bluuebunny/crossref_metadata_2025 huggingface dataset:
Design and preliminary evaluation of a low-cost three-dimensional biomechanical force plate
Authors: Zhu Disha , Wang Xuefeng , Shang Shaomei
Published: November 2023

Objective:

The three-dimensional (3D) force plate is a widely used device in biomechanical research, capable of measuring the ground reaction force (GRF) exerted on the sole of the foot. The forces of human joints are calculated by combining GRF with motion capture data. In the field of nursing and rehabilitation, evaluation of joint pressure can inform further therapy. However, its high cost often limits its application to a small population. Therefore, we aimed to design and manufacture a low-cost 3D force plate to address this issue, which will advance the evaluation of joint pressure in nursing practices.

Methods:

Through mechanical derivation and finite element method simulation, the feasibility of this 3D force plate was tested. We proposed a method based on simulation results to assist in calibration. Furthermore, we collected the GRF data of the author using the 3D force plate designed in this study. Then we imported this GRF data and the data obtained from motion capture into OpenSim.

Results:

The 3D force plate consisted of two 3D force sensors and a 600

300 mm board. The 3D force plate could measure the 3D reaction force between the sole of a subject’s foot and the ground. The 3D force plate was validated the usability in this study through theoretical calculation and a complete musculoskeletal analysis process.

Conclusion:

We have completed the design and practicality verification of this low-cost 3D force plate and provided a calibration method based on finite element method simulation assistance. Low-cost 3D force plates can accelerate the popularization and application of musculoskeletal analysis in the field of nursing and rehabilitation, which is helpful for precision health.
Usefulness of Heart-Type Fatty Acid–Binding Protein Measurement in Postmortem Urine Specimens
Authors: Hisamura Waka , Takasu Shojiro , Iwadate Kimiharu
Published: November 2023

Heart-type fatty acid–binding protein (HFABP) is a 15-kDa substance reported to pass through the renal tubules and be renally excreted. Therefore, it is possible that its concentration in the urine collected postmortem may reflect antemortem blood levels. We measured the postmortem urine concentration of HFABP in 94 forensic autopsy cases and compared it between acute myocardial infarction (AMI), sepsis, heat stroke cases, and asphyxia cases as control cases to examine its diagnostic validity. Kidney tissue collected at autopsy was immunostained with antibodies against HFABP to evaluate the correlation with the urinary measurements. Urinary HFABP was significantly higher in AMI, sepsis, and heat stroke cases than in asphyxia cases. Quantitative immunostaining results showed no significant differences between any 2 groups. The usefulness of kidney immunostaining for HFABP in elucidating the cause of death was low. Two reasons may explain the lack of significant differences in kidney immunostaining: nonspecific leakage of tubular epithelial HFABP into the tubules because of postmortem changes and oliguria due to dehydration caused by heat stroke. In conclusion, the measurement of urinary HFABP may be useful in elucidating the cause of death; however, the kidney HFABP immunostaining was not significantly different from AMI.
Lesions of the Cardiac Conduction System and Sudden Death
Authors: Cohle Stephen D. , Wygant Cassandra Maria
Published: November 2023

When a young previously healthy person dies suddenly, occasionally, the scene is noncontributory and the autopsy and drug screen are negative. In such cases, additional studies, including genetic assessment and cardiac conduction system examination, should be performed. We performed a literature search and reviewed our own material to identify possible or definite conduction system anomalies that may cause death. We identified intrinsic conduction system disease including cystic tumor of the atrioventricular node, atrioventricular node (cystic tumor of the AV node), and fibromuscular dysplasia of the atrioventricular node artery to be likely causes of death. Extrinsic causes, in which a generalized disease affects the conduction system, include tumors, autoimmune disease, infiltrative disorders, and others, are a second category of diseases that can affect the conduction system and cause atrioventricular block and sudden death.
Multiparametric Approach to Breast Cancer With Emphasis on Magnetic Resonance Imaging in the Era of Personalized Breast Cancer Treatment
Authors: Kataoka Masako , Iima Mami , Miyake Kanae Kawai , Honda Maya
Published: November 2023

A multiparametric approach to breast cancer imaging offers the advantage of integrating the diverse contributions of various parameters. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is the most important MRI sequence for breast imaging. The vascularity and permeability of lesions can be estimated through the use of semiquantitative and quantitative parameters. The increased use of ultrafast DCE-MRI has facilitated the introduction of novel kinetic parameters. In addition to DCE-MRI, diffusion-weighted imaging provides information associated with tumor cell density, with advanced diffusion-weighted imaging techniques such as intravoxel incoherent motion, diffusion kurtosis imaging, and time-dependent diffusion MRI opening up new horizons in microscale tissue evaluation. Furthermore, T2-weighted imaging plays a key role in measuring the degree of tumor aggressiveness, which may be related to the tumor microenvironment. Magnetic resonance imaging is, however, not the only imaging modality providing semiquantitative and quantitative parameters from breast tumors. Breast positron emission tomography demonstrates superior spatial resolution to whole-body positron emission tomography and allows comparable delineation of breast cancer to MRI, as well as providing metabolic information, which often precedes vascular and morphological changes occurring in response to treatment. The integration of these imaging-derived factors is accomplished through multiparametric imaging. In this article, we explore the relationship among the key imaging parameters, breast cancer diagnosis, and histological characteristics, providing a technical and theoretical background for these parameters. Furthermore, we review the recent studies on the application of multiparametric imaging to breast cancer and the significance of the key imaging parameters.
Financial Toxicity in Breast Implant–Associated Anaplastic Large Cell Lymphoma
Authors: Tesfaye Eliora A. , O'Neill Rebecca C. , McGregor Terri , Clemens Mark W.
Published: November 2023

