bluuebunny/crossref_metadata_2025_split huggingface dataset:
Greenhouse gas emissions from sandy soils amended with lime and gypsum under different initial soil pH and nitrogen sources
Authors: Ribeiro Pablo Lacerda , Hamta Zainuddin , Mühling Karl Hermann 
Published: July 2024

AbstractLime (CaCO3) application has led to an inconsistent mitigation of greenhouse gas emissions (GHGs) from agricultural soils. In addition, only a few studies have investigated the impact of gypsum (CaSO4) on the release of GHGs. Therefore, here we investigated the impact of initial soil pH and nitrogen sources on CaSO4 and CaCO3 effectiveness in reducing the production of GHGs. We hypothesized that (i) liming presents the highest effectiveness in reducing GHGs when performed in acidic soil and under NO3−‐N fertilizer application, and (ii) application of CaSO4 is not effective in reducing GHG irrespective of the initial soil pH or nitrogen (N) source. Firstly, an incubation experiment was carried out to evaluate the effect of initial soil pH using acidic soil and neutral soil amended with CaSO4 and CaCO3. Subsequently, a second incubation experiment was conducted to investigate the effect of N source by applying calcium nitrate and urea in an acidic soil amended with CaSO4, CaCO3 and CaSO4 + CaCO3. The measured variables were soil , daily and cumulative emissions of N2O‐N, CO2‐C and CH4‐C, as well as NH4+‐N and NO3−‐N concentrations. CaCO3 did not affect N2O‐N emission under neutral soil pH, and NO3−‐N fertilizer application. However, CaCO3 increased N2O‐N release under acidic soil (+96%), and urea fertilizer application (+97%). Furthermore, CaCO3 and CaSO4 reduced CO2‐C emission from the neutral pH soil by 31%, and CaSO4 decreased the mean cumulative N2O‐N release from the soil fertilized with urea‐N by 43%. In conclusion, this study did not confirm liming as an alternative to reduce N2O‐N release under different initial soil pH and N sources. Furthermore, our results indicated that CaSO4 may decrease GHG emissions. Finally, these results suggest caution for considering liming as a strategy to mitigate N2O‐N emission from agriculture.
Spatial and temporal heterogeneity of land surface phenology in Shanxi Province from 2001 to 2020
Authors: Zhao Haipeng , Deng Xiangzheng , Wang Zehao 
Published: July 2024

AbstractLand surface phenology encompasses variations in the life cycle events of plants induced by seasonal changes in environmental factors, primarily meteorological conditions. This study leverages Google Earth Engine to extract a comprehensive time series of two‐band Enhanced Vegetation Index (EVI 2) from Landsat images. Utilizing relatively sparse data spanning from 2001 to 2020, a Bayesian hierarchical model is applied at a 30 m resolution to capture the continuous temporal evolution of phenology. The fitting results of this study demonstrate excellent performance, with annual correlation coefficients consistently exceeding 0.89. The findings indicate that between 2001 and 2020, the Start of Season in Shanxi advanced by an average of 0.79 days per year, the End of Season was delayed by an average of 0.83 days per year, and the Length of Season (LOS) extended by an average of 0.80 days per year. Spatial disparities in phenological periods in Shanxi are evident, with an average LOS of 192 days on 35–36° N and only 122 days on 40–41° N. Below 1200 m, phenological periods exhibit significant changes influenced by human activities, while between 1200 m and 2600 m, LOS shows a weak trend of shortening. Above 2600 m, there is a noticeable reduction in LOS. With an increasing slope, LOS increases from an average of 175 days to 187 days (>25°). This study, utilizing Shanxi as a case study, explores the spatiotemporal evolution characteristics of vegetation phenology, aiming to support fine land management and enhance agricultural productivity.
Evaluation of oral herpes simplex virus shedding among solid organ transplant recipients: A pilot study
Authors: Fischer Molly D. , Green Margaret L. , Selke Stacy , Limaye Ajit P. , Wald Anna , Boeckh Michael J. , Phipps Amanda I. , Pergam Steven A. , Johnston Christine 
Published: July 2024

