bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small body size is associated with increased evolutionary lability of wing skeleton proportions in birds
Authors: Orkney Andrew , Hedrick Brandon P. 
Published: May 2024

AbstractBirds are represented by 11,000 species and a great variety of body masses. Modular organisation of trait evolution across birds has facilitated simultaneous adaptation of different body regions to divergent ecological requirements. However, the role modularity has played in avian body size evolution, especially small-bodied, rapidly evolving and diverse avian subclades, such as hummingbirds and songbirds, is unknown. Modularity is influenced by the intersection of biomechanical restrictions, adaptation, and developmental controls, making it difficult to uncover the contributions of single factors such as body mass to skeletal organisation. We develop a novel framework to decompose this complexity, assessing factors underlying the modularity of skeletal proportions in fore-limb propelled birds distributed across a range of body masses. We demonstrate that differences in body size across birds triggers a modular reorganisation of flight apparatus proportions consistent with biomechanical expectations. We suggest weakened integration within the wing facilitates radiation in small birds. Our framework is generalisable to other groups and has the capacity to untangle the multi-layered complexity intrinsic to modular evolution.
Crykey: Rapid identification of SARS-CoV-2 cryptic mutations in wastewater
Authors: Liu Yunxi , Sapoval Nicolae , Gallego-García Pilar , Tomás Laura , Posada David , Treangen Todd J. , Stadler Lauren B. 
Published: May 2024

AbstractWastewater surveillance for SARS-CoV-2 provides early warnings of emerging variants of concerns and can be used to screen for novel cryptic linked-read mutations, which are co-occurring single nucleotide mutations that are rare, or entirely missing, in existing SARS-CoV-2 databases. While previous approaches have focused on specific regions of the SARS-CoV-2 genome, there is a need for computational tools capable of efficiently tracking cryptic mutations across the entire genome and investigating their potential origin. We present Crykey, a tool for rapidly identifying rare linked-read mutations across the genome of SARS-CoV-2. We evaluated the utility of Crykey on over 3,000 wastewater and over 22,000 clinical samples; our findings are three-fold: i) we identify hundreds of cryptic mutations that cover the entire SARS-CoV-2 genome, ii) we track the presence of these cryptic mutations across multiple wastewater treatment plants and over three years of sampling in Houston, and iii) we find a handful of cryptic mutations in wastewater mirror cryptic mutations in clinical samples and investigate their potential to represent real cryptic lineages. In summary, Crykey enables large-scale detection of cryptic mutations in wastewater that represent potential circulating cryptic lineages, serving as a new computational tool for wastewater surveillance of SARS-CoV-2.
A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions
Authors: Liu Yuan , Li Dianke , Zhang Xin , Xia Simin , Qu Yingjie , Ling Xinping , Li Yang , Kong Xiangren , Zhang Lingqiang , Cui Chun-Ping , Li Dong 
Published: May 2024

AbstractProtein ubiquitination regulates a wide range of cellular processes. The degree of protein ubiquitination is determined by the delicate balance between ubiquitin ligase (E3)-mediated ubiquitination and deubiquitinase (DUB)-mediated deubiquitination. In comparison to the E3-substrate interactions, the DUB-substrate interactions (DSIs) remain insufficiently investigated. To address this challenge, we introduce a protein sequence-based ab initio method, TransDSI, which transfers proteome-scale evolutionary information to predict unknown DSIs despite inadequate training datasets. An explainable module is integrated to suggest the critical protein regions for DSIs while predicting DSIs. TransDSI outperforms multiple machine learning strategies against both cross-validation and independent test. Two predicted DUBs (USP11 and USP20) for FOXP3 are validated by “wet lab” experiments, along with two predicted substrates (AR and p53) for USP22. TransDSI provides new functional perspective on proteins by identifying regulatory DSIs, and offers clues for potential tumor drug target discovery and precision drug application.
ARPES detection of superconducting gap sign in unconventional superconductors
Authors: Gao Qiang , Bok Jin Mo , Ai Ping , Liu Jing , Yan Hongtao , Luo Xiangyu , Cai Yongqing , Li Cong , Wang Yang , Yin Chaohui , Chen Hao , Gu Genda , Zhang Fengfeng , Yang Feng , Zhang Shenjin , Peng Qinjun , Zhu Zhihai , Liu Guodong , Xu Zuyan , Xiang Tao , Zhao Lin , Choi Han-Yong , Zhou X. J. 
Published: May 2024

