bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of BCR::ABL1 transcript type on RT-qPCR amplification performance and molecular response to therapy
Authors: Salmon Matthew , White Helen E. , Zizkova Hana , Gottschalk Andrea , Motlova Eliska , Cerveira Nuno , Colomer Dolors , Coriu Daniel , Franke Georg N. , Gottardi Enrico , Izzo Barbara , Jurcek Tomas , Lion Thomas , Schäfer Vivien , Venturi Claudia , Vigneri Paolo , Zawada Magdalena , Zuna Jan , Hovorkova Lenka , Koblihova Jitka , Klamova Hana , Markova Marketa Stastna , Srbova Dana , Benesova Adela , Polivkova Vaclava , Zackova Daniela , Mayer Jiri , Roeder Ingo , Glauche Ingmar , Ernst Thomas , Hochhaus Andreas , Polakova Katerina Machova , Cross Nicholas C. P. 
Published: June 2022

AbstractSeveral studies have reported that chronic myeloid leukaemia (CML) patients expressing e14a2BCR::ABL1have a faster molecular response to therapy compared to patients expressing e13a2. To explore the reason for this difference we undertook a detailed technical comparison of the commonly used Europe Against Cancer (EAC)BCR::ABL1reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) assay in European Treatment and Outcome Study (EUTOS) reference laboratories (n = 10). We found the amplification ratio of the e13a2 amplicon was 38% greater than e14a2 (p = 0.015), and the amplification efficiency was 2% greater (P = 0.17). This subtle difference led to measurable transcript-type dependent variation in estimates of residual disease which could be corrected by (i) taking the qPCR amplification efficiency into account, (ii) using alternative RT-qPCR approaches or (iii) droplet digital PCR (ddPCR), a technique which is relatively insensitive to differences in amplification kinetics. In CML patients, higher levels ofBCR::ABL1/GUSBwere identified at diagnosis for patients expressing e13a2 (n = 67) compared to e14a2 (n = 78) when analysed by RT-qPCR (P = 0.0005) but not ddPCR (P = 0.5). These data indicate that widely used RT-qPCR assays result in subtly different estimates of disease depending onBCR::ABL1transcript type; these differences are small but may need to be considered for optimal patient management.
Histone H3K27 demethylase UTX compromises articular chondrocyte anabolism and aggravates osteoarthritic degeneration
Authors: Lian Wei-Shiung , Wu Re-Wen , Ko Jih-Yang , Chen Yu-Shan , Wang Shao-Yu , Yu Chun-Ping , Jahr Holger , Wang Feng-Sheng 
Published: June 2022

AbstractEpigenome alteration in chondrocytes correlates with osteoarthritis (OA) development. H3K27me3 demethylase UTX regulates tissue homeostasis and deterioration, while its role was not yet studied in articulating joint tissue in situ. We now uncovered that increased UTX and H3K27me3 expression in articular chondrocytes positively correlated with human knee OA. Forced UTX expression upregulated the H3K27me3 enrichment at transcription factor Sox9 promoter, inhibiting key extracellular matrix molecules collagen II, aggrecan, and glycosaminoglycan in articular chondrocytes. Utx overexpression in knee joints aggravated the signs of OA, including articular cartilage damage, synovitis, osteophyte formation, and subchondral bone loss in mice. Chondrocyte-specific Utx knockout mice developed thicker articular cartilage than wild-type mice and showed few gonarthrotic symptoms during destabilized medial meniscus- and collagenase-induced joint injury. In vitro, Utx loss changed H3K27me3-binding epigenomic landscapes, which contributed to mitochondrial activity, cellular senescence, and cartilage development. Insulin-like growth factor 2 (Igf2) and polycomb repressive complex 2 (PRC2) core components Eed and Suz12 were, among others, functional target genes of Utx. Specifically, Utx deletion promoted Tfam transcription, mitochondrial respiration, ATP production and Igf2 transcription but inhibited Eed and Suz12 expression. Igf2 blockade or forced Eed or Suz12 expression increased H3K27 trimethylation and H3K27me3 enrichment at Sox9 promoter, compromising Utx loss-induced extracellular matrix overproduction. Taken together, UTX repressed articular chondrocytic activity, accelerating cartilage loss during OA. Utx loss promoted cartilage integrity through epigenetic stimulation of mitochondrial biogenesis and Igf2 transcription. This study highlighted a novel noncanonical role of Utx, in concert with PRC2 core components, in controlling H3K27 trimethylation and articular chondrocyte anabolism and OA development.
Cost increase in the electricity supply to achieve carbon neutrality in China
Authors: Zhuo Zhenyu , Du Ershun , Zhang Ning , Nielsen Chris P. , Lu Xi , Xiao Jinyu , Wu Jiawei , Kang Chongqing 
Published: June 2022

