bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variant histology is associated with more non‐urothelial tract recurrence but less intravesical recurrence for upper tract urothelial carcinoma after radical nephroureterectomy
Authors: Yu Tsung Yu , Wang Hung Jen , Sung Min Tse , Chuang Yao Chi , Chen Yen Ta , Cheng Yuan Tso , Kang Chih Hsiung , Liu Hui Ying , Chang Yin Lun , Luo Hao Lun 
Published: January 2024

PurposeTo investigate the prognostic impact of variant histology (VH) on oncological outcomes in patients with upper urinary tract urothelial carcinoma (UTUC) who had undergone radical nephroureterectomy (RNU).Patients and methodsA total of 1239 patients with clinically localized UTUC who underwent RNU at a single institution between January 2005 and June 2020 were included. The VH was reviewed by a uro‐pathologist at our institution. The Cox regression model was used to perform multivariate analysis, including VH and other established prognostic factors for post‐RNU oncological outcomes (intravesical recurrence [IVR], non‐urothelial recurrence, and cancer‐specific death).ResultsOf the 1239 patients with UTUC, 384 patients (31%) were found to have VH. Advanced tumor stage, lymph node metastasis, high tumor grade, lymphovascular invasion, open surgery, and renal pelvis had a significantly larger proportion of UTUC with VH compared to pure UTUC (all p < 0.05). VH was an independent prognostic factor associated with less IVR identified by multivariate analysis, more non‐urothelial recurrence, and more cancer‐specific mortality.ConclusionPatients with VH account for 31% with UTUC treated with RNU in this cohort. VH was an independent prognostic factor associated with more non‐urothelial recurrence and cancer‐specific mortality but less IVR.
Accumulation of extracellular elastin‐derived peptides disturbed neuronal morphology and neuron–microglia crosstalk in aged brain
Authors: Ma Jun , Wang Bingqian , Wei Xiaoxi , Tian Meng , Bao Xingfu , Zhang Yifan , Qi Huichuan , Zhang Yi , Hu Min 
Published: January 2024

AbstractExtracellular elastin‐derived peptides (EDPs) accumulate in the aging brain and have been associated with vascular dementia and Alzheimer's disease (AD). The activation of inflammatory processes in glial cells with EDP treatment has received attention, but not in neurons. To properly understand EDPs' pathogenic significance, the impact on neuronal function and neuron–microglia crosstalk was explored further. Among the EDP molecules, Val‐Gly‐Val‐Ala‐Pro‐Gly (VGVAPG) is a typical repeating hexapeptide. Here, we observed that EDPs‐VGVAPG influenced neuronal survival and morphology in a dose‐dependent manner. High concentrations of VGVAPG induced synapse loss and microglia hyperactivation in vivo and in vitro. Following EDP incubation, galectin 3 (Gal‐3) released by neurons served as a chemokine, attracting microglial engulfment. Blocking Gal‐3 and EDP binding remedied synapse loss in neurons and phagocytosis in microglia. In response to the accumulation of EDPs, proteomics in matrix remodeling and cytoskeleton dynamics, such as a disintegrin and metalloproteinase (ADAM) family, were engaged. These findings in extracellular EDPs provided more evidence for the relationship between aging and neuron dysfunction, increasing the insight of neuroinflammatory responses and the development of new specialized extracellular matrix remolding‐targeted therapy options for dementia or other neurodegenerative disease.image
From the Great Divergence to South–South Divergence: New comparative horizons in global economic history
Authors: Frankema Ewout 
Published: January 2024

AbstractThe Great Divergence debate has been the leading conversation in economic history for the past 25 years. This review article explores new comparative horizons in global economic history. I argue that questions of South–South Divergence form a logical and timely extension to the Great Divergence research agenda. Asia's economic renaissance did not only put an end to a century‐spanning process of widening global income disparities, it also set a new process of divergence within the global south in motion. Deeper understandings of the historical nature and origins of this transition are pertinent in light of the increasing demographic and economic weight of the global south. South–south comparisons also offer an opportunity to counter the dominance of western‐centered and north–south perspectives and incentivize the development of new approaches and theories that go beyond mainstream concepts designed by development economists and political scientists. I argue that these novel approaches will have to grapple with the opportunities and constraints to “late” development being shaped by the quadruple challenge of vast technology gaps, limited state autonomy, global competition, and rapidly closing land and resource frontiers.
Experimental measurement and computational prediction of bacterial Hanks‐type Ser/Thr signaling system regulatory targets
Authors: Grunfeld Noam , Levine Erel , Libby Elizabeth 
Published: January 2024

