bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proinflammatory gene expression is associated with prospective risk for adolescent suicidal thoughts and behaviors over twelve months
Authors: Clayton Matthew G. , Cole Steve W. , Giletta Matteo , Hastings Paul D. , Nock Matthew K. , Rudolph Karen D. , Slavich George M. , Prinstein Mitchell J. 
Published: January 2025

Abstract

Objective:
Recent theories have implicated inflammatory biology in the development of psychopathology and maladaptive behaviors in adolescence, including suicidal thoughts and behaviors (STB). Examining specific biological markers related to inflammation is thus warranted to better understand risk for STB in adolescents, for whom suicide is a leading cause of death.

Method:
Participants were 211 adolescent females (ages 9–14 years; Mage = 11.8 years, SD = 1.8 years) at increased risk for STB. This study examined the prospective association between basal levels of inflammatory gene expression (average of 15 proinflammatory mRNA transcripts) and subsequent risk for suicidal ideation and suicidal behavior over a 12-month follow-up period.

Results:
Controlling for past levels of STB, greater proinflammatory gene expression was associated with prospective risk for STB in these youth. Similar effects were observed for CD14 mRNA level, a marker of monocyte abundance within the blood sample. Sensitivity analyses controlling for other relevant covariates, including history of trauma, depressive symptoms, and STB prior to data collection, yielded similar patterns of results.

Conclusions:
Upregulated inflammatory signaling in the immune system is prospectively associated with STB among at-risk adolescent females, even after controlling for history of trauma, depressive symptoms, and STB prior to data collection. Additional research is needed to identify the sources of inflammatory up-regulation in adolescents (e.g., stress psychobiology, physiological development, microbial exposures) and strategies for mitigating such effects to reduce STB.
Age and anxiety symptoms jointly moderated the curvilinear changes in trial-level ERN following repeated errors on a Go/No-Go task during early adolescence
Authors: Tan Jaron X.Y. , Hamm Jeremy M. , Liu Pan 
Published: January 2025

Abstract
The ability to detect and monitor errors enables us to maintain optimal performance across tasks. One neurophysiological index of error monitoring is the error-related negativity (ERN), a fronto-central negative deflection peaking between 0 and 150 ms following an erroneous response. While the developmental literature has illustrated age-related differences in the ERN and its association with anxiety, the literature has mainly focused on the between-person differences of the ERN. Our study examined the within-person variations of the ERN in 115 community-dwelling 9- to 12-year-olds (66 girls; mean age/SD = 11.00/1.16 years). Participants completed an EEG Go/No-Go task and reported their anxiety symptoms. Multilevel growth analyses yielded significant within-person, curvilinear changes in the ERN throughout the task. Youths’ trial-level ERN increased (i.e., became more negative) with early errors, but decreased with subsequent errors. This curvilinear pattern was evident in older, but not younger, youths. Age also interacted with anxiety symptoms: younger youths with higher anxiety showed a continuous increase in the ERN throughout the task, whereas older youths with higher anxiety showed an initial increase followed by a decline in the ERN. Our study contributed novel evidence for the development of the ERN and the underlying mechanisms of the ERN-anxiety relationship that cannot be captured by between-person approaches.
Concurrent Heat Extremes in Relation to Global Warming, High Atmospheric Pressure and Low Soil Moisture in the Northern Hemisphere
Authors: Nasong Dalai , Zhou Sha , Kornhuber Kai , Yu Bofu 
Published: January 2025

AbstractSummer heat extremes increasingly co‐occur worldwide, posing disastrous impacts on our society and the environment. However, the spatial pattern and underlying mechanisms of concurrent heat extremes remain unclear. We used a statistical framework to estimate the spatial concurrence strength of heat extremes in the Northern Hemisphere and identified their relationships to global warming, atmospheric circulation, and land‐atmosphere feedbacks. Concurrent heat extremes over different regions have significantly increased in the Northern Hemisphere from 1950 to 2023. Moreover, heat extremes show strong spatial concurrence strength, and the driving factors vary geographically. Global warming is responsible for long‐term increases in the frequency and strength of concurrent heat extremes, with most pronounced impact in tropical regions. In the absence of warming trends, the temporal and spatial variations in concurrent heat extremes are mainly caused by simultaneous high atmospheric pressure controlled by large‐scale circulations, particularly in mid‐latitude regions. While low soil moisture enhances regional heat extremes through land‐atmosphere feedbacks, it plays a minor role in driving concurrent heat extremes alone but can contribute in combination with high‐pressure anomalies. Given the ever‐increasing risks of heat extremes, our study underscores the importance of identifying the mechanisms of spatially concurrent heat extremes to improve prediction and mitigation of widespread heatwaves and their adverse impacts on socio‐economic sustainability and human well‐being.
Relationship Between Rupture Length and Magnitude of Oceanic Transform Fault Earthquakes
Authors: de Melo Guilherme W. S. , Grevemeyer Ingo , Lange Dietrich , Metz Dirk , Kopp Heidrun 
Published: January 2025

