bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal Constraints in the Life and Social Sciences
Authors: Ross Lauren N. 
Published: December 2023

AbstractThis paper examines constraints and their role in scientific explanation. Common views in the philosophical literature suggest that constraints are non-causal and that they provide non-causal explanations. While much of this work focuses on examples from physics, this paper explores constraints from other fields, including neuroscience, physiology, and the social sciences. I argue that these cases involve constraints that are causal and that provide a unique type of causal explanation. This paper clarifies what it means for a factor to be a constraint, when such constraints are causal, and how they figure in scientific explanation.
The effect of Coenzyme Q10 on mitochondrial biogenesis in mouse ovarian follicles during in vitro culture
Authors: Harsini Roya , Zavareh Saeed , Nasiri Meysam , Seyfi Sara 
Published: December 2023

SummaryThe aim of this research was to investigate the effect of Coenzyme Q10 (CoQ10) on the expression of the Transcription Factor A Mitochondrial (Tfam) gene and mtDNA copy number in preantral follicles (PFs) of mice during in vitro culture. To conduct this experimental study, PFs were isolated from 14-day-old National Medical Research Institute mice and cultured in the presence of 50 µm CoQ10 for 12 days. On the 12th day, human chorionic gonadotropin was added to stimulate ovulation. The fundamental parameters, including preantral follicle developmental rate and oocyte maturation, were evaluated. Additionally, the Tfam gene expression and mtDNA copy number of granulosa cells and oocytes were assessed using the real-time polymerase chain reaction. The results revealed that CoQ10 significantly increased the diameter of PFs, survival rate, antrum formation, and metaphase II (MII) oocytes (P < 0.05). Moreover, in the CoQ10-treated groups, the Tfam gene expression in granulosa cells and oocytes increased considerably compared with the control group. The mtDNA copy number of granulosa cells and oocytes cultured in the presence of CoQ10 was substantially higher compared with the control groups (P < 0.05). The addition of CoQ10 to the culture medium enhances the developmental competence of PFs during in vitro culture by upregulating Tfam gene expression and increasing mtDNA copy number in oocyte and granulosa cells.
Temporal Variations of Earthquake Magnitude‐Frequency Relation in the Source Area of M ≥ 6.0 Earthquakes: A Systematic Survey in Taiwan
Authors: Chen Sean Kuanhsiang , Chen Po‐Yuan , Wu Yih‐Min , Chen Chien‐Chih , Chan Chung‐Han 
Published: December 2023

AbstractRecent studies in the earthquake magnitude‐frequency relation (b‐value) found that the b‐value can decrease with time before large earthquakes in the source area. Such a decrease even coincided with a burst of foreshocks immediately before the earthquakes implying a preslip migrating toward the nucleation zone. We systematically survey the b‐value variations in space and time in the source area of 17 earthquakes with magnitudes greater than ML 6.0 in Taiwan. We relocated the earthquakes released by the Central Weather Administration of Taiwan since 2012 as timing can provide a sufficiently low completeness magnitude (MC) of 1.5. We carefully determine the spatiotemporal search criteria on seismicity in the source area of all targeted earthquakes. We surveyed the temporal b‐value systematically using moving time windows with a given number of earthquake events with the magnitudes greater than MC. We found the b‐value decreased clearly for 2 days before the 2018 ML 6.3 Hualien earthquake, coinciding with a burst of ML 5.8 earthquake and its aftershocks nearby as foreshocks. The foreshocks migrated updip toward the hypocenter of the 2018 ML 6.3 Hualien earthquake and revealed a second decrease in the b‐value 10 hours before it occurred. The b‐value precursor primarily comes from a rapid reduction of small earthquakes in the foreshocks and agrees with recent key findings of preslip. However, there is no strong correlation between the b‐value precursor and coseismic slip. Apart from this, the b‐values did not change significantly in most cases of earthquakes in Taiwan before and after they occurred.
Survey and Analysis of Whistler‐ and Z‐Mode Emission in the Juno Extended Mission
Authors: Menietti J. D. , Averkamp T. F. , Kurth W. S. , Faden J. B. , Bolton S. J. 
Published: December 2023

