bluuebunny/crossref_metadata_2025_split huggingface dataset:
The spatial distribution of the photosynthetic picoeukaryotes community structure in Lake Hongze
Authors: Wu Fan , Zhang Min , Liu Changqing , Yang Jinsheng , Ren Mindong , Wu Qing Long , Shi Xiaoli 
Published: July 2021

ABSTRACT
The spatial dynamics of picophytoplankton were investigated by flow cytometry and high-throughput sequencing in Lake Hongze, a large river-connecting lake. Picophytoplankton were mainly composed of phycocyanin-rich picocyanobacteria (PCY) and photosynthetic picoeukaryotes (PPEs). Picocyanobacteria was the dominant picophytoplankton group since the contribution of PPEs to total picophytoplankton was only 11.78%. However, PPEs were highly diverse and were composed of Chlorophyta, Bacillariophyta and Chrysophyceae. Environmental factors showed spatial differences, particularly in total phosphorus (TP), suspended solids (SS) and chemical oxygen demand (CODMn), which showed relatively high concentrations around the river channel. The abundances of PPEs and PCY showed similar spatial patterns, which were relatively low in the river course since they were negatively related to SS and CODMn. The top 10 OTUs contributed 79.18% of the total PPEs reads and affiliated with main species in PPEs. CCA results showed that, PPEs community composition was significantly impacted by temperature and DO at sites away from river channel, while was only influenced by nitrite at sites around the river channel.
Human Molecular Genetics and the long road to treating cystic fibrosis
Authors: Harris Ann 
Published: July 2021

AbstractThe causative gene in cystic fibrosis (CF) was identified in 1989, 3 years before the publication of the first issue of Human Molecular Genetics. The cystic fibrosis transmembrane conductance regulator (CFTR) gene was among the first underlying a common inherited disorder to be cloned, and hence, its subsequent utilization toward a cure for CF provides a roadmap for other monogenic diseases. Over the past 30 years, the advances that built upon knowledge of the gene and the CFTR protein to develop effective therapeutics have been remarkable, and yet, the setbacks have also been challenging. Technological progress in other fields has often circumvented the barriers. This review focuses on key aspects of CF diagnostics and current approaches to develop new therapies for all CFTR mutations. It also highlights the major research advances that underpinned progress toward treatments and considers the remaining obstacles.
Endoscopic Prediction of Crohn’s Disease Postoperative Recurrence
Authors: De Cruz Peter , Hamilton Amy L , Burrell Kathryn J , Gorelik Alexandra , Liew Danny , Kamm Michael A 
Published: July 2021

Abstract

Background
The presence and severity of endoscopic recurrence after Crohn's disease intestinal resection predicts subsequent disease course. The Rutgeerts postoperative endoscopic recurrence score is unvalidated but has proven prognostically useful in many clinical studies. This study aimed to investigate the association between specific early endoscopic findings and subsequent disease course.

Methods
In the setting of a randomized controlled trial (the POCER study), 85 patients underwent colonoscopy at 6 and 18 months after intestinal resection. Patients received 3 months of metronidazole, and high-risk patients received a thiopurine (or adalimumab if they were thiopurine intolerant). For endoscopic recurrence (Rutgeerts score ≥i2) at 6 months, patients stepped up to a thiopurine, fortnightly adalimumab with thiopurine, or weekly adalimumab. Central readers confirmed Rutgeerts, Simple Endoscopic Score for Crohn’s Disease, Crohn’s Disease Endoscopic Index of Severity scores, and 5 newly tested endoscopic parameters: anastomotic ulcer depth (superficial vs deep), number of ulcers (0, ≤2, &gt;2), ulcer size (1-5 mm, ≥6 mm), circumferential extent of ulceration (&lt;25%, ≥25%), and the presence or absence of stenosis. The POCER index, based on the 6-month postoperative findings, was then developed in relation to predicting the endoscopic outcome at 18 months.

