bluuebunny/crossref_metadata_2025 huggingface dataset:
Anatomic and Magnetic Resonance Imaging-Based Correction of Upper-Eyelid Depression and Blepharoptosis in Senile Patients
Authors: Li Pengcheng , Li Kongying , Li Silei , Wang Yongqian
Published: March 2023

In senile patients with sunken superior sulcus, involutional ptosis, and higher eyelid crease, a single operation to correct depression or ptosis cannot achieve good results. We demonstrated the anatomy of periorbital septum fibers, which may contribute to the levator muscle’s volume depletion and dynamic power transmission disorder, and described a procedure for correcting upper-eyelid depression and blepharoptosis in senile patients. The fibrous webs in these patients connected the posterior aspect of the orbicularis and the orbital septum and extended to the orbital fat and levator aponeurosis. These fibers were dissected to release the periorbital septal fibers, and the orbital septal fat flap was transferred to the depressed region. Advancement or plication of the levator aponeurosis was performed in patients with uncorrected blepharoptosis after the procedures described above. The technique was applied to 13 Chinese patients (25 eyes) between May 2021 and April 2022. Postoperative magnetic resonance imaging revealed that the preaponeurotic fat was displaced forward and down to the upper margin of the tarsus, and the curvature of the upper-eyelid depression was significantly improved. Moreover, the superior sulcus deformity improved, the ptosis was corrected, and the uppermost crease decreased in all patients. No recurrence of ptosis or abnormal adhesion was observed. We believe this is the first study using magnetic resonance imaging to evaluate eyelid anatomy and the effects of surgery in this patient group. Releasing periorbital septum fibers is crucial for correcting a portion of the sunken eyelid and ptosis in Asians.
Tapentadol for the management of cancer pain in adults: an update
Authors: Boland Jason W.
Published: March 2023

Purpose of review

Tapentadol is the first of a new class of analgesics, having synergistic µ-opioid receptor agonist and noradrenaline reuptake inhibitory actions. It has been widely researched in many areas of pain, often in noninferiority studies against potent opioids. This review describes all randomized and recent nonrandomized studies of tapentadol in adults with cancer pain.

Recent findings

Tapentadol has been shown to be at least as effective as morphine and oxycodone in five randomized (two of which were multicenter and double-blind) and a range of nonrandomized trials, although caution is needed when interpreting these results. It is effective in both opioid-naive patients and those already taking opioids. By having a lower µ-opioid receptor binding affinity, it has fewer opioid-related toxicities such as constipation and nausea. A recent randomized trial comparing tapentadol to tapentadol plus duloxetine in patients with chemotherapy-induced peripheral neuropathy shows similar improvement in both groups in a range of pain relieving and quality of life measures, with similar adverse effects.

Tapentadol has been shown in a range of studies to be an effective analgesic and thus should be considered as an alternative to morphine and oxycodone, especially when opioid toxicities are an issue.
Parameters, architecture and emergent properties of the
Pseudomonas aeruginosa
LasI/LasR quorum-sensing circuit
Authors: Schuster Martin , Li Christina , Smith Parker , Kuttler Christina
Published: March 2023

Quorum sensing is a widespread process in bacteria that controls collective behaviours in response to cell density. Populations of cells coordinate gene expression through the perception of self-produced chemical signals. Although this process is well-characterized genetically and biochemically, quantitative information about network properties, including induction dynamics and steady-state behaviour, is scarce. Here we integrate experiments with mathematical modelling to quantitatively analyse the LasI/LasR quorum sensing pathway in the opportunistic pathogen
Pseudomonas aeruginosa
. We determine key kinetic parameters of the pathway and, using the parametrized model, show that quorum sensing behaves as a bistable hysteretic switch, with stable on and off states. We investigate the significance of feedback architecture and find that positive feedback on signal production is critical for induction dynamics and bistability, whereas positive feedback on receptor expression and negative feedback on signal production play a minor role. Taken together, our data-based modelling approach reveals fundamental and emergent properties of a bacterial quorum sensing circuit, and provides evidence that native quorum sensing can indeed function as the gene expression switch it is commonly perceived to be.
Excess labile carbon promotes diazotroph abundance in heat-stressed octocorals
Authors: Xiang Nan , Meyer Achim , Pogoreutz Claudia , Rädecker Nils , Voolstra Christian R. , Wild Christian , Gärdes Astrid
Published: March 2023

