bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the efficiency of single-cell genome sequencing based on overlapping pooling strategy and CNV analysis
Authors: Tu Jing , Yang Zengyan , Lu Na , Lu Zuhong
Published: January 2022

Single-cell genome sequencing has become a useful tool in medicine and biology studies. However, an independent library is required for each cell in single-cell genome sequencing, so that the cost grows with the number of cells. In this study, we report a study which efficiently analyses single-cell copy number variation (CNV) using overlapping pooling strategy and branch and bound (
B&B
) algorithm. Single cells were overlapped pooled before sequencing, and later were assorted into specific types by estimating their CNV patterns by
B&B
algorithm. Instead of constructing libraries for each cell, a library is required only for each pool. As the number of pools is smaller than the cells, fewer libraries are required, which means lower cost. Through computer simulations, we overlapped pooled 80 cells into 40 or 27 pools and classified them into cell types based on CNV pattern. The results showed that 84% cells in 40 pools and 76.5% cells in 27 pools were correctly classified on average, while only half or one-third of the sequencing libraries were required. Combining with traditional approaches, our method is expected to significantly improve the efficiency of single-cell genome sequencing.
Probing the chemical constituents of
Cassia javanica
and its
in vitro
analyses as a potent drug
Authors: Haleem Muhammad Abdul , ul-Ain Qurrat , Saadiq Muhammad , Iqbal Muhammad , Gulab Hussain , Ali Sajid , Khan Sabir
Published: January 2022

The phytochemical screening of the crude methanolic stem extracts of
Cassia javanica
plant showed the presence of different classes of organic compounds like alkaloids, tannins, flavonoids, saponins, phlobatanins, steroids, anthraquinone and cardiac glycoside. The starching frequencies of these functional groups were determined from FT-IR spectroscopic data. The crude and their fractions were examined for antibacterial potential against
Klebsiella pneumoniae
and
Proteus mirabilis
. The antibacterial assay showed maximum zone of inhibition for ethyl acetate fraction, i.e. 20 mm against
Proteus mirabilis
and 18 mm against
Klebsiella pneumoniae
in the comparison with Levofloxacin used as standard (40 mm). Meanwhile for methanolic crude extract, the inhibition zone was recorded 14 mm against
Klebsiella pneumoniae
and 22 mm against
Proteus mirabilis
. The minimum inhibitory concentrations and minimum bactericidal concentrations were recorded as 187.5 µg ml
−1
against
Proteus mirabilis
and 93.75 µg ml
−1
against
Klebsiella pneumoniae.
The scavenging free radical assay was noted as 69.61% at the concentration of 100 ppm.
A robust transition to homochirality in complex chemical reaction networks
Authors: Laurent Gabin , Gaspard Pierre , Lacoste David
Published: January 2022

Homochirality, i.e. the dominance across all living matter of one enantiomer over the other among chiral molecules, is thought to be a key step in the emergence of life. Building on ideas put forward by Frank and many others, we proposed recently one such mechanism in Laurentet al.(Laurent, 2021Proc. Natl Acad. Sci. USA118, e2012741118. (doi:10.1073/pnas.2012741118)) based on the properties of large out of equilibrium chemical networks. We showed that in such networks, a phase transition towards a homochiral state is likely to occur as the number of chiral species in the system becomes large or as the amount of free energy injected into the system increases. This paper aims at clarifying some important points in that scenario, not covered by our previous work. We first analyse the various conventions used to measure chirality, introduce the notion of chiral symmetry of a network and study its implications regarding the relative chiral signs adopted by different groups of molecules. We then propose a generalization of Frank’s model for large chemical networks, which we characterize completely using methods of random matrices. This analysis is extended to sparse networks, which shows that the emergence of homochirality is a robust transition.
Weyl almost automorphic solutions in distribution sense of Clifford-valued stochastic neural networks with time-varying delays
Authors: Li Yongkun , Wang Xiaohui , Huo Nina
Published: January 2022

In this paper, the existence and stability of Weyl almost automorphic solutions in distribution sense for a class of Clifford-valued stochastic neural networks with time-varying delays are studied by using the direct method. Firstly, the existence and uniqueness of Weyl almost automorphic solutions in distribution sense for this class of neural networks are studied by using the Banach fixed point theorem and the relationship between several different senses of random almost automorphy. Then, the global exponential stability in

p

th mean of the unique Weyl almost automorphic solution in distribution sense is proved by inequality technique and counter proof method. Even when this class of neural networks we consider is real-valued, our results are new. Meanwhile, the method proposed in this paper can be used to study the existence of Weyl almost automorphic solutions of other types of neural networks including stochastic and deterministic neural networks. Finally, an example is given to illustrate the feasibility of our results.
Silencing
Doublesex
expression triggers three-level pheromonal feminization in
Nasonia vitripennis
males
Authors: Wang Yidong , Sun Weizhao , Fleischmann Sonja , Millar Jocelyn G. , Ruther Joachim , Verhulst Eveline C.
Published: January 2022

