bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Pattern of Leaf N:P Ratio Along Plantation Age: A Global Synthesis
Authors: Zhang Hui , Sun Meng , Wen Yuxiang , Tong Ran , Wang Geoff , Wu Qiqian , Li Yan , Wu Tonggui 
Published: November 2021

Abstract
Background

Plant stoichiometry displayed flexible over age sequences in previous studies, but effect of stand age on stoichiometry showed large uncertainties for different plantations at the global scale. In this study, we want to obtain the general pattern of leaf N:P ratio for global plantations across age gradients through the compilation and analysis of published data from the individual studies.
Results

Stand age, together with life forms, and climatic variables strongly affected leaf N:P ratio. This result indicates that the stand age is an indispensable underlying mechanism on stoichiometry. Leaf N:P ratio increased with stand age for all plantations pooled together, revealing the existence of the general pattern in leaf stoichiometry for plantations across age gradients. Leaf N:P ratio exhibited no trend in evergreen trees, but an increasing trend was obtained in deciduous trees along age sequences. Meanwhile, leaf N:P ratio rose with stand age for plantations in humid subtropical regions, but it did not vary in dry temperate regions.
Conclusions

Our results reveal the effects of age on tree stoichiometry cannot be neglected. These age-related patterns of stoichiometry verified that global plantations changed from N limitation to P limitation with increasing stand age, particularly for deciduous plantations and in plantations in humid regions. The study highlights the importance of considering stand age when exploring nutrient patterns in plantations, which contributes to improving the plant stoichiometry theory and offers a guidance for the nutrient management of plantations at regional to global scales.
Gas6 Induces Inflammation And Reduces Plaque Burden But Worsens Behavior In The APP/PS1 Model of Alzheimer’s Disease
Authors: Owlett Laura D. , Karaahmet Berke , Le Linh , Belcher Elizabeth K. , Dionisio-Santos Dawling , Olschowka John A. , Elliott Michael R. , O'Banion M. Kerry 
Published: November 2021

Abstract
Background: Alzheimer’s disease is the leading cause of dementia worldwide. TAM receptor tyrosine kinases (Tyro3, Axl, MerTK) are known for their role in engagement of phagocytosis and modulation of inflammation, and recent evidence suggests a complex relationship between Axl, Mer, and microglial phagocytosis of amyloid plaques in AD. Gas6, the primary CNS TAM ligand, reduces neuroinflammation and improves outcomes in murine models of CNS disease. Therefore, we hypothesized that AAV-mediated overexpression of Gas6 would alleviate plaque pathology, reduce neuroinflammation, and improve behavior in the APP/PS1 model of Alzheimer’s disease.Methods: Adeno-associated viral vectors were used to overexpress Gas6 in the APP/PS1 model of Alzheimer’s disease. Nine-month-old male and female APP/PS1 and nontransgenic littermates received bilateral stereotactic hippocampal injections of AAV-Gas6 or AAV-control, which expresses a non-functional Gas6 protein. One month after injections, mice underwent a battery of behavioral tasks to assess cognitive function and brains were processed for immunohistochemical and transcriptional analyses. Results: Gas6 overexpression reduced plaque burden in male APP/PS1 mice. However, contrary to our hypothesis, Gas6 increased pro-inflammatory microglial gene expression and worsened contextual fear conditioning compared to control-treated mice. Gas6 overexpression appeared to have no effect on phagocytic mechanisms in vitro or in vivo as measured by CD68 immunohistochemistry, microglial methoxy-04 uptake, and primary microglial uptake of fluorescent fibrillary amyloid beta. Conclusion: Our data describes a triad of worsened behavior, reduced plaque number, and an increase in proinflammatory signaling. While Gas6 has historically induced anti-inflammatory signatures in the peripheral nervous system, our data suggest an alternative, proinflammatory role in the context of Alzheimer’s disease pathology.
Long-Term Renal Safety Between Patients With Chronic Hepatitis B Receiving Tenofovir vs. Entecavir Therapy: A Multicenter Study
Authors: Chon Young Eun , Park Soo Young , Kim Seung Up , Hong Han Pyo , Lee Jae Seung , Lee Hye Won , Kim Mi Na , Park Jun Yong , Kim Do Young , Ahn Sang Hoon , Kim Beom Kyung 
Published: November 2021

