bluuebunny/crossref_metadata_2025 huggingface dataset:
Rare internalin A premature stop codon on Listeria monocytogenes on Italian PDO cheeses isolates
Authors: Magagna G , Filipello V , Spinelli E , Gori M , Tanzi E , Finazzi G
Published: October 2021

Background

Listeria monocytogenes is a widespread foodborne pathogen that causes listeriosis, a human infection with low morbidity but high mortality. Internalin A (InlA), a L. monocytogenes virulence factor, has a key role in the invasion of human intestinal epithelium through the interaction with E-cadherin receptor. Truncated InlA caused by premature stop-codons (PMSC) have been correlated with attenuated virulence. To date, 29 mutations leading to a PMSC have been reported. In this study, we identified a rare PMSC mutation widespread in isolates from the production chain of the Gorgonzola and Taleggio PDO cheeses.

Methods

Within an ongoing monitoring plan for the characterization of L. monocytogenes, a total of 81 isolates collected in Lombardy (Northern Italy) from food, food processing environments, and clinical cases, between 2013-2021, were characterized using multilocus sequence tying (MLST) and then screened for the presence of PMSC by sequencing the 2400 pb inlA gene.

Results

A mutation leading to PMSC was identified on the position 277 (PMSC mutation type 26). To date, this mutation has been reported only on a CC7 strain from a clinical case. In our study, all isolates harbouring this mutation (n = 21) belong to ST325 (CC31, serotype 1/2a). Among these, 86% (n = 18) belong to the production chain of the Gorgonzola and Taleggio PDO cheeses.

Conclusions

To the best of our knowledge, this is the first report of PMSC mutation type 26 on food and environmental isolates. Although PMSC 26 is rarely found worldwide, our findings suggest that ST325 with this mutation is widespread in the production chain of the two PDO cheeses, and the presence of this PMSC may be correlated with the low incidence of ST325 clinical cases.

Key messages

A rare mutation leading to truncated InlA has been identified in a cluster of isolates correlated to the production chain of two PDO cheeses. Truncated inlA is suggestive of adaptation to the niche to the detriment of virulence.
Italian flu season 2020-2021: reasons for the drop and insights for the future
Authors: Cugudda E , Bert F , Galvagno PF , Lo Moro G , Tatti R , Siliquini R
Published: October 2021

Background

Having seen the trend of 2020 flu season in the Southern hemisphere, the objectives of this study were to describe the trend of 2020-21 flu season in Italy, relating it with containment measures undertaken due to COVID-19, and to provide insights for next flu seasons and prevention of airborne diseases.

Methods

We collected data on Italian influenza virological samples on FluNet. We also collected French, German and Spanish data as a comparison. Data on Italian ILI (influenza-like illness) surveillance system were assessed with InfluNet. We used the Containment and Health Index of the Oxford COVID-19 Government Response Tracker (OxCGRT) to evaluate the impact of containment measures on Italian ILI incidence (Spearman's correlation).

Results

No sample out of 6818 tested positive to influenza virus in Italy in 2020-21 flu season; 21.6% of the samples tested positive to SARS-CoV-2. France, Germany and Spain registered a maximum of 0.10% of positive samples to influenza virus. In Italy the mean of positive samples to influenza virus in seasons from 2015-16 to 2019-20 was 28.8%; the mean number of processed samples in those seasons was 14008. ILI incidence in Italy remained at interseasonal levels during all flu season (mean 1.44/1000; range 0.85-2.04). According to the Containment and Health Index, with increasing containment measures a deflection of ILI incidence in Italy was described (p = 0.015).

Conclusions

Containment measures, along with rise of seasonal flu vaccination, are the most likely factors to explain the drop in cases in Italian 2020-21 flu season. The reduction of cases in neighbouring countries lower the role of the downsizing of Italian surveillance system seen in 2020-21 compared to seasons from 2015-16 to 2019-20. Rules and conducts may perpetrate the benefit on the decreased disease activity seen in 2020-21 flu season.

Key messages

Containment measures and flu vaccinations are the most impacting factors on the drop of influenza cases in 2020-21 in Italy. Though the Italian surveillance system was downsized in 2020-21, the experience of neighbouring countries suggests that the decreased flu activity was factual.
Health care costs for residents diagnosed with diabetes type 2 in Malmö, Sweden between 2011 and 2018
Authors: Zdravkovic S , Jonsson C , Annersten Gershater M , Ericsson Å , Grahn M , Rämgård M , Dozet A
Published: October 2021

Background

During the last decade, type 2 diabetes (T2D) prevalence has increased worldwide, especially among children and young adults. Diabetes is a chronic disease that if not diagnosed in time can lead to serious health complications and put pressure on the societal resources. The aim of this study was to evaluate the economic impact of the increased T2D prevalence in Malmö over time on the regional health care organization.

Methods

A longitudinal population-based study in Malmö, within the Cities Changing Diabetes project. Data was collected from the Patient Administrative System in Region Skåne, classifying T2D by the ICD E11 code. The health care cost (HCC) has been adjusted by the Consumer Price Index (CPI) to 2020 prices.