Doublesex (Dsx) has a conserved function in controlling sexual morphological differences in insects, but our knowledge of its role in regulating sexual behaviour is primarily limited to
Drosophila
. Here, we show with the parasitoid wasp
Nasonia vitripennis
that males whose
Dsx
gene had been silenced (
NvDsx
-i) underwent a three-level pheromonal feminization: (i)
NvDsx
-i males were no longer able to attract females from a distance, owing to drastically reduced titres of the long-range sex pheromone; (ii)
NvDsx
-i males were courted by wild-type males as though they were females, which correlated with a lower abundance of alkenes in their cuticular hydrocarbon (CHC) profiles. Supplementation with realistic amounts of synthetic (
Z
)-9-hentriacontene (
Z
9C31), the most significantly reduced alkene in
NvDsx
-i males, to
NvDsx
-i males interrupted courtship by wild-type conspecific males. Supplementation of female CHC profiles with
Z
9C31 reduced courtship and mating attempts by wild-type males. These results prove that
Z
9C31 is crucial for sex discrimination in
N. vitripennis
; and (iii)
Nvdsx
-i males were hampered in eliciting female receptivity and thus experienced severely reduced mating success, suggesting that they are unable to produce the to-date unidentified oral aphrodisiac pheromone reported in
N. vitripennis
males. We conclude that Dsx is a multi-level key regulator of pheromone-mediated sexual communication in
N. vitripennis
.
Decoding alarm signal propagation of seed-harvester ants using automated movement tracking and supervised machine learning
Authors: Guo Xiaohui , Lin Michael R. , Azizi Asma , Saldyt Lucas P. , Kang Yun , Pavlic Theodore P. , Fewell Jennifer H.
Published: January 2022

Alarm signal propagation through ant colonies provides an empirically tractable context for analysing information flow through a natural system, with useful insights for network dynamics in other social animals. Here, we develop a methodological approach to track alarm spread within a group of harvester ants,
Pogonomyrmex californicus
. We initially alarmed three ants and tracked subsequent signal transmission through the colony. Because there was no actual standing threat, the false alarm allowed us to assess amplification and adaptive damping of the collective alarm response. We trained a random forest regression model to quantify alarm behaviour of individual workers from multiple movement features. Our approach translates subjective categorical alarm scores into a reliable, continuous variable. We combined these assessments with automatically tracked proximity data to construct an alarm propagation network. This method enables analyses of spatio-temporal patterns in alarm signal propagation in a group of ants and provides an opportunity to integrate individual and collective alarm response. Using this system, alarm propagation can be manipulated and assessed to ask and answer a wide range of questions related to information and misinformation flow in social networks.
Colour constancy failures expected in colourful environments
Authors: Foster David H. , Reeves Adam
Published: January 2022

Colour constancy refers to the constant perceived or apparent colour of a surface despite changes in illumination spectrum. Laboratory measurements have often found it imperfect. The aim here was to estimate the frequency of constancy failures in natural outdoor environments and relate them to colorimetric surface properties. A computational analysis was performed with 50 hyperspectral reflectance images of outdoor scenes undergoing simulated daylight changes. For a chromatically adapted observer, estimated colour appearance changed noticeably for at least 5% of the surface area in 60% of scenes, and at least 10% of the surface area in 44% of scenes. Somewhat higher frequencies were found for estimated changes in perceived colour relations represented by spatial ratios of cone-photoreceptor excitations. These estimated changes correlated with surface chroma and saturation. Outdoors, the colour constancy of some individual surfaces seems likely to fail, particularly if those surfaces are colourful.
A Novel Barrier Device and Method for Protection against Airborne Pathogens During Endotracheal Intubation
Authors: Alonso Julio M. , Lipman Jeffrey , Shekar Kiran
Published: January 2022

Background

The risk of SARS-CoV-2 transmission to healthcare workers increases during aerosol-generating procedures such as endotracheal intubation.

Objectives

We tested the effectiveness of a novel barrier mouthpiece in reducing clinician exposure to aerosols and droplets during endotracheal intubation.

Design

A prospective case control study was carried out, with a single operator performing eight simulated intubations with and without the device on two different high-fidelity manikin models which produced aerosols and droplets.

Setting

The study was performed during June 2020, at the Clinical Skills Development Service, Brisbane, Australia.

Interventions

Simulated scenarios included 1) intubation during cardiopulmonary resuscitation 2) intubation while pre-oxygenating via high flow nasal cannula. Photographic images were obtained during each intubation and digitally analyzed using ImageJ v2.1.0/1.53c.

Patients

Not applicable.

Main outcome measures

Aerosol and droplets were quantified using pixel counts. Overall results were expressed as means (± SD), with comparisons between groups made using a two-tailed Student’s T-test under the assumption of unequal variances. A P value of ≤ 0.05 was considered as statistically significant.

Results

First pass intubation was achieved in all scenarios, with and without the barrier device. Pixel counts demonstrated significant overall reduction in aerosol and droplet exposure when the barrier device was used during intubation [Mean (SD) count:509 (860) vs 10169 (11600); P=0.014]. The highest exposure risk to airborne particles was observed during simulated induction, prior to laryngoscopy and intubation.

Conclusions

The novel barrier device was effective in reducing environmental exposure to aerosols and droplets during intubation without negatively affecting first pass intubation. The highest risk of exposure to airborne particles was during induction, before intubation takes place. Clinical trials are indicated to further test the feasibility and efficacy of this device.

Trial registration

Not applicable.

KEY POINTS

This prospective, preclinical study represents a pilot trial of a novel barrier mouthpiece for reducing clinician exposure to aerosols and droplets during endotracheal intubation.

In eight simulated intubations with and without the barrier mouthpiece, the device proved effective in reducing environmental exposure to aerosols and droplets (measured in pixels) during intubation, without negatively affecting first pass intubation.

