bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cerebro-cerebellar network for learning visuomotor associations
Authors: Sendhilnathan Naveen , Bostan Andreea C. , Strick Peter L. , Goldberg Michael E. 
Published: March 2024

AbstractConsensus is rapidly building to support a role for the cerebellum beyond motor function, but its contributions to non-motor learning remain poorly understood. Here, we provide behavioral, anatomical and computational evidence to demonstrate a causal role for the primate posterior lateral cerebellum in learning new visuomotor associations. Reversible inactivation of the posterior lateral cerebellum of male monkeys impeded the learning of new visuomotor associations, but had no effect on movement parameters, or on well-practiced performance of the same task. Using retrograde transneuronal transport of rabies virus, we identified a distinct cerebro-cerebellar network linking Purkinje cells in the posterior lateral cerebellum with a region of the prefrontal cortex that is critical in learning visuomotor associations. Together, these results demonstrate a causal role for the primate posterior lateral cerebellum in non-motor, reinforcement learning.
Dynamics of the charge transfer to solvent process in aqueous iodide
Authors: Lan Jinggang , Chergui Majed , Pasquarello Alfredo 
Published: March 2024

AbstractCharge-transfer-to-solvent states in aqueous halides are ideal systems for studying the electron-transfer dynamics to the solvent involving a complex interplay between electronic excitation and solvent polarization. Despite extensive experimental investigations, a full picture of the charge-transfer-to-solvent dynamics has remained elusive. Here, we visualise the intricate interplay between the dynamics of the electron and the solvent polarization occurring in this process. Through the combined use of ab initio molecular dynamics and machine learning methods, we investigate the structure, dynamics and free energy as the excited electron evolves through the charge-transfer-to-solvent process, which we characterize as a sequence of states denoted charge-transfer-to-solvent, contact-pair, solvent-separated, and hydrated electron states, depending on the distance between the iodine and the excited electron. Our assignment of the charge-transfer-to-solvent states is supported by the good agreement between calculated and measured vertical binding energies. Our results reveal the charge transfer process in terms of the underlying atomic processes and mechanisms.
Coherent phonon and unconventional carriers in the magnetic kagome metal Fe3Sn2
Authors: Gonçalves-Faria Marcos V. , Pashkin Alexej , Wang Qi , Lei Hechang C. , Winnerl Stephan , Tsirlin Alexander A. , Helm Manfred , Uykur Ece 
Published: March 2024

AbstractTemperature- and fluence-dependent carrier dynamics of the magnetic kagome metal Fe3Sn2 were studied using the ultrafast optical pump-probe technique. Two carrier relaxation processes and a laser-induced coherent optical phonon were observed. We ascribe the shorter relaxation (~1 ps) to hot electrons transferring their energy to the crystal lattice via electron–phonon scattering. The second relaxation (~30 ps), on the other hand, cannot be explained as a conventional process, and we attributed it to the unconventional (localized) carriers in the material. The observed coherent oscillation is assigned to be a totally symmetric A1g optical phonon dominated by Sn displacements out of the kagome planes and possesses a prominently large amplitude, on the order of 10−3, comparable to the maximum of the reflectivity change (ΔR/R). This amplitude is similar to what has been observed for coherent phonons in charge-density-wave (CDW) systems, although no signs of such instability were hitherto reported in Fe3Sn2. Our results suggest an unexpected connection between Fe3Sn2 and kagome metals with CDW instabilities and a strong interplay between phonon and electron dynamics in this compound.
Expert review of the science underlying nature-based climate solutions
Authors: Buma B. , Gordon D. R. , Kleisner K. M. , Bartuska A. , Bidlack A. , DeFries R. , Ellis P. , Friedlingstein P. , Metzger S. , Morgan G. , Novick K. , Sanchirico J. N. , Collins J. R. , Eagle A. J. , Fujita R. , Holst E. , Lavallee J. M. , Lubowski R. N. , Melikov C. , Moore L. A. , Oldfield E. E. , Paltseva J. , Raffeld A. M. , Randazzo N. A. , Schneider C. , Uludere Aragon N. , Hamburg S. P. 
Published: March 2024

