bluuebunny/crossref_metadata_2025_split huggingface dataset:
SpyChIP identifies cell type-specific transcription factor occupancy from complex tissues
Authors: Feng Siqian , Mann Richard S. 
Published: June 2022

Chromatin immunoprecipitation (ChIP) is an important technique for characterizing protein–DNA binding in vivo. One drawback of ChIP-based techniques is the lack of cell type-specificity when profiling complex tissues. To overcome this limitation, we developed SpyChIP to identify cell type-specific transcription factor (TF) binding sites in native physiological contexts without tissue dissociation or nuclei sorting. SpyChIP takes advantage of a specific covalent isopeptide bond that rapidly forms between the 15-amino acid SpyTag and the 17-kDa protein SpyCatcher. In SpyChIP, the target TF is fused with SpyTag by genome engineering, and an epitope tagged SpyCatcher is expressed in cell populations of interest, where it covalently binds to SpyTag-TF. Cell type-specific ChIP is obtained by immunoprecipitating chromatin prepared from whole tissues using antibodies directed against the epitope-tagged SpyCatcher. Using SpyChIP, we identified the genome-wide binding profiles of the Hox protein Ultrabithorax (Ubx) in two distinct cell types of the
Drosophila
haltere imaginal disc. Our results revealed extensive region-specific Ubx–DNA binding events, highlighting the significance of cell type-specific ChIP and the limitations of whole-tissue ChIP approaches. Analysis of Ubx::SpyChIP results provided insights into the relationship between chromatin accessibility and Ubx–DNA binding, as well as different mechanisms Ubx employs to regulate its downstream
cis
-regulatory modules. In addition to SpyChIP, we suggest that SpyTag–SpyCatcher technology, as well as other protein pairs that form covalent isopeptide bonds, will facilitate many additional in vivo applications that were previously impractical.
Genome-wide analysis of the
in vivo
tRNA structurome reveals RNA structural and modification dynamics under heat stress
Authors: Yamagami Ryota , Sieg Jacob P. , Assmann Sarah M. , Bevilacqua Philip C. 
Published: June 2022

RNA structure plays roles in myriad cellular events including transcription, translation, and RNA processing. Genome-wide analyses of RNA secondary structure in vivo by chemical probing have revealed critical structural features of mRNAs and long ncRNAs. Here, we examine the in vivo secondary structure of a small RNA class, tRNAs. Study of tRNA structure is challenging because tRNAs are heavily modified and strongly structured. We introduce “tRNA structure-seq,” a new workflow that accurately determines in vivo secondary structures of tRNA. The workflow combines dimethyl sulfate (DMS) probing, ultra-processive RT, and mutational profiling (MaP), which provides mutations opposite DMS and natural modifications thereby allowing multiple modifications to be identified in a single read. We applied tRNA structure-seq to
E. coli
under control and stress conditions. A leading folding algorithm predicts
E. coli
tRNA structures with only ∼80% average accuracy from sequence alone. Strikingly, tRNA structure-seq, by providing experimental restraints, improves structure prediction under in vivo conditions to ∼95% accuracy, with more than 14 tRNAs predicted completely correctly. tRNA structure-seq also quantifies the relative levels of tRNAs and their natural modifications at single nucleotide resolution, as validated by LC-MS/MS. Our application of tRNA structure-seq yields insights into tRNA structure in living cells, revealing that it is not immutable but has dynamics, with partial unfolding of secondary and tertiary tRNA structure under heat stress that is correlated with a loss of tRNA abundance. This method is applicable to other small RNAs, including those with natural modifications and highly structured regions.
Lectal contamination
Authors: Pijpops Dirk 
Published: June 2022

Abstract
This paper presents evidence from both corpora and agent-based simulation for the effect of lectal contamination.
By doing so, it shows how agent-based simulation can be used as a complementary technique to corpus research in the study of
language variation. Lectal contamination is an effect whereby the words that are typical of a language variety more often appear
in a morphosyntactic variant typical of that same variety, even among language use from a different variety. This study looks at
the Dutch partitive genitive construction, which exhibits variation between a “Netherlandic” variant with -s
ending and a “Belgian” variant without -s ending. It is shown that the probability of the Belgian variant without
-s increases among more “Belgian” words, in the language use of both Belgians and people from the Netherlands. Meanwhile, an
agent-based simulation reveals the crucial theoretical preconditions that lead to this effect.
Object agreement in Hungarian
Authors: Coppock Elizabeth 
Published: June 2022

