bluuebunny/crossref_metadata_2025 huggingface dataset:
Interpreting vaccine efficacy trial results for infection and transmission
Authors: Lipsitch Marc , Kahn Rebecca
Published: February 2021

Randomized controlled trials (RCTs) have shown high efficacy of multiple vaccines against SARS-CoV-2 disease (COVID-19), and recent studies have shown the vaccines are also effective against infection. Evidence for the effect of each of these vaccines on ability to transmit the virus is also beginning to emerge. We describe an approach to estimate these vaccines’ effects on viral positivity, a prevalence measure which under the reasonable assumption that vaccinated individuals who become infected are no more infectious than unvaccinated individuals forms a lower bound on efficacy against transmission. Specifically, we recommend separate analysis of positive tests triggered by symptoms (usually the primary outcome) and cross-sectional prevalence of positive tests obtained regardless of symptoms. The odds ratio of carriage for vaccine vs. placebo provides an unbiased estimate of vaccine effectiveness against viral positivity, under certain assumptions, and we show through simulations that likely departures from these assumptions will only modestly bias this estimate. Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more. We describe how these approaches can be translated into observational studies of vaccine effectiveness.

Highlights

SARS-CoV-2 vaccine trials did not directly estimate vaccine efficacy against transmission.

We describe an approach to estimate a lower bound of vaccine efficacy against transmission.

We estimate one dose of the Moderna vaccine reduces the potential for transmission by at least 61%.

We recommend separate analysis of tests triggered by symptoms vs. cross-sectional tests.
Brazil Nut Effect Drives Pattern Formation in Early Mammalian Embryos
Authors: Guo Zheng , Yao Jie , Zheng Xu , Cao Jialing , Gao Zheng , Guo Shuyu , Qin Dandan , Tan Min , Wang Bo , Meng Fanzhe , Zhang Jing , Li Lei , Du Jing , Fan Yubo
Published: February 2021

The formation of three-dimensional ordered spatial patterns, which is essential for embryonic development, tissue regeneration, and cancer metastasis, is mainly guided by the chemical concentration gradient of morphogens. However, since no chemical concentration gradient has been observed in the early embryonic development (pre-implantation) of mammals, the pattern formation mechanism has been unsolved for a long time. During the second cell fate decision of mouse embryos, the inner cell mass (ICM) segregates into topographically regionalized epiblast (EPI) and primitive endoderm (PrE) layers. Here, we report that the segregation process of PrE/EPI precursors coincides with an emerged periodic expansion-contraction vibration of the blastocyst cavity, which induces phase transition in the ICM compartment to a higher fluidity state and generates directional tissue flows. By experiments and modeling, we demonstrate that the spatial segregation of PrE and EPI precursors is mediated by a “Brazil nut effect”-like viscous segregation mechanism in which PrE precursors with low affinity gradually migrate to the surface of ICM along with the tissue flow, while EPI precursors with high affinity remains inside ICM under cavity vibration. Artificially manipulation of the frequency and amplitude of cavity vibration could control the process of spatial separation as well as lineage specification of PrE/EPI. Furthermore, disruption of the cavity vibration in the initial stage after segregation could reverse the ICM cells back to a mixed state. Therefore, this study reveals a fundamental mechanism that guarantees the robustness of cell segregation and pattern formation without specific morphogens in early mammalian embryos. Our model also emphasizes a conserved function of cavity structure that widely exists in organisms as an energy reservoir and converter between different forms, such as chemical and mechanical energy.
A unicellular walker controlled by a microtubule-based finite state machine
Authors: Larson Ben T. , Garbus Jack , Pollack Jordan B. , Marshall Wallace F.
Published: February 2021

Cells are complex biochemical systems whose behavior emerges from interactions among myriad molecular components. Computation is often invoked as a general framework for navigating this cellular complexity. However, it is unclear how cells might embody computational processes such that theories of computation, including finite state machine models, could be productively applied. Here, we demonstrate finite state machine-like processing embodied in cells using the walking behavior ofEuplotes eurystomus, a ciliate that walks across surfaces using fourteen motile appendages (cirri). We found that cellular walking entails regulated transitions between a discrete set of gait states. The set of observed transitions decomposes into a small group of high-probability, temporally irreversible transitions and a large group of low-probability time-symmetric transitions, thus revealing stereotypy in sequential patterns of state transitions. Simulations and experiments suggest that the sequential logic of the gait is functionally important. Taken together, these findings implicate a finite state machine-like process. Cirri are connected by microtubule bundles (fibers), and we found that the dynamics of cirri involved in different state transitions are associated with the structure of the fiber system. Perturbative experiments revealed that the fibers mediate gait coordination, suggesting a mechanical basis of gait control.
Quantitative consequences of protein carriers in immunopeptidomics and tyrosine phosphorylation MS2analyses
Authors: Stopfer Lauren E. , Conage-Pough Jason E. , White Forest M.
Published: February 2021

