bluuebunny/crossref_metadata_2025 huggingface dataset:
Increased 68Ga-FAPI Activity in Hepatic Inflammatory Myofibroblastoma
Authors: Ou Lei , Zhou Yue , Sun Rui , Zhang Chunyin , Chen XiaoLiang
Published: April 2023

Hepatic inflammatory myofibroblastoma is an uncommon borderline tumor. We present 68Ga-FAPI PET/CT findings of hepatic inflammatory myofibroblastoma in a 58-year-old man. The rare hepatic inflammatory myofibroblastoma demonstrated intense tracer uptake on 68Ga-FAPI PET/CT. This case demonstrates the potential value of 68Ga-FAPI PET/CT for the evaluation of hepatic inflammatory myofibroblastoma.
Global Smile Foundation’s Cleft Surgical Outreach Program: Clinical and Economic Impact During the Past 14 Years
Authors: Younan Robert A. , Melhem Antonio M. , Haddad Mario , Annan Beyhan , Najjar Wassim , Kantar Rami S. , Hamdan Usama S.
Published: April 2023

Clefts of the lip and/or palate can result in significant morbidity as well as economic and psychosocial distress for patients and families. Global Smile Foundation is a non-profit organization committed to providing comprehensive cleft care to patients with cleft of the lip/palate around the world. Primary cleft lip and primary cleft palate repairs performed by the Global Smile Foundation in the last decade were reviewed. Averted disability-adjusted life years were estimated and assessed for their economic value. A total of 15,310 disability-adjusted life years were averted. The financial gain was estimated between $78,323,624 and $152,906,604, with an average financial benefit of $48,021 to $93,750 per patient.
A Clinical Review of the Classification and Management of Prefrailty in Older Adults
Authors: Prevett Christina , Tang Ada
Published: April 2023

Frailty is a clinical geriatric syndrome where loss of physical resiliency increases vulnerability to external stressors. Frailty is predictive of many adverse health outcomes. Frailty exists across a spectrum where prefrailty is an intermediary, subclinical state of frailty. Evidence suggests that it is easier to reverse prefrailty states than to reverse established frailty, and therefore may be an ideal target for preventative interventions. This narrative review discusses clinical methods of identifying individuals with prefrailty, and interventions shown to be effective in improving frailty status in older adults.
Mobility and Frailty Rehabilitation in Older Adults
Authors: Treacy Daniel , Sherrington Catherine
Published: April 2023

Mobility is a broad term which is defined as the ability to move around and change positions such as walking, rising from a chair, and maintaining balance while standing. Mobility has been shown to be key determinant in older individuals' overall health and quality of life. High rates of mobility and functional limitation are evident in older people with frailty. Exercise-based rehabilitation interventions including mobility and balance training are effective in improving mobility in individuals with frailty.
Using Laser Speckle Contrast Imaging to Quantify Perfusion Quality in Kidney and Pancreas Grafts on Vascular Reperfusion: A Proof-of-Principle Study
Authors: Gopal Jeevan Prakash , Vaz Osborne , Varley Rebecca , Spiers Harry , Goldsworthy Matthew A. , Siddagangaiah Vishwanath , Lock Brian , Sharma Videha , Summers Angela , Moinuddin Zia , van Dellen David , Augustine Titus
Published: April 2023

Introduction.

The accuracy of intraoperative graft perfusion assessment still remains subjective, with doppler examination being the only objective adjunct. Laser speckle contrast imaging (LSCI) has been used to assess intraoperative blood flow in neurosurgery and in various surgical specialties. Despite its ability to accurately quantify perfusion at the microvascular level, it has not been clinically evaluated in kidney/kidney-pancreas transplantation for perfusion characterization. We aimed to evaluate the utility of LSCI and identify objective parameters that can be quantified at reperfusion.

Methods.

This study was registered in ClinicalTrials.gov (NCT04202237). The Moor FLPI-2 blood flow imager was used in 4 patients (1 Simultaneous Pancreas and Kidney, 2 deceased, and 1 living donor kidney transplants) during reperfusion to capture reperfusion data. The following parameters were measured: flux (average speed × concentration of moving red blood cells in the sample volume), doppler centroid, total and valid pixels, valid rate, and total and valid area. Flux data were analyzed with Moor FLPI analysis software.

Results.

The perfusion characteristics and flux images correlated with initial graft function.

Conclusions.

LSCI is a safe, noncontact imaging modality that provides real-time, accurate, high-resolution, full field blood flow images and a wide range of flux data to objectively quantify organ reperfusion intraoperatively in kidney/kidney-pancreas transplantation. This modality could be used to develop a robust numerical quantification system for the evaluation and reporting of intraoperative organ perfusion, and aid intraoperative decision-making. Perfusion data could be combined with biomarkers and immunological parameters to more accurately predict graft outcomes.
Cost-effectiveness of Interventions to Increase Utilization of Kidneys From Deceased Donors With Primary Brain Malignancy in an Australian Setting
Authors: Hedley James A. , Kelly Patrick J. , Wyld Melanie , Shah Karan , Morton Rachael L. , Byrnes Juliet , Rosales Brenda M. , De La Mata Nicole L. , Wyburn Kate , Webster Angela C.
Published: April 2023

Background.

