bluuebunny/crossref_metadata_2025_split huggingface dataset:
Draft genome sequencing of
Naganishia
species isolated from the polar environments
Authors: Leo Patrick , Onofri Silvano , Zucconi Laura , Selbmann Laura , Turchetti Benedetta , Buzzini Pietro , Chander Atul M. , Simpson Anna , Singh Nitin , Vellone Daniel , Tighe Scott , Venkateswaran Kasthuri 
Published: September 2023

ABSTRACT

The draft genomes of five
Naganishia
strains were sequenced using MinION and annotated using Funannotate pipeline. Phylogenetic and genomic analyses were performed to provide their genetic relationships, diversity, and potential functional capabilities. This approach will aid in understanding their potential to survive under microgravity and their resilience to extreme environments.
Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development
Authors: Sieradzki Ella T. , Nuccio Erin E. , Pett-Ridge Jennifer , Firestone Mary K. 
Published: September 2023

ABSTRACT

Interactions between plant roots and rhizosphere bacteria modulate nitrogen (N)-cycling processes and create habitats rich in low molecular weight compounds (exudates) and complex organic molecules (decaying root litter) compared to those of bulk soil. Microbial N-cycling is regulated by edaphic conditions and genes from many interconnected metabolic pathways, but most studies of soil N-cycling gene expression have focused on single pathways. Currently, we lack a comprehensive understanding of the interplay between soil N-cycling gene regulation, spatial habitat, and time. We present results from a replicated time series of soil metatranscriptomes; we followed gene expression of multiple N transformations in four soil habitats (rhizosphere, detritusphere, rhizo-detritusphere, and bulk soil) during active root growth for the annual grass,
Avena fatua
. The presence of root litter and living roots significantly altered the trajectories of N-cycling gene expression. Upregulation of assimilatory nitrate reduction in the rhizosphere suggests that rhizosphere bacteria were actively competing with roots for nitrate. Simultaneously, ammonium assimilatory pathways were upregulated in both rhizosphere and detritusphere soil, which could have limited N availability to plants. The detritusphere supported dissimilatory processes DNRA and denitrification. Expression of nitrification genes was dominated by three phylotypes of
Thaumarchaeota
and was upregulated in bulk soil. Unidirectional ammonium assimilation and its regulatory genes (GS/GOGAT) were upregulated near relatively young roots and highly decayed root litter, suggesting N may have been limiting in these habitats (GS/GOGAT is typically activated under N limitation). Our comprehensive analysis indicates that differences in carbon and inorganic N availability control contemporaneous transcription of N-cycling pathways in soil habitats.

IMPORTANCE
Plant roots modulate microbial nitrogen (N) cycling by regulating the supply of root-derived carbon and nitrogen uptake. These differences in resource availability cause distinct micro-habitats to develop: soil near living roots, decaying roots, near both, or outside the direct influence of roots. While many environmental factors and genes control the microbial processes involved in the nitrogen cycle, most research has focused on single genes and pathways, neglecting the interactive effects these pathways have on each other. The processes controlled by these pathways determine consumption and production of N by soil microorganisms. We followed the expression of N-cycling genes in four soil microhabitats over a period of active root growth for an annual grass. We found that the presence of root litter and living roots significantly altered gene expression involved in multiple nitrogen pathways, as well as tradeoffs between pathways, which ultimately regulate N availability to plants.
The impact of Parkinson’s disease-associated gut microbiota on the transcriptome in
Drosophila
Authors: Liu Xin , Yang Meng , Liu Runzhou , Zhou Fan , Zhu Haibing , Wang Xiaoyun 
Published: September 2023