Nitrogen limitation is the foundation of stable coral-algal symbioses. Diazotrophs, prokaryotes capable of fixing N
2
into ammonia, support the productivity of corals in oligotrophic waters, but could contribute to the destabilization of holobiont functioning when overstimulated. Recent studies on reef-building corals have shown that labile dissolved organic carbon (DOC) enrichment or heat stress increases diazotroph abundance and activity, thereby increasing nitrogen availability and destabilizing the coral-algal symbiosis. However, the (a)biotic drivers of diazotrophs in octocorals are still poorly understood. We investigated diazotroph abundance (via relative quantification of
nifH
gene copy numbers) in two symbiotic octocorals, the more mixotrophic soft coral
Xenia umbellata
and the more autotrophic gorgonian
Pinnigorgia flava,
under (i) labile DOC enrichment for 21 days, followed by (ii) combined labile DOC enrichment and heat stress for 24 days. Without heat stress, relative diazotroph abundances in
X. umbellata
and
P. flava
were unaffected by DOC enrichment. During heat stress, DOC enrichment (20 and 40 mg glucose l
−1
) increased the relative abundances of diazotrophs by sixfold in
X. umbellata
and fourfold in
P. flava
, compared with their counterparts without excess DOC. Our data suggest that labile DOC enrichment and concomitant heat stress could disrupt the nitrogen limitation in octocorals by stimulating diazotroph proliferation. Ultimately, the disruption of nitrogen cycling may further compromise octocoral fitness by destabilizing symbiotic nutrient cycling. Therefore, improving local wastewater facilities to reduce labile DOC input into vulnerable coastal ecosystems may help octocorals cope with ocean warming.
Correlated energy from radial density–energy relations
Authors: Baskerville Adam L. , Gray Conor , Cox Hazel
Published: March 2023

Here, we demonstrate that the radial distribution function can be mapped into a radial density–energy space and the relationship between the radial density and radial energy is linear for the ground and excited states of helium-like systems; the gradient of the resulting straight line delivers the energy of the state considered. To utilize this finding, a simple analytical expression for the total energy in terms of the density at the most probable nucleus–electron distance of the systems considered is derived using a fitting procedure.
How predictable are mass extinction events?
Authors: Foster William J. , Allen Bethany J. , Kitzmann Niklas H. , Münchmeyer Jannes , Rettelbach Tabea , Witts James D. , Whittle Rowan J. , Larina Ekaterina , Clapham Matthew E. , Dunhill Alexander M.
Published: March 2023

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to ‘predict’ the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.
Widespread sex ratio polymorphism inCaenorhabditisnematodes
Authors: Huang Yun , Lo Yun-Hua , Hsu Jung-Chen , Le Tho Son , Yang Fang-Jung , Chang Tiffany , Braendle Christian , Wang John
Published: March 2023

Although equal sex ratio is ubiquitous and represents an equilibrium in evolutionary theory, biased sex ratios are predicted for certain local conditions. Cases of sex ratio bias have been mostly reported for single species, but little is known about its evolution above the species level. Here, we surveyed progeny sex ratios in 23 species of the nematode genusCaenorhabditis,including 19 for which we tested multiple strains.For the species with multiple strains, five species had female-biased and two had non-biased sex ratios in all strains, respectively. The other 12 species showed polymorphic sex ratios across strains. Female-biased sex ratios could be due to sperm competition whereby X-bearing sperm outcompete nullo-X sperm during fertilization. In this model, when sperm are limited allowing all sperm to be used, sex ratios are expected to be equal. However, in assays limiting mating to a few hours, most strains showed similarly biased sex ratios compared with unlimited mating experiments, except that oneC. beceistrain showed significantly reduced female bias compared with unlimited mating. Our study shows frequent polymorphism in sex ratios withinCaenorhabditisspecies and that sperm competition alone cannot explain the sex ratio bias.
Detection of dairy products from multiple taxa in Late Neolithic pottery from Poland: an integrated biomolecular approach
Authors: Evans Miranda , Lundy Jasmine , Lucquin Alexandre , Hagan Richard , Kowalski Łukasz , Wilczyńki Jarosław , Bickle Penny , Adamczak Kamil , Craig Oliver E. , Robson Harry K. , Hendy Jessica
Published: March 2023

The detection of dairy processing is pivotal to our understanding of ancient subsistence strategies. This culinary process is linked to key arguments surrounding the evolution of lactase persistence in prehistory. Despite extensive evidence indicating the presence of dairy products in ceramics in the European Neolithic, questions remain about the nature and extent of milk (and lactose) processing and consumption. In order to investigate past patterns of dairy processing, here we analyse ancient proteins identified from Late Neolithic Funnel Beaker ceramics, scrutinizing the principle that curd and whey proteins partition during the production of dairy foods from milk. Our results indicate the presence of casein-rich dairy products in these vessels suggesting the creation of curd-enriched products from raw milk. Moreover, this analysis reveals the use of multiple species for their dairy products in the Late Neolithic, adding to a growing body of evidence for the period. Alongside palaeoproteomic analysis, we applied well-established lipid residue analysis. Differential interpretations between these two approaches show that palaeoproteomics is especially useful where the effects from isotope mixing may underestimate the frequency of dairy products in archaeological ceramics, highlighting the potential utility of a multi-stranded approach to understand life histories of vessel use.
Fermentation characteristics of yakju containing
different amounts of steam-cooked Jerusalem artichoke (Helianthus
tuberosus L.)
Authors: Choi Jun-Su , Choi Kyu-Taek , Kim Chan-Woo , Park Heui-Dong , Lee Sae-Byuk
Published: March 2023