The novel barrier mouthpiece represents a possible solution for reducing the risk of respiratory pathogen transmission during endotracheal intubation without hampering the procedure itself, although larger preclinical and clinical trials are necessary.
Hilab system, a new point-of-care hematology analyzer supported by the Internet of Things and Artificial Intelligence
Authors: Gasparin Aléxia Thamara , Franco Araujo Claudiane Isabel , Perussolo Maiara Carolina , de Jesus Thainá Caroline Schuartz , Santiago Erika Bergamo , Reis Silva Ivan Lucas , de Sousa Ricardo Gurgel , Teng Flavia Zhu , Severo Evair Borges , Alves Ribeiro Victor Henrique , Cardoso Milena Andreuzo , Silva Fernanda D’Amico , de Araujo Perazzoli Carolina Rodrigues , de Holanda Farias João Samuel , de Almeida Bernardo Montesanti Machado , Rogal Sergio , Mazega Figueredo Marcus Vinícius
Published: January 2022

The complete blood count (CBC) is one of the most requested tests by physicians. Mostly realized in conventional hematological analyzers, CBC tests are restricted to centralized laboratories, due to frequent maintenance, size of devices, and expensive costs that these analyzers require. On the other hand, most handheld CBC devices commercially available present high costs and are not liable to calibration or control procedures, which results in poor quality compared to standard hematology instruments. The Hilab system is a small-handed novel hematological platform that uses microscopy and chromatography techniques for blood cells and hematimetric parameters analysis. Combining artificial intelligence, machine learning, and deep learning techniques, provides the main parameters evaluated in the CBC test and four-part differential WBC. For clinical evaluation, accuracy, precision, method comparison, and flagging capabilities of the Hilab System were compared with the Sysmex XE-2100 (Sysmex, Japan) results. Over the entire measuring range, a strong correlation (r > 0.9) between both methodologies was obtained for most parameters evaluated. Also, high accuracy (> 0.85), and adequate precision values were observed. The anticoagulant influence and the sample source (venous and capillary) effect were also evaluated, and no significant differences were observed (p > 0.05). Thus, considering the need for blood count point-of-care tests, especially for quickly patient management, the study indicated that the Hilab system provides fast, accurate, low cost, and robust blood cell analysis for reliable clinical use.

Key points

The Hilab system presents a high correlation with a standardized reference analyzer for all evaluated CBC parameters;

The flagging capabilities of the Hilab system present high accuracy compared to results provided by specialized hematologists.
Establishment of human post-vaccination SARS-CoV-2 standard reference sera
Authors: Xiang Jinhua , Katz Louis , Winokur Patricia L. , Chaudhary Ashok , Bradford Rebecca , Rashid Sujatha , Ghosh Sudakshina , Robertson Angela , Menetski Joseph , Lee Taylor , Poelaert Brittany , Eastman Richard T. , Hall Matthew D. , Stapleton Jack T.
Published: January 2022

As SARS-CoV-2 variants emerge, there is a critical need to understand the effectiveness of serum elicited by different SARS-CoV-2 vaccines. A reference reagent comprised of post-vaccination sera from recipients of different vaccines allows evaluation of in vitro variant neutralization, and provides a reference for comparing assay results across laboratories. We prepared and pooled >1 L serum from donors who received the SARS-CoV-2 mRNA vaccines (BNT162b2, Pfizer and mRNA-1273, Moderna), a replication-incompetent adenovirus type 26 vaccine (Ad26.COV2.S, Johnson and Johnson), or recombinant spike protein expressed by baculovirus incorporated into a nanoparticle vaccine plus Matrix-M adjuvant (NVX-CoV2373, Novavax). Twice frozen sera were aliquoted and are available for distribution to the research community (BEI Resources). The calculated WHO titer of pooled sera to spike protein was 1,312, 1,447, 1,936, and 587 and the reciprocal RBD binding to ACE-2 IC90-titers were 60, 64, 118, and 46 for BNT162b2, mRNA1273, Ad26.CoV2373, and NVX-CoV2373 sera, respectively.
Effects of vaccination against COVID-19 on the emotional health of Peruvian older adults
Authors: Alarcon-Ruiz Christoper A. , Romero-Albino Zoila , Soto-Becerra Percy , Huarcaya-Victoria Jeff , Runzer-Colmenares Fernando M. , Romani-Huacani Elisa , Villarreal-Zegarra David , Maguiña Jorge L. , Apolaya-Segura Moises , Cuba-Fuentes Sofía
Published: January 2022

Background

COVID-19 vaccination may reduce anxiety and depression. However, the pandemic significantly impacted the elderly from low-middle-income countries. Therefore, we aimed to estimate the effect of vaccination against COVID-19 on the emotional health of older adults.

Methods

We selected a nationally stratified sample of non-hospitalized adults aged 60 to 79 years who intended to receive the COVID-19 vaccine or had already received it during recruitment. We assess the fear, anxiety, and worry about COVID-19, general anxiety, and depression at baseline and after a month. We estimated the adjusted odds ratios (aOR) and 95% confidence intervals (95% CI) for each altered emotional health outcomes in those who had one and two doses, compared with those who were not vaccinated using multilevel logistic regression with mixed effects.

Results

We recruited 861 older adults. Loss to follow-up was 20.8%. At baseline, 43.9% had only one dose of the vaccine, and 49.1% had two doses. In the analysis during follow-up, those who had two doses had less fear (ORa: 0.19; CI95%: 0.07 to 0.51) and anxiety to COVID-19 (ORa: 0.45; CI95%: 0.22 to 0.89), compared to non-vaccinated. We observed no effects in those with only one dose.

