bluuebunny/crossref_metadata_2025 huggingface dataset:
Wound infiltrating adipocytes are not myofibroblasts
Authors: Kalgudde Gopal Shruthi , Dai Ruoxuan , Stefanska Ania Maria , Ansari Meshal , Zhao Jiakuan , Ramesh Pushkar , Bagnoli Johannes W. , Correa-Gallegos Donovan , Lin Yue , Christ Simon , Angelidis Ilias , Lupperger Valerio , Marr Carsten , Davies Lindsay C. , Enard Wolfgang , Machens Hans-Günther , Schiller Herbert B. , Jiang Dongsheng , Rinkevich Yuval
Published: May 2023

The origins of wound myofibroblasts and scar tissue remains unclear, but it is assumed to involve conversion of adipocytes into myofibroblasts. Here, we directly explore the potential plasticity of adipocytes and fibroblasts after skin injury. Using genetic lineage tracing and live imaging in explants and in wounded animals, we observe that injury induces a transient migratory state in adipocytes with vastly distinct cell migration patterns and behaviours from fibroblasts. Furthermore, migratory adipocytes, do not contribute to scar formation and remain non-fibrogenic in vitro, in vivo and upon transplantation into wounds in animals. Using single-cell and bulk transcriptomics we confirm that wound adipocytes do not convert into fibrogenic myofibroblasts. In summary, the injury-induced migratory adipocytes remain lineage-restricted and do not converge or reprogram into a fibrosing phenotype. These findings broadly impact basic and translational strategies in the regenerative medicine field, including clinical interventions for wound repair, diabetes, and fibrotic pathologies.
Bimodal ionic photomemristor based on a high-temperature oxide superconductor/semiconductor junction
Authors: El Hage Ralph , Humbert Vincent , Rouco Victor , Sánchez-Santolino Gabriel , Lagarrigue Aurelien , Seurre Kevin , Carreira Santiago J. , Sander Anke , Charliac Jérôme , Mesoraca Salvatore , Trastoy Juan , Briatico Javier , Santamaría Jacobo , Villegas Javier E.
Published: May 2023

Memristors, a cornerstone for neuromorphic electronics, respond to the history of electrical stimuli by varying their electrical resistance across a continuum of states. Much effort has been recently devoted to developing an analogous response to optical excitation. Here we realize a novel tunnelling photo-memristor whose behaviour is bimodal: its resistance is determined by the dual electrical-optical history. This is obtained in a device of ultimate simplicity: an interface between a high-temperature superconductor and a transparent semiconductor. The exploited mechanism is a reversible nanoscale redox reaction between both materials, whose oxygen content determines the electron tunnelling rate across their interface. The redox reaction is optically driven via an interplay between electrochemistry, photovoltaic effects and photo-assisted ion migration. Besides their fundamental interest, the unveiled electro-optic memory effects have considerable technological potential. Especially in combination with high-temperature superconductivity which, in addition to facilitating low-dissipation connectivity, brings photo-memristive effects to the realm of superconducting electronics.
Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach
Authors: Feehily Conor , O’Neill Ian J. , Walsh Calum J. , Moore Rebecca L. , Killeen Sarah Louise , Geraghty Aisling A. , Lawton Elaine M. , Byrne David , Sanchez-Gallardo Rocio , Nori Sai Ravi Chandra , Nielsen Ida Busch , Wortmann Esther , Matthews Elizabeth , O’Flaherty Roisin , Rudd Pauline M. , Groeger David , Shanahan Fergus , Saldova Radka , McAuliffe Fionnuala M. , Van Sinderen Douwe , Cotter Paul D.
Published: May 2023

A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.
Fabricating strong and tough aramid fibers by small addition of carbon nanotubes
Authors: Luo Jiajun , Wen Yeye , Jia Xiangzheng , Lei Xudong , Gao Zhenfei , Jian Muqiang , Xiao Zhihua , Li Lanying , Zhang Jiangwei , Li Tao , Dong Hongliang , Wu Xianqian , Gao Enlai , Jiao Kun , Zhang Jin
Published: May 2023

Synthetic high-performance fibers present excellent mechanical properties and promising applications in the impact protection field. However, fabricating fibers with high strength and high toughness is challenging due to their intrinsic conflicts. Herein, we report a simultaneous improvement in strength, toughness, and modulus of heterocyclic aramid fibers by 26%, 66%, and 13%, respectively, via polymerizing a small amount (0.05 wt%) of short aminated single-walled carbon nanotubes (SWNTs), achieving a tensile strength of 6.44 ± 0.11 GPa, a toughness of 184.0 ± 11.4 MJ m−3, and a Young’s modulus of 141.7 ± 4.0 GPa. Mechanism analyses reveal that short aminated SWNTs improve the crystallinity and orientation degree by affecting the structures of heterocyclic aramid chains around SWNTs, and in situ polymerization increases the interfacial interaction therein to promote stress transfer and suppress strain localization. These two effects account for the simultaneous improvement in strength and toughness.
An Aurora B-RPA signaling axis secures chromosome segregation fidelity
Authors: Roshan Poonam , Kuppa Sahiti , Mattice Jenna R. , Kaushik Vikas , Chadda Rahul , Pokhrel Nilisha , Tumala Brunda R. , Biswas Aparna , Bothner Brian , Antony Edwin , Origanti Sofia
Published: May 2023