Background

Financial toxicity is a growing concern due to its considerable effects on medical adherence, quality of life, and mortality. The cost associated with breast implant-associated anaplastic large cell lymphoma (BIA-ALCL) is substantial from diagnosis to treatment, including adjuvant therapy and surgery. This study aims to assess the prevalence of financial toxicity in BIA-ALCL patients.

Methods

We performed a cross-sectional, survey-based study on women with confirmed cases of BIA-ALCL from December 2019 to March 2023. The primary study outcomes were financial toxicity measured by Comprehensive Score for Financial Toxicity (COST) score and patient-reported financial burden measured by the responses to the Evaluation of the Financial Impact of BIA-ALCL survey. Lower COST scores signify higher financial toxicity. Responses were linked to patient data extracted from the medical records.

Results

Thirty-two women treated for confirmed BIA-ALCL were included. Patients were all White and were diagnosed at a median age of 51 years (range, 41–65 years). The mean COST score was 27.9 ± 2.23. Lower COST scores were associated with receipt of radiotherapy (P = 0.033), exceeding credit card limits (P = 0.036), living paycheck to paycheck (P = 0.00027), requiring financial support from friends and family (P = 0.00044), and instability in household finances (P = 0.034).

Conclusions

Financial toxicity is prevalent in BIA-ALCL patients and has a substantial impact on patient reported burden. Insurance denial is frequent for patients with a prior history of cosmetic augmentation. Risk assessments and cost discussions should occur throughout the care continuum to minimize financial burden.
Liver transplantation for severe hepatic trauma: A multicenter analysis from the UNOS data set
Authors: Orozco Gabriel , Gupta Meera , Ancheta Alexandre , Shah Malay B. , Warriner Zachary , Marti Francesc , Mei Xiaonan , Desai Siddharth , Bernard Andrew , Gedaly Roberto
Published: November 2023

BACKGROUND

Orthotopic liver transplantation (OLT) is rarely indicated after hepatic trauma but it can be the only therapeutic option in some patients. There are scarce data analyzing the surgical outcomes of OLT after trauma.

METHODS

We used the UNOS data set to identify patients who underwent OLT for trauma from 1987 to 2022 and compared them to a cohort of patients transplanted for other indications. Cox proportional hazard and multivariable logistic regression analyses were performed to assess predictors of graft and patient survival.

RESULTS

Seventy-two patients underwent OLT for trauma during the study period. Patients with trauma were more frequently on mechanical ventilation at the time of transplantation (26.4% vs. 7.6%, p < 0.001) and had a greater incidence of pretransplant portal vein thrombosis (12.5% vs. 4%, p = 0.002). Our 4:1 matched analysis showed that trauma patients had significantly shorter wait times, higher incidence of pretransplant portal vein thrombosis and prolonged length of stay. Trauma was associated with decreased overall graft survival (hazards ratio, 1.42; 95% confidence interval, 1.01–1.98), and increased length of stay (p = 0.048). There were no significant differences in long-term patient survival.

CONCLUSION

Unique physiological and vascular challenges after severe hepatic trauma might be associated with decreased graft survival in patients requiring liver transplantation.

LEVEL OF EVIDENCE

Prognostic and Epidemiological; Level III.
Engineering mice for female-biased progeny without impacting genetic integrity and litter size
Authors: Yosef Ido , Mahata Tridib , Xie Xuefeng , Chen Yuhuang , Bar-Joseph Hadas , Sun Qing-Yuan , Shalgi Ruth , Munitz Ariel , Gerlic Motti , Qimron Udi
Published: November 2023

Generating mammalian gametes with a skewed sex ratio has thus far eluded empirical confirmation. The utilization of such genetically engineered organisms would offer the potential to curtail the necessity for culling animals of undesirable sex, mitigate resource wastage, and alleviate superfluous labor burdens. In this study, we introduce a transgenic male mouse lineage, which consistently yields predominantly female progeny (comprising up to ∼90% of the total offspring). This accomplishment was made possible by integrating a controllable genetic cassette onto the Y chromosome. The cassette encodes dCas9 and RNA guides that selectively silence a spermatid maturation gene. After the separation of X and Y gametes during meiosis, gametes containing an X chromosome develop normally, while those harboring the engineered Y chromosome, subjected to dCas9 silencing of the spermatid maturation gene, do not mature properly. Indeed, some spermatozoa from the transgenic mice exhibit a unique morphology, associated with the absence of the maturation gene. Notably, the resultant female offspring do not inherit the genetically engineered Y chromosome and are thus not genetically modified. Importantly, the litter size of the transgenic mice remains unchanged compared to the wild type. These findings represent the potential of genetic engineering to yield sex-biased litters of full size without compromising genetic integrity, marking a pioneering advancement in this field of study.