AbstractWhistler‐mode and Z‐mode waves may have significant impact on electron scattering and acceleration at Jupiter as recent stochastic models indicate. New observations of these waves in the Juno extended mission expand the orbital coverage from previous surveys, extending especially to smaller radial distances near the magnetic equator, and to extended ranges of dusk‐side magnetic local time. M‐shells transiting the Io torus and the orbit of Europa are recognized as a significant source region for whistler‐mode lower and upper band chorus emission with intensity peaks near 9 RJ. Ganymede is a significant source of intense whistler‐mode chorus confined to the local moon environment. New Z‐mode observations now extend from a few kHz to over 80 kHz. Inferred source regions for Z‐mode are consistent with the outer edge of the Io torus and with auroral field lines that may also support broadband kilometric or decametric emission.
Comparison of Simulated Warm‐Rain Microphysical Processes in a Record‐Breaking Rainfall Event Using Polarimetric Radar Observations
Authors: Wang Hong , Xue Ming , Yin Jinfang , Deng Hua 
Published: December 2023

AbstractDuring 6–7 May 2017, a record‐breaking nocturnal rainfall event occurred in Guangzhou, China, and it was a typical warm‐sector heavy rainfall event under weak synoptic forcing. A prior observational study by the authors revealed that warm‐rain microphysical processes were dominant and responsible for the record‐breaking precipitation. In this study, the double‐moment Morrison, Thompson and NSSL microphysics schemes in WRF are evaluated against polarimetric radar observations in their ability of reproducing observed microphysical characteristics. The Thompson scheme shows the greatest fidelity to the observed raindrop size distribution (RSD) median value, corresponding to the most amount of precipitation forecast. While the Morrison and NSSL simulations overestimate (underestimate) the raindrop size (number concentration), exhibiting continental‐type convective precipitation. The three experiments slightly overestimate differential reflectivity (ZDR), but significantly underestimate specific differential phase (KDP) and liquid water content by about 30%–50%, implying the undervaluation of number of medium‐sized raindrops. Examinations of the occurrence frequencies of ZDR, KDP, mass‐weighted diameter, and logarithmic normalized intercept parameter for rain suggest that all three schemes fail to reproduce the full variability of observed RSD for the extreme rainfall. The vertical variations of RSD parameters and the Kumjian‐Ryzhkov parameter space suggest that the collision–coalescence is the dominant warm‐rain microphysical process but the simulated process is too weak. This may be attributed to the misrepresented RSD near the melting layer, where the raindrops with lower number concentration and larger sizes cannot grow through the collision–coalescence process as actively.
Impact of Reservoir Operation Policies on Spatiotemporal Dynamics of Sediment Methane Production and Release in a Large Reservoir
Authors: Xu Zhihao , Li Yunying , Cai Ximing , Cai Yanpeng , Yang Zhifeng 
Published: December 2023

AbstractReservoir operation policies affect sediment methane (CH4) production and pathways through complex influence on hydrodynamic and biogeochemical processes in reservoir water and sediment. However, the underlying influencing mechanisms, especially the impact of operations on sediment CH4 production and pathways, remain poorly understood. This study combines a physical‐biogeochemical model with a reservoir operation model to evaluate operation impacts on spatiotemporal sediment CH4 production and release dynamics and to analyze affiliated processes and driving factors. Three typical operation policies (i.e., standard, hedging, eco‐friendly) are selected to create the operation scenarios, and a coupled physical‐biogeochemical model is adopted to simulate and compare sediment CH4 production, consumption, diffusion, and ebullition under these scenarios. The methods are applied in the second largest reservoir in China (i.e., Danjiangkou Reservoir) as a case study. Results show that annual total sediment CH4 production among the scenarios ranges from 285.9 to 298.3 Gg C year−1, while operation scenario outcomes significantly differ. Specifically, a significant CH4 percentage (34%–39%) is oxidized in surface sediment while the remaining escapes sediment through diffusion and ebullition. Although diffusion accounts for >60% of the annual sediment CH4 release, sediment ebullition ultimately dominates atmospheric CH4 emissions. Annual total atmospheric CH4 emissions range from 42.8 to 71.1 Gg C year−1 and account for 14%–25% of the annual total sediment production among the three scenarios. The differences demonstrate that reservoir operations significantly impact CH4 pathways and atmospheric emissions. This study provides implications for reservoir managers to coordinate socioeconomic and ecological protection while mitigating CH4 emission targets.
Neural network assisted high-spatial-resolution polarimetry with non-interleaved chiral metasurfaces
Authors: Chen Chen , Xiao Xingjian , Ye Xin , Sun Jiacheng , Ji Jitao , Yu Rongtao , Song Wange , Zhu Shining , Li Tao 
Published: December 2023