Kidneys from potential deceased donors with brain cancer are often foregone due to concerns of cancer transmission risk to recipients. There may be uncertainty around donors’ medical history and their absolute transmission risk or risk-averse decision-making among clinicians. However, brain cancer transmissions are rare, and prolonging waiting time for recipients is harmful.

Methods.

We assessed the cost-effectiveness of increasing utilization of potential deceased donors with brain cancer using a Markov model simulation of 1500 patients waitlisted for a kidney transplant, based on linked transplant registry data and with a payer perspective (Australian government). We estimated costs and quality-adjusted life-years (QALYs) for three interventions: decision support for clinicians in assessing donor risk, improved cancer classification accuracy with real-time data-linkage to hospital records and cancer registries, and increased risk tolerance to allow intermediate-risk donors (up to 6.4% potential transmission risk).

Results.

Compared with current practice, decision support provided 0.3% more donors with an average transmission risk of 2%. Real-time data-linkage provided 0.6% more donors (1.1% average transmission risk) and increasing risk tolerance (accepting intermediate-risk 6.4%) provided 2.1% more donors (4.9% average transmission risk). Interventions were dominant (improved QALYs and saved costs) in 78%, 80%, and 87% of simulations, respectively. The largest benefit was from increasing risk tolerance (mean +18.6 QALYs and AU$2.2 million [US$1.6 million] cost-savings).

Conclusions.

Despite the additional risk of cancer transmission, accepting intermediate-risk donors with brain cancer is likely to increase the number of donor kidneys available for transplant, improve patient outcomes, and reduce overall healthcare expenditure.
Microbial communities in freshwater used for hydraulic fracturing are unable to withstand the high temperatures and pressures characteristic of fractured shales
Authors: Nixon Sophie L. , Plominsky Alvaro M. , Hernandez-Becerra Natali , Boothman Christopher , Bartlett Douglas H.
Published: April 2023

Natural gas is recovered from shale formations by hydraulic fracturing, a process known to create microbial ecosystems in the deep subsurface. Microbial communities that emerge in fractured shales include organisms known to degrade fracturing fluid additives and contribute to corrosion of well infrastructure. In order to limit these negative microbial processes, it is essential to constrain the source of the responsible micro-organisms. Previous studies have identified a number of potential sources, including fracturing fluids and drilling muds, yet these sources remain largely untested. Here, we apply high-pressure experimental approaches to assess whether the microbial community in synthetic fracturing fluid made from freshwater reservoir water can withstand the temperature and pressure conditions of hydraulic fracturing and the fractured shale environment. Using cell enumerations, DNA extraction and culturing, we show that the community can withstand high pressure or high temperature alone, but the combination of both is fatal. These results suggest that initial freshwater-based fracturing fluids are an unlikely source of micro-organisms in fractured shales. These findings indicate that potentially problematic lineages, such as sulfidogenic strains of

Halanaerobium

that have been found to dominate fractured shale microbial communities, likely derive from other input sources into the downwell environment, such as drilling muds.
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)
Authors: Honma Hajime , Takahashi Nobuyuki , Arisue Nobuko , Sugishita Tomohiko
Published: April 2023

Malarial parasites exhibit extensive genomic plasticity, which induces the antigen diversification and the development of antimalarial drug resistance. Only a few studies have examined the genome maintenance mechanisms of parasites. The study aimed at elucidating the impact of a mutation in a DNA mismatch repair gene on genome stability by maintaining the mutant and wild-type parasites through serial in vitro cultures for approximately 400 days and analysing the subsequent spontaneous mutations. A P513T mutant of the DNA mismatch repair protein PfMSH2-1 from Plasmodium falciparum 3D7 was created. The mutation did not influence the base substitution rate but significantly increased the insertion/deletion (indel) mutation rate in short tandem repeats (STRs) and minisatellite loci. STR mutability was affected by allele size, genomic category and certain repeat motifs. In the mutants, significant telomere healing and homologous recombination at chromosomal ends caused extensive gene loss and generation of chimeric genes, resulting in large-scale chromosomal alteration. Additionally, the mutant showed increased tolerance to N-methyl-Nʹ-nitro-N-nitrosoguanidine, suggesting that PfMSH2-1 was involved in recognizing DNA methylation damage. This work provides valuable insights into the role of PfMSH2-1 in genome stability and demonstrates that the genomic destabilization caused by its dysfunction may lead to antigen diversification.
Bacterial secretion system functions: evidence of interactions and downstream implications
Authors: Maphosa Silindile , Moleleki Lucy N. , Motaung Thabiso E.
Published: April 2023

Unprecedented insights into the biology and functions of bacteria have been and continue to be gained through studying bacterial secretion systems in isolation. This method, however, results in our understanding of the systems being primarily based on the idea that they operate independently, ignoring the subtleties of downstream interconnections. Gram-negative bacteria are naturally able to adapt to and navigate their frequently varied and dynamic surroundings, mostly because of the covert connections between secretion systems. Therefore, to comprehend some of the linked downstream repercussions for organisms that follow this discourse, it is vital to have mechanistic insights into how the intersecretion system functions in bacterial rivalry, virulence, and survival, among other things. To that purpose, this paper discusses a few key instances of molecular antagonistic and interdependent relationships between bacterial secretion systems and their produced functional products.
VoroIF-GNN: Voronoi tessellation-derived protein-protein interface assessment using a graph neural network
Authors: Olechnovič Kliment , Venclovas Česlovas
Published: April 2023

