bluuebunny/crossref_metadata_2025_split huggingface dataset:
A step towards measuring connectivity in the deep sea: elemental fingerprints of mollusk larval shells discriminate hydrothermal vent sites
Authors: Mouchi Vincent , Pecheyran Christophe , Claverie Fanny , Cathalot Cécile , Matabos Marjolaine , Germain Yoan , Rouxel Olivier , Jollivet Didier , Broquet Thomas , Comtet Thierry 
Published: January 2023

AbstractDeep-sea hydrothermal-vent systems are under investigation for base and precious metal exploitations. The impact of mining will depend critically on the ability of larval dispersal to connect and replenish endemic populations. However, assessing connectivity is extremely challenging, especially in the deep sea. Here, we investigate the potential of elemental fingerprinting of mollusc larval shells to discriminate larval origins between multiple hydrothermal sites in the Southwest Pacific Ocean. The gastropodShinkailepas tollmannirepresents a suitable candidate as it uses capsules to hold larvae before dispersal, which facilitates sampling and ensures mineralization occurs on the site of origin. Multielemental microchemistry was performed using cutting-edge femtosecond laser ablation Inductively Coupled Plasma Mass Spectrometry analysis to obtain individual measurements on 600 encapsulated larval shells. We used classification methods to discriminate the origin of individuals from 14 hydrothermal sites spanning over 3,500 km, with an overall success rate of 70%. When considering less sites within more restricted areas, reflecting dispersal distances reported by genetic and modelling approaches, the success rate increased up to 86%. We conclude that individual larval shells register site-specific elemental signatures that can be used to assess their origin. These results open new perspectives to get direct estimates on population connectivity from the geochemistry of pre-dispersal shell of recently settled juveniles.
Molecular architecture of the ciliary tip revealed by cryo-electron tomography
Authors: Legal T. , Tong M. , Black C. , Valente Paterno M. , Gaertig J. , Bui K.H. 
Published: January 2023

AbstractCilia are essential organelles that protrude from the cell body. Cilia are made of a microtubule-based structure called the axoneme. In most types of cilia, the ciliary tip is distinct from the rest of the cilium. Here, we used cryo-electron tomography and subtomogram averaging to obtain the structure of the ciliary tip of the ciliateTetrahymena thermophila. We show the microtubules in the tip are highly cross-linked with each other and stabilised by luminal proteins, plugs and cap proteins at the plus ends. In the tip region, the central pair lacks the typical projections and twists significantly. By analysing cells lacking a ciliary tip-enriched proteinCEP104/FAP256by cryo-electron tomography and proteomics, we discovered candidates for the central pair cap complex and explain potential functions ofCEP104/FAP256. These data provide new insights into the function of the ciliary tip and inform about the mechanisms of ciliary assembly and length regulation.
Structural mechanism ofLIN28Bnucleosome targeting by OCT4 for pluripotency
Authors: Guan Ruifang , Lian Tengfei , Zhou Bing-Rui , Bai Yawen 
Published: January 2023

SUMMARYPioneer transcription factors are essential for cell fate changes by targeting closed chromatin. OCT4 is a crucial pioneer factor that can induce cell reprogramming. However, the structural basis of how pioneer factors recognize thein vivonucleosomal DNA targets is unknown. Here, we determine the high-resolution structures of the nucleosome containing humanLIN28BDNA and its complexes with the OCT4 DNA binding region. Three OCT4s bind the pre-positioned nucleosome by recognizing non-canonical DNA motifs. Two use their POUS domains by forming extensive hydrogen bonds. The other uses the POUS-loop-POUHD region; POUHD serves as a wedge to unwrap ∼25 base pair DNA. Biochemical studies suggest that multiple OCT4s cooperatively open the H1-condensed nucleosome array containing theLIN28Bnucleosome. Our study suggests a mechanism whereby OCT4s target theLIN28Bnucleosome by forming multivalent interactions with nucleosomal motifs, unwrapping nucleosomal DNA, evicting H1, and cooperatively open closed chromatin to initiate cell reprogramming.
MYC disrupts transcriptional and metabolic circadian oscillations in cancer and promotes enhanced biosynthesis
Authors: Cazarin Juliana , DeRollo Rachel E. , Ahmad Shahidan Siti Noor Ain Binti , Burchett Jamison B. , Mwangi Daniel , Krishnaiah Saikumari , Hsieh Annie L. , Walton Zandra E. , Brooks Rebekah , Mello Stephano S. , Weljie Aalim M. , Dang Chi V. , Altman Brian J. 
Published: January 2023

