bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative ichnology: a novel framework to determine the producers of locomotory trace fossils with the ichnogenus Gordia as a case study
Authors: Wang Zekun , Rahman Imran A. 
Published: December 2023

AbstractTrace fossils record the interactions between organisms and their surroundings, and can therefore provide unique insights into the coevolution of trace makers and the environment. However, identifying the producers of trace fossils is challenging because different animals can create very similar traces and many ichnotaxa can therefore only be attributed to broad morphological grades. For example, simple horizontal traces like Gordia are generally suggested to have been produced by vermiform organisms, potentially encompassing a range of animal phyla. This uncertainty makes it difficult to decipher their palaeobiological significance through major evolutionary events and episodes of environmental change. We have developed new mathematical approaches for identifying previously unrecognized signatures left by the trace makers of simple marine locomotory traces. We calculated the deviation angle series of self‐crossing traces made by extant isopods, polychaetes, gastropods and nematodes, computing the frequency spectrum and autocorrelation function in each case. The results reveal that each of these taxa left unique markers during the trace‐making process, reflecting differences in their anatomy and locomotory behaviour. We were able to identify the possible trace makers of several early Palaeozoic Gordia specimens, demonstrating that ichnospecies within the same ichnogenus can be created by distantly related animals with very different morphologies and/or behaviours. This novel mathematical framework has great potential for identifying the possible producers of diverse trace fossils through deep time, helping to uncover the earliest evidence of certain animals or behaviours. It also has great potential for quantifying ichnotaxonomy, consolidating the link between ichnology and palaeobiology.
New wine in old bottles: Modification of the Na+/K+‐ATPase enzyme activity assay and its application in salmonid aquaculture
Authors: Takvam Marius , Sundell Kristina , Sundh Henrik , Gharbi Naouel , Kryvi Harald , Nilsen Tom Ole 
Published: December 2023

AbstractThe Na+, K+ ATPase (NKA) enzyme is important to generate the transmembrane ion gradient in the gills, intestine, and kidneys, hence, is vital for secondary transport of fluids and different solutes in teleosts. Gill NKA enzyme activity is often used as a proxy for parr–smolt transformation (PST) during which anadromous salmonids prepare for seawater (SW). Increased intensification and production of larger smolts in modern salmonid aquaculture has resulted in reports of gill NKA activity being less reliable as a proxy for smolt quality. Consequently, changes in mRNA nka‐α1b/α1a ratios in gills are increasingly used as indicators of PST. However, nka isoform mRNA abundance may not reflect translation into the functional protein, nor the activity of the mature enzyme. This may limit the predictive power of molecular markers under certain environmental conditions, rearing regimes and biological scenarios. During PST, the osmoregulatory transformations necessary for SW tolerance and survival does not only occur in the gills. Equally important are the changes in ion transporting activities, including NKA activity, in the intestine and kidneys. However, to our knowledge, there are no previous studies addressing the timing and concurrent changes in NKA activity in the three osmoregulatory tissue during PST. Here we present modifications and optimization of the NKA enzyme activity protocols for gill, intestinal and kidney tissue and outline how to best utilize NKA activity measurements as part of a more holistic approach to evaluate overall smolt quality in modern aquaculture.
Fossilized autogenic responses of grain‐size transition to sediment supply and water discharge: Alluvial fan experiments
Authors: Shin Haein , Kim Wonsuck , Lee Hyojae , Johnson Joel P. L. , Paola Chris 
Published: December 2023

ABSTRACTAutogenic feedbacks can produce large‐scale, organized stratigraphic patterns in alluvial fans, but autogenic depositional signatures of specific upstream boundary conditions remain challenging to interpret. Here, a combination of theory, experiment and field application is used to explore how autogenic lithofacies changes can be interpreted as stratigraphic indicators of upstream boundary conditions. Six experiments were conducted to test the effects of sediment supply and water discharge rates on autogenic advance and retreat of the lithofacies boundary (grain‐size transition) in an alluvial fan with two dominant grain sizes. Migration of the grain‐size transition caused a short‐term zigzag pattern in the grain‐size transition position in the dip‐directional deposit section. For each experiment, time‐lapse images and laser topographic scans of the fan surface and stratigraphic cross‐sections of the final deposits were used to quantify characteristic timescales of autogenic processes. Timescales for fan‐margin migration, surface wet‐fraction change and grain‐size transition migration generally shorten as sediment supply rate increases and water discharge rate decreases. Increasing the sediment supply rate shortens the duration of the fluvial sediment storage and release cycle, producing higher frequency zigzags in the grain‐size transition trajectory. Increasing the water discharge tends to widen channels and lengthens the duration of the fluvial sediment storage and release cycle, constructing lower frequency zigzags in the grain‐size transition trajectory. Increasing the water discharge also enables more sediment to transport further downstream during release events, leading to higher magnitude zigzags in the grain‐size transition trajectory. These relationships between upstream boundary conditions and the grain‐size transition trajectory demonstrate how autogenic stratigraphic signals could be used as a tool to infer relative changes in boundary conditions.
An evolutionary view of vanillylamine synthase pAMT, a key enzyme of capsaicinoid biosynthesis pathway in chili pepper
Authors: Kusaka Hirokazu , Nakasato Saika , Sano Kaori , Kobata Kenji , Ohno Sho , Doi Motoaki , Tanaka Yoshiyuki 
Published: December 2023

