bluuebunny/crossref_metadata_2025 huggingface dataset:
Neurocognitive measures of self-blame and risk prediction models of recurrence in major depressive disorder
Authors: Lawrence Andrew J. , Stahl Daniel , Duan Suqian , Fennema Diede , Jaeckle Tanja , Young Allan H. , Dazzan Paola , Moll Jorge , Zahn Roland
Published: January 2021

Background

Overgeneralised self-blaming emotions, such as self-disgust, are core symptoms of major depressive disorder (MDD) and prompt specific actions (i.e. “action tendencies”), which are more functionally relevant than the emotions themselves. We have recently shown, using a novel cognitive task, that when feeling self-blaming emotions, maladaptive action tendencies (feeling like “hiding” and like “creating a distance from oneself”) and an overgeneralised perception of control are characteristic of MDD, even after remission of symptoms. Here, we probed the potential of this cognitive signature, and its combination with previously employed fMRI measures, to predict individual recurrence risk. For this purpose, we developed a user-friendly hybrid machine-/statistical-learning tool which we make freely available.

Methods

52 medication-free remitted MDD patients, who had completed the Action Tendencies Task and our self-blame fMRI task at baseline, were followed up clinically over 14-months to determine recurrence. Prospective prediction models included baseline maladaptive self-blame-related action tendencies and anterior temporal fMRI connectivity patterns across a set of fronto-limbic a priori regions of interest, as well as established clinical and standard psychological predictors. Prediction models used elastic-net regularised logistic regression with nested 10-fold cross-validation.

Results

Cross-validated discrimination was highly promising (AuC≥0.86), and positive predictive values over 80% were achieved when including fMRI in multi-modal models, but only up to 71% (AuC≤.74) when solely relying on cognitive and clinical measures.

Conclusions

This shows the high potential of multi-modal signatures of self-blaming biases to predict recurrence risk at an individual level, and calls for external validation in an independent sample.
Mucoricin is a Ricin-Like Toxin that is Critical for the Pathogenesis of Mucormycosis
Authors: Soliman Sameh S. M. , Baldin Clara , Gu Yiyou , Singh Shakti , Gebremariam Teclegiorgis , Swidergall Marc , Alqarihi Abdullah , Youssef Eman G. , Alkhazraji Sondus , Pikoulas Antonis , Perske Christina , Venkataramani Vivek , Rich Abigail , Bruno Vincent M. , Hotopp Julie Dunning , Mantis Nicolas J. , Edwards John E. , Filler Scott G. , Chamilos Georgios , Vitetta Ellen S. , Ibrahim Ashraf S.
Published: January 2021

Fungi of the order Mucorales cause mucormycosis, a lethal infection with an incompletely understood pathogenesis. We now demonstrate that Mucorales fungi produce a toxin that plays a central role in virulence. Polyclonal antibodies against this toxin inhibit its ability to damage human cellsin vitro,and prevent hypovolemic shock, organ necrosis, and death in mice with mucormycosis. RNAi inhibition of the toxin inRhizopus delemar,compromises the ability of the fungus to damage host cells and attenuates virulence in mice. This 17 kDa toxin has structural and functional features of the plant toxin, ricin, including the ability to inhibit protein synthesis by its N-glycosylase activity, the existence of a motif that mediates vascular leak, and a lectin sequence. Antibodies against the toxin inhibitR. delemar-or toxin-mediated vascular permeabilityin vitroand cross-react with ricin. A monoclonal anti-ricin B chain antibody binds to the toxin and also inhibits its ability to cause vascular permeability. Therefore, we propose the name “mucoricin” for this toxin. Not only is mucoricin important in the pathogenesis of mucormycosis but our data suggest that a ricin- like toxin is produced by organisms beyond the plant and bacterial kingdoms. Importantly, mucoricin should be a promising therapeutic target.
Prevalence of floating toe and its relationship with static postural stability in children: The Yamanashi adjunct study of the Japan Environment and Children’s Study (JECS-Y)
Authors: Fujimaki Taro , Wako Masanori , Koyama Kensuke , Furuya Naoto , Shinohara Ryoji , Otawa Sanae , Kobayashi Anna , Horiuchi Sayaka , Kushima Megumi , Yamagata Zentaro , Haro Hirotaka
Published: January 2021

Floating toe (FT) is a frequently seen condition in which a toe is inadequately in contact with the ground. Although toes play an important role in stabilizing standing posture and walking, many aspects of the effects of FT on the body remain unclear. To our knowledge, there have been no reports about the relationship between FT and postural stability, especially in children. This study aimed to clarify the prevalence of FT and its relationship with static postural stability in children. Of the 400 children aged 8 years who participated in our cohort study, 396, who were examined for static postural stability, were included in this study. Postural stability and FT were assessed using a foot pressure plate. The sway path length of the center of pressure and the area of the ellipse defined as the size of the area marked by the center of pressure were measured as an evaluation of static postural stability. We calculated the “floating toe score (FT score: small FT score indicates insufficient ground contact of the toes)” using the image of the plantar footprint obtained at the postural stability measurement. The FT rate was very high at more than 90%, and the FT score in the eyes-closed condition was significantly higher than that in the eyes-open condition in both sexes. The FT score significantly correlated with the center of pressure path and area. Our results suggest that ground contact of the toes is not directly related to static postural stability in children, but it may function to stabilize the body when the condition becomes unstable, such as when the eyes are closed.
Assessing biomass and primary production of microphytobenthos in depositional coastal systems using spectral information
Authors: Jacobs Pascalle , Pitarch Jaime , Kromkamp Jacco C. , Philippart Catharina J.M.
Published: January 2021