AbstractBackgroundHerpes simplex viruses (HSVs) frequently reactivate during immunosuppression and may be a risk factor for adverse outcomes after solid organ transplant (SOT). While suppressive antiviral therapy reduces the risk of symptomatic HSV reactivation, the kinetics of asymptomatic viral shedding with chronic immunosuppression after transplant are not well understood. We report the characteristics of oral HSV shedding among 15 HSV‐1 seropositive SOT recipients (n = 8 liver, n = 7 kidney, median age 58.5 years, median 20 months post‐transplant) who were not taking daily antiviral suppressive therapy.MethodsParticipants self‐collected oral swabs three times daily for 6 weeks for HSV quantification and recorded the presence of oral symptoms or lesions in a diary.ResultsSample collection adherence was high (median 122 swabs/person, range: 85.7%–101.6% of expected swabs). Most participants (n = 12, 80%) experienced at least one shedding episode, with a median shedding rate of 8.9% (range: 0%–33.6%). There were 32 total shedding episodes, 24 (75%) of which occurred without symptoms or lesions. For episodes of known duration, the median length was 21.8 hrs (interquartile range: 10.8–46.1 hrs).ConclusionMost shedding episodes (78.1%) lasted >12 hrs, suggesting that twice‐daily sampling may be sufficient to detect most episodes. These data show that self‐collection of oral swabs is feasible for patients who have undergone SOTs and can provide insight into the frequency of oral HSV reactivation, which can be used to design future studies in this population.
Clinical approach to donor‐derived infection in solid organ transplant recipients
Authors: Phadke Varun K. 
Published: July 2024

AbstractDonor‐derived infection is an uncommon but potentially devastating complication of solid organ transplantation (SOT). Accurate and timely identification of unexpected infectious disease transmission events has implications not only for the recipient(s) experiencing infection, but also other recipients of organs or tissues from the same donor who may require additional testing or risk mitigation, as well as the broader organ transplant regulatory framework. This narrative review synthesizes data from published reports of symptomatic unexpected donor‐derived infections in SOT recipients to provide clinicians with a systematic approach to the evaluation of undifferentiated illnesses that may be of donor origin. Key reasons to consider donor‐derived infection include certain microbiologically proven infections in the recipient, especially early after transplant, characteristics of the donor or their management that suggest potential exposure to or infection with specific pathogens prior to organ procurement, and select clinical syndromes that occur in the post‐transplant period. Syndromes for which expedited consideration and evaluation of donor‐derived infection may be warranted include central nervous system infection, graft or perigraft complications developing in the absence of typical risk factors, and unexplained critical illness/sepsis syndrome in the early post‐transplant period. When embarking on an investigation of a suspected donor‐derived infection, clinicians should apply knowledge of the entire continuum of the organ procurement and transplant process to ensure unbiased and comprehensive data collection that will facilitate appropriate adjudication of these uncommon but high‐consequence events.
Canine corneal endothelial cell analysis using vital dyes and light microscopy
Authors: Soueid Yamit , Baransy Shaden , Goncharov Yulia , Keinan Yael , Sebbag Lionel 
Published: July 2024

AbstractPurposeTo evaluate the use of vital dyes and light microscopy for assessing canine corneal endothelial morphology ex vivo.MethodsThe corneas of 40 canine eyes (n = 20 dogs) enucleated <24 h following euthanasia or death were isolated and flat‐mounted on a slide. Corneal endothelium was stained via 0.25% trypan blue followed by 0.5% alizarin red (pH 4.2), photographed, then the following morphological features were calculated using ImageJ: mean cell density (MCD), mean cell area (MCA), polymegathism (coefficient of variation of cell area), and pleomorphism (% hexagonality).ResultsMean ± standard deviation (range) outcomes were: MCD, 2544 ± 541 cells/mm2 (1750–3922 cells/mm2); MCA, 431 ± 97 μm2 (251–626 μm2); polymegathism, 17 ± 2% (14%–22%); pleomorphism, 84 ± 3% (80%–90%). No significant differences (p ≥ .122) were noted for any outcome between male versus female or brachycephalic versus non‐brachycephalic dogs. Young dogs (<10 years) had lower MCA (p = .044), lower pleomorphism (p = .003), and higher MCD (p = .035) when compared to older dogs (≥10 years). Age was significantly (p ≤ .049) correlated with MCA (r = 0.467), MCD (r = −0.476), polymegathism (r = 0.444), and pleomorphism (r = 0.609).ConclusionsThe combination of vital dyes and light microscopy allowed for clear visualization and evaluation of the corneal endothelium in canine eyes ex vivo. Our findings can be used in future studies to deepen our understanding of the corneal endothelium in health and disease.
Comparative Study of Machine Learning Methods for State of Health Estimation of Maritime Battery Systems
Authors: Grindheim Christian Alm , Stakkeland Morten , Glad Ingrid Kristine , Vanem Erik 
Published: July 2024