AbstractThe rupture behavior of large oceanic strike‐slip earthquakes remains largely unresolved using seismic signals recorded thousands of kilometers away from the source area. Large submarine earthquakes, however, generate hydroacoustic T‐waves propagating through the ocean over long distances. Here, we show that these T‐waves recorded at regional distances on the Ascension hydrophone array of the International Monitoring System can provide critical information on the earthquake location and rupture behavior. We use recordings from 47 events in oceanic transform faults, ranging in magnitude from 5.6 ≤ Mw ≤ 7.1, to investigate the rupture processes. We find that most strike‐slip earthquakes show unilateral rupture behavior, while a few larger events were more complex. Furthermore, earthquakes in oceanic transforms have longer ruptures than events of the same magnitude in continental faults. We argue that differences in the scaling relation of oceanic and continental strike‐slip earthquakes support a lower rigidity in the oceanic lithosphere caused by hydration.
Enhancing Hectare‐Scale Groundwater Recharge Estimation by Integrating Data From Cosmic‐Ray Neutron Sensing Into Soil Hydrological Modeling
Authors: Scheiffele Lena M. , Munz Matthias , Francke Till , Baroni Gabriele , Oswald Sascha E. 
Published: January 2025

AbstractVadose zone models, calibrated with state variables, may offer a robust approach for deriving groundwater recharge. Cosmic‐ray neutron sensing (CRNS) provides soil moisture over a large support volume (horizontal extent of hectares) and offers the opportunity to estimate water fluxes at this scale. However, the horizontal and vertical sensitivity of the method results in an inherently weighted water content, which poses a challenge for its application in soil hydrologic modeling. We systematically assess calibrating a soil hydraulic model in HYDRUS 1D at a cropped field site. Calibration was performed using different field‐scale soil moisture time series and the ability of the model to represent root zone soil moisture and derive groundwater recharge was assessed. As our benchmark, we used a distributed point sensor network from within the footprint of the CRNS. Models calibrated on CRNS data or combinations of CRNS with deeper point measurements resulted in cumulative groundwater recharge comparable to the benchmark. While models based exclusively on CRNS data do not represent the root zone soil moisture dynamics adequately, combining CRNS with profile soil moisture overcomes this limitation. Models calibrated on CRNS data also perform well in timing the downward flux compared to an independent estimate based on soil water tension measurements. However, the latter provides quantitative groundwater recharge estimates spanning a wide range of values, including unrealistic highs exceeding local annual precipitation. Conversely, modeled groundwater recharge based on the distributed sensor network or on CRNS resulted in estimates ranging between 30% and 40% of annual precipitation.
Observing non-Hermiticity induced chirality breaking in a synthetic Hall ladder
Authors: Ye Rui , He Yanyan , Li Guangzhen , Wang Luojia , Wu Xiaoxiong , Qiao Xin , Zheng Yuanlin , Jin Liang , Wang Da-Wei , Yuan Luqi , Chen Xianfeng 
Published: January 2025

AbstractNon-Hermitian topological photonics plays a key role in bridging topological matter with gain and loss engineering in optics. Here we report the experimental observation of the break of chiral currents in a Hall ladder from the non-Hermiticity by constructing synthetic frequency dimension in two rings, where currents on both legs of the ladder co-propagate in the same direction. The origin of such phenomena is resulted from the interplay between the effective magnetic flux and the on-site gain and loss. Such non-Hermitian co-propagating currents exhibit characteristics of unidirectional frequency conversion in both rings, and moreover, different from the counterpart in Hermitian systems, can provide a method to probe the signatures of the non-Hermitian skin effect from steady-state bulk dynamics. Our model is further extended to models including next-nearest-neighbor couplings, pointing to a way for observing the non-Hermitian signature with higher winding number, and provides a new control knob for light manipulation with the topological dissipation engineering.
Experimental demonstration of 8190-km long-haul semiconductor-laser chaos synchronization induced by digital optical communication signal
Authors: Wang Anbang , Wang Junli , Jiang Lin , Wang Longsheng , Wang Yuncai , Yan Lianshan , Qin Yuwen 
Published: January 2025

