bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic assessment of measurable residual disease in favorable-risk acute myeloid leukemia in first remission, treatment, and outcomes
Authors: Yu Sijian , Lin Tong , Nie Danian , Zhang Yu , Sun Zhiqiang , Zhang Qing , Wang Caixia , Xiong Mujun , Fan Zhiping , Huang Fen , Xu Na , Liu Hui , Yu Guopan , Zhang Hongyu , Shi Pengcheng , Xu Jun , Xuan Li , Guo Ziwen , Wu Meiqing , Han Lijie , Xiong Yiying , Sun Jing , Wang Yu , Liu Qifa 
Published: December 2021

AbstractWe aimed to investigate outcomes of different post-remission treatment (PRT) choices based on dynamic measurable residual disease (MRD) by multiparameter flow cytometry in favorable-risk AML (FR-AML). Four hundred and three younger patients with FR-AML in first complete remission (CR1) were enrolled in this registry-based cohort study, including 173 who received chemotherapy (CMT), 92 autologous stem cell transplantation (auto-SCT), and 138 allogeneic SCT (allo-SCT). The primary endpoint was the 5-year overall survival (OS). Subgroup analyses were performed based on dynamic MRD after the 1st, 2nd, and 3rd courses of chemotherapy. In subgroups of patients with negative MRD after 1 or 2 course of chemotherapy, comparable OS was observed among the CMT, auto-SCT, and allo-SCT groups (p = 0.340; p = 0.627, respectively). But CMT and auto-SCT had better graft-versus-host-disease-free, relapse-free survival (GRFS) than allo-SCT in both subgroups. For patients with negative MRD after three courses of chemotherapy, allo-SCT had better disease-free-survival than CMT (p = 0.009). However, OS was comparable among the three groups (p = 0.656). For patients with persistently positive MRD after 3 courses of chemotherapy or recurrent MRD, allo-SCT had better OS than CMT and auto-SCT (p = 0.011; p = 0.029, respectively). Dynamic MRD might improve therapy stratification and optimize PRT selection for FR-AML in CR1.
A geometric criterion for the optimal spreading of active polymers in porous media
Authors: Kurzthaler Christina , Mandal Suvendu , Bhattacharjee Tapomoy , Löwen Hartmut , Datta Sujit S. , Stone Howard A. 
Published: December 2021

AbstractEfficient navigation through disordered, porous environments poses a major challenge for swimming microorganisms and future synthetic cargo-carriers. We perform Brownian dynamics simulations of active stiff polymers undergoing run-reverse dynamics, and so mimic bacterial swimming, in porous media. In accord with experiments ofEscherichia coli, the polymer dynamics are characterized by trapping phases interrupted by directed hopping motion through the pores. Our findings show that the spreading of active agents in porous media can be optimized by tuning their run lengths, which we rationalize using a coarse-grained model. More significantly, we discover a geometric criterion for the optimal spreading, which emerges when their run lengths are comparable to the longest straight path available in the porous medium. Our criterion unifies results for porous media with disparate pore sizes and shapes and for run-and-tumble polymers. It thus provides a fundamental principle for optimal transport of active agents in densely-packed biological and environmental settings.
Single cell atlas for 11 non-model mammals, reptiles and birds
Authors: Chen Dongsheng , Sun Jian , Zhu Jiacheng , Ding Xiangning , Lan Tianming , Wang Xiran , Wu Weiying , Ou Zhihua , Zhu Linnan , Ding Peiwen , Wang Haoyu , Luo Lihua , Xiang Rong , Wang Xiaoling , Qiu Jiaying , Wang Shiyou , Li Haimeng , Chai Chaochao , Liang Langchao , An Fuyu , Zhang Le , Han Lei , Zhu Yixin , Wang Feiyue , Yuan Yuting , Wu Wendi , Sun Chengcheng , Lu Haorong , Wu Jihong , Sun Xinghuai , Zhang Shenghai , Sahu Sunil Kumar , Liu Ping , Xia Jun , Zhang Lijing , Chen Haixia , Fang Dongming , Zeng Yuying , Wu Yiquan , Cui Zehua , He Qian , Jiang Sanjie , Ma Xiaoyan , Feng Weimin , Xu Yan , Li Fang , Liu Zhongmin , Chen Lei , Chen Fang , Jin Xin , Qiu Wei , Wang Tianjiao , Li Yang , Xing Xiumei , Yang Huanming , Xu Yanchun , Hua Yan , Liu Yahong , Liu Huan , Xu Xun 
Published: December 2021

