bluuebunny/crossref_metadata_2025_split huggingface dataset:
ALPK2 acts as tumor promotor in development of bladder cancer through targeting DEPDC1A
Authors: Wang Yuchen , Wu Jie , Luo Wenjie , Zhang Hailiang , Shi Guohai , Shen Yijun , Zhu Yao , Ma Chunguang , Dai Bo , Ye Dingwei , Zhu Yiping 
Published: July 2021

AbstractBladder cancer is one of the most common malignant tumors in the urinary system. The development and improvement of treatment efficiency require the deepening of the understanding of its molecular mechanism. This study investigated the role of ALPK2, which is rarely studied in malignant tumors, in the development of bladder cancer. Our results showed the upregulation of ALPK2 in bladder cancer, and data mining of TCGA database showed the association between ALPK2 and pathological parameters of patients with bladder cancer. In vitro and in vivo experiments demonstrated that knockdown of ALPK2 could inhibit bladder cancer development through regulating cell proliferation, cell apoptosis, and cell migration. Additionally, DEPDC1A is identified as a potential downstream of ALPK2 with direct interaction, whose overexpression/downregulation can inhibit/promote the malignant behavioral of bladder cancer cells. Moreover, the overexpression of DEPDC1A can rescue the inhibitory effects of ALPK2 knockdown on bladder cancer. In conclusion, ALPK2 exerts a cancer-promoting role in the development of bladder cancer by regulating DEPDC1A, which may become a promising target to improve the treatment strategy of bladder cancer.
Interactions between ShPP2-1, an F-box family gene, and ACR11A regulate cold tolerance of tomato
Authors: Song Jianwen , Shang Lele , Chen Shiwei , Lu Yongen , Zhang Yuyang , Ouyang Bo , Ye Zhibiao , Zhang Junhong 
Published: July 2021

AbstractThere is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress. We found that the expression of an F-box gene family member named ShPP2-1 from Solanum habrochaites is cold inducible and studied its contribution to cold tolerance. Overexpression of ShPP2-1 in cultivated tomato (AC) reduced cold tolerance by intensifying damage to cell membranes. To explore the underlying molecular mechanism, we conducted a yeast two-hybrid library screen and found that a protein containing ACT domain repeats named ACR11A interacts with PP2-1. Overexpression of SlACR11A in AC enhanced the cold tolerance of seedlings and germinating seeds. Cold tolerance decreased in tomato plants that overexpressed both of these genes. Additionally, we performed seed germination experiments in the cold with 177 tomato accessions and identified two alleles of SlACR11A that differ in one single-nucleotide polymorphism. We found that one of these alleles, SlACR11AG, is significantly enriched in cold-tolerant tomato plants. Taken together, our findings indicate that the combination of low expression levels of PP2-1 and high expression levels of ACR11A can promote cold tolerance. These genes may therefore serve as direct targets for both genetic engineering and improvement projects that aim to enhance the cold tolerance of tomato.
Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit
Authors: Leitão Susana T. , Santos Carmen , Araújo Susana de Sousa , Rubiales Diego , Vaz Patto Maria Carlota 
Published: July 2021

AbstractCommon bean (Phaseolus vulgaris L.), one of the most consumed food legumes worldwide, is threatened by two main constraints that are found frequently together in nature, water deficit (WD) and fusarium wilt (Fop). To understand the shared and unique responses of common bean to Fop and WD, we analyzed the transcriptomic changes and phenotypic responses in two accessions, one resistant and one susceptible to both stresses, exposed to single and combined stresses. Physiological responses (photosynthetic performance and pigments quantification) and disease progression were also assessed. The combined FopWD imposition negatively affected the photosynthetic performance and increased the susceptible accession disease symptoms. The susceptible accession revealed a higher level of transcriptional changes than the resistant one, and WD single stress triggered the highest transcriptional changes. While 89 differentially expressed genes were identified exclusively in combined stresses for the susceptible accession, 35 were identified in the resistant one. These genes belong mainly to “stress”, “signaling”, “cell wall”, “hormone metabolism”, and “secondary metabolism” functional categories. Among the up-regulated genes with higher expression in the resistant accession, the cysteine-rich secretory, antigen 5 and Pr-1 (CAP) superfamily protein, a ribulose bisphosphate carboxylase family protein, and a chitinase A seem promising targets for multiple stress breeding.
The apple C2H2-type zinc finger transcription factor MdZAT10 positively regulates JA-induced leaf senescence by interacting with MdBT2
Authors: Yang Kuo , An Jian-Ping , Li Chong-Yang , Shen Xue-Na , Liu Ya-Jing , Wang Da-Ru , Ji Xing-Long , Hao Yu-Jin , You Chun-Xiang 
Published: July 2021

