bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre-Pandemic COVID-19 in New York City: A descriptive analysis of COVID-19 illness prior to February 29, 2020
Authors: Keating Page , Sell Jessica , Chen Judy , Ackelsberg Joel , Wu Winfred , Tsoi Benjamin , Weiss Don
Published: April 2022

Background

On January 30, 2020 the COVID-19 pandemic was declared a Public Health Emergency of International Concern (PHEIC) by the World Health Organization. Almost a month later on February 29, 2020, the first case in New York City (NYC) was diagnosed.

Methods

Three-hundred-sixty persons with COVID-like illness was reported to the NYC Department of Health and Mental Hygiene (DOHMH) before February 29, but 37 of these tested negative and 237 were never tested for SARS-COV-2. Records of 86 persons with confirmed COVID-19 and symptom onset prior to February 29, 2020 were reviewed by four physician-epidemiologists. Case-patients were classified as likely early onset COVID-19, or insufficient evidence to determine onset. Clinical and epidemiological factors collected by DOHMH and supplemented with emergency department records were analyzed.

Results

Thirty-nine likely early onset COVID-19 cases were identified. The majority had severe disease with 69% presenting to an ED visit within 2 weeks of symptom onset. The first likely COVID-19 case on record had symptom onset on January 28, 2020. Only 7 of the 39 cases (18%) had traveled internationally within 14 days of onset (none to China).

Conclusions

SARS-CoV-2 and COVID-19 was in NYC before being classified as a PHEIC, and eluded surveillance for another month. The delay in recognition limited mitigation effort and by the time that city and state-wide mandates were enacted 16 and 22 days later there was already community transmission.

Key Points

Records of 86 persons with confirmed COVID-19 and symptom onset prior to February 29, 2020 were reviewed for likelihood of early onset COVID-19. Thirty-nine likely early onset COVID-19 cases were identified, suggesting that early COVID-19 transmission in NYC went undetected.
Beyond Common Outcomes: Client’s Perspectives on the Benefits of Prenatal Care Coordination
Authors: Greene Madelyne Z. , Tran-Smith Bikki , Moua Pahder
Published: April 2022

Prenatal Care Coordination (PNCC) is a fee-for-service Medicaid benefit available in Wisconsin and several other states. It provides for home visiting, health education, care coordination and other supportive services to high-risk mothers. However, PNCC is not supported by an evidence-based model, its impact is not systematically evaluated, and the benefit is not currently reaching all eligible mothers. The purpose of this qualitative descriptive study was to describe PNCC clients’ perspectives on the experience of receiving the PNCC benefit and the value and impact of PNCC in the context of their own lives. We interviewed recent clients of PNCC programs in two PNCC sites that varied by racial/ethnic community makeup, rural/urban geography, and health department size. PNCC clients identified two major benefits of PNCC: 1) social and emotional support from the PNCC nurse; and 2) assistance with obtaining or getting connected to other resources they needed. These two program benefits were especially meaningful to PNCC clients in the context of difficult life events and circumstances. Findings from this study highlight the impact of PNCC services on social and emotional health through trusting and supportive nurse-client relationships. Our findings also suggest that a longer program period and the development of standards to assess program effectiveness would improve PNCC client outcomes and reduce disparities in maternal health.
Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater
Authors: Fuzzen Meghan , Harper Nathanael B.J. , Dhiyebi Hadi A. , Srikanthan Nivetha , Hayat Samina , Peterson Shelley W. , Yang Ivy , Sun J.X. , Edwards Elizabeth A. , Giesy John P. , Mangat Chand S. , Graber Tyson E. , Delatolla Robert , Servos Mark R.
Published: April 2022

Wastewater-based surveillance (WBS) has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Quantities of viral fragments of SARS-CoV-2 in wastewater are related to numbers of clinical cases of COVID-19 reported within the corresponding sewershed. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) or sequencing. A multiplex RT-qPCR assay to detect and estimate the prevalence of multiple VOCs, including Omicron/Alpha, Beta, Gamma, and Delta, in wastewater RNA extracts was developed and validated. The probe-based multiplex assay, named “N200” focuses on amino acids 199-202, a region of the N gene that contains several mutations that are associated with variants of SARS- CoV-2 within a single amplicon. Each of the probes in the N200 assay are specific to the targeted mutations and worked equally well in single- and multi-plex modes. To estimate prevalence of each VOC, the abundance of the targeted mutation was compared with a non- mutated region within the same amplified region. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from six sewersheds in Ontario, Canada collected between December 1, 2021, and January 4, 2022. Using the N200 assay, the replacement of the Delta variant along with the introduction and rapid dominance of the Omicron variant were monitored in near real-time, as they occurred nearly simultaneously at all six locations. The N200 assay is robust and efficient for wastewater surveillance can be adopted into VOC monitoring programs or replace more laborious assays currently being used to monitor SARS- CoV-2 and its VOCs.
Modeling vital rates and age-sex structure of Pacific arctic phocids: influence on aerial survey correction factors
Authors: Conn Paul B. , Trukhanova Irina S.
Published: April 2022