AbstractThe availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening of animal cells could reveal the expression patterns of viral entry genes in different hosts. However, such exploration for SARS-CoV-2 remains limited. Here, we perform single-nucleus RNA sequencing for 11 non-model species, including pets (cat, dog, hamster, and lizard), livestock (goat and rabbit), poultry (duck and pigeon), and wildlife (pangolin, tiger, and deer), and investigated the co-expression of ACE2 and TMPRSS2. Furthermore, cross-species analysis of the lung cell atlas of the studied mammals, reptiles, and birds reveals core developmental programs, critical connectomes, and conserved regulatory circuits among these evolutionarily distant species. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and putative zoonotic reservoirs.
Widespread homogenization of plant communities in the Anthropocene
Authors: Daru Barnabas H. , Davies T. Jonathan , Willis Charles G. , Meineke Emily K. , Ronk Argo , Zobel Martin , Pärtel Meelis , Antonelli Alexandre , Davis Charles C. 
Published: December 2021

AbstractNative biodiversity decline and non-native species spread are major features of the Anthropocene. Both processes can drive biotic homogenization by reducing trait and phylogenetic differences in species assemblages between regions, thus diminishing the regional distinctiveness of biotas and likely have negative impacts on key ecosystem functions. However, a global assessment of this phenomenon is lacking. Here, using a dataset of >200,000 plant species, we demonstrate widespread and temporal decreases in species and phylogenetic turnover across grain sizes and spatial extents. The extent of homogenization within major biomes is pronounced and is overwhelmingly explained by non-native species naturalizations. Asia and North America are major sources of non-native species; however, the species they export tend to be phylogenetically close to recipient floras. Australia, the Pacific and Europe, in contrast, contribute fewer species to the global pool of non-natives, but represent a disproportionate amount of phylogenetic diversity. The timeline of most naturalisations coincides with widespread human migration within the last ~500 years, and demonstrates the profound influence humans exert on regional biotas beyond changes in species richness.
A plant virus satellite RNA directly accelerates wing formation in its insect vector for spread
Authors: Jayasinghe Wikum H. , Kim Hangil , Nakada Yusuke , Masuta Chikara 
Published: December 2021

AbstractCucumber mosaic virus (CMV) often accompanies a short RNA molecule called a satellite RNA (satRNA). When infected with CMV in the presence of Y-satellite RNA (Y-sat), tobacco leaves develop a green mosaic, then turn yellow. Y-sat has been identified in the fields in Japan. Here, we show that the yellow leaf colour preferentially attracts aphids, and that the aphids fed on yellow plants, which harbour Y-sat-derived small RNAs (sRNAs), turn red and subsequently develop wings. In addition, we found that leaf yellowing did not necessarily reduce photosynthesis, and that viral transmission was not greatly affected despite the low viral titer in the Y-sat-infected plants. Y-sat-infected plants can therefore support a sufficient number of aphids to allow for efficient virus transmission. Our results demonstrate that Y-sat directly alters aphid physiology via Y-sat sRNAs to promote wing formation, an unprecedented survival strategy that enables outward spread via the winged insect vector.
Glucocorticoid receptor regulates PD-L1 and MHC-I in pancreatic cancer cells to promote immune evasion and immunotherapy resistance
Authors: Deng Yalan , Xia Xianghou , Zhao Yang , Zhao Zilong , Martinez Consuelo , Yin Wenjuan , Yao Jun , Hang Qinglei , Wu Weiche , Zhang Jie , Yu Yang , Xia Weiya , Yao Fan , Zhao Di , Sun Yutong , Ying Haoqiang , Hung Mien-Chie , Ma Li 
Published: December 2021

AbstractDespite unprecedented responses of some cancers to immune checkpoint blockade (ICB) therapies, the application of checkpoint inhibitors in pancreatic cancer has been unsuccessful. Glucocorticoids and glucocorticoid receptor (GR) signaling are long thought to suppress immunity by acting on immune cells. Here we demonstrate a previously undescribed tumor cell-intrinsic role for GR in activating PD-L1 expression and repressing the major histocompatibility complex class I (MHC-I) expression in pancreatic ductal adenocarcinoma (PDAC) cells through transcriptional regulation. In mouse models of PDAC, either tumor cell-specific depletion or pharmacologic inhibition of GR leads to PD-L1 downregulation and MHC-I upregulation in tumor cells, which in turn promotes the infiltration and activity of cytotoxic T cells, enhances anti-tumor immunity, and overcomes resistance to ICB therapy. In patients with PDAC, GR expression correlates with high PD-L1 expression, low MHC-I expression, and poor survival. Our results reveal GR signaling in cancer cells as a tumor-intrinsic mechanism of immunosuppression and suggest that therapeutic targeting of GR is a promising way to sensitize pancreatic cancer to immunotherapy.
A tough nitric oxide-eluting hydrogel coating suppresses neointimal hyperplasia on vascular stent
Authors: Chen Yin , Gao Peng , Huang Lu , Tan Xing , Zhou Ningling , Yang Tong , Qiu Hua , Dai Xin , Michael Sean , Tu Qiufen , Huang Nan , Guo Zhihong , Zhou Jianhua , Yang Zhilu , Wu Hongkai 
Published: December 2021

