bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study
Authors: Anscombe Catherine , Lissauer Samantha , Thole Herbert , Rylance Jamie , Dula Dingase , Menyere Mavis , Kutambe Belson , van der Veer Charlotte , Phiri Tamara , Banda Ndaziona P. , Mndolo Kwazizira S. , Mponda Kelvin , Phiri Chimota , Mallewa Jane , Nyirenda Mulinda , Katha Grace , Mwandumba Henry , Gordon Stephen B. , Jambo Kondwani C. , Cornick Jennifer , Feasey Nicholas , Barnes Kayla G. , Morton Ben , Ashton Philip M. ,   Blantyre COVID-19 Consortium
Published: February 2022

AbstractBackgroundCompared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome.MethodsWe enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION™ in Blantyre.ResultsWe enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection.ConclusionsOur data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.SummaryWe used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.
Enhancing imagery rehearsal therapy for nightmares with targeted memory reactivation
Authors: Schwartz Sophie , Clerget Alice , Perogamvros Lampros 
Published: February 2022

SummaryNightmare disorder (ND) is characterized by dreams with strong negative emotions occurring during rapid-eye movement (REM) sleep. ND is mainly treated by imagery rehearsal therapy (IRT), where the patients are asked to change the negative story line of their nightmare to a more positive one. We here used targeted memory reactivation (TMR) during REM sleep to strengthen IRT-related memories and accelerate remission of ND. Thirty-six patients with ND were asked to perform an initial IRT session and, while they generated a positive outcome of their nightmare, half of the patients were exposed to a sound (TMR group), while no such pairing took place for the other half (control group). During the next two weeks, all patients performed IRT every evening at home, and were exposed to the sound during REM sleep with a wireless headband, which automatically detected sleep stages. The frequency of nightmares per week at two weeks was used as the primary outcome measure. We found that the TMR group had less frequent nightmares and more positive dream emotions than the control group after two weeks of IRT, and a sustained decrease of nightmares after three months. By demonstrating the effectiveness of TMR during sleep to potentiate therapy, these results have clinical implications for the management of ND, with relevance to other psychiatric disorders too. Additionally, these findings show that TMR applied during REM sleep can modulate emotions in dreams.
Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant
Authors: Kanjilal Sanjat , Chalise Sujata , Shah Adnan Shami , Cheng Chi-An , Senussi Yasmeen , Uddin Rockib , Thiriveedhi Vamsi , Cho Ha Eun , Carroll Seamus , Lemieux Jacob , Turbett Sarah , Walt David R 
Published: February 2022

AbstractRapid antigen detection tests (RADTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now in widespread use in the United States. RADTs play an important role in maintaining an open society but require periodic reassessment to ensure test performance remains intact as the virus evolves. The nucleocapsid (N) protein is the target for the majority of RADTs and the SARS-CoV-2 Omicron variant has several N protein mutations that are previously uncharacterized. We sought to assess the impact of these mutations by testing 30 Omicron variant samples across a wide range of viral loads on three widely used RADTs: the iHealth COVID-19 Antigen Rapid Test, the ACON Laboratories FlowFlex COVID-19 Antigen Home Test, and the Abbott BinaxNOW COVID-19 Antigen Card, using 30 Delta variant samples as a comparator. We found no change in the analytic sensitivity of all three RADTs for detection of Omicron versus Delta, but noted differences in performance between assays. No RADT was able to detect samples with a cycle threshold (Ct) value of ≥27.5 for the envelope gene target on the Roche cobas RT-PCR assay. Epidemiologic studies are necessary to correlate these findings with their real-world performance.
GPX4-associated Sedaghatian Type Spondylometaphyseal Dysplasia: A Protein Interactome Perspective
Authors: Karunakaran Kalyani B. , Balakrishnan N. , Ganapathiraju Madhavi K. 
Published: February 2022

