data
Authors: Isci Senol , Kalender Derya Sema Yaman , Bayraktar Firat , Yaman Alper 
Published: June 2020

ABSTRACTAccurate classification of Cushing’s Syndrome (CS) plays a critical role in providing early and correct diagnosis of CS that may facilitate treatment and improve patient outcomes. Diagnosis of CS is a complex process, which requires careful and concurrent interpretation of signs and symptoms, multiple biochemical test results, and findings of medical imaging by physicians with a high degree of specialty and knowledge to make correct judgments. In this article, we explore the state of the art machine learning algorithms to demonstrate their potential as a clinical decision support system to analyze and classify CS in order to facilitate the diagnosis, prognosis, and treatment of CS. Prominent algorithms are compared using nested cross-validation and various class comparison strategies including multiclass, one vs. all, and one vs. one binary classification. Our findings show that Random Forest (RF) algorithm is most suitable for the classification of CS. We demonstrate that the proposed approach can classify CS subjects with an average accuracy of 92% and an average F1 score of 91.5%, depending on the class comparison strategy and selected features. RF-based one vs. all binary classification model achieves sensitivity of 97.6%, precision of 91.1%, and specificity of 87.1% to discriminate CS from non-CS on the test dataset. RF-based multiclass classification model achieves average per class sensitivity of 91.8%, average per class specificity of 97.1%, and average per class precision of 92.1% to classify different subtypes of CS on the test dataset. Clinical performance evaluation suggests that the developed models can help improve physician’s judgment in diagnosing CS.
Peripersonal and reaching space differ: evidence from their spatial extent and multisensory facilitation pattern
Authors: Zanini A. , Patané I. , Blini E. , Salemme R. , Koun E. , Farnè A. , Brozzoli C. 
Published: June 2020

AbstractPeripersonal space (PPS) is a multisensory representation of the space near body parts facilitating interactions with the close environment. Studies on non-human and human primates converge in showing that PPS is a body-part-centred representation that guides actions. Because of these characteristics, growing confusion conflates peripersonal and arm-reaching space (ARS), that is the space one’s arm can reach. Despite neuroanatomical evidence favors their distinction, no study has contrasted directly their respective extent and behavioral features. Here, in five experiments (N=140) we found that PPS differs from ARS, as evidenced both by participants’ spatial and temporal performance and its modeling. We mapped PPS and ARS using both their respective gold standard tasks and a novel multisensory facilitation paradigm. Results show that 1) PPS is smaller than ARS; 2) multivariate analyses of spatial patterns of multisensory facilitation predict participants’ hand locations within ARS; 3) the multisensory facilitation map shifts isomorphically following hand positions, revealing hand-centred coding of PPS, therefore pointing to a functional similarity to the receptive fields of monkeys’ multisensory neurons. A control experiment further corroborated these results and additionally ruled out the orienting of attention as driving mechanism for the increased multisensory facilitation near the hand. In sharp contrast, ARS mapping results in a larger spatial extent, with undistinguishable patterns across hand positions, cross-validating the conclusion that PPS and ARS are distinct spatial representations. These findings urge for a refinement of theoretical models of PPS, which is relevant to constructs as diverse as self-representation, social interpersonal distance, and motor control.
Recording site placement on planar silicon-based probes affects neural signal quality: edge sites enhance acute recording performance
Authors: Fiáth Richárd , Meszéna Domokos , Boda Mihály , Barthó Péter , Ruther Patrick , Ulbert István 
Published: June 2020

AbstractObjectiveMultisite, silicon-based probes are widely used tools to record the electrical activity of neuronal populations. Several physical features of these devices (e.g. shank thickness, tip geometry) are designed to improve their recording performance. Here, our goal was to investigate whether the position of recording sites on the silicon shank might affect the quality of the recorded neural signal in acute experiments.ApproachNeural recordings obtained with five different types of high-density, single-shank, planar silicon probes from anesthetized rats were analyzed. Wideband data were filtered (500 - 5000 Hz) to extract spiking activity, then various quantitative properties (e.g. amplitude distribution of the filtered potential, single unit yield) of the recorded cortical and thalamic activity were compared between sites located at different positions of the silicon shank, focusing particularly on edge and center sites.Main resultsEdge sites outperformed center sites: mean values of the examined properties of the spiking activity were in most cases higher for edge sites (~94%, 33/35) and a large fraction of these differences were also statistically significant (~45%, 15/33) with effect sizes ranging from small to large. Although the single unit yield was similar between site positions, the difference in signal quality was remarkable in the range corresponding to high-amplitude spikes. Furthermore, the advantage of edge sites slightly decreased for probes having a narrower shank.SignificanceThe better signal quality on edge sites might be the result of the reduced shielding effect of the silicon shank providing a larger field of view for edge sites to detect spikes, or the less tissue damage caused near the edges of the shank. Our results might aid the design of novel neural implants in enhancing their recording performance by identifying more efficient recording site placements.
Extensive genetic diversity inPlasmodium vivaxfrom Sudan and its genetic relationships with other geographical isolates
Authors: Albsheer Musab M Ali. , Gebremeskel Eyoab Iyasu , Kepple Daniel , Lo Eugenia , Rougeron Virginie , Ibrahim Muntaser E. , Abdel Hamid Muzamil M. 
Published: June 2020

