bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing and controlling nanoscale self-assembly of suckerin-12
Authors: Hershewe Jasmine M. , Wiseman William D. , Kath James E. , Buck Chelsea C. , Gupta Maneesh K. , Dennis Patrick B. , Naik Rajesh R. , Jewett Michael C. 
Published: August 2020

AbstractStructural proteins such as the “suckerins” present promising avenues for fabricating functional materials. Suckerins are a family of naturally occurring block copolymer-type proteins that comprise the sucker ring teeth of cephalopods and are known to self-assemble into supramolecular networks of nanoconfinedβ-sheets. Here, we report characterization and controllable, nanoscale self-assembly of suckerin-12 (S12). We characterize impacts of salt, pH, and protein concentration on S12 solubility, secondary structure, and self-assembly. In doing so, we identify conditions for fabricating ~100 nm nanoassemblies (NAs) with narrow size distributions. Finally, by installing a non-canonical amino acid (ncAA) into S12, we demonstrate the assembly of NAs that are covalently conjugated with a hydrophobic fluorophore, and the ability to change self-assembly andβ-sheet content by PEGylation. This work presents new insights into the biochemistry of suckerin-12 and demonstrates how ncAAs can be used to expedite and fine-tune the design of protein materials.
Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology
Authors: Siegle Joshua H. , Ledochowitsch Peter , Jia Xiaoxuan , Millman Daniel , Ocker Gabriel K. , Caldejon Shiella , Casal Linzy , Cho Andrew , Denman Daniel J. , Durand Séverine , Groblewski Peter A. , Heller Greggory , Kato India , Kivikas Sara , Lecoq Jerome , Nayan Chelsea , Ngo Kiet , Nicovich Philip R. , North Kat R. , Ramirez Tamina K. , Swapp Jackie , Waughman Xana , Williford Ali , Olsen Shawn R. , Koch Christof , Buice Michael A. , de Vries Saskia E. J. 
Published: August 2020

AbstractExtracellular electrophysiology and two-photon calcium imaging are widely used methods for measuring physiological activity with single-cell resolution across large populations of neurons in the brain. While these two modalities have distinct advantages and disadvantages, neither provides complete, unbiased information about the underlying neural population. Here, we compare evoked responses in visual cortex recorded in awake mice under highly standardized conditions using either imaging or electrophysiology. Across all stimulus conditions tested, we observe a larger fraction of responsive neurons in electrophysiology and higher stimulus selectivity in calcium imaging. This work explores which data transformations are most useful for explaining these modality-specific discrepancies. We show that the higher selectivity in imaging can be partially reconciled by applying a spikes-to-calcium forward model to the electrophysiology data. However, the forward model could not reconcile differences in responsiveness without sub-selecting neurons based on event rate or level of signal contamination. This suggests that differences in responsiveness more likely reflect neuronal sampling bias or cluster-merging artifacts during spike sorting of electrophysiological recordings, rather than flaws in event detection from fluorescence time series. This work establishes the dominant impacts of the two modalities’ respective biases on a set of functional metrics that are fundamental for characterizing sensory-evoked responses.
An RNA-centric global view ofClostridioides difficilereveals broad activity of Hfq in a clinically important Gram-positive bacterium
Authors: Fuchs Manuela , Lamm-Schmidt Vanessa , Ponath Falk , Jenniches Laura , Barquist Lars , Vogel Jörg , Faber Franziska 
Published: August 2020

