bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antibodies utilizing VL6-57 light chains target a convergent cryptic epitope on SARS-CoV-2 spike protein and potentially drive the genesis of Omicron variants
Authors: Yan Qihong , Gao Xijie , Liu Banghui , Hou Ruitian , He Ping , Ma Yong , Zhang Yudi , Zhang Yanjun , Li Zimu , Chen Qiuluan , Wang Jingjing , Huang Xiaohan , Liang Huan , Zheng Huiran , Yao Yichen , Chen Xianying , Niu Xuefeng , He Jun , Chen Ling , Zhao Jincun , Xiong Xiaoli 
Published: August 2024

AbstractContinued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.
Direct observation of a few-photon phase shift induced by a single quantum emitter in a waveguide
Authors: Staunstrup Mathias J. R. , Tiranov Alexey , Wang Ying , Scholz Sven , Wieck Andreas D. , Ludwig Arne , Midolo Leonardo , Rotenberg Nir , Lodahl Peter , Le Jeannic Hanna 
Published: August 2024

AbstractRealizing a sensitive photon-number-dependent phase shift on a light beam is required both in classical and quantum photonics. It may lead to new applications for classical and quantum photonics machine learning or pave the way for realizing photon-photon gate operations. Nonlinear phase-shifts require efficient light-matter interaction, and recently quantum dots coupled to nanophotonic devices have enabled near-deterministic single-photon coupling. We experimentally realize an optical phase shift of 0.19π ± 0.03 radians ( ≈ 34 degrees) using a weak coherent state interacting with a single quantum dot in a planar nanophotonic waveguide. The phase shift is probed by interferometric measurements of the light scattered from the quantum dot in the waveguide. The process is nonlinear in power, the saturation at the single-photon level and compatible with scalable photonic integrated circuitry. The work may open new prospects for realizing high-efficiency optical switching or be applied for proof-of-concept quantum machine learning or quantum simulation demonstrations.
Single-molecule force spectroscopy of toehold-mediated strand displacement
Authors: Walbrun Andreas , Wang Tianhe , Matthies Michael , Šulc Petr , Simmel Friedrich C. , Rief Matthias 
Published: August 2024

AbstractToehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.
Disinhibition enables vocal repertoire expansion after a critical period
Authors: Heim Fabian , Mendoza Ezequiel , Koparkar Avani , Vallentin Daniela 
Published: August 2024

AbstractThe efficiency of motor skill acquisition is age-dependent, making it increasingly challenging to learn complex manoeuvres later in life. Zebra finches, for instance, acquire a complex vocal motor programme during a developmental critical period after which the learned song is essentially impervious to modification. Although inhibitory interneurons are implicated in critical period closure, it is unclear whether manipulating them can reopen heightened motor plasticity windows. Using pharmacology and a cell-type specific optogenetic approach, we manipulated inhibitory neuron activity in a premotor area of adult zebra finches beyond their critical period. When exposed to auditory stimulation in the form of novel songs, manipulated birds added new vocal syllables to their stable song sequence. By lifting inhibition in a premotor area during sensory experience, we reintroduced vocal plasticity, promoting an expansion of the syllable repertoire without compromising pre-existing song production. Our findings provide insights into motor skill learning capacities, offer potential for motor recovery after injury, and suggest avenues for treating neurodevelopmental disorders involving inhibitory dysfunctions.
A catalog of small proteins from the global microbiome
Authors: Duan Yiqian , Santos-Júnior Célio Dias , Schmidt Thomas Sebastian , Fullam Anthony , de Almeida Breno L. S. , Zhu Chengkai , Kuhn Michael , Zhao Xing-Ming , Bork Peer , Coelho Luis Pedro 
Published: August 2024

AbstractSmall open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.
Excitonic signatures of ferroelectric order in parallel-stacked MoS2
Authors: Deb Swarup , Krause Johannes , Faria Junior Paulo E. , Kempf Michael Andreas , Schwartz Rico , Watanabe Kenji , Taniguchi Takashi , Fabian Jaroslav , Korn Tobias 
Published: August 2024

