bluuebunny/crossref_metadata_2025_split huggingface dataset:
Squid adjust their body color according to substrate
Authors: Nakajima Ryuta , Lajbner Zdeněk , Kuba Michael J. , Gutnick Tamar , Iglesias Teresa L. , Asada Keishu , Nishibayashi Takahiro , Miller Jonathan 
Published: March 2022

AbstractColeoid cephalopods camouflage on timescales of seconds to match their visual surroundings. To date, studies of cephalopod camouflage-to-substrate have been focused primarily on benthic cuttlefish and octopus, because they are readily found sitting on the substrate. In contrast to benthic cephalopods, oval squid (Sepioteuthis lessoniana species complex) are semi-pelagic animals that spend most of their time in the water column. In this study, we demonstrate that in captivity, S. lessoniana Sp.2 (Shiro-ika, white-squid) from the Okinawa archipelago, Japan, adapts the coloration of their skin using their chromatophores according to the background substrate. We show that if the animal moves between substrates of different reflectivity, the body patterning is changed to match. Chromatophore matching to substrate has not been reported in any loliginid cephalopod under laboratory conditions. Adaptation of the chromatophore system to the bottom substrate in the laboratory is a novel experimental finding that establishes oval squid as laboratory model animals for further research on camouflage.
Arginine glycosylation regulates UDP-GlcNAc biosynthesis in Salmonella enterica
Authors: El Qaidi Samir , Scott Nichollas E. , Hays Michael P. , Hardwidge Philip R. 
Published: March 2022

AbstractThe Salmonella enterica SseK1 protein is a type three secretion system effector that glycosylates host proteins during infection on specific arginine residues with N-acetyl glucosamine (GlcNAc). SseK1 also Arg-glycosylates endogenous bacterial proteins and we thus hypothesized that SseK1 activities might be integrated with regulating the intrabacterial abundance of UPD-GlcNAc, the sugar-nucleotide donor used by this effector. After searching for new SseK1 substrates, we found that SseK1 glycosylates arginine residues in the dual repressor-activator protein NagC, leading to increased DNA-binding affinity and enhanced expression of the NagC-regulated genes glmU and glmS. SseK1 also glycosylates arginine residues in GlmR, a protein that enhances GlmS activity. This Arg-glycosylation improves the ability of GlmR to enhance GlmS activity. We also discovered that NagC is a direct activator of glmR expression. Salmonella lacking SseK1 produce significantly reduced amounts of UDP-GlcNAc as compared with Salmonella expressing SseK1. Overall, we conclude that SseK1 up-regulates UDP-GlcNAc synthesis both by enhancing the DNA-binding activity of NagC and by increasing GlmS activity through GlmR glycosylation. Such regulatory activities may have evolved to maintain sufficient levels of UDP-GlcNAc for both bacterial cell wall precursors and for SseK1 to modify other bacterial and host targets in response to environmental changes and during infection.
Antimicrobial resistance determinants in silage
Authors: Nagy Sára Ágnes , Tóth Adrienn Gréta , Papp Márton , Kaplan Selçuk , Solymosi Norbert 
Published: March 2022

AbstractAnimal products may play a role in developing and spreading antimicrobial resistance in several ways. On the one hand, residues of antibiotics not adequately used in animal farming can enter the human body via food. However, resistant bacteria may also be present in animal products, which can transfer the antimicrobial resistance genes (ARG) to the bacteria in the consumer’s body by horizontal gene transfer. As previous studies have shown that fermented foods have a meaningful ARG content, it is indicated that such genes may also be present in silage used as mass feed in the cattle sector. In our study, we aspired to answer what ARGs occur in silage and what mobility characteristics they have? For this purpose, we have analyzed bioinformatically 52 freely available deep sequenced silage samples from shotgun metagenome next-generation sequencing. A total of 16 perfect matched ARGs occurred 54 times in the samples. More than half of these ARGs are mobile because they can be linked to integrative mobile genetic elements, prophages or plasmids. Our results point to a neglected but substantial ARG source in the food chain.
Hypovitaminosis D among newly diagnosed pulmonary TB patients and their household contacts in Uganda
Authors: Acen Ester Lilian , Biraro Irene Andia , Bbuye Mudarshiru , Kateete David Patrick , Joloba Moses L. , Worodria William 
Published: March 2022

