bluuebunny/crossref_metadata_2025 huggingface dataset:
Intertwined maritime Silk Road and Austronesian routes: A Taiwanese archaeological perspective
Authors: Liu Jiun-Yu
Published: October 2023

This article analyses recent archaeological work on the flow of materials and their influences on the communities in the South China Sea maritime regions, primarily from a local, Taiwanese perspective. The intertwined Austronesian Routes and maritime Silk Road acted as the primary conduit for the movement of both people and materials. Archaeological findings demonstrate intermittent interaction and cultural exchange between Taiwan and the regions around the South China Sea during the period 1,500-500 BCE. However, starting from 500 BCE, the gradual increase of glass beads, agate beads, and metal products which were made in mainland Southeast Asia and adjacent regions indicate an intensified interaction between Taiwan and Southeast Asia via the Maritime Silk Road and the Austronesian Routes. The author hypothesizes that trade diasporic craftspeople were the carriers of these exotic materials and knowledge, and that external cultural elements had a profound impact on the development of contemporary prehistoric Formosan society. This can be seen most notably in the shifting of decoration systems, the changing methods of subsistence, and technological leaps. Some of the impacts have faded into the archaeological records, but others are still traceable in the modern Indigenous society of Taiwan.
Kongomania and the Numbers Game
Authors: Thornton John
Published: October 2023

In response to two pieces I wrote in the 1990s, and a section of my book Cultural History of the Atlantic World (2012), David Geggus has charged me with fomenting “Kongomania.” I am a specialist in the history of the Kingdom of Kongo, it is true, and in both pieces, Kongo's history was an important part of the argument. In spite of my own fondness for Kongo and its role in the world, I plead not guilty.
Kraken kennen keine Berge
Authors: Ihle Sabine , Krohn Julia , Hirsig Sabine
Published: October 2023

Ob Tinti wohl eines Tages mit in die Berge kommen darf?

Mit Humor und Feingefühl wird das Abenteuer rund um die Frühgeburt des Mädchens Tilda und ihrem Freund, der Krake Tinti, erzählt. Die beiden durchleben gemeinsam Tildas erste Lebenswochen auf der Neonatologie – eine besondere Zeit mit Höhen und Tiefen, lustigen und schwierigen Momenten und einem Gefühlskarussell für die ganze Familie.
Denn nicht nur Tilda wurde frühgeboren, sondern ihre ganze Familie.

Zum Vorlesen und Erzählen für Kinder ab 3 Jahren.
Mit psychologisch fundiertem Begleittext.

„Das Bilderbuch bietet die ideale Grundlage für die ganze Familie, die Frühgeburt spielerisch zu verarbeiten, und dient Fachpersonen als Unterstützung bei der ­Begleitung der frühgeborenen Kinder und ihren Bezugspersonen.“
PD Dr. med. André Kidszun, Leiter Neonatologie, Universitätsklinik für Kinderheilkunde Bern.
High intensity perturbations induce an abrupt shift in soil microbial state
Authors: Cordero Irene , Leizeaga Ainara , Hicks Lettice C , Rousk Johannes , Bardgett Richard D
Published: October 2023

Soil microbial communities play a pivotal role in regulating ecosystem functioning. But they are increasingly being shaped by human-induced environmental change, including intense “pulse” perturbations, such as droughts, which are predicted to increase in frequency and intensity with climate change. While it is known that soil microbial communities are sensitive to such perturbations and that effects can be long-lasting, it remains untested whether there is a threshold in the intensity and frequency of perturbations that can trigger abrupt and persistent transitions in the taxonomic and functional characteristics of soil microbial communities. Here we demonstrate experimentally that intense pulses of drought equivalent to a 30-year drought event (<15% WHC) induce a major shift in the soil microbial community characterised by significantly altered bacterial and fungal community structures of reduced complexity and functionality. Moreover, the characteristics of this transformed microbial community persisted after returning soil to its previous moisture status. As a result, we found that drought had a strong legacy effect on bacterial community function, inducing an enhanced growth rate following subsequent drought. Abrupt transitions are widely documented in aquatic and terrestrial plant communities in response to human-induced perturbations. Our findings demonstrate that such transitions also occur in soil microbial communities in response to high intensity pulse perturbations, with potentially deleterious consequences for soil health.
Population genomic diversity and structure in the golden bandicoot: a history of isolation, extirpation, and conservation
Authors: Rick Kate , Byrne Margaret , Cameron Skye , Cooper Steve J. B. , Dunlop Judy , Hill Brydie , Lohr Cheryl , Mitchell Nicola J. , Moritz Craig , Travouillon Kenny J. , von Takach Brenton , Ottewell Kym
Published: October 2023