Jerusalem artichoke (JA, Helianthus tuberosus L.) has a great
potential to enhance the quality of yakju due to the plentiful
inulin content which is functional and indigestible carbohydrate in human. In
this study, the optimal preparation conditions such as the added amount and
steam treatment of JA were investigated to improve the quality of
yakju. As the amount of JA added to yakju
increased, alcohol production decreased, whereas fermentation was performed well
when the steam-cooked JA was added to yakju. The pH and total
acidity of yakju decreased and increased, respectively, when
the amount of JA added to yakju increased, whereas pH and total
acidity of yakju increased and decreased, respectively, when
the steam-cooked JA was added to yakju. The free sugar and
organic acid contents of yakju increased and decreased,
respectively, when the amount of JA added to yakju increased,
whereas those of yakju decreased when the steam-cooked JA was
added to Yakju. Amino acid content of JA decreased as the
amount of JA added to yakju increased and that of JA
significantly decreased when the steam-cooked JA was added to
yakju. In the sensory evaluation analysis, the addition of
10% unsteam-cooked JA to yakju was the best when
considering sweetness, flavor, sourness, and overall preference of
yakju supplemented with JA. Consequently, utilizing JA to
yakju may contribute to the improvement of the quality of
yakju.
Method validation for quantitative analyzing aflatoxin productivity
in Aspergillus sp. isolated from soybean paste
Authors: Yoo SeongEui , Jeong WooSoo , Yeo Soo-Hwan , Kim So-Young
Published: March 2023

Non-aflatoxigenic Aspergillus oryzae and aflatoxigenic
A. flavus cannot be clearly identified by partial
sequencing of the internal transcribed spacer (ITS) and 18S ribosomal
ribonucleic acid (18S rRNA) regions. This study aimed to compare the accuracy
among three aflatoxin detection methods using ultra-performance liquid
chromatography (UPLC), high-performance liquid chromatography (HPLC), and an
enzyme-linked immunosorbent assay (ELISA) kit and to select the
non-aflatoxigenic Aspergillus sp. isolated from soybean paste.
All analytical methods were suitable according to the international standards of
Codex Alimentarius FAO-WHO (CODEX) or the Ministry of Food and Drug Safety
(MFDS). UPLC exhibited the best of limit of detection (LOD) and limit of
quantification (LOQ). Based on UPLC, HPLC, and the ELISA kit assay, the P5 and
P7 strains isolated from soybean paste had 1,663.49, 1,468.12, and ⟩20
μg/kg and 1,470.08, 1,056.73, and ⟩20
μg/kg, respectively, detected and re-identified as
A. flavus. In contrast, the P3 and P4 strains (A.
oryzae), which were detected below the MFDS standards in all
assays, were confirmed as non-aflatoxigenic fungi. Among the methods evaluated
for quantitative analysis of aflatoxin, UPLC and HPLC are superior in terms of
accuracy, and the ELISA kit rapidly detects low concentrations of aflatoxin.
Furthermore, this study demonstrates that any Aspergillus sp.
isolated for use as a fermentation starter should be analyzed for potential
aflatoxin production using UPLC and HPLC for accurate quantitative analysis or
ELISA for the rapid detection of low-level concentrations of aflatoxin.
Informing individualized multi-scale neural signatures of clozapine response in patients with treatment-refractory schizophrenia
Authors: Ji Jie Lisa , Lencz Todd , Gallego Juan , Neufeld Nicholas , Voineskos Aristotle , Malhotra Anil , Anticevic Alan
Published: March 2023

Clozapine is currently the only antipsychotic with demonstrated efficacy in treatment-refractory schizophrenia (TRS). However, response to clozapine differs widely between TRS patients, and there are no available clinical or neural predictive indicators that could be used to increase or accelerate the use of clozapine in patients who stand to benefit. Furthermore, it remains unclear how the neuropharmacology of clozapine contributes to its therapeutic effects. Identifying the mechanisms underlying clozapine’s therapeutic effects across domains of symptomatology could be crucial for development of new optimized therapies for TRS.

Here, we present results from a prospective neuroimaging study that quantitatively related heterogeneous patterns of clinical clozapine response to neural functional connectivity at baseline. We show that we can reliably capture specific dimensions of clozapine clinical response by quantifying the full variation across item-level clinical scales, and that these dimensions can be mapped to neural features that are sensitive to clozapine-induced symptom change. Thus, these features may act as “failure modes” that can provide an early indication of treatment (non-)responsiveness. Lastly, we related the response-relevant neural maps to spatial expression profiles of genes coding for receptors implicated in clozapine’s pharmacology, demonstrating that distinct dimensions of clozapine symptom-informed neural features may be associated with specific receptor targets. Collectively, this study informs prognostic neuro-behavioral measures for clozapine as a more optimal treatment for selected patients with TRS. We provide support for the identification of neuro-behavioral targets linked to pharmacological efficacy that can be further developed to inform optimal early treatment decisions in schizophrenia.
Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats
Authors: Steinfeldt Jakob , Wild Benjamin , Buergel Thore , Pietzner Maik , Upmeier zu Belzen Julius , Vauvelle Andre , Hegselmann Stefan , Denaxas Spiros , Hemingway Harry , Langenberg Claudia , Landmesser Ulf , Deanfield John , Eils Roland
Published: March 2023