Utilizing a protein carrier in combination with isobaric labeling to “boost” the signal of other low-level samples in multiplexed analyses has emerged as an attractive strategy to enhance data quantity while minimizing protein input in mass spectrometry analyses. Recent applications of this approach include pMHC profiling and tyrosine phosphoproteomics, two applications that are often limited by large sample requirements. While including a protein carrier has been shown to increase the number of identifiable peptides in both applications, the impact of a protein carrier on quantitative accuracy remains to be thoroughly explored, particularly in relevant biological contexts where samples exhibit dynamic changes in abundance across peptides. Here, we describe two sets of analyses comparing MS2-based quantitation using a 20x protein carrier in pMHC analyses and a high (∼100x) and low (∼9x) protein carrier in pTyr analyses, using CDK4/6 inhibitors and EGF stimulation to drive dynamic changes in the immunopeptidome and phosphoproteome, respectively. In both applications, inclusion of a protein carrier resulted in an increased number of MHC peptide or phosphopeptide identifications, as expected. At the same time, quantitative accuracy was adversely affected by the presence of the protein carrier, altering interpretation of the underlying biological response to perturbation. Moreover, for tyrosine phosphoproteomics, the presence of high levels of protein carrier led to a large number of missing values for endogenous phosphopeptides, leading to fewer quantifiable peptides relative to the “no-boost” condition. These data highlight the unique limitations and future experimental considerations for both analysis types and provide a framework for assessing quantitative accuracy in protein carrier experiments moving forward.
Hyperspectral sensing of photosynthesis, stomatal conductance, and transpiration for citrus tree under drought condition
Authors: Zhou Jing-Jing , Zhang Ya-Hao , Han Ze-Min , Liu Xiao-Yang , Jian Yong-Feng , Hu Chun-Gen , Dian Yuan-Yong
Published: February 2021

Obtaining variation in water use and photosynthetic capacity is a promising route toward yield increases, but it is still too laborious for large-scale rapid monitoring and prediction. We tested the application of hyperspectral reflectance as a high-throughput phenotyping approach for early identification of water stress and rapid assessment of leaf photosynthetic traits in citrus trees. To this end, photosynthetic CO2assimilation rate (Pn), stomatal conductance (Cond) and transpiration rate (Trmmol) were measured with gas-exchange approaches alongside measurements of leaf hyperspectral reflectance from citrus grown across a gradient of soil drought levels. Water stress causedPn, CondandTrmmolrapid and continuous decreases in whole drought period. Upper layer was more sensitive to drought than middle and lower layers. Original reflectance spectra of three drought treatments were surprisingly of low diversity and could not track drought responses, whereas specific hyperspectral spectral vegetation indices (SVIs) and absorption features or wavelength position variables presented great potential. Performance of four machine learning algorithms were assessed and random forest (RF) algorithm yielded the highest predictive power for predicting photosynthetic parameters. Our results indicated that leaf hyperspectral reflectance was a reliable and stable method for monitoring water stress and yield increasing in large-scale orchards.

Highlight

An efficient and stable methods using hyperspectral features for early and pre-visual identification of drought and machine learning techniques for predicting photosynthetic capacity.
A new murineRpl5(uL18) mutation provides a unique model of variably penetrant Diamond Blackfan Anemia
Authors: Yu Lei , Lemay Philippe , Ludlow Alexander , Guyot Marie-Claude , Jones Morgan , Mohamed Fatma F. , Saroya Ghazi-Abdullah , Panaretos Christopher , Schneider Emily , Wang Yu , Myers Greggory , Khoriaty Rami , Li Qing , Franceschi Renny , Engel James Douglas , Kaartinen Vesa , Rothstein Thomas L. , Justice Monica J. , Kibar Zoha , Singh Sharon A.
Published: February 2021

Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins (RPs) are found in the majority of individuals with Diamond Blackfan anemia (DBA) while somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human DBA patients. The spontaneous anemia remission observed in some DBA patients occurs via unknown mechanism(s) and has not been previously described in animal models. Here we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations and increased mortality. Following genetic mapping and whole exome sequencing, we identified an intronicRpl5mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent withRpl5haploinsufficiency.Rpl5Skax23-Jusmutant animals had a profound delay in erythroid maturation and increased mortality at embryonic day E12.5, which improved by E14.5. Surviving mutant animals had a macrocytic anemia at birth as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novelRpl5Skax23-Jusmutant mouse will be useful to study the factors influencing the variable penetrance and anemia remission that are observed in DBA.
Ade novoparadigm for male infertility
Authors: Oud MS , Smits RM , Smith HE , Mastrorosa FK , Holt GS , Houston BJ , de Vries PF , Alobaidi BKS , Batty LE , Ismail H , Greenwood J , Sheth H , Mikulasova A , Astuti GDN , Gilissen C , McEleny K , Turner H , Coxhead J , Cockell S , Braat DDM , Fleischer K , D’Hauwers KWM , Schaafsma E ,   GEMINI Consortium, Nagirnaja L , Conrad DF , Friedrich C , Kliesch S , Aston KI , Riera-Escamilla A , Krausz C , Gonzaga-Jauregui C , Santibanez-Koref M , Elliott DJ , Vissers LELM , Tüttelmann F , O’Bryan MK , Ramos L , Xavier MJ , van der Heijden GW , Veltman JA
Published: February 2021

