bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of salinity on the simultaneous anammox and denitrification process: performance, sludge morphology and shifts in microbial communities
Authors: Wang Zhaozhao , Gao Peng , Ji Ying , Zhang Huan , Wu Xinjuan , Ma Jun , Li Simin
Published: May 2021

In this study, the long-term effects of different salinities on the performance, sludge morphology and shifts in microbial communities were studied in a simultaneous anammox and denitrification (SAD) process at a C/N ratio of 0.5. Stable nitrogen removal efficiencies of 86.96 and 84.58% and nitrogen removal rates of 0.95 and 0.93 kg (m
3
d)
−1
could be achieved under low (25 mmol l
−1
) and moderate (50 mmol l
−1
) salinity, respectively. However, the performance collapsed when the system was exposed to high salinity (100 mmol l
−1
). The content of extracellular polymeric substances increased as salinity increased, which resulted in larger sizes of granular sludge under low and moderate salinities. Nevertheless, high salinity shock disintegrated granular sludge, thereby decreasing the average granule size. The Illumina-Miseq sequencing results revealed that
Candidatus Jettenia
was the sole salinity-tolerant AnAOB genus during the entire operation, whereas the main denitrification bacterial genera shifted from
Denitrisoma
under low salinity to
Denitrisoma
,
Thauera
and
Ignavibacterium
under high salinity. The results of this study provide a comprehensive and practical evaluation of the SAD process for organic nitrogen-rich saline wastewater treatment.
Reinfection by the SARS-CoV-2 Gamma variant in blood donors in Manaus, Brazil
Authors: Prete Carlos A. , Buss Lewis F. , Buccheri Renata , Abrahim Claudia M. M. , Salomon Tassila , Crispim Myuki A. E. , Oikawa Marcio K. , Grebe Eduard , da Costa Allyson G. , Fraiji Nelson A. , Carvalho Maria do P. S. S. , Whittaker Charles , Alexander Neal , Faria Nuno R. , Dye Christopher , Nascimento Vítor H. , Busch Michael P. , Sabino Ester C.
Published: May 2021

Background

The city of Manaus, north Brazil, was stricken by a second epidemic wave of SARS-CoV-2 despite high seroprevalence estimates, coinciding with the emergence of the Gamma (P.1) variant. Reinfections were postulated as a partial explanation for the second surge. However, accurate calculation of reinfection rates is difficult when stringent criteria as two time-separated RT-PCR tests and/or genome sequencing are required. To estimate the proportion of reinfections caused by the Gamma variant during the second wave in Manaus and the protection conferred by previous infection, we analyzed a cohort of repeat blood donors to identify anti-SARS-CoV-2 antibody boosting as a means to infer reinfection.

Methods

We tested serial blood samples from unvaccinated repeat blood donors in Manaus for the presence of anti-SARS-CoV-2 IgG antibody. Donors were required to have three or more donations and at least one donation during each epidemic wave. Donors were tested with two assays that display waning in early convalescence, enabling the detection of reinfection-induced boosting. The serial samples were used to divide donors into six groups defined based on the inferred sequence of infection and reinfection with non-Gamma and Gamma variants.

Results

From 3,655 repeat blood donors, 238 met all inclusion criteria, and 223 had enough residual sample volume to perform both serological assays. Using a strict serological definition of reinfection, we found 13.6% (95% CI 7.0% - 24.5%) of all presumed Gamma infections that were observed in 2021 were reinfections. If we also include cases of probable or possible reinfections, these percentages increase respectively to 22.7% (95% CI 14.3% - 34.2%) and 39.3% (95% CI 29.5% - 50.0%). Previous infection conferred a protection against reinfection of 85.3% (95% CI 71.3% - 92.7%), decreasing to respectively 72.5% (95% CI 54.7% - 83.6%) and 39.5% (95% CI 14.1% - 57.8%) if probable and possible reinfections are included.

Conclusions

Reinfection due to Gamma is common and may play a significant role in epidemics where Gamma is prevalent, highlighting the continued threat variants of concern pose even to settings previously hit by substantial epidemics.
Temporal changes in the risk of superspreading events of coronavirus disease 2019
Authors: Lim Jun-Sik , Noh Eunbi , Shim Eunha , Ryu Sukhyun
Published: May 2021

In order to identify the temporal change in the possible risk of superspreading events (SSE), we estimated the overdispersion parameter in two different periods of COVID-19 pandemic. We identified the possible risk of SSE was reduced 34% during the second epidemic period in South Korea.
Identifying risk factors for COVID-19 severity and mortality in the UK Biobank
Authors: Madakkatel Iqbal , King Catherine , Zhou Ang , Mulugeta Anwar , Lumsden Amanda , McDonnell Mark , Hyppönen Elina
Published: May 2021

Severe acute respiratory syndrome coronavirus has infected over 114 million people worldwide as of March 2021, with worldwide mortality rates ranging between 1-10%. We use information on up to 421,111 UK Biobank participants to identify possible predictors for long-term susceptibility to severe COVID-19 infection (N=1,088) and mortality (N=376). We include 36,168 predictors in our analyses and use a gradient boosting decision tree (GBDT) algorithm and feature attribution based on Shapley values, together with traditional epidemiological approaches to identify possible risk factors. Our analyses show associations between socio-demographic factors (e.g. age, sex, ethnicity, education, material deprivation, accommodation type) and lifestyle indicators (e.g. smoking, physical activity, walking pace, tea intake, and dietary changes) with risk of developing severe COVID-19 symptoms. Blood (cystatin C, C-reactive protein, gamma glutamyl transferase and alkaline phosphatase) and urine (microalbuminuria) biomarkers measured more than 10 years earlier predicted severe COVID-19. We also confirm increased risks for several pre-existing disease outcomes (e.g. lung diseases, type 2 diabetes, hypertension, circulatory diseases, anemia, and mental disorders). Analyses on mortality were possible within a sub-group testing positive for COVID-19 infection (N=1,953) with our analyses confirming association between age, smoking status, and prior primary diagnosis of urinary tract infection.