AbstractViable nature-based climate solutions (NbCS) are needed to achieve climate goals expressed in international agreements like the Paris Accord. Many NbCS pathways have strong scientific foundations and can deliver meaningful climate benefits but effective mitigation is undermined by pathways with less scientific certainty. Here we couple an extensive literature review with an expert elicitation on 43 pathways and find that at present the most used pathways, such as tropical forest conservation, have a solid scientific basis for mitigation. However, the experts suggested that some pathways, many with carbon credit eligibility and market activity, remain uncertain in terms of their climate mitigation efficacy. Sources of uncertainty include incomplete GHG measurement and accounting. We recommend focusing on resolving those uncertainties before broadly scaling implementation of those pathways in quantitative emission or sequestration mitigation plans. If appropriate, those pathways should be supported for their cobenefits, such as biodiversity and food security.
DiagSet: a dataset for prostate cancer histopathological image classification
Authors: Koziarski Michał , Cyganek Bogusław , Niedziela Przemysław , Olborski Bogusław , Antosz Zbigniew , Żydak Marcin , Kwolek Bogdan , Wąsowicz Paweł , Bukała Andrzej , Swadźba Jakub , Sitkowski Piotr 
Published: March 2024

AbstractCancer diseases constitute one of the most significant societal challenges. In this paper, we introduce a novel histopathological dataset for prostate cancer detection. The proposed dataset, consisting of over 2.6 million tissue patches extracted from 430 fully annotated scans, 4675 scans with assigned binary diagnoses, and 46 scans with diagnoses independently provided by a group of histopathologists can be found at https://github.com/michalkoziarski/DiagSet. Furthermore, we propose a machine learning framework for detection of cancerous tissue regions and prediction of scan-level diagnosis, utilizing thresholding to abstain from the decision in uncertain cases. The proposed approach, composed of ensembles of deep neural networks operating on the histopathological scans at different scales, achieves 94.6% accuracy in patch-level recognition and is compared in a scan-level diagnosis with 9 human histopathologists showing high statistical agreement.
Efficient and high-quality absorption enhancement using epsilon-near-zero cylindrical nano-shells constructed by graphene
Authors: Raad Shiva Hayati , Afshari-Bavil Mehdi , Liu Dong 
Published: March 2024

AbstractThis paper presents a detailed scattering analysis of a hollow-core plasmonic-shell cylindrical wire to design an efficient, compact, narrowband, and reconfigurable optical absorber. The shell is formed by a thin graphene material, investigated in its epsilon-near-zero (ENZ) plasmonic region. Compared to the graphene plasmonic resonances in the terahertz(THz)/far-infrared (FIR) frequencies, the ENZ plasmonic resonances offer a blue shift in the operating frequency of the second-order plasmonic resonances by increasing the geometrical dimensions. This feature is successfully used to design efficient optical wave absorbers with absorption cross-sections much larger than geometrical and scattering cross-sections. The observed blue shift in the resonance spectrum, which is the key point of the design, is further verified by defining each particle with its polarizability and fulfilling the resonant scattering condition in the framework of Mie’s theory. Furthermore, graphene relaxation time and chemical potential can be used to manipulate the absorption rate. Observed resonances have narrow widths, achieved with simple geometry. To consider more practical scenarios, the one-dimensional arrangement of the cylindrical elements as a dense and sparse array is also considered and the design key point regarding graphene quality is revealed. The quality factor of the sparse array resonance is 2272.8 and it demands high-quality graphene material in design. It is also observed that due to the use of small particles in the design, the near-field and cooperative effects are not visible in the absorption cross-section of the array and a clear single peak is attained. This polarization-insensitive absorber can tolerate a wide range of incident angles with an absorption rate above 90%.
Cross-sectional and longitudinal analyses of urinary extracellular vesicle mRNA markers in urothelial bladder cancer patients
Authors: Murakami Taku , Minami Keita , Harabayashi Toru , Maruyama Satoru , Takada Norikata , Kashiwagi Akira , Miyata Haruka , Sato Yasuyuki , Matsumoto Ryuji , Kikuchi Hiroshi , Abe Takashige , Ito Yoichi M. , Murai Sachiyo , Shinohara Nobuo , Harada Hiroshi , Osawa Takahiro 
Published: March 2024

