bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigations into differential glyphosate sensitivity between two horseweed (Conyza canadensis) growth types
Authors: Fisher Justine L. , Sprague Christy L. , Patterson Eric L. , Schramski John A. 
Published: January 2023

AbstractHorseweed [Conyza canadensis (L.) Cronquist] grows in one of two distinct growth phenotypes, “rosette” and “upright” growth types, and they have recently been observed co-occurring in Michigan fields. Previous research found that upright plants from two glyphosate-resistant populations were 3- and 4-fold less sensitive to glyphosate than their rosette siblings. Further experiments were conducted to investigate whether differential glyphosate sensitivity of the growth types was due to glyphosate retention, absorption, or translocation. The total amount of glyphosate retained on the C. canadensis leaf surface was similar for both growth types; however, on a per-weight and per-area bases, the upright growth type retained 21% and 18% less glyphosate, respectively. Glyphosate absorption was up to 85% at 168 h after treatment (HAT), and was not different between the rosette and upright growth types or between the susceptible (S) and resistant (R) biotypes. Additionally, there was no difference in translocation between the two growth types within each biotype at any time point. Interestingly, at 168 HAT, [14C]glyphosate translocation was higher in the S rosette compared with the two growth types from the R biotype; however, the S upright type was similar to both R growth types. Thus, glyphosate resistance in the R biotype may be due to an alternative mechanism rather than impaired translocation, which has been cited as the primary mechanism of glyphosate resistance in C. canadensis. These results suggest that reduced glyphosate retention on a per-weight and per-area bases of the upright growth type may contribute to increased glyphosate tolerance due to a diluted concentration of glyphosate in the plant. However, another factor is likely related to the mechanism of resistance within the R biotype, which is contributing to a 3-fold difference in glyphosate sensitivity between the two growth types, such as alterations in EPSPS gene expression or changes in undescribed metabolism genes.
Prediction of the Diurnal Variation of Summertime Precipitation Over the Sichuan Basin by a Regional Model
Authors: Li Juan , Jiang Xingwen , Schiemann Reinhard , Chen Haoming , Li Yueqing , Heng Zhiwei 
Published: January 2023

AbstractThe nocturnal precipitation over the Sichuan Basin (SCB) exhibits obvious spatial variation, most of the existing numerical research of precipitation event over the SCB is based on case studies. In this study, the long‐term climatological evaluation of the prediction of diurnal spatio‐temporal evolution of precipitation and relevant physical mechanism over the SCB by 9 and 3 km operational numerical weather prediction model is carried out. It is found that the SWC‐WARMS model with 9 km grid spacing overestimates the summer precipitation, especially over the western slopes of the SCB. The northeastward timing delay of the precipitation peak over the SCB is well reproduced in the model, with predicted precipitation peaking at midnight over the southwestern SCB and in the early morning over the northeastern SCB. However, the predicted diurnal peak of precipitation appears 2–3 hr earlier than the observed peak. Increasing horizontal resolution to 3 km reduces the wet bias and improves the diurnal phase of precipitation. Compared to reanalysis, the predicted easterly anomalous wind appears earlier and the anomalous wind speed is stronger. Moreover, the predicted atmosphere is too unstable, which is associated with “warm below and cold above” vertical biases in temperature and wet biases in specific humidity. Thus, model precipitation peaks too early in the day over the SCB, and is overestimated. The weakening of the predicted southwesterly flow in the middle troposphere weakens the northeastward propagation of precipitation after midnight over the SCB. The most significant improvements are found for the diurnal variation of low‐level anomalous wind speed in the 3 km resolution model, contributing to a more realistic representation of precipitation over the SCB.
A Compact Passive Quad‐Band Negative Group Delay Circuit With Stepped Impedance Resonator and Defected Microstrip Structure
Authors: Zhang Li , Yang Shuhui , Guo Qingxin , Xiao Huaibao , Wang Ling , Li Bin , Zhang Hui 
Published: January 2023