AbstractBacteria possess diverse classes of signaling systems that they use to sense and respond to their environments and execute properly timed developmental transitions. One widespread and evolutionarily ancient class of signaling systems are the Hanks‐type Ser/Thr kinases, also sometimes termed “eukaryotic‐like” due to their homology with eukaryotic kinases. In diverse bacterial species, these signaling systems function as critical regulators of general cellular processes such as metabolism, growth and division, developmental transitions such as sporulation, biofilm formation, and virulence, as well as antibiotic tolerance. This multifaceted regulation is due to the ability of a single Hanks‐type Ser/Thr kinase to post‐translationally modify the activity of multiple proteins, resulting in the coordinated regulation of diverse cellular pathways. However, in part due to their deep integration with cellular physiology, to date, we have a relatively limited understanding of the timing, regulatory hierarchy, the complete list of targets of a given kinase, as well as the potential regulatory overlap between the often multiple kinases present in a single organism. In this review, we discuss experimental methods and curated datasets aimed at elucidating the targets of these signaling pathways and approaches for using these datasets to develop computational models for quantitative predictions of target motifs. We emphasize novel approaches and opportunities for collecting data suitable for the creation of new predictive computational models applicable to diverse species.
The EIN3/EIL‐ERF9‐HAK5 transcriptional cascade positively regulates high‐affinity K+ uptake in Gossypium hirsutum
Authors: Xiao Shuang , Yang Doudou , Li Fangjun , Tian Xiaoli , Li Zhaohu 
Published: January 2024

Summary

High‐affinity K+ (HAK) transporters play essential roles in facilitating root K+ uptake in higher plants. Our previous studies revealed that GhHAK5a, a member of the HAK family, is crucial for K+ uptake in upland cotton. Nevertheless, the precise regulatory mechanism governing the expression of GhHAK5a remains unclear.

The yeast one‐hybrid screening was performed to identify the transcription factors responsible for regulating GhHAK5a, and ethylene response factor 9 (GhERF9) was identified as a potential candidate.

Subsequent dual‐luciferase and electrophoretic mobility shift assays confirmed that GhERF9 binds directly to the GhHAK5a promoter, thereby activating its expression. Silencing of GhERF9 decreased the expression of GhHAK5a and exacerbated K+ deficiency symptoms in leaves, also decreased K+ uptake rate and K+ content in roots. Additionally, it was observed that the application of ethephon (an ethylene‐releasing reagent) resulted in a significant upregulation of GhERF9 and GhHAK5a, accompanied by an increased rate of K+ uptake. Expectedly, GhEIN3b and GhEIL3c, the two key components involved in ethylene signaling, bind directly to the GhERF9 promoter.

These findings provide valuable insights into the molecular mechanisms underlying the expression of GhHAK5a and ethylene‐mediated K+ uptake and suggest a potential strategy to genetically enhance cotton K+ uptake by exploiting the EIN3/EILs‐ERF9‐HAK5 module.
Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis
Authors: Chen C. , Luo D. , Wang Z. , Miao Y. , Liu Q. , Zhao T. , Liu D. 
Published: January 2024

Abstract

Artemisia L. is the largest genus in the Asteraceae, and well known for its high medicinal value. The morphological features of Artemisia species are similar, making taxonomic identification and evolutionary research difficult.

We sequenced chloroplast genomes of eight Artemisia species, all of which are common adulterants of A. argyi. We used novel genetic data and compared these data to the published A. argyi chloroplast genome in to develop molecular markers for species identification and reconstructing phylogenetic relationships between Artemisia species.

