bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Two‐Dimensional Closed‐Form Analytical Solution for Heat Transport With Nonvertical Flow in Riparian Zones
Authors: Shi Wenguang , Zhan Hongbin , Wang Quanrong , Xie Xianjun 
Published: August 2023

AbstractHeat as a tracer has received increasing attention in recent decades and has become a popular and widely used tool for quantifying streambed fluxes, among many other applications. Nonvertical flow component is an important parameter for heat transport in riparian zones. However, previous investigations using heat as a tracer in the quantification of streambed fluxes frequently overlooked or simplified nonvertical flow component with erroneous presumptions. In this study, a novelty two‐dimensional closed‐form analytical solution for heat transport with vertical and nonvertical flow components and arbitrary initial and boundary conditions under losing conditions is presented for the first time using Green's function method. The new model is tested by finite‐element solution and stochastic modeling. The capabilities of the new analytical solution are demonstrated using field data. Results show that the nonvertical flow component has a significant impact on heat transport in streambed. The temperature difference between the streambed and the surface water increases as the nonvertical flow component increases, and the amplitude of the temperature curves decreases with increasing horizontal distance from the center of stream at the same depth due to the influences of nonvertical flow. Stochastic modeling shows that an increasing nonuniform flow can result in overestimation of vertical and nonvertical flow components near the bank of stream, and the new analytical model works well in a heterogeneous streambed when the variance of natural logarithm of the streambed hydraulic conductivity is less than 0.10 (). The vertical and nonvertical flow components are more sensitive to temperature‐time data than the other parameters. The new analytical model is a significant advancement of the previous one‐dimensional analytical models which only considered vertical flow.
Surface‐Plasma Interactions at Europa in Draped Magnetospheric Fields: The Contribution of Energetic Electrons to Energy Deposition and Sputtering
Authors: Addison Peter , Liuzzo Lucas , Simon Sven 
Published: August 2023

AbstractWe calculate the time‐varying spatial distribution of energetic magnetospheric electron influx onto Europa's surface by combining a hybrid model of the moon's draped electromagnetic environment with a relativistic particle tracer. We generate maps of the energetic electron influx patterns at four distinct locations of Europa relative to the center of the Jovian magnetospheric current sheet. For a full synodic rotation of Jupiter, these results are applied to constrain the averaged number and energy influx patterns as well as the O2 sputtering rates associated with energetic electron precipitation. We also determine the relative contributions of magnetospheric ions and electrons to surface erosion and exospheric genesis at Europa. Our major results are: (a) Except for a small region near Europa's downstream apex, the moon's entire surface is exposed to heavy irradiation by magnetospheric electrons. (b) The spatial distribution of energetic electron influx onto Europa's surface is only slightly modified by field line draping and the induced magnetic field from the moon's subsurface ocean. (c) The contributions of magnetospheric electron and ion impacts to energy deposition onto Europa's surface are of the same order of magnitude. (d) Within uncertainties, impinging magnetospheric electrons and ions make similar contributions to O2 sputtering from Europa's surface. (e) The spatial distribution of electron energy influx and the observed concentrations of sulfuric acid (H2SO4) are only weakly correlated, suggesting that energy deposition by magnetospheric electron impacts is not a necessary agent for H2SO4 production within Europa's surface.
3-year follow-up of a prospective, multicenter study of the Amplatzer Piccolo™ Occluder for transcatheter patent ductus arteriosus closure in children ≥ 700 grams
Authors: Morray Brian H. , Sathanandam Shyam K. , Forbes Thomas , Gillespie Matthew , Berman Darren , Armstrong Aimee K. , Shahanavaz Shabana , Jones Thomas , Rockefeller Toby , Justino Henri , Nykanen David , Weiler Courtney , Gutfinger Dan , Zahn Evan M. 
Published: August 2023

Abstract
Objective
This study describes 3-year follow-up of 200 infants weighing ≥ 700 grams who underwent transcatheter patent ductus arteriosus (PDA) closure with the Amplatzer Piccolo™ Occluder.

Study Design
Between June 2017 and February 2019, 200 children were enrolled in this U.S. study (NCT03055858). PDA closure, survival, and device- or procedure-related events were evaluated. A total of 156 of the available 182 patients (86%) completed the study.

Results
The implant success rate was 95.5% (191/200). At 3 years, PDA closure was observed in 100% (33/33) of patients. Survival was >95% with 9 reported deaths. No deaths were adjudicated as device- or procedure-related. Notable events included aortic obstruction (2) requiring stent placement and tricuspid regurgitation (5), for which no interventions were required.