Introduction

De novo mutations (DNMs) are known to play a prominent role in sporadic disorders with reduced fitness1. We hypothesize that DNMs play an important role in male infertility and explain a significant fraction of the genetic causes of this understudied disorder. To test this hypothesis, we performed trio-based exome-sequencing in a unique cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare protein altering DNMs were classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of Loss-of-Function (LoF) DNMs in LoF-intolerant genes (p-value=1.00×10-5) as well as predicted pathogenic missense DNMs in missense-intolerant genes (p-value=5.01×10-4). One DNM gene identified, RBM5, is an essential regulator of male germ cell pre-mRNA splicing2. In a follow-up study, 5 rare pathogenic missense mutations affecting this gene were observed in a cohort of 2,279 infertile patients, with no such mutations found in a cohort of 5,784 fertile men (p-value=0.009). Our results provide the first evidence for the role of DNMs in severe male infertility and point to many new candidate genes affecting fertility.
Circulating miRNAs associated with bone mineral density in healthy adult baboons
Authors: Quillen Ellen. E. , Foster Jaydee , Sheldrake Anne , Stainback Maggie , Bredbenner Todd L.
Published: February 2021

MicroRNAs (miRNAs) regulate gene expression post-transcriptionally and circulate in the blood, making them attractive biomarkers of disease state for tissues like bone that are challenging to interrogate directly. Here we report on five miRNAs – miR-197-3p, miR-320a, miR-320b, miR-331-5p, and miR-423-5p – that are associated with bone mineral density (BMD) in 147 healthy adult baboons. These baboons range in age from 15 to 25 years (45 to 75 human equivalent years) and were 65% female with a broad range of BMDs including a minority of osteopenic individuals. miRNAs were generated via RNA sequencing from buffy coats collected at necropsy and areal BMD evaluated via DXA of the lumbar vertebrae post-mortem. Differential expression analysis controlled for the underlying pedigree structure of these animals to account for genetic variation which may be driving miRNA abundance and BMD values. While many of these miRNAs have been associated with risk of human osteoporosis, this finding is of interest because the cohort represent a model of normal aging and bone metabolism rather than a disease cohort. The replication of miRNA associations with osteoporosis or other bone metabolic disorders in animals with healthy BMD suggests an overlap in normal variation and disease states. We suggest that these miRNAs are involved in the regulation of cellular proliferation, apoptosis, and protein composition in the extracellular matrix throughout life. However, age-related dysregulation of these systems may lead to disease causing associations of the miRNAs among individuals with clinically defined disease.
Flor yeasts rewire the central carbon metabolism during wine alcoholic fermentation
Authors: Peltier Emilien , Vion Charlotte , Saada Omar Abou , Friedrich Anne , Schacherer Joseph , Marullo Philippe
Published: February 2021

The identification of natural allelic variations controlling quantitative traits could contribute to decipher metabolic adaptation mechanisms within different populations of the same species. Such variations could result from man-mediated selection pressures and participate to the domestication. In this study, the genetic causes of the phenotypic variability of the central carbon metabolismSaccharomyces cerevisiaewere investigated in the context of the enological fermentation. Carbon dioxide and glycerol production as well as malic acid consumption modulate the fermentation yield revealing a high level of genetic complexity. Their genetic determinism was found out by a multi environment QTL mapping approach allowing the identification of 14 quantitative trait loci from which 8 of them were validated down to the gene level by genetic engineering. Most of the validated genes had allelic variations involving flor yeast specific alleles. Those alleles were brought in the offspring by one parental strain that is closely related to the flor yeast genetic group while the second parental strain is part of the wine group. The causative genes identified are functionally linked to quantitative proteomic variations that would explain divergent metabolic features of wine and flor yeasts involving the tricarboxylic acid cycle (TCA), the glyoxylate shunt and the homeostasis of proton and redox cofactors. Overall, this work led to the identification of genetic factors that are hallmarks of adaptive divergence between flor yeast and wine yeast in the wine biotope. These alleles can also be used in the context of yeast selection to improve oenological traits linked to fermentation yield.
G9a and Sirtuin6 epigenetically modulate host cholesterol accumulation to facilitate mycobacterial survival
Authors: Prakhar Praveen , Bhatt Bharat , Mukherjee Tanushree , Lohia Gaurav Kumar , Kolthur-Seetharam Ullas , Sundaresan Nagalingam Ravi , Rajmani R.S. , Balaji Kithiganahalli Narayanaswamy
Published: February 2021

