bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pine wilt disease: A global threat to forestry
Authors: Back Matthew A. , Bonifácio Luís , Inácio Maria L. , Mota Manuel , Boa Eric 
Published: February 2024

AbstractPines are the most economically important trees in the world and, together with eucalyptus, they dominate commercial forests. But the success of a relatively small number of widely planted species, such as Pinus pinaster, the maritime pine, comes at a price. Pines are attractive to damaging pathogens and insect pests, including the pinewood nematode (PWN), Bursaphelenchus xylophilus, the causal agent of pine wilt disease (PWD). Originally described in Japan, PWD has caused widespread destruction to forests in countries such as China, Taiwan, Portugal, Spain and the United States. PWN causes irreparable damage to the vascular system of its pine hosts, leading to mortality within 3 months. Pine sawyer beetles (Monochamus spp.) are key vectors of PWD, introducing the PWN to healthy trees during feeding. Other organisms contribute to PWD spread and development, including bacteria, fungi and bark beetles. Control measures include tree felling to prevent vector transmission of PWN, insecticide treatments, trapping of Monochamus spp. and tree breeding for plant resistance. The PWN is a quarantine pathogen and subject to regular legislation and phytosanitary measures aimed at restricting movement and preventing introduction to new areas. Current research is investigating the use of biopesticides against PWN and Monochamus spp. This review examines the biology, epidemiology, impact and management of PWD through published research, grey literature and interviews with people directly involved in the management of the disease in Portugal.
Metabolomics Analyses Revealed the Key Metabolites and Pathways of Panax notoginseng under Heavy Drought Stress
Authors: Zhang Shuai , Yang Kuan , Ye Kunhao , Wang Huiling , Zhu Youyong , He Xiahong , Guo Liwei 
Published: February 2024

AbstractDrought is the most common abiotic stress that hinders plantgrowth. To clarify the changes in the growth and metabolism of Panax notoginseng following drought stress, here the effects of drought stress on the growth and metabolism of P. notoginseng are investigated using gas chromatography–mass spectrometry based on a widely targeted metabolomic approach. We conducted drought stress treatments (DS) and re‐watering treatments after drought stress (RW) with no drought stress as the control group. The results showed that DS treatment significantly inhibited biomass accumulation and root development of P. notoginseng. Single saponin Rg1 and total saponin in the roots were the highest in the control group, while the total saponins in the leaves were the highest in DS. A total of 120 metabolites were identified using metabolomics and they were classified into eight categories. The metabolites of P. notoginseng under DS were significantly different from the control and RW treatment. Caffeic acid was significantly enriched in all comparison groups, suggesting its important role in the drought resistance of P. notoginseng. Enrichment analysis of differential metabolites showed that the ATP‐binding cassette (ABC) transporters, the metabolic pathway of valine, leucine, and isoleucine were closely associated with the drought resistance of P. notoginseng. We also verified that significantly upregulated differential metabolites such as 5‐aminolevulinic acid (5‐ALA) and quinic acid can enhance the drought resistance of P. notoginseng through exogenous application.
Abiotic and biotic factors regulate the timing of floral induction: a review
Authors: Patra Sanjib , Chatterjee Debdatta , Dutta Rijhdyuti , Mandal Arunava 
Published: February 2024

AbstractTime of flowering is an important phenomenon which ensures reproductive success and better adaptability to various environmental conditions. There are a few proteins that function as master regulators of flowering. The expression of these proteins highly depends on many extrinsic and intrinsic factors along with several biotic components. Further, alterations in these factors result in drastic changes in the transition from the vegetative to the reproductive phase that ultimately results in yield loss. Different abiotic stresses, such as drought, salinity, cold, heat, nutrient scarcity, sugar availability and exogenous chemicals, collectively affect the whole ambit of the floral induction process. Nevertheless, biotic stresses like bacterial (Pseudomonas syringae) and fungal (Fusarium oxysporum) infections promote the expression of the FT gene, which further accelerates the flowering phenomenon. Soil‐dwelling microorganisms, herbivores, pollinators and a few endophytes are associated with the promotion of flowering. Although plants have adapted several strategies to cope with the stress conditions and manage to maintain their reproductive physiology, it is noteworthy that flowering in plants under stress conditions shows species‐specific response patterns by accelerating or retarding the floral induction. Several transcription factors and some miRNAs were also involved in the regulation of flowering under stress conditions. In this review, we have summarised the different biotic and abiotic stresses that affect the flowering time and also include several strategies that plants adapt to escape the stress condition.
A cotton APS REDUCTASE represses root hair elongation via sulfur assimilation and hydrogen peroxide‐mediated cell wall damage
Authors: Mao Xiaonan , Wei Zhenzhen , Xu Zhenzhen , Qanmber Ghulam , Liu Ji , Li Yonghui , Lu Lili , Wang Ye , Peng Jun , Wang Zhi 
Published: February 2024