AbstractThe superconducting gap symmetry is crucial in understanding the underlying superconductivity mechanism. Angle-resolved photoemission spectroscopy (ARPES) has played a key role in determining the gap symmetry in unconventional superconductors. However, it has been considered so far that ARPES can only measure the magnitude of the superconducting gap but not its phase; the phase has to be detected by other phase-sensitive techniques. Here we propose a method to directly detect the superconducting gap sign by ARPES. This method is successfully validated in a cuprate superconductor Bi2Sr2CaCu2O8+δ with a well-known d-wave gap symmetry. When two bands have a strong interband interaction, the resulted electronic structures in the superconducting state are sensitive to the relative gap sign between the two bands. Our present work provides an approach to detect the gap sign and can be applied to various superconductors, particularly those with multiple orbitals like the iron-based superconductors.
Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms
Authors: Inamo Jun , Suzuki Akari , Ueda Mahoko Takahashi , Yamaguchi Kensuke , Nishida Hiroshi , Suzuki Katsuya , Kaneko Yuko , Takeuchi Tsutomu , Hatano Hiroaki , Ishigaki Kazuyoshi , Ishihama Yasushi , Yamamoto Kazuhiko , Kochi Yuta 
Published: May 2024

AbstractAlternative splicing events are a major causal mechanism for complex traits, but they have been understudied due to the limitation of short-read sequencing. Here, we generate a full-length isoform annotation of human immune cells from an individual by long-read sequencing for 29 cell subsets. This contains a number of unannotated transcripts and isoforms such as a read-through transcript of TOMM40-APOE in the Alzheimer’s disease locus. We profile characteristics of isoforms and show that repetitive elements significantly explain the diversity of unannotated isoforms, providing insight into the human genome evolution. In addition, some of the isoforms are expressed in a cell-type specific manner, whose alternative 3’-UTRs usage contributes to their specificity. Further, we identify disease-associated isoforms by isoform switch analysis and by integration of several quantitative trait loci analyses with genome-wide association study data. Our findings will promote the elucidation of the mechanism of complex diseases via alternative splicing.
Memory CD8 T cells are vulnerable to chronic IFN-γ signals but not to CD4 T cell deficiency in MHCII-deficient mice
Authors: Setoguchi Ruka , Sengiku Tomoya , Kono Hiroki , Kawakami Eiryo , Kubo Masato , Yamamoto Tadashi , Hori Shohei 
Published: May 2024

AbstractThe mechanisms by which the number of memory CD8 T cells is stably maintained remains incompletely understood. It has been postulated that maintaining them requires help from CD4 T cells, because adoptively transferred memory CD8 T cells persist poorly in MHC class II (MHCII)-deficient mice. Here we show that chronic interferon-γ signals, not CD4 T cell-deficiency, are responsible for their attrition in MHCII-deficient environments. Excess IFN-γ is produced primarily by endogenous colonic CD8 T cells in MHCII-deficient mice. IFN-γ neutralization restores the number of memory CD8 T cells in MHCII-deficient mice, whereas repeated IFN-γ administration or transduction of a gain-of-function STAT1 mutant reduces their number in wild-type mice. CD127high memory cells proliferate actively in response to IFN-γ signals, but are more susceptible to attrition than CD127low terminally differentiated effector memory cells. Furthermore, single-cell RNA-sequencing of memory CD8 T cells reveals proliferating cells that resemble short-lived, terminal effector cells and documents global downregulation of gene signatures of long-lived memory cells in MHCII-deficient environments. We propose that chronic IFN-γ signals deplete memory CD8 T cells by compromising their long-term survival and by diverting self-renewing CD127high cells toward terminal differentiation.
Control of artificial membrane fusion in physiological ionic solutions beyond the limits of electroformation
Authors: Kim Bong Kyu , Kang Dong-Hyun , Woo Junhyuk , Yoon Wooseung , Ryu Hyunil , Han Kyungreem , Chung Seok , Kim Tae Song 
Published: May 2024

AbstractMembrane fusion, merging two lipid bilayers, is crucial for fabricating artificial membrane structures. Over the past 40 years, in contrast to precise and controllable membrane fusion in-vivo through specific molecules such as SNAREs, controlling the fusion in-vitro while fabricating artificial membrane structures in physiological ionic solutions without fusion proteins has been a challenge, becoming a significant obstacle to practical applications. We present an approach consisting of an electric field and a few kPa hydraulic pressure as an additional variable to physically control the fusion, enabling tuning of the shape and size of the 3D freestanding lipid bilayers in physiological ionic solutions. Mechanical model analysis reveals that pressure-induced parallel/normal tensions enhance fusion among membranes in the microwell. In-vitro peptide-membrane assay, mimicking vesicular transport via pressure-assisted fusion, and stability of 38 days with in-chip pressure control via pore size-regulated hydrogel highlight the potential for diverse biological applications.
Uniformly elevated future heat stress in China driven by spatially heterogeneous water vapor changes
Authors: Wang Fan , Gao Meng , Liu Cheng , Zhao Ran , McElroy Michael B. 
Published: May 2024