Limitations

Inability to obtain the planned sample size for primary analysis. There is a selection bias during recruitment and a measurement bias because of self-reported vaccination.

Conclusions

COVID-19 vaccination with two doses in elders improves the perception of COVID-19 infection consequences. This information could be integrated into the vaccination campaign as its beneficial effect.

Highlights

Up to 90% of elders in a Peruvian sample had at least one dose of COVID-19 vaccine

Two doses of COVID-19 vaccine reduced the levels of fear and anxiety for COVID-19

Only one dose of vaccine didn’t had effect in any emotional mental outcome
Predictive and analysis of COVID-19 cases cumulative total: ARIMA model based on machine learning
Authors: Yan Zehui , Wang Yanding , Yang Meitao , Li Zhiqiang , Gong Xinran , Wu Di , Zhang Wenyi , Wang Yong
Published: January 2022

At present, COVID-19 poses a serious threat to global human health, and the cumulative confirmed cases in America, Brazil and India continue to grow rapidly. Therefore, the prediction models of cumulative confirmed cases in America, Brazil and India from August 1, 2021 to December 31, 2021 were established. In this study, the prevalence data of COVID-19 from 1 August 2021 to 31 December 2021 were collected from the World Health Organization website. Several ARIMA models were formulated with different ARIMA parameters. ARIMA (7,2,0), ARIMA (3,2,1), and ARIMA (10,2,4) models were selected as the best models for America, Brazil, and India, respectively. Initial combinations of model parameters were selected using the automated ARIMA model, and the optimized model parameters were then found based on Bayesian information criterion (BIC). The analytical tools autocorrelation function (ACF), and partial autocorrelation function (PACF) were used to evaluate the reliability of the model. The performance of different models in predicting confirmed cases from January 1, 2022 to January 5, 2022 was compared by using root mean square error (RMSE), mean absolute error (MAE), and mean absolute percentage error (MAPE). This study shows that ARIMA models are suitable for predicting the prevalence of COVID-19 in the future. The results of the analysis can shed light on understanding the trends of the outbreak and give an idea of the epidemiological stage of these regions. Besides, the prediction of COVID-19 prevalence trends of America, Brazil, and India can help take precautions and policy formulation for this epidemic in other countries.
The effect of COVID-19 mRNA vaccine on human lung carcinoma cells in vitro by means of Raman spectroscopy and imaging
Authors: Abramczyk Halina , Surmacki Jakub
Published: January 2022

The effect of COVID-19 mRNA vaccine on human lung carcinoma epithelial cells (A549) in vitro as a convenient preclinical model has been studied by means of Raman spectroscopy and imaging. The paper focuses on Raman imaging as a tool to explore apoptosis and oxidative phosphorylation in mitochondrial dysfunctions. The Raman results demonstrate alterations in the oxidation-reduction pathways associated with cytochrome c. We found that the COVID-19 mRNA vaccine downregulates the concentration of cytochrome c upon incubation with tumorous lung cells. Concentration of oxidized form of cytochrome c in mitochondria of lung cells decreases upon incubation the COVID-19 mRNA vaccine. Lower concentration of oxidized cytochrome c in mitochondria illustrates lower effectiveness of oxidative phosphorylation (respiration), reduced apoptosis and lessened ATP production. Moreover, mRNA vaccine increases significantly de novo lipids synthesis in lipid droplets up to 96 hours and alterations in biochemical composition. It seems that lipid composition of cells returns to the normal level for longer incubation time (14 days). In cell nucleus the mRNA vaccine does not produce statistically significant changes. The observed alterations in biochemical profiles upon incubation with mRNA vaccine in the specific organelles of the tumorous lung cells are similar to those we observe for other types of cancers, particularly brain glial cells.
Transcriptomics informs design of a planar human enterocyte culture system that reveals metformin enhances fatty acid export
Authors: Gomez-Martinez Ismael , Bliton R. Jarrett , Breau Keith A. , Czerwinski Michael J. , Williamson Ian A. , Wen Jia , Rawls John F. , Magness Scott T.
Published: January 2022

Background & Aims

Absorption, metabolism, and export of dietary lipids occurs in the small intestinal epithelium. Caco-2 and organoids have been used to study these processes but are limited in physiological relevance or preclude simultaneous apical and basal access. Here, we develop a high-throughput planar human absorptive enterocyte (AE) monolayer system for investigating lipid-handling, then evaluate the role of fatty acid oxidation (FAO) in fatty acid (FA) export, using etomoxir, C75, and anti-diabetic drug, metformin.

Methods

Single-cell RNA-sequencing (scRNAseq), transcriptomics, and lineage trajectory was performed on primary human jejunum.In vivoAE maturational states informed conditions used to differentiate human intestinal stem cells (ISCs) that mimicin vivoAE maturation. The system was scaled for high-throughput drug screening. Fatty acid oxidation (FAO) was pharmacologically modulated and BODIPY™ (B)-labelled FAs were used to evaluate FA-handling via fluorescence and thin layer chromatography (TLC).

Results

scRNAseq shows increasing expression of lipid-handling genes as AEs mature. Culture conditions promote ISC differentiation into confluent AE monolayers. FA-handling gene expression mimicsin vivomaturational states. FAO inhibitor, etomoxir, decreased apical-to-basolateral export of medium-chain B-C12 and long-chain B-C16 FAs whereas CPT1 agonist, C75, and antidiabetic drug, metformin, increased apical-to-basolateral export. Short-chain B-C5 was unaffected by FAO inhibition and diffused through AEs.

