bluuebunny/crossref_metadata_2025 huggingface dataset:
Biology and non-chemical management of Spermacoce verticillata and Spermacoce densiflora
Authors: Castilho Juliana , Forti Victor Augusto , Monquero Patricia Andrea
Published: September 2021

The weed species Spermacoce densiflora DC. and Spermacoce verticillata L. have shown an increase in their occurrence in cultivated areas in the northeast region of Brazil, and field observations have reported their ineffective control with chemicals. This study aimed to evaluate the germination of S. densiflora and S. verticillata under constant (15, 20, 25, 30 and 35°C) and alternating temperatures (20–30°C) in dark and in constant light; the emergence of seedlings from seven sowing depths (0, 0.5, 1, 2, 4, 6 and 10 cm); the emergence of seedlings under five types of cover crop straw (Crotalaria juncea L., Pennisetum glaucum (L.) R. Br., Sorghum bicolor (L.) Moench, Dolichos lablab L., and Cajanus cajan L.) and four amounts (nil and the average, half and twice the amount of straw produced in the field); and germination at different aqueous cover crop extract concentrations (0, 20, 40, 60 and 100%) to measure allelopathic potential of cover crop straw. The results showed that S. densiflora has positive photoblastic behavior. The alternating temperature provided the highest percentage of germination and germination speed index (GSI) for both species. S. densiflora and S. verticillata seedling emergence decreased with an increase in depth, with no germination at a depth of 10 cm. The presence of straw impaired the emergence of seedlings of S. densiflora and S. verticillata by delaying and even preventing germination from occurring. The gradual increase in the aqueous extract concentrations was accompanied by lower percentages of germination and GSI for S. densiflora and S. verticillata.
SELF-REFERENCE UPFRONT: A STUDY OF SELF-REFERENTIAL GÖDEL NUMBERINGS
Authors: GRABMAYR BALTHASAR , VISSER ALBERT
Published: September 2021

In this paper we examine various requirements on the formalisation choices under which self-reference can be adequately formalised in arithmetic. In particular, we study self-referential numberings, which immediately provide a strong notion of self-reference even for expressively weak languages. The results of this paper suggest that the question whether truly self-referential reasoning can be formalised in arithmetic is more sensitive to the underlying coding apparatus than usually believed. As a case study, we show how this sensitivity affects the formal study of certain principles of self-referential truth.
Ungewöhnliche Ursache einer bilateralen Ptose
Authors: Chaloulos-Iakovidis Panagiotis , Aicher Marie Louise , Chilver-Stainer Lara
Published: September 2021

Zusammenfassung. Immun-Checkpoint-Inhibitoren (ICI) werden zunehmend bei verschiedenen Tumorerkrankungen eingesetzt. Autoimmune Nebenwirkungen (irAE) wie Colitis, Hepatitis oder Hautreaktionen sind den meisten Ärztinnen und Ärzten bekannt, allerdings gibt es viele weitere, seltenere, u.a. neurologische Nebenwirkungen wie myasthene Syndrome, Myopathien sowie Myasthenie/Myopathie-Overlap-Syndrome mit potenziell lebensbedrohlichen Komplikationen. Eine genaue Diagnose hat weitreichende therapeutische Konsequenzen. Hier präsentieren wir den Fall eines Patienten unter einer Immun-Checkpoint-Inhibitor-Therapie, bei dem sich die Diagnosestellung aufgrund des Vorhandenseins von Overlap-Symptomen als herausfordernd darstellte, die korrekte Diagnose allerdings aufgrund der therapeutischen Konsequenzen wichtig war.
CME-Sonografie 101: Ultraschall am Bewegungsapparat – Update 2021 CME- Fragen
Authors: Tamborrini Giorgio , Dubs Beat , Krebs Andreas , Ziswiler Hans-Rudolf , Bianchi Stefano
Published: September 2021

Zusammenfassung. In der Ultraschalltechnologie in der Medizin (und in vielen anderen Lebensbereichen) erleben wir andauernd enorme Fortschritte. Die Automatisierung in der Medizin nimmt zu, so auch in der bildgebenden Diagnostik. Dieser Artikel beschreibt den aktuellen technischen Stand im Ultraschall am Bewegungsapparat und wir wagen einen Ausblick in die nahe Zukunft.
Parsing Weather Variability and Wildfire Effects on the Post‐Fire Changes in Daily Stream Flows: A Quantile‐Based Statistical Approach and Its Application
Authors: Beyene Mussie T. , Leibowitz Scott G. , Pennino Michael J.
Published: September 2021

Determining wildland fire impacts on streamflow can be problematic as the hydrology in burned watersheds is influenced by post‐fire weather conditions. This study presents a quantile‐based analytical framework for assessing fire impacts on low and peak daily flow magnitudes, while accounting for post‐fire weather influences. This framework entails (a) the bootstrap method to compute the relative change in the post‐fire annual flow and weather statistics, (b) double mass analysis to detect if post‐fire baseflow and quick‐flow yield ratios are significantly altered, and (c) a quantile regression method to parse fire effects on flow at a specific quantile. We illustrate the applicability of this analytical framework using 44 western US streams with at least 5% of their watershed area burned. Results indicate that large, high‐severity burns in upland watersheds can raise the streamflow magnitude at the 0. and 0. quantiles for at least the five post‐fire years. Quantile regression results show that the median fire‐related increase in flow for the five post‐fire years can be up to 5,000% (Standard Error; 2%) at the 0. quantile and 161% ( 10%) at the 0. quantile. The fire‐related increase in flow was often pronounced at the 0. quantile for streams in the Pacific Northwest and California regions. The difference in fire effects on flow (at both quantiles) across streams was related to post‐fire weather, pyrology, physiography, and land cover. The proposed analytical framework can be useful for detecting and quantifying fire effects on the low and peak stream flows in burned watersheds without overlapping disturbances.
Suspended Sediment Concentration Profile in a Typha Latifolia Canopy
Authors: Xu Yuan , Nepf Heidi
Published: September 2021

