bluuebunny/crossref_metadata_2025 huggingface dataset:
Do cover crops suppress weeds in the U.S. Southeast? A meta-analysis
Authors: Weisberger David A. , Bastos Leonardo M. , Sykes Virginia R. , Basinger Nicholas T.
Published: April 2023

Cover crops (CCs) have shown great potential for suppressing annual weeds within agronomic cropping systems across the United States. However, the weed suppressive potential of CCs may be moderated by environmental and management factors that are specific to certain geographic areas and their associated characteristics. This may be particularly true within the U.S. Southeast, where higher mean annual temperature and precipitation generate favorable conditions for both CC and weed growth. To understand the effects of this regional context on CCs and weeds, a meta-analysis examining paired comparisons of weed biomass and/or weed density under CC and bare ground conditions from studies conducted within the Southeast was conducted. Data were identified and extracted from 28 journal articles in which weed biomass and/or weed density were measured along with cash crop yield data, if they were provided. Fourteen studies provided 142 comparisons for weed biomass; 23 studies provided 139 comparisons for weed density; and 22 studies, pooled over both weed response variables, provided 144 comparisons for cash crop yield. CCs had a negative effect on weed density (P = 0.0016) but no effect on either weed biomass (P = 0.16) or cash crop yield (P = 0.88). The mean relative reduction in weed density under CCs was 44%. Subsequent analyses indicated that CC biomass was the key factor associated with this reduction. Weed density suppression was linearly related to CC biomass; a 50% decrease in weed density was associated with 6,600 kg ha−1 of CC biomass. Edaphic, geographic, and other management factors had no bearing on this suppressive effect. This highlights the importance of generating adequate CC biomass if weed suppression is the primary objective of CC use and the potential for CCs to reduce weed density over diverse soil, climate, and farm management conditions.
Changing the Unpredictable Nature of Internal Tides Through Deep Learning
Authors: Li Bingtian , Wang Yufei , Wei Zexun , Pan Haidong , Xu Tengfei , Lv Xianqing
Published: April 2023

Nonstationary internal tides (ITs) are formed from their interactions with background currents. Harmonic analysis (HA), which cannot be used to estimate the incoherent component, is almost exclusively used method to predict ITs from observations. This remains ITs prediction challenge. In this study, we establish a deep learning framework to predict semidiurnal ITs. The model is established and trained with observed semidiurnal internal tidal currents that are 172 days long, and then ITs over the next 42 days are forecasted. The prediction accuracy is greatly improved using the deep learning framework. The magnitudes of errors using the deep learning framework are approximately 35% of those obtained using HA. Most temporal and spatial variations in baroclinic currents can successfully be forecasted using deep learning. In addition, the kinetic energy and incoherent components of ITs can be accurately predicted. Moreover, the relatively high adoptability of the established deep learning model is shown.
Formation and Motion of Horse Collar Aurora Events
Authors: Bower G. E. , Milan S. E. , Paxton L. J. , Spanswick E. , Hairston M. R.
Published: April 2023

The polar cap can become teardrop shaped through the poleward expansion of the dusk and dawn sectors of the auroral oval, to form what is called horse collar aurora (HCA). The formation of HCA has been linked to dual‐lobe reconnection (DLR) where magnetic flux is closed at the dayside magnetopause. A prolonged period of northward IMF is required for the formation of HCA. HCA have previously been identified in UV images captured by the Special Sensor Ultraviolet Spectrographic Imager (SSUSI) instrument on‐board the Defense Meteorological Satellite Program (DMSP) spacecraft F16, F17 and F18. Events that have concurrent 630.0 nm all‐sky camera (ASC) data from the Redline Geospace Observatory (REGO) Resolute Bay site are now studied in more detail, making use of the higher cadence of the ASC images compared to DMSP/SSUSI. 11 HCA events are studied and classified based on the IMF conditions at the end of the event. Five of the events were found to end via a southward turning of the IMF, two end with positive By dominated IMF and four with negative By dominance. Under positive (negative) By the arcs move duskward (dawnward) in the northern hemisphere with the opposite true in the southern hemisphere. Under a southward turning the arcs move equatorward. One event is of particular interest as it occurred while there was a transpolar arc (TPA) also present. Understanding the evolution of HCA will allow DLR to be studied in more detail.
Estimating Coccolithophore PIC:POC Based on Coccosphere and Coccolith Geometry
Authors: Jin Xiaobo , Liu Chuanlian
Published: April 2023

The marine biological calcification and photosynthesis, which can produce particulate inorganic and organic carbon (PIC and POC), have the opposite effects on seawater pCO2. Coccolithophores are a kind of marine unicellular algae with both of the two biological processes, and PIC and POC productions of them can shape the water column rain ratio as a dominant driver for Earth's carbon cycle. Thus, the changes in ancient coccolithophore PIC:POC can be important for the paleoceanographic and paleoclimatic studies of carbon cycle modeling. However, ancient coccolithophore PIC:POC is poorly constrained because of the occasional occurrences of intact coccospheres in deep ocean sediments, as detached coccoliths are commonly the remnants of fossilized coccolithophores. Here, we carry out the biometric analysis of coccosphere and coccolith from the living cells of Emiliania huxleyi and Gephyrocapsa oceanica in the South China Sea, and confirm a significant correlationship between their PIC:POC and lateral coccolith aspect ratio (ARL). ARL here is defined by the ratio of mean coccolith thickness with respect to coccolith length. A linear regression is given, (R2 = 0.59, n = 121), for the reconstruction of ancient Noelaerhabdaceae coccolithophore PIC:POC based on individual coccoliths in marine sediments. Based on this equation, we reconstruct ancient Noelaerhabdaceae coccolithophore PIC:POC since 14 million years ago (Ma) using published coccolith data, which reveal a long‐term decrease in PIC:POC from 7 to 4 Ma. We suggest that such a change in coccolithophore physiology may be induced by a simultaneous long‐term decline in seawater calcium concentration.
Using Lagrangian Filtering to Remove Waves From the Ocean Surface Velocity Field
Authors: Jones C. Spencer , Xiao Qiyu , Abernathey Ryan P. , Smith K. Shafer
Published: April 2023