Cholesterol derived from the host milieu forms a critical factor for mycobacterial pathogenesis. However, the molecular circuitry co-opted byMycobacterium tuberculosis(Mtb) to accumulate cholesterol in host cells remains obscure. Here, we report that a functional amalgamation of WNT-responsive histone modifiers G9a (H3K9 methyltransferase) and Sirt6 (H3K9 deacetylase) orchestrate cholesterol build-up inin-vitroandin-vivomodels of Mtb infection. Mechanistically, G9a, along with SREBP2, drives the expression of cholesterol biosynthesis and uptake genes; while Sirt6 represses the genes involved in cholesterol efflux. The accumulated cholesterol promotes the expression of antioxidant genes leading to reduced oxidative stress, thereby supporting Mtb survival. In corroboration, loss-of-function of G9ain vitroandin vivoby pharmacological inhibition; or utilization of BMDMs derived fromSirt6KO mice orin vivoinfection inSirt6heterozygous mice; hampers host cholesterol accumulation and restricts Mtb burden. These findings shed light on the novel roles of G9a and Sirt6 during Mtb infection and highlight the previously unknown contribution of host cholesterol in potentiating anti-oxidative responses for aiding Mtb survival.
Post-transcriptional dysregulation in autism, schizophrenia and bipolar disorder
Authors: Wang Yuanyuan , Liu Liya , Lin Mingyan
Published: February 2021

Post-transcriptional gene regulation (PTGR) contributes to numerous aspects of RNA metabolism. While multiple regulators of PTGR have been associated with the occurrence and development of psychiatric disorders, a systematic investigation of the role of PTGR in the context of neuropsychiatric disorders is still lacking. In this work, we developed a new transcriptome -based algorithm to estimate PTGR and applied it to an RNA-Seq dataset of 2160 brain samples from individuals with autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BD) and controls. The results showed that the contribution of PTGR abnormality to gene differential expression between three common psychiatric disorders and controls was about 30% of that of transcriptional gene regulation (TGR) abnormality. Besides, aberrant PTGR tended to decrease RNA stability in SCZ/BD, while increase RNA stability in ASD, implicating contrasting pathologies among diseases. The abnormal alteration of PTGR in SCZ/BD converged on the inhibition of neurogenesis and neural differentiation, whereas dysregulation of PTGR in ASD induced enhanced activity of apoptosis. This suggested that heterogeneity in disease mechanism and clinical manifestation across different psychiatric disorders may be partially attributed to the diverse role of PTGR. Intriguingly, we identified a promising RBP (RNA bind protein) ELAVL3 (ELAV-Like Protein 3) that have a profound role in all three psychiatric disorders. Our systematic study expands the understanding of the link between PTGR and psychiatric disorders and also open a new avenue for deciphering the pathogenesis of psychiatric disorders.
Beyond Carbon Pricing: Tax Reform is Climate Policy
Authors: Green Jessica F.
Published: February 2021

The incrementalism of carbon pricing, which includes carbon taxes and emissions trading, has led us astray. It has been proffered as a key component of climate policy, yet evidence clearly shows that its effects are marginal. It provides limited emissions reductions and has provoked considerable political controversy in key large‐emitting countries. More importantly, pricing carbon means viewing climate change as a market failure, rather than as a problem of societal transformation. But rapid decarbonization will require more than market corrections; it demands strong state intervention to reorganize the economy. In this maximalist view, the state must create public goods, rather than merely prevent public bads. This article seeks to expand our collective political imagination about climate policy, moving beyond mundane fights about the appropriate design of carbon pricing. Instead, we need to think bigger. Aggressive climate policy begins with a reassertion of state sovereignty. Multinational corporations use ‘offshore’ tax havens to avoid paying taxes. By closing loopholes on corporate tax evasion, states reaffirm one of their fundamental functions: taxation. This reform would repatriate billions of dollars in missing capital, and help create the political conditions for meaningful action on decarbonization. Tax reform, not just carbon pricing, is climate policy too.
Estimating peptide half‐life in serum from tunable, sequence‐related physicochemical properties
Authors: Cavaco Marco , Valle Javier , Flores Isabel , Andreu David , A. R. B. Castanho Miguel
Published: February 2021

Proteolytic instability is a critical limitation for peptide‐based products. Although significant efforts are devoted to stabilize sequences against proteases/peptidases in plasma/serum, such approaches tend to be rather empirical, unspecific, time‐consuming, and frequently not cost‐effective. A more rational and potentially rewarding alternative is to identify the chemical grounds of susceptibility to enzymatic degradation of peptides so that proteolytic resistance can be tuned by manipulation of key chemical properties. In this regard, we conducted a meta‐analysis of literature published over the last decade reporting experimental data on the lifetimes of peptides exposed to proteolytic conditions. Our initial database contained 579 entries and was curated with regard to amino acid sequence, chemical modification, terminal half‐life (t1/2) or other stability readouts, type of stability assay, and biological application of the study. Although the majority of entries in the database corresponded to (slightly or substantially) modified peptides, we chose to focus on unmodified ones, as we aimed to decipher intrinsic characteristics of peptide proteolytic susceptibility. Specifically, we developed a multivariable regression model to unravel those peptide properties with most impact on proteolytic stability and thus potential t1/2 predicting ability. Model validation was done by two different approaches. First, a library of peptides spanning a large interval of properties that modulate stability was synthesized and their t1/2 in human serum were experimentally determined. Second, the t1/2 of 21 selected peptides approved for clinical use or in clinical trials were recorded and matched with the model‐estimated values. With both approaches, good correlation between experimental and predicted t1/2 data was observed.
Temporal changes in the relative abundance of anadromous Arctic charr, brown trout, and Atlantic salmon in northern Europe: Do they reflect changing climates?
Authors: Svenning Martin‐A. , Falkegård Morten , Dempson J. Brian , Power Michael , Bårdsen Bård‐Jørgen , Guðbergsson Gudni , Fauchald Per
Published: February 2021