The COVID-19 pandemic exposed, with few exceptions, a global deficiency in delivering systematic, data-driven guidance to protect citizens and coordinate vaccination programs. At the same time, medical histories are routinely recorded in most healthcare systems and are instantly available for risk assessment. Here, we demonstrate the utility of medical history in determining the risk for 1,883 diseases across clinical specialties and facilitating the rapid response to emerging health threats at the example of COVID-19. We developed a neural network to learn disease-specific risk states from routinely collected health records of 502,460 UK Biobank participants, demonstrating risk stratification for nearly all conditions, and validated this model on 229,830 individuals from the All of US cohort. When integrated into Cox Proportional Hazard Models, we observed significant discriminative improvements over basic demographic predictors for 1,774 (94.3%). After transferring the unmodified risk models to the All of US cohort, the discriminate improvements were replicated for 1,347 (89.8%) of 1,500 investigated endpoints, demonstrating model generalizability across healthcare systems and historically underrepresented groups. We then show that these risk states can be used to identify individuals vulnerable to severe COVID-19 and mortality. Our study demonstrates the currently underused potential of medical history to rapidly respond to emerging health threats by systematically estimating risk for thousands of diseases at once at minimal cost.
Human immunoglobulin gene allelic variation impacts germline-targeting vaccine priming
Authors: deCamp Allan C. , Corcoran Martin M. , Fulp William J. , Willis Jordan R. , Cottrell Christopher A. , Bader Daniel L.V. , Kalyuzhniy Oleksandr , Leggat David J. , Cohen Kristen W. , Hyrien Ollivier , Menis Sergey , Finak Greg , Ballweber-Fleming Lamar , Srikanth Abhinaya , Plyler Jason R. , Rahaman Farhad , Lombardo Angela , Philiponis Vincent , Whaley Rachael E. , Seese Aaron , Brand Joshua , Ruppel Alexis M. , Hoyland Wesley , Mahoney Celia R. , Cagigi Alberto , Taylor Alison , Brown David M. , Ambrozak David R. , Sincomb Troy , Mullen Tina-Marie , Maenza Janine , Kolokythas Orpheus , Khati Nadia , Bethony Jeffrey , Roederer Mario , Diemert David , Koup Richard A. , Laufer Dagna S. , McElrath Juliana M. , McDermott Adrian B. , Hedestam Gunilla B. Karlsson , Schief William R.
Published: March 2023

Vaccine priming immunogens that activate germline precursors for broadly neutralizing antibodies (bnAbs) have promise for development of precision vaccines against major human pathogens. In a clinical trial of the eOD-GT8 60mer germline-targeting immunogen, higher frequencies of vaccine-induced VRC01-class bnAb-precursor B cells were observed in the high dose compared to the low dose group. Through immunoglobulin heavy chain variable (IGHV) genotyping, statistical modeling, quantification of IGHV1-2 allele usage and B cell frequencies in the naive repertoire for each trial participant, and antibody affinity analyses, we found that the difference between dose groups in VRC01-class response frequency was best explained by IGHV1-2 genotype rather than dose and was most likely due to differences in IGHV1-2 B cell frequencies for different genotypes. The results demonstrate the need to define population-level immunoglobulin allelic variations when designing germline-targeting immunogens and evaluating them in clinical trials.

One-Sentence Summary

Human genetic variation can modulate the strength of vaccine-induced broadly neutralizing antibody precursor B cell responses.
Live-trapping of rodents in urban green spaces across Los Angeles
Authors: Friscia Anthony R. , Helman Sarah , Maloney Molly , Molina-Echavarria Alexandra K. , Nugen Sarah , Punjabi Nihal , Tweedt Isobel , Lynch Jessica W.
Published: March 2023

Urban green spaces have the potential to function as multi-benefit spaces, for both human enjoyment and sustaining native wildlife populations. In our study, we trapped for small nocturnal mammals across a series of Los Angeles green spaces. Our results show that native rodents are only present in habitats that support native vegetation; in particular we highlight the native rodent biodiversity on Sage Hill, a coastal sage scrub remnant on the UCLA campus. Other urban parks that are composed of non-native grasses and non-native shrubbery yielded only invasive species of rodents, including Brown Rats (Rattus norvegicus) and House Mice (Mus musculus). Our study points to the ability of renovated green space in Los Angeles to support native fauna. In addition, our study demonstrates some of the difficulties in doing trapping studies in heavily urbanized environments.
Metabolic memory of Δ9-tetrahydrocannabinol exposure in pluripotent stem cells and primordial germ cells-like cells
Authors: Verdikt Roxane , Armstrong Abigail A. , Cheng Jenny , Hwang Young Sun , Clark Amander T. , Yang Xia , Allard Patrick
Published: March 2023