AbstractSulfur is a critical element for plant growth and development, and it is assimilated through a pathway called the sulfur assimilation pathway. APS REDUCTASE (APR) is a key rate‐limiting enzyme in this pathway, and it plays a vital role in regulating sulfur flow and plant development. However, the exact role and mechanism of APR in cotton fiber and root hair development are still not fully understood. This study used in vitro cultured ovules grown on a sulfur‐deficient medium to explore the role of sulfur in fiber development. Genetic approaches such as virus‐induced gene silencing (VIGS) was used to determine the role of target genes. In vitro assays revealed the role of sulfur in fiber development and identified GhAPR2 as a key candidate gene. The GhAPR2 negatively regulates fiber cell initiation and Arabidopsis root hair elongation. Further studies demonstrated that overexpression of GhAPR2 increased the contents of sulfite and GSH to enhance sulfur assimilation in Arabidopsis, leading to abnormal accumulation of ROS in root hair. This down‐regulates the transcription of proline‐rich cell wall protein‐coding genes such as AtEXTs and AtPRPs, reducing the content of hydroxyproline in the cell wall, disrupting the development of the root hair cell wall, and inhibiting root hair elongation. This study elucidated the functional pathway of APR2 in the regulation of root hair development. APR2 first affects sulfur assimilation, which affects the content of reactive oxygen species (ROS), and finally affects the content of hydroxyproline‐rich glycoprotein, which in turn affects the development of root hair. This model also contributes to the understanding of the role of sulfur in fiber development, as well as cell differentiation and development.
Plant–plant interactions affect seasonal nitrogen uptake of subalpine conifer seedlings by altering root traits and soil nitrogen availabilities
Authors: Xie Lulu , Hu Xuefeng , Li Wanting , Liu Qinghua , Yin Chunying 
Published: February 2024

AbstractAlthough it is known that plant–plant interaction is an important factor influencing plant nitrogen (N) uptake and biomass productivity, its effects on seasonal inorganic N uptake, preference, and allocation remain unclear. In this study, two conifer species (Picea asperataandAbies faxoniana) were planted in three different planting modes (i.e., single, intraspecific, and interspecific interaction). Using15N stable isotope tracer, we quantified plant biomass, ammonium (NH4+), and nitrate (NO3−) uptake rate (mass) and allocation in the middle (July) and the end (September) of the growing season, respectively, followed by analyses of root traits and soil properties so as to explore the underlying mechanism. Across the two seasons, intraspecific interaction decreased plant biomass and inorganic N‐uptake rate, which triggered intense competition for both species. Intraspecific competition ofP. asperatawas stronger than that ofA. faxoniana. In contrast, interspecific interaction revealed significant facilitative effects onA. faxoniana, particularly in September. From the middle to the late growing season, the inorganic N‐uptake rate ofP. asperatareduced, whereas that ofA. faxonianaincreased under interspecific interaction. The seasonal variation in plant N uptake was regulated by changes in root traits (such as root nitrogen concentration, specific root length, and branching intensity) and soil N availabilities. Both species indicated a preference for NO3−across seasons. Furthermore, we observed that15N allocation to shoots ofA. faxonianaunder interspecific interaction was higher than that ofP. asperataand declined from July to September. These findings on how plant–plant interactions affect plant N uptake seasonally can facilitate our understanding of species co‐existence and community assembly in forest ecosystems.
A retrospective Italian Society of Veterinary Oncology (SIONCOV) study of 56 cats with appendicular osteosarcoma
Authors: Marconato Laura , Annoni Maurizio , Massari Federico , Zanardi Stefano , Stefanello Damiano , Ferrari Roberta , Rossi Federica , Montinaro Vincenzo , Morello Emanuela , Chalfon Carmit , De Lorenzi Marco , Murgia Daniela , Drudi Dario , Truncellito Gabriele , Cabibbo Emanuele , Sabattini Silvia 
Published: February 2024