Warming temperatures resulting from climate change may alter the distribution and abundance of many freshwater fish species, especially those in northern latitudes. Owing to interspecific differences in temperature adaptations and tolerances, warming may lead to changes in the fish community as a result of shifts in the abundance of co‐existing species.

We investigated how increased temperatures have potentially affected the abundance and catch composition of anadromous salmonids in northern Europe. We used national angling catch statistics over a period of several decades (1993–2018) as a proxy of relative annual abundance of adult Atlantic salmon (Salmo salar), brown trout (Salmo trutta), and Arctic charr (Salvelinus alpinus) in water courses in Iceland and in northern Norway. These are the only locations in the world where the three species coexist naturally as anadromous forms, and where they are distributed across latitudinal gradients characterised by varying temperatures.

Interpolated data on average annual air temperatures proximate to the study rivers increased 1–1.7°C in northern Norway and 1.0–1.5°C in Iceland during the 26‐year study period.

While the overall total number of fish caught has remained relatively stable during the period of study, gradual climate warming has been accompanied by a marked change in the catch composition of the three species in both countries. Increased temperatures were related to a decreased proportion of Arctic charr and an increased proportion of brown trout, while no temperature effect was found for Atlantic salmon. Controlling for the difference between fluvial and lacustrine systems, brown trout has begun to replace Arctic charr in all regions, whereas the relative catch of Atlantic salmon has been stable.

Interpretation of angling data can facilitate understanding of longer‐term trends in catch data and provide insights into possible underlying changes in fish species and alert managers to shifts in abundance that might be mitigated by management actions. However, care must be taken to avoid the confounding effects that changes in fisheries management measures, angler preferences, and effort might have on the metrics of relative change used to make inferences about long‐term trends.
Integrated analysis of gait parameters and gene expression profiles in a murine model of subarachnoid hemorrhage
Authors: Zheng Zhi Yuan , Lu Gang , Xiong Zhi Qiang , Leung Chi Kwan , Su Xian Wei , Li Tu , Poon Wai Sang , Chan Wai Yee , Wong George Kwok Chu
Published: February 2021

Gait analysis has been widely used to examine the behavioral presentation of numerous neurological disorders. Thorough murine model evaluation of the subarachnoid hemorrhage (SAH)‐associated gait deficits is missing. This study measures gait deficits using a clinically relevant murine model of SAH to examine associations between gait variability and SAH‐associated gene expressions. A total of 159 dynamic and static gait parameters from the endovascular perforation murine model for simulating clinical human SAH were determined using the CatWalk system. Eighty gait parameters and the mRNA expression levels of 35 of the 88 SAH‐associated genes were differentially regulated in the diseased models. Totals of 42 and 38 gait parameters correlated with the 35 SAH‐associated genes positively and negatively with Pearson's correlation coefficients of >0.7 and <−0.7, respectively. p‐SP1453 expression in the motor cortex in SAH animal models displays a significant correlation with a subset of gait parameters associated with muscular strength and coordination of limb movements. Our data highlights a strong correlation between gait variability and SAH‐associated gene expression. p‐SP1453 expression could act as a biomarker to monitor SAH pathological development and a therapeutic target for SAH.
Prenylflavonoids isolated from Macaranga tanarius stimulate odontoblast differentiation of human dental pulp stem cells and tooth root formation via the mitogen‐activated protein kinase and protein kinase B pathways
Authors: Nam S. H. , Yamano A. , Kim J. A. , Lim J. , Baek S. H. , Kim J. E. , Kwon T.G. , Saito Y. , Teruya T. , Choi S. Y. , Kim Y. K. , Bae Y. C. , Shin H. I. , Woo J. T. , Park E. K.
Published: February 2021

Aim

To identify odontogenesis‐promoting compounds and examine the molecular mechanism underlying enhanced odontoblast differentiation and tooth formation.

Methodology

Five different nymphaeols, nymphaeol B (NB), isonymphaeol B (INB), nymphaeol A (NA), 3’‐geranyl‐naringenin (GN) and nymphaeol C (NC) were isolated from the fruit of Macaranga tanarius. The cytotoxic effect of nymphaeols on human DPSCs was observed using a 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide (MTT) assay. The effect of nymphaeols on odontoblast differentiation was analysed with Alizarin Red S staining and odontoblast marker expression was assessed using real‐time polymerase chain reaction and Western blot analysis. The molecular mechanism was investigated with Western blot analysis. In order to examine the effect of INB on dentine formation in the developing tooth germ, INB‐soaked beads were placed under the tooth bud explants in the collagen gel; thereafter, the tooth bud explant‐bead complexes were implanted into the sub‐renal capsules for 3 weeks. Tooth root formation was analysed using micro‐computed tomography and histological analysis. Data are presented as mean ± standard error (SEM) values of three independent experiments, and results are compared using a two‐tailed Student's t‐test. The data were considered to have statistical significance when the P‐value was less than 0.05.