Results

The prevalence of T2D increased from 2,5% in 2011 to 4,3% in 2018. The increase in T2D prevalence was most noticeable for residents 18 - 64 years. The overall HCC for treating residents with T2D was approximately €47,2 million in 2011 and €90,7 million in 2018. The HCC in 2018 was higher for males than for females (€54,6 million vs €36,2 million). In 2018, the cost was €49,9 million for those 18 - 64 years and €40,5 million for those being 65 years or older. The overall HCC increased during the study period (3,3 times for those 18 - 64 years and 1,4 times for those being 65 years or older). For the age group 18 - 64 the HCC per resident was €5 000 in 2011 and €5 300 in 2018. The HCC per resident for all age groups, has not changed markedly, from €6 200 in 2011 to €6 100 in 2018 as well as the number of health care visits (23 in 2011 and 29 in 2018).

Conclusions

The HCC for T2D has increased markedly since 2011. This increase is most noticeable for people under 65 years. The overall HCC for these patients and its change over time puts an increased strain on the health care provider Region Skåne, mainly due to increased prevalence.

Key messages

The overall HCC during 2011 – 2018 has increased 2 times for residents with T2D and 1.5 times for residents without T2D. This increase is likely to continue if the current trend remains. The main driving force behind the increase in HCC over time is the increase in T2D prevalence and not in HCC per resident.
Use of cancer e-referral data to monitor health-seeking behaviours during the COVID-19 pandemic
Authors: McCarthy T , Dawkins I , Burns H , Nolan E
Published: October 2021

At the outset of the pandemic, concern arose that people with concerning symptoms would not attend their GP and delayed presentations would impact cancer survival. Ireland lacks a national database of GP attendances from which to observe this. Ireland has rapid access clinics in designated cancer centres, providing a streamlined pathway for the diagnosis of certain common cancers. Referral to these clinics can be made electronically from primary care, using a national messaging system Healthlink. Healthlink agreed to report on the volume of referrals at weekly intervals, given the concern regarding non-presentation. Rolling descriptive analytics included the comparison of referral numbers to pre-pandemic weeks in 2020 (Weeks 2-11) and to corresponding time periods in 2019. A marked reduction was observed in wave 1 of the pandemic. Weekly e-referrals dropped by more than 60% in weeks 12-14 (breast 62.5%; lung 57.9%; prostate 61.1%). This was not replicated in subsequent waves. By end-2020, the volume of referrals equated to 112.4% of total referrals in 2019. The objective demonstration of a fall in cancer referrals prompted a media campaign to highlight the importance of early diagnosis and to reassure that cancer diagnostic and treatment services continued to operate. It also prompted national communication in relation to other essential health services. Challenges identified included occasional misinterpretation of referral data as reflective of attendance and investigation at clinics and the potential influence of increased uptake of e-referral systems. While caveats exist in relation to interpretation, e-referral data from primary care to cancer centres is a useful tool to monitor trends in patient presentations with suspected cancer. Automated collection of cancer e-referral data at a national level provides real-time information, compared to manual data collection systems within hospitals which were challenged through redeployment of staff to the Covid response.

Key messages

Monitoring of e-referral rates provided a useful and timely proxy measure of health-seeking behaviour during the Covid pandemic. The significant drop in referrals during the first wave of the pandemic was not repeated, suggesting an improved understanding among the public of the need to investigate symptoms of possible cancer.
The power of genomic estimated breeding values for selection when using a finite population size in genetic improvement of tetraploid potato
Authors: Selga Catja , Reslow Fredrik , Pérez-Rodríguez Paulino , Ortiz Rodomiro
Published: October 2021

Potato breeding relies heavily on visual phenotypic scoring for clonal selection. Obtaining robust phenotypic data can be labor intensive and expensive, especially in the early cycles of a potato breeding program where the number of genotypes is very large. We have investigated the power of genomic estimated breeding values (GEBVs) for selection from a limited population size in potato breeding. We collected genotypic data from 669 tetraploid potato clones from all cycles of a potato breeding program, as well as phenotypic data for eight important breeding traits. The genotypes were partitioned into a training and a test population distinguished by cycle of selection in the breeding program. GEBVs for seven traits were predicted for individuals from the first stage of the breeding program (T1) which had not undergone any selection, or individuals selected at least once in the field (T2). An additional approach in which GEBVs were predicted within and across full-sib families from unselected material (T1) was tested for four breeding traits. GEBVs were obtained by using a Bayesian Ridge Regression model estimating single marker effects and phenotypic data from individuals at later stages of selection of the breeding program. Our results suggest that, for most traits included in this study, information from individuals from later stages of selection cannot be utilized to make selections based on GEBVs in earlier clonal generations. Predictions of GEBVs across full-sib families yielded similarly low prediction accuracies as across generations. The most promising approach for selection using GEBVs was found to be making predictions within full-sib families.
A versatile framework to solve the Helmholtz equation using physics-informed neural networks
Authors: Song Chao , Alkhalifah Tariq , Waheed Umair Bin
Published: October 2021