The transport of sediment in regions with vegetation plays an important role in aquatic ecosystems and landform evolution in river deltas. In this study, flow parameters and suspended sediment concentration (SSC) within an emergent canopy with real plant morphology (Typha latifolia) were measured in a laboratory channel. T. latifolia is a common marsh species with multiple thin leaves emerging from a tight bundle (culm) at the bed. The observed equilibrium SSC profile differed significantly from a Rouse profile, the classic model for SSC over bare beds. The vertical distribution of SSC was nearly uniform in the culm region of the canopy, and decreased with height in the upper canopy region of distributed leaves. The profile of SSC reflected the vertically nonuniform turbulent diffusion, which arose from the plant morphology. A diffusivity model based on cylinder arrays was first validated with tracer data and then adapted to the T. latifolia morphology, providing a way to model turbulent diffusivity in marsh systems. The diffusivity model was successfully used within a random displacement model to predict the spatial evolution and equilibrium SSC profile within the T. latifolia canopy.
Phospholipase D2 is a positive regulator of sirtuin 1 and modulates p53-mediated apoptosis via sirtuin 1
Authors: Lee Hyesung , Jung Taek-Yeol , Lim Seong Hun , Choi Eun Ju , Lee Jinu , Min Do Sik
Published: September 2021

Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide-dependent histone deacetylase that plays diverse physiological roles. However, little is known about the regulation of SIRT1 activity. Here, we show that phospholipase D2 (PLD2), but not PLD1, selectively interacts with SIRT1 and increases the deacetylase activity of SIRT1. PLD2 does not interact with the other isozymes of SIRT (SIRT2–7). Two leucine residues in the LXXLL motif (L173 and L174) in the phox domain of PLD2 interact with the region essential for SIRT1 activity. PLD2 stimulates the SIRT1-mediated deacetylation of p53 independent of its lipase activity. In our study, mutagenesis of the LXXLL motif suppressed the interaction of PLD2 with SIRT1 and inhibited SIRT1-mediated p53 deacetylation and p53-induced transactivation of proapoptotic genes. Ultimately, overexpression of wild-type PLD2 but not that of LXXLL-mutant PLD2 protected cells against etoposide-induced apoptosis. Moreover, PLD2 did not protect against apoptosis induced by SIRT1 depletion under genotoxic stress. Collectively, our results suggest that PLD2 is a positive regulator of SIRT1 and modulates p53-mediated apoptosis via SIRT1.
Naloxone precipitated withdrawal increases dopamine release in the dorsal striatum of opioid dependent men
Authors: Shokri-Kojori Ehsan , Wang Gene-Jack , Volkow Nora D.
Published: September 2021

Dopamine (DA) neurotransmission is critical in the neurobiology of reward and aversion, but its contribution to the aversive state of opioid withdrawal remains unknown in humans. To address this, we used updated voxelwise methods and retrospectively analyzed a [11C]raclopride-PET dataset to measure D2/3receptor availability and relative cerebral blood flow (R1) in male opioid use disorder (OUD) participants (n = 10) during placebo and acute opioid withdrawal conditions. We found that acute withdrawal precipitated by the opioid antagonist naloxone significantly increased dorsal striatal DA release in OUD participants (pFWE < 0.05). Net changes in striatal DA were significantly correlated with a subjective index of withdrawal aversion such that greater DA increases were associated with more aversive responses (r(8) = 0.82,p < 0.005). Withdrawal also affected brain function, as indexed by increases in relative cerebral blood flow in the insula and putamen (pFWE < 0.05). Our findings are different from preclinical studies that have primarily reported decreases in ventral striatal DA during naloxone precipitated withdrawal, whereas this effect was not significant in OUD participants (p = 0.79). In sum, we provide evidence for the contribution of increases in dorsal striatal DA to the aversive state of naloxone precipitated withdrawal in humans.
SARS-CoV-2-specific T cells in infection and vaccination
Authors: Bertoletti Antonio , Le Bert Nina , Qui Martin , Tan Anthony T.
Published: September 2021

During viral infections, antibodies and T cells act together to prevent pathogen spread and remove virus-infected cells. Virus-specific adaptive immunity can, however, also trigger pathological processes characterized by localized or systemic inflammatory events. The protective and/or pathological role of virus-specific T cells in SARS-CoV-2 infection has been the focus of many studies in COVID-19 patients and in vaccinated individuals. Here, we review the works that have elucidated the function of SARS-CoV-2-specific T cells in patients and in vaccinated individuals. Understanding whether SARS-CoV-2-specific T cells are more linked to protection or pathogenesis is pivotal to define future therapeutic and prophylactic strategies to manage the current pandemic.
Cytotoxic T cells are able to efficiently eliminate cancer cells by additive cytotoxicity
Authors: Weigelin Bettina , den Boer Annemieke Th. , Wagena Esther , Broen Kelly , Dolstra Harry , de Boer Rob J. , Figdor Carl G. , Textor Johannes , Friedl Peter
Published: September 2021