Conclusions

Primary human ISCs in culture undergo programmed maturation. AE monolayers demonstratein vivomaturational states and lipid-handling gene expression profiles. AEs create strong epithelial barriers in 96-Transwell format. FA export is proportional to FAO. Metformin enhances FAO and increases basolateral FA export, supporting an intestine-specific role.
Human sialomucin CD164 is an essential entry factor for lymphocytic choriomeningitis virus
Authors: Liu Jamin , Knopp Kristeene A. , Rackaityte Elze , Wang Chung Yu , Laurie Matthew T. , Sunshine Sara , Puschnik Andreas S , DeRisi Joseph L
Published: January 2022

Lymphocytic choriomeningitis virus (LCMV) is a well-studied mammarenavirus that can be fatal in congenital infections. However, our understanding of LCMV and its interactions with human host factors remain incomplete. Here, host determinants affecting LCMV infection were investigated through a genome-wide CRISPR knockout screen in A549 cells, a human lung adenocarcinoma line. We identified and validated a variety of novel host factors that play a functional role in LCMV infection. Among these, knockout of the sialomucin CD164, a heavily glycosylated transmembrane protein, was found to ablate infection with multiple LCMV strains but not other hemorrhagic mammarenaviruses, in several cell types. Further characterization revealed a dependency of LCMV entry on the cysteine-rich domain of CD164, including a N-linked glycosylation site at residue 104 in that region. Given the documented role of LCMV with respect to transplacental human infections, CD164 expression was investigated in human placental tissue and placental cell lines. CD164 was found to be highly expressed in the cytotrophoblast cells, an initial contact site for pathogens within the placenta, and LCMV infection in placental cells was effectively blocked using a monoclonal antibody specific to the cysteine-rich domain of CD164. Together, this study identifies novel factors associated with LCMV infection of human tissues, and highlights the importance of CD164, a sialomucin that has previously not been associated with viral infection.
Computationally efficient assembly of a Pseudomonas aeruginosa gene expression compendium
Authors: Doing Georgia , Lee Alexandra J. , Neff Samuel L. , Holt Jacob D. , Stanton Bruce A. , Greene Casey S. , Hogan Deborah A.
Published: January 2022

Over the past two decades, thousands of RNA sequencing (RNA-seq) gene expression profiles of Pseudomonas aeruginosa have been made publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In the work we present here, we draw on over 2,300 P. aeruginosa transcriptomes from hundreds of studies performed by over seventy-five different research groups. We first developed a pipeline, using the Salmon pseudo-aligner and two different P. aeruginosa reference genomes (strains PAO1 and PA14), that transformed raw sequence data into a uniformly processed data in the form of sample-wise normalized counts. In this workflow, P. aeruginosa RNA-seq data are filtered using technically and biologically driven criteria with characteristics tailored to bacterial gene expression and that account for the effects of alignment to different reference genomes. The filtered data are then normalized to enable cross experiment comparisons. Finally, annotations are programmatically collected for those samples with sufficient meta-data and expression-based metrics are used to further enhance strain assignment for each sample. Our processing and quality control methods provide a scalable framework for taking full advantage of the troves of biological information hibernating in the depths of microbial gene expression data. The re-analysis of these data in aggregate is a powerful approach for hypothesis generation and testing, and this approach can be applied to transcriptome datasets in other species.

Significance

Pseudomonas aeruginosa causes a wide range of infections including chronic infections associated with cystic fibrosis. P. aeruginosa infections are difficult to treat and people with CF-associated P. aeruginosa infections often have poor clinical outcomes. To aid the study of this important pathogen, we developed a methodology that facilitates analyses across experiments, strains, and conditions. We aligned, filtered for quality and normalized thousands of P. aeruginosa RNA-seq gene expression profiles that were publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The workflow that we present can be efficiently scaled to incorporate new data and applied to the analysis of other species.
Characterization and identification of a novel daidzein reductase involved in (S)-equol biosynthesis in Clostridium C1
Authors: Hu Yun-fei , Yang Chun-Fang , Song Can , Zhong Wei-Xuan , Li Bai-yuan , Cao Lin-yan , Chen Hua-hai , Zhao Chang-Hui , Yin Ye-shi
Published: January 2022

(S)-equol is an isoflavone with high estrogen-like activity and no toxic effects in the human body, and is only produced by some gut bacteria in vivo. It plays an important role in maintaining individual health, however, the dearth of resources associated with (S)-equol-producing bacteria has seriously restricted the production and application of (S)-equol. We report here a novel functional gene C1-07020 that was identified from a chick (S)-equol-producing bacterium (Clostridium C1). We found that recombinant protein of C1-07020 possessed similar function to daidzein reductase (DZNR), which can convert daidzein (DZN) into R/S-dihydrodaidzein (R/S-DHD). Interestingly, C1-07020 can reverse convert (R/S)-DHD (DHD oxidases) into DZN even without cofactors or anaerobic conditions. Additionally, high concentrations of (S)-equol can directly promote DHD oxidase but inhibit DZNR activity. Molecular docking and site-directed mutagenesis revealed that the amino acid Arg 75 was the active site of DHD oxidases. Subsequently, an engineered E. coli strain based on C1-07020 was constructed and showed higher yield of (S)-equol than the engineered bacteria from our previous work. Metagenomics analysis and PCR detection surprisingly revealed that C1-07020 and related bacteria may be prevalent in the gut of humans and animals and their (S)-equol production state may cause differed between (S)-equol producer and non-producer. Overall, a novel DZNR from Clostridium C1 was found and identified in this study, and its bidirectional enzyme activities and wide distribution in the gut of humans and animals provide alternative strategies for revealing the individual regulatory mechanisms of (S)-equol-producing bacteria.

