bluuebunny/crossref_metadata_2025_split huggingface dataset:
Point-to-point associations of drusen and hyperreflective foci volumes with retinal sensitivity in non-exudative age-related macular degeneration
Authors: Reiter Gregor S. , Bogunovic Hrvoje , Schlanitz Ferdinand , Vogl Wolf-Dieter , Seeböck Philipp , Ramazanova Dariga , Schmidt-Erfurth Ursula 
Published: May 2023

Abstract
Objectives
To evaluate the quantitative impact of drusen and hyperreflective foci (HRF) volumes on mesopic retinal sensitivity in non-exudative age-related macular degeneration (AMD).

Methods
In a standardized follow-up scheme of every three months, retinal sensitivity of patients with early or intermediate AMD was assessed by microperimetry using a custom pattern of 45 stimuli (Nidek MP-3, Gamagori, Japan). Eyes were consecutively scanned using Spectralis SD-OCT (20° × 20°, 1024 × 97 × 496). Fundus photographs obtained by the MP-3 allowed to map the stimuli locations onto the corresponding OCT scans. The volume and mean thickness of drusen and HRF within a circle of 240 µm centred at each stimulus point was determined using automated AI-based image segmentation algorithms.

Results
8055 individual stimuli from 179 visits from 51 eyes of 35 consecutive patients were matched with the respective OCT images in a point-to-point manner. The patients mean age was 76.85 ± 6.6 years. Mean retinal sensitivity at baseline was 25.7 dB. 73.47% of all MP-spots covered drusen area and 2.02% of MP-spots covered HRF. A negative association between retinal sensitivity and the volume of underlying drusen (p < 0.001, Estimate −0.991 db/µm3) and HRF volume (p = 0.002, Estimate -5.230 db/µm3) was found. During observation time, no eye showed conversion to advanced AMD.

Conclusion
A direct correlation between drusen and lower sensitivity of the overlying photoreceptors can be observed. For HRF, a small but significant correlation was shown, which is compromised by their small size. Biomarker quantification using AI-methods allows to determine the impact of sub-clinical features in the progression of AMD.
Value of prolonged scrotal drainage after penile prosthesis implantation: a multicenter prospective nonrandomized pilot study
Authors: Osmonov D. , Ragheb A. M. , Petry T. , Eraky A. , Bettocchi C. , Lamers K. G. , Van Renterghem K. , Tropmann-Frick M. , Chung E. , Jünemann K. P. , Garaffa G. , Porst H. , Mohamed A. G. , Wilson S. K. 
Published: May 2023

AbstractWe aimed to understand the risks and benefits of post-inflatable penile prosthesis (IPP) implantation drainage and optimal duration. Our patients were divided into 3 groups: Group 1 (n = 114) had no drain placed, Group 2 had a drain placed for 24 h (n = 114) and Group 3 had a drain placed for 72 h (n = 117). Postoperative scrotal hematoma and prosthesis infection rates were compared between the groups. The patients from Group 3 demonstrated a statistically significant lower incidence of hematoma on the 10th postoperative day: (n = 1, 0.9%) compared to Group 2: (n = 11, 9.6%) and Group 1: (n = 8, 7%), (p = 0.013). However, on the 3rd postoperative day, there was a statistically significant lower incidence of hematoma in both Groups 3 and 2: (0.9% and 6.1%, respectively) vs. Group 1: (11.4%), (p = 0.004). Hematoma rates followed the same group order after the first day of surgery: 1.7% (n = 2), 5.3% (n = 6), and 8.8% (n = 10), respectively, (p = 0.05). Five patients (4.4%) in Group 1 and four patients (3.5%) in Group 2 developed an IPP associated infection, opposed to only a single patient (0.85%) in Group 3, (p = 0.210). We concluded that prolonged scrotal drainage for 72 h after virgin IPP implantation significantly reduces hematoma and infection rates.
Seismically imaged lithospheric delamination and its controls on the Mesozoic Magmatic Province in South China
Authors: Zhang Haijiang , Lü Qing-Tian , Wang Xiao-Lei , Han Shoucheng , Liu Lijun , Gao Lei , Wang Rui , Hou Zeng-Qian 
Published: May 2023