AbstractPolarimetry plays an indispensable role in modern optics. Nevertheless, the current strategies generally suffer from bulky system volume or spatial multiplexing scheme, resulting in limited performances when dealing with inhomogeneous polarizations. Here, we propose a non-interleaved, interferometric method to analyze the polarizations based on a tri-channel chiral metasurface. A deep convolutional neural network is also incorporated to enable fast, robust and accurate polarimetry. Spatially uniform and nonuniform polarizations are both measured through the metasurface experimentally. Distinction between two semblable glasses is also demonstrated. Our strategy features the merits of compactness and high spatial resolution, and would inspire more intriguing design for detecting and sensing.
The oral health of secondary school pupils: baseline data from the Brushing RemInder 4 Good oral HealTh (BRIGHT) trial
Authors: Marshman Zoe , Fairhurst Caroline , El Yousfi Sarab , Whiteside Katie , Ainsworth Hannah , Chestnutt Ivor G. , Day Peter F. , Dey Donna , Hewitt Catherine , Hicks Katie , Pavitt Sue , Robertson Mark , Robinson-Smith Lyn , Sykes Debbie , Torgerson David , Turner Emma , Innes Nicola 
Published: December 2023

AbstractBackground This paper describes the sociodemographics and oral health of UK secondary school pupils. They were participants of the BRIGHT trial, which was designed to evaluate the effectiveness of a toothbrushing intervention to reduce dental caries.Methods Overall, 4,680 pupils aged 11-13 years attending 42 secondary schools in England, Scotland and Wales with above average proportion of pupils eligible for free school meals, were recruited to the trial. Sociodemographic data were collected. Participants had a clinical assessment for caries, plaque and bleeding and completed measures of oral and general health-related quality of life and oral health behaviours (frequency of toothbrushing, dental attendance and cariogenic food/drinks consumed). Regression analyses were performed.Results Over one-third (34.7%) of participants had caries experience, with 44.5% reporting their oral health had an impact on their daily lives. Factors associated with a statistically significant increased likelihood of caries experience were older age, being female, eligibility for free school meals, worse oral health-related quality of life, higher cariogenic diet, less than twice-daily toothbrushing, living in a more deprived area and lower school attendance.Conclusions The prevalence and impact of dental caries on the lives of pupils remains high, with further oral health promotion activities needed in targeted secondary schools.
First in man study of intravitreal tripeptidyl peptidase 1 for CLN2 retinopathy
Authors: Wawrzynski James , Martinez Ana Rodriguez , Thompson Dorothy Ann , Ram Dipak , Bowman Richard , Whiteley Rebecca , Gan Chin , Harding Louise , Mortensen Amanda , Mills Philippa , Gissen Paul , Henderson Robert H. 
Published: December 2023

Abstract
Background/Objectives
CLN2 Batten Disease is a fatal neurodegenerative condition of childhood associated with retinal dystrophy and blindness. Intracerebroventricular infusion of rhTPP1 greatly slows the rate of neurodegenerative decline but not retinopathy. Intravitreal rhTPP1 is known to slow retinal degeneration in a canine model of CLN2. We report a first-in-man controlled clinical trial of intravitreal rhTPP1 for CLN2 associated retinal dystrophy.

Subjects/methods
8 children aged 5–9 with CLN2 Batten Disease were prospectively enroled. Severely affected patients were preferentially selected, provided that vision was better than no perception of light. Children underwent 8 weekly intravitreal injections of rhTPP1 (0.2 mg in 0.05 ml) into the right eye for 12–18 months. The left eye was untreated and acts as a paired control. The primary outcome was safety based on the clinical detection of complications. A secondary outcome was paracentral macular volume (PMV) measured by spectral domain OCT. Linear regression/paired t tests were used to compare rates of decline.