AbstractThis paper contributes another round in the debate over how to analyze object agreement in Hungarian, a form of differential object marking that is found among other Uralic languages as well. I have previously argued that the choice of conjugation is determined not by the syntactic category of the object, but rather on the basis of semantic factors, primarily: on the Lexical Familiarity Hypothesis (LFH), selected lexical items are assigned a definiteness feature in virtue of a certain type of familiarity presupposition that they carry. Subsequent work has raised challenges for the LFH. This paper considers what would be necessary in order for these challenges to be met. I conclude that the LFH can be defended, if supplemented by a certain set of independently-motivated assumptions. In fact, this theory enjoys certain advantages over the most recent alternative.
Light, moderate and vigorous physical activities: New insights into a virtuous circle with happiness
Authors: Castellanos‐García Pablo , Lera‐López Fernando , Sánchez‐Santos José Manuel 
Published: June 2022

ABSTRACTThe study of the physical activity engagement (PA) has given rise to a relevant research agenda in a wide range of fields, such as its close relationship with subjective well‐being, self‐perceived health and social capital. Previous evidence has identified interrelationships among these variables, but without considering different levels of physical activity. We have thus considered three levels of activity: light (walking), moderate and vigorous. Structural Equation Modelling (SEM) is undertaken on data from Spain's National Health Survey in 2011–2012 to analyse these interrelationships. The SEM shows a simultaneous and bidirectional relationship between different levels of PA (moderate and vigorous activities) and happiness, with a more robust association stemming from happiness to PA than vice versa. This relationship is mediated through health. From a policy perspective, this implies a virtuous circle: involvement in different levels of PA increases happiness and self‐perceived health, while happiness involves higher PA and subsequent positive increases in health and happiness. Nevertheless, this virtuous circle does not always run successfully when social capital is considered to mediate the relationship between PA and happiness, which might explain why it has proven to be very difficult for health policymakers to fight against inactivity and a sedentary lifestyle within a great part of the population.
The effects of acute respiratory illness on exercise and sports performance outcomes in athletes – A systematic review by a subgroup of the IOC consensus group on “Acute respiratory illness in the athlete”
Authors: Kaulback Kelly , Pyne David B. , Hull James H. , Snyders Carolette , Sewry Nicola , Schwellnus Martin 
Published: June 2022

ABSTRACTAcute respiratory infections (ARinf) are common in athletes, but their effects on exercise and sports performance remain unclear. This systematic review aimed to determine the acute (short‐term) and longer‐term effects of ARinf, including SARS‐CoV‐2 infection, on exercise and sports performance outcomes in athletes. Data sources searched included PubMed, Web of Science and EBSCOhost, from January 1990 to 31 December 2021. Eligibility criteria included original research studies published in English, measuring exercise and/or sports performance outcomes in athletes/physically active/military aged 15–65 years with ARinf. Information regarding the study cohort, diagnostic criteria, illness classification and quantitative data on the effect on exercise/sports performance were extracted. Database searches identified 1707 studies. After full‐text screening, 17 studies were included (n = 7793). Outcomes were acute or longer‐term effects on exercise (cardiovascular or pulmonary responses), or sports performance (training modifications, change in standardised point scoring systems, running biomechanics, match performance or ability to start/finish an event). There was substantial methodological heterogeneity between studies. ARinf was associated with acute decrements in sports performance outcomes (four studies) and pulmonary function (three studies), but minimal effects on cardiorespiratory endurance (seven studies in mild ARinf). Longer‐term detrimental effects of ARinf on sports performance (six studies) were divided. Training mileage, overall training load, standardised sports performance‐dependent points and match play can be affected over time. Despite few studies, there is a trend towards impairment in acute and longer‐term exercise and sports outcomes after ARinf in athletes. Future research should consider a uniform approach to explore relationships between ARinf and exercise/sports performance.PROSPERO (CRD42020159259)
A quantitative study of the dynamic response of compliant microfluidic chips in a microfluidics context
Authors: Hébert Marie , Huissoon Jan , Ren Carolyn L 
Published: June 2022

