bluuebunny/crossref_metadata_2025 huggingface dataset:
Application of Augmented Reality Navigation in Treatment With Fibrosis Dysplasia
Authors: Lin Li , Han Wenqing , Chai Gang , Xu Haisong
Published: December 2021

Objective:

In order to reduce the possibility of accidental injury to neurovascular and important tissues, this research conduct preoperative design and intraoperative guidance for fibrous dysplasia through augmented reality technology.

Methods:

Five patients with fibrous dysplasia were selected for three-dimensional (3D) Computed Tomography (CT) scan and 3D model was reconstructed. Considering the navigation plan was comprehensively, the guide plate (composed of card groove, connector, and fixator) was designed and 3D printed. Threedimensional software was used to unify the coordinates of the surgical plan and the guide plate, and the relative position was fixed. Then, the virtual and real overlapping registration is completed on the physical model. Pattern recognition technology is used to identify pre-defined markers in the video images before operation. Finally, the registration results are superimposed into the surgical field of vision to guide and remind surgeons.

Results:

In this study, the navigation based on augmented reality technology was used in the surgical treatment of 5 cases patients with fibrous dysplasia. The 3D navigation information was displayed in real time in the operative field. The operation was accurate and the postoperative effect was good.

Conclusions:

This paper introduces an effective visual navigation surgical method in treatment with fibrous dysplasia. The augmented- reality based navigation system achieves individualized precise treatment by displaying 3D navigation directly in the surgical field. It is an effective auxiliary method for future research on craniofacial surgery.
Specialized Proresolving Lipid Meditators Agonistic to Formyl Peptide Receptor Type 2 Attenuate Ischemia-reperfusion Injury in Rat Lung
Authors: Oda Hiromi , Tanaka Satona , Shinohara Masakazu , Morimura Yuki , Yokoyama Yuhei , Kayawake Hidenao , Yamada Yoshito , Yutaka Yojiro , Ohsumi Akihiro , Nakajima Daisuke , Hamaji Masatsugu , Menju Toshi , Date Hiroshi
Published: December 2021

Background.

Lung ischemia-reperfusion injury (IRI) is a form of acute lung injury characterized by nonspecific alveolar damage and lung edema due to robust inflammation. Little is known about the roles of specialized proresolving lipid mediators (SPMs) in lung IRI. Therefore, we aimed to evaluate the dynamic changes in endogenous SPMs during the initiation and resolution of lung IRI and to determine the effects of SPM supplementation on lung IRI.

Methods.

We used a rat left hilar clamp model with 90 min of ischemia, followed by reperfusion. Dynamic changes in endogenous SPMs were evaluated using liquid chromatography-tandem mass spectrometry.

Results.

Endogenous SPMs in the left lung showed a decreasing trend after 1 h of reperfusion. Oxygenation improved between 3 and 7 d following reperfusion; however, the level of endogenous SPMs remained low compared with that in the naïve lung. Among SPM receptors, only formyl peptide receptor type 2 (ALX/FPR2) gene expression in the left lung was increased 3 h after reperfusion, and the inflammatory cells were immunohistochemically positive for ALX/FPR2. Administration of aspirin-triggered (AT) resolvin D1 (AT-RvD1) and AT lipoxin A4 (AT-LXA4), which are agonistic to ALX/FPR2, immediately after reperfusion improved lung function, reduced inflammatory cytokine levels, attenuated lung edema, and decreased neutrophil infiltration 3 h after reperfusion. The effects of AT-RvD1 and AT-LXA4 were not observed after pretreatment with the ALX/FPR2 antagonist.

Conclusions.

The level of intrapulmonary endogenous SPMs decreased during lung IRI process and the administration of AT-RvD1 and AT-LXA4 prevented the exacerbation of lung injury via ALX/FPR2.
Sequence diversity of the Pseudomonas aeruginosa population in loci that undergo microevolution in cystic fibrosis airways
Authors: Fischer Sebastian , Klockgether Jens , Gonzalez Sorribes Marina , Dorda Marie , Wiehlmann Lutz , Tümmler Burkhard
Published: December 2021

Five hundred and thirty-four unrelated

Pseudomonas aeruginosa

isolates from inanimate habitats, patients with cystic fibrosis (CF) and other human infections were sequenced in 19 genes that had been identified previously as the hot spots of genomic within-host evolution in serial isolates from 12 CF lungs. Amplicon sequencing confirmed a significantly higher sequence diversity of the 19 loci in

P. aeruginosa

isolates from CF patients compared to those from other habitats, but this overrepresentation was mainly due to the larger share of synonymous substitutions. Correspondingly, non-synonymous substitutions were either rare (gltT, lepA, ptsP) or benign (nuoL, fleR, pelF) in some loci. Other loci, however, showed an accumulation of non-neutral coding variants. Strains from the CF habitat were often mutated at evolutionarily conserved positions in the elements of stringent response (RelA, SpoT), LPS (PagL), polyamine transport (SpuE, SpuF) and alginate biosynthesis (AlgG, AlgU). The strongest skew towards the CF lung habitat was seen for amino acid sequence variants in AlgG that clustered in the carbohydrate-binding/sugar hydrolysis domain. The master regulators of quorum sensing lasR and rhlR were frequent targets for coding variants in isolates from chronic and acute human infections. Unique variants in lasR showed strong evidence of positive selection indicated by d
N/d
S values of ~4. The pelA gene that encodes a multidomain enzyme involved in both the formation and dispersion of Pel biofilms carried the highest number of single-nucleotide variants among the 19 genes and was the only gene with a higher frequency of missense mutations in