The Surface Water and Ocean Topography satellite will measure altimetry on scales down to about 15 km: at these scales, the sea‐surface‐height signature of inertia‐gravity waves, including barotropic tides and internal tides, will be visible. However, tides and inertia‐gravity waves have little impact on tracer transport. Recent work has shown that Lagrangian filtering can be used to isolate the inertia‐gravity wave part of the flow. This manuscript presents a recipe for removing barotropic motions and inertia‐gravity waves from the surface velocities and from the sea‐surface height (SSH), to estimate the non‐wave part of the flow in the Agulhas region of a high‐resolution ocean model (LLC4320). First, two methods for removing the barotropic component of SSH variability are presented. Then Lagrangian filtering, a method that accounts for Doppler shifting of high‐frequency motions by the low‐frequency velocity field, is applied to both the SSH and the ocean surface velocity field. The results of Lagrangian filtering are presented in spectral space. Lagrangian filtering preserves motions that appear super‐inertial in the reference frame of the Earth, while other methods do not preserve these motions as effectively. In some locations most of the energy at high frequencies comes from these Doppler shifted balanced motions. We show that the non‐wave part of the velocity field that is preserved more effectively by Lagrangian filtering includes convergent motions near regions of frontogenesis.
Quantification of Physical and Numerical Mixing in a Coastal Ocean Model Using Salinity Variance Budgets
Authors: Schlichting Dylan , Qu Lixin , Kobashi Daijiro , Hetland Robert
Published: April 2023

Numerical mixing, the spurious mixing primarily generated by the discretization of advection, is often significant in estuarine and coastal models due to sharp, energetic fronts. We compare on‐ and offline estimates of numerical mixing in a submesoscale‐resolving realistic simulation of the ocean state over the Texas‐Louisiana continental shelf. While offline estimates of numerical mixing differ from online estimates, offline methods may be the only analysis available. We use two methods to estimate numerical mixing offline based on the residuals of the salinity squared s2 and volume‐mean salinity variance budgets. The budget overestimates the time‐averaged online numerical mixing by 60% at hourly output. The s2 budget compares poorly due to large truncation errors associated with the tendency and advection terms. The residual of the s2 budget starts to converge to the budget as output frequency increases to 10 min—an unrealistic frequency for long‐term coastal ocean simulations—but neither method unconditionally converges to the online method and therefore cannot be recommended for generic analysis of numerical mixing. We also investigate the effects of horizontal resolution on numerical mixing using a two‐way nested grid with the online method. The volume‐integrated numerical mixing constitutes 57% of the bulk physical mixing—the mixing prescribed by the turbulence closure scheme—in the coarse model and may exceed the physical mixing by half an order of magnitude. We find numerical mixing is reduced by 35% on average in the nested model, likely due to new dynamical processes that emerge in the nested simulation.
Giving Some Tooth to Precambrian Carbonates and the Tales They Tell About Ancient Oceans
Authors: Lyons Timothy W. , Tu Chenyi , Hancock Leanne
Published: April 2023

Enigmatic is a word that often comes up in discussions about Proterozoic molar tooth carbonate structures (MTS). But when unusual features such as these are common in rocks of a particular age, there is almost always an important message waiting to be discovered. In this case, the observed temporal patterns for MTS likely track first‐order trends in evolving compositions in the oceans during Earth's middle history when CO2 in the atmosphere and carbonate saturation in the ocean were high but declining and oxygen (O2) in the ocean‐atmosphere system was on the rise. A new paper by Tang et al. (2023, https://doi.org/10.1029/2022JG007077) gives us a new way to think about MTS origins, and nested within their model are wide ranging implicit and explicit linkages to Earth surface evolution as life was becoming more complex in a slow march toward the world we know today.
PRR15 deficiency facilitates malignant progression by mediating PI3K/Akt signaling and predicts clinical prognosis in triple-negative rather than non-triple-negative breast cancer
Authors: Guo Fengzhu , Ma Jialu , Li Cong , Liu Shuning , Wu Weizheng , Li Chunxiao , Wang Jiani , Wang Jinsong , Li Zhijun , Zhai Jingtong , Sun Fangzhou , Zhou Yantong , Guo Changyuan , Qian Haili , Xu Binghe
Published: April 2023