AbstractThe wet bulb temperature (Tw) has gained considerable attention as a crucial indicator of heat-related health risks. Here we report south-to-north spatially heterogeneous trends of Tw in China over 1979-2018. We find that actual water vapor pressure (Ea) changes play a dominant role in determining the different trend of Tw in southern and northern China, which is attributed to the faster warming of high-latitude regions of East Asia as a response to climate change. This warming effect regulates large-scale atmospheric features and leads to extended impacts of the South Asia high (SAH) and the western Pacific subtropical high (WPSH) over southern China and to suppressed moisture transport. Attribution analysis using climate model simulations confirms these findings. We further find that the entire eastern China, that accommodates 94% of the country’s population, is likely to experience widespread and uniform elevated thermal stress the end of this century. Our findings highlight the necessity for development of adaptation measures in eastern China to avoid adverse impacts of heat stress, suggesting similar implications for other regions as well.
Emergence of a short peptide based reductase via activation of the model hydride rich cofactor
Authors: Chatterjee Ayan , Goswami Surashree , Kumar Raushan , Laha Janmejay , Das Dibyendu 
Published: May 2024

AbstractIn extant biology, large and complex enzymes employ low molecular weight cofactors such as dihydronicotinamides as efficient hydride transfer agents and electron carriers for the regulation of critical metabolic processes. In absence of complex contemporary enzymes, these molecular cofactors are generally inefficient to facilitate any reactions on their own. Herein, we report short peptide-based amyloid nanotubes featuring exposed arrays of cationic and hydrophobic residues that can bind small molecular weak hydride transfer agents (NaBH4) to facilitate efficient reduction of ester substrates in water. In addition, the paracrystalline amyloid phases loaded with borohydrides demonstrate recyclability, substrate selectivity and controlled reduction and surpass the capabilities of standard reducing agent such as LiAlH4. The amyloid microphases and their collaboration with small molecular cofactors foreshadow the important roles that short peptide-based assemblies might have played in the emergence of protometabolism and biopolymer evolution in prebiotic earth.
XPD stalled on cross-linked DNA provides insight into damage verification
Authors: Kuper Jochen , Hove Tamsanqa , Maidl Sarah , Neitz Hermann , Sauer Florian , Kempf Maximilian , Schroeder Till , Greiter Elke , Höbartner Claudia , Kisker Caroline 
Published: May 2024

AbstractThe superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.
Solar-matched S-scheme ZnO/g-C3N4 for visible light-driven paracetamol degradation
Authors: Hassan Fahad , Backer Sumina Namboorimadathil , Almanassra Ismail W. , Ali Atieh Muataz , Elbahri Mady , Shanableh Abdallah 
Published: May 2024

AbstractIn pursuit of an efficient visible light driven photocatalyst for paracetamol degradation in wastewater, we have fabricated the ZnO/g-C3N4 S-Scheme photocatalysts and explored the optimal percentage to form a composite of graphitic carbon nitride (g-C3N4) with zinc oxide (ZnO) for enhanced performance. Our study aimed to address the urgent need for a catalyst capable of environmentally friendly degradation of paracetamol, a common pharmaceutical pollutant, using visible light conditions. Here, we tailored the band gap of a photocatalyst to match solar radiation as a transformative advancement in environmental catalysis. Notably, the optimized composite, containing 10 wt.% g-C3N4 with ZnO, demonstrated outstanding paracetamol degradation efficiency of 95% within a mere 60-min exposure to visible light. This marked enhancement represented a 2.24-fold increase in the reaction rate compared to lower wt. percentage composites (3 wt.% g-C3N4) and pristine g-C3N4. The exceptional photocatalytic activity of the optimized composite can be attributed to the band gap narrowing that closely matched the maximum solar radiation spectrum. This, coupled with efficient charge transfer mechanisms through S-scheme heterojunction formation and an abundance of active sites due to increased surface area and reduced particle size, contributed to the remarkable performance. Trapping experiments identified hydroxyl radicals as the primary reactive species responsible for paracetamol photoreduction. Furthermore, the synthesized ZnO/g-C3N4 composite exhibited exceptional photostability and reusability, underscoring its practical applicability. Thus, this research marks a significant stride towards the development of an effective and sustainable visible light photocatalyst for the removal of pharmaceutical contaminants from aquatic environments.
Modeling security evaluation framework for IoHT-driven systems using integrated decision-making methodology
Authors: Khan Habib Ullah , Ali Yasir 
Published: May 2024

