bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial Ecology and Site Characteristics Underlie Differences in Salinity‐Methane Relationships in Coastal Wetlands
Authors: Bueno de Mesquita Clifton P. , Hartman Wyatt H. , Ardón Marcelo , Bernhardt Emily S. , Neubauer Scott C. , Weston Nathaniel B. , Tringe Susannah G. 
Published: June 2024

AbstractMethane (CH4) is a potent greenhouse gas emitted by archaea in anaerobic environments such as wetland soils. Tidal freshwater wetlands are predicted to become increasingly saline as sea levels rise due to climate change. Previous work has shown that increases in salinity generally decrease CH4 emissions, but with considerable variation, including instances where salinization increased CH4 flux. We measured microbial community composition, biogeochemistry, and CH4 flux from field samples and lab experiments from four different sites across a wide geographic range. We sought to assess how site differences and microbial ecology affect how CH4 emissions are influenced by salinization. CH4 flux was generally, but not always, positively correlated with CO2 flux, soil carbon, ammonium, phosphate, and pH. Methanogen guilds were positively correlated with CH4 flux across all sites, while methanotroph guilds were both positively and negatively correlated with CH4 depending on site. There was mixed support for negative relationships between CH4 fluxes and concentrations of alternative electron acceptors and abundances of taxa that reduce them. CH4/salinity relationships ranged from negative, to neutral, to positive and appeared to be influenced by site characteristics such as pH and plant composition, which also likely contributed to site differences in microbial communities. The activity of site‐specific microbes that may respond differently to low‐level salinity increases is likely an important driver of CH4/salinity relationships. Our results suggest several factors that make it difficult to generalize CH4/salinity relationships and highlight the need for paired microbial and flux measurements across a broader range of sites.
Molecular testing for gastrointestinal pathogens in intestinal tissue of infants with necrotizing enterocolitis or spontaneous intestinal perforation
Authors: Talavera-Barber Maria M. , Sánchez Pablo J. , Conces Miriam , Kaptsan Irina , Everhart Kathy , Leber Amy , Malleske Daniel T. , Moallem Mohannad , Panesso-Gómez Santiago , Shimamura Masako 
Published: June 2024

Abstract
Objective
The objective of this study was to determine the frequency of common gastrointestinal bacterial, parasitic, and viral pathogen detection in necrotizing enterocolitis (NEC) or spontaneous intestinal perforation (SIP) -associated intestinal tissue.

Study design
Retrospective cohort study examined formalin fixed, paraffin embedded (FFPE) surgical or autopsy intestinal tissue from NEC or SIP specimens. DNA and RNA were extracted and analyzed by multiplex PCR panel (GIFA Biofire). DNA or RNA from stool samples containing each pathogen were extracted for positive controls.

Results
The total number of intestinal tissue samples were 193 from 310 infants (156 NEC, 37 SIP). Six (3%) infants with stage III NEC tested positive for a target pathogen; 2, C. difficile; 3, Enteroaggregtive E. coli; and 1, Giardia. No gastrointestinal viral pathogens were detected.

Conclusion
Molecular testing yielded few GI pathogens suggesting that these organisms are likely not major causes or facilitators of NEC or SIP.
Epigenetic alterations in patients with anorexia nervosa—a systematic review
Authors: Käver Larissa , Hinney Anke , Rajcsanyi Luisa Sophie , Maier Hannah Benedictine , Frieling Helge , Steiger Howard , Voelz Clara , Beyer Cordian , Trinh Stefanie , Seitz Jochen 
Published: June 2024