AbstractJasmonic acid (JA) plays an important role in regulating leaf senescence. However, the molecular mechanisms of leaf senescence in apple (Malus domestica) remain elusive. In this study, we found that MdZAT10, a C2H2-type zinc finger transcription factor (TF) in apple, markedly accelerates leaf senescence and increases the expression of senescence-related genes. To explore how MdZAT10 promotes leaf senescence, we carried out liquid chromatography/mass spectrometry screening. We found that MdABI5 physically interacts with MdZAT10. MdABI5, an important positive regulator of leaf senescence, significantly accelerated leaf senescence in apple. MdZAT10 was found to enhance the transcriptional activity of MdABI5 for MdNYC1 and MdNYE1, thus accelerating leaf senescence. In addition, we found that MdZAT10 expression was induced by methyl jasmonate (MeJA), which accelerated JA-induced leaf senescence. We also found that the JA-responsive protein MdBT2 directly interacts with MdZAT10 and reduces its protein stability through ubiquitination and degradation, thereby delaying MdZAT10-mediated leaf senescence. Taken together, our results provide new insight into the mechanisms by which MdZAT10 positively regulates JA-induced leaf senescence in apple.
Microbial short-chain fatty acids modulate CD8+ T cell responses and improve adoptive immunotherapy for cancer
Authors: Luu Maik , Riester Zeno , Baldrich Adrian , Reichardt Nicole , Yuille Samantha , Busetti Alessandro , Klein Matthias , Wempe Anne , Leister Hanna , Raifer Hartmann , Picard Felix , Muhammad Khalid , Ohl Kim , Romero Rossana , Fischer Florence , Bauer Christian A. , Huber Magdalena , Gress Thomas M. , Lauth Matthias , Danhof Sophia , Bopp Tobias , Nerreter Thomas , Mulder Imke E. , Steinhoff Ulrich , Hudecek Michael , Visekruna Alexander 
Published: July 2021

AbstractEmerging data demonstrate that the activity of immune cells can be modulated by microbial molecules. Here, we show that the short-chain fatty acids (SCFAs) pentanoate and butyrate enhance the anti-tumor activity of cytotoxic T lymphocytes (CTLs) and chimeric antigen receptor (CAR) T cells through metabolic and epigenetic reprograming. We show that in vitro treatment of CTLs and CAR T cells with pentanoate and butyrate increases the function of mTOR as a central cellular metabolic sensor, and inhibits class I histone deacetylase activity. This reprogramming results in elevated production of effector molecules such as CD25, IFN-γ and TNF-α, and significantly enhances the anti-tumor activity of antigen-specific CTLs and ROR1-targeting CAR T cells in syngeneic murine melanoma and pancreatic cancer models. Our data shed light onto microbial molecules that may be used for enhancing cellular anti-tumor immunity. Collectively, we identify pentanoate and butyrate as two SCFAs with therapeutic utility in the context of cellular cancer immunotherapy.
One-way dependent clusters and stability of cluster synchronization in directed networks
Authors: Lodi Matteo , Sorrentino Francesco , Storace Marco 
Published: July 2021

AbstractCluster synchronization in networks of coupled oscillators is the subject of broad interest from the scientific community, with applications ranging from neural to social and animal networks and technological systems. Most of these networks are directed, with flows of information or energy that propagate unidirectionally from given nodes to other nodes. Nevertheless, most of the work on cluster synchronization has focused on undirected networks. Here we characterize cluster synchronization in general directed networks. Our first observation is that, in directed networks, a cluster A of nodes might be one-way dependent on another cluster B: in this case, A may remain synchronized provided that B is stable, but the opposite does not hold. The main contribution of this paper is a method to transform the cluster stability problem in an irreducible form. In this way, we decompose the original problem into subproblems of the lowest dimension, which allows us to immediately detect inter-dependencies among clusters. We apply our analysis to two examples of interest, a human network of violin players executing a musical piece for which directed interactions may be either activated or deactivated by the musicians, and a multilayer neural network with directed layer-to-layer connections.
Bcl-2-dependent autophagy disruption during aging impairs amino acid utilization that is restored by hochuekkito
Authors: Nahata Miwa , Mogami Sachiko , Sekine Hitomi , Iizuka Seiichi , Okubo Naoto , Fujitsuka Naoki , Takeda Hiroshi 
Published: July 2021