AbstractAn estimated one billion people globally live with hypovitaminosis D. Studies have indicated that vitamin D deficiency is a risk factor for active tuberculosis (TB) disease. The aim of this study was to determine the association between vitamin D deficiency and TB status among patients with active TB, latent TB infection (LTBI) and those without TB infection. In a cross-sectional study of active TB patients, LTBI, QuantiFERON GOLD testpositive and (QFN+TST+) household contact and controls QuantiFERON GOLD testnegative (QFN−TST−) samples vitamin D levels were compared. Vitamin D status was determined by measurement of total vitamin D levels with 56 samples of active TB patients, 17 with LTBI, and 22 without TB infection using electrochemiluminescence. The median interquartile range (IQR) age of the study participants was 28 (20–35) years, and the majority (63%) were females. The median (IQR) vitamin D levels were 18 ng/ml (14–24). All groups had vitamin D hypovitaminosis with significantly lower levels among active TB patients (17 ng/ml, 13, 2) than among LTBI individuals (23 ng/ml 16–29) and those without TB infection (22 ng/ml, 17–28).
CubeSat constellations provide enhanced crop phenology and digital agricultural insights using daily leaf area index retrievals
Authors: Johansen Kasper , Ziliani Matteo G. , Houborg Rasmus , Franz Trenton E. , McCabe Matthew F. 
Published: March 2022

AbstractSatellite remote sensing has great potential to deliver on the promise of a data-driven agricultural revolution, with emerging space-based platforms providing spatiotemporal insights into precision-level attributes such as crop water use, vegetation health and condition and crop response to management practices. Using a harmonized collection of high-resolution Planet CubeSat, Sentinel-2, Landsat-8 and additional coarser resolution imagery from MODIS and VIIRS, we exploit a multi-satellite data fusion and machine learning approach to deliver a radiometrically calibrated and gap-filled time-series of daily leaf area index (LAI) at an unprecedented spatial resolution of 3 m. The insights available from such high-resolution CubeSat-based LAI data are demonstrated through tracking the growth cycle of a maize crop and identifying observable within-field spatial and temporal variations across key phenological stages. Daily LAI retrievals peaked at the tasseling stage, demonstrating their value for fertilizer and irrigation scheduling. An evaluation of satellite-based retrievals against field-measured LAI data collected from both rain-fed and irrigated fields shows high correlation and captures the spatiotemporal development of intra- and inter-field variations. Novel agricultural insights related to individual vegetative and reproductive growth stages were obtained, showcasing the capacity for new high-resolution CubeSat platforms to deliver actionable intelligence for precision agricultural and related applications.
Micro-scale foundation with error quantification for the approximation of dynamics on networks
Authors: Ward Jonathan A. , Tapper Alice , Simon Péter L. , Mann Richard P. 
Published: March 2022

AbstractEpidemics, voting behaviour and cascading failures in power grids are examples of natural, social and technological phenomena that can be modelled as dynamical processes on networks. The study of such important complex systems requires approximation, but the assumptions that underpin the standard mean-field approaches are routinely violated by dynamics on real-world networks, leading to uncontrolled errors and even controversial results. Consequently, determining the approximation precision has been recognised as a key challenge. We present a micro-scale foundation for mean-field approximation of a wide range of dynamics on networks that facilitates quantification of approximation error, elucidating its connection to network structure and model dynamics. We show that our coarse-graining approach minimises approximation error and we obtain an upper bound on this uncertainty. We illustrate our approach using epidemic dynamics on real-world networks.
Stochastic modeling of antibody binding predicts programmable migration on antigen patterns
Authors: Hoffecker Ian T. , Shaw Alan , Sorokina Viktoria , Smyrlaki Ioanna , Högberg Björn 
Published: March 2022