AbstractBased on two‐stage stepped impedance resonator (SIR) and defected microstrip structure (DMS) with an E‐shaped slot, a novel compact passive quad‐band negative group delay circuit (NGDC) is proposed whose resonation frequencies and group delay performance are mainly determined by the SIR and the DMS. In order to help reveal the working mechanism of the quad‐band NGDC, an equivalent circuit of the NGDC is developed. It is composed of the transmission lines and serial‐parallel LC networks, and its S‐parameters are derived by using the theory of transmission matrix. The theoretical and simulated results for the transmission characteristics of the NGDC agree well with each other. To validate the design concept, a prototype of the proposed quad‐band NGDC was fabricated and measured. The measured results show that at the frequencies of 2.64, 7.88, 13.08, and 18.18 GHz, the negative group delay values achieve −5.4, −3.1, −1.18, and −1.14 ns, with |S21| values of −17.2, −20.5, −12.8, and −18.1 dB, respectively. Compared with the recently reported works, the proposed NGDC exhibits the largest number of operation frequency bands. Furthermore, it does not use lumped resistors and has miniaturized dimension.
Systems Biology Graphical Notation: Process Description language Level 1
Authors: Moodie Stuart , Le Novere Nicolas , Demir Emek , Mi Huaiyu , Schreiber Falk 
Published: January 2023

AbstractStandard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
PathExpand: Extending biological pathways using molecular interaction networks
Authors: Glaab Enrico , Baudot Anais , Krasnogor Natalio , Valencia Alfonso 
Published: January 2023

AbstractWe present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyze their enrichment in cancer mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes.
Maximizing decision rate in multisensory integration
Authors: Drugowitsch Jan , Pouget Alexandre , DeAngelis Gregory , Angelaki Dora 
Published: January 2023

AbstractEffective decision-making in an uncertain world requires making use of all available information, even if distributed across different sensory modalities, as well as trading off the speed of a decision with its accuracy. In tasks with a fixed stimulus presentation time, animal and human subjects have previously been shown to combine information from several modalities in a statistically optimal manner. Furthermore, for easily discriminable stimuli and under the assumption that reaction times result from a race-to-threshold mechanism, multimodal reaction times are typically faster than predicted from unimodal conditions when assuming independent (parallel) races for each modality. However, due to a lack of adequate ideal observer models, it has remained unclear whether subjects perform optimal cue combination when they are allowed to choose their response times freely.Based on data collected from human subjects performing a visual/vestibular heading discrimination task, we show that the subjects exhibit worse discrimination performance in the multimodal condition than predicted by standard cue combination criteria, which relate multimodal discrimination performance to sensitivity in the unimodal conditions. Furthermore, multimodal reaction times are slower than those predicted by a parallel race model, opposite to what is commonly observed for easily discriminable stimuli.Despite violating the standard criteria for optimal cue combination, we show that subjects still accumulate evidence optimally across time and cues, even when the strength of the evidence varies with time. Additionally, subjects adjust their decision bounds, controlling the trade-off between speed and accuracy of a decision, such that they feature correct decision rates close to the maximum achievable value.
Histone deacetylase inhibitors promote breast cancer metastasis by elevating NEDD9 expression
Authors: Hu Zonglong , Wei Fan , Su Yi , Wang Yafang , Shen Yanyan , Fang Yanfen , Ding Jian , Chen Yi 
Published: January 2023