Abstract
Polydimethylsiloxane (PDMS) is a widely used material for microfluidic devices due to its low cost, superior optical properties and fast iterative design process. Its softness however creates challenges for the device design and operation because part of the applied pressures contributes to deform chips instead of controlling the flow. The resulting dynamic behaviour is often ignored in passive microfluidic that focuses on the static behaviour of the chip, however, can cause low accuracy to active microfluidic that actuates flow frequently. Therefore, understanding the dynamic behaviour of microfluidic devices due to material compliance is of fundamental and practical importance. In this study, the microfluidic chip compliance is carefully considered by separating it from the sample tubing compliance. The capacitance is retrieved by assuming a symmetric RC circuit based on the experimentally determined time constant and chip resistance. The experimental capacitance is compared to a theoretical formula for chip designs with different height-to-width ratios and height-to-length ratios and for various fluids. The accuracy is within one order of magnitude that is much closer than previous approximations.
Comparison of different algorithms based on TKEO for EMG change point detection
Authors: Wang Shenglin , Zhu Shifan , Shang Zhen 
Published: June 2022

Abstract

Objective. A significant challenge in surface electromyography (EMG) is the accurate identification of onset and offset of muscle activation while maintaining high real-time performance. Teager–Kaiser energy operator (TKEO) is widely used in muscle activity monitoring systems because of its computational simplicity and strong real-time performance. However, in contrast to TKEO ontology, few studies have examined how well the energy operator variants from multiple fields perform in conditioning EMG signals. This paper aims to investigate the role of the energy operator and its variants in EMG change point detection by a threshold detector. Approach. To compare the stability and accuracy of TKEO and its variants for EMG change point detection, the EMG data of extensor carpi radialis longus and flexor carpi radialis were acquired from twenty participants operating a controller under normal and disturbed conditions, and EMG change point detection was performed by four energy operators and their rectified versions. Main results. Based on the ‘standard’ change points collected by the controller, the detection results were evaluated by three evaluation indexes: detection rate, F1 Score, and accuracy. The experimental results show that the multiresolution energy operator and the TKEO with rectified (abs-TKEO) are more suitable for EMG change point detection. Significance. This paper compared the effect of the energy operator and its variants on a threshold-based EMG change point detector. The experimental results in this paper can provide a reference for the selection of EMG signal conditioning methods to improve the detection performance of the EMG change point detector.
Anisotropic angular scattering models of elastic electron-neutral collisions for Monte Carlo plasma simulations
Authors: Park Ryan M , Kupets Willem , Zammit Mark C , Colgan James , Fontes Christopher J , Scheiner Brett S , Timmermans Eddy , Tang Xian-Zhu , Scarlett Liam H , Fursa Dmitry V , Bray Igor , Garland Nathan A 
Published: June 2022

Abstract
Many laboratory and industrial plasma applications require accurate modeling techniques to understand the interplay between microscopic and macroscopic processes. A prime example of this interplay is how particle and Monte Carlo (MC) simulation codes describe angular scattering of electrons following elastic scattering events. The forward peaked nature of high energy electron elastic scattering is relatively trivial to accurately describe in plasma simulations. However, for lower energy collisions, which produce near isotropic or backward peaked differential cross sections, there is not a strong consensus among the plasma modeling community on how to best describe these angular scattering trends. In this study, we propose a systematic method to approximate the aforementioned non-trivial angular scattering behavior with a formula that can be readily implemented in particle-in-cell (PIC) and/or MC plasma simulation codes. The present approach is specifically applied to fusion relevant atomic hydrogen and helium, as well as for molecular hydrogen, and results are also applicable to the atomic isotopes and homonuclear molecular isotopologues of these species. Comparisons between the present angular distribution function and benchmark scattering data were used to validate the proposed models. In addition, two-term Boltzmann calculations and PIC direct simulation MC simulations revealed that the proposed angular distribution function is accurate, agreeing very well with benchmark convergent close-coupling scattering calculations, and electron transport measurements. These studies confirmed that the present angular distribution function model can be utilized without the need of renormalization to the momentum transfer cross section (as opposed to using the elastic scattering integrated cross section), which has been suggested by several studies in order to correct for deficient angular scattering models, and to agree with transport measurements. Hence, the present anisotropic angular scattering model can be utilized to accurately model the momentum transfer as well as the electron trajectories of elastic collisions.
Electric field strengths within a micro cavity plasma array measured by Stark shift and splitting of a helium line pair
Authors: Dzikowski Sebastian , Steuer David , Iséni Sylvain , Golda Judith , Böke Marc , Schulz-von der Gathen Volker 
Published: June 2022