To estimate abundance, surveys of marine mammals often rely on samples of satellite-tagged individuals to correct counts for the proportion of animals that are unavailable to be detected. However, naïve application of this correction relies on the key assumption that availability of the tagged sample resembles that of the population. Here, we show how matrix population models can be used to estimate the stable stage structure of bearded seals (Erignathus barbatus), ribbon seals (Histriophoca fasciata), ringed seals (Pusa hispida), and spotted seals (Phoca largha) in the Bering and Chukchi Seas, and how these proportions can be used to adjust aerial survey correction factors so that they represent population-level availability. We find that correction factors ignoring age-sex composition can positively bias spotted seal abundance by an average of 13% and negatively bias ribbon seal abundance by an average of 5%. Note that we did not examine potential bias for bearded or ringed seals due to low sample sizes; as such, we urge caution in interpretation of abundance estimates for these species.
Legacy effect of microplastics on plant-soil feedbacks
Authors: Lozano Y.M , Rillig M.C
Published: April 2022

Microplastics are a complex contaminant suite that are now understood to affect plants and soil biota and the processes they drive. However, the role of microplastic in plant-soil feedbacks, a key feature in plant-soil interactions, is still unknown. We address this here, using soil from a previous experiment, which has been conditioned with 12 different microplastic types including fibers, films, foams, and fragments. To evaluate the feedback effect, we grew a native and a range-expanding plant species with inocula extracted from each one of these soils. At harvest, plant biomass and root morphological traits were measured.

Films gave rise to a positive feedback on shoot mass (higher mass with soil inocula conditioned with microplastics than without), likely via negative effects on harmful soil biota. Foams and fragments also caused positive feedback on shoot mass likely via effects on enzymatic activities and mutualistic soil biota. Fibers led to negative feedback on root mass as they may promote the abundance of soil pathogens.

Microplastics also have a legacy effect on root traits: Daucus had thicker roots probably for promoting mycorrhizal associations while Calamagrostis had reduced root diameter probably for diminishing pathogenic infection. Microplastic legacy on plants is species-specific and may affect plant biomass primarily via root traits. Microplastics, as a function of their shape and polymer type, have a feedback effect on plant performance.
Defining tertiary sulci in lateral prefrontal cortex in chimpanzees using human predictions
Authors: Hathaway Catherine B. , Voorhies Willa I. , Sathishkumar Neha , Mittal Chahat , Yao Jewelia K. , Miller Jacob A. , Parker Benjamin J. , Weiner Kevin S.
Published: April 2022

Similarities and differences in brain structure and function across species is of major interest in systems neuroscience, comparative biology, and brain mapping. Recently, increased emphasis has been placed on tertiary sulci, which are shallow indentations of the cerebral cortex that appear last in gestation, continue to develop after birth, and are largely either human- or hominoid-specific. While tertiary sulcal morphology in lateral prefrontal cortex (LPFC) has been linked to functional representations and cognition in humans, it is presently unknown if LPFC tertiary sulci also exist in non-human hominoids. To fill this gap in knowledge, we leveraged two freely available multimodal datasets to address the following main question: Can LPFC tertiary sulci be defined in chimpanzee cortical surfaces from human predictions? We found that 1-3 components of the posterior middle frontal sulcus (pmfs) in the posterior middle frontal gyrus are identifiable in nearly all chimpanzee hemispheres. In stark contrast to the consistency of the pmfs components, we could only identify components of the paraintermediate frontal sulcus (pimfs) in two chimpanzee hemispheres. LPFC tertiary sulci were relatively smaller and shallower in chimpanzees compared to humans. In both species, two of the pmfs components were deeper in the right compared to the left hemisphere. As these results have direct implications for future studies interested in the functional and cognitive role of LPFC tertiary sulci across species, we share probabilistic predictions of the three pmfs components to guide the definitions of these sulci in future studies.
Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons
Authors: Owuor D. Collins , de Laurent Zaydah R. , Nyawanda Bryan O. , Emukule Gideon O. , Kondor Rebecca , Barnes John R. , Nokes D. James , Agoti Charles N. , Chaves Sandra S.
Published: April 2022

Background

Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making.

Methods

We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and determinants of clinical outcome.

Results

We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity reduced with increase in age among children aged <5 years.

Conclusion

Our study highlights the utility of genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on the severity of circulating strains could improve selection of influenza strains for inclusion in vaccines.
A Sepsis Treatment Algorithm to Improve Early Antibiotic De-escalation While Maintaining Adequacy of Coverage (Early-IDEAS): A Prospective Observational Study
Authors: Bucheeri Mohamed , Elligsen Marion , Lam Philip W. , Daneman Nick , MacFadden Derek
Published: April 2022

Background

Empiric antibiotic treatment selection should provide adequate coverage for potential pathogens while minimizing unnecessary broad-spectrum antibiotic use. We sought to pilot a rule- and model-based early sepsis treatment algorithm (Early-IDEAS) to make optimal individualized antibiotic recommendations.

