bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretation of T cell states from single-cell transcriptomics data using reference atlases
Authors: Andreatta Massimo , Corria-Osorio Jesus , Müller Sören , Cubas Rafael , Coukos George , Carmona Santiago J. 
Published: May 2021

AbstractSingle-cell RNA sequencing (scRNA-seq) has revealed an unprecedented degree of immune cell diversity. However, consistent definition of cell subtypes and cell states across studies and diseases remains a major challenge. Here we generate reference T cell atlases for cancer and viral infection by multi-study integration, and develop ProjecTILs, an algorithm for reference atlas projection. In contrast to other methods, ProjecTILs allows not only accurate embedding of new scRNA-seq data into a reference without altering its structure, but also characterizing previously unknown cell states that “deviate” from the reference. ProjecTILs accurately predicts the effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. A meta-analysis of tumor-infiltrating T cells from several cohorts reveals a strong conservation of T cell subtypes between human and mouse, providing a consistent basis to describe T cell heterogeneity across studies, diseases, and species.
Data driven discovery of conjugated polyelectrolytes for optoelectronic and photocatalytic applications
Authors: Wan Yangyang , Ramirez Fernando , Zhang Xu , Nguyen Thuc-Quyen , Bazan Guillermo C. , Lu Gang 
Published: May 2021

AbstractConjugated polyelectrolytes (CPEs), comprised of conjugated backbones and pendant ionic functionalities, are versatile organic materials with diverse applications. However, the myriad of possible molecular structures of CPEs render traditional, trial-and-error materials discovery strategy impractical. Here, we tackle this problem using a data-centric approach by incorporating machine learning with high-throughput first-principles calculations. We systematically examine how key materials properties depend on individual structural components of CPEs and from which the structure–property relationships are established. By means of machine learning, we uncover structural features crucial to the CPE properties, and these features are then used as descriptors in the machine learning to predict the properties of unknown CPEs. Lastly, we discover promising CPEs as hole transport materials in halide perovskite-based optoelectronic devices and as photocatalysts for water splitting. Our work could accelerate the discovery of CPEs for optoelectronic and photocatalytic applications.
Cost-effectiveness analysis of COPD screening programs in primary care for high-risk patients in China
Authors: Qu Shuli , You Xuedan , Liu Tianyi , Wang Lijiao , Yin Zheng , Liu Yanjun , Ye Chong , Yang Ting , Huang Mao , Li Hongchao , Fang Liwen , Zheng Jinping 
Published: May 2021

AbstractWe built a decision-analytic model to compare the cost-effectiveness of using portable spirometer and questionnaire to screen chronic obstructive pulmonary diseases (COPD) with no screening (i.e. usual care) among chronic bronchitis patient in China. A lifetime horizon and a payer perspective were adopted. Cost data of health services including spirometry screening and treatment costs covered both maintenance and exacerbation. The result indicated that portable spirometer screening was cost-saving compared with questionnaire screening and no screening, with an incremental cost-effectiveness ratio (ICER) of −5026 and −1766 per QALY, respectively. Sensitivity analyses confirmed the robustness of the results. In summary, portable spirometer screening is likely the optimal option for COPD screening among chronic bronchitis patients China.
Rational design of innate defense regulator peptides as tumor vaccine adjuvants
Authors: Tian Yaomei , Hu Qiuyue , Zhang Rui , Zhou Bailing , Xie Daoyuan , Wang Yuanda , Zhang Xueyan , Yang Li 
Published: May 2021