Results
Of the 5 parameters, the combination of ulcer depth and circumference at the anastomosis at 6 months was associated with endoscopic recurrence at 18 months (odds ratio [OR], 1.6; 95% confidence interval [CI], 1.03-2.50; P = 0.035) with an area under the receiver operating characteristic curve of 0.62 (95% CI, 0.5-0.75). The combination of these 2 parameters formed the basis of the POCER index (range, 0-4 with 0 denoting no ulcers and 4 denoting deep ulceration with &gt;25% circumferential involvement). The new index had a strong correlation with the Rutgeerts score measured at the same time points: Spearmans’ r = .80 at 6 months and r = .77 at 18 months (P &lt; 0.001 at both time points). A POCER index of ≥2 and a Rutgeerts score of ≥i2 both had a sensitivity of 0.41 for recurrence; however, the POCER index had a higher specificity (0.8 and 0.67, respectively). The POCER index at 6 months was associated with endoscopic recurrence at 18 months (OR, 1.5; 95% CI, 1.2-2.0; P = 0.002; area under the receiver operating characteristic curve of 0.70; 95% CI, 0.57-0.82), but the Rutgeerts score was not (OR, 1.2; 95% CI, 0.8-1.8; P = 0.402).

Conclusions
The POCER postoperative index comprises 2 key endoscopic factors related to the anastomosis that are associated with subsequent disease progression. A higher score, comprising the adverse prognostic factors of deep or circumferentially extensive anastomotic ulceration, may help identify patients who require more intensive therapy.
A new approach to the complex Helmholtz equation with applications to diffusion wave fields, impedance spectroscopy and unsteady Stokes flow
Authors: Hauge Jordan C , Crowdy Darren 
Published: July 2021

Abstract
A new transform pair representing solutions to the complex Helmholtz equation in a convex 2D polygon is derived using the theory of Bessel’s functions and Green’s second identity. The derivation is a direct extension of that given by Crowdy (2015, A transform method for Laplace’s equation in multiply connected circular domains. IMA J. Appl. Math., 80, 1902–1931) for ‘Fourier–Mellin transform’ pairs associated with Laplace’s equation in various domain geometries. It is shown how the new transform pair fits into the collection of ideas known as the Fokas transform where the key step in solving any given boundary value problem is the analysis of a global relation. Here we contextualize those global relations from the point of view of ‘reciprocal theorems’, which are familiar tools in the study of the effective properties of physical systems. A survey of the many uses of this new transform approach to the complex Helmholtz equation in applications is given. This includes calculation of effective impedance in electrochemical impedance spectroscopy and in other spectroscopy methods in diffusion wave field theory, application to the 3$\omega $ method for measuring thermal conductivity and to unsteady Stokes flow. A theoretical connection between this analysis of the global relations and Lorentz reciprocity in mathematical physics is also pointed out.
Emerging Themes in the Molecular Pathogenesis of Enterotoxigenic Escherichia coli
Authors: Fleckenstein James M , Sheikh Alaullah 
Published: July 2021

Abstract
Enterotoxigenic Escherichia coli (ETEC) are ubiquitous diarrheal pathogens that thrive in areas lacking basic human needs of clean water and sanitation. These genetically plastic organisms cause tremendous morbidity among disadvantaged young children, in the form of both acute diarrheal illness and sequelae of malnutrition and growth impairment. The recent discovery of additional plasmid-encoded virulence factors and elucidation of their critical role in the molecular pathogenesis of ETEC may inform new approaches to the development of broadly protective vaccines. Although the pathogens have been closely linked epidemiologically with nondiarrheal sequelae, these conditions remain very poorly understood. Similarly, while canonical effects of ETEC toxins on cellular signaling promoting diarrhea are clear, emerging data suggest that these toxins may also drive changes in intestinal architecture and associated sequelae. Elucidation of molecular events underlying these changes could inform optimal approaches to vaccines that prevent acute diarrhea and ETEC-associated sequelae.
Vagus nerve-mediated intestinal immune regulation: therapeutic implications of inflammatory bowel diseases
Authors: Mikami Yohei , Tsunoda Junya , Kiyohara Hiroki , Taniki Nobuhito , Teratani Toshiaki , Kanai Takanori 
Published: July 2021