Methods

The Early-IDEAS decision support algorithm was derived from previous Gram-negative and Gram-positive prediction rules and models. The Gram-negative prediction consists of multiple parametric regression models which predict the likelihood of susceptibility for each commonly used antibiotic for Gram-negative pathogens, based on epidemiologic predictors and prior culture results and recommends the narrowest spectrum agent that exceeds a predefined threshold of adequate coverage. The Gram-positive rules direct the addition or cessation of vancomycin based on prior culture results. We applied the algorithm to prospectively identified consecutive adults within 24-hours of suspected sepsis. The primary outcome was the proportion of patients for whom the algorithm recommended de-escalation of the primary antibiotic regimen. Secondary outcomes included: (1) the proportion of patients for whom escalation was recommended; (2) the number of recommended de-escalation steps along a pre-specified antibiotic cascade; and (3) the adequacy of therapy in the subset of patients with culture-confirmed infection.

Results

We screened 578 patients, of whom 107 eligible patients with sepsis were included. The Early-IDEAS treatment recommendation was informed by Gram-negative models in 76 (71%) of patients, Gram-positive rules in 66 (61.7%), and local guidelines in 27 (25%). Antibiotic de-escalation was recommended by the algorithm in almost half of all patients (n=50, 47%), no treatment change was recommended in 48 patients (45%), and escalation was recommended in 9 patients (8%). Amongst the patients where de-escalation was recommended, the median number of steps down the a priori antibiotic treatment cascade was 2. Among the 17 patients with relevant culture-positive blood stream infection, the clinician prescribed regimen provided adequate coverage in 14 (82%) and the algorithm recommendation would have provided adequate coverage in 13 (76%), p=1. Among the 25 patients with positive relevant (non-blood) cultures, the clinician prescribed regimen provided adequate coverage in 22 (88%) and the algorithm recommendation would have provided adequate coverage in 21 (84%), p=1.

Conclusions

An individualized decision support algorithm in early sepsis could lead to substantial antibiotic de-escalation without compromising adequate antibiotic coverage.
Stimulated emission depletion microscopy with a single depletion laser using five fluorochromes and fluorescence lifetime phasor separation
Authors: Pisfil Mariano Gonzalez , Nadelson Iliya , Bergner Brigitte , Rottmeier Sonja , Thomae Andreas W. , Dietzel Steffen
Published: April 2022

Stimulated emission depletion (STED) microscopy achieves super-resolution by exciting a diffraction-limited volume and then suppressing fluorescence in its outer parts by depletion. Multiple depletion lasers may introduce misalignment and bleaching. Hence, a single depletion wavelength is preferable for multi-color analyses. However, this limits the number of usable spectral channels. Using cultured cells, common staining protocols, and commercially available fluorochromes and microscopes we exploit that the number of fluorochromes in STED or confocal microscopy can be increased by phasor based fluorescence lifetime separation of two dyes with similar emission spectra but different fluorescent lifetimes. In our multi-color FLIM-STED approach two fluorochromes in the near red (exc. 594 nm, em. 600-630) and two in the far red channel (633/641-680), supplemented by a single further redshifted fluorochrome (670/701-750) were depleted with 775 nm. To the best of our knowledge, these are the first published five color STED images. Generally, this approach doubles the number of fully distinguishable colors in laser scanning microscopy. We provide evidence that eight color FLIM-STED with a single depletion laser would be possible if suitable fluorochromes were identified and we confirm that a fluorochrome may have different lifetimes depending on the molecules to which it is coupled.
Mutations in DNA polymerase δ subunit 1 mediate CMD2-type resistance to Cassava Mosaic Geminiviruses
Authors: Lim Y.W. , Mansfeld B.N. , Schläpfer P. , Gilbert K.B. , Narayanan N.N. , Qi W. , Wang Q. , Zhong Z. , Boyher A. , Gehan J. , Beyene G. , Lin Z.D. , Esuma W. , Feng S. , Chanez C. , Eggenberger N. , Adiga G. , Alicai T. , Jacobsen S.E. , Taylor N.J , Gruissem W. , Bart R.S.
Published: April 2022

Cassava mosaic disease suppresses cassava yields across the tropics. The dominant CMD2 locus confers resistance to the cassava mosaic geminiviruses. It has been reported that CMD2-type landraces lose resistance after regeneration through de novo morphogenesis. As full genome bisulfite sequencing failed to uncover an epigenetic mechanism for loss of resistance, we performed whole genome sequencing and genetic variant analysis and fine-mapped the CMD2 locus to a 190 kilobase interval. Data suggest that CMD2-type resistance is caused by a nonsynonymous, single nucleotide polymorphism in DNA polymerase δ subunit 1 (MePOLD1) located within this region. Virus-induced gene silencing of MePOLD1 in a Cassava mosaic disease-susceptible cassava variety produced a recovery phenotype typical of CMD2-type resistance. Analysis of other CMD2-type cassava varieties identified additional resistance alleles within MePOLD1. MePOLD1 resistance alleles represent important genetic resources for resistance breeding or genome editing, and elucidating mechanisms of resistance to geminiviruses.
A systems approach reveals species differences in hepatic stress response capacity
Authors: Russomanno Giusy , Sison-Young Rowena , Livoti Lucia A. , Coghlan Hannah , Jenkins Rosalind E. , Kunnen Steven J. , Fisher Ciarán P. , Reddyhoff Dennis , Gardner Iain , Rehman Adeeb H. , Fenwick Stephen W. , Jones Andrew R. , De Conchard Guy Vermeil , Simonin Gilles , Bertheux Helene , Weaver Richard J. , Liguori Michael J. , Clausznitzer Diana , Stevens James L. , Goldring Christopher E. , Copple Ian M.
Published: April 2022

