bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of computational metabolic-pathway predictions for
Helicobacter pylori
Authors: Paley Suzanne M. , Karp Peter D. 
Published: July 2002

Abstract
Motivation: We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway databases used by those algorithms, to the prediction accuracy.
Results: The comparisons we performed were as follows. (1) We compared two predictions of the pathway complements of Helicobacter pylori that were computed by an early version of our pathway-prediction algorithm: prediction A used the EcoCyc E. coli pathway DB as the reference database (DB) for prediction, and prediction B used the MetaCyc pathway DB (a superset of EcoCyc) as the reference pathway DB. The MetaCyc-based prediction contained 75% more pathway predictions, but we believe a significant number of those predictions were false positives. (2) We compared two predictions of the pathway complement of H. pylori that used MetaCyc as the reference pathway DB, but that used different algorithms: the original PathoLogic algorithm, and an enhanced version of the algorithm designed to eliminate false-positive pathway predictions. The improved algorithm predicted 30\% fewer metabolic pathways than the original algorithm; all of the eliminated pathways are believed to be false-positive predictions. (3)~We compared the 98 pathways predicted by the enhanced algorithm with the results of a manual analysis of the pathways of H. pylori. Results: 40 of the computationally predicted pathways were consistent with the manual analysis, 13 pathways are considered false-positive predictions, and four pathways had partially overlapping topologies. Twenty-six predicted pathways were not mentioned in the manual analysis; we believe these are correct predictions by PathoLogic that were not found by the manual analysis. Five pathways from the manual analysis were not found computationally. Agreement between the computational and manual predictions was good overall, with the computational analysis inferring many pathways that the manual analysis did not identify. Ultimately the manual analysis is also partially speculative, and therefore is not an absolute measure of correctness. The algorithm is designed to err on the side of more false positives to bring more potential pathways to the user's attention. The resulting H. pylori pathway DB is freely available at http://ecocyc.org:1555/HPY/organism-summary?object=HPY.
Availability: The Pathway Tools software is freely available to academic users, and is available to commercial users for a fee. Contact pkarp@ai.sri.com for information on obtaining the software.
Contact: paley@ai.sri.com; pkarp@ai.sri.com
* To whom correspondence should be addressed.
Does natural selection organize ecosystems for the maintenance of high productivity and diversity?
Authors: Giles Leigh Egbert , Vermeij Geerat Jacobus 
Published: July 2002

Three types of evidence suggest that natural ecosystems are organized for high productivity and diversity: (i) changes not previously experienced by a natural ecosystem, such as novel human disturbances, tend to diminish its productivity and/or diversity, just as ‘random’ changes in a machine designed for a function usually impair its execution of that function; (ii) humans strive to recreate properties of natural ecosystems to enhance productivity of artificial ones, as farmers try to recreate properties of natural soils in their fields; and (iii) productivity and diversity have increased during the Earth's history as a whole, and after every major biotic crisis.Natural selection results in ecosystems organized to maintain high productivity of organic matter and diversity of species, just as competition among individuals in Adam Smith's ideal economy favours high production of wealth and diversity of occupations. In nature, poorly exploited energy attracts more efficient users. This circumstance favours the opening of new ways of life and more efficient recycling of resources, and eliminates most productivity–reducing ‘ecological monopolies’. Ecological dominants tend to be replaced by successors with higher metabolism, which respond to more stimuli and engage in more varied interactions. Finally, increasingly efficient predators and herbivores favour faster turnover of resources.
High-Throughput Imaging of Brain Gene Expression
Authors: Brown Vanessa M. , Ossadtchi Alex , Khan Arshad H. , Cherry Simon R. , Leahy Richard M. , Smith Desmond J. 
Published: July 2002

Voxelation is a new method for acquisition of three dimensional (3D) gene expression patterns in the brain. It employs high-throughput analysis of spatially registered voxels (cubes) to produce multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 24 voxel images of coronal hemisections at the level of the hippocampus of both the normal human brain and Alzheimer's disease brain were acquired for 2000 genes. The analysis revealed a common network of coregulated genes, and allowed identification of putative control regions. In addition, singular value decomposition (SVD), a mathematical method used to provide economical explanations of complex data sets, produced images that distinguished between brain structures, including cortex, caudate, and hippocampus. The results suggest that voxelation will be a useful approach for understanding how the genome constructs the brain.[All study results are available as a web supplement athttp://www.pharmacology.ucla.edu/smithlab/genome_research_data and at http://www.genome.org.]
A study on the home modifications required for discharged patients from hospital to home
Authors: Nishino Akiko , Tsukuda Kazunori , Okamoto Kazuhiko , Nishide Kazuhiko 
Published: April 2022