AbstractVascular stent is viewed as one of the greatest advancements in interventional cardiology. However, current approved stents suffer from in-stent restenosis associated with neointimal hyperplasia or stent thrombosis. Herein, we develop a nitric oxide-eluting (NOE) hydrogel coating for vascular stents inspired by the biological functions of nitric oxide for cardiovascular system. Our NOE hydrogel is mechanically tough and could selectively facilitate the adhesion of endothelial cells. Besides, it is non-thrombotic and capable of inhibiting smooth muscle cells. Transcriptome analysis unravels the NOE hydrogel could modulate the inflammatory response and induce the relaxation of smooth muscle cells. In vivo study further demonstrates vascular stents coated with it promote rapid restoration of native endothelium, and persistently suppress inflammation and neointimal hyperplasia in both leporine and swine models. We expect such NOE hydrogel will open an avenue to the surface engineering of vascular implants for better clinical outcomes.
Janus acoustic metascreen with nonreciprocal and reconfigurable phase modulations
Authors: Zhu Yifan , Cao Liyun , Merkel Aurélien , Fan Shi-Wang , Vincent Brice , Assouar Badreddine 
Published: December 2021

AbstractIntegrating different reliable functionalities in metastructures and metasurfaces has become of remarkable importance to create innovative multifunctional compact acoustic, optic or mechanical metadevices. In particular, implementing different wave manipulations in one unique material platform opens an appealing route for developing integrated metamaterials. Here, the concept of Janus acoustic metascreen is proposed and demonstrated, producing two-faced and independent wavefront manipulations for two opposite incidences. The feature of two-faced sound modulations requires nonreciprocal phase modulating elements. An acoustic resonant unit cell with rotating inner core, which produces a bias by a circulating fluid, is designed to achieve high nonreciprocity, leading to decoupled phase modulations for both forward and backward directions. In addition, the designed unit cell consisting of tunable phase modulators is reconfigurable. A series of Janus acoustic metascreens including optional combinations of extraordinary refraction, acoustic focusing, sound absorption, acoustic diffusion, and beam splitting are demonstrated through numerical simulations and experiments, showing their great potential for acoustic wavefront manipulation.
High efficiency laser resonance ionization of plutonium
Authors: Galindo-Uribarri Alfredo , Liu Yuan , Romero Romero Elisa , Stracener Daniel W. 
Published: December 2021

AbstractThree-step resonance photoionization spectra of plutonium have been studied with Ti:Sapphire lasers for the development of efficient laser ionization schemes for ultra-trace analysis of Pu isotopes by resonance ionization mass spectrometry. We observed eighteen intermediate excited states of even parity in the energy range 35568–36701 $${\text {cm}}^{-1}$$

cm

-
1

, thirteen of them have not been previously documented, and a larger number of high-lying excited states and autoionizing states of odd-parity between 48238 and 49510 $${\text {cm}}^{-1}$$

cm

-
1

. Three-color, three-photon ionization schemes via six intermediate states were evaluated under similar ion source operating conditions. This led to a highly efficient three-step scheme with an overall ionization efficiency of $$51.1 \pm 1.3\%$$

51.1
±
1.3
%

, which is an order of magnitude improvement over the previously reported ionization efficiency for Pu.
Systems biology and machine learning approaches identify drug targets in diabetic nephropathy
Authors: Abedi Maryam , Marateb Hamid Reza , Mohebian Mohammad Reza , Aghaee-Bakhtiari Seyed Hamid , Nassiri Seyed Mahdi , Gheisari Yousof 
Published: December 2021

