bluuebunny/crossref_metadata_2025_split huggingface dataset:
Allometric tissue-scale forces activate mechanoresponsive immune cells to drive pathological foreign body response to biomedical implants
Authors: Padmanabhan Jagannath , Chen Kellen , Sivaraj Dharshan , Kuehlmann Britta A. , Bonham Clark A. , Dohi Teruyuki , Henn Dominic , Stern-Buchbinder Zachary A. , Than Peter A. , Hosseini Hadi S. , Barrera Janos A. , Kussie Hudson C. , Magbual Noah J. , Borrelli Mimi R. , Trotsyuk Artem A. , Kwon Sun Hyung , Dunn James C.Y. , Maan Zeshaan N. , Januszyk Michael , Prantl Lukas , Gurtner Geoffrey C. 
Published: January 2022

AbstractFor decades, it has been assumed that the foreign body response (FBR) to biomedical implants is primarily a reaction to the chemical and mechanical properties of the implant. Here, we show for the first time that a third independent variable, allometric tissue-scale forces (which increase exponentially with body size), can drive the biology of FBR in humans. We first demonstrate that pathological FBR in humans is mediated by immune cell-specific Rac2 mechanotransduction signaling, independent of implant chemistry or mechanical properties. We then show that mice, which are typically poor models of human FBR, can be made to induce a strikingly human-like pathological FBR by altering these extrinsic tissue forces. Altering these extrinsic tissue forces alone activates Rac2 signaling in a unique subpopulation of immune cells and results in a human-like pathological FBR at the molecular, cellular, and local tissue levels. Finally, we demonstrate that blocking Rac2 signaling negates the effect of increased tissue forces, dramatically reducing FBR. These findings highlight a previously unsuspected mechanism for pathological FBR and may have profound implications for the design and safety of all implantable devices in humans.One-Sentence SummaryAllometric tissue-scale forces at the implant-tissue interface drive pathological foreign body response.
dsRNA-induced condensation of antiviral proteins promotes PKR activation
Authors: Corbet Giulia A. , Burke James M. , Bublitz Gaia R. , Parker Roy 
Published: January 2022

ABSTRACTMammalian cells respond to dsRNA in multiple manners. One key response to dsRNA is the activation of PKR, an eIF2α kinase, which triggers translational arrest and the formation of stress granules. However, the process of PKR activation in cells is not fully understood. In response to increased endogenous or exogenous dsRNA, we observed that PKR forms novel cytosolic condensates, referred to as dsRNA-induced foci (dRIFs). dRIFs contain dsRNA, form in proportion to dsRNA, and are enhanced by longer dsRNAs. dRIFs also enrich several other dsRNA-binding proteins including ADAR1, Stau1, NLRP1, and PACT. Strikingly, dRIFs correlate with and form prior to translation repression by PKR and localize to regions of cells where PKR activation is initiated. We suggest that dRIF formation is a mechanism cells utilize to enhance the sensitivity of PKR activation in response to low levels of dsRNA, or to overcome viral inhibitors of PKR activation.
ART duration and immunometabolic state determine efficacy of DC-based treatment restoring functional HIV- specific CD8+ T cells in PLWH
Authors: Calvet-Mirabent Marta , Sánchez-Cerrillo Ildefonso , Martín-Cófreces Noa , de la Fuente Hortensia , Tsukalov Ilya , Delgado-Arévalo Cristina , Calzada María José , de los Santos Ignacio , Sanz Jesús , García-Fraile Lucio , Sánchez-Madrid Francisco , Alfranca Arantzazu , Muñoz-Fernández María Ángeles , Buzón Maria J. , Martín-Gayo Enrique 
Published: January 2022