Importance

(S)-equol is a final product of DZN that metabolized by some enteric bacteria. Although (S)-equol played very important roles in maintaining human health, larger differences in equol production varied between different populations. Here, a novel DZNR gene C1-07020, which related to (S)-equol production, was reported. The bidirectional enzyme functions and wide distribution of C1-07020 in human and animal gut provided additional insights into the metabolic regulation of (S)-equol. Additionally, C1-07020 can be used for improving the production of (S)-equol in vitro.
Lung Perfusion Disturbances Detected with MRI in Non-Hospitalized Post-COVID-19 Individuals with Dyspnea 3 -13 Months after the Acute Disease
Authors: Yu Jimmy , Granberg Tobias , Shams Roya , Petersson Sven , Sköld Magnus , Nyrén Sven , Lundberg Johan
Published: January 2022

Background

Dyspnea is a prevalent symptom in the post-COVID-19 condition, though its mechanisms are largely unknown. Lung perfusion abnormalities have been reported in acute COVID-19 and could be suspected in patients with lingering dyspnea after the acute phase.

Objectives

To detect pulmonary perfusion disturbances in non-hospitalized post-COVID condition with persistent dyspnea 4-13 months after the disease onset.

Methods

Non-hospitalized individuals reporting persistent dyspnea after COVID-19 and matched healthy controls were prospectively recruited between October 2020 and May 2021 to undergo pulmonary dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), six-minute walk test, and self-reported scales questionnaires on dyspnea and physical activity. The DCE-MRI perfusion images were quantified into two parametric values: mean time-to-peak (TTP) and TTP ratio.

Results

Twenty-eight persons with post-COVID condition and persistent dyspnea (mean age 46.5±8.0 years, 75% women) and 22 healthy controls (mean age 44.1±10.8 years, 73% women) were included. The post-COVID group had higher mean pulmonary TTP (0.43±0.04 vs. 0.41±0.03, P=0.011) and higher TTP ratio (0.096±0.052 vs. 0.068±0.027, P=0.032). Notably, post-COVID males had the highest values (mean TTP 0.47±0.02, TTP ratio 0.160±0.039, P<0.001 for both values compared to male controls and post-COVID females). Correlation between dyspnea and perfusion parameters was demonstrated in the males (r=0.83, P<0.001 for mean TTP; r=0.76, P=0.003 for TTP ratio), but not in females.

Conclusions

Lung perfusion disturbances were detected in males reporting post-COVID dyspnea using perfusion parameters from DCE-MRI. The distinct sex difference has implications for understanding the perplexing post-COVID pathophysiology and warrants future studies. DCE-MRI could provide biomarkers for such studies.
Comparative immunogenicity of heterologous versus homologous 3rd SARS-CoV-2 vaccine doses in kidney transplant recipients
Authors: Thomson Tina , Prendecki Maria , Gleeson Sarah , Martin Paul , Spensley Katrina , Seneschall Charlotte , Gan Jaslyn , Clarke Candice L. , Lewis Shanice , Pickard Graham , Thomas David , McAdoo Stephen P. , Lightstone Liz , Cox Alison , Kelleher Peter , Willicombe Michelle
Published: January 2022

Background

Solid organ transplant recipients have attenuated immune responses to SARS-CoV-2 vaccines. Emerging evidence suggests at least equivalent immunogenicity of heterologous compared with homologous vaccine regimens in the general population. In this study, we report on immune responses to 3rd dose BNT162b2 vaccines in transplant recipients either primed with ChAdOx1 or BNT162b2.

Methods

700 kidney transplant recipients were prospectively screened for serological responses (median time of 33 (21-52) days) following 3 primary doses of a SARS-CoV2 vaccine. All vaccine doses were received post-transplant, and all 3rd doses were BNT162b2. All participants had serological testing performed post-2nd vaccination at a median time of 34 (IQR 26-46) days following the 2nd inoculation, and at least once prior to their 1st dose of vaccine.

Results

366/700 (52.3%) participants were primed with BNT162b2, whilst 334/700 (47.7) had received ChAdOx1. Overall, 139/700 (19.9%) participants had evidence of prior infection. Of 561 infection naïve participants, 263 (46.9%) had no detectable anti-S following 2-doses of vaccine (V2). 134 (23.9%) participants remained seronegative post 3rd vaccine (V3); 54/291 (18.6%) and 79/270 (29.3%) of participants receiving BNT162b2 and ChAdOx1 respectively, p=0.0029. Median anti-S concentrations were significantly higher post-V3 in patients who had received BNT162b2 compared with ChAdOx1, at 612 (27-234) versus 122 (7.1-1111) BAU/ml respectively, p<0.0001.

Cellular responses were investigated in 30 infection naïve participants at a median time of 35 (24-46) days post-V3. Eighteen of 30 (60.0%) participants had undetectable T-cell responses. There were neither qualitative or quantitative differences in T-cell responses between those patients who received BNT162b2 or ChAdOx1 as their first 2-doses, with 10/16 (62.5%) and 8/14 (57.1%) respectively having undetectable T-cell responses, p=0.77.