One sentence summary

Y chromosome manipulation yields mostly female mice, preserving litter size without genetic alteration in females.

Significance statement

This study demonstrates a groundbreaking approach to producing predominantly female offspring in mice without altering the genetic makeup of the females. By engineering a male mouse’s Y chromosome to prevent the proper development of male sperm, we can bias the offspring toward females while maintaining normal litter sizes and without genetically modifying the females. This technique has significant potential for reducing waste, labor, and ethical concerns in animal breeding.

Graphical Abstract

A proof of concept for the first mammal producing sexed semen may revolutionize the way for breeding animals such as cattle for the dairy industry and swine for the meat industry.
Phenology across scales: an intercontinental analysis of leaf-out dates in temperate deciduous tree communities
Authors: Delpierre Nicolas , Garnier Suzon , Treuil-Dussouet Hugo , Hufkens Koen , Lin Jianhong , Beier Colin , Bell Michael , Berveiller Daniel , Cuntz Matthias , Curioni Giulio , Dahlin Kyla , Denham Sander O. , Desai Ankur R. , Domec Jean-Christophe , Hart Kris M. , Ibrom Andreas , Joetzjer Emilie , King John , Klosterhalfen Anne , Koebsch Franziska , Hale Peter Mc , Morfin Alexandre , Munger J. William , Noormets Asko , Pilegaard Kim , Pohl Felix , Rebmann Corinna , Richardson Andrew D. , Rothstein David , Schwartz Mark D. , Wilkinson Matthew , Soudani Kamel
Published: November 2023

Aim

To quantify the intra-community variability of leaf-out (ICVLo) among dominant trees in temperate deciduous forests, assess its links with specific and phylogenetic diversity, identify its environmental drivers, and deduce its ecological consequences with regard to radiation received and exposure to late frost.

Location

Eastern North America (ENA) and Europe (EUR).

Time period

2009-2022

Major taxa studied

Temperate deciduous forest trees.

Methods

We developed an approach to quantify ICVLo through the analysis of RGB images taken from phenological cameras. We related ICVLo to species richness, phylogenetic diversity and environmental conditions. We quantified the intra-community variability of the amount of radiation received and of exposure to late frost.

Results

Leaf-out occurred over a longer time interval in ENA than in EUR. The sensitivity of leaf-out to temperature was identical in both regions (-3.4 days per °C). The distributions of ICVLo were similar in EUR and ENA forests, despite the latter being more species-rich and phylogenetically diverse. In both regions, cooler conditions and an earlier occurrence of leaf-out resulted in higher ICVLo. ICVLo resulted in a ca. 8% difference of radiation absorption over spring among individual trees. Forest communities in ENA had shorter safety margins as regards the exposure to late frosts, and were actually more frequently exposed to late frosts.

Main conclusions

We conducted the first intercontinental analysis of the variability of leaf-out at the scale of tree communities. North American and European forests showed similar ICVLo, in spite of their differences in terms of species richness and phylogenetic diversity, highlighting the relevance of environmental controls on ICVLo. We quantified two ecological implications of ICVLo (difference in terms of radiation absorption and exposure to late frost), which should be explored in the context of ongoing climate change, which affects trees differently according to their phenological niche.
Giant genes are rare but implicated in cell wall degradation by predatory bacteria
Authors: West-Roberts Jacob , Valentin-Alvarado Luis , Mullen Susan , Sachdeva Rohan , Smith Justin , Hug Laura A. , Gregoire Daniel S. , Liu Wentso , Lin Tzu-Yu , Husain Gabriel , Amano Yuki , Ly Lynn , Banfield Jillian F.
Published: November 2023

Across the tree of life, gene lengths vary, but most are no more than a few thousand base pairs in length. The largest protein often reported is the ∼40,000 aa eukaryotic Titin. Even larger proteins may occur in the rapidly expanding set of metagenome-derived sequences, but their existence may be obscured by assembly fragmentation. Here, we leverage genome curation to complete metagenome-derived sequences that encode predicted proteins of up to 85,804 aa. Overall, the findings illuminate a huge knowledge gap related to giant proteins. Although predicted proteins of >30,000 aa occur in bacterial phyla such asFirmicutesandActinobacteria, they are most common in ca.Omnitrophota,ultra small bacteria that adopt predatory lifestyles. All full length giant genes encode numerous transmembrane regions and most encode divergent secA DEAD helicase domains.In silicostructural prediction of protein subregions was required to identify domains in unannotated protein segments, and revealed putative domains implicated in attachment and carbohydrate degradation. Many giant genes in new complete and near-completeOmnitrophotagenomes occur in close proximity to genes homologous to type II secretion systems as well as carbohydrate import systems. This, in combination with the domain content, suggests that many bacterial giant proteins enable prey adhesion and cell wall digestion during bacterial predation.
Inflammatory Recruitment of Healthy Hematopoietic Stem and Progenitor Cells in the Acute Myeloid Leukemia Niche
Authors: Chen Ding-Wen , Fan Jian-Meng , Schrey Julie M. , Mitchell Dana V. , Jung Seul K. , Hurwitz Stephanie N. , Perez Empar B. , Muraro Mauro , Carroll Martin , Taylor Deanne M. , Kurre Peter
Published: November 2023