AbstractDiabetic nephropathy (DN), the leading cause of end-stage renal disease, has become a massive global health burden. Despite considerable efforts, the underlying mechanisms have not yet been comprehensively understood. In this study, a systematic approach was utilized to identify the microRNA signature in DN and to introduce novel drug targets (DTs) in DN. Using microarray profiling followed by qPCR confirmation, 13 and 6 differentially expressed (DE) microRNAs were identified in the kidney cortex and medulla, respectively. The microRNA-target interaction networks for each anatomical compartment were constructed and central nodes were identified. Moreover, enrichment analysis was performed to identify key signaling pathways. To develop a strategy for DT prediction, the human proteome was annotated with 65 biochemical characteristics and 23 network topology parameters. Furthermore, all proteins targeted by at least one FDA-approved drug were identified. Next, mGMDH-AFS, a high-performance machine learning algorithm capable of tolerating massive imbalanced size of the classes, was developed to classify DT and non-DT proteins. The sensitivity, specificity, accuracy, and precision of the proposed method were 90%, 86%, 88%, and 89%, respectively. Moreover, it significantly outperformed the state-of-the-art (P-value ≤ 0.05) and showed very good diagnostic accuracy and high agreement between predicted and observed class labels. The cortex and medulla networks were then analyzed with this validated machine to identify potential DTs. Among the high-rank DT candidates are Egfr, Prkce, clic5, Kit, and Agtr1a which is a current well-known target in DN. In conclusion, a combination of experimental and computational approaches was exploited to provide a holistic insight into the disorder for introducing novel therapeutic targets.
A rapid point of care CC16 kit for screening of occupational silica dust exposed workers for early detection of silicosis/silico-tuberculosis
Authors: Nandi Shyam Sundar , Lambe Upendra P. , Sarkar Kamalesh , Sawant Sonali , Deshpande Jagadish 
Published: December 2021

AbstractSilicosis is an irreversible, incurable and progressive occupational disease caused by prolonged exposure to crystalline-silica dust while working in the relevant industries. Conventionally diagnosis is done by chest radiology, often in an advanced stage as early symptoms often go unnoticed. Early detection and necessary intervention (secondary prevention) could be a realistic possible control strategy for controlling silicosis as no effective treatment is available to stop and/or reverse the pathological process. Additionally, these patients are also vulnerable to pulmonary tuberculosis, which often becomes difficult to treat and with uncertain treatment outcome. Considering India has a huge burden of silicosis and silico-tuberculosis, a rapid and inexpensive screening method was realized to be an urgent need for early detection of silicosis among silica dust exposed workers. Serum club cell protein 16 (CC16) is evidenced to be a useful proxy screening marker for early detection of silicosis as evidenced from the recent research work of ICMR-National Institute of Occupational Health (ICMR-NIOH), India. In this study a lateral-flow assay for semi-quantitative estimation of serum CC16 level was developed. The detection was performed using gold nanoparticles conjugated anti-CC16 monoclonal antibodies. A sum of 106 serum samples was tested to do the performance evaluation of the assay. A concentration of 6 ng/ml or less produced one band, 6.1–9 ng/ml produced two bands, while more than 9 ng/ml produced all the three bands at the test zone. The sensitivity of the assay was 100% while the specificity was 95%. This assay may be used as a sensitive tool for periodic screening of silica dust exposed vulnerable workers for early detection of silicosis in them.
A host-directed macrocyclic peptide therapeutic for MDR gram negative bacterial infections
Authors: Schaal Justin B. , Eriguchi Yoshihiro , Tran Dat Q. , Tran Patti A. , Hawes Chase , Cabebe Anthony E. , Pike Kaitlyn , Trinh Katie , Ouellette André J. , Selsted Michael E. 
Published: December 2021

AbstractThe emergence of infections by carbapenem resistant Enterobacteriaceae (CRE) pathogens has created an urgent public health threat, as carbapenems are among the drugs of last resort for infections caused by a growing fraction of multi-drug resistant (MDR) bacteria. There is global consensus that new preventive and therapeutic strategies are urgently needed to combat the growing problem of MDR bacterial infections. Here, we report on the efficacy of a novel macrocyclic peptide, minimized theta-defensin (MTD)-12813 in CRE sepsis. MTD12813 is a theta-defensin inspired cyclic peptide that is highly effective against CRE pathogens K. pneumoniae and E. coli in vivo. In mouse septicemia models, single dose administration of MTD12813 significantly enhanced survival by promoting rapid host-mediated bacterial clearance and by modulating pathologic cytokine responses, restoring immune homeostasis, and preventing lethal septic shock. The peptide lacks direct antibacterial activity in the presence of mouse serum or in peritoneal fluid, further evidence for its indirect antibacterial mode of action. MTD12813 is highly stable in biological matrices, resistant to bacterial proteases, and nontoxic to mice at dose levels 100 times the therapeutic dose level, properties which support further development of the peptide as a first in class anti-infective therapeutic.
In vitro additive effects of dalbavancin and rifampicin against biofilm of Staphylococcus aureus
Authors: Jacob Benjamin , Makarewicz Oliwia , Hartung Anita , Brodt Steffen , Roehner Eric , Matziolis Georg 
Published: December 2021

