bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nested non-covalent interactions expand the functions of supramolecular polymer networks
Authors: Lundberg David J. , Brown Christopher M. , Bobylev Eduard O. , Oldenhuis Nathan J. , Alfaraj Yasmeen S. , Zhao Julia , Kevlishvili Ilia , Kulik Heather J. , Johnson Jeremiah A. 
Published: May 2024

AbstractSupramolecular polymer networks contain non-covalent cross-links that enable access to broadly tunable mechanical properties and stimuli-responsive behaviors; the incorporation of multiple unique non-covalent cross-links within such materials further expands their mechanical responses and functionality. To date, however, the design of such materials has been accomplished through discrete combinations of distinct interaction types in series, limiting materials design logic. Here we introduce the concept of leveraging “nested” supramolecular crosslinks, wherein two distinct types of non-covalent interactions exist in parallel, to control bulk material functions. To demonstrate this concept, we use polymer-linked Pd2L4 metal–organic cage (polyMOC) gels that form hollow metal–organic cage junctions through metal–ligand coordination and can exhibit well-defined host-guest binding within their cavity. In these “nested” supramolecular network junctions, the thermodynamics of host-guest interactions within the junctions affect the metal–ligand interactions that form those junctions, ultimately translating to substantial guest-dependent changes in bulk material properties that could not be achieved in traditional supramolecular networks with multiple interactions in series.
Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88
Authors: Lauer Simon M. , Reepmeyer Maren , Berendes Ole , Klepacki Dorota , Gasse Jakob , Gabrielli Sara , Grubmüller Helmut , Bock Lars V. , Krizsan Andor , Nikolay Rainer , Spahn Christian M. T. , Hoffmann Ralf 
Published: May 2024

AbstractProline-rich antimicrobial peptides (PrAMPs) inhibit bacterial protein biosynthesis by binding to the polypeptide exit tunnel (PET) near the peptidyl transferase center. Api137, an optimized derivative of honeybee PrAMP apidaecin, inhibits protein expression by trapping release factors (RFs), which interact with stop codons on ribosomes to terminate translation. This study uses cryo-EM, functional assays and molecular dynamic (MD) simulations to show that Api137 additionally occupies a second binding site near the exit of the PET and can repress translation independently of RF-trapping. Api88, a C-terminally amidated (-CONH2) analog of Api137 (-COOH), binds to the same sites, occupies a third binding pocket and interferes with the translation process presumably without RF-trapping. In conclusion, apidaecin-derived PrAMPs inhibit bacterial ribosomes by multimodal mechanisms caused by minor structural changes and thus represent a promising pool for drug development efforts.
An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries
Authors: Petersen Brian M. , Kirby Monica B. , Chrispens Karson M. , Irvin Olivia M. , Strawn Isabell K. , Haas Cyrus M. , Walker Alexis M. , Baumer Zachary T. , Ulmer Sophia A. , Ayala Edgardo , Rhodes Emily R. , Guthmiller Jenna J. , Steiner Paul J. , Whitehead Timothy A. 
Published: May 2024

AbstractAntibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of nine different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.
Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data
Authors: Su Yaqi , Yu Zhejian , Jin Siqian , Ai Zhipeng , Yuan Ruihong , Chen Xinyi , Xue Ziwei , Guo Yixin , Chen Di , Liang Hongqing , Liu Zuozhu , Liu Wanlu 
Published: May 2024

AbstractThe advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors. In this study, we conducted a benchmark analysis of thirteen methods implemented in nine tools capable of identifying isoform structures from long-read RNA-seq data. We evaluated their performances using simulated data, which represented diverse sequencing platforms generated by an in-house simulator, RNA sequins (sequencing spike-ins) data, as well as experimental data. Our findings demonstrate IsoQuant as a highly effective tool for isoform detection with LRS, with Bambu and StringTie2 also exhibiting strong performance. These results offer valuable guidance for future research on alternative splicing analysis and the ongoing improvement of tools for isoform detection using LRS data.
Efficient characterizations of multiphoton states with an ultra-thin optical device
Authors: An Kui , Liu Zilei , Zhang Ting , Li Siqi , Zhou You , Yuan Xiao , Wang Leiran , Zhang Wenfu , Wang Guoxi , Lu He 
Published: May 2024