Abstract
This paper tests two data-driven approaches for predicting the state of health (SOH) of lithium-ion-batteries (LIBs) for the purpose of monitoring maritime battery systems. First, non-sequential approaches are investigated and various models are tested: ridge, lasso, support vector regression, and gradient boosted trees. Binning is proposed for feature engineering for these types of models to capture the temporal structure in the data. Such binning creates histograms for the accumulated time the LIB has been within various voltage, temperature, and current ranges. Further binning to combine these histograms into 2D or 3D histograms is explored in order to capture relationships between voltage, temperature, and current. Second, a sequential approach is explored where different deep learning architectures are tried out: long short-term memory, transformer, and temporal convolutional network. Finally, the various models and the two approaches are compared in terms of their SOH prediction ability. Results indicate that the binning with ridge regression models performed best. The same publicly available sensor data from laboratory cycling tests are used for both approaches.
Modeling Development of a Receiver–Reactor of Type R2Mx for Thermochemical Water Splitting
Authors: Vega Puga Estefanía , Brendelberger Stefan , Weber Anika , Sattler Christian 
Published: July 2024

Abstract
This work reports on the development of a transient heat transfer model for a prototype reactor of type R2Mx for thermochemical water splitting by temperature and pressure swing of ceria. Key aspects of the R2Mx concept, which are also incorporated in the prototype design, include a movable monolithic redox structure combined with a linear transport system, a reduction reactor, as well as a dedicated oxidation reactor. With the model, the operation of the prototype is simulated for consecutive water splitting cycles, in which ceria is reduced in a continuously heated reactor, oxidized in a separate oxidation reactor, and transported in between the reaction zones. A 2D axisymmetric numerical model of the prototype reactor was developed in ansys mechanical. The model includes heat transfer calculations in combination with an approximated simulation of the transport of the redox material during cyclic operation. It incorporates the chemical reaction by means of a modified heat capacity for ceria and accounts for internal radiation heat transfer inside the porous redox material by applying effective heat transfer properties. A parametric analysis has been undertaken to evaluate different modes of operation of the oxidation reactor. Model results are used to size the power demand of the reduction reactor and vacuum pump, to define durations of the process steps, as well as to assess operational parameters with respect to achieved temperatures. Findings suggest that suitable operation of the prototype reactor involves reduction durations ranging from 8 to 10 min and oxidations of 6 to 10 min.
Automated Classification of Manual Exploratory Behaviors Using Sensorized Objects and Machine Learning: A Preliminary Proof-of-Concept Study
Authors: Patel Priya , Pandya Harsh , Ranganathan Rajiv , Lee Mei-Hua 
Published: July 2024