The eight chloroplast sequences were highly similar in gene order, content, and structure, encoding a total of 114 genes (82 protein‐coding genes, 28 tRNAs, and four rRNAs). All species harboured similar repeat sequences and simple sequence repeats (SSRs), ranging from 47 to 49 and 38 to 40 repeats, respectively. In addition, we identified five hypervariable regions (rpl32‐trnL, rps16‐trnQ, petN‐psbM, trnE‐rpoB, and atpA‐trnR) and ten variable coding genes (ycf1, psbG, rpl36, psaC, psaI, accD, psbT, ndhD, ndhE, and psbH), which can be used to develop chloroplast molecular markers. Finally, phylogenetic reconstructions based on six datasets produced similar topologies, revealing A. argyi is closely related to species often found as adulterants, as expected.

Our research provides valuable new information on the evolution and phylogenetic relationships between Artemisia chloroplast genomes and identifies valuable molecular makers to distinguish it from closely related species.
Plant hormone ethylene: A leading edge in conferring drought stress tolerance
Authors: Nazir Faroza , Peter Poor , Gupta Ravi , Kumari Sarika , Nawaz Kashif , Khan M. Iqbal R. 
Published: January 2024

AbstractAgricultural sufficient productivity is of paramount importance for ensuring food security and conserving soil health to support the world's agronomy. Climatic abruptions have been emerging as one of the most nerve‐pressing issues for the sustainment of the planet Earth in the twenty‐first century. Among the various environmental constraints, drought stress stands out as a potent factor restricting crop growth and productivity. It triggers a myriad of intricate responses in plants to combat the underlying stress‐mediated adversities. Gaining a comprehensive understanding of the key physiological and molecular mechanisms that enable plants to withstand drought stress is crucial for developing effective strategies to enhance crop resilience. Ethylene, a gaseous plant hormone, influences the adaptive measures adopted by plants subjected to drought stress by regulating the drought stress‐mediated signal transduction‐associated responses. The present review article provides an in‐depth understanding of the critical roles of ethylene in enhancing plants' ability to restrain the severity of drought stress. It also highlights the significance of ethylene signaling components in regulating plant survival and drought stress tolerance. Additionally, we have illustrated the additive and antagonistic interactions of ethylene with other plant growth regulators, which instigate the tolerance responses. Conclusively, this review emphasizes the significance of complex networks involved in ethylene‐mediated drought tolerance, providing valuable insights for future research and uncovering novel studies in the field of ethylene biology.
Complex plant responses to drought and heat stress under climate change
Authors: Sato Hikaru , Mizoi Junya , Shinozaki Kazuo , Yamaguchi‐Shinozaki Kazuko 
Published: January 2024

SUMMARYGlobal climate change is predicted to result in increased yield losses of agricultural crops caused by environmental conditions. In particular, heat and drought stress are major factors that negatively affect plant development and reproduction, and previous studies have revealed how these stresses induce plant responses at physiological and molecular levels. Here, we provide a comprehensive overview of current knowledge concerning how drought, heat, and combinations of these stress conditions affect the status of plants, including crops, by affecting factors such as stomatal conductance, photosynthetic activity, cellular oxidative conditions, metabolomic profiles, and molecular signaling mechanisms. We further discuss stress‐responsive regulatory factors such as transcription factors and signaling factors, which play critical roles in adaptation to both drought and heat stress conditions and potentially function as ‘hubs’ in drought and/or heat stress responses. Additionally, we present recent findings based on forward genetic approaches that reveal natural variations in agricultural crops that play critical roles in agricultural traits under drought and/or heat conditions. Finally, we provide an overview of the application of decades of study results to actual agricultural fields as a strategy to increase drought and/or heat stress tolerance. This review summarizes our current understanding of plant responses to drought, heat, and combinations of these stress conditions.
Clonorchiasis and opisthorchiasis: epidemiology, transmission, clinical features, morbidity, diagnosis, treatment, and control
Authors: Qian Men-Bao , Keiser Jennifer , Utzinger Jürg , Zhou Xiao-Nong 
Published: January 2024