AbstractMetasurface enables the generation and manipulation of multiphoton entanglement with flat optics, providing a more efficient platform for large-scale photonic quantum information processing. Here, we show that a single metasurface optical device would allow more efficient characterizations of multiphoton entangled states, such as shadow tomography, which generally requires fast and complicated control of optical setups to perform information-complete measurements, a demanding task using conventional optics. The compact and stable device here allows implementations of general positive operator valued measures with a reduced sample complexity and significantly alleviates the experimental complexity to implement shadow tomography. Integrating self-learning and calibration algorithms, we observe notable advantages in the reconstruction of multiphoton entanglement, including using fewer measurements, having higher accuracy, and being robust against experimental imperfections. Our work unveils the feasibility of metasurface as a favorable integrated optical device for efficient characterization of multiphoton entanglement, and sheds light on scalable photonic quantum technologies with ultra-thin optical devices.
Three concurrent mechanisms generate gene copy number variation and transient antibiotic heteroresistance
Authors: Nicoloff Hervé , Hjort Karin , Andersson Dan I. , Wang Helen 
Published: May 2024

AbstractHeteroresistance is a medically relevant phenotype where small antibiotic-resistant subpopulations coexist within predominantly susceptible bacterial populations. Heteroresistance reduces treatment efficacy across diverse bacterial species and antibiotic classes, yet its genetic and physiological mechanisms remain poorly understood. Here, we investigated a multi-resistant Klebsiella pneumoniae isolate and identified three primary drivers of gene dosage-dependent heteroresistance for several antibiotic classes: tandem amplification, increased plasmid copy number, and transposition of resistance genes onto cryptic plasmids. All three mechanisms imposed fitness costs and were genetically unstable, leading to fast reversion to susceptibility in the absence of antibiotics. We used a mouse gut colonization model to show that heteroresistance due to elevated resistance-gene dosage can result in antibiotic treatment failures. Importantly, we observed that the three mechanisms are prevalent among Escherichia coli bloodstream isolates. Our findings underscore the necessity for treatment strategies that address the complex interplay between plasmids, resistance cassettes, and transposons in bacterial populations.
Mutational dissection of a hole hopping route in a lytic polysaccharide monooxygenase (LPMO)
Authors: Ayuso-Fernández Iván , Emrich-Mills Tom Z. , Haak Julia , Golten Ole , Hall Kelsi R. , Schwaiger Lorenz , Moe Trond S. , Stepnov Anton A. , Ludwig Roland , Cutsail III George E. , Sørlie Morten , Kjendseth Røhr Åsmund , Eijsink Vincent G. H. 
Published: May 2024

AbstractOxidoreductases have evolved tyrosine/tryptophan pathways that channel highly oxidizing holes away from the active site to avoid damage. Here we dissect such a pathway in a bacterial LPMO, member of a widespread family of C-H bond activating enzymes with outstanding industrial potential. We show that a strictly conserved tryptophan is critical for radical formation and hole transference and that holes traverse the protein to reach a tyrosine-histidine pair in the protein’s surface. Real-time monitoring of radical formation reveals a clear correlation between the efficiency of hole transference and enzyme performance under oxidative stress. Residues involved in this pathway vary considerably between natural LPMOs, which could reflect adaptation to different ecological niches. Importantly, we show that enzyme activity is increased in a variant with slower radical transference, providing experimental evidence for a previously postulated trade-off between activity and redox robustness.
Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression
Authors: Li-Bao Lin , Díaz-Díaz Covadonga , Raiola Morena , Sierra Rocío , Temiño Susana , Moya Francisco J. , Rodriguez-Perales Sandra , Santos Elisa , Giovinazzo Giovanna , Bleckwehl Tore , Rada-Iglesias Álvaro , Spitz Francois , Torres Miguel 
Published: May 2024

AbstractMYC plays various roles in pluripotent stem cells, including the promotion of somatic cell reprogramming to pluripotency, the regulation of cell competition and the control of embryonic diapause. However, how Myc expression is regulated in this context remains unknown. The Myc gene lies within a ~ 3-megabase gene desert with multiple cis-regulatory elements. Here we use genomic rearrangements, transgenesis and targeted mutation to analyse Myc regulation in early mouse embryos and pluripotent stem cells. We identify a topologically-associated region that homes enhancers dedicated to Myc transcriptional regulation in stem cells of the pre-implantation and early post-implantation embryo. Within this region, we identify elements exclusively dedicated to Myc regulation in pluripotent cells, with distinct enhancers that sequentially activate during naive and formative pluripotency. Deletion of pluripotency-specific enhancers dampens embryonic stem cell competitive ability. These results identify a topologically defined enhancer cluster dedicated to early embryonic expression and uncover a modular mechanism for the regulation of Myc expression in different states of pluripotency.
Distributed representations of prediction error signals across the cortical hierarchy are synergistic
Authors: Gelens Frank , Äijälä Juho , Roberts Louis , Komatsu Misako , Uran Cem , Jensen Michael A. , Miller Kai J. , Ince Robin A. A. , Garagnani Max , Vinck Martin , Canales-Johnson Andres 
Published: May 2024