Cannabis, the most consumed illicit psychoactive drug in the world, is increasingly used by pregnant women. However, while cannabinoid receptors are expressed in the early embryo, the impact of phytocannabinoids exposure on early embryonic processes is lacking. Here, we leverage a stepwise in vitro differentiation system that captures early embryonic developmental cascade to investigate the impact of exposure to the most abundant phytocannabinoid, Δ9-tetrahydrocannabinol (Δ9-THC). We demonstrate that Δ9-THC increases the proliferation of naïve mouse embryonic stem cells (ESCs) but not of their primed counterpart. Surprisingly, this increased proliferation, dependent on the CB1 receptor binding, is only associated with moderate transcriptomic changes. Instead, Δ9-THC capitalizes on ESCs’ metabolic bivalence by increasing their glycolytic rates and anabolic capabilities. A memory of this metabolic rewiring is retained throughout differentiation to Primordial Germ Cell-Like Cells in the absence of direct exposure and is associated with an alteration of their transcriptional profile. These results represent the first in-depth molecular characterization of the impact of Δ9-THC exposure on early stages of germline development.
Successful Modulation of Temporoparietal Junction Activity and Stimulus-Driven Attention by fNIRS-based Neurofeedback – a Randomized Controlled Proof-of-Concept Study
Authors: Kohl Simon H. , Melies Pia , Uttecht Johannes , Lührs Michael , Bell Laura , Mehler David M. A. , Soekadar Surjo R. , Viswanathan Shivakumar , Konrad Kerstin
Published: March 2023

The right temporoparietal junction (rTPJ) is a core hub in neural networks associated with reorienting of attention and social cognition. However, it remains unknown whether participants can learn to actively modulate their rTPJ activity via neurofeedback. Here, we explored the feasibility of functional near-infrared spectroscopy (fNIRS)-based neurofeedback in modulating rTPJ activity and its effect on rTPJ functions such as reorienting of attention and visual perspective taking. In a bidirectional regulation control group design, 50 healthy participants were either reinforced to up- or downregulate rTPJ activation over four days of training.

Both groups showed an increase in rTPJ activity right from the beginning of the trainingbut only the upregulation group maintained this effect, while the downregulation group showed a decline from the initial rTPJ activation. This suggests a learning effect in the downregulation exclusively, making it challenging to draw definitive conclusions about the effectiveness of rTPJ upregulation training. However, we observed group-specific effects on the behavioral level. We found a significant group x time interaction effect in the performance of the reorienting of attention task and group-specific changes, with decreased reaction times (RTs) in the upregulation group and increased RTs in the downregulation group across all conditions after the neurofeedback training. Those with low baseline performance showed greater improvements. In the perspective-taking task, however, only time effects were observed that were non-group-specific.These findings demonstrate that fNIRS-based neurofeedback is a feasible method to modulate rTPJ functions with preliminary evidence of neurophysiologically specific effects, thus paving the way for future applications of non-invasive rTPJ modulation in neuropsychiatric disorders.

Graphical abstract

Highlights

the right temporoparietal junction (rTPJ) as a core hub for attentive and socio-cognitive functions is a promising target for neuromodulatory interventions

first single-blinded, randomized controlled study demonstrates feasibility and effectiveness of the fNIRS-based neurofeedback training of the rTPJ in healthy adults

subjects are able to regulate the rTPJ with different learning characteristics

first evidence of a neurophysiologically specific effect on stimulus-driven attention

findings have important implications for clinical translation of neurofeedback interventions targeting the rTPJ
Lactiplantibacillus plantarumuses ecologically relevant, exogenous quinones for extracellular electron transfer
Authors: Stevens Eric T. , Van Beeck Wannes , Blackburn Benjamin , Tejedor-Sanz Sara , Rasmussen Alycia R. M. , Mevers Emily , Ajo-Franklin Caroline M. , Marco Maria L.
Published: March 2023