AbstractPlasmodium vivaxmalaria is a neglected tropical disease in Africa due to low occurrence rates and lack of accurate diagnosis. Recently, there has been a dramatic increase inP. vivaxcases in East Africa and reportedly spreading to western countries. This study investigated the geographical origin and genetic diversity ofP. vivaxin Sudan by 14 microsatellite markers. A total of 113 clinicalP. vivaxsamples were collected from two districts, New Halfa and Khartoum in Sudan. In addition, data from 841 geographical samples retrieved from the database for global genetic analysis were included in the analysis to further the genetic relationships among theP. vivaxisolates at regional and worldwide scales. On a regional scale, we observed 91 unique and 8 shared haplotypes amongst the Sudan samples. Such a high genetic diversity compared to other geographical isolates lends support to hypothesis thatP. vivaxwas originated from Africa. On a global scale, as already demonstrated, we observed distinct genetic clustering ofP. vivaxisolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) with limited admixture in all three clusters. The principal component analysis and phylogenetic tree showed similar clustering patterns and highlighted the contribution of the African isolates to the genetic variation observed globally. The East AfricanP. vivaxshowed similarity with some of the Asian isolates suggesting potential recent introductions. Our results show extensive genetic diversity co-occurring with significant multi-locus linkage disequilibrium, demonstrating the effectiveness of using microsatellite markers to implement effective control measures.
Outcomes of Isoniazid Preventive Therapy among people living with HIV in Kenya: A retrospective study of routine health care data
Authors: Karanja Muthoni , Kingwara Leonard , Kiende Polly , Owiti Philip , Kirui Elvis , Ngari Faith , Onyango Elizabeth , Ngugi Catherine , Maina Maurice , Masini Enos 
Published: June 2020

AbstractIntroductionIsoniazid preventive therapy (IPT) taken by People Living with HIV (PLHIV) protects against tuberculosis (TB). Despite its recommendation, there is scarcity of data on the uptake of IPT among PLHIV and factors associated with treatment outcomes. We aimed to determine the proportion of PLHIV initiated on IPT, IPT treatment outcomes and screening for TB during and after IPT.MethodsA retrospective cohort study of a representative sample of PLHIV initiated on IPT between July 2015 and June 2018 in Kenya. We abstracted information on socio-demographic, TB screening practices, IPT initiation, follow up, and outcomes from health facilities’ patient record cards, IPT cards and IPT registers. Further, we assessed baseline characteristics as potential correlates of developing TB during and after treatment and IPT completion using multivariable logistic regression.ResultsWe enrolled 138,442 PLHIV into ART during the study period and initiated 95,431 (68.9%) into IPT. Abstracted files for 4708 patients initiated on IPT, out of which 3891(82.6%) had IPT treatment outcomes documented, 4356(92.5%) had ever been screened for TB at every clinic visit and 4,243(90.1%) had documentation of TB screening on the IPT tool before IPT initiation. 3712(95.4%) of patients with documented IPT treatment outcomes completed their treatment. 42(0.89%) of the abstracted patients developed active TB, 16(38.1%) during and 26(61.9%) after completing IPT. Follow up for TB at 6-month post-IPT completion was done for 2729(73.5%) of patients with IPT treatment outcomes. Sex, Viral load suppression and clinic type were associated with TB development (p<0.05). Levels 4, 5, FBO, and private facilities and IPT prescription practices were associated with IPT completion (p<0.05).ConclusionTwo-thirds of PLHIV were initiated on IPT, with a high completion rate. TB screening practices were better during IPT than after completion. Development of TB during and after IPT emphasises need for keen follow up.
Predicting Collaborative Learning Quality through Physiological Synchrony Recorded by Wearable Biosensors
Authors: Liu Yang , Wang Tingting , Wang Kun , Zhang Yu 
Published: June 2020

