bluuebunny/crossref_metadata_2025_split huggingface dataset:
PhyloBLAST: facilitating phylogenetic analysis of BLAST results
Authors: Brinkman Fiona S. L. , Wan Ivan , Hancock Robert E. W. , Rose Ann M. , Jones Steven J. 
Published: July 2002

Abstract
Summary: PhyloBLAST is an internet-accessed application based on CGI/Perl programming that compares a users protein sequence to a SwissProt/TREMBL database using BLAST2 and then allows phylogenetic analyses to be performed on selected sequences from the BLAST output. Flexible features such as ability to input your own multiple sequence alignment and use PHYLIP program options provide additional web-based phylogenetic analysis functionality beyond the analysis of a BLAST result.
Availability: This program is available from http://www.pathogenomics.bc.ca/phyloBLAST/ and the source code is freely available from the authors.
Contact: info@pathogenomics.bc.ca
* To whom correspondence should be addressed.
The utility of different representations of protein sequence
for predicting functional class
Authors: King Ross D. , Karwath Andreas , Clare Amanda , Dehaspe Luc 
Published: July 2002

Abstract
Motivation: Data Mining Prediction (DMP) is a novel approach to predicting protein functional class from sequence. DMP works even in the absence of a homologous protein of known function. We investigate the utility of different ways of representing protein sequence in DMP (residue frequencies, phylogeny, predicted structure) using the Escherichia coli genome as a model.
Results: Using the different representations DMP learnt prediction rules that were more accurate than default at every level of function using every type of representation. The most effective way to represent sequence was using phylogeny (75% accuracy and 13% coverage of unassigned ORFs at the most general level of function: 69% accuracy and 7% coverage at the most detailed). We tested different methods for combining predictions from the different types of representation. These improved both the accuracy and coverage of predictions, e.g. 40% of all unassigned ORFs could be predicted at an estimated accuracy of 60% and 5% of unassigned ORFs could be predicted at an estimated accuracy of 86%.
Availability: The rules and data are freely available. Warmr is free to academics.
Contact: rdk@aber.ac.uk
Supplementary information: http://www.aber.ac.uk/~dcswww/Research/bio/ProteinFunction
* To whom correspondence should be addressed.
MAC5: Bayesian inference of phylogenetic trees from DNA

sequences incorporating gaps
Authors: McGuire Gráinne , Denham Michael C. , Balding David J. 
Published: July 2002

Abstract
Summary: MAC5 implements MCMC sampling of the posterior distribution of tree topologies from DNA sequences containing gaps by using a five state model of evolution (the four nucleotides and the gap character).
Availability: MAC5 is available from http://www.reading.ac.uk/statistics/genetics/ under the software link.
Contact: gmcguire@hgmp.mrc.ac.uk
Prevention of severe ovarian hyperstimulation syndrome in IVF with or without ICSI and embryo transfer: a modified `coasting' strategy based on ultrasound for identification of high-risk patients
Authors: Al-Shawaf T. , Zosmer A. , Hussain S. , Tozer A. , Panay N. , Wilson C. , Lower A.M. , Grudzinskas J.G. 
Published: July 2002

AbstractOvarian hyperstimulation syndrome (OHSS) can be a severe and potentially life-threatening complication of ovarian stimulation for IVF. Coasting or withholding gonadotrophin stimulation relies on frequent estimation of serum oestradiol to identify patients at risk. A modified coasting protocol was developed in which identification of patients at risk of severe OHSS was based on ultrasound monitoring. Serum oestradiol concentrations were measured only in patients with >20 follicles on ultrasound (high risk). If serum oestradiol concentrations were <3000 pmol/l, the gonadotrophin dose was maintained; if concentrations were ≥3000 pmol/l but <13200 pmol/l and ≥25% of the follicles had a diameter of ≥13 mm, the gonadotrophin dose was halved; and if serum oestradiol concentrations were ≥13 200 pmol/l and ≥25% of the follicles had a diameter of ≥15 mm, patients were coasted. In the latter group, human chorionic gonadotrophin (HCG) 10000 IU was administered when at least three follicles had a diameter of ≥18 mm and serum oestradiol concentrations were <10000 pmol/l. Over a 10 month period, serum oestradiol concentrations were measured in 123 out of 580 cycles (24%) and in 50 cycles, gonadotrophins were withheld. Overall, moderate OHSS occurred in three patients (0.7%) and severe OHSS in one patient (0.2%). The pregnancy rates in the cycles where the gonadotrophin dose was reduced or withheld were 39.6 and 40% per cycle respectively; corresponding implantation rates were 30.7 and 25.6%. It is concluded that the modified coasting strategy is associated with a low risk of moderate and severe OHSS to a minimum without compromising pregnancy rates. Identification of patients at risk by ultrasound reduces the number of serum oestradiol measurements and thus inconvenience to patients as well as costs and workload.
Association of Allostatic Load With Overall Mortality Among Patients With Metastatic Non–Small Cell Lung Cancer
Authors: Obeng-Gyasi Samilia , Li Yaming , Carson William E. , Reisinger Sarah , Presley Carolyn J. , Shields Peter G. , Carbone David P. , Ceppa DuyKhanh P. , Carlos Ruth C. , Andersen Barbara L. 
Published: July 2022