Extracellular electron transfer (EET) is a metabolic process that frequently uses quinones to couple intracellular redox reactions with extracellular electron acceptors. The physiological relevance of this metabolism for microorganisms that are capable of EET, but unable to synthesize their own quinones, remains to be determined. To address this question, we investigated quinone utilization byLactiplantibacillus plantarum,a microorganism required for food fermentations, performs EET, and is also a quinone auxotroph. L. plantarumselectively used 1,4-dihydroxy-2-naphthoic acid (DHNA), 2-amino-3-carboxy-1,4-naphthoquinone (ACNQ), 1,4-naphthoquinone, and menadione for EET reduction of insoluble iron (ferrihydrite). However, those quinones used for EET also inhibitedL. plantarumgrowth in non-aerated conditions. Transcriptomic analysis showed that DHNA induced oxidative stress inL. plantarumand this was alleviated by the inclusion of an electron acceptor, soluble ferric ammonium citrate (FeAC), in the laboratory culture medium. The presence of DHNA and FeAC during growth also inducedL. plantarumEET metabolism, although activity was still dependent on the presence of exogenous electron shuttles. To determine whether quinone-producing bacteria frequently found together withL. plantarumin food fermentations could be a source of those electron shuttles,L. plantarumEET was measured after incubation withLactococcus lactisandLeuconostoc mesenteroides.Quinone-producingL. lactis,but not a quinone-deficientL. lactisΔmenCmutant, increasedL. plantarumferrihydrite reduction and medium acidification through an EET-dependent mechanism.L. plantarumEET was also stimulated byL. mesenteroides, and this resulted in greater environmental acidification and transient increases inL. plantarumgrowth. Overall, our findings revealed thatL. plantarumovercomes the toxic effects of exogenous quinones to use those compounds, including those made by related bacteria, for EET-conferred, ecological advantages during the early stages of food fermentations.
Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG
Authors: Tielemans Birger , Llambrich Sergi , Seldeslachts Laura , Cremer Jonathan , Tsui Hung Chang , Jonckheere Anne-Charlotte , Marain Fopke , Riedel Mirko , Wouters Jens , Herzen Julia , Leszczyński Bartosz , Verbeken Erik , Vanoirbeek Jeroen , Velde Greetje Vande
Published: March 2023

In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. Although these clinical comorbidities are well described, no preclinical models for DS are fully characterized for cardiopulmonary alterations, preventing research to understanding the development and pharmacological modulation of lungs, heart and immune system. Our objective is to characterize the cardiopulmonary and immunological phenotype in Ts65Dn mice and investigate the modulatory effects green tea extract enriched in epigallocatechin 3 gallate (GTE-EGCG). GTE-EGCG administration started at embryonic day 9 and was discontinued at postnatal day (PD) 180. Newborns were longitudinally monitored until PD210 using micro-computed tomography. At endpoint, we characterized the structural, functional and immunological alterations and persistent effects of GTE-EGCG administration. This study revealed normal lung development in the Ts65Dn mice and highlighted RV hypertrophy and immunological alterations. GTE-EGCG administration resulted in genotype-specific and genotype-independent alterations resulting in lung immaturation and airway hyperreactivity. Our results highlight the cardiovascular and immunological phenotype of Ts65Dn mice and potential use for safety studies of therapeutic agents in a DS-specific context.

Summary statement

This study longitudinally follows respiratory and cardiac alterations in the Ts65Dn mouse model and describes the impact of prenatal EGCG modulation on the euploid and trisomic phenotype
Behavioral and neuroimaging correlates of attentional biases to angry faces in individuals in remission from depression: a population-derived study
Authors: Nagrodzki Jakub , Passamonti Luca , Schweizer Suzanne , Stretton Jason , Knights Ethan , Henson Richard ,   Cam-CAN, Wolpe Noham
Published: March 2023

Background

Depressed individuals show attentional biases in the processing of emotional stimuli, such as negative face expressions. Some of these biases persist in previously depressed individuals, but their mechanisms remain largely unknown.

Methods

A population-derived cohort (n= 134, 68 females; 21 - 92 years) was recruited by Cam-CAN. Functional MRI was acquired during a gender discrimination task, which used angry and neutral faces. Drift diffusion modelling (DDM) was used to investigate the latent components of the decision process, focusing on the effect of emotional valence. DDM parameters were correlated with activity in brain regions.

Results

14% of participants reported a history of depression in remission. The best fitting DDM specified a different drift rate for angry and neutral faces. A slower drift rate for angry faces predicted depression in remission (OR 0.092,p= 0.048). This effect persisted after accounting for current depression symptoms and drift rate for neutral faces. Participants with a slower drift rate for angry faces demonstrated increased activations in the bilateral insula, bilateral inferior frontal gyrus and bilateral parietal cortex when viewing angry relative to neutral faces.

Conclusions

Our results suggest a persistent attentional bias in the processing of angry faces in individuals with depression in remission, over and above their current depressive symptoms. The imaging findings suggest that the slowing is associated with changes in areas involved in emotional regulation and evidence accumulation. Attentional biases in the processing of emotional information may reflect a trait, rather than state, in individuals with depression.
Delayed postglacial colonization ofBetulain Iceland and the circum North Atlantic
Authors: Harning David J. , Sacco Samuel , Anamthawat-Jónsson Kesara , Ardenghi Nicolò , Thordarson Thor , Raberg Jonathan H. , Sepúlveda Julio , Geirsdóttir Áslaug , Shapiro Beth , Miller Gifford H.
Published: March 2023