Abstract
The electric field is a fundamental parameter for plasma sources and devices. Its knowledge is a dominant setscrew for many processes such as controllable fluxes and energies of charged particles onto surfaces and for the electron energy distribution function. However, experimental data of electric field strengths in micro-structured surface dielectric barrier discharges are rare. Due to geometric configurations and dimensions in micrometer scale, probe-based investigations are challenging. To tackle these issues, we exploit the optical access into micro cavities of a plasma array operated with pure helium to use the Stark effect of the allowed 492.19 nm

(

D

1

↦

P

0

1

)

and forbidden 492.06 nm helium line

(

F

0

1

↦

P

0

1

)

. Based on it, we present spatially-integrated and time-resolved electric field strengths in a range between 20 kV cm−1 and 60 kV cm−1 depending on various parameters such as cavity diameters in 100 μm range and excitation properties. The obtained electric fields can be controlled just by bipolarity of applied voltage and show a good agreement to previous simulated field strengths in pore and silicon-based devices. As expected from simulation dealing with discharges in pores, a smaller cavity dimension yields higher electric field strengths. Due to these high electric fields and the option of this plasma source to easily integrate a catalyst in the discharge volume, this micro cavity plasma array promises further insights into plasma-enhanced catalysis.
Review and prospects of world-wide superconducting undulator development for synchrotrons and FELs
Authors: Zhang Kai , Calvi Marco 
Published: June 2022

Abstract
Superconducting undulators (SCUs) with a period >15 mm can offer a much higher on-axis undulator field B
0 than state-of-the-art cryogenic permanent magnet undulators with the same period and vacuum gap. The commissioned NbTi planar SCUs for user operation in the Karlsruhe Institute of Technology synchrotron and the advanced photon source storage ring are operated stably without quenches, producing outperformed photon flux in the high energy part of the hard x-ray spectrum. Another potential advantage of deploying SCU is its radiation hardness, a crucial characteristic for being used in free electron lasers (FELs) driven by high repetition rate superconducting linear accelerators (LINACs) and diffraction limited storage rings (DLSRs) with small vacuum gap and large averaged beam current. The development of shorter period but high field SCU is an important mission in an EU founded CompactLight project as this technology would reduce both the length of undulators and the length of LINACs. This review paper first overviews the research and development of SCUs worldwide from the late 1970s to 2021, then presents the SCU design requirements and compares the theory limits of different types of planar and helical SCUs, and finally reviews the technical challenges including the SCU cryostat, the magnetic field measurement, the integral/local field correction and the high-temperature superconductor (HTS) challenges and prospects the research needs for SCUs.
Entropy-based inference of transition states and cellular trajectory for single-cell transcriptomics
Authors: Gan Yanglan , Guo Cheng , Guo Wenjing , Xu Guangwei , Zou Guobing 
Published: June 2022