AbstractInterfacial ferroelectricity, prevalent in various parallel-stacked layered materials, allows switching of out-of-plane ferroelectric order by in-plane sliding of adjacent layers. Its resilience against doping potentially enables next-generation storage and logic devices. However, studies have been limited to indirect sensing or visualization of ferroelectricity. For transition metal dichalcogenides, there is little knowledge about the influence of ferroelectric order on their intrinsic valley and excitonic properties. Here, we report direct probing of ferroelectricity in few-layer 3R-MoS2 using reflectance contrast spectroscopy. Contrary to a simple electrostatic perception, layer-hybridized excitons with out-of-plane electric dipole moment remain decoupled from ferroelectric ordering, while intralayer excitons with in-plane dipole orientation are sensitive to it. Ab initio calculations identify stacking-specific interlayer hybridization leading to this asymmetric response. Exploiting this sensitivity, we demonstrate optical readout and control of multi-state polarization with hysteretic switching in a field-effect device. Time-resolved Kerr ellipticity reveals direct correspondence between spin-valley dynamics and stacking order.
Rock glaciers across the United States predominantly accelerate coincident with rise in air temperatures
Authors: Kääb Andreas , Røste Julie 
Published: August 2024

AbstractDespite their extensive global presence and the importance of variations in their speed as an essential climate variable, only about a dozen global time series document long-term changes in the velocity of rock glaciers – large tongue-shaped flows of frozen mountain debris. By analysing historical aerial photographs, we reconstruct here 16 new time series, a type of data that has not previously existed for the North American continent. We observe substantial accelerations, as much as 2–3 fold, in the surface displacement rates of rock glaciers across the mountains of the western contiguous United States over the past six to seven decades, most consistent with strongly increasing air temperatures in that region. Variations between individual time series suggest that different local and internal conditions of the frozen debris bodies modulate this overall climate response. Our observations indicate fundamental long-term environmental changes associated with frozen ground in the study region.
The ontogeny of human fetal trabecular bone architecture occurs in a limb-specific manner
Authors: Wiles Crispin Charles , Suh Sarah Holly , Brown Katharine Robson , Abel Richard Leslie 
Published: August 2024

AbstractGestational growth and development of bone is an understudied process compared to soft tissues and has implications for lifelong health. This study investigated growth and development of human fetal limb bone trabecular architecture using 3D digital histomorphometry of microcomputed tomography data from the femora and humeri of 35 skeletons (17 female and 18 male) with gestational ages between 4 and 9 months. Ontogenetic data revealed: (i) fetal trabecular architecture is similar between sexes; (ii) the proximal femoral metaphysis is physically larger, with thicker trabeculae and greater bone volume fraction relative to the humerus, but other aspects of trabecular architecture are similar between the bones; (iii) between 4 and 9 months gestation there is no apparent sexual or limb dimorphism in patterns of growth, but the size of the humerus and femur diverges early in development. Additionally, both bones exhibit significant increases in mean trabecular thickness (and for the femur alone, bone volume fraction) but minimal trabecular reorganisation (i.e., no significant changes in degree of anisotropy, connectivity density, or fractal dimension). Overall, these data suggest that in contrast to data from the axial skeleton, prenatal growth of long bones in the limbs is characterised by size increase, without major reorganizational changes in trabecular architecture.
Optical fibre sensing of turbulent-frequency motions in the oceanic environment
Authors: Spingys Carl P. , Garabato Alberto C. Naveira , Belal Mohammad 
Published: August 2024

AbstractObservations of turbulence in the oceanic environment are sparse, with very few cases of coherent measurements with significant spatio-temporal extent due primarily to limitations of current observational tools. Here we propose submarine cables with embedded optical fibres as a potential solution to fill this observational gap, and utilise a recent 12-h observational optical fibre data set from a fast-flowing tidal channel to demonstrate such potential. Firstly, the presence of turbulent-scale signals driven by flow-topography interaction is shown at frequencies of 1 Hz and higher. These signals are consistent with the timing of the tidal flow as recorded by a nearby conventional sensor. Secondly, we show the presence of surface gravity waves with periods of 10 s, which are tight in frequency space further offshore but leak energy into the turbulent frequency range on parts of the cable closer to shore. This is compatible with shoreward-propagating surface waves that break in shallow water. Finally, we fit a theoretical spectral structure to the observations to show that much of the collected data (i) has a spectral slope that is consistent with the turbulent inertial subrange, and (ii) has a range of spectral energy consistent with that expected from turbulence generation by bottom drag acting on the tidal flow. In combination, these results highlight the potential for optical fibre sensing of turbulence, and call for a targeted experiment to characterise the fibre’s turbulence-sensing capabilities.
Optimizing Gaussian process regression (GPR) hyperparameters with three metaheuristic algorithms for viscosity prediction of suspensions containing microencapsulated PCMs
Authors: Hai Tao , Basem Ali , Alizadeh As’ad , Sharma Kamal , jasim Dheyaa J. , Rajab Husam , Ahmed Mohsen , Kassim Murizah , Singh Narinderjit Singh Sawaran , Maleki Hamid 
Published: August 2024