Manual exploratory behaviors during object interaction that form the basis of tool use behavior, are mostly qualitatively characterized in terms of their frequency and duration of occurrence. To fully understand their functional and clinical significance, quantitative movement characterization is needed alongside their qualitative analysis. However, there are two challenges in quantifying them—(a) reliably classifying the type of movement and (b) performing this classification on a time series automatically. Here, we propose a machine learning-based classification method to address these challenges. We measured three common exploratory behaviors (object rotation, fingering, and throwing) in college-aged adults using “sensorized objects” that had wireless Inertial Measurement Units embedded in them. We then calculated several statistical features based on linear acceleration and angular velocity data to train machine learning classifiers to identify these behaviors. All classifiers identified the behaviors with a substantially higher accuracy (average accuracy = 84.95 ± 4.16%) than chance level (33.33%). Of all models tested, Support Vector Machine Quadratic, Support Vector Machine Medium Gaussian, and Narrow Neural Network were the best models in classifying the three behaviors (average accuracy = 89.34 ± 0.12%). This classification method shows potential for automating movement characterization of exploratory behaviors, thereby may aid early assessment of neurodevelopmental disorders.
Glyphosate effects on growth and biofilm formation in bee gut symbionts and diverse associated bacteria
Authors: Motta Erick V. S. , de Jong Tyler K. , Gage Alejandra , Edwards Joseph A. , Moran Nancy A. 
Published: July 2024

ABSTRACT

Biofilm formation is a common adaptation enabling bacteria to thrive in various environments and withstand external pressures. In the context of host–microbe interactions, biofilms play vital roles in establishing microbiomes associated with animals and plants and are used by opportunistic microbes to facilitate survival within hosts. Investigating biofilm dynamics, composition, and responses to environmental stressors is crucial for understanding microbial community assembly and biofilm regulation in health and disease. In this study, we explore
in vivo
colonization and
in vitro
biofilm formation abilities of core members of the honey bee (
Apis mellifera
) gut microbiota. Additionally, we assess the impact of glyphosate, a widely used herbicide with antimicrobial properties, and a glyphosate-based herbicide formulation on growth and biofilm formation in bee gut symbionts as well as in other biofilm-forming bacteria associated with diverse animals and plants. Our results demonstrate that several strains of core bee gut bacterial species can colonize the bee gut, which probably depends on their ability to form biofilms. Furthermore, glyphosate exposure elicits variable effects on bacterial growth and biofilm formation. In some instances, the effects correlate with the bacteria’s ability to encode a susceptible or tolerant version of the enzyme inhibited by glyphosate in the shikimate pathway. However, in other instances, no such correlation is observed. Testing the herbicide formulation further complicates comparisons, as results often diverge from glyphosate exposure alone, suggesting that co-formulants influence bacterial growth and biofilm formation. These findings highlight the nuanced impacts of environmental stressors on microbial biofilms, with both ecological and host health-related implications.

IMPORTANCE

Biofilms are essential for microbial communities to establish and thrive in diverse environments. In the honey bee gut, the core microbiota member
Snodgrassella alvi
forms biofilms, potentially aiding the establishment of other members and promoting interactions with the host. In this study, we show that specific strains of other core members, including
Bifidobacterium
,
Bombilactobacillus
,
Gilliamella
, and
Lactobacillus
, also form biofilms
in vitro
. We then examine the impact of glyphosate, a widely used herbicide that can disrupt the bee microbiota, on bacterial growth and biofilm formation. Our findings demonstrate the diverse effects of glyphosate on biofilm formation, ranging from inhibition to enhancement, reflecting observations in other beneficial or pathogenic bacteria associated with animals and plants. Thus, glyphosate exposure may influence bacterial growth and biofilm formation, potentially shaping microbial establishment on host surfaces and impacting health outcomes.
Promoting public engagement in interdisciplinary biological systems education by leveraging American sports-inspired bracket contests on social media and web
Authors: Myer Phillip R. , Blair Susan , Mason Katie M. , Shepherd Elizabeth A. , Downey Blair C. , McLean Kyle J. , Rowan Troy N. , Eckelkamp Elizabeth A. , Schrick F. Neal , Zambito Ivey Jennie L. 
Published: July 2024