Errors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of Ser-384 phosphorylation in RPA70 leads to defects in chromosome segregation with loss of viability and a feedback modulation of Aurora B activity. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical Aurora B-RPA signaling axis in mitosis that is essential for maintaining genomic integrity.
Polarization patterning in ferroelectric nematic liquids via flexoelectric coupling
Authors: Sebastián Nerea , Lovšin Matija , Berteloot Brecht , Osterman Natan , Petelin Andrej , Mandle Richard J. , Aya Satoshi , Huang Mingjun , Drevenšek-Olenik Irena , Neyts Kristiaan , Mertelj Alenka
Published: May 2023

The recently discovered ferroelectric nematic liquids incorporate to the functional combination of fluidity, processability and anisotropic optical properties of nematic liquids, an astonishing range of physical properties derived from the phase polarity. Among them, the remarkably large values of second order optical susceptibility encourage to exploit these new materials for non-linear photonic applications. Here we show that photopatterning of the alignment layer can be used to structure polarization patterns. To do so, we take advantage of the flexoelectric effect and design splay structures that geometrically define the polarization direction. We demonstrate the creation of periodic polarization structures and the possibility of guiding polarization by embedding splay structures in uniform backgrounds. The demonstrated capabilities of polarization patterning, open a promising new route for the design of ferroelectric nematic based photonic structures and their exploitation.
Machine learning-enabled exploration of the electrochemical stability of real-scale metallic nanoparticles
Authors: Bang Kihoon , Hong Doosun , Park Youngtae , Kim Donghun , Han Sang Soo , Lee Hyuck Mo
Published: May 2023

Surface Pourbaix diagrams are critical to understanding the stability of nanomaterials in electrochemical environments. Their construction based on density functional theory is, however, prohibitively expensive for real-scale systems, such as several nanometer-size nanoparticles (NPs). Herein, with the aim of accelerating the accurate prediction of adsorption energies, we developed a bond-type embedded crystal graph convolutional neural network (BE-CGCNN) model in which four bonding types were treated differently. Owing to the enhanced accuracy of the bond-type embedding approach, we demonstrate the construction of reliable Pourbaix diagrams for very large-size NPs involving up to 6525 atoms (approximately 4.8 nm in diameter), which enables the exploration of electrochemical stability over various NP sizes and shapes. BE-CGCNN-based Pourbaix diagrams well reproduce the experimental observations with increasing NP size. This work suggests a method for accelerated Pourbaix diagram construction for real-scale and arbitrarily shaped NPs, which would significantly open up an avenue for electrochemical stability studies.
An ancient metabolite damage-repair system sustains photosynthesis in plants
Authors: Leister Dario , Sharma Anurag , Kerber Natalia , Nägele Thomas , Reiter Bennet , Pasch Viviana , Beeh Simon , Jahns Peter , Barbato Roberto , Pribil Mathias , Rühle Thilo
Published: May 2023

Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major catalyst in the conversion of carbon dioxide into organic compounds in photosynthetic organisms. However, its activity is impaired by binding of inhibitory sugars such as xylulose-1,5-bisphosphate (XuBP), which must be detached from the active sites by Rubisco activase. Here, we show that loss of two phosphatases in Arabidopsis thaliana has detrimental effects on plant growth and photosynthesis and that this effect could be reversed by introducing the XuBP phosphatase from Rhodobacter sphaeroides. Biochemical analyses revealed that the plant enzymes specifically dephosphorylate XuBP, thus allowing xylulose-5-phosphate to enter the Calvin-Benson-Bassham cycle. Our findings demonstrate the physiological importance of an ancient metabolite damage-repair system in degradation of by-products of Rubisco, and will impact efforts to optimize carbon fixation in photosynthetic organisms.
Retrosynthesis prediction using an end-to-end graph generative architecture for molecular graph editing
Authors: Zhong Weihe , Yang Ziduo , Chen Calvin Yu-Chian
Published: May 2023

Retrosynthesis planning, the process of identifying a set of available reactions to synthesize the target molecules, remains a major challenge in organic synthesis. Recently, computer-aided synthesis planning has gained renewed interest and various retrosynthesis prediction algorithms based on deep learning have been proposed. However, most existing methods are limited to the applicability and interpretability of model predictions, and further improvement of predictive accuracy to a more practical level is still required. In this work, inspired by the arrow-pushing formalism in chemical reaction mechanisms, we present an end-to-end architecture for retrosynthesis prediction called Graph2Edits. Specifically, Graph2Edits is based on graph neural network to predict the edits of the product graph in an auto-regressive manner, and sequentially generates transformation intermediates and final reactants according to the predicted edits sequence. This strategy combines the two-stage processes of semi-template-based methods into one-pot learning, improving the applicability in some complicated reactions, and also making its predictions more interpretable. Evaluated on the standard benchmark dataset USPTO-50k, our model achieves the state-of-the-art performance for semi-template-based retrosynthesis with a promising 55.1% top-1 accuracy.
Bridging the immunogenicity of a tetravalent dengue vaccine (TAK-003) from children and adolescents to adults
Authors: LeFevre Inge , Bravo Lulu , Folschweiller Nicolas , Medina Eduardo Lopez , Moreira Edson Duarte , Nordio Francesco , Sharma Mayuri , Tharenos Leslie M. , Tricou Vianney , Watanaveeradej Veerachai , Winkle Peter J. , Biswal Shibadas
Published: May 2023