ABSTRACTThe Gram-positive human pathogenClostridioides difficilehas emerged as the leading cause of antibiotic-associated diarrhea. Despite growing evidence for a role of Hfq in RNA-based gene regulation inC. difficile, little is known about the bacterium’s transcriptome architecture and mechanisms of post-transcriptional control. Here, we have applied a suite of RNA-centric techniques, including transcription start site mapping, transcription termination mapping and Hfq RIP-seq, to generate a single-nucleotide resolution RNA map ofC. difficile630. Our transcriptome annotation provides information about 5’ and 3’ untranslated regions, operon structures and non-coding regulators, including 42 sRNAs. These transcriptome data are accessible via an open-access browser called ‘Clost-Base’. Our results indicate functionality of many conserved riboswitches and predict novelcis-regulatory elements upstream of MDR-type ABC transporters and transcriptional regulators. Recent studies have revealed a role of sRNA-based regulation in several Gram-positive bacteria but their involvement with the RNA-binding protein Hfq remains controversial. Here, sequencing the RNA ligands of Hfq revealsin vivoassociation of many sRNAs along with hundreds of potential target mRNAs inC. difficileproviding evidence for a global role of Hfq in post-transcriptional regulation in a Gram-positive bacterium. Through integration of Hfq-bound transcripts and computational approaches we predict regulated target mRNAs for the novel sRNA AtcS encoding several adhesins and the conserved oligopeptide transporteroppBthat influences sporulation initiation inC. difficile. Overall, these findings provide a potential mechanistic explanation for increased biofilm formation and sporulation in anhfqdeletion strain and lay the foundation for understanding clostridial ribo regulation with implications for the infection process.
The intrinsically disordered protein SPE-18 promotes localized assembly of the major sperm protein inC. elegansspermatocytes
Authors: Price Kari L. , Presler Marc , Uyehara Christopher M. , Shakes Diane C. 
Published: August 2020

ABSTRACTMany specialized cells use unconventional strategies of cytoskeletal control. Nematode spermatocytes discard their actin and tubulin following meiosis, and instead employ the regulated assembly/disassembly of the Major Sperm Protein (MSP) to drive sperm motility. However prior to the meiotic divisions, MSP is effectively sequestered as it exclusively assembles into paracrystalline structures called fibrous bodies (FBs). The accessory proteins that direct this sequestration process have remained mysterious. This study reveals SPE-18 as an intrinsically disordered protein that that is essential for MSP assembly within FBs. Inspe-18mutant spermatocytes, MSP remains cytosolic, and the cells arrest in meiosis. In wildtype spermatocytes, SPE-18 localizes to pre-FB complexes and functions with the kinase SPE-6 to recruit MSP. Changing patterns of SPE-18 localization revealed unappreciated complexities in FB maturation. Later, within newly individualized spermatids, SPE −18 is rapidly lost, yet SPE-18 loss alone is insufficient for MSP disassembly. Our findings reveal an alternative strategy for sequestering cytoskeletal elements, not as monomers but in localized, bundled polymers. Additionally, these studies provide an important example of disordered proteins promoting ordered cellular structures.Summary StatementIntrinsically disordered proteins are increasingly recognized as key regulators of localized cytoskeletal assembly. Expanding that paradigm, SPE-18 localizes MSP assembly withinC. elegansspermatocytes.
BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database
Authors: Brůna Tomáš , Hoff Katharina J. , Lomsadze Alexandre , Stanke Mario , Borodovsky Mark 
Published: August 2020

AbstractFull automation of gene prediction has become an important bioinformatics task since the advent of next generation sequencing. The eukaryotic genome annotation pipeline BRAKER1 had combined self-training GeneMark-ET with AUGUSTUS to generate genes’ coordinates with support of transcriptomic data. Here, we introduce BRAKER2, a pipeline with GeneMark-EP+ and AUGUSTUS externally supported by cross-species protein sequences aligned to the genome. Among the challenges addressed in the development of the new pipeline was generation of reliable hints to the locations of protein-coding exon boundaries from likely homologous but evolutionarily distant proteins. Under equal conditions, the gene prediction accuracy of BRAKER2 was shown to be higher than the one of MAKER2, yet another genome annotation pipeline. Also, in comparison with BRAKER1 supported by a large volume of transcript data, BRAKER2 could produce a better gene prediction accuracy if the evolutionary distances to the reference species in the protein database were rather small. All over, our tests demonstrated that fully automatic BRAKER2 is a fast and accurate method for structural annotation of novel eukaryotic genomes.
AlphaSimR: An R-package for Breeding Program Simulations
Authors: Gaynor R. Chris , Gorjanc Gregor , Hickey John M. 
Published: August 2020