Lethal hit delivery by cytotoxic T lymphocytes (CTL) towards B lymphoma cells occurs as a binary, “yes/no” process. In non-hematologic solid tumors, however, CTL often fail to kill target cells during 1:1 conjugation. Here we describe a mechanism of “additive cytotoxicity” by which time-dependent integration of sublethal damage events, delivered by multiple CTL transiting between individual tumor cells, mediates effective elimination. Reversible sublethal damage includes perforin-dependent membrane pore formation, nuclear envelope rupture and DNA damage. Statistical modeling reveals that 3 serial hits delivered with decay intervals below 50 min discriminate between tumor cell death or survival after recovery. In live melanoma lesions in vivo, sublethal multi-hit delivery is most effective in interstitial tissue where high CTL densities and swarming support frequent serial CTL-tumor cell encounters. This identifies CTL-mediated cytotoxicity by multi-hit delivery as an incremental and tunable process, whereby accelerating damage magnitude and frequency may improve immune efficacy.
Improved modeling of human AD with an automated culturing platform for iPSC neurons, astrocytes and microglia
Authors: Bassil Reina , Shields Kenneth , Granger Kevin , Zein Ivan , Ng Shirley , Chih Ben
Published: September 2021

Advancement in human induced pluripotent stem cell (iPSC) neuron and microglial differentiation protocols allow for disease modeling using physiologically relevant cells. However, iPSC differentiation and culturing protocols have posed challenges to maintaining consistency. Here, we generated an automated, consistent, and long-term culturing platform of human iPSC neurons, astrocytes, and microglia. Using this platform we generated a iPSC AD model using human derived cells, which showed signs of Aβ plaques, dystrophic neurites around plaques, synapse loss, dendrite retraction, axon fragmentation, phospho-Tau induction, and neuronal cell death in one model. We showed that the human iPSC microglia internalized and compacted Aβ to generate and surround the plaques, thereby conferring some neuroprotection. We investigated the mechanism of action of anti-Aβ antibodies protection and found that they protected neurons from these pathologies and were most effective before pTau induction. Taken together, these results suggest that this model can facilitate target discovery and drug development efforts.
Epistatic Net allows the sparse spectral regularization of deep neural networks for inferring fitness functions
Authors: Aghazadeh Amirali , Nisonoff Hunter , Ocal Orhan , Brookes David H. , Huang Yijie , Koyluoglu O. Ozan , Listgarten Jennifer , Ramchandran Kannan
Published: September 2021

Despite recent advances in high-throughput combinatorial mutagenesis assays, the number of labeled sequences available to predict molecular functions has remained small for the vastness of the sequence space combined with the ruggedness of many fitness functions. While deep neural networks (DNNs) can capture high-order epistatic interactions among the mutational sites, they tend to overfit to the small number of labeled sequences available for training. Here, we developed Epistatic Net (EN), a method for spectral regularization of DNNs that exploits evidence that epistatic interactions in many fitness functions are sparse. We built a scalable extension of EN, usable for larger sequences, which enables spectral regularization using fast sparse recovery algorithms informed by coding theory. Results on several biological landscapes show that EN consistently improves the prediction accuracy of DNNs and enables them to outperform competing models which assume other priors. EN estimates the higher-order epistatic interactions of DNNs trained on massive sequence spaces-a computational problem that otherwise takes years to solve.
A CDK-regulated chromatin segregase promoting chromosome replication
Authors: Chacin Erika , Bansal Priyanka , Reusswig Karl-Uwe , Diaz-Santin Luis M. , Ortega Pedro , Vizjak Petra , Gómez-González Belen , Müller-Planitz Felix , Aguilera Andrés , Pfander Boris , Cheung Alan C. M. , Kurat Christoph F.
Published: September 2021

The replication of chromosomes during S phase is critical for cellular and organismal function. Replicative stress can result in genome instability, which is a major driver of cancer. Yet how chromatin is made accessible during eukaryotic DNA synthesis is poorly understood. Here, we report the characterization of a chromatin remodeling enzyme—Yta7—entirely distinct from classical SNF2-ATPase family remodelers. Yta7 is a AAA+ -ATPase that assembles into ~1 MDa hexameric complexes capable of segregating histones from DNA. The Yta7 chromatin segregase promotes chromosome replication both in vivo and in vitro. Biochemical reconstitution experiments using purified proteins revealed that the enzymatic activity of Yta7 is regulated by S phase-forms of Cyclin-Dependent Kinase (S-CDK). S-CDK phosphorylation stimulates ATP hydrolysis by Yta7, promoting nucleosome disassembly and chromatin replication. Our results present a mechanism for how cells orchestrate chromatin dynamics in co-ordination with the cell cycle machinery to promote genome duplication during S phase.
Olfactory bulb astrocytes mediate sensory circuit processing through Sox9 in the mouse brain
Authors: Ung Kevin , Huang Teng-Wei , Lozzi Brittney , Woo Junsung , Hanson Elizabeth , Pekarek Brandon , Tepe Burak , Sardar Debosmita , Cheng Yi-Ting , Liu Gary , Deneen Benjamin , Arenkiel Benjamin R.
Published: September 2021

The role of transcription factors during astrocyte development and their subsequent effects on neuronal development has been well studied. Less is known about astrocytes contributions towards circuits and behavior in the adult brain. Astrocytes play important roles in synaptic development and modulation, however their contributions towards neuronal sensory function and maintenance of neuronal circuit architecture remain unclear. Here, we show that loss of the transcription factor Sox9 results in both anatomical and functional changes in adult mouse olfactory bulb (OB) astrocytes, affecting sensory processing. Indeed, astrocyte-specific deletion of Sox9 in the OB results in decreased odor detection thresholds and discrimination and it is associated with aberrant neuronal sensory response maps. At functional level, loss of astrocytic Sox9 impairs the electrophysiological properties of mitral and tufted neurons. RNA-sequencing analysis reveals widespread changes in the gene expression profiles of OB astrocytes. In particular, we observe reduced GLT-1 expression and consequential alterations in glutamate transport. Our findings reveal that astrocytes are required for physiological sensory processing and we identify astrocytic Sox9 as an essential transcriptional regulator of mature astrocyte function in the mouse OB.
Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation
Authors: Lioy Virginia S. , Lorenzi Jean-Noël , Najah Soumaya , Poinsignon Thibault , Leh Hervé , Saulnier Corinne , Aigle Bertrand , Lautru Sylvie , Thibessard Annabelle , Lespinet Olivier , Leblond Pierre , Jaszczyszyn Yan , Gorrichon Kevin , Varoquaux Nelle , Junier Ivan , Boccard Frédéric , Pernodet Jean-Luc , Bury-Moné Stéphanie
Published: September 2021

