bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using eDNA to Supplement Population Genetic Analyses for Cryptic Marine Species: Identifying Population Boundaries for Alaska Harbour Porpoises
Authors: Parsons Kim M. , May Samuel A. , Gold Zachary , Dahlheim Marilyn , Gabriele Christine , Straley Janice M. , Moran John R. , Goetz Kimberly , Zerbini Alexandre N. , Park Linda , Morin Phillip A. 
Published: October 2024

ABSTRACTIsolation by distance and biogeographical boundaries define patterns of population genetic structure for harbour porpoise along the Pacific coast from California to British Columbia. Until recently, inadequate sample sizes in many regions constrained efforts to characterise population genetic structure throughout the coastal waters of Alaska. Here, tissue samples from beachcast strandings and fisheries bycatch were supplemented with targeted environmental DNA (eDNA) samples in key regions of Alaska coastal and inland waters. Using a geographically explicit, hierarchical approach, we examined the genetic structure of Alaska harbour porpoises, using both mitochondrial DNA (mtDNA) sequence data and multilocus SNP genotypes. Despite a lack of evidence of genetic differentiation from nuclear SNP loci, patterns of relatedness and genetic differentiation from mtDNA suggest natal philopatry at multiple geographic scales, with limited gene flow among sites possibly mediated by male dispersal. A priori clustering of sampled areas at an intermediate scale (eastern and western Bering Sea, Gulf of Alaska and Southeast Alaska) best explained the genetic variance (12.37%) among regions. In addition, mtDNA differentiation between the Gulf of Alaska and eastern Bering Sea, and among regions within the Gulf of Alaska, indicated significant genetic structuring of harbour porpoise populations in Southeast Alaska. The targeted collection of eDNA samples from strata within Southeast Alaska was key for elevating the statistical power of our mtDNA dataset, and findings indicate limited dispersal between neighbouring strata within coastal and inland waters. These results provide evidence supporting a population boundary within the currently recognised Southeast Alaska Stock. Together, these findings will prove useful for ongoing management efforts to reduce fisheries conflict and conserve genetic diversity in this iconic coastal species.
A reassessment of spinal cord pathology in severe infantile spinal muscular atrophy
Authors: Allardyce Hazel , Lawrence Benjamin D. , Crawford Thomas O. , Sumner Charlotte J. , Parson Simon H. 
Published: October 2024

AbstractAimsSpinal muscular atrophy (SMA) is a life‐limiting paediatric motor neuron disease characterised by lower motor neuron loss, skeletal muscle atrophy and respiratory failure, if untreated. Revolutionary treatments now extend patient survival. However, a limited understanding of the foundational neuropathology challenges the evaluation of therapeutic success. As opportunities to study treatment‐naïve tissue decrease, we have characterised spinal cord pathology in severe infantile SMA using gold‐standard techniques, providing a baseline to measure treatment success and therapeutic limitations.MethodsDetailed histological analysis, stereology and transmission electron microscopy were applied to post‐mortem spinal cord from severe infantile SMA patients to estimate neuron number at the end of life; characterise the morphology of ventral horn, lateral horn and Clarke's column neuron populations; assess cross‐sectional spinal cord area; and observe myelinated white matter tracts in the clinically relevant thoracic spinal cord.ResultsVentral horn neuron loss was substantial in all patients, even the youngest cases. The remaining ventral horn neurons were small with abnormal, occasionally chromatolytic morphology, indicating cellular damage. In addition to ventral horn pathology, Clarke's column sensory–associated neurons displayed morphological features of cellular injury, in contrast to the preserved sympathetic lateral horn neurons. Cellular changes were associated with aberrant development of grey and white matter structures that affected the overall dimensions of the spinal cord.ConclusionsWe provide robust quantification of the neuronal deficit found at the end of life in SMA spinal cord. We question long‐accepted dogmas of SMA pathogenesis and shed new light on SMA neuropathology out with the ventral horn, which must be considered in future therapeutic design.
Splenectomy prevents brain orexin, ghrelin, or oxytocin but not GLP‐1‐induced improvement of intestinal barrier function in rats
Authors: Funayama Takuya , Nozu Tsukasa , Ishioh Masatomo , Igarashi Sho , Tanaka Hiroki , Sumi Chihiro , Saito Takeshi , Toki Yasumichi , Hatayama Mayumi , Yamamoto Masayo , Shindo Motohiro , Takahashi Shuichiro , Okumura Toshikatsu 
Published: October 2024