Abstract
The pathophysiology of inflammatory bowel diseases (IBDs) involves immunological, genetic and environmental factors. Through its ability to sense environmental stimuli, the autonomic nervous system plays a key role in the development and persistence of IBDs. The vagus nerve (VN), which contains sensory and motor neurons, travels throughout the body to innervate the gut and other visceral organs in the thoracic and abdominopelvic cavities. Recent studies show that the VN has anti-inflammatory effects via the release of acetylcholine, in what is known as the cholinergic anti-inflammatory pathway (CAIP). In the gut immune system, the CAIP is proposed to be activated directly by signals from the gut and indirectly by signals from the liver, which receives gut-derived bioactive substances via the portal vein and senses the status of the gut. The gut–brain axis and liver–brain–gut reflex arc regulate a wide variety of peripheral immune cells to maintain homeostasis in the gut. Therefore, targeting the neural reflex by methods such as VN stimulation is now under investigation for suppressing intestinal inflammation associated with IBDs. In this review, we describe the role of the VN in the regulation of intestinal immunity, and we discuss novel therapeutic approaches for IBDs that target neuroimmune interactions.
Ankle intention detection algorithm using electromyography signal
Authors: Kim Inwoo , Lee Taehoon , Lee Soo-Hong 
Published: July 2021

AbstractIn this study, an ankle intention detection algorithm was developed to calculate the torque the user wants to exert from the ankle starting from the user’s EMG signal. Since the subtalar joint axis of the ankle is very important for stability, the intent detection algorithm also calculates the torque of the eversion motion of the subtalar joint axis. A dry EMG sensor was used to measure the EMG signal, and an ankle biaxial torque measurement device was manufactured to measure the ankle torque to perform the experiment. The experiment was conducted on four healthy subjects (mean ± SD: height, 177.6 ± 7.3 cm; weight 70.2 ± 8.9 kg; and age, 27 ± 2 years), and the EMG signals and ankle torque were measured. Using the experimental results and a neural network, we developed an intention detection algorithm. When you input an EMG signal, the algorithm estimates the torque of eversion, dorsiflexion, and plantar flexion. The error of the algorithm is 0.37 Nm (subtalar) and 0.57 Nm (talocrural), which is 0.5% (subtalar) and 1.5% (talocrural) of the torque required for walking. Using the algorithm of this study, more accurate and stable exoskeleton robot control becomes possible.
Tissue-level transcriptomic responses to local and distal chilling reveal potential chilling survival mechanisms in maize
Authors: Xue Chunmei , Jiang Yuan , Wang Zhixue , Shan Xiaohui , Yuan Yaping , Hua Jian 
Published: July 2021

Abstract
Chilling is a major stress to plants of subtropical and tropical origins, including maize (Zea mays L.). To reveal the molecular mechanisms underlying chilling tolerance and survival in maize, we investigated transcriptomic responses to chilling stress in differentiated leaves and roots as well as in crowns with meristem activity. The application of chilling stress to shoots or roots each contributed to seedling lethality in maize. Comparison of maize lines with different chilling tolerance capacities revealed that chilling survival is highly associated with the up-regulation of abscisic acid biosynthesis and responses as well as transcriptional regulators in leaves and crowns. It was also associated with the down-regulation of translation in leaves and the heat response in crowns. Chilling treatment of all or part of the plants revealed that the response to distal chilling is very distinct from, and sometimes opposite to, the response to local or whole-plant chilling in both leaves and roots, suggesting communication between shoots and roots in the environmental response. This study thus provides information on transcriptomic responses in leaves, roots, and crowns under different chilling stresses in maize, and reveals potential chilling tolerance and survival mechanisms, which lay the ground for improving chilling tolerance in crop plants.
Four ‘Peculiar’ RRd stars observed by K2
Authors: Nemec James M , Moskalik Paweł 
Published: July 2021