Bacteria of the genus Streptomyces are prolific producers of specialized metabolites, including antibiotics. The linear chromosome includes a central region harboring core genes, as well as extremities enriched in specialized metabolite biosynthetic gene clusters. Here, we show that chromosome structure in Streptomyces ambofaciens correlates with genetic compartmentalization during exponential phase. Conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends tend to be transcriptionally quiescent compartments with different structural features. The onset of metabolic differentiation is accompanied by a rearrangement of chromosome architecture, from a rather ‘open’ to a ‘closed’ conformation, in which highly expressed specialized metabolite biosynthetic genes form new boundaries. Thus, our results indicate that the linear chromosome of S. ambofaciens is partitioned into structurally distinct entities, suggesting a link between chromosome folding, gene expression and genome evolution.
Aurora kinase A inhibition reverses the Warburg effect and elicits unique metabolic vulnerabilities in glioblastoma
Authors: Nguyen Trang T. T. , Shang Enyuan , Shu Chang , Kim Sungsoo , Mela Angeliki , Humala Nelson , Mahajan Aayushi , Yang Hee Won , Akman Hasan Orhan , Quinzii Catarina M. , Zhang Guoan , Westhoff Mike-Andrew , Karpel-Massler Georg , Bruce Jeffrey N. , Canoll Peter , Siegelin Markus D.
Published: September 2021

Aurora kinase A (AURKA) has emerged as a drug target for glioblastoma (GBM). However, resistance to therapy remains a critical issue. By integration of transcriptome, chromatin immunoprecipitation sequencing (CHIP-seq), Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq), proteomic and metabolite screening followed by carbon tracing and extracellular flux analyses we show that genetic and pharmacological AURKA inhibition elicits metabolic reprogramming mediated by inhibition of MYC targets and concomitant activation of Peroxisome Proliferator Activated Receptor Alpha (PPARA) signaling. While glycolysis is suppressed by AURKA inhibition, we note an increase in the oxygen consumption rate fueled by enhanced fatty acid oxidation (FAO), which was accompanied by an increase of Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1α). Combining AURKA inhibitors with inhibitors of FAO extends overall survival in orthotopic GBM PDX models. Taken together, these data suggest that simultaneous targeting of oxidative metabolism and AURKAi might be a potential novel therapy against recalcitrant malignancies.
The basis of easy controllability in Boolean networks
Authors: Borriello Enrico , Daniels Bryan C.
Published: September 2021

Effective control of biological systems can often be achieved through the control of a surprisingly small number of distinct variables. We bring clarity to such results using the formalism of Boolean dynamical networks, analyzing the effectiveness of external control in selecting a desired final state when that state is among the original attractors of the dynamics. Analyzing 49 existing biological network models, we find strong numerical evidence that the average number of nodes that must be forced scales logarithmically with the number of original attractors. This suggests that biological networks may be typically easy to control even when the number of interacting components is large. We provide a theoretical explanation of the scaling by separating controlling nodes into three types: those that act as inputs, those that distinguish among attractors, and any remaining nodes. We further identify characteristics of dynamics that can invalidate this scaling, and speculate about how this relates more broadly to non-biological systems.
Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice
Authors: Kim Kwang-eun , Park Isaac , Kim Jeesoo , Kang Myeong-Gyun , Choi Won Gun , Shin Hyemi , Kim Jong-Seo , Rhee Hyun-Woo , Suh Jae Myoung
Published: September 2021

Secretory proteins are an essential component of interorgan communication networks that regulate animal physiology. Current approaches for identifying secretory proteins from specific cell and tissue types are largely limited to in vitro or ex vivo models which often fail to recapitulate in vivo biology. As such, there is mounting interest in developing in vivo analytical tools that can provide accurate information on the origin, identity, and spatiotemporal dynamics of secretory proteins. Here, we describeiSLET (in situ Secretory protein Labeling via ER-anchored TurboID) which selectively labels proteins that transit through the classical secretory pathway via catalytic actions of Sec61b-TurboID, a proximity labeling enzyme anchored in the ER lumen. To validateiSLET in a whole-body system, we expressiSLET in the mouse liver and demonstrate efficient labeling of liver secretory proteins which could be tracked and identified within circulating blood plasma. Furthermore, proteomic analysis of the labeled liver secretome enriched from liveriSLET mouse plasma is highly consistent with previous reports of liver secretory protein profiles. Taken together,iSLET is a versatile and powerful tool for studying spatiotemporal dynamics of secretory proteins, a valuable class of biomarkers and therapeutic targets.
Correlation of bone density to screw loosening in dynamic stabilization: an analysis of 176 patients
Authors: Chang Hsuan-Kan , Ku Jason , Ku Johnson , Kuo Yi-Hsuan , Chang Chih-Chang , Wu Ching-Lan , Lirng Jiing-Feng , Wu Jau-Ching , Huang Wen-Cheng , Cheng Henrich , Hsu Shih-Ming
Published: September 2021