ABSTRACT

The complexity of modern biology poses challenges in fostering interdisciplinary understanding, particularly between practicing scientists and the public. Furthermore, scientists often lack formal training in science communication, despite various motivations to engage the public. The science literacy of the public in the biological sciences can also vary across socio-economic and cultural backgrounds. Leveraging popular culture and informal learning practices to promote active learning offers promising avenues to enhance public understanding of biological systems. Organized sports hold collective recognition across various communities and cultures, serving as a means to bring people together. Notably, the NCAA March Madness event holds widespread national and international popularity, presenting an opportunity to laterally apply this concept to promote science communication within STEM and biology education. An educational social media and web-based contest tool was developed integrating NCAA-inspired brackets with animal biological systems concepts. The tool featured tournament-style matchups based on animal biological systems, interesting animal facts, and a voting system, all housed within a user-friendly interface. To encourage regular user access to the tool, graphic designs were developed for all social media posts to aid in visual recruitment to the voting website. Based on online metrics, the use of social media garnered repeat users across both the public and educators. The latter noted the tool’s simplicity and informative content. Application of this social media and web-based bracket contest tool, which leverages informal settings for active learning for use in biology education, can foster science communication to engage audiences, improve comprehension, and promote interdisciplinary biology education.
Structure and
in vivo
psoralen DNA crosslink repair activity of mycobacterial Nei2
Authors: Warren Garrett M. , Shuman Stewart 
Published: July 2024

ABSTRACT

Mycobacterium smegmatis
Nei2 is a monomeric enzyme with AP β-lyase activity on single-stranded DNA. Expression of Nei2, and its operonic neighbor Lhr (a tetrameric 3′-to-5′ helicase), is induced in mycobacteria exposed to DNA damaging agents. Here, we find that
nei2
deletion sensitizes
M. smegmatis
to killing by DNA inter-strand crosslinker trimethylpsoralen but not to crosslinkers mitomycin C and cisplatin. By contrast, deletion of
lhr
sensitizes to killing by all three crosslinking agents. We report a 1.45 Å crystal structure of recombinant Nei2, which is composed of N and C terminal lobes flanking a central groove suitable for DNA binding. The C lobe includes a tetracysteine zinc complex. Mutational analysis identifies the N-terminal proline residue (Pro2 of the ORF) and Lys51, but not Glu3, as essential for AP lyase activity. We find that Nei2 has 5-hydroxyuracil glycosylase activity on single-stranded DNA that is effaced by alanine mutations of Glu3 and Lys51 but not Pro2. Testing complementation of psoralen sensitivity by expression of wild-type and mutant
nei2
alleles in ∆
nei2
cells established that AP lyase activity is neither sufficient nor essential for crosslink repair. By contrast, complementation of psoralen sensitivity of ∆
lhr
cells by mutant
lhr
alleles depended on Lhr’s ATPase/helicase activities and its tetrameric quaternary structure. The
lhr–nei2
operon comprises a unique bacterial system to rectify inter-strand crosslinks.

IMPORTANCE

The DNA inter-strand crosslinking agents mitomycin C, cisplatin, and psoralen–UVA are used clinically for the treatment of cancers and skin diseases; they have been invaluable in elucidating the pathways of inter-strand crosslink repair in eukaryal systems. Whereas DNA crosslinkers are known to trigger a DNA damage response in bacteria, the roster of bacterial crosslink repair factors is incomplete and likely to vary among taxa. This study implicates the DNA damage-inducible mycobacterial
lhr–nei2
gene operon in protecting
Mycobacterium smegmatis
from killing by inter-strand crosslinkers. Whereas interdicting the activity of the Lhr helicase sensitizes mycobacteria to mitomycin C, cisplatin, and psoralen–UVA, the Nei2 glycosylase functions uniquely in evasion of damage caused by psoralen–UVA.
Complete genome of
Allorhizobium
(previously
Agrobacterium
)
vitis
strain CG957=AA25 from Afghanistan
Authors: Gan Han Ming , Liew Li Yuan , Savka Michael A. 
Published: July 2024

ABSTRACT

Using Nanopore Q20+ sequencing, we report the complete genome of
Allorhizobium
(
Agrobacterium
)
vitis
strain CG957=AA25, isolated nearly 40 years ago from a grapevine crown gall in Afghanistan. The assembled genome size is 6 Mb, comprising a circular chromosome, a linear chromid, a Ti plasmid, and two non-Ti plasmids.