bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term follow-up of patients with acute myeloid leukemia undergoing allogeneic hematopoietic stem cell transplantation after primary induction failure
Authors: Mozaffari Jovein Miriam , Ihorst Gabriele , Duque-Afonso Jesús , Wäsch Ralph , Bertz Hartmut , Wehr Claudia , Duyster Justus , Zeiser Robert , Finke Jürgen , Scherer Florian 
Published: December 2023

AbstractPrimary induction failure (PIF) in acute myeloid leukemia (AML) patients is associated with poor outcome, with allogeneic hematopoietic stem cell transplantation (HCT) being the sole curative therapeutic option. Here, we retrospectively evaluated long-term outcomes of 220 AML patients undergoing allogeneic HCT after PIF who never achieved remission, and identified clinical and molecular risk factors associated with treatment response and ultimate prognosis. In this high-risk population, disease-free survival was 25.2% after 5 years and 18.7% after 10 years, while overall survival rates were 29.8% and 21.6% after 5 and 10 years of HCT, respectively. 10-year non-relapse mortality was 32.5%, and 48.8% of patients showed disease relapse within 10 years after allogeneic HCT. Adverse molecular risk features determined at initial diagnosis, poor performance status at the time of allogeneic HCT, and long diagnosis-to-HCT intervals were associated with unfavorable prognosis. Collectively, our data suggests that immediate allogeneic HCT after PIF offers long-term survival and cure in a substantial subset of cases and that high-risk AML patients who never achieved complete response during induction might benefit from early donor search.
A minority of final stacks yields superior amplitude in single-particle cryo-EM
Authors: Zhu Jianying , Zhang Qi , Zhang Hui , Shi Zuoqiang , Hu Mingxu , Bao Chenglong 
Published: December 2023

AbstractCryogenic electron microscopy (cryo-EM) is widely used to determine near-atomic resolution structures of biological macromolecules. Due to the low signal-to-noise ratio, cryo-EM relies on averaging many images. However, a crucial question in the field of cryo-EM remains unanswered: how close can we get to the minimum number of particles required to reach a specific resolution in practice? The absence of an answer to this question has impeded progress in understanding sample behavior and the performance of sample preparation methods. To address this issue, we develop an iterative particle sorting and/or sieving method called CryoSieve. Extensive experiments demonstrate that CryoSieve outperforms other cryo-EM particle sorting algorithms, revealing that most particles are unnecessary in final stacks. The minority of particles remaining in the final stacks yield superior high-resolution amplitude in reconstructed density maps. For some datasets, the size of the finest subset approaches the theoretical limit.
Geometric constraint-triggered collagen expression mediates bacterial-host adhesion
Authors: Feng Yuting , Wang Shuyi , Liu Xiaoye , Han Yiming , Xu Hongwei , Duan Xiaocen , Xie Wenyue , Tian Zhuoling , Yuan Zuoying , Wan Zhuo , Xu Liang , Qin Siying , He Kangmin , Huang Jianyong 
Published: December 2023

AbstractCells living in geometrically confined microenvironments are ubiquitous in various physiological processes, e.g., wound closure. However, it remains unclear whether and how spatially geometric constraints on host cells regulate bacteria-host interactions. Here, we reveal that interactions between bacteria and spatially constrained cell monolayers exhibit strong spatial heterogeneity, and that bacteria tend to adhere to these cells near the outer edges of confined monolayers. The bacterial adhesion force near the edges of the micropatterned monolayers is up to 75 nN, which is ~3 times higher than that at the centers, depending on the underlying substrate rigidities. Single-cell RNA sequencing experiments indicate that spatially heterogeneous expression of collagen IV with significant edge effects is responsible for the location-dependent bacterial adhesion. Finally, we show that collagen IV inhibitors can potentially be utilized as adjuvants to reduce bacterial adhesion and thus markedly enhance the efficacy of antibiotics, as demonstrated in animal experiments.
Resin acids play key roles in shaping microbial communities during degradation of spruce bark
Authors: Ristinmaa Amanda Sörensen , Tafur Rangel Albert , Idström Alexander , Valenzuela Sebastian , Kerkhoven Eduard J. , Pope Phillip B. , Hasani Merima , Larsbrink Johan 
Published: December 2023

AbstractThe bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.
Inhibition of host PARP1 contributes to the anti-inflammatory and antitubercular activity of pyrazinamide
Authors: Krug Stefanie , Gupta Manish , Kumar Pankaj , Feller Laine , Ihms Elizabeth A. , Kang Bong Gu , Srikrishna Geetha , Dawson Ted M. , Dawson Valina L. , Bishai William R. 
Published: December 2023