Conclusion

A significant proportion of transplant recipients remain seronegative following 3 doses of SARS-CoV-2 vaccines, with anti-S concentrations lower in patients receiving heterologous versus homologous vaccinations.
Incontinence and Healthcare Utilization of Medicare Patients
Authors: Duncan Ian , Stocking Andrew , Fitzner Karen , Ahmed Tamim , Huynh Nhan
Published: January 2022

Purpose

Claims data are used to directly measure the prevalence of incontinence and incontinence-related events within a large Medicare population.

Design

Retrospective analysis.

Subjects and Settings

The study relied on administrative claims data from the CMS Medicare Limited Data Set (5% sample) in 2018. The analysis was limited to fee-for-service (FFS) Medicare beneficiaries with minimum of 3-month enrollment in Parts A & B and at least 65 years old.

Methods

We used diagnosis codes to identify members with incontinence in their 2018 claims experience and grouped these members into 3 categories (urinary incontinent only, fecal incontinent only, and dual incontinent (DI)) and four sites-of-service (nursing home, Skilled-nursing Facility (SNF), home health, and self-care). We then determined the incidence of four types of incontinence-related events for each cohort: 1) Urinary Tract Infections (UTIs), 2) Incontinence-Associated Dermatitis (IAD), 3) Slips and falls, and 4) Behavioral disruptions.

Results

We found that 11.2 percent of Medicare members had a claims-based diagnosis of incontinence in 2018. This result falls below the estimated share of the over-65 population who are incontinent, as reported in the literature. The prevalence of the four incontinence-related events is significantly higher (between 2 percentage points to 17 percentage points) for members who experience dual incontinence relative to those with only urinary incontinence. On average, those diagnosed with incontinence experienced 5 times more UTIs, two times as many dermatitis events, more than twice as many slips and falls, and 2.8 times more behavior disruptions compared to those without an incontinence diagnosis.

Conclusions

Although we find that the prevalence of incontinence is under-reported relative to the literature, our results show that those who are diagnosed as incontinent experience a much higher prevalence of UTIs, IAD, slips and falls, and behavioral deterioration compared to those who are not diagnosed as incontinent. Our results suggest that incontinence may be an important indicator diagnosis of many other conditions and, if not well-managed, may challenge the desire for those who are incontinent to age at home.
Pharmacological treatment for connective tissue disease-associated interstitial lung involvement: Protocol for an overview of systematic reviews and meta-analyses
Authors: Karassa Fotini B. , Bougioukas Konstantinos I. , Pelechas Eleftherios , Skalkou Anastasia , Argyriou Evangelia , Haidich Anna-Bettina
Published: January 2022

Background

Interstitial lung disease (ILD) is the most important pulmonary manifestation of the connective tissue diseases (CTDs) since it is associated with high morbidity and mortality. However, there is uncertainty on what constitutes the optimal treatment options from a variety of competing interventions. The aim of the overview is to summarize existing evidence of the effectiveness and harm of pharmacological therapies for adults with CTD-ILD.

Methods

A literature search will be conducted in MEDLINE, the Cochrane Database of Systematic Reviews, DARE, the Centre for Reviews and Dissemination Health Technology Assessment database, Epistemonikos.org, KSR Evidence, and PROSPERO. We will search for systematic reviews and meta-analyses that examine pharmacological treatment for CTD-ILD. Updated supplemental search will also be undertaken to identify additional randomized controlled trials. The primary outcomes will be changes in lung function measures and adverse events. Methodological quality of the included reviews will be assessed using the AMSTAR 2 tool. The overall quality of the evidence will be evaluated using the GRADE rating. Summarized outcome data extracted from systematic reviews will be described in narrative form or in tables. For each meta-analysis we will estimate the summary effect size by use of random-effects and fixed-effects models with 95% confidence intervals, the between-study heterogeneity expressed by I2, and the 95% prediction interval. If feasible, given sufficient data, network meta-analysis will be conducted to combine direct and indirect evidence of class and agent comparisons.

Discussion

While many factors are crucial in selecting an appropriate treatment for patients with CTD-ILD, evidence for the efficacy and safety of a drug is essential in guiding this decision. Thus, this overview will aid clinicians in balancing risks versus benefits of the available therapies by providing high-quality evidence to support informed decision making and may contribute to future guideline development.

Systematic review registration

pending
Mitigating isolation: further comparing the effect of LFD testing for early release from self-isolation for COVID-19 cases
Authors: Bays Declan , Whiteley Timothy , Williams Hannah , Finnie Thomas , Gent Nick
Published: January 2022

In a recent paper, we described how lateral flow device (LFD) testing might be used to reduce the amount of excess time individuals spend in isolation following confirmation of a COVID-19 infection. Through the work presented here, we look to expand upon this and explore in more detail the benefit that such an approach might provide. We use our previously described model to study scenarios through the metrics “proportion released still infectious”, “excess time spent in isolation” (time isolated while no longer infectious), and “time spent infectious after early release”. We also look to consider the effect on these metrics by comparing values obtained when a single negative LFD test is required for early release, versus requiring two and three sequential negative LFD tests. Results show that jointly employing self-isolation and LFD testing may deliver sizeable reductions to the proportion of individuals being release while still infection, the average amount of excess time spent in isolation by those no longer a public health threat, and the average amount of time spent infectious by those released early. These effects considered in conjunction could provide a considerable decrease in the public health risk posed by still infectious individuals being released back into the population by actively monitoring their infection status throughout their isolation period. Such an approach could also help lighten the impact incurred on the individual by reducing the amount of time spent in isolation while posing no further public health risk, in addition to alleviating pressures on the economy and in healthcare settings caused by mass isolation in times of high prevalence.
Immunogenetics of Gastrointestinal Cancers: A Systematic Review of Inborn Errors of Immunity in Humans
Authors: Zheng Beishi , Chung Howard , Bing Chen , Sun Siming , Green Peter H.R. , Wang Timothy C. , Kong Xiao-Fei
Published: January 2022