AbstractThe molecular circadian clock, which controls rhythmic 24-hour oscillation of genes, proteins, and metabolites in healthy tissues, is disrupted across many human cancers. Deregulated expression of the MYC oncoprotein has been shown to alter expression of molecular clock genes, leading to a disruption of molecular clock oscillation across cancer types. It remains unclear what benefit cancer cells gain from suppressing clock oscillation, and how this loss of molecular clock oscillation impacts global gene expression and metabolism in cancer. We hypothesized that MYC or its paralog N-MYC (collectively termed MYC herein) suppress oscillation of gene expression and metabolism to upregulate pathways involved in biosynthesis in a static, non-oscillatory fashion. To test this, cells from distinct cancer types with inducible MYC were examined, using time-series RNA-sequencing and metabolomics, to determine the extent to which MYC activation disrupts global oscillation of genes, gene expression pathways, and metabolites. We focused our analyses on genes, pathways, and metabolites that changed in common across multiple cancer cell line models. We report here that MYC disrupted over 85% of oscillating genes, while instead promoting enhanced ribosomal and mitochondrial biogenesis and suppressed cell attachment pathways. Notably, when MYC is activated, biosynthetic programs that were formerly circadian flipped to being upregulated in an oscillation-free manner. Further, activation of MYC ablates the oscillation of nutrient transporter proteins while greatly upregulating transporter expression, cell surface localization, and intracellular amino acid pools. Finally, we report that MYC disrupts metabolite oscillations and the temporal segregation of amino acid metabolism from nucleotide metabolism. Our results demonstrate that MYC disruption of the molecular circadian clock releases metabolic and biosynthetic processes from circadian control, which may provide a distinct advantage to cancer cells.
Application of nanopore sequencing for accurate identification of bacterial colonies
Authors: Marshall Austin , Fuller Daniel T. , Dougall Paul , Kumaragama Kavindra , Dhaniyala Suresh , Sur Shantanu 
Published: January 2023

AbstractCulture based detection remains to be one of the most reliable and acceptable techniques to detect extremely low quantity pathogens present in a sample. The process typically involves inoculating the sample on an agar plate to allow growth of the microorganisms to form colonies, followed by the identification of the individual colonies, commonly by DNA sequencing of a PCR-amplified targeted gene. Sanger method is often the default choice of sequencing as it offers affordable and accurate results for a single species. However, the technique could pose limitations in certain situations such as identification of multi-species microbial colonies. In this work, we compared the performance of Sanger sequencing with MinION nanopore sequencing in identifying bacterial colonies derived from bioaerosol samples. We conducted Sanger and nanopore sequencing of full-length 16S rRNA genes from seven bacterial colonies derived from bioaerosol samples and compared the outcome by alignment against NCBI 16S reference database. We found that for five out of seven colonies both techniques indicated the presence of the same bacterial genus. For one of the remaining colonies, a noisy Sanger electropherogram failed to generate a meaningful sequence, but nanopore sequencing identified it to be a mix of two bacterial generaAlkalihalobacillusandKocuria. For the other remaining colony, the Sanger sequencing suggestedMicrococcuswith a clean electropherogram, however, the nanopore sequencing suggested the presence of an additional genusParaburkholderia. Further corroborating these findings with mock multispecies colonies from pure bacterial DNA samples, we confirm that nanopore sequencing is comparable to the Sanger method in identifying colonies with single bacterial species but is the superior method in classifying individual bacterial components with their relative abundances in multispecies colonies. Our results suggest that nanopore sequencing could be advantageous over Sanger sequencing for colony identification in culture-based analysis of environmental samples such as bioaerosol where direct inoculation of the sample to culture plate might lead to formation of multispecies colonies.
EpiMix: an integrative tool for epigenomic subtyping using DNA methylation
Authors: Zheng Yuanning , Jun John , Brennan Kevin , Gevaert Olivier 
Published: January 2023