Solving the wave equation to obtain wavefield solutions is an essential step in illuminating the subsurface using seismic imaging and waveform inversion methods. Here, we utilize a recently introduced machine-learning based framework called physics-informed neural networks (PINNs) to solve the frequency-domain wave equation, which is also referred to as the Helmholtz equation, for isotropic and anisotropic media. Like functions, PINNs are formed by using a fully connected neural network (NN) to provide the wavefield solution at spatial points in the domain of interest, in which the coordinates of the point form the input to the network. We train such a network by backpropagating the misfit in the wave equation for the output wavefield values and their derivatives for many points in the model space. Generally, a hyperbolic tangent activation is used with PINNs, however, we use an adaptive sinusoidal activation function to optimize the training process. Numerical results show that PINNs with adaptive sinusoidal activation functions are able to generate frequency-domain wavefield solutions that satisfy wave equations. We also show the flexibility and versatility of the proposed method for various media, including anisotropy, and for models with strong irregular topography.
Do laws promoting gender equity and freedom from violence benefit the most vulnerable? A multilevel analysis of women’s and adolescent girls’ experiences in 15 low- and-middle-income countries
Authors: Maxwell Lauren , Khan Zara , Yount Kathryn M
Published: October 2021

In this analysis, we assess whether laws that promote gender equity and freedom from violence are associated with a lower risk of prior-year physical and sexual intimate partner violence (IPV) among adolescent girls and adult women (AGW) and whether these laws protect more and less vulnerable AGW equally. We included all 15 countries that administered the Domestic Violence Module in a Demographic and Health Survey since 2015. The primary exposure was a validated, country-level index of laws on violence against women and girls (LoVI). A multilevel approach was used to model five forms of violence (prior-year partner physical, sexual, physical or sexual violence and prior-year non-partner physical violence or sexual violence) among ever-partnered, non-widowed adolescent girls 13–19 years (n = 6691) and women 20–49 years (n = 119 343). Across countries, partner physical violence ranged from 0% to 33% and sexual violence from 0% to 23%. Laws on marital rape, child marriage and sexual harassment were negatively associated with prior-year physical and sexual IPV for women and girls. Comprehensive domestic violence legislation was unrelated to girls’ experiences of prior-year physical or prior-year sexual IPV. No interaction was observed between LoVI component laws and a score meant to capture adolescent vulnerability. Three of the four LoVI component laws had consistent, negative associations with partner violence for girls and women, but negative associations were stronger for women than girls. Thus, while laws promoting gender equity and freedom from violence are generally protective, they may be more so for women than adolescent girls. Future research should explore the impact of gender equitable laws on women’s and adolescent girls’ experiences of violence, and countries may consider more comprehensive legal protections against violence for adolescent girls.
Combined supplementation of sodium humate and glutamine reduced diarrhea incidence of weaned calves by intestinal microbiota and metabolites changes
Authors: Wang Dong , Du Yuanyi , Huang Siqi , You Zhendong , Zheng Duo , Liu Yun
Published: October 2021

This study was conducted to investigate the effects of combined supplementation of sodium humate (HNa) and glutamine (Gln) on growth performance, diarrhea incidence, serum parameters, intestinal microbiome, and metabolites of weaned calves. In Exp. 1, 40 calves were randomly assigned to four treatments: 1) NC (negative control, basal diet), 2) 1% H+1% G (basal diet extra orally gavaged with 1 g of HNa and 1 g of Gln daily), 3) 3% H+1% G (basal diet extra orally gavaged with 3 g of HNa and 1 g of Gln daily), and 4) 5% H+1% G (basal diet extra orally gavaged with 5 g of HNa and 1 g of Gln daily). The HNa and Gln were together mixed with 100 mL of milk replacer (51 to 58 d of age) or water (59 to 72 d of age) and orally administrated to each calf from a bottle before morning feeding. In a 21-d trial, calves on the 5% HNa+1% Gln group had higher (P < 0.05) average daily gain (ADG) and lower (P < 0.05) diarrhea incidence than those in the control group. In Exp. 2, 20 calves were randomly assigned to two treatments fed with a basal diet and a basal diet supplemented with 100 mL of 5% HNa+1% Gln. In a 21-d trial, calves supplemented with HNa and Gln had higher (P < 0.05) ADG, IgG concentration and glutathione peroxidase (GSH-Px), and total antioxidant capacity (T-AOC) activities in the serum, but lower (P < 0.05) diarrhea incidence, as well as serum diamine oxidase (DAO), D-isomer of lactic acid (D-lac), tumor necrosis factor-α (TNF-α), and malondialdehyde (MDA) concentrations compared with control group. Results of intestinal microbiota indicated that supplementation with HNa and Gln significantly increased (P < 0.05) the abundance of intestinal beneficial microbiota. Moreover, supplementation with HNa and Gln altered 18 metabolites and enriched 6 Kyoto Encyclopedia of Genes and Genomes pathways in weaned calves. In conclusion, combined supplementation with HNa and Gln could decrease diarrhea incidence of weaned calves via altering intestinal microbial ecology and metabolism profile.
Phlebotomus neglectus (Diptera: Psychodidae): New Insights on Its Presence in Iran Based on Three Independent Genetic Loci
Authors: Badakhshan M , Moin-Vaziri V , Sadraei J
Published: October 2021