AbstractThe Chinese government has set long-term carbon neutrality and renewable energy (RE) development goals for the power sector. Despite a precipitous decline in the costs of RE technologies, the external costs of renewable intermittency and the massive investments in new RE capacities would increase electricity costs. Here, we develop a power system expansion model to comprehensively evaluate changes in the electricity supply costs over a 30-year transition to carbon neutrality. RE supply curves, operating security constraints, and the characteristics of various generation units are modelled in detail to assess the cost variations accurately. According to our results, approximately 5.8 TW of wind and solar photovoltaic capacity would be required to achieve carbon neutrality in the power system by 2050. The electricity supply costs would increase by 9.6 CNY¢/kWh. The major cost shift would result from the substantial investments in RE capacities, flexible generation resources, and network expansion.
Altered predictive control during memory suppression in PTSD
Authors: Leone Giovanni , Postel Charlotte , Mary Alison , Fraisse Florence , Vallée Thomas , Viader Fausto , de La Sayette Vincent , Peschanski Denis , Dayan Jaques , Eustache Francis , Gagnepain Pierre 
Published: June 2022

AbstractAberrant predictions of future threat lead to maladaptive avoidance in individuals with post-traumatic stress disorder (PTSD). How this disruption in prediction influences the control of memory states orchestrated by the dorsolateral prefrontal cortex is unknown. We combined computational modeling and brain connectivity analyses to reveal how individuals exposed and nonexposed to the 2015 Paris terrorist attacks formed and controlled beliefs about future intrusive re-experiencing implemented in the laboratory during a memory suppression task. Exposed individuals with PTSD used beliefs excessively to control hippocampal activity during the task. When this predictive control failed, the prediction-error associated with unwanted intrusions was poorly downregulated by reactive mechanisms. This imbalance was linked to higher severity of avoidance symptoms, but not to general disturbances such as anxiety or negative affect. Conversely, trauma-exposed participants without PTSD and nonexposed individuals were able to optimally balance predictive and reactive control during the memory suppression task. These findings highlight a potential pathological mechanism occurring in individuals with PTSD rooted in the relationship between the brain’s predictive and control mechanisms.
Taf2 mediates DNA binding of Taf14
Authors: Klein Brianna J. , Feigerle Jordan T. , Zhang Jibo , Ebmeier Christopher C. , Fan Lixin , Singh Rohit K. , Wang Wesley W. , Schmitt Lauren R. , Lee Thomas , Hansen Kirk C. , Liu Wenshe R. , Wang Yun-Xing , Strahl Brian D. , Anthony Weil P. , Kutateladze Tatiana G. 
Published: June 2022

AbstractThe assembly and function of the yeast general transcription factor TFIID complex requires specific contacts between its Taf14 and Taf2 subunits, however, the mechanism underlying these contacts remains unclear. Here, we determined the molecular and structural basis by which the YEATS and ET domains of Taf14 bind to the C-terminal tail of Taf2 and identified a unique DNA-binding activity of the linker region connecting the two domains. We show that in the absence of ligands the linker region of Taf14 is occluded by the surrounding domains, and therefore the DNA binding function of Taf14 is autoinhibited. Binding of Taf2 promotes a conformational rearrangement in Taf14, resulting in a release of the linker for the engagement with DNA and the nucleosome. Genetic in vivo data indicate that the association of Taf14 with both Taf2 and DNA is essential for transcriptional regulation. Our findings provide a basis for deciphering the role of individual TFIID subunits in mediating gene transcription.
Optomechanical crystal with bound states in the continuum
Authors: Liu Shengyan , Tong Hao , Fang Kejie 
Published: June 2022