ABSTRACT

Parkinson’s disease (PD) is a common neurodegenerative disease in middle-aged and elderly people, and many studies have confirmed that the disorder of gut microbiota is involved in the pathophysiological process of PD. However, the molecular mechanism of gut microbiota in regulating the pathogenesis of PD is still lacking. In this study, to investigate the impact of PD-associated gut microbiota on host transcriptome, we established various PD models with fecal microbiota transplantation (FMT) in the model organism
Drosophila
followed by integrative data analysis of microbiome and transcriptome. We first constructed rotenone-induced PD models in
Drosophila
followed by FMT in different groups. Microbial analysis by 16S rDNA sequencing showed that gut microbiota from PD
Drosophila
could affect bacterial structure of normal
Drosophila
, and gut microbiota from normal
Drosophila
could affect bacterial structure of PD
Drosophila
. Transcriptome analysis revealed that PD-associated gut microbiota influenced expression patterns of genes enriched in neuroactive ligand-receptor interaction, lysosome, and diverse metabolic pathways. Importantly, to verify our findings, we transplanted
Drosophila
with fecal samples from clinical PD patients. Compared to the control,
Drosophila
transplanted with fecal samples from PD patients had reduced microbiota
Acetobacter
and
Lactobacillus
, and differentially expressed genes enriched in diverse metabolic pathways. In summary, our results reveal the influence of PD-associated gut microbiota on host gene expression, and this study can help better understand the link between gut microbiota and PD pathogenesis through gut-brain axis.

IMPORTANCE

Gut microbiota plays important roles in regulating host gene expression and physiology through complex mechanisms. Recently, it has been suggested that disorder of gut microbiota is involved in the pathophysiological process of Parkinson’s disease (PD). However, the molecular mechanism of gut microbiota in regulating the pathogenesis of PD is still lacking. In this study, to investigate the impact of PD-associated gut microbiota on host transcriptome, we established various PD models with fecal microbiota transplantation in the model organism
Drosophila
followed by integrative data analysis of microbiome and transcriptome. We also verified our findings by transplanting
Drosophila
with fecal samples from clinical PD patients. Our results demonstrated that PD-associated gut microbiota can induce differentially expressed genes enriched in diverse metabolic pathways. This study can help better understand the link between gut microbiota and PD pathogenesis through gut-brain axis.
The essential role of intestinal microbiota in cytomegalovirus reactivation
Authors: Kohda Chikara , Ino Satoshi , Ishikawa Hiroki , Kuno Yoshihiro , Nagashima Ryuichi , Iyoda Masayuki 
Published: September 2023

ABSTRACT
Human cytomegalovirus (HCMV) is a member of Herpesviridae. It has been reported that HCMV is reactivated in the breast milk of HCMV-seropositive lactating women. As we have reported various aspects of the roles of indigenous microbiota, its role in the murine CMV (MCMV) reactivation was examined in this study. MCMV was latently infected in the salivary gland, mammary tissues, and colon in the pregnant mice. When the salivary gland, mammary tissues, and colon were removed 5 days after delivery, MCMV reactivation of latent infection in each organ was confirmed by the detection of MCMV IE1 mRNA using reverse transcription-quantitative PCR. MCMV reactivation was observed in 100% of the mice during pregnancy. Next, for the elimination of intestinal microbiota, the pregnant mice were treated with low-dose or high-dose non-absorbable antibiotics. Although the numbers of aerobe/anaerobe in cecal content in low-dose antibiotic-treated mice were comparable to those in untreated controls, high-dose antibiotic treatment decreased the number of aerobe/anaerobe microbes from ca.9.0 Log10 to ca.3.0 Log10 (cfu/g). However, it could not be confirmed in 16S rRNA analysis that specific bacterial phylum or genus was eliminated by this high-dose treatment. Interestingly, MCMV reactivation was also observed in 100% of low-dose antibiotic-treated mice, whereas, in high-dose antibiotic-treated mice, MCMV reactivation was not observed in the salivary gland or colon. MCMV IE1 mRNA was detected only in 33% of the mammary tissues of those high-dose-treated mice. These results suggest that the indigenous microbiota played a crucial role in the reactivation of latent infection.