AbstractOsteosarcoma is the most common malignant primary bone cancer, but it is infrequently reported in cats. Feline appendicular osteosarcoma typically exhibits good prognosis when treated with surgery alone. A retrospective multi‐institutional study was conducted to identify possible prognostic factors. Cats diagnosed with appendicular osteosarcoma were included if initial staging and follow‐up information were available. Data including signalment, tumour characteristics, treatment modalities, and survival outcomes were collected and analysed. Fifty‐six cats were included; the femur was the most frequently affected bone. Eight cats had distant metastasis at admission and an additional 9 developed metastatic disease during follow‐up, resulting in an overall metastatic rate of 30%. Forty‐nine (87.5%) cats underwent surgery, and 4 also received adjuvant chemotherapy. Among operated cats, median time to local progression (TTLP), time to distant progression and tumour‐specific survival (TSS) were not reached. One‐ and 2‐year survival rates were 66% and 55%, respectively. Seven (12.5%) cats received no treatment; 1‐ and 2‐year survival rates were 25% and 0%, respectively. Operated cats had significantly longer TTLP (P < .001) and TSS (P = .001) compared with non‐operated cats. Among operated cats, young age negatively impacted local tumour progression, while the presence of distant metastasis at diagnosis was associated with a higher risk of tumour‐related death. This study reaffirms the good prognosis for cats with appendicular osteosarcoma undergoing surgery, but sheds light on some additional factors to consider. Accurate initial staging is recommended, as the metastatic rate may exceed many previous estimations. Surgery substantially extends survival time, whereas the role of chemotherapy remains uncertain.
Bayesian approach for meta-analyses in biomedical research: a scoping review protocol
Authors: Santos Joseph Alvin , Riggi Emilia , Grant Robert , Ingale Samiksha , Bhaumik Soumyadeep , Di Tanna Gian Luca 
Published: February 2024

Objective:
The overarching aim of this scoping review is to describe and analyze the scope of use and reporting of Bayesian methods in meta-analyses in biomedical research.

Introduction:
The Bayesian approach provides a powerful and flexible framework for meta-analysis, particularly suited for dealing with complex, sparse, or heterogeneous data. Due to these advantages and its appeal, Bayesian methods have been increasingly used in many areas of biomedical research; however, their use in meta-analysis remains scarce.

Inclusion criteria:
This review will include studies that used Bayesian methods for meta-analysis of primary studies in biomedical research.

Methods:
The proposed review will be conducted in accordance with the JBI methodology for scoping reviews. PubMed, Embase, CINAHL, and the Cochrane Database of Systematic Reviews will be searched to identify relevant full-text papers published since 2016 in English. No geographical restriction will be applied. Two reviewers will screen the articles and extract the data using a tool that will be pilot-tested and revised, as necessary. Analysis will involve frequency counts, narrative synthesis, and mapping concepts to propose an appropriate workflow. The details of the scoping review will be reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews guideline.

Review registration:
Open Science Framework https://osf.io/jenp4/
Atherosclerotic Calcifications Have a Local Effect on the Peel Behavior of Human Aortic Media
Authors: Donahue Carly L. , Badal Ruturaj M. , Younger Thomas S. , Guan Weihua , Tolkacheva Elena G. , Barocas Victor H. 
Published: February 2024