ABSTRACT
Four stars pulsating simultaneously with a dominant period PD ∈ (0.28, 0.39) d and an additional period PA ∈ (0.20, 0.27) d have been identified from among the more than 3000 RR Lyrae stars observed by the Kepler space telescope during NASA’s K2 Mission. All four stars are located in the direction of the Galactic Bulge and have period ratios, PA/PD, significantly smaller than those of most double-mode RR Lyrae (RRd) stars: PA/PD ∈ (0.694, 0.710) versus P1/P0 ∈ (0.726, 0.748). Three of the stars are faint (〈V〉 = 18–20 mag) and distant and are among the ‘peculiar’ RRd (pRRd) stars discovered by Prudil et al. (2017); the fourth star, EPIC 216764000 (=  V1125 Sgr), is a newly discovered pRRd star several magnitudes brighter than the other three stars. In this paper, the high-precision long-cadence K2 photometry is analysed in detail and used to study the cycle-to-cycle light variations. The pulsational characteristics of pRRd stars are compared with those of ‘classical’ and ‘anomalous’ RRd (cRRd, aRRd) stars. The conclusion by Prudil et al. that pRRd stars form a separate group of double-mode pulsators and are not simply very short-period cRRd stars is confirmed. V1127 Aql and AH Cam are identified as other probable members of the class of pRRd stars.
Quenched fractions in the IllustrisTNG simulations: comparison with observations and other theoretical models
Authors: Donnari Martina , Pillepich Annalisa , Nelson Dylan , Marinacci Federico , Vogelsberger Mark , Hernquist Lars 
Published: July 2021

ABSTRACT
We make an in-depth comparison of the IllustrisTNG cosmological simulations with observed quenched fractions of central and satellite galaxies, for Mstars = 109–12 M⊙ at 0 ≤ z ≤ 3. We show how measurement choices [aperture, quenched definition, and star formation rate (SFR) indicator time-scale], as well as sample selection issues (projection effects, satellite/central misclassification, and host mass distribution sampling), impact this comparison. The quenched definition produces differences of up to 70 (30) percentage points for centrals (satellites) above ∼1010.5 M⊙. At z ≳ 2, a larger aperture within which SFR is measured suppresses the quenched fractions by up to ∼50 percentage points. Proper consideration of the stellar and host mass distributions is crucial: Naive comparisons to volume-limited samples from simulations lead to misinterpretation of the quenched fractions as a function of redshift by up to 20 percentage points. Including observational uncertainties to theoretical values of Mstars and SFR changes the quenched fraction values and their trend and/or slope with mass. Taking projected rather than three-dimensional distances for satellites decreases the quenched fractions by up to 10 per cent. TNG produces quenched fractions for both centrals and satellites broadly consistent with observations and predicts up to ∼80 (90) per cent of quenched centrals at z = 0 (z = 2), in line with recent observations, and higher than other theoretical models. The quantitative agreement of TNG and Sloan Digital Sky Survey for satellite quenched fractions in groups and clusters depends strongly on the galaxy and host mass range. Our mock comparison highlights the importance of properly accounting for observational effects and biases.
On the interaction between fast tides and convection
Authors: Barker Adrian J , Astoul Aurélie A V 
Published: July 2021

ABSTRACT
The interaction between equilibrium tides and convection in stellar envelopes is often considered important for tidal evolution in close binary and extrasolar planetary systems. Its efficiency for fast tides has however long been controversial, when the tidal frequency exceeds the turnover frequency of convective eddies. Recent numerical simulations indicate that convection can act like an effective viscosity which decays quadratically with tidal frequency for fast tides, resulting in inefficient dissipation in many applications involving pre- and main-sequence stars and giant planets. A new idea was however recently proposed by Terquem (2021), who suggested Reynolds stresses involving correlations between tidal flow components dominate the interaction instead of correlations between convective flow components as usually assumed. They further showed that this can potentially significantly enhance tidal dissipation for fast tides in many applications. Motivated by the importance of this problem for tidal dissipation in stars and planets, we directly compute this new term using analytical arguments and global spherical simulations using Boussinesq and anelastic hydrodynamic models. We demonstrate that the new term proposed by Terquem vanishes identically for equilibrium tides interacting with convection in both Boussinesq and anelastic models; it is therefore unlikely to contribute to tidal dissipation in stars and planets.
Visualization and characterization of RNA–protein interactions in living cells
Authors: Duan Ningjun , Arroyo Maria , Deng Wen , Cardoso M Cristina , Leonhardt Heinrich 
Published: July 2021