ImportanceAdverse social determinants of health (SDHs) (eg, poverty) are associated with poor oncologic outcomes among patients with lung cancer. However, no studies have evaluated biological correlates of adverse SDHs, operationalized as allostatic load (AL), with mortality due to lung cancer.ObjectiveTo examine the association among AL, SDHs, and mortality among patients with metastatic non–small cell lung cancer (NSCLC).Design, Setting, and ParticipantsThis cross-sectional study of an observational cohort was performed at a National Cancer Institute–designated comprehensive cancer center with data accrued from June 1, 2017, to August 31, 2019. Patients with metastatic (stage IV) NSCLC enrolled at diagnosis into a prospective observational cohort study were included in the present analysis if they had all the biomarkers to calculate an AL score (N = 143). Follow-up was completed on August 31, 2021, and data were analyzed from July 1 to September 30, 2021.ExposuresSocial determinants of health.Main Outcomes and MeasuresOverall mortality and AL.ResultsA total of 143 patients met the study criteria with a median age of 63 (IQR, 55-71) years (89 men [62.2%] and 54 women [37.8%]). In terms of race and ethnicity, 1 patient (0.7%) was Asian, 7 (4.9%) were Black, 117 (81.8%) were White, 17 (11.9%) were of multiple races, and 1 (0.7%) was of other race or ethnicity. The mean (SD) AL was 2.90 (1.37). Elevated AL covaried with lower educational level (r = −0.26; P = .002), male sex (r = 0.19; P = .02), limited mobility (r = 0.19; P = .04), worsening self-care (r = 0.30; P &amp;lt; .001), problems engaging in usual activities (r = 0.21; P = .01), depressive symptoms (r = 0.23; P = .005), and a high number of stressful life events (r = 0.30; P &amp;lt; .001). Multivariable analysis found only increasing difficulty with mobility (r = 0.37 [95% CI, 0.13-0.60]; P = .002) and male sex (r = 0.63 [95% CI, 0.19-1.08]; P = .005) associated with higher AL. On adjusted analysis, elevated AL (hazard ratio, 1.43 [95% CI, 1.16-1.79]; P = .001) and low educational level (hazard ratio, 2.11 [95% CI, 1.03-4.34]; P = .04) were associated with worse overall mortality.Conclusions and RelevanceThe findings of this cross-sectional study suggest that higher AL was associated with adverse SDHs and worse overall mortality among patients with advanced NSCLC. These results provide a framework for replication and further studies of AL as a biological correlate for SDH and future prognostic marker.
Controlled Formation of Conduction Channels in Memristive Devices Observed by X‐ray Multimodal Imaging
Authors: Liu Huajun , Dong Yongqi , Galib Mirza , Cai Zhonghou , Stan Liliana , Zhang Lei , Suwardi Ady , Wu Jing , Cao Jing , Tan Chee Kiang Ivan , Sankaranarayanan Subramanian K. R. S. , Narayanan Badri , Zhou Hua , Fong Dillon D. 
Published: July 2022

AbstractNeuromorphic computing provides a means for achieving faster and more energy efficient computations than conventional digital computers for artificial intelligence (AI). However, its current accuracy is generally less than the dominant software‐based AI. The key to improving accuracy is to reduce the intrinsic randomness of memristive devices, emulating synapses in the brain for neuromorphic computing. Here using a planar device as a model system, the controlled formation of conduction channels is achieved with high oxygen vacancy concentrations through the design of sharp protrusions in the electrode gap, as observed by X‐ray multimodal imaging of both oxygen stoichiometry and crystallinity. Classical molecular dynamics simulations confirm that the controlled formation of conduction channels arises from confinement of the electric field, yielding a reproducible spatial distribution of oxygen vacancies across switching cycles. This work demonstrates an effective route to control the otherwise random electroforming process by electrode design, facilitating the development of more accurate memristive devices for neuromorphic computing.
Scaling Laws for Perovskite Nanolasers With Photonic and Hybrid Plasmonic Modes
Authors: Huang Zhen‐Ting , Chen Jia‐Wei , Li Heng , Zhu Yizhi , Cui Qiannan , Xu Chunxiang , Lu Tien‐Chang 
Published: July 2022