AbstractInterpersonal physiological synchrony has been consistently found during collaborative tasks. However, few studies have applied synchrony to predict collaborative learning quality in real classroom. This study collected electrodermal activity (EDA) and heart rate (HR) in naturalistic class sessions, and compared the physiological synchrony between independent task and group discussion task. Since each student learn differently and not everyone prefers collaborative learning, participants were sorted into collaboration and independent dyads based on collaborative behaviors before data analysis. The result showed that during groups discussions, high collaboration pairs produced significantly higher synchrony than low collaboration dyads (p= 0.010). Given the equivalent engagement level during independent and collaborative tasks, the difference of physiological synchrony between high and low collaboration dyads was triggered by collaboration quality. Building upon this result, the classification analysis was conducted, indicating that EDA synchrony can predict collaboration quality (AUC = 0.767,p= 0.015).
Bacterial isolates from CSF sample and their antimicrobial resistance patters in among under-five children suspected for meningitis in Dilla University Referral Hospital
Authors: Awulachew Ephrem , Diriba Kuma , Awoke Netsanet 
Published: June 2020

AbstractIntroductionBacterial meningitis is medical emergency that requires immediate medical attention. It is a cause of an estimated 288, 649 deaths worldwide per year, of which 94 883 death occur among Under-five children. Up to 24% of the survivors suffer from long-term sequelae such as epilepsy, mental retardation, or sensorineural deafness especially when the disease is contracted during early childhood.Objectivethe aim of this study was to assess bacterial isolates of CSF sample and their antimicrobial resistance patterns among under-five children in Dilla University Referral Hospital.Material and MethodsHospital based cross-sectional study design was used to collect clinical data and CSF sample from under-five children who was suspected for meningitis. Sediment of CSF sample was inoculated to Blood Agar plate, Chocolate Agar plate and Mackonkey Agar for bacterial isolation and identification. Chemical analysis and cytological analysis was also conducted based on standard operating procedures.ResultsFrom a total of 287 CSF sample cultured, causative bacteria were detected in 38 (13.2%). From culture positive cases the most frequent isolate wasStreptococcus pneumoniae13 (34.2%) followed byStaphylococcus aureas7 (18.4%),Neisseria meningitidis6 (16%) andEscherichia coli6 (16%).Haemophilus influenzaeb was isolated in 4 (10.5%) of children with meningitis. The other cause of meningitis wasStreptococcus agalactiaewhich accounted (10.5%). Cryptococcus neoformans have been detected in 4 (1.9%) cases of meningitis. Of all bacterial isolates about 42.1% (16/38) bacterial isolates were multidrug resistant. About 38.5% ofS. pneumoniaewas multidrug resistance while about 33.3%N. meningitis, 50% of H. influenzae, 57.1% of S. aureasand 40% ofE. colishowed multidrug resistanceConclusionsHigh prevalence of bacterial meningitis and high rate of drug resistance were observed.S. pneumoniaewas the leading cause of bacterial meningitis among under-five children.
Detection of Envelope Glycoprotein Assembly from Old-World Hantaviruses in the Golgi Apparatus of Living Cells
Authors: Petazzi R. A. , Koikkarah A. A. , Tischler N.D. , Chiantia S. 
Published: June 2020

AbstractHantaviruses are emerging pathogens that occasionally cause deadly outbreaks in the human population. While the structure of the viral envelope has been characterized with high precision, the protein-protein interactions leading to the formation of new virions in infected cells are not fully understood yet. In this work, we use quantitative fluorescence microscopy (i.e. Number&Brightness analysis and fluorescence fluctuation spectroscopy) to quantify the interactions that lead to oligomeric spike complex formation in the physiological context of living cells. To this aim, we have analyzed proteins from Puumala and Hantaan orthohantaviruses in several cellular models. For the first time, we quantified the oligomerization state of each protein in relation to its subcellular localization, concentration and the concentration of its interaction partner. Our results indicate that when expressed separately, both glycoproteins can form homo-multimers in a concentration-dependent manner. Fluorescence fluctuation analysis was applied to prove that Gc:Gc contacts observed on virions are also relevant for Gc-Gc interactions in living cells, in the absence of Gn. Furthermore, we proved that the membrane-distal lobes of Gn are not necessary for Gn homo-multimerization. In cells co-expressing both glycoproteins, we observe clear indication of Gn-Gc interactions and the formation of protein complexes with different sizes, while using various labelling schemes to minimize the influence of the fluorescent tags. Our data are compatible with an assembly model according to which hantavirus spikes are formed via the assembly of Gn-Gc hetero-dimers. Furthermore, our results indicate the interconnection of large Gn-Gc hetero-multimers in the Golgi apparatus. Such large glycoprotein multimers may be identified as multiple interacting viral spikes and provide a possible first evidence for the initial assembly steps of the viral envelope, within this organelle, directly in living cells.
De novo enteric neurogenesis in post-embryonic zebrafish from Schwann cell precursors rather than resident cell types
Authors: El-Nachef Wael Noor , Bronner Marianne E. 
Published: June 2020