AbstractThis paper introduces AlphaSimR, an R package for stochastic simulations of plant and animal breeding programs. AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. AlphaSimR utilizes a scripting approach to building simulations that is particularly well suited for modeling highly complex breeding programs, such as commercial breeding programs. The primary benefit of this scripting approach is that it frees users from preset breeding program designs and allows them to model nearly any breeding program design. This paper lists the main features of AlphaSimR and provides a brief example simulation to show how to use the software.
Perceptual difficulty modulates the direction of information flow in familiar face recognition
Authors: Karimi-Rouzbahani Hamid , Ramezani Farzad , Woolgar Alexandra , Rich Anina , Ghodrati Masoud 
Published: August 2020

AbstractHumans are fast and accurate when they recognize familiar faces. Previous neurophysiological studies have shown enhanced representations for the dichotomy of familiar vs. unfamiliar faces. As familiarity is a spectrum, however, any neural correlate should reflect graded representations for more vs. less familiar faces along the spectrum. By systematically varying familiarity across stimuli, we show a neural familiarity spectrum using electroencephalography. We then evaluated the spatiotemporal dynamics of familiar face recognition across the brain. Specifically, we developed a novel informational connectivity method to test whether peri-frontal brain areas contribute to familiar face recognition. Results showed that feed-forward flow dominates for the most familiar faces and top-down flow was only dominant when sensory evidence was insufficient to support face recognition. These results demonstrate that perceptual difficulty and the level of familiarity influence the neural representation of familiar faces and the degree to which peri-frontal neural networks contribute to familiar face recognition.
Dietary propionate induces intestinal oxidative stress via inhibition of SIRT3-mediated SOD2 depropionylation
Authors: Ding Qian-wen , Zhang Zhen , Li Yu , Liu Hong-liang , Hao Qiang , Yang Ya-lin , Ringø Einar , Olsen Rolf Erik , Clarke Jihong Liu , Ran Chao , Zhou Zhi-gang 
Published: August 2020

AbstractPropionate is a commonly used preservative in various food and feedstuffs and has been regarded as a food additive without safety concerns. However, we observed that dietary propionate supplementation induced intestinal damage in the context of high fat diet (HFD) in zebrafish. The intestinal damage was attributable to oxidative stress owing to impaired antioxidant capacity, which was caused by compromised SOD2 activity in the intestine. Global lysine propionylation analysis of the intestinal samples showed that SOD2 was propionylated at K132, and further biochemical assays demonstrated that K132 propionylation suppressed SOD2 activity. In addition, SIRT3 could directly interact with SOD2 and played an important role in regulating SOD2 activity via modulating depropionylation, and the enhanced SOD2 propionylation in zebrafish fed high fat plus propionate diet was attributable to reduced SIRT3 expression. Finally, we reveal that intestinal oxidative stress resulting from SOD2 propionylation contributed to the compositional change of gut microbiota, which further deteriorated intestinal oxidative stress independent of SIRT3. Collectively, the results in this study reveal a link between protein propionylation and intestine health, and suggest potential risk of a widely used food preservative in HFD context.
Naturally acquired immunity among Kenyan adults suppresses the West African P. falciparum NF54 strain in controlled human malaria infection (CHMI)
Authors: Kapulu Melissa C , Njuguna Patricia , Hamaluba Mainga , Kimani Domtila , Ngoi Joyce M. , Musembi Janet , Ngoto Omar , Otieno Edward , Billingsley Peter F ,   CHMI-SIKA Study Team
Published: August 2020

AbstractWe used controlled human malaria infection (CHMI) to study naturally acquired immunity of Kenyan adults. We administered 3.2×103 cryopreserved Plasmodium falciparum sporozoites (SPZ, NF54 West African strain) and undertook clinical monitoring and serial quantitative PCR (qPCR). Of the 142 volunteers who were eligible for analysis: 26 (18.3%) had febrile symptoms and were treated; 30 (21.1%) reached ≥500 parasites/μl and were treated; 53 (37.3%) had parasitaemia without meeting thresholds for treatment and; 33 (23.2%) remained qPCR negative. We find that the immunity acquired by some Kenyan adults can completely suppress in vivo growth of a parasite strain originating from outside Kenya.
Proteomics reveals synergy in biomass conversion between fungal enzymes and inorganic Fenton chemistry in leaf-cutting ant colonies
Authors: Schiøtt Morten , Boomsma Jacobus J. 
Published: August 2020