AbstractAnorexia nervosa (AN) is a complex metabolic and psychological disorder that is influenced by both heritable genetic components and environmental factors. Exposure to various environmental influences can lead to epigenetically induced changes in gene expression. Epigenetic research in AN is still in its infancy, and studies to date are limited in determining clear, valid links to disease onset and progression are limited. Therefore, the aim of this systematic review was to compile and critically evaluate the available results of epigenetic studies specifically in AN and to provide recommendations for future studies. In accordance with the PRISMA guidelines, a systematic literature search was performed in three different databases (PubMed, Embase, and Web of Science) through May 2023. Twenty-three original papers or conference abstracts on epigenetic studies in AN were collected. Epigenome-wide association studies (EWASs), which analyze DNA methylation across the genome in patients with AN and identify potential disease-relevant changes in promoter/regulatory regions of genes, are the most promising for future research. To date, five EWASs on AN have been published, suggesting a potential reversibility of malnutrition-induced epigenetic changes once patients recover. Hence, determining differential DNA methylation levels could serve as a biomarker for disease status or early diagnosis and might be involved in disease progression or chronification. For future research, EWASs with a larger sample size, longitudinal study design and uniform methods should be performed to contribute to the understanding of the pathophysiology of AN, the development of individual interventions and a better prognosis for affected patients.
Cross-cultural validation of Malay version of perceived professionalism among dental patients
Authors: Pandarathodiyil Anitha Krishnan , Mani Shani Ann , Veerabhadrappa Suresh Kandagal , Danaee Mahmoud , Zamzuri Ahmad Termizi Bin 
Published: June 2024

Abstract
Background
Professionalism is a dynamic construct that requires constant revision based on contemporary practices and attitudes.

Objectives
The purpose of this study was to cross-culturally adapt an already validated English questionnaire assessing patient perceptions of professionalism among dentists, into the Malay language.

Methods
An original 24-item questionnaire was cross-cultural adapted in the Malaysian context through two phases. Phase I included content and face validity from experts’ evaluation which was followed by translation into the Malay language. Phase II involved psychometric assessment including construct validity and reliability analysis.

Results
Expert evaluation indicated that all items demonstrated excellent content validity for the characteristics of relevance (CVI = 0.75–1.00 Kappa = 0.72–1.00) and clarity (CVI = 0.75–1.00 and Kappa= 0.72–1.00). A total of 300 dental patients completed the questionnaire. EFA was done on the first dataset and the second dataset was subjected to CFA which showed composite reliability (CR) ranging between 0.741 and 0.897 indicating acceptable reliability among items. The final questionnaire had 20 items with 3 domains; Patient expectation of a dental care provider, Ethics and Dentist’s professional responsibilities, Patient communication and confidentiality.

Conclusion
This study has successfully validated the questionnaire for patient perception of professionalism in the Malaysian context.
Additional copies of 1q negatively impact the outcome of multiple myeloma patients and induce transcriptomic deregulation in malignant plasma cells
Authors: D’Agostino Mattia , Rota-Scalabrini Delia , Belotti Angelo , Bertamini Luca , Arigoni Maddalena , De Sabbata Giovanni , Pietrantuono Giuseppe , Pascarella Anna , Tosi Patrizia , Pisani Francesco , Pescosta Norbert , Ruggeri Marina , Rogers Jennifer , Olivero Martina , Garzia Mariagrazia , Galieni Piero , Annibali Ombretta , Monaco Federico , Liberati Anna Marina , Palmieri Salvatore , Stefanoni Paola , Zamagni Elena , Bruno Benedetto , Calogero Raffaele Adolfo , Boccadoro Mario , Musto Pellegrino , Gay Francesca 
Published: June 2024

AbstractAdditional copies of chromosome 1 long arm (1q) are frequently found in multiple myeloma (MM) and predict high-risk disease. Available data suggest a different outcome and biology of patients with amplification (Amp1q, ≥4 copies of 1q) vs. gain (Gain1q, 3 copies of 1q) of 1q. We evaluated the impact of Amp1q/Gain1q on the outcome of newly diagnosed MM patients enrolled in the FORTE trial (NCT02203643). Among 400 patients with available 1q data, 52 (13%) had Amp1q and 129 (32%) Gain1q. After a median follow-up of 62 months, median progression-free survival (PFS) was 21.2 months in the Amp1q group, 54.9 months in Gain1q, and not reached (NR) in Normal 1q. PFS was significantly hampered by the presence of Amp1q (HR 3.34 vs. Normal 1q, P < 0.0001; HR 1.99 vs. Gain1q, P = 0.0008). Patients with Gain1q had also a significantly shorter PFS compared with Normal 1q (HR 1.68, P = 0.0031). Concomitant poor prognostic factors or the failure to achieve MRD negativity predicted a median PFS < 12 months in Amp1q patients. Carfilzomib–lenalidomide–dexamethasone plus autologous stem cell transplantation treatment improved the adverse effect of Gain1q but not Amp1q. Transcriptomic data showed that additional 1q copies were associated with deregulation in apoptosis signaling, p38 MAPK signaling, and Myc-related genes.
Effect of antimony additions on the microstructure and performance of Zn–Mg–Al alloy coatings
Authors: Britton Daniel A. , Penney David , Malla Amar D. , Mehraban Shahin , Sullivan James , Goldsworthy Mathew , McGettrick James , Johnston Richard , Mitchell Ria L. , Challinor Clive 
Published: June 2024