We present VoroIF-GNN, a novel single-model method for assessing inter-subunit interfaces in protein-protein complexes. Given a multimeric protein structural model, we derive interface contacts from the Voronoi tessellation of atomic balls, construct a graph of those contacts, and predict accuracy of every contact using an attention-based graph neural network. The contact-level predictions are then summarized to produce whole interface-level scores. VoroIF-GNN was blindly tested for its ability to estimate accuracy of protein complexes during CASP15 and showed strong performance in selecting the best multimeric model out of many. The method implementation is freely available athttps://klimentolechnovic.github.io/voronota/expansion_js/.
Tracking insulin- and glucagon-expressing bihormonal cells during differentiation using anINSULINandGLUCAGONdouble reporter human embryonic stem cell line
Authors: Mar Samantha , Filatov Ekaterina , Nian Cuilan , Sasaki Shugo , Zhang Dahai , Lynn Francis C.
Published: April 2023

Human embryonic stem cell (hESC)-derived pancreatic alpha and beta cells can be used to develop cell replacement therapies to treat diabetes. However, recent published differentiation protocols yield varying amounts of alpha and beta cells amidst heterogeneous cell populations. To visualize and isolate hESC-derived alpha and beta cells, we generated aGLUCAGON-2A- mScarletandINSULIN-2A-EGFPdual fluorescent reporter (INSEGFPGCGmScarlet) hESC line using CRISPR/Cas9. We established robust expression of EGFP and mScarlet fluorescent proteins in insulin- and glucagon-expressing cells respectively without compromising the differentiation or function of these cells. We also showed the insulin- and glucagon-expressing bihormonal population at the maturing endocrine cell stage (Stage 6) lose insulin expression over time, while maintaining an alpha-like expression profile, suggesting these bihormonal cells are preferentially fated to become alpha-like cellsin vitro. Together, the INSEGFPGCGmScarlethESC line provides an efficient strategy for tracking populations of hESC-derived beta- and alpha-like cells.
Validating a low-cost, open-source, locally manufactured workstation and computational pipeline for automated histopathology evaluation using deep learning
Authors: Choudhury Divya , Dolezal James , Dyer Emma , Kochanny Sara , Ramesh Siddi , Howard Frederick M. , Margalus Jayson R. , Schroeder Amelia , Schulte Jefree , Garassino Marina C. , Kather Jakob N. , Pearson Alexander T.
Published: April 2023

Deployment and access to state-of-the-art diagnostic technologies remains a fundamental challenge in providing equitable global cancer care to low-resource settings. The expansion of digital pathology in recent years and its interface with computational biomarkers provides an opportunity to democratize access to personalized medicine. Here we describe a low-cost platform for digital side capture and computational analysis composed of open-source components. The platform provides low-cost ($200) digital image capture from glass slides and is capable of real-time computational image analysis using an open-source deep learning (DL) algorithm and Raspberry Pi ($35) computer. We validate the performance of deep learning models’ performance using images captured from the open-source workstation and show similar model performance when compared against significantly more expensive standard institutional hardware.
DECODING COMPLEXITY IN BIOMOLECULAR RECOGNITION OF DNA I-MOTIFS
Authors: Yazdani Kamyar , Seshadri Srinath , Tillo Desiree , Vinson Charles , Schneekloth John S.
Published: April 2023

DNA i-motifs (iMs) are non-canonical C-rich secondary structures implicated in numerous cellular processes. Though iMs exist throughout the genome, our understanding of iM recognition by proteins or small molecules is limited to a few examples. We designed a DNA microarray containing 10,976 genomic iM sequences to examine the binding profiles of four iM-binding proteins, mitoxantrone, and the iMab antibody. iMab microarray screens demonstrated that pH 6.5, 5% BSA buffer was optimal, and fluorescence was correlated with iM C-tract length. hnRNP K broadly recognizes diverse iM sequences, favoring 3-5 cytosine repeats flanked by thymine-rich loops of 1-3 nucleotides. Array binding mirrored public ChIP-Seq datasets, in which 35% of well-bound array iMs are enriched in hnRNP K peaks. In contrast, other reported iM-binding proteins had weaker binding or preferred G-quadruplex (G4) sequences instead. Mitoxantrone broadly binds both shorter iMs and G4s, consistent with an intercalation mechanism. These results suggest that hnRNP K may play a role in iM-mediated regulation of gene expressionin vivo, whereas hnRNP A1 and ASF/SF2 are possibly more selective in their binding preferences. This powerful approach represents the most comprehensive investigation of how biomolecules selectively recognize genomic iMs to date.
Alternative splicing impacts microRNA regulation within coding regions
Authors: Hackl Lena Maria , Fenn Amit , Louadi Zakaria , Baumbach Jan , Kacprowski Tim , List Markus , Tsoy Olga
Published: April 2023