Immunobridging is an important methodology that can be used to extrapolate vaccine efficacy estimates to populations not evaluated in clinical studies, and that has been successfully used in developing many vaccines. Dengue, caused by a mosquito-transmitted flavivirus endemic to many tropical and subtropical regions, is traditionally thought of as a pediatric disease but is now a global threat to both children and adults. We bridged immunogenicity data from a phase 3 efficacy study of a tetravalent dengue vaccine (TAK-003), performed in children and adolescents living in endemic areas, with an immunogenicity study in adults in non-endemic areas. Neutralizing antibody responses were comparable in both studies following receipt of a two-dose TAK-003 schedule (months 0 and 3). Similar immune responses were observed across exploratory assessments of additional humoral responses. These data support the potential for clinical efficacy of TAK-003 in adults.
Strong immune responses and protection of PcrV and OprF-I mRNA vaccine candidates against Pseudomonas aeruginosa
Authors: Wang Xingyun , Liu Cong , Rcheulishvili Nino , Papukashvili Dimitri , Xie Fengfei , Zhao Jiao , Hu Xing , Yu Kaiwei , Yang Nuo , Pan Xuehua , Liu Xueyan , Wang Peng George , He Yunjiao
Published: May 2023

Pseudomonas aeruginosa (PA) is a leading cause of hospital-acquired and ventilator-associated pneumonia. The multidrug-resistance (MDR) rate of PA is increasing making the management of PA a global challenge. Messenger RNA (mRNA) vaccines represent the most promising alternative to conventional vaccines and are widely studied for viral infection and cancer immunotherapy while rarely studied for bacterial infections. In this study, two mRNA vaccines encoding PcrV– the key component of the type III secretion system in Pseudomonas and the fusion protein OprF-I comprising outer membrane proteins OprF and OprI were constructed. The mice were immunized with either one of these mRNA vaccines or with the combination of both. Additionally, mice were vaccinated with PcrV, OprF, or the combination of these two proteins. Immunization with either mRNA-PcrV or mRNA-OprF-I elicited a Th1/Th2 mixed or slighted Th1-biased immune response, conferred broad protection, and reduced bacterial burden and inflammation in burn and systemic infection models. mRNA-PcrV induced significantly stronger antigen-specific humoral and cellular immune responses and higher survival rate compared with the OprF-I after challenging with all the PA strains tested. The combined mRNA vaccine demonstrated the best survival rate. Moreover, the mRNA vaccines showed the superiority over protein vaccines. These results suggest that mRNA-PcrV as well as the mixture of mRNA-PcrV and mRNA-OprF-I are promising vaccine candidates for the prevention of PA infection.
Transverse oscillations and an energy source in a strongly magnetized sunspot
Authors: Yuan Ding , Fu Libo , Cao Wenda , Kuźma Błażej , Geeraerts Michaël , Trelles Arjona Juan C. , Murawski Kris , Van Doorsselaere Tom , Srivastava Abhishek K. , Miao Yuhu , Feng Song , Feng Xueshang , Noda Carlos Quintero , Cobo Basilio Ruiz , Su Jiangtao
Published: May 2023

The solar corona is two to three orders of magnitude hotter than the underlying photosphere, and the energy loss of coronal plasma is extremely strong, requiring a heating flux of over 1,000 W m−2 to maintain its high temperature. Using the 1.6 m Goode Solar Telescope, we report a detection of ubiquitous and persistent transverse waves in umbral fibrils in the chromosphere of a strongly magnetized sunspot. The energy flux carried by these waves was estimated to be 7.52 × 106 W m−2, three to four orders of magnitude stronger than the energy loss rate of plasma in active regions. Two-fluid magnetohydrodynamic simulations reproduced the high-resolution observations and showed that these waves dissipate significant energy, which is vital for coronal heating. Such transverse oscillations and the associated strong energy flux may exist in a variety of magnetized regions on the Sun, and could be the observational target of next-generation solar telescopes.
Fibril formation and ordering of disordered FUS LC driven by hydrophobic interactions
Authors: Maltseva Daria , Chatterjee Sayantan , Yu Chun-Chieh , Brzezinski Mateusz , Nagata Yuki , Gonella Grazia , Murthy Anastasia C. , Stachowiak Jeanne C. , Fawzi Nicolas L. , Parekh Sapun H. , Bonn Mischa
Published: May 2023