AbstractThe intensification of the Internet of Health Things devices created security concerns due to the limitations of these devices and the nature of the healthcare data. While dealing with the security challenges, several authentication schemes, protocols, processes, and standards have been adopted. Consequently, making the right decision regarding the installation of a secure authentication solution or procedure becomes tricky and challenging due to the large number of security protocols, complexity, and lack of understanding. The major objective of this study is to propose an IoHT-based assessment framework for evaluating and prioritizing authentication schemes in the healthcare domain. Initially, in the proposed work, the security issues related to authentication are collected from the literature and consulting experts’ groups. In the second step, features of various authentication schemes are collected under the supervision of an Internet of Things security expert using the Delphi approach. The collected features are used to design suitable criteria for assessment and then Graph Theory and Matrix approach applies for the evaluation of authentication alternatives. Finally, the proposed framework is tested and validated to ensure the results are consistent and accurate by using other multi-criteria decision-making methods. The framework produces promising results such as 93%, 94%, and 95% for precision, accuracy, and recall, respectively in comparison to the existing approaches in this area. The proposed framework can be picked as a guideline by healthcare security experts and stakeholders for the evaluation and decision-making related to authentication issues in IoHT systems
Investigates the ability of plant extracts from Lens culinaris to protect zucchini from the Zucchini yellow mosaic virus (ZYMV)
Authors: Ali Rania , Eldidamony Gamal , Askora Ahmed , Galal Abdelmoneim 
Published: May 2024

AbstractEvaluate the impact of extracts from the Lens culinaris plant on a number of physiological and biochemical parameters in squash leaves infected with ZYMV in this work. Compared to the untreated leaves, ZYMV infected leaves showed a range of symptoms, such as severe mosaic, size reduction, stunting, and deformation. Analysis of physiological data revealed that L. culinaris extract lectin therapies and viral infections had an impact on metabolism. Protein, carbohydrate, and pigment levels were all lowered by viral infection. However, phenolic compounds, total protein, total carbohydrates, total amino acids, proline, total chlorophyll and peroxidases levels are considerably elevated with all extract therapies. The other biochemical parameters also displayed a variety of changes. Moreover shoot length, number of leaves and number of flowers was significantly increased compared to viral control in all treatments. The L. culinaris extract treatment increases the plant’s ZYMV resistance. This is detectable through reduction of the plants treated with lentil lectin pre and post virus inoculation, reduction in disease severity and viral concentration, and percentage of the infected plants has a virus. All findings demonstrate significant metabolic alterations brought by viral infections or L. culinaris extract treatments, and they also suggest that exogenous extract treatments is essential for activating the body’s defences against ZYMV infection.
Temperature-dependent iron motion in extremophile rubredoxins – no need for ‘corresponding states’
Authors: Jenney Francis E. , Wang Hongxin , George Simon J. , Xiong Jin , Guo Yisong , Gee Leland B. , Marizcurrena Juan José , Castro-Sowinski Susana , Staskiewicz Anna , Yoda Yoshitaka , Hu Michael Y. , Tamasaku Kenji , Nagasawa Nobumoto , Li Lei , Matsuura Hiroaki , Doukov Tzanko , Cramer Stephen P. 
Published: May 2024

AbstractExtremophile organisms are known that can metabolize at temperatures down to − 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins – rubredoxins – from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of ‘corresponding states’ posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although ‘corresponding states’ would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.
Fully-automated CT derived body composition analysis reveals sarcopenia in functioning adrenocortical carcinomas
Authors: Santhanam Prasanna , Dinparastisaleh Roshan , Popuri Karteek , Faisal Beg Mirza , Chen Cardenas Stanley M. , Hamrahian Amir 
Published: May 2024

AbstractDetermination of body composition (the relative distribution of fat, muscle, and bone) has been used effectively to assess the risk of progression and overall clinical outcomes in different malignancies. Sarcopenia (loss of muscle mass) is especially associated with poor clinical outcomes in cancer. However, estimation of muscle mass through CT scan has been a cumbersome, manually intensive process requiring accurate contouring through dedicated personnel hours. Recently, fully automated technologies that can determine body composition in minutes have been developed and shown to be highly accurate in determining muscle, bone, and fat mass. We employed a fully automated technology, and analyzed images from a publicly available cancer imaging archive dataset (TCIA) and a tertiary academic center. The results show that adrenocortical carcinomas (ACC) have relatively sarcopenia compared to benign adrenal lesions. In addition, functional ACCs have accelerated sarcopenia compared to non-functional ACCs. Further longitudinal research might shed further light on the relationship between body component distribution and ACC prognosis, which will help us incorporate more nutritional strategies in cancer therapy.