In depositional intertidal coastal systems, primary production is dominated by benthic microalgae (microphytobenthos) inhabiting the mudflats. This benthic productivity is supporting secondary production and supplying important services to humans including food provisioning. Increased frequencies of extreme events in weather (such as heatwaves, storm surges and cloudbursts) are expected to strongly impact the spatiotemporal dynamics of the microphytobenthos and subsequently their contribution to coastal food webs. Within north-western Europe, the years 2018 and 2019 were characterized by record-breaking summer temperatures and accompanying droughts. Field-calibrated satellite data (Sentinel 2) were used to quantify the seasonal dynamics of microphytobenthos biomass and production at an unprecedented spatial and temporal resolution during these years. We demonstrate that the Normalized Difference Vegetation Index (NDVI) should be used with caution in depositional coastal intertidal systems, because it may reflect import of remains of allochthonous pelagic productivity rather than local benthic biomass. We show that the reduction in summer biomass of the benthic microalgae cannot be explained by grazing but was most probably due to the high temperatures. The fivefold increase in salinity from January to September 2018, resulting from reduced river run-off during this exceptionally dry year, cannot have been without consequences for the vitality of the microphytobenthos community and its resistance to wind stress and cloud bursts. Comparison to historical information revealed that primary productivity of microphytobenthos may vary at least fivefold due to variations in environmental conditions. Therefore, ongoing changes in environmental conditions and especially extreme events because of climate change will not only lead to changes in spatiotemporal patterns of benthic primary production but also to changes in biodiversity of life under water and ecosystem services including food supply. Satellite MPB data allows for adequate choices in selecting coastal biodiversity conservation and coastal food supply.

HIGHLIGHTS

Expected seasonality changes require large-scale and high-resolution coastal data

NDVI of tidal flats reflects local benthic biomass and allochthonous phytoplankton

High summer temperatures reduced biomass and productivity of benthic microalgae

Long-term data revealed a five-fold variation in MPB biomass and production

Satellite MPB data allow for adequate conservation of coastal biodiversity
Female gametophyte expressedArabidopsis thalianalipid transfer proteins AtLtpI.4 and AtLtpI.8 provide a link between callose homeostasis, pollen tube guidance, and fertilization success
Authors: Kumari Khushbu , Zhao Meng , Britz Sebastian , Weiste Christine , Dröge-Laser Wolfgang , Stigloher Christian , Deeken Rosalia , Becker Dirk
Published: January 2021

Non-specific lipid transfer proteins (LTPs) represent a sub-class among the large family of Cysteine-rich proteins (CRPs) specific to land plants. LTPs possess a hydrophobic cavity, enabling them to bind and stabilize a variety of lipid molecules outside membranes. In line with the existence of an N-terminal signal peptide, secreted LTPs represent a well-suited mobile signal carrier in the plant’s extracellular matrix. Thus, LTPs are currently considered as key players to mediate the bulk flow of lipids between membranes/compartments as well as the buildup of lipid barrier polymers including cutin and suberin.

Here, we show that floral expressedArabidopsis thalianaAtLtpI.4 (AtLTP2) and AtLtpI.8 (AtLTP5), mutually control cell-cell communication between growing pollen tubes and ovules during fertilization. Arabidopsis mutants lacking functional AtLtpI.4 and AtLtpI.8 exhibit significantly reduced fertilization success. Cross-pollination and cell biological analyses revealed thatAtLtpI.4/I.8double mutants are impaired in pollen tube guidance towards ovules. Our finding that theAtLtpI.4/I.8phenotype correlates with aberrant callose depositions in the micropylar region during ovule development suggests that both LTPs represent novel players of a joint signaling pathway that controls callose homeostasis in the female gametophyte.
Molecular dynamic simulation reveals E484K mutation enhances spike RBD-ACE2 affinity and the combination of E484K, K417N and N501Y mutations (501Y.V2 variant) induces conformational change greater than N501Y mutant alone, potentially resulting in an escape mutant
Authors: Nelson Gard , Buzko Oleksandr , Spilman Patricia , Niazi Kayvan , Rabizadeh Shahrooz , Soon-Shiong Patrick
Published: January 2021