Biomolecular condensates, protein-rich and dynamic membrane-less organelles, play critical roles in a range of subcellular processes, including membrane trafficking and transcriptional regulation. However, aberrant phase transitions of intrinsically disordered proteins in biomolecular condensates can lead to the formation of irreversible fibrils and aggregates that are linked to neurodegenerative diseases. Despite the implications, the interactions underlying such transitions remain obscure. Here we investigate the role of hydrophobic interactions by studying the low-complexity domain of the disordered ‘fused in sarcoma’ (FUS) protein at the air/water interface. Using surface-specific microscopic and spectroscopic techniques, we find that a hydrophobic interface drives fibril formation and molecular ordering of FUS, resulting in solid-like film formation. This phase transition occurs at 600-fold lower FUS concentration than required for the canonical FUS low-complexity liquid droplet formation in bulk. These observations highlight the importance of hydrophobic effects for protein phase separation and suggest that interfacial properties drive distinct protein phase-separated structures.
Very short-lived halogens amplify ozone depletion trends in the tropical lower stratosphere
Authors: Villamayor Julián , Iglesias-Suarez Fernando , Cuevas Carlos A. , Fernandez Rafael P. , Li Qinyi , Abalos Marta , Hossaini Ryan , Chipperfield Martyn P. , Kinnison Douglas E. , Tilmes Simone , Lamarque Jean-François , Saiz-Lopez Alfonso
Published: May 2023

In contrast to the general stratospheric ozone recovery following international agreements, recent observations show an ongoing net ozone depletion in the tropical lower stratosphere (LS). This depletion is thought to be driven by dynamical transport accelerated by global warming, while chemical processes have been considered to be unimportant. Here we use a chemistry–climate model to demonstrate that halogenated ozone-depleting very short-lived substances (VSLS) chemistry may account for around a quarter of the observed tropical LS negative ozone trend in 1998–2018. VSLS sources include both natural and anthropogenic emissions. Future projections show the persistence of the currently unaccounted for contribution of VSLS to ozone loss throughout the twenty-first century in the tropical LS, the only region of the global stratosphere not projecting an ozone recovery by 2100. Our results show the need for mitigation strategies of anthropogenic VSLS emissions to preserve the present and future ozone layer in low latitudes.
Grooved electrodes for high-power-density fuel cells
Authors: Lee ChungHyuk , Kort-Kamp Wilton J. M. , Yu Haoran , Cullen David A. , Patterson Brian M. , Arman Tanvir Alam , Komini Babu Siddharth , Mukundan Rangachary , Borup Rod L. , Spendelow Jacob S.
Published: May 2023

Proton exchange membrane fuel cells (PEMFCs) are leading candidates to decarbonize the transport sector, but widespread deployment will require improvements in lifetime, fuel economy and cost. Here we present the grooved electrode, an alternative electrode structure that enhances PEMFC performance and durability by coupling high ionomer (ion-conducting binder) content for improved H+ transport with grooves for rapid O2 transport. Grooved electrodes provide up to 50% higher performance than state-of-the-art conventional electrodes under standard operating conditions. Fuel cell diagnostics combined with multiphysics modelling demonstrate that grooved electrodes provide facile O2 transport despite their high ionomer content, enabling improved reaction rate uniformity. Grooved electrodes also provide improved durability, with less performance loss after carbon corrosion compared with baseline electrodes. Machine learning analysis demonstrates the potential to further optimize grooved structures for next-generation PEMFCs with enhanced performance and durability, enabling smaller and cheaper fuel cell stacks with higher fuel efficiency.
IngridKG: A FAIR Knowledge Graph of Graffiti
Authors: Sherif Mohamed Ahmed , da Silva Ana Alexandra Morim , Pestryakova Svetlana , Ahmed Abdullah Fathi , Niemann Sven , Ngomo Axel-Cyrille Ngonga
Published: May 2023

Graffiti is an urban phenomenon that is increasingly attracting the interest of the sciences. To the best of our knowledge, no suitable data corpora are available for systematic research until now. The Information System Graffiti in Germany project (Ingrid) closes this gap by dealing with graffiti image collections that have been made available to the project for public use. Within Ingrid, the graffiti images are collected, digitized and annotated. With this work, we aim to support the rapid access to a comprehensive data source on Ingrid targeted especially by researchers. In particular, we present IngridKG, an RDF knowledge graph of annotated graffiti, abides by the Linked Data and FAIR principles. We weekly update IngridKG by augmenting the new annotated graffiti to our knowledge graph. Our generation pipeline applies RDF data conversion, link discovery and data fusion approaches to the original data. The current version of IngridKG contains 460,640,154 triples and is linked to 3 other knowledge graphs by over 200,000 links. In our use case studies, we demonstrate the usefulness of our knowledge graph for different applications.
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Authors: Zheng Zhe , Lai Zhuoxin , Wu Bin , Song Xinlin , Zhao Wei , Zhong Ruzhuo , Zhang Jiawei , Liao Yongshan , Yang Chuangye , Deng Yuewen , Mei Junpu , Yue Zhen , Jian Jianbo , Wang Qingheng
Published: May 2023