AbstractMicroscopy, electrochemical techniques and mechanical testing are used to investigate the effect of varying antimony additions (0.45–1.8 wt%) on the microstructure and corrosion properties of zinc-magnesium-aluminium coating alloys. Samples were produced by splat casting to produce high cooling rates similar to those seen in a continuous galvanising line. X-Ray Microscopy reveals that the Sb additions produce disk-shaped Mg3Sb2 intermetallics, subsequently reducing or eliminating the MgZn2 eutectic. Electrochemical testing in 1 wt% NaCl shows that the Mg3Sb2 phase is cathodic with respect to the bulk alloy with slower oxygen reduction kinetics. The decrease in eutectic content leads to less intense anodic activity. The combined effect is anodic and cathodic deactivation, which leads to a 43% reduction in corrosion rate as measured through LPR compared to the base alloy. This work shows that quaternary additions to ZMA coating alloys can be a potential route to improved corrosion resistance for galvanic protection.
Influenza virus uses mGluR2 as an endocytic receptor to enter cells
Authors: Ni Zixin , Wang Jinliang , Yu Xiaofei , Wang Yifan , Wang Jingfei , He Xijun , Li Chengjun , Deng Guohua , Shi Jianzhong , Kong Huihui , Jiang Yongping , Chen Pucheng , Zeng Xianying , Tian Guobin , Chen Hualan , Bu Zhigao 
Published: June 2024

AbstractInfluenza virus infection is initiated by the attachment of the viral haemagglutinin (HA) protein to sialic acid receptors on the host cell surface. Most virus particles enter cells through clathrin-mediated endocytosis (CME). However, it is unclear how viral binding signals are transmitted through the plasma membrane triggering CME. Here we found that metabotropic glutamate receptor subtype 2 (mGluR2) and potassium calcium-activated channel subfamily M alpha 1 (KCa1.1) are involved in the initiation and completion of CME of influenza virus using an siRNA screen approach. Influenza virus HA directly interacted with mGluR2 and used it as an endocytic receptor to initiate CME. mGluR2 interacted and activated KCa1.1, leading to polymerization of F-actin, maturation of clathrin-coated pits and completion of the CME of influenza virus. Importantly, mGluR2-knockout mice were significantly more resistant to different influenza subtypes than the wild type. Therefore, blocking HA and mGluR2 interaction could be a promising host-directed antiviral strategy.
Haplotype-resolved chromosome-level genome assembly of Huyou (Citrus changshanensis)
Authors: Miao Changjiu , Wu Yijing , Wang Lixia , Zhao Siqing , Grierson Donald , Xu Changjie , Chen Wenbo , Chen Kunsong 
Published: June 2024

AbstractHuyou (Citrus changshanensis) is a significant citrus species that originated in Zhejiang Province, China, where it is also primarily cultivated. It is valued for its distinctive flavor and notable health benefits, owing to its high content of bioactive compounds like naringin and limonin. However, the absence of a high quality reference genome has limited the exploration of these health-promoting compounds in Huyou and hindered research into the mechanisms behind its medicinal properties. In this study, we present a phased chromosome-level genome assembly of Huyou. By combining PacBio and Hi-C sequencing, we generated a primary genome assembly and two haplotypes, comprising nine pseudo-chromosomes, with sizes of 339.91 Mb, 323.51 Mb, and 311.89 Mb, respectively. By integrating transcriptome data and annotations of homologous species, we identified a total of 29,775 protein-coding genes in the genome of Huyou. Additionally, we detected lots of structural variants between the two haplotypes. This represents the first reference genome of Huyou, providing a valuable resource for future studies on its agricultural characteristics and medicinal applications.
Experimental data on filling and emptying of a large-scale pipeline
Authors: Chen Xifeng , Hou Qingzhi , Laanearu Janek , Tijsseling Arris S. 
Published: June 2024