AbstractBackgroundAccumulating evidence has suggested that neuropeptides such as orexin, ghrelin, or oxytocin act centrally in the brain to regulate intestinal barrier function through the vagus nerve. It has been reported that the vagal cholinergic anti‐inflammatory pathway was blocked by splenectomy. In the present study, we therefore examined the effect of splenectomy on neuropeptides‐induced improvement of increased intestinal permeability.MethodsColonic permeability was determined in vivo by quantifying the absorbed Evans blue in colonic tissue for 15 min spectrophotometrically in rats.ResultsSplenectomy increased colonic permeability. The increased permeability by splenectomy was significantly blocked by vagal activation induced by carbachol or 2‐deoxy‐d‐glucose which was prevented by atropine, suggesting vagal activation could prevent colonic hyperpermeability in splenectomized rats. In the splenectomized rats, intracisternal injection of orexin, ghrelin, oxytocin, or butyrate failed to inhibit increased colonic permeability while intracisternal glucagon‐like peptide‐1 (GLP‐1) analogue, liraglutide, potently blocked the increased colonic permeability in a dose‐dependent manner. The liraglutide‐induced improvement of increased colonic permeability was blocked by atropine in splenectomized rats. Intracisternal injection of GLP‐1 receptor antagonist attenuated 2‐deoxy‐d‐glucose‐induced improvement of colonic hyperpermeability in splenectomized rats.ConclusionThe present results suggested that the spleen is important in the improvement of intestinal barrier function by brain orexin, ghrelin or oxytocin, and butyrate. On the other hand, GLP‐1 acts centrally in the brain to improve colonic hyperpermeability in a spleen‐independent manner. All these results suggest that dual mechanisms (spleen dependent or independent) may exist for the brain‐gut regulation in intestinal barrier function.
Branched‐chain amino acid metabolism: Pathophysiological mechanism and therapeutic intervention in metabolic diseases
Authors: Mansoori Shama , Ho Melody Yuen‐man , Ng Kelvin Kwun‐wang , Cheng Kenneth King‐yip 
Published: October 2024

SummaryBranched‐chain amino acids (BCAAs), including leucine, isoleucine, and valine, are essential for maintaining physiological functions and metabolic homeostasis. However, chronic elevation of BCAAs causes metabolic diseases such as obesity, type 2 diabetes (T2D), and metabolic‐associated fatty liver disease (MAFLD). Adipose tissue, skeletal muscle, and the liver are the three major metabolic tissues not only responsible for controlling glucose, lipid, and energy balance but also for maintaining BCAA homeostasis. Under obese and diabetic conditions, different pathogenic factors like pro‐inflammatory cytokines, lipotoxicity, and reduction of adiponectin and peroxisome proliferator‐activated receptors γ (PPARγ) disrupt BCAA metabolism, leading to excessive accumulation of BCAAs and their downstream metabolites in metabolic tissues and circulation. Mechanistically, BCAAs and/or their downstream metabolites, such as branched‐chain ketoacids (BCKAs) and 3‐hydroxyisobutyrate (3‐HIB), impair insulin signaling, inhibit adipogenesis, induce inflammatory responses, and cause lipotoxicity in the metabolic tissues, resulting in multiple metabolic disorders. In this review, we summarize the latest studies on the metabolic regulation of BCAA homeostasis by the three major metabolic tissues—adipose tissue, skeletal muscle, and liver—and how dysregulated BCAA metabolism affects glucose, lipid, and energy balance in these active metabolic tissues. We also summarize therapeutic approaches to restore normal BCAA metabolism as a treatment for metabolic diseases.
Fatigue in severe pediatric asthma patients: Results of the PANDA study
Authors: van Dijk Yoni E. , Keuker Valerie S. L. , Hashimoto Simone , Rutjes Niels W. , van Muilekom Maud M. , Golebski Kornel , Van Litsenburg Raphaële R. L. , Terheggen‐Lagro Suzanne W. J. , van Ewijk Bart E. , Gemke Reinoud J. B. J. , Maitland‐van der Zee Anke H. , Vijverberg Susanne J. H. 
Published: October 2024