Although osteoporosis has negative impacts on lumbar fusion, its effects on screw loosening in dynamic stabilization remain elusive. We aimed to correlate bone mineral density (BMD) with screw loosening in Dynesys dynamic stabilization (DDS). Consecutive patients who underwent 2- or 3-level DDS for spondylosis, recurrent disc herniations, or low-grade spondylolisthesis at L3-5 were retrospectively reviewed. BMD was assessed by the Hounsfield Unit (HU) in vertebral bodies (VB) and pedicles with and without cortical bone (CB) on pre-operative computed tomography (CT). Screw loosening was assessed by radiographs and confirmed by CT. HU values were compared between the loosened and intact screws. 176 patients and 918 screws were analyzed with 78 loosened screws found in 36 patients (mean follow-up: 43.4 months). The HU values of VB were similar in loosened and intact screws (p = 0.14). The HU values of pedicles were insignificantly less in loosened than intact screws (including CB: 286.70 ± 118.97 vs. 297.31 ± 110.99, p = 0.45; excluding CB: 238.48 ± 114.90 vs. 240.51 ± 108.91, p = 0.88). All patients had clinical improvements. In conclusion, the HU values, as a surrogate for BMD, were unrelated to screw loosening in DDS. Therefore, patients with compromised BMD might be potential candidates for dynamic stabilization rather than fusion.
Impact of shredding degree on papermaking potential of recycled waste
Authors: Lipkiewicz Aneta , Małachowska Edyta , Dubowik Marcin , Przybysz Piotr
Published: September 2021

The properties of paper products depend on the structure of the cellulose fibres therein. Although fibre properties in virgin pulps can be modified by a refining process, this is more difficult in pulp from recovered fibre, particularly waste from office shredders that tend to shorten fibres during shredding. The shorter fibres in shredded paper make it difficult to easily reconstitute them into high-quality paper products. Moreover, because of high energy usage during the recycling process and transportation inefficiencies, there is a need to determine how to responsibly shred paper to alleviate this environmental burden. With this in mind, the influence of initial fibre length on the tensile properties of paper was investigated. Changes in initial fibre length significantly influenced many pulp and paper properties. It was found that cutting the paper into pieces with an area less than 25 mm2caused significant changes in the important morphological parameters of the fibres and a sharp decrease in the tensile properties of the reconstituted paper.
20 Years nitrogen dynamics study by using APSIM nitrogen model simulation for sustainable management in Jilin China
Authors: Tahir Nazia , Li Jumei , Ma Yibing , Ullah Aman , Zhu Ping , Peng Chang , Hussain Babar , Danish Subhan
Published: September 2021

The tremendous increase in industrial development and urbanization has become a severe threat to the Chinese climate and food security. The Agricultural Production System Simulator model was used to simulate soil nitrogen in black soil in Yangling Jilin Province for 20 years. The observed values are consistent with the simulated values. The predicted values of total soil NO3−–N and NH4+–N nitrogen are 10 kg ha−1 and 5 kg ha−1 higher than the observed values. The total soil NO3−–N loss has the same trend as the rainfall, and it increases with the number of rainfall days over the years. The average 20 years losses of NO3−–N and NH4+–N observed were 1375.91 kg ha−1, and 9.24 kg ha−1, while in the simulation increase was 1387.01 kg ha−1 and 9.28 kg ha−1, respectively. The difference between the observed and simulated values of NO3−–N and NH4+–N of mean loss was 11.15 kg ha−1 and 0.04 kg ha−1 respectively. Moreover, our findings highlight the opportunity further to improve management policies (especially for nitrogen) to maintain crop yield.
Predictive value of m5C regulatory gene expression in pancreatic adenocarcinoma
Authors: Yu Xiao , Zhang Qiyao , Gao Fang , Zhang Menggang , Zheng Qingyuan , He Yuting , Guo Wenzhi
Published: September 2021

Pancreatic adenocarcinoma (PAAD) is the most malignant digestive tumor. The global incidence of pancreatic cancer has been rapidly trending upwards, necessitating an exploration of potential prognostic biomarkers and mechanisms of disease development. One of the most prevalent RNA modifications is 5-methylcytosine (m5C); however, its contribution to PAAD remains unclear. Data from The Cancer Genome Atlas (TCGA) database, including genes, copy number variations (CNVs), and simple nucleotide variations (SNVs), were obtained in the present study to identify gene signatures and prognostic values for m5C regulators in PAAD. Regulatory gene m5C changes were significantly correlated with TP53, BRCA1, CDKN2A, and ATM genes, which play important roles in PAAD pathogenesis. In particular, there was a significant relationship between m5C regulatory gene CNVs, especially in genes encoding epigenetic “writers”. According to m5C-regulated gene expression in clinically graded cases, one m5C-regulated genes, DNMT3A, showed both a strong effect on CNVs and a significant correlation between expression level and clinical grade (P < 0.05). Furthermore, low DNMT3A expression was not only associated with poor PAAD patient prognosis but also with the ribosomal processing. The relationship between low DNMT3A expression and poor prognosis was confirmed in an International Cancer Genome Consortium (ICGC) validation dataset.
Transcriptome analysis reveals key genes associated with root-lesion nematode Pratylenchus thornei resistance in chickpea
Authors: Channale Sonal , Kalavikatte Danamma , Thompson John P. , Kudapa Himabindu , Bajaj Prasad , Varshney Rajeev K. , Zwart Rebecca S. , Thudi Mahendar
Published: September 2021