Conclusions
This follow-up study demonstrates high rates of PDA closure, low serious complication rates, and survival > 95% at 3 years. The Amplatzer Piccolo™ Occluder is a safe and effective therapy for PDA treatment in premature infants. ClinicalTrials.gov identifier: NCT0305585.
The mitophagy pathway and its implications in human diseases
Authors: Wang Shouliang , Long Haijiao , Hou Lianjie , Feng Baorong , Ma Zihong , Wu Ying , Zeng Yu , Cai Jiahao , Zhang Da-wei , Zhao Guojun 
Published: August 2023

AbstractMitochondria are dynamic organelles with multiple functions. They participate in necrotic cell death and programmed apoptotic, and are crucial for cell metabolism and survival. Mitophagy serves as a cytoprotective mechanism to remove superfluous or dysfunctional mitochondria and maintain mitochondrial fine-tuning numbers to balance intracellular homeostasis. Growing evidences show that mitophagy, as an acute tissue stress response, plays an important role in maintaining the health of the mitochondrial network. Since the timely removal of abnormal mitochondria is essential for cell survival, cells have evolved a variety of mitophagy pathways to ensure that mitophagy can be activated in time under various environments. A better understanding of the mechanism of mitophagy in various diseases is crucial for the treatment of diseases and therapeutic target design. In this review, we summarize the molecular mechanisms of mitophagy-mediated mitochondrial elimination, how mitophagy maintains mitochondrial homeostasis at the system levels and organ, and what alterations in mitophagy are related to the development of diseases, including neurological, cardiovascular, pulmonary, hepatic, renal disease, etc., in recent advances. Finally, we summarize the potential clinical applications and outline the conditions for mitophagy regulators to enter clinical trials. Research advances in signaling transduction of mitophagy will have an important role in developing new therapeutic strategies for precision medicine.
CDK7-YAP-LDHD axis promotes D-lactate elimination and ferroptosis defense to support cancer stem cell-like properties
Authors: Lv Mengzhu , Gong Ying , Liu Xuesong , Wang Yan , Wu Qingnan , Chen Jie , Min Qingjie , Zhao Dongyu , Li Xianfeng , Chen Dongshao , Yang Di , Yeerken Danna , Liu Rui , Li Jinting , Zhang Weimin , Zhan Qimin 
Published: August 2023

AbstractReprogrammed cellular metabolism is essential for maintaining cancer stem cells (CSCs) state. Here, we report that mitochondrial D-lactate catabolism is a necessary initiating oncogenic event during tumorigenesis of esophageal squamous cell carcinoma (ESCC). We discover that cyclin-dependent kinase 7 (CDK7) phosphorylates nuclear Yes-associated protein 1 (YAP) at S127 and S397 sites and enhances its transcription function, which promotes D-lactate dehydrogenase (LDHD) protein expression. Moreover, LDHD is enriched significantly in ESCC-CSCs rather than differentiated tumor cells and high LDHD status is connected with poor prognosis in ESCC patients. Mechanistically, the CDK7-YAP-LDHD axis helps ESCC-CSCs escape from ferroptosis induced by D-lactate and generates pyruvate to satisfy energetic demands for their elevated self-renewal potential. Hence, we conclude that esophageal CSCs adopt a D-lactate elimination and pyruvate accumulation mode dependent on CDK7-YAP-LDHD axis, which drives stemness-associated hallmarks of ESCC-CSCs. Reasonably, targeting metabolic checkpoints may serve as an effective strategy for ESCC therapy.
Heimdall, an alternative protein issued from a ncRNA related to kappa light chain variable region of immunoglobulins from astrocytes: a new player in neural proteome
Authors: Capuz Alice , Osien Sylvain , Cardon Tristan , Karnoub Mélodie Anne , Aboulouard Soulaimane , Raffo-Romero Antonella , Duhamel Marie , Cizkova Dasa , Trerotola Marco , Devos David , Kobeissy Firas , Vanden Abeele Fabien , Bonnefond Amélie , Fournier Isabelle , Rodet Franck , Salzet Michel 
Published: August 2023