AbstractLaboratory-scale experiments are one of the most important means to explore the evolution of air-water interfaces and the mechanisms of pressure oscillations in pipelines during rapid filling and emptying processes. This study presents a dataset obtained from the experimental results of the flow behaviours during the pressure-gradient-driven filling and emptying processes of a large-scale pipeline. Based on these data, it is possible to study the evolution of the water-air and air-water interfaces and their breaking during pipe filling and emptying. The experimental equipment includes a variety of components (such as tanks, valves, bends, pipes of different materials and diameters, anchors, supports and water basin) and the operation procedures are rather complex. The flow behaviours are measured by various instruments; hence a thorough hydrodynamic analysis is possible. All these features and data frameworks make the current study particularly useful as a test case for real rapid filling and emptying processes and syphoning.
Biomechanics of sound production in high-pitched classical singing
Authors: Echternach Matthias , Burk Fabian , Köberlein Marie , Döllinger Michael , Burdumy Michael , Richter Bernhard , Titze Ingo R. , Elemans Coen P. H. , Herbst Christian T. 
Published: June 2024

AbstractVoice production of humans and most mammals is governed by the MyoElastic-AeroDynamic (MEAD) principle, where an air stream is modulated by self-sustained vocal fold oscillation to generate audible air pressure fluctuations. An alternative mechanism is found in ultrasonic vocalizations of rodents, which are established by an aeroacoustic (AA) phenomenon without vibration of laryngeal tissue. Previously, some authors argued that high-pitched human vocalization is also produced by the AA principle. Here, we investigate the so-called “whistle register” voice production in nine professional female operatic sopranos singing a scale from C6 (≈ 1047 Hz) to G6 (≈ 1568 Hz). Super-high-speed videolaryngoscopy revealed vocal fold collision in all participants, with closed quotients from 30 to 73%. Computational modeling showed that the biomechanical requirements to produce such high-pitched voice would be an increased contraction of the cricothyroid muscle, vocal fold strain of about 50%, and high subglottal pressure. Our data suggest that high-pitched operatic soprano singing uses the MEAD mechanism. Consequently, the commonly used term “whistle register” does not reflect the physical principle of a whistle with regard to voice generation in high pitched classical singing.
Machine learning-assisted chemical design of highly efficient deicers
Authors: Ito Kai , Fukatsu Arisa , Okada Kenji , Takahashi Masahide 
Published: June 2024

AbstractThe use of deicers in urban areas, on runways and aircrafts has raised concerns about their environmental impact. Understanding the ice-melting mechanism is crucial for developing environmentally friendly deicers, yet it remains challenging. This study employs machine learning to investigate the ice penetration capacity (IPC) of 21 salts and 16 organic solvents as deicers. Relationships between their IPC and various physical properties were analysed using extreme gradient boosting (XGBoost) and Shapley additive explanation (SHAP). Three key ice-melting mechanisms were identified: (1) freezing-point depression, (2) interactions between deicers and H2O molecules and (3) infiltration of ions into ice crystals. SHAP analysis revealed different ice-melting factors and mechanisms for salts and organic solvents, suggesting a potential advantage in combining the two. A mixture of propylene glycol (PG) and sodium formate demonstrated superior environmental impact and IPC. The PG and sodium formate mixture exhibited higher IPC when compared to six commercially available deicers, offering promise for sustainable deicing applications. This study provides valuable insights into the ice-melting process and proposes an effective, environmentally friendly deicer that combines the strengths of organic solvents and salts, paving the way for more sustainable practices in deicing.
A new label free spiral sensor using impedance spectroscopy to characterize hepatocellular carcinoma in tissue and serum samples
Authors: Abdelbaset Reda , Shawky Sherif M. , Abdullah Mohammed A. A. , Morsy Omar E. , Yahia Yahia A. , Ghallab Yehya H. , Matboli Marwa , Ismail Yehea 
Published: June 2024

