bluuebunny/crossref_metadata_2025 huggingface dataset:
Muscle Strength and Power in People With Parkinson Disease: A Systematic Review and Meta-analysis
Authors: Gamborg Mads , Hvid Lars Grøndahl , Thrue Cecilie , Johansson Sverker , Franzén Erika , Dalgas Ulrik , Langeskov-Christensen Martin
Published: November 2022

Background and Purpose:

No studies have synthesized the literature regarding mechanical muscle function (ie, strength, power, rate of force development [RFD]) in people with Parkinson disease (PD). Here, we aimed to expand our understanding of mechanical muscle function in people with PD (PwPD) by systematically reviewing (1) the psychometric properties of isokinetic/isometric dynamometry in PD, (2) the literature comparing mechanical muscle function in PwPD with healthy controls (HC), and (3) reported associations between muscle mechanical muscle function and functional capacity and/or disease severity.

Methods:

Systematic literature search in 6 databases. Included studies had to (1) enroll and report data on PwPD, (2) include assessment(s) of psychometric properties (ie, validity, reliability, responsiveness) of isokinetic/isometric dynamometry in PD, and/or (3) assess mechanical muscle function in both PwPD and HC using isokinetic/isometric dynamometry.

Results:

A total of 40 studies were included. Aim 1 studies (n = 2) showed high reliability for isometric dynamometry (hip-abductor/dorsiflexor/trunk flexor-extensor/handgrip: intraclass correlations coefficients range = 0.92-0.98). Aim 2 studies (n = 40) showed impaired mechanical muscle function (ie, strength, power, RFD) in PwPD compared with HC (effect sizes range = 0.52-1.89). Aim 3 studies (n = 11) showed weak-to-strong associations between overall and lower extremities muscle strength and functional capacity and/or disease severity outcomes (ie, Unified Parkinson Disease Rating Scale).

Discussion and Conclusions:

Sparse methodological evidence suggests high reliability when using dynamometry in PwPD. Muscle strength, power, and RFD are impaired in PwPD compared with HC. Muscle strength is associated with functional capacity and disease severity.

Video Abstract availablefor more insights from the authors (see the Video, Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A403).
Association Between Antibiotic Redosing Before Incision and Risk of Incisional Site Infection in Children With Appendicitis
Authors: Cramm Shannon L. , Chandler Nicole M. , Graham Dionne A. , Kunisaki Shaun M. , Russell Robert T. , Blakely Martin L. , Lipskar Aaron M. , Allukian Myron , Aronowitz Danielle I. , Campbell Brendan T. , Collins Devon T. , Commander Sarah J. , Cowles Robert A. , DeFazio Jennifer R. , Esparaz Joseph R. , Feng Christina , Griggs Cornelia L. , Guyer Richard A. , Hanna David N. , Kahan Anastasia M. , Keane Olivia A. , Lamoshi Abdulraouf , Lopez Carla M. , Pace Elizabeth , Regan Maia D. , Santore Matthew T. , Scholz Stefan , Tracy Elisabeth T. , Williams Sacha A. , Zhang Lucy , Rangel Shawn J.
Published: November 2022

Objective:

To evaluate whether redosing antibiotics within an hour of incision is associated with a reduction in incisional surgical site infection (iSSI) in children with appendicitis.

Background:

Existing data remain conflicting as to whether children with appendicitis receiving antibiotics at diagnosis benefit from antibiotic redosing before incision.

Methods:

This was a multicenter retrospective cohort study using data from the Pediatric National Surgical Quality Improvement Program augmented with antibiotic utilization and operative report data obtained though supplemental chart review. Children undergoing appendectomy at 14 hospitals participating in the Eastern Pediatric Surgery Network from July 2016 to June 2020 who received antibiotics upon diagnosis of appendicitis between 1 and 6 hours before incision were included. Multivariable logistic regression was used to compare odds of iSSI in those who were and were not redosed with antibiotics within 1 hour of incision, adjusting for patient demographics, disease severity, antibiotic agents, and hospital-level clustering of events.

Results:

A total of 3533 children from 14 hospitals were included. Overall, 46.5% were redosed (hospital range: 1.8%–94.4%, P<0.001) and iSSI rates were similar between groups [redosed: 1.2% vs non-redosed: 1.3%; odds ratio (OR) 0.84, (95%,CI, 0.39–1.83)]. In subgroup analyses, redosing was associated with lower iSSI rates when cefoxitin was used as the initial antibiotic (redosed: 1.0% vs nonredosed: 2.5%; OR: 0.38, (95% CI, 0.17–0.84)], but no benefit was found with other antibiotic regimens, longer periods between initial antibiotic administration and incision, or with increased disease severity.

Conclusions:

Redosing of antibiotics within 1 hour of incision in children who received their initial dose within 6 hours of incision was not associated with reduction in risk of incisional site infection unless cefoxitin was used as the initial antibiotic.
Seizure EEG Quality in Right Unilateral Ultrabrief ECT
Authors: Yeap Samantha , Gupta Neeraj Kumar , Gill Shane , Dinesh Anthony , Woodman Richard John
Published: November 2022

Objective

The aims of this study were to compare threshold and suprathreshold ictal electroencephalograms (EEGs) in right unilateral (RUL) ultrabrief (UB) electroconvulsive therapy (ECT) and to identify the differences between these EEGs.