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast neoplasms with a higher risk of recurrence and metastasis than non-TNBC. Nevertheless, the factors responsible for the differences in the malignant behavior between TNBC and non-TNBC are not fully explored. Proline rich 15 (PRR15) is a protein involved in the progression of several tumor types, but its mechanisms are still controversial. Therefore, this study aimed to investigate the biological role and clinical applications of PRR15 on TNBC. PRR15 gene was differentially expressed between TNBC and non-TNBC patients, previously described as an oncogenic factor in breast cancer. However, our results showed a decreased expression of PRR15 that portended a favorable prognosis in TNBC rather than non-TNBC. PRR15 knockdown facilitated the proliferation, migration, and invasive ability of TNBC cells in vitro and in vivo, which was abolished by PRR15 restoration, without remarkable effects on non-TNBC. High-throughput drug sensitivity revealed that PI3K/Akt signaling was involved in the aggressive properties of PRR15 silencing, which was confirmed by the PI3K/Akt signaling activation in the tumors of PRR15Low patients, and PI3K inhibitor reversed the metastatic capacity of TNBC in mice. The reduced PRR15 expression in TNBC patients was positively correlated with more aggressive clinicopathological characteristics, enhanced metastasis, and poor disease-free survival. Collectively, PRR15 down-regulation promotes malignant progression through the PI3K/Akt signaling in TNBC rather than in non-TNBC, affects the response of TNBC cells to antitumor agents, and is a promising indicator of disease outcomes in TNBC.
RIPK3 promoter hypermethylation in hepatocytes protects from bile acid-induced inflammation and necroptosis
Authors: Hoff Jessica , Xiong Ling , Kammann Tobias , Neugebauer Sophie , Micheel Julia M. , Gaßler Nikolaus , Bauer Michael , Press Adrian T.
Published: April 2023

Necroptosis facilitates cell death in a controlled manner and is employed by many cell types following injury. It plays a significant role in various liver diseases, albeit the cell-type-specific regulation of necroptosis in the liver and especially hepatocytes, has not yet been conceptualized. We demonstrate that DNA methylation suppresses RIPK3 expression in human hepatocytes and HepG2 cells. In diseases leading to cholestasis, the RIPK3 expression is induced in mice and humans in a cell-type-specific manner. Overexpression of RIPK3 in HepG2 cells leads to RIPK3 activation by phosphorylation and cell death, further modulated by different bile acids. Additionally, bile acids and RIPK3 activation further facilitate JNK phosphorylation, IL-8 expression, and its release. This suggests that hepatocytes suppress RIPK3 expression to protect themselves from necroptosis and cytokine release induced by bile acid and RIPK3. In chronic liver diseases associated with cholestasis, induction of RIPK3 expression may be an early event signaling danger and repair through releasing IL-8.
Disease-related p63 DBD mutations impair DNA binding by distinct mechanisms and varying degree
Authors: Osterburg Christian , Ferniani Marco , Antonini Dario , Frombach Ann-Sophie , D’Auria Ludovica , Osterburg Susanne , Lotz Rebecca , Löhr Frank , Kehrloesser Sebastian , Zhou Huiqing , Missero Caterina , Dötsch Volker
Published: April 2023

The transcription factor p63 shares a high sequence identity with the tumour suppressor p53 which manifests itself in high structural similarity and preference for DNA sequences. Mutations in the DNA binding domain (DBD) of p53 have been studied in great detail, enabling a general mechanism-based classification. In this study we provide a detailed investigation of all currently known mutations in the p63 DBD, which are associated with developmental syndromes, by measuring their impact on transcriptional activity, DNA binding affinity, zinc binding capacity and thermodynamic stability. Some of the mutations we have further characterized with respect to their ability to convert human dermal fibroblasts into induced keratinocytes. Here we propose a classification of the p63 DBD mutations based on the four different mechanisms of DNA binding impairment which we identified: direct DNA contact, zinc finger region, H2 region, and dimer interface mutations. The data also demonstrate that, in contrast to p53 cancer mutations, no p63 mutation induces global unfolding and subsequent aggregation of the domain. The dimer interface mutations that affect the DNA binding affinity by disturbing the interaction between the individual DBDs retain partial DNA binding capacity which correlates with a milder patient phenotype.
PHF14 enhances DNA methylation of SMAD7 gene to promote TGF-β-driven lung adenocarcinoma metastasis
Authors: Tian Han , Liu Chenying , Yu Jianchen , Han Jian , Du Jianan , Liang Shujun , Wang Wenting , Liu Qin , Lian Rong , Zhu Ting , Wu Shanshan , Tao Tianyu , Ye Yaokai , Zhao Jingjing , Yang Yi , Zhu Xun , Cai Junchao , Wu Jueheng , Li Mengfeng
Published: April 2023

Aberrant activation of TGF-β signaling plays a pivotal role in cancer metastasis and progression. However, molecular mechanisms underlying the dysregulation of TGF-β pathway remain to be understood. Here, we found that SMAD7, a direct downstream transcriptional target and also a key antagonist of TGF-β signaling, is transcriptionally suppressed in lung adenocarcinoma (LAD) due to DNA hypermethylation. We further identified that PHF14 binds DNMT3B and serves as a DNA CpG motif reader, recruiting DNMT3B to the SMAD7 gene locus, resulting in DNA methylation and transcriptional suppression of SMAD7. Our in vitro and in vivo experiments showed that PHF14 promotes metastasis through binding DNMT3B to suppress SMAD7 expression. Moreover, our data revealed that PHF14 expression correlates with lowered SMAD7 level and shorter survival of LAD patients, and importantly that SMAD7 methylation level of circulating tumor DNA (ctDNA) can potentially be used for prognosis prediction. Together, our present study illustrates a new epigenetic mechanism, mediated by PHF14 and DNMT3B, in the regulation of SMAD7 transcription and TGF-β-driven LAD metastasis, and suggests potential opportunities for LAD prognosis.
Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation
Authors: Hughes Laetitia A. , Rudler Danielle L. , Siira Stefan J. , McCubbin Tim , Raven Samuel A. , Browne Jasmin M. , Ermer Judith A. , Rientjes Jeanette , Rodger Jennifer , Marcellin Esteban , Rackham Oliver , Filipovska Aleksandra
Published: April 2023

