bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-operating-temperature MWIR photodetector based on a InAs/GaSb superlattice grown by MOCVD
Authors: Hao Xiujun , Teng Yan , Zhu He , Liu Jiafeng , Zhu Hong , Huai Yunlong , Li Meng , Chen Baile , Huang Yong , Yang Hui 
Published: January 2022

Abstract
We demonstrate a high-operating-temperature (HOT) mid-wavelength InAs/GaSb superlattice heterojunction infrared photodetector grown by metal–organic chemical vapor deposition. High crystalline quality and the near-zero lattice mismatch of a InAs/GaSb superlattice on an InAs substrate were evidenced by high-resolution X-ray diffraction. At a bias voltage of –0.1 V and an operating temperature of 200 K, the device exhibited a 50% cutoff wavelength of ~ 4.9 μm, a dark current density of 0.012 A/cm2, and a peak specific detectivity of 2.3 × 109 cm·Hz1/2 /W.
Characterisation of supersonic gas jets for different nozzle geometries for laser-plasma acceleration experiments at SPARC_LAB
Authors: Costa G. , Anania M.P. , Biagioni A. , Bisesto F.G. , Del Franco M. , Galletti M. , Ferrario M. , Pompili R. , Romeo S. , Rossi A.R. , Zigler A. , Cianchi A. 
Published: January 2022

Abstract
Plasma-based technology promises a tremendous reduction in size of accelerators used for research, medical, and industrial applications, making it possible to develop tabletop machines accessible for a broader scientific community. The use of high-power laser pulses on gaseous targets is a promising method for the generation of accelerated electron beams at energies on the GeV scale, in extremely small sizes, typically millimetres. The gaseous target in question can be a collimated supersonic gasjet from a nozzle. In this work, a technique for optimising the so generated plasma channel is presented. In detail, a study on the influence of the nozzle throat shape in relation to the uniformity and density of the generated plasma profile is reported. These considerations are discussed first of all from a theoretical point of view, by means of a stationary one-dimensional mathematical model of the neutral gas, thus exploiting the possibility of comparing the properties of the output flow for different nozzle geometries. This is combined with an experimental approach using interferometric longitudinal density measurements of the plasma channel. The latter is generated by a high-power laser pulse focused on a helium gasjet, in the SPARC_LAB laboratories.
Biomimetic porous scaffolds containing decellularized small intestinal submucosa and Sr2+/Fe3+ co-doped hydroxyapatite accelerate angiogenesis/osteogenesis for bone regeneration
Authors: Cui Wei , Yang Liang , Ullah Ismat , Yu Keda , Zhao Zhigang , Gao Xinfeng , Liu Tao , Liu Ming , Li Peng , Wang Junwen , Guo Xiaodong 
Published: January 2022

Abstract
The design of bone scaffolds is predominately aimed to well reproduce the natural bony environment by imitating the architecture/composition of host bone. Such biomimetic biomaterials are gaining increasing attention and acknowledged quite promising for bone tissue engineering. Herein, novel biomimetic bone scaffolds containing decellularized small intestinal submucosa matrix (SIS-ECM) and Sr2+/Fe3+ co-doped hydroxyapatite (SrFeHA) are fabricated for the first time by the sophisticated self-assembled mineralization procedure, followed by cross-linking and lyophilization post-treatments. The results indicate the constructed SIS/SrFeHA scaffolds are characterized by highly porous structures, rough microsurface and improved mechanical strength, as well as efficient releasing of bioactive Sr2+/Fe3+ and ECM components. These favorable physico-chemical properties endow SIS/SrFeHA scaffolds with an architectural/componential biomimetic bony environment which appears to be highly beneficial for inducing angiogenesis/osteogenesis both in vitro and in vivo. In particular, the cellular functionality and bioactivity of endotheliocytes/osteoblasts are significantly enhanced by SIS/SrFeHA scaffolds, and the cranial defects model further verifies the potent ability of SIS/SrFeHA to accelerate in vivo vascularization and bone regeneration following implantation. In this view these results highlight the considerable angiogenesis/osteogenesis potential of biomimetic porous SIS/SrFeHA scaffolds for inducing bone regeneration and thus may afford a new promising alternative for bone tissue engineering.
Air pollution is linked to higher cancer rates among black or impoverished communities in Louisiana
Authors: Terrell Kimberly A , St Julien Gianna 
Published: January 2022