AbstractHistone deacetylase (HDAC) is a kind of protease that modifies histone to regulate gene expression, and is usually abnormally activated in tumors. The approved pan-HDAC inhibitors have demonstrated clinical benefits for patients in some hematologic malignancies. Only limited therapeutic success in breast cancer has been observed in clinical trials. In this study, we declare that pan-HDAC inhibitors targeting NEDD9-FAK pathway exacerbate breast cancer metastasis in preclinical models, which may severely impede their clinical success. NEDD9 is not an oncogene, however, it has been demonstrated recently that there are high level or activity changes of NEDD9 in a variety of cancer, including leukemia, colon cancer, and breast cancer. Mechanistically, pan-HDAC inhibitors enhance H3K9 acetylation at the nedd9 gene promoter via inhibition of HDAC4 activity, thus increase NEDD9 expression, and then activate FAK phosphorylation. The realization that pan-HDAC inhibitors can alter the natural history of breast cancer by increasing invasion warrants clinical attention. In addition, although NEDD9 has been reported to have a hand in breast cancer metastasis, it has not received much attention, and no therapeutic strategies have been developed. Notably, we demonstrate that FAK inhibitors can reverse breast cancer metastasis induced by upregulation of NEDD9 via pan-HDAC inhibitors, which may offer a potential combination therapy for breast cancer.
COVID-19-associated monocytic encephalitis (CAME): histological and proteomic evidence from autopsy
Authors: Zhang Pei-Pei , He Zhi-Cheng , Yao Xiao-Hong , Tang Rui , Ma Jie , Luo Tao , Zhu Chuhong , Li Tian-Ran , Liu Xindong , Zhang Dingyu , Zhang Shuyang , Ping Yi-Fang , Leng Ling , Bian Xiu-Wu 
Published: January 2023

AbstractSevere neurological symptoms are associated with Coronavirus disease 2019 (COVID-19). However, the morphologic features, pathological nature and their potential mechanisms in patient brains have not been revealed despite evidence of neurotropic infection. In this study, neuropathological damages and infiltrating inflammatory cells were quantitatively evaluated by immunohistochemical staining, ultrastructural examination under electron microscopy, and an image threshold method, in postmortem brains from nine critically ill COVID-19 patients and nine age-matched cadavers of healthy individuals. Differentially expressed proteins were identified by quantitative proteomic assays. Histopathological findings included neurophagocytosis, microglia nodules, satellite phenomena, extensive edema, focal hemorrhage, and infarction, as well as infiltrating mononuclear cells. Immunostaining of COVID-19 brains revealed extensive activation of both microglia and astrocytes, severe damage of the blood–brain barrier (BBB) and various degrees of perivascular infiltration by predominantly CD14+/CD16+/CD141+/CCR7+/CD11c+ monocytes and occasionally CD4+/CD8+ T lymphocytes. Quantitative proteomic assays combined with bioinformatics analysis identified upregulated proteins predominantly involved in immune responses, autophagy and cellular metabolism in COVID-19 patient brains compared with control brains. Proteins involved in brain development, neuroprotection, and extracellular matrix proteins of the basement membrane were downregulated, potentially caused by the activation of transforming growth factor β receptor and vascular endothelial growth factor signaling pathways. Thus, our results define histopathological and molecular profiles of COVID-19-associated monocytic encephalitis (CAME) and suggest potential therapeutic targets.
Impaired belief updating and devaluation in adult women with bulimia nervosa
Authors: Berner Laura A. , Fiore Vincenzo G. , Chen Joanna Y. , Krueger Angeline , Kaye Walter H. , Viranda Thalia , de Wit Sanne 
Published: January 2023

AbstractRecent models of bulimia nervosa (BN) propose that binge-purge episodes ultimately become automatic in response to cues and insensitive to negative outcomes. Here, we examined whether women with BN show alterations in instrumental learning and devaluation sensitivity using traditional and computational modeling analyses of behavioral data. Adult women with BN (n = 30) and group-matched healthy controls (n = 31) completed a task in which they first learned stimulus-response-outcome associations. Then, participants were required to repeatedly adjust their responses in a “baseline test”, when different sets of stimuli were explicitly devalued, and in a “slips-of-action test”, when outcomes instead of stimuli were devalued. The BN group showed intact behavioral sensitivity to outcome devaluation during the slips-of-action test, but showed difficulty overriding previously learned stimulus-response associations on the baseline test. Results from a Bayesian learner model indicated that this impaired performance could be accounted for by a slower pace of belief updating when a new set of previously learned responses had to be inhibited (p = 0.036). Worse performance and a slower belief update in the baseline test were each associated with more frequent binge eating (p = 0.012) and purging (p = 0.002). Our findings suggest that BN diagnosis and severity are associated with deficits in flexibly updating beliefs to withhold previously learned responses to cues. Additional research is needed to determine whether this impaired ability to adjust behavior is responsible for maintaining automatic and persistent binge eating and purging in response to internal and environmental cues.
Interactions between perceived stress and microbial-host immune components: two demographically and geographically distinct pregnancy cohorts
Authors: Peñalver Bernabé Beatriz , Maki Pauline M. , Cunningham Janet L. , Eisenlohr-Moul Tory , Tussing-Humphreys Lisa , Carroll Ian M. , Meltzer-Brody Samantha , Gilbert Jack A. , Kimmel Mary 
Published: January 2023