The number of tRNA isodecoders has increased dramatically in mammals, but the specific molecular and physiological reasons for this expansion remain elusive. To address this fundamental question we used CRISPR editing to knockout the seven-membered phenylalanine tRNA gene family in mice, both individually and combinatorially. Using ATAC-Seq, RNA-seq, ribo-profiling and proteomics we observed distinct molecular consequences of single tRNA deletions. We show that tRNA-Phe-1-1 is required for neuronal function and its loss is partially compensated by increased expression of other tRNAs but results in mistranslation. In contrast, the other tRNA-Phe isodecoder genes buffer the loss of each of the remaining six tRNA-Phe genes. In the tRNA-Phe gene family, the expression of at least six tRNA-Phe alleles is required for embryonic viability and tRNA-Phe-1-1 is most important for development and survival. Our results reveal that the multi-copy configuration of tRNA genes is required to buffer translation and viability in mammals.
Damage dynamics and the role of chance in the timing of E. coli cell death
Authors: Yang Yifan , Karin Omer , Mayo Avi , Song Xiaohu , Chen Peipei , Santos Ana L. , Lindner Ariel B. , Alon Uri
Published: April 2023

Genetically identical cells in the same stressful condition die at different times. The origin of this stochasticity is unclear; it may arise from different initial conditions that affect the time of demise, or from a stochastic damage accumulation mechanism that erases the initial conditions and instead amplifies noise to generate different lifespans. To address this requires measuring damage dynamics in individual cells over the lifespan, but this has rarely been achieved. Here, we used a microfluidic device to measure membrane damage in 635 carbon-starved Escherichia coli cells at high temporal resolution. We find that initial conditions of damage, size or cell-cycle phase do not explain most of the lifespan variation. Instead, the data points to a stochastic mechanism in which noise is amplified by a rising production of damage that saturates its own removal. Surprisingly, the relative variation in damage drops with age: cells become more similar to each other in terms of relative damage, indicating increasing determinism with age. Thus, chance erases initial conditions and then gives way to increasingly deterministic dynamics that dominate the lifespan distribution.
Highly conductive tissue-like hydrogel interface through template-directed assembly
Authors: Chong Jooyeun , Sung Changhoon , Nam Kum Seok , Kang Taewon , Kim Hyunjun , Lee Haeseung , Park Hyunchang , Park Seongjun , Kang Jiheong
Published: April 2023

Over the past decade, conductive hydrogels have received great attention as tissue-interfacing electrodes due to their soft and tissue-like mechanical properties. However, a trade-off between robust tissue-like mechanical properties and good electrical properties has prevented the fabrication of a tough, highly conductive hydrogel and limited its use in bioelectronics. Here, we report a synthetic method for the realization of highly conductive and mechanically tough hydrogels with tissue-like modulus. We employed a template-directed assembly method, enabling the arrangement of a disorder-free, highly-conductive nanofibrous conductive network inside a highly stretchable, hydrated network. The resultant hydrogel exhibits ideal electrical and mechanical properties as a tissue-interfacing material. Furthermore, it can provide tough adhesion (800 J/m2) with diverse dynamic wet tissue after chemical activation. This hydrogel enables suture-free and adhesive-free, high-performance hydrogel bioelectronics. We successfully demonstrated ultra-low voltage neuromodulation and high-quality epicardial electrocardiogram (ECG) signal recording based on in vivo animal models. This template-directed assembly method provides a platform for hydrogel interfaces for various bioelectronic applications.
Phase I study of A166, an antibody‒drug conjugate in advanced HER2-expressing solid tumours
Authors: Zhang Jian , Liu Rujiao , Gao Shuiping , Li Wenhua , Chen Yang , Meng Yanchun , Liu Chang , Jin Wenyue , Wu Junyan , Wang Ying , Hao Yanrong , Yi Shuli , Qing Yan , Ge Junyou , Hu Xichun
Published: April 2023