Abstract
Aortic dissections, characterized by the propagation of a tear through the layers of the vessel wall, are critical, life-threatening events. Aortic calcifications are a common comorbidity in both acute and chronic dissections, yet their impact on dissection mechanics remains unclear. Using micro-computed tomography (CT) imaging, peel testing, and finite element modeling, this study examines the interplay between atherosclerotic calcifications and dissection mechanics. Samples cut from cadaveric human thoracic aortas were micro-CT imaged and subsequently peel-tested to map peel tension curves to the location of aortic calcifications. Empirical mode decomposition separated peel tension curves into high and low-frequency components, with high-frequency effects corresponding to interlamellar bonding mechanics and low-frequency effects to peel tension fluctuations. Finally, we used an idealized finite element model to examine how stiff calcifications affect aortic failure mechanics. Results showed that atherosclerosis influences dissection behavior on multiple length scales. Experimentally, atherosclerotic samples exhibited higher peel tensions and greater variance in the axial direction. The variation was driven by increased amplitudes of low-frequency tension fluctuations in diseased samples, indicating that more catastrophic propagations occur near calcifications. The simulations corroborated this finding, suggesting that the low-frequency changes resulted from the presence of a stiff calcification in the vessel wall. There were also modifications to the high-frequency peel mechanics, a response likely attributable to alterations in the microstructure and interlamellar bonding within the media. Considered collectively, these findings demonstrate that dissection mechanics are modified in aortic media nearby and adjacent to aortic calcifications.
Cold Ambient Temperature Does Not Alter Subcutaneous Abdominal Adipose Tissue Lipolysis and Blood Flow in Endurance-Trained Cyclists
Authors: Bach Christopher W. , Saracino Patrick G. , Baur Daniel A. , Willingham Brandon D. , Ruby Brent C. , Ormsbee Michael J. 
Published: February 2024

This study sought to investigate the effect of cold ambient temperature on subcutaneous abdominal adipose tissue (SCAAT) lipolysis and blood flow during steady-state endurance exercise in endurance-trained cyclists. Ten males (age: 23 ± 3 years; peak oxygen consumption: 60.60 ± 4.84 ml·kg−1·min−1; body fat: 18.4% ± 3.5%) participated in baseline lactate threshold (LT) and peak oxygen consumption testing, two familiarization trials, and two experimental trials. Experimental trials consisted of cycling in COLD (3 °C; 42% relative humidity) and neutral (NEU; 19 °C; 39% relative humidity) temperatures. Exercise consisted of 25 min cycling at 70% LT and 25 min at 90% LT. In situ SCAAT lipolysis and blood flow were measured via microdialysis. Heart rate, core temperature, carbohydrate and fat oxidation, blood glucose, and blood lactate were also measured. Heart rate, core temperature, oxygen consumption, and blood lactate increased with exercise but were not different between COLD and NEU. SCAAT blood flow did not change from rest to exercise or between COLD and NEU. Interstitial glycerol increased during exercise (p < .001) with no difference between COLD and NEU. Fat oxidation increased (p < .001) at the onset of exercise and remained elevated thereafter with no difference between COLD and NEU. Carbohydrate oxidation increased with increasing exercise intensity and was greater at 70% LT in COLD compared to NEU (p = .030). No differences were observed between conditions for any other variable. Cycling exercise increased SCAAT lipolysis but not blood flow. Ambient temperature did not alter SCAAT metabolism, SCAAT blood flow, or fat oxidation in well-trained cyclists, though cold exposure increased whole-body carbohydrate oxidation at lower exercise intensities.
Biochemical characterization of the L1-like metallo-β-lactamase from
Stenotrophomonas lactitubi
Authors: Yamada Kageto , Ishii Yoshikazu , Tateda Kazuhiro 
Published: February 2024

ABSTRACT

L1-like metallo-β-lactamases (MBLs) exhibit diversity and are highly conserved. Although the presence of the
bla
L1-like
gene is known, the biochemical characteristics are unclear. This study aimed to characterize an L1-like MBL from
Stenotrophomonas lactitubi
. It showed 70.9–99.7% similarity to 50 L1-like amino acid sequences. The characteristic kinetic parameter was its high hydrolyzing efficiency for ampicillin and nitrocefin. Furthermore, L1-like from
S. lactitubi
was distinctly more susceptible to inhibition by EDTA than that to inhibition by 2,6-pyridinedicarboxylic acid.
Epidemiological, clinical, and laboratory characteristics of human granulocytic anaplasmosis in North India
Authors: Vinayaraj E. V. , Thakur Chandan Kumar , Negi Preeti , Sreenath K. , Upadhyay Priyanka , Verma Nishant , Das Bimal Kumar , Kabra S. K. , Wig Naveet , Chaudhry Rama 
Published: February 2024