Methods

This study is a retrospective review of 125 pairs EEGs from titration and subsequent sessions across a 2-year period. All EEGs were independently rated for by 2 assessors using a scale based on qualities of an EEG used to guide ECT treatment dose adequacy, for example, midictal amplitude, regularity, interhemispheric coherence, seizure end point, and postictal suppression. The scores of threshold and suprathreshold EEGs were compared within and between groups based on 2 ECT types, that is, RUL UB ECT and RUL brief pulse (BP) ECT.

Results

Paired t tests showed a statistically significant difference in between threshold and suprathreshold EEG scores in RUL UB ECT. There were no statistically significant differences between corresponding scores for RUL UB ECT and RUL BP ECT threshold and suprathreshold EEGs.

Conclusions

There is a significant difference between the quality of threshold and suprathreshold EEGs in RUL UB ECT when measured with an EEG rating scale. Visual rating of ictal EEGs is as reliable in discriminating between threshold and suprathreshold seizure in RUL UB ECT as it is in RUL BP ECT.
Markers of psoriatic skin phenotype: androgen/estrogen and cortisone/cortisol imbalance, and DNA damage
Authors: Kılıç Şeyma Başar , Taheri Serpil , Mehmetbeyoğlu Ecmel , Öksüm Solak Eda , Rassoulzadegan Minoo , Borlu Murat
Published: November 2022

Patients prone to psoriasis suffer after a breakdown of the epidermal barrier and develop poorly healing lesions with abnormal proliferation of keratinocytes.

Strong inflammatory reactions with genotoxicity (short telomeres) suggest impaired immune defences with DNA damage repair response (DDR) in patients with psoriasis. Recent evidence indicates the existence of crosstalk mechanisms linking the DDR machinery and hormonal signalling pathways that cooperate to influence both progressions of many diseases and responses to treatment.

The aim of this study was to clarify whether steroid biosynthesis and genomic stability markers are altered in parallel during the formation of psoriatic skin. Understanding between the interaction of the steroid pathway and DNA damage response is crucial to addressing underlying fundamental issues and managing resulting epidermal barrier disruption in psoriasis.

Twenty patients with psoriasis and fifteen healthy volunteers were included in this study. Transcription levels of estrogen (ESR1, ESR2), androgen (AR), glucocorticoid/mineralocorticoid receptors (NR3C1, NR3C2),HSD11B1/HSD11B2genes, and DNA damage sensors (SMC1A, TREX1, TREX2, SSBP3, RAD1, RAD18, EXO1, POLH, HUS1) were determined by Real-Time-PCR in blood and skin samples (Lesional, non-lesional) from psoriasis and control groups.

Results

We found thatESR1, ESR2, HSD11B1, NR3C1, NR3C2, POLH, andSMC1Atranscripts were significantly decreased andAR, TREX1, RAD1, andSSBP3transcripts were increased dramatically in the lesional skin compared to skin samples of controls.

As a result, we found that the regulation of the steroidogenic pathway was disrupted in the lesional tissue of psoriasis patients and that a sufficient glucocorticoid and mineralocorticoid response did not form and the estrogen/androgen balance was altered in favour of androgens. We suggest that an increased androgen response in the presence of DDR increases the risk of developing psoriasis. Although this situation may be the cause or the consequence of a disruption of the epidermal barrier, our data suggest developing new therapeutic strategies.
Older Adults’ Attitudes Regarding COVID-19 and Associated Infection Control Measures in Shanghai, and Impact on Well-Being
Authors: Cui Lixian , Xu Zhiming , Ghisi Gabriela Lima de Melo , Liu Xia , Grace Sherry L
Published: November 2022

This cross-sectional study investigated health management, well-being, and pandemic-related perspectives in Shanghainese adults ≥50 years during early and strict COVID-19 control measures. A self-report survey was administered via Wenjuanxing between March-April/2020. Items from the Somatic Symptom Scale, Patient Health Questionnaire-9 and Generalized Anxiety Disorder-7 were administered, as well as pandemic-specific questions. 1181 primarily married, retired females participated; Many had hypertension (n=521, 44.1%), coronary artery disease (CAD; n=201, 17.8%) and diabetes (n=171, 14.5%). While most respondents (n=868; 73.5%) were strictly following control measures (including limiting visits with children; n=390, 33.0%) and perceived they could tolerate that beyond 6 months (n=555;47.0%), they were optimistic about the future if control measures were continued (n=969;82.0%), and perceived impact would be temporary (n=646;64.7%). 52 of those with any condition (8.2%) and 19 of those without a condition (3.5%) reported the pandemic was impacting their health. Somatic symptoms were high (29.4±7.1/36), with Sleep & Cognitive symptoms highest. 24.4% and 18.9% of respondents had elevated depressive and anxious symptoms, respectively; greater distress was associated with lower income (p=0.018), having hypertension (p=0.001) and CAD (p<0.001), more negative perceptions of global COVID-19 control (p=0.004), COVID-19 spread (p≤0.001), impact on life and health (p<0.001), compliance with control measures (p<0.001), and shorter time control measures could be tolerated (p<0.001) in adjusted analyses. In the initial COVID-19 outbreak, most older adults were optimistic and resilient with regard to the epidemic and control measures. However, the distress of older adults is not trivial, particularly in those with health issues.
Therapeutic impact of dance therapy on adult individuals with psychological trauma: a systematic review
Authors: Tomaszewski Crystal , Belot Rose-Angélique , Essadek Aziz , Onumba-Bessonnet Héloïse , Clesse Christophe
Published: November 2022

Context

Dance therapy is a therapeutic tool adapted for people that struggle with classical language-based therapeutic devices (e.g., people facing migration). As dance therapy significantly mobilizes mental, physiological, and somatic dimensions affected by psychological trauma, its therapeutic effect on psychological trauma needs to be evaluated.