Rapidly spreading SARS-CoV-2 variants present not only an increased threat to human health due to the confirmed greater transmissibility of several of these new strains but, due to conformational changes induced by the mutations, may render first-wave SARS-CoV-2 convalescent sera, vaccine-induced antibodies, or recombinant neutralizing antibodies (nAbs) ineffective. To be able to assess the risk of viral escape from neutralization by first-wave antibodies, we leveraged our capability for Molecular Dynamic (MD) simulation of the spike receptor binding domain (S RBD) and its binding to human angiotensin-converting enzyme 2 (hACE2) to predict alterations in molecular interactions resulting from the presence of the E484K, K417N, and N501Y variants found in the South African 501Y.V2 strain – alone and in combination. We report here the combination of E484K, K417N and N501Y results in the highest degree of conformational alterations of S RBD when bound to hACE2, compared to either E484K or N501Y alone. Both E484K and N501Y increase affinity of S RBD for hACE2 and E484K in particular switches the charge on the flexible loop region of RBD which leads to the formation of novel favorable contacts. Enhanced affinity of S RBD for hACE2 very likely underpins the greater transmissibility conferred by the presence of either E484K or N501Y; while the induction of conformational changes may provide an explanation for evidence that the 501Y.V2 variant, distinguished from the B.1.1.7 UK variant by the presence of E484K, is able to escape neutralization by existing first-wave anti-SARS-CoV-2 antibodies and re-infect COVID-19 convalescent individuals.
High prevalence of Plasmodium malariae and Plasmodium ovale in co-infections with Plasmodium falciparum in asymptomatic malaria parasite carriers in Southwest Nigeria
Authors: Abdulraheem Muhydeen Abiodun , Ernest Medard , Ugwuanyi Ifeoma , Abkallo Hussein M. , Nishikawa Saori , Adeleke Mofeyisade , Orimadegun Adebola E. , Culleton Richard
Published: January 2021

Asymptomatic malaria parasite carriers do not seek anti-malarial treatment and may constitute a silent infectious reservoir. In order to assess the level of asymptomatic and symptomatic carriage amongst adolescents in a highly endemic area, and to identify the risk factors associated with such carriage, we conducted a cross sectional survey of 1032 adolescents (ages 10-19) from eight schools located in Ibadan, Southwest Nigeria in 2016. Blood films and blood spot filter paper samples were prepared for microscopy and DNA analysis. The prevalence of asymptomatic malaria was determined using microscopy, rapid diagnostic tests and PCR for 658 randomly selected samples. Of these, we found that 80% of asymptomatic schoolchildren were positive for malaria parasites by PCR, compared to 47% and 9% determined by RDT and microscopy, respectively. Malaria parasite species typing was performed using PCR targeting the mitochondrial CoxIII gene, and revealed high rates of carriage of Plasmodium malariae (53%) and Plasmodium ovale (24%). Most asymptomatic infections were co-infections of two or more species (62%), with P. falciparum + P. malariae the most common (35%), followed by P. falciparum + P. malariae + P. ovale (21%) and P. falciparum + P. ovale (6%). Single infections of P. falciparum, P. malariae and P. ovale accounted for 24%, 10% and 4% of all asymptomatic infections respectively. To compare the species composition of asymptomatic and symptomatic infections, further sample collection was carried out in 2017 at one of the previously sampled schools, and at a nearby hospital. Whilst the species composition of the asymptomatic infections was similar to that observed in 2016, the symptomatic infections were markedly different, with single infections of P. falciparum observed in 91% of patients, P. falciparum + P. malariae in 5% and P. falciparum + P. ovale in 4%.
Vaginal bacterial load in the second trimester is associated with early preterm birth recurrence: a nested case-control study
Authors: Goodfellow Laura , Verwijs Marijn C. , Care Angharad , Sharp Andrew , Ivandic Jelena , Poljak Borna , Roberts Devender , Bronowski Christina , Gill A. Christina , Darby Alistair C. , Alfirevic Ana , Muller-Myhsok Bertram , Alfirevic Zarko , van de Wijgert Janneke H.H.M.
Published: January 2021

Objective

To assess the association between vaginal microbiome (VMB) composition and recurrent early spontaneous preterm birth (sPTB)/preterm prelabour rupture of membranes (PPROM).

Design

Nested case-control study.

Setting

UK tertiary referral hospital.

Sample

High-risk women with previous sPTB/PPROM <34+0 weeks gestation who had a recurrence (n=22) or delivered at ≥37+0 weeks without PPROM (n=87).

Methods

Vaginal swabs collected between 15-22 weeks gestation were analysed by 16S rRNA gene sequencing and 16S quantitative PCR.

Main outcome measure

Recurrent early sPTB/PPROM.

Results

28/109 high-risk women had anaerobic vaginal dysbiosis, with the remainder dominated by lactobacilli (L. iners 36/109, L. crispatus 23/109, or other 22/109). VMB type, diversity, and stability were not associated with recurrence. Women with a recurrence, compared to those without, had a higher median vaginal bacterial load (8.64 vs. 7.89 log10 cells/μl, adjusted odds ratio (aOR)=1.90, 95% confidence interval (CI)=1.01-3.56, p=0.047) and estimated Lactobacillus concentration (8.59 vs. 7.48 log10 cells/μl, aOR=2.35, CI=1.20-4.61, p=0.013). A higher recurrence risk was associated with higher median bacterial loads for each VMB type after stratification, although statistical significance was reached only for L. iners-domination (aOR=3.44, CI=1.06-11.15, p=0.040). Women with anaerobic dysbiosis or L. iners-domination had a higher median vaginal bacterial load than women with a VMB dominated by L. crispatus or other lactobacilli (8.54, 7.96, 7.63, and 7.53 log10 cells/μl, respectively).

Conclusions

Vaginal bacterial load is associated with early sPTB/PPROM recurrence. Domination by lactobacilli other than L. iners may protect women from developing high bacterial loads. Future PTB studies should quantify vaginal bacteria and yeasts.