Inflammation in the bone marrow (BM) microenvironment is a constitutive component of leukemogenesis in acute myeloid leukemia (AML). Current evidence suggests that both leukemic blasts and stroma secrete proinflammatory factors that actively suppress the function of healthy hematopoietic stem and progenitor cells (HSPCs). HSPCs are also cellular components of the innate immune system, and we reasoned that they may actively propagate the inflammation in the leukemic niche. In two separate congenic models of AML we confirm by evaluation of the BM plasma secretome and HSPC-selective single-cell RNA sequencing (scRNA-Seq) that multipotent progenitors and long-lived stem cells adopt inflammatory gene expression programs, even at low BM leukemic burden. In particular, we observe interferon gamma (IFN-γ) pathway activation, along with secretion of its chemokine target, CXCL10. We show that AML-derived nanometer-sized extracellular vesicles (EVAML) are sufficient to trigger this inflammatory HSPC response, bothin vitroandin vivo. Altogether, our studies indicate that HSPCs are an unrecognized component of the inflammatory adaptation of the BM by leukemic cells. The pro-inflammatory conversion and long-lived presence of HSPC in the BM along with their regenerative re-expansion during remission may impact clonal selection and disease evolution.
Cell-cycle dependent inhibition of BRCA1 signaling by the lysine methyltransferase SET8
Authors: Perez Yannick , Alhourani Fatima , Patouillard Julie , Ribeyre Cyril , Larroque Marion , Baldin Véronique , Lleres David , Grimaud Charlotte , Julien Eric
Published: November 2023

Although the inverse affinities of 53BP1 and BRCA1-BARD1 complexes for distinct methylation states of lysine (K) 20 at histone H4 have underscored a role of this epigenetic mark in the regulation of DNA-repair pathways choice, how the different H4K20 methyltransferases are involved remained unclear. Here, we show that the replication-coupled degradation of the lysine methyltransferase SET8 responsible for H4K20 mono-methylation (H4K20me1) is required for the onset of the recombinogenic functions of BRCA1 during unperturbed DNA replication. Indeed, we demonstrate that SET8 can work as a primary inhibitor of homologous recombination by tipping the balance from BRCA1-BARD1 to 53BP1 complexes in a manner depending on the single switch from un-methyl to mono-methyl H4K20 and the recruitment of the ubiquitin ligase RNF168 on post-replicated chromatin. Conversely, the lack of SET8 and K20 mono-methylation on newly assembly chromatin after DNA replication led to the untimely chromatin accumulation of BRCA1 at the exit of mitosis, which contributes to the improper progression from G1 to S-phase in daughter cells. Altogether, these results establish thede novoactivity of SET8 on chromatin as a primordial epigenetic lock of BRCA1-mediated HR pathway during the cell cycle.
Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization
Authors: Sun Qiang , Zhou Qin , Qiao Yulong , Sun Hao , Wang Huating
Published: November 2023

Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary associated RBPs (baRBPs). We also characterize chromatin features of baRBP binding and uncover clustering among baRBPs and with transcription factors (TFs). Moreover, we found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF independent manner. Further analyses revealed that baRBP binding is associated with nascent promoter transcription thus RBP/transcription may synergistically demarcate TADs. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown ofRBFox2in K562 cells causes remarkable TAD reorganization and boundary loss. Moreover, we found RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is down-regulated and its bound boundaries are remodeled during MB differentiation into myotubes (MTs). Knockout ofRbfox2in MBs also causes significant boundary reorganization. Finally, transcriptional inhibition in C2C12 cells indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play active role in modulating TAD organization through co-transcriptional association and synergistic action with nascent promoter transcripts.
Helicobacter pylori cancer associated CagA protein drives intestinal metaplastic transition in human gastric organoids
Authors: Reines Mar , Soerensen Meike , Berger Hilmar , Patel Mihir , Schlärmann Philipp , Meyer Thomas F.
Published: November 2023

Gastric intestinal metaplasia (GIM) constitutes a pre-neoplastic stage in the development of stomach cancer. While strong evidence points to a role of infection with CagA positiveHelicobacter pyloriin the development of GIM, currently available experimental models have not provided mechanistic clues on this association. Here, we ectopically expressed theH. pyloriCagA protein in human gastric organoids derived from normal, primary epithelial cells. Native CagA protein was produced and rapidly processed to yield a tyrosine-phosphorylated C-terminal fragment of ∼35 kDa. It led to an activation of the STAT3 pathway and aberrant elevation of CDX2 expression, a marker of intestinal type of cells, as well as other intestinal markers. Thus, CagA drives re-programming of gastric cells towards an intestinal-like phenotype, towards GIM. In summary, we describe a cooperative mechanism of CagA-induced STAT3 signaling and intestinal-like trans-differentiation, promoting a pre-neoplastic state. Our model provides mechanistic evidence for a direct role of CagA in driving premalignancy in gastric pathogenesis.
Successful gall induction byDiplolepis rosaeandD. mayrion the sweet briar (Rosa rubiginosa) under laboratory conditions
Authors: László Zoltán , Biró Mátyás , Iordache Constantin-Teodor , Macalik Borbála , Nicula Marco , Szilágyi Bálint , Podar Dorina
Published: November 2023

Plant galls are unique outgrowths caused by various organisms, including insects, serving as nourishment for the inducer’s larvae. Despite the taxonomists and ecologists attempts to elucidate the mechanisms behind plant gall formation, its understanding is still incomplete. Modern genetic techniques allow in depth analysis of the molecular processes, but variations across species entangle the analysis. Establishing laboratory-friendly plant-gall inducer communities is crucial, yet past attempts have faced challenges.