Objectives

To identify the potential therapeutic effects of dance therapy in adults with psychological trauma (trauma-focused and non-trauma-focused impact) as well as the barriers and facilitators associated with its therapeutic employment.

Method

Articles published between 2000 and 2022 have been selected with the help of five relevant keyword combinations applied on seven databases. Two reviewers independently screened titles and abstracts against inclusion and exclusion criteria. Bias evaluation has been conducted with the help of the NIH and JBI. A report of the results has been organized with the help of thematic analysis.

Results

Of the thirteen articles included, only one case study directly reports a diminution of pathognomic symptoms of trauma. Other studies present improvements in key dimensions targeted by non-trauma-focused treatment: bodily sensations and perceptions, psychological processes, and interpersonal skills. These improvements depend on the skill set of the therapists and the stability of the intervention.

Conclusion

Dance therapy is an effective non-trauma-focused treatment, as it mobilizes the mandatory dimensions for the management of psychological trauma. It is specially adapted to women survivors of violence, and people facing migration. Researchers and professionals should investigate dance therapy as a trauma-focused treatment.

Highlights

While the non-trauma-focused effects of dance therapy have been particularly evaluated, there is a lack of evidence about studies evaluating the effect of dance therapy as a trauma-focused intervention.

Dance therapy improves key dimensions targeted by non-trauma-focused intervention therapies: sensory-motor perceptions, motor skills, identification, expression, and externalization of emotions, reflexivity, creativity, interpersonal skills, and verbal expression.

The effectiveness of dance therapy interventions is correlated with the therapist’s skill set, the intervention’s stability, and the patient’s flow state.
Frequent shedding of multi-drug resistant pneumococci among adults living with HIV on suppressive antiretroviral therapy in Malawi
Authors: Sibale Lusako , Phiri Joseph , Mitole Ndaona , Kalata Newton , Nyazika Tinashe , Kalirani Alice , Khwiya Mercy , Sagawa Gift , Thindwa Deus , Swarthout Todd D , French Neil , Malisita Ken , Kamng’ona Arox , Ferreira Daniela M , Heyderman Robert S. , Kwambana-Adams Brenda A. , Jambo Kondwani
Published: November 2022

People living with human immunodeficiency virus (PLHIV) on antiretroviral therapy (ART) are reported to have three times higher carriage ofStreptococcus pneumoniaethan their HIV-uninfected counterparts in point prevalence studies. Using a longitudinal cohort study design, we assessed pneumococcal carriage density, shedding and antibiotic resistance profiles, as well as nasal mucosal immunity, in otherwise healthy PLHIV on ART for at least one year, compared to HIV-uninfected participants in Malawi. Pneumococcal carriage density was higher among PLHIV compared to HIV-uninfected participants. Moreover, PLHIV were twice more likely to shed pneumococci than HIV-uninfected participants. In PLHIV, aerosol shed pneumococci were more often multi-drug resistant (MDR) than nasopharyngeal carried isolates recovered from the same individual. Consistent with high shedding, PLHIV exhibited heightened neutrophil-mediated nasal mucosa inflammation. We propose that PLHIV should be considered in intervention strategies, such as vaccination, as they could be an important reservoir for transmission of MDRS. pneumoniae.
Evaluation of the Peterborough Public Health COVID-19 Rapid Antigen Test Self-Report Tool: Implications for COVID-19 Surveillance
Authors: Smith Erin , Pigeau Carolyn , Ahmadian-Yazdi Jamal , Kharbouch Mohamed , Hoffmeyer Jane , Piggott Thomas
Published: November 2022

Background

The ongoing COVID-19 pandemic has necessitated novel testing strategies, including the use of Rapid Antigen Tests (RATs). The widespread distribution of RATs to the public prompted Peterborough Public Health to launch a pilot RAT self-report tool to assess its utility in COVID-19 surveillance.

Objective

To investigate the utility of a RAT self-report tool through an analysis of the temporal association between RAT results, PCR test results, and wastewater levels of COVID-19.

Methods

We investigated the association between RAT results, PCR test results, and wastewater levels of COVID-19 using Pearson’s correlation coefficient. Percent positivity and count of positive tests for RATs and PCR tests were analyzed.

Results

PCR percent positivity and wastewater were weakly correlated (r=0.33p=0.022), as were RAT percent positivity and wastewater (r=0.33p=0.002). RAT percent positivity and PCR percent positivity were not significantly correlated (r=-0.035,p=0.75). Count of positive RAT tests and count of positive PCR tests were moderately correlated (r=0.59,p<0.001). Wastewater was not significantly correlated to count of positive RAT tests (r=0.019,p=0.864) or count of positive PCR tests (r=0.004,p=0.971).