AbstractThe development of adjuvants has been an empirical process. Efforts to develop a new design and evaluation system for novel adjuvants are not only desirable but also necessary. Moreover, composite adjuvants that contain two or more types of adjuvants to synergistically enhance the immune response are important for adjuvant and vaccine design. Innate defense regulator peptides (IDRs) are promising adjuvants for clinical immunotherapy because they exhibit multifaceted immunomodulatory capabilities. However, the rational design and discovery of IDRs that have improved immunomodulatory activities have been hampered by the lack of screening techniques and the great challenges in the identification of their interaction partners. Here, we describe a screening and evaluation system for IDR design. On the basis of in vitro screening, the optimized IDR DP7 recruited neutrophils, monocytes and macrophages to the site of infection. The adjuvant, comprising the DP7 and CpG oligonucleotide (CpG), induced chemokine/cytokine expression, enhanced the antigen uptake by dendritic cells and upregulated surface marker expression in dendritic cells. Vaccination with the NY-ESO-1 or OVA antigens combined with the adjuvant alum/CpG/DP7 strongly suppressed tumor growth in mice which was due to the improvement of antigen-specific humoral and cellular immunity. Regarding the mechanism of action, GPR35 may be the potential interaction partner of DP7. Our study revealed the potential application of the screening and evaluation system as a strategy for rationally designing effective IDRs or composite adjuvants and identifying their mechanism of action.
Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Authors: Cuperlovic-Culf Miroslava , Cunningham Emma L. , Teimoorinia Hossen , Surendra Anuradha , Pan Xiaobei , Bennett Steffany A. L. , Jung Mijin , McGuiness Bernadette , Passmore Anthony Peter , Beverland David , Green Brian D. 
Published: May 2021

AbstractDelirium is an acute change in attention and cognition occurring in ~ 65% of severe SARS-CoV-2 cases. It is also common following surgery and an indicator of brain vulnerability and risk for the development of dementia. In this work we analyzed the underlying role of metabolism in delirium-susceptibility in the postoperative setting using metabolomic profiling of cerebrospinal fluid and blood taken from the same patients prior to planned orthopaedic surgery. Distance correlation analysis and Random Forest (RF) feature selection were used to determine changes in metabolic networks. We found significant concentration differences in several amino acids, acylcarnitines and polyamines linking delirium-prone patients to known factors in Alzheimer’s disease such as monoamine oxidase B (MAOB) protein. Subsequent computational structural comparison between MAOB and angiotensin converting enzyme 2 as well as protein–protein docking analysis showed that there potentially is strong binding of SARS-CoV-2 spike protein to MAOB. The possibility that SARS-CoV-2 influences MAOB activity leading to the observed neurological and platelet-based complications of SARS-CoV-2 infection requires further investigation.
Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction
Authors: Rasmy Laila , Xiang Yang , Xie Ziqian , Tao Cui , Zhi Degui 
Published: May 2021

AbstractDeep learning (DL)-based predictive models from electronic health records (EHRs) deliver impressive performance in many clinical tasks. Large training cohorts, however, are often required by these models to achieve high accuracy, hindering the adoption of DL-based models in scenarios with limited training data. Recently, bidirectional encoder representations from transformers (BERT) and related models have achieved tremendous successes in the natural language processing domain. The pretraining of BERT on a very large training corpus generates contextualized embeddings that can boost the performance of models trained on smaller datasets. Inspired by BERT, we propose Med-BERT, which adapts the BERT framework originally developed for the text domain to the structured EHR domain. Med-BERT is a contextualized embedding model pretrained on a structured EHR dataset of 28,490,650 patients. Fine-tuning experiments showed that Med-BERT substantially improves the prediction accuracy, boosting the area under the receiver operating characteristics curve (AUC) by 1.21–6.14% in two disease prediction tasks from two clinical databases. In particular, pretrained Med-BERT obtains promising performances on tasks with small fine-tuning training sets and can boost the AUC by more than 20% or obtain an AUC as high as a model trained on a training set ten times larger, compared with deep learning models without Med-BERT. We believe that Med-BERT will benefit disease prediction studies with small local training datasets, reduce data collection expenses, and accelerate the pace of artificial intelligence aided healthcare.
Mechanosensitive channel YnaI has lipid-bound extended sensor paddles
Authors: Hu Wenxin , Wang Zhiming , Zheng Hongjin 
Published: May 2021