AbstractThe dogma “One gene, one protein” is clearly obsolete since cells use alternative splicing and generate multiple transcripts which are translated into protein isoforms, but also use alternative translation initiation sites (TISs) and termination sites on a given transcript. Alternative open reading frames for individual transcripts give proteins originate from the 5′- and 3′-UTR mRNA regions, frameshifts of mRNA ORFs or from non-coding RNAs. Longtime considered as non-coding, recent in-silico translation prediction methods enriched the protein databases allowing the identification of new target structures that have not been identified previously. To gain insight into the role of these newly identified alternative proteins in the regulation of cellular functions, it is crucial to assess their dynamic modulation within a framework of altered physiological modifications such as experimental spinal cord injury (SCI). Here, we carried out a longitudinal proteomic study on rat SCI from 12 h to 10 days. Based on the alternative protein predictions, it was possible to identify a plethora of newly predicted protein hits. Among these proteins, some presented a special interest due to high homology with variable chain regions of immunoglobulins. We focus our interest on the one related to Kappa variable light chains which is similarly highly produced by B cells in the Bence jones disease, but here expressed in astrocytes. This protein, name Heimdall is an Intrinsically disordered protein which is secreted under inflammatory conditions. Immunoprecipitation experiments showed that the Heimdall interactome contained proteins related to astrocyte fate keepers such as “NOTCH1, EPHA3, IPO13” as well as membrane receptor protein including “CHRNA9; TGFBR, EPHB6, and TRAM”. However, when Heimdall protein was neutralized utilizing a specific antibody or its gene knocked out by CRISPR-Cas9, sprouting elongations were observed in the corresponding astrocytes. Interestingly, depolarization assays and intracellular calcium measurements in Heimdall KO, established a depolarization effect on astrocyte membranes KO cells were more likely that the one found in neuroprogenitors. Proteomic analyses performed under injury conditions or under lipopolysaccharides (LPS) stimulation, revealed the expression of neuronal factors, stem cell proteins, proliferation, and neurogenesis of astrocyte convertor factors such as EPHA4, NOTCH2, SLIT3, SEMA3F, suggesting a role of Heimdall could regulate astrocytic fate. Taken together, Heimdall could be a novel member of the gatekeeping astrocyte-to-neuroprogenitor conversion factors.
Coronary artery disease, its associations with ocular, genetic and blood lipid parameters
Authors: Matulevičiūtė Indrė , Tatarūnas Vacis , Skipskis Vilius , Čiapienė Ieva , Veikutienė Audronė , Lesauskaitė Vaiva , Dobilienė Olivija , Žaliūnienė Dalia 
Published: August 2023

Abstract
Background/objectives
To investigate the associations between ophthalmic parameters, CYP4F2 (rs2108622) and ABCA1 (rs1883025) polymorphisms and coronary artery disease, considering the accessibility, non-invasive origin of retinal examination and its possible resemblance to coronary arteries.

Subjects/methods
Overall 165 participants divided into groups based on the coronary angiography results and clinical status: control group (N = 73), MI group (N = 63), 3VD (three vessel disease) (N = 24). All the participants underwent total ophthalmic examination – optical coherence tomography (OCT) and OCT angiography of the macula region were performed and evaluated. Total cholesterol, high-density lipoprotein, low-density lipoprotein and triglyceride cholesterol (Tg-C) were tested. A standard manufacturer’s protocol for CYP4F2 (rs2108622) and ABCA1 (rs1883025) was used for genotyping with TaqMan probes.

Results
GCL+ layer was thicker in control group vs. 3VD group (74.00; 62.67–94.67 (median; min.-max.) vs. 71.06; 51.33–78.44, p = 0.037). T allele carriers under ABCA1 rs1883025 dominant model were shown to have ticker retina and smaller foveal avascular zone in superficial capillary plexus and smaller Tg-C concentration. ABCA1 rs1883025 was associated with retinal thickness (OR = 0.575, 95% CI 0.348–0.948, p = 0.030). Univariate logistic regression showed that ABCA1 rs1883025 CT genotype is associated with decreased risk for coronary artery disease development under overdominant genetic model (OR = 0.498, 95% CI 0.254–0.976; p = 0.042) and codominant genetic model (OR = 0.468, 95% CI 0.232–0.945, p = 0.034).

Conclusions
Results of this study confirmed that non-invasive methods such as OCT of eye might be used for identification of patients at risk of CAD.
Pharmacological perturbation of the phase-separating protein SMNDC1
Authors: Enders Lennart , Siklos Marton , Borggräfe Jan , Gaussmann Stefan , Koren Anna , Malik Monika , Tomek Tatjana , Schuster Michael , Reiniš Jiří , Hahn Elisa , Rukavina Andrea , Reicher Andreas , Casteels Tamara , Bock Christoph , Winter Georg E. , Hannich J. Thomas , Sattler Michael , Kubicek Stefan 
Published: August 2023