Conclusion

Our results provide evidence in support of the use of RAT self-reporting as a low-cost simple adjunctive COVID-19 surveillance tool, and may suggest that its utility is greatest when considering an absolute count of positive RAT tests rather than percent positivity due to reporting bias towards positive tests. These results can help inform COVID-19 surveillance strategies of local Public Health Units and encourage the use of a RAT self-report tool.
The multivalent G-quadruplex (G4)-ligands MultiTASQs allow for versatile click chemistry-based investigations
Authors: Sperti Francesco Rota , Mitteaux Jérémie , Zell Joanna , Pipier Angélique , Valverde Ibai E. , Monchaud David
Published: November 2022

Chemical biology hinges on multivalent molecular tools that uniquely allow for interrogating and/or manipulating cellular circuitries from the inside. The success of many of these approaches relies on molecular tools that make it possible to visualize biological targets in cells and then isolate them for identification purposes. To this end, click chemistry has become in just a few years a vital tool in offering practically convenient solutions to address highly complicated biological question. We report here on two clickable molecular tools, the biomimetic G-quadruplex (G4) ligands MultiTASQ andazMultiTASQ, which benefit from the versatility of two types of bioorthogonal chemistry, CuAAC and SPAAC (the discovery of which was very recently awarded the Nobel Prize of chemistry). These two MultiTASQs are here used to both visualize G4s in, and identify G4s from human cells. To this end, we developed click chemo-precipitation of G-quadruplexes (G4-click-CP) andin situG4 click imaging protocols, which provide unique insights into G4 biology in a straightforward and reliable manner.
Heritability estimation of cognitive phenotypes in the ABCD Study®using mixed models
Authors: Smith Diana M. , Loughnan Robert , Friedman Naomi P. , Parekh Pravesh , Frei Oleksandr , Thompson Wesley K. , Andreassen Ole A. , Neale Michael , Jernigan Terry L. , Dale Anders M.
Published: November 2022

Twin and family studies have historically aimed to partition phenotypic variance into components corresponding to additive genetic effects (A), common environment (C), and unique environment (E). Here we present the ACE Model and several extensions in the Adolescent Brain Cognitive Development Study (ABCD Study®), employed using the new Fast Efficient Mixed Effects Analysis (FEMA) package. In the twin sub-sample (n= 924; 462 twin pairs), heritability estimates were similar to those reported by prior studies for height (twin heritability = 0.86) and cognition (twin heritability between 0.00 and 0.61), respectively. Incorporating SNP-derived genetic relatedness and using the full ABCD Study®sample (n= 9,742) led to narrower confidence intervals for all parameter estimates. By leveraging the sparse clustering method used by FEMA to handle genetic relatedness only for participants within families, we were able to take advantage of the diverse distribution of genetic relatedness within the ABCD Study®sample.
Using spatio-temporal information in weather radar data to detect and track communal bird roosts
Authors: Perez Gustavo , Zhao Wenlong , Cheng Zezhou , T. D. Belotti Maria Carolina , Deng Yuting , Simons Victoria F. , Tielens Elske , Kelly Jeffrey F. , Horton Kyle G. , Maji Subhransu , Sheldon Daniel
Published: November 2022

The exodus of swallows from communal nighttime roosts is often visible as an expanding ring-shaped pattern in weather radar data. The WSR-88D network operated by the National Weather Service archives more than 25 years of data across 143 stations in the contiguous US. However, access to information about the roosting behavior of swallows is limited by the cost of manual annotation of these scans.

We develop an AI system to detect and track swallow roosts in weather radar data. Our model is based on the Faster R-CNN architecture and is customized to incorporate multiple spatial and temporal channels in volumetric radar scans using novel adaptor layers. We systematically study the impact of network architecture and input representation for this task. We incorporate our detection outputs into an AI-assisted system with an interface for human screening to collect research-grade data about roosting behavior. We deploy the system to collect information from 12 radar stations in the Great Lakes region of the US spanning 21 years.

The addition of temporal information improves roost detection performance from 47.0% mean average precision to 54.7%. Temporal information helps the model recognize the expanding pattern of roosts and filter false positives due to rain and static structures. Our system allowed the annotation of 15,628 roost signatures with 64,620 single-frame detections in 612,786 radar scans with 183.6 total hours of human screening, or 1.08 seconds per radar scan.

Our AI-assisted system provides research-quality roost data with far less human effort than manual annotation of radar scans. The data contains critical information about the phenology and population trends of swallows and martins, a declining group of aerial insectivores. Our successful deployment to collect historical data for 8% of the radar stations in the contiguous US lays the groundwork for continentscale analysis of swallow roosts, and provides a starting point for analysis of other family-specific phenomena in weather radar, such as bat roosts and mayfly hatches.
LAD: an R package to estimate leaf angle distribution from measured leaf inclination angles
Authors: Chianucci Francesco , Cesaretti Lorenzo
Published: November 2022

Leaf angle distribution (LAD) is an important factor for characterizing the optical features of vegetation canopies. The characterization of LAD requires direct measurements of leaf inclination angles, which can be obtained from manual clinometer measurements or leveled digital photography.