MicroRNAs (miRNAs) are small non-coding RNA molecules that bind to target sites in different gene regions and regulate post-transcriptional gene expression. Approximately 95% of human multi-exon genes can be spliced alternatively, which enables the production of functionally diverse transcripts and proteins from a single gene. Through alternative splicing, transcripts might lose the exon with the miRNA target site and become unresponsive to miRNA regulation. To check this hypothesis, we studied the role of miRNA target sites in both coding and noncoding regions using six cancer data sets from The Cancer Genome Atlas (TCGA). First, we predicted miRNA target sites on mRNAs from their sequence using TarPmiR. To check whether alternative splicing interferes with this regulation, we trained linear regression models to predict miRNA expression from transcript expression. Using nested models, we compared the predictive power of transcripts with miRNA target sites in the coding regions to that of transcripts without target sites. Models containing transcripts with target sites perform significantly better. We conclude that alternative splicing does interfere with miRNA regulation by skipping exons with miRNA target sites within the coding region.
Suprabasal cells retaining stem cell identity programs drive basal cell hyperplasia in eosinophilic esophagitis
Authors: Clevenger Margarette H. , Karami Adam L. , Carlson Dustin A. , Kahrilas Peter J. , Gonsalves Nirmala , Pandolfino John E. , Winter Deborah R. , Whelan Kelly A. , Tétreault Marie-Pier
Published: April 2023

Eosinophilic esophagitis (EoE) is an esophageal immune-mediated disease characterized by eosinophilic inflammation and epithelial remodeling, including basal cell hyperplasia (BCH) and loss of differentiation. Although BCH correlates with disease severity and with persistent symptoms in patients in histological remission, the molecular processes driving BCH remain poorly defined. Here, we demonstrate that despite the presence of BCH in all EoE patients examined, no increase in basal cell proportion was observed by scRNA-seq. Instead, EoE patients exhibited a reduced pool ofKRT15+ COL17A1+quiescent cells, a modest increase inKI67+dividing epibasal cells, a substantial increase inKRT13+ IVL+suprabasal cells, and a loss of differentiated identity in superficial cells. Suprabasal and superficial cell populations demonstrated increased quiescent cell identity scoring in EoE with the enrichment of signaling pathways regulating pluripotency of stem cells. However, this was not paired with increased proliferation. Enrichment and trajectory analyses identified SOX2 and KLF5 as potential drivers of the increased quiescent identity and epithelial remodeling observed in EoE. Notably, these findings were not observed in GERD. Thus, our study demonstrates that BCH in EoE results from an expansion of non-proliferative cells that retain stem-like transcriptional programs while remaining committed to early differentiation.
Nfe2l1-mediated proteasome function controls muscle energy metabolism in obesity
Authors: Lemmer Imke L. , Haas Daniel T. , Willemsen Nienke , Kotschi Stefan , Toksöz Irmak , Gjika Ejona , Khani Sajjad , Rohm Maria , Diercksen Nick , Nguyen Phong B.H. , Menden Michael P. , Egu Desalegn T. , Waschke Jens , Larsen Steen , Ma Tao , Gerhart-Hines Zachary , Herzig Stephan , Dyar Kenneth , Krahmer Natalie , Bartelt Alexander
Published: April 2023

Muscle function is an important denominator of energy balance and metabolic health. Adapting the proteome to energetic challenges, in response to diet or fasting, is facilitated by programs of proteostasis, but the adaptive role of the ubiquitin-proteasome system (UPS) in muscle remains unclear. Here, using a multi-omics approach, we uncover that the distinct metabolic condition of obesity is associated with recalibration of the UPS in muscle. Interestingly, obesity is associated with the activation of the transcription factor Nuclear factor, erythroid derived 2,- like 1 (Nfe2l1, also known as Nrf1), and loss of myocyte Nfe2l1 diminishes proteasomal activity and leads to hyperubiquitylation. Mice lacking Nfe2l1 display hormetic energy metabolism and resistance to diet-induced obesity, associated with a lean phenotype and muscle fiber type switching. In conclusion, we define a new adaptive role for UPS in remolding of muscle proteome and function, which is controlled by fine-tuning of proteasome function by Nfe2l1.
Automatic recognition of complementary strands: Lessons regarding machine learning abilities in RNA folding
Authors: Chasles Simon , Major François
Published: April 2023

Prediction of RNA secondary structure from single sequences still needs substantial improvements. The application of machine learning (ML) to this problem has become increasingly popular. However, ML algorithms are prone to overfitting, limiting the ability to learn more about the inherent mechanisms governing RNA folding. It is natural to use high-capacity models when solving such a difficult task, but poor generalization is expected when too few examples are available. Here, we report the relation between capacity and performance on a fundamental related problem: determining whether two sequences are fully complementary. Our analysis focused on the impact of model architecture and capacity as well as dataset size and nature on classification accuracy. We observed that low-capacity models are better suited for learning with mislabelled training examples, while large capacities improve the ability to generalize to structurally dissimilar data. It turns out that neural networks struggle to grasp the fundamental concept of base complementarity, especially in lengthwise extrapolation context. Given a more complex task like RNA folding, it comes as no surprise that the scarcity of usable examples hurdles the applicability of machine learning techniques to this field.
Convergence of multiple RNA-silencing pathways on GW182/TNRC6
Authors: Welte Thomas , Goulois Alison , Stadler Michael B. , Hess Daniel , Soneson Charlotte , Neagu Anca , Azzi Chiara , Lübke Marlena J. , Seebacher Jan , Schmidt Isabel , Estoppey David , Nigsch Florian , Reece-Hoyes John , Hoepfner Dominic , Großhans Helge
Published: April 2023