ABSTRACTThe enteric nervous system is essential for normal gastrointestinal function, but evidence regarding postnatal enteric neurogenesis is conflicting. Using zebrafish as a model, we explored the origin of enteric neurons that arise in post-embryonic life in normal development and injury, and tested effects of the 5-HT4receptor agonist, prucalopride.To assess enteric neurogenesis, all enteric neurons were photoconverted prior to time-lapse imaging to detect emergence of new neurons. Injury was modeled by two-photon laser ablation of enteric neurons. Lineage tracing was performed with neural tube injections of lipophilic dye and with an inducible Sox10-Cre line. Lastly, we tested prucalopride’s effect on post-embryonic enteric neurogenesis.The post-embryonic zebrafish intestine appears to lack resident neurogenic precursors and enteric glia. However, enteric neurogenesis persists post-embryonically during development and after injury. New enteric neurons arise from trunk neural crest-derived Schwann cell precursors. Prucalopride increases enteric neurogenesis in normal development and after injury if exposure occurs prior to injury.Enteric neurogenesis persists in the post-embryonic period in both normal development and injury, appears to arise from gut-extrinsic Schwann cell precursors, and is promoted by prucalopride.SUMMARY STATEMENTTrunk crest-derived enteric neurogenesis is poorly understood. We find post-embryonic zebrafish lack resident neuronal precursors yet enteric neurogenesis from trunk crest-derived precursors occurs in development, injury, and is promoted by prucalopride.
R7 photoreceptor axon targeting depends on the relative levels oflost and foundexpression in R7 and its synaptic partners
Authors: Douthit Jessica , Hairston Ariel , Lee Gina , Morrison Carolyn A. , Holguera Isabel , Treisman Jessica E. 
Published: June 2020

AbstractAs neural circuits form, growing processes select the correct synaptic partners through interactions between cell surface proteins. The presence of such proteins on two neuronal processes may lead to either adhesion or repulsion; however, the consequences of mismatched expression have rarely been explored. Here we show that theDrosophilaCUB-LDL protein Lost and found (Loaf) is required in the UV-sensitive R7 photoreceptor for normal axon targeting only when Loaf is also present in its synaptic partners. Although targeting occurs normally inloafmutant animals, removingloaffrom photoreceptors or expressing it in their postsynaptic neurons Tm5a/b or Dm9 in aloafmutant causes mistargeting of R7 axons. Loaf localizes primarily to intracellular vesicles including endosomes. We propose that Loaf regulates the trafficking or function of one or more cell surface proteins, and an excess of these proteins on the synaptic partners of R7 prevents the formation of stable connections.
Novel ionic liquids-based extraction method that preserves molecular structure from cutin
Authors: Moreira Carlos J.S. , Bento Artur , Pais Joana , Petit Johann , Escórcio Rita , Correia Vanessa G. , Pinheiro Ângela , Haliński Łukasz P. , Mykhaylyk Oleksandr O. , Rothan Christophe , Pereira Cristina Silva 
Published: June 2020

AbstractThe biopolyester cutin is ubiquitous in land plants, building the polymeric matrix of the plant’s outermost defensive barrier - the cuticle. Cutin influences many biological processesin plantahowever due to its complexity and highly branched nature, the native structure remains partially unresolved. Our aim was to define an original workflow for the purification and systematic characterisation of the molecular structure of cutin. To purify cutin we tested the ionic liquids cholinium hexanoate and 1-butyl-3-methyl-imidazolium acetate. The ensuing polymers are highly esterified, amorphous and have the typical monomeric composition as demonstrated by solid state NMR, complemented by spectroscopic (GC-MS), thermal (DSC) and x-ray scattering (WAXS) analyses. A systematic study by solution-state NMR of cryogenically milled cutins extracted from Micro-Tom tomatoes (the wild type and thegpat6andcus1mutants) was undertaken. Their molecular structures, relative distribution of ester aliphatics, free acid end-groups and free hydroxyl groups, differentiating between those derived from primary and secondary esters, were solved. The acquired data demonstrate the existence of free hydroxyl groups in cutin and reveal novel insights on how the mutations impact the esterification arrangement of cutin. Compared to conventional approaches, the usage of ionic liquids for the study of plant polyesters opens new avenues since simple modifications can be applied to recover a biopolymer carrying distinct types/degrees of modifications (e.g. preservation of esters or cuticular polysaccharides), which in combination with the solution NMR methodologies developed here, constitutes now essential tools to fingerprint the multi-functionality and the structure of cutinin planta.