The idea of the existence of Phlebotomus (Larroussius) neglectus (Diptera: Psychodidae) Tonnoir, 1921 in Iran and the skepticism about the existence of Phlebotomus major s.str. Annandale, 1910 had been grown recently in the country. This study reports a combined analysis of mitochondrial and ribosomal DNA target regions of P. major s.l.Annandale, 1910, specimens collected from different parts of Iran. Two different morphotypes were found among the collected samples based on the shape of the aedeagus, ventrally located hairs of the coxite, and parameral sheets. One morphotype seemed similar to P. neglectus Tonnoir 1921 or P. major krimensis Perfiliv1966 (called here MI.N.K.); the other one was similar to P. neglectus and to some extent to P. notus Artemiev & Neronov 1984 (here called MII.N.NO). Cytochrome B, elongation factor 1-alpha, and internal transcribed spacer II loci were amplified, sequenced, and characterized. High sequence homology (98–100%) was observed between P. neglectus and these morphotypes, and phylogenetic analysis was also concordant. Phlebotomus neglectus sequences available in GenBank are located as the sister group of sequences here, particularly near to morphotype MII.N.NO. Moreover, ITS2 locus provides the maximum resolution for differentiation of two morphotypes. Based on achieving results, although a strong support for the presence of P. neglectus was provided, but it is too early to say that P. major s.str. does/does not exist in Iran. This question could be resolved by studying more samples and, most importantly, by comparing the topotypes of P. neglectus and P. major s. str. if possible in the future.
The formation of massive stellar clusters in converging galactic flows with photoionization
Authors: Dobbs C L , Bending T J R , Pettitt A R , Bate M R
Published: October 2021

We have performed simulations of cluster formation along two regions of a spiral arm taken from a global Milky Way simulation, including photoionizing feedback. One region is characterized by strongly converging flows, the other represents a more typical spiral arm region. We find that more massive clusters are able to form on shorter time-scales for the region with strongly converging flows. Mergers between clusters are frequent in the case of the strongly converging flows and enable the formation of massive clusters. We compare equivalent clusters formed in simulations with and without ionization. Photoionization does not prevent massive cluster formation, but can be seen to limit the masses of the clusters. On average, the mass is reduced by around 20 per cent, but we see a large spread from ionization having minimal difference to leading to a 50 per cent reduction in mass. Photoionization is also able to clear out the gas in the vicinity of the clusters on Myr time-scales, which can produce clusters with larger radii that are surrounded by more massive stellar haloes. We find that the ionizing feedback has more impact in our second region that is less dense and has less strongly converging flows.
The impact of precession on the observed population of ULXs
Authors: Khan Norman , Middleton Matthew J , Wiktorowicz Grzegorz , Dauser Thomas , Roberts Timothy P , Wilms Joern
Published: October 2021

The discovery of neutron stars powering several ultraluminous X-ray sources (ULXs) raises important questions about the nature of the underlying population. In this paper we build on previous work studying simulated populations by incorporating a model where the emission originates from a precessing, geometrically beamed wind-cone, created by a super-critical inflow. We obtain estimates – independent of the prescription for the precession period of the wind – for the relative number of ULXs that are potentially visible (persistent or transient) for a range of underlying factors such as the relative abundance of black holes or neutron stars within the population, maximum precessional angle, and LMXB duty cycle. We make initial comparisons to existing data using a catalogue compiled from XMM-Newton. Finally, based on estimates for the precession period, we determine how the eROSITA all-sky survey (eRASS) will be able to constrain the underlying demographic.
Orion Bar as a window to the evolution of PAHs
Authors: Murga Maria S , Kirsanova Maria S , Wiebe Dmitry S , Boley Paul A
Published: October 2021

We investigate the mid-infrared (IR) emission in the Orion Bar photodissociation region (PDR), using archival photometric and spectroscopic observations from the United Kingdom Infrared Telescope (UKIRT), Spitzer, Infrared Space Observatory(ISO), and Stratospheric Observatory for Infrared Astronomy (SOFIA) telescopes. Specifically, we consider flux densities of the emission bands at 3.3, 3.4, 3.6, 6.6, 7.7, and 11.2 $\mu$m in several locations and a spectrum from 3 to 45 $\mu$m in one location. We study the behaviour of band flux ratios, which are sensitive to external conditions, as revealed by their variations with the distance from an ionizing source. Assuming that the mid-IR emission arises mostly from polycyclic aromatic hydrocarbons (PAHs), and that a weak emission feature at 3.4 $\mu$m is related to PAHs with extra hydrogen atoms (H-PAHs), we trace variations of the ratios using a model for PAH evolution. Namely, we estimate how populations of PAHs of different sizes, hydrogenation and ionization states change across the Orion Bar over a time interval approximately equal to its lifetime. The obtained ensembles of PAHs are further used to calculate the corresponding synthetic spectra and band flux densities. The model satisfactorily describes the main features of the ratios I3.6/I11.2, I7.7/I11.2, I7.7/I3.6, and I3.3/I3.4. We conclude that the best coincidence between modelling and observations is achieved if C loss of PAHs is limited by the number of carbon atoms NC = 60, and the band at 3.4 $\mu$m may indeed be attributed to H-PAHs. We confirm that large cations dominate at the surface of the PDR but small neutral PAHs and anions are abundant deeper in the molecular cloud.
Burst properties of the highly active FRB20201124A using uGMRT
Authors: Marthi V R , Bethapudi S , Main R A , Lin H-H , Spitler L G , Wharton R S , Li D Z , Gautam T , Pen U-L , Hilmarsson G H
Published: October 2021