AbstractThe current lithospheric root of the South China Block has been partly removed, yet what mechanisms modified the lithospheric structure remain highly controversial. Here we use a new joint seismic inversion algorithm to image tabular high-velocity anomalies at depths of ~90–150 km in the asthenosphere beneath the convergent belt between the Yangtze and Cathaysia blocks that remain weakly connected with the stable Yangtze lithosphere. Based on obtained seismic images and available geochemical data, we interpret these detached fast anomalies as partially destabilized lower lithosphere that initially delaminated at 180–170 Ma and has relaminated to their original position after warming up in the mantle by now. We conclude that delamination is the most plausible mechanism for the lithospheric modification and the formation of a Mesozoic Basin and Range-style magmatic province in South China by triggering adiabatic upwelling of the asthenosphere and consequent lithospheric extension and extensive melting of the overlying crust.
Cryo-electron microscopy of the f1 filamentous phage reveals insights into viral infection and assembly
Authors: Conners Rebecca , León-Quezada Rayén Ignacia , McLaren Mathew , Bennett Nicholas J. , Daum Bertram , Rakonjac Jasna , Gold Vicki A. M. 
Published: May 2023

AbstractPhages are viruses that infect bacteria and dominate every ecosystem on our planet. As well as impacting microbial ecology, physiology and evolution, phages are exploited as tools in molecular biology and biotechnology. This is particularly true for the Ff (f1, fd or M13) phages, which represent a widely distributed group of filamentous viruses. Over nearly five decades, Ffs have seen an extraordinary range of applications, yet the complete structure of the phage capsid and consequently the mechanisms of infection and assembly remain largely mysterious. In this work, we use cryo-electron microscopy and a highly efficient system for production of short Ff-derived nanorods to determine a structure of a filamentous virus including the tips. We show that structure combined with mutagenesis can identify phage domains that are important in bacterial attack and for release of new progeny, allowing new models to be proposed for the phage lifecycle.
meQTL mapping in the GENOA study reveals genetic determinants of DNA methylation in African Americans
Authors: Shang Lulu , Zhao Wei , Wang Yi Zhe , Li Zheng , Choi Jerome J. , Kho Minjung , Mosley Thomas H. , Kardia Sharon L. R. , Smith Jennifer A. , Zhou Xiang 
Published: May 2023

AbstractIdentifying genetic variants that are associated with variation in DNA methylation, an analysis commonly referred to as methylation quantitative trait locus (meQTL) mapping, is an important first step towards understanding the genetic architecture underlying epigenetic variation. Most existing meQTL mapping studies have focused on individuals of European ancestry and are underrepresented in other populations, with a particular absence of large studies in populations with African ancestry. We fill this critical knowledge gap by performing a large-scale cis-meQTL mapping study in 961 African Americans from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. We identify a total of 4,565,687 cis-acting meQTLs in 320,965 meCpGs. We find that 45% of meCpGs harbor multiple independent meQTLs, suggesting potential polygenic genetic architecture underlying methylation variation. A large percentage of the cis-meQTLs also colocalize with cis-expression QTLs (eQTLs) in the same population. Importantly, the identified cis-meQTLs explain a substantial proportion (median = 24.6%) of methylation variation. In addition, the cis-meQTL associated CpG sites mediate a substantial proportion (median = 24.9%) of SNP effects underlying gene expression. Overall, our results represent an important step toward revealing the co-regulation of methylation and gene expression, facilitating the functional interpretation of epigenetic and gene regulation underlying common diseases in African Americans.
Replication fork binding triggers structural changes in the PriA helicase that govern DNA replication restart in E. coli
Authors: Duckworth Alexander T. , Ducos Peter L. , McMillan Sarah D. , Satyshur Kenneth A. , Blumenthal Katelien H. , Deorio Haley R. , Larson Joseph A. , Sandler Steven J. , Grant Timothy , Keck James L. 
Published: May 2023