PackageLADallows to calculate the Leaf angle distribution (LAD) function and the G-function from measured leaf inclination angles. Using the package, the LAD distribution and G-function is derived by fitting a two parameter Beta distribution. Summary leaf angle statistics and distribution type is also calculated, by comparing the obtained LAD against theoretical distribution by de Wit (1965).
Retrieval and Savings of Contextual Fear Memories Across an Extended Retention Interval in Juvenile and Adult Male and Female Rats
Authors: Odynocki Natalie , Isaacs Zerah , Poulos Andrew M.
Published: November 2022

Adult rodents exhibit an exceptional ability to retrieve context fear memories across lengthy retention intervals. In contrast, these same memories established in juvenile rodents are susceptible to significant forgetting. While much of this original work has focused on male rodents, emerging research indicates that the mechanisms of context fear conditioning in females may be sexually dimorphic. If so, these female memories may exhibit a unique mnemonic profile from male rats that may be probed using single-trial conditioning, extended retention intervals, and savings procedures. The current study aimed to examine the longevity of contextual fear memories established in 24-day-old juvenile and 90-day-old Long-Evans male and female rats. Testing at the 1-day retention interval, adults exhibited greater conditioning than juvenile males, while in females, conditioning did not differ between juvenile and adult rats. In adults, males displayed greater conditioning than females, while in juveniles, males and females reached similar conditioning levels. At the 60-day retention interval, adult sex differences were maintained; however, juvenile rats failed to retrieve this remote contextual fear memory. Next, we examined whether a savings trial and test procedure could recover these remotely established juvenile memories in both males and females. Following a 60-day retention test, the now adult rats were presented with an additional context-shock pairing to assess the level of saving in both male and female rats. While this procedure produced greater conditioning in males than females, the relative amounts of the savings of this early life memory were similar in males and females. Lastly, the recovery of this memory exhibited significant generalization relative to previously unshocked juveniles and was similar in males and females. The results of these experiments indicate that adult sex differences in contextual fear memory are maintained across an extended retention interval, while in juveniles, there were no significant sex differences. In addition, male and female rats failed to retrieve an initial juvenile memory at an extended retention interval. However, these memories could be recovered with a single reminder of the original juvenile experience.
Automated simulation-based membrane-protein refinement into cryo-EM data
Authors: Yvonnesdotter Linnea , Rovšnik Urška , Blau Christian , Lycksell Marie , Howard Rebecca J. , Lindahl Erik
Published: November 2022

I.

The resolution revolution has increasingly enabled single-particle cryogenic electron microscopy (cryo-EM) reconstructions of previously inaccessible systems, including membrane proteins – a category that constitutes a disproportionate share of drug targets. We present a protocol for using density-guided molecular dynamics simulations to automatically refine atomistic models into membrane-protein cryo-EM maps. Using adaptive-force density-guided simulations as implemented in the GROMACS molecular dynamics package, we show how automated model refinement of a membrane protein is achieved without the need to manually tune the fitting force ad hoc. We also present selection criteria to choose the best fit model which balances stereochemistry and goodness-of-fit. The proposed protocol was used to refine models into a new cryo-EM density of the membrane protein maltoporin, either in a lipid bilayer or detergent micelle, and we found that results do not substantially differ from fitting in solution. Fitted structures satisfied classical model-quality metrics and improved the quality and the model-to-map correlation of the X-ray starting structure. Additionally, the density-guided fitting in combination with generalized orientation-dependent all-atom potential (GOAP) was used to correct the pixel-size estimation of the experimental cryo-EM density map. This work demonstrates the applicability of a straightforward automated approach to fitting membrane-protein cryo-EM densities. Such computational approaches promise to facilitate rapid refinement of proteins under different conditions or with various ligands present, including targets in the highly relevant superfamily of membrane proteins.

II.

STATEMENT OF SIGNIFICANCE

Cryo-EM is an increasingly critical method of structure determination. As data collection and model generation become more efficient, iteratively fitting an experimental density can still require considerable time and expertise. Membrane proteins are particularly important targets in pharmacology and bioengineering, but can present distinctive challenges to data quality and modeling. Here, we tested a new tool to drive density fitting with molecular dynamics simulations, in context of a new structure of the membrane protein maltoporin. Fitting performed well in detergent, lipids, or solution, offering simpler options for fully automated simulation protocols. We were also able to apply fitting to adjust the microscope’s pixel size. The approach described here should be applicable to rapid, accurate refinement of a variety of membrane-protein structures.
Rapid evolution of flower phenology and clonality in restored populations of multiple grassland species
Authors: Bucharova Anna , Conrady Malte , Klein-Raufhake Theresa , Schultz Franziska , Hölzel Norbert
Published: November 2022

Restoration of terrestrial ecosystems often requires re-introduction of plants. In restored sites, the plants often face environment that differs from the one in natural populations. This which can affect plant traits, reduce performance and impose novel selection pressures. As a response, restored populations might rapidly evolve and adapt to the novel conditions. This may enhance population survival and contribute to restoration success, but has been rarely tested so far. Here, we focused on populations of three grassland species restored 20 years ago (Galium wirtgenii, Inula salicinaandCentaurea jacea) by the transfer of green hay, and compared them with populations that were source of the hay. We measured plants both in-situ, and in common garden under control and three stress conditions.In-situ, restored and natural populations differed in flowering phenology in two out of the three species. In the common garden, plants of the restored population flowered earlier (inGalium) or showed increased plasticity of clonal propagation in response to clipping (Inula). Both these traits suggest rapid adaptation to the contrasting mowing regimes in restored in comparison to the natural donor sites. InCentaurea, we detected no differentiation, neither in-situ, nor in the common garden. Rapid evolution in two out of three species indicates that evolution in restoration may be rather common, yet not ubiquitous across species.
Reversing gut microbiome-driven adipose tissue inflammation alleviates metabolic syndrome
Authors: Newman N. K. , Zhang Y. , Padiadpu J. , Miranda C. L. , Magana A. A. , Wong C.P. , Hioki K. A. , Pederson J. W. , Li Z. , Gurung M. , Bruce A. M. , Brown K , Bobe G. , Sharpton T. J. , Shulzhenko N. , Maier C. S. , Stevens J. F. , Gombart A. F. , Morgun A.
Published: November 2022