We report the observations of the highly active FRB20201124A with the upgraded Giant Metrewave Radio Telescope at 550-750 MHz. These observations in the incoherent array mode simultaneously provided an arcsecond localization of bursts from FRB20201124A, the discovery of persistent radio emission associated with the host galaxy, and the detection of 48 bursts. Using the brightest burst in the sample (F = 108 Jy ms) we find a structure-maximizing dispersion measure of 410.8 ± 0.5 pc cm−3. We find that our observations are complete down to a fluence level of 10 Jy ms, above which the cumulative burst rate scales as a power-law R( > F) = 10 hr−1(F/10 Jy ms)γ with γ = −1.2 ± 0.2. We find that the bursts are on average wider than those reported for other repeating FRBs. We find that the waiting time between bursts is well approximated by an exponential distribution with a mean of ∼2.9 min during our observations. We searched for periodicities using both a standard Fourier domain method and the Fast Folding Algorithm, but found no significant candidates. We measure bulk spectro-temporal drift rates between −0.75 and −20 MHz ms−1. Finally, we use the brightest burst to set an upper limit to the scattering time of 11.1 ms at 550 MHz. The localization of FRB20201124A adds strength to the proof-of-concept method described in our earlier work and serves as a potential model for future localizations and follow-up of repeating FRBs with the uGMRT.
The IntAct database: efficient access to fine-grained molecular interaction data
Authors: del Toro Noemi , Shrivastava Anjali , Ragueneau Eliot , Meldal Birgit , Combe Colin , Barrera Elisabet , Perfetto Livia , How Karyn , Ratan Prashansa , Shirodkar Gautam , Lu Odilia , Mészáros Bálint , Watkins Xavier , Pundir Sangya , Licata Luana , Iannuccelli Marta , Pellegrini Matteo , Martin Maria Jesus , Panni Simona , Duesbury Margaret , Vallet Sylvain D , Rappsilber Juri , Ricard-Blum Sylvie , Cesareni Gianni , Salwinski Lukasz , Orchard Sandra , Porras Pablo , Panneerselvam Kalpana , Hermjakob Henning
Published: October 2021

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way.
lncRNAfunc: a knowledgebase of lncRNA function in human cancer
Authors: Yang Mengyuan , Lu Huifen , Liu Jiajia , Wu Sijia , Kim Pora , Zhou Xiaobo
Published: October 2021

The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3′-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
Enhancing biological signals and detection rates in single-cell RNA-seq experiments with cDNA library equalization
Authors: Bacher Rhonda , Chu Li-Fang , Argus Cara , Bolin Jennifer M , Knight Parker , Thomson James A , Stewart Ron , Kendziorski Christina
Published: October 2021

Considerable effort has been devoted to refining experimental protocols to reduce levels of technical variability and artifacts in single-cell RNA-sequencing data (scRNA-seq). We here present evidence that equalizing the concentration of cDNA libraries prior to pooling, a step not consistently performed in single-cell experiments, improves gene detection rates, enhances biological signals, and reduces technical artifacts in scRNA-seq data. To evaluate the effect of equalization on various protocols, we developed Scaffold, a simulation framework that models each step of an scRNA-seq experiment. Numerical experiments demonstrate that equalization reduces variation in sequencing depth and gene-specific expression variability. We then performed a set of experiments in vitro with and without the equalization step and found that equalization increases the number of genes that are detected in every cell by 17–31%, improves discovery of biologically relevant genes, and reduces nuisance signals associated with cell cycle. Further support is provided in an analysis of publicly available data.
eQuilibrator 3.0: a database solution for thermodynamic constant estimation
Authors: Beber Moritz E , Gollub Mattia G , Mozaffari Dana , Shebek Kevin M , Flamholz Avi I , Milo Ron , Noor Elad
Published: October 2021

eQuilibrator (equilibrator.weizmann.ac.il) is a database of biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts around 1,000 distinct monthly users, its design could not accommodate larger compound databases and it lacked a scalable Application Programming Interface (API) for integration into other tools developed by the systems biology community. Here, we report on the recent updates to the database as well as the addition of a new Python-based interface to eQuilibrator that adds many new features such as a 100-fold larger compound database, the ability to add novel compounds, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, the new interface can compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modelling. We foresee that these improvements will make thermodynamic modelling more accessible and facilitate the integration of eQuilibrator into other software platforms.
Nursing Care of 26 Infants Born to Mothers With COVID-19
Authors: Ding Lingli , Xiong Xiaoju , Yu Genzhen , Li Changyan , Wang Hui , Yang Yiran , Wu Shanshan , Cai Xianglian
Published: October 2021

Background:

Novel coronavirus disease (COVID-19) has spread throughout the world; yet, there are few reports of neonatal cases. Thus, information about related clinical care experience is scarce.