IMPORTANCE
Human cytomegalovirus (HCMV) infection via breast milk is a serious problem for very preterm infants such as developing a sepsis-like syndrome, cholestasis, or bronchopulmonary dysplasia, among others. It has been reported that HCMV is reactivated in the breast milk of HCMV-seropositive lactating women. In this study, the roles of indigenous microbiota in the murine CMV (MCMV) reactivation were examined using a mouse model. In MCMV latently infected mice, MCMV reactivation was observed in 100% of the mice during pregnancy. For the elimination of intestinal microbiota, MCMV-latent mice were treated with non-absorbable antibiotics. After delivery, MCMV reactivation was not observed in antibiotic-treated mice. This result suggested that the indigenous microbiota played a crucial role in the reactivation of latent infection.
Cellular localization of the hybrid pyruvate/2-oxoglutarate dehydrogenase complex in the actinobacteriumCorynebacterium glutamicum
Authors: Sundermeyer Lea , Folkerts Jan-Gerrit , Lückel Benita , Mack Christina , Baumgart Meike , Bott Michael 
Published: September 2023

ABSTRACTFor many bacterial proteins, specific localizations within the cell have been demonstrated, but enzymes involved in central metabolism are usually considered to be homogenously distributed within the cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex found in actinobacteria, the hybrid pyruvate/2-oxoglutarate dehydrogenase complex (PDH-ODH). In non-actinobacterial cells, PDH and ODH form separate multienzyme complexes of megadalton size composed of three different subunits, E1, E2, and E3. The actinobacterial PDH-ODH complex is composed of four subunits, AceE (E1p), AceF (E2p), Lpd (E3), and OdhA (E1oE2o). Using fluorescence microscopy, we observed that inCorynebacterium glutamicum, all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots are present at mid-cell. These results further confirm the existence of the hybrid complex. The unphosporylated OdhI protein, which binds to OdhA and inhibits ODH activity, was co-localized with OdhA at the poles, whereas phosphorylated OdhI, which does not bind OdhA, was distributed in the entire cytoplasm. Isocitrate dehydrogenase and glutamate dehydrogenase, both metabolically linked to ODH, were evenly distributed in the cytoplasm. Based on the available structural data for individual PDH-ODH subunits, a novel supramolecular architecture of the hybrid complex differing from classical PDH and ODH complexes has to be postulated. Our results suggest that localization at the poles or at mid-cell is most likely caused by nucleoid exclusion and results in a spatially organized metabolism in actinobacteria, with consequences yet to be studied.IMPORTANCEEnzymes involved in the central metabolism of bacteria are usually considered to be distributed within the entire cytoplasm. Here, we provide an example for a spatially defined localization of a unique enzyme complex of actinobacteria, the hybrid pyruvate dehydrogenase/2-oxoglutarate dehydrogenase (PDH-ODH) complex composed of four different subunits. Using fusions with mVenus or mCherry and fluorescence microscopy, we show that all four subunits are co-localized in distinct spots at the cell poles, and in larger cells, additional spots were observed at mid-cell. These results clearly support the presence of the hybrid PDH-ODH complex and suggest a similar localization in other actinobacteria. The observation of a defined spatial localization of an enzyme complex catalyzing two key reactions of central metabolism poses questions regarding possible consequences for the availability of substrates and products within the cell and other bacterial enzyme complexes showing similar behavior.
Prediction of mammalian virus cross-species transmission based on host proteins
Authors: Zhang Zheng , Lu Congyu , Mo Bocheng , Bai Kehan , Ge Xing-Yi , Deng Li , Peng Yousong 
Published: September 2023

ABSTRACT

Most emerging viruses are spilled over from mammals. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of newly emerging viruses. This study systematically investigated the host proteins associated with the cross-species transmission of mammalian viruses based on 1,271 pairs of virus-mammal interactions including 382 viruses from 33 viral families and 73 mammal species from 11 orders. Numerous host proteins were found to contribute to the cross-species transmission of mammalian viruses. Host proteins potentially contributing to virus cross-species transmission are specific to viral families, and few overlaps of such host proteins are observed in different viral families. Based on these host proteins, the random-forest (RF) models were built to predict the cross-species transmission potential of mammalian viruses. Moderate performance was obtained when using all viruses together. However, when modeling by viral family, the performance of the RF models varied much among viral families. In 13 viral families such as
Flaviviridae
,
Retroviridae,
and
Poxviridae
, the AUC of the RF model was greater than 0.8. Finally, the contribution of virus receptors to cross-species transmission was evaluated, and the virus receptor was found to have a minor effect in predicting the cross-species transmission of mammalian viruses. The study deepens our understanding of the mechanism of virus cross-species transmission and provides a framework for predicting the cross-species transmission of mammalian viruses.