In this phase I study, the safety, pharmacokinetics, and antitumour activity of the HER2-targeted antibody–drug conjugate A166 were evaluated in patients with HER2-expressing advanced solid tumours. Patients with advanced solid tumours refractory to standard therapies received A166 at doses of 0.1, 0.3, 0.6, 1.2, 2.4, 3.6, 4.8 or 6.0 mg/kg Q3W in a standard “3 + 3” design. Dose cohorts were expanded at 4.8 and 6.0 mg/kg Q3W. Primary endpoints were assessment of the safety and tolerability of A166 and identification of the maximum tolerated dose or recommended phase II dose. In total, 81 patients were enroled and received A166 (n = 1 for 0.1 mg/kg;n = 3 for each of 0.3, 0.6, 1.2, 2.4 and 3.6 mg/kg doses;n = 27 for 4.8 mg/kg;n = 38 for 6.0 mg/kg). No dose-limiting toxicity or drug-related deaths occurred. The most common treatment-related adverse events at grade 3 or higher were corneal epitheliopathy (30.9%), blurred vision (18.5%), dry eyes (7.4%), and peripheral sensory neuropathy (6.2%). The Cmaxand area under the curve of Duo-5, its free payload, were approximately 0.1% and 0.2% of those of the ADC, respectively. For all assessable HER2-positive breast cancer patients enroled in the 4.8 mg/kg and 6.0 mg/kg cohorts, the corresponding ORRs were 73.9% (17/23) and 68.6% (24/35), respectively, and the median PFS was 12.3 and 9.4 months, respectively. A166 has a recommended phase II dose of 4.8 mg/kg Q3W, manageable toxicity, good stability in the circulation and promising antitumour activities in HER2-positive breast cancer patients.
Free-living bacteria stimulate sugarcane growth traits and edaphic factors along soil depth gradients under contrasting fertilization
Authors: Fallah Nyumah , Tayyab Muhammad , Yang Ziqi , Pang Ziqin , Zhang Caifang , Lin Zhaoli , Stewart Lahand James , Ntambo Mbuya Sylvain , Abubakar Ahmad Yusuf , Lin Wenxiong , Zhang Hua
Published: April 2023

Free-living bacterial community and abundance have been investigated extensively under different soil management practices. However, little is known about their nitrogen (N) fixation abilities, and how their contributions to N budgets impact plant growth, yield, and carbon (C) and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons. Here, nifH gene amplicon was used to investigate diazotrophs bacterial community and abundance by leveraging high-throughput sequencing (HTS). Moreover, edaphic factors in three soil depths (0–20, 20–40, and 40–60 cm) under control (CK), organic matter (OM), biochar (BC), and filter mud (FM) amended soils were investigated. Our analysis revealed that β-glucosidase activity, acid phosphatase activity, ammonium (NH4+-N), nitrate (NO3–N), total carbon (TC), total nitrogen (TN), and available potassium (AK) were considerably high in 0–20 cm in all the treatments. We also detected a significantly high proportion of Proteobacteria and Geobacter in the entire sample, including Anabaena and Enterobacter in 0–20 cm soil depth under the BC and FM amended soils, which we believed were worthy of promoting edaphic factors and sugarcane traits. This phenomenon was further reinforced by network analysis, where diazotrophs bacteria belonging to Proteobacteria exhibited strong and positive associations soil electrical conductivity (EC), soil organic matter content (SOM) available phosphorus (AP), TN, followed by NH4+-N and NO3–N, a pattern that was further validated by Mantel test and Pearson’s correlation coefficients analyses. Furthermore, some potential N-fixing bacteria, including Burkholderia, Azotobacter, Anabaena, and Enterobacter exhibited a strong and positive association with sugarcane agronomic traits, namely, sugarcane stalk, ratoon weight, and chlorophyll content. Taken together, our findings are likely to broaden our understanding of free-living bacteria N-fixation abilities, and how their contributions to key soil nutrients such as N budgets impact plant growth and yield, including C and N cycling enzymes in a long-term consecutive sugarcane monoculture farming system, under contrasting amendments, along different soil horizons.
Association between adherence to the Dietary Approaches to Stop Hypertension diet and serum uric acid
Authors: Feng Jie , Huang Yuchai , Wang Haozhuo , Wang Chao , Xu Hongbin , Ke Pan , He Yan , Tian Qingfeng , Cao Shiyi , Lu Zuxun
Published: April 2023

To explore the relationship between Dietary Approaches to Stop Hypertension (DASH) diet and serum uric acid (SUA) levels among the Chinese adult population, and verify the mediating effect of BMI between DASH diet and SUA levels. A total of 1125 adults were investigated using a self-administered food frequency questionnaire. SUA levels were determined by uricase colorimetry. The total DASH score ranged from 9 to 72. The relationship between the DASH diet and SUA levels was examined by multiple adjusted regression analysis. Method of Bootstrap was used to test the mediation effect of BMI in the correlation of the DASH diet and SUA levels. After multivariable adjustment, there was a significant linear relationship between the DASH diet and SUA (P < 0.001). Compared with the lowest group, SUA of participants in group of highest DASH diet score decreased by 34.907 (95% CI − 52.227, − 17.588; P trend < 0.001) μmol/L. The association between the DASH diet scores and SUA levels was partly mediated by BMI (− 0.26, Bootstrap 95% CI − 0.49, − 0.07), with 10.53% of the total effect being mediated. Adopting the DASH diet might be helpful in reducing SUA level, and the effect might be partly mediated by BMI.
Single-particle properties of topological Wannier excitons in bismuth chalcogenide nanosheets
Authors: Maisel Licerán Lucas , García Flórez Francisco , Siebbeles Laurens D. A. , Stoof Henk T. C.
Published: April 2023