The RNA-binding protein TRIM71/LIN-41 is a phylogenetically conserved developmental regulator that functions in mammalian stem cell reprogramming, brain development and cancer. TRIM71 recognizes target mRNAs through hairpin motifs and silences them through molecular mechanisms that await identification. Here, we uncover that TRIM71 silences its targets by recruiting TNRC6/GW182, a core component of the miRNA-induced silencing complex (miRISC). Co-immunoprecipitation reveals interaction of TNRC6A with additional RNA-binding proteins and we demonstrate that AGO2, TRIM71, and UPF1 each recruit TNRC6 to specific, largely distinct sets of transcripts to silence them. As cellular TNRC6 levels are limiting, competition occurs among the silencing pathways, such that loss of AGO2 protein, or of AGO2 binding to TNRC6, enhances the activities of the other pathways. We conclude that a miRNA-like silencing activity is shared among different mRNA silencing pathways and that use of TNRC6 as a central hub provides a means to integrate their activities.
p73 activates transcriptional signatures of basal lineage identity and ciliogenesis in pancreatic ductal adenocarcinoma
Authors: Hur Stella K. , Somerville Tim D.D. , Wu Xiaoli S. , Maia-Silva Diogo , Demerdash Osama E. , Tuveson David A. , Notta Faiyaz , Vakoc Christopher R.
Published: April 2023

During the progression of pancreatic ductal adenocarcinoma (PDAC), tumor cells are known to acquire transcriptional and morphological properties of the basal (also known as squamous) epithelial lineage, which leads to more aggressive disease characteristics. Here, we show that a subset of basal-like PDAC tumors aberrantly express p73 (TA isoform), which is a known transcriptional activator of basal lineage identity, ciliogenesis, and tumor suppression in normal tissue development. Using gain- and loss- of function experiments, we show that p73 is necessary and sufficient to activate genes related to basal identity (e.g.KRT5), ciliogenesis (e.g.FOXJ1), and p53-like tumor suppression (e.g.CDKN1A) in human PDAC models. Owing to the paradoxical combination of oncogenic and tumor suppressive outputs of this transcription factor, we propose that PDAC cells express a low level of p73 that is optimal for promoting lineage plasticity without severe impairment of cell proliferation. Collectively, our study reinforces how PDAC cells exploit master regulators of the basal epithelial lineage during disease progression.
Association of Oxytetracycline and Florfenicol affects zebrafish larvae behavioral repertoire
Authors: Gusso Darlan , Gobbo Marilia Oberto da Silva , Rübensam Gabriel , Bonan Carla Denise
Published: April 2023

The fish farms are increasingly growing and, consequently, the use of antibiotics in aquaculture. Oxytetracycline (OTC) and Florfenicol (FF) are the most common antibiotics applied in the fish production sector and livestock farming. The elucidation of the effects of the antibiotics is essential to control their use and their physiological and pharmacological implications. Here we studied the behavioral effects of the 96 h-exposure to OTC (2, 10, 20, and 100 mg/L), FF (0.01, 0.05, 2 and 10 mg/L) or OTC (10 mg/L) + FF (10 mg/L) in zebrafish larvae. We observed that the covered distance and the movement increased in animals exposed to OTC + FF when compared to control. In addition, fish entered the center of the plate test more often and stayed there longer. The turn angle was reduced at OTC + FF. We also observed that the optomotor response was compromised by 10 and 20 mg/L OTC and to OTC + FF. Our data demonstrated that there is an increase in the number of entries in the center area and time spent in center area for FF- and OTC + FF-treated groups. These data showed that the antibiotics promoted a reduction of anxiety-like behavior allowing larvae to explore more the novel environment as well as a detrimental performance for the optomotor response.

Highlights

Florfenicol (FF) did not alter exploratory and anxiety-like behavior in zebrafish larvae.

Oxytetracycline (OTC) did not alter exploratory behavior, but there was an increase in the time spent in the center area

OTC plus FF increased distance and movement in zebrafish larvae.

OTC plus FF reduced the anxiety-like behavior in zebrafish larvae.

Optomotor behavior was compromised by treatments with OTC or OTC + FF.
Shedding light (… electrons) on human bone ultrastructure with correlative on-axis electron tomography and energy dispersive X-ray spectroscopy tomography
Authors: Micheletti Chiara , Shah Furqan A. , Palmquist Anders , Grandfield Kathryn
Published: April 2023

Mineralized collagen fibrils are the building block units of bone at the nanoscale. While it is known that collagen fibrils are mineralized both inside their gap zones (intra-fibrillar mineralization) and on their outer surfaces (extra-fibrillar mineralization), a clear visualization of this architecture in three dimensions (3D), combining structural and compositional information over large volumes, but without compromising the resolution, remains challenging. In this study, we demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with a diameter up to 700 nm prepared from individual osteonal lamellae in the human femur. Our work mainly focuses on two aspects: i) low-contrast nanosized circular spaces (“holes”) observed in sections of bone oriented perpendicular to the long axis of a long bone; and ii) extra-fibrillar mineral, especially in terms of morphology and spatial relationship with respect to intra-fibrillar mineral and collagen fibrils. From our analyses, it emerges quite clearly that most “holes” are cross-sectional views of collagen fibrils. While this had been postulated before, our 3D reconstructions and reslicing along meaningful two-dimensional (2D) cross-sections provide a direct visual confirmation. Extra-fibrillar mineral appears composed of thin plates that are interconnected and span over several collagen fibrils, confirming that mineralization is cross-fibrillar, at least for the extra-fibrillar phase. EDX tomography shows mineral signature (Ca and P) within the gap zones, but the signal appears weaker than that associated to the extra-fibrillar mineral, pointing towards the existence of dissimilarities between the two types of mineralization.
A discrete model for the growth and spread of the Scottish populations of red squirrels (Sciurus vulgaris) and grey squirrels (Sciurus carolinensis)
Authors: Gramain Jean-Baptiste
Published: April 2023