P. aeruginosa

strains from non-CF habitats than in isolates from CF airways. PelA protein variants are widely distributed in the

P. aeruginosa

population. In conclusion, coding variants in a subset of the examined loci are indeed characteristic for the adaptation of

P. aeruginosa

to the CF airways, but for other loci the elevated mutation rate is more indicative of infections in human habitats (lasR, rhlR) or global diversifying selection (pelA).
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1
Authors: Koong Jonathan , Johnson Claire , Rafei Rayane , Hamze Monzer , Myers Garry S. A. , Kenyon Johanna J. , Lopatkin Allison J. , Hamidian Mohammad
Published: December 2021

Acinetobacter baumannii

is an opportunistic pathogen that is difficult to treat due to its resistance to extreme conditions, including desiccation and antibiotics. Most strains causing outbreaks around the world belong to two main global lineages, namely global clones 1 and 2 (GC1 and GC2). Here, we used a combination of Illumina short read and MinION (Oxford Nanopore) long-read sequence data with a hybrid assembly approach to complete the genome sequence of two antibiotic-sensitive GC1 strains, Ex003 and Ax270, recovered in Lebanon from water and a rectal swab of a cat, respectively. Phylogenetic analysis of Ax270 and Ex003 with 186 publicly available GC1 genomes revealed two major clades, including five main lineages (L1–L5), and four single-isolate lineages outside of the two clades. Ax270 and Ex003, along with AB307-0294 and MRSN7213 (both predicted antibiotic-susceptible isolates) represent these individual lineages. Antibiotic resistance islands and transposons interrupting the comM gene remain important features in L1–L5, with L1 associated with the AbaR-type resistance islands, L2 with AbaR4, L3 strains containing either AbaR4 or its variants as well as Tn6022::ISAba42, and L4 and L5 associated with Tn6022 or its variants. Analysis of the capsule (KL) and outer core (OCL) polysaccharide loci further revealed a complex evolutionary history probably involving many recombination events. As more genomes become available, more GC1 lineages continue to emerge. However, genome sequence data from more diverse geographical regions are needed to draw a more accurate population structure of this globally distributed clone.
Stressors, Manifestations and Course of COVID-19 Related Distress Among Nurses and Midwives in Tasmania
Authors: Marsden Kathryn M. , Porter Julie M. , Robertson IK.
Published: December 2021

The deleterious effects relating to the COVID-19 pandemic on the mental health of healthcare workers has now been widely established. Understanding how COVID-19 affects their work and life is complex and multidimensional. This study describes the critical stressors and how they manifest within both the work and larger social environment for nurses and midwives in Tasmania, Australia.

A longitudinal, descriptive survey was designed to explore the trajectory of the psychological health of Tasmanian public sector nurses and midwives during the COIVD-19 pandemic. The survey was distributed at 3 timepoints over a 12-month period and consisted of a battery of psychological tests which included the Patient Health Questionnaire, General Anxiety Disorder, Insomnia Severity Index, and the Impact of Events Scale-Revised, together with free text comments.

The associations between outcome and predictor variables were assessed using mixed effects linear regression and linear mixed model analyses. Free text comments were themed.

High levels of stress and mental exhaustion were attributed to threatened workplace team culture; compromised quality of patient care; the impact on family, home, financial and economic domains; lack of clear communication; issues surrounding personal protective equipment; and female gender. Study data show younger nurses and midwives suffered higher levels of stress and mental exhaustion than older.

This study highlights the need for stable and functional relationships at home and at work for nurses and midwives.

Factors which will help preserve the mental health of nurses and midwives include strong workplace culture with ongoing processes to monitor organisational burnout; building resilience, particularly among younger nurses and midwives; protection of healthcare worker safety; clear communication processes and supporting stable and functional relationships at home. The health service has an imperative to ensure optimum service delivery by safeguarding staff, despite the inevitable health stress imposed by the nature of the work.
A mitochondria-specific mutational signature of aging: increased rate of A>G substitutions on a heavy chain
Authors: Mikhaylova A. G. , Mikhailova A. A. , Ushakova K. , Tretiakov E.O. , Iliushchenko D. , Shamansky V. , Iurchenko A. , Zazhytska M. , Kozenkova E. , Zdobnov E. , Makeev V. , Yurov V. , Tanaka M. , Gostimskaya I. , Fleischmann Z. , Annis S. , Franco M. , Wasko K. , Kunz W.S , Knorre D.A. , Mazunin I. , Nikolaev S. , Fellay J. , Reymond A. , Khrapko K. , Gunbin K. , Popadin K.
Published: December 2021