AbstractChipscale micro- and nano-optomechanical systems, hinging on the intangible radiation-pressure force, have shown their unique strength in sensing, signal transduction, and exploration of quantum physics with mechanical resonators. Optomechanical crystals, as one of the leading device platforms, enable simultaneous molding of the band structure of optical photons and microwave phonons with strong optomechanical coupling. Here, we demonstrate a new breed of optomechanical crystals in two-dimensional slab-on-substrate structures empowered by mechanical bound states in the continuum (BICs) at 8 GHz. We show symmetry-induced BIC emergence with optomechanical couplings up to g/2π ≈ 2.5 MHz per unit cell, on par with low-dimensional optomechanical crystals. Our work paves the way towards exploration of photon-phonon interaction beyond suspended microcavities, which might lead to new applications of optomechanics from phonon sensing to quantum transduction.
The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis
Authors: Wilson L. F. L. , Dendooven T. , Hardwick S. W. , Echevarría-Poza A. , Tryfona T. , Krogh K. B. R. M. , Chirgadze D. Y. , Luisi B. F. , Logan D. T. , Mani K. , Dupree P. 
Published: June 2022

AbstractHeparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of alternating β-d-glucuronosyl and N-acetyl-α-d-glucosaminyl residues by exostosins. These enzymes generally possess two glycosyltransferase domains (GT47 and GT64)—each thought to add one type of monosaccharide unit to the backbone. Although previous structures of murine exostosin-like 2 (EXTL2) provide insight into the GT64 domain, the rest of the bi-domain architecture is yet to be characterised; hence, how the two domains co-operate is unknown. Here, we report the structure of human exostosin-like 3 (EXTL3) in apo and UDP-bound forms. We explain the ineffectiveness of EXTL3’s GT47 domain to transfer β-d-glucuronosyl units, and we observe that, in general, the bi-domain architecture would preclude a processive mechanism of backbone extension. We therefore propose that heparan sulfate backbone polymerisation occurs by a simple dissociative mechanism.
Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates
Authors: Gharechahi Javad , Sarikhan Sajjad , Han Jian-Lin , Ding Xue-Zhi , Salekdeh Ghasem Hosseini 
Published: June 2022

AbstractRumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.
Continuous Bose–Einstein condensation
Authors: Chen Chun-Chia , González Escudero Rodrigo , Minář Jiří , Pasquiou Benjamin , Bennetts Shayne , Schreck Florian 
Published: June 2022

AbstractBose–Einstein condensates (BECs) are macroscopic coherent matter waves that have revolutionized quantum science and atomic physics. They are important to quantum simulation1 and sensing2,3, for example, underlying atom interferometers in space4 and ambitious tests of Einstein’s equivalence principle5,6. A long-standing constraint for quantum gas devices has been the need to execute cooling stages time-sequentially, restricting these devices to pulsed operation. Here we demonstrate continuous Bose–Einstein condensation by creating a continuous-wave (CW) condensate of strontium atoms that lasts indefinitely. The coherent matter wave is sustained by amplification through Bose-stimulated gain of atoms from a thermal bath. By steadily replenishing this bath while achieving 1,000 times higher phase-space densities than previous works7,8, we maintain the conditions for condensation. Our experiment is the matter wave analogue of a CW optical laser with fully reflective cavity mirrors. This proof-of-principle demonstration provides a new, hitherto missing piece of atom optics, enabling the construction of continuous coherent-matter-wave devices.
Nanoscale imaging of phonon dynamics by electron microscopy
Authors: Gadre Chaitanya A. , Yan Xingxu , Song Qichen , Li Jie , Gu Lei , Huyan Huaixun , Aoki Toshihiro , Lee Sheng-Wei , Chen Gang , Wu Ruqian , Pan Xiaoqing 
Published: June 2022