AbstractSurface plasmons exhibit an extraordinary capability to reduce the structural size and improve light−matter interaction. However, for small‐sized plasmonic cavities, the optical diffraction limit makes the near‐field difficult to observe, complicating the analysis of exact lasing characteristics. In this study, a 4f measurement system is used to extract the mode parity from the interference pattern and reconstruct the near‐field of the hybrid plasmonic perovskite nanolasers. In conjunction with other measurements, a series of rigorous methods for determining the exact resonance mode and obtaining the precise lasing characteristics of perovskite nanolasers are described. By applying these methods, the scaling laws for wire‐type hybrid plasmonic perovskite lasers are successfully determined and an appropriate size is selected for achieving outstanding lasing performance with low threshold power consumption and a high group index. These methods can be applied to nanowire plasmon‐based lasers to advance the development of plasmonic devices.
Tunable Luminescence of Sb3+ Doped 0D Cs4PbCl6 Nanocrystals from Three Distinct Emission Centers
Authors: Zhang Anran , Jin Jiance , Xia Zhiguo 
Published: July 2022

AbstractMetal halide nanocrystals (NCs) with multiple emission centers are high‐potential luminescent materials used in versatile optoelectronic applications. However, technical challenges hinder the achievement of tunable emission bands in single‐component NCs. In this study, by elaborately using 0D Cs4PbCl6 to design Cs4PbCl6:Sb3+ NCs, multiple photoluminescence excited at specific energies without energy transfer occurred owing to the isolated and distinct centers in the 0D frame. The three emission centers at 368, 450 and 570 nm can be assigned to the 3P1 → 1S0 transition of Pb2+ ions, D‐state emission of Pb2+ ions, and 3P1 → 1S0 transition of Sb3+ ions, respectively. The emission colors of Cs4PbCl6:Sb3+ NCs can be easily tuned from ultraviolet to yellow by precisely modulating the excitation wavelength, and white‐light emission at 360 nm excitation with a color coordinate of (0.3026, 0.3264) is obtained owing to the simultaneous activation of Sb3+ ions and the D‐state. This study not only demonstrates a feasible scheme for designing multiple‐emitting metal halide NCs but also provides guidance for expansion of their applications in flexible optoelectronic devices.
A Single‐Dose Qβ VLP Vaccine against S100A9 Protein Reduces Atherosclerosis in a Preclinical Model
Authors: Ortega‐Rivera Oscar A. , Shin Matthew D. , Moreno‐Gonzalez Miguel A. , Pokorski Jonathan K. , Steinmetz Nicole F. 
Published: July 2022

AbstractThe standard therapy for cardiovascular disease (CVD) is the administration of statins to reduce plasma cholesterol levels, but this requires lifelong treatment. A CVD vaccine candidate that targets the pro‐inflammatory mediator calprotectin by eliciting antibodies against the S100A9 protein is developed. The vaccine, based on bacteriophage Qβ virus‐like particles (VLPs) displaying S100A9 peptide epitopes, is formulated as a slow‐release PLGA:VLP implant by hot–melt extrusion. The single‐dose implant elicits S100A9‐specific antibody titers comparable to a three‐dose injection schedule with soluble VLPs. In an animal model of CVD (ApoE−/− mice fed on a high‐fat diet), the implant reduces serum levels of calprotectin, IL‐1β, IL‐6, and MCP‐1, resulting in less severe aortic lesions. This novel implant is therefore able to attenuate atherosclerosis over a sustained period and offers a novel and promising strategy to replace the repetitive administration of statins for the treatment of CVD.
Triple Conductive Wiring by Electron Doping, Chelation Coating and Electrochemical Conversion in Fluffy Nb2O5 Anodes for Fast‐Charging Li‐Ion Batteries
Authors: Zheng Yongjian , Qiu Wujie , Wang Lei , Liu Jianjun , Chen Shuangqiang , Li Chilin 
Published: July 2022