Using genetic information to develop and implement conservation programs is vital for maintaining biodiversity and ecosystem resilience. Evaluation of the genetic variability within and among remnant populations can inform management of both natural and translocated populations to maximise species’ adaptive potential, mitigate negative impacts of inbreeding, and subsequently minimise risk of extinction. Here we use reduced representation sequencing to undertake a genetic assessment of the golden bandicoot (Isoodon auratus), a threatened marsupial endemic to Australia. The currently recognised taxon consists of three subspecies distributed among multiple natural and translocated populations. After confirming the genetic distinctiveness of I. auratus from two closely related taxa, I. fusciventer and I. macrourus, we identified four genetic clusters within I. auratus. These clusters exhibited substantial genetic differentiation (pairwise FST values ranging from 0.18 to 0.65, pairwise DXY ranging from 0.1 to 0.168), reflecting long-term isolation of some populations on offshore islands and the influence of genetic drift. Mainland natural populations in the Kimberley region had the highest genetic diversity and the largest contribution to overall allelic and gene diversity compared to both natural and translocated island populations. A population translocated to Guluwuru Island in the Northern Territory had the lowest genetic diversity. Our data suggest that island populations can appear genetically unique due to genetic drift and this needs to be taken into account when considering genetic diversity in conservation efforts to maintain overall genetic diversity of the species. We effectively demonstrate how genomic information can guide practical conservation planning, especially when declining species are represented by multiple isolated populations.
Over 200,000 kilometers of free-flowing river habitat in Europe is altered due to impoundments
Authors: Parasiewicz Piotr , Belka Kamila , Łapińska Małgorzata , Ławniczak Karol , Prus Paweł , Adamczyk Mikołaj , Buras Paweł , Szlakowski Jacek , Kaczkowski Zbigniew , Krauze Kinga , O’Keeffe Joanna , Suska Katarzyna , Ligięza Janusz , Melcher Andreas , O’Hanley Jesse , Birnie-Gauvin Kim , Aarestrup Kim , Jones Peter E. , Jones Joshua , Garcia de Leaniz Carlos , Tummers Jeroen S. , Consuegra Sofia , Kemp Paul , Schwedhelm Hannah , Popek Zbigniew , Segura Gilles , Vallesi Sergio , Zalewski Maciej , Wiśniewolski Wiesław
Published: October 2023

European rivers are disconnected by more than one million man-made barriers that physically limit aquatic species migration and contribute to modification of freshwater habitats. Here, a Conceptual Habitat Alteration Model for Ponding is developed to aid in evaluating the effects of impoundments on fish habitats. Fish communities present in rivers with low human impact and their broad environmental settings enable classification of European rivers into 15 macrohabitat types. These classifications, together with the estimated fish sensitivity to alteration of their habitat are used for assessing the impacts of six main barrier types (dams, weirs, sluices, culverts, fords, and ramps). Our results indicate that over 200,000 km or 10% of previously free-flowing river habitat has been altered due to impoundments. Although they appear less frequently, dams, weirs and sluices cause much more habitat alteration than the other types. Their impact is regionally diverse, which is a function of barrier height, type and density, as well as biogeographical location. This work allows us to foresee what potential environmental gain or loss can be expected with planned barrier management actions in rivers, and to prioritize management actions.
Regulation of CTCF loop formation during pancreatic cell differentiation
Authors: Lyu Xiaowen , Rowley M. Jordan , Kulik Michael J. , Dalton Stephen , Corces Victor G.
Published: October 2023

Transcription reprogramming during cell differentiation involves targeting enhancers to genes responsible for establishment of cell fates. To understand the contribution of CTCF-mediated chromatin organization to cell lineage commitment, we analyzed 3D chromatin architecture during the differentiation of human embryonic stem cells into pancreatic islet organoids. We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of H3K9me3 to H3K9me2, demethylation of DNA, recruitment of pioneer factors, and positioning of nucleosomes flanking the new CTCF sites. Existing CTCF sites not involved in loop formation become functional loop anchors via the establishment of new cohesin loading sites containing NIPBL and YY1 at sites between the new anchors. In both cases, formation of new CTCF loops leads to strengthening of enhancer promoter interactions and increased transcription of genes adjacent to loop anchors. These results suggest an important role for CTCF and cohesin in controlling gene expression during cell differentiation.
A human antibody against pathologic IAPP aggregates protects beta cells in type 2 diabetes models
Authors: Wirth Fabian , Heitz Fabrice D. , Seeger Christine , Combaluzier Ioana , Breu Karin , Denroche Heather C. , Thevenet Julien , Osto Melania , Arosio Paolo , Kerr-Conte Julie , Verchere C. Bruce , Pattou François , Lutz Thomas A. , Donath Marc Y. , Hock Christoph , Nitsch Roger M. , Grimm Jan
Published: October 2023

In patients with type 2 diabetes, pancreatic beta cells progressively degenerate and gradually lose their ability to produce insulin and regulate blood glucose. Beta cell dysfunction and loss is associated with an accumulation of aggregated forms of islet amyloid polypeptide (IAPP) consisting of soluble prefibrillar IAPP oligomers as well as insoluble IAPP fibrils in pancreatic islets. Here, we describe a human monoclonal antibody selectively targeting IAPP oligomers and neutralizing IAPP aggregate toxicity by preventing membrane disruption and apoptosis in vitro. Antibody treatment in male rats and mice transgenic for human IAPP, and human islet-engrafted mouse models of type 2 diabetes triggers clearance of IAPP oligomers resulting in beta cell protection and improved glucose control. These results provide new evidence for the pathological role of IAPP oligomers and suggest that antibody-mediated removal of IAPP oligomers could be a pharmaceutical strategy to support beta cell function in type 2 diabetes.
Bone disease imaging through the near-infrared-II window
Authors: Mi Chao , Zhang Xun , Yang Chengyu , Wu Jianqun , Chen Xinxin , Ma Chenguang , Wu Sitong , Yang Zhichao , Qiao Pengzhen , Liu Yang , Wu Weijie , Guo Zhiyong , Liao Jiayan , Zhou Jiajia , Guan Ming , Liang Chao , Liu Chao , Jin Dayong
Published: October 2023