The gut microbiota contributes to macrophage-mediated inflammation in adipose tissue with consumption of an obesogenic diet, thus driving the development of metabolic syndrome. There is a need to identify and develop interventions that abrogate this condition. The hops-derived prenylated flavonoid xanthohumol (XN) and its semi-synthetic derivative tetrahydroxanthohumol (TXN) attenuate high-fat diet-induced obesity, hepatosteatosis and metabolic syndrome in C57Bl/6J mice. This coincides with a decrease in pro-inflammatory gene expression in the gut and adipose tissue, together with alterations in the gut microbiota and bile acid composition. In this study, we integrated and interrogated multi-omics data from different organs with fecal 16S sequences and systemic metabolic phenotypic data using a transkingdom network analysis. By incorporating cell type information from single cell RNA-seq data, we discovered TXN attenuates macrophage inflammatory processes in adipose tissue. TXN treatment also reversed levels of inflammation-inducing microbes, such asOscillibacter valericigenes, that lead to adverse metabolic phenotypes. Furthermore,in vitrovalidation in macrophage cell lines andin vivomouse supplementation showed addition ofO. valericigenessupernatant induced the expression of metabolic macrophage signature genes that are downregulated by TXNin vivo. Our findings establish an important mechanism by which TXN mitigates adverse phenotypic outcomes from diet-induced obesity and metabolic syndrome. It primarily reduces the abundance of pro-inflammatory gut microbes that can otherwise promote macrophage-associated inflammation in adipose tissue.
Small immunological clocks identified by Deep Learning and Gradient Boosting
Authors: Kalyakulina Alena , Yusipov Igor , Kondakova Elena , Bacalini Maria Giulia , Franceschi Claudio , Vedunova Maria , Ivanchenko Mikhail
Published: November 2022

Background

The aging process affects all systems of the human body, and the observed increase in inflammatory components affecting the immune system in old age can lead to the development of age-associated diseases and systemic inflammation.

Results

We propose a small clock model SImAge based on a limited number of immunological biomarkers. To regress the chronological age from cytokine data, we first use a baseline Elastic Net model, gradient-boosted decision trees models, and several deep neural network architectures. For the full dataset of 46 immunological parameters, DANet, SAINT, FT-Transformer and TabNet models showed the best results for the test dataset. Dimensionality reduction of these models with SHAP values revealed the 10 most age-associated immunological parameters, taken to construct the SImAge small immunological clock. The best result of the SImAge model shown by the FT-Transformer deep neural network model has mean absolute error of 6.94 years and Pearsonρ= 0.939 on the independent test dataset. Explainable artificial intelligence methods allow for explaining the model solution for each individual participant.

Conclusions

We developed an approach to construct a model of immunological age based on just 10 immunological parameters, coined SImAge, for which the FT-Transformer deep neural network model had proved to be the best choice. The model shows competitive results compared to the published studies on immunological profiles, and takes a smaller number of features as an input. Neural network architectures outperformed gradient-boosted decision trees, and can be recommended in the further analysis of immunological profiles.
Heart cockle shells transmit sunlight to photosymbiotic algae using bundled fiber optic cables and condensing lenses
Authors: McCoy Dakota E. , Burns Dale H. , Klopfer Elissa , Herndon Liam K. , Ogunlade Babatunde , Dionne Jennifer A. , Johnsen Sönke
Published: November 2022

Many animals convergently evolved photosynthetic symbioses. In bivalves, giant clams (Cardiidae: Tridacninae) gape open to irradiate their symbionts, but heart cockles (Cardiidae: Fraginae) stay closed because sunlight passes through transparent windows in their shells. Here, we show that heart cockles (Corculum cardissaand spp.) use biophotonic adaptations to transmit sunlight for photosynthesis. Heart cockles transmit 11-62% of photosynthetically active radiation (mean=31%) but only 5-28% of potentially harmful UV radiation (mean=14%) to their symbionts. Beneath each window, microlenses condense light to penetrate more deeply into the symbiont-rich tissue. Within each window, aragonite forms narrow fibrous prisms perpendicular to the surface. These bundled “fiber optic cables’’ project images through the shell with a resolution of >100 lines/mm. Parameter sweeps show that the aragonite fibers’ size (∼1µm diameter), morphology (long fibers rather than plates), and orientation (along the optical c-axis) transmit more light than many other possible designs. Heart cockle shell windows are thus: (i) the first instance of fiber optic cable bundles in an organism to our knowledge; (ii) a second evolution, with epidermal cells in angiosperm plants, of condensing lenses for photosynthesis; and (iii) a photonic system that efficiently transmits useful light while protecting photosymbionts from UV radiation.
Influence of anthropogenic light on puma road crossing movement
Authors: Abelson Eric S. , Sikich Jeff A. , Riley Seth P.D. , Blumstein Daniel T.
Published: November 2022