As the Arctic continues to warm, woody shrubs are expected to expand northward. This process, known as “shrubification”, has important implications for regional biodiversity, food web structure, and high-latitude temperature amplification. While the future rate of shrubification remains poorly constrained, past records of plant immigration to newly deglaciated landscapes in the Arctic may serve as useful analogues. We provide one new postglacial Holocene sedimentary ancient DNA (sedaDNA) record of vascular plants from Iceland and place a second Iceland postglacialsedaDNA record on an improved geochronology; both show Salicaceae present shortly after deglaciation whereas Betulaceae first appears more than 1000 years later. We find a similar pattern of delayed Betulaceae colonization in eight previously published postglacial sedaDNA records from across the glaciated circum North Atlantic. In nearly all cases, we find that Salicaceae colonizes earlier than Betulaceae and that Betulaceae colonization is increasingly delayed for locations farther from glacial-age woody plant refugia. These trends in Salicaceae and Betulaceae colonization are consistent with the plant families’ environmental tolerances, species diversity, reproductive strategies, seed sizes, and soil preferences. As these reconstructions capture the efficiency of postglacial vascular plant migration during a past period of high-latitude warming, a similarly slow response of some woody shrubs to current warming in glaciated regions, and possibly non-glaciated tundra, may delay Arctic shrubification and future changes in the structure of tundra ecosystems and temperature amplification.
Prostaglandin E2controls the metabolic adaptation of T cells to the intestinal microenvironment
Authors: Villa Matteo , Sanin David E. , Apostolova Petya , Corrado Mauro , Kabat Agnieszka M. , Cristinzio Carmine , Regina Annamaria , Carrizo Gustavo E. , Rana Nisha , Stanczak Michal A. , Baixauli Francesc , Grzes Katarzyna M. , Cupovic Jovana , Solagna Francesca , Hackl Alexandra , Globig Anna-Maria , Hässler Fabian , Puleston Daniel J. , Kelly Beth , Cabezas-Wallscheid Nina , Hasselblatt Peter , Bengsch Bertram , Zeiser Robert , Sagar  , Buescher Joerg M. , Pearce Edward J , Pearce Erika L.
Published: March 2023

Immune cells must adapt to different environments during the course of an immune response. We studied the adaptation of CD8+T cells to the intestinal microenvironment and how this process shapes their residency in the gut. CD8+T cells progressively remodel their transcriptome and surface phenotype as they acquire gut residency, and downregulate expression of mitochondrial genes. Human and mouse gut-resident CD8+T cells have reduced mitochondrial mass, but maintain a viable energy balance to sustain their function. We found that the intestinal microenvironment is rich in prostaglandin E2(PGE2), which drives mitochondrial depolarization in CD8+T cells. Consequently, these cells engage autophagy to clear depolarized mitochondria, and enhance glutathione synthesis to scavenge reactive oxygen species (ROS) that result from mitochondrial depolarization. Impairing PGE2sensing promotes CD8+T cell accumulation in the gut, while tampering with autophagy and glutathione negatively impacts the T cell population. Thus, a PGE2-autophagy-glutathione axis defines the metabolic adaptation of CD8+T cells to the intestinal microenvironment, to ultimately influence the T cell pool.
Fast Approximate IsoRank for Scalable Global Alignment of Biological Networks
Authors: Devkota Kapil , Blumer Anselm , Cowen Lenore , Hu Xiaozhe
Published: March 2023

A well-studied approximate version of the graph matching problem is directly relevant for the study of protein-protein interaction networks. Called by the computational biology community Global Network Alignment, the two networks to be matched are derived from the protein-protein interaction (PPI) networks from organisms of two different species. If these two species evolved recently from a common ancestor, we can view the two PPI networks as a single network that evolved over time. It is the two versions of this network that we want to align using approximate graph matching. The first spectral method for the PPI global alignment problem proposed by the biological community was the IsoRank method of Singh et al. This method for global biological network alignment is still used today. However, with the advent of many more experiments, the size of the networks available to match has grown considerably, making running IsoRank unfeasible on these networks without access to state of the art computational resources. In this paper, we develop a new IsoRank approximation, which exploits the mathematical properties of IsoRank’s linear system to solve the problem in quadratic time with respect to the maximum size of the two PPI networks. We further propose a computationally cheaper refinement to this initial approximation so that the updated result is even closer to the original IsoRank formulation. In experiments on synthetic and real PPI networks, we find that the results of our approximate IsoRank are not only nearly as accurate as the original IsoRank results but are also much faster, which makes the global alignment of large-scale biological networks feasible and scalable.
Plant diversity stabilizes soil temperature
Authors: Huang Yuanyuan , Stein Gideon , Kolle Olaf , Kübler Karl , Schulze Ernst-Detlef , Dong Hui , Eichenberg David , Gleixner Gerd , Hildebrandt Anke , Lange Markus , Roscher Christiane , Schielzeth Holger , Schmid Bernhard , Weigelt Alexandra , Weisser Wolfgang W. , Shadaydeh Maha , Denzler Joachim , Ebeling Anne , Eisenhauer Nico
Published: March 2023