AbstractBackgroundFatigue is a commonly reported clinical symptom, yet research on fatigue in children with severe asthma is missing. We aimed to explore the extent of fatigue in severe pediatric asthma and identify associated factors.MethodThis study was conducted within the Pediatric Asthma Non‐Invasive Diagnostic Approaches (PANDA), an observational cohort of 6‐ to 17‐year‐old Dutch children with severe asthma. The Pediatric Quality of Life Inventory Multidimensional Fatigue Scale (PedsQL™‐MFS) was used to measure self‐reported fatigue. Fatigue levels were compared with a general pediatric Dutch population using linear regression, and quantifying the prevalence of “fatigued” (−2 < Standard deviations [SD] ≤ −1) and “severely fatigued” (SD ≤ −2) children. Secondly, we performed linear regression analyses to explore whether fatigue levels were independently associated with asthma attacks, comorbidities, medication, pulmonary function, symptom control, and asthma‐related quality of life (QoL).ResultsSevere pediatric asthma patients (n = 78, mean age 11.8 ± 3.1 years) reported significantly more fatigue than Dutch peers (n = 328, mean age 11.8 ± 3.2 years) mean difference in z‐score: −0.68; 95%CI −0.96, −0.40. In the severe asthma group, 28.2% scored as “fatigued” and 15.4% as “severely fatigued,” compared with 14.0% and 3.4% in the general population. In pediatric asthma patients, asthma‐related QoL (β = 0.77, p < .01, ΔR2 = .43), symptom control (β = 0.56, p < .01, ΔR2 = .24) and a dysfunctional breathing pattern (β = −0.36, p < .01, ΔR2 = .12) were most strongly associated with fatigue scores.ConclusionFatigue is a common symptom in children with severe asthma and is associated with multiple clinical factors and patient‐reported outcomes. It should be considered as an important treatment target.
Narrative review: Managing buprenorphine and opioid use disorder in the perioperative setting
Authors: Kohan Lynn , Barreveld Antje , Potru Sudheer , Abd‐Elsayed Alaa , Viscusi Eugene R. 
Published: October 2024

AbstractThe opioid epidemic continues to have a staggering impact on millions of individuals and families across all socioeconomic levels and communities. Recent studies suggest high numbers of patients presenting for surgery with reported opioid misuse and/or opioid use disorder (OUD). Anesthesiologists often lack basic education to treat patients suffering with OUD or patients in recovery from this treatable disease. This manuscript will provide a review of the American Society of Anesthesiology and Pain Medicine Multisociety Working Group Practice Advisory recommendations on existing OUD treatment barriers and perioperative management best practices; it will also demonstrate the benefits that greater involvement of the anesthesiologist can have in managing patients with OUD perioperatively.
Assessing Rapid Adaptation Through Epigenetic Inheritance: A New Experimental Approach
Authors: Huber Meret , Chávez Alexandra 
Published: October 2024

Summary statementEpigenetic inheritance is hypothesized to lead to rapid adaptation, yet evidence is scarce, possibly because of the current experimental approaches. We propose a new approach to simultaneously assess whether species adapt through selection of epimutations or formation of stress‐induced epialleles.
Astrocytes Can Be Key Players Against Cerebral Leishmaniasis: In Vitro Co‐Culture Model for the Assessment of Infection
Authors: Islek Zeynep , Ucisik Mehmet Hikmet , Sahin Fikrettin 
Published: October 2024