In this article, a model, discrete in space and time, is developed to describe the growth and spread of the Scottish populations of red squirrels (Sciurus vulgaris) and grey squirrel (Sciurus carolinensis). The initial state for the model is designed using a large dataset of records of sightings of individuals of both species reported by members of the public. Choices of parameters involved in the model and their values are informed by the analysis of this dataset for the period 2011-2016, and model predictions are compared to records for the years 2006-2019.
Pyroptosis inhibiting nanobodies block Gasdermin D pore formation
Authors: Kopp Anja , Hagelueken Gregor , Jamitzky Isabell , Moecking Jonas , Schiffelers Lisa D. J. , Schmidt Florian I. , Geyer Matthias
Published: April 2023

Gasdermin D (GSDMD) is a key mediator of pyroptosis, a pro-inflammatory form of cell death occurring downstream of inflammasome activation as part of the innate immune defence. Upon cleavage by inflammatory caspases, the N-terminal domain of GSDMD forms pores in the plasma membrane resulting in cytokine release and eventually cell death. Targeting GSDMD is an attractive way to dampen inflammation. In this study, six GSDMD targeting nanobodies were characterized in terms of their binding affinity, stability, and effect on GSDMD pore formation. Three of the nanobodies inhibited GSDMD pore formation in a liposome leakage assay, although caspase cleavage was not perturbed. We determined the crystal structure of human GSDMD in complex with two nanobodies at 1.9 Å resolution, providing detailed insights into the GSDMD–nanobody interactions and epitope binding. The pore formation is sterically blocked by one of the nanobodies that binds to the oligomerization interface of the N-terminal domain in the multi-subunit assembly. Our biochemical and structural findings provide new tools for studying inflammasome biology and build a framework for the design of novel GSDMD targeting drugs.
The Role of MAP3K1 in the Development of the Female Reproductive Tract
Authors: Kimura Eiki , Mongan Maureen , Xiao Bo , Wang Jingjing , Carreira Vinicius S , Bolon Brad , Zhang Xiang , Burns Katherine A. , Biesiada Jacek , Medvedovic Mario , Puga Alvaro , Xia Ying
Published: April 2023

Mitogen-Activated Protein 3 Kinase 1 (MAP3K1) is a dynamic signaling molecule with a plethora of cell-type specific functions, most of which are yet to be understood. Here we describe a role for MAP3K1 in the development of female reproductive tract (FRT). MAP3K1 kinase domain-deficient (Map3k1ΔKD) females exhibit imperforate vagina, labor failure, and infertility. These defects correspond to a shunted Müllerian duct (MD), the principle precursor of the FRT, in embryos, while they manifest as a contorted caudal vagina with abrogated vaginal-urogenital sinus fusion in neonates. In epithelial cells, MAP3K1 acts through JNK and ERK to activate WNT, yetin vivoMAP3K1 is crucial for WNT activity in mesenchyme associated with the caudal MD. Expression ofWnt7bis high in wild type, but low inMap3k1knockout MD epithelium and MAP3K1-deficient keratinocytes. Correspondingly, conditioned media derived from MAP3K1-competent epithelial cells activate TCF/Lef-luciferase reporter in fibroblasts, suggesting that MAP3K1-induced factors released from epithelial cells trans-activate WNT signaling in fibroblasts. Our results reveal a temporal-spatial and paracrine MAP3K1-WNT crosstalk contributing to MD caudal elongation and FRT development.

Highlights

MAP3K1 deficient female mice exhibit imperforate vagina and infertility

Loss of MAP3K1 kinase activity impedes Müllerian duct (MD) caudal elongation and fusion with urogenital sinus (UGS) in embryogenesis

The MAP3K1-MAPK pathway up-regulates WNT signaling in epithelial cells

MAP3K1 deficiency down-regulates Wnt7b expression in the MD epithelium and prevents WNT activity in mesenchyme of the caudal MD
The Promise and Pitfalls of Prophages
Authors: McKerral Jody C. , Papudeshi Bhavya , Inglis Laura K. , Roach Michael J. , Decewicz Przemyslaw , McNair Katelyn , Luque Antoni , Dinsdale Elizabeth A. , Edwards Robert A.
Published: April 2023

Phages dominate every ecosystem on the planet. While virulent phages sculpt the microbiome by killing their bacterial hosts, temperate phages provide unique growth advantages to their hosts through lysogenic conversion. Many prophages benefit their host, and prophages are responsible for genotypic and phenotypic differences that separate individual microbial strains. However, the microbes also endure a cost to maintain those phages: additional DNA to replicate and proteins to transcribe and translate. We have never quantified those benefits and costs. Here, we analysed over two and a half million prophages from over half a million bacterial genome assemblies. Analysis of the whole dataset and a representative subset of taxonomically diverse bacterial genomes demonstrated that the normalised prophage density was uniform across all bacterial genomes above 2 Mbp. We identified a constant carrying capacity of phage DNA per bacterial DNA. We estimated that each prophage provides cellular services equivalent to approximately 2.4 % of the cell’s energy or 0.9 ATP per bp per hour. We demonstrate analytical, taxonomic, geographic, and temporal disparities in identifying prophages in bacterial genomes that provide novel targets for identifying new phages. We anticipate that the benefits bacteria accrue from the presence of prophages balance the energetics involved in supporting prophages. Furthermore, our data will provide a new framework for identifying phages in environmental datasets, diverse bacterial phyla, and from different locations.
Protein multiple conformations prediction using multi-objective evolution algorithm
Authors: Hou Ming-Hua , Jin Si-Rong , Cui Xin-Yue , Peng Chun-Xiang , Zhao Kai-Long , Song Le , Zhang Gui-Jun
Published: April 2023