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria is tightly involved in aerobic energy production, it is expected that mtDNA mutational spectra is affected by the oxidative damage. Assuming that oxidative damage increases with age, we analyze mtDNA mutagenesis of different species. Analysing (i) dozens thousands of somatic mtDNA mutations in samples of different age (ii) 70053 polymorphic synonymous mtDNA substitutions, reconstructed in 424 mammalian species with different generation length and (iii) synonymous nucleotide content of 650 complete mitochondrial genomes of mammalian species we observed that the frequency of AH>GH substitutions (H - heavy chain notation) is twice higher in species with high versus low generation length making their mtDNA more AH poor and GH rich. Considering that AH>GH substitutions are also sensitive to the time spent single stranded (TSSS) during asynchroniuos mtDNA replication we demonstrated that AH>GH substitution rate is a function of both species-specific generation length and position specific TSSS. We propose that AH>GH is a mitochondria-specific signature of oxidative damage associated with both aging and TSSS.
Interactions of SARS-CoV-2 protein E with cell junctions and polarity PDZ-containing proteins
Authors: Zhu Yanlei , Alvarez Flavio , Wolff Nicolas , Mechaly Ariel , Brûlé Sébastien , Neitthoffer Benoit , Etienne-Manneville Sandrine , Haouz Ahmed , Boëda Batiste , Caillet-Saguy Célia
Published: December 2021

The C-terminus of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein E contains a PBM (PDZ binding motif) targeting PDZ (PSD-95/Dlg/ZO-1) domains identical to the PBM of SARS-CoV. The latter is involved in the pathogenicity of the virus. Recently, we identified ten human PDZ-containing proteins showing significant interactions with SARS-CoV-2 protein E PBM. We selected several of them involved in cellular junctions and cell polarity (TJP1, PARD3, MLLT4, LNX2) and MPP5/Pals1 previously shown to interact with SARS-CoV E PBM. Targeting cellular junctions and polarity components is a common strategy by viruses to hijack cell machinery to their advantage. In this study, we showed that these host PDZ domains TJP1, PARD3, MLLT4, LNX2 and MPP5/PALS1 interact in a PBM-dependent manner in vitro and colocalize with the full-length E protein in cellulo, sequestrating the PDZ domains to the Golgi compartment. We solved three crystal structures of complexes between human LNX2, MLLT4 and MPP5 PDZs and SARS-CoV-2 E PBM highlighting its binding preferences for several cellular targets. Finally, we showed different affinities for the PDZ domains with the original SARS-CoV-2 C-terminal sequence containing the PBM and the one of the beta variant that contains a mutation close to the PBM. The acquired mutations in E protein localized near the PBM might have important effects both on the structure and the ion-channel activity of the E protein and on the host machinery targeted by the variants during the infection.
The High Transmission of SARS-CoV-2 Omicron (B.1.1.529) Variant is Not Only Due to Its hACE2 binding: A Free Energy of Perturbation Study
Authors: Fratev Filip
Published: December 2021

The mutations in the spike protein of SARS-CoV-2 Omicron variant (B.1.1.529 lineage) gave rise to questions, but the data on the mechanism of action at the molecular level is limited. In this study, we present the Free energy of perturbation (FEP) data about the RBD-hACE2 binding of this new variant.

We identified two groups of mutations located close to the most contributing substitutions Q498R and Q493R, which altered significantly the RBD-hACE2 interactions. The Q498R, Y505H and G496S mutations, in addition to N501Y, highly increased the binding to hACE2. They enhanced the binding by 98, 14 and 13 folds, respectively, which transforms the S1-RBD to a picomolar binder. However, in contrast to the case in mice the Q493R/K mutations, in a combination with K417N and T478K, dramatically reduced the S1 RBD binding by over 100 folds. The N440K, G446S and T478K substitutions had lesser contribution. Thus, the total effect of these nine mutations located on the interaction surface of RBD-hACE2 turns out to be similar to that observed in the Alpha variant. In a special circumstances it could be further altered by the E484A and S477N mutations and even lower binding capacity is likely to be detected. Finally, we provide a structural basis of the observed changes in the interactions.

These data may explain only partially the observed in South Africa extremely high Omicron spread and is in support to the hypothesis for multiple mechanisms of actions involved in the transmission.

Graphical abstract
Waning antibody levels after vaccination with mRNA BNT162b2 and inactivated CoronaVac COVID-19 vaccines in Hong Kong blood donors
Authors: Kwok Shirley LL , Cheng Samuel MS , Leung Jennifer NS , Leung Kathy , Lee Cheuk-Kwong , Peiris JS Malik , Wu Joseph T
Published: December 2021

Both inactivated vaccine (CoronaVac; Sinovac) and mRNA vaccine (Comirnaty/BNT162b2; Fosun-Pharma/BioNTech) are available in Hong Kong’s COVID-19 Vaccination Programme. We reported waning antibody levels by enzyme-linked immunosorbent assays (ELISA) and surrogate virus neutralization test (sVNT) among 850 fully vaccinated blood donors (i.e., received two doses). The BNT162b2 group’s antibody levels remain over the 50% protection threshold within six months, and the CoronaVac’s group’s median antibody levels begin to fall below the 50% protection threshold two months after vaccination.
Sleep Dependent Changes of Lactate Concentration in Human Brain
Authors: Yildiz Selda , Lim Miranda M. , Sammi Manoj K. , Powers Katherine , Murchison Charles F. , Iliff Jeffrey J. , Rooney William D.
Published: December 2021