Wildlife may be attracted or repelled by anthropogenic stimuli – by understanding these responses we gain powerful tools to modify their behavior. Anthropogenic lighting is ubiquitous but little is known about how it influences carnivores. We focused on pumas (Puma concolor) living around Los Angeles, California for which vehicular collision is an important source of mortality. We used GPS collars to track their movement around roads and combined this with ground-level and remotely sensed data of human generated nighttime light to see how that influenced activity around roads. There are multiple landscape level scales, and metrics of light relevant at each scale, that influence the perceptual landscape of wildlife and thus these different scales must be considered. We found that, at a broad spatial scale, pumas crossed roads more frequently in areas with low levels of anthropogenic light (controlling for distance to urbanization). However, while pumas crossed roads in darker parts of the landscape at a broad-landscape scale, we did not find a statistically significant relationship between puma eye-level light intensity and predicted road crossing locations.

Regarding pumas and nighttime light, it appears that having dark swaths of land, at a broad spatial scale, is important. This is important for puma conservation and road design as little is currently known about wildlife movement response to nighttime light and the ideal placement for mitigation structures. Ultimately, anthropogenic light at night is a landscape aspect that needs to be better understood and integrated into conservation as the human footprint increases.
Deep model predictive control of gene expression in thousands of single cells
Authors: Lugagne Jean-Baptiste , Blassick Caroline M. , Dunlop Mary J.
Published: November 2022

Gene expression is inherently dynamic, due to complex regulation and stochastic biochemical events. However, the effects of these dynamics on cell phenotypes can be difficult to determine. Researchers have historically been limited to passive observations of natural dynamics, which can preclude studies of elusive and noisy cellular events where large amounts of data are required to reveal statistically significant effects. Here, using recent advances in the fields of machine learning and control theory, we train a deep neural network to accurately predict the response of an optogenetic system inEscherichia colicells. We then use the network in a deep model predictive control framework to impose arbitrary and cell-specific gene expression dynamics on thousands of single cells in real time, applying the framework to generate complex time-varying patterns. We also showcase the framework’s ability to link expression patterns to dynamic functional outcomes by controlling expression of thetetAantibiotic resistance gene. This study highlights how deep learning-enabled feedback control can be used to tailor distributions of gene expression dynamics with high accuracy and throughput.
GGSDT: A unified signal detection framework for confidence data analysis
Authors: Miyoshi Kiyofumi , Nishida Shin’ya
Published: November 2022

Human decision behavior entails a graded awareness of its certainty, known as a feeling of confidence. Until now, considerable interest has been paid to behavioral and computational dissociations of decision and confidence, which has raised an urgent need for measurement frameworks that can quantify the efficiency of confidence rating relative to decision accuracy (metacognitive efficiency). As a unique addition to such frameworks, we have developed a new signal detection theory paradigm utilizing the generalized gaussian distribution (GGSDT). This framework evaluates the observer’s internal standard deviation ratio and metacognitive efficiency through the scale and shape parameters respectively. The shape parameter quantifies the kurtosis of internal distributions and can practically be understood in reference to the proportion of the gaussian ideal observer’s confidence being disrupted with random guessing (metacognitive lapse rate). This interpretation holds largely irrespective of the contaminating effects of decision accuracy or operating characteristic asymmetry. Thus, the GGSDT enables hitherto unexplored research protocols (e.g., direct comparison of yes/no versus forced-choice metacognitive efficiency), expected to find applications in various fields of behavioral science. This paper provides a detailed walkthrough of the GGSDT analysis with an accompanying R package (ggsdt).
Affected cell types for hundreds of Mendelian diseases revealed by analysis of human and mouse single-cell data
Authors: Hekselman Idan , Vital Assaf , Ziv-Agam Maya , Kerber Lior , Yeger-Lotem Esti
Published: November 2022

Hereditary diseases manifest clinically in certain tissues, however their affected cell types typically remain elusive. Single-cell expression studies showed that overexpression of disease-associated genes may point to the affected cell types. Here, we developed a method that infers disease-affected cell types from the preferential expression of disease-associated genes in cell types (PrEDiCT). We applied PrEDiCT to single-cell expression data of six human tissues, to infer the cell types affected in 1,113 hereditary diseases. Overall, we identified 110 cell types affected by 714 diseases. We corroborated our findings by literature text-mining and recapitulation in mouse corresponding tissues. Based on these findings, we explored features of disease-affected cell types and cell classes, highlighted cell types affected by mitochondrial diseases and heritable cancers, and identified diseases that perturb intercellular communication. This study expands our understanding of disease mechanisms and cellular vulnerability.
Mixed Models Quantify Annual Volume Change; Linear Regression Determines Thalamic Volume as the Best Subcortical Structure Volume Predictor in Alzheimer’s Disease and Aging
Authors: Leger Charles S. , Herbert Monique , Dale Stevens W. , DeSouza Joseph F. ,   Alzheimer’s Disease Neuroimaging Initiative
Published: November 2022

Background

Thalamus-hippocampus-putamen and thalamus-cerebellar interconnections are dense. The extent this connectivity is paralleled by each structure’s volume impact on another is unquantified in Alzheimer’s disease (AD). Mixed model quantification of annual volume change in AD is scarce and absent inclusive of the cerebellum, hippocampus, putamen and lateral ventricles and thalamus. Among these structures, autopsy evidence of early-stage AD seems largely but not entirely restricted to the hippocampus and thalamus.