AbstractWe designed this multi-center prospective study with the following objectives: (1) the cross-sectional validation of extracellular vesicles (EV) mRNA markers to detect urothelial bladder cancer (UBC) before transurethral resection of bladder cancer (TURBT), and (2) the longitudinal validation of EV mRNA markers to monitor non-muscle invasive bladder cancer (NMIBC) recurrence after TURBT. EV mRNA markers evaluated in this study were KRT17, GPRC5A, and SLC2A1 in addition to two additional markers from literatures, MDK and CXCR2, and measured by quantitative RT-PCR with normalization by a reference gene (ALDOB). Diagnostic performances of EV mRNA markers were compared to conventional markers. Regarding the first objective, we confirmed that EV mRNA biomarkers in urine were higher in UBC patients, particularly those with higher stage/grade tumors, than in those without UBC (n = 278 in total) and the diagnostic performance of EV mRNA MDK and KRT17 outperformed conventional biomarkers with AUC 0.760 and 0.730, respectively. Concerning the second objective, we prospectively analyzed the time courses of EV mRNA markers while NMIBC patients (n = 189) (median follow-up 19 months). The expression of EV mRNA KRT17 was significantly high in patients with recurrence, while it gradually decreased over time in those without recurrence (p < 0.01).
N-benzyl-N-methyldecan-1-amine, derived from garlic, and its derivative alleviate 2,4-dinitrochlorobenzene-induced atopic dermatitis-like skin lesions in mice
Authors: Kim Ji Eun , Budluang Phatcharaporn , Park Jumin , Lee Kon Ho , Pakdeepromma Sirichatnach , Kaewpiboon Chutima , Kang Ho Young , Hwang Dae Youn , Chung Young-Hwa 
Published: March 2024

AbstractGiven the intricate etiology and pathogenesis of atopic dermatitis (AD), the complete cure of AD remains challenging. This study aimed to investigate if topically applying N-benzyl-N-methyldecan-1-amine (BMDA), derived from garlic, and its derivative [decyl-(4-methoxy-benzyl)-methyl-1-amine] (DMMA) could effectively alleviate AD-like skin lesions in 2,4-dinitrochlorobenzene (DNCB)-treated mice. Administering these compounds to the irritated skin of DNCB-treated mice significantly reduced swelling, rash, and excoriation severity, alongside a corresponding decrease in inflamed epidermis and dermis. Moreover, they inhibited spleen and lymph node enlargement and showed fewer infiltrated mast cells in the epidermis and dermis through toluidine-blue staining. Additionally, they led to a lower IgE titer in mouse sera as determined by ELISA, compared to vehicle treatment. Analyzing skin tissue from the mice revealed decreased transcript levels of inflammatory cytokines (TNF-α, IL-1β, and IL-6), IL-4, iNOS, and COX-2, compared to control mice. Simultaneously, the compounds impeded the activation of inflammation-related signaling molecules such as JNK, p38 MAPK, and NF-κB in the mouse skin. In summary, these findings suggest that BMDA and DMMA hold the potential to be developed as a novel treatment for healing inflammatory AD.
Analysis of the air stream flow parameters generated by the positive pressure ventilator—full scale experiment and CFD simulation
Authors: Kaczmarzyk Piotr , Małozięć Daniel , Burdzy Tomasz , Ziegler Bartosz , Krawiec Piotr , Dziechciarz Anna , Warguła Łukasz 
Published: March 2024

AbstractPositioning the positive pressure ventilator in front of the door opening affects the effectiveness of the rescue operation carried out during a fire. An important factor determining the effectiveness of the positive pressure ventilator is also the layout of the rooms within the gas exchange path and the obstacles present there. The purpose of this article is to assess the feasibility of using analyses such as large eddy simulation (LES) to verify the efficiency of mobile fans under simulation conditions, without the need for time-consuming experimentation (also for complex room volumes of buildings). The article presents a comparative analysis to assess the degree of convergence of flow parameters obtained during an experiment (in a multi-story building) and computational fluid dynamics (CFD) simulations. For volumetric flow rate, convergence was achieved at levels ranging from 0.4% (for 5 m) to 11.5% (1 m), and for pressure values, the differences achieved ranged from 0.6% (5 m) to 30.1% (4 m). This paper demonstrates that the LES model can be used to perform CFD simulations in the area of assessing the performance of a positive pressure ventilator. The article also describes a test methodology for determining the flow parameters of an air stream, which can be used to perform numerical simulations.
Training-related changes in neural beta oscillations associated with implicit and explicit motor sequence learning
Authors: Dyck Susanne , Klaes Christian 
Published: March 2024