The root-lesion nematode, Pratylenchus thornei, is one of the major plant-parasitic nematode species causing significant yield losses in chickpea (Cicer arietinum). In order to identify the underlying mechanisms of resistance to P. thornei, the transcriptomes of control and inoculated roots of three chickpea genotypes viz. D05253 > F3TMWR2AB001 (resistant advanced breeding line), PBA HatTrick (moderately resistant cultivar), and Kyabra (susceptible cultivar) were studied at 20 and 50 days post inoculation using the RNA-seq approach. On analyzing the 633.3 million reads generated, 962 differentially expressed genes (DEGs) were identified. Comparative analysis revealed that the majority of DEGs upregulated in the resistant genotype were downregulated in the moderately resistant and susceptible genotypes. Transcription factor families WRKY and bZIP were uniquely expressed in the resistant genotype. The genes Cysteine-rich receptor-like protein kinase 10, Protein lifeguard-like, Protein detoxification, Bidirectional sugar transporter Sugars Will Eventually be Exported Transporters1 (SWEET1), and Subtilisin-like protease were found to play cross-functional roles in the resistant chickpea genotype against P. thornei. The identified candidate genes for resistance to P. thornei in chickpea can be explored further to develop markers and accelerate the introgression of P. thornei resistance into elite chickpea cultivars.
Long-term data reveal unimodal responses of ground beetle abundance to precipitation and land use but no changes in taxonomic and functional diversity
Authors: Zajicek Petr , Welti Ellen A. R. , Baker Nathan J. , Januschke Kathrin , Brauner Oliver , Haase Peter
Published: September 2021

While much of global biodiversity is undoubtedly under threat, the responses of ecological communities to changing climate, land use intensification, and long-term changes in both taxonomic and functional diversity over time, has still not been fully explored for many taxonomic groups, especially invertebrates. We compiled time series of ground beetles covering the past two decades from 40 sites located in five regions across Germany. We calculated site-based trends for 21 community metrics representing taxonomic and functional diversity of ground beetles, activity density (a proxy for abundance), and activity densities of functional groups. We assessed both overall and regional temporal trends and the influence of the global change drivers of temperature, precipitation, and land use on ground beetle communities. While we did not detect overall temporal changes in ground beetle taxonomic and functional diversity, taxonomic turnover changed within two regions, illustrating that community change at the local scale does not always correspond to patterns at broader spatial scales. Additionally, ground beetle activity density had a unimodal response to both annual precipitation and land use. Limited temporal change in ground beetle communities may indicate a shifting baseline, where community degradation was reached prior to the start of our observation in 1999. In addition, nonlinear responses of animal communities to environmental change present a challenge when quantifying temporal trends.
Lower extremity energy absorption strategies at different phases during single and double-leg landings with knee valgus in pubertal female athletes
Authors: Dadfar Mahdis , Soltani M. , Novinzad Mohammadreza Basohbat , Raahemifar Kaamran
Published: September 2021

Dynamic knee valgus (DKV) malalignment affects the biomechanical characteristic during sports activities. This cross-sectional study was conducted to evaluate mechanical energy absorption (MEA) strategies at initial contact (IC) and total landing (TL) phases during single-leg landing (SLL), and double-leg landing (DLL). Twenty-eight female athletes with DKV (age 10–14) were invited. MEA analysis of lower extremity joints was done in sagittal and frontal motion planes employing 8 Vicon motion capture cameras and 2 Kistler force plates. Statistical analysis was done using IBM Statistics (version24) by Bivariate Pearson Correlation Coefficient test. Knee extensors MEA during SLL (IC: P = 0.008, R = 0.522/TL: P < 0.001, R = 0.642) and DLL (IC: P < 0.001, R = 0.611/TL: P = 0.011, R = 0.525), and knee abductors during SLL (IC: P = 0.021, R = 0.474) were positively correlated with increased DKV angle. Ankle plantar flexors during SLL (TL: P = 0.017, R = − 0.477) and DLL (TL: P = 0.028, R = − 0.404), and hip extensors during SLL (TL: P = 0.006, R = − 0.5120) were negatively correlated with increased DKV angle. Compensated MEA in knee extensors was correlated with less ankle plantar flexion MEA during SLL (IC: P = 0.027, R = − 0.514/TL: P = 0.007, R = − 0.637) and DLL (IC: P = 0.033, R = − 00.412/TL: P = 0.025, R = − 0.485). These outcomes indicated a knee-reliant MEA strategy in female athletes with DKV during puberty, putting them at higher risks of ACL injuries during landing.
Molecular epidemiology and genotype/subtype distribution of Blastocystis sp., Enterocytozoon bieneusi, and Encephalitozoon spp. in livestock: concern for emerging zoonotic infections
Authors: Mohammad Rahimi Hanieh , Mirjalali Hamed , Zali Mohammad Reza
Published: September 2021

Intestinal parasitic infections have high prevalence rate in many regions especially in developing countries. The aim of this study was to determine the presence and genotype/subtype of some intestinal protozoa in livestock in Iran. Stool samples were collected from cattle, sheep, chickens, and horses. The presence of targeted parasites was evaluated using real-time PCR. Genotyping/subtyping of positive samples was characterized using sequencing of the ITS and barcoding region, respectively. Blastocystis sp., 27.7% (48/173) and Enterocytozoon bieneusi 26.0% (45/173) were the most frequent protozoa followed by Encephalitozoon spp., 0.57% (1/173). Cryptosporidium spp. were not detected among samples. Encephalitozoon spp., was detected only in chickens 2.2% (1/45). A statistically correlation was seen between animals and the prevalence of targeted protozoa. E. bieneusi genotypes I (9/38; 23.68%), BEB6 (22/38; 57.89%), D (6/38; 15.79%), and horse1 (1/38; 2.63%) were detected among samples. A statistically significant correlation was seen between the genotypes and animals (P ≤ 0.05). Blastocystis sp., ST1 (1/45; 2.22%), ST5 3/45; 6.66%), ST7 (1/45; 2.22%), ST10 (24/45; 53.33%), and ST14 (16/45; 35.55%) were characterized among samples. There was no significant correlation between certain subtypes and animals (P = 0.173). The presence of zoonotic potential genotypes of E. bieneusi in animals and zoonotic potential subtypes ST1 and ST7 among our samples provide a clue about the transmission dynamic of E. bieneusi and Blastocystis sp. between animals–animals and humans–animals.
Revealing the molecular interplay of curcumin as Culex pipiens Acetylcholine esterase 1 (AChE1) inhibitor
Authors: Rao Priyashi , Goswami Dweipayan , Rawal Rakesh M.
Published: September 2021