Our hypothesis-free approach combining machine learning with traditional epidemiological methods finds a number of risk factors (sociodemographic, lifestyle, and psychosocial factors, biomarkers, disease outcomes and treatments) associated with developing severe COVID-19 symptoms and COVID-19 mortality.
The global rarity of intact coastal regions
Authors: Williams Brooke A , Watson James E M , Beyer Hawthorne L , Klein Carissa J , Montgomery Jamie , Runting Rebecca K , Roberson Leslie A , Halpern Benjamin S , Grantham Hedley S , Kuempel Caitlin D. , Frazier Melanie , Venter Oscar , Wenger Amelia
Published: May 2021

Management of the land-sea interface is considered essential for global conservation and sustainability objectives, as coastal regions maintain natural processes that support biodiversity and the livelihood of billions of people. However, assessments of coastal regions have focused on either strictly the terrestrial or marine realm, and as a consequence, we still have a poor understanding of the overall state of Earth’s coastal regions. Here, by integrating the terrestrial human footprint and marine cumulative human impact maps, we provide a global assessment of the anthropogenic pressures affecting coastal areas. Just 15.5% of coastal areas globally can be considered having low anthropogenic pressure, mostly found in Canada, Russia, and Greenland. Conversely, 47.9% of coastal regions are heavily impacted by humanity with most countries (84.1%) having >50% of their coastal regions degraded. Nearly half (43.3%) of protected areas across coastal regions are exposed to high human pressures. In order to meet global sustainability objectives, we identify those nations that must undertake greater actions to preserve and restore coastal regions so as to ensure global sustainable development objectives can be met.
Autophagy gene-dependent intracellular immunity triggered by interferon-γ
Authors: McAllaster Michael R. , Bhushan Jaya , Balce Dale R. , Orvedahl Anthony , Park Arnold , Hwang Seungmin , Sullender Meagan E. , Sibley L. David , Virgin Herbert W.
Published: May 2021

Genes required for the lysosomal degradation pathway of autophagy play key roles in topologically distinct cellular processes with significant physiologic importance. One of the first-described of theseATGgene-dependent processes is the requirement for a subset ofATGgenes in interferon-γ (IFNγ)-induced inhibition of norovirus andToxoplasma gondiireplication. Herein we identified new genes that are required for or that negatively regulate this immune mechanism. Enzymes involved in the conjugation of UFM1 to target proteins including UFC1 and UBA5, negatively regulated IFNγ-induced inhibition of norovirus replication via effects ofErn1. IFNγ-induced inhibition of norovirus replication requiredWipi2bandAtg9a, but notBecn1(encoding Beclin1),Atg14, orSqstm1. The phosphatidylinositol-3-phosphate and ATG16L1 binding domains of WIPI2B were required for IFNγ-induced inhibition of norovirus replication. BothWIPI2andSQSTM1were required for IFNγ-induced inhibition ofToxoplasma gondiireplication in HeLa cells. These studies further delineate the mechanisms of a programmable form of cytokine-induced intracellular immunity that relies on an expanding cassette of essentialATGgenes to restrict the growth of phylogenetically diverse pathogens.

Importance

Interferon-γ is a critical mediator of cell-intrinsic immunity to intracellular pathogens. Understanding the complex cellular mechanisms supporting robust interferon-γ-induced host defenses could aid in developing new therapeutics to treat infections. Here, we examined the impact of autophagy in the interferon-γ induced host response. We demonstrate that CRISPR-Cas9 screens specifically targeting the autophagy pathway uncover a role for WIPI2 in IFNγ-induced inhibition ofNorovirusreplication in mouse cells and IFNγ mediated restriction of theToxoplasma gondiiparasitophorous vacuole in human cells. Furthermore, we found perturbation of UFMylation pathway components led to more robust IFNγ-induced inhibition ofNorovirusdue to ER stressin vitro. Enhancing or inhibiting these dynamic cellular components could serve as a strategy to weaken intracellular pathogens and maintain an effective immune response.
Deep neural networks allow expert-level brain meningioma detection, segmentation and improvement of current clinical practice
Authors: Boaro Alessandro , Kaczmarzyk Jakub R. , Kavouridis Vasileios K. , Harary Maya , Mammi Marco , Dawood Hassan , Shea Alice , Cho Elise Y. , Juvekar Parikshit , Noh Thomas , Rana Aakanksha , Ghosh Satrajit , Arnaout Omar
Published: May 2021