AbstractMany motor actions we perform have a sequential nature while learning a motor sequence involves both implicit and explicit processes. In this work, we developed a task design where participants concurrently learn an implicit and an explicit motor sequence across five training sessions, with EEG recordings at sessions 1 and 5. This intra-subject approach allowed us to study training-induced behavioral and neural changes specific to the explicit and implicit components. Based on previous reports of beta power modulations in sensorimotor networks related to sequence learning, we focused our analysis on beta oscillations at motor-cortical sites. On a behavioral level, substantial performance gains were evident early in learning in the explicit condition, plus slower performance gains across training sessions in both explicit and implicit sequence learning. Consistent with the behavioral trends, we observed a training-related increase in beta power in both sequence learning conditions, while the explicit condition displayed stronger beta power suppression during early learning. The initially stronger beta suppression and subsequent increase in beta power specific to the explicit component, correlated with enhanced behavioral performance, possibly reflecting higher cortical excitability. Our study suggests an involvement of motor-cortical beta oscillations in the explicit component of motor sequence learning.
THOUSAND-GRAIN WEIGHT 6, which is an IAA-glucose hydrolase, preferentially recognizes the structure of the indole ring
Authors: Akabane Tatsuki , Suzuki Nobuhiro , Ikeda Kazuyoshi , Yonezawa Tomoki , Nagatoishi Satoru , Matsumura Hiroyoshi , Yoshizawa Takuya , Tsuchiya Wataru , Kamino Satoshi , Tsumoto Kouhei , Ishimaru Ken , Katoh Etsuko , Hirotsu Naoki 
Published: March 2024

AbstractAn indole-3-acetic acid (IAA)-glucose hydrolase, THOUSAND-GRAIN WEIGHT 6 (TGW6), negatively regulates the grain weight in rice. TGW6 has been used as a target for breeding increased rice yield. Moreover, the activity of TGW6 has been thought to involve auxin homeostasis, yet the details of this putative TGW6 activity remain unclear. Here, we show the three-dimensional structure and substrate preference of TGW6 using X-ray crystallography, thermal shift assays and fluorine nuclear magnetic resonance (19F NMR). The crystal structure of TGW6 was determined at 2.6 Å resolution and exhibited a six-bladed β-propeller structure. Thermal shift assays revealed that TGW6 preferably interacted with indole compounds among the tested substrates, enzyme products and their analogs. Further analysis using 19F NMR with 1,134 fluorinated fragments emphasized the importance of indole fragments in recognition by TGW6. Finally, docking simulation analyses of the substrate and related fragments in the presence of TGW6 supported the interaction specificity for indole compounds. Herein, we describe the structure and substrate preference of TGW6 for interacting with indole fragments during substrate recognition. Uncovering the molecular details of TGW6 activity will stimulate the use of this enzyme for increasing crop yields and contributes to functional studies of IAA glycoconjugate hydrolases in auxin homeostasis.
Occurrence of plant hormones in composts made from organic fraction of agri-food industry waste
Authors: Sienkiewicz Aneta , Krasowska Małgorzata , Kowczyk-Sadowy Małgorzata , Obidziński Sławomir , Piotrowska-Niczyporuk Alicja , Bajguz Andrzej 
Published: March 2024

AbstractUtilizing the organic fraction of agri-food industry waste for fertilization represents one approach to waste management, with composting emerging as a popular method. Composts derived from this waste may contain plant hormones alongside primary macronutrients. This study aimed to evaluate the content of plant hormones in composts crafted from the organic fraction of agri-food industry waste. The presence of these substances was ascertained using liquid chromatography–mass spectrometry (LC-MS) analysis, applied to extracted samples from three composts produced in a bioreactor and three obtained from companies. The results indicate the presence of 35 compounds, which belong to six types of plant hormones: auxins, cytokinins, gibberellins, brassinosteroids, abscisic acid, and salicylic acid, in composts for the first time. The highest amount of plant hormones was noted in buckwheat husk and biohumus extract (35 compounds), and the lowest in hemp chaff and apple pomace (14 compounds). Brassinosteroids (e.g., brassinolide, 28-homobrassinolide, 24-epicastasterone, 24-epibrassinolide, and 28-norbrassinolide) and auxins (e.g., indolilo-3-acetic acid) are dominant. The highest concentration of total phytohormones was reported in biohumus extract (2026.42 ng g−1dry weight), and the lowest in organic compost (0.18 ng g−1dry weight).
Growers’ perceptions and attitudes towards fungicide resistance extension services
Authors: Olita Toto , Stankovic Michelle , Sung Billy , Jones Megan , Gibberd Mark 
Published: March 2024