AbstractCommon-signal-induced synchronization of semiconductor lasers have promising applications in physical-layer secure transmission with high speed and compatibility with the current fiber communication. Here, we propose an ultra-long-distance laser synchronization scheme by utilizing random digital optical communication signal as the common drive signal. By utilizing the long-haul optical coherent communication techniques, high-fidelity fiber transmission of the digital drive can be achieved and thus ultra-long-distance synchronization is expected. Experiments were implemented with distributed feedback lasers injected by a random-digital phase-modulated drive light. Results show that high-quality synchronization can be achieved as the drive signal rate is larger than the laser relaxation frequency and the transmission bit error ratio is below a critical value. Chaos synchronization over 8191-km fiber transmission was experimentally achieved. Compared to traditional common-signal-induced synchronization using analog drive signal such as chaos, the distance is increased by 8 times, and complicated hardware devices for channel impairment compensation are no longer required. In addition, the proposed method does not sacrifice communication capacity like traditional methods which need a channel to transmit analog drive signal. It is therefore believed that this common-digital-signal induced laser synchronization paves a way for secure backbone and submarine transmission.
Transverse optical gradient force in untethered rotating metaspinners
Authors: Engay Einstom , Shanei Mahdi , Mylnikov Vasilii , Wang Gan , Johansson Peter , Volpe Giovanni , Käll Mikael 
Published: January 2025

AbstractNanostructured dielectric metasurfaces offer unprecedented opportunities to control light-matter momentum exchange, and thereby the forces and torques that light can exert on matter. Here we introduce optical metasurfaces as components of ultracompact untethered microscopic metaspinners capable of efficient light-induced rotation in a liquid environment. Illuminated by weakly focused light, a metaspinner generates torque via photon recoil through the metasurfaces’ ability to bend light towards high angles despite their sub-wavelength thickness, thereby creating orbital angular momentum. We find that a metaspinner is subject to an anomalous transverse lateral optical gradient force that acts in concert with the classical gradient force. Consequently, when two or more metaspinners are trapped together in a laser beam, they collectively orbit the optical axis in the opposite direction to their spinning motion, in stark contrast to rotors coupled through hydrodynamic or mechanical interactions. The metaspinners delineated herein not only serve to illustrate the vast possibilities of utilizing optical metasurfaces for fundamental exploration of optical torques, but they also represent potential building-blocks of artificial active matter systems, light-driven micromachinery, and general-purpose optomechanical devices.
A light-driven device for neuromorphic computing
Authors: Nath Shimul Kanti 
Published: January 2025

AbstractA unique optoelectronic synaptic device has been developed, leveraging the negative photoconductance property of a single-crystal material system called Cs2CoCl4. This device exhibits a simultaneous volatile resistive switching response and sensitivity to optical stimuli, positioning Cs2CoCl4 as a promising candidate for optically enhanced neuromorphic applications.
Micro-vibration assisted dual-layer spiral microneedles to rapidly extract dermal interstitial fluid for minimally invasive detection of glucose
Authors: Saifullah Khaled Mohammed , Mushtaq Asim , Azarikhah Pouria , Prewett Philip D. , Davies Graham J. , Faraji Rad Zahra 
Published: January 2025