Lactate is an important cellular metabolite that is present at high concentrations in the brain, both within cells and in the extracellular space between cells. Small animal studies demonstrated high extracellular concentrations of lactate during wakefulness with reductions during sleep and/or anesthesia with a recent study suggesting the glymphatic activity as the mechanism for the reduction of lactate concentrations. We have recently developed a rigorous non-invasive imaging approach combining simultaneous magnetic resonance spectroscopy (MRS) and polysomnography (PSG) measurements, and here, we present the first in-vivo evaluation of brain lactate levels during sleep-wake cycles in young healthy humans. First, we collected single voxel proton MRS (1H-MRS) data at the posterior cingulate with high temporal resolution (every 7.5 sec), and simultaneously recorded PSG data while temporally registering with 1H-MRS time-series. Second, we evaluated PSG data in 30 s epochs, and classified into four stages Wake (W), Non-REM sleep stage 1 (N1), Non-REM sleep stage 2 (N2), and Non-REM sleep stage 3 (N3). Third, we determined lactate signal intensity from each 7.5-s spectrum, normalized to corresponding water signal, and averaged over 30-s for each PSG epoch. In examinations of nine healthy participants (four females, five males; mean age 24.2 (±2; SD) years; age range: 21-27 years) undergoing up to 3-hour simultaneous MRS/PSG recordings, we observed a group mean reduction of [4.9 ± 4.9] % in N1, [10.4 ± 5.2] % in N2, and [24.0 ± 5.8] % in N3 when compared to W. Our finding is consistent with more than 70 years of invasive lactate measurements from small animal studies. In addition, reduced brain lactate was accompanied by a significant reduction the apparent diffusion coefficient of brain lactate. Taken together, these findings are consistent with the loss of lactate from the extracellular space during sleep while suggesting lactate metabolism is altered and/or lactate clearance via glymphatic exchange is increased during sleep.

Significance Statement

This study describes a non-invasive magnetic resonance spectroscopy/polysomnography technique that allows rigorous measurement of brain metabolite levels together with simultaneous characterization of brain arousal state as either wakeful or one of the several sleep states. The results provide the first in-vivo demonstration of reductions in brain lactate concentration and diffusivity during sleep versus wakefulness in young healthy human brain. These findings are consistent with invasive small-animal studies showing the loss of extracellular lactate during sleep, and support the notion of altered lactate metabolism and/or increased glymphatic activity in sleeping human brain.
A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern
Authors: Tyrkalska Sylwia D. , Martínez-López Alicia , Arroyo Ana B. , Martínez-Morcillo Francisco J. , Candel Sergio , García-Moreno Diana , Mesa-del-Castillo Pablo , Cayuela María L. , Mulero Victoriano
Published: December 2021

The sudden and unexpected appearance of the COVID-19 pandemic turned the whole world upside down in a very short time. One of the main challenges faced has been to understand COVID-19 patient heterogeneity, as a minority develop life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). Using the unique advantages of the zebrafish model we report here the proinflammatory role of Spike (S) proteins from different SARS-CoV-2 variants of concern after injection into the hindbrain ventricle, a cavity filled with cerebrospinal fluid to which immune cells can be easily recruited and that mimics the alveolar environment of the human lung. We found that wild type/Wuhan variant S1 (S1WT) protein promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1γ protein was more proinflammatory and S1δ was less proinflammatory than S1WT and, strikingly, S1β promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome robustly alleviated S1 protein-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and the administration of angiopoietin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.

Highlights

S proteins of SARS-CoV-2 promote hyperinflammation, neutrophilia, monocytosis and hemorrhages in zebrafish.

S protein effects in zebrafish are mediated via the canonical inflammasome and the Ace2/Angiopoietin (1-7) axis.

Delta S1 is less proinflammatory than wild type S1 and fails to induce emergency myelopoiesis in zebrafish.

Naïve and primed human white blood cells are unable to respond to S proteins.
PACAP-PAC1 Receptor Inhibition is Effective in Models of Opioid-Induced Medication Overuse Headache
Authors: Bertels Zachariah , Mangutov Elizaveta , Siegersma Kendra , Tipton Alycia , Pradhan Amynah A
Published: December 2021

Opioids are regularly prescribed for migraine and can result in medication overuse headache and dependence. We recently showed that pituitary adenylate cyclase activating polypeptide (PACAP) is upregulated following opioid administration or in a model of chronic migraine. The goal of this study was to determine if PACAP was a link between opioid use and headache chronification. We tested the effect of PACAP-PAC1 receptor inhibition in novel models of opioid-exacerbated migraine pain and aura; and examined the co-expression between mu opioid receptor (MOR), PAC1, and PACAP in headache-associated brain and peripheral regions.