Abstract
Background
Renal safety is a critical issue in chronic hepatitis B (CHB) patients receiving long-term entecavir (ETV) or tenofovir disofuroxil fumarate (TDF) therapy. We investigated their effects on estimated glomerular filtration rate (eGFR).
Methods
Treatment-naïve CHB patients receiving ETV or TDF for ≥1 year were recruited. The eGFR was assessed using the Chronic Kidney Disease Epidemiology Collaboration equation. We calculated average annual percent change (AAPC) in eGFR using Joinpoint regression.
Results
At beginning of observation, ETV group had unfavorable conditions than TDF group: lower eGFR and higher FIB-4 and APRI than TDF group (all P<0.001). After 6 years antiviral therapy, the mean eGFR in ETV group (n=1,793) was maintained (96.0 at first year to 95.6 mL/min/1.73 m2 at sixth year; AAPC -0.09%; P=0.322), whereas that in TDF group (n=1,240) significantly decreased annually (101.9 at first year to 96.9 mL/min/1.73 m2 at sixth year; AAPC -0.88%; P<0.001). Notably, in TDF group, even patients without diabetes (AAPC -0.80%; P=0.001) or hypertension (AAPC -0.87%; P=0.001) experienced significant decrease in eGFR. Expectably, accompanying diabetes (AAPC -1.59%; p=0.011) or hypertension (AAPC -1.00%; p=0.002) tended to accelerate eGFR decrease. TDF treatment (odds ratio 1.66, P<0.001), along with eGFR<60 mL/min/1.73 m2, serum albumin<3.5 mg/dL, and hypertension, were independently associated with ongoing renal dysfunction, defined as a negative slope of the mean eGFR change.
Conclusions
Compared to ETV, long-term TDF treatment induced slow, but progressive renal dysfunction. Although the annual eGFR change by TDF was small, careful monitoring is necessary, especially in patients requiring life-long therapy.
Analytical validity of DecisionDx-SCC, a gene expression profile test to identify risk of metastasis in cutaneous squamous cell carcinoma (SCC) patients
Authors: Borman Sherri , Wilkinson Jeff , Meldi-Sholl Lauren , Johnson Clare , Carter Kelsey , Covington Kyle R. , Fitzgerald Alison , Kurley Sarah J. , Farberg Aaron S. , Goldberg Matthew S. , Monzon Federico A. , Oelschlager Kristen , Cook Robert W. 
Published: November 2021

Abstract
Background
To improve identification of patients with cutaneous squamous cell carcinoma (SCC) at high risk for metastatic disease, the DecisionDx-SCC assay, a prognostic 40-gene expression profile (40-GEP) test, was developed and validated. The 40-GEP assay utilizes RT-PCR gene expression analysis on primary tumor biopsy tissue to evaluate the expression of 34 signature gene targets and 6 normalization genes. The test provides classifications of low risk (Class 1), moderate risk (Class 2A), and high risk (Class 2B) of metastasis within 3 years of diagnosis. The primary objective of this study was to validate the analytical performance of the 40 gene expression signature.
Methods
The repeatability and reproducibility of the 40-GEP test was evaluated by performance of inter-assay, intra-assay, and inter-operator precision experiments along with monitoring the reliability of sample and reagent stability for class call concordance. The technical performance of clinical orders from September 2020 through July 2021 for the 40-GEP test was assessed.
Results
Patient hematoxylin and eosin (H&E) stained slides were reviewed by a board-certified pathologist to assess minimum acceptable tumor content. Class specific controls (Class 1 and Class 2B) were evaluated with Levey Jennings analysis and demonstrated consistent and reproducible results. Inter-assay, inter-operator and intra-assay concordance were all ≥90%, with short-term and long-term RNA stability also meeting minimum concordance requirements. Of the 2,446 orders received, 93.4% remained eligible for testing, with 96.8% of all tested samples that completed the assay demonstrating actionable class call results.
Conclusion
DecisionDx-SCC demonstrates a high degree of analytical precision, yielding high concordance rates across multiple performance experiments, along with exhibiting robust technical reliability on clinical samples.
Revisiting Nonoperative Treatment of Lateral Compression Pelvic Fractures. Analysis of Rehabilitation and Radiologic Outcomes in a Historical Cohort Using Today's AO Stability Criteria.
Authors: Rojas Claudio , EWERTZ ERNESTO , Hormazabal Jose Miguel 
Published: November 2021