IMPORTANCE
Emerging viruses pose serious threats to humans. Understanding the mechanism of virus cross-species transmission and identifying zoonotic viruses before their emergence are critical for the prevention and control of emerging viruses. This study systematically identified host factors associated with cross-species transmission of mammalian viruses and further built machine-learning models for predicting cross-species transmission of the viruses based on host factors including virus receptors. The study not only deepens our understanding of the mechanism of virus cross-species transmission but also provides a framework for predicting the cross-species transmission of mammalian viruses based on host factors.
Validating Synthetic Usage Data in Living Lab Environments
Authors: Breuer Timo , Fuhr Norbert , Schaer Philipp 
Published: September 2023

Evaluating retrieval performance without editorial relevance judgments is challenging, but instead, user interactions can be used as relevance signals. Living labs offer a way for small-scale platforms to validate information retrieval systems with real users. If enough user interaction data are available, then click models can be parameterized from historical sessions to evaluate systems before exposing users to experimental rankings. However, interaction data are sparse in living labs, and little is studied about how click models can be validated for reliable user simulations when click data are available in moderate amounts.
This work introduces an evaluation approach for validating synthetic usage data generated by click models in data-sparse human-in-the-loop environments like living labs. We ground our methodology on the click model’s estimates about a system ranking compared to a reference ranking for which the relative performance is known. Our experiments compare different click models and their reliability and robustness as more session log data become available. In our setup, simple click models can reliably determine the relative system performance with already 20 logged sessions for 50 queries. In contrast, more complex click models require more session data for reliable estimates, but they are a better choice in simulated interleaving experiments when enough session data are available. While it is easier for click models to distinguish between more diverse systems, it is harder to reproduce the system ranking based on the same retrieval algorithm with different interpolation weights. Our setup is entirely open, and we share the code to reproduce the experiments.
Detection of lung pathology using the fractal method
Authors: Abdikerimova Gulzira , Shekerbek Ainur , Tulenbayev Murat , Sultanova Bakhyt , Beglerova Svetlana , Dzhaulybaeva Elvira , Zhumakanova Kamshat , Rysbekkyzy Bakhytgul 
Published: September 2023

<span lang="EN-US">Currently, the detection of pathology of lung cavities and their digitalization is one of the urgent problems of the healthcare industry in Kazakhstan. In this paper, the method of fractal analysis was considered to solve the task set. Diagnosis of lung pathology based on fractal analysis is an actively developing area of medical research. Conducted experiments on a set of clinical data confirm the effectiveness of the proposed methodology. The results obtained show that fractal analysis can be a useful tool for early detection of lung pathologies. It allows you to detect even minor changes in the structure and texture of lung tissues, which may not be obvious during visual analysis. The article deals with images of pathology of the pulmonary cavity, taken from an open data source. Based on the analysis of fractal objects, they were pre-assembled. Software algorithms for the operation of the information system for screening diagnostics have been developed. Based on the information contained in the fractal image of the lungs, mathematical models have been developed to create a diagnostic rule. A reference set of information features has been created that allows you to create algorithms for diagnosing the lungs: healthy and with pathologies of tuberculosis. </span>
Rainfall analysis and prediction using ensemble learning for Karnataka State
Authors: Meti Govardhana , Krishnegowda Ravi Kumar Guralamata , Swamy Gudihalli Savitha 
Published: September 2023

<span lang="EN-US">Accurate <span lang="EN-US">prediction of rainfall can save farmers from crop damage as erratic rains in India have caused agricultural losses. Due to continuous climate change, rainfall and weather prediction has become essential. Rain causes damage to people and property. So, rainfall forecasting is crucial for crop as our country’s economy is still heavily dependent on agriculture. Using machine learning (ML) and deep learning (DL) models, we can train these models for the rainfall dataset and make predictions. In this paper, we estimate rainfall over the Karnataka region using a stacking ensemble model on a rainfall dataset collected between 1901 and 2015.</span></span>
Tracing the Origin and Development of the Black Ink Marks Daubed onto the Upper Edges of Bamboo Slips in Warring States, Qin, and Han Manuscripts: With the Term jiang 江 from Slip 118 of Vol. 5 of the Yuelu Qin Slips Serving as a Guide
Authors: Lu Jialiang 
Published: September 2023