SUMMARY

Clonorchis sinensis
,
Opisthorchis viverrini
, and
Opisthorchis felineus
are important liver flukes that cause a considerable public health burden in eastern Asia, southeastern Asia, and eastern Europe, respectively. The life cycles are complex, involving humans, animal reservoirs, and two kinds of intermediate hosts. An interplay of biological, cultural, ecological, economic, and social factors drives transmission. Chronic infections are associated with liver and biliary complications, most importantly cholangiocarcinoma. With regard to diagnosis, stool microscopy is widely used in epidemiologic surveys and for individual diagnosis. Immunologic techniques are employed for screening purposes, and molecular techniques facilitate species differentiation in reference laboratories. The mainstay of control is preventive chemotherapy with praziquantel, usually combined with behavioral change through information, education and communication, and environmental control. Tribendimidine, a drug registered in the People’s Republic of China for soil-transmitted helminth infections, shows potential against both
C. sinensis
and
O. viverrini
and, hence, warrants further clinical development. Novel control approaches include fish vaccine and biological control. Considerable advances have been made using multi-omics which may trigger the development of new interventions. Pressing research needs include mapping the current distribution, disentangling the transmission, accurately estimating the disease burden, and developing new diagnostic and treatment tools, which would aid to optimize control and elimination measures.
Virology—the path forward
Authors: Rasmussen Angela L. , Gronvall Gigi K. , Lowen Anice C. , Goodrum Felicia , Alwine James , Andersen Kristian G. , Anthony Simon J. , Baines Joel , Banerjee Arinjay , Broadbent Andrew J. , Brooke Christopher B. , Campos Samuel K. , Caposio Patrizia , Casadevall Arturo , Chan Gary C. , Cliffe Anna R. , Collins-McMillen Donna , Connell Nancy , Damania Blossom , Daugherty Matthew D. , Debbink Kari , Dermody Terence S. , DiMaio Daniel , Duprex W. Paul , Emerman Michael , Galloway Denise A. , Garry Robert F. , Goldstein Stephen A. , Greninger Alexander L. , Hartman Amy L. , Hogue Brenda G. , Horner Stacy M. , Hotez Peter J. , Jung Jae U. , Kamil Jeremy P. , Karst Stephanie M. , Laimins Lou , Lakdawala Seema S. , Landais Igor , Letko Michael , Lindenbach Brett , Liu Shan-Lu , Luftig Micah , McFadden Grant , Mehle Andrew , Morrison Juliet , Moscona Anne , Mühlberger Elke , Munger Joshua , Münger Karl , Murphy Eain , Neufeldt Christopher J. , Nikolich Janko Z. , O'Connor Christine M. , Pekosz Andrew , Permar Sallie R. , Pfeiffer Julie K. , Popescu Saskia V. , Purdy John G. , Racaniello Vincent R. , Rice Charles M. , Runstadler Jonathan A. , Sapp Martin J. , Scott Rona S. , Smith Gregory A. , Sorrell Erin M. , Speranza Emily , Streblow Daniel , Tibbetts Scott A. , Toth Zsolt , Van Doorslaer Koenraad , Weiss Susan R. , White Elizabeth A. , White Timothy M. , Wobus Christiane E. , Worobey Michael , Yamaoka Satoko , Yurochko Andrew 
Published: January 2024

ABSTRACT
In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.
Polymyxin B and ethylenediaminetetraacetic acid act synergistically against
Pseudomonas aeruginosa
and
Staphylococcus aureus
Authors: Hale Samuel J. M. , Cameron Alan J. , Lux Christian A. , Biswas Kristi , Kim Raymond , O'Carroll Mark , Harris Paul W. R. , Douglas Richard G. , Wagner Mackenzie Brett 
Published: January 2024