AbstractThe objective of this study is to find out the actual situations of discharged patients' home modifications to mitigate the environmental gap between a recovery rehabilitation hospital and their own homes, as well as to identify their potential needs for home improvement. The results of this study show: (1) Patients have many potential needs for home modification which are hard for a physical therapist (PT) or occupational therapist (OT) to discover at one‐time‐only home inspections 1 month before discharge. (2) The typical suggestion from a PT or OT is to install handrails, whereas architectural experts have limited opportunity to give professional advice; therefore, a collaboration system should be established.
Cost‐Effectiveness of the Early Arthritis Clinic Organizational Model
Authors: Zanetti Anna , Sakellariou Garifallia , Zambon Antonella , Carrara Greta , Argnani Lisa , Mantovani Lorenzo G. , Cortesi Paolo A. , Bugatti Serena , Montecucco Carlomaurizio , Scirè Carlo A. 
Published: April 2022

ObjectiveEarly diagnosis and tight control improve outcomes of rheumatoid arthritis (RA). However, whether establishing an early arthritis clinic (EAC) is sustainable for national health systems is not known. This analysis aimed to compare effectiveness and costs of an EAC compared to patients followed by the current standard of care.MethodsA retrospective study on administrative health databases of patients with a new diagnosis of RA was conducted: 430 patients followed in an EAC were enrolled, and 4 non‐EAC controls were randomly matched for each. During 2 years of follow‐up, the mean health care costs (outpatient, inpatient, pharmaceutical, and global) and 3 effectiveness measures (number and length of hospitalization and quality of care) of the EAC and non‐EAC were estimated. The incremental cost‐effectiveness ratio was calculated as well as the cost‐effectiveness acceptability curve.ResultsThe cohorts included patients with a mean age of 55.4 years, and 1,506 patients (70%) were female. The mean pharmaceutical (2,602 versus 1,945 euros) and outpatient (2,447 versus 1,778 euros) costs were higher in the EAC cohort. Conversely, a higher rate of non‐EAC patients had a low adherence to quality‐of‐care indicators. The expected number of hospitalizations and the length of stay were statistically significantly higher in the non‐EAC versus EAC.ConclusionDespite an expected increase in outpatient costs (visits and diagnostic tests) and pharmaceutical costs, the reduction in terms of number and length of hospitalizations and the higher adherence to international quality‐of‐care guidelines support the effectiveness of the EAC model.
A distributed optimal power management system for microgrids with plug&play capabilities
Authors: Hosseinzadeh Mehdi , Schenato Luca , Garone Emanuele 
Published: April 2022

AbstractIn this article we consider the problem of managing the power flow among different components of a microgrid while ensuring that the demands of all loads are satisfied. In order to address this problem, we propose a distributed scheme where only one sensor (for each subgrid in the microgrid) broadcasts a single scalar variable though a wireless communication network (e.g., WiFi, ZigBee, cellular communication network). More precisely, in the proposed scheme each generation/storage subsystem is able to adjust its operating set‐point only making use of the feedback from the sensors. This architecture provides the system with plug&play capabilities. Interestingly enough, the proposed scheme provides the optimal power flow for the whole microgrid without any information on the demanded load. In this article we apply the proposed approach to hybrid ac/dc microgrids; however, the scheme is general and can be applied to any type of microgrid. The effectiveness of the proposed scheme is evaluated through extensive simulations and compared with a centralized optimal strategy.
Single‐Junction Organic Solar Cells with 19.17% Efficiency Enabled by Introducing One Asymmetric Guest Acceptor
Authors: Sun Rui , Wu Yao , Yang Xinrong , Gao Yuan , Chen Zeng , Li Kai , Qiao Jiawei , Wang Tao , Guo Jing , Liu Chao , Hao Xiaotao , Zhu Haiming , Min Jie 
Published: April 2022