Sipuncula is a class of exocoelomic unsegmented animals whose evolutionary relationships are unresolved. The peanut worm Sipunculus nudus is a globally distributed, economically important species belonging to the class Sipuncula. Herein, we present the first high-quality chromosome-level assembly of S. nudus based on HiFi reads and high-resolution chromosome conformation capture (Hi-C) data. The assembled genome was 1,427 Mb, with a contig N50 length of 29.46 Mb and scaffold N50 length of 80.87 Mb. Approximately 97.91% of the genome sequence was anchored to 17 chromosomes. A BUSCO assessment showed that 97.7% of the expectedly conserved genes were present in the genome assembly. The genome was composed of 47.91% repetitive sequences, and 28,749 protein-coding genes were predicted. A phylogenetic tree demonstrated that Sipuncula belongs to Annelida and diverged from the common ancestor of Polychaeta. The high-quality chromosome-level genome of S. nudus will serve as a valuable reference for studies of the genetic diversity and evolution of Lophotrochozoa.
Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing
Authors: Lau Billy , Chandak Shubham , Roy Sharmili , Tatwawadi Kedar , Wootters Mary , Weissman Tsachy , Ji Hanlee P.
Published: May 2023

The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling errors, and limitations with scaling up read operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. By conjugating synthesized DNA to magnetic agarose beads, we enabled repeated data readouts while preserving the original DNA analyte and maintaining data readout quality. MDRAM utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.
Stochastic gradient descent for optimization for nuclear systems
Authors: Williams Austin , Walton Noah , Maryanski Austin , Bogetic Sandra , Hines Wes , Sobes Vladimir
Published: May 2023

The use of gradient descent methods for optimizing k-eigenvalue nuclear systems has been shown to be useful in the past, but the use of k-eigenvalue gradients have proved computationally challenging due to their stochastic nature. ADAM is a gradient descent method that accounts for gradients with a stochastic nature. This analysis uses challenge problems constructed to verify if ADAM is a suitable tool to optimize k-eigenvalue nuclear systems. ADAM is able to successfully optimize nuclear systems using the gradients of k-eigenvalue problems despite their stochastic nature and uncertainty. Furthermore, it is clearly demonstrated that low-compute time, high-variance estimates of the gradient lead to better performance in the optimization challenge problems tested here.
A network meta-analysis assessing the effectiveness of various radical and conservative surgical approaches regarding recurrence in treating solid/multicystic ameloblastomas
Authors: Hendra Faqi Nurdiansyah , Helder Marco N. , Ruslin Muhammad , Van Cann Ellen M. , Forouzanfar Tymour
Published: May 2023

Multiple treatment approaches have been undertaken to reduce the incidence of recurrence in solid/multicystic ameloblastoma (SMA), both conservative and radical. A network meta-analysis (NMA) was conducted to assess and compare the effectiveness of these various treatment approaches concurrently. This study was reported based on the Preferred Reporting Items for Systematic Reviews for Network Meta-Analysis (PRISMA-NMA) statement. PubMed (MEDLINE), ScienceDirect, Scopus, and Web of Science were searched until August 10, 2021. The NMA was conducted using the STATA program. Of 1153 records identified in the search, seven observational studies with 180 patients were included. Six different treatment approaches were identified. Segmental resection ranked highest for reducing the recurrence rate with the highest SUCRA score (77.7), followed by curettage with cryotherapy (66.9) and marginal resection (49.3). Network inconsistencies and publication bias appeared to be absent. According to the Confidence in Network Meta-Analysis (CINeMa) method, the evidence's certainty was low for all comparisons due to imprecision and within-study bias. In conclusion, this study is the first NMA in the field of ameloblastoma. Segmental resection seemed to be the most effective treatment approach for minimizing recurrence in SMA patients. Nevertheless, weak certainty of evidence makes that the results must be regarded with caution.
Association between food-based dietary inflammatory potential and ulcerative colitis: a case–control study
Authors: Khademi Zeinab , Saneei Parvane , Hassanzadeh-Keshteli Ammar , Daghaghzadeh Hamed , Tavakkoli Hamid , Adibi Peyman , Esmaillzadeh Ahmad
Published: May 2023

Despite several studies on the link between dietary inflammatory potential and risk of several conditions, limited studies investigated the association between pro-inflammatory diet and ulcerative colitis (UC). The objective of the present study was to examine the link between food-based dietary inflammatory potential (FDIP) and odds of UC in Iranian adults. This case–control study was carried out among 109 cases and 218 randomly chosen healthy controls. UC was diagnosed and confirmed by a gastroenterologist. Patients with this condition were recruited from Iranian IBD registry. Age- and sex-matched controls were selected randomly from participants of a large cross-sectional study. Dietary data were obtained using a validated 106-item semi-quantitative food frequency questionnaire (FFQ). We calculated FDIP score using subjects’ dietary intakes of 28 pre-defined food groups. In total 67% of subjects were female. There was no significant difference in mean age between cases and controls (39.5 vs. 41.5y; p = 0.12). The median (interquartile range) of FDIP scores for cases and controls were − 1.36(3.25) and − 1.54(3.15), respectively. We found no significant association between FDIP score and UC in the crude model (OR 0.93; 95% CIs 0.53–1.63). Adjustment for several potential confounders in multivariate model did not change this association (OR 1.12; 95% CIs 0.46–2.71). We failed to observe any significant association between greater adherence to a pro-inflammatory diet and risk of UC in this study. Prospective cohort studies are needed to further assess this relationship.
New evidence for the Ontong Java Nui hypothesis
Authors: Tejada M. L. G. , Sano T. , Hanyu T. , Koppers A. A. P. , Nakanishi M. , Miyazaki T. , Ishikawa A. , Tani K. , Shimizu S. , Shimizu K. , Vaglarov B. , Chang Q.
Published: May 2023