To minimise unexpected toxicities in early phase clinical studies of new drugs, it is vital to understand fundamental similarities and differences between preclinical test species and humans. We have used physiologically-based pharmacokinetic modelling to identify doses of the model hepatotoxin acetaminophen yielding similar hepatic burdens of the reactive metabolite N-acetyl-p-benzoquinoneimine in mice and rats, to enable comparison of tissue adaptive responses under conditions of equivalent chemical insult. Mice exhibited a greater degree of liver injury than rats, despite the equivalent hepatic NAPQI burden. Transcriptomic and proteomic analyses highlighted the stronger activation of stress response pathways (including the Nrf2 oxidative stress response and autophagy) in the livers of rats. Components of these pathways were also found to be expressed at a higher basal level in the livers of rats compared with both mice and humans. Our findings exemplify a systems approach to understanding differential species sensitivity to hepatotoxicity, and have important implications for species selection and human translation in the safety testing of new drug candidates.
Bacillus thuringiensis Cry1A toxins divert progenitor cells toward enteroendocrine fate by decreasing cell adhesion with intestinal stem cells
Authors: Jneid Rouba , Loudhaief Rihab , Zucchini-Pascal Nathalie , Nawrot-Esposito Marie-Paule , Fichant Arnaud , Rousset Raphaël , Bonis Mathilde , Osman Dani , Gallet Armel
Published: April 2022

Bacillus thuringiensis subsp. kurstaki (Btk) is a strong pathogen toward lepidopteran larvae thanks to specific Cry toxins causing leaky gut phenotypes. Hence, Btk and its toxins are used worldwide as microbial insecticide and in genetically modified crops, respectively, to fight crop pests. However, Btk belongs to the B. cereus group, some strains of which are well known human opportunistic pathogens. Therefore, ingestion of Btk along with food may threaten organisms not susceptible to Btk infection. Here we show that Cry1A toxins induce enterocyte death and intestinal stem cell (ISC) proliferation in the midgut of Drosophila melanogaster, an organism non-susceptible to Btk. Surprisingly, a high proportion of the ISC daughter cells differentiate into enteroendocrine cells instead of their initial enterocyte destiny. We show that Cry1A toxins weaken the Cadherin-dependent adherens junction between the ISC and its immediate daughter progenitor, leading the latter to adopt an enteroendocrine fate. Hence, though not lethal to non-susceptible organisms, Cry toxins can interfere with conserved cell adhesion mechanisms, thereby disrupting intestinal homeostasis and enteroendocrine functions.
Perceptual expectations and false percepts generate stimulus-specific activity in distinct layers of the early visual cortex
Authors: Haarsma Joost , Deveci Narin , Corbin Nadège , Callaghan Martina F. , Kok Peter
Published: April 2022

Perception has been proposed to result from the integration of feedforward sensory signals with internally generated feedback signals. The latter are believed to play an important role in driving false percepts, i.e., seeing things that are not actually there. Feedforward and feedback influences on perception can be studied using layer-specific fMRI, which we used here to interrogate neural activity underlying high confidence false percepts while healthy participants (N=25) performed a perceptual orientation discrimination task. Orientation-specific BOLD activity in the deep and superficial layers of V2 reflected perceptual expectations induced by predictive auditory cues. However, these expectations did not influence participants’ perception. Instead, high confidence false percepts were reflected by orientation-specific activity in the middle input layers of V2, suggesting a feedforward signal contributing to false percepts. The prevalence of high confidence false percepts was related to everyday hallucination severity in a separate online sample (N=100), suggesting a possible link with abnormal perceptual experiences. These results reveal a feedforward mechanism underlying false percepts, reflected by spontaneous stimulus-like activity in the input layers of the visual cortex, independent of top-down perceptual expectations.
The role of neuropeptides in regulating ecdysis and reproduction in the hemimetabolous insect Rhodnius prolixus
Authors: Sterkel Marcos , Volonté Mariano , Albornoz Maximiliano G. , Wulff Juan Pedro , del Huerto Sánchez Mariana , Terán Paula María , Ajmat María Teresa , Ons Sheila
Published: April 2022

In ecdysozoan animals, moulting entails the production of a new exoskeleton and the shedding of the old one during ecdysis. It is induced by a pulse of ecdysone that regulates the expression of different hormonal receptors and activates a peptide-mediated signalling cascade. In Holometabola, the peptidergic cascade regulating ecdysis has been well described. However, very little functional information regarding the neuroendocrine regulation of ecdysis is available for Hemimetabola, which displays an incomplete metamorphosis.

Here, we studied neuropeptides related to ecdysis regulation in the hemi-metabolous insect Rhodnius prolixus. The RNA interference-mediated reduction of ETH expression in fourth instar nymphs resulted in lethality at the expected time of ecdysis, thereby showing its crucial role in this process. Furthermore, the results revealed the involvement of ETH in the regulation of reproductive fitness. Different from holometabolous, the knockdown of ETH in adult females led to failures in egg hatching without affecting the oviposition. Most of the first instar nymphs hatched from the eggs laid by females injected with dsEH, dsCCAP and dsOKA died at the expected time of ecdysis, indicating the crucial involvement of these genes for post-embryonic development. No phenotypes were observed upon CZ knockdown in nymphs or adult females. The conservation of the role of these neuropeptides in regulating ecdysis and reproduction throughout the class Insecta is discussed.