AbstractSpatially resolved vibrational mapping of nanostructures is indispensable to the development and understanding of thermal nanodevices1, modulation of thermal transport2 and novel nanostructured thermoelectric materials3–5. Through the engineering of complex structures, such as alloys, nanostructures and superlattice interfaces, one can significantly alter the propagation of phonons and suppress material thermal conductivity while maintaining electrical conductivity2. There have been no correlative experiments that spatially track the modulation of phonon properties in and around nanostructures due to spatial resolution limitations of conventional optical phonon detection techniques. Here we demonstrate two-dimensional spatial mapping of phonons in a single silicon–germanium (SiGe) quantum dot (QD) using monochromated electron energy loss spectroscopy in the transmission electron microscope. Tracking the variation of the Si optical mode in and around the QD, we observe the nanoscale modification of the composition-induced red shift. We observe non-equilibrium phonons that only exist near the interface and, furthermore, develop a novel technique to differentially map phonon momenta, providing direct evidence that the interplay between diffuse and specular reflection largely depends on the detailed atomistic structure: a major advancement in the field. Our work unveils the non-equilibrium phonon dynamics at nanoscale interfaces and can be used to study actual nanodevices and aid in the understanding of heat dissipation near nanoscale hotspots, which is crucial for future high-performance nanoelectronics.
Core control principles of the eukaryotic cell cycle
Authors: Basu Souradeep , Greenwood Jessica , Jones Andrew W. , Nurse Paul 
Published: June 2022

AbstractCyclin-dependent kinases (CDKs) lie at the heart of eukaryotic cell cycle control, with different cyclin–CDK complexes initiating DNA replication (S-CDKs) and mitosis (M-CDKs)1,2. However, the principles on which cyclin–CDK complexes organize the temporal order of cell cycle events are contentious3. One model proposes that S-CDKs and M-CDKs are functionally specialized, with substantially different substrate specificities to execute different cell cycle events4–6. A second model proposes that S-CDKs and M-CDKs are redundant with each other, with both acting as sources of overall CDK activity7,8. In this model, increasing CDK activity, rather than CDK substrate specificity, orders cell cycle events9,10. Here we reconcile these two views of core cell cycle control. Using phosphoproteomic assays of in vivo CDK activity in fission yeast, we find that S-CDK and M-CDK substrate specificities are remarkably similar, showing that S-CDKs and M-CDKs are not completely specialized for S phase and mitosis alone. Normally, S-CDK cannot drive mitosis but can do so when protein phosphatase 1 is removed from the centrosome. Thus, increasing S-CDK activity in vivo is sufficient to overcome substrate specificity differences between S-CDK and M-CDK, and allows S-CDK to carry out M-CDK function. Therefore, we unite the two opposing views of cell cycle control, showing that the core cell cycle engine is largely based on a quantitative increase in CDK activity through the cell cycle, combined with minor and surmountable qualitative differences in catalytic specialization of S-CDKs and M-CDKs.
Thermal enhancement in Falkner–Skan flow of the nanofluid by considering molecular diameter and freezing temperature
Authors: Adnan  , Murtaza Rashid , Hussain Iftikhar , Rehman Ziaur , Khan Ilyas , Andualem Mulugeta 
Published: June 2022

AbstractThe analysis of nanofluids heat transfer over a wedge is very important due to their wider applications in applied thermal engineering, chemical engineering and biomedical engineering etc. Therefore, aim of the study is to explore the heat transport in nanofluid over a wedge (Falkner Skan flow) under viscous dissipation and thermal radiation over a wedge. The proper model formulation is carried out via similarity relations and empirical correlations of the nanofluids. After successful model transformation, numerical scheme (RK technique along with shooting technique) applied and furnished the results over the desired domain under varying effects of preemenant flow parameters. The results revealed that the velocity rises for opposing ($$\gamma <0$$