Motivation

With the breakthrough of AlphaFold2 and the publication of AlphaFold DB, the protein structure prediction has made remarkable progress, which may further promote many potential applications of proteomics in all areas of life. However, it should be noted that AlphaFold2 models tend to represent only a single static structure, and accurately predicting multiple conformations remains a challenge. Therefore, it is essential to develop methods for predicting multiple conformations, which enable us to gain knowledge of multiple conformational states and the broader conformational landscape to better understand the mechanism of action.

Results

In this work, we proposed a multiple conformational states folding method using the distance-based multi-objective evolutionary algorithm framework, named MultiSFold. First, a multi-objective energy landscape with multiple competing constraints generated by deep learning is constructed. Then, an iterative modal exploration and exploitation strategy based on multi-objective optimization, geometric optimization and structural similarity clustering is designed to perform conformational sampling. Finally, the final population is generated using a loop-specific perturbation strategy to adjust the spatial orientations. MultiSFold was compared with state-of-the-art methods on a developed benchmark testset containing 81 proteins with two representative conformational states. Based on the proposed metric, the success ratio of MultiSFold predicting multiple conformations was 70.4% while that of AlphaFold2 was 9.88%, which may indicate that conformational sampling combined with knowledge gained through deep learning has the potential to produce conformations spanned the range between two experimental structures. In addition, MultiSFold was tested on 244 human proteins with low structural accuracy in AlphaFold DB to test whether it could further improve the accuracy of static structures. The experimental results demonstrate that the TM-score of MultiSFold is 2.97% and 7.72% higher than that of AlphaFold2 and RoseTTAFold, respectively, supporting our hypothesis that multiple competing optimization objectives can further assist conformational search to improve prediction accuracy.
Environmental impacts of cultured meat: A cradle-to-gate life cycle assessment
Authors: Risner Derrick , Kim Yoonbin , Nguyen Cuong , Siegel Justin B. , Spang Edward S.
Published: April 2023

Interest in animal cell-based meat (ACBM) or cultured meat as a viable environmentally conscious replacement for livestock production has been increasing, however a life cycle assessment for the current production methods of ACBM has not been conducted. Currently, ACBM products are being produced at a small scale and at an economic loss, however ACBM companies are intending to industrialize and scale-up production. This study assesses the potential environmental impact of near term ACBM production. Updated findings from recent technoeconomic assessments (TEAs) of ACBM and a life cycle assessment of Essential 8™ were utilized to perform a life cycle assessment of near-term ACBM production. A scenario analysis was conducted utilizing the metabolic requirements examined in the TEAs of ACBM and a purification factor from the Essential 8™ life cycle assessment was utilized to account for growth medium component processing. The results indicate that the environmental impact of near-term ACBM production is likely to be orders of magnitude higher than median beef production if a highly refined growth medium is utilized for ACBM production.
Identification of FAM53C as a cytosolic-anchoring inhibitory binding protein of the kinase DYRK1A
Authors: Miyata Yoshihiko , Nishida Eisuke
Published: April 2023

The protein kinase DYRK1A encoded in human chromosome 21 is the major contributor to the multiple symptoms observed in Down syndrome patients. In addition, DYRK1A malfunction is associated with various other neurodevelopmental disorders such as autism spectrum disorder. Here we identified FAM53C with no hitherto known biological function as a novel suppressive binding partner of DYRK1A. FAM53C bound to the catalytic protein kinase domain of DYRK1A, whereas DCAF7/WDR68, the major DYRK1A-binding protein, binds to the N-terminal domain of DYRK1A. The binding of FAM53C inhibited autophosphorylation activity of DYRK1A and its kinase activity to an exogenous substrate MAPT/Tau. FAM53C did not bind directly to DCAF7/WDR68, whereas DYRK1A tethered FAM53C and DCAF7/WDR68 by binding concurrently to both of them, forming a tri-protein complex. DYRK1A possesses a nuclear localization signal and accumulates in the nucleus when overexpressed in cells. Co-expression of FAM53C induced cytoplasmic re-localization of DYRK1A, revealing the cytoplasmic anchoring function of FAM53C to DYRK1A. Moreover, the binding of FAM53C to DYRK1A suppressed the DYRK1A-dependent nuclear localization of DCAF7/WDR68. All the results show that FAM53C binds to DYRK1A, suppresses its kinase activity, and anchors it in the cytoplasm. In addition, FAM53C bound to the DYRK1A-related kinase DYRK1B with an Hsp90/Cdc37-independent manner. The results explain for the first time why endogenous DYRK1A is distributed in the cytoplasm in normal brain tissue. FAM53C-dependent regulation of the kinase activity and intracellular localization of DYRK1A may play a significant role in gene expression regulation caused by normal and aberrant levels of DYRK1A.
AI and supportive technology experiences of customers with visual impairments in hotel, restaurant, and travel contexts
Authors: Liu Aijing , Ma Emily , Wang Yao-Chin , Xu Shi (Tracy) , Grillo Tyran
Published: April 2023

Purpose

The purpose of this study is to critically reflect on visually impaired customers’ technology assistance needs and the perceptions of existing technologies’ performance in the contexts of hospitality and tourism.