Skeletal disorders are commonly diagnosed by X-ray imaging, but the radiation limits its use. Optical imaging through the near-infrared-II window (NIR-II, 1000–1700 nm) can penetrate deep tissues without radiation risk, but the targeting of contrast agent is non-specific. Here, we report that lanthanide-doped nanocrystals can passively target the bone marrow, which can be effective for over two months. We therefore develop the high-resolution NIR-II imaging method for bone disease diagnosis, including the 3D bone imaging instrumentation to show the intravital bone morphology. We demonstrate the monitoring of 1 mm bone defects with spatial resolution comparable to the X-ray imaging result. Moreover, NIR-II imaging can reveal the early onset inflammation as the synovitis in the early stage of rheumatoid arthritis, comparable to micro computed tomography (μCT) in diagnosis of osteoarthritis, including the symptoms of osteophyte and hyperostosis in the knee joint.
Single-cell allele-specific expression analysis reveals dynamic and cell-type-specific regulatory effects
Authors: Qi Guanghao , Strober Benjamin J. , Popp Joshua M. , Keener Rebecca , Ji Hongkai , Battle Alexis
Published: October 2023

Differential allele-specific expression (ASE) is a powerful tool to study context-specific cis-regulation of gene expression. Such effects can reflect the interaction between genetic or epigenetic factors and a measured context or condition. Single-cell RNA sequencing (scRNA-seq) allows the measurement of ASE at individual-cell resolution, but there is a lack of statistical methods to analyze such data. We present Differential Allelic Expression using Single-Cell data (DAESC), a powerful method for differential ASE analysis using scRNA-seq from multiple individuals, with statistical behavior confirmed through simulation. DAESC accounts for non-independence between cells from the same individual and incorporates implicit haplotype phasing. Application to data from 105 induced pluripotent stem cell (iPSC) lines identifies 657 genes dynamically regulated during endoderm differentiation, with enrichment for changes in chromatin state. Application to a type-2 diabetes dataset identifies several differentially regulated genes between patients and controls in pancreatic endocrine cells. DAESC is a powerful method for single-cell ASE analysis and can uncover novel insights on gene regulation.
Multivalent insulin receptor activation using insulin–DNA origami nanostructures
Authors: Spratt Joel , Dias José M. , Kolonelou Christina , Kiriako Georges , Engström Enya , Petrova Ekaterina , Karampelias Christos , Cervenka Igor , Papanicolaou Natali , Lentini Antonio , Reinius Björn , Andersson Olov , Ambrosetti Elena , Ruas Jorge L. , Teixeira Ana I.
Published: October 2023

Insulin binds the insulin receptor (IR) and regulates anabolic processes in target tissues. Impaired IR signalling is associated with multiple diseases, including diabetes, cancer and neurodegenerative disorders. IRs have been reported to form nanoclusters at the cell membrane in several cell types, even in the absence of insulin binding. Here we exploit the nanoscale spatial organization of the IR to achieve controlled multivalent receptor activation. To control insulin nanoscale spatial organization and valency, we developed rod-like insulin–DNA origami nanostructures carrying different numbers of insulin molecules with defined spacings. Increasing the insulin valency per nanostructure markedly extended the residence time of insulin–DNA origami nanostructures at the receptors. Both insulin valency and spacing affected the levels of IR activation in adipocytes. Moreover, the multivalent insulin design associated with the highest levels of IR activation also induced insulin-mediated transcriptional responses more effectively than the corresponding monovalent insulin nanostructures. In an in vivo zebrafish model of diabetes, treatment with multivalent—but not monovalent—insulin nanostructures elicited a reduction in glucose levels. Our results show that the control of insulin multivalency and spatial organization with nanoscale precision modulates the IR responses, independent of the insulin concentration. Therefore, we propose insulin nanoscale organization as a design parameter in developing new insulin therapies.
Chiral and nematic phases of flexible active filaments
Authors: Dunajova Zuzana , Mateu Batirtze Prats , Radler Philipp , Lim Keesiang , Brandis Dörte , Velicky Philipp , Danzl Johann Georg , Wong Richard W. , Elgeti Jens , Hannezo Edouard , Loose Martin
Published: October 2023

The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division.
Age-dependent topic modeling of comorbidities in UK Biobank identifies disease subtypes with differential genetic risk
Authors: Jiang Xilin , Zhang Martin Jinye , Zhang Yidong , Durvasula Arun , Inouye Michael , Holmes Chris , Price Alkes L. , McVean Gil
Published: October 2023