AbstractA relevant question concerning inter-areal communication in the cortex is whether these interactions are synergistic. Synergy refers to the complementary effect of multiple brain signals conveying more information than the sum of each isolated signal. Redundancy, on the other hand, refers to the common information shared between brain signals. Here, we dissociated cortical interactions encoding complementary information (synergy) from those sharing common information (redundancy) during prediction error (PE) processing. We analyzed auditory and frontal electrocorticography (ECoG) signals in five common awake marmosets performing two distinct auditory oddball tasks and investigated to what extent event-related potentials (ERP) and broadband (BB) dynamics encoded synergistic and redundant information about PE processing. The information conveyed by ERPs and BB signals was synergistic even at lower stages of the hierarchy in the auditory cortex and between auditory and frontal regions. Using a brain-constrained neural network, we simulated the synergy and redundancy observed in the experimental results and demonstrated that the emergence of synergy between auditory and frontal regions requires the presence of strong, long-distance, feedback, and feedforward connections. These results indicate that distributed representations of PE signals across the cortical hierarchy can be highly synergistic.
Human-induced intensified seasonal cycle of sea surface temperature
Authors: Liu Fukai , Song Fengfei , Luo Yiyong 
Published: May 2024

AbstractChanges in the seasonal cycle of sea surface temperature (SST) have far-reaching ecological and societal implications. Previous studies have found an intensified SST seasonal cycle under global warming, but whether such changes have emerged in historical records remains largely unknown. Here, we reveal that the SST seasonal cycle globally has intensified by 3.9 ± 1.6% in recent four decades (1983–2022), with hotspot regions such as the northern subpolar gyres experiencing an intensification of up to 10%. Increased greenhouse gases are the primary driver of this intensification, and decreased anthropogenic aerosols also contribute. These changes in anthropogenic emissions lead to shallower mixed layer depths, reducing the thermal inertia of upper ocean and enhancing the seasonality of SST. In addition, the direct impacts of increased ocean heat uptake and suppressed seasonal amplitude of surface heat flux also contribute in the North Pacific and North Atlantic. The temperature seasonal cycle is intensified not only at the ocean surface, but throughout the mixed layer. The ramifications of this intensified SST seasonal cycle extend to the seasonal variation in upper-ocean oxygenation, a critical factor for most ocean ecosystems.
A nascent riboswitch helix orchestrates robust transcriptional regulation through signal integration
Authors: Chauvier Adrien , Dandpat Shiba S. , Romero Rosa , Walter Nils G. 
Published: May 2024

Abstract
Widespread manganese-sensing transcriptional riboswitches effect the dependable gene regulation needed for bacterial manganese homeostasis in changing environments. Riboswitches – like most structured RNAs – are believed to fold co-transcriptionally, subject to both ligand binding and transcription events; yet how these processes are orchestrated for robust regulation is poorly understood. Through a combination of single-molecule and bulk approaches, we discover how a single Mn2+ ion and the transcribing RNA polymerase (RNAP), paused immediately downstream by a DNA template sequence, are coordinated by the bridging switch helix P1.1 in the representative Lactococcus lactis riboswitch. This coordination achieves a heretofore-overlooked semi-docked global conformation of the nascent RNA, P1.1 base pair stabilization, transcription factor NusA ejection, and RNAP pause extension, thereby enforcing transcription readthrough. Our work demonstrates how a central, adaptable RNA helix functions analogous to a molecular fulcrum of a first-class lever system to integrate disparate signals for finely balanced gene expression control.
Implementing no-signaling correlations as a service
Authors: Koniorczyk Mátyás , Naszvadi Péter , Bodor András , Hanyecz Ottó , Adam Peter , Pintér Miklós 
Published: May 2024

AbstractWe deal with no-signaling correlations that include Bell-type quantum nonlocality. We consider a logical implementation using a trusted central server with encrypted connections to clients. We show that in this way it is possible to implement two-party no-signaling correlations in an asynchronous manner. While from the point of view of physics our approach can be considered as the computer emulation of the results of measurements on entangled particles, from the software engineering point of view it introduces a primitive in communication protocols that can be capable of coordinating agents without revealing the details of their actions. We present an actual implementation in the form of a Web-based application programming interface (RESTful Web API). We demonstrate the use of the API via the simple implementation of the Clauser–Horne–Shimony–Holt game.
Spatial–temporal transmission dynamics of HIV-1 CRF01_AE in Indonesia
Authors: Khairunisa Siti Qamariyah , Indriati Dwi Wahyu , Megasari Ni Luh Ayu , Ueda Shuhei , Kotaki Tomohiro , Fahmi Muhamad , Ito Masahiro , Rachman Brian Eka , Hidayati Afif Nurul , Nasronudin  , Kameoka Masanori 
Published: May 2024