Objective

Variation in annual volume related to time and baseline age was assessed for the hippocampus, putamen, cerebellum, lateral ventricles and thalamus. Which subcortical structure’s volume had the largest explanatory effect of volume variation in other subcortical structures was also determined.

Method

The intraclass correlation coefficient was used to assess test-retest reliability of structure automated segmentation. Linear regression (N= 45) determined which structure’s volume most impacted volume of other structures. Finally, mixed models (N= 36; 108 data points) quantified annual structure volume change from baseline to 24-months.

Results

High test-retest reliability was indicated by a mean ICC score of .989 (SD= .012). Thalamic volume consistently had the greatest explanatory effect of hippocampal, putamen, cerebellar and lateral ventricular volume. The group variable proxy for AD significantly contributed to the best-fitting hippocampal linear regression model, hippocampal and thalamic longitudinal mixed models, and approached significance in the longitudinal lateral ventricular mixed model. Mixed models determined time (1 year) had a negative effect on hippocampal, cerebellar and thalamic volume, no effect on putamen volume, and a positive effect on lateral ventricular volume. Baseline age had a negative effect on hippocampal and thalamic volume, no effect on cerebellar or putamen volume and a positive effect on lateral ventricular volume.

Interpretation

Linear regression determined thalamic volume as a virtual centralized index of hippocampal, cerebellar, putamen, and lateral ventricular volume. Relative to linear regression, longitudinal mixed models had greater sensitivity to detect contribution of early AD, or potential AD pathology (MCI), via the group variable not just to volume reduction in the hippocampus but also in the thalamus.
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations
Authors: Lauterbur M. Elise , Cavassim Maria Izabel A. , Gladstein Ariella L. , Gower Graham , Pope Nathaniel S. , Tsambos Georgia , Adrion Jeff , Belsare Saurabh , Biddanda Arjun , Caudill Victoria , Cury Jean , Echevarria Ignacio , Haller Benjamin C. , Hasan Ahmed R. , Huang Xin , Iasi Leonardo Nicola Martin , Noskova Ekaterina , Obšteter Jana , Pavinato Vitor Antonio Corrêa , Pearson Alice , Peede David , Perez Manolo F. , Rodrigues Murillo F. , Smith Chris C. R. , Spence Jeffrey P. , Teterina Anastasia , Tittes Silas , Unneberg Per , Vazquez Juan Manuel , Waples Ryan K. , Wohns Anthony Wilder , Wong Yan , Baumdicker Franz , Cartwright Reed A. , Gorjanc Gregor , Gutenkunst Ryan N. , Kelleher Jerome , Kern Andrew D. , Ragsdale Aaron P. , Ralph Peter L. , Schrider Daniel R. , Gronau Ilan
Published: November 2022

Simulation is a key tool in population genetics for both methods development and empirical research, but producing simulations that recapitulate the main features of genomic data sets remains a major obstacle. Today, more realistic simulations are possible thanks to large increases in the quantity and quality of available genetic data, and to the sophistication of inference and simulation software. However, implementing these simulations still requires substantial time and specialized knowledge. These challenges are especially pronounced for simulating genomes for species that are not well-studied, since it is not always clear what information is required to produce simulations with a level of realism sufficient to confidently answer a given question. The community-developed frameworkstdpopsimseeks to lower this barrier by facilitating the simulation of complex population genetic models using up-to-date information. The initial version ofstdpopsimfocused on establishing this framework using six well-characterized model species (Adrion et al., 2020). Here, we report on major improvements made in the new release ofstdpopsim(version 0.2), which includes a significant expansion of the species catalog and substantial additions to simulation capabilities. Features added to improve the realism of the simulated genomes include non-crossover recombination and provision of species-specific genomic annotations. Through community-driven efforts, we expanded the number of species in the catalog more than three-fold and broadened coverage across the tree of life. During the process of expanding the catalog, we have identified common sticking points and developed best practices for setting up genome-scale simulations. We describe the input data required for generating a realistic simulation, suggest good practices for obtaining the relevant information from the literature, and discuss common pitfalls and major considerations. These improvements tostdpopsimaim to further promote the use of realistic whole-genome population genetic simulations, especially in non-model organisms, making them available, transparent, and accessible to everyone.
Spatial structure imposes sex-specific costs but does not reduce interlocus sexual conflict
Authors: Halder Subhasish , Kar Shramana , Sethi Simran , Tewari Swadha , Verma Tanya , Nandy Bodhisatta
Published: November 2022

Spatial structure is a common feature of all naturally occurring populations. Theoretically, spatial structuring of a habitat could modulate the intensity of Interlocus sexual conflict (ISC) in a population, possibly by modulating intersexual encounter rate. We tested this theory using laboratory populations ofDrosophila melanogasterby measuring male induced fitness decline in females in three-patch habitat systems under two alternative habitat types – structured-interconnected and unstructured. Our results on reproductive and survival costs in females suggested significant costs due to (a) male presence (i.e., ISC) and (b) living on structured habitat. However, there was only a weak evidence supporting the theory of modulation of ISC by habitat structuring only. Through a follow up experiment, we further showed that the effect of habitat on ISC is also robust to the alteration of female conditions. Therefore, it appears that spatial structuring per se is unlikely to modulate ISC, but can impose additional survival costs. We further showed such survival cost could be sex-specific possibly reflecting female biased spontaneous dispersal.