Background/Aims

The immune system plays a key role in cancer surveillance and modulation of the tumor microenvironment. Humans with inborn errors of immunity (IEI), or primary immunodeficiencies, may be prone to recurrent mucosal bacterial and viral infections and chronic inflammation, associated with intrinsic or secondary epithelium dysfunction, a potential risk factor for early-onset gastrointestinal (GI) cancer.

Methods

We systematically reviewed all cases with clinical diagnoses of both an IEI and a GI cancer in three databases (MEDLINE, SCOPUS, EMBASE). In total, 76 publications satisfying our inclusion criteria were identified, and data for 149 cases were analyzed.

Results

Of the 149 patients with IEIs, 95 presented with gastric cancer, 13 with small bowel cancer, 35 with colorectal cancer, and six with unspecified cancer or cancer at another site. Gastric and colonic adenocarcinoma was the most common. For both gastric and colorectal cancer, age at onset was significantly earlier in patients with IEIs than in the general population, based on the SEER database. Common variable immune deficiency (CVID) was the most common IEI associated with gastrointestinal cancer. About 12% of patients had molecular genetic diagnoses, the three most frequently implicated genes beingATM, CARMIL2, CTLA4. Impaired humoral immunity and Epstein-Barr virus (EBV) infection were frequently reported as the factors potentially underlying early-onset GI malignancy in patients with IEIs.

Conclusion

Patients with IEIs should be considered at risk of early-onset GI cancers, and should therefore undergo cancer screening at an earlier age. Surveillance guidance based on stratifications for genetic risk should be revised to take into account the immunogenetic contribution to GI cancers.
Multiple Ciliary Localization Signals Control INPP5E Ciliary Targeting
Authors: Cilleros-Rodriguez Dario , Martin-Morales Raquel , Barbeito Pablo , Roy Abhijit Deb , Loukil Abdelhalim , Sierra-Rodero Belen , Herranz Gonzalo , Pampliega Olatz , Redrejo-Rodriguez Modesto , Goetz Sarah C. , Izquierdo Manuel , Inoue Takanari , Garcia-Gonzalo Francesc R.
Published: January 2022

Primary cilia are sensory membrane protrusions whose dysfunction causes diseases named ciliopathies. INPP5E is a ciliary phosphoinositide phosphatase mutated in ciliopathies like Joubert syndrome. INPP5E regulates numerous ciliary functions, such as cilium stability, trafficking, signaling, or exovesicle release. Despite its key ciliary roles, how INPP5E accumulates in cilia remains poorly understood. Herein, we show that INPP5E ciliary targeting requires its folded catalytic domain and is controlled by four ciliary localization signals (CLSs), the first two of which we newly discover: LLxPIR motif (CLS1), W383 (CLS2), FDRxLYL motif (CLS3) and CaaX box (CLS4). We answer two long-standing questions in the field. First, partial redundancy between CLS1 and CLS4 explains why CLS4 is dispensable for ciliary targeting. Second, the essential need for CLS2 on the catalytic domain surface clarifies why CLS3 and CLS4 are together insufficient for ciliary accumulation. Furthermore, we reveal that some Joubert syndrome mutations in INPP5E catalytic domain affect its ciliary targeting, and shed light on the mechanisms of action of each CLS. Thus, we find that CLS2 and CLS3 promote interaction with TULP3 and ARL13B, while downregulating CEP164 binding. On the other hand, CLS4 recruits PDE6D, RPGR and ARL13B, and cooperates with CLS1 in ATG16L1 binding. Lastly, we show INPP5E immune synapse targeting is CLS-independent. Altogether, we reveal unusual complexity in INPP5E ciliary targeting mechanisms, likely reflecting its multiple key roles in ciliary biology.
Potentially prebiotic synthesis of aminoacyl-RNA via a bridging phosphoramidate-ester intermediate
Authors: Roberts Samuel J. , Liu Ziwei , Sutherland John D.
Published: January 2022

Translation according to the genetic code is made possible by selectivity both in aminoacylation of tRNA and in anticodon:codon recognition. In extant biology, tRNAs are selectively aminoacylated by enzymes using high-energy intermediates, but how this might have been achieved prior to the advent of protein synthesis has been a largely unanswered question in prebiotic chemistry. We have now elucidated a novel, prebiotically plausible stereoselective aminoacyl-RNA synthesis which starts from RNA-amino acid phosphoramidates and proceeds via phosphoramidate-ester intermediates which subsequently undergo conversion to aminoacyl-esters by mild acid hydrolysis. The chemistry avoids the intermediacy of high-energy mixed carboxy-phosphate anhydrides and is greatly favored under eutectic conditions, which also potentially allow for the requisite pH fluctuation through the variable solubility of CO2 in solid/liquid water.