Results

Three of the compounds, NB, INB, and GN, did not exert a cytotoxic effect on human DPSCs. However, INB was most effective in promoting the deposition of calcium minerals in vitro (P < 0.001) and induced the expression of odontogenic marker genes (P < 0.05). Moreover, this compound strongly induced the phosphorylation of mitogen‐activated protein (MAP) kinases and protein kinase B (AKT) (P < 0.05). The inhibition of p38 MAP, c‐Jun N‐terminal kinase (JNK), and AKT substantially suppressed the INB‐induced odontoblast differentiation (P < 0.001). In addition, isonymphaeol B significantly induced the formation of dentine and elongation of the tooth root in vivo (P < 0.05).

Conclusions

Prenylflavonoids, including INB, exerted stimulatory effects on odontoblast differentiation and tooth root and dentine formation via the MAP kinase and AKT signalling pathways. These results suggest that nymphaeols could stimulate the repair processes for dentine defects or injuries.
Effects of enzymatic treatment conditions on dietary fibre content of wheat bran and use of cellulase‐treated bran in cookie
Authors: Nguyen Si Nhat , Vien Man Dat , Le Thi Thu Trang , Tran Thi Thu Tra , Ton Nu Minh Nguyet , Le Van Viet Man
Published: February 2021

A commercial cellulase preparation (Viscozyme Cassava C) was employed to process wheat bran to improve the ratio of insoluble to soluble dietary fibre. The effects of initial moisture content, enzyme dosage, and incubation time on the content of soluble and insoluble fibre during the enzymatic treatment were investigated. The appropriate conditions for the cellulase treatment were initial moisture content of 0.75 g water g−1 dry matter, enzyme dosage of 9 U g−1 dry matter and incubation time of 120 min under which the ratio of insoluble to soluble fibre of wheat bran was lowered by 42%. Untreated and cellulase‐treated wheat bran was incorporated into cookies at levels of 0%, 20%, 30%, 40% and 50%. Cookie with 50% cellulase‐treated bran showed 21% lower ratio of insoluble to soluble fibre as well as 14% lower hardness and 13% higher overall acceptability than sample with the same amount of untreated bran.
Intensive care unit trainee perception of end‐of‐life care provided during medical emergency team activation events
Authors: Rotherham Hannah J. , Jones Daryl A. , Presneill Jeffrey J. ,   the Victorian EOLC MET Investigators
Published: February 2021

Background

Hospital medical emergency team (MET) activation events involving end‐of‐life care (EOLC) are common. The issues faced by medical staff attending these events are incompletely described.

Aims

The purpose of this study was to measure the perceptions of Victorian hospital medical staff, training in the speciality of intensive care, about multiple aspects of EOLC MET calls. We sought to determine the overall extent of formal training in MET and EOLC and assess the domains of self‐perceived confidence, barriers to communication, frequency of clinician agreement and trainee distress.

Methods

We conducted an anonymous, voluntary, Internet‐based survey of registered trainees of the College of Intensive Care Medicine of Australia and New Zealand in May 2019. The participants eligible were those trainees working in an adult intensive care unit in Victoria, Australia, during the study period. The main outcome measures were self‐reported levels of confidence, barriers to communication, frequency of conflict and distress, senior support, supervision and access to training.

Results

Of 124 trainees surveyed, 75 (60%) responded. Overall, 78% of respondents felt confident to manage EOLC MET calls, but the frequently reported barriers to effective patient/next of kin communication included: (i) lack of private meeting rooms; (ii) resource and time constraints; and (iii) lack of patient and family availability during a MET call to discuss medical treatment limitations. Two‐thirds of respondents reported emotional distress at least occasionally, this being frequent in one in five. Most (68%) trainees experienced conflict with other medical teams at least occasionally. Factors associated with experiencing distress at least occasionally include greater trainee age, patients' being unable to participate in discussion due to illness, resource and time constraints and negative encounters with other medical teams.