Abstract
Background: Type I lateral compression pelvic fractures (LC-I) have historically been treated conservatively. Inferior outcomes in a distinctive subset of these injuries has been reported, therefore their management has shifted towards surgery. Revisiting historical series of LC-I allows us to determine whether non-operative management of these unstable patterns result in poorer outcomes. The objective was to evaluate the differences in the rehabilitation progress, fracture consolidation and displacement in non-operatively treated LC-I fractures that would be considered unstable using today´s AO criteria.Methods: We conducted a retrospective review of conservatively treated LC-I injuries in a single level I trauma center, between June 2010 and June 2014. Patients were distributed in Stable (Group A) and unstable (Group B) groups according to 2018 AO classification. Time to walk independently (TWI), time to return to work (TRW), fracture consolidation and displacement were analyzed. Results: 34 patients, mean aged 45.5 ±14.5 years, were included. Mean TWI in groups A and B were 71.2 ±31.9 and 105.9 ±50.9 days (p=0.027). Mean TRW was 106 ±51.3 and 157 ±84 days in Groups A and B respectively (p=0.038). A difference in mean TWI and TRW of 34.7 and 51.3 days between groups was observed. No significant differences in fracture consolidation or displacement were observed.Conclusion: Unstable fractures presented significantly longer TWI and TRW. The revised AO classification contributes in the identification of fracture patterns that correlate with prolonged rehabilitation in which additional treatment strategies might be considered.
Genomics Analysis and Degradation Characteristics of Lignin by Streptomyces Thermocarboxydus Strain DF3-3
Authors: Tan Fangyun , Cheng Jun , Zhang Yu , Jiang Xingfu , Liu Yueqiu 
Published: November 2021

Abstract
Background: Lignocellulose is an important raw material for biomass-to-energy conversion, and it exhibits a complex but inefficient degradation mechanism. Microbial degradation is promising due to its environmental adaptability and biochemical versatility, but the pathways used by microbes for lignin degradation have not been fully studied. Degradation intermediates and complex metabolic pathways require more study.Results: A novel actinomycete DF3-3, with the potential for lignin degradation, was screened and isolated. After morphological and molecular identification, DF3-3 was determined to be Streptomyces thermocarboxydus. The degradation of alkali lignin reached 31% within 15 days. Manganese peroxidase and laccase demonstrated their greatest activity levels, 1821.66 UL-1 and 1265.58 UL-1, respectively, on the sixth day. The highest lignin peroxidase activity was 480.33 UL-1 on the fourth day. A total of 19 lignin degradation intermediates were identified by gas chromatography-mass spectrometry (GC-MS), including 10 aromatic compounds. Genome sequencing and annotation identified 107 lignin-degrading enzyme-coding genes containing three core enzymatic systems for lignin depolymerization: laccases, peroxidases and manganese peroxidase. In total, 7 lignin metabolic pathways were predicted.Conclusions: Streptomyces thermocarboxydus strain DF3-3 has good lignin degradation ability. Degradation products and genomics analyses of DF3-3 show that it has a relatively complete lignin degradation pathway, including the β-ketoadipate pathway and peripheral reactions; gentisate pathway; anthranilate pathway; homogentisic pathway; and catabolic pathway for resorcinol. Two other pathways, the phenylacetate-CoA pathway and the 2,3-dihydroxyphenylpropionic acid pathway, are predicted based on genome data alone. This study provides the basis for future characterization of potential biotransformation enzyme systems for biomass energy conversion.
Multiple distinct domains of human XIST are required to coordinate gene silencing and subsequent heterochromatin formation
Authors: Dixon-McDougall Thomas Alan , Brown Carolyn J. 
Published: November 2021