AbstractDNA methylation (DNAme) is a major epigenetic factor influencing gene expression with alterations leading to cancer, immunological, and cardiovascular diseases. Recent technological advances enable genome-wide quantification of DNAme in large human cohorts. So far, existing methods have not been evaluated to identify differential DNAme present in large and heterogeneous patient cohorts. We developed an end-to-end analytical framework named “EpiMix” for population-level analysis of DNAme and gene expression. Compared to existing methods, EpiMix showed higher sensitivity in detecting abnormal DNAme that was present in only small patient subsets. We extended the model-based analyses of EpiMix to cis-regulatory elements within protein-coding genes, distal enhancers, and genes encoding microRNAs and lncRNAs. Using cell-type specific data from two separate studies, we discovered novel epigenetic mechanisms underlying childhood food allergy and survival-associated, methylation-driven non-coding RNAs in non-small cell lung cancer.
Small cell lung cancer co-culture organoids provide insights into cancer cell survival after chemotherapy
Authors: Sen Chandani , Koloff Caroline , Kundu Souvik , Wilkinson Dan C , Yang Juliette , Shia David W , Meneses Luisa K , Rickabaugh Tammy M , Gomperts Brigitte N 
Published: January 2023

AbstractSmall-cell-lung-cancer (SCLC) has the worst prognosis of all lung cancers because of a high incidence of relapse after therapy. We developed a bioengineered 3-dimensional (3D) SCLC co-culture organoid as a phenotypic tool to study SCLC tumor kinetics and SCLC-fibroblast interactions during relapse. We used functionalized alginate microbeads as a scaffold to mimic lung alveolar architecture and co-cultured SCLC cell lines with primary adult lung fibroblasts (ALF). We found that SCLCs in the model proliferated extensively, invaded the microbead scaffold and formed tumors within just 7 days. We compared the bioengineered tumors with patient tumors and found them to recapitulate the pathology and immunophenotyping of the patient tumors better than the PDX model developed from the same SCLC cell line. When treated with standard chemotherapy drugs, etoposide and cisplatin, the organoid recapitulated relapse after chemotherapy. Co-culture of the SCLC cells with ALFs revealed that the fibroblasts play a key role in inducing faster and more robust SCLC cell regrowth in the model. This was a paracrine effect as conditioned medium from the same fibroblasts was responsible for this accelerated cell regrowth. This model is also amenable to high throughput phenotypic or targeted drug screening to find new therapeutics for SCLC.
Manipulating mitochondrial dynamics in the NTS prevents diet-induced deficits in brown fat morphology and glucose uptake
Authors: Fozzato Arianna , New Lauryn E. , Griffiths Joanne C. , Patel Bianca , Deuchars Susan A. , Filippi Beatrice M. 
Published: January 2023

AbstractBrown adipose tissue (BAT) uptakes and metabolises both glucose and triglycerides to produce heat and is activated by the central nervous system (CNS) through direct noradrenergic sympathetic innervation. Dysregulation of signalling modules in selective CNS areas such as the nucleus of tractus solitarius (NTS) are linked with altered BAT activity, obesity and diabetes. High-fat diet (HFD)-feeding increases mitochondrial fragmentation in the NTS triggering insulin resistance, hyperphagia and weight gain. Here we sought to determine whether changes in mitochondrial dynamics in the NTS can affect BAT glucose uptake. Our findings demonstrated that short-term HFD feeding reduces BAT’s ability to take up glucose, as measured by PET/CT scan. However, inhibiting mitochondrial fragmentation in NTS-astrocytes of HFD-fed rats improved BAT glucose uptake while lowering blood glucose and insulin levels. Compared with HFD-fed rats, HFD fed animals, where mitochondrial fragmentation was inhibited in the NTS-astrocytes, had higher levels of catecholaminergic innervation of BAT, and did not present HFD-dependent infiltration of enlarged white fat droplets in the BAT. In regular chow-fed rats, increasing mitochondrial fragmentation in the NTS-astrocytes reduced BAT glucose uptake, catecholaminergic innervation and β3-adrenergic receptor levels. Our data suggest that targeting mitochondrial dynamics in the NTS-astrocytes could be a beneficial strategy to increase glucose utilization and protect from developing obesity and diabetes.
A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity
Authors: Bottone Sara , Cakil Zeyneb Vildan , Joliot Octave , Boncompain Gaelle , Perez Franck , Gautier Arnaud 
Published: January 2023