AbstractThe herbivorous symbiosis between leaf-cutting ants and fungal cultivars processes biomass via ant fecal fluid mixed with munched plant substrate before fungal degradation. Here we present a full proteome of the fecal fluid ofAcromyrmexleaf-cutting ants, showing that most proteins function as biomass degrading enzymes and that ca. 80% are produced by the fungal cultivar and ingested, but not digested, by the ants. Hydrogen peroxide producing oxidoreductases were remarkably common in the fecal proteome, inspiring us to test a scenario in which hydrogen peroxide reacts with iron in the fecal fluid to form reactive oxygen radicals after which oxidized iron is reduced by other fecal-fluid enzymes. Our biochemical assays confirmed that these cyclical Fenton reactions do indeed take place in special substrate pellets, presumably to degrade recalcitrant lignocellulose. This implies that the symbiosis manages a combination of chemical and enzymatic degradation, an achievement that surpasses current human bioconversion technology.
Genetic-substructure and complex demographic history of South African Bantu speakers
Authors: Sengupta Dhriti , Choudhury Ananyo , Fortes-Lima Cesar , Aron Shaun , Whitelaw Gavin , Bostoen Koen , Gunnink Hilde , Chousou-Polydouri Natalia , Delius Peter , Tollman Stephen , Casas F Gomez-Olive , Norris Shane , Mashinya Felistas , Alberts Marianne , Hazelhurst Scott , Schlebusch Carina M. , Ramsay Michèle ,   as members and collaborators of AWI-Gen and the H3Africa Consortium
Published: August 2020

AbstractSouth Eastern Bantu-speaking (SEB) groups constitute more than 80% of the population in South Africa. Despite clear linguistic and geographic diversity, the genetic differences between these groups have not been systematically investigated. Based on genome-wide data of over 5000 individuals, representing eight major SEB groups, we provide strong evidence for fine-scale population structure that broadly aligns with geographic distribution and is also congruent with linguistic phylogeny (separation of Nguni, Sotho-Tswana and Tsonga speakers). Although differential Khoe-San admixture plays a key role, the structure persists after Khoe-San ancestry-masking. The timing of admixture, levels of sex-biased gene flow and population size dynamics also highlight differences in the demographic histories of individual groups. The comparisons with five Iron Age farmer genomes further support genetic continuity over ∼400 years in certain regions of the country. Simulated trait genome-wide association studies further show that the observed population structure could have major implications for biomedical genomics research in South Africa.
Mapping multicellular programs from single-cell profiles
Authors: Jerby-Arnon Livnat , Regev Aviv 
Published: August 2020

ABSTRACTTissue homeostasis relies on orchestrated multicellular circuits, where interactions between different cell types dynamically balance tissue function. While single-cell genomics identifies tissues’ cellular components, deciphering their coordinated action remains a major challenge. Here, we tackle this problem through a new framework of multicellular programs: combinations of distinct cellular programs in different cell types that are coordinatedtogetherin the tissue, thus forming a higher order functional unit at the tissue, rather than only cell, level. We develop the open-access DIALOGUE algorithm to systematically uncover such multi-cellular programs not only from spatial data, but even from tissue dissociated and profiled as single cells,e.g., by single-cell RNA-Seq. Tested on spatial transcriptomes from the mouse hypothalamus, DIALOGUE recovered spatial information, predicted the properties of a cell’s environment only based on its transcriptome, and identified multicellular programs that mark animal behavior. Applied to brain samples and colon biopsies profiled by scRNA-Seq, DIALOGUE identified multicellular configurations that mark Alzheimer’s disease and ulcerative colitis (UC), including a program spanning five cell types that is predictive of response to anti-TNF therapy in UC patients and enriched for UC risk genes from GWAS, each acting in different cell types, but all cells acting in concert. Taken together, our study provides a novel conceptual and methodological framework to unravel multicellular regulation in health and disease.
Real-time transient stability assessment using stacked auto-encoders
Authors: Azarbik Masoud , Sarlak Mostafa 
Published: August 2020