To model opioid exacerbated migraine pain, mice were injected daily with morphine (10 mg/kg) or vehicle for 11 days. On days 3,5,7,9, and 11 they also received the known human migraine trigger nitroglycerin (0.1 mg/kg) or vehicle. To model opioid exacerbated aura, mice were treated with vehicle or morphine twice daily for 4 days (20 mg/kg on days 1-3, 40 mg/kg on day 4), a well-established paradigm for causing opioid-induced hyperalgesia. On day 5 they underwent cortical spreading depression, a physiological correlate of migraine aura. The effect of the PAC1 inhibitor, M65 (0.1 mg/kg), was tested in these models. Fluorescent in situ hybridization was used to investigate the expression of MOR, PAC1, and PACAP.

Only mice treated with combined morphine and nitroglycerin developed chronic cephalic allodynia (n=18/group). M65 reversed this hypersensitivity (n=9/group). Morphine significantly increased the number of CSD events (n=8-9/group); and M65 decreased this exacerbation by morphine (n=8-12/group). PAC1 and/or PACAP were highly co-expressed with MOR, and varied by region (n=6/group). MOR and PACAP were co-expressed in the trigeminal ganglia, while MOR and PAC1 receptor showed near complete overlap in the trigeminal nucleus caudalis and periaqueductal gray. The cortex showed similar cellular co-expression between MOR-PACAP and MOR-PAC1.

These results show that opioids facilitate the transition to chronic headache through induction of PACAPergic mechanisms. Antibodies or pharmacological agents targeting PACAP or PAC1 receptor may be particularly beneficial for the treatment of opioid-induced medication overuse headache.
“It was brutal. It still is”: A qualitative analysis of the challenges of bereavement during the COVID-19 pandemic reported in two national surveys
Authors: Torrens-Burton Anna , Goss Silvia , Sutton Eileen , Barawi Kali , Longo Mirella , Seddon Kathy , Carduff Emma , Farnell Damian JJ , Nelson Annmarie , Byrne Anthony , Phillips Rhiannon , Selman Lucy E. , Harrop Emily
Published: December 2021

The COVID-19 pandemic has been a devastating, mass bereavement event characterised by sudden unexpected deaths and high levels of disruption to end-of-life, grieving and coping processes, as well as social life more broadly. We analysed qualitative free-text data from two independent UK-wide online surveys to describe in depth the experiences of 881 people bereaved during the Covid-19 pandemic using. We analysed the data in two phases, conducting an inductive thematic analysis and then applying Stroebe and Schut’s Dual Process Model (DPM) (1999; 2010) as an analytic lens to further contextualise and interpret the data. The DPM identifies loss-oriented and restoration-oriented coping processes between which grieving people naturally oscillate. Loss-oriented coping involves coming to terms with the death and lost relationship, while restoration-oriented coping involves adapting to new ways of life. We identified six main themes: troubled deaths (guilt, anger and unanswered questions); mourning, memorialisation and death administration; mass bereavement, the media and the ongoing threat of the pandemic; grieving and coping (alone and with others); work and employment; and support from the health and social care system. Examples of loss-oriented stressors included being unable to visit or say goodbye, the sudden and traumatic nature of many deaths, and restricted funeral and memorialisation practices. Associated reactions were feelings of guilt and anger, and problems accepting the death and starting to grieve. Examples of restoration-oriented stressors and reactions were stressful death-related administration and severely curtailed social networks, support systems and social/recreational activities, which impacted people’s ability to cope. Study results demonstrate the exceptionally difficult sets of experiences associated with pandemic bereavement, and the utility of the DPM for conceptualizing these additional challenges and their impacts on grieving. Our analysis builds and expands on previous use of the DPM (Stroebe and Schut, 2021) in explicating the impact of the pandemic on bereavement. We make recommendations for statutory, private and third sector organisations for improving the experiences of people bereaved during and following this and future pandemics.
Age-specific effects of body size on fracture risk in later life: A lifecourse Mendelian randomization study
Authors: Power Grace M. , Tobias Jon H. , Frayling Timothy M. , Tyrrell Jess , Hartley April , Heron Jon , Smith George Davey , Richardson Tom G.
Published: December 2021

Musculoskeletal conditions, including fractures, can have severe and long-lasting consequences. Higher body mass index in adulthood is widely acknowledged to be protective for most fracture sites, indicated through previous clinical and epidemiological observational research. However, the association between weight and bone health is complex and sources of bias, induced by confounding factors, may have distorted earlier findings. Employing a lifecourse Mendelian randomization (MR) approach by using genetic instruments to separate effects at different life stages, this investigation aims to explore how prepubertal and adult body size independently influence fracture risk in later life.

Using data from a large UK-based prospective cohort, univariable and multivariable MR with inverse variance weighted meta-analysis were conducted to simultaneously estimate the effects of age-specific genetic proxies for body size (n=453,169) on the odds of fracture in later life (n=416,795). A two-step MR framework was additionally applied to elucidate potential mediators. Univariable and multivariable MR indicated strong evidence that higher body size in childhood reduced fracture risk in later life (OR, 95% CI: 0.89, 0.82 to 0.96, P=0.005 and OR, 95% CI: 0.76, 0.69 to 0.85, P=1×10−6, respectively). Conversely, higher body size in adulthood increased fracture risk (OR, 95% CI: 1.08, 1.01 to 1.16, P=0.023 and OR, 95% CI: 1.26, 1.14 to 1.38, P=2×10−6, respectively). Two-step MR analyses suggested that the effect of higher body size in childhood on reduced fracture risk was mediated by its influence on higher estimated bone mineral density (eBMD) in adulthood.