ABSTRACTProximity between proteins plays an essential and ubiquitous role in many biological processes. Molecular tools enabling to control and observe the proximity of proteins are essential for studying the functional role of physical distance between two proteins. Here we present CATCHFIRE (Chemically Assisted Tethering of CHimera by Fluorogenic Induced REcognition), a chemically induced proximity technology with intrinsic fluorescence imaging and sensing capabilities. CATCHFIRE relies on genetic fusion to small dimerizing domains that interact upon addition of fluorogenic inducers of proximity that fluoresce upon formation of the ternary assembly, allowing real-time monitoring of the chemically induced proximity. CATCHFIRE is rapid and fully reversible, and allows the control and tracking of protein localization, protein trafficking, organelle transport and cellular processes, opening new avenues for studying or controlling biological processes with high spatiotemporal resolution. Its fluorogenic nature allowed furthermore the design of innovative biosensors for the study of various processes, such as signal transduction and apoptosis.
Activity of Sotrovimab against BQ.1.1 and XBB.1 Omicron sublineages in a hamster model
Authors: Driouich Jean-Sélim , Bernadin Ornéllie , Touret Franck , de Lamballerie Xavier , Nougairède Antoine 
Published: January 2023

AbstractThe successive emergence of SARS-CoV-2 Omicron variants has completely changed the modalities of use of therapeutic monoclonal antibodies. Recent in vitro studies indicated that only Sotrovimab has maintained partial activity against BQ.1.1 and XBB.1. In the present study, we used the hamster model to determine whether Sotrovimab retains antiviral activity against these Omicron variants in vivo. Our results show that at exposures consistent with those observed in humans, Sotrovimab remains active against BQ.1.1 and XBB.1, although for BQ.1.1 the efficacy is lower than that observed against the first globally dominant Omicron sublineages BA.1 and BA.2.
Calmness instead of panicking: re-thinking the resource allocation strategies in an era of uncertainty: a case of a developing country
Authors: Blouch Riffat , Khan Muhammad Majid 
Published: January 2023

PurposeDrawing on the concept of superior resource, capability and processes of the resource-based theory of the firm, the purpose of the current study is to analyze the influence of firms’ winner-picking strategic approach on firm performance (FP) via a direct and indirect mechanism.Design/methodology/approachUsing survey data of 104 diversified manufacturing firms, the current study analyzed the conditional indirect effect of firms’ strategic approach on efficient resource allocation with the help of Statistical Analysis Software (SAS) process macros.FindingsThe study found that firms’ choices of winner-picking approach can undermine the resource allocation efficiency when not perfectly blended with firms’ access to the resource. Furthermore, the effect of winner-picking strategy (WPS) on resource allocation efficiency via firms’ competitive advantage (CA) can be greater when both strategic choice and resources are employed adequately.Research limitations/implicationsDespite making a unique contribution, the present study has a few limitations requiring researchers’ attention to be tackled in the forthcoming. This includes a little amount of data, a self-reporting technique and failure to include all the possible reasons that could lead to inefficient resource allocation.Practical implicationsThe present research has potential applications for managers of the manufacturing industry in a period of sheer uncertainty [coronavirus disease 2019 (COVID-19)]. First, the study alerts managers about the challenges of underinvestment and overinvestment while allocating resources. At the same time, this study provides an important implication for managing the importance of firms’ access to capital (AC).Originality/valueThe current study has made a sizeable impression in the literature on internal resource allocation and resource-based theory of the firm by recommending a model that augments the theoretical foundation of strategic management of the firms. As there are only a handful of studies on this grave issue in the context of developing economies, thus, closely considering these insights would be helping for the firms for allocating resources efficiently in the manufacturing industry.
A survey of corporate communication professionals' perspective on social listening and analytics
Authors: Yavuz Şenay , Tire Engin 
Published: January 2023