Our study aimed to create a sustainable laboratory community involving wild roses (Rosasp.) and as gall-inducing insects rose gall wasps belonging to the genusDiplolepis. Controlled indoor conditions were optimized for plant growth. Wild roses were transplanted, then exposed to gall inducers, and monitored.

Successfully initialized gall growth was measures and analysed, revealing insights into the impact of plant vigour on gall size.

Our study successfully established a novel laboratory community for further research on gall formation mechanisms.
Unraveling the Power of NAP-CNB’s Machine Learning-enhanced Tumor Neoantigen Prediction
Authors: Méndez-Pérez Almudena , Acosta-Moreno Andrés M. , Wert-Carvajal Carlos , Ballesteros-Cuartero Pilar , Sánchez-García Rubén , Macías José R , Sanz-Pamplona Rebeca , Alemany Ramon , Sorzano Carlos Óscar S. , Muñoz-Barrutia Arrate , Veiga Esteban
Published: November 2023

In this study, we present a proof-of-concept classical vaccination experiment that validates thein silicoidentification of tumor neoantigens (TNAs) using a machine learning-based platform called NAP-CNB. Unlike other TNA predictors, NAP-CNB leverages RNAseq data to consider the relative expression of neoantigens in tumors. Our experiments show the efficacy of NAP-CNB. Predicted TNAs elicited potent antitumor responsesin vivofollowing classical vaccination protocols. Notably, optimal antitumor activity was observed when targeting the antigen with higher expression in the tumor, which was not the most immunogenic. Additionally, the vaccination combining different neoantigens resulted in vastly improved responses compared to each one individually, showing the worth of multiantigen-based approaches. These findings validate NAP-CNB as an innovative TNA-identification platform and make a substantial contribution to advancing the next generation of personalized immunotherapies
Age-related differences in electrophysiological correlates of visuospatial reorientation
Authors: Naveilhan Clément , Delaux Alexandre , Durteste Marion , Lebrun Jerome , Zory Raphaël , Arleo Angelo , Ramanoël Stephen
Published: November 2023

Spatial navigation abilities decline with age. Recent studies revealed a specific impairment in landmark-based reorientation, linked to changes in scene-selective brain regions activity. While fMRI studies suggest that these cortical modulations might be compensatory, a more precise investigation of the brain dynamics associated with visuospatial processing is warranted. We analyzed Event-Related Potentials and Event-Related Spectral Perturbations recorded from electrodes over scene-selective regions. 28 young adults and 28 older adults completed a desktop-based reorientation task using landmarks. Our findings show poorer reorientation performance among older adults. Signatures of age-related modulation of EEG activity imputable to scene-selective regions were predominantly observed within the right hemisphere. EEG analysis disclosed a tripartite worsening of scene processing accounting for older adults’ difficulties. Firstly, a delayed and reduced P1 component likely reflects a slower and less efficient stimulus discrimination. Secondly, an increased N1 amplitude and theta-band activity suggest a higher demand on cognitive resources associated with more effortful processing of visuospatial information. Thirdly, a decreased P2 amplitude may imply deficient attentional mechanisms to select task-relevant stimuli.
Efficient Analysis of Annotation Colocalization Accounting for Genomic Contexts
Authors: Gafurov Askar , Vinař Tomáš , Medvedev Paul , Brejová Broňa
Published: November 2023

An annotation is a set of genomic intervals sharing a particular function or property. Examples include genes or their exons, evolutionarily conserved elements, and regions with a particular epigenetic state. A common task is to compare two annotations to determine if one is enriched or depleted in the regions covered by the other. We study the problem of assigning statistical significance to such a comparison based on a null model representing two random unrelated annotations. To incorporate more background information into such analyses, we propose a new null model based on a Markov chain which differentiates among several genomic contexts. These contexts can capture various confounding factors, such as GC content or assembly gaps. We then develop a new algorithm for estimating p-values by computing the exact expectation and variance of the test statistics and then estimating the p-value using a normal approximation. Compared to the previous algorithm by Gafurov et al., the new algorithm provides three advances: (1) the running time is improved from quadratic to linear or quasi-linear, (2) the algorithm can handle two different test statistics, and (3) the algorithm can handle both simple and context-dependent Markov chain null models.

We demonstrate the efficiency and accuracy of our algorithm on synthetic and real data sets, including the recent human telomere-to-telomere assembly. In particular, our algorithm computed p-values for 450 pairs of human genome annotations using 24 threads in under three hours. Moreover, the use of genomic contexts to correct for GC bias resulted in the reversal of some previously published findings.