ABSTRACT

Human granulocytic anaplasmosis (HGA) is an emerging, rickettsial tick-borne disease caused by
Anaplasma phagocytophilum
. Sero-epidemiological data demonstrate that this pathogen has a worldwide distribution. The diagnosis of HGA requires a high index of clinical suspicion, even in endemic areas. In recent years, HGA has increasingly been reported from Asia and described in China, Japan, and Korea. We serologically and molecularly screened 467 patients with clinical suspicion of Anaplasmosis. The present study describes the epidemiology, clinical, and laboratory details of 6 confirmed and 43 probable cases of human granulocytic anaplasmosis. One of the HGA patients developed secondary invasive opportunistic
Aspergillus fumigatus
and
Acinetobacter baumanii
infection during the illness, which resulted in a fatal infection. The HGA patients without severe complications had excellent treatment responses to doxycycline. The emergence of this newly recognized tick-borne zoonotic HGA in North India is a significant concern for public health and is likely underdiagnosed, underreported, and untreated. Hence, it is also essential to establish a well-coordinated system for actively conducting tick surveillance, especially in the forested areas of the country.

IMPORTANCE

The results of the present study show the clinical and laboratory evidence of autochthonous cases of
Anaplasma phagocytophilum
in North India. The results suggest the possibility of underdiagnosis of HGA in this geographical area. One of the HGA patients developed secondary invasive opportunistic
Aspergillus fumigatus
and
Acinetobacter baumanii
infection during the illness, which resulted in a fatal infection.
Revisiting host identification of bacteriophage Enc34: from biochemical to molecular
Authors: Cernooka Elina , Dislers Andris , Kazaks Andris 
Published: February 2024

ABSTRACT

In our 2012 genome announcement (J Virol 86:11403–11404, 2012,
https://doi.org/10.1128/JVI.01954-12
), we initially identified the host bacterium of bacteriophage Enc34 as
Enterobacter cancerogenus
using biochemical tests. However, later in-house DNA sequencing revealed that the true host is a strain of
Hafnia alvei
. Capitalizing on our new DNA-sequencing capabilities, we also refined the genomic termini of Enc34, confirming a 60,496-bp genome with 12-nucleotide 5′ cohesive ends.

IMPORTANCE

Our correction reflects the evolving landscape of bacterial identification, where molecular methods have supplanted traditional biochemical tests. This case underscores the significance of revisiting past identifications, as seemingly known bacterial strains may yield unexpected discoveries, necessitating essential updates to the scientific record. Despite the host identity correction, our genome announcement retains importance as the first complete genome sequence of a
Hafnia alvei
bacteriophage.
Rhodobacteraceae methanethiol oxidases catalyze methanethiol degradation to produce sulfane sulfur other than hydrogen sulfide
Authors: Cao Qun , Liu Xuanyu , Wang Qingda , Liu Zongzheng , Xia Yongzhen , Xun Luying , Liu Huaiwei 
Published: February 2024

ABSTRACT

Methanethiol (MT) is a sulfur-containing compound produced during dimethylsulfoniopropionate (DMSP) degradation by marine bacteria. The C–S bond of MT can be cleaved by methanethiol oxidases (MTOs) to release a sulfur atom. However, the cleaving process remains unclear, and the species of sulfur product is uncertain. It has long been assumed that MTOs produce hydrogen sulfide (H
2
S) from MT. Herein, we studied the MTOs in the Rhodobacteraceae family—whose members are important DMSP degraders ubiquitous in marine environments. We identified 57 MTOs from 1,904 Rhodobacteraceae genomes. These MTOs were grouped into two major clusters. Cluster 1 members share three conserved cysteine residues, while cluster 2 members contain one conserved cysteine residue. We examined the products of three representative MTOs both
in vitro
and
in vivo
. All of them produced sulfane sulfur other than H
2
S from MT. Their conserved cysteines are substrate-binding sites in which the MTO–S–S–CH
3
complex is formed. This finding clarified the sulfur product of MTOs and enlightened the MTO-catalyzing process. Moreover, this study connected DMSP degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.

IMPORTANCE

This study overthrows a long-time assumption that methanethiol oxidases (MTOs) cleave the C–S bond of methanethiol to produce both H
2
S and H
2
O
2
—the former is a strong reductant and the latter is a strong oxidant. From a chemistry viewpoint, this reaction is difficult to happen. Investigations on three representative MTOs indicated that sulfane sulfur (S
0
) was the direct product, and no H
2
O
2
was produced. Finally, the products of MTOs were corrected to be S
0
and H
2
O. This finding connected dimethylsulfoniopropionate (DMSP) degradation with sulfane sulfur metabolism, filling a critical gap in the DMSP degradation pathway and representing new knowledge in the marine sulfur cycle field.