SUMMARYPungent capsaicinoid is synthesized only in chili pepper (Capsicum spp.). The production of vanillylamine from vanillin is a unique reaction in the capsaicinoid biosynthesis pathway. Although putative aminotransferase (pAMT) has been isolated as the vanillylamine synthase gene, it is unclear how Capsicum acquired pAMT. Here, we present a phylogenetic overview of pAMT and its homologs. The Capsicum genome contained 5 homologs, including pAMT, CaGABA‐T1, CaGABA‐T3, and two pseudogenes. Phylogenetic analysis indicated that pAMT is a member of the Solanaceae cytoplasmic GABA‐Ts. Comparative genome analysis found that multiple copies of GABA‐T exist in a specific Solanaceae genomic region, and the cytoplasmic GABA‐Ts other than pAMT are located in the region. The cytoplasmic GABA‐T was phylogenetically close to pseudo‐GABA‐T harboring a plastid transit peptide (pseudo‐GABA‐T3). This suggested that Solanaceae cytoplasmic GABA‐Ts occurred via duplication of a chloroplastic GABA‐T ancestor and subsequent loss of the plastid transit signal. The cytoplasmic GABA‐T may have been translocated from the specific Solanaceae genomic region during Capsicum divergence, resulting in the current pAMT locus. A recombinant protein assay demonstrated that pAMT had higher vanillylamine synthase activity than those of other plant GABA‐Ts. pAMT was expressed exclusively in the placental septum of mature green fruit, whereas tomato orthologs SlGABA‐T2/4 exhibit a ubiquitous expression pattern in plants. These findings suggested that both the increased catalytic efficiency and transcriptional changes in pAMT may have contributed to establish vanillylamine synthesis in the capsaicinoid biosynthesis pathway. This study provides insights into the establishment of pungency in the evolution of chili peppers.
Seismic Assessment Formula for a Buried Pipeline With Local Wall Thinning
Authors: Onuki Shoma , Mitsuya Masaki 
Published: December 2023

Abstract
The structural strength of buried pipeline may be reduced by local wall thinning owing to corrosion in long-term operations. In seismic active area, it is necessary to ensure the integrity of buried pipeline with wall thinning against seismic motion. This study proposed a seismic assessment formula for a pipe with wall thinning subjected to cyclic axial loading assuming seismic motion. Cyclic axial loading experiments using pipes with wall thinning and finite element analysis (FEA) were conducted to study the failure behavior. The pipe with wall thinning deformed starting from the wall-thinning part, and finally plastic collapse due to elephant foot buckling or leakage at the wall thinning due to low-cycle fatigue occurred in several to ten and several cycles. Based on the deformation mechanism at wall thinning, a seismic assessment formula was proposed. The proposed formula can easily evaluate the seismic performance of the pipe with wall thinning against design seismic motion. The formula was validated by the results of experiments and FEA. In addition, based on the proposed formula, the assessment curves for an allowable wall-thinning size against design seismic motion were illustrated. The formula can be used to formulate standards and assess the safety of pipes with wall thinning that are subjected to seismic motion.
Transient Process Analysis of Oscillating Motion in Oscillating Heat Pipes
Authors: Núñez Roberto , Ma Hongbin 
Published: December 2023

Abstract
During the startup phase, oscillating heat pipes (OHPs) exhibit a transient process in which the working fluid moves erratically until a steady-state oscillatory flow is attained. Understanding the transient process is important to predict how long it takes an oscillating heat pipe to reach normal operation and realize its heat transfer potential after it is started. In this paper, we perform a theoretical study of the transient process of oscillating heat pipes. Based on a one-dimensional mathematical model, we obtain an analytic solution that allows us to predict transient process characteristics of oscillating motions in an oscillating heat pipe, as well as the impact that different design and operating parameters have on this transient process.
Simulation of Heat and Mass Transfer in a Moving Bed Part-Fluidized Boiler
Authors: Wan Guang-Zhong , Guo Qiang , Li Yang , Ma Gui-Yang , Xu Chi , Li Ya-Ya 
Published: December 2023