AbstractSMNDC1 is a Tudor domain protein that recognizes di-methylated arginines and controls gene expression as an essential splicing factor. Here, we study the specific contributions of the SMNDC1 Tudor domain to protein-protein interactions, subcellular localization, and molecular function. To perturb the protein function in cells, we develop small molecule inhibitors targeting the dimethylarginine binding pocket of the SMNDC1 Tudor domain. We find that SMNDC1 localizes to phase-separated membraneless organelles that partially overlap with nuclear speckles. This condensation behavior is driven by the unstructured C-terminal region of SMNDC1, depends on RNA interaction and can be recapitulated in vitro. Inhibitors of the protein’s Tudor domain drastically alter protein-protein interactions and subcellular localization, causing splicing changes for SMNDC1-dependent genes. These compounds will enable further pharmacological studies on the role of SMNDC1 in the regulation of nuclear condensates, gene regulation and cell identity.
EGFR-targeted fluorescence molecular imaging for intraoperative margin assessment in oral cancer patients: a phase II trial
Authors: de Wit Jaron G. , Vonk Jasper , Voskuil Floris J. , de Visscher Sebastiaan A. H. J. , Schepman Kees-Pieter , Hooghiemstra Wouter T. R. , Linssen Matthijs D. , Elias Sjoerd G. , Halmos Gyorgy B. , Plaat Boudewijn E. C. , Doff Jan J. , Rosenthal Eben L. , Robinson Dominic , van der Vegt Bert , Nagengast Wouter B. , van Dam Gooitzen M. , Witjes Max J. H. 
Published: August 2023

AbstractInadequate surgical margins occur frequently in oral squamous cell carcinoma surgery. Fluorescence molecular imaging (FMI) has been explored for intraoperative margin assessment, but data are limited to phase-I studies. In this single-arm phase-II study (NCT03134846), our primary endpoints were to determine the sensitivity, specificity and positive predictive value of cetuximab-800CW for tumor-positive margins detection. Secondary endpoints were safety, close margin detection rate and intrinsic cetuximab-800CW fluorescence. In 65 patients with 66 tumors, cetuximab-800CW was well-tolerated. Fluorescent spots identified in the surgical margin with signal-to-background ratios (SBR) of ≥2 identify tumor-positive margins with 100% sensitivity, 85.9% specificity, 58.3% positive predictive value, and 100% negative predictive value. An SBR of ≥1.5 identifies close margins with 70.3% sensitivity, 76.1% specificity, 60.5% positive predictive value, and 83.1% negative predictive value. Performing frozen section analysis aimed at the fluorescent spots with an SBR of ≥1.5 enables safe, intraoperative adjustment of surgical margins.
Giant room-temperature nonlinearities in a monolayer Janus topological semiconductor
Authors: Shi Jiaojian , Xu Haowei , Heide Christian , HuangFu Changan , Xia Chenyi , de Quesada Felipe , Shen Hongzhi , Zhang Tianyi , Yu Leo , Johnson Amalya , Liu Fang , Shi Enzheng , Jiao Liying , Heinz Tony , Ghimire Shambhu , Li Ju , Kong Jing , Guo Yunfan , Lindenberg Aaron M. 
Published: August 2023

AbstractNonlinear optical materials possess wide applications, ranging from terahertz and mid-infrared detection to energy harvesting. Recently, the correlations between nonlinear optical responses and certain topological properties, such as the Berry curvature and the quantum metric tensor, have attracted considerable interest. Here, we report giant room-temperature nonlinearities in non-centrosymmetric two-dimensional topological materials—the Janus transition metal dichalcogenides in the 1 T’ phase, synthesized by an advanced atomic-layer substitution method. High harmonic generation, terahertz emission spectroscopy, and second harmonic generation measurements consistently show orders-of-the-magnitude enhancement in terahertz-frequency nonlinearities in 1 T’ MoSSe (e.g., > 50 times higher than 2H MoS2 for 18th order harmonic generation; > 20 times higher than 2H MoS2 for terahertz emission). We link this giant nonlinear optical response to topological band mixing and strong inversion symmetry breaking due to the Janus structure. Our work defines general protocols for designing materials with large nonlinearities and heralds the applications of topological materials in optoelectronics down to the monolayer limit.
H2 formation via non-Born-Oppenheimer hydrogen migration in photoionized ethane
Authors: Yang Yizhang , Ren Hao , Zhang Ming , Zhou Shengpeng , Mu Xiangxu , Li Xiaokai , Wang Zhenzhen , Deng Ke , Li Mingxuan , Ma Pan , Li Zheng , Hao Xiaolei , Li Weidong , Chen Jing , Wang Chuncheng , Ding Dajun 
Published: August 2023