PurposeThis paper aims to report how one can assess the transient stability of a power system by using stacked auto-encoders.Design/methodology/approachThe proposed algorithm works in a power system equipped with the wide area measurement system. To be more exact, it needs pre- and post-disturbance values of frequency sent from phasor measurement units.FindingsThe authors have investigated the performance of the proposed method. Going through details, the authors have simulated many contingencies, and then have predicted the transient stability in each of which by using the proposed algorithm.Originality/valueThe results demonstrate that the algorithm is fast, and it has acceptable performance under different circumstances including the change of system topology and failures of telecommunication channels.
Quality of working life and career engagement of cancer survivors: the mediating role of effect of disease and treatment
Authors: Hamzah Siti Raba’ah , Musa Siti Nur Syuhada , Muda Zulaiha , Ismail Maimunah 
Published: August 2020

PurposeThis study aims at investigating the relationship between the quality of working life and career engagement of cancer survivors and the mediating role of the effect of disease and treatment.Design/methodology/approachA cross-sectional study was conducted on 400 cancer survivors in Malaysia. The participants, aged between 18 and 40, were Malaysian citizens undergoing follow-up sessions at the Kuala Lumpur General Hospital and the National Cancer Institute of Malaysia. Data were analysed using descriptive statistics, Pearson’s correlation coefficient and regression analysis that implemented Baron and Kenny’s method for mediation were used for analyses.FindingsThe effect of treatment and disease was found to significantly mediate the relationship between quality of work-life and career engagement of cancer survivors.Research limitations/implicationsThe instrument for this study was a self-reported questionnaire, with participants responding to specific items on a five-point Likert scale under the supervision of the researchers. As results from the survey were subjective in nature, the bias in the participants could not be eliminated completely. This study was also limited to the two main parameters, namely, quality of working life and career engagement and a mediator, namely, effects of the disease and treatment. Moreover, as the survey was conducted in only two hospitals in the Klang Valley area, the results cannot be generalized to other cancer survivors in other regions of Malaysia.Practical implicationsThe results of this study indicated that the mediating role of the effects of disease and treatment on the relationship of the quality of working life subscales with career engagement. Practical implications, cancer survivor consciousness of the effects of disease and treatment is very important and should be addressed and could be notable to improve the quality of working life.Originality/valueThis study gives valuable insight to managers and practitioners by investigating the relationship between the quality of working life and career engagement and mediates by the effects of disease and treatment. The findings highlight the challenges cancer survivors face on their return to working life. The findings also highlight the need for management to take steps to help cancer survivors cope with career engagement for better work performance.
From displacement to resettlement: how current policies shape eviction narratives among urban poor in the Philippines
Authors: Collado Zaldy C. , Orozco Noella May-i G. 
Published: August 2020

Purpose
This study aims to examine the experiences of urban poor relocatees in their resettlement communities, specifically those who were relocated from the Caloocan, Malabon, Navotas, Valenzuela and Quezon City areas to the province of Bulacan, Philippines. This study hopes to convey the importance of revisiting the law on socialized housing in the Philippines.

Design/methodology/approach
This study gathered qualitative data through 2 focus group discussions among 28 participants who came from 3 resettlement sites in San Jose del Monte City, Bulacan Province, Philippines. The resettlement areas are owned and managed by the National Housing Authority of the Philippine Government.

Findings
Results show that resettlement experiences are stories of survival under impoverished conditions. Lack of housing facilities or poorly built units characterize their relocation experience aside from having no immediate access to basic utilities such as electricity and water, despite a law that supposedly secures these rights to relocatees. The expensive cost of transportation and the lack of livelihood also heavily strain the lives of the relocated population.

Originality/value
This study illustrates that involuntary displacement predicts poor living conditions upon resettlement. This study is an inquiry not only of existing conditions of socialized housing in resettlement areas but also past realities of these housing communities at the onset of the displacees’ relocation.