Abstract
The phrase “make wet its upper part” (jiang qi shang 江其上), which appears in the protocol inscribed on slip nos. 117–118 of Accessory Ordinance C no. 4 卒令丙四 in vol. 5 of the Yuelu shuyuan cang Qin jian 岳麓書院藏秦簡 (“Qin Slips Housed at the Yuelu Academy”) as an instruction for the marking of document label slips, should be read as “[inscribe] a plank-mark onto its upper part” (gang qi shang 杠其上). This phrase in the protocol instructs clerks to mark label slips by inscribing a horizontal “plank” mark (heng gang 橫杠) onto the upper part of a rectangular slip (fang 方). The marks that were produced by this clerical custom are the visually conspicuous markers modern scholars describe as “blackened bamboo slip tops” (jian shou tu hei 簡首塗黑) that frequently appear in caches of early Chinese textual materials. However, rather than using the phrase “blackened bamboo slip tops,” it would be more precise to refer to these as “horizontal oblong black ink marks” (mo heng 墨橫) or “black ink plank marks” (mo gang 墨杠).
After the Miners’ Strike
Authors: Farmer Paul , Kilburn Mark 
Published: September 2023

In this rich memoir, the first of two volumes, Paul Farmer traces the story of A39, the Cornish political theatre group he co-founded and ran from the mid-1980s to the early 1990s. Farmer offers a unique insight into A39’s creation, operation, and artistic practice during a period of convulsive political and social change.
The reader is plunged into the national miners’ strike and the collapse of Cornish tin mining, the impact of Thatcherism and ‘Reaganomics’, and the experience of touring Germany on the brink of reunification, alongside the influence on A39 of writers Bertolt Brecht, John McGrath and Keith Johnstone. Farmer, a former bus driver turned artistic director, details the theatre group’s inception and development as it fought to break down social barriers, attract audiences, and survive with little more than a beaten-up Renault 12, a photocopier and two second-hand stage lights at its disposal: the book traces the progress from these raw materials to the development of an integrated community theatre practice for Cornwall.
Farmer’s candour and humour enliven this unique insight into 1980s theatre and politics. It will appeal to anyone with an interest in theatre history, life in Cornwall, and the relationship between performance and society during a turbulent era.
Automated Lightning Jump (LJ) Detection from Geostationary Satellite Data
Authors: Erdmann Felix , Poelman Dieter R. 
Published: September 2023

Abstract
Rapid increases in the flash rate (FR) of a thunderstorm, so-called lightning jumps (LJs), have potential for nowcasting applications and to increase lead times for severe weather warnings. To date, there are some automated LJ algorithms that were developed and tuned for ground-based lightning locating systems. This study addresses the optimization of an automated LJ algorithm for the Geostationary Lightning Mapper (GLM) lightning observations from space. The widely used σ-LJ algorithm is used in its original form and in an adapted calculation including the footprint area of the storm cell (FRarea LJ algorithm). In addition, a new relative increase level (RIL) LJ algorithm is introduced. All algorithms are tested in different configurations, and detected LJs are verified against National Centers for Environmental Information severe weather reports. Overall, the FRarea algorithm with an activation FR threshold of 15 flashes per minute and a σ-level threshold of 1.0–1.5 as well as the RIL algorithm with FR threshold of 15 flashes per minute and RIL threshold of 1.1 are recommended. These algorithms scored the best critical success index (CSI) of ∼0.5, with a probability of detection of 0.6–0.7 and a false alarm ratio of ∼0.4. For daytime warm-season thunderstorms, the CSI can exceed 0.5, reaching 0.67 for storms observed during three consecutive days in April 2021. The CSI is generally lower at night and in winter.