The analysis of longitudinal data from electronic health records (EHRs) has the potential to improve clinical diagnoses and enable personalized medicine, motivating efforts to identify disease subtypes from patient comorbidity information. Here we introduce an age-dependent topic modeling (ATM) method that provides a low-rank representation of longitudinal records of hundreds of distinct diseases in large EHR datasets. We applied ATM to 282,957 UK Biobank samples, identifying 52 diseases with heterogeneous comorbidity profiles; analyses of 211,908 All of Us samples produced concordant results. We defined subtypes of the 52 heterogeneous diseases based on their comorbidity profiles and compared genetic risk across disease subtypes using polygenic risk scores (PRSs), identifying 18 disease subtypes whose PRS differed significantly from other subtypes of the same disease. We further identified specific genetic variants with subtype-dependent effects on disease risk. In conclusion, ATM identifies disease subtypes with differential genome-wide and locus-specific genetic risk profiles.
Population-level integration of single-cell datasets enables multi-scale analysis across samples
Authors: De Donno Carlo , Hediyeh-Zadeh Soroor , Moinfar Amir Ali , Wagenstetter Marco , Zappia Luke , Lotfollahi Mohammad , Theis Fabian J.
Published: October 2023

The increasing generation of population-level single-cell atlases has the potential to link sample metadata with cellular data. Constructing such references requires integration of heterogeneous cohorts with varying metadata. Here we present single-cell population level integration (scPoli), an open-world learner that incorporates generative models to learn sample and cell representations for data integration, label transfer and reference mapping. We applied scPoli on population-level atlases of lung and peripheral blood mononuclear cells, the latter consisting of 7.8 million cells across 2,375 samples. We demonstrate that scPoli can explain sample-level biological and technical variations using sample embeddings revealing genes associated with batch effects and biological effects. scPoli is further applicable to single-cell sequencing assay for transposase-accessible chromatin and cross-species datasets, offering insights into chromatin accessibility and comparative genomics. We envision scPoli becoming an important tool for population-level single-cell data integration facilitating atlas use but also interpretation by means of multi-scale analyses.
Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control
Authors: Mahata Barun , Cabrera Alan , Brenner Daniel A. , Guerra-Resendez Rosa Selenia , Li Jing , Goell Jacob , Wang Kaiyuan , Guo Yannie , Escobar Mario , Parthasarathy Abinand Krishna , Szadowski Hailey , Bedford Guy , Reed Daniel R. , Kim Sunghwan , Hilton Isaac B.
Published: October 2023

Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR–Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain poorly tolerated elements and/or are prohibitively large for many applications. Here, we defined and optimized minimal TADs built from human mechanosensitive transcription factors. We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS and eN3x9) and to build the CRISPR–dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific and robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci. We also showed that MSN and NMS were portable across Type I, II and V CRISPR systems, transcription activator-like effectors and zinc finger proteins. Further, as proofs of concept, we used dCas9-NMS to efficiently reprogram human fibroblasts into induced pluripotent stem cells and demonstrated that mechanosensitive transcription factor TADs are efficacious and well tolerated in therapeutically important primary human cell types. Finally, we leveraged the compact and potent features of these engineered TADs to build dual and all-in-one CRISPRa AAV systems. Altogether, these compact human TADs, fusion modules and delivery architectures should be valuable for synthetic transcriptional control in biomedical applications.
An evaluation tool for backbone extraction techniques in weighted complex networks
Authors: Yassin Ali , Haidar Abbas , Cherifi Hocine , Seba Hamida , Togni Olivier
Published: October 2023

Networks are essential for analyzing complex systems. However, their growing size necessitates backbone extraction techniques aimed at reducing their size while retaining critical features. In practice, selecting, implementing, and evaluating the most suitable backbone extraction method may be challenging. This paper introduces , a Python package designed for assessing the performance of backbone extraction techniques in weighted networks. Its comparison framework is the standout feature of . Indeed, the tool incorporates state-of-the-art backbone extraction techniques. Furthermore, it provides a comprehensive suite of evaluation metrics allowing users to evaluate different backbones techniques. We illustrate the flexibility and effectiveness of through the US air transportation network analysis. We compare the performance of different backbone extraction techniques using the evaluation metrics. We also show how users can integrate a new backbone extraction method into the comparison framework. is publicly available as an open-source tool, ensuring its accessibility to researchers and practitioners. Promoting standardized evaluation practices contributes to the advancement of backbone extraction techniques and fosters reproducibility and comparability in research efforts. We anticipate that will serve as a valuable resource for researchers and practitioners enabling them to make informed decisions when selecting backbone extraction techniques to gain insights into the structural and functional properties of complex systems.
Impact of proton therapy on the DNA damage induction and repair in hematopoietic stem and progenitor cells
Authors: Sioen Simon , Vanhove Oniecha , Vanderstraeten Barbara , De Wagter Carlos , Engelbrecht Monique , Vandevoorde Charlot , De Kock Evan , Van Goethem Marc-Jan , Vral Anne , Baeyens Ans
Published: October 2023