AbstractHuman immunodeficiency virus type 1 (HIV-1) remains a serious health threat in Indonesia. In particular, the CRF01_AE viruses were the predominant HIV-1 strains in various cities in Indonesia. However, information on the dynamic transmission characteristics and spatial–temporal transmission of HIV-1 CRF01_AE in Indonesia is limited. Therefore, the present study examined the spatial–temporal transmission networks and evolutionary characteristics of HIV-1 CRF01_AE in Indonesia. To clarify the epidemiological connection between CRF01_AE outbreaks in Indonesia and the rest of the world, we performed phylogenetic studies on nearly full genomes of CRF01_AE viruses isolated in Indonesia. Our results showed that five epidemic clades, namely, IDN clades 1–5, of CRF01_AE were found in Indonesia. To determine the potential source and mode of transmission of CRF01_AE, we performed Bayesian analysis and built maximum clade credibility trees for each clade. Our study revealed that CRF01_AE viruses were commonly introduced into Indonesia from Southeast Asia, particularly Thailand. The CRF01_AE viruses might have spread through major pandemics in Asian countries, such as China, Vietnam, and Laos, rather than being introduced directly from Africa in the early 1980s. This study has major implications for public health practice and policy development in Indonesia. The contributions of this study include understanding the dynamics of HIV-1 transmission that is important for the implementation of HIV disease control and prevention strategies in Indonesia.
Development of a dual point humidity sensor using POF based on twisted fiber structure
Authors: Hussian Sadam , Mehdi Mujahid , Ghaffar Abdul , Lan Kun , Hu Yanjun , Lin Huan , Qaisrani Mumtaz A. , Ali Sikandar , Lin Jie , Mehdi Rehan , Ma Rui 
Published: May 2024

AbstractThe humidity has often been measured through a single point sensor. Where, the humidity could be varied at different locations as well as depending on environmental conditions. The present paper developed the dual point humidity measuring sensor by using a polymer optical fiber (POF) based on a single illuminating fiber. The sensor’s basic structure is to twist two fibers and bend them at a certain radius. However, the dual point sensor is developed through the cascading of twisted micro bend (TMB-1 and TMB-2). The twisting of fibers couples the light from one fiber to another fiber through the side coupling method. An increase in the humidity level leads to a change in the reflective index, which helps to get variation in coupled light intensity. To measure the humidity, the dual point sensors are placed into the control humidity chamber at two random positions. The power reading variation is significantly linear when the humidity level increases from 30 to 80%. The sensor has a fast response of about 1 s and a recovery time of about 4 s. Furthermore, the chemical coating is applied to improve the sensor’s sensitivity. Between 30 and 80% range of humidity, the both sensors of dual point TMB-1 and TMB-2 have appropriate sensitivity and detection limits, which is about 680.8 nW/% and 763.9 nW/% and 1.37% and 1.98%, respectively. To measure the humidity at variable positions, the present dual points humidity sensor is well-stable, easy, and straightforward, which uses a less expensive method.
Enhanced adsorption and removal of Cd(II) from aqueous solution by amino-functionalized ZIF-8
Authors: Khosravi Amir , Habibpour Razieh , Ranjbar Maryam 
Published: May 2024

AbstractZeolite imidazolate framework-8 (ZIF-8), which is a special subgroup of metal–organic frameworks (MOFs), was synthesized and modified by ethylenediamine (ZIF-8-EDA) to prepare an efficient adsorbent for the high sorption of Cd2+ions from solution. The synthesized and modified ZIF-8 (ZIF-8-EDA) were characterized by X-ray diffraction (XRD), Fourier-transform infrared (FT-IR) spectroscopy, Brunauer–Emmett–Teller (BET), field emission scanning electron microscopy (FE-SEM) with energy dispersive spectroscopy (EDS), and transmission electron microscopy (TEM) analysis. The optimum conditions for dosage of adsorbent, initial ion concentration, pH, and contact time were 0.05 g/l, 50 mg/l, 6, and 60 min, respectively, for cadmium ion sorption from aqueous solutions with a removal efficiency of 89.7% for ZIF-8 and 93.5% for ZIF-8-EDA. Adsorption kinetics and equilibrium data were analyzed using the Langmuir and Freundlich equations. The Langmuir model fitted the equilibrium data better than the Freundlich model. According to the Langmuir equation, the maximum uptake for the cadmium ions was 294.11(mg/g). The calculated thermodynamic parameters (ΔG°, ΔH°, and ΔS°) indicated that the adsorption process was feasible, spontaneous, and endothermic at 20–50 °C. Based on the results, the amino functionalized ZIF-8 had improved adsorption performance due to the replacing of the starting linker with organic ligands that had effective functional groups, leading to chemical coordination due to the interaction of metal ions with the non-bonding pair of electrons on the N atoms of the amino functional group. The selectivity toward metal ion adsorption by ZIF-8-EDA was Cd2+ > Pb2+ > Ni2+‏.