AbstractVarious hydrogels have been explored to create minimally invasive microneedles (MNs) to extract interstitial fluid (ISF). However, current methods are time-consuming and typically require 10–15 min to extract 3–5 mg of ISF. This study introduces two spiral-shaped swellable MN arrays: one made of gelatin methacryloyl (GelMA) and polyvinyl alcohol (PVA), and the other incorporating a combination of PVA, polyvinylpyrrolidone (PVP), and hyaluronic acid (HA) for fast ISF extraction. These MN arrays demonstrated a rapid swelling ratio of 560 ± 79.6% and 370 ± 34.1% in artificial ISF within 10 min, respectively. Additionally, this study proposes a novel method that combines MNs with a custom-designed Arduino-based applicator vibrating at frequency ranges (50–100 Hz) to improve skin penetration efficiency, thereby enhancing the uptake of ISF in ex vivo. This dynamic combination enables GelMA/PVA MNs to rapidly uptake 6.41 ± 1.01 mg of ISF in just 5 min, while PVA/PVP/HA MNs extract 5.38 ± 0.77 mg of ISF within the same timeframe. To validate the capability of the MNs to recover glucose as the target biomarker, a mild heating procedure is used, followed by determining glucose concentration using a d-glucose content assay kit. The efficient extraction of ISF and glucose detection capabilities of the spiral MNs suggest their potential for rapid and minimally invasive biomarker sensing.
Auditory evoked-potential abnormalities in a mouse model of 22q11.2 Deletion Syndrome and their interactions with hearing impairment
Authors: Lu Chen , Linden Jennifer F. 
Published: January 2025

AbstractThe 22q11.2 deletion is a risk factor for multiple psychiatric disorders including schizophrenia and also increases vulnerability to middle-ear problems that can cause hearing impairment. Up to 60% of deletion carriers experience hearing impairment and ~30% develop schizophrenia in adulthood. It is not known if these risks interact. Here we used the Df1/+ mouse model of the 22q11.2 deletion to investigate how hearing impairment might interact with increased genetic vulnerability to psychiatric disease to affect brain function. We measured brain function using cortical auditory evoked potentials (AEPs), which are commonly measured non-invasively in humans. After identifying one of the simplest and best-validated methods for AEP measurement in mice from the diversity of previous approaches, we measured peripheral hearing sensitivity and cortical AEPs in Df1/+ mice and their WT littermates. We exploited large inter-individual variation in hearing ability among Df1/+ mice to distinguish effects of genetic background from effects of hearing impairment. Central auditory gain and adaptation were quantified by comparing brainstem activity and cortical AEPs and by analyzing the growth of cortical AEPs with increasing sound level or inter-tone interval duration. We found that level-dependent AEP growth was abnormally large in Df1/+ mice regardless of hearing impairment, but other AEP measures of central auditory gain and adaptation depended on both genotype and hearing phenotype. Our results demonstrate the relevance of comorbid hearing loss to auditory brain dysfunction in 22q11.2DS and also identify potential biomarkers for psychiatric disease that are robust to hearing impairment.
High-coverage whole-genome sequencing of a Jakun individual from the “Orang Asli” Proto-Malay subtribe from Peninsular Malaysia
Authors: Yap Wai-Sum , Cengnata Alvin , Saw Woei-Yuh , Abdul Rahman Thuhairah , Teo Yik-Ying , Lim Renee Lay-Hong , Hoh Boon-Peng 
Published: January 2025

AbstractJakun, a Proto-Malay subtribe from Peninsular Malaysia, is believed to have inhabited the Malay Archipelago during the period of agricultural expansion approximately 4 thousand years ago (kya). However, their genetic structure and population history remain inconclusive. In this study, we report the genome structure of a Jakun female, based on whole-genome sequencing, which yielded an average coverage of 35.97-fold. We identified approximately 3.6 million single-nucleotide variations (SNVs) and 517,784 small insertions/deletions (indels). Of these, 39,916 SNVs were novel (referencing dbSNP151), and 10,167 were nonsynonymous (nsSNVs), spanning 5674 genes. Principal Component Analysis (PCA) revealed that the Jakun genome sequence closely clustered with the genomes of the Cambodians (CAM) and the Metropolitan Malays from Singapore (SG_MAS). The ADMIXTURE analysis further revealed potential admixture from the EA and North Borneo populations, as corroborated by the results from the F3, F4, and TreeMix analyses. Mitochondrial DNA analysis revealed that the Jakun genome carried the N21a haplogroup (estimated to have occurred ~19 kya), which is commonly found among Malays from Malaysia and Indonesia. From the whole-genome sequence data, we identified 825 damaging and deleterious nonsynonymous single-nucleotide polymorphisms (nsSNVs) affecting 720 genes. Some of these variants are associated with age-related macular degeneration, atrial fibrillation, and HDL cholesterol level. Additionally, we located a total of 3310 variants on 32 core adsorption, distribution, metabolism, and elimination (ADME) genes. Of these, 193 variants are listed in PharmGKB, and 21 are nsSNVs. In summary, the genetic structure identified in the Jakun individual could enhance the mapping of genetic variants for disease-based population studies and further our understanding of the human migration history in Southeast Asia.
Small variant benchmark from a complete assembly of X and Y chromosomes
Authors: Wagner Justin , Olson Nathan D. , McDaniel Jennifer , Harris Lindsay , Pinto Brendan J. , Jáspez David , Muñoz-Barrera Adrián , Rubio-Rodríguez Luis A. , Lorenzo-Salazar José M. , Flores Carlos , Sahraeian Sayed Mohammad Ebrahim , Narzisi Giuseppe , Byrska-Bishop Marta , Evani Uday S. , Xiao Chunlin , Lake Juniper A. , Fontana Peter , Greenberg Craig , Freed Donald , Mootor Mohammed Faizal Eeman , Boutros Paul C. , Murray Lisa , Shafin Kishwar , Carroll Andrew , Sedlazeck Fritz J. , Wilson Melissa , Zook Justin M. 
Published: January 2025