AbstractNeutral H2 formation via intramolecular hydrogen migration in hydrocarbon molecules plays a vital role in many chemical and biological processes. Here, employing cold target recoil ion momentum spectroscopy (COLTRIMS) and pump-probe technique, we find that the non-adiabatic coupling between the ground and excited ionic states of ethane through conical intersection leads to a significantly high yield of neutral H2 fragment. Based on the analysis of fingerprints that are sensitive to orbital symmetry and electronic state energies in the photoelectron momentum distributions, we tag the initial electronic population of both the ground and excited ionic states and determine the branching ratios of H2 formation channel from those two states. Incorporating theoretical simulation, we established the timescale of the H2 formation to be ~1300 fs. We provide a comprehensive characterization of H2 formation in ionic states of ethane mediated by conical intersection and reveals the significance of non-adiabatic coupling dynamics in the intramolecular hydrogen migration.
Extreme environments offer an unprecedented opportunity to understand microbial eukaryotic ecology, evolution, and genome biology
Authors: Rappaport Hannah B. , Oliverio Angela M. 
Published: August 2023

AbstractResearch in extreme environments has substantially expanded our understanding of the ecology and evolution of life on Earth, but a major group of organisms has been largely overlooked: microbial eukaryotes (i.e., protists). In this Perspective, we summarize data from over 80 studies of protists in extreme environments and identify focal lineages that are of significant interest for further study, including clades within Echinamoebida, Heterolobosea, Radiolaria, Haptophyta, Oomycota, and Cryptophyta. We argue that extreme environments are prime sampling targets to fill gaps in the eukaryotic tree of life and to increase our understanding of the ecology, metabolism, genome architecture, and evolution of eukaryotic life.
Astroglial Hmgb1 regulates postnatal astrocyte morphogenesis and cerebrovascular maturation
Authors: Freitas-Andrade Moises , Comin Cesar H. , Van Dyken Peter , Ouellette Julie , Raman-Nair Joanna , Blakeley Nicole , Liu Qing Yan , Leclerc Sonia , Pan Youlian , Liu Ziying , Carrier Micaël , Thakur Karan , Savard Alexandre , Rurak Gareth M. , Tremblay Marie-Ève , Salmaso Natalina , da F. Costa Luciano , Coppola Gianfilippo , Lacoste Baptiste 
Published: August 2023

AbstractAstrocytes are intimately linked with brain blood vessels, an essential relationship for neuronal function. However, astroglial factors driving these physical and functional associations during postnatal brain development have yet to be identified. By characterizing structural and transcriptional changes in mouse cortical astrocytes during the first two postnatal weeks, we find that high-mobility group box 1 (Hmgb1), normally upregulated with injury and involved in adult cerebrovascular repair, is highly expressed in astrocytes at birth and then decreases rapidly. Astrocyte-selective ablation ofHmgb1at birth affects astrocyte morphology and endfoot placement, alters distribution of endfoot proteins connexin43 and aquaporin-4, induces transcriptional changes in astrocytes related to cytoskeleton remodeling, and profoundly disrupts endothelial ultrastructure. While lack of astroglialHmgb1does not affect the blood-brain barrier or angiogenesis postnatally, it impairs neurovascular coupling and behavior in adult mice. These findings identify astroglialHmgb1as an important player in postnatal gliovascular maturation.
The first chromosome-level genome assembly of Entomobrya proxima Folsom, 1924 (Collembola: Entomobryidae)
Authors: Jin Jianfeng , Zhao Yuxin , Zhang Guoqiang , Pan Zhixiang , Zhang Feng 
Published: August 2023

AbstractThe Entomobryoidea, the largest superfamily of Collembola, encompasses over 2,000 species in the world. However, the lack of high-quality genomes hinders our understanding of the evolution and ecology of this group. This study presents a chromosome-level genome of Entomobrya proxima by combining PacBio long reads, Illumina short reads, and Hi-C data. The genome has a size of 362.37 Mb, with a scaffold N50 size of 57.67 Mb, and 97.12% (351.95 Mb) of the assembly is located on six chromosomes. The BUSCO analysis of our assembly indicates a completeness of 96.1% (n = 1,013), including 946 (93.4%) single-copy BUSCOs and 27 (2.7%) duplicated BUSCOs. We identified that the genome contains 22.16% (80.06 Mb) repeat elements and 20,988 predicted protein-coding genes. Gene family evolution analysis of E. proxima identified 177 gene families that underwent significant expansions, which were primarily associated with detoxification and metabolism. Moreover, our inter-genomic synteny analysis showed strong chromosomal synteny between E. proxima and Sinella curviseta. Our study provides valuable genomic information for comprehending the evolution and ecology of Collembola.