Extreme weather events are occurring more frequently, and research has shown that plant diversity can help mitigate impacts of climate change by increasing plant productivity and ecosystem stability1,2. Although soil temperature and its stability are key determinants of essential ecosystem processes related to water and nutrient uptake3as well as soil respiration and microbial activity4, no study has yet investigated whether plant diversity can buffer soil temperature fluctuations. Using 18 years of a continuous dataset with a resolution of 1 minute (∼795,312,000 individual measurements) from a large-scale grassland biodiversity experiment, we show that plant diversity buffers soil temperature throughout the year. Plant diversity helped to prevent soil heating in hot weather, and cooling in cold weather. Moreover, this effect of plant diversity increased over the 18-year observation period with the aging of experimental communities and was even stronger under extreme conditions, i.e., on hot days or in dry years. Using structural equation modelling, we found that plant diversity stabilized soil temperature by increasing soil organic carbon concentrations and, to a lesser extent, by increasing the plant leaf area index. We suggest that the diversity-induced stabilization of soil temperature may help to mitigate the negative effects of extreme climatic events such as soil carbon release, thus slow global warming.
Effect of elevated embryonic incubation temperature on the temperature preference of juvenile lake (Coregonus clupeaformis) and round whitefish (Prosopium cylindraceum)
Authors: Harman Adam A. , Mahoney Hannah , Thompson William Andrew , Fuzzen Meghan L.M. , Aggarwhal Bhuvan , Laframboise Lisa , Boreham Douglas R. , Manzon Richard G. , Somers Christopher M. , Wilson Joanna Y.
Published: March 2023

Anthropogenic impacts can lead to increased temperatures in freshwater environments through thermal effluent and climate change. Thermal preference of aquatic organisms can be modulated by abiotic and biotic factors including environmental temperature. Whether increased temperature during embryogenesis can lead to long-term alterations in thermal preference has not been explicitly tested in native freshwater species. Lake (Coregonus clupeaformis) and round (Prosopium cylindraceum) whitefish were incubated at natural and elevated temperatures until hatching, following which, all groups were moved to common garden conditions (15°C) during the post-hatching stage. Temperature preference was determined at 8 (Lake whitefish only) and 12-months of age (both species), using a shuttlebox system. Round whitefish preferred a cooler temperature when incubated at 2°C and 6°C compared to 0.5°C. Lake whitefish had similar temperature preferences regardless of age, weight, and incubation temperature. These results reveal that temperature preference in freshwater fish can be programmed during early development, and that round whitefish may be more sensitive to incubation temperature. This study highlights the effects that small increases in temperature caused by anthropogenic impacts may have on cold-adapted freshwater fish.
Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data
Authors: Dai Rujia , Chu Tianyao , Zhang Ming , Wang Xuan , Jourdon Alexandre , Wu Feinan , Mariani Jessica , Vaccarino Flora M. , Lee Donghoon , Fullard John F. , Hoffman Gabriel E. , Roussos Panos , Wang Yue , Wang Xusheng , Pinto Dalila , Wang Sidney H. , Zhang Chunling ,   PsychENCODE consortium, Chen Chao , Liu Chunyu
Published: March 2023

Sample-wise deconvolution methods have been developed to estimate cell-type proportions and gene expressions in bulk-tissue samples. However, the performance of these methods and their biological applications has not been evaluated, particularly on human brain transcriptomic data. Here, nine deconvolution methods were evaluated with sample-matched data from bulk-tissue RNAseq, single-cell/nuclei (sc/sn) RNAseq, and immunohistochemistry. A total of 1,130,767 nuclei/cells from 149 adult postmortem brains and 72 organoid samples were used. The results showed the best performance of dtangle for estimating cell proportions and bMIND for estimating sample-wise cell-type gene expression. For eight brain cell types, 25,273 cell-type eQTLs were identified with deconvoluted expressions (decon-eQTLs). The results showed that decon-eQTLs explained more schizophrenia GWAS heritability than bulk-tissue or single-cell eQTLs alone. Differential gene expression associated with multiple phenotypes were also examined using the deconvoluted data. Our findings, which were replicated in bulk-tissue RNAseq and sc/snRNAseq data, provided new insights into the biological applications of deconvoluted data.
Shared input and recurrency in neural networks for metabolically efficient information transmission
Authors: Barta Tomas , Kostal Lubomir
Published: March 2023

Shared input to a population of neurons induces noise correlations, which decreases the information carried by a population activity. Inhibitory feedback in recurrent neural networks can reduce the noise correlations and thus increase the information carried by the averaged population activity. However, the activity of inhibitory neurons is costly. This inhibitory feedback decreases the gain of the population. Thus, depolarization of its neurons requires stronger excitatory synaptic input, which is associated with higher ATP consumption. Given that the goal of neural populations is to transmit as much information as possible at minimal metabolic costs, it is unclear whether the increased information transmission reliability provided by inhibitory feedback compensates for the additional costs. We analyze this problem in a network of leaky integrate-and-fire neurons receiving correlated input. By maximizing mutual information with metabolic cost constraints, we show that there is an optimal strength of recurrent connections in the network, which maximizes the value of mutual information-per-cost. For higher values of input correlation, the mutual information-per-cost is higher for recurrent networks with inhibitory feedback compared to feedforward networks without any inhibitory neurons. Our results, therefore, show that the optimal synaptic strength of a recurrent network can be inferred from metabolically efficient coding arguments and that decorrelation of the input by inhibitory feedback compensates for the associated increased metabolic costs.