AbstractThe sex chromosomes contain complex, important genes impacting medical phenotypes, but differ from the autosomes in their ploidy and large repetitive regions. To enable technology developers along with research and clinical laboratories to evaluate variant detection on male sex chromosomes X and Y, we create a small variant benchmark set with 111,725 variants for the Genome in a Bottle HG002 reference material. We develop an active evaluation approach to demonstrate the benchmark set reliably identifies errors in challenging genomic regions and across short and long read callsets. We show how complete assemblies can expand benchmarks to difficult regions, but highlight remaining challenges benchmarking variants in long homopolymers and tandem repeats, complex gene conversions, copy number variable gene arrays, and human satellites.
Reconstitution of human DNA licensing and the structural and functional analysis of key intermediates
Authors: Wells Jennifer N. , Edwardes Lucy V. , Leber Vera , Allyjaun Shenaz , Peach Matthew , Tomkins Joshua , Kefala-Stavridi Antonia , Faull Sarah V. , Aramayo Ricardo , Pestana Carolina M. , Ranjha Lepakshi , Speck Christian 
Published: January 2025

AbstractHuman DNA licensing initiates replication fork assembly and DNA replication. This reaction promotes the loading of the hMCM2-7 complex on DNA, which represents the core of the replicative helicase that unwinds DNA during S-phase. Here, we report the reconstitution of human DNA licensing using purified proteins. We showed that the in vitro reaction is specific and results in the assembly of high-salt resistant hMCM2-7 double-hexamers. With ATPγS, an hORC1-5-hCDC6-hCDT1-hMCM2-7 (hOCCM) assembles independent of hORC6, but hORC6 enhances double-hexamer formation. We determined the hOCCM structure, which showed that hORC-hCDC6 recruits hMCM2-7 via five hMCM winged-helix domains. The structure highlights how hORC1 activates the hCDC6 ATPase and uncovered an unexpected role for hCDC6 ATPase in complex disassembly. We identified that hCDC6 binding to hORC1-5 stabilises hORC2-DNA interactions and supports hMCM3-dependent recruitment of hMCM2-7. Finally, the structure allowed us to locate cancer-associated mutations at the hCDC6-hMCM3 interface, which showed specific helicase loading defects.
Site-saturation mutagenesis of 500 human protein domains
Authors: Beltran Antoni , Jiang Xiang’er , Shen Yue , Lehner Ben 
Published: January 2025

Abstract
Missense variants that change the amino acid sequences of proteins cause one-third of human genetic diseases1. Tens of millions of missense variants exist in the current human population, and the vast majority of these have unknown functional consequences. Here we present a large-scale experimental analysis of human missense variants across many different proteins. Using DNA synthesis and cellular selection experiments we quantify the effect of more than 500,000 variants on the abundance of more than 500 human protein domains. This dataset reveals that 60% of pathogenic missense variants reduce protein stability. The contribution of stability to protein fitness varies across proteins and diseases and is particularly important in recessive disorders. We combine stability measurements with protein language models to annotate functional sites across proteins. Mutational effects on stability are largely conserved in homologous domains, enabling accurate stability prediction across entire protein families using energy models. Our data demonstrate the feasibility of assaying human protein variants at scale and provides a large consistent reference dataset for clinical variant interpretation and training and benchmarking of computational methods.