AbstractHigher stress during pregnancy associates with negative outcomes and elevated inflammation. The gut microbiota, reflecting environment and social interactions, alongside host immune responses have the potential to better understand perceived stress and identify when stress is excessive in pregnancy. Two U.S. cohorts of 84 pregnant individuals, composed of urban women of color and suburban white women, completed the Perceived Stress Scale-10 (PSS-10) and provided fecal and blood samples at two time points. Confirmatory Factor Analysis assessed the robustness of a two-factor PSS-10 model (Emotional Distress/ED and Self-Efficacy/SE). Gut microbiota composition was measured by 16 S rRNA amplicon sequencing and the immune system activity was assessed with a panel of 21 T-cell related cytokines and chemokines. ED levels were higher in the suburban compared to the urban cohort, but levels of SE were similar. ED and SE levels were associated with distinct taxonomical signatures and the gut microbiota data improved the prediction of SE levels compared with models based on socio-demographic characteristics alone. Integration of self-reported symptoms, microbial and immune information revealed a possible mediation effect ofBacteroides uniformisbetween the immune system (through CXCL11) and SE. The study identified links between distinct taxonomical and immunological signatures with perceived stress. The data are congruent with a model where gut microbiome and immune factors, both impacting and reflecting factors such as close social relationships and dietary fiber, may modulate neural plasticity resulting in increased SE during pregnancy. The predictive value of these peripheral markers merit further study.
A potassium-chloride co-transporter promotes tumor progression and castration resistance of prostate cancer through m6A reader YTHDC1
Authors: Yuan Shuai , He Shao-Hua , Li Lu-Yao , Xi Shu , Weng Hong , Zhang Jin-Hui , Wang Dan-Qi , Guo Meng-Meng , Zhang Haozhe , Wang Shuang-Ying , Ming Dao-Jing , Liu Meng-Yang , Hu Hailiang , Zeng Xian-Tao 
Published: January 2023

AbstractSLC12A5, a neuron-specific potassium-chloride co-transporter, has been reported to promote tumor progression, however, the underlying mechanism remains unclear. Here we report that SLC12A5 functions as an oncogene to promote tumor progression and castration resistance of prostate cancer through the N6-methyladenosine (m6A) reader YTHDC1 and the transcription factor HOXB13. We have shown that the level of SLC12A5 was increased in prostate cancer, in comparison to its normal counterparts, and further elevated in castration-resistant prostate cancer (CRPC). The enhanced expression of SLC12A5 mRNA was associated with neuroendocrine prostate cancer (NEPC) progression and poor survival in prostate cancer. Furthermore, we demonstrated that SLC12A5 promoted the castration resistance development of prostate cancer in addition to the cell proliferation and migration. Interestingly, SLC12A5 was detected in the cell nucleus and formed a complex with nuclear m6A reader YTHDC1, which in turn upregulated HOXB13 to promote the prostate cancer progression. Therefore, our findings reveal a mechanism that how the potassium-chloride cotransporter SLC12A5 promotes the tumor progression and provide a therapeutic opportunity for prostate cancer to apply the neurological disorder drug SLC12A5 inhibitors.
Illustrating new understanding of adsorbed water on silica for inducing tetrahedral cobalt(II) for propane dehydrogenation
Authors: Huang Zijun , He Dedong , Deng Weihua , Jin Guowu , Li Ke , Luo Yongming 
Published: January 2023