Accurate brain meningioma detection, segmentation and volumetric assessment are critical for serial patient follow-up, surgical planning and monitoring response to treatment. Current gold standard of manual labeling is a time-consuming process, subject to inter-user variability. Fully-automated algorithms for meningioma detection and segmentation have the potential to bring volumetric analysis into clinical and research workflows by increasing accuracy and efficiency, reducing inter-user variability and saving time. Previous research has focused solely on segmentation tasks without assessment of impact and usability of deep learning solutions in clinical practice. Herein, we demonstrate a three-dimensional convolutional neural network (3D-CNN) that performs expert-level, automated meningioma segmentation and volume estimation on MRI scans. A 3D-CNN was initially trained by segmenting entire brain volumes using a dataset of 10,099 healthy brain MRIs. Using transfer learning, the network was then specifically trained on meningioma segmentation using 806 expert-labeled MRIs. The final model achieved a median performance of 88.2% reaching the spectrum of current inter-expert variability (82.6% - 91.6%) and compared to current workflows, reduced processing time by 99%. We demonstrate in a simulated clinical setting that a deep learning approach to meningioma segmentation is feasible, highly accurate and has the potential to improve current clinical practice.
Characteristics of SARS-CoV-2 Positive Individuals in California From Two Periods During Notable Decline in Incident Infection
Authors: Allan-Blitz Lao-Tzu , Turner Isaac , Hertlein Fred , Klausner Jeffrey D.
Published: May 2021

Despite declining SARS-CoV-2 incidence, continued epidemic monitoring is warranted. We collected SARS-CoV-2 test results from 150 drive-through testing centers across California from two observation periods: February 23rd-March 3rd 2021 and April 15th-April 30th 2021. We assessed SARS-CoV-2 positivity, stratified by Hispanic heritage among sociodemographic characteristics and potential exposures. We analyzed 114,789 test results (5.1% and 2.6% positive during the respective observation periods). Nearly half of all positive tests were among testers reporting a recent exposure (48.8% and 45.3% during the respective observation periods). Those findings may provide insight into evolving local transmission dynamics and support targeted public health strategies.
COVID-19: A comparative study of severity of patients hospitalized during the first and the second wave in South Africa
Authors: Maslo Caroline , Messina Angeliki , Laubscher Anchen , Toubkin Mande , Sitharam Liza , Feldman Charles , Richards Guy A
Published: May 2021

Background

South Africa has experienced two waves of COVID-19 infections, the second of which was inter alia attributed to the emergence of a novel SARS-CoV2 variant, 501Y.V2. This variant possibly has increased virulence and may be associated with increased mortality. The objective of this study was to determine if patients admitted in the second wave had more severe illness and higher mortality than those admitted in the first.

Methods

We analysed and compared the characteristics, biological severity markers, treatments, level of care and outcomes of patients hospitalised in a private hospital in the Eastern Cape Province, South Africa.

Results

Compared to the first wave, patients admitted in the second were older and less likely to have co-morbidities. In contrast, the D-dimer and interleukin-6 (IL-6) levels were significantly higher. Despite this, significantly less patients were admitted to ICU and/or were mechanically ventilated. The total length of hospital stay was identical in both groups. Whereas the overall mortality was not significantly higher during the second wave, the ICU mortality was. Those that died in the second wave were older than those in the first wave. Multivariable logistic regression showed that being admitted during the second wave was an independent risk factor for mortality.

Conclusion

This study appears to confirm previous reports that the 501Y.V2 variant is possibly more virulent as indicated by the higher levels of D-dimer and IL-6, the slight increase in mortality of hospitalised patients and the higher ICU mortality in the second wave.
Restoring persistent accessibility to memories after sleep deprivation-induced amnesia
Authors: Bolsius Youri G. , Heckman Pim R.A. , Raven Frank , Meijer Elroy L. , Kas Martien J.H. , Ramirez Steve , Meerlo Peter , Havekes Robbert
Published: May 2021

It is well established that sleep deprivation after learning impairs hippocampal memory processes and causes amnesia. It is unknown, however, whether it leads to the actual loss of information or merely suppresses the retrievability of this information stored under suboptimal conditions. Here, we reveal that hippocampal memories formed under sleep deprivation conditions can be successfully retrieved multiple days following training using optogenetic memory engram activation or treatment with the clinically-approved phosphodiesterase 4 (PDE4) inhibitor roflumilast. Moreover, when optogenetic memory engram activation and roflumilast treatment were combined two days following training and subsequent sleep deprivation, it resulted in a more persistent memory trace that allowed for natural (i.e., manipulation free) retrieval several days later. Our studies in mice demonstrate that sleep deprivation does not necessarily cause memory loss, but instead leads to the suboptimal storage of information that is difficult to retrieve. We also provide proof of principle that these suboptimally stored memories can be made accessible again far beyond the learning episode and that the clinically-approved PDE4 inhibitor roflumilast may be used to successfully retrieve information thought to be lost.
Intracellular Vesicle Entrapment of Nanobubble Ultrasound Contrast Agents Targeted to PSMA Promotes Prolonged Enhancement and StabilityIn VivoandIn Vitro
Authors: Perera Reshani H. , Abenojar Eric , Nittayacharn Pinunta , Wang Xinning , Ramamurthy Gopal , Peiris Pubudu , Bederman Ilya , Basilion James P. , Exner Agata A.
Published: May 2021