AbstractViruses and bacteria commonly exhibit spatial repetition of the surface molecules that directly interface with the host immune system. However, the complex interaction of patterned surfaces with immune molecules containing multiple binding domains is poorly understood. We developed a pipeline for constructing mechanistic models of antibody interactions with patterned antigen substrates. Our framework relies on immobilized DNA origami nanostructures decorated with precisely placed antigens. The results revealed that antigen spacing is a spatial control parameter that can be tuned to influence the antibody residence time and migration speed. The model predicts that gradients in antigen spacing can drive persistent, directed antibody migration in the direction of more stable spacing. These results depict antibody–antigen interactions as a computational system where antigen geometry constrains and potentially directs the antibody movement. We propose that this form of molecular programmability could be exploited during the co-evolution of pathogens and immune systems or in the design of molecular machines.
Grid‐forming inverter control design for PV sources considering DC‐link dynamics
Authors: Ray Ishita , Tolbert Leon M. 
Published: March 2022

AbstractA grid‐forming inverter in an inverter‐dominated grid should operate as a dispatchable voltage source, which is difficult to achieve when the inverter is interfaced with nonlinear dc sources such as photovoltaic (PV) arrays. This paper presents a new grid‐forming controller which considers the PV source dynamics and limitations and maintains dc‐link stability under transient and overload conditions. A single‐loop voltage controller without ac current feedback is used, and the synchronization is achieved using dc voltage‐frequency droop. Additional dc current‐virtual impedance feedforward compensation is included to improve the ac output passivity. The controller limits the operation of the PV source inverter in the linear portion of its characteristic by regulating its modulation index, thus preventing dc voltage collapse. The proposed controller is implemented and tested on a controller‐in‐the‐loop simulation platform. The simulation results show that the controller shares power in proportion to the dc source capacities of parallel inverters, effectively limits the output current during faults, and limits dc‐link voltage drop when the inverter is overloaded. The controller is also validated on a hardware testbed.
Intellectual discourse on Chinese media in times of the coronavirus
Authors: Tang Xuefei 
Published: March 2022

Abstract
This paper investigates intellectual discourse in China during the COVID-19 coronavirus crisis through two discourse analyses, aiming to see the role of intellectuals in leading public discussion and perception on government decisions in times of crisis. Digital ethnography and digital discourse analysis are implemented to do a micro and in-depth analysis of texts and the media engagement of the Chinese intellectuals. In the context in which the presence and reception of public intellectuals in China has been transformed from pro-West gongzhi (公知) to intellectuals in the system (体制内), this study reviews the moral values and norms that promoted governmental policies and social coherence embedded in a new intellectual discourse. It contributes to the analysis of the dynamics and flexibility of China’s public communication in times of crisis within the social context in which online activities and offline realities are closely bonded in modern China.
The discourse of Xinmin
Authors: Cao Qing 
Published: March 2022

Abstract
Focusing on Liang Qichao’s campaign of national moral character reform, this article examines the discourse of xinmin (新民 new people) as a social engineering project that sought to remold the mindset and behaviors of the people a means of nation-building in the 1900s. Drawing on Koselleck’s idea of conceptual history, it analyses how the idea of qun (群) was deployed as a discursive building block of xinmin to cultivate a sense of membership in the political community of Chinese nation. It argues that the xinmin discourse facilitated a fundamental restructuring of the mental-cognitive framing of society in changing China from a Confucian cultural entity to a national political identity.
From transitive to intransitive and voiceless to voiced in Proto-Sino-Tibetan
Authors: Gates Jesse P. , Honkasalo Sami , Lai Yunfan 
Published: March 2022

Abstract
This paper offers new evidence from Stau, Geshiza, and Khroskyabs to address the question of directionality in valency-changing derivations in Sino-Tibetan. Examining Stau, Geshiza, and Khroskyabs causative and anticausative verb stem pairs adds to the evidence that in Proto-Sino-Tibetan, a number of intransitive stems are derived from transitive stems, in some cases as the result of *N‑ prefixation, and in other cases from voicing alternation independent of *N‑ prefixation. In addition, the proto-sigmatic prefix (*s-) does not cause devoicing in Stau, Geshiza, and Khroskyabs, but rather often undergoes voicing assimilation, and has more than just a causativization function. Furthermore, by looking at Gyalrong, Minyag, Tangut, Middle Chinese, and Old Chinese we emphasize that there is no synchronic evidence to support devoicing induced by *s‑, nor is there historical evidence to support the claim that *s‑ caused devoicing in Proto-Gyalrongic, or even at genetically deeper stages.
Strain-induced alignment of printed silver nanowires for stretchable electrodes
Authors: Moon Yoon Jae , Kang Kyung-Tae 
Published: March 2022