AbstractChronic undernutrition contributes to the increase in frailty observed among elderly adults, which is a pressing issue in the sector of health care for older people worldwide. Autophagy, an intracellular recycling system, is closely associated with age-related pathologies. Therefore, decreased autophagy in aging could be involved in the disruption of energy homeostasis that occurs during undernutrition; however, the physiological mechanisms underlying this process remain unknown. Here, we showed that 70% daily food restriction (FR) induced fatal hypoglycemia in 23–26-month-old (aged) mice, which exhibited significantly lower hepatic autophagy than 9-week-old (young) mice. The liver expressions of Bcl-2, an autophagy-negative regulator, and Beclin1–Bcl-2 binding, were increased in aged mice compared with young mice. The autophagy inducer Tat-Beclin1 D11, not the mTOR inhibitor rapamycin, decreased the plasma levels of the glucogenic amino acid and restored the blood glucose levels in aged FR mice. Decreased liver gluconeogenesis, body temperature, physical activity, amino acid metabolism, and hepatic mitochondrial dynamics were observed in the aged FR mice. These changes were restored by treatment with hochuekkito that is a herbal formula containing several autophagy-activating ingredients. Our results indicate that Bcl-2 upregulation in the liver during the aging process disturbs autophagy activation, which increases the vulnerability to undernutrition. The promotion of liver autophagy may offer clinical therapeutic benefits to frail elderly patients.
Genetic discrimination: introducing the Asian perspective to the debate
Authors: Kim Hannah , Ho Calvin W. L. , Ho Chih-Hsing , Athira P. S. , Kato Kazuto , De Castro Leonardo , Kang Hui , Huxtable Richard , Zwart Hub , Ives Jonathan , Lee Ilhak , Joly Yann , Kim So Yoon 
Published: July 2021

AbstractOur article aims to provide a comprehensive portrayal of how seven Asian jurisdictions have sought to address the challenge of genetic discrimination (GD) by presenting an analysis of the relevant legislation, policies, and practices. Based on our findings, policy discussion and action on preventing or mitigating GD have been narrowly framed in terms of employment, insurance, disability, marriage, and family planning. Except for South Korea, none of the jurisdictions we examined has adopted specific legislation to prevent GD. However, for Asia to truly benefit from its recent scientific and technological progress in genomics, we highlight the need for these jurisdictions to engage more proactively with the challenges of GD through a coordinated regulatory and governance mechanism.
A method for gaining a deeper insight into the aroma profile of olive oil
Authors: Suzuki Daisuke , Sato Yuko , Mori Akane , Tamura Hirotoshi 
Published: July 2021

AbstractVolatile compounds in food play a crucial role in affecting food quality and consumer preference, but the volatile compounds in olive oil are not fully understood due to the matrix effect of oil. The oiling-out assisted liquid–liquid extraction (OA-LLE), which we previously reported, is an effective method for isolating volatile compounds from edible oils with a strong matrix effect. However, when we apply OA-LLE to extra virgin olive oil (EVOO), the aromatic extracts contain non-volatile compounds such as pigments because of solvent-based extraction. Solvent-assisted flavor evaporation (SAFE) can remove such non-volatiles from extracts, but SAFE is affected by a matrix effect during distillation, resulting in a decrease in performance. By combining the advantages of OA-LLE and SAFE, we propose an effective approach, OA-LLE followed by SAFE (OA-LLE + SAFE), for extracting aroma compounds from EVOO. The “two assists” should help to better understand the native aroma profile of EVOO.
Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq
Authors: Philpott Martin , Watson Jonathan , Thakurta Anjan , Brown Tom , Brown Tom , Oppermann Udo , Cribbs Adam P. 
Published: July 2021