Funding

Wellbeing of Women, London, UK

Tweetable abstract

Increased vaginal bacterial load in the second trimester may be associated with recurrent early spontaneous preterm birth.
COVID-19 dynamics in an Ohio prison
Authors: KhudaBukhsh Wasiur R. , Khalsa Sat Kartar , Kenah Eben , Rempala Grzegorz A. , Tien Joseph H.
Published: January 2021

Importance

Incarcerated individuals are a vulnerable population for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Understanding SARS-CoV-2 dynamics in prisons is crucial for curbing transmission both within correctional facilities and in the surrounding community.

Objective

The purpose of this study was to identify transmission scenarios that could underly rapid, widespread SARS-CoV-2 infection among inmates in Marion Correctional Institution (MCI).

Design

Publicly available data reported by the Ohio Department of Rehabilitation and Corrections (ODRC) was analyzed using mathematical and statistical models.

Setting

We consider SARS-CoV-2 transmission dynamics among MCI inmates prior to and including April 16, 2020.

Participants

This study uses de-identified, publicly available SARS-CoV-2 test result data for MCI inmates.

Exposures

Inmates at MCI were considered exposed to potential infection with SARS-CoV-2.

Main outcome and measures

Results from mass testing conducted on April 16, 2020 were analyzed together with time of first reported SARS-CoV-2 infection among MCI inmates.

Results

Rapid, widespread infection of MCI inmates was reported, with nearly 80% of inmates infected within three weeks of first reported inmate case. These data are consistent with i) a basic reproduction number greater than 14, together with a single initially infected inmate, ii) an initial super-spreading event resulting in several hundred initially infected inmates, together with a basic reproduction number of approximately three, and iii) earlier undetected circulation of virus among inmates prior to April.

Conclusions and relevance

Mass testing data are consistent with extreme transmissibility, super-spreading events, or undetected circulation of virus among inmates. All scenarios consistent with these data attest to the vulnerabilities of prisoners to COVID-19.

Key points

Question

To identify transmission characteristics consistent with timing and extent of SARS-CoV-2 infection among inmates in Marion Correctional Institution.

Findings

Mathematical and statistical modeling finds three scenarios that are consistent with the observed widespread infection in Marion Correctional Institution: i) very high transmissibility corresponding to a basic reproduction number in the double digits, ii) an initial super-spreading event involving exposure of several hundred inmates, iii) undetected circulation of virus prior to the first documented case among inmates.

Meaning

High transmissibility, super-spreading events, and challenges with disease surveillance all attest to the vulnerabilities of prison populations to SARS-CoV-2.
SARS-Cov-2 prevalence, transmission, health-related outcomes and control strategies in homeless shelters: systematic review and meta-analysis
Authors: Mohsenpour Amir Mohsen , Bozorgmehr Kayvan , Rohleder Sven , Stratil Jan , Costa Diogo
Published: January 2021

Background: People experiencing homelessness (PEH) may be at particular risk for COVID19. We synthesised the evidence on SARS-Cov-2 infection, transmission, outcomes of disease, effects of non-pharmaceutical interventions (NPI), and the effectiveness of targeted strategies for infection prevention and control (IPC).
Methods: Systematic review of articles, reports and grey-literature indexed in electronic databases (EMBASE, WHO-Covid19, Web of Science), pre-print repositories, institutional websites, and handsearching. Empirical papers of any study design addressing Covid-19 in PEH or homeless shelters' staff in English were included. (PROSPERO 2020 CRD42020187033)
Findings: Of 194 publications, 13 studies were included (two modelling, ten observational and one qualitative study). All were conducted in high-income countries. Random-effect meta-analysis of prevalence estimates yields a baseline SARS-Cov-2 prevalence of 2.14% (95% Confidence-Interval, 95%CI=1.02-3.27) in PEH and 1.72 % (95%CI=0.31-3.12) in staff. In outbreaks, the pooled prevalence increases to 29.49% (95%CI=16.44-29.55) in PEH and 15.18% (95%CI=8.95-21.42) in staff. Main IPC strategies were universal and rapid testing, expansion of non-congregate housing support, and individual measures in shelters (bed spacing, limited staff rotation).
Interpretation: Up to 30% PEH and 17% staff are infected during outbreaks of SARS-Cov-2 in homeless shelters. Most studies were conducted in the USA. No studies were found on health-related outcomes or health effects of NPI. An overview and evaluation of IPC strategies for PEH, including a better understanding of disease transmission, and reliable data on PEH within Covid-19 notification systems is needed. Qualitative studies may serve to voice PEH experiences and guide future evaluations and IPC strategies.
Funding: No source of funding.
N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2
Authors: McCallum Matthew , Marco Anna De , Lempp Florian , Tortorici M. Alejandra , Pinto Dora , Walls Alexandra C. , Beltramello Martina , Chen Alex , Liu Zhuoming , Zatta Fabrizia , Zepeda Samantha , di Iulio Julia , Bowen John E. , Montiel-Ruiz Martin , Zhou Jiayi , Rosen Laura E. , Bianchi Siro , Guarino Barbara , Fregni Chiara Silacci , Abdelnabi Rana , Caroline Foo Shi-Yan , Rothlauf Paul W. , Bloyet Louis-Marie , Benigni Fabio , Cameroni Elisabetta , Neyts Johan , Riva Agostino , Snell Gyorgy , Telenti Amalio , Whelan Sean P.J. , Virgin Herbert W. , Corti Davide , Pizzuto Matteo Samuele , Veesler David
Published: January 2021