Abstract
Moving bed part-fluidized boiler is a new type of furnace. The new combustion method in the furnace has attracted a lot of attention and shown attractive prospects. Two-dimensional computational fluid dynamic (CFD) simulations were performed for a 116 MW moving bed part-fluidized boiler to investigate the different combustion patterns of coal particles of different particle sizes inside the furnace chamber. A low-NOX combustion method based on the combination of laminar combustion and fluidized combustion is proposed. By comparing the effects of different air distributions on the fluidization state of coal particles, the air distribution values required for optimal fluidized combustion were obtained. The temperature field and pollutant distribution in the furnace chamber for the conventional combustion method and the new combustion method were also simulated. The results show that the combustion technology combining laminar combustion and fluidization of a moving bed part-fluidized boiler can significantly improve the combustion rate and reduce the NOX concentration at the furnace exit. When the secondary air speed is up to 15 m/s, the coal particles smaller than 5 mm are fully fluidized and burned in the whole furnace chamber. The coal particles larger than 5 mm are burned on the bed. The pollutant emission of the boiler can reach the best condition. The new type of boiler can reach a super clean emission in which the NOX emission value is below 47 mg/m3, and the SO2 emission value is reduced to 0.15 mg/m3.
Study on Radiofrequency Ablation of Lung and Kidney Tumors With and Without Nanoparticles Using Multi-Tined Electrode
Authors: Ahammed Md. Ezaz , Peravali Mrunal Swaroop , Naik Santosh S. , Yadav Ajay Kumar , Laxminidhi T. 
Published: December 2023

Abstract
Radio frequency ablation (RFA) is an alternative method for the cure of malign tumors in the liver, lung, and kidney. In the present work, finite element method (FEM) analysis is conducted to study the effect of nanoparticles on the temporal and spatial temperature distribution during RFA. Three-dimensional thermoelectrically FEM model consisting of a multitined radio frequency electrode (nine-tine, deployed up to 2 cm) and a cubical tumor of size 50 mm3 is developed. Numerical simulation is carried out under the temperature-controlled mode (95 °C) with 10 min ablation time. A study using multitined electrodes is carried out on different tissues, i.e., lung and kidney, with and without nanoparticles. Results show that the nanoparticles increase the heat conduction rate and decrease the ablation time up to 13% for the inclusion of 6% nanoparticles. It has been found that the spatial temperature distribution becomes uniform with nanoparticle assistance.
Development of an agar-based screening method for terbinafine, itraconazole, and amorolfine susceptibility testing of
Trichophyton
spp.
Authors: Siopi Maria , Efstathiou Ioanna , Arendrup Maiken C. , Meletiadis Joseph 
Published: December 2023

ABSTRACT

Resistance in dermatophytes is an emerging global public health issue. We, therefore, developed an agar-based method for screening
Trichophyton
spp. susceptibility to terbinafine (TRB), itraconazole (ITC), and amorolfine (AMF) and validated it using molecularly characterized isolates. Α total of 40
Trichophyton
spp. isolates, 28 TRB wild type (WT) (13
T. rubrum
, 10
T. mentagrophytes
, 5
T. interdigitale
) and 12 TRB non-WT (7
T. rubrum
, 5
T. indotineae
) with different alterations in the squalene epoxidase (SQLE) gene, were used. The optimal test conditions (inoculum and drug concentrations, incubation time, and temperature) and stability over time were evaluated. The method was then applied for 86 WT
Trichophyton
spp. clinical isolates (68
T. rubrum
, 7
T. interdigitale
, 6
T. tonsurans
, 5
T. mentagrophytes
) and 4 non-WT
T. indotineae
. Optimal growth of drug-free controls was observed using an inoculum of 20 µL 0.5 McFarland after 5–7 days of incubation at 30°C. The optimal concentrations that prevented the growth of WT isolates were 0.016 mg/L of TRB, 1 mg/L of ITC, and 0.25 mg/L of AMF, whereas 0.125 mg/L of TRB was used for the detection of
Trichophyton
strong SQLE mutants (MIC ≥0.25 mg/L). The agar plates were stable up to 4 months. Inter-observer and inter-experimental agreement were 100%, and the method successfully detected TRB non-WT
Trichophyton
spp. strains showing 100% agreement with the reference EUCAST methodology. An agar-based method was developed for screening
Trichophyton
spp. in order to detect TRB non-WT weak and strong mutant isolates facilitating their detection in non-expert routine diagnostic laboratories.
Precision-cut lung slices as an
ex vivo
model to study
Pneumocystis murina
survival and antimicrobial susceptibility
Authors: Munyonho Ferris T. , Clark Robert D. E. , Lin Dong , Khatun Mst Shamima , Pungan Dora , Dai Guixiang , Kolls Jay K. 
Published: December 2023