AbstractHere we describe single-cell corrected long-read sequencing (scCOLOR-seq), which enables error correction of barcode and unique molecular identifier oligonucleotide sequences and permits standalone cDNA nanopore sequencing of single cells. Barcodes and unique molecular identifiers are synthesized using dimeric nucleotide building blocks that allow error detection. We illustrate the use of the method for evaluating barcode assignment accuracy, differential isoform usage in myeloma cell lines, and fusion transcript detection in a sarcoma cell line.
Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa
Authors: Happi Anise N. , Ogunsanya Olusola A. , Oguzie Judith U. , Oluniyi Paul E. , Olono Alhaji S. , Heeney Jonathan L. , Happi Christian T. 
Published: July 2021

AbstractRabbit Haemorrhagic Disease (RHD) causes high morbidity and mortality in rabbits and hares. Here, we report the first genomic characterization of lagovirus GI.2 virus in domestic rabbits from sub-Saharan Africa. We used an unbiased microbial metagenomic Next Generation Sequencing (mNGS) approach to diagnose the pathogen causing the suspected outbreak of RHD in Ibadan, Nigeria. The liver, spleen, and lung samples of five rabbits from an outbreak in 2 farms were analyzed. The mNGS revealed one full and two partial RHDV2 genomes on both farms. Phylogenetic analysis showed close clustering with RHDV2 lineages from Europe (98.6% similarity with RHDV2 in the Netherlands, and 99.1 to 100% identity with RHDV2 in Germany), suggesting potential importation. Subsequently, all the samples were confirmed by RHDV virus-specific RT-PCR targeting the VP60 gene with the expected band size of 398 bp for the five rabbits sampled. Our findings highlight the need for increased genomic surveillance of RHDV2 to track its origin, understand its diversity and to inform public health policy in Nigeria, and Sub-Saharan Africa.
Gender differences in BaYaka forager sleep-wake patterns in forest and village contexts
Authors: Kilius Erica , Samson David R. , Lew-Levy Sheina , Sarma Mallika S. , Patel Ujas A. , Ouamba Yann R. , Miegakanda Valchy , Gettler Lee T. , Boyette Adam H. 
Published: July 2021

AbstractSleep studies in small-scale subsistence societies have broadened our understanding of cross-cultural sleep patterns, revealing the flexibility of human sleep. We examined sleep biology among BaYaka foragers from the Republic of Congo who move between environmentally similar but socio-ecologically distinct locations to access seasonal resources. We analyzed the sleep–wake patterns of 51 individuals as they resided in a village location (n = 39) and a forest camp (n = 23) (362 nights total). Overall, BaYaka exhibited high sleep fragmentation (50.5) and short total sleep time (5.94 h), suggestive of segmented sleep patterns. Sleep duration did not differ between locations, although poorer sleep quality was exhibited in the village. Linear mixed effect models demonstrated that women’s sleep differed significantly from men’s in the forest, with longer total sleep time (β ± SE =  − 0.22 ± 0.09, confidence interval (CI) = [− 0.4, − 0.03]), and higher sleep quality (efficiency; β ± SE =  − 0.24 ± 0.09, CI = [− 0.42, − 0.05]). These findings may be due to gender-specific social and economic activities. Circadian rhythms were consistent between locations, with women exhibiting stronger circadian stability. We highlight the importance of considering intra-cultural variation in sleep–wake patterns when taking sleep research into the field.
Communication breakdown: Limits of spectro-temporal resolution for the perception of bat communication calls
Authors: Hörpel Stephen Gareth , Baier A. Leonie , Peremans Herbert , Reijniers Jonas , Wiegrebe Lutz , Firzlaff Uwe 
Published: July 2021