Abstract
Despite longstanding concerns about environmental injustice in Louisiana’s industrialized communities, including the area known as Cancer Alley, there is a lack of environmental health research in this state. This research gap has direct consequences for residents of industrialized neighborhoods because state regulators have cited a lack of evidence for adverse health outcomes when making industrial permitting decisions. We investigated how cancer incidence relates to cancer risk from toxic air pollution, race, poverty, and occupation across Louisiana census tracts, while controlling for parish-level smoking and obesity rates, using linear regression and Akaike information criterion model selection. We used the most recent cancer data from the Louisiana Tumor Registry (2008–2017), estimates of race, poverty, and occupation from the US Census Bureau’s American Community Survey (2011–2015), and estimated cancer risk due to point sources from the US Environmental Protection Agency’s 2005 National Air Toxics Assessment (accounting for cancer latency). Because race and poverty were strongly correlated (r = 0.69, P < 0.0001), we included them in separate, analogous models. Results indicated that higher estimated cancer risk from air toxics was associated with higher cancer incidence through an interaction with poverty or race. Further analysis revealed that the tracts with the highest (i.e. top quartile) proportions of impoverished residents (or Black residents) were driving the association between toxic air pollution and cancer incidence. These findings may be explained by well-established disparities that result in greater exposure/susceptibility to air toxics in Black or impoverished neighborhoods. Regardless, our analysis provides evidence of a statewide link between cancer rates and carcinogenic air pollution in marginalized communities and suggests that toxic air pollution is a contributing factor to Louisiana’s cancer burden. These findings are consistent with the firsthand knowledge of Louisiana residents from predominantly Black, impoverished, and industrialized neighborhoods who have long maintained that their communities are overburdened with cancer.
Evidence that modern fires may be unprecedented during the last 3400 years in permafrost zone of Central Siberia, Russia
Authors: Novenko Elena Yu , Kupryanov Dmitry A , Mazei Natalia G , Prokushkin Anatoly S , Phelps Leanne N , Buri Aline , Davis Basil A S 
Published: January 2022

Abstract
Recent climate change in Siberia is increasing the probability of dangerous forest fires. The development of effective measures to mitigate and prevent fires is impossible without an understanding of long-term fire dynamics. This paper presents the first multi-site palaeo-fire reconstruction based on macroscopic charcoal data from peat and lake sediment cores located in different landscapes across the permafrost area of central Siberia. The obtained results show similar temporal patterns of charcoal accumulation rates in the cores under study, and near synchronous changes in fire regimes. The paleo-fire record revealed moderate biomass burning between 3.4 and 2.6 ka BP, followed by the period of lower burning occurring from 2.6 to 1.7 ka BP that coincided with regional climate cooling and moistening. Minimal fire activity was also observed during the Little Ice Age (0.7–0.25 ka BP). Fire frequencies increased during the interval from 1.7 to 0.7 ka BP and appears to be partly synchronous with climate warming during the Medieval Climate Anomaly. Regional reconstructions of long-term fire history show that recent fires are unprecedented during the late Holocene, with modern high biomass burning lying outside millennial and centennial variability of the last 3400 years.
Asymptotic and numerical analysis of slowly varying two-dimensional quantum waveguides
Authors: Barrera-Figueroa Víctor , Rabinovich Vladimir S , Cristina Loredo-Ramírez Samantha Ana 
Published: January 2022

Abstract
The work is devoted to the asymptotic and numerical analysis of the wave function propagating in two-dimensional quantum waveguides with confining potentials supported on slowly varying tubes. The leading term of the asymptotics of the wave function is determined by an adiabatic approach and the WKB approximation. Unlike other similar studies, in the present work we consider arbitrary bounded potentials and obtain exact solutions for the thresholds, and for the transverse modes in the form of power series of the spectral parameter. Our approach leads to an effective numerical method for the analysis of such quantum waveguides and for the tunnel effect observed in sections of the waveguide that shrink or widen too much. Several examples of interest show the applicability of the method.
Quantum process in probability representation of quantum mechanics
Authors: Przhiyalkovskiy Y V 
Published: January 2022