Clinical Findings:

This case report includes 26 infants admitted to the neonatal intensive care unit (NICU) of Tongji Hospital in Wuhan City who were born to mothers with suspected/confirmed COVID-19. The nursing and medical staff implemented care of these infants in strict accordance with infection control measures.

Intervention:

Emergency measures for the prevention and control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the NICU were developed, and neonatal isolation, observation, and treatment were performed.

Outcomes:

Vital signs of the 26 infants remained stable during isolation and treatment, and no complications occurred. During the study period, neither the infants nor the nursing and medical staff were infected with SARS-CoV-2.

Practice Recommendations:

Based on our strict practices, infants born to mothers with suspected/confirmed COVID-19 should receive care in a single-patient room to support infection control and provide enhanced observation. During initial contact and nursing care, increased attention should be given to the protection of infants born to mothers with suspected/confirmed COVID-19.
Laryngoscopic Screening Before Revision Anterior Cervical Spine Surgery
Authors: Seok Sang Yun , Lee Dong-Ho , Park Se Han , Lee Hyung Rae , Cho Jae Hwan , Hwang Chang Ju , Lee Choon Sung
Published: October 2021

Study Design:

Retrospective study.

Objectives:

The aim was to evaluate the exact incidence of vocal cord palsy (VCP) caused by previous anterior cervical spine surgery (ACSS) and aid surgeons in deciding the approach direction in revision ACSS.

Summary of Background Data:

The incidence of VCP detected by preoperative laryngoscopic screening before revision ACSS appeared to be much higher in previous reports than in our experience.

Materials and Methods:

We reviewed the data of 64 patients who underwent revision ACSS. Preoperative laryngoscopy was performed in all patients to detect VCP and/or structural abnormalities of the vocal cords. The patients’ characteristics, laryngoscopy results, and symptoms before revision surgery that were potentially caused by previous recurrent laryngeal nerve injuries (voice change, foreign body sensation, and chronic aspiration) were recorded.

Results:

Laryngoscopy demonstrated no complete VCP or decreased vocal cord motility. Eleven patients (17.2%) showed vocal cord-related symptoms and 13 patients (20.3%) showed abnormal laryngoscopic findings without VCP. Four patients (6.2%) showed vocal cord-related symptoms and abnormal laryngoscopic findings simultaneously. At the initial operative level, no significant differences in vocal cord-related symptoms were observed between the upper and lower levels (C3-4-5 vs. C5-6-7). However, the frequency of vocal cord-related symptoms was significantly high at the larger number of levels (≥3 segments) (P=0.010).

Conclusions:

In contrast to previous reports, this study demonstrated that VCP is rarely detected before revision ACSS. Therefore, deciding the approach direction with only vocal cord motility can be dangerous, and more attention is required in setting the approach direction in patients who show both vocal cord-related symptoms and abnormal laryngoscopic finding. In other cases, a contralateral approach which has a low risk of bilateral VCP could be utilized if necessary.
Effects of dipeptidyl peptidase-4 inhibition on portal hypertensive and cirrhotic rats
Authors: Huang Hui-Chun , Hsu Shao-Jung , Chuang Chiao-Lin , Hsiung Shao-Yu , Chang Ching-Chih , Hou Ming-Chih , Lee Fa-Yauh
Published: October 2021

Background:

Portal hypertension is a pathophysiological abnormality with distinct vascular derangements associated with liver cirrhosis. Dipeptidyl peptidase-4 (DPP-4) inhibitors are antidiabetic agents which exert pleiotropic vascular effects, but their relevant impact on portal hypertension and liver cirrhosis remains unclear. This study aims to clarify this issue.

Methods:

Rats receiving partial portal vein ligation (PVL) and common bile duct ligation (BDL) served as experimental models for portal hypertension and cirrhosis, respectively. After linagliptin (a DPP-4 inhibitor) treatment, the survival rate, hemodynamics, biochemistry parameters and liver histopathology were evaluated. In addition, the collateral vascular responsiveness and severity of portal-systemic shunting were examined. mRNA and protein expression in the vasculature and liver were also examined.

Results:

Linagliptin significantly reduced portal pressure (control vs linagliptin: 12.9 ± 1.2 vs 9.1 ± 2.0 mmHg, p = 0.001) and upregulated nitric oxide synthase expression in the collateral vessel, superior mesentery artery, and liver of PVL rats. However, the portal hypotensive effect was insignificant in BDL rats. Glucose plasma levels, liver and renal biochemistry parameters were not significantly altered by linagliptin. The degree of portal-systemic shunting and collateral vascular responsiveness were also not significantly altered by linagliptin treatment. Linagliptin did not improve liver fibrosis and hepatic inflammation in BDL rats.