AbstractThe ternary strategy has been widely identified as an effective approach to obtain high‐efficiency organic solar cells (OSCs). However, for most ternary OSCs, the nonradiative voltage loss lies between those of the two binary devices, which limits further efficiency improvements. Herein, an asymmetric guest acceptor BTP‐2F2Cl is designed and incorporated into a PM1:L8‐BO host blend. Compared with the L8‐BO neat film, the L8‐BO:BTP‐2F2Cl blend film shows higher photoluminescence quantum yield and larger exciton diffusion length. Introducing BTP‐2F2Cl into the host blend extends its absorption spectrum, improves the molecular packing of host materials, and suppresses the nonradiative charge recombination of the ternary OSCs. Consequently, the power conversion efficiency is improved up to 19.17% (certified value 18.7%), which represents the highest efficiency value reported for single‐junction OSCs so far. The results show that improving the exciton behaviors is a promising approach to reducing the nonradiative voltage loss and realizing high‐performance OSCs.
Steric Engineering Enables Efficient and Photostable Wide‐Bandgap Perovskites for All‐Perovskite Tandem Solar Cells
Authors: Wen Jin , Zhao Yicheng , Liu Zhou , Gao Han , Lin Renxing , Wan Sushu , Ji Chenglong , Xiao Ke , Gao Yuan , Tian Yuxi , Xie Jin , Brabec Christoph J. , Tan Hairen 
Published: April 2022

AbstractWide‐bandgap (WBG, ≈1.8 eV) perovskite is a crucial component to pair with narrow‐bandgap perovskite in low‐cost monolithic all‐perovskite tandem solar cells. However, the stability and efficiency of WBG perovskite solar cells (PSCs) are constrained by the light‐induced halide segregation and by the large photovoltage deficit. Here, a steric engineering to obtain high‐quality and photostable WBG perovskites (≈1.8 eV) suitable for all‐perovskite tandems is reported. By alloying dimethylammonium and chloride into the mixed‐cation mixed‐halide perovskites, wide bandgaps are obtained with much lower bromide contents while the lattice strain and trap densities are simultaneously minimized. The WBG PSCs exhibit considerably improved performance and photostability, retaining >90% of their initial efficiencies after 1000 h of operation at maximum power point. With the triple‐cation/triple‐halide WBG perovskites enabled by steric engineering, a stabilized power conversion efficiency of 26.0% in all‐perovskite tandem solar cells is further obtained. The strategy provides an avenue to fabricate efficient and stable WBG subcells for multijunction photovoltaic devices.
Flexible Confinement and Manipulation of Mie Resonances via Nano Rectangular Hollow Metasurfaces
Authors: Li Zhancheng , Geng Guangzhou , Cheng Jiaqi , Liu Wenwei , Yu Shiwang , Xie Boyang , Cheng Hua , Li Junjie , Zhou Wenyuan , Tian Jianguo , Chen Shuqi 
Published: April 2022

AbstractMie resonances excited in high‐index all‐dielectric metasurfaces provide a powerful platform for the constraint and manipulation of light at the subwavelength scale, which enable tremendous advanced developments in optical field manipulation, imaging, and sensing. Recently, how to manipulate and confine Mie resonances in the frequency domain has attracted tremendous interest since it is invaluable for the implementation of frequency‐selective and ‐multiplexed optical devices. Here, the authors theoretically analyze and experimentally demonstrate that the nano rectangular hollow (NRH) metasurfaces are promising candidates for the flexible confinement and effective manipulation of Mie resonances in the frequency domain. They reveal that the diameter of the hollow in the NRH can provide an efficient degree of freedom for the constraint of displace currents in the space domain, which results in the confinement of Mie resonances in the frequency domain. The excitation wavelength of the Mie resonance can also be manipulated by adjusting the side length of the NRH. The potential uses of NRH metasurfaces in the implementation of frequency‐selective intensity encoding and optical encryption are theoretically and experimentally demonstrated. The results provide a fertile ground for confining Mie resonances in the frequency domain and can be further applied in frequency‐multiplexed optical devices.
Facile Polydimethylsiloxane Treatment of Indium Gallium Zinc Oxide Phototransistor for Visible Light‐Based Multilevel Photomemory
Authors: Park Kyungho , Lee Jin Hyeok , Kang Byung Ha , Chung Jusung , Kim Hee Jun , Kwak Kyungmoon , Kim Hyun Jae 
Published: April 2022