ABSTRACTLeishmaniasis is a neglected tropical disease, caused by protozoan parasites of Leishmania (L.), and is transmitted by bite of phlebotomine sandflies. There are several studies on central nervous system infection to indicate that Leishmania can cross the blood–brain barrier, resulting in neurological manifestations, known as “cerebral leishmaniasis.” This study highlighted the notions: (i) polarisation of bone marrow‐derived macrophages (BMDM) incubated following stimulation with lipopolysaccharide (LPS) or soluble Leishmania antigen (SLA), (ii) quantification of parasites within co‐culture of Leishmania‐infected macrophages, and astrocytes, and (iii) effect of interferon‐gamma (IFN‐γ) on the infection rate of co‐culture populations. Accordingly, 83% of overall macrophage population was identified on day 7 for CD11b and F4/80 macrophage markers. Flow cytometry analysis revealed significant increases in CD11b and F4/80 surface markers in LPS and SLA‐stimulated BMDMs at 24 h, compared to untreated cells. TNF‐α levels increased significantly in both LPS and SLA‐treated BMDMs after 48 h. Additionally, SLA treatment induced a more elongated, spindle‐like shape in the cells, indicative of M2 macrophage polarisation over the M1 phenotype. When non‐infected astrocytes with/without stimulation with IFN‐γ before co‐culture, gp63 FITC‐labelled parasite populations (%) in co‐culture decreased to 25% at 72 h, thus indicating a lower infection rate in a time‐dependent manner. IFN‐γ and IL‐6 levels significantly increased to 71.66 ± 3.51 and 184 ± 14.42 pg/mL, resulting in the inflammatory response in the co‐culture system at 48 h (p ≤ 0.0001), when compared to the control (30 ± 2.52 pg/mL for IFN‐γ and 8.66 ± 2.37 pg/mL for IL‐6) at 0 h of the incubation. It is the first study to emphasize the communication between Leishmania‐infected macrophages and astrocytes regarding Leishmania parasite load. The results suggest that astrocytes can lead to the reduction in Leishmania parasites, thereby controlling the incidence of cerebral leishmaniasis.
Rigid lid limit in shallow water over a flat bottom
Authors: Melinand Benjamin 
Published: October 2024

AbstractWe perform the so‐called rigid lid limit on different shallow water models such as the abcd Bousssinesq systems or the Green–Naghdi equations. To do so, we consider an appropriate nondimensionalization of these models where two small parameters are involved: the shallowness parameter and a parameter which can be interpreted as a Froude number. When the parameter tends to zero, the surface deformation formally goes to the rest state, hence the name rigid lid limit. We carefully study this limit for different topologies. We also provide rates of convergence with respect to and careful attention is given to the dependence on the shallowness parameter .
Efficient numerical approximations for a nonconservative nonlinear Schrödinger equation appearing in wind‐forced ocean waves
Authors: Athanassoulis Agissilaos , Katsaounis Theodoros , Kyza Irene 
Published: October 2024

AbstractWe consider a nonconservative nonlinear Schrödinger equation (NCNLS) with time‐dependent coefficients, inspired by a water waves problem. This problem does not have mass or energy conservation, but instead mass and energy change in time under explicit balance laws. In this paper, we extend to the particular NCNLS two numerical schemes which are known to conserve energy and mass in the discrete level for the cubic nonlinear Schrödinger equation. Both schemes are second‐order accurate in time, and we prove that their extensions satisfy discrete versions of the mass and energy balance laws for the NCNLS. The first scheme is a relaxation scheme that is linearly implicit. The other scheme is a modified Delfour–Fortin–Payre scheme, and it is fully implicit. Numerical results show that both schemes capture robustly the correct values of mass and energy, even in strongly nonconservative problems. We finally compare the two numerical schemes and discuss their performance.
Fluorescent Reporters, Imaging, and Artificial Intelligence Toolkits to Monitor and Quantify Autophagy, Heterophagy, and Lysosomal Trafficking Fluxes
Authors: Rudinskiy Mikhail , Morone Diego , Molinari Maurizio 
Published: October 2024

ABSTRACTLysosomal compartments control the clearance of cell‐own material (autophagy) or of material that cells endocytose from the external environment (heterophagy) to warrant supply of nutrients, to eliminate macromolecules or parts of organelles present in excess, aged, or containing toxic material. Inherited or sporadic mutations in lysosomal proteins and enzymes may hamper their folding in the endoplasmic reticulum (ER) and their lysosomal transport via the Golgi compartment, resulting in lysosomal dysfunction and storage disorders. Defective cargo delivery to lysosomal compartments is harmful to cells and organs since it causes accumulation of toxic compounds and defective organellar homeostasis. Assessment of resident proteins and cargo fluxes to the lysosomal compartments is crucial for the mechanistic dissection of intracellular transport and catabolic events. It might be combined with high‐throughput screenings to identify cellular, chemical, or pharmacological modulators of these events that may find therapeutic use for autophagy‐related and lysosomal storage disorders. Here, discuss qualitative, quantitative and chronologic monitoring of autophagic, heterophagic and lysosomal protein trafficking in fixed and live cells, which relies on fluorescent single and tandem reporters used in combination with biochemical, flow cytometry, light and electron microscopy approaches implemented by artificial intelligence‐based technology.
Has trade facilitation of the ‘Belt and Road’ countries promoted China's cross‐border E‐commerce exports?
Authors: Guo Ping , Hamzah Hanny Zurina , Chin Lee 
Published: October 2024