Availability

The software is freely available athttps://github.com/fmfi-compbio/mcdp2under the MIT licence. All data for reproducibility are available athttps://github.com/fmfi-compbio/mcdp2-reproducibility
Impaired oxytocin signaling in the central amygdala in rats with chronic heart failure
Authors: Althammer Ferdinand , Roy Ranjan K. , Kirchner Matthew K. , Lira Elba Campos , Schimmer Stephanie , Charlet Alexandre , Grinevich Valery , Stern Javier E.
Published: November 2023

Aims

Heart failure (HF) patients often suffer from cognitive decline, depression, and mood impairments, but the molecular signals and brain circuits underlying these effects remain elusive. The hypothalamic neuropeptide oxytocin (OT) is critically involved in the regulation of mood, and OTergic signaling in the central amygdala (CeA) is a key mechanism controlling emotional responses including anxiety-like behaviors. Based on this, we used in this study a well-established ischemic rat HF model and aimed to study alterations in the hypothalamus-to-CeA OTergic circuit.

Methods and Results

To study potential HF-induced changes in the hypothalamus-to-CeA OTertic circuit, we combined patch-clamp electrophysiology, immunohistochemical analysis, RNAScope assessment of OTR mRNA, brain region-specific stereotaxic injections of viral vectors and retrograde tracing, optogenetic stimulation and OT biosensors in the ischemic HF model. We found that most of OTergic innervation of the central amygdala (CeA) originated from the hypothalamic supraoptic nucleus (SON). While no differences in the numbers of SON➜CeA OTertic neurons (or their OT content) was observed between sham and HF rats, we did observe a blunted content and release of OT from axonal terminals within the CeA. Moreover, we report downregulation of neuronal and astrocytic OT receptors, and impaired OTR-driven GABAergic synaptic activity within the CeA microcircuit of rats with HF.

Conclusions

Our study provides first evidence that HF rats display various perturbations in the hypothalamus-to-amygdala OTergic circuit, and lays the foundation for future translational studies targeting either the OT system or GABAergic amygdala GABA microcircuit to ameliorate depression or mood impairments in rats or patients with chronic HF.
Transmission dynamics of MERS-CoV in a transgenic human DPP4 mouse model
Authors: Doremalen Neeltje van , Bushmaker Trenton , Fischer Robert J. , Okumura Atsushi , Figueroa Dania , McMinn Rebekah J. , Letko Michael , Saturday Greg , Munster Vincent J.
Published: November 2023

Since 2002, three novel coronavirus outbreaks have occurred: severe acute respiratory syndrome coronavirus (SARS-CoV-1), Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV-2. A better understanding of the transmission potential of coronaviruses will result in adequate infection control precautions and an early halt of transmission within the human population. Experiments on the stability of coronaviruses in the environment, as well as transmission models, are thus pertinent. Here, we show that transgenic mice expressing human DPP4 can be infected with MERS-CoV via the aerosol route. Exposure to 5×106TCID50and 5×104TCID50MERS-CoV per cage via fomites resulted in transmission in 15 out of 20 and 11 out of 18 animals, respectively. Exposure of sentinel mice to donor mice one day post inoculation with 105TCID50MERS-CoV resulted in transmission in 1 out of 38 mice via direct contact and 4 out of 54 mice via airborne contact. Exposure to donor mice inoculated with 104TCID50MERS-CoV resulted in transmission in 0 out of 20 pairs via direct contact and 0 out of 5 pairs via the airborne route. Our model shows limited transmission of MERS-CoV via the fomite, direct contact, and airborne routes. The hDPP4 mouse model will allow assessment of the ongoing evolution of MERS-CoV in the context of acquiring enhanced human-to-human transmission kinetics and will inform the development of other transmission models.
Collection of Non Timber Forest Products (NTFPs) and their contribution to sustainable rural livelihoods in selected areas around Ayubia National Park, Pakistan
Authors: Zaman Mehwish , Jabeen Asma , Shabbir Rabia
Published: November 2023

This study shows the Collection of Non Timber Forest Products (NTFPs) and their contribution to sustainable rural livelihoods in selected areas around Ayubia National Park, Pakistan. Forests are an important component for daily life of rural residents living near forested areas. A protected area is a geographically designated area for the purpose of biological conservation. Ayubia National Park (ANP) is a protected area in KPK, Pakistan that was designated with the purpose of management and preservation of nature. Non Timber Forest Products (NTFPs) have been defined as “All biological materials, excluding timber, which are extracted from forests for human use”. NTFPs play an important role in income generation for indigenous people. Malaach Village, Pasala Village and Khanuspur Town present around ANP were selected study areas. Purposive sampling was used for selection of study areas. Quantitative research was done. Field visits were done for Questionnaire survey. 50 questionnaires were filled from each selected village/town and results were analysed using SPSS. Cross tabulation was done and Chi Square test was applied. It was found that Wild Vegetables, Wild Fruits, Medicinal Plants and Mushrooms are collected from forests in and around ANP by indigenous people. Chi square results showed significant relationship between gender and collection of NTFPs. Poverty is found to be the main reason for collecting NTFPs. Contribution of NTFPs to annual income of people is mostly less than 20% but this contribution is also 21%-40% and even 41%-60% for few people. ANP should be managed properly to inhibit the collection of NTFPs within the park. Indigenous people should cooperate in sustainable collection and use of NTFPs. The role of NTFPs to livelihoods in and around ANP are clearly understood by study and will be useful in the awareness and implementation of the conservation practices in the Ayubia National Park.
Contribution of B-1 cells in the cytotoxicity of CD8 T lymphocytes in encephalitozoonosis
Authors: de Oliveira Cristina Gabriela Nascimento , Perez Elizabeth Cristina , Alvares-Saraiva Anuska Marcelino , Lallo Maria Anete
Published: November 2023