SARS-CoV-2 entry into host cells is orchestrated by the spike (S) glycoprotein that contains an immunodominant receptor-binding domain (RBD) targeted by the largest fraction of neutralizing antibodies (Abs) in COVID-19 patient plasma. Little is known about neutralizing Abs binding to epitopes outside the RBD and their contribution to protection. Here, we describe 41 human monoclonal Abs (mAbs) derived from memory B cells, which recognize the SARS-CoV-2 S N-terminal domain (NTD) and show that a subset of them neutralize SARS-CoV-2 ultrapotently. We define an antigenic map of the SARS-CoV-2 NTD and identify a supersite recognized by all known NTD-specific neutralizing mAbs. These mAbs inhibit cell-to-cell fusion, activate effector functions, and protect Syrian hamsters from SARS-CoV-2 challenge. SARS-CoV-2 variants, including the 501Y.V2 and B.1.1.7 lineages, harbor frequent mutations localized in the NTD supersite suggesting ongoing selective pressure and the importance of NTD-specific neutralizing mAbs to protective immunity.
SARS-CoV-2 spike protein arrested in the closed state induces potent neutralizing responses
Authors: Carnell George W. , Ciazynska Katarzyna A. , Wells David A. , Xiong Xiaoli , Aguinam Ernest T. , McLaughlin Stephen H. , Mallery Donna , Ebrahimi Soraya , Ceron-Gutierrez Lourdes , James Leo C. , Doffinger Rainer , Heeney Jonathan L. , Briggs John A. G.
Published: January 2021

The majority of SARS-CoV-2 vaccines in use or in advanced clinical development are based on the viral spike protein (S) as their immunogen. S is present on virions as pre-fusion trimers in which the receptor binding domain (RBD) is stochastically open or closed. Neutralizing antibodies have been described that act against both open and closed conformations. The long-term success of vaccination strategies will depend upon inducing antibodies that provide long-lasting broad immunity against evolving, circulating SARS-CoV-2 strains, while avoiding the risk of antibody dependent enhancement as observed with other Coronavirus vaccines. Here we have assessed the results of immunization in a mouse model using an S protein trimer that is arrested in the closed state to prevent exposure of the receptor binding site and therefore interaction with the receptor. We compared this with a range of other modified S protein constructs, including representatives used in current vaccines. We found that all trimeric S proteins induce a long-lived, strongly neutralizing antibody response as well as T-cell responses. Notably, the protein binding properties of sera induced by the closed spike differed from those induced by standard S protein constructs. Closed S proteins induced more potent neutralising responses than expected based on the degree to which they inhibit interactions between the RBD and ACE2. These observations suggest that closed spikes recruit different, but equally potent, virus-inhibiting immune responses than open spikes, and that this is likely to include neutralizing antibodies against conformational epitopes present in the closed conformation. Together with their improved stability and storage properties we suggest that closed spikes may be a valuable component of refined, next-generation vaccines.
Role of the mobilome in the global dissemination of the carbapenem resistance geneblaNDM
Authors: Acman Mislav , Wang Ruobing , van Dorp Lucy , Shaw Liam P. , Wang Qi , Luhmann Nina , Yin Yuyao , Sun Shijun , Chen Hongbin , Wang Hui , Balloux Francois
Published: January 2021

The mobile resistance geneblaNDMencodes the NDM enzyme which hydrolyses carbapenems, a class of antibiotics used to treat some of the most severe bacterial infections.blaNDMis globally distributed across a variety of Gram-negative bacteria on multiple plasmids, typically located within a highly recombining and transposon-rich genomic region. This complexity means the dynamics underlying the dissemination ofblaNDMremain poorly resolved. In this work, we compile a dataset of over 6000 bacterial genomes harbouring theblaNDMgene including 104 newly generated PacBio hybrid assemblies from clinical and livestock associated isolates across China. We develop a novel computational approach to track structural variants surroundingblaNDMin bacterial genomes. This allows us to identify the prevalent genomic contexts ofblaNDMand reconstruct the key mobile genetic elements and events in its global spread. We estimate thatblaNDMemerged on a Tn125transposon before 1985 but only reached a global prevalence around a decade after its first recorded observation in 2005. We find that the Tn125transposon played an important role in early plasmid-mediated jumps ofblaNDMbut was overtaken by other elements in recent years including IS26-flanked pseudo-composite transposons and Tn3000. Lastly, we observe a notable correlation between plasmid backbones bearingblaNDMand the sampling location of isolates. This observation suggests that the dissemination of resistance genes is mainly driven by successive between-plasmid transposon jumps, with plasmid exchange much more restricted due to the adaptation of plasmids to specific bacterial hosts.
Divalent ligand-monovalent molecule binding
Authors: Janssen Mathijs , Stenmark Harald , Carlson Andreas
Published: January 2021