Conclusions

Victorian intensive care trainees were confident managing EOLC MET activation events. However, distress was reported commonly and strategies are required to address the areas of concern.
Characterisation of stemness and multipotency of ovine muscle‐derived stem cells from various muscle sources
Authors: Elashry Mohamed I. , Gaertner Kateryna , Klymiuk Michele C. , Eldaey Asmaa , Wenisch Sabine , Arnhold Stefan
Published: February 2021

Muscle stem cells (MSCs) are a promising tool for cell‐based therapy and tissue regeneration in veterinary medicine. Evaluation of MSCs from muscles of different origins improves our understanding of their regenerative potential. The present study compared the stemness, cell proliferation, migration potential, myogenic differentiation (MD), and multipotency of MSCs for four developmentally different muscles of ovine origin. MSCs were isolated from the hind limb (HL), diaphragm (DI), extraocular (EO), and masseter (MS) muscles. Cell proliferation, migration, and stemness were examined using sulforhodamine B, and colony formation assays. Evaluation of multipotency was examined using histological and morphometric analyses, alkaline phosphatase (ALP) activity, and the expression of myogenic, adipogenic, and osteogenic markers using RT‐qPCR. Data were statistically analysed using analysis of variance. The results revealed that all experimental groups expressed stem cell markers paired box transcription factor Pax7, α7‐integrin, CD90, and platelet‐derived growth factor receptor alpha. DI and HL muscle cells displayed higher proliferation, migration, and colony formation capacities compared to the EO and MS muscle cells. HL and DI muscle cells showed increased MD, as indicated by myotube formation and relative expression of MyoD at day 7 and Myogenin at day 14. Although MS and EO muscle cells displayed impaired MD, these cells were more prone to adipogenic differentiation, as indicated by Oil Red O staining and upregulated fatty acid‐binding protein 4 and peroxisome proliferator‐activated receptor gamma expression. DI muscle cells demonstrated a higher osteogenic differentiation capability, as shown by the upregulation of osteopontin expression and an elevated ALP activity. Our data indicate that ovine HL and DI MSCs have a higher regenerative and multipotent potential than the EO and MS muscle cells. These results could be valuable for regional muscle biopsies and cell‐based therapies.
Effects of oxidative stress‐induced increases in Zn2+ concentrations in human gingival epithelial cells
Authors: Yagi Hiroko , Fujihara Chiharu , Murakami Shinya
Published: February 2021

Background and objective

Previous studies have reported that oxidative stress increases intracellular Zn2+ concentrations and induces cytotoxicity. However, no studies have investigated whether oxidative stress induces such changes in periodontal tissue cells. In the present study, we investigated the effect of oxidative stress on intracellular Zn2+ concentration in periodontium constituent cells and its potential relationship with periodontal disease.

Methods

We analyzed changes in intracellular Zn2+ concentrations in human gingival epithelial (epi4) cells treated with hydrogen peroxide (H2O2). The fluorescent probes FluoZin‐3 AM and CellTracker Green CMFDA were used to detect intracellular Zn2+ and thiol groups, respectively. Western blot analyses, luciferase reporter assays, and real‐time polymerase chain reaction (PCR) analyses were performed to examine the effect of intracellular Zn2+ on epi4 cells.

Results

H2O2 treatment increased intracellular concentrations of Zn2+ in epi4 cells by facilitating the movement of Zn2+ from cellular nonprotein thiols to the cytoplasm and promoting cell membrane permeability to Zn2+. Furthermore, H2O2‐induced increases in intracellular Zn2+ activated the p38 cAMP response element‐binding protein/mitogen‐activated protein kinase (p38 CREB/MAPK) cascade, upregulated nuclear factor kappa B (NF‐κB) DNA binding, and increased the expression of inflammatory cytokines and matrix metallopeptidase‐9 (MMP‐9).

Conclusion

Increases in intracellular Zn2+ induced by oxidative stress activate signaling pathways involved in inflammation, potentially contributing to the progression of periodontal disease.
Mesenchymal stem cell‐derived small extracellular vesicles as cell‐free therapy: Perspectives in periodontal regeneration
Authors: Novello Solen , Pellen‐Mussi Pascal , Jeanne Sylvie
Published: February 2021

Mesenchymal stem cells (MSC) are involved in the regeneration of the different missing or compromised periodontal tissues. MSC‐derived small extracellular vesicles (sEV) have recently been explored as a favorable substitution for stem cell therapy, as they are capable of producing therapeutic effects comparable to those of their parent cells, with advantages over cell therapy. The aim of this review is to evaluate the use of mesenchymal stem cells (MSC)‐derived sEV as cell‐free therapy in periodontal regeneration. A review of the scientific literature on sEV and their use in periodontal regeneration was performed. The main characteristics of sEV are described, and their mechanisms of action and potential biological effects in periodontal regeneration are studied. A summary of existing preclinical studies conducted in animals is performed. The results indicate that sEV derived from MSC are emerging as a promising new therapeutic tool in the field of periodontal regeneration and may become an ideal therapeutic option. In this review, we have summarized recent advances in this regard in order to better understand this newly emerging treatment. First results in vivo are promising and show a favorable potential for cell‐free therapy in periodontal regeneration.
SPARC inhibition accelerates NAFLD‐associated hepatocellular carcinoma development by dysregulating hepatic lipid metabolism
Authors: M. Onorato Agostina , Fiore Esteban , Bayo Juan , Casali Cecilia , Fernandez‐Tomé María , Rodríguez Marcelo , Domínguez Luciana , Argemi Josepmaría , Hidalgo Florencia , Favre Cristian , García Mariana , Atorrasagasti Catalina , Mazzolini Guillermo D.
Published: February 2021

Background and aims

Non‐alcoholic fatty liver (NAFLD) and its more serious form non‐alcoholic steatohepatitis increase risk of hepatocellular carcinoma (HCC). Lipid metabolic alterations and its role in HCC development remain unclear. SPARC (Secreted Protein, Acidic and Rich in Cysteine) is involved in lipid metabolism, NAFLD and diabetes, but the effects on hepatic lipid metabolism and HCC development is unknown. The aim of this study was to evaluate the role of SPARC in HCC development in the context of NAFLD.