Encephalitozoon cuniculiis an opportunistic intracellular pathogen that establishes a balanced relationship with immunocompetent individuals depending on the activity of their CD8+T cells lymphocytes. However, lower resistance to experimental infection withE. cuniculiwas found in B-1 deficient mice (Xid), besides increased the number of CD8 T lymphocytes. Here, we evaluated the cytotoxic activity of CD8+T lymphocytes from Balb/c wild-type (WT) or Balb/c Xid mice (with B-1 cell deficiency) on the microbicidal activity of macrophages challenged withE. cuniculi. CD8 T lymphocytes from WT or Xid mice previously infected or not withE cuniculiwere co-cultured with macrophages challenged withE. cuniculi. We evaluated macrophages viability and microbicidal activity, and proliferation, viability, and presence of activating molecules (CD62L, CD69, and CD107a) in CD8 T lymphocytes. Macrophages co-cultured with CD8 T lymphocytes from WT demonstrated high microbicidal activity. CD8 T lymphocytes obtained from uninfected WT mice had a higher proliferative capacity and a higher expression of CD69 and LAMP-1-activating molecules compared to Xid CD8+T lymphocytes. CD8 T lymphocytes from infected Xid mice proliferated more than those from WT mice, however, when the expression of the activating molecule CD69 associated with the expression of CD62L was kept low. In conclusion, the absence of B-1 cells in Xid mice might be associated with the lower expression of activating molecules in CD8+T lymphocytes and their cytotoxic activity. However, after a previous infection withE. cuniculi, CD8 T lymphocytes were more effective in killing macrophages infected withE. cuniculi.
METTL3 alters capping enzyme expression and its activity on ribosomal proteins
Authors: del Valle-Morales Daniel , Romano Giulia , Le Patricia , Saviana Michela , Brown Rachel , Micalo Lavender , Li Howard , Ferlita Alessandro La , Nigita Giovanni , Nana-Sinkam Patrick , Acunzo Mario
Published: November 2023

The 5’ cap, catalyzed by RNA guanylyltransferase and 5’-phosphatase (RNGTT), is a vital mRNA modification for the functionality of mRNAs. mRNA capping occurs in the nucleus for the maturation of the functional mRNA and in the cytoplasm for fine-tuning gene expression. Given the fundamental importance of RNGTT in mRNA maturation and expression there is a need to further investigate the regulation of RNGTT. N6-methyladenosine (m6A) is one of the most abundant RNA modifications involved in the regulation of protein translation, mRNA stability, splicing, and export. We sought to investigate whether m6A could regulate the expression and activity of RNGTT. A motif for the m6A writer methyltransferase 3 (METTL3) in the 3’UTR of RNGTT mRNA was identified. Knockdown of METTL3 resulted in destabilizing RNGTT mRNA, and reduced protein expression. Sequencing of capped mRNAs identified an underrepresentation of ribosomal protein mRNA overlapping with 5’ terminal oligopyrimidine (TOP) mRNAs and genes are dysregulated when cytoplasmic capping is inhibited. Pathway analysis identified disruptions in the mTOR and p70S6K pathways. A reduction in RPS6 mRNA capping, protein expression, and phosphorylation was detected with METTL3 knockdown.
SHC-3: a previously unidentifiedC. elegansShc family member functions in the insulin-like signaling pathway to enhance survival during L1 arrest
Authors: Guerrero Victoria L. León , Di Bernardo Mercedes , Hardy W. Rod , Sutoski Jacob C. , MacNeil Lesley T.
Published: November 2023

Shc proteins function in many different signaling pathways where they mediate phosphorylation-dependent protein-protein interactions. These proteins are characterized by the presence of two phosphotyrosine-binding domains, an N-terminal PTB and a C-terminal SH2. We describe a previously unrecognizedC. elegansShc gene,shc-3and characterize its role of in stress response. Bothshc-3andshc-1are required for long-term survival in L1 arrest, however, they do not act redundantly but rather play distinct roles in this process. SHC-3 function in survival during L1 arrest is DAF-16-dependent, demonstrating that like SHC-1, SHC-3 functions in the Insulin-like signaling pathway. In the absence of SHC-3, nuclear entry and exit are slowed suggesting that SHC-3 is required for rapid changes in DAF-16 signaling.
LDER-GE estimates phenotypic variance component of gene-environment interactions in human complex traits accurately with GE interaction summary statistics and full LD information
Authors: Dong Zihan , Jiang Wei , Li Hongyu , DeWan Andrew T. , Zhao Hongyu
Published: November 2023