AbstractHigh‐rate anode material is the kernel of developing fast‐charging lithium ion batteries (LIBs). T–Nb2O5, well‐known for its “room and pillar” structure and bulk pseudocapacitive effect, is expected to enable the fast lithium (de)intercalation. But this property is still limited by the low electronic conductivity or insufficient wiring manner. Herein, a strategy of triple conductive wiring through electron doping, chelation coating, and electrochemical conversion inside the microsized porous spheres consisting of dendrite‐like T–Nb2O5 primary particles is proposed to achieve the fast‐charging and durable anodes for LIBs. The penetrative implanting of conformal carbon coating (derivative from polydopamine chelate) and NbO domains (induced by excess discharging) reinforces the global supply of electronically conductive wires, apart from those from Co/Mn heteroatom or O vacancy doping. The polydopamine etching on T–Nb2O5 spheres promotes their evolution into fluffy morphology with better electrolyte infiltration. The synergic electron and ion wiring at different scales endow the modified T–Nb2O5 anode with ultralong cycling life (143 mAh g−1 at 1 A g−1 after 8500 cycles) and high‐rate performance (144.1 mAh g−1 at 10.0 A g−1). The permeation of multiple electron wires also enables a high mass loading of T–Nb2O5 (4.5 mg cm−2) with a high areal capacity of 0.668 mAh cm−2 even after 150 cycles.
The Effect of the Charge Transfer Transition of the Tetravalent Terbium on the Photostability of Oxide Thin‐Film Transistors
Authors: Lan Linfeng , Li Xiao , Ding Chunchun , Chen Siting , Su Huimin , Huang Bo , Chen Baozhong , Zhou Hongkun , Peng Junbiao 
Published: July 2022

AbstractThe development of the next‐generation display technologies requires thin‐film transistors (TFTs) with high mobility and good negative‐bias‐illumination stress (NBIS) stability. Here, a tetravalent‐terbium‐doped indium oxide (Tb:In2O3) semiconductor is reported, which can effectively improve the NBIS stability of the TFT while ensuring high mobility. The TFT with Tb:In2O3 channel layer exhibited remarkable performance with a saturation mobility of 45.0 cm2 V–1 s–1 (with average mobility of 38.6 cm2 V–1 s–1), a turn‐on voltage (Von) of −1.1 V, and an on‐off current ratio of 108. In addition, the Tb:In2O3 TFT showed greatly improved NBIS stability with Von shift (ΔVon) of −3.9 V (with average ΔVon of 4.0 V) under 3600 s stress with −20 V gate voltage and white light illumination (compared to ΔVon of −11.7 V for the pure In2O3 TFT). Comprehensive studies reveal that the effective improvement of NBIS stability after Tb4+ doping is mainly attributed to the wide‐band absorption of the incident blue light by the Tb4f 7—O2p6 to Tb4f 8—O2p5 charge transfer (CT) transition that has smaller overall lattice expansion/contraction and shorter relaxation time compared to VO ionization.
Temporal Pattern Coding in Ionic Memristor‐Based Spiking Neurons for Adaptive Tactile Perception
Authors: Xie Zhuolin , Zhu Xiaojian , Wang Wei , Guo Zhecheng , Zhang Yuejun , Liu Huiyuan , Sun Cui , Tang Minghua , Gao Shuang , Li Run‐Wei 
Published: July 2022

AbstractBiological neurons encode signals through firing voltage spike trains having unique temporal patterns, enabling efficient information representation and processing. Realization of these rich neuronal firing characteristics in a single electronic device, without circuitry and software assistance, promise compact and functional neuromorphic hardware for advanced artificial intelligence applications. Here, a Pt/Co3O4‐x/ITO‐based ionic memristor is reported that can faithfully produce voltage spike trains exhibiting diverse temporal patterns of biological neurons, under electric current stimulation. The spiking behaviors stem from the redistribution of ions in the device, governed by the current induced electric field and Joule heating effects. Tonic, phasic, burst, and adaptive firing patterns of neurons are demonstrated. Particularly, the adaptive firing characteristics allow the memristor to reduce the response to invariant current stimulation and to respond to current changes with enhanced sensitivity, implementing neuronal adaptive coding function. Integrating such memristors with pressure sensors yields an artificial tactile sensory system that can adaptively perceive small pressure variations in the presence of strong static pressure backgrounds, enabling accurate identification of touched objects in ever‐changing environments. This work opens up an avenue toward advanced neuromorphic hardware for smart neural prosthetics and bionic robotics applications.
Insights into the Origins of Minority Carrier Traps in Solution‐Processed Organic Semiconductors and Their Effects on Transistor Photostability
Authors: Ruan Xiaobin , Cheng Shuiling , Deng Wei , Tan Yuan , Lu Zhengjun , Shi Jialin , Zhang Xiujuan , Jie Jiansheng 
Published: July 2022