AbstractSpondylometaphyseal dysplasia, Sedaghatian type (SMDS) is a rare and lethal skeletal dysplasia inherited in an autosomal recessive manner and caused by mutations in GPX4. In order to expand the functional landscape of this poorly studied disorder and accelerate the discovery of biologically insightful and clinically actionable targets, we constructed SMDS-centric and GPX4-centric protein-protein interaction (PPI) networks, augmented with novel protein interactors predicted by our HiPPIP algorithm. The SMDS-centric networks included those that showed the interconnections of GPX4 with other putative SMDS-associated genes and genes associated with other skeletal dysplasias. The GPX4-centric network showed the interconnections of GPX4 with genes whose perturbation has been known to affect GPX4 expression. We discovered that these networks either contained or were enriched with genes associated with specific SMDS pathophenotypes, tissue-naïve/fetus-specific functional modules and genes showing elevated expression in brain and/or testis similar to GPX4. We identified 7 proteins as novel interactors of GPX4 (APBA3, EGR4, FUT5, GAMT, GTF2F1, MATK and ZNF197) and showed their potential biological relevance to GPX4 or SMDS. Comparative transcriptome analysis of expression profiles associated with chondroplasia and immune-osseous dysplasia versus drug-induced profiles revealed 11 drugs that targeted the neighborhood network of GPX4 and other putative SMDS-associated genes. Additionally, resveratrol, which is currently being tested against a skeletal dysplasia in a clinical trial, was identified as another potential candidate based on the proximity of its targets to GPX4.
Specific attenuation of purinergic signaling during bortezomib-induced peripheral neuropathy
Authors: Holzer Anna-Katharina , Suciu Ilinca , Goj Thomas , Karreman Christiaan , Leist Marcel 
Published: February 2022

AbstractHuman peripheral neuropathies are poorly-understood, and the availability of experimental models limits further research. The PeriTox test uses immature dorsal root ganglia (DRG)-like neurons, derived from induced pluripotent stem cells (iPSC), to assess cell death and neurite damage. Here, we explored the suitability of matured peripheral neuron cultures for detection of sub-cytotoxic endpoints, such as altered responses of pain-related P2X receptors. A 2-step differentiation protocol, involving transient expression of ectopic neurogenin-1 (NGN1), allowed for the generation of homogeneous cultures of sensory neurons. After > 38 days-of-differentiation, they showed a robust response (Ca2+-signalling) to the P2X3 ligand α,β-methylene ATP. The clinical proteasome inhibitor bortezomib abolished the P2X3 signal at ≥ 5 nM, while 50-200 nM were required in the PeriTox test to identify neurite damage and cell death. A 24 h treatment with low nM concentrations of bortezomib led to moderate increases in resting cell intracellular [Ca2+], but signalling through transient receptor potential-V1 (TRPV1) receptors or depolarization-triggered Ca2+-influx remained unaffected. We interpret the specific attenuation of purinergic signalling as functional cell stress response. A reorganization of tubulin to dense structures around the cell somata confirmed a mild, non-cytotoxic stress triggered by low concentrations of bortezomib. The proteasome inhibitors carfilzomib, delanzomib, epoxomycin and MG-132 showed similar stress responses. Thus, the model presented here may be used for profiling of new proteasome inhibitors as to their side effect (neuropathy) potential, or for pharmacological studies on the attenuation of their neurotoxicity. P2X3 signalling proved useful as endpoint to assess potential neurotoxicants in peripheral neurons.
Fisheries genomics of snapper (Chrysophrys auratus) along the western Australian coast
Authors: Bertram Andrea , Fairclough David , Sandoval-Castillo Jonathan , Brauer Chris , Fowler Anthony , Wellenreuther Maren , Beheregaray Luciano B. 
Published: February 2022