ABSTRACTDysfunction of CD8+ T cells in people living with HIV-1 (PLWH) receiving anti-retroviral therapy (ART) has restricted the efficacy of dendritic cell (DC)-based immunotherapies against HIV-1. Heterogeneous immune exhaustion and metabolic states of CD8+ T cells might differentially associate with dysfunction. However, specific parameters associated to functional restoration of CD8+ T cells after DC treatment have not been investigated in detail. Here, we studied the association of ART duration with memory subsets, exhaustion and metabolic profiles of CD8+ T cells from PLWH and improvement of polyfunctional and effector HIV-1 specific responses after stimulation with Gag-adjuvant-primed DC. HIV-1-specific CD8+ T cell responses from a larger proportion PLWH on ART for more than 10 years (LT-ARTp) improved polyfunctionality and capacity to eliminate autologous p24+ infected CD4+ T cellsin vitro. In contrast, CD8+ T cells from PLWH on ART for less than a decade (ST-ARTp) were less responsive to DC treatment and functional improvement was limited in this group. This was associated with lower frequencies of central memory CD8+ T cells, increased co-expression of PD1 and TIGIT and reduced mitochondrial respiration and glycolytic induction upon TCR activation. In contrast, CD8+ T cells from LT-ARTp showed increased frequencies of TIM3+PD1-cells and preserved induction of glycolysis. Treatment of dysfunctional CD8+ T cells from ST-ARTp with combined anti-PD1 and anti-TIGIT antibodies plus a glycolysis promoting drug restored their ability to eliminate infected CD4+ T cells. Together, our study identifies specific immunometabolic parameters for different PLWH subgroups potentially useful for future personalized DC-based HIV-1 vaccines.
Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum
Authors: Baker Christopher R. , Patel Dhruv , Cole Benjamin J. , Ching Lindsey G. , Dautermann Oliver , Kelikian Armen C. , Allison Cayci , Pedraza Julie , Sievert Julie , Bilbao Aivett , Lee Joon-Yong , Kim Young-Mo , Kyle Jennifer E. , Bloodsworth Kent J. , Paurus Vanessa , Hixson Kim K. , Hutmacher Robert , Dahlberg Jeffery , Lemaux Peggy G. , Niyogi Krishna K. 
Published: January 2022

AbstractClimate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a drought-tolerant cereal capable of producing high yields under water scarcity conditions. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling in terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in control and terminal post-flowering drought field plots in the Central Valley of California. Photosynthetic, photoprotective, water dynamics, and biomass traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during drought. Physiological and metabolomic data was then compared to longitudinal RNA sequencing data collected from these two genotypes. The metabolic response to drought highlights the uniqueness of the post-flowering drought acclimation relative to pre-flowering drought. The functional stay-green genotype BTx642 specifically induced photoprotective responses in post-flowering drought supporting a putative role for photoprotection in the molecular basis of the functional stay-green trait. Specific genes are highlighted that may contribute to post-flowering drought tolerance and that can be targeted in crops to maximize yields under limited water input conditions.HighlightPathways contributing to the long-term maintenance of photosynthetic activity in terminal post-flowering drought are revealed by a comprehensive approach combining in-field photosynthetic physiological analysis, metabolomics, and transcriptomics.
Absence of the fragile X mental retardation protein alters response patterns to sounds in the auditory midbrain
Authors: Sibille Jérémie , Kremkow Jens , Koch Ursula 
Published: January 2022

AbstractAmong the different autism spectrum disorders, Fragile X Syndrome (FXS) is the most common inherited cause of mental retardation. Sensory and especially auditory hypersensitivity is a key symptom in patients, which is well mimicked in the Fmr1 -/- mouse model. However, the physiological mechanisms underlying FXS’s acoustic hypersensitivity in particular remain poorly understood. Here, we categorized spike response patterns to pure tones of different frequencies and intensities from neurons in the Inferior Colliculus (IC), a central integrator in the ascending auditory pathway. Based on this categorization we analyzed differences in response patterns between IC neurons of WT and Fmr1 -/- mice. Our results report broadening of frequency tuning, an increased firing in response to monaural as well as binaural stimuli, an altered balance of excitation-inhibition, and reduced response latencies, all expected features of acoustic hypersensitivity. Furthermore, we were surprised to notice that all neuron response types in Fmr1 -/- mice displayed enhanced offset-rebound activity outside their excitatory frequency response area. These results provide evidence that the loss of Fmr1 not only increases spike responses in IC neurons similar to auditory brainstem neurons, but also changes response patterns such as offset spiking. One can speculate this to be an underlying aspect of the receptive language problems associated with Fragile X syndrome.
Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats
Authors: Blanton Jessica M. , Peoples Logan M. , Gerringer Mackenzie E. , Iacuniello Caroline M. , Gallo Natalya D. , Linley Thomas D. , Jamieson Alan J. , Drazen Jeffrey C. , Bartlett Douglas H. , Allen Eric E. 
Published: January 2022