Abstract
In this work, the operator-sum representation of a quantum process is extended to the probability representation of quantum mechanics. It is shown that each process admitting the operator-sum representation is assigned a kernel, convolving of which with the initial tomogram set characterizing the system state gives the tomographic state of the transformed system. This kernel, in turn, is broken into the kernels of partial operations, each of them incorporating the symbol of the evolution operator related to the joint evolution of the system and an ancillary environment. Such a kernel decomposition for the projection to a certain basis state and a Gaussian-type projection is demonstrated as well as qubit flipping and amplitude damping processes.
Age, Period, and Cohort Effects of Internalizing Symptoms Among US Students and the Influence of Self-Reported Frequency of Attaining 7 or More Hours of Sleep: Results From the Monitoring the Future Survey 1991–2019
Authors: Kaur Navdep , Hamilton Ava D , Chen Qixuan , Hasin Deborah , Cerda Magdalena , Martins Silvia S , Keyes Katherine M 
Published: January 2022

Abstract
Adolescent internalizing symptoms have increased since 2010, whereas adequate sleep has declined for several decades. It remains unclear how self-reported sleep attainment has affected internalizing-symptoms trends. Using 1991–2019 data from the Monitoring the Future Study (n ~ 390,000), we estimated age-period-cohort effects in adolescent internalizing symptoms (e.g., loneliness, self-esteem, self-derogation, depressive affect) and the association with yearly prevalence of a survey-assessed, self-reported measure of attaining ≥7 hours of sleep most nights. We focused our main analysis on loneliness and used median odds ratios to measure variance in loneliness associated with period differences. We observed limited signals for cohort effects and modeled only period effects. The feeling of loneliness increased by 0.83% per year; adolescents in 2019 had 0.68 (95% CI: 0.49, 0.87) increased log odds of loneliness compared with the mean, which was consistent by race/ethnicity and parental education. Girls experienced steeper increases in loneliness than boys (P &lt; 0.0001). The period-effect median odds ratio for loneliness was 1.16 (variance = 0.09; 95% CI: 0.06, 0.17) before adjustment for self-reported frequency of getting ≥7 hours sleep versus 1.07 (variance = 0.02; 95% CI: 0.01, 0.03) after adjustment. Adolescents across cohorts are experiencing worsening internalizing symptoms. Self-reported frequency of &lt;7 hours sleep partially explains increases in loneliness, indicating the need for feasibility trials to study the effect of increasing sleep attainment on internalizing symptoms.
Skate-skin mucin, rich in sulfated sugars and threonine, promotes proliferation of Akkermansia muciniphila in feeding tests in rats and in vitro fermentation using human feces
Authors: Miyata Takaaki , Mizushima Takayasu , Miyamoto Nobuyuki , Yamada Takahiro , Hase Koji , Fukushima Michihiro , Nishimura Naomichi , Hino Shingo , Morita Tatsuya 
Published: January 2022

ABSTRACT
Dietary factors, affect Akkermansia muciniphila (AM) abundance in the colon, have attracted attention, driven by the inverse correlation between AM abundance and metabolic disorders. We prepared skate-skin mucin (SM), porcine stomach mucin (PM), and rat gastrointestinal mucin (RM). SM contained more sulfated sugars and threonine than PM or RM. Rats were fed a control diet or diets including SM, PM, or RM (15 g/kg), or SM (12 g/kg) from 5 different threonine contents for 14 d. Cecal total bacteria and AM were less and more numerous, respectively, in SM-fed rats than the others, but SM did not affect microbial species richness. Low-threonine SM did not induce AM proliferation. The in vitro fermentation with human feces showed that the rate of AM increase was greater with SM than PM. Collectively, heavy SM sulfation facilitates a priority supply of SM-derived amino sugars and threonine that promotes AM proliferation in rats and human feces.
Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network
Authors: Khalili Elham , Ramazi Shahin , Ghanati Faezeh , Kouchaki Samaneh 
Published: January 2022