Proton therapy is of great interest to pediatric cancer patients because of its optimal depth dose distribution. In view of healthy tissue damage and the increased risk of secondary cancers, we investigated DNA damage induction and repair of radiosensitive hematopoietic stem and progenitor cells (HSPCs) exposed to therapeutic proton and photon irradiation due to their role in radiation-induced leukemia. Human CD34+ HSPCs were exposed to 6 MV X-rays, mid- and distal spread-out Bragg peak (SOBP) protons at doses ranging from 0.5 to 2 Gy. Persistent chromosomal damage was assessed with the micronucleus assay, while DNA damage induction and repair were analyzed with the γ-H2AX foci assay. No differences were found in induction and disappearance of γ-H2AX foci between 6 MV X-rays, mid- and distal SOBP protons at 1 Gy. A significantly higher number of micronuclei was found for distal SOBP protons compared to 6 MV X-rays and mid- SOBP protons at 0.5 and 1 Gy, while no significant differences in micronuclei were found at 2 Gy. In HSPCs, mid-SOBP protons are as damaging as conventional X-rays. Distal SOBP protons showed a higher number of micronuclei in HSPCs depending on the radiation dose, indicating possible changes of the in vivo biological response.
Volcanic glass from the 1.8 ka Taupō eruption (New Zealand) detected in Antarctic ice at ~ 230 CE
Authors: Piva Stephen B. , Barker Simon J. , Iverson Nels A. , Winton V. Holly L. , Bertler Nancy A. N. , Sigl Michael , Wilson Colin J. N. , Dunbar Nelia W. , Kurbatov Andrei V. , Carter Lionel , Charlier Bruce L. A. , Newnham Rewi M.
Published: October 2023

Chemical anomalies in polar ice core records are frequently linked to volcanism; however, without the presence of (crypto)tephra particles, links to specific eruptions remain speculative. Correlating tephras yields estimates of eruption timing and potential source volcano, offers refinement of ice core chronologies, and provides insights into volcanic impacts. Here, we report on sparse rhyolitic glass shards detected in the Roosevelt Island Climate Evolution (RICE) ice core (West Antarctica), attributed to the 1.8 ka Taupō eruption (New Zealand)—one of the largest and most energetic Holocene eruptions globally. Six shards of a distinctive geochemical composition, identical within analytical uncertainties to proximal Taupō glass, are accompanied by a single shard indistinguishable from glass of the ~25.5 ka Ōruanui supereruption, also from Taupō volcano. This double fingerprint uniquely identifies the source volcano and helps link the shards to the climactic phase of the Taupō eruption. The englacial Taupō-derived glass shards coincide with a particle spike and conductivity anomaly at 278.84 m core depth, along with trachytic glass from a local Antarctic eruption of Mt. Melbourne. The assessed age of the sampled ice is 230 ± 19 CE (95% confidence), confirming that the published radiocarbon wiggle-match date of 232 ± 10 CE (2 SD) for the Taupō eruption is robust.
Revision of the Schistura cincticauda species group (Teleostei, Nemacheilidae) using molecular and morphological markers
Authors: Dvořák Tomáš , Bohlen Jörg , Kottelat Maurice , Šlechtová Vendula
Published: October 2023

To approach the taxonomy of large and complex animal groups it is of advantage to focus on species groups with shared derived character state. We investigate the composition, morphological characteristics and relationships of and within the Schistura cincticauda species group, whose members are small freshwater fishes that inhabit streams and rivers in eastern Myanmar and western and southern Thailand. A phylogenetic analysis using molecular genetic markers demonstrated the monophyly of this group; a combined genetic and morphological analysis revealed the inclusion of at least twelve species. They share the presence of a pair of black marks on the lower lip, one on each side of the median interruption (these marks may be reduced to few melanophores or even missing in some individuals). Additionally, all species share a small body size (max. 60 mm SL), an incomplete lateral line reaching at most to vertical through anal-fin base, and the absence of sexual dimorphism. Each of the 12 species is diagnosed by a unique combination of character states in fin ray numbers, anus position, presence/absence of an axillary pelvic lobe, and colour pattern. The distribution areas of several species overlap and five cases of syntopic occurrence are known. Five unnamed species are described herein.
Fully automated sequential immunofluorescence (seqIF) for hyperplex spatial proteomics
Authors: Rivest François , Eroglu Deniz , Pelz Benjamin , Kowal Joanna , Kehren Alexandre , Navikas Vytautas , Procopio Maria Giuseppina , Bordignon Pino , Pérès Emilie , Ammann Marco , Dorel Emmanuel , Scalmazzi Sylvain , Bruno Lorenzo , Ruegg Matthieu , Campargue Gabriel , Casqueiro Gilles , Arn Lionel , Fischer Jérôme , Brajkovic Saska , Joris Pierre , Cassano Marco , Dupouy Diego
Published: October 2023