AbstractThis paper investigates the impact of trade facilitation level on China's exports in cross‐border e‐commerce (CBEC) in 56 major ‘Belt and Road’ countries using PPML panel estimation. The total sample and sub‐sample regressions based on the classification of developed and developing countries show that (1) the trade facilitation level of ‘Belt and Road’ countries has a significant positive impact on China's CBEC exports, but the impact of developed countries is greater than that of developing countries. (2) All five trade facilitation sub‐indicators of the ‘Belt and Road’ countries have an impact on China's CBEC exports, but the impact of the logistics and e‐commerce environments are prominent. (3) The impact of the customs environment of developed countries on China's CBEC exports is second only to that of the logistics environment, and the impact of the e‐commerce environment in developing countries is greater than that of the logistics environment. To promote China's CBEC exports to the ‘Belt and Road’ countries, the Chinese government needs to prioritise cooperation in the logistics and e‐commerce environments. In addition, cooperation with developed countries in particular needs to strengthen the customs environment construction, whilst cooperation with developing countries should prioritise the improvement of the e‐commerce environment.
The Digital Displacement Pump As a Frequency Generator
Authors: Dumnov Daniil , Melling Jonathan , Caldwell Niall , Johnston Nigel , Plummer Andrew , Sell Nathan 
Published: October 2024

Abstract
Digital Displacement® pumps are a type of variable displacement, radial piston hydraulic pump currently being developed for use in efficient mobile hydraulic systems. The pump displacement is controlled by selective enabling of solenoid valves at the inlet of each cylinder and since the pump displacement can be controlled directly by software it is possible to use the pump as a flow source with any arbitrary demand. By enabling precise flow control and reducing leakage and throttling losses they can provide a significant improvement in efficiency over conventional pumps; however, this also leads to a decrease in the overall sources of damping in the system and may result in increased transmission of vibration and fluid-borne noise.
This paper presents a method for characterising vibration sensitivity of a hydraulic system, using the pump as a frequency generator whose flow output follows a sinusoidal ‘chirp’ demand. Simulation results are presented of the pump open-loop frequency response, which show the control bandwidth and demonstrates that the pump can modulate its output flow at frequencies into the audible range. This enables the possibility of using the pump to identify potential sensitivities in a downstream hydraulic system up to 200 Hz. A method is described for characterising the noise and vibration of the connected system within this frequency range. Test data from a hydraulic excavator are presented and analysed to create a characteristic transfer function for the system, relating pump output flow to pressure ripple and vibration in the downstream system.
These system transfer functions can be used to develop control methods to reduce the impact of vibration, either by active damping, filtering of the control signals or choice of cylinder enabling strategy. Test data are presented also showing the effect of some mitigation strategies in the same hydraulic excavator, leading to a reduction of overall vibration in the vehicle cabin.
Development of Boundary/Mixed Friction Models for Cylinder Block/Valve Plate Interface in a Novel Aerospace Electro-Hydrostatic Module
Authors: Lyu Dingchong , Fu Jian , Zhao Shoujun , Chen Siyuan 
Published: October 2024

Abstract
The highly compact Electro-Hydrostatic Module (EHM) is the key technology of future Electro-Hydrostatic Actuation (EHA) in the aerospace industry. Improving the frictional performance of the critical friction pairs is crucial for EHM. To address this issue, this study develops a specific friction model for the cylinder block/valve plate interface that combines rotor dynamics with boundary/mixed friction characteristics. The boundary/mixed friction properties of the interface are characterized by combining a viscous friction model based on Reynolds lubrication theory and the measurement results of a special simulated friction experiment of cylinder block/valve plate. A finite element model for the rotor dynamics is developed, and the rotor models under a wide range of rotational speeds are determined by harmonic response analysis. By merging the rotor dynamics model with the friction model through the exchange of rotor model data and bearing parameters, the coupling effects of rotor vortices and oil film hydrodynamics at the cylinder block/valve plate interface are simulated. The model’s accuracy is verified through experiments to be 85%. It is found that the integrated structure has a critical speed near 20000 rpm through simulation analysis, and the interface friction characteristics near the critical speed are significantly increased. From the perspective of the two critical attributes of reliability and efficiency, this study provides theoretical reference points for the structural optimization of the novel EHM.