Emergence of vector borne diseases has continued to take toll on millions of lives since its inception. The use of insecticides began as vector control strategy in the early 1900’s but the menace of insects is still prevalent. Additionally, the inadequate use of organophosphates and carbamates which target acetylcholine esterase (AChE), are known to develop resistance amongst vectors of transmission and are toxic to humans. In this study, extensive computational screening was performed using homology modelling, molecular docking, molecular dynamics (MD) simulation and free energy change calculation, which highlighted curcumin as a lead molecule out of ~ 1700 phytochemicals against Culex pipiens AChE. In vivo larvicidal activity was carried out along with in vivo and in vitro AChE inhibition assay to determine the biochemical efficacy of curcumin. Our study reveals that curcumin induces mortality in Cx. pipiens at an early stage of its life cycle by AChE inhibition. This also underlines the use of curcumin as a coming-age natural product insecticide.
Control of axillary bud growth in tobacco through toxin gene expression system
Authors: Lv Jing , Chen Ya-Qiong , Ding An-Ming , Lei Bo , Yu Jing , Gao Xiao-Ming , Dai Chang-Bo , Sun Yu-He
Published: September 2021

The control of axillary bud development after removing the terminal buds (topping) of plants is a research hotspot, and the control of gene expression, like switching on and off, allows us to further study biological traits of interest, such as plant branching and fertility. In this study, a toxin gene control system for plants based on dexamethasone (DEX) induction was constructed, and the positive transgenic tobacco exhibited growth retardation in the application area (axillary bud). The expression level of the lethal Diphtheria toxin A (DTA) gene under different DEX concentrations at different application days was analyzed. The highest expression levels appeared at 5 days after the leaf injection of DEX. The DTA transcripts were induced by 5 µM DEX and peaked in response to 50 µM DEX at 5 days after leaf injection. Here, a chemical induction system, combined with a toxin gene, were used to successfully control the growth of tobacco axillary buds after topping. The DTA expression system under DEX induction was sensitive and efficient, therefore, can be used to control axillary bud growth and development in tobacco.
Electronic cigarette smoke reduces ribosomal protein gene expression to impair protein synthesis in primary human airway epithelial cells
Authors: Park Hae-Ryung , Vallarino Jose , O’Sullivan Michael , Wirth Charlotte , Panganiban Ronald A. , Webb Gabrielle , Shumyatcher Maya , Himes Blanca E. , Park Jin-Ah , Christiani David C. , Allen Joseph , Lu Quan
Published: September 2021

The widespread use of electronic cigarettes (e-cig) is a serious public health concern; however, mechanisms by which e-cig impair the function of airway epithelial cells—the direct target of e-cig smoke—are not fully understood. Here we report transcriptomic changes, including decreased expression of many ribosomal genes, in airway epithelial cells in response to e-cig exposure. Using RNA-seq we identify over 200 differentially expressed genes in air–liquid interface cultured primary normal human bronchial epithelial (NHBE) exposed to e-cig smoke solution from commercial e-cig cartridges. In particular, exposure to e-cig smoke solution inhibits biological pathways involving ribosomes and protein biogenesis in NHBE cells. Consistent with this effect, expression of corresponding ribosomal proteins and subsequent protein biogenesis are reduced in the cells exposed to e-cig. Gas chromatography/mass spectrometry (GC/MS) analysis identified the presence of five flavoring chemicals designated as ‘high priority’ in regard to respiratory health, and methylglyoxal in e-cig smoke solution. Together, our findings reveal the potential detrimental effect of e-cig smoke on ribosomes and the associated protein biogenesis in airway epithelium. Our study calls for further investigation into how these changes in the airway epithelium contribute to the current epidemic of lung injuries in e-cig users.
Magnetic silica particles functionalized with guanidine derivatives for microwave-assisted transesterification of waste oil
Authors: Chipurici Petre , Vlaicu Alexandru , Călinescu Ioan , Vînătoru Mircea , Busuioc Cristina , Dinescu Adrian , Ghebaur Adi , Rusen Edina , Voicu Georgeta , Ignat Maria , Diacon Aurel
Published: September 2021

This study aimed to develop a facile synthesis procedure for heterogeneous catalysts based on organic guanidine derivatives superbases chemically grafted on silica-coated Fe3O4 magnetic nanoparticles. Thus, the three organosilanes that were obtained by reacting the selected carbodiimides (N,N′-dicyclohexylcarbodiimide (DCC), N,N′-diisopropylcarbodiimide (DIC), respectively 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) with 3-aminopropyltriethoxysilane (APTES) were used in a one-pot synthesis stage for the generation of a catalytic active protective shell through the simultaneous hydrolysis/condensation reaction with tetraethyl orthosilicate (TEOS). The catalysts were characterized by FTIR, TGA, SEM, BET and XRD analysis confirming the successful covalent attachment of the organic derivatives in the silica shell. The second aim was to highlight the capacity of microwaves (MW) to intensify the transesterification process and to evaluate the activity, stability, and reusability characteristics of the catalysts. Thus, in MW-assisted transesterification reactions, all catalysts displayed FAME yields of over 80% even after 5 reactions/activation cycles. Additionally, the influence of FFA content on the catalytic activity was investigated. As a result, in the case of Fe3O4@SiO2-EDG, a higher tolerance towards the FFA content can be noticed with a FAME yield of over 90% (for a 5% (weight) vs oil catalyst content) and 5% weight FFA content.
A novel mitochondrial-targeting fluorescent probe based on 1,4-dihydropyridine to visualize and monitor the viscosity of live cells and mice in vivo
Authors: Xue Longqi , Lv Jialin , Li Ronghang , Xinyu Wang  , Li Yapeng , Du Jianshi , Qi Shaolong , Yang Qingbiao , Shan Yaming , Li Yaoxian
Published: September 2021