This investigation provides novel evidence that higher body size in childhood has a direct effect on reduced fracture risk in later life through its influence on increased eBMD. Results indicate that higher body size in adulthood is a risk factor for fractures, opposing findings from earlier research. Protective effect estimates previously observed are likely attributed to childhood effects.
Neural dynamics of causal inference in the macaque frontoparietal circuit
Authors: Qi Guangyao , Fang Wen , Li Shenghao , Li Junru , Wang Liping
Published: December 2021

Natural perception relies inherently on inferring causal structure in the environment. However, the neural mechanisms and functional circuits that are essential for representing and updating the hidden causal structure and corresponding sensory representations during multisensory processing are unknown. To address this, monkeys were trained to infer the probability of a potential common source from visual and proprioceptive signals on the basis of their spatial disparity in a virtual reality system. The proprioceptive drift reported by monkeys demonstrated that they combined historical information and current multisensory signals to estimate the hidden common source and subsequently updated both the causal structure and sensory representation. Single-unit recordings in premotor and parietal cortices revealed that neural activity in premotor cortex represents the core computation of causal inference, characterizing the estimation and update of the likelihood of integrating multiple sensory inputs at a trial-by-trial level. In response to signals from premotor cortex, neural activity in parietal cortex also represents the causal structure and further dynamically updates the sensory representation to maintain consistency with the causal inference structure. Thus, our results indicate how premotor cortex integrates historical information and sensory inputs to infer hidden variables and selectively updates sensory representations in parietal cortex to support behavior. This dynamic loop of frontal-parietal interactions in the causal inference framework may provide the neural mechanism to answer long-standing questions regarding how neural circuits represent hidden structures for body-awareness and agency.
TargetGeneReg 2.0: a comprehensive web-atlas for p53, p63, and cell cycle-dependent gene regulation
Authors: Fischer Martin , Riege Konstantin , Schwarz Robert , DeCaprio James A. , Hoffmann Steve
Published: December 2021

In recent years, our web-atlas at www.TargetGeneReg.org has enabled many researchers to uncover new biological insights and to identify novel regulatory mechanisms that affect p53 and the cell cycle – signaling pathways that are frequently dysregulated in diseases like cancer. Here, we provide a substantial upgrade of the database that comprises an extension to include non-coding genes and the transcription factors ΔNp63 and RFX7. TargetGeneReg 2.0 combines gene expression profiling and transcription factor DNA binding data to determine, for each gene, the response to p53, ΔNp63, and cell cycle signaling. It can be used to dissect common, cell type, and treatment-specific effects, identify the most promising candidates, and validate findings. We demonstrate the increased power and more intuitive layout of the resource using realistic examples.
Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation
Authors: Soskic Blagoje , Cano-Gamez Eddie , Smyth Deborah J. , Ambridge Kirsty , Ke Ziying , Bossini-Castillo Lara , Kaplanis Joanna , Ramirez-Navarro Lucia , Nakic Nikolina , Esparza-Gordillo Jorge , Rowan Wendy , Wille David , Tough David F. , Bronson Paola G. , Trynka Gosia
Published: December 2021

During activation, T cells undergo extensive changes in gene expression which shape the properties of cells to exert their effector function. Therefore, understanding the genetic regulation of gene expression during T cell activation provides essential insights into how genetic variants influence the response to infections and immune diseases. We generated a single-cell map of expression quantitative trait loci (eQTL) across a T cell activation time-course. We profiled 655,349 CD4+ naive and memory T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. We identified 38 cell clusters, including stable clusters such as central and effector memory T cells and transient clusters that were only present at individual time points of activation, such as interferon-responding cells. We mapped eQTLs using a T cell activation trajectory and identified 6,407 eQTL genes, of which a third (2,265 genes) were dynamically regulated during T cell activation. We integrated this information with GWAS variants for immune-mediated diseases and observed 127 colocalizations, with significant enrichment in dynamic eQTLs. Immune disease loci colocalized with genes that are involved in the regulation of T cell activation, and genes with similar functions tended to be perturbed in the same direction by disease risk alleles. Our results emphasize the importance of mapping context-specific gene expression regulation, provide insights into the mechanisms of genetic susceptibility of immune diseases, and help prioritize new therapeutic targets.
Polyunsaturated fatty acid arachidonic acid increases the virulence of gut pathogen, Yersinia enterocolitica
Authors: Chac Denise , Crebs Kelly , Yee Cara , DePaolo R. William
Published: December 2021