Design/methodology/approach

Following a qualitative approach, this study used in-depth semistructured interviews with 19 participants with visual impairments.

Findings

Positive and negative sides of technology-assisted experiences in the hotel, restaurant, and travel domains were summarized, and room for improvement was discussed to enhance the quality of life and travel experience of visually impaired customers.

Practical implications

Findings from this study offer actionable implications and future directions to technicians and managers to make hospitality and travel experiences more inclusive.

Originality/value

This timely reflection addresses a critical situation by offering original ideas and calling for more discussion of under-represented groups with visual impairments.
Do human capital and relational capital influence knowledge-intensive firm competitiveness? The roles of export orientation and marketing knowledge capability
Authors: Mohammad Shafiee Majid , Warkentin Merrill , Motamed Setare
Published: April 2023

Purpose

This study aims to investigate the key roles of human and relational capital in the export orientation and competitiveness of knowledge-intensive cooperative companies. It is also aimed to examine the moderating role of marketing knowledge capabilities.

Design/methodology/approach

Data from 552 managers at 86 companies, selected from knowledge-intensive export cooperatives, were analyzed with structural equation modeling with the partial least squares approach.

Findings

Results indicate that both human and relational capital exert considerable effects on competitiveness. Export orientation was a driving factor for cooperatives’ competitiveness. Human and relational capital fostered the effects of export orientation on competitiveness. Moreover, marketing knowledge capabilities were found to moderate the relationships between human and relational capital and export orientation, as well as between export orientation and competitiveness.

Originality/value

By highlighting the role of human capital and relational capital in export orientation and competitiveness, this study offers an analysis of important managerial processes within cooperative companies, which have not been sufficiently addressed in previous research. This research also demonstrated the moderating role of marketing knowledge capabilities in strengthening relationships between human and relational capital and export orientation, as well as between export orientation and competitiveness, which has been neglected in previous studies. These findings provide academics and practitioners with a new framework for examining the relationships between these constructs, which will enable them to establish strategies for achieving a competitive advantage.
Entrepreneurs' preference for corporate venture capital – The influence of exit strategies and resource requirements
Authors: Weniger Stefanie , Jarchow Svenja , Nenadić Oleg
Published: April 2023

Purpose

Literature on entrepreneurial finance has long overcome the view of an investor as a sole provider of financial capital. Entrepreneurs need to consider more aspects when deciding on an investor. Especially the depiction of corporate venture capital (CVC) investors has long highlighted advantages and disadvantages compared to independent VC (IVC) investors. The authors investigate what drives entrepreneurs' preferences for CVC relative to IVC and thereby focus on two key issues in the entrepreneur's consideration – the role of resource requirements and exit strategies.

Design/methodology/approach

The data were collected in an online survey that gathered information on several characteristics of entrepreneurs and their ventures. The resulting data set of 105 German entrepreneurs was analyzed using logistic regression and revealed important drivers for entrepreneurs' investor preferences.

Findings

The study’s findings confirm that the venture's resource needs, specifically the need for marketing resources and access to the corporate network, which play a significant role in the decision on whether a CVC or IVC investor is preferred. Moreover, the analysis debunks the hypothesis that entrepreneurs view a CVC investment as the first step toward acquisition. However, those entrepreneurs striving for an IPO are less likely to prefer CVC.

Originality/value

The study expands the literature on CVC attractiveness and specifically considers the entrepreneurs' intentions and needs. The results confirm but also debunk some widespread perceptions about why entrepreneurs choose to pursue financing from a CVC investor.
Citric acid-crosslinked nanosilver finishing of indigo-dyed denim for potential surgical gowns
Authors: Habib Saima , Raza Zulfiqar Ali , Kishwar Farzana , Abid Sharjeel
Published: April 2023

Purpose

This paper aims to develop an indigo-dyed denim fabric treated with a nanosilver colloid in the presence of a natural crosslinker of citric acid for possible surgical gown fabrication applications.

Design/methodology/approach

A bleached denim fabric was dyed with the sustainable indigo dye followed by silver nanofinishing through citric acid crosslinking under the pad-dry-cure method. The prepared denim samples were analyzed for chemo-physical, textile, dyeing, antibacterial and finish release properties.

Findings

The results demonstrated that the comfort and textile characteristics of nanosilver-treated/indigo-dyed cellulosic fabric were affected due to the crosslinking, surface amphiphilicity and air permeability. These properties were, still, in the acceptable range for the fabrication of naturally dyed and antibacterial nanofinished denim gowns.

Practical implications

The dyeing of denim with synthetic dyes may cause harmful effects on the skin and health of the wearer, and the authors present an eco-friendly sustainable approach.

Originality/value

The authors used the fabric substrate, natural indigo dye and reducing/crosslinker agent of citric acid, all being bio-based, in the fabrication of antibacterial dyed fabric for health care garments.