AbstractAgricultural extension services have been successful in promoting knowledge sharing and innovation in agriculture. However, the adoption of new agricultural practices, particularly in integrated pest management, has been slow. Using a case study with a co-designed survey instrument, this research aimed to understand how growers in the Southwest Western Australian Grainbelt access information and resources to manage fungicide resistance. We found that the growers rely on a combination of paid agronomists, government or research institutes, local grower groups, and field days for fungicide resistance information. Growers seek information from trusted experts who can simplify complex research, value easy-to-understand communication and prefer resources tailored to their local context. Additionally, growers valued information regarding new fungicide developments and having access to rapid fungicide resistance diagnostic services. These findings highlight the importance of providing growers with effective agricultural extension services to manage the risk of fungicide resistance.
Glucose tolerance test with a single abnormal value as a predictor of type 2 diabetes mellitus: a multicenter retrospective study
Authors: Lee Seon Ui , Hong Subeen , Choi Sae Kyung , Kim Su Mi , Shin Jae Eun , Kil Ki Cheol , Kim Yeon Hee , Wie Jeong Ha , Jo Yun Sung , Ko Hyun Sun 
Published: March 2024

AbstractClinical implication of a single abnormal value (SAV) in the 100 g oral glucose tolerance test during pregnancy has not been established. We aimed to evaluate the risk of postpartum type 2 diabetes mellitus (T2DM) and investigate adverse pregnancy outcomes in women with SAV, using a retrospective database, from seven medical centers of Korea. Based on the Carpenter-Coustan criteria using two-step approach, pregnancy and postpartum outcomes were compared, among normoglycemic, SAV, and gestational diabetes mellitus (GDM) groups. Among 9353 women, 342 (3.66%) and 418(4.47%) women were included in SAV and GDM groups, respectively. SAV and GDM groups showed significantly higher rates of postpartum T2DM than normoglycemic group (7.60%, 14.83%, and 1.82%, respectively, p < 0.001). And SAV group showed significantly higher rates of pregnancy associated hypertension, preterm birth, and neonatal hypoglycemia and sepsis, compared to normoglycemic group (neonatal sepsis, p = 0.008; the others, p < 0.001). In multivariate analysis, postpartum T2DM was associated with SAV, GDM (with/without insulin), nulliparity, pre-pregnancy BMI, chronic hypertension, hyperlipidemia, and DM family history. A scoring model to predict postpartum T2DM within 5 years, achieved an area under the curve of 0.74. This study demonstrated that not only GDM, but also SAV is a significant risk factor for postpartum T2DM.
A single laccase acts as a key component of environmental sensing in a broad host range fungal pathogen
Authors: Westrick Nathaniel M. , Dominguez Eddie G. , Bondy Madeline , Hull Christina M. , Smith Damon L. , Kabbage Mehdi 
Published: March 2024

AbstractSecreted laccases are important enzymes on a broad ecological scale for their role in mediating plant-microbe interactions, but within ascomycete fungi these enzymes have been primarily associated with melanin biosynthesis. In this study, a putatively secreted laccase, Sslac2, was characterized from the broad-host-range plant pathogen Sclerotinia sclerotiorum, which is largely unpigmented and is not dependent on melanogenesis for plant infection. Gene knockouts of Sslac2 demonstrate wide ranging developmental phenotypes and are functionally non-pathogenic. These mutants also displayed indiscriminate growth behaviors and enhanced biomass formation, seemingly as a result of their inability to respond to canonical environmental growth cues, a phenomenon further confirmed through chemical stress, physiological, and transcriptomic analyses. Transmission and scanning electron microscopy demonstrate apparent differences in extracellular matrix structure between WT and mutant strains that likely explain the inability of the mutants to respond to their environment. Targeting Sslac2 using host-induced gene silencing significantly improved resistance to S. sclerotiorum, suggesting that fungal laccases could be a valuable target of disease control. Collectively, we identified a laccase critical to the development and virulence of the broad-host-range pathogen S. sclerotiorum and propose a potentially novel role for fungal laccases in modulating environmental sensing.