AbstractHadal snailfishes are the deepest-living fishes in the ocean, inhabiting trenches from depths of ∼6,000 to 8,000 m. While the microbial communities in trench environments have begun to be characterized, the microbes associated with hadal megafauna remain relatively unknown. Here, we describe the gut microbiomes of two hadal snailfishes, Pseudoliparis swirei (Mariana Trench) and Notoliparis kermadecensis (Kermadec Trench) using 16S rRNA gene amplicon sequencing. We contextualize these microbiomes with comparisons to the abyssal macrourid Coryphaenoides yaquinae and the continental shelf-dwelling snailfish Careproctus melanurus. The microbial communities of the hadal snailfishes were distinct from their shallower counterparts and were dominated by the same sequences related to the Mycoplasmataceae and Desulfovibrionaceae. These shared taxa indicate that symbiont lineages may have remained similar to the ancestral symbiont since their geographic separation or that they are dispersed between geographically distant trenches and subsequently colonize specific hosts. The abyssal and hadal fishes contained sequences related to known, cultured piezophiles, microbes that grow optimally under high hydrostatic pressure, including Psychromonas, Moritella, and Shewanella. These taxa are adept at colonizing nutrient-rich environments present in the deep ocean, such as on particles and in the guts of hosts, and we hypothesize they could make a dietary contribution to deep-sea fishes by degrading chitin and producing fatty acids. We characterize the gut microbiota within some of the deepest fishes to provide new insight into the diversity and distribution of host-associated microbial taxa and the potential of these animals, and the microbes they harbor, for understanding adaptation to deep-sea habitats.ImportanceHadal trenches, characterized by high hydrostatic pressures and low temperatures, are one of the most extreme environments on our planet. By examining the microbiome of abyssal and hadal fishes, we provide insight into both the physiology of the deepest-living vertebrates and the microbes which colonize them. Our findings show that there are similar microbial populations in fishes geographically separated by thousands of miles, reflecting strong selection for specific microbial lineages. Only a handful of psychropiezophilic taxa, which do not reflect the diversity of microbial life at great depth, have been successfully isolated in the laboratory. Our examination of deep-sea fish microbiomes shows that typical high-pressure culturing methodologies, which have largely remained unchanged since the pioneering work of Claude ZoBell in the 1950s, may simulate the chemical environment found in animal guts and helps explain why the same deep-sea genera are consistently isolated.
IL-33 regulates age-dependency of long-term immune dysfunction induced by sepsis
Authors: Colon David F. , Wanderley Carlos W. , Turato Walter M. , Borges Vanessa F. , Franchin Marcelo , Castanheira Fernanda V. S. , Nascimento Daniele , Prado Douglas , de Lima Mikhael Haruo Fernandes , Volpon Leila C , Kavaguti Silvia K. , Ramalho Fernando , Carlotti Ana P. , Carmona Fabio , Franklin Bernardo S , Alves-Filho Jose C. , Cunha Fernando Q. 
Published: January 2022

AbstractSepsis survival in adults is commonly followed by immunosuppression and increased susceptibility to secondary infections. However, the long-term immune consequences of pediatric sepsis are unknown. Here, we compared the frequency of Tregs, the activation of the IL-33/ILC2s axis in M2 macrophages, and the DNA methylation of epithelial lung cells from post-septic infant and adult mice. In contrast to adults, infant mice were resistant to secondary infection and did not show impairment in tumour controls upon melanoma challenge. Mechanistically, increased IL-33 levels, Tregs expansion, and activation of ILC2s and M2-macrophages were observed in post-septic adults but not infant mice. Impaired IL-33 production in post-septic infant mice was associated with increased DNA-methylation on lung epithelial cells. Notably, IL-33 treatment boosted the expansion of Tregs and induced immunosuppression in infant mice. Clinically, adults but not pediatric post-septic patients exhibited higher counts of Tregs and sera IL-33 levels. Hence, we describe a crucial and age-dependent role for IL-33 in post-sepsis immunosuppression.
Culture and genomic analysis of Symbiopectobacterium purcellii, gen.nov. sp. nov., isolated from the leafhopper Empoasca decipiens
Authors: Nadal-Jimenez Pol , Siozios Stefanos , Halliday Nigel , Cámara Miguel , Hurst Gregory D.D. 
Published: January 2022