AbstractHighly dispersed metal sites on the surface of silica, achieved from immobilization of metal precursor within hydroxyl groups, has gained increasing attention in the field of heterogeneous catalyst. However, the special role of adsorbed water derived by hydroxyl groups on the silica is generally ignored. Herein, a new understanding of adsorbed water on the formation of highly dispersed tetrahedral Co(II) (Td-cobalt(II)) sites is illustrated. It is indicated that sufficient adsorbed water induces the transformation of precursor of Co(NO3)2 into intermediate of [Co(H2O)6]2+. Subsequently, [Co(H2O)6]2+ makes the highly dispersed Td-cobalt(II) sites to be available during direct H2-reduction process. A systematic characterization and DFT calculation prove the existence of the adsorbed water and the importance of the intermediate of [Co(H2O)6]2+, respectively. The as-synthesized catalyst is attempted to the propane dehydrogenation, which shows better reactivity when compared with other reported Co based catalysts.
A phase II study of palbociclib plus letrozole plus trastuzumab as neoadjuvant treatment for clinical stages II and III ER+ HER2+ breast cancer (PALTAN)
Authors: Ademuyiwa Foluso O. , Northfelt Donald W. , O’Connor Tracey , Levine Ellis , Luo Jingqin , Tao Yu , Hoog Jeremy , Laury Marie L. , Summa Tracy , Hammerschmidt Trish , Guo Zhanfang , Frith Ashley , Weilbaecher Katherine , Opyrchal Mateusz , Aft Rebecca , Clifton Katherine , Suresh Rama , Bagegni Nusayba , Hagemann Ian S. , Iglesia Michael D. , Ma Cynthia X. 
Published: January 2023

AbstractPatients with ER+/HER2+ breast cancer (BC) are less likely to achieve pathological complete response (pCR) after chemotherapy with dual HER2 blockade than ER−/HER2+ BC. Endocrine therapy plus trastuzumab is effective in advanced ER+/HER2+ BC. Inhibition of CDK4/6 and HER2 results in synergistic cell proliferation reduction. We combined palbociclib, letrozole, and trastuzumab (PLT) as a chemotherapy-sparing regimen. We evaluated neoadjuvant PLT in early ER+/HER2+ BC. Primary endpoint was pCR after 16 weeks. Research biopsies were performed for whole exome and RNA sequencing, PAM50 subtyping, and Ki67 assessment for complete cell cycle arrest (CCCA: Ki67 ≤ 2.7%). After 26 patients, accrual stopped due to futility. pCR (residual cancer burden—RCB 0) was 7.7%, RCB 0/I was 38.5%. Grade (G) 3/4 treatment-emergent adverse events occurred in 19. Among these, G3/4 neutropenia was 50%, hypertension 26.9%, and leucopenia 7.7%. Analysis indicated CCCA in 85% at C1 day 15 (C1D15), compared to 27% at surgery after palbociclib was discontinued. Baseline PAM50 subtyping identified 31.2% HER2-E, 43.8% Luminal B, and 25% Luminal A. 161 genes were differentially expressed comparing C1D15 to baseline. MKI67, TK1, CCNB1, AURKB, and PLK1 were among the genes downregulated, consistent with CCCA at C1D15. Molecular Signatures Database gene-sets analyses demonstrated downregulated processes involved in proliferation, ER and mTORC1 signaling, and DNA damage repair at C1D15, consistent with the study drug’s mechanisms of action. Neoadjuvant PLT showed a pCR of 7.7% and an RCB 0/I rate of 38.5%. RNA sequencing and Ki67 data indicated potent anti-proliferative effects of study treatments. ClinicalTrials.gov- NCT02907918.