AbstractThe efficacy of fisheries management strategies depends on stock assessment and management actions being carried out at appropriate spatial scales. This requires understanding of spatial and temporal population structure and connectivity, which is challenging in weakly structured and highly connected marine populations. We carried out a population genomics study of the heavily exploited snapper (Chrysophrys auratus) along ∼2,600 km of the Australian coastline, with a focus on Western Australia (WA). We used 10,903 filtered SNPs in 341 individuals from eight locations to characterise population structure and connectivity in snapper across WA and to assess if current spatial scales of stock assessment and management agree with evidence from population genomics. Our dataset also enabled us to investigate temporal stability in population structure as well as connectivity between WA and its nearest, eastern jurisdictional neighbor. As expected for a species influenced by the extensive ocean boundary current in the region, low genetic differentiation and high connectivity was uncovered across WA. However, we did detect strong isolation by distance and genetic discontinuities in the mid-west and south-east. The discontinuities correlate with boundaries between biogeographic regions, influenced by on-shelf oceanography, and the sites of important spawning aggregations. We also detected temporal instability in genetic structure at one of our sites, possibly due to interannual variability in recruitment in adjacent regions. Our results partly contrast with the current spatial management of snapper in WA, highlighting the need for a review. This study supports the value of population genomic surveys in informing the management of weakly-structured and wide-ranging marine fishery resources.
LLIN Evaluation in Uganda Project (LLINEUP) – The durability of long-lasting insecticidal nets treated with and without piperonyl butoxide (PBO) in Uganda
Authors: Mechan Frank , Katureebe Agaba , Tuhaise Violet , Mugote Martin , Oruni Ambrose , Onyige Ismail , Bumali Kawesa , Thornton Jonathan , Maxwell Kilama , Kyohere Mary , Kamya Moses R , Mutungi Peter , Kigozi Simon P , Yeka Adoke , Opigo Jimmy , Maiteki-Sebuguzi Catherine , Gonahasa Samuel , Hemingway Janet , Dorsey Grant , Reimer Lisa J , Staedke Sarah G , Donnelly Martin J , Lynd Amy 
Published: February 2022

ABSTRACTLong Lasting Insecticidal Nets (LLINs) supplemented with the synergist piperonyl butoxide have been developed in response to growing pyrethroid resistance however their durability in the field remains poorly described. A pragmatic cluster-randomised trial was embedded into Uganda’s 2017-2018 distribution to compare the durability of LLINs with and without PBOA total of 104 clusters were included with each receiving one of four LLIN products, two with pyrethroid+PBO (Olyset Plus and PermaNet 3.0) and two pyrethroid-only (Olyset Net and PermaNet 2.0). Nets were sampled at baseline, 12, and 25 months post-distribution to assess physical condition, chemical content, and bioefficacy. Physical condition was quantified using proportionate Hole Index and chemical content measured using high-performance liquid chromatography. Bioefficacy was assessed with three-minute WHO Cone and Wireball assays using pyrethroid-resistant An. gambiae, with 1hr knockdown and 24hr mortality recorded.There was no difference in physical durability between LLIN products assessed (p=0.644). The pyrethroid content of all products remained relatively stable across timepoints but PBO content declined by 55% (p<0.001) and 58% (p<0.001) for Olyset Plus and PermaNet 3.0 respectively. Both PBO LLINs were highly effective against pyrethroid-resistant mosquitoes when new, knocking down all mosquitoes. However, bioefficacy declined over time with Olyset Plus knocking down 45.72% (95% CI: 22.84-68.62, p=0.021) and Permanet 3.0 knocking down 78.57% (95% CI: 63.57-93.58, p<0.001) after 25 months.Here we demonstrate that both Olyset Plus and PermaNet 3.0 are as durable as their pyrethroid-only equivalents and had superior bioefficacy against pyrethroid-resistant An. gambiae. However, the superiority of PBO-LLINs decreased with operational use, correlating with a reduction in total PBO content. This decline in bioefficacy after just two years is concerning and there is an urgent need to assess the durability of PBO LLINs in other settings.
Reducing structural non-identifiabilities in upstream bioprocess models using profile-likelihood
Authors: Babel Heiko , Omar Ola , Paul Albert , Bär Joachim 
Published: February 2022