Cell viscosity is related to some diseases, such as diabetes, atherosclerosis, and Alzheimer's disease.
Recent advances in catalytic synthesis of medium-ring lactones and their derivatives
Authors: Liu Zi-Kui , Gao Yang , Hu Xiao-Qiang
Published: September 2021

In light of the ever-increasing significance of medium-sized lactones across the range of chemical sciences, this review summarizes the recent advances in catalytic synthesis of medium-ring lactones with emphasis on reaction scope and mechanism.
Exogenous electricity flowing through cyanobacterial photosystem I drives CO2 valorization with high energy efficiency
Authors: Li Zhaodong , Wu Chao , Gao Xiang , Addison Bennett , Shinde Shrameeta , Wang Xin , Chen Xihan , Yu Jianping , Svedruzic Drazenka , Blackburn Jeffrey L. , Xiong Wei
Published: September 2021

An integrated photoelectrochemical architecture, with cyanobacteria lacking photosystem II activity, uses photons and exogenous electrons to convert carbon dioxide into carbon fuel products.
Conversion and storage of solar energy for cooling
Authors: Wang Wenbin , Shi Yusuf , Zhang Chenlin , Li Renyuan , Wu Mengchun , Zhuo Sifei , Aleid Sara , Wang Peng
Published: September 2021

A passive no electricity and sustainable cooling on-demand (NESCOD) system can convert and store solar energy for cooling.
Extracellular vesicles from adipose stromal cells combined with a thermoresponsive hydrogel prevent esophageal stricture after extensive endoscopic submucosal dissection in a porcine model
Authors: Coffin Elise , Grangier Alice , Perrod Guillaume , Piffoux Max , Marangon Iris , Boucenna Imane , Berger Arthur , M'Harzi Leila , Assouline Jessica , Lecomte Thierry , Chipont Anna , Guérin Coralie , Gazeau Florence , Wilhelm Claire , Cellier Christophe , Clément Olivier , Silva Amanda Karine Andriola , Rahmi Gabriel
Published: September 2021

We show herein that a combination of a biomaterial and extracellular vesicles (produced at a high yield by a turbulence stimulation from stromal cells) was effective in the prevention of esophageal stricture in a clinically relevant porcine model.
A ruthenium nanoframe/enzyme composite system as a self-activating cascade agent for the treatment of bacterial infections
Authors: Liu Yanan , Huo Dongliang , Zhu Xufeng , Chen Xu , Lin Ange , Jia Zhi , Liu Jie
Published: September 2021

The cascade catalytic strategy could effectively enhance the antibacterial activity by regulating the production of hydroxyl radicals (˙OH) in the sites of bacterial infection.
Switching interlayer magnetic order in bilayer CrI3 by stacking reversal
Authors: Kong Xiangru , Yoon Hongkee , Han Myung Joon , Liang Liangbo
Published: September 2021

First-principles calculations predict that rotating one layer by 180° over the other layer can switch the interlayer magnetic order in bilayer CrI3, demonstrating stacking rotation as an effective strategy to manipulate the magnetism in 2D magnets.
Improving the knock-in efficiency of the MOF-encapsulated CRISPR/Cas9 system through controllable embedding structures
Authors: Liu Chang , Xu Xiaoyu , Koivisto Oliver , Zhou Wenhui , Jacquemet Guillaume , Rosenholm Jessica M. , Zhang Hongbo
Published: September 2021

A rapid and convenient method was developed to load gene molecules into nanostructures, exploring structure–function relationship for efficient intracellular delivery and gene editing, opening up new avenues for the MOF-based non-viral vectors.
Facile fabrication of soy protein isolate-functionalized nanofibers with enhanced biocompatibility and hemostatic effect on full-thickness skin injury
Authors: Ke Meifang , Wang Zijian , Dong Qi , Chen Feixiang , He Liu , Huselstein Céline , Wang Xinghuan , Chen Yun
Published: September 2021

SPNF-n electrospinning nanofibers can promote fibroblast proliferation and diminish inflammation. In particular, SPNF-80 is hemostatic, and accelerates wound healing by interfering multiple biological processes.
Molecular simulation of the diffusion mechanism of nanorods in cross-linked networks
Authors: Zhao Bo-Ran , Li Bin , Shi Xinghua
Published: September 2021

We study the diffusion of rod-shaped nanocarriers with different rigidities and aspect ratios in cross-linked networks using coarse-grained molecular dynamics simulations, the diffusion of nanorods mainly occurs by hopping between cages in networks.
A guide towards safe, functional and renewable BPA alternatives by rational molecular design: structure–property and structure–toxicity relationships
Authors: Trullemans L. , Koelewijn S.-F. , Scodeller I. , Hendrickx T. , Van Puyvelde P. , Sels B. F.
Published: September 2021

Putting the pieces together: a guide for rational molecular design of safe, functional and renewable BPA alternatives.
CDK4/6 inhibitors: a brief overview and prospective research directions
Authors: Adon Tenzin , Shanmugarajan Dhivya , Kumar Honnavalli Yogish
Published: September 2021

The discovery of cyclin-dependent kinases (CDK) and their mechanism in regulating the cell cycle process was considered a game-changer in cancer therapy.