The formation of the Ontong Java Nui super oceanic plateau (OJN), which is based on the model that the submarine Ontong Java Plateau (OJP), Manihiki Plateau (MP), and Hikurangi Plateau (HP) were once its contiguous fragments, could have been the largest globally consequential volcanic event in Earth’s history. This OJN hypothesis has been debated given the paucity of evidence, for example, the differences in crustal thickness, the compositional gap between MP and OJP basalts and the apparent older age of both plateaus relative to HP remain unresolved. Here we investigate the geochemical and 40Ar-39Ar ages of dredged rocks recovered from the OJP’s eastern margin. Volcanic rocks having compositions that match the low-Ti MP basalts are reported for the first time on the OJP and new ~ 96–116 Ma and 67–68 Ma 40Ar-39Ar age data bridge the temporal gap between OJP and HP. These results provide new evidence for the Ontong Java Nui hypothesis and a framework for an integrated tectonomagmatic evolution of the OJP, MP, and HP. The isotopic data imply four mantle components in the source of OJN that are also expressed in present-day Pacific hotspots sources, indicating origin from (and longevity of) the Pacific Large Low Shear-wave Velocity Province.
Development of a calculated panel reactive antibody calculator for the United Arab Emirates: a proof of concept study
Authors: Alvares Marion , Anwar Siddiq , Hashmi Shahrukh K. , Zaman Muhammad Badar , Al Mahri Ayeda , Alvares Christabelle , Al Katheeri Layla , Purushothaman Ananthanayagi , Ralonya Mesele Emily , Sangalang Marie Glo , Jannang Raysha , Abdulle Abdulkadir , Al Qubaisi Alyazia , Al Ahmed Maitha , Khamis Amar Hassan , Al Seiari Mohamed , Al Obaidli Ali , Al Yafei Zain , ElGhazali Gehad
Published: May 2023

Calculated panel reactive antibody (CPRA) is used to help increase sensitized patient’s access to transplantation. United Arab Emirates (UAE) has a diverse resident population hence we developed a UAE–CPRA calculator based on HLA antigen frequencies of the different ethnic groups that represent the UAE population. HLA antigen frequencies at serological split antigen level for HLA-A, -B, -C, -DRB1 and -DQB1 of 1002 healthy unrelated donors were performed. We subsequently compared the performance of the UAE CPRA calculator with the Organ Procurement and Transplantation Network (OPTN) and the Canadian CPRA calculators in 110 Kidney Transplant waitlist patients from January 2016 to December 2018. Lin’s concordance correlation coefficient showed a moderate agreement between the UAE and OPTN calculator (Rc = 0.949, 95% CI 0.929–0.963) and the UAE and Canadian calculators (Rc = 0.952, 95% CI 0.932–0.965). While there continued to be a moderate agreement (Rc = 0.937, UAE versus OPTN calculator) in the lower sensitized group, a poor agreement (Rc = 0.555, UAE versus OPTN calculator) was observed in the higher sensitized group. In this study, we provide a template for countries to develop their own population-specific CPRA calculator. Implementation of the CPRA algorithm based on HLA frequencies of the multi-ethnic UAE population will be more fitting to increase access to transplantation and improve transplant outcomes. Our study demonstrates that the CPRA calculators developed using the data from the western population had poor correlation in our higher sensitized patients disadvantaging them in potential organ allocations systems. We plan to further refine this calculator by using high resolution HLA typing to address the problem of a genetically diverse population.
Transcriptomic and metabolic studies on the role of inorganic and organic iodine compounds in lettuce plants
Authors: Smoleń Sylwester , Czernicka Małgorzata , Kęska-Izworska Kinga , Kowalska Iwona , Grzebelus Dariusz , Pitala Joanna , Halka Mariya , Skoczylas Łukasz , Tabaszewska Małgorzata , Liszka-Skoczylas Marta , Grzanka Marlena , Ledwożyw-Smoleń Iwona , Koronowicz Aneta , Krzemińska Joanna , Sularz Olga , Kiełbasa Daniel , Neupauer Jakub , Kováčik Peter
Published: May 2023

Iodine (I) is considered a beneficial element or even micronutrient for plants. The aim of this study was to determine the molecular and physiological processes of uptake, transport, and metabolism of I applied to lettuce plants. KIO3, KIO3 + salicylic acid, 5-iodosalicylic acid and 3,5-diiodosalicylic acid were applied. RNA-sequencing was executed using 18 cDNA libraries constructed separately for leaves and roots from KIO3, SA and control plants. De novo transcriptome assembly generated 1937.76 million sequence reads resulting in 27,163 transcripts with N50 of 1638 bp. 329 differentially expressed genes (DEGs) in roots were detected after application of KIO3, out of which 252 genes were up-regulated, and 77 were down-regulated. In leaves, 9 genes revealed differential expression pattern. DEGs analysis indicated its involvement in such metabolic pathways and processes as: chloride transmembrane transport, phenylpropanoid metabolism, positive regulation of defense response and leaf abscission, and also ubiquinone and other terpenoid-quinone biosynthesis, protein processing in endoplasmic reticulum, circadian rhythm including flowering induction as well as a putative PDTHA (i.e. Plant Derived Thyroid Hormone Analogs) metabolic pathway. qRT-PCR of selected genes suggested their participation in the transport and metabolism of iodine compounds, biosynthesis of primary and secondary metabolites, PDTHA pathway and flowering induction.
Simple combination of multiple somatic variant callers to increase accuracy
Authors: Trevarton Alexander J. , Chang Jeffrey T. , Symmans W. Fraser
Published: May 2023