AbstractProcess models are increasingly used to support upstream process development in the biopharmaceutical industry for process optimization, scale-up and to reduce experimental effort. Parametric unstructured models based biological mechanisms are highly promising, since they do not require large amounts of data. The critical part in the application is the certainty of the parameter estimates, since uncertainty of the parameter estimates propagates to model predictions and can increase the risk associated with those predictions. Currently Fisher-Information-Matrix based approximations or Monte-Carlo approaches are used to estimate parameter confidence intervals and regularization approaches to decrease parameter uncertainty.Here we apply profile likelihood to determine parameter identifiability of a recent upstream process model. We have investigated the effect of data amount on identifiability and found out that addition of data reduces non-identifiability. The likelihood profiles of non-identifiable parameters were then used to uncover structural model changes. These changes effectively alleviate the remaining non-identifiabilities except for a single parameter out of 21 total parameters.We present the first application of profile likelihood to a complete upstream process model. Profile likelihood is a highly suitable method to determine parameter confidence intervals in upstream process models and provides reliable estimates even with non-linear models and limited data.
Prefrontally Modulated Vagal Tone Inhibits Inflammatory Responses to Prevent Telomere Damage in Healthy Participants
Authors: Ask Torvald F. , Sütterlin Stefan 
Published: February 2022

AbstractBackgroundAccumulated senescent cells are proposed to be one of the main drivers of age-related pathology through disruption of tissue structure and function. We recently proposed the Neuro-Immuno-Senescence Integrative Model (NISIM; Ask et al., 2018) which relates prefrontally modulated vagal tone and subsequent balance between vagal and sympathetic input to the spleen to inflammatory responses leading to generation of reactive oxygen species and oxidative telomere damage. The NISIM is based on converging evidence and argues for the existence of a prefrontal cortex-autonomic nervous system-spleen (PAS) axis, suggesting that the inflammation that induces reactive oxygen species-generation is downstream of this axis.AimIn this study, we aim to assess inflammation as a mediator in the relationship between prefrontally modulated vagal tone and leukocyte telomere length to test the hypothesis that PAS axis dysregulation accelerates cellular aging. We also assess the relationship between a recently proposed index of vagal immunomodulation (vagal tone/inflammation ratio; NIM index; Gidron et al., 2018) and telomere length, and compare results between the NIM index and vagal tone as predictors of telomere length.MethodsThis study uses participant data from a large nationally representative longitudinal study since 1974 with a total of 45,000 Norwegian residents so far. A sub-sample of 1372 participants from which vagal tone, C Reactive Protein, and leukocyte telomere length could be obtained were included in the study. Relationships were analyzed with hierarchical multiple linear regression using either vagal tone and C Reactive Protein or the NIM index to predict telomere length. Sleeping problems, tobacco use status, alcohol use status, time since last meal, and symptoms of depression were included as control variables.ResultsIn the mediation analysis, vagal tone was a significant positive predictor of telomere length, while C Reactive Protein was a significant negative predictor of telomere length. This relationship remained significant when individually controlling for some but not all confounding variables. The NIM index was a significant positive predictor of telomere length. This relationship remained significant when controlling for all confounding variables except one. In a reduced dataset excluding all participants where confounders were present, the NIM index remained a significant predictor of telomere length.ConclusionThis is the first study suggesting that PAS axis activity is associated with telomere length thus supporting the NISIM. Results indicate that the NIM index is a more sensitive indicator of PAS axis activity than vagal tone and C Reactive Protein in isolation. Clinical relevance and suggestions for future research are discussed.
Genomic characterization of SARS-CoV-2 from Islamabad, Pakistan by Rapid Nanopore sequencing
Authors: Badar Nazish , Ikram Aamer , Salman Muhammad , Umair Massab , Rehman Zaira , Ahad Abdul , Mirza Hamza Ahmed , Alam Masroor , mehmood Nayab , Bashir Uzma 
Published: February 2022