AbstractBacterial replisomes often dissociate from replication forks before chromosomal replication is complete. To avoid the lethal consequences of such situations, bacteria have evolved replication restart pathways that reload replisomes onto prematurely terminated replication forks. To understand how the primary replication restart pathway in E. coli (PriA-PriB) selectively acts on replication forks, we determined the cryogenic-electron microscopy structure of a PriA/PriB/replication fork complex. Replication fork specificity arises from extensive PriA interactions with each arm of the branched DNA. These interactions reshape the PriA protein to create a pore encircling single-stranded lagging-strand DNA while also exposing a surface of PriA onto which PriB docks. Together with supporting biochemical and genetic studies, the structure reveals a switch-like mechanism for replication restart initiation in which restructuring of PriA directly couples replication fork recognition to PriA/PriB complex formation to ensure robust and high-fidelity replication re-initiation.
Convergent evolution of SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant
Authors: Ito Jumpei , Suzuki Rigel , Uriu Keiya , Itakura Yukari , Zahradnik Jiri , Kimura Kanako Terakado , Deguchi Sayaka , Wang Lei , Lytras Spyros , Tamura Tomokazu , Kida Izumi , Nasser Hesham , Shofa Maya , Begum Mst Monira , Tsuda Masumi , Oda Yoshitaka , Suzuki Tateki , Sasaki Jiei , Sasaki-Tabata Kaori , Fujita Shigeru , Yoshimatsu Kumiko , Ito Hayato , Nao Naganori , Asakura Hiroyuki , Nagashima Mami , Sadamasu Kenji , Yoshimura Kazuhisa , Yamamoto Yuki , Nagamoto Tetsuharu , Kuramochi Jin , Schreiber Gideon ,   The Genotype to Phenotype Japan (G2P-Japan) Consortium, Suzuki Saori , Kato Marie , Ferdous Zannatul , Mouri Hiromi , Shishido Kenji , Misawa Naoko , Kimura Izumi , Kosugi Yusuke , Lin Pan , Suganami Mai , Chiba Mika , Yoshimura Ryo , Yasuda Kyoko , Iida Keiko , Ohsumi Naomi , Strange Adam P. , Sauter Daniel , Nakagawa So , Wu Jiaqi , Watanabe Yukio , Sakamoto Ayaka , Yasuhara Naoko , Nakajima Yukari , Yajima Hisano , Shirakawa Kotaro , Takaori-Kondo Akifumi , Nagata Kayoko , Kazuma Yasuhiro , Nomura Ryosuke , Horisawa Yoshihito , Tashiro Yusuke , Kawa Yugo , Irie Takashi , Kawabata Ryoko , Shimizu Ryo , Takahashi Otowa , Ichihara Kimiko , Motozono Chihiro , Toyoda Mako , Ueno Takamasa , Shibatani Yuki , Nishiuchi Tomoko , Saito Akatsuki , Matsuno Keita , Takayama Kazuo , Hashiguchi Takao , Tanaka Shinya , Fukuhara Takasuke , Ikeda Terumasa , Sato Kei 
Published: May 2023

AbstractIn late 2022, various Omicron subvariants emerged and cocirculated worldwide. These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. Here, we characterize the convergent evolution of Omicron subvariants and the properties of one recent lineage of concern, BQ.1.1. Our phylogenetic analysis suggests that these five substitutions are recurrently acquired, particularly in younger Omicron lineages. Epidemic dynamics modelling suggests that the five substitutions increase viral fitness, and a large proportion of the fitness variation within Omicron lineages can be explained by these substitutions. Compared to BA.5, BQ.1.1 evades breakthrough BA.2 and BA.5 infection sera more efficiently, as demonstrated by neutralization assays. The pathogenicity of BQ.1.1 in hamsters is lower than that of BA.5. Our multiscale investigations illuminate the evolutionary rules governing the convergent evolution for known Omicron lineages as of 2022.
In-plane hyperbolic polariton tuners in terahertz and long-wave infrared regimes
Authors: Huang Wuchao , Folland Thomas G. , Sun Fengsheng , Zheng Zebo , Xu Ningsheng , Xing Qiaoxia , Jiang Jingyao , Chen Huanjun , Caldwell Joshua D. , Yan Hugen , Deng Shaozhi 
Published: May 2023

AbstractOne of the main bottlenecks in the development of terahertz (THz) and long-wave infrared (LWIR) technologies is the limited intrinsic response of traditional materials. Hyperbolic phonon polaritons (HPhPs) of van der Waals semiconductors couple strongly with THz and LWIR radiation. However, the mismatch of photon − polariton momentum makes far-field excitation of HPhPs challenging. Here, we propose an In-Plane Hyperbolic Polariton Tuner that is based on patterning van der Waals semiconductors, here α-MoO3, into ribbon arrays. We demonstrate that such tuners respond directly to far-field excitation and give rise to LWIR and THz resonances with high quality factors up to 300, which are strongly dependent on in-plane hyperbolic polariton of the patterned α-MoO3. We further show that with this tuner, intensity regulation of reflected and transmitted electromagnetic waves, as well as their wavelength and polarization selection can be achieved. Our results can help the development of THz and LWIR miniaturized devices.
Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures
Authors: Inagaki Masahito , Abe Naoko , Li Zhenmin , Nakashima Yuko , Acharyya Susit , Ogawa Kazuya , Kawaguchi Daisuke , Hiraoka Haruka , Banno Ayaka , Meng Zheyu , Tada Mizuki , Ishida Tatsuma , Lyu Pingxue , Kokubo Kengo , Murase Hirotaka , Hashiya Fumitaka , Kimura Yasuaki , Uchida Satoshi , Abe Hiroshi 
Published: May 2023