ABSTRACT

Polymyxin B and ethylenediaminetetraacetic acid are antimicrobials possessing antibiofilm activity. They act by displacement and chelation, respectively, of divalent cations in bacterial membranes and may therefore act synergistically when applied in combination. If so, this combination of agents may be useful for the treatment of diseases like cystic fibrosis (CF), in which biofilms are present on the respiratory epithelium. We used checkerboard assays to investigate the synergy between these agents using reference strains
Pseudomonas aeruginosa
ATCC 27853 and
Staphylococcus aureus
ATCC 6538 in planktonic form. We then determined the efficacy of each agent against biofilms of both species grown on 96-pin lids and proceeded to combination testing against the
P. aeruginosa
reference strain and 10 clinical isolates from patients with CF. Synergism was observed for planktonic forms of both species and for biofilms of
P. aeruginosa
. The susceptibility of biofilms of
P. aeruginosa
clinical isolates to these agents was variable compared to the laboratory reference strain. This combination of agents may be useful in the management of biofilm-associated conditions, particularly those amenable to topical therapies. These results provide a basis upon which the antimicrobial and antibiofilm efficacy of preparations containing these agents may be enhanced.

IMPORTANCE

Bacteria living in biofilms produce a protective matrix which makes them difficult to kill. Patients with severe respiratory disease often have biofilms. Polymyxin B is an antibiotic commonly used in topical medications, such as eye drops and nasal sprays. Ethylenediaminetetraacetic acid (EDTA) is used widely as a preservative in medication but also has antimicrobial properties. It has been hypothesized that Polymyxin B and EDTA could have a synergistic relationship: when used in combination their antimicrobial effect is enhanced. Here, we evaluated the levels at which Polymyxin B and EDTA work together to kill common pathogens
Pseudomonas aeruginosa
and
Staphylococcus aureus
. We found that Polymyxin B and EDTA were synergistic. This synergy may be useful in the management of planktonic infection with
P. aeruginosa
and
S. aureus
, or biofilm infection with
P. aeruginosa
. This synergy may be beneficial in the treatment of respiratory biofilms, in which
P. aeruginosa
biofilms are common.
Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice
Authors: Matějková Tereza , Dodoková Alica , Kreisinger Jakub , Stopka Pavel , Stopková Romana 
Published: January 2024

ABSTRACT

Symbiotic microbial communities affect the host immune system and produce molecules contributing to the odor of an individual. In many mammalian species, saliva and vaginal fluids are important sources of chemical signals that originate from bacterial metabolism and may act as honest signals of health and reproductive status. In this study, we aimed to define oral and vaginal microbiomes and their dynamics throughout the estrous cycle in wild house mice. In addition, we analyzed a subset of vaginal proteomes and metabolomes to detect potential interactions with microbiomes. 16S rRNA sequencing revealed that both saliva and vagina are dominated by
Firmicutes
and
Proteobacteria
but differ at the genus level. The oral microbiome is more stable during the estrous cycle and most abundant bacteria belong to the genera
Gemella
and
Streptococcus
, while the vaginal microbiome shows higher bacterial diversity and dynamics during the reproductive cycle and is characterized by the dominance of
Muribacter
and
Rodentibacter
. These two genera cover around 50% of the bacterial community during estrus. Proteomic profiling of vaginal fluids revealed specific protein patterns associated with different estrous phases. Highly expressed proteins in estrus involve the keratinization process thus providing estrus markers (e.g., Hrnr) while some proteins are downregulated such as immune-related proteins that limit bacterial growth (Camp, Clu, Elane, Lyz2, and Ngp). The vaginal metabolome contains volatile compounds potentially involved in chemical communication, for example, ketones, aldehydes, and esters of carboxylic acids. Data integration of all three OMICs data sets revealed high correlations, thus providing evidence that microbiomes, host proteomes, and metabolomes may interact.

IMPORTANCE
Our data revealed dynamic changes in vaginal, but not salivary, microbiome composition during the reproductive cycle of wild mice. With multiple OMICs platforms, we provide evidence that changes in microbiota in the vaginal environment are accompanied by changes in the proteomic and metabolomics profiles of the host. This study describes the natural microbiota of wild mice and may contribute to a better understanding of microbiome-host immune system interactions during the hormonal and cellular changes in the female reproductive tract. Moreover, analysis of volatiles in the vaginal fluid shows particular substances that can be involved in chemical communication and reproductive behavior.