Tissues are complex environments where different cell types are in constant interaction with each other and with non-cellular components. Preserving the spatial context during proteomics analyses of tissue samples has become an important objective for different applications, one of the most important being the investigation of the tumor microenvironment. Here, we describe a multiplexed protein biomarker detection method on the COMET instrument, coined sequential ImmunoFluorescence (seqIF). The fully automated method uses successive applications of antibody incubation and elution, and in-situ imaging enabled by an integrated microscope and a microfluidic chip that provides optimized optical access to the sample. We show seqIF data on different sample types such as tumor and healthy tissue, including 40-plex on a single tissue section that is obtained in less than 24 h, using off-the-shelf antibodies. We also present extensive characterization of the developed method, including elution efficiency, epitope stability, repeatability and reproducibility, signal uniformity, and dynamic range, in addition to marker and panel optimization strategies. The streamlined workflow using off-the-shelf antibodies, data quality enabling downstream analysis, and ease of reaching hyperplex levels make seqIF suitable for immune-oncology research and other disciplines requiring spatial analysis, paving the way for its adoption in clinical settings.
A personalized classification of behavioral severity of autism spectrum disorder using a comprehensive machine learning framework
Authors: Ali Mohamed T. , Gebreil Ahmad , ElNakieb Yaser , Elnakib Ahmed , Shalaby Ahmed , Mahmoud Ali , Sleman Ahmed , Giridharan Guruprasad A. , Barnes Gregory , Elbaz Ayman S.
Published: October 2023

Autism Spectrum Disorder (ASD) is characterized as a neurodevelopmental disorder with a heterogeneous nature, influenced by genetics and exhibiting diverse clinical presentations. In this study, we dissect Autism Spectrum Disorder (ASD) into its behavioral components, mirroring the diagnostic process used in clinical settings. Morphological features are extracted from magnetic resonance imaging (MRI) scans, found in the publicly available dataset ABIDE II, identifying the most discriminative features that differentiate ASD within various behavioral domains. Then, each subject is categorized as having severe, moderate, or mild ASD, or typical neurodevelopment (TD), based on the behavioral domains of the Social Responsiveness Scale (SRS). Through this study, multiple artificial intelligence (AI) models are utilized for feature selection and classifying each ASD severity and behavioural group. A multivariate feature selection algorithm, investigating four different classifiers with linear and non-linear hypotheses, is applied iteratively while shuffling the training-validation subjects to find the set of cortical regions with statistically significant association with ASD. A set of six classifiers are optimized and trained on the selected set of features using 5-fold cross-validation for the purpose of severity classification for each behavioural group. Our AI-based model achieved an average accuracy of 96%, computed as the mean accuracy across the top-performing AI models for feature selection and severity classification across the different behavioral groups. The proposed AI model has the ability to accurately differentiate between the functionalities of specific brain regions, such as the left and right caudal middle frontal regions. We propose an AI-based model that dissects ASD into behavioral components. For each behavioral component, the AI-based model is capable of identifying the brain regions which are associated with ASD as well as utilizing those regions for diagnosis. The proposed system can increase the speed and accuracy of the diagnostic process and result in improved outcomes for individuals with ASD, highlighting the potential of AI in this area.
Genetic diversity of hepatitis B virus quasispecies in different biological compartments reveals distinct genotypes
Authors: do Lago Bárbara Vieira , Bezerra Cristianne Sousa , Moreira Daniel Andrade , Parente Thiago Estevam , Portilho Moyra Machado , Pessôa Rodrigo , Sanabani Sabri Saeed , Villar Livia Melo
Published: October 2023

The selection pressure imposed by the host immune system impacts hepatitis B virus (HBV) quasispecies variability. This study evaluates HBV genetic diversity in different biological fluids. Twenty paired serum, oral fluid, and DBS samples from chronic HBV carriers were analyzed using both Sanger and next generation sequencing (NGS). The mean HBV viral load in serum was 5.19 ± 4.3 log IU/mL (median 5.29, IQR 3.01–7.93). Genotype distribution was: HBV/A1 55% (11/20), A2 15% (3/20), D3 10% (2/20), F2 15% (3/20), and F4 5% (1/20). Genotype agreement between serum and oral fluid was 100% (genetic distances 0.0–0.006), while that between serum and DBS was 80% (genetic distances 0.0–0.115). Two individuals presented discordant genotypes in serum and DBS. Minor population analysis revealed a mixed population. All samples displayed mutations in polymerase and/or surface genes. Major population analysis of the polymerase pointed to positions H122 and M129 as the most polymorphic (≥ 75% variability), followed by V163 (55%) and I253 (50%). Neither Sanger nor NGS detected any antiviral primary resistance mutations in the major populations. Minor population analysis, however, demonstrated the rtM204I resistance mutation in all individuals, ranging from 2.8 to 7.5% in serum, 2.5 to 6.3% in oral fluid, and 3.6 to 7.2% in DBS. This study demonstrated that different fluids can be used to assess HBV diversity, nonetheless, genotypic differences according to biological compartments can be observed.
RETRACTED ARTICLE: Sign language recognition using the fusion of image and hand landmarks through multi-headed convolutional neural network
Authors: Pathan Refat Khan , Biswas Munmun , Yasmin Suraiya , Khandaker Mayeen Uddin , Salman Mohammad , Youssef Ahmed A. F.
Published: October 2023