AbstractFor visible light‐based multilevel photomemories, indium‐gallium‐zinc‐oxide (IGZO, In:Ga:Zn = 1:2.8:1.4)‐based phototransistors capable of detection and storage in the visible light region are fabricated through the facile polydimethylsiloxane (PDMS) treatment, a process of exfoliating the hardened PDMS after coating on the gate insulator (GI) via a drop‐casting process. Here, PDMS residues form on the GI by exfoliation induced subgap states in the front channel of IGZO. Subgap states are composed of interface trap states by the less‐hardened PDMS and organic‐related trap states by diffusion of organic residues into the IGZO front region during the 300 °C annealing step. PDMS‐treated IGZO phototransistors exhibit improved optoelectronic characteristics due to increased subgap states. Photoresponsivity, photosensitivity, and detectivity under red light irradiation with an intensity of 5 mW mm−2 are improved compared with untreated IGZO phototransistors, from 69.56 to 718.15 A W−1, from 7.64 × 103 to 4.63 × 107, and from 3.16 × 108 to 1.25 × 1012 Jones, respectively. Additionally, the possibility of multilevel photomemory is evaluated using the same devices. These devices are able to not only hold data for 18 000 s after red light irradiation for 1 s but also exhibit stable operation for up to 60 repetitive programming/erasing cycles.
Hypertension, a dementia polygenic risk score, APOE genotype, and incident dementia
Authors: Littlejohns Thomas J. , Collister Jennifer A. , Liu Xiaonan , Clifton Lei , Tapela Neo M. , Hunter David J. 
Published: April 2022

AbstractIntroductionThere is inconsistent evidence on whether genetic risk for dementia modifies the association between hypertension and dementia.MethodsIn 198,965 dementia‐free participants aged ≥60 years, Cox proportional‐hazards models were used to investigate the association between hypertension and incident dementia. A polygenic risk score (PRS) based on 38 non‐apolipoprotein E (APOE) single nucleotide polymorphisms and APOE ε4 status were used to determine genetic risk for dementia.ResultsOver 15 years follow‐up, 6270 participants developed dementia. Hypertension was associated with a 19% increased risk of dementia (hazard ratio = 1.19, 95% confidence interval 1.11–1.27). The associations remained similar when stratifying by genetic risk, with no evidence for multiplicative interaction by dementia PRS (P = 0.20) or APOE ε4 status (P = 0.16). However, the risk difference between those with and without hypertension was larger among those at higher genetic risk.DiscussionHypertension was associated with an increased risk of dementia regardless of genetic risk for dementia.
Validating the trauma care system developed by Yokohama City local government
Authors: Takeuchi Ichiro , Morimura Naoto , Iwashita Masayuki , Kitano Mitsuhide , Doi Tomoki , Hayashi Munetaka , Fujita Takashi , Yamasaki Motoyasu , Shuri Jun 
Published: April 2022

BackgroundSince becoming the city with the first government‐designated major trauma center in 2014, Yokohama has been striving to centralize care for extensive trauma patients. Hence, in this study, the Yokohama City Major Trauma Care Advisory Committee tested the efficacy of the centralization of care for trauma patients.MethodsThis investigation included all cases of deaths due to road traffic accidents that occurred in the 2‐year period following the establishment of the major trauma center. The probability of survival was calculated using data provided by the police and fire departments. Cases that died despite having a probability of survival of 50% or more were included in the survey undertaken by physicians recommended by the Japanese Association for the Surgery of Trauma, who visited the hospitals.ResultsOf those surveyed, preventable trauma death accounted for 1 case (1.7%) and potentially preventable trauma death accounted for 7 (11.9%), compared with 5 (9.8%) and 11 (21%) cases, respectively, in the period 2009–2010.ConclusionsComparing the survey conducted before establishment of the major trauma center, those results support the benefits of centralizing care for severe trauma cases. We aim to continue improving trauma care provided through the center along with the Yokohama Medical Control Council and to overcome challenges that were identified through the peer review.
Membrane‐Bound Inward‐Growth of Artificial Cytoskeletons and Their Selective Disassembly
Authors: Xu Qingsong , Li Shanlong , Qi Meiwei , Gao Jing , Chen Chuanshuang , Huang Pei , Wang Yuling , Yu Chunyang , Huang Wei , Zhou Yongfeng 
Published: April 2022