Previous work has shown that active targeting of nanobubble (NB) ultrasound contrast agents to the prostate-specific membrane antigen (PSMA) significantly prolongs ultrasound signal enhancement in PSMA-expressing prostate cancer. However, the specific mechanism behind this effect is not well understood. Furthermore, prior studies were carried out using clinical ultrasound scanners in a single imaging plane. Because tumor heterogeneity can have a drastic effect on bubble kinetics and resulting contrast enhancement, a single region of interest in one imaging plane over time may not fully represent the contrast dynamics of the entire tumor. Accordingly, in the current work, we used high-frequency dynamic parametric contrast-enhanced ultrasound (DCE-US) imaging to gain a detailed understanding of NB kinetics in prostate tumors in mice. Specifically, we examined the differences in enhancement between the tumor periphery and tumor core in the same imaging plane. We also quantified intact nanobubble retention in the entire tumor volume. To better understand the mechanism behind prolonged tumor enhancement, intracellular retention and the acoustic activity of PSMA-NB were evaluated in cell culture. DCE-US US data suggest that both tumor wash-in and retention of PSMA-NB are delayed due to biomarker interaction and binding. The longer retention of PSMA-NB signal in tumor core supported target-driven bubble extravasation.In vitrostudies demonstrated a higher level of internalization and prolonged-acoustic activity of internalized PSMA-NB. GC/MS analysis confirmed gas persistence in the cells after PSMA-NB internalization. The active-targeting of NB results in cellular internalization via receptor-mediated endocytosis, and the location with intracellular vesicles (late-stage endosomes/lysosomes) significantly prolongs gas retention within the cells. These features can enable background-free diagnostic imaging of the target cells/tissues, as well as highly focused ultrasound-modulated therapeutic interventions.
Polymorphisms and gene expression in the almond IGT family are not correlated to variability in growth habit in major commercial almond cultivars
Authors: Montesinos Álvaro , Dardick Chris , Rubio-Cabetas María José , Grimplet Jérôme
Published: May 2021

Almond breeding programs aimed at selecting cultivars adapted to intensive orchards have recently focused on the optimization of tree architecture. This multifactorial trait is defined by numerous components controlled by processes such as hormonal responses, gravitropism and light perception. Gravitropism sensing is crucial to control the branch angle and therefore, the tree habit. A gene family, denominated IGT family after a share conserved domain, has been described as involved in the regulation of branch angle in several species, including rice and Arabidopsis, and even in fruit trees like peach. Here we identified six members of this family in almond: LAZY1, LAZY2, TAC1, DRO1, DRO2, IGT-like. After analyzing their protein sequences in forty-one almond cultivars and wild species, little variability was found, pointing a high degree of conservation in this family. Gene expression was analyzed in fourteen cultivars of agronomical interest comprising diverse tree habit phenotypes. Only LAZY1, LAZY2 and TAC1 were expressed in almond shoot tips during the growing season. No relation was established between the expression profile of these genes and the tree habit. However, some insight has been gained in how LAZY1 and LAZY2 are regulated, identifying the IPA1 almond homologues and other transcription factors involved in hormonal responses as regulators of their expression. Besides, we have found various polymorphisms that could not be discarded as involved in a potential polygenic origin of regulation of architectural phenotypes. Therefore, we have established that unlike many species, IGT family genes do not play a critical role in the control of tree habit in currently commercialized almond cultivars, with other gene families contributing to the variability of these traits.
ontoFAST: An R package for interactive and semi-automatic annotation of characters with biological ontologies
Authors: Tarasov Sergei , MIko Istvan , Yoder Matthew Jon
Published: May 2021

The commonly used Entity-Quality (EQ) syntax provides rich semantics and high granularity for annotating phenotypes and characters using ontologies. However, EQ syntax might be time inefficient if this granularity is unnecessary for downstream analysis. We present an R package ontoFAST that aid production of fast annotations of characters and character matrices with biological ontologies. Its interactive interface allows quick and convenient tagging of character statements with necessary ontology terms. The annotations produced in ontoFAST can be exported in csv format for downstream analysis. Additinally, OntoFAST provides: (i) functions for constructing simple queries of characters against ontologies, and (ii) helper function for exporting and visualising complex ontological hierarchies and their relationships. OntoFAST enhances data interoperability between various applications and support further integration of ontological and phylogenetic methods. Ontology tools are underrepresented in R environment and we hope that ontoFAST will stimulate their further development.
Convergent loss of chemoreceptors across independent origins of slave-making in ants
Authors: Jongepier Evelien , Séguret Alice , Labutin Anton , Feldmeyer Barbara , Gstöttl Claudia , Foitzik Susanne , Heinze Jürgen , Bornberg-Bauer Erich
Published: May 2021