AbstractRNA–protein interactions are the structural and functional basis of significant numbers of RNA molecules. RNA–protein interaction assays though, still mainly depend on biochemical tests in vitro. Here, we establish a convenient and reliable RNA fluorescent three-hybrid (rF3H) method to detect/interrogate the interactions between RNAs and proteins in cells. A GFP tagged highly specific RNA trap is constructed to anchor the RNA of interest to an artificial or natural subcellular structure, and RNA–protein interactions can be detected and visualized by the enrichment of RNA binding proteins (RBPs) at these structures. Different RNA trapping systems are developed and detection of RNA–protein complexes at multiple subcellular structures are assayed. With this new toolset, interactions between proteins and mRNA or noncoding RNAs are characterized, including the interaction between a long noncoding RNA and an epigenetic modulator. Our approach provides a flexible and reliable method for the characterization of RNA–protein interactions in living cells.
Predicting stability of DNA bulge at mononucleotide microsatellite
Authors: Bae Jin H , Zhang David Yu 
Published: July 2021

Abstract
Mononucleotide microsatellites are clinically and forensically crucial DNA sequences due to their high mutability and abundance in the human genome. As a mutagenic intermediate of an indel in a microsatellite and a consequence of probe hybridization after such mutagenesis, a bulge with structural degeneracy sliding within a microsatellite is formed. Stability of such dynamic bulges, however, is still poorly understood despite their critical role in cancer genomics and neurological disease studies. In this paper, we have built a model that predicts the thermodynamics of a sliding bulge at a microsatellite. We first identified 40 common bulge states that can be assembled into any sliding bulges, and then characterized them with toehold exchange energy measurement and the partition function. Our model, which is the first to predict the free energy of sliding bulges with more than three repeats, can infer the stability penalty of a sliding bulge of any sequence and length with a median prediction error of 0.22 kcal/mol. Patterns from the prediction clearly explain landscapes of microsatellites observed in the literature, such as higher mutation rates of longer microsatellites and C/G microsatellites.
piRNAclusterDB 2.0: update and expansion of the piRNA cluster database
Authors: Rosenkranz David , Zischler Hans , Gebert Daniel 
Published: July 2021

Abstract
PIWI-interacting RNAs (piRNAs) and their partnering PIWI proteins defend the animal germline against transposable elements and play a crucial role in fertility. Numerous studies in the past have uncovered many additional functions of the piRNA pathway, including gene regulation, anti-viral defense, and somatic transposon repression. Further, comparative analyses across phylogenetic groups showed that the PIWI/piRNA system evolves rapidly and exhibits great evolutionary plasticity. However, the presence of so-called piRNA clusters as the major source of piRNAs is common to nearly all metazoan species. These genomic piRNA-producing loci are highly divergent across taxa and critically influence piRNA populations in different evolutionary lineages. We launched the initial version of the piRNA cluster database to facilitate research on regulation and evolution of piRNA-producing loci across tissues und species. In recent years the amount of small RNA sequencing data that was generated and the abundance of species that were studied has grown rapidly. To keep up with this recent progress, we have released a major update for the piRNA cluster database (https://www.smallrnagroup.uni-mainz.de/piRNAclusterDB), expanding it from 12 to a total of 51 species with hundreds of new datasets, and revised its overall structure to enable easy navigation through this large amount of data.