Abstract
Silver nanowires (Ag NWs) have been in the spotlight as a nanomaterials for roll-to-roll printed stretchable electrode because of excellent mechanical properties. Electrical conductivity of Ag NWs was affected by the nanowire orientation. Here, we printed Ag NWs ink with the drop-on-demand dispenser and stretched the Ag NWs electrode on silicone rubber and thermoplastic polyurethane (TPU) up to 140% in length. The averaged resistance at released state of 50 test samples of Ag NWs electrodes on silicone rubber film after 10% stretching test was approximately 14% lower than before stretching test. During the stretching test, both electrodes and film were stretched and strain was induced. However, the resistance at released state of Ag NWs electrodes on TPU film was increased as strain increased. The Ag NWs alignment to the stretching direction was observed on silicone rubber film by FESEM images, but alignment of Ag NWs on TPU film by stretching did not occur. Because the adhesion class (ASTM D 3359) of Ag NWs electrodes with the silicone rubber film is 1B and TPU film is 5B, Ag NWs could slide and rotate on silicone rubber film as applying the strain. We confirmed that alignment of Ag NWs on the silicone rubber film by stretching resulted in reduction of electrical resistance.
Experimental investigation on abrasive water jet machining of neem wood plastic composite
Authors: Boopathi Sampath , Thillaivanan Alagu , Azeem Mohammed Abdul , Shanmugam P , Pramod V R 
Published: March 2022

Abstract
In this article, the neem wood plastic composite material has been fabricated by mixing neem wood saw powder with polypropylene (PP) matrix by injection molding method to study the machining characteristics of the abrasive water jet machining process. The volume percentage of neem wood saw powder, the volume percentage of additive agent talc mixed with PP matrix (A), table traveling speed (Ts), and water-jet pressure (Wp) have been considered as process parameters. The experiments were conducted and analyzed to predict the optimum parameters setting for surface roughness (SR) and kerf angle (KA) using the Taguchi method. It was observed that KA and SR have been greatly impacted by the percentage of neem wood saw powder, table traveling speed, and water-jet pressure. The SR and KA were minimized by reducing the percentage of neem wood powder, table traveling speed, and water-jet pressure. The SR has been decreased by adding talc agent, conversely, the KA has been increased. The concurrent optimum process parameters setting to minimize both SR and KA had been estimated by the weighted product method (WPM). The predicted results from Taguchi and WPM had been verified by microscopic analysis and confirmation experiments.
PyLiger: scalable single-cell multi-omic data integration in Python
Authors: Lu Lu , Welch Joshua D 
Published: March 2022

Abstract

Motivation
LIGER (Linked Inference of Genomic Experimental Relationships) is a widely used R package for single-cell multi-omic data integration. However, many users prefer to analyze their single-cell datasets in Python, which offers an attractive syntax and highly optimized scientific computing libraries for increased efficiency.

Results
We developed PyLiger, a Python package for integrating single-cell multi-omic datasets. PyLiger offers faster performance than the previous R implementation (2–5× speedup), interoperability with AnnData format, flexible on-disk or in-memory analysis capability and new functionality for gene ontology enrichment analysis. The on-disk capability enables analysis of arbitrarily large single-cell datasets using fixed memory.

Availability and implementation
PyLiger is available on Github at https://github.com/welch-lab/pyliger and on the Python Package Index.