Conclusion:

DPP-4 inhibition by linagliptin reduced portal pressure in portal hypertensive rats but not in cirrhotic rats. It may act by decreasing intrahepatic resistance via upregulation of hepatic nitric oxide synthase in portal hypertensive rats.
Implantation of monocusp valve prolongs the duration of chest tube drainage in children with tetralogy of fallot after corrective surgery
Authors: Huang Shao-Wei , Hsu Wan-Fu , Li Hsing-Yuan , Hwang Betau , Wu Fei-Yi , Weng Zen-Chung , Chuang Chieh-Mao , Chen Shyi-Jou , Wang Chih-Chien , Wang Der-Shiun , Lee Pi-Chang
Published: October 2021

Background:

Right ventricular outflow tract obstruction relief is one of the major procedures during the total correction of tetralogy of Fallot (TOF). Pulmonary insufficiency (PI) is usually inevitable after a transannular incision with a patch repair is performed. Therefore, some surgeons advocate to place a monocusp valve within the transannular patch (TAP) in order to decrease the severity of the PI. However, the monocusp valve seemed not be very effective in some patients who underwent the complete TOF repair.

Methods:

Patients who had the classic form of TOF between January 2009 and January 2017 and underwent the corrective surgery with a TAP by the same cardiovascular surgeon were identified for further analysis. Clinical information including demographics at operation, perioperative data, and postoperative outcome were collected retrospectively and compared between the group with and without a monocusp valve.

Results:

A total of 24 TOF cases were included in the final analysis, and 16 (66.7%) patients received a monocusp valve placement. The patients’ characteristics before and during the surgery were similar between the two groups. The median duration of chest tube drainage after the total correction in the monocusp group was longer than those without the valve (p = 0.04). There was no difference in the immediate postoperative data, including the inflammation/infection status, the duration of mechanical ventilation, and the length of ICU and hospital stay.

Conclusion:

Implantation of a monocusp valve during the total TOF correction using a TAP did not bring benefit to improve the immediate postoperative outcomes, especially the duration of the pleural drainage. Further study with a prospective design and a larger number of cases is needed.
New-Onset Solitary Black Lesion on the Heel
Authors: Ingrasci Giuseppe , Yosipovitch Gil
Published: October 2021

The new onset of a darkly pigmented lesion of the heel is a common reason for patients to present to their dermatology clinic. Herein, we describe a photo quiz of a case of a darkly pigmented lesion that appeared on the heel of a middle-aged adult. The answer choices include the differentials for a new-onset darkly pigmented lesion on the heel, and the correct answer can only be elucidated given the patient history, appearance of the lesion, and findings upon dermoscopy and paring of the lesion. Accurate diagnosis and proper management are important to reduce significant morbidity and costs associated with unnecessary invasive procedures or treatments.
Cardamom
Authors: Singletary Keith
Published: October 2021

The spice cardamom, also known historically as the “queen of spices,” is produced from the seeds of the plant Elettaria cardamomum, which is cultivated commercially on plantations in the south of India, Sri Lanka, Central America, and Southeast Asia. It enhances both sweet and savory dishes in many regions around the world. In ancient traditional medicines, cardamom was used to alleviate digestive disorders and obesity, and even today, it is used in local cultures for individuals with ailments such as bronchitis, depression, dysentery, influenza, and infections. This narrative review discusses human investigations of cardamom's effects on blood glucose and lipid regulation, inflammation and hypertension, and gastrointestinal discomfort of pregnancy. To date, the limited and inconsistent outcomes from these trials are insufficient to support recommendations for human use. Related animal studies are also summarized, and recommendations for future research are highlighted.
Functional and Aesthetic Lower Lip Reconstruction Using the Yotsuyanagy Flap
Authors: Alfonso Amanda , Parra Carreño Andrés , Beltrán Paloma P.
Published: October 2021

Lower lip defects are a major challenge from a reconstructive perspective. The lower lip is an anatomical region formed by different types of tissue, and it is essential to obtain adequate functional and aesthetic results. When local tissue is available to be a donor area, it becomes the best option to repair the defect. This article's purpose is to present our experience in reconstruction of partial or transfixing total defects of the lower lip with the musculocutaneous flap of the depressor anguli oris described by Yotsuyanagi.
The Application of Modified Kite Flap in Repairing Facial Skin Defects After Tumor Resection
Authors: Wu Yi , Peng Jianzhong , Luo Xianyan , Wang Tao
Published: October 2021

Introduction

The kite flap is widely used in the repair of facial skin defects because of its high survival rate and simple operation. However, the flap mobility of traditional kite flap is limited and needs to be improved. We conducted this survey to evaluate clinical efficacy of modified kite flap in repairing facial skin defects after tumor resection.

Methods

Clinical data of 25 patients with facial skin tumors were collected and analyzed. All patients received skin defect repair with modified kite flaps after Mohs surgery. The survival conditions of the flaps were observed 24 hours after the surgery. The patients were followed up at the first month and the third month after surgery and then every 3 months thereafter. The shape and texture of the flaps, as well as the matching degree with surrounding tissues, were evaluated.