The evolution of an obligate parasitic lifestyle often leads to the reduction of morphological and physiological traits, which may be accompanied by loss of genes and functions. Slave-maker ants are social parasites that exploit the work force of closely related ant species for social behaviours such as brood care and foraging. Recent divergence between these social parasites and their hosts enables comparative studies of gene family evolution. We sequenced the genomes of eight ant species, representing three independent origins of ant slavery. During the evolution of eusociality, chemoreceptor genes multiplied due to the importance of chemical communication in societies. We investigated evolutionary patterns of chemoreceptors in relation to slave-making in ants. We found that slave-maker ant genomes harboured only half as many gustatory receptors as their hosts, potentially mirroring the outsourcing of foraging tasks to host workers. In addition, parasites had fewer odorant receptors and their loss shows patterns of convergence across origins of parasitism, representing a rare case of convergent molecular evolution. This convergent loss of specific odorant receptors suggests that selective deprivation of receptors is adaptive. The 9-exon odorant receptor subfamily, previously linked to social evolution in insects, was significantly enriched for convergent loss across the three origins of slavery in our study, indicating that the transition to social parasitism in ants is accompanied by the loss of receptors that are likely important for mediating eusocial behaviour. Overall, gene loss in slave-maker ants suggests that a switch to a parasitic lifestyle accompanies relaxed selection on chemical perception.
The Drosophila orthologue of the primary ciliary dyskinesia-associated gene, DNAAF3, is required for axonemal dynein assembly
Authors: zur Lage Petra , Xi Zhiyan , Lennon Jennifer , Hunter Iain , Chan Wai Kit , Carrancio Alfonso Bolado , von Kriegsheim Alex , Jarman Andrew P.
Published: May 2021

Ciliary motility is powered by a suite of highly conserved axoneme-specific dynein motor complexes. In humans the impairment of these motors through mutation results in the disease, Primary Ciliary Dyskinesia (PCD). Studies in Drosophila have helped to validate several PCD genes whose products are required for cytoplasmic pre-assembly of axonemal dynein motors. Here we report the characterisation of the Drosophila homologue of the less known assembly factor, DNAAF3. This gene, CG17669 (Dnaaf3), is expressed exclusively in developing mechanosensory chordotonal (Ch) neurons and spermatocytes, the only two Drosophila cell types bearing motile cilia/flagella. Mutation of Dnaaf3 results in larvae that are deaf and adults that are uncoordinated, indicating defective Ch neuron function. The mutant Ch neuron cilia of the antenna specifically lack dynein arms, while Ca imaging in larvae reveals a complete loss of Ch neuron response to vibration stimulus, confirming that mechanotransduction relies on ciliary dynein motors. Mutant males are infertile with immotile sperm whose flagella lack dynein arms and show axoneme disruption. Analysis of proteomic changes suggest a reduction in heavy chains of all axonemal dynein forms, consistent with an impairment of dynein pre-assembly.

SUMMARY STATEMENT

DNAAF3 function as a dynein assembly factor for motile cilia is conserved in Drosophila.
Pseudohypoxic HIF pathway activation dysregulates collagen structure-function in human lung fibrosis
Authors: Brereton Christopher , Yao Liudi , Zhou Yilu , Vukmirovic Milica , Bell Joseph , Ridley Robert A. , Davies Elizabeth R. , Dean Lareb S.N. , Andriotis Orestis G. , Conforti Franco , Mohammed Soran , Wallis Tim , Tavassoli Ali , Ewing R. , Alzetani Aiman , Marshall Ben G. , Fletcher Sophie V. , Thurner Phillipp J. , Fabre Aurelie , Kaminski Naftali , Richeldi Luca , Bhaskar Atul , Loxham Matthew , Davies Donna E. , Wang Yihua , Jones Mark G.
Published: May 2021

Extracellular matrix (ECM) stiffening with downstream activation of mechanosensitive pathways is strongly implicated in fibrosis. We previously reported that altered collagen nanoarchitecture is a key determinant of pathogenetic ECM structure-function in human fibrosis (Jones et al., 2018). Here, through human tissue, bioinformatic and ex vivo studies we show that hypoxia-inducible factor (HIF) pathway activation is a critical pathway for this process regardless of oxygen status (pseudohypoxia). Whilst TGFβ increased rate of fibrillar collagen synthesis, HIF pathway activation was required to dysregulate post-translational modification of fibrillar collagen, promoting ‘bone-type’ cross-linking, altering collagen nanostructure, and increasing tissue stiffness. In vitro, knock down of Factor Inhibiting HIF (FIH) or oxidative stress caused pseudohypoxic HIF activation in normal fibroblasts. In contrast, endogenous FIH activity was reduced in fibroblasts from patients with lung fibrosis in association with significantly increased normoxic HIF pathway activation. In human lung fibrosis tissue, HIF mediated signalling was increased at sites of active fibrogenesis whilst subpopulations of IPF lung mesenchymal cells had increases in both HIF and oxidative stress scores. Our data demonstrate that oxidative stress can drive pseudohypoxic HIF pathway activation which is a critical regulator of pathogenetic collagen structure-function in fibrosis.
ZFP36L1 regulates Fgf21 mRNA turnover and modulates alcoholic hepatic steatosis and inflammation in mice
Authors: Bathula Chandra S. , Chen Jian , Blackshear Perry J. , Saini Yogesh , Patial Sonika
Published: May 2021