ABSTRACTBacterial endosymbionts are found in multiple arthropod species, where they play crucial roles as nutritional symbionts, defensive symbionts or reproductive parasites. Recent work has highlighted a new clade of heritable microbes within the gammaproteobacteria that enter into both obligate and facultative symbioses, with an obligately required unculturable symbiont recently given the name Cand. Symbiopectobacterium. In this study, we describe a culturable rod shaped non-flagellated bacterial symbiont from this clade isolated from the leafhopper Empoasca decipiens. The symbiont is related to the transovarially-transmitted ‘BEV’ bacterium that was first isolated from the leafhopper Euscelidius variegatus by Alexander Purcell, and we therefore name the symbiont Symbiopectobacterium purcellii sp. nov. gen. nov. We further report the closed genome sequence for S. purcellii. The genome is atypical for a heritable microbe, being large in size, without profound AT bias and with little evidence of pseudogenization. The genome is predicted to encode Type II, III and VI secretion systems and associated effectors and a non-ribosomal peptide synthase array likely to produce bioactive small molecules. Predicted metabolism is more complete than for other symbionts in the Symbiopectobacterium clade, and the microbe is predicted to synthesize a range of B vitamins. However, Biolog plate analysis indicate metabolism is depauperate compared to the sister clade, represented by Pectobacterium carotovorum. A quorum-sensing pathway related to that of Pectobacterium spp. (containing an overlapping expI-expR1 pair in opposite directions and a “solo” expR2) is evidenced, and LC-MS/MS analysis reveals the presence of 3-hydroxy-C10-HSL as the sole N-acylhomoserine lactone (AHL) in our strain. This AHL profile is profoundly divergent from that of other Erwinia and Pectobacterium spp., which produce mostly 3-oxo-C6- and 3-oxo-C8-HSL and could aid group identification. Thus, this microbe denotes one that has lost certain pathways associated with a saprophytic lifestyle but represents an important baseline against which to compare other members of the genus Symbiopectobacterium that show more profound integration into host biology.
MeShClust v3.0: High-quality clustering of DNA sequences using the mean shift algorithm and alignment-free identity scores
Authors: Girgis Hani Z. 
Published: January 2022

AbstractBackgroundTools for accurately clustering biological sequences are among the most important tools in computational biology. Two pioneering tools for clustering sequences are CD-HIT and UCLUST, both of which are fast and consume reasonable amounts of memory; however, there is a big room for improvement in terms of cluster quality. Motivated by this opportunity for improving cluster quality, we applied the mean shift algorithm in MeShClust v1.0. The mean shift algorithm is an instance of unsupervised learning. Its strong theoretical foundation guarantees the convergence to the true cluster centers. Our implementation of the mean shift algorithm in MeShClust v1.0 was a step forward; however, it was not the original algorithm. In this work, we make progress toward applying the original algorithm while utilizing alignment-free identity scores in a new tool: MeShClust v3.0.ResultsWe evaluated CD-HIT, MeShClust v1.0, MeShClust v3.0, and UCLUST on 22 synthetic sets and five real sets. These data sets were designed or selected for testing the tools in terms of scalability and different similarity levels among sequences comprising clusters. On the synthetic data sets, MeShClust v3.0 outperformed the related tools on all sets in terms of cluster quality. On two real data sets obtained from human microbiome and maize transposons, MeShClust v3.0 outperformed the related tools by wide margins, achieving 55%—300% improvement in cluster quality. On another set that includes degenerate viral sequences, MeShClust v3.0 came third. On two bacterial sets, MeShClust v3.0 was the only applicable tool because of the long sequences in these sets. MeShClust v3.0 requires more time and memory than the related tools; almost all personal computers at the time of this writing can accommodate such requirements. MeShClust v3.0 can estimate an important parameter that controls cluster membership with high accuracy.ConclusionsThese results demonstrate the high quality of clusters produced by MeShClust v3.0 and its ability to apply the mean shift algorithm to large data sets and long sequences. Because clustering tools are utilized in many studies, providing high-quality clusters will help with deriving accurate biological knowledge.
Forecasting the next revolution: food technology’s impact on consumers' acceptance and satisfaction
Authors: Recuero-Virto Nuria , Valilla-Arróspide Cristina 
Published: January 2022