AbstractThe general mechanism of bacterial mechanosensitive channels (MS) has been characterized by extensive studies on a small conductance channel MscS from Escherichia coli (E. coli). However, recent structural studies on the same channel have revealed controversial roles of various channel-bound lipids in channel gating. To better understand bacterial MscS-like channels, it is necessary to characterize homologs other than MscS. Here, we describe the structure of YnaI, one of the closest MscS homologs in E. coli, in its non-conducting state at 3.3 Å resolution determined by cryo electron microscopy. Our structure revealed the intact membrane sensor paddle domain in YnaI, which was stabilized by functionally important residues H43, Q46, Y50 and K93. In the pockets between sensor paddles, there were clear lipid densities that interact strongly with residues Q100 and R120. These lipids were a mixture of natural lipids but may be enriched in cardiolipin and phosphatidylserine. In addition, residues along the ion-conducting pathway and responsible for the heptameric assembly were discussed. Together with biochemical experiments and mutagenesis studies, our results provide strong support for the idea that the pocket lipids are functionally important for mechanosensitive channels.
Structural analysis of the SRP Alu domain from Plasmodium falciparum reveals a non-canonical open conformation
Authors: Soni Komal , Kempf Georg , Manalastas-Cantos Karen , Hendricks Astrid , Flemming Dirk , Guizetti Julien , Simon Bernd , Frischknecht Friedrich , Svergun Dmitri I. , Wild Klemens , Sinning Irmgard 
Published: May 2021

AbstractThe eukaryotic signal recognition particle (SRP) contains an Alu domain, which docks into the factor binding site of translating ribosomes and confers translation retardation. The canonical Alu domain consists of the SRP9/14 protein heterodimer and a tRNA-like folded Alu RNA that adopts a strictly ‘closed’ conformation involving a loop-loop pseudoknot. Here, we study the structure of the Alu domain from Plasmodium falciparum (PfAlu), a divergent apicomplexan protozoan that causes human malaria. Using NMR, SAXS and cryo-EM analyses, we show that, in contrast to its prokaryotic and eukaryotic counterparts, the PfAlu domain adopts an ‘open’ Y-shaped conformation. We show that cytoplasmic P. falciparum ribosomes are non-discriminative and recognize both the open PfAlu and closed human Alu domains with nanomolar affinity. In contrast, human ribosomes do not provide high affinity binding sites for either of the Alu domains. Our analyses extend the structural database of Alu domains to the protozoan species and reveal species-specific differences in the recognition of SRP Alu domains by ribosomes.
Ratio of products of mixture gamma variates with applications to wireless communications systems
Authors: Al‐Hmood Hussien , Al‐Raweshid Hamed 
Published: May 2021

AbstractThe fading scenario of many realistic wireless communication transmission systems, such as, multi‐hop communications and spectrum sharing in cognitive radio networks (CRNs), can be modelled by the product and the ratio of the product of the random variables (RVs) of the channel distribution. However, there is no work has been investigated in the literature to provide unified statistics of the product and the ratio of the products that can be used for a wide range of non‐composite and composite fading conditions. Accordingly, in this paper, the statistical properties, namely, probability density function (PDF), cumulative distribution function (CDF), and moment generating function (MGF) of the product and the ratio of the product of independent and non‐identically distributed (i.n.d.) mixture Gamma (MG) RVs are derived. A MG distribution has been widely employed to approximate with high accuracy most of the conventional fading models, for example, Rayleigh, Nakagami‐m, Nakagami‐q (Hoyt), and Nakagami‐n (Rician) as well as the generalised composite fading channels, such as, generalised‐/gamma, /gamma, and /gamma. Hence, the derived PDF, CDF, and MGF are utilized for the Beaulieu–Xie and shadowed fading channels that have not been yet presented by the previous works due to mathematical intractability of their statistics. Thus, the equivalent parameters of a MG distribution for these channels are given. To this end, simple closed‐form mathematically tractable expressions of the performance metrics are obtained. The derived statistics are applied to analyse the outage probability (OP), the average error probability for different modulation schemes, the effective rate (ER) of wireless communication systems and the average area under the receiver operating characteristics (AUC) curve of energy detection over cascaded fading channels. Moreover, the OP of the multi‐hop communications systems with co‐channel interference (CCI), both the lower bound of secure OP (SOPL) and probability of non‐zero secrecy capacity (PNSC) of the physical layer security (PLS), and the outage and delay‐limited capacities of CRNs are studied via using the statistics of the ratio of the product of MG variates. A comparison between the numerical results and the Monte Carlo simulations is presented to verify the validation of our analysis.
Event‐triggered scheduling for pinning networks of coupled dynamical systems under stochastically fast switching
Authors: Han Yujuan , Lu Wenlian , Chen Tianping 
Published: May 2021