Zinc finger protein 36 like 1 (ZFP36L1) enhances the turnover of mRNAs containing AU-rich elements (AREs) in their 3’untranslated regions (3’UTR). The physiological and pathological functions of ZFP36L1 in liver, however, remain largely unknown. To investigate the role of ZFP36L1 in liver physiology and pathology, we generated liver-specific ZFP36L1-deficient (Zfp36l1flox/flox /Cre+; L1LKO) mice. Under normal conditions, the L1LKO mice and their littermate controls (Zfp36l1flox/flox/Cre-; L1FLX) appeared normal. When fed a Lieber-DeCarli liquid diet containing alcohol, L1LKO mice were significantly protected from developing alcohol-induced hepatic steatosis and inflammation compared to L1FLX mice. Serum ALT levels were significantly increased in alcohol-fed L1FLX versus alcohol-fed L1LKO mice. RNA-Seq analysis revealed 584 differentially-expressed transcripts in L1FLX alcohol-fed mice, many of which were inflammatory mediators, compared to only 159 in alcohol-fed L1LKO mice. Most importantly, fibroblast growth factor 21 (Fgf21) mRNA was significantly increased in the livers of alcohol-fed L1LKO mice but not in the alcohol-fed control group. The Fgf21 mRNA contains three AREs in its 3’UTR, and Fgf21 3’UTR was directly regulated by ZFP36L1 in luciferase reporter assays. Steady state levels of Fgf21 mRNA were significantly decreased by wildtype ZFP36L1, but not by a non-binding zinc-finger ZFP36L1 mutant. Finally, wildtype ZFP36L1, but not the ZFP36L1 mutant, bound to Fgf21 3’UTR ARE RNA probe. Our results demonstrate that ZFP36L1 inactivation protects against alcohol-induced hepatic steatosis and liver injury, possibly by stabilizing Fgf21 mRNA. Our findings suggest that the modulation of ZFP36L1 may be beneficial in the prevention or treatment of human alcoholic liver disease.
Atmospheric plasma jet device for versatile electron microscope grid treatment
Authors: Ahn Eungjin , Tang Tianyu , Kim Byungchul , Lee Hae June , Cho Uhn-Soo
Published: May 2021

Atmospheric pressure plasmas have been widely applied in surface modification and biomedical treatment due to its ability to generate highly reactive radicals and charged particles. In negative-stain electron microscopy (Neg-EM) and cryogenic electron microscopy (cryo-EM), plasmas have been used in eliminating the surface contaminants as well as generating the hydrophilic surface to embed the specimen on grids. Plasma treatment is a prerequisite for negative stain and quantifoil grids, which are coated with hydrophobic carbon on the grid surface. Here we introduce a non-thermal atmospheric plasma jet system as an alternative new tool for surface treatment. Unlike the conventional glow discharger, we found that the plasma jet system successfully cleans the grid surface and introduces hydrophilicity on grids in the ambient environment without introducing a vacuum. Therefore, we anticipate the plasma jet system will be beneficial in many aspects, such as cost-effective, convenient, versatile, and potential applications in surface modification for both negative stain and cryo-EM grid treatment.
Neural correlates of semantic number: A cross-linguistic investigation
Authors: Dunagan Donald , Zhang Shulin , Li Jixing , Bhattasali Shohini , Pallier Christophe , Whitman John , Yang Yiming , Hale John
Published: May 2021

One aspect of natural language comprehension is understanding how many of what or whom a speaker is referring to. While previous work has documented the neural correlates of general number comprehension and quantity comparison, we investigate semantic number from a cross-linguistic perspective with the goal of identifying cortical regions involved in distinguishing plural from singular nouns. We use three fMRI datasets in which Chinese, French, and English native speakers listen to an audiobook of a children’s story in their native language. We select these three languages because they differ in their number semantics. While Chinese lacks nominal pluralization, French and English nouns are overtly marked for number. We find a number of known semantic processing regions in common, including dorsomedial prefrontal cortex and the pars orbitalis, in which cortical activation is greater for plural than singular nouns and posit a cross-linguistic role for number in semantic comprehension.
Genetic analysis argues for a coactivator function for theSaccharomyces cerevisiaeTup1 corepressor
Authors: Parnell Emily J. , Parnell Timothy J. , Stillman David J.
Published: May 2021

The Tup1-Cyc8 corepressor complex ofSaccharomyces cerevisiaeis recruited to promoters by DNA-binding proteins to repress transcription of genes, including thea-specific mating type genes. We report here atup1(S649F)mutant that displays mating irregularities similar to atup1null and an α-predominant growth defect. RNA-Seq and ChIP-Seq were used to analyze gene expression and Tup1 occupancy changes in mutant vs. wild-type in bothaand α cells. Increased Tup1(S649F) occupancy tended to occur upstream of upregulated genes, whereas locations with decreased occupancy usually did not show changes in gene expression, suggesting this mutant not only loses corepressor function but also behaves as a coactivator. Based upon studies demonstrating a dual role of Tup1 in both repression and activation, we postulate that the coactivator function of Tup1(S649F) results from diminished interaction with repressor proteins, including α2. We also found that large changes in mating type-specific gene expression betweenaand α or between mutant and wild-type were not easily explained by the range of Tup1 occupancy levels within their promoters, as predicted by the classic model ofa-specific gene repression by Tup1. Most surprisingly, we observed Tup1 occupancy upstream of thea-specific geneMFA2and the α-specific geneMF(ALPHA)1in cells in which each gene was expressed rather than repressed. These results, combined with identification of additional mating related genes upregulated in thetup1(S649F)α strain, illustrate that the role of Tup1 in distinguishing mating types in yeast appears to be both more comprehensive and more nuanced than previously appreciated.
Multiscale light-sheet organoid imaging framework
Authors: de Medeiros Gustavo , Ortiz Raphael , Strnad Petr , Boni Andrea , Moos Franziska , Repina Nicole , Chalet Meylan Ludivine , Maurer Francisca , Liberali Prisca
Published: May 2021