PurposeIn a sector that needs to satisfy a fast-increasing population, advancements like cultivated meat and bio-circular economy are basic to sustain the industry and the society. As innovations are key for economic and social progress, it is crucial to understand consumers' position on this matter.Design/methodology/approachBased on text data mining, 7,030 tweets were collected and organised into 14 different food-related topics. Of the total, 6 of these categories were positive, 5 were negative and 3 were neutral.FindingsIn total, 6 categories related to food technologies were positively perceived by Twitter users, such as innovative solutions and sustainable agriculture, while 5 like the virtual dimensions of the industry or crisis-related scenarios were negatively perceived. It is remarkable that 3 categories had a neutral sentiment, which gives ground to improvement before consumers have a negative opinion and consequently will be more complicated to change their minds.Originality/valueTechnological innovations are becoming predominant in the food industry. The SARS-CoV-2 pandemic has made the sector improve even faster. Traditional methods needed to be substituted and technologies such as robots, artificial intelligence, blockchain and genetics are here to stay.
Exploring the university research scholars’ information literacy competency: a focus on the knowledge and skills
Authors: Senthur Selvi Kalai , Ganesan Perumal 
Published: January 2022

PurposeThis study aims to determine the level of knowledge in searching, evaluating, information management competency and to find differences among research scholars’ in terms of their information literacy (IL) competency with regards to gender and academic designation.Design/methodology/approachA survey method was conducted to collect the data from the research scholars’ pursuing their doctoral degrees in Manonmaniam Sundaranar University, Tamil Nadu, India.FindingsThe results of this study revealed that the majority have used simple search and were not using the Online Public Access Catalogue. They were not able to assess the information retrieved and the assistance from the library staff to locate the resources was found to be minimal. This study also highlighted some of the problems faced by the research scholars and provided some suggestions based on the findings. This study highlights the need to adopt a new IL framework and conduct user literacy training programmes for effective use of the resources.Practical implicationsThis study also has practical implications in terms of assessing the IL competency among the research scholars and significant variations which identified through demographics and assessment of IL competency will enable policymakers to develop a framework for brand new literacy instructions. The results may help to frame long-term strategies to motivate and train the research scholars in the effective use of technologies for improving their academic performance.Originality/valueThis study used a questionnaire as tool to collect the data. The outcome of the results will help the librarians and authorities to discuss research scholars’ IL competency and take appropriate decisions to improve their IL skills.
Assessment of early warning signs in hospital projects' front-end phase
Authors: Larsen Anne Strand Alfredsen , Karlsen Anniken Th , Lund Jo-Åsmund , Andersen Bjørn Sørskot 
Published: January 2022

PurposeThe front-end phase plays an important role in achieving project success, and establishment of performance measurement systems considering project challenges or pitfalls is a way of keeping track of this phase. Early warning signs, a type of proactive performance indicators, may serve as means for improving decision-making and project processes aiming for short- and long-term project success. In this paper, the authors present findings from a study on early warning signs (EWS) in hospital projects' front-end. A preliminary systematisation of identified signs as a contribution to front-end improvement is provided.Design/methodology/approachThe paper is based on a mixed methods approach, using a sequential, exploratory research design comprising document studies, interviews and a survey.FindingsThe authors identified 62 challenges for hospital projects' front-end performance and further established four categories of EWS as follows: (1) structure and tools, (2) context and frame factors, (3) management and (4) relational factors and properties. This mirrors the presence of hard and soft issues from previous studies. There is need for clarifying terminology and raising consciousness on EWS. Processual approaches to identify EWS are considered more useful than subsequent established indicators.Originality/valueThe findings from this paper provide insight into EWS in hospital projects' front-end phase. This adds to the general understanding of EWS and contributes to more knowledge on the front-end phase in general.