ABSTRACT

Pneumocystis
pneumonia (PCP) is a serious fungal lung infection caused by
Pneumocystis jirovecii
in immunosuppressed individuals. The lack of viable
in vitro/ex vivo
PCP models has greatly hindered the progress in studying the biology of these fungi, the host/pathogen interactions, as well as antifungal susceptibility testing. In this study, we show the utility of precision-cut lung slices (PCLS) to support the survival of
Pneumocystis murina in vitro
. We cultured PCLS tissue derived from wild type and immunocompromised mice with a
P. murina
inoculum in submerged or air-liquid interface models for up to 14 days. We isolated total RNA from the cultured lung tissues at days 0, 3, 7, 10, and 14 and analyzed for the expression of host lung genes and
P. murina
genes (
Gsc1
for asci and
Sp
for trophs) by real-time quantitative PCR. When cultured in media alone,
P. murina
died gradually within a few days. However, when cultured on PCLS, both the troph and ascus forms survived throughout the incubation period of 2 weeks. Moreover, immunohistochemistry staining of
P. murina
inoculated PCLS sections using polyclonal anti-
Pneumocystis
sera and showed evidence of fungal aggregation and possible biofilm formation. Additionally,
in vitro
(PCLS) antibiotic susceptibility testing using commonly used antifungal drugs confirmed successful targeting of the troph and ascus forms by trimethoprim sulfamethoxazole and the ascus form by echinocandins.

IMPORTANCE

Our study reveals the potential of precision-cut lung slices as an
ex vivo
platform to study the growth/survival of
Pneumocystis
spp. that can facilitate the development of new anti-fungal drugs.
Complete genome sequence of eight LEE-negative Shiga toxin-producing
Escherichia coli
strains isolated from patients with hemolytic-uremic syndrome
Authors: Kubomura Akiko , Lee Kenichi , Ohnishi Makoto , Iyoda Sunao , Akeda Yukihiro , Working Group EHEC 
Published: December 2023

ABSTRACT

Major serotypes of Shiga toxin-producing
Escherichia coli
(STEC) carry a locus of enterocyte effacement (LEE), which is required for attaching and effacing lesion formation. Genome information of LEE-negative STEC is scarce despite their virulence potential. We present the complete genome sequences of eight LEE-negative STEC isolates from hemolytic-uremic syndrome patients.
Draft genome sequence of
Kluyvera ascorbata
HAK22 isolated from human feces
Authors: Yadav Asha , Shinde Pratik Balwant , Dhar Mahesh S. , Ponnusamy Kalaiarasan , Marwal Robin , V. S. Radhakrishnan , Sharma Krishna Kant 
Published: December 2023

ABSTRACT

The whole genome sequence of rare human pathogen
Kluyvera ascorbata
strain HAK22 is reported. The
K. ascorbata
HAK22 was isolated from healthy human from Gurugram, Haryana, India. The draft genome has a length of 4.7 Mbp, with 54.36% GC content and 4,411 proteins, 4,470 genes, and 18 antimicrobial resistance genes.
Lifetime measurement of the yrast 2$$^+$$ state in $$^{118}$$Te
Authors: Cederlöf E. Ahlgren , Bäck T. , Nyberg J. , Qi C. , Ataç A. , Badran H. , Braunroth T. , Calverley T. , Cox D. M. , Doncel M. , Grahn T. , Greenlees P. , Hilton J. , Julin R. , Juutinen S. , Konki J. , Li H. , Matta S. , Modamio V. , Singh B. S. Nara , Pakarinen J. , Papadakis P. , Partanen J. , Rahkila P. , Ruotsalainen P. , Sandzelius M. , Sarén J. , Scholey C. , Stolze S. , Subramaniam P. , Uusitalo J. , Valiente-Dobón J. J. 
Published: December 2023