Organoids provide an accessible in-vitro system to mimic the dynamics of tissue regeneration and development. However, long-term live-imaging of organoids remains challenging. Here we present an experimental and image-processing framework capable of turning long-term light-sheet imaging of intestinal organoids into digital organoids. The framework combines specific imaging optimization combined with data processing via deep learning techniques to segment single organoids, their lumen, cells and nuclei in 3D over long periods of time. By linking lineage trees with corresponding 3D segmentation meshes for each organoid, the extracted information is visualized using a web-based “Digital Organoid Viewer” tool allowing unique understanding of the multivariate and multiscale data. We also show backtracking of cells of interest, providing detailed information about their history within entire organoid contexts. Furthermore, we show cytokinesis failure of regenerative cells and that these cells never reside in the intestinal crypt, hinting at a tissue scale control on cellular fidelity.
A ten-year literature review of content-based image retrieval (CBIR) studies in the tourism industry
Authors: Ammatmanee Chanattra , Gan Lu
Published: May 2021

Purpose

Due to the worldwide growth of digital image sharing and the maturity of the tourism industry, the vast and growing collections of digital images have become a challenge for those who use and/or manage these image data across tourism settings. To overcome the image indexing task with less labour cost and improve the image retrieval task with less human errors, the content-based image retrieval (CBIR) technique has been investigated for the tourism domain particularly. This paper aims to review the relevant literature in the field to understand these previous works and identify research gaps for future directions.

Design/methodology/approach

A systematic and comprehensive review of CBIR studies in tourism from the year 2010 to 2019, focussing on journal articles and conference proceedings in reputable online databases, is conducted by taking a comparative approach to critically analyse and address the trends of each fundamental element in these research experiments.

Findings

Based on the review of the literature, the trends of CBIR studies in tourism is to improve image representation and retrieval by advancing existing feature extraction techniques, contributing novel techniques in the feature extraction process through fine-tuning fusion features and improving image query of CBIR systems. Co-authorship, tourist attraction sector and fusion image features have been in focus. Nonetheless, the number of studies in other tourism sectors and available image databases could be further explored.

Originality/value

The fact that no existing academic review of CBIR studies in tourism makes this paper a novel contribution.
Knowledge and practice regarding menstrual hygiene management among the Rohingya refugee adolescent girls in Cox’s Bazar, Bangladesh: a mixed method study
Authors: Rakhshanda Shagoofa , Ahmed Sahlil , Saidu Samuel , Nderitu Christine , Thapa Basanta , Awal Abdul , Farnaz Nadia , Rahman Atiya , Aktar Bachera , Faruque A.S.G.
Published: May 2021

Purpose

About half of the 16% adolescents in the world experience menstruation. Menstrual hygiene management (MHM) is a health concern and challenge especially in humanitarian situations as experienced by Myanmar Rohingya refugees living in Cox’s Bazar, Bangladesh. This study aims to assess knowledge, practice and influencing factors for MHM among Rohingya refugee adolescent girls of 14–18 years.

Design/methodology/approach

The study used both quantitative (a cross-sectional survey with 340 adolescent girls through a structured questionnaire) and qualitative (7 in-depth interviews with adolescent girls and 2 focus group discussions with the mothers) approaches. Quantitative data, analyzed using STATA version 13.0, were supported by qualitative data, grouped into themes and presented as matrix.

Findings

Around 51% adolescent girls learned about menstruation after menarche, at the mean age of 12 years, from their mothers and older sisters. About 75% used sanitary pads as absorbents which they got mostly as relief material or bought from local stores (83%); the rest used cloths and other materials (25%). About 57% of the respondents disposed of their absorbent by burying. Those who used reusable absorbents washed them with soap and water (40%) and mostly dried them indoors (17%). Factors influencing healthy MHM practice included the use of absorbent, privacy, disposal, washing and drying of clothes, physical activities, hygiene and pain management. Adolescents with secondary or higher education were four times more likely to have better MHM practice (odds ratio = 4.27; confidence interval = 1.19–15.31) than those with no formal schooling.

Originality/value

This paper is based on a research undertaken as part of academic requirement.
Microstructure evolution and shear strength of full Cu3Sn- microporous copper composite joint by thermo-compression bonding
Authors: Sun F , Pan Zhen , Liu Yang , Li Xiang , Liu Haoyu , Li Wenpeng
Published: May 2021

Purpose

The purpose of this paper is to quickly manufacture full Cu3Sn-microporous copper composite joints for high-temperature power electronics applications and study the microstructure evolution and the shear strength of Cu3Sn at different bonding times.

Design/methodology/approach

In this paper, a novel structure of Cu/composite solder sheet/Cu was designed. The composite solder sheet was made of microporous copper filled with Sn. The composite joint was bonded by thermo-compression bonding under pressure of 0.6 MPa at 300°C. The microstructure evolution and the growth behavior of Cu3Sn at different bonding times were observed by electron microscope and metallographic microscope. The shear strength of the joint was measured by shear machine.

Findings

At initial bonding stage the copper atoms in the substrate and the copper atoms in the microporous copper dissolved into the liquid Sn. Then the scallop-liked Cu6Sn5 phases formed at the interface of liquid Sn/microporous copper and liquid Sn/Cu substrates. During the liquid Sn changing to Cu6Sn5 phases, Cu3Sn phases formed and grew at the interface of Cu6Sn5/Cu substrates and Cu6Sn5/microporous copper. After that the Cu3Sn phases continued to grow and the Cu3Sn-microporous copper composite joint with a thickness of 100 µm was successfully obtained. The growth rule of Cu3Sn was parabolic growth. The shear strength of the composite joints was about 155 MPa.