AbstractThe cytoskeleton is one of the most important cellular components. Up to now, most of the reported artificial cytoskeletons are based on a gel‐in‐vesicle strategy. Herein, we report a membrane‐bound inward‐growth pathway to prepare cytoskeleton‐like and radially aligned nanofibers grown from capsule membranes to get membrane‐bound artificial cytoskeletons (MACs). The mechanism therein is disclosed through the direct observation of the intermediates in both dried and liquid states. Furthermore, the as‐prepared MACs show a selective disassembly behavior in the presence of reductants: both capsule membranes and MACs can be disassembled or only MACs can be disassembled through the selective introduction of dynamic disulfide bonds (DS) into them and by the switch of ultraviolet (UV) irradiation. The present work provides a new hierarchical self‐assembly way to construct artificial cytoskeletons with controlled compositions and orientations.
Synthesis and research of basalt microfiber‐reinforced polyurethane elastomer composites
Authors: Wang Danhui , Li Xiaodong , Ge Mengchen , Lei Lisha , Yang Yi , Liu Shuang , Zou Meishuai 
Published: April 2022

AbstractBasalt microfiber‐reinforced polyurethane elastomer composites (BMF/PUE) were prepared by semi‐prepolymer method in this study. The degree of microphase separation and quantitative analysis of H‐bonding formation in polyurethane were determined by infrared spectroscopy. The fiber surface and the morphology at the tensile fracture interface of the composite materials were observed by scanning electron microscopy. The mechanical properties of composite materials were further measured on an electronic universal testing machine. Dynamic thermomechanical analysis and acoustic impedance tube were used to study the damping and acoustic properties of composite materials, respectively. The results indicated that the composite material prepared by adding 6 g of basalt microfibers treated with 3 min' crushing had the best overall performance. Compared with the matrix, BMF/PUE showed good sound insulation performance with a much wider effective damping temperature range. On the basis of ensuring its excellent overall performance, the mechanical properties were increased by 50.4% in tensile strength, 28.1% in elongation at break, and 14.2% in tear strength.
Interleukin‐13 Receptor α1–Mediated Signaling Regulates Age‐Associated/Autoimmune B Cell Expansion and Lupus Pathogenesis
Authors: Chen Zhu , Flores Castro Danny , Gupta Sanjay , Phalke Swati , Manni Michela , Rivera‐Correa Juan , Jessberger Rolf , Zaghouani Habib , Giannopoulou Eugenia , Pannellini Tania , Pernis Alessandra B. 
Published: April 2022

ObjectiveAge‐associated/autoimmune B cells (ABCs) are an emerging B cell subset with aberrant expansion in systemic lupus erythematosus. ABC generation and differentiation exhibit marked sexual dimorphism, and Toll‐like receptor 7 (TLR‐7) engagement is a key contributor to these sex differences. ABC generation is also controlled by interleukin‐21 (IL‐21) and its interplay with interferon‐γ and IL‐4. This study was undertaken to investigate whether IL‐13 receptor α1 (IL‐13Rα1), an X‐linked receptor that transmits IL‐4/IL‐13 signals, regulates ABCs and lupus pathogenesis.MethodsMice lacking DEF‐6 and switch‐associated protein 70 (double‐knockout [DKO]), which preferentially develop lupus in females, were crossed with IL‐13Rα1–knockout mice. IL‐13Rα1–knockout male mice were also crossed with Y chromosome autoimmune accelerator (Yaa) DKO mice, which overexpress TLR‐7 and develop severe disease. ABCs were assessed using flow cytometry and RNA‐Seq. Lupus pathogenesis was evaluated using serologic and histologic analyses.ResultsABCs expressed higher levels of IL‐13Rα1 than follicular B cells. The absence of IL‐13Rα1 in either DKO female mice or Yaa DKO male mice decreased the accumulation of ABCs, the differentiation of ABCs into plasmablasts, and autoantibody production. Lack of IL‐13Rα1 also prolonged survival and delayed the development of tissue inflammation. IL‐13Rα1 deficiency diminished in vitro generation of ABCs, an effect that, surprisingly, could be observed in response to IL‐21 alone. RNA‐Seq revealed that ABCs lacking IL‐13Rα1 down‐regulated some histologic characteristics of B cells but up‐regulated myeloid markers and proinflammatory mediators.ConclusionOur findings indicate a novel role for IL‐13Rα1 in controlling ABC generation and differentiation, suggesting that IL‐13Rα1 contributes to these effects by regulating a subset of IL‐21–mediated signaling events. These results also suggest that X‐linked genes besides TLR7 participate in the regulation of ABCs in lupus.