Abstract
The development of single-cell RNA-seq (scRNA-seq) technology allows researchers to characterize the cell types, states and transitions during dynamic biological processes at single-cell resolution. One of the critical tasks is to infer pseudo-time trajectory. However, the existence of transition cells in the intermediate state of complex biological processes poses a challenge for the trajectory inference. Here, we propose a new single-cell trajectory inference method based on transition entropy, named scTite, to identify transitional states and reconstruct cell trajectory from scRNA-seq data. Taking into account the continuity of cellular processes, we introduce a new metric called transition entropy to measure the uncertainty of a cell belonging to different cell clusters, and then identify cell states and transition cells. Specifically, we adopt different strategies to infer the trajectory for the identified cell states and transition cells, and combine them to obtain a detailed cell trajectory. For the identified cell clusters, we utilize the Wasserstein distance based on the probability distribution to calculate distance between clusters, and construct the minimum spanning tree. Meanwhile, we adopt the signaling entropy and partial correlation coefficient to determine transition paths, which contain a group of transition cells with the largest similarity. Then the transitional paths and the MST are combined to infer a refined cell trajectory. We apply scTite to four real scRNA-seq datasets and an integrated dataset, and conduct extensive performance comparison with nine existing trajectory inference methods. The experimental results demonstrate that the proposed method can reconstruct the cell trajectory more accurately than the compared algorithms. The scTite software package is available at https://github.com/dblab2022/scTite.
The a-average Degree Edge-Connectivity of Bijective Connection Networks
Authors: Yang Yayu , Zhang Mingzu , Meng Jixiang , Chen Rongda 
Published: June 2022

Abstract
The conditional edge-connectivity is an important parameter to evaluate the reliability and fault tolerance of multi-processor systems. The $n$-dimensional bijective connection networks $B_{n}$ contain hypercubes, crossed cubes, Möbius cubes and twisted cubes, etc. The conditional edge-connectivity of a connected graph $G$ is the minimum cardinality of edge sets, whose deletion disconnects $G$ and results in each remaining component satisfying property $\mathscr{P}$. And let $F$ be the edge set as desired. For a positive integer $a$, if $\mathscr{P}$ denotes the property that the average degree of each component of $G-F$ is no less than $a$, then the conditional edge-connectivity can be called the $a$-average degree edge-connectivity $\overline{\lambda }_{a}(G)$. In this paper, we determine that the exact value of the $a$-average degree edge-connectivity of an $n$-dimensional bijective connection network $\overline{\lambda }_{a}(B_{n})$ is $(n-a)2^a$ for each $0\leq a \leq n-1 $ and $n\geq 1$. 1
A pharmacokinetic-pharmacodynamic (PKPD) model-based analysis of tedizolid against enterococci using the hollow-fibre infection model
Authors: Iqbal K , Rohde H , Huang J , Tikiso T , Amann L F , Zeitlinger M , Wicha S G 
Published: June 2022

Abstract

Background
Tedizolid is a novel oxazolidinone antibiotic. Considering the higher antibacterial effect in immunocompetent compared with immunosuppressed animals, it is not recommended in immunocompromised patients.

Objectives
In this study, we assessed the ‘pure’ pharmacokinetic-pharmacodynamic (PKPD) relationship for tedizolid against Enterococcus in the hollow-fibre infection model (HFIM).

Methods
Unbound plasma concentration time profiles (200–5000 mg/day IV) were simulated in the HFIM over 120 h against an Enterococcus faecalis strain and two clinical isolates of Enterococcus faecium (VRE-vanB and VRE-vanA). Next, a PKPD model describing tedizolid efficacy against bacterial isolates was developed. A population PK model was linked to the developed PKPD model and utilized to predict the bacterial kinetics in plasma and in target tissues [adipose, muscle, epithelial lining fluid (ELF) and sputum] over 120 h of therapy.

Results
The PKPD model adequately described the bacterial kill kinetics for all bacterial populations. At the human recommended dose of 200 mg/day, bacterial growth was predicted in plasma and all tissues, except for ELF. Bacteriostasis was observed only at a higher dose of 1200 mg/day over 120 h. An fAUC/MIC of 80 related to stasis over 120 h. Subpopulations resistant to 3 × MIC were amplified in plasma and target tissues, except for ELF, at doses of 200–800 mg/day.

Conclusions
The human dose of 200 mg/day was insufficient to suppress bacterial growth in the HFIM, indicating that further components contribute to the clinical effect of tedizolid. This study supports the warning/precaution for tedizolid to limit its use in immunocompromised patients.