Publications comparing variant caller algorithms present discordant results with contradictory rankings. Caller performances are inconsistent and wide ranging, and dependent upon input data, application, parameter settings, and evaluation metric. With no single variant caller emerging as a superior standard, combinations or ensembles of variant callers have appeared in the literature. In this study, a whole genome somatic reference standard was used to derive principles to guide strategies for combining variant calls. Then, manually annotated variants called from the whole exome sequencing of a tumor were used to corroborate these general principles. Finally, we examined the ability of these principles to reduce noise in targeted sequencing.
Effect of modified waste introduction methods over short-term and long-term use of onsite sanitation systems
Authors: Astete Vasquez L. , Mladenov N.
Published: May 2023

Insufficiently treated wastes contained within onsite sanitation systems (OSS) commonly used by disadvantaged and developing communities contribute to public and environmental health concerns, calling for practical alternative solutions. At the basic level, an improved understanding of the evolution of chemical and physical constituents under different waste introduction methods and for short-term and long-term operation is needed. While receiving non-dilute waste under mixed, unmixed, toilet paper exclusion, and urine diversion (UD) regimes, self-flushing OSS simulated using anaerobic digesters (ADs) were compared during three operational stages: (1) 0–1 month service for unsheltered encampments; (2) 1–3 month disaster relief scenario; and (3) ≥ 3 months representing refugee camps and long-term household use. Although stratification was found to promote suitable conditions for short-term use of self-flushing toilets, mixing increased beneficial biodegradation of organic constituents. Urine-containing ADs demonstrated a shift from sulfide to ammonia odor accompanied by high pH (> 8) after ~ 240 d. E. coli reduction following elevated nitrogen and dissolved solids levels pointed to decreased pathogen survival in ADs with urine. The benefits of bacterial disinfection, reduction of sulfurous odors, and heightened organics degradation in mixed, urine-containing ADs suggest this format as more desirable for prolonged use of self-flushing OSS over unmixed or urine-diverting formats.
Unravelling the resilience of the KGK VI population from the Gumelnița site (Romania) through stable isotopes
Authors: García-Vázquez Ana , Bălășescu Adrian , Vasile Gabriel , Golea Mihaela , Radu Valentin , Opriș Vasile , Ignat Theodor , Culea Mihaela , Covătaru Cristina , Sava Gabriela , Lazăr Cătălin
Published: May 2023

The Gumelnița site belongs to the Kodjadermen-Gumelnița-Karanovo VI (KGK VI) communities (c. 4700–3900 cal BC) and comprises the tell-type settlement and its corresponding cemetery. This paper reconstructs the diet and lifeways of the Chalcolithic people in the northeastern Balkans using archaeological remains found at the Gumelnița site (Romania). A multi-bioarchaeological investigation (archaeobotany, zooarchaeology, anthropology) was conducted on vegetal, animal, and human remains, alongside radiocarbon dating and stable isotope analyses (δ13C, δ15N) of humans (n = 33), mammals (n = 38), reptiles (n = 3), fishes (n = 8), freshwater mussels shells (n = 18), and plants (n = 24). According to the results of δ13C and δ15N values and FRUITS, the inhabitants of Gumelnița had a diet based on crops and using natural resources, such as fish, freshwater molluscs and game. Although domestic fauna was occasionally exploited for meat, it had a role in providing secondary products. Crops were heavily manured, and chaff and other crop waste may have been necessary fodder for cattle and sheep. Dogs and pigs fed on human waste, although the diet of the latter is more similar to that of wild boars. Foxes had a diet close to dogs, which may indicate synanthropic behaviour. Radiocarbon dates were calibrated with the percentage of freshwater resources obtained by FRUITS. As a result, the corrected dates for the freshwater reservoir effect (FRE) have a delay of an average of 147 years. According to our data, this agrarian community developed a subsistence strategy under the pressure of some climatic changes that started after 4300 cal BC, corresponding to KGK VI rapid collapse/decline episode tracked recently (that begins around 4350 cal BC). This matching of our data in the two models (climatic and chrono-demographic) allowed us to capture the economic strategies that led to the resilience of those people more than other contemporary KGK VI communities.
The nonlinear energy model and stress–strain model of sandstone
Authors: Zheng Zhiming , Yang Yu , Pan Cheng
Published: May 2023