AbstractSuspensions containing microencapsulated phase change materials (MPCMs) play a crucial role in thermal energy storage (TES) systems and have applications in building materials, textiles, and cooling systems. This study focuses on accurately predicting the dynamic viscosity, a critical thermophysical property, of suspensions containing MPCMs and MXene particles using Gaussian process regression (GPR). Twelve hyperparameters (HPs) of GPR are analyzed separately and classified into three groups based on their importance. Three metaheuristic algorithms, namely genetic algorithm (GA), particle swarm optimization (PSO), and marine predators algorithm (MPA), are employed to optimize HPs. Optimizing the four most significant hyperparameters (covariance function, basis function, standardization, and sigma) within the first group using any of the three metaheuristic algorithms resulted in excellent outcomes. All algorithms achieved a reasonable R-value (0.9983), demonstrating their effectiveness in this context. The second group explored the impact of including additional, moderate-significant HPs, such as the fit method, predict method and optimizer. While the resulting models showed some improvement over the first group, the PSO-based model within this group exhibited the most noteworthy enhancement, achieving a higher R-value (0.99834). Finally, the third group was analyzed to examine the potential interactions between all twelve HPs. This comprehensive approach, employing the GA, yielded an optimized GPR model with the highest level of target compliance, reflected by an impressive R-value of 0.999224. The developed models are a cost-effective and efficient solution to reduce laboratory costs for various systems, from TES to thermal management.
Digital spatial profiling identifies the tumor center as a topological niche in prostate cancer characterized by an upregulation of BAD
Authors: Huber Ann-Kathrin , Kaczorowski Adam , Schneider Felix , Böning Sarah , Görtz Magdalena , Langhoff David , Schwab Constantin , Stenzinger Albrecht , Hohenfellner Markus , Duensing Anette , Duensing Stefan 
Published: August 2024

AbstractProstate cancer is characterized by a high degree of intratumoral heterogeneity. However, little is known about the spatial distribution of cancer cells with respect to specific functional characteristics and the formation of spatial niches. Here, we used digital spatial profiling (DSP) to investigate differences in protein expression in the tumor center versus the tumor periphery. Thirty-seven regions of interest were analyzed for the expression of 47 proteins, which included components of the PI3K-AKT, MAPK, and cell death signaling pathways as well as immune cell markers. A total of 1739 data points were collected from five patients. DSP identified the BCL-2 associated agonist of cell death (BAD) protein as the most significantly upregulated protein in the tumor center. BAD upregulation was confirmed by conventional immunohistochemistry, which furthermore showed a phosphorylation of BAD at serine 112 indicating its inactivation. Knockdown of BAD in prostate cancer cells in vitro led to decreased cell viability and colony growth. Clinically, high BAD expression was associated with a shorter time to biochemical recurrence in 158 mostly high-risk prostate cancer patients. Collectively, our results suggest that the tumor center is a topological niche with high BAD expression that may drive prostate cancer progression.
Effect of the underlayer on the elastic parameters of the CoFeB/MgO heterostructures
Authors: Shekhar S. , Mielcarek S. , Otani Y. , Rana B. , Trzaskowska A. 
Published: August 2024

AbstractWe investigated the thermally induced surface acoustic waves in CoFeB/MgO heterostructures with different underlayer materials. Our results show a direct correlation between the density and elastic parameters of the underlayer materials and the surface phonon dispersion. Using finite element method-based simulations, we calculate the effective elastic parameters (such as elastic tensor, Young’s modulus, and Poisson’s ratio) for multilayers with different underlayer materials. The simulation results, either considering the elastic parameters of individual layers or considering the effective elastic parameters of whole stacks, exhibit good agreement with the experimental data. This study will help us deepen our understanding of phonon properties and their interactions with other quasiparticles or magnetic textures with the help of these estimated elastic properties.
CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder
Authors: Folimonova Varvara , Chen Xiang , Negi Hitendra , Schwieters Charles D. , Li Jess , Byrd R. Andrew , Taylor Naomi , Youkharibache Philippe , Walters Kylie J. 
Published: August 2024