AbstractThe antibiotic pyrazinamide (PZA) is a cornerstone of tuberculosis (TB) therapy that shortens treatment durations by several months despite being only weakly bactericidal. Intriguingly, PZA is also an anti-inflammatory molecule shown to specifically reduce inflammatory cytokine signaling and lesion activity in TB patients. However, the target and clinical importance of PZA’s host-directed activity during TB therapy remain unclear. Here, we identify the host enzyme Poly(ADP-ribose) Polymerase 1 (PARP1), a pro-inflammatory master regulator strongly activated in TB, as a functionally relevant host target of PZA. We show that PZA inhibits PARP1 enzymatic activity in macrophages and in mice where it reverses TB-induced PARP1 activity in lungs to uninfected levels. Utilizing a PZA-resistant mutant, we demonstrate that PZA’s immune-modulatory effects are PARP1-dependent but independent of its bactericidal activity. Importantly, PZA’s bactericidal efficacy is impaired in PARP1-deficient mice, suggesting that immune modulation may be an integral component of PZA’s antitubercular activity. In addition, adjunctive PARP1 inhibition dramatically reduces inflammation and lesion size in mice and may be a means to reduce lung damage and shorten TB treatment duration. Together, these findings provide insight into PZA’s mechanism of action and the therapeutic potential of PARP1 inhibition in the treatment of TB.
Strong and ductile high temperature soft magnets through Widmanstätten precipitates
Authors: Han Liuliu , Maccari Fernando , Soldatov Ivan , Peter Nicolas J. , Souza Filho Isnaldi R. , Schäfer Rudolf , Gutfleisch Oliver , Li Zhiming , Raabe Dierk 
Published: December 2023

AbstractFast growth of sustainable energy production requires massive electrification of transport, industry and households, with electrical motors as key components. These need soft magnets with high saturation magnetization, mechanical strength, and thermal stability to operate efficiently and safely. Reconciling these properties in one material is challenging because thermally-stable microstructures for strength increase conflict with magnetic performance. Here, we present a material concept that combines thermal stability, soft magnetic response, and high mechanical strength. The strong and ductile soft ferromagnet is realized as a multicomponent alloy in which precipitates with a large aspect ratio form a Widmanstätten pattern. The material shows excellent magnetic and mechanical properties at high temperatures while the reference alloy with identical composition devoid of precipitates significantly loses its magnetization and strength at identical temperatures. The work provides a new avenue to develop soft magnets for high-temperature applications, enabling efficient use of sustainable electrical energy under harsh operating conditions.
One-dimensionally oriented self-assembly of ordered mesoporous nanofibers featuring tailorable mesophases via kinetic control
Authors: Peng Liang , Peng Huarong , Wang Steven , Li Xingjin , Mo Jiaying , Wang Xiong , Tang Yun , Che Renchao , Wang Zuankai , Li Wei , Zhao Dongyuan 
Published: December 2023

AbstractOne-dimensional (1D) nanomaterials have sparked widespread research interest owing to their fascinating physicochemical properties, however, the direct self-assembly of 1D porous nanomaterials and control over their porosity still presents a grand challenge. Herein, we report a monomicelle oriented self-assembly approach to fabricate 1D mesoporous nanostructures with uniform diameter, high aspect ratio and ordered mesostructure. This strategy features the introduction of hexamethylenetetramine as a curing agent, which can subtly control the monomicelle self-assembly kinetics, thus enabling formation of high-quality 1D ordered mesostructures. Meanwhile, the micellar structure can be precisely manipulated by changing the reactant stoichiometric ratio, resulting in tailorable mesophases from 3D cubic (Im-3m) to 2D hexagonal (p6mm) symmetries. More interestingly, the resultant mesoporous nanofibers can be assembled into 3D hierarchical cryogels on a large scale. The 1D nanoscale of the mesoporous nanofibers, in combination with small diameter (~65 nm), high aspect ratio (~154), large surface area (~452 m2 g−1), and 3D open mesopores (~6 nm), endows them with excellent performances for sodium ion storage and water purification. Our methodology opens up an exciting way to develop next-generation ordered mesoporous materials for various applications.
Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines
Authors: Zhu Qionghua , Zhao Xin , Zhang Yuanhang , Li Yanping , Liu Shang , Han Jingxuan , Sun Zhiyuan , Wang Chunqing , Deng Daqi , Wang Shanshan , Tang Yisen , Huang Yaling , Jiang Siyuan , Tian Chi , Chen Xi , Yuan Yue , Li Zeyu , Yang Tao , Lai Tingting , Liu Yiqun , Yang Wenzhen , Zou Xuanxuan , Zhang Mingyuan , Cui Huanhuan , Liu Chuanyu , Jin Xin , Hu Yuhui , Chen Ao , Xu Xun , Li Guipeng , Hou Yong , Liu Longqi , Liu Shiping , Fang Liang , Chen Wei , Wu Liang 
Published: December 2023