We analyze the topology, dispersion, and optical selection rules of bulk Wannier excitons in nanosheets of Bi2Se3, a topological insulator in the family of the bismuth chalcogenides. Our main finding is that excitons also inherit the topology of the electronic bands, quantified by the skyrmion winding numbers of the constituent electron and hole pseudospins as a function of the total exciton momentum. The excitonic bands are found to be strongly indirect due to the band inversion of the underlying single-particle model. At zero total momentum, we predict that the s-wave and d-wave states of two exciton families are selectively bright under left- or right-circularly polarized light. We furthermore show that every s-wave exciton state consists of a quartet with a degenerate and quadratically dispersing nonchiral doublet, and a chiral doublet with one linearly dispersing mode as in transition metal dichalcogenides. Finally, we discuss the potential existence of topological edge states of chiral excitons arising from the bulk-boundary correspondence.
Rational peptide design for inhibition of the KIX–MLL interaction
Authors: Sato Nao , Suetaka Shunji , Hayashi Yuuki , Arai Munehito
Published: April 2023

The kinase-inducible domain interacting (KIX) domain is an integral part of the general transcriptional coactivator CREB-binding protein, and has been associated with leukemia, cancer, and various viral diseases. Hence, the KIX domain has attracted considerable attention in drug discovery and development. Here, we rationally designed a KIX inhibitor using a peptide fragment corresponding to the transactivation domain (TAD) of the transcriptional activator, mixed-lineage leukemia protein (MLL). We performed theoretical saturation mutagenesis using the Rosetta software to search for mutants expected to bind KIX more tightly than the wild-type MLL TAD. Mutant peptides with higher helical propensities were selected for experimental characterization. We found that the T2857W mutant of the MLL TAD peptide had the highest binding affinity for KIX compared to the other 12 peptides designed in this study. Moreover, the peptide had a high inhibitory effect on the KIX–MLL interaction with a half-maximal inhibitory concentration close to the dissociation constant for this interaction. To our knowledge, this peptide has the highest affinity for KIX among all previously reported inhibitors that target the MLL site of KIX. Thus, our approach may be useful for rationally developing helical peptides that inhibit protein–protein interactions implicated in the progression of various diseases.
Factor-specific generative pattern from large-scale drug-induced gene expression profile
Authors: Ahn Se Hwan , Kim Ju Han
Published: April 2023

Drug discovery is a complex and interdisciplinary field that requires the identification of potential drug targets for specific diseases. In this study, we present FacPat, a novel approach that identifies the optimal factor-specific pattern explaining the drug-induced gene expression profile. FacPat uses a genetic algorithm based on pattern distance to mine the optimal factor-specific pattern for each gene in the LINCS L1000 dataset. We applied Benjamini–Hochberg correction to control the false discovery rate and identified significant and interpretable factor-specific patterns consisting of 480 genes, 7 chemical compounds, and 38 human cell lines. Using our approach, we identified genes that show context-specific effects related to chemical compounds and/or human cell lines. Furthermore, we performed functional enrichment analysis to characterize biological features. We demonstrate that FacPat can be used to reveal novel relationships among drugs, diseases, and genes.
Anaerobic co-digestion of grass and cow manure: kinetic and GHG calculations
Authors: Ulukardesler Ayse Hilal
Published: April 2023

Grass is a highly desirable substrate for anaerobic digestion because of its higher biodegradability and biogas/methane yield. In this study, anaerobic co-digestion of grass, cow manure and sludge was studied under mesophilic conditions for 65 days. Experiments were performed on a feed ratio of grass/manure from 5 to 25%, respectively. The maximum cumulative biogas and methane yield was obtained as 331.75 mLbiogas/gVS and 206.64 mLCH4/gVS for 25% ratio. Also, the results of the experiments were tested on the three different kinetics model which are the first order kinetic model, modified Gompertz model and Logistics model. As a result of the study, it was found that by using grass nearly 480 × 106 kWh/year electricity may be produced and 0.5 × 106 tons/year CO2 greenhouse gas emission mitigation may be reached.
A pathogenicity locus of Streptococcus gallolyticus subspecies gallolyticus
Authors: Taylor John Culver , Kumar Ritesh , Xu Juan , Xu Yi
Published: April 2023

Streptococcus gallolyticus subspecies gallolyticus (Sgg) is known to be strongly associated with colorectal cancer (CRC). Recent functional studies further demonstrated that Sgg actively stimulates CRC cell proliferation and promotes the development of colon tumors. However, the Sgg factors important for the pro-proliferative and pro-tumor activities of Sgg remain unclear. Here, we identified a chromosomal locus in Sgg strain TX20005. Deletion of this locus significantly reduced Sgg adherence to CRC cells and abrogated the ability of Sgg to stimulate CRC cell proliferation. Thus, we designate this locus as the Sgg pathogenicity-associated region (SPAR). More importantly, we found that SPAR is important for Sgg pathogenicity in vivo. In a gut colonization model, mice exposed to the SPAR deletion mutant showed significantly reduced Sgg load in the colonic tissues and fecal materials, suggesting that SPAR contributes to the colonization capacity of Sgg. In a mouse model of CRC, deletion of SPAR abolished the ability of Sgg to promote the development of colon tumors growth. Taken together, these results highlight SPAR as a critical pathogenicity determinant of Sgg.
Investigating mechanism of the effect of emotional facial expressions on attentional processing by data clustering approach
Authors: Li Yuezhi , Zhao Weifeng , Peng Xiaobo
Published: April 2023