AbstractThis paper studies the stability of linearly coupled dynamical systems with feedback pinning algorithms. Here, both the coupling matrix and the set of pinned‐nodes are time‐varying, induced by stochastic processes. Event‐triggered rules are employed in both diffusion coupling and feedback pinning terms, which can reduce the actuation and communication loads. Two event‐triggered rules are proposed and it is proved that if the system with time‐average couplings and pinning gains is stable and the switching of coupling matrices and pinned nodes is sufficiently fast, the proposed event‐triggered strategies can stabilize the system. Moreover, Zeno behaviour can be excluded for all nodes. Numerical examples of networks of mobile agents are presented to illustrate the theoretical results.
A wide input range energy harvesting system for AM broadcast with capacitor load
Authors: Wang Maodong , Zhang Yichao , Tang Kuanfeng , Yan Na , Min Hao 
Published: May 2021

AbstractA high efficiency, wide input range radio frequency (RF) energy harvesting system with capacitor load is presented, applied for harvesting the energy from amplitude modulation (AM) broadcast. The chip is fabricated in 55 nm complementary metal‐oxide‐semiconductor (CMOS) technology, and the active chip area is 1.63 mm2. The number of stages of the rectifier is reconfigurable to improve the power efficiency when the voltage across the capacitor changes during charge accumulation. A dual‐path rectifier with the switch in parallel is adopted to extend the input power range of high power efficiency (>20%). Meanwhile, to achieve the high sensitivity, a 4 nA static current‐voltage reference supplying for low‐power loop controller is also proposed. The measurement results show that the average power efficiency is improved up to 48.7% when the capacitor load is charged from 0 to 2 V and at least 6.3% improvement compared to fixed stages rectifier. The high power efficiency range is improved by 20 dB, while the single‐path reconfigurable rectifiers can only maintain the high power conversion efficiency range for a 14‐dB range. The measured RF input power sensitivity is −34.2 dBm for a 1 V output voltage.
Optimal operation of small, numerous, and disparate DERs via aggregation in transactive distribution systems with universal metering
Authors: Sabillon Carlos , Mohamed Amr A. , Golriz Ali , Venkatesh Bala 
Published: May 2021

AbstractTransactive energy distribution systems (TEDS) have unleashed new economic opportunities in the distribution sector via a new local distribution operator (LDO) that enables transactions between peers and the LDO (P2LDO) and peer‐to‐peer transactions. Aiming to unleash full benefits from existing distributed energy resources (DERs), this paper introduces an optimization algorithm for the operation of small, numerous, and disparate DER aggregations. The proposed algorithm seeks to maximize aggregator profits obtained via P2LDO and peer‐to‐peer transactions for energy and demand response, while being cognizant of capacity obligations acquired during transactive energy distribution system planning phases. In addition, the concept of universal metering is introduced to upgrade the economic opportunity of DERs. Results obtained via case studies show that the proposed approach can help DER owners to increase their revenue. An aggregated case study for 300 m shows that the overall revenue can be increased by more than 100% when operating DERs in an aggregated fashion.
Assessment of stratification of the breeds of the underground cavity roof
Authors: Makeeva Tamara , Trofimov Vitaly 
Published: May 2021