Methods

Primary hepatocyte cultures from knockout (SPARC−/−) or wild‐type (SPARC+/+) mice, and HepG2 cells were used to assess the effects of free fatty acids on lipid accumulation, expression of lipogenic genes and de novo triglyceride (TG) synthesis. A NAFLD‐HCC model was stabilized on SPARC−/− or SPARC+/+ mice. Correlations among SPARC, lipid metabolism‐related gene expression patterns and clinical prognosis were studied using HCC gene expression dataset.

Results

SPARC−/− mice increases hepatic lipid deposits over time. Hepatocytes from SPARC−/− mice or inhibition of SPARC by an antisense adenovirus in HepG2 cells resulted in increased TG deposit, expression of lipid‐related genes and nuclear translocation of SREBP1c. Human HCC database analysis revealed that SPARC negatively correlated with genes involved in lipid metabolism, and with poor survival. In NAFLD‐HCC murine model, the absence of SPARC accelerates HCC development. RNA‐seq study revealed that pathways related to lipid metabolism, cellular detoxification and proliferation were upregulated in SPARC−/− tumour‐bearing mice.

Conclusions

The absence of SPARC is associated with an altered hepatic lipid metabolism, and an accelerated NAFLD‐related HCC development.
Overcoming insect immune response: The role of Pseudomonas aeruginosa alkaline protease in phenoloxidase inhibition
Authors: Andrejko Mariola , Siemińska‐Kuczer Anna , Iwański Bartłomiej , Cytryńska Małgorzata
Published: February 2021

The role of Pseudomonas aeruginosa alkaline protease, one of the important virulence factors of these bacteria, in the prophenoloxidase (proPO) system activation in Galleria mellonella haemolymph was investigated. Immunization of G. mellonella larvae with alkaline protease led to an increase in phenoloxidase (PO) activity in haemolymph 2–8 h after the injection. However, 15 h after the challenge, almost no PO activity was detected, in contrast to insects immunized with heat‐killed P. aeruginosa, where an elevated PO activity in haemolymph persisted at all the time points of the experiment (2–24 h). To test the effect of alkaline protease on already activated PO in vitro, non‐immune G. mellonella haemolymph with proPO system pre‐activated in vitro by heat‐killed P. aeruginosa was used. Subsequently, direct incubation of the protease with non‐immune haemolymph was carried out to test the effect of the alkaline protease on the proPO system activation. It can be postulated that P. aeruginosa alkaline protease affected not only the active PO, but also significantly inhibited proPO cascade activation in the haemolymph of G. mellonella.
EVALUATION OF PARAMETERS FOR SUBCRITICAL WATER EXTRACTION OF ZINGIBER ZERUMBET USING FRACTIONAL FACTORIAL DESIGN
Authors: Mohd Amir Siti Nur Khairunisa , Mad Nordin Mariam Firdhaus , Shameli Kamyar , Mohamad Abdul Wahab Izzati , Abdul Hamid Mariani
Published: February 2021

Zingiber zerumbet (Z. zerumbet) is recognized for decades for its usability as spice and condiment in food flavoring as well as having high medicinal properties. Up to date, there are limited literature on evaluation of the effects of multiple variables in details especially in pilot-scale subcritical water extraction (SWE) of Z. zerumbet. The aim for this study is to implement the fractional factorial design with five variables which are temperature (100-170°C), time (10-40 minutes), pressure (10-20 bar), particle size (0.89-3.56 mm) and solvent to solid ratio (20-40 ml/g) in SWE of Z. zerumbet. Analysis of variance for all responses stated that temperature, time, particle size and solvent to solid ratio are significant variables. Temperature is the most significant factor for zerumbone concentration and antioxidant activity with a p-value of <0.0001 and 0.0002, respectively. The solvent to solid ratio was the most significant factor for the yield of extraction with a p-value of 0.0002. Time and particle size were significant towards all responses, however pressure was not significant on zerumbone concentration and yield. Thus, the fractional factorial design could give a broad overview in selecting the significant variables for further optimization in SWE from the findings.
THE EFFECT OF TRANSFER DISTANCE TO LOWER BACK TWISTING AND BENDING PATTERNS IN MANUAL TRANSFER TASK
Authors: Radin Umar Radin Zaid , Khafiz Muhammad Naqiuddin , Abdullasim Nazreen , Mohd Azli Lee Fatin Ayuni , Ahmad Nadiah
Published: February 2021

Manual material handling (MMH) activities utilize human’s effort with minimal aid from mechanical