Results

All the flaps were survived without infection and healed by the first intervention. The shape and color of the flaps were all good without obvious scar. Satisfactory functional and cosmetic results were achieved in both donor sites and recipient sites.

Conclusions

The modified kite flap is effective for the repair of facial skin defects, which has a high survival rate and larger mobility.
Trusting and learning from others: immediate and long-term effects of learning from observation and advice
Authors: Hertz Uri , Bell Vaughan , Raihani Nichola
Published: October 2021

Social learning underpins our species's extraordinary success. Learning through observation has been investigated in several species, but learning from advice—where information is intentionally broadcast—is less understood. We used a pre-registered, online experiment (n= 1492) combined with computational modelling to examine learning through observation and advice. Participants were more likely to immediately follow advice than to copy an observed choice, but this was dependent upon trust in the adviser: highly paranoid participants were less likely to follow advice in the short term. Reinforcement learning modelling revealed two distinct patterns regarding the long-term effects of social information: some individuals relied fully on social information, whereas others reverted to trial-and-error learning. This variation may affect the prevalence and fidelity of socially transmitted information. Our results highlight the privileged status of advice relative to observation and how the assimilation of intentionally broadcast information is affected by trust in others.
Coral reef fishes reveal strong divergence in the prevalence of traits along the global diversity gradient
Authors: Parravicini V. , Bender M. G. , Villéger S. , Leprieur F. , Pellissier L. , Donati F. G. A. , Floeter S. R. , Rezende E. L. , Mouillot D. , Kulbicki M.
Published: October 2021

Coral reefs are experiencing declines due to climate change and local human impacts. While at a local scale these impacts induce biodiversity loss and shifts in community structure, previous biogeographical analyses recorded consistent taxonomic structure of fish communities across global coral reefs. This suggests that regional communities represent a random subset of the global species and traits pool, whatever their species richness. Using distributional data on 3586 fish species and latest advances in species distribution models, we show marked gradients in the prevalence of size classes and diet categories across the biodiversity gradient. This divergence in trait structure is best explained by reef isolation during past unfavourable climatic conditions, with large and piscivore fishes better represented in isolated areas. These results suggest the risk of a global community re-organization if the ongoing climate-induced reef fragmentation is not halted.
Antibiotics accelerate growth at the expense of immunity
Authors: Galarza Juan A. , Murphy Liam , Mappes Johanna
Published: October 2021

Antibiotics have long been used in the raising of animals for agricultural, industrial or laboratory use. The use of subtherapeutic doses in diets of terrestrial and aquatic animals to promote growth is common and highly debated. Despite their vast application in animal husbandry, knowledge about the mechanisms behind growth promotion is minimal, particularly at the molecular level. Evidence from evolutionary research shows that immunocompetence is resource-limited, and hence expected to trade off with other resource-demanding processes, such as growth. Here, we ask if accelerated growth caused by antibiotics can be explained by genome-wide trade-offs between growth and costly immunocompetence. We explored this idea by injecting broad-spectrum antibiotics into wood tiger moth (Arctia plantaginis) larvae during development. We follow several life-history traits and analyse gene expression (RNA-seq) and bacterial (r16S) profiles. Moths treated with antibiotics show a substantial depletion of bacterial taxa, faster growth rate, a significant downregulation of genes involved in immunity and significant upregulation of growth-related genes. These results suggest that the presence of antibiotics may aid in up-keeping the immune system. Hence, by reducing the resource load of this costly process, bodily resources may be reallocated to other key processes such as growth.
SARS-CoV-2 IgG antibody responses in rt-PCR-positive cases: first report from India
Authors: Dash Girish Chandra , Parai Debaprasad , Choudhary Hari Ram , Peter Annalisha , Rout Usha Kiran , Nanda Rashmi Ranjan , Kshatri Jaya Singh , Kanungo Srikanta , Palo Subrata Kumar , Mandal Nityananda , Pati Sanghamitra , Bhattacharya Debdutta
Published: October 2021

Introduction. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody responses remain poorly understood and the clinical utility of serological testing is still unclear.

Aim. To understand the relationship between the antibody response to SARS-CoV-2 infection and the demographics and cycle threshold (C
t) values of confirmed RT-PCR patients.

Methodology. A total of 384 serum samples were collected from individuals between 4–6 weeks after confirmed SARS-CoV-2 infection and tested for the development of immunoglobulin class G (IgG) against SARS-CoV-2. The C
t values, age, gender and symptoms of the patients were correlated with the development of antibodies.

Results. IgG positivity was found to be 80.2 % (95 % CI, 76.2–84.2). Positivity increased with a decrease in the C
t value, with the highest (87.6 %) positivity observed in individuals with C
t values <20. The mean (±sd) C
t values for IgG positives and negatives were 23.34 (±6.09) and 26.72 (±7.031), respectively. No significant difference was found for demographic characteristics such as age and sex and symptoms and antibody response. The current study is the first of its kind wherein we have assessed the correlation of the RT-PCR C
t with the development of IgG against SARS-CoV-2.

Conclusion. Although C
t values might not have any relation with the development of symptoms, they are associated with the antibody response among SARS-CoV-2-infected individuals.