AbstractDuring vocal communication, the spectro-temporal structure of vocalizations conveys important contextual information. Bats excel in the use of sounds for echolocation by meticulous encoding of signals in the temporal domain. We therefore hypothesized that for social communication as well, bats would excel at detecting minute distortions in the spectro-temporal structure of calls. To test this hypothesis, we systematically introduced spectro-temporal distortion to communication calls of Phyllostomus discolor bats. We broke down each call into windows of the same length and randomized the phase spectrum inside each window. The overall degree of spectro-temporal distortion in communication calls increased with window length. Modelling the bat auditory periphery revealed that cochlear mechanisms allow discrimination of fast spectro-temporal envelopes. We evaluated model predictions with experimental psychophysical and neurophysiological data. We first assessed bats’ performance in discriminating original versions of calls from increasingly distorted versions of the same calls. We further examined cortical responses to determine additional specializations for call discrimination at the cortical level. Psychophysical and cortical responses concurred with model predictions, revealing discrimination thresholds in the range of 8–15 ms randomization-window length. Our data suggest that specialized cortical areas are not necessary to impart psychophysical resilience to temporal distortion in communication calls.
Mosquito species identification using convolutional neural networks with a multitiered ensemble model for novel species detection
Authors: Goodwin Autumn , Padmanabhan Sanket , Hira Sanchit , Glancey Margaret , Slinowsky Monet , Immidisetti Rakhil , Scavo Laura , Brey Jewell , Sai Sudhakar Bala Murali Manoghar , Ford Tristan , Heier Collyn , Linton Yvonne-Marie , Pecor David B. , Caicedo-Quiroga Laura , Acharya Soumyadipta 
Published: July 2021

Abstract
With over 3500 mosquito species described, accurate species identification of the few implicated in disease transmission is critical to mosquito borne disease mitigation. Yet this task is hindered by limited global taxonomic expertise and specimen damage consistent across common capture methods. Convolutional neural networks (CNNs) are promising with limited sets of species, but image database requirements restrict practical implementation. Using an image database of 2696 specimens from 67 mosquito species, we address the practical open-set problem with a detection algorithm for novel species. Closed-set classification of 16 known species achieved 97.04 ± 0.87% accuracy independently, and 89.07 ± 5.58% when cascaded with novelty detection. Closed-set classification of 39 species produces a macro F1-score of 86.07 ± 1.81%. This demonstrates an accurate, scalable, and practical computer vision solution to identify wild-caught mosquitoes for implementation in biosurveillance and targeted vector control programs, without the need for extensive image database development for each new target region.
Positive evidence for clinical pharmacist interventions during interdisciplinary rounding at a psychiatric hospital
Authors: Stuhec Matej , Tement Valentina 
Published: July 2021

AbstractClinical pharmacists have not yet become an integral part of interdisciplinary ward rounds in most psychiatric hospitals across the European Union. This retrospective observational pre-post study examined the impact of clinical pharmacist recommendations in an interdisciplinary medical team during psychiatric hospital rounding. The study included all patients in a Slovenian psychiatric hospital who were hospitalized 2019–2020. The clinical pharmacist made 315 recommendations for a total of 224 participants (average age M = 59.4, median = 56). Psychiatrists accepted 295 (93.7%) of the recommendations. After the recommendations, the number of expressed and potential drug-related problems decreased in 166 (93.8%) and 129 (93.8%) interventions, respectively. Three months after discharge, 222 accepted recommendations were continued (70.5%). The most common recommendations were related to antipsychotics (19.4%, N = 61) followed by antidepressants (16.8%, N = 53). Including a clinical pharmacist in the interdisciplinary ward rounds at a psychiatric hospital reduced the number of expressed and potential drug-related problems with a very high recommendation acceptance rate. These results are the first in Central Europe to explore the benefits of including a clinical pharmacist in ward rounding.
Novel mumps virus epitopes reveal robust cytotoxic T cell responses after natural infection but not after vaccination
Authors: Kaaijk Patricia , Emmelot Maarten E. , Meiring Hugo D. , van Els Cécile A. C. M. , de Wit Jelle 
Published: July 2021

AbstractMumps is nowadays re-emerging despite vaccination. The contribution of T cell immunity to protection against mumps has not been clearly defined. Previously, we described a set of 41 peptides that were eluted from human leukocyte antigen (HLA) class I molecules of mumps virus (MuV)-infected cells. Here, we confirmed immunogenicity of five novel HLA-B*07:02- and HLA-A*01:01-restricted MuV T cell epitopes from this set of peptides. High frequencies of T cells against these five MuV epitopes could be detected ex vivo in all tested mumps patients. Moreover, these epitope-specific T cells derived from mumps patients displayed strong cytotoxic activity. In contrast, only marginal T cell responses against these novel MuV epitopes could be detected in recently vaccinated persons, corroborating earlier findings. Identifying which MuV epitopes are dominantly targeted in the mumps-specific CD8+ T- response is an important step towards better understanding in the discrepancies between natural infection or vaccination-induced cell-mediated immune protection.