Summary statement

The information provided here is of interest for evolutive studies on the neuroendocrine regulation of ecdysis and reproduction in insects, and the research for new targets to control pest insects.
Co-expression of recombinant human collagen α1(III) chain with viral prolyl 4-Hydroxylase in P. pastoris GS115
Authors: Fang Jiayuan , Ma Ze , Liu Dongyue , Wang Zhaoguo , Zheng Shuo , Wu Hongyan , Xia Peijun , Chen Xi , Yang Rui , Hao Linlin
Published: April 2022

Prolyl 4-hydroxylase (P4H) is essential to maintain the stable triple-helix structure and function of human collagen α1(Ш) chain (COL3A1). To obtain hydroxylated human COL3A1, the human COL3A1 and the viral P4H A085R were co-expressed in P. pastoris GS115. The sequence of human COL3A1 without N-terminal and C-terminal was selected for expression. Colony PCR analysis and sequencing after transfection showed that the target gene had inserted successfully. Real-time quantitative PCR (RT-qPCR) indicated that human COL3A1 and P4H were expressed at the mRNA levels. SDS-PAGE and Western blotting analysis of supernatant from the recombinant methylotrophic yest culture showed that recombinant human COL3A1 (rhCOL3A1) was secreted into the culture medium with an apparent molecular mass of approximately 130 kDa. It was noted that the rhCOL3A1 expession quantity was higest at 120 h of induction. Furthermore, mass spectrometry analysis demonstrated that the rhCOL3A1 was expressed successfully. His-tagged rhCOL3A1 protein was purified by Ni-affinity column.
The Computational Neuroanatomy of Predictive Dynamics of Pain Perception
Authors: Ishikawa Ryota , Izawa Jun
Published: April 2022

Pain perception is an active process that regulates nociceptive inputs by descending opioidergic signals, in which the brain encodes pain-related predictive and corrective terms, after having made Bayesian-like inferences about noxious amplitudes. Offset analgesia (OA), a large reduction of tonic pain after a small nociceptive termination, is typical empirical evidence of on-line pain modulation through prediction and its correction. However, the basic computational structure underlying OA is not understood. Here, we adopted a constructive approach, formulated the inference of noxious amplitudes with a Kalman filter model, i.e., a recursive Bayesian computation, and then deduced the computational structure for OA, in which an interaction between two latent state variables was implemented. Simulation results suggested that the unidirectional interaction of the two states with two dissociable roles (an integral over time and a derivative of stimulus changes) is crucial for OA. Our results, combined with previous anatomical studies, suggest a computational basis of neural connectivity for pain. The ACC and aINS interact to compute a descending prediction to the brainstem, i.e. PAG, while ascending inputs are filtered in the thalamus and delivered to the cortices as prediction errors. Thus, we suggest dissociable, computational roles of the ACC and aINS in pain processing.

Author Summary

Understanding the computational theory of pain perception is crucial for clarifying why some painful syndromes become chronic. Here, we propose a computational neuroanatomical model of endogenous pain modulation and we simulate a model for offset analgesia. We first demonstrate through model comparisons that the brain encodes at least two distinct states to estimate ongoing nociception: a derivative of input changes and its integral. We suggest that its neural substrate comprises hierarchical circuits composed of cortices, the thalamus, and brainstem. Second, we show that the computational basis of disrupted pain modulation in patients is pseudo-neglect of actual sensory inputs, with bias toward the internal prediction. Our results are the first to provide a neurocomputational mechanism of pain perception dynamics and a factor that determines its functionality.
Isolation, purification, and characterisation of a phage tail-like bacteriocin from the insect pathogenic bacterium Brevibacillus laterosporus
Authors: Babar Tauseef Khan , Glare Travis R. , Hampton John G. , Hurst Mark R.H. , Narciso Josefina O.
Published: April 2022