Simultaneous binding of divalent ligands to two identical molecules is a widespread phenomenon in biology and chemistry. Here, we describe this binding event as a divalent ligand AA that can bind to two identical monovalent molecules B to form the complex AA · B2. Cases where the total concentration [AA]Tis either much larger or much smaller than the total concentration [B]Thave been studied earlier, but a description of intermediate concentrations is missing. In this paper, we describe the general case of any ratio ofξ≡ [B]T/[AA]T. We show that the concentration of the intermediate complex AA · B is governed by a cubic equation and discuss several scenarios in which this cubic equation simplifies. Our numerical results, which cover the entire range of 0 <ξ< ∞, are relevant to processes wherein the concentrations of free ligands and proteins both decrease upon binding. Such ligand and protein depletion is expected to be important in cellular contexts, e.g., in antigen detection and in coincidence detection of proteins or lipids.
Structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in Nucleotide Excision Repair
Authors: van Eeuwen Trevor , Shim Yoonjung , Kim Hee Jong , Zhao Tingting , Basu Shrabani , Garcia Benjamin A. , Kaplan Craig , Min Jung-Hyun , Murakami Kenji
Published: January 2021

The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit core TFIIH assembled on a carcinogen-DNA adduct lesion at 3.9–9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3’ and 5’ side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 would extend the DNA opening at the lesion and deliver the damaged strand to Rad3 (XPD) in an unwound form suitable for subsequent lesion scanning and verification.
Can prognostic factors for indirect muscle injuries in elite football (soccer) players be identified using data from preseason screening? An exploratory analysis using routinely-collected periodic health examination records
Authors: Hughes Tom , Riley Richard D. , Callaghan Michael J. , Sergeant Jamie C.
Published: January 2021

This study used periodic health examination (PHE) data from 134 outfield elite male football players, over 5 seasons (1st July 2013 to 19th May 2018). Univariable and multivariable logistic regression models were used to determine prognostic associations between 36 variables and time-loss, lower extremity index indirect muscle injuries (I-IMIs). Non-linear associations were explored using fractional polynomials. During 317 participant-seasons, 138 I-IMIs were recorded. Univariable associations were determined for previous calf indirect muscle injury (IMI) frequency (OR=1.80, 95% confidence interval (CI) = 1.09 to 2.97), hamstring IMI frequency (OR=1.56, 95% CI=1.17 to 2.09), if the most recent hamstring IMI occurred > 12 months but < 3 years prior to PHE (OR= 2.95, 95% CI = 1.51 to 5.73) and age (OR =1.12 per 1-year increase, 95% CI = 1.06 to 1.18). Multivariable analyses demonstrated that if a player’s most recent previous hamstring IMI was >12 months but <3 years prior to PHE (OR= 2.24, 95% CI = 1.11 to 4.53), then this was the only variable with added prognostic value over and above age (OR=1.12 per 1-year increase, 95%CI = 1.05 to 1.18). Allowing non-linear associations conferred no advantage over linear ones. Therefore, PHE has limited use for injury risk prediction.
Sleep disorders predict the one-year onset, persistence, but not remission of psychotic experiences in pre-adolescence: a longitudinal analysis of the ABCD cohort data
Authors: Reeve Sarah , Bell Vaughan
Published: January 2021

The relationship between sleep disorder and psychotic experiences in preadolescence has not been extensively studied despite the potential for intervention. The current study addresses this relationship using the Adolescent Brain Cognitive Development (ABCD) cohort, which provides baseline data from 11,830 10 to 11-year-olds; for 4910 of these 1-year follow-up data is also available. A set of pre-registered multi-level regression models were applied to test whether a) sleep disorder is associated with psychotic experiences at baseline; b) baseline sleep disorder predicts psychotic experiences at follow-up; c) the persistence of sleep disorder predicts persistence of psychotic experiences at follow-up; d) the remission of sleep disorder predicts the remission of psychotic experiences at follow-up. After controlling for potential confounders, sleep disorder was associated with psychotic experiences cross-sectionally (OR=1.40, 95% CI 1.20-1.63), at one-year follow-up (OR=1.32, 95% CI 1.11-1.57), and the persistence of sleep disorder predicted the persistence of psychotic experiences (OR=1.72, 95% CI 1.44-2.04). However, remission of sleep problems did not predict remission of psychotic experiences (OR=1.041, 95% CI 0.80-1.35). The results indicate that sleep disorders in preadolescence are common and associated with psychotic experiences, although the lack of co-remission raises questions about the mechanism of association. However, given these findings, and existing evidence in later adolescence and adults, further investigation of sleep as a preventative mental health intervention in this age group is warranted.
Inequalities and policy gaps in maternal health among Empowered Action Group (EAG) States in India: Evidence from Demographic Health Survey
Authors: Malik Manzoor Ahmad , Akhtar Saddaf Naaz
Published: January 2021