AbstractStarting with the clinical application of two vaccines in 2020, mRNA therapeutics are currently being investigated for a variety of applications. Removing immunogenic uncapped mRNA from transcribed mRNA is critical in mRNA research and clinical applications. Commonly used capping methods provide maximum capping efficiency of around 80–90% for widely used Cap-0- and Cap-1-type mRNAs. However, uncapped and capped mRNA possesses almost identical physicochemical properties, posing challenges to their physical separation. In this work, we develop hydrophobic photocaged tag-modified cap analogs, which separate capped mRNA from uncapped mRNA by reversed-phase high-performance liquid chromatography. Subsequent photo-irradiation recovers footprint-free native capped mRNA. This approach provides 100% capping efficiency even in Cap-2-type mRNA with versatility applicable to 650 nt and 4,247 nt mRNA. We find that the Cap-2-type mRNA shows up to 3- to 4-fold higher translation activity in cultured cells and animals than the Cap-1-type mRNA prepared by the standard capping method.
Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes
Authors: Nepal Chirag , Andersen Jesper B. 
Published: May 2023

AbstractTranscriptional regulation is commonly governed by alternative promoters. However, the regulatory architecture in alternative and reference promoters, and how they differ, remains elusive. In 100 CAGE-seq libraries from hepatocellular carcinoma patients, here we annotate 4083 alternative promoters in 2926 multi-promoter genes, which are largely undetected in normal livers. These genes are enriched in oncogenic processes and predominantly show association with overall survival. Alternative promoters are narrow nucleosome depleted regions, CpG island depleted, and enriched for tissue-specific transcription factors. Globally tumors lose DNA methylation. We show hierarchical retention of intragenic DNA methylation with CG-poor regions rapidly losing methylation, while CG-rich regions retain it, a process mediated by differential SETD2, H3K36me3, DNMT3B, and TET1 binding. This mechanism is validated in SETD2 knockdown cells and SETD2-mutated patients. Selective DNA methylation loss in CG-poor regions makes the chromatin accessible for alternative transcription. We show alternative promoters can control tumor transcriptomes and their regulatory architecture.
Allocating capital-associated CO2 emissions along the full lifespan of capital investments helps diffuse emission responsibility
Authors: Ye Quanliang , Krol Maarten S. , Shan Yuli , Schyns Joep F. , Berger Markus , Hubacek Klaus 
Published: May 2023

AbstractCapital assets such as machinery and infrastructure contribute substantially to CO2 emissions over their lifetime. Unique features of capital assets such as their long durability complicate the assignment of capital-associated CO2 emissions to final beneficiaries. Whereas conventional approaches allocate emissions required to produce capital assets to the year of formation, we propose an alternative perspective through allocating required emissions from the production of assets over their entire lifespans. We show that allocating CO2 emissions embodied in capital assets over time relieves emission responsibility for the year of formation, with 25‒46% reductions from conventional emission accounts. This temporal allocation, although virtual, is important for assessing the equity of CO2 emissions across generations due to the inertia of capital assets. To re-allocate emission responsibilities to the future, we design three capital investment scenarios with different investment purposes until 2030. Overall, the existing capital in 2017 will still carry approximately 10% responsibilities of China’s CO2 emissions in 2030, and could reach more than 40% for capital-intensive service sectors.
Neonatal immune challenge poses a sex-specific risk for epigenetic microglial reprogramming and behavioral impairment
Authors: Schwabenland Marius , Mossad Omar , Sievert Annika , Peres Adam G. , Ringel Elena , Baasch Sebastian , Kolter Julia , Cascone Giulia , Dokalis Nikolaos , Vlachos Andreas , Ruzsics Zsolt , Henneke Philipp , Prinz Marco , Blank Thomas 
Published: May 2023

AbstractWhile the precise processes underlying a sex bias in the development of central nervous system (CNS) disorders are unknown, there is growing evidence that an early life immune activation can contribute to the disease pathogenesis. When we mimicked an early systemic viral infection or applied murine cytomegalovirus (MCMV) systemically in neonatal female and male mice, only male adolescent mice presented behavioral deficits, including reduced social behavior and cognition. This was paralleled by an increased amount of infiltrating T cells in the brain parenchyma, enhanced interferon-γ (IFNγ) signaling, and epigenetic reprogramming of microglial cells. These microglial cells showed increased phagocytic activity, which resulted in abnormal loss of excitatory synapses within the hippocampal brain region. None of these alterations were seen in female adolescent mice. Our findings underscore the early postnatal period’s susceptibility to cause sex-dependent long-term CNS deficiencies following infections.
Solvent control of water O−H bonds for highly reversible zinc ion batteries
Authors: Wang Yanyan , Wang Zhijie , Pang Wei Kong , Lie Wilford , Yuwono Jodie A. , Liang Gemeng , Liu Sailin , Angelo Anita M. D’ , Deng Jiaojiao , Fan Yameng , Davey Kenneth , Li Baohua , Guo Zaiping 
Published: May 2023