Results
No severe adverse reactions (uveitis, raised IOP, media opacity) occurred. The mean baseline PMV was 1.28 mm3(right), 1.27 mm3(left). 3 of the youngest patients exhibited bilateral progressive retinal thinning (p < 0.05), whereas retinal volume was stable in the remaining 5 patients. In the 3 patients undergoing retinal degeneration, the rate of PMV loss was slower in the treated vs. untreated eye (p = 0.000042, p = 0.0011, p = 0.00022).

Conclusions
Intravitreal rhTPP1 appears to be a safe and effective treatment for CLN2 related retinopathy however commencement of treatment early in the course of disease is more likely to be efficacious.
Autoencoder neural networks enable low dimensional structure analyses of microbial growth dynamics
Authors: Baig Yasa , Ma Helena R. , Xu Helen , You Lingchong 
Published: December 2023

AbstractThe ability to effectively represent microbiome dynamics is a crucial challenge in their quantitative analysis and engineering. By using autoencoder neural networks, we show that microbial growth dynamics can be compressed into low-dimensional representations and reconstructed with high fidelity. These low-dimensional embeddings are just as effective, if not better, than raw data for tasks such as identifying bacterial strains, predicting traits like antibiotic resistance, and predicting community dynamics. Additionally, we demonstrate that essential dynamical information of these systems can be captured using far fewer variables than traditional mechanistic models. Our work suggests that machine learning can enable the creation of concise representations of high-dimensional microbiome dynamics to facilitate data analysis and gain new biological insights.
Engineering artificial photosynthesis based on rhodopsin for CO2 fixation
Authors: Tu Weiming , Xu Jiabao , Thompson Ian P. , Huang Wei E. 
Published: December 2023

AbstractMicrobial rhodopsin, a significant contributor to sustaining life through light harvesting, holds untapped potential for carbon fixation. Here, we construct an artificial photosynthesis system which combines the proton-pumping ability of rhodopsin with an extracellular electron uptake mechanism, establishing a pathway to drive photoelectrosynthetic CO2 fixation by Ralstonia eutropha (also known as Cupriavidus necator) H16, a facultatively chemolithoautotrophic soil bacterium. R. eutropha is engineered to heterologously express an extracellular electron transfer pathway of Shewanella oneidensis MR-1 and Gloeobacter rhodopsin (GR). Employing GR and the outer-membrane conduit MtrCAB from S. oneidensis, extracellular electrons and GR-driven proton motive force are integrated into R. eutropha’s native electron transport chain (ETC). Inspired by natural photosynthesis, the photoelectrochemical system splits water to supply electrons to R. eutropha via the Mtr outer-membrane route. The light-activated proton pump - GR, supported by canthaxanthin as an antenna, powers ATP synthesis and reverses the ETC to regenerate NADH/NADPH, facilitating R. eutropha’s biomass synthesis from CO2. Overexpression of a carbonic anhydrase further enhances CO2 fixation. This artificial photosynthesis system has the potential to advance the development of efficient photosynthesis, redefining our understanding of the ecological role of microbial rhodopsins in nature.
CXCL12 targets the primary cilium cAMP/cGMP ratio to regulate cell polarity during migration
Authors: Atkins Melody , Wurmser Maud , Darmon Michèle , Roche Fiona , Nicol Xavier , Métin Christine 
Published: December 2023

AbstractDirected cell migration requires sustained cell polarisation. In migrating cortical interneurons, nuclear movements are directed towards the centrosome that organises the primary cilium signalling hub. Primary cilium-elicited signalling, and how it affects migration, remain however ill characterised. Here, we show that altering cAMP/cGMP levels in the primary cilium by buffering cAMP, cGMP or by locally increasing cAMP, influences the polarity and directionality of migrating interneurons, whereas buffering cAMP or cGMP in the apposed centrosome compartment alters their motility. Remarkably, we identify CXCL12 as a trigger that targets the ciliary cAMP/cGMP ratio to promote sustained polarity and directed migration. We thereby uncover cAMP/cGMP levels in the primary cilium as a major target of extrinsic cues and as the steering wheel of neuronal migration.
A structure of the relict phycobilisome from a thylakoid-free cyanobacterium
Authors: Jiang Han-Wei , Wu Hsiang-Yi , Wang Chun-Hsiung , Yang Cheng-Han , Ko Jui-Tse , Ho Han-Chen , Tsai Ming-Daw , Bryant Donald A. , Li Fay-Wei , Ho Meng-Chiao , Ho Ming-Yang 
Published: December 2023

AbstractPhycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a “paddle-shaped” PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity
Authors: Hoffmann Maximilian , Henninger Jörg , Veith Johannes , Richter Lars , Judkewitz Benjamin 
Published: December 2023

AbstractDue to the size and opacity of vertebrate brains, it has until now been impossible to simultaneously record neuronal activity at cellular resolution across the entire adult brain. As a result, scientists are forced to choose between cellular-resolution microscopy over limited fields-of-view or whole-brain imaging at coarse-grained resolution. Bridging the gap between these spatial scales of understanding remains a major challenge in neuroscience. Here, we introduce blazed oblique plane microscopy to perform brain-wide recording of neuronal activity at cellular resolution in an adult vertebrate. Contrary to common belief, we find that inferences of neuronal population activity are near-independent of spatial scale: a set of randomly sampled neurons has a comparable predictive power as the same number of coarse-grained macrovoxels. Our work thus links cellular resolution with brain-wide scope, challenges the prevailing view that macroscale methods are generally inferior to microscale techniques and underscores the value of multiscale approaches to studying brain-wide activity.
Operando dynamics of trapped carriers in perovskite solar cells observed via infrared optical activation spectroscopy
Authors: Pan Jiaxin , Chen Ziming , Zhang Tiankai , Hu Beier , Ning Haoqing , Meng Zhu , Su Ziyu , Nodari Davide , Xu Weidong , Min Ganghong , Chen Mengyun , Liu Xianjie , Gasparini Nicola , Haque Saif A. , Barnes Piers R. F. , Gao Feng , Bakulin Artem A. 
Published: December 2023

AbstractConventional spectroscopies are not sufficiently selective to comprehensively understand the behaviour of trapped carriers in perovskite solar cells, particularly under their working conditions. Here we use infrared optical activation spectroscopy (i.e., pump-push-photocurrent), to observe the properties and real-time dynamics of trapped carriers within operando perovskite solar cells. We compare behaviour differences of trapped holes in pristine and surface-passivated FA0.99Cs0.01PbI3 devices using a combination of quasi-steady-state and nanosecond time-resolved pump-push-photocurrent, as well as kinetic and drift-diffusion models. We find a two-step trap-filling process: the rapid filling (~10 ns) of low-density traps in the bulk of perovskite, followed by the slower filling (~100 ns) of high-density traps at the perovskite/hole transport material interface. Surface passivation by n-octylammonium iodide dramatically reduces the number of trap states (~50 times), improving the device performance substantially. Moreover, the activation energy (~280 meV) of the dominant hole traps remains similar with and without surface passivation.
Prostate lineage-specific metabolism governs luminal differentiation and response to antiandrogen treatment
Authors: Giafaglione Jenna M. , Crowell Preston D. , Delcourt Amelie M. L. , Hashimoto Takao , Ha Sung Min , Atmakuri Aishwarya , Nunley Nicholas M. , Dang Rachel M. A. , Tian Mao , Diaz Johnny A. , Tika Elisavet , Payne Marie C. , Burkhart Deborah L. , Li Dapei , Navone Nora M. , Corey Eva , Nelson Peter S. , Lin Neil Y. C. , Blanpain Cedric , Ellis Leigh , Boutros Paul C. , Goldstein Andrew S. 
Published: December 2023

AbstractLineage transitions are a central feature of prostate development, tumourigenesis and treatment resistance. While epigenetic changes are well known to drive prostate lineage transitions, it remains unclear how upstream metabolic signalling contributes to the regulation of prostate epithelial identity. To fill this gap, we developed an approach to perform metabolomics on primary prostate epithelial cells. Using this approach, we discovered that the basal and luminal cells of the prostate exhibit distinct metabolomes and nutrient utilization patterns. Furthermore, basal-to-luminal differentiation is accompanied by increased pyruvate oxidation. We establish the mitochondrial pyruvate carrier and subsequent lactate accumulation as regulators of prostate luminal identity. Inhibition of the mitochondrial pyruvate carrier or supplementation with exogenous lactate results in large-scale chromatin remodelling, influencing both lineage-specific transcription factors and response to antiandrogen treatment. These results establish reciprocal regulation of metabolism and prostate epithelial lineage identity.