PurposeThe present research aimed to identify the motivations, needs, wants, preferences and limitations of corporate professionals with regard to business social analytics.Design/methodology/approachOnline interviews were conducted with 26 professionals the majority of whom work at the management level at 20 reputable corporations in Turkey. Both qualitative and quantitative data was collected during these interviews, which lasted an average of one hour.FindingsThe findings shed light on the motivations of corporate professionals for monitoring social media and other digital media, their perceived capability and limitations in doing so, the media that they monitor and wanted to monitor if possible, their criteria and processes for working with service providers in the field of business social analytics, their needs which are not fully met by service providers, their suggestions on service improvement and their reflections on how internal and external customer data can be analyzed with an integrated approach.Originality/valueThis research is an attempt to bridge the gap between the priorities of engineers who generate artificial intelligence for the purposes of social listening and analytics and the end users, e.g. corporate communication professionals. Only by doing so, this field, which is getting more and more important as people spend more time online, will reach its full potential and benefit corporations by providing fruitful insight upon which strategic steps can be taken.
International human rights law and the intangible face of ageism
Authors: Mikołajczyk Barbara 
Published: January 2023

PurposeThe purpose of this paper is to show the potential of international human rights law to raise awareness of the international community about ageism and its three aspects – old age discrimination, stereotyping and prejudices against older persons. The author evaluates the ability of international human rights law to encourage states to take action against these phenomena and looks for new solutions. The author also intends to examine if there are international law instruments compelling states to reject stereotypes and prejudices on older persons if there is no treaty devoted to them.Design/methodology/approachThe author applies methods relevant to legal science. The core human rights treaties, soft law documents and activities of human rights bodies are selected, analysed and interpreted.FindingsThe core human rights treaties require going beyond their literal interpretation to observe older persons' rights. States should interpret them in good faith, relying on the ageing mainstreaming approach. Instruction to states on how to do so lies in the soft law and output of the international human rights bodies. However, there is also room for improvement. Therefore, the author proposes adopting a targeted resolution on counteracting ageism and its components, updating positions by international treaty bodies, and involving various human rights procedures and specialised agencies in the fight against intangible dimensions of ageism.Originality/valueIt is the first study analysing awareness about stereotyping and prejudices against older persons from international human rights law. The author indicates untapped possibilities of the fight against ageism and its intangible dimensions under international law.
Adaptation re-use of traditional cafés in Erbil, Iraq
Authors: Agha Rand H.M. , Hussein Amna Nassir 
Published: January 2023

PurposeThis paper aims to shed light on adaptive reuse in traditional architecture (TA) in Erbil, Iraq.Design/methodology/approachAn inductive approach and qualitative method were used in this study. The inductive research approach was used because there was no clear image of adaptive reuse in traditional cafés (TCs) in Erbil. Besides, there are no studies of TCs in Erbil particularly. Thus, there is a lack of knowledge about what adaptations took place in TCs in Erbil. The qualitative method extracted themes and issues from case studies of four TCs in Erbil citadel's buffer zone. This included a physical survey and observation of the TCs in Erbil and 18 semi-structured interviews with the owners, servers and visitors.FindingsThe analysis shows the flexibility of the TCs in Erbil as a face of adaptive re-use (AR) which is explained through the capacity linked to space modifications, the addition of modern devices, the function linked to space modifications, service addition, the condition linked to space modifications and the addition of modern devices. Also, TCs in Erbil has a spatial identity and architectural value that proves it is worthy enough to be preserved through unique spirituality linked to preserving the place.Research limitations/implicationsThe findings are limited to the cases of TCs in mountain regain and may not be applicable or appropriate to other cafés in other different countries.Originality/valueThere are three aspects of authenticity in the current research. Firstly, the TCs in Erbil have not been studied before. Secondly, TCs that have been discovered have made AR of themselves whilst maintaining their original function-serving beverages, to stimulate creativity. Thirdly, most of the studies of AR have dealt with historical and heritage architecture, whilst the current research paper is dealing with TA.