AbstractPhosphorylation of proteins is one of the most significant post-translational modifications (PTMs) and plays a crucial role in plant functionality due to its impact on signaling, gene expression, enzyme kinetics, protein stability and interactions. Accurate prediction of plant phosphorylation sites (p-sites) is vital as abnormal regulation of phosphorylation usually leads to plant diseases. However, current experimental methods for PTM prediction suffers from high-computational cost and are error-prone. The present study develops machine learning-based prediction techniques, including a high-performance interpretable deep tabular learning network (TabNet) to improve the prediction of protein p-sites in soybean. Moreover, we use a hybrid feature set of sequential-based features, physicochemical properties and position-specific scoring matrices to predict serine (Ser/S), threonine (Thr/T) and tyrosine (Tyr/Y) p-sites in soybean for the first time. The experimentally verified p-sites data of soybean proteins are collected from the eukaryotic phosphorylation sites database and database post-translational modification. We then remove the redundant set of positive and negative samples by dropping protein sequences with &gt;40% similarity. It is found that the developed techniques perform &gt;70% in terms of accuracy. The results demonstrate that the TabNet model is the best performing classifier using hybrid features and with window size of 13, resulted in 78.96 and 77.24% sensitivity and specificity, respectively. The results indicate that the TabNet method has advantages in terms of high-performance and interpretability. The proposed technique can automatically analyze the data without any measurement errors and any human intervention. Furthermore, it can be used to predict putative protein p-sites in plants effectively.The collected dataset and source code are publicly deposited at https://github.com/Elham-khalili/Soybean-P-sites-Prediction.
Inverse Potts model improves accuracy of phylogenetic profiling
Authors: Fukunaga Tsukasa , Iwasaki Wataru 
Published: January 2022

Abstract

Motivation
Phylogenetic profiling is a powerful computational method for revealing the functions of function-unknown genes. Although conventional similarity metrics in phylogenetic profiling achieved high prediction accuracy, they have two estimation biases: an evolutionary bias and a spurious correlation bias. While previous studies reduced the evolutionary bias by considering a phylogenetic tree, few studies have analyzed the spurious correlation bias.

Results
To reduce the spurious correlation bias, we developed metrics based on the inverse Potts model (IPM) for phylogenetic profiling. We also developed a metric based on both the IPM and a phylogenetic tree. In an empirical dataset analysis, we demonstrated that these IPM-based metrics improved the prediction performance of phylogenetic profiling. In addition, we found that the integration of several metrics, including the IPM-based metrics, had superior performance to a single metric.

Availability and implementation
The source code is freely available at https://github.com/fukunagatsu/Ipm.

Supplementary information
Supplementary data are available at Bioinformatics online.
Patterns of Demand and Provision in English Adult Social Care Services
Authors: Hood Rick , Goldacre Allie , Abbott Simon , Jones Ray 
Published: January 2022

Abstract
This article reports on a quantitative study of the national datasets for adult social care in England. Building on recent analysis of trends in demand and expenditure, the aim of the study was to investigate the relationship between local authority (LA) characteristics, levels of demand for state-funded services and rates of short- and long-term provision. Publicly available data on short- and long-term activity and finances were collected for all LAs in England from 2016 to 2019 and combined with other indicators including population demographics and the Index of Multiple Deprivation. Correlation analysis was undertaken to investigate patterns of demand and provision and their link to contextual factors. Findings showed that variation between LAs was to some extent shaped by contextual factors such as deprivation and demographics, but was also subject to the effects of rationing and the impact of the self-funded market on levels of demand. Implications are discussed for efforts to reform the adult social system and address longstanding inequalities that have been both highlighted and exacerbated by the COVID-19 pandemic.
A neuron-to-astrocyte Wnt5a signal governs astrogliosis during HIV-associated pain pathogenesis
Authors: Liu Xin , Bae Chilman , Gelman Benjamin B , Chung Jin Mo , Tang Shao-Jun 
Published: January 2022