Health inequality in maternal health is one of the serious challenges currently faced by public health experts. Maternal mortality in Empowered Action Group (EAG) states is highest and so are the health inequalities prevalent. We have made a comprehensive attempt to understand maternal health inequality and the risk factors concerning the EAG states in India, using recent data of Demography Health Survey of India (2015-16). Bi-variate, multivariate logistic regression, and concentration indices were used. The study has measured the four outcome variables of maternal health namely antenatal care of at least 4 visits, institutional delivery, contraceptive use, and unmet need. The study revealed that better maternal health is heavily concentrated among the richer households, while the negative concentration index of unmet need clearly reflected the greater demand for higher unmet need among the poor households in the EAG states of India. Challenges of inequalities still persist at large in maternal health, but to achieve better health these inequalities must be reduced. Since inequality mainly affects the poor households due to a lower level of income. Therefore, specific measures must be taken from a demand-side perspective in order to enhance their income and reduce the disparities in the EAG states of India.
Combining symbolic regression with the Cox proportional hazards model improves prediction of heart failure deaths
Authors: Wilstup Casper , Cave Chris
Published: January 2021

Heart failure is a clinical syndrome characterised by a reduced ability of the heart to pump blood. Patients with heart failure have a high mortality rate, and physicians need reliable prognostic predictions to make informed decisions about the appropriate application of devices, transplantation, medications, and palliative care. In this study, we demonstrate that combining symbolic regression with the Cox proportional hazards model improves the ability to predict death due to heart failure compared to using the Cox proportional hazards model alone.

We used a newly invented symbolic regression method called the QLat-tice to analyse a data set of medical records for 299 Pakistani patients diagnosed with heart failure. The QLattice identified a minimal set of mathematical transformations of the available covariates, which we then used in a Cox model to predict survival.

An exponential function of age, the inverse of ejection fraction, and the inverse of serum creatinine were identified as the best risk factors for predicting heart failure deaths. A Cox model fitted on these transformed covariates had improved predictive performance compared with a Cox model on the same covariates without mathematical transformations.

Symbolic regression is a way to find transformations of covariates from patients’ medical records which can improve the performance of survival regression models. At the same time, these simple functions are intuitive and easy to apply in clinical settings. The direct interpretability of the simple forms may help researchers gain new insights into the actual causal pathways leading to deaths.
Does International Financial Reporting Standard 8 improve the firms' information environment?
Authors: Lenormand Gaëlle , Touchais Lionel
Published: January 2021

Purpose

This article analyzes the effect of International Financial Reporting Standard (IFRS) 8 on the informational content of segment data. It aims to assess the change in quality of the financial analysts' and the shareholders' information environment due to the new segment reporting standard to verify the International Accounting Standards Board’s (IASB) expectations and the conclusions of its post-implementation review.

Design/methodology/approach

Based on a sample of 250 companies listed on Euronext Paris in France, a country with poor legal protection for shareholders, over a nine-year period, the authors test whether the new standard makes the financial analysts' forecasts more accurate and reduces the implied cost of equity capital.

Findings

The findings show that IFRS 8 partially improves the informational content of segment data, partially supporting the outcome of IASB. The management approach may have forced some firms to change their segmentation to provide a more economic view of the business. The poor legal protection for shareholders in France may explain this result.

Research limitations/implications

Due to proprietary and agency costs, firms may withhold segment information whatever the standard used.

Practical implications

This study contributes to the ongoing debate about IFRS 8 and may interest financial statement users and the international standard-setter for such a criticized standard.

Originality/value

The results contribute to the segment reporting literature by addressing the partial improvement of information environment under the managerial approach in a country with lower investor protection.
Documenting social justice in library and information science research: a literature review
Authors: Winberry Joseph , Bishop Bradley Wade
Published: January 2021

Purpose

The purpose of this study is to provide an overview of social justice research in library and information science (LIS) literature in order to identify the research quantity, what populations or settings were included and future directions for this area of the discipline through examination of when related research was published, what contexts it covered and what contributions LIS researchers have made in this research area.

Design/methodology/approach

This study reviews results from two LIS literature databases—Library, Information Science and Technology Abstracts (LISTA) and Library and Information Science Source (LISS)—that use the term “social justice” in title, abstract or full text to explicitly or implicitly describe their research.

Findings

This review of the literature using the term social justice to describe LIS research recognizes the significant increase in quantities of related research over the first two decades of the 21st century as well as the emergence of numerous contexts in which that research is situated. The social justice research identified in the literature review is further classified into two primary contribution categories: indirect action (i.e. steps necessary for making change possible) or direct action (i.e. specific steps, procedures and policies to implement change).

Research limitations/implications

The findings of this study provide a stronger conceptualization of the contributions of existing social justice research through examination of past work and guides next steps for the discipline.

Practical implications

The conceptualizations and related details provided in this study help identify gaps that could be filled by future scholarship.

Originality/value

While social justice research in LIS has increased in recent years, few studies have explored the landscape of existing research in this area.
Social environment: Trait, context and agent for selection in a meta‐population
Authors: Vander Wal Eric
Published: January 2021

In Focus: Formica, V., Donald, H., Marti, H., Irgebay, Z., Brodie III, E. Social network position experiences more variable selection than weaponry in wild subpopulations of forked fungus beetles. Journal of Animal Ecology, 90, 168–182, https://doi.org/10.1111/1365‐2656.13322. That social network traits can exhibit consistent‐individual differences among individuals and confer a fitness benefit or cost is increasingly well‐established. However, how selection—natural or sexual—affects those social traits and at what scale remains an open question. In this Special Feature, Formica and colleagues employ a meta‐population of forked fungus beetles to test and contrast whether sexual selection on social network traits contrasted to morphological traits occurs at the local (soft) or global (hard) scales. The authors demonstrate that morphological traits are largely under hard directional positive selection, whereas social traits are under soft and variable selection. The findings are compelling and raise interesting discussion of multi‐level selection and the evolution of social traits in a meta‐population.
Nutrient availability predicts multiple stem frequency, an indicator of species resprouting capacity in tropical forests
Authors: Heineman Katherine D. , Turner Benjamin L. , Dalling James W.
Published: January 2021

Resprouting capacity is a key component of plant life history. While resprouting requires substantial nutrient reserves to support new growth, the influence of soil fertility on resprouting is largely unknown.