Supplementary information
Supplementary data are available at Bioinformatics online.
Timescale separation and models of symbiosis: state space reduction, multiple attractors and initialization
Authors: Pfab Ferdinand , Brown Alexandra Lynne , Detmer A Raine , Baxter Ethan C , Moeller Holly V , Cunning Ross , Nisbet Roger M 
Published: March 2022

Abstract
Dynamic Energy Budget models relate whole organism processes such as growth, reproduction and mortality to suborganismal metabolic processes. Much of their potential derives from extensions of the formalism to describe the exchange of metabolic products between organisms or organs within a single organism, for example the mutualism between corals and their symbionts. Without model simplification, such models are at risk of becoming parameter-rich and hence impractical. One natural simplification is to assume that some metabolic processes act on ‘fast’ timescales relative to others. A common strategy for formulating such models is to assume that ‘fast’ processes equilibrate immediately, while ‘slow’ processes are described by ordinary differential equations. This strategy can bring a subtlety with it. What if there are multiple, interdependent fast processes that have multiple equilibria, so that additional information is needed to unambiguously specify the model dynamics? This situation can easily arise in contexts where an organism or community can persist in a ‘healthy’ or an ‘unhealthy’ state with abrupt transitions between states possible. To approach this issue, we offer the following: (a) a method to unambiguously complete implicitly defined models by adding hypothetical ‘fast’ state variables; (b) an approach for minimizing the number of additional state variables in such models, which can simplify the numerical analysis and give insights into the model dynamics; and (c) some implications of the new approach that are of practical importance for model dynamics, e.g. on the bistability of flux dynamics and the effect of different initialization choices on model outcomes. To demonstrate those principles, we use a simplified model for root-shoot dynamics of plants and a related model for the interactions between corals and endosymbiotic algae that describes coral bleaching and recovery.
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe
Authors: Bhattacharyya Teerna , Nayak Soumya , Goswami Smit , Gadiyaram Vasundhara , Mathew Oommen K , Sowdhamini Ramanathan 
Published: March 2022

Abstract

Sequence alignments are models that capture the structural, functional and evolutionary relationships between proteins. Structure-guided sequence alignments are helpful in the case of distantly related proteins with poor sequence identity, thus rendering routine sequence alignment methods ineffective. Protein Alignment organized as Structural Superfamilies or PASS2 database provides such sequence alignments of protein domains within a superfamily as per the Structural Classification of Proteins extended (SCOPe) database. The current update of PASS2 (i.e. PASS2.7) is following the latest release of SCOPe (2.07) and we provide data for 14 323 protein domains that are &lt;40% identical and are organized into 2024 superfamilies. Several useful features derived from the alignments, such as conserved secondary structural motifs, HMMs and residues conserved across the superfamily, are also reported. Protein domains that are deviant from the rest of the members of a superfamily may compromise the quality of the alignment, and we found this to be the case in ∼7% of the total superfamilies we considered. To improve the alignment by objectively identifying such ‘outliers’, in this update, we have used a k-means-based unsupervised machine learning method for clustering superfamily members, where features provided were length of domains aligned, Cα-RMSD derived from the rigid-body superposition of all members and gaps contributed to the alignment by each domain. In a few cases, we have split the superfamily as per the clusters predicted and provided complete data for each cluster. A new feature included in this update is absolutely conserved interactions (ACIs) between residue backbones and side chains, which are obtained by aligning protein structure networks using structure-guided sequence alignments of superfamilies. ACIs provide valuable information about functionally important residues and the structure–function relationships of proteins. The ACIs and the corresponding conserved networks for backbone and sidechain have been marked on the superimposed structure separately.

Database URL
The updated version of the PASS2 database is available at http://caps.ncbs.res.in/pass2/.
On reduced form estimation of the effect of policy interventions on the COVID-19 pandemic
Authors: Korolev Ivan 
Published: March 2022

Summary
Several studies have estimated the effects of various nonpharmaceutical interventions on the COVID-19 pandemic using a ‘reduced form’ approach. In this paper, I show that many different SIR models can generate virtually identical dynamics of the number of reported cases during the early stages of the epidemic and lead to the same reduced form estimates. In some of these models, policy interventions effectively reduce the transmission rate; in others, the growth of the reported number of cases slows down even though policy has little or no effect on the transmission rate. Thus, the effect of policy cannot be uniquely determined based on the reduced form estimates. This result holds regardless of whether time series or panel data is used in reduced form estimation. I also demonstrate that the reduced form estimates of the policy effect based on panel data specifications with two-way fixed effects can have the wrong sign.