AbstractHuman cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
Astrocytic insulin receptor controls circadian behavior via dopamine signaling in a sexually dimorphic manner
Authors: González-Vila Antía , Luengo-Mateos María , Silveira-Loureiro María , Garrido-Gil Pablo , Ohinska Nataliia , González-Domínguez Marco , Labandeira-García Jose Luis , García-Cáceres Cristina , López Miguel , Barca-Mayo Olga 
Published: December 2023

AbstractMammalian circadian clocks respond to feeding and light cues, adjusting internal rhythms with day/night cycles. Astrocytes serve as circadian timekeepers, driving daily physiological rhythms; however, it’s unknown how they ensure precise cycle-to-cycle rhythmicity. This is critical for understanding why mistimed or erratic feeding, as in shift work, disrupts circadian physiology- a condition linked to type 2 diabetes and obesity. Here, we show that astrocytic insulin signaling sets the free-running period of locomotor activity in female mice and food entrainment in male mice. Additionally, ablating the insulin receptor in hypothalamic astrocytes alters cyclic energy homeostasis differently in male and female mice. Remarkably, the mutants exhibit altered dopamine metabolism, and the pharmacological modulation of dopaminergic signaling partially restores distinct circadian traits in both male and female mutant mice. Our findings highlight the role of astrocytic insulin-dopaminergic signaling in conveying time-of-feeding or lighting cues to the astrocyte clock, thus governing circadian behavior in a sex-specific manner.
Limitations to sustainable renewable jet fuels production attributed to cost than energy-water-food resource availability
Authors: Chong Cheng Tung , Ng Jo-Han 
Published: December 2023

AbstractRenewable jet fuel (RJF) is often touted as the only viable sustainable energy source for the aviation sector, given the difficulties faced by other low-carbon energy sources in overcoming technological barriers. Despite that, the sustainability of RJF is still in dispute due to the conflicting requirements in natural resource for producing the fuels. We introduce a holistic 25-indicator sustainability index encompassing the four domains of energy-water-food nexus and governance, that measures the potential impact of RJF production on 154 countries (and territories) through the oil-to-jet, alcohol-to-jet and gas-to-jet conversion methods. Countries and territories are ranked according to the composite index scores of the four domains. The sustainability index model provides insights on how RJF affords the aviation sector a clean slate in determining the manner of development in a sustainably and equitable way, while also marching towards the long-term goal of carbon neutrality, in alignment with the Sustainable Development Goals.
In-plane charged antiphase boundary and 180° domain wall in a ferroelectric film
Authors: Cai Xiangbin , Chen Chao , Xie Lin , Wang Changan , Gui Zixin , Gao Yuan , Kentsch Ulrich , Zhou Guofu , Gao Xingsen , Chen Yu , Zhou Shengqiang , Gao Weibo , Liu Jun-Ming , Zhu Ye , Chen Deyang 
Published: December 2023

AbstractThe deterministic creation and modification of domain walls in ferroelectric films have attracted broad interest due to their unprecedented potential as the active element in non-volatile memory, logic computation and energy-harvesting technologies. However, the correlation between charged and antiphase states, and their hybridization into a single domain wall still remain elusive. Here we demonstrate the facile fabrication of antiphase boundaries in BiFeO3 thin films using a He-ion implantation process. Cross-sectional electron microscopy, spectroscopy and piezoresponse force measurement reveal the creation of a continuous in-plane charged antiphase boundaries around the implanted depth and a variety of atomic bonding configurations at the antiphase interface, showing the atomically sharp 180° polarization reversal across the boundary. Therefore, this work not only inspires a domain-wall fabrication strategy using He-ion implantation, which is compatible with the wafer-scale patterning, but also provides atomic-scale structural insights for its future utilization in domain-wall nanoelectronics.
Language experience matters for the emergence of early numerical concepts
Authors: Santos Stacee , Brownell Hiram , Coppola Marie , Shusterman Anna , Cordes Sara 
Published: December 2023

AbstractResearch has shown a link between the acquisition of numerical concepts and language, but exactly how linguistic input matters for numerical development remains unclear. Here, we examine both symbolic (number word knowledge) and non-symbolic (numerical discrimination) numerical abilities in a population in which access to language is limited early in development—oral deaf and hard of hearing (DHH) preschoolers born to hearing parents who do not know a sign language. The oral DHH children demonstrated lower numerical discrimination skills, verbal number knowledge, conceptual understanding of the word “more”, and vocabulary relative to their hearing peers. Importantly, however, analyses revealed that group differences in the numerical tasks, but not vocabulary, disappeared when differences in the amount of time children had had auditory access to spoken language input via hearing technology were taken into account. Results offer insights regarding the role language plays in emerging number concepts.
Labelled dataset for Ultra-Low Temperature Freezer to aid dynamic modelling & fault detection and diagnostics
Authors: Huang Tao , Nøstvik Silas , Bacher Peder , Jensen Jonas Kjær , Markussen Wiebke Brix , Møller Jan Kloppenborg 
Published: December 2023