The gram-positive and spore-forming bacterium Brevibacillus laterosporus (Bl) belongs to the Brevibacillus brevis phylogenetic cluster. Isolates of the species have demonstrated pesticidal potency against a wide range of invertebrate pests and plant diseases. Two New Zealand isolates, Bl 1821L and Bl 1951, are under development as biopesticides for control of diamondback moth and other pests. However, due to often restricted growth of these endemic isolates, production can be an issue. During investigations of the cause of the disrupted growth, electron micrographs of crude lysate of Bl 1821L showed the presence of phages tail-like structures. PEG 8000 precipitated lysate harbouring the putative phage tail-like particles demonstrated broad-spectrum activity against several gram-positive bacteria. SDS-PAGE of purified and concentrated lysate showed a prominent protein band of ∼48 kD from where transmission electron microscopy revealed the presence of polysheath-like structures. N-terminal sequencing of the ∼48 kD protein mapped to a gene with weak predicted amino acid homology to a Bacillus PBSX phage-like element xkdK, the translated product of which shared >90% amino acid similarity to the phage tail-sheath protein of another Bl published genome, LMG15441. An xkdK homolog was also identified in the Bl 1951 genome. However, genome comparison of the region around the xkdK gene between Bl 1821L and Bl 1951 found differences including two glycine rich protein encoding genes which contain imperfect repeats (1700 bp) in Bl 1951, while a putative phage region resides in the analogous Bl 1821L region. Although comparative analysis of the genomic organisation of Bl 1821L and Bl 1951 PBSX-like region with the defective phages PBSX, PBSZ, and PBP 180 of Bacillus subtilis isolates 168 and W23, and Bacillus phage PBP180 revealed low amino acids similarity, the genes encode similar functional proteins in similar arrangements, including phage tail-sheath (XkdK), tail (XkdO), holin (XhlB), and N-acetylmuramoyl-L-alanine (XlyA). AMPA analysis identified a bactericidal stretch of 13 amino acids in the ∼48 kD sequenced protein of Bl 1821L. Assays of purified ∼48 kD protein of Bl 1821L caused a decrease of 34.2% in the number of viable cells of Bl 1951, 18 hours after treatment as compared to the control.

Significance of the study

This study for the first time isolated, purified, and characterised putative phage tail-like bacteriocins (PTLBs) from the insect pathogenic isolates of Brevibacillus laterosporus. Identified PTLBs caused a decrease in the number of viable cells of Bl 195, 18 hours after treatment as compared to control. Therefore, it is likely that the putative PTLBs might have implications in harnessing the insecticidal potential of this useful bacterium.
Self-avoidance alone does not explain the function of Dscam1 in mushroom body axonal wiring
Authors: Dong Haiyang , Guo Pengjuan , Zhang Jian , Wu Lili , Fu Ying , Li Lei , Zhu Yanda , Du Yiwen , Shi Jilong , Zhang Shixin , Li Guo , Xu Bingbing , Bian Lina , Zhu Xiaohua , You Wendong , Shi Feng , Yang Xiaofeng , Huang Jianhua , Jin Yongfeng
Published: April 2022

Alternative splicing of Drosophila Dscam1 into 38,016 isoforms provides neurons with a unique molecular code for self-recognition and self-avoidance. A canonical model suggests that homophilic binding of identical Dscam1 isoforms on sister branches of mushroom body (MB) axons supports segregation with high fidelity, even when only a single isoform is expressed. Here we generated a series of mutant flies with a single exon 4, 6, or 9 variant, encoding 1,584, 396, or 576 potential isoforms, respectively. Surprisingly, most of the mutants in the latter two groups exhibited obvious defects in the growth, branching, and segregation of MB axonal sister branches. This demonstrates that repertoires of 396 and 576 Dscam1 isoforms were not sufficient for normal patterning of axonal branches. Moreover, reducing Dscam1 levels largely reversed the defects caused by reduced isoform diversity, suggesting a functional link between Dscam1 expression levels and isoform diversity. Taken together, these results indicate that canonical self-avoidance alone does not explain the function of Dscam1 in MB axonal wiring.
The sphingolipid inhibitor myriocin increases susceptibility of Candida auris to amphotericin B
Authors: Stieber Hanna , Junghanns Lara , Wilhelm Hannah , Batliner Maria , Aldejohann Alexander Maximilian , Kurzai Oliver , Martin Ronny
Published: April 2022

The emerging human fungal pathogen Candida auris can cause of hospital outbreaks by transmission between patients and / or medical care staff. It is known for a fast adaption to environmental stress and antifungal treatment. Besides resistance to fluconazole in most isolates, C. auris frequently shows limited susceptibility to echinocandins and even to amphotericin B. Therefore, multidrug resistance (MDR) is frequently found in clinical isolates, leading to a need for new therapeutic targets and compounds. One of those targets could be sphingolipids which are an integral part of the cell membrane and are important for membrane fluidity and the formation of lipid rafts. Here, we show that myriocin-mediated inhibition of the de novo sphingolipid biosynthesis caused severe growth defects in C. auris. Sublethal myriocin concentrations increase fungal susceptibility to amphotericin B and anidulafungin. While the effect is limited for anidulafungin, even isolates that show phenotypic resistance to amphotericin B became susceptible in presence of myriocin. A large-scale screening of 59 clinical isolates validated these initial results and showed that inhibition of the de novo sphingolipid biosynthesis increases C. auris susceptibility to amphotericin B. These observations open new options for future therapeutic strategies and illustrate that sphingolipids might play a pivotal role for the ability of C. auris to develop resistance against amphotericin B.
Cis mutagenesis in vivo reveals extensive noncanonical functions of Dscam1 isoforms in neuronal wiring
Authors: Zhang Shixin , Yang Xi , Dong Haiyang , Xu Bingbing , Wu Lili , Zhang Jian , Li Guo , Guo Pengjuan , Li Lei , Fu Ying , Du Yiwen , Zhu Yanda , Shi Feng , Huang Jianhua , He Haihuai , Jin Yongfeng
Published: April 2022