Sign Language Recognition is a breakthrough for communication among deaf-mute society and has been a critical research topic for years. Although some of the previous studies have successfully recognized sign language, it requires many costly instruments including sensors, devices, and high-end processing power. However, such drawbacks can be easily overcome by employing artificial intelligence-based techniques. Since, in this modern era of advanced mobile technology, using a camera to take video or images is much easier, this study demonstrates a cost-effective technique to detect American Sign Language (ASL) using an image dataset. Here, “Finger Spelling, A” dataset has been used, with 24 letters (except j and z as they contain motion). The main reason for using this dataset is that these images have a complex background with different environments and scene colors. Two layers of image processing have been used: in the first layer, images are processed as a whole for training, and in the second layer, the hand landmarks are extracted. A multi-headed convolutional neural network (CNN) model has been proposed and tested with 30% of the dataset to train these two layers. To avoid the overfitting problem, data augmentation and dynamic learning rate reduction have been used. With the proposed model, 98.981% test accuracy has been achieved. It is expected that this study may help to develop an efficient human–machine communication system for a deaf-mute society.
Male sex and pretreatment weight loss are associated with poor outcome in patients with advanced non-small cell lung cancer treated with immunotherapy: a retrospective study
Authors: Jin Jingxiao , Visina Jacqueline , Burns Timothy F. , Diergaarde Brenda , Stabile Laura P.
Published: October 2023

The influence of sex and body mass index (BMI) on the efficacy of immune checkpoint inhibitors (ICIs) in advanced non-small cell lung cancer (NSCLC) patients remains unclear. We conducted a retrospective study to evaluate the relationship between sex, BMI, pretreatment weight loss (PWL), and clinical outcomes in 399 stage IV NSCLC patients treated with ICIs using data abstracted from medical records. Multivariable Cox proportional hazards models were used to assess the impact on overall survival and progression-free survival. Females were significantly more likely to experience immune-related adverse events and had a significantly lower risk of death compared to males in our patient cohort. In stratified analyses, the latter was limited to those receiving first-line monotherapy. BMI was overall not significantly associated with outcome. However, underweight patients had a significantly higher risk of both progression and death compared to normal weight patients in the first-line monotherapy group. When stratified by sex, underweight males had a significantly higher risk of progression and death compared to normal weight males. This was not observed among females. Those with PWL had overall significantly worse outcomes compared to those without. In stratified analyses, PWL was associated with significantly worse OS in both females and males. Stratified by treatment, the worse outcome was limited to those receiving ICI monotherapy. In summary, utilizing real-world data, this study suggests that male sex, being underweight, and PWL negatively impact ICI efficacy in NSCLC patients. Therapeutic approaches to improve ICI outcomes in underweight patients and those with PWL should be investigated.
Study on the effect of excavation sequence of three-hole shield tunnel on surface settlement and segment deformation
Authors: Wang You , Dai Fang , Ding Bosong , Zhong Ming , Zhang Heng
Published: October 2023

In order to study the influence of excavation sequence of three-hole parallel shield tunnel on surface settlement and segment convergence, an improved “three-stage analysis method” was proposed to calculate the surface settlement of three-hole parallel shield tunnel. Based on Peck's existing theory, this method deduced the ground settlement formula under the three-hole parallel condition, and can calculate the ground settlement more accurately. Based on the engineering background of a shield tunnel section in Jiangsu Province, a three-dimensional model of a three-hole parallel shield tunnel was established by using Flac3d software, and the three-hole parallel shield tunnel was simulated under four working conditions: right–center–left, right–left–center, right–left–right and right–center (reverse)–left. This paper analyzed the influence of tunnel excavation sequence on surface settlement, soil displacement and deformation of tunnel segments. The construction sequence was optimized based on the above influencing factors. It was found that Case 4, S-type sequential excavation, produced the least ground settlement. The surface settlement value caused by S-type excavation sequence was only 11.41 mm, and the convergence value of the segments generated by S-type excavation sequence was relatively small. Considering the economic factors such as construction efficiency and benefit, the S-shaped excavation sequence was better. The new calculation method of tunnel surface settlement and the optimal sequence of tunnel construction proposed in this paper can provide reference for actual construction.
Influence of the strain effect on magnetocrystalline anisotropy in Co2Fe0.4Mn0.6Si Heusler alloys
Authors: Nabiałek A. , Chumak O. M. , Aleshkevych P. , Domagala J. Z. , Pacewicz A. , Salski B. , Krupka J. , Seki T. , Takanashi K. , Baczewski L. T. , Szymczak H.
Published: October 2023

The perpendicular magnetocrystalline anisotropy, magnetoelastic properties as well as the Gilbert damping factor in Co2Fe0.4Mn0.6Si thin films were found to depend on a magnetic layer thickness, and they can be also tuned by the application of additional Ag buffer layer. The tetragonal distortion of a magnetic layer was found to increase with decreasing thickness, and after the application of an additional Ag buffer layer, the character of this distortion was changed from tensile to compressive in the plane of a film. A correlation between the tetragonal distortion and perpendicular magnetocrystalline anisotropy was found. However, the magnitude of the observed tetragonal distortion for most samples seems to be too small to explain alone the experimentally found large magnitude of the perpendicular magnetocrystalline anisotropy. For these samples, other mechanisms including both surface and volume effects must be taken into account.
Joint analysis of the metabolomics and transcriptomics uncovers the dysregulated network and develops the diagnostic model of high-risk neuroblastoma
Authors: Du Bang , Zhang Fei , Zhou Qiumei , Cheng Weyland , Yu Zhidan , Li Lifeng , Yang Jianwei , Zhang Xianwei , Zhou Chongchen , Zhang Wancun
Published: October 2023