AbstractSince the start of COVID-19 pandemic, Pakistan has experienced four waves of pandemic. The fourth wave ended in October, 2021 while the fifth wave of pandemic starts in January, 2022. The data regarding the circulating strains after the fourth wave of pandemic from Pakistan is not available. The current study explore the genomic diversity of SARS-CoV-2 after fourth wave and before fifth wave of pandemic through whole genome sequencing. The results showed the circulation of different strains of SARS-CoV-2 during November-December, 2021. We have Omicron BA.1 (n=4), Lineage A (n=2) and delta AY.27 (n=1) variants of SARS-CoV-2 in the population of Islamabad. All the isolates harbors characteristics mutations of omicron and delta variant in the genome. The lineage A isolate harbors a nine amino acid (68-76) and a ten amino acid (679-688) deletion in the genome. The circulation of omicron in the population before the fifth wave of pandemic and subsequent upsurges of COVID-19 positive cases in Pakistan highlights the importance of genomic surveillance.
Species richness and community structure of bats along a forest elevational transect in Papua New Guinea
Authors: Sivault Elise , Amick Pita K. , Armstrong Kyle N. , Novotny Vojtech , Sam Katerina 
Published: February 2022

ABSTRACTOver the past decades, elevational gradients have become a powerful tool with which to understand the underlying cause(s) of biodiversity. The Mt. Wilhelm elevational transect is one such example, having been used to study the birds, insects, and plants of Papua New Guinea (PNG). However, a survey of mammals from this forest elevational transect was lacking. We thus aimed to investigate patterns in the community structure and species richness of bats (Chiroptera) along the transect, link the species to available regional data, and explain the observed patterns by including environmental characteristics. Bat communities were surveyed between 200 m and a timberline at 3,700 m a.s.l. at eight study sites separated by 500 m in elevation. We conducted mist-netting and acoustic surveys to detect and identify species at each site. Regional data were compiled to compare local with regional diversity. Finally, biotic (i.e., food availability, habitat features) and abiotic (i.e., mean daily temperature, available land area) factors were included in our analyses to disentangle the ecological drivers underlying bat diversity. Results revealed that species richness decreases with ascending elevation and was best explained by a corresponding decrease in both area and temperature. We also observed community turnover along the transect at local and regional scales, along with the increase of species’ elevational ranges. Consequently, despite that the study was restricted to one mountain in PNG, it demonstrates how basic inventory surveys can be used to address ecological questions in other similar and undisturbed tropical mountains.
Maximizing citizen scientists’ contribution to automated species recognition
Authors: Koch Wouter , Hogeweg Laurens , Nilsen Erlend B. , Finstad Anders G. 
Published: February 2022

AbstractTechnological advances and data availability have enabled artificial intelligence-driven tools that can increasingly successfully assist in identifying species from images. Especially within citizen science, an emerging source of information filling the knowledge gaps needed to solve the biodiversity crisis, such tools can allow participants to recognize and report more poorly known species. This can be an important tool in addressing the substantial taxonomic bias in biodiversity data, where broadly recognized, charismatic species are highly overrepresented. Meanwhile, the recognition models are trained using the same biased data, so it is important to consider what additional images are needed to improve recognition models. In this study, we investigated how the amount of training data influenced the performance of species recognition models for various taxa. We utilized a large Citizen Science dataset collected in Norway, where images are added independently from identification. We demonstrate that while adding images of currently under-represented taxa will generally improve recognition models more, there are important deviations from this general pattern. Thus, a more focused prioritization of data collection beyond the basic paradigm that “more is better” is likely to significantly improve species recognition models and advance the representativeness of biodiversity data.