Gene-environment (GE) interactions are essential in understanding human complex traits. Identifying these interactions is necessary for deciphering the biological basis of such traits. In this study, we introduce a statistical method Linkage-Disequilibrium Eigenvalue Regression for Gene-Environment interactions (LDER-GE). LDER-GE improves the accuracy of estimating the phenotypic variance component explained by genome-wide GE interactions using large-scale biobank association summary statistics. LDER-GE leverages the complete Linkage Disequilibrium (LD) matrix, as opposed to only the diagonal squared LD matrix utilized by LDSC (Linkage Disequilibrium Score)-based methods. Our extensive simulation studies demonstrate that LDER-GE performs better than LDSC-based approaches by enhancing statistical efficiency by approximately 23%. This improvement is equivalent to a sample size increase of around 51%. Additionally, LDER-GE effectively controls type-I error rate and produces unbiased results. We conducted an analysis using UK Biobank data, comprising 307,259 unrelated European-Ancestry subjects and 966,766 variants, across 151 environmental covariate-phenotype (E-Y) pairs. LDER-GE identified 35 significant E-Y pairs while LDSC-based method only identified 25 significant E-Y pairs with 23 overlapped with LDER-GE. Furthermore, we employed LDER-GE to estimate the aggregated variance component attributed to multiple GE interactions, leading to an increase in the explained phenotypic variance with GE interactions compared to considering main genetic effects only. Our results suggest the importance of impacts of GE interactions on human complex traits.
Epigenetic clocks, sex markers, and age-class diagnostics in three harvested large mammals
Authors: Czajka Natalie , Northrup Joseph M. , Jones Meaghan J. , Shafer Aaron B.A.
Published: November 2023

The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range: white-tailed deer, black bear, and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples (N=141) of all three species. We used a penalized regression model (elastic net) to build highly explanatory (black bearr= 0.95; white-tailed deerr= 0.99; mountain goatr= 0.97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age (clocks). We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. Our results demonstrate promising tools for the large-scale estimation of age in wild animals, which have the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.
Comparingin vitrocytotoxic drug sensitivity in colon and pancreatic cancer using 2D and 3D cell models: contrasting viability and growth inhibition in clinically relevant dose and repeated drug cycles
Authors: Tidwell Tia R. , Røsland Gro , Tronstad Karl Johan , Søreide Kjetil , Hagland Hanne R.
Published: November 2023

In vitrodrug screening that is more translatable to thein vivotumor environment can reduce both time and cost of cancer drug development. Here we address some of the shortcomings in screening and show how treatment with 5-fluorouracil (5-FU) in 2D and 3D culture models of colorectal cancer (CRC) and pancreatic ductal adenocarcinomas (PDAC) give different responses regarding growth inhibition.

The sensitivity of the cell lines at clinically relevant 5-FU concentrations was monitored over 4 days of treatment in both 2D and 3D cultures for CRC (SW948 and HCT116) and PDAC (Panc-1 and MIA-Pa-Ca-2) cell lines. The 3D cultures were maintained beyond this point to enable a second treatment cycle at day 14, following the timeline of a standard clinical 5-FU regimen. Evaluation after one cycle did not reveal significant growth inhibition in any of the CRC or PDAC 2D models. By the end of the second cycle of treatment the CRC spheroids reached 50% inhibition at clinically achievable concentrations in the 3D model, but not in the 2D model. The PDAC models were not sensitive to clinical doses even after two cycles. High content viability metrics point to even lower response in the resistant PDAC models.

This study reveals the limitations of testing drugs in 2D cancer models and short exposure in 3D models, and the importance of using appropriate growth inhibition analysis. We found that screening with longer exposure and several cycles of treatment in 3D models suggests a more reliable way to assess drug sensitivity.
Adaptive Coding Explains the Paradoxical Relationship between hippocampus size and memory function in Alzheimer’s Disease, Autism Spectrum Disorder, and PTSD
Authors: Stocco Andrea , Hake Holly S. , Leonard Bridget , Li Xinyue
Published: November 2023

The relationship between hippocampal volume and memory function has produced mixed results in neuroscience research, which suggests an additional influencing mechanism. To explore the role of an experience-dependent encoding mechanism, we developed an autoencoder model of the cortex-hippocampus loop and examined how its memory representation is affected by a penalty that prioritizes sparseness. We trained our model with the Fashion MNIST database and a loss function to modify synapses via backpropagation of mean squared recall error. The model exhibited experience-dependent efficient encoding, representing frequently-repeated objects with fewer neurons and smaller loss penalties; representations of similar sizes were found for objects repeated equally. Our findings clarify perplexing results from neurodevelopmental studies by linking increased hippocampal size and memory impairments in autism spectrum disorder (ASD) to decreased sparseness, and explaining dementia symptoms of forgetting with varied neuronal integrity. Our findings propose a novel model that connects observed relationships between hippocampal size and memory to the environmental demands and the underlying biological constraints, contributing to the development of a larger theory on experience-dependent encoding and storage and its failure.

Author Summary

The hippocampus is the brain region where memories are initially formed. A larger hippocampus seems to be associated with better memory performance, but this is not a static relationship; studies suggest that its size might grows with demand (e.g., the need to memorize more information) and that, in certain conditions, larger or smaller volumes of the hippocampus are not associated with better or worse memory. We demonstrate that it is possible to make sense of these findings by assuming that the hippocampus balances the need to correctly remember with the need to minimize resources used to store it, and that the hippocampal size might change as a function of memory demands (the characteristics of the information to memorize) and the underlying biology (e.g., the presence of hippocampal cell damage, or a reduction in hippocampal GABA receptors). We test this hypothesis by building a neural network model; the model correctly predicts existing, puzzling findings in the literature, and can even capture subtle interactions between different phenomena, such as predicting that individuals with Autism Spectrum Disorder would be more susceptible to memory loss in dementia.