Drosophila Dscam1 encodes ten thousand of cell recognition molecules via alternative splicing, which is required for nervous function. However, the underlying mechanism has not fully understood. Here we revealed extensive noncanonical functions of Dscam1 isoform diversity in neuronal wiring. We generated a series of allelic cis mutations in Dscam1, encoding normal number of isoforms albeit with altered isoform composition. Despite normal dendritic self-avoidance and self/non-self discrimination in da neurons, which is consistent with canonical self-avoidance model, these mutants exhibited strikingly distinct spectra of phenotypic defects in three classes of neurons: up to ∼60% defects in mushroom bodies, a significantly increased branching and growth in da neurons, and mild axonal branching defects in mechanosensory neurons. These data suggest that proper Dscam1 isoform composition is required for axon and dendrite growth in diverse neurons. This unprecedented splicing-tuned regulation unlocks new insights into the molecular mechanisms that Dscam1 isoform diversity is engaged in.
High-throughput proteomics of nanogram-scale samples with Zeno SWATH DIA
Authors: Wang Ziyue , Mülleder Michael , Batruch Ihor , Chelur Anjali , Textoris-Taube Kathrin , Schwecke Torsten , Hartl Johannes , Causon Jason , Castro-Perez Jose , Demichev Vadim , Tate Stephen , Ralser Markus
Published: April 2022

The ability to conduct high-quality proteomic experiments in high throughput has opened new avenues in clinical research, drug discovery, and systems biology. Next to an increase in quantitative precision, recent developments in high-throughput proteomics have also gained proteomic depth, to the extent that earlier gaps between classic and high-throughput experiments have significantly narrowed. Here we introduce and benchmark Zeno SWATH, a data-independent acquisition technique that employs a linear ion trap pulsing (Zeno trap pulsing) in order to increase proteomic depth and dynamic range in proteomic experiments. Combined with the high acquisition speed, these gains in sensitivity are particularly attractive for conducting high-throughput proteomics experiments with high chromatographic flow rates and fast gradients. We demonstrate that when combined with either micro-flow- or analytical-flow-rate chromatography, Zeno SWATH increases protein identification in complex samples 5- to 10-fold when compared to current SWATH acquisition methods on the same instrument. Using 20-min micro-flow chromatography, Zeno SWATH identified > 6,000 proteins from a 62.5 ng load of human cell lysate with more than 5,000 proteins consistently quantified in triplicate injections with a median CV of 6%. Using 5-min analytical-flow-rate chromatography (800 µl/min), Zeno SWATH identified 4,907 proteins from a triplicate injection of 2 µg of a human cell lysate; or more than 3,000 proteins from 250 ng tryptic digest. Zeno SWATH hence facilitates precise proteomic experiments with small sample amounts using a fast and robust high flow-rate chromatographic method, broadening the application space that requires precise proteomic experiments on a large scale.
AlphaFold2 can predict single-mutation effects
Authors: McBride John M. , Polev Konstantin , Abdirasulov Amirbek , Reinharz Vladimir , Grzybowski Bartosz A. , Tlusty Tsvi
Published: April 2022

AlphaFold2 (AF) is a promising tool, but is it accurate enough to predict single mutation effects? Here, we report that the localized structural deformation between protein pairs differing by only 1-3 mutations – as measured by the effective strain – is correlated across 3,901 experimental and AF-predicted structures. Furthermore, analysis of ∼11,000 proteins shows that the local structural change correlates with various phenotypic changes. These findings suggest that AF can predict the range and magnitude of single-mutation effects on average, and we propose a method to improve precision of AF predictions and to indicate when predictions are unreliable.
Pneumococcal Evasion of Antibiotics via Metabolic Adaptation During Infection
Authors: Dao Tina H. , Echlin Haley , McKnight Abigail , Marr Enolia S. , Junker Julia , Jia Qidong , Hayden Randall , Rosch Jason W.
Published: April 2022

Streptococcus pneumoniae is a major human pathogen of global health concern, causing a range of mild to severe infections, including acute otitis media, pneumonia, sepsis, and meningitis. The rapid emergence of antibiotic resistance among S. pneumoniae isolates poses a serious public health problem worldwide. Resistant pneumococcal strains have rendered the mainstay treatment with beta-lactams, fluoroquinolones, and macrolides, ineffective. Antibiotic resistance in S. pneumoniae has spread globally via the emergence of de novo mutations and horizontal transfer of resistance. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage, as is often the case with other classes of antibiotics. In this study, we demonstrated that deleterious fitness costs constrain the emergence of individual fluoroquinolone resistance mutations in either topoisomerase IV or gyrase A in S. pneumoniae. Generation of double point mutations in the target enzymes in topoisomerase IV and gyrase A conferred high-level fluoroquinolone resistance while restoring fitness comparable to the sensitive wild-type. During an in vivo model of antibiotic resistance evolution, S. pneumoniae was able to circumvent deleterious fitness costs imposed by resistance determinants through development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, an effect that could be recapitulated pharmacologically. The metabolic mutants conferring tolerance resulted in a fitness benefit during infection following antibiotic treatment with fluroquinolones. These data suggest that emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by host fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes may be an important contributor to the evasion of antibiotic mediated killing.
CanSig: a tool for benchmarking malignant state discovery in single-cell RNA-Seq data
Authors: Barkmann Florian , Yates Josephine , Czyz Pawel , Kraft Agnieszka , Glettig Marc , Beerenwinkel Niko , Boeva Valentina
Published: April 2022