AbstractT-cell therapies based on chimeric antigen receptor (CAR) targeting of a tumor-specific antigen offer hope for patients with relapsed or refractory cancers. CAR hinge and transmembrane regions link antigen recognition domains to intracellular signal transduction domains. Here, we apply biophysical methods to characterize the structure and dynamic properties of the CD28 CAR hinge (CD28H) used in an FDA-approved CD19 CAR for the treatment of B-lineage leukemia/lymphoma. By using nuclear Overhauser effect spectroscopy (NOESY), which detects even transiently occupied structural motifs, we observed otherwise elusive local structural elements amidst overall disorder in CD28H, including a conformational switch from a native β-strand to a 310-helix and polyproline II helix-like structure. These local structural motifs contribute to an overall loosely formed extended geometry that could be captured by NOESY data. All FDA-approved CARs use prolines in the hinge region, which we find in CD28, and previously in CD8α, isomerize to promote structural plasticity and dynamics. These local structural elements may function in recognition and signaling events and constrain the spacing between the transmembrane and antigen recognition domains. Our study thus demonstrates a method for detecting local and transient structure within intrinsically disordered systems and moreover, our CD28H findings may inform future CAR design.
Deposition temperature-mediated growth of helically shaped polymers and chevron-type graphene nanoribbons from a fluorinated precursor
Authors: Teeter Jacob D. , Sarker Mamun , Lu Wenchang , Tao Chenggang , Baddorf Arthur P. , Huang Jingsong , Hong Kunlun , Bernholc Jerry , Sinitskii Alexander , Li An-Ping 
Published: August 2024

AbstractGraphene nanoribbons (GNRs) of precise size and shape, critical for controlling electronic properties and future device applications, can be realized via precision synthesis on surfaces using rationally designed molecular precursors. Fluorine-bearing precursors have the potential to form GNRs on nonmetallic substrates suitable for device fabrication. Here, we investigate the deposition temperature-mediated growth of a new fluorine-bearing precursor, 6,11-diiodo-1,4-bis(2-fluorophenyl)-2,3-diphenyltriphenylene (C42H24F2I2), into helically shaped polymer intermediates and chevron-type GNRs on Au(111) by combining scanning tunneling microscopy, X-ray photoelectron spectroscopy, and density functional theory simulations. The fluorinated precursors do not adsorb on the Au(111) surface at lower temperatures, necessitating an optimum substrate temperature to achieve maximum polymer and GNR lengths. We compare the adsorption behavior with that of pristine chevron precursors and discuss the effects of C-H and C-F bonds. The results elucidate the growth mechanism of GNRs with fluorine-bearing precursors and establish a foundation for future synthesis of GNRs on nonmetallic substrates.
Acute Type A aortic dissection surgical repair in Octogenarians: A meta-analysis
Authors: Hasan Mohammed Tarek , Rezq Hazem Salah , Saleh Othman , Aboeldahab Heba , El khashab Mohammad K. , Hamouda Salah Mahmoud , Elkersh Hassan , Gbreel Mohamed Ibrahim , Hassaballa Aly Sherif , Awad Ahmed K. 
Published: August 2024

AbstractAortic dissection (AD), a life-threatening condition resulting from aortic wall tears, is especially concerning in the elderly. However, few studies have investigated long-term surgical outcomes in octogenarians with Type A aortic dissection (TAAD). Our paper addresses this critical knowledge gap. Four electronic databases were searched from inception till November 2022 to include any observational or randomized controlled trials (RCT) that evaluate long-term surgical outcomes of TAAD in octogenarians alone or compared with Septuagint focusing on factors including surgical approach, comorbidities, and preoperative status. The Mantel-Haenszel method was used to pool study estimates and calculate odds ratios (OR) with 95% confidence intervals (CI). We included 18,057 participants (10,253 males, 7804 females). In octogenarians and compared to medical treatment, surgical repair achieved significantly lower rates of re-exploration (9%), antegrade cerebral perfusion (33%), stroke (10%), and respiratory failure (19%). In terms of operative data, octogenarians had shorter cardiopulmonary bypass time (161.89 min), cross-clamp time (103.18 min), and myocardial ischemic time (90.89 min). Compared to septuagenarians, octogenarians had significantly shorter cardiopulmonary bypass and systemic cardiac arrest times (−13.84 min and −2.46 min, respectively). Additionally, octogenarians had a higher risk of respiratory complications (RR = 1.60). No significant differences were found for tracheostomy, antegrade cerebral perfusion, neurologic complications, and renal failure. In conclusion, octogenarians undergoing surgical repair for TAAD face relatively lower complication rates, but a higher risk of respiratory issues compared to septuagenarians, emphasizing the unique surgical challenges in this elderly fragile population.