Originality/value

This paper presents a novel full Cu3Sn-microporous copper composite joint with high shear strength for high-temperature applications based on transient liquid phase bonding. The microstructure evolution and the growth behavior of Cu3Sn in the composite joints were studied. The shear strength and the fracture mechanism of the composite joints were studied.
The role of quality perceptions and perceived ubiquity in adoption intention of mobile knowledge management systems (MKMS) in semiconductor industry
Authors: Cheak Audrey Poh Choo , Chong Chin Wei , Yuen Yee Yen
Published: May 2021

Purpose

First, this study aims to investigate the effects of quality perceptions (i.e. system quality, information quality and service quality) and perceived ubiquity on engineers’ perceived benefits and perceived user-friendly of mobile knowledge management systems (MKMS). Second, it aims to examine the influence of perceived benefits and perceived user-friendly on MKMS adoption intention.

Design/methodology/approach

Quantitative empirical research using an integrated technology acceptance model and information systems success model was used, among semiconductors engineers in Malaysia. There were only 375 usable responses collected, which are at a response rate of 59.52%. The partial least squares version 3.0 was used to analyze the valid data collected.

Findings

The results suggest that service quality plays an important role that would increase the engineers’ perception of MKMS benefits and its user-friendliness. Intention to adopt MKMS was found to be strongly predicted by perceived MKMS benefits as compared to perceived user-friendly.

Practical implications

The findings are valuable for managers, engineers, knowledge management (KM) practitioners, MKMS developers and mobile device producers to enhance MKMS adoption intention.

Originality/value

Despite KM has been well accepted and established in the management science and practice area of study, yet it is still neglected in a “mobile” context. Accordingly, this paper contributes to the research gap.
Smc5/6 in the rDNA modulates lifespan independently of Fob1​
Authors: Moradi‐Fard Sarah , Mojumdar Aditya , Chan Megan , Harkness Troy A.A. , Cobb Jennifer A.
Published: May 2021

The ribosomal DNA (rDNA) in Saccharomyces cerevisiae is in one tandem repeat array on Chromosome XII. Two regions within each repetitive element, called intergenic spacer 1 (IGS1) and IGS2, are important for organizing the rDNA within the nucleolus. The Smc5/6 complex localizes to IGS1 and IGS2. We show that Smc5/6 has a function in the rDNA beyond its role in homologous recombination (HR) at the replication fork barrier (RFB) located in IGS1. Fob1 is required for optimal binding of Smc5/6 at IGS1 whereas the canonical silencing factor Sir2 is required for its optimal binding at IGS2, independently of Fob1. Through interdependent interactions, Smc5/6 stabilizes Sir2 and Cohibin at both IGS and its recovery at IGS2 is important for nucleolar compaction and transcriptional silencing, which in turn supports rDNA stability and lifespan.
A life‐threatening dental implant: A case report
Authors: Dalle Carbonare Marco , Yeung Elizabeth , Siddiqui Juveria , Kandasamy Naga , Fan Kathleen
Published: May 2021

Background

Intraoral bleeding complications in implant surgery are infrequent; nevertheless, serious and life‐threatening complications have been described, generally related to mandibular implants.

Purpose

This article presents the exceptional case of a 24‐year‐old woman who underwent repeated delayed life‐threatening episodes of intraoral bleeding following uncovering of a maxillary dental implant. Local measures afforded only temporary control.

Results

The episodes were successfully managed by embolising the greater descending palatine artery, and the patient remains now under close follow‐up.

Conclusions

Early recognition of shock secondary to hemorrhage following intraoral surgery is of paramount importance.
Obstetric and long‐term graft outcomes in pregnant kidney transplant recipients: A single‐center experience
Authors: Akcay Omer Faruk , Yeter Haci Hasan , Karcaaltincaba Deniz , Bayram Merih , Guz Galip , Erten Yasemin
Published: May 2021

Background

Kidney transplantation (KT) is the best option for many women with end‐stage renal disease desiring pregnancy. The aim of this study was to investigate obstetric and graft outcomes among KT recipient women in our center.

Methods

Maternal and fetal data were assessed in 29 pregnancies of 18 female KT recipients. Each patient was matched with two controls without pregnancy history for factors known to affect graft function. According to pre‐pregnancy levels, serum creatinine and eGFR slope in the gestational and postpartum periods were calculated as percentages.

Results

The main maternal and fetal complications were preeclampsia (38%) and preterm births (38%), respectively. Pregnancy (odds ratio [OR]: 5.09; p = .02), proteinuria in the third trimester (OR: 5.52; p = .02), proteinuria in postpartum third months (OR: 7.4; p = .008) and stable creatinine levels in the first 6 months of pregnancy (OR: 11.25 p = .03) were associated with graft dysfunction. Postpartum first year eGFR decline (−16.8% vs. −6.7%; p = .04) and second‐year eGFR decline (−18.5% vs. −8.3%; p = .04) were significantly higher in the pregnancy group than those matched controls.

Conclusion

Pregnancy after KT is associated with high rates of maternal and fetal complications. The sustained decline of eGFR may suggest an increased risk of graft loss compared to recipients with similar clinical characteristics.