Single-cell RNA sequencing (scRNA-seq) facilitates the discovery of gene signatures that define cell states across patients, which could be used in patient stratification and drug discovery. However, the lack of standardization in computational methodologies to analyse these data impedes the reproducibility of signature detection. To address this, we developed CanSig, a comprehensive benchmarking tool that evaluates methods for identifying transcriptional signatures in cancer. CanSig integrates metrics for batch correction and biological signal conservation with a gene signature correlation metric to score according to rediscovery, cross-dataset reproducibility, and clinical relevance. We applied CanSig to ten methods and to ten scRNA-seq datasets from four human cancer types—glioblastoma, breast cancer, lung adenocarcinoma, and cutaneous squamous cell carcinoma— representing 116 patients and 105,000 malignant cells. Our results identify BBKNN as a leading method. We showed that the signatures identified with these methods correlate with clinically relevant outcomes, including patient survival and lymph node metastasis. Thus, CanSig establishes a standardized framework for reproducible cancer transcriptomics analysis.
This is GlycoQL
Authors: Hayes Catherine , Daponte Vincenzo , Mariethoz Julien , Lisacek Frederique
Published: April 2022

Motivation

We have previously designed and implemented a tree-based ontology to represent glycan structures with the aim of searching these structures with a glyco-driven syntax. This resulted in creating the GlySTreeM knowledge-base as a linchpin of the matching procedure and we now introduce a query language, called GlycoQL, for the actual implementation of a glycan structure search.

Results

The methodology is described and illustrated with a use-case focused on SARS-CoV-2 spike protein glycosylation. We show how to enhance site annotation with federated queries involving UniProt and GlyConnect, our glycoprotein database.

Availability

currently only available for reviewers at:https://beta.glyconnect.expasy.org/glycoql/

Contact

catherine.hayes@unige.ch;frederique.lisacek@sib.swiss

Supplementary information

Supplementary data are available athttps://glyconnect.expasy.org/glystreem/wiki.
Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly
Authors: Shipilina Daria , Näsvall Karin , Höök Lars , Vila Roger , Talavera Gerard , Backström Niclas
Published: April 2022

Gene family expansions and crossing over are two main mechanisms for the generation of novel genetic variants that can be picked up by natural selection. Here, we developed a high-density, pedigree-based linkage map of the painted lady butterfly (Vanessa cardui) – a non-diapausing, highly polyphagous species famous for its long-distance migratory behavior. We also performed detailed annotations of genes and interspersed repetitive elements for a previously developed genome assembly, characterized species-specific gene family expansions and the relationship between recombination rate variation and genomic features. Identified expanded gene families consisted of clusters of tandem duplications with functions associated with protein and fat metabolism, detoxification, and defense against infection - key functions for the painted lady’s unique lifestyle. The detailed assessment of recombination rate variation demonstrated a negative association between recombination rate and chromosome size. Moreover, the recombination landscape along the holocentric chromosomes was bimodal. The regional recombination rate was positively associated with the proportion of short interspersed elements (SINEs), but not the other repeat classes, potentially a consequence of SINEs hijacking the recombination machinery for proliferation. The detailed genetic map developed here will contribute to the understanding of the mechanisms and evolutionary consequences of recombination rate variation in Lepidoptera in general. We conclude that the structure of the painted lady genome has been shaped by a complex interplay between recombination, gene duplications and TE-activity and that specific gene family expansions have been key for the evolution of long-distance migration and the ability to utilize a wide range of host plants.
The EGFR/ErbB inhibitor neratinib modifies the neutrophil phosphoproteome and promotes apoptosis and clearance by airway macrophages
Authors: Herman Kimberly D , Wright Carl G , Marriott Helen M , McCaughran Sam C , Collins Mark O , Renshaw Stephen A , Prince Lynne R
Published: April 2022

Dysregulated neutrophilic inflammation can be highly destructive in chronic inflammatory diseases due to prolonged neutrophil lifespan and continual release of histotoxic mediators in inflamed tissues. Therapeutic induction of neutrophil apoptosis, an immunologically silent form of cell death, may be beneficial in these diseases, provided that the apoptotic neutrophils are efficiently cleared from the tissue. Our previous research identified ErbB inhibitors as able to induce neutrophil apoptosis and reduce neutrophilic inflammation bothin vitroandin vivo(Rahman et al., 2019). Here we extend that work using a clinical ErbB inhibitor, neratinib, which has the potential to be repurposed in inflammatory diseases. We show that neratinib reduces neutrophilic migration to an inflammatory site in zebrafish larvae. Neratinib upregulates efferocytosis and reduces the number of persisting neutrophil corpses in mouse models of acute, but not chronic, lung injury, suggesting the drug may have therapeutic benefits in acute inflammatory settings. Phosphoproteomics analysis of human neutrophils shows that neratinib modifies the phosphorylation of proteins regulating apoptosis, migration and efferocytosis. This work identifies a potential mechanism for neratinib in treating acute lung inflammation by upregulating the clearance of dead neutrophils and, through examination of the neutrophil phosphoproteome, provides important insights into the mechanisms by which this may be occurring.