AbstractMinority carrier traps in the bandgap of organic semiconductors (OSCs) are pervasive and of vital importance in determining the performance and stability of the optoelectronic device. Understanding their origins is one critical issue at both the fundamental and applied levels. However, relevant research has rarely been performed due to the lack of an effective strategy for quantitatively assessing the minority carrier traps buried in OSCs. Here, organic field‐effect transistors (OFETs) operated under strong and long‐term light illumination can be used as a model device to assess the amount of minority carrier traps in solution‐processed OSCs, are proposed. Based on the experimental results and theoretical calculations, first identified hydrated impurities (water and oxygen) in the residual organic solvents primarily contribute to formation of minority carrier traps within the OSC bandgap, giving rise to photo‐induced electrical instability of OFETs. To address this problem, a molecular additive strategy is developed to improve the OFET photostability by releasing trapped electrons from the levels of minority carrier traps. This work not only elucidates the significant role of water and oxygen in the residual organic solvents in forming minority carrier traps but also provides guidelines for improving OFET photostability for practical applications.
Cover crop effects on μCT‐measured geometrical pore characteristics
Authors: Rankoth Lalith Mahendra , Udawatta Ranjith P. , Gantzer Clark J. , Anderson Stephen H. 
Published: July 2022

AbstractCover crops (CC) could improve soil physical, chemical, and biological properties; however, the micrometer scale quantification of geometric pore characteristics in CC soil is limited in the literature. The objective of this study was to differentiate geometrical pore characteristics between CC and no CC (NCC) by computed tomography (CT). The study design consisted of winter CC and summer corn (Zea mays L.)–soybean [Glycine max (L.) Merr.] rotation with no‐till management. The sample cores were collected after 7 yr of mixed species CC establishment. Six 0‐to‐65‐mm‐long soil cores (28‐mm diam.) were imaged at 29‐μm resolution, and three‐dimensional volumes were analyzed using Fiji‐ImageJ2 software. Slice thickness was 29 μm, and the minimum achievable voxel size was 90 nm. Images within the top and bottom 7.25 mm were removed, and two depths within a core were analyzed for soil pore parameters. The total pore volume was significantly greater (P < .05) in CC compared with NCC, with 8.4 and 2.5 times greater values in CC at 7.25–27.25 and 37.25–57.25 mm, respectively. The total (individual + branched) and the individual pore count were significantly greater (P < .05) in CC compared with NCC for both depths. The porosity of CC soil at 7.25‐to‐27.25‐mm depth was 10 times greater than that of NCC. The branched pore count was not significantly different between two treatments. Overall, the micrometer scale determination of geometrical pore network characteristics showed added benefits of CC use compared with NCC; thus, the use of CC can be beneficial in improving soil pore networks.
BRD4 degradation blocks expression of MYC and multiple forms of stem cell resistance in Ph+ chronic myeloid leukemia
Authors: Peter Barbara , Eisenwort Gregor , Sadovnik Irina , Bauer Karin , Willmann Michael , Rülicke Thomas , Berger Daniela , Stefanzl Gabriele , Greiner Georg , Hoermann Gregor , Keller Alexandra , Wolf Dominik , Čulen Martin , Winter Georg E. , Hoffmann Thomas , Schiefer Ana‐Iris , Sperr Wolfgang R. , Zuber Johannes , Mayer Jiří , Valent Peter 
Published: July 2022

AbstractIn most patients with chronic myeloid leukemia (CML) clonal cells can be kept under control by BCR::ABL1 tyrosine kinase inhibitors (TKI). However, overt resistance or intolerance against these TKI may occur. We identified the epigenetic reader BRD4 and its downstream‐effector MYC as growth regulators and therapeutic targets in CML cells. BRD4 and MYC were found to be expressed in primary CML cells, CD34+/CD38− leukemic stem cells (LSC), and in the CML cell lines KU812, K562, KCL22, and KCL22T315I. The BRD4‐targeting drug JQ1 was found to suppress proliferation in KU812 cells and primary leukemic cells in the majority of patients with chronic phase CML. In the blast phase of CML, JQ1 was less effective. However, the BRD4 degrader dBET6 was found to block proliferation and/or survival of primary CML cells in all patients tested, including blast phase CML and CML cells exhibiting the T315I variant of BCR::ABL1. Moreover, dBET6 was found to block MYC expression and to synergize with BCR::ABL1 TKI in inhibiting the proliferation in the JQ1‐resistant cell line K562. Furthermore, BRD4 degradation was found to overcome osteoblast‐induced TKI resistance of CML LSC in a co‐culture system and to block interferon‐gamma‐induced upregulation of the checkpoint antigen PD‐L1 in LSC. Finally, dBET6 was found to suppress the in vitro survival of CML LSC and their engraftment in NSG mice. Together, targeting of BRD4 and MYC through BET degradation sensitizes CML cells against BCR::ABL1 TKI and is a potent approach to overcome multiple forms of drug resistance in CML LSC.