Abstract
Chronic pain is the most common neurological disorder of HIV patients. Multiple neuropathologies were identified in the pain pathway. Among them is the prominent astrocytic reaction (also know an astrogliosis). However, the pathogenic role and mechanism of the astrogliosis are unclear. Here, we show that the astrogliosis is crucial for the pain development induced by a key neurotoxic HIV protein gp120 and that a neuron-to-astrocyte Wnt5a signal controls the astrogliosis. Ablation of astrogliosis blocked the development of gp120-induced mechanical hyperalgesia, and concomitantly the expression of neural circuit polarization in the spinal dorsal horn. We demonstrated that conditional knockout of either Wnt5a in neurons or its receptor ROR2 in astrocytes abolished not only gp120-induced astrogliosis but also hyperalgesia and neural circuit polarization. Furthermore, we found that the astrogliosis promoted expression of hyperalgesia and NCP via IL-1β regulated by a Wnt5a-ROR2-MMP2 axis.
Our results shed light on the role and mechanism of astrogliosis in the pathogenesis of HIV-associated pain.
Brain-wide ongoing activity is responsible for significant cross-trial BOLD variability
Authors: Zhang Qingqing , Cramer Samuel R , Ma Zilu , Turner Kevin L , Gheres Kyle W , Liu Yikang , Drew Patrick J , Zhang Nanyin 
Published: January 2022

Abstract
A notorious issue of task-based functional magnetic resonance imaging (fMRI) is its large cross-trial variability. To quantitatively characterize this variability, the blood oxygenation level-dependent (BOLD) signal can be modeled as a linear summation of a stimulation-relevant and an ongoing (i.e. stimulation-irrelevant) component. However, systematic investigation on the spatiotemporal features of the ongoing BOLD component and how these features affect the BOLD response is still lacking. Here we measured fMRI responses to light onsets and light offsets in awake rats. The neuronal response was simultaneously recorded with calcium-based fiber photometry. We established that between-region BOLD signals were highly correlated brain-wide at zero time lag, including regions that did not respond to visual stimulation, suggesting that the ongoing activity co-fluctuates across the brain. Removing this ongoing activity reduced cross-trial variability of the BOLD response by ~30% and increased its coherence with the Ca2+ signal. Additionally, the negative ongoing BOLD activity sometimes dominated over the stimulation-driven response and contributed to the post-stimulation BOLD undershoot. These results suggest that brain-wide ongoing activity is responsible for significant cross-trial BOLD variability, and this component can be reliably quantified and removed to improve the reliability of fMRI response. Importantly, this method can be generalized to virtually all fMRI experiments without changing stimulation paradigms.
Clinical Characteristics and Outcomes of Coronavirus Disease 2019 (COVID-19) in Pregnant Women: A Propensity Score–Matched Analysis of Data From the COVID-19 Registry Japan
Authors: Shoji Kensuke , Tsuzuki Shinya , Akiyama Takayuki , Matsunaga Nobuaki , Asai Yusuke , Suzuki Setsuko , Iwamoto Noriko , Funaki Takanori , Yamada Masaki , Ozawa Nobuaki , Yamaguchi Koushi , Miyairi Isao , Ohmagari Norio 
Published: January 2022

Abstract

Background
Several studies have investigated whether pregnancy is a risk factor for developing severe coronavirus disease 2019 (COVID-19); however, the results remain controversial. In addition, the information regarding risk factors for developing severe COVID-19 in pregnant women is limited.

Methods
A retrospective cohort study analyzing the data from the nationwide COVID-19 registry in Japan was conducted. Propensity score–matched analysis was performed to compare COVID-19 severity between pregnant and nonpregnant women. Multivariate analysis was also conducted to evaluate risk factors for developing moderate-to-severe COVID-19 in pregnant women.

Results
During the study period, 254 pregnant and 3752 nonpregnant women of reproductive age were identified. After propensity score matching, 187 pregnant women and 935 nonpregnant women were selected. A composite outcome of moderate-to-severe COVID-19 was more frequently observed in pregnant women than that of nonpregnant women (n = 18 [9.6%] vs n = 46 [4.9%]; P = .0155). In multivariate analysis, the presence of underlying diseases and being in the second-to-third trimester of pregnancy were recognized as risk factors for moderate-to-severe COVID-19 in pregnant women (odds ratio [95% confidence interval]: 5.295 [1.21–23.069] and 3.871 [1.201–12.477], respectively).

Conclusions
Pregnancy could be a risk factor for moderate-to-severe COVID-19 for women in Japan. In addition to the presence of comorbidities, advanced pregnancy stages may contribute to greater risks for developing moderate-to-severe COVID-19 in pregnant women.