AbstractThe electromagnetic transition probabilities of the yrast $$2^+$$

2
+

states in the midshell Te isotopes, two protons above the closed shell at Sn, are of great importance for the understanding of nuclear collectivity in these isotopes and the role played by the neutron-proton interactions and cross-shell excitations. However, the large uncertainty of the experimental data for the midshell nucleus 118Te and the missing data for 116Te make it difficult to pin down the general trend of the evolution of transition probabilities as a function of the neutron number. In this work, the lifetime of the yrast $$2^+$$

2
+

state in 118Te was measured, with the aim of reducing the uncertainty of the previous measurement. The result is $$\tau _{2+}=7.46(19)$$

τ

2
+

=
7.46

(
19
)

ps. In addition, the lifetime of the $$4^+$$

4
+

state was measured to be $$\tau _{4+} = 4.25(23)$$

τ

4
+

=
4.25

(
23
)

ps. The experimental transition rates are extracted from the measured lifetimes and compared with systematic large-scale shell-model calculations. The trend of the $$B(\textrm{E2};0^+\rightarrow 2^+)$$

B
(
E2
;

0
+

→

2
+

)

values in the midshell area is in good agreement with the calculations and the calculated $$B_{4/2}$$

B

4
/
2

ratio provide evidence for 118Te as a near perfect harmonic vibrator.
Phospholipase PLCE1 Promotes Transcription and Phosphorylation of MCM7 to Drive Tumor Progression in Esophageal Cancer
Authors: Shi Qi , Xu Guixuan , Jiang Yuliang , Yang Ju , Han Xueping , Wang Qian , Li Ya , Zhang Zhiyu , Wang Kaige , Peng Hao , Chen Fangfang , Ma Yandi , Zhao Linyue , Chen Yunzhao , Liu Zheng , Yang Lan , Jia Xingyuan , Wen Tao , Tong Zhaohui , Cui Xiaobin , Li Feng 
Published: December 2023

Abstract

Phospholipase C epsilon 1 (PLCE1) is a well-established susceptibility gene for esophageal squamous cell carcinoma (ESCC). Identification of the underlying mechanism(s) regulated by PLCE1 could lead to a better understanding of ESCC tumorigenesis. In this study, we found that PLCE1 enhances tumor progression by regulating the replicative helicase MCM7 via two pathways. PLCE1 activated PKCα-mediated phosphorylation of E2F1, which led to the transcriptional activation of MCM7 and miR-106b-5p. The increased expression of miR-106b-5p, located in intron 13 of MCM7, suppressed autophagy and apoptosis by targeting Beclin-1 and RBL2, respectively. Moreover, MCM7 cooperated with the miR-106b-25 cluster to promote PLCE1-dependent cell-cycle progression both in vivo and in vitro. In addition, PLCE1 potentiated the phosphorylation of MCM7 at six threonine residues by the atypical kinase RIOK2, which promoted MCM complex assembly, chromatin loading, and cell-cycle progression. Inhibition of PLCE1 or RIOK2 hampered MCM7-mediated DNA replication, resulting in G1–S arrest. Furthermore, MCM7 overexpression in ESCC correlated with poor patient survival. Overall, these findings provide insights into the role of PLCE1 as an oncogenic regulator, a promising prognostic biomarker, and a potential therapeutic target in ESCC.

Significance:
PLCE1 promotes tumor progression in ESCC by activating PKCα-mediated phosphorylation of E2F1 to upregulate MCM7 and miR-106b-5p expression and by potentiating MCM7 phosphorylation by RIOK2.
Spatial Sensory References for Vestibular Self-Motion Perception
Authors: Zanchi Silvia , Cuturi Luigi F. , Sandini Giulio , Gori Monica , Ferrè Elisa R. 
Published: December 2023

Abstract
While navigating through the surroundings, we constantly rely on inertial vestibular signals for self-motion along with visual and acoustic spatial references from the environment. However, the interaction between inertial cues and environmental spatial references is not yet fully understood. Here we investigated whether vestibular self-motion sensitivity is influenced by sensory spatial references. Healthy participants were administered a Vestibular Self-Motion Detection Task in which they were asked to detect vestibular self-motion sensations induced by low-intensity Galvanic Vestibular Stimulation. Participants performed this detection task with or without an external visual or acoustic spatial reference placed directly in front of them. We computed the d prime () as a measure of participants’ vestibular sensitivity and the criterion as an index of their response bias. Results showed that the visual spatial reference increased sensitivity to detect vestibular self-motion. Conversely, the acoustic spatial reference did not influence self-motion sensitivity. Both visual and auditory spatial references did not cause changes in response bias. Environmental visual spatial references provide relevant information to enhance our ability to perceive inertial self-motion cues, suggesting a specific interaction between visual and vestibular systems in self-motion perception.