AbstractAqueous Zn-ion batteries have attracted increasing research interest; however, the development of these batteries has been hindered by several challenges, including dendrite growth, Zn corrosion, cathode material degradation, limited temperature adaptability and electrochemical stability window, which are associated with water activity and the solvation structure of electrolytes. Here we report that water activity is suppressed by increasing the electron density of the water protons through interactions with highly polar dimethylacetamide and trimethyl phosphate molecules. Meanwhile, the Zn corrosion in the hybrid electrolyte is mitigated, and the electrochemical stability window and the operating temperature of the electrolyte are extended. The dimethylacetamide alters the surface energy of Zn, guiding the (002) plane dominated deposition of Zn. Molecular dynamics simulation evidences Zn2+ions are solvated with fewer water molecules, resulting in lower lattice strain in the NaV3O8·1.5H2O cathode during the insertion of hydrated Zn2+ions, boosting the lifespan of Zn|| NaV3O8·1.5H2O cell to 3000 cycles.
Mantle heterogeneity caused by trapped water in the Southwest Basin of the South China Sea
Authors: Tian Jinyu , Ma Zhitu , Lin Jian , Xu Min , Yu Xun , Le Ba Manh , Zhang Xubo , Zhang Fan , Guo Laiyin 
Published: May 2023

AbstractWater is the most common volatile component inside the Earth. A substantial amount of water can be carried down to the interior of the Earth by subducting plates. However, how the subducted water evolves after the subducting slab breaks off remains poorly understood. Here we use the data from a passive seismic experiment using ocean bottom seismometers (OBSs) together with the land stations to determine the high-resolution, three-dimensional seismic structure of the Southwest Sub-basin (SWSB) of the South China Sea (SCS). At depths below 40 km, the mantle shear velocity (Vsv) beneath the northern side of the SWSB is similar to that of the conventional oceanic pyrolite mantle, but roughly 3% shear-velocity reduction is found beneath the southern side of the SWSB. Results of thermal dynamic modeling reveal that the observed shear-velocity reduction could be explained by the presence of 150–300 ppm of water and 5–10% of lower continental crust. The inferred high-water content at the southern side of the SWSB is consistent with a model in which the Proto-SCS plate subducted southward prior to and during the formation of the SCS basin, releasing water into the upper mantle of the SWSB.
Task-specific modulation of corticospinal neuron activity during motor learning in mice
Authors: Serradj Najet , Marino Francesca , Moreno-López Yunuen , Bernstein Amanda , Agger Sydney , Soliman Marwa , Sloan Andrew , Hollis Edmund 
Published: May 2023

AbstractMotor skill learning relies on the plasticity of the primary motor cortex as task acquisition drives cortical motor network remodeling. Large-scale cortical remodeling of evoked motor outputs occurs during the learning of corticospinal-dependent prehension behavior, but not simple, non-dexterous tasks. Here we determine the response of corticospinal neurons to two distinct motor training paradigms and assess the role of corticospinal neurons in the execution of a task requiring precise modulation of forelimb movement and one that does not. In vivo calcium imaging in mice revealed temporal coding of corticospinal activity coincident with the development of precise prehension movements, but not more simplistic movement patterns. Transection of the corticospinal tract and optogenetic regulation of corticospinal activity show the necessity for patterned corticospinal network activity in the execution of precise movements but not simplistic ones. Our findings reveal a critical role for corticospinal network modulation in the learning and execution of precise motor movements.
Many-body screening effects in liquid water
Authors: Reshetnyak Igor , Lorin Arnaud , Pasquarello Alfredo 
Published: May 2023

AbstractThe screening arising from many-body excitations is a crucial quantity for describing absorption and inelastic X-ray scattering (IXS) of materials. Similarly, the electron screening plays a critical role in state-of-the-art approaches for determining the fundamental band gap. However, ab initio studies of the screening in liquid water have remained limited. Here, we use a combined analysis based on the Bethe-Salpeter equation and time-dependent density functional theory. We first show that absorption spectra at near-edge energies are insufficient to assess the accuracy by which the screening is described. Next, when the energy range under scrutiny is extended, we instead find that the IXS spectra are highly sensitive and allow for the selection of the optimal theoretical scheme. This leads to good agreement with experiment over a large range of transferred energies and momenta, and enables establishing the elusive fundamental band gap of liquid water at 9.3 eV.