Abstract
Background
Mammalian dosage compensation is achieved by the inactivation of one X chromosome in XX individuals. In eutheria this process is initiated early in development by the long non-coding RNA XIST. Studies of the initiation of silencing by XIST have focussed on mouse models, so the domains of XIST required to induce silencing in humans, and their relationship with domains required to establish heterochromatin remain to be determined.
Methods
We have previously established an inducible XIST cDNA in somatic cells and shown it can induce silencing and recruit heterochromatic features. We now assess a series of deletions across the construct for the ability to induce silencing and integrate these results with time-course and chromatin remodelling inhibitor treatments to follow the steps of XIST-induced silencing and heterochromatinization.
Discussion
We find that in addition to the previously reported necessity of the 5’ A repeat region for XIST-induced silencing, the F repeat region and a non-repetitive region at the 3’ end of the RNA are also required to silence genes. Silencing of genes up to 17Mb from the XIST integration occurs within two days, while formation of a Cot-1 depleted domain is slower, and more dependent on repeat F. The role of Repeat F in both the silencing of actively transcribed genes, the spread of H3K27me3 and the formation of a transcriptionally inert domain suggests a role in a pathway crucial for the spread of XIST across the chromatin to target distal regions of inactivation. Histone deacetylation requires only the A repeat region, with HDAC3 inhibition showing limited effect on silencing, but an impact on H3K27me3 recruitment, and as a result the recruitment of MacroH2A. Global HDAC inhibition impacted silencing in both a distance and dose-dependent fashion. The E repeat region was required for CIZ1 and H4K20me1 recruitment as well as H3K27me3; however, these appeared to act relatively independently. The H3K27me3 mark established by PRC2 integrated silencing and many of the heterochromatic features, while the PRC1 mark ubH2A appeared to be downstream of silencing in these human somatic cells.
Enteric Methane Emission Estimates for the Zimbabwean Sanga Cattle Breeds of Tuli and Mashona
Authors: Gwatibaya Showman , Murungweni Chrispen , Mpofu Irvine , Jingura Raphael , Tigere Accadius Tinarwo , Tererai Bosiwe 
Published: November 2021

Abstract
The effectiveness of methane mitigation in ruminant livestock production systems depends on the accuracy of estimating methane emission factors and providing accurate emission inventories. Following the Paris Climate agreement, it is recommended that countries adopt the Tier-2 approach for estimating enteric methane emissions from ruminants instead of the Tier-1 approach currently used by most countries. This study sought to provide base line enteric methane emission estimates for the Tuli and Mashona Sanga cattle breeds in Zimbabwe using the IPCC Tier-2 model. Using animal characterization data collected from 412 cattle from Grasslands Research Institute and 406 cattle from Makoholi Research Institute, net energy requirements were estimated. From this and the estimate for digestibility, gross energy intake and dry matter intake were estimated. Gross energy intakes and the estimated methane conversion factor were used to estimate enteric methane emissions. Mean emission factors for Tuli were 45.1, 56, 28.5, 28.4, 20.6kg CH4/head/year for cows, bulls, heifers, steers and calves respectively. For Mashona, they were 47.8, 51.9, 29, 29.1 and 20.7kgCH4/head/year for cows, bulls, heifers, steers and calves respectively. Generally, estimated Tier-2 emission factors were significantly different from the IPCC Tier-1 default emission factors. This study concluded that enteric methane emission factors estimated using the IPCC Tier-2 model offer insights into the controversial use of the default IPCC Tier-1 emission factors.
B Cell Subsets in Colombian Adults With Predominantly Antibody Deficiencies, Bronchiectasis or Recurrent Pneumonia
Authors: Giraldo-Ocampo Sebastian , Perdomo Anilza Bonelo , Zea-Vera Andrés Felipe 
Published: November 2021

Abstract
Purpose.

To evaluate lymphocyte’s populations and B cell subsets in patients presenting with PAD diagnosed with bronchiectasis or recurrent pneumonia seen in Cali (Colombian Southwest region).
Methods.

16 patients with PAD, 20 with bronchiectasis or recurrent pneumonia and 20 healthy controls were included. Lymphocyte populations (T, B & NK cells) and B cell subsets were evaluated in Peripheral Blood mononuclear cells (PBMC) using flow cytometry, using the T/B/NK reagent and the pre-germinal center antibody panel proposed by the EUROflow consortium, respectively. Clinical and sociodemographic data was collected (hospital records and interview). EUROclass and the classification proposed by Driessen et al were implemented.
Results.

B cell subsets were disturbed when compared to the age range matched healthy donors. Among B cell subsets,memory B cellcompartment was the most affected, especially switched memory B cells. Four participants were classified as B- and two CVID as smB-Trnorm and smB-21lo groups according to EUROclass classification. The most frequent pattern proposed by Driessen et al were B-cell production and germinal center defect. PAD participants also showed alteration in the B cell subsets correlation. Non-PAD participants with pulmonary complication also had alteration in B cell subsets.
Blockade of Myd88 Signaling by Novel MyD88 Inhibitor Prevents Colitis-associated Colorectal Cancer From Development by Impairing Myeloid-Derived Suppressor Cells
Authors: Wang Lu , Hu Dan , Xie Bin , Xie Lin 
Published: November 2021