The relationship between strain and elastic energy is simplified by introducing a stress state parameter based on the generalised Hooke’s law. It is assumed that the micro-element strengths satisfy the Weibull distribution and a new model for the non-linear evolution of energy is developed by introducing the concept of rock micro-element strengths. A sensitivity analysis of the model parameters is carried out on this basis. The results show that the model agrees well with the experimental data. The model is close to the deformation and damage laws of the rock and is able to reflect the relationship between the elastic energy and strain of the rock. By comparing with other model curves, the model of this paper is more suitable for the experimental curve. They show that the improved model could better describe the stress–strain relationship of rock. Finally, according to the analysis of the influence of the distribution parameter on the variation pattern of the elastic energy of the rock, the magnitude of the distribution parameter can directly reflect the peak energy of the rock.
Uric acid level in climacteric women and its association with clinical and metabolic parameters
Authors: Cota e Souza Laura Alves , D’Angelo Georgia Carvalho de Oliveira , da Silva Glenda Nicioli , Lima Angélica Alves
Published: May 2023

Climacteric women often experience unfavorable metabolic changes. Consequently, identifying markers that may contribute to such undesirable changes is imperative. This study aimed to evaluate serum uric acid (UA) concentration and its association with metabolic and clinical parameters in climacteric women. We selected 672 women between 40 and 65 years and performed interviews, biochemical analyses, blood pressure, and anthropometric measurements. UA levels were determined using the enzymatic-colorimetric method. We compared variables according to the quartiles of UA using the Kruskal–Wallis test. The mean UA level was 4.9 ± 1.5 mg/dl, ranging from 2.0 to 11.6 mg/dl. We found that UA levels greater than 4.8 mg/dl were associated with adverse metabolic parameters in climacteric women. For all anthropometric and biochemical variables, we observed significantly better results in women who had lower UA levels (p < 0.05). Similarly, we observed a significant increase in blood pressure, frequency of metabolic syndrome, and cardiovascular risk as UA levels increased (p < 0.05). Our findings showed that climacteric women with high levels of UA were more likely to have adverse metabolic and clinical parameters than those with lower UA levels. Further studies may determine the causal relationship between UA and metabolic changes in climacteric women.
Effect of far-infrared radiation on inhibition of colonies on packaging during storage of sterilised surgical instruments
Authors: Fann Li-Yun , Cheng Chih-Chien , Chien Yung-Chen , Hsu Cheng-Wei , Chien Wu-Chien , Huang Yao-Ching , Chung Ren-Jei , Huang Shi-Hao , Jiang Ying-Hua , Yin Shih-Han , Cheng Kai-Wen , Wu Yi-Ping , Hsiao Sheng-Huang , Hsu Shao-Yuan , Huang Ying-Che , Chu Chi-Ming
Published: May 2023

The sterilisation of surgical instruments is a major factor in infection control in the operating room (OR). All items used in the OR must be sterile for patient safety. Therefore, the present study evaluated the effect of far-infrared radiation (FIR) on the inhibition of colonies on packaging surface during the long-term storage of sterilised surgical instruments. From September 2021 to July 2022, 68.2% of 85 packages without FIR treatment showed microbial growth after incubation at 35 °C for 30 days and at room temperature for 5 days. A total of 34 bacterial species were identified, with the number of colonies increasing over time. In total, 130 colony-forming units were observed. The main microorganisms detected wereStaphylococcusspp. (35%) andBacillusspp. (21%) ,Kocuria marinaandLactobacillusspp. (14%), and mould (5%). No colonies were found in 72 packages treated with FIR in the OR. Even after sterilisation, microbial growth can occur due to movement of the packages by staff, sweeping of floors, lack of high-efficiency particulate air filtration, high humidity, and inadequate hand hygiene. Thus, safe and simple far-infrared devices that allow continuous disinfection for storage spaces, as well as temperature and humidity control, help to reduce microorganisms in the OR.
Subpopulations of hypocretin/orexin neurons differ in measures of their cell proliferation, dynorphin co-expression, projections, and response to embryonic ethanol exposure
Authors: Yasmin Nushrat , Collier Adam D. , Karatayev Olga , Abdulai Abdul R. , Yu Boyi , Fam Milisia , Khalizova Nailya , Leibowitz Sarah F.
Published: May 2023

Numerous studies in animals demonstrate that embryonic exposure to ethanol (EtOH) at low-moderate doses stimulates neurogenesis and increases the number of hypothalamic neurons expressing the peptide, hypocretin/orexin (Hcrt). A recent study in zebrafish showed that this effect on the Hcrt neurons in the anterior hypothalamus (AH) is area specific, evident in the anterior (aAH) but not posterior (pAH) part of this region. To understand specific factors that may determine the differential sensitivity to EtOH of these Hcrt subpopulations, we performed additional measures in zebrafish of their cell proliferation, co-expression of the opioid dynorphin (Dyn), and neuronal projections. In association with the increase in Hcrt neurons in the aAH but not pAH, EtOH significantly increased only in the aAH the proliferation of Hcrt neurons and their number lacking Dyn co-expression. The projections of these subpopulations differed markedly in their directionality, with those from the pAH primarily descending to the locus coeruleus and those from the aAH ascending to the subpallium, and they were both stimulated by EtOH, which induced specifically the most anterior subpallium-projecting Hcrt neurons to become ectopically expressed beyond the aAH. These differences between the Hcrt subpopulations suggest they are functionally distinct in their regulation of behavior.