Authors of the research consider the approach to the assessment of possibility of formation of stratification and shift cracks in the roof of extended horizontal cavity, based on the method of boundary elements.	The algorithm implements the iterative procedure of variation of the formed crack length with control of tension in its tip. At the same time, the angle of the crack coasts closing is defined by the tensile strength of the layer material. The crack with smooth closing of coasts is formed in case of equality to zero this durability. The mechanism of failure forming over the developed space with vertical pipe type walls is considered. The results received by the authors, can be useful as the offered approach allows to model the destructions localization in the massif of rocks, location and sizes of the arising cracks of stretching and shift if there are strength defects in the massif
Moral values and environmental responsibility for future generations: case study of Russia
Authors: Kazantseva Dina , Tkach Elena , Sokolovskaya Irina 
Published: May 2021

Annotation.
Spiritual and moral values and motives are historically the basis of the mental matrix of the Russian citizen, determining the development and acting as a psychological coping mechanism in a crisis. In the modern world, it is spiritual values and motives that are being transformed. Mental protection of a personality based on the integrity of primal archetypes of the collective unconscious, creating mental traits and identity is interrupted, which leads to destructive changes, specifically, deprivation, alienation, deviance. In this regard, the purpose of the article is to identify the features of the transformation of spiritual and moral values of modern Russians. In the course of four sociological studies in 2007, 2009, 2010, 2019 in the regions of Russia, the values of schoolchildren (15-17 years), students (17-22 years), working youth (23-29 years) were studied. The research was based on personal, activity oriented, systemic and subjective approaches. It resulted in the consideration of the dynamics of personal values’ changes from 2007 to 2019, revealing the integrity of basic, spiritual, and moral values, which are fundamental for the personality formation of a Russian living in a particular historical and geographical environment.
Determination of the time norms for excavating soil with a mini excavator
Authors: Galiev Ilyas , Ibragimov Ruslan 
Published: May 2021

Since 2010, there has been a growing trend in the market for mini-excavators from various manufacturers. The range of manufactured equipment is increasing, as well as the technological capabilities of construction equipment are growing. At the same time, in the modern standards of Russia are no figures on the complexity of soil excavation with this type of technology.
The article shows the timing of soil excavation using the example of a mini-excavator with a bucket volume of 0.03-0.04 m3. The object of the study is the amount of time the mini-excavator works on II group of soils. The timekeeping method is used to determine the operating time of a mini-excavator with a bucket volume of 0.03 and 0.04 m3. It is experimentally obtained that the norm of time for operation of a mini-excavator with a bucket volume of 0.03m3 is 5.82 mach *hours, and for a bucket volume of 0.04 m3 is 5.37 mach*hour.
Recycling building materials is the ideal way to protect the environment
Authors: Larionov Arkadiy , Al-Rubaye Saba Jasim Raheem 
Published: May 2021

Annotation.
At the present time, the issues of combating environmental pollution are especially acute in the world. At various scientific and public platforms, the sources of the negative impact on the environment and ways to restore the ecosystem are discussed. The purpose of this article is to consider one of the main sources of environmental pollution - construction waste. Having studied a number of works on this topic and summarizing the results obtained, the authors give a detailed description of environmentally hazardous construction waste. At the same time, the authors propose a solution to this problem, which consists in the recycling of waste, that is, in the reuse of unnecessary things for the purpose of subsequent use as raw materials, energy, materials and consumer products. The authors argue that recycling waste can be safe and profitable, with great returns. Thus, the recycling of environmentally hazardous, in this particular case, construction waste will contribute not only to solving environmental issues, but also to improve the economic situation of the state.