We tested whether the frequency of multi‐stemmed trees, a potential indicator of resprouting history, is associated with low soil fertility, reflecting selection for conservative life histories that enhance survival, or with high fertility, reflecting greater resource availability to support regrowth.

Data from the Barro Colorado Island (BCI) 50‐ha plot in Panama showed that multi‐stemmed trees are more likely to resprout during their lifetime than single‐stemmed trees, and that multiple stem frequency has a strong taxonomic signal for adult trees.

To test how multiple stem frequency varies with demographic rates and nutrient allocation strategies, we compiled functional trait datasets for 71 species from lowland forest on BCI and 43 species from lower montane forest in western Panama. We also assessed environmental correlates of community‐wide multiple stem frequency in thirty‐seven 1‐ha lowland plots in the Panama Canal watershed and twelve 1‐ha montane plots in western Panama, spanning gradients of rainfall and soil fertility.

Multiple stem frequency was not correlated with species demographic rates or wood density, suggesting that resprouting is unrelated to classical ‘persistence’ traits in neotropical tree species. Multiple stem frequency of tree species occurring on BCI was weakly but significantly positively correlated with regional soil phosphorus associations, but unrelated to foliar nutrient concentrations.

Multiple stem frequency covaried strongly with soil and tissue nutrient status across fertility gradients. It was significantly positively correlated with nutrient allocation traits, including foliar phosphorus and wood nitrogen and phosphorus, among species sampled across soil habitats in western Panama. At the community level, the proportion of woody stems >10 cm DBH with at least one multiple stem increased with plant available soil phosphorus.

Synthesis. These results suggest a novel mechanism by which soil phosphorus availability influences tree recruitment and forest dynamics by facilitating resprouting. Future experiments should seek to understand whether soil fertility mediates resprouting frequency through nutrient supply directly, or via the formation of enhanced wood nutrient reserves.
Foreign Venture Capitalists and Access to Foreign Research: The Case of US Initial Public Offerings
Authors: Chahine Salim , Goergen Marc , Saade Samer
Published: January 2021

We investigate whether foreign venture capital (VC) firms create value above and beyond the value created by domestic VC firms in US initial public offering (IPO) firms. Contributing to an emerging literature on the role and effects of foreign VC firms, we study whether such VC firms enhance innovation by their investee firms. While high levels of innovation are a prerequisite for future value creation, as well as for maintaining the firm's competitive advantage, the extant literature nevertheless suggests that investors struggle with valuing innovation input when firms are about to go public. Ultimately, this results in greater rather than lower IPO underpricing. We argue that foreign VC firms, especially those from countries with high patent activity, increase the innovation levels of their investee firms. In turn, their presence in the VC syndicate signals the greater likelihood of the investee firm successfully turning innovation input (i.e. research and development (R&D) expenditures) into innovation output (i.e. patents), resulting in lower IPO underpricing. Studying a sample of 995 US IPOs conducted during 2000–2016, we find strong and consistent support for the above arguments.
The Guardian and Press Reform: a Wheel Come Full Circle
Authors: Cathcart Brian
Published: January 2021

In the decade 2008–18, between the eruption of the phone hacking scandal and the cancellation of part two of the Leveson Inquiry, the editorial position of The Guardian on press regulation went from indifference to demanding wholesale reform, and then back to indifference and even active opposition to change. Inevitably, this entailed reversals and contradictions, yet these were not acknowledged to the newspaper’s readers, who are left with a misleading impression of continuity. This study, by an academic and journalist who campaigned for regulatory reform throughout this period, aims to shed light on The Guardian’s 360‐degree progression by reference to its editorials and other published statements.
Secondary hypereosinophilic syndrome: an unusual manifestation in a patient with syringotropic mycosis fungoides and human immunodeficiency virus infection
Authors: Reguero‐Del Cura Leandra , Pérez‐Paredes María Genma , Cortés‐Vázquez Miguel Angel , López‐Sundh Ana Elisabet , González‐Vela María Carmen , Gómez‐Fernández Cristina , González‐López Marcos Antonio
Published: January 2021

Syringotropic mycosis fungoides is a very rare variant of cutaneous T‐cell lymphomas characterised by prominent involvement of the eccrine glands. Hypereosinophilic syndrome refers to a rare group of conditions that are associated with persistent eosinophilia with organ involvement. It is classified into idiopathic, primary and secondary (reactive). We report herein an unusual case of hypereosinophilic syndrome with great impact on morbidity, which developed in a patient with human immunodeficiency virus infection and long‐time misdiagnosed syringotropic mycosis fungoides.