AbstractDalbavancin is a novel glycopeptide antibiotic approved for the treatment of acute bacterial skin and skin structure infections (ABSSSIs). It is characterized by a potent activity against numerous Gram-positive pathogens, a long elimination half-life and a favorable safety profile. Most recently, its application for the treatment of periprosthetic joint infections (PJIs) was introduced. The aim of this study was to proof our hypothesis, that dalbavancin shows superior efficacy against staphylococcal biofilms on polyethylene (PE) disk devices compared with vancomycin and additive behavior in combination with rifampicin. Staphylococcus aureus biofilms were formed on PE disk devices for 96 h and subsequently treated with dalbavancin, vancomycin, rifampicin and dalbavancin-rifampicin combination at different concentrations. Quantification of antibacterial activity was determined by counting colony forming units (CFU/ml) after sonification of the PE, serial dilution of the bacterial suspension and plating on agar-plates. Biofilms were additionally life/dead-stained and visualized using fluorescence microscopy. Dalbavancin presented superior anti-biofilm activity compared to vancomycin. Additive effects of the combination dalbavancin and rifampicin were registered. Dalbavancin combined with rifampicin presents promising anti-biofilm activity characteristics in vitro. Further in vivo studies are necessary to establish recommendations for the general use of dalbavancin in the treatment of PJIs.
Comparable genetic alteration profiles between gastric cancers with current and past Helicobacter pylori infection
Authors: Tsuyuki Sho , Takeshima Hideyuki , Sekine Shigeki , Yamagata Yukinori , Ando Takayuki , Yamashita Satoshi , Maeda Shin , Yoshikawa Takaki , Ushijima Toshikazu 
Published: December 2021

AbstractGastric cancers can develop even after Helicobacter pylori (H. pylori) eradication in 0.2–2.9% cases per year. Since H. pylori is reported to directly activate or inactivate cancer-related pathways, molecular profiles of gastric cancers with current and past H. pylori infection may be different. Here, we aimed to analyze whether profiles of point mutation and gene amplification are different between the two groups. Current or past infection by H. pylori was determined by positive or negative amplification of H. pylori jhpr3 gene by PCR, and past infection was established by the presence of endoscopic atrophy. Among the 90 gastric cancers analyzed, 55 were with current infection, and 35 were with past infection. Target sequencing of 46 cancer-related genes revealed that 47 gastric cancers had 68 point mutations of 15 different genes, such as TP53 (36%), KRAS (4%), and PIK3CA (4%) and that gene amplification was present for ERBB2, KRAS, PIK3CA, and MET among the 26 genes assessed for copy number alterations. Gastric cancers with current and past infection had similar frequencies of TP53 mutations (38% and 31%, respectively; p = 0.652) and oncogene activation (20% and 29%, respectively; p = 0.444). Gastric cancers with current and past infection had comparable profiles of genetic alterations.
Design and implementation of an illumination system to mimic skyglow at ecosystem level in a large-scale lake enclosure facility
Authors: Jechow Andreas , Schreck Günther , Kyba Christopher C. M. , Berger Stella A. , Bistarelli Lukas Thuile , Bodenlos Matthias , Gessner Mark O. , Grossart Hans-Peter , Kupprat Franziska , Nejstgaard Jens C. , Pansch Andreas , Penske Armin , Sachtleben Michael , Shatwell Tom , Singer Gabriel A. , Stephan Susanne , Walles Tim J. W. , Wollrab Sabine , Zielinska-Dabkowska Karolina M. , Hölker Franz 
Published: December 2021

AbstractLight pollution is an environmental stressor of global extent that is growing exponentially in area and intensity. Artificial skyglow, a form of light pollution with large range, is hypothesized to have environmental impact at ecosystem level. However, testing the impact of skyglow at large scales and in a controlled fashion under in situ conditions has remained elusive so far. Here we present the first experimental setup to mimic skyglow at ecosystem level outdoors in an aquatic environment. Spatially diffuse and homogeneous surface illumination that is adjustable between 0.01 and 10 lx, resembling rural to urban skyglow levels, was achieved with white light-emitting diodes at a large-scale lake enclosure facility. The illumination system was enabled by optical modeling with Monte-Carlo raytracing and validated by measurements. Our method can be adapted to other outdoor and indoor skyglow experiments, urgently needed to understand the impact of skyglow on ecosystems.