γ
<
0

) and assisting ($$\gamma >0$$

γ
>
0

) flows against $$\lambda$$
λ
and significant contribution of Ec and imposed thermal radiations (Rd number) observed in thermal performance of the nanofluid. The temperature declines by strengthen $$\lambda$$
λ
and optimum decrement is noted for opposing flow. Finally, a comparison is provided for various values of $$\lambda$$
λ
($$\lambda =\mathrm{0,0.014}, 0.04, 0.09, 0.1429, 0.2, \mathrm{0.333,0.5}$$

λ
=

0
,
0.014

,
0.04
,
0.09
,
0.1429
,
0.2
,

0.333
,
0.5

) with previously published work under certain restrictions and found an excellent agreement.
Experimental investigation of the mechanical properties of mud shale under water-bearing conditions and its applications
Authors: Fang Xinxin , Feng Hong , Li Fengling , Wang Hao 
Published: June 2022

AbstractMud shale, used in drilling engineering, is prone to hydration and expansion, resulting in creep deformation that leads to wellbore shrinkage and pipe sticking incidents. Studying the creep characteristics of mud shale is significant for designing a reasonable well structure and determining the lower limit of drilling fluid density. The influence of moisture content on rock strength and creep mechanical properties were studied using water absorption, uniaxial compression, and creep tests. Test results show that with an increase in the moisture content, the mud shale was damaged and softened; moreover, the elastic modulus decreased with increase in moisture content. Under the same load level, the instantaneous strain increased with increasing moisture content. Under different loading stresses, the creep of the rock had nonlinear characteristics, which could be divided into three different creep stages: attenuation, second, and accelerated creep. A new improved creep model based on the Nishihara model was established to describe the accelerated creep characteristics of mud shale under different moisture contents. The ageing degradation and water-bearing weakening effects were introduced. The Levenberg–Marquardt nonlinear least-squares method was applied to invert the creep parameters. The results show that the simulated creep curves, generated using the new creep model, conform to the experimental ones. The relationship between the drilling fluid density and wellbore shrinkage ratio can be defined using this model; it provides a reference for reasonably determining the drilling fluid density.
The cause of acute lethality of mice exposed to a laser-induced shock wave to the brainstem
Authors: Yamamura Koji , Kiriu Nobuaki , Tomura Satoshi , Kawauchi Satoko , Murakami Kaoru , Sato Shunichi , Saitoh Daizoh , Yokoe Hidetaka 
Published: June 2022

AbstractAir embolism is generally considered the most common cause of death within 1 h of a blast injury. Shock lung, respiratory arrest, and circulatory failure caused by vagal reflexes contribute to fatal injuries that lead to immediate death; however, informative mechanistic data are insufficient. Here we used a laser-induced shock wave (LISW) to determine the mechanism of acute fatalities associated with blast injuries. We applied the LISW to the forehead, upper neck, and thoracic dorsum of mice and examined their vital signs. Moreover, the LISW method is well suited for creating site-specific damage. Here we show that only mice with upper neck exposure, without damage elsewhere, died more frequently compared with the other injured groups. The peripheral oxygen saturation (SpO2) of the former mice significantly decreased for < 1 min [p < 0.05] but improved within 3 min. The LISW exposure to the upper neck region was the most lethal factor, affecting the respiratory function. Protecting the upper neck region may reduce fatalities that are related to blast injuries.
A resource saving FPGA implementation approach to fractional Kalman filter
Authors: Xu Bo , Bai Libing , Chen Kai , Tian Lulu 
Published: June 2022

AbstractThe efficiency of the hardware implementations of fractional Kalman filter (FKF) heavily relies on the efficiency of realising the fractional‐order derivative operator. In this paper, a generic software and hardware implementation of the FKF based on the Grunwald–Letnikov approximation is proposed and verified on a field‐programmable gate array. The main advantage of this particular realisation is its resource saving capability on both software and hardware components (e.g. digital signal processing chips), and this enables fast and efficient real‐time computation of the FKF. Furthermore, the performance of the FKF is evaluated via studying the mean square boundedness of the filtering error. At last, a mass‐spring‐damper example is implemented via Matlab simulations to verify the applicability of the proposed approach and moreover, a hardware experiment is also conducted to demonstrate the advantage of resource saving.