Abstract
Background: Myeloid-derived suppressor cells (MDSCs) are currently confirmed to be due to escaping the host immune system of tumor by developing a highly suppressive environment. MDSC elimination provides an ideal target for tumor immunotherapy. However, little is still known about the exact molecular mechanism behind MDSC-mediated tumor immune evasion. Methods: We used a novel myeloid differentiation factor 88 (MyD88) inhibitor TJ-M2010-5 to block the MyD88 signaling and prevent colitis-associated colorectal cancer (CAC) development in mice. Results: We showed that CAC growth inhibition was involved in diminished MDSC generation, expansion, and suppressive function, and that the MDSC-mediated immune escape was dependent on the MyD88 signaling pathway activation. The MyD88 inhibitor treatment decreased accumulation of CD11b+Gr1+ MDSC in mice with CAC, thereby reducing cytokine (GM-CSF, G-CSF, IL-1β, IL-6 and TGF-β) secretion associated with MDSC accumulation, and reducing expression of molecules (iNOS, Arg-1 and IDO) associated with the suppressive capacity of MDSC. In addition, the MyD88 inhibitor treatment reduced the differentiation of MDSC from myeloid cells and the suppressive capacity of MDSC on proliferation of activated CD4+ T cell in vitro. Conclusion: Therefore, MDSC is a primary cellular target of the novel MyD88 inhibitor during CAC development. Our findings prove that MyD88 signaling is involved in the regulation of the immunosuppressive functions of MDSC. Our novel MyD88 inhibitor, TJ-M2010-5, is a new and effective agent that modulates MyD88 signaling to overcome MDSC suppressive functions and to enable the development of a successful antitumor immunotherapy.
Becoming Entangled: Queer Attachments with Hemiparasites
Authors: Instone Lesley , D'Costa Rhett 
Published: November 2021

What is that queer plant that drapes itself chaotically over the top of trees and bushes? You know the one along the road on the way into town?
Ah yes! You mean the one with no leaves, that looks like tangled yarn caught up in the branches?
Yes, it looks like its floating airborne on top of the canopy, smothering and embracing at the same time.
Well, that's the one with the common name of snotty gobble or Dodder-Laurel!!! Dodder may look chaotic but that only demands on how you view it.
I can’t stop thinking about it, Let’s find out what it’s doing.
‘Learning to be affected’ says Bruno Latour is to be 'moved, put into motion by other entities, humans or non-humans’(2004). And this is what happened to Down the Road Projects when we became intrigued with local plant parasites where we live in central Victoria, Australia.
This paper explores how we became ensnared by planty agencies. By charting our multispecies and human interactions in the course of developing the art project, Becoming Differently (2018), we trace how parasites came to be an important theme of the art, how they infiltrated the art works, how they changed our understanding of parasites, how they enticed us into the bush and developed our style of collaboration.
We ‘queery’ what it means to be ‘drawn towards’ particular plants, we wonder who or what is ‘drawing’, and how these particular plants inflected our art and writing. We consider how we were moved towards different ways of figuring identity and belonging, and how we grappled with practices and modes of engagement with complex issues of identity, belonging and nature in a settler-colonial situation, and how this led to us to become differently entangled in the place where we live.
Structural Proteomics: Detection of Neurodegenerative Protein Modifications
Authors: Khurana Mallika , Rahman Syed Obaidur , Agarwal Shivani , Akhtar Md. Sayeed , Aldughaim Mohammed S. , Pottoo Faheem Hyder , Najmi Abul Kalam 
Published: November 2021

:
For decades now, neurodegenerative disorders have been explored, but their prompt detection
is still very strenuous due to the complexity of the brain. This entails the demand for identification
and development of clinical biomarkers in order to comply with the criteria of precision,
specificity and repeatability. The use of rapidly evolving technologies such as Mass Spectrometry
(MS) in proteomics has opened new ways to speed up the discovery of biomarkers, both for diagnostic
and prognostic purposes. The wide range of possibilities for the detection of differentially expressed
proteins in specific diseases has been opened by several novel proteomic techniques such
as cross-linking mass spectrometry, hydrogen-deuterium exchange mass spectrometry, protein foot
printing and more. Still, much research is required to give a deep insight into the complex system
of the brain and its related disorders for unraveling prognostic and diagnostic biomarkers, which
can be used to either enhance a certain function of our brain or to cure a particular disease/disorder.
This review summarizes the latest developments in neuroproteomics and analyzes existing and potential
directions for the discovery of biomarkers for neurodegenerative diseases.