Food-borne illnesses are a major health concern worldwide. While 1 in 6 individuals are infected in the United States yearly, there is little research into which dietary factors can alter the risk of infection. Despite evidence suggesting a correlation between obesity and enteric infection, the few reported studies focus on the role of dietary factors and the impact on host tissues and susceptibility. The direct impact of dietary constituents on the virulence of a pathogen has largely been ignored. One component of the Western diet that has been correlated with increasing inflammatory diseases is increased consumption of omega-6 polyunsaturated fatty acids such as arachidonic acid. Here, we show that arachidonic acid directly alters the pathogenicity of the food-borne pathogen Yersinia enterocolitica. Using in vitro cellular adherence assays, proteomic peptide mass fingerprint profiles and in vivo mouse models, we show that arachidonic acid can alter the pathogenesis of Y. enterocolitica by increasing proliferation and intracellular invasion. These findings have major implications in more than food safety, potentially revealing how current dietary habits may increase the virulence of food-borne pathogens.
Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR- V7 splice variant chromatin binding and transcriptional activities
Authors: Basil Paul , Robertson Matthew J. , Bingman William E. , Dash Amit K. , Krause William C. , Shafi Ayesha A. , Piyarathna Badrajee , Coarfa Cristian , Weigel Nancy L.
Published: December 2021

The constitutively active androgen receptor (AR) splice variant, AR-V7, plays an important role in resistance to androgen deprivation therapy in castration resistant prostate cancer (CRPC). Studies seeking to determine whether AR-V7 is a partial mimic of the AR, or also has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conflicting results. One limitation in many studies has been the low level of AR variant compared to AR. Here, LNCaP and VCaP cell lines in which AR-V7 expression can be induced to match the level of AR, were used to compare the activities of AR and AR-V7. The two AR isoforms shared many targets, but overall had distinct transcriptomes. Optimal induction of novel targets sometimes required more receptor isoform than classical targets such as PSA. The isoforms displayed remarkably different cistromes with numerous differential binding sites. Some of the unique AR-V7 sites were located proximal to the transcription start sites (TSS). A de novo binding motif similar to a half ARE was identified in many AR-V7 preferential sites and, in contrast to conventional half ARE sites that bind AR-V7, FOXA1 was not enriched at these sites. This supports the concept that the AR isoforms have unique actions with the potential to serve as biomarkers or novel therapeutic targets.
Task-dependent switching of feedback controllers
Authors: Česonis Justinas , Franklin David W.
Published: December 2021

The separation of distinct motor memories by contextual cues is a well known and well studied phenomenon of feedforward human motor control. However, there is no clear evidence of such context-induced separation in feedback control. Here we test both experimentally and computationally if context-dependent switching of feedback controllers is possible in the human motor system. Specifically, we probe visuomotor feedback responses of our human participants in two different tasks – stop and hit – and under two different schedules. The first, blocked schedule, is used to measure the behaviour of stop and hit controllers in isolation, showing that it can only be described by two independent controllers with two different sets of control gains. The second, mixed schedule, is then used to compare how such behaviour evolves when participants regularly switch from one task to the other. Our results support our hypothesis that there is contextual switching of feedback controllers, further extending the accumulating evidence of shared features between feedforward and feedback control.
Omicron BA.1 and BA.2 Variants Increase the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2
Authors: Golcuk Mert , Yildiz Ahmet , Gur Mert
Published: December 2021

SARS-CoV-2 infection is initiated by binding of the receptor-binding domain (RBD) of its spike glycoprotein to the peptidase domain (PD) of angiotensin-converting enzyme 2 (ACE2) receptors in host cells. Recently detected Omicron variant of SARS-CoV-2 (B.1.1.529) is heavily mutated on RBD. Currently, the most common Omicron variants are the original BA.1 Omicron strain and the BA.2 variant, which became more prevalent since it first appeared. To investigate how these mutations affect RBD-PD interactions, we performed all-atom molecular dynamics simulations of the BA.1 and BA.2 RBD-PD in the presence of full-length glycans, explicit water and ions. Simulations revealed that RBDs of BA.1 and BA.2 variants exhibit a more dispersed interaction network and make an increased number of salt bridges and hydrophobic interactions with PD compared to wild-type RBD. Although BA.1 and BA.2 differ in two residues at the RBD-ACE2 interface, no major difference in RBD-PD interactions and binding strengths were observed between these variants. Using the conformations sampled in each trajectory, the Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) method estimated ~34% and ~51% stronger binding free energies for BA.1 and BA.2 RBD, respectively, than wild-type RBD, which may result in higher binding efficiency of the Omicron variant to infect host cells.
Homeostatic Synaptic Plasticity Rescues Neural Coding Reliability
Authors: Rozenfeld Eyal , Ehmann Nadine , Manoim Julia E. , Kittel Robert J. , Parnas Moshe
Published: December 2021

To survive, animals must recognize reoccurring stimuli. A key requirement for repeated identification of stimuli is reliable representation by the neural code on each encounter. Synaptic transmission underlies neural codes propagation between brain regions. A hallmark of chemical synapses is their plasticity, which enables signal transfer to be modified in an activity-dependent manner. Despite many decades of intense research on synapses, it remains unclear how the plastic features of synaptic transmission can maintain reliable neural coding. By studying the olfactory system of Drosophila melanogaster, we aimed to obtain a deeper mechanistic understanding of how synaptic function shapes neural coding reliability in the live, behaving animal. We show that the properties of the active zone (AZ), the presynaptic site of neurotransmitter release, are critical for generating a reliable neural code. Reducing neurotransmitter release probability specifically at AZs of olfactory sensory neurons disrupted both neural coding and behavioral reliability. Strikingly, these defects were rescued within a day by target-specific synaptic plasticity, whereby a homeostatic increase in the number of AZs compensated the drop in release probability. These findings demonstrate an important role for synaptic plasticity in maintaining neural coding reliability and are of pathophysiological interest by uncovering an elegant mechanism through which the neural circuitry can counterbalance perturbations.
Nucleotide imbalance decouples cell growth from cell proliferation
Authors: Diehl Frances F. , Miettinen Teemu P. , Elbashir Ryan , Nabel Christopher S. , Manalis Scott R. , Lewis Caroline A. , Vander Heiden Matthew G.
Published: December 2021

Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can accordingly inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is also not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways, causing aberrant biomass production and excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signaling to survive during, and recover from, nucleotide imbalance during S phase. In fact, replication stress signaling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signaling to cope with this metabolic problem, and disrupting the coordination of cell growth and division.
Frontal plane ankle stiffness increases with axial load independent of muscle activity
Authors: Villamar Zoe , Perreault Eric J. , Ludvig Daniel
Published: December 2021

Ankle sprains are the most common musculoskeletal injury, typically resulting from excessive inversion of the ankle. One way to prevent excessive inversion and maintain ankle stability is to generate a stiffness that is sufficient to resist externally imposed rotations. Frontal-plane ankle stiffness increases as participants place more weight on their ankle, but whether this effect is due to muscle activation or axial loading of the ankle is unknown. Identifying whether and to what extent axial loading affects ankle stiffness is important in understanding what role the passive mechanics of the ankle joint play in maintaining its stability. The objective of this study was to determine the effect of passive axial load on frontal-plane ankle stiffness. We had subjects seated in a chair as an axial load was applied to the ankle ranging from 10% to 50% body weight. Small rotational perturbations were applied to the ankle in the frontal plane to estimate stiffness. We found a significant, linear, 3-fold increase in ankle stiffness with axial load from the range of 0% bodyweight to 50% bodyweight. This increase could not be due to muscle activity as we observed no significant axial-load-dependent change in any of the recorded muscle activations. These results demonstrate that axial loading is a significant contributor to maintaining frontal-plane ankle stability, and that disruptions to the mechanism mediating this sensitivity of stiffness to axial loading may result in pathological cases of ankle instability.
TRAP1 and cyclophilin D compete at OSCP subunit to regulate enzymatic activity and permeability transition pore opening by F-ATP synthase
Authors: Cannino Giuseppe , Urbani Andrea , Gaspari Marco , Varano Mariaconcetta , Negro Alessandro , Filippi Antonio , Ciscato Francesco , Masgras Ionica , Gerle Christoph , Tibaldi Elena , Brunati Anna Maria , Lippe Giovanna , Bernardi Paolo , Rasola Andrea
Published: December 2021

Binding of the mitochondrial chaperone TRAP1 to client proteins shapes cell bioenergetic and proteostatic adaptations, but the panel of TRAP1 clients is only partially defined. Here we show that TRAP1 interacts with F-ATP synthase, the protein complex that provides most cellular ATP. TRAP1 competes with the peptidyl-prolylcis-transisomerase cyclophilin D (CyPD) for binding to the oligomycin sensitivity-conferring protein (OSCP) subunit of F-ATP synthase, increasing its catalytic activity and counteracting the inhibitory effect of CyPD. Moreover, TRAP1 inhibits opening of the permeability transition pore (PTP) formed by F-ATP synthase and effectively antagonizes the PTP-inducing effect of CyPD, which elicits mitochondrial depolarization and cell death. Consistently, electrophysiological measurements indicate that TRAP1 and CyPD compete in the modulation of channel activity of purified F-ATP synthase, resulting in PTP inhibition and activation, respectively, and outcompeting each other effect on the channel. Moreover, TRAP1 counteracts PTP induction by CyPD, whereas CyPD reverses TRAP1-mediated PTP inhibition. Our data identify TRAP1 as a F-ATP synthase regulator that can influence cell bioenergetics and survival and can be targeted in pathological conditions where these processes are dysregulated, such as cancer.
A convolutional neural network highlights mutations relevant to antimicrobial resistance in Mycobacterium tuberculosis
Authors: Green Anna G. , Yoon Chang H. , Chen Michael L. , Freschi Luca , Gröschel Matthias I. , Kohane Isaac , Beam Andrew , Farhat Maha
Published: December 2021

Long diagnostic wait times hinder international efforts to address multi-drug resistance in M. tuberculosis. Pathogen whole genome sequencing, coupled with statistical and machine learning models, offers a promising solution. However, generalizability and clinical adoption have been limited in part by a lack of interpretability and verifiability, especially in deep learning methods. Here, we present a deep convolutional neural network (CNN) that predicts the antibiotic resistance phenotypes of M. tuberculosis isolates. The CNN performs with state-of-the-art levels of predictive accuracy. Evaluation of salient sequence features permits biologically meaningful interpretation and validation of the CNN’s predictions, with promising repercussions for functional variant discovery, clinical applicability, and translation to phenotype prediction in other organisms.