AbstractHepatocellular carcinoma (HCC) stands as the most prevalent form of primary liver cancer, predominantly affecting patients with chronic liver diseases such as hepatitis B or C-induced cirrhosis. Diagnosis typically involves blood tests (assessing liver functions and HCC biomarkers), imaging procedures such as Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), and liver biopsies requiring the removal of liver tissue for laboratory analysis. However, these diagnostic methods either entail lengthy lab processes, require expensive imaging equipment, or involve invasive techniques like liver biopsies. Hence, there exists a crucial need for rapid, cost-effective, and noninvasive techniques to characterize HCC, whether in serum or tissue samples. In this study, we developed a spiral sensor implemented on a printed circuit board (PCB) technology that utilizes impedance spectroscopy and applied it to 24 tissues and sera samples as proof of concept. This newly devised circuit has successfully characterized HCC and normal tissue and serum samples. Utilizing the distinct dielectric properties between HCC cells and serum samples versus the normal samples across a specific frequency range, the differentiation between normal and HCC samples is achieved. Moreover, the sensor effectively characterizes two HCC grades and distinguishes cirrhotic/non-cirrhotic samples from tissue specimens. In addition, the sensor distinguishes cirrhotic/non-cirrhotic samples from serum specimens. This pioneering study introduces Electrical Impedance Spectroscopy (EIS) spiral sensor for diagnosing HCC and liver cirrhosis in clinical serum—an innovative, low-cost, rapid (< 2 min), and precise PCB-based technology without elaborate sample preparation, offering a novel non-labeled screening approach for disease staging and liver conditions.
Investigating the impact of motion visual synchrony on self face recognition using real time morphing
Authors: Kasahara Shunichi , Kumasaki Nanako , Shimizu Kye 
Published: June 2024

AbstractFace recognition is a crucial aspect of self-image and social interactions. Previous studies have focused on static images to explore the boundary of self-face recognition. Our research, however, investigates the dynamics of face recognition in contexts involving motor-visual synchrony. We first validated our morphing face metrics for self-face recognition. We then conducted an experiment using state-of-the-art video processing techniques for real-time face identity morphing during facial movement. We examined self-face recognition boundaries under three conditions: synchronous, asynchronous, and static facial movements. Our findings revealed that participants recognized a narrower self-face boundary with moving facial images compared to static ones, with no significant differences between synchronous and asynchronous movements. The direction of morphing consistently biased the recognized self-face boundary. These results suggest that while motor information of the face is vital for self-face recognition, it does not rely on movement synchronization, and the sense of agency over facial movements does not affect facial identity judgment. Our methodology offers a new approach to exploring the ‘self-face boundary in action’, allowing for an independent examination of motion and identity.
CellMarkerPipe: cell marker identification and evaluation pipeline in single cell transcriptomes
Authors: Jia Yinglu , Ma Pengchong , Yao Qiuming 
Published: June 2024

AbstractAssessing marker genes from all cell clusters can be time-consuming and lack systematic strategy. Streamlining this process through a unified computational platform that automates identification and benchmarking will greatly enhance efficiency and ensure a fair evaluation. We therefore developed a novel computational platform, cellMarkerPipe (https://github.com/yao-laboratory/cellMarkerPipe), for automated cell-type specific marker gene identification from scRNA-seq data, coupled with comprehensive evaluation schema. CellMarkerPipe adaptively wraps around a collection of commonly used and state-of-the-art tools, including Seurat, COSG, SC3, SCMarker, COMET, and scGeneFit. From rigorously testing across diverse samples, we ascertain SCMarker’s overall reliable performance in single marker gene selection, with COSG showing commendable speed and comparable efficacy. Furthermore, we demonstrate the pivotal role of our approach in real-world medical datasets. This general and opensource pipeline stands as a significant advancement in streamlining cell marker gene identification and evaluation, fitting broad applications in the field of cellular biology and medical research.