AbstractUltra-low temperature (ULT) freezers are used to store perishable biological contents and are among the most energy-intensive equipment in laboratory buildings, biobanks, and similar settings. To ensure reliable and efficient operation, it is essential to implement data-driven fault detection and diagnostic algorithms, along with energy optimization techniques. This study presents labelled and long-term ULT-freezer performance dataset, the first of its kind, derived from 53 ULT freezers featuring two different control strategies. The dataset comprises high-resolution historical operation data spanning up to 10 years. More than 10 attributes are recorded from the freezing chamber and critical locations in the refrigeration systems. The dataset is labelled with regular events, such as door openings, as well as fault events obtained from 46 service reports. A scalable data pipeline, consisting of extraction, transformation, and loading processes, is developed to convert the raw data into a format ready for analysis. The dataset can be utilized to support the development of data-driven models and algorithms that advance the intelligent digital operation of ULT freezers.
The species composition, richness and diversity studies of fruit flies captured from the orchard of Nagpur mandarin
Authors: Nage Sonal , Kulkarni U. S. , Undirwade D. B. , Meshram N. M. , Sant Swati 
Published: December 2023

AbstractThe present experiment was conducted to study the diversity of fruit flies in Nagpur mandarin orchard from different agro-ecological zones ofVidarbharegion of Maharashtra, India. The fruit flies samples were collected from 18 places falling under 9 agro-ecological zone using methyl eugenol traps. Out of the total collected catches of fruit flies from each zones,Bactrocera dorsaliswas found to be the most prominent species followed byBactrocera zonata. TheZ. cucurbitaeandB. correctawhich occupied third and fourth rank in species composition, respectively. The species viz.,Zeugodacus duplicatusandZeugodacus gavisusrecorded very less abundance at all locations. Shannons index of diversity was maximum in Morshi followed by Katol. Simpson index was more at Tiwasa and Achalpur locations which indicated minimum diversity in the population of fruit flies. Higher diversity of fruit flies were recorded in Morshi and Katol followed by Amravati.
Low-cost prototyping of nitinol wires/frames using polymeric cores and sacrificial fixtures with application in individualized frames anchoring through the atrial septum
Authors: Dulal Hemanta , Swan Trey , Al’Aref Subhi J. , Alaie Seyedhamidreza 
Published: December 2023

AbstractSelf-expanding frames for minimally invasive implants are typically made from nitinol wires and are heat treated to maintain the desired shapes. In the process of heat treatment, nitinol structures are placed in a high-temperature oven, while they are confined by a fixture. During this process, nitinol exerts a high amount of force. Accordingly, a fixture requires high mechanical strength and temperature resistance; this is why fixtures are typically made from metals. The use of metal fixture also increases the turnaround time and cost. However, accelerating this process is beneficial in many applications, such as rapid development of medical implants that are patient-specific. Inspired by the use of sacrificial layers in microfabrication technology, here we propose a novel method for shape setting nitinol wires using a sacrificial metal fixture. In this process, the nitinol wires are first aligned inside copper hypotubes. Next, the forming process is done using hand-held tools to shape complex geometrical structures, annealing the nitinol reinforced by copper, and then selectively etching copper hypotubes in ammonium persulfate solutions. In this process, other sacrificial cores, which are 3D printed or cast from low-cost polymers, are also used. This combination of polymeric cores and minimal use of metals enables reducing the cost and the turnaround time. As a proof of concept, we showed that this process was capable of fabricating springs with mm or sub-mm diameters. The result showed a change of less than 5% in the intended diameter of the nitinol spring with diameters ranging from ~ 0.7 to 1.9 mm, which confirms copper as a suitable sacrificial fixture to obtain the desired complex geometry for nitinol. A metric, based on the elastic strain stored in copper is suggested to predict the possible variation of the intended dimensions in this process. Finally, to demonstrate the potential of this method, as proof of concept, we fabricated NiTi wire frames designed for anchoring through the atrial septum. These frames demonstrated septal defect occluders that were designed based on a patient’s cardiac image available in the public domain. This low-cost rapid fabrication technique is highly beneficial for a variety of applications in engineering and medicine with specific applications in rapid prototyping of medical implants.