High-risk neuroblastoma (HR-NB) has a significantly lower survival rate compared to low- and intermediate-risk NB (LIR-NB) due to the lack of risk classification diagnostic models and effective therapeutic targets. The present study aims to characterize the differences between neuroblastomas with different risks through transcriptomic and metabolomic, and establish an early diagnostic model for risk classification of neuroblastoma.Plasma samples from 58 HR-NB and 38 LIR-NB patients were used for metabolomics analysis. Meanwhile, NB tissue samples from 32 HR-NB and 23 LIR-NB patients were used for transcriptomics analysis. In particular, integrative metabolomics and transcriptomic analysis was performed between HR-NB and LIR-NB. A total of 44 metabolites (P < 0.05 and fold change > 1.5) were altered, including 12 that increased and 32 that decreased in HR-NB. A total of 1,408 mRNAs (P < 0.05 and |log2(fold change)|> 1) showed significantly altered in HR-NB, of which 1,116 were upregulated and 292 were downregulated. Joint analysis of both omic data identified 4 aberrant pathways (P < 0.05 and impact ≥ 0.5) consisting of glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism. Importantly, a HR-NB risk classification diagnostic model was developed using plasma circulating-free S100A9, CDK2, and UNC5D, with an area under receiver operating characteristic curve of 0.837 where the sensitivity and specificity in the validation set were both 80.0%. This study presents a novel pioneering study demonstrating the metabolomics and transcriptomics profiles of HR-NB. The glycerolipid metabolism, retinol metabolism, arginine biosynthesis and linoleic acid metabolism were altered in HR-NB. The risk classification diagnostic model based on S100A9, CDK2, and UNC5D can be clinically used for HR-NB risk classification.
Safety assessment of slope on in-service dump under severe dry–wet cycles at high-altitude
Authors: Dong Jianjun , Jiang Hao , Yang Di , Gao Ke
Published: October 2023

This study aimed to evaluate the safety of dump slopes in high-altitude areas subjected to severe dry–wet cycles. The slope of No. 1 and No. 2 in-service dumps in limestone mining areas for cement in high-altitude mining areas is taken as the research object. The unsaturated soil shear strength and matrix suction distribution equations were imported based on the unsaturated–saturated seepage theory. Therefore, the evolution characteristics of the unsaturated–saturated seepage field in the dump are analyzed by numerical calculation, and the safety state of the dump slope is evaluated. The results indicated the following rules: under the action of four dry–wet cycles, the surface soil of the dump slope changes from an unsaturated state to a saturated state. Furthermore, with the increase in the times of the dry–wet cycle, the maximum vertical displacement of the No. 1 and No. 2 dump slopes increased. The numerical calculations of the maximum cumulative vertical displacement of the slope were consistent with the actual monitoring data. The factor of safety of the dump slope decreased continuously with the increase in the times of dry–wet cycles. Nevertheless, it still met the safety and stability standards. It was concluded that the slope of the in-service dump remains stable after enduring four severe cycles of dry–wet.
AutoGIS processing for site selection for solar pond development as efficient water treatment plants in Egypt
Authors: Altahan Mahmoud Fatehy , Nower Mohamed
Published: October 2023

The increasing demand for renewable and environmentally friendly energy sources is a top priority for many countries around the world. It is obvious that renewable solar energy will help to meet most of the energy demand in the coming years. A solar pond is a huge Salt artificial Lake that serves as a solar energy collection system. However, site selection is a critical factor that affects the effectiveness and lifetime of a solar pond. Here, we present an innovative methodology for site selection based on three environmental factors, including direct solar irradiance (DNI), temperature, and wind speed. Our approach uses Python programming and clustering analysis with several libraries, including Pandas, Geopandas, Rasterio, Osgeo, and Sklearn, to analyse and process data collected over a 30-year period from NASA power. This method was applied to the geographic boundaries of Egypt, but the methods can be applied to any spatial context if the same dataset is available. The results show that Egypt has a potential land area of 500 km2 suitable for solar ponds construction along the border with Sudan throughout the year, including 2000 km2 in winter (between January and March), 800 km2 in spring (between April and June), 900 km2 in summer (between July and September), and the largest area of 3700 km2 (between October and December), most of which is located in the south of the Eastern Desert and around the Nile River. Notably, the northwestern region, close to the Mediterranean Sea on the border with Libya, exhibits suitability for solar pond development, with consistent performance throughout the year. Our results provide an efficient way for GIS and data processing and could be useful for implementing new software to find the best location for solar ponds development. This could be beneficial for those interested in investing in renewable energy and using solar ponds as an efficient water treatment plant.