To explore the mechanism of the effect of emotional facial expression on attentional process, time course and topographic map of Electroencephalographic activities affected by emotional stimuli were investigated. Emotional Stroop task was used to collect 64-channel event-related potentials (ERP) in nonclinical participants, and data clustering was applied to find significant effect of sad and happy facial expression on ERP. Several significant ERP clusters were found in the sad and happy conditions respectively. In the sad condition, the decreased N170 in the bilateral parietooccipital areas, the increased P3 in the right centroparietal region and the increased negative deflection between 600 and 650 ms in the prefrontal regions were observed, these alterations reflected inhibited perceptual processing of sad facial expression, and increased activations of the orienting network and the executive control network in attentional system, respectively. In the happy condition, increased negative slow wave was found in the left centroparietal region indicating strengthened awareness and readiness for successive trials. Importantly, nonpathological attentional bias to sad facial expression in nonclinical participants was associated with inhibited perceptual processing and increased activations of the orienting and executive control networks. It provides the basis for better understanding and application of attentional bias in psychiatric clinical utilization.
Characterization of aortic aging using 3D multi-parametric MRI-long-term follow-up in a population study
Authors: Loose Sophie , Solou Demetris , Strecker Christoph , Hennemuth Anja , Hüllebrand Markus , Grundmann Sebastian , Asmussen Alexander , Treppner Martin , Urbach Horst , Harloff Andreas
Published: April 2023

We comprehensively studied morphological and functional aortic aging in a population study using modern three-dimensional MR imaging to allow future comparison in patients with diseases of the aortic valve or aorta. We followed 80 of 126 subjects of a population study (20 to 80 years of age at baseline) using the identical methodology 6.0 ± 0.5 years later. All underwent 3 T MRI of the thoracic aorta including 3D T1 weighted MRI (spatial resolution 1 mm3) for measuring aortic diameter and plaque thickness and 4D flow MRI (spatial/temporal resolution = 2 mm3/20 ms) for calculating global and regional aortic pulse wave velocity (PWV) and helicity of aortic blood flow. Mean diameter of the ascending aorta (AAo) decreased and plaque thickness increased significantly in the aortic arch (AA) and descending aorta (DAo) in females. PWV of the thoracic aorta increased (6.4 ± 1.5 to 7.0 ± 1.7 m/s and 6.8 ± 1.5 to 7.3 ± 1.8 m/s in females and males, respectively) over time. Local normalized helicity volumes (LNHV) decreased significantly in the AAo and AA (0.33 to 0.31 and 0.34 to 0.32 in females and 0.34 to 0.32 and 0.32 to 0.28 in males). By contrast, helicity increased significantly in the DAo in both genders (0.28 to 0.29 and 0.29 to 0.30, respectively). 3D MRI was able to characterize changes in aortic diameter, plaque thickness, PWV and helicity during six years in our population. Aortic aging determined by 3D multi-parametric MRI is now available for future comparisons in patients with diseases of the aortic valve or aorta.
Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm
Authors: Shikha Kumari , Madhumal Thayil Vinayan , Shahi J. P. , Zaidi P. H. , Seetharam Kaliyamoorthy , Nair Sudha K , Singh Raju , Tosh Garg , Singamsetti Ashok , Singh Saurabh , Sinha B.
Published: April 2023

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05–3.06), 5 (bin5.03), 8 (bin8.05–8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines.
Echo chamber effects on short video platforms
Authors: Gao Yichang , Liu Fengming , Gao Lei
Published: April 2023

In recent years, short videos have become an increasingly vital source of information. To compete for users’ attention, short video platforms have been overusing algorithmic technology, making the group polarization intensify, which is likely to push users into the homogeneous “echo chamber”. However, echo chambers can contribute to the spread of misleading information, false news, or rumors, which have negative social impacts. Therefore, it is necessary to explore echo chamber effects in short video platforms. Moreover, the communication paradigms between users and feed algorithms greatly vary across short video platforms. This paper investigated echo chamber effects of three popular short video platforms (Douyin, TikTok, and Bilibili) using social network analysis and explored how user features influenced the generation of echo chambers. We quantified echo chamber effects through two primary ingredients: selective exposure and homophily, in both platform and topic dimensions. Our analyses indicate that the gathering of users into homogeneous groups dominates online interactions on Douyin and Bilibili. We performed performance comparison of echo chamber effects and found that echo chamber members tend to display themselves to attract the attention of their peers and that cultural differences can prevent the development of echo chambers. Our findings are of great value in designing targeted management strategies to prevent the spread of misleading information, false news, or rumors.
Comparative study of Dapagliflozin versus Glimepiride effect on insulin regulated aminopeptidase (IRAP) and interleukin-34 (IL-34) in patient with type 2 diabetes mellitus
Authors: Zekry Rania , Omran Gamal A. , El-Gharbawy Nashwa M. , Werida Rehab H.
Published: April 2023

Type 2 diabetes mellitus (T2DM) is one of the most common diseases, that managed by several medications such as Glimepiride and Dapagliflozin. This study aims to compare the effects of Dapagliflozin versus Glimepiride on glycemic control, insulin resistance, and biomarkers as (extracellular domain of insulin regulated aminopeptidase) IRAPe, (interleukin-34) IL-34, and (N-terminal pro b-type natriuretic peptide) NT-proBNP. This study included 60 type 2 diabetic patients, who are randomized to receive either Glimepiride 4 mg/day (group 1) or Dapagliflozin 10 mg/day (group 2). Blood samples were collected at baseline and after 3 months of treatment for biochemical analysis. Additionally, HOMA-IR is calculated. After 3 months of receiving the intervention, there is no significant difference between the effects of Glimepiride and Dapagliflozin on FBG, PPBG, HbA1C%, fasting insulin, and HOMA-IR. The difference between both groups is significant for IL-34 (p = 0.002) and non-significant for IRAPe (p = 0.12) and NT-Pro BNP (p = 0.68). Both Glimepiride and Dapagliflozin significantly improve glycemic control, and HOMA-IR with no significant difference between them. Both drugs significantly improved the level of NT-proBNP. Dapagliflozin has a borderline significant effect on IRAPe but not IL-34, and Glimepiride has significant effect on IL-34 but not IRAPe.

Clinical Trial Registration: This trial was registered on clinicaltrial.gov (NCT04240171).
CBGA ameliorates inflammation and fibrosis in nephropathy
Authors: Suzuki Sayuri , Fleig Andrea , Penner Reinhold
Published: April 2023

Cannabidiol (CBD) is thought to have multiple biological effects, including the ability to attenuate inflammatory processes. Cannabigerols (CBGA and its decarboxylated CBG molecule) have pharmacological profiles similar to CBD. The endocannabinoid system has recently emerged to contribute to kidney disease, however, the therapeutic properties of cannabinoids in kidney disease remain largely unknown. In this study, we determined whether CBD and CBGA can attenuate kidney damage in an acute kidney disease model induced by the chemotherapeutic cisplatin. In addition, we evaluated the anti-fibrosis effects of these cannabinoids in a chronic kidney disease model induced by unilateral ureteral obstruction (UUO). We find that CBGA, but not CBD, protects the kidney from cisplatin-induced nephrotoxicity. CBGA also strongly suppressed mRNA of inflammatory cytokines in cisplatin-induced nephropathy, whereas CBD treatment was only partially effective. Furthermore, both CBGA and CBD treatment significantly reduced apoptosis through inhibition of caspase-3 activity. In UUO kidneys, both CBGA and CBD strongly reduced renal fibrosis. Finally, we find that CBGA, but not CBD, has a potent inhibitory effect on the channel-kinase TRPM7. We conclude that CBGA and CBD possess reno-protective properties, with CBGA having a higher efficacy, likely due to its dual anti-inflammatory and anti-fibrotic effects paired with TRPM7 inhibition.
Randomized clinical trial on the clinical effects of a toothpaste containing extra virgin olive oil, xylitol, and betaine in gingivitis
Authors: Rodríguez-Agurto Alejandro , Bravo Manuel , Magán-Fernandez Antonio , López-Toruño Ana , Muñoz Ricardo , Ferrer Joaquín , Mesa Francisco
Published: April 2023

To determine the effects on gingival bleeding, dental biofilm, and salivary flow and pH in patients with gingivitis of using toothpaste with extra-virgin olive oil (EVOO), xylitol, and betaine in comparison to a placebo or commercial toothpaste. This controlled, double blinded, and multicenter randomized clinical trial included patients with gingivitis randomly assigned to one of three groups: test group (EVOO, xylitol, and betaine toothpaste), control group 1 (placebo toothpaste), or control group 2 (commercial toothpaste). Percentage supragingival biofilm and gingival bleeding were evaluated at baseline (T0), 2 months (T2), and 4 months (T4), measuring non-stimulated salivary flow and salivary pH. Comparisons were performed between and within groups. The final study sample comprised 20 in the test group, 21 in control group 1, and 20 in control group 2. In comparison to control group 1, the test group showed significantly greater decreases in gingival bleeding between T4 and T0 (p = 0.02) and in biofilm between T2 and T0 (p = 0.02) and between T4 and T0 (p = 0.01). In the test group, salivary flow significantly increased between T2 and T0 (p = 0.01), while pH alkalization was significantly greater between T4 and T0 versus control group 2 (p = 0.01) and close-to-significantly greater versus control group 1 (p = 0.06). The toothpaste with EVOO, xylitol, and betaine obtained the best outcomes in patients with gingivitis, who showed reductions in gingival bleeding and supragingival biofilm and an increase in pH at 4 months in comparison to a commercial toothpaste.
Effects of fine grinding on mid-infrared spectroscopic analysis of plant leaf nutrient content
Authors: Whatley Caleb R. , Wijewardane Nuwan K. , Bheemanahalli Raju , Reddy K. Raja , Lu Yuzhen
Published: April 2023

Fourier transform mid infrared (FT-MIR) spectroscopy combined with modeling techniques has been studied as a useful tool for multivariate chemical analysis in agricultural research. A drawback of this method is the sample preparation requirement, in which samples must be dried and fine ground for accurate model calibrations. For research involving large sample sets, this may dramatically increase the time and cost of analysis. This study investigates the effect of fine grinding on model performance using leaf tissue from a variety of crop species. Dried leaf samples (N = 300) from various environmental conditions were obtained with data on 11 nutrients measured using chemical methods. The samples were scanned with attenuated total reflectance (ATR) and diffuse reflectance (DRIFT) FT-MIR techniques. Scanning was repeated after fine grinding for 2, 5, and 10 min. The spectra were analyzed for the 11 nutrients using partial least squares regression with a 75%/25% split for calibration and validation and repeated for 50 iterations. All analytes except for boron, iron, and zinc were well-modeled (average R2 > 0.7), with higher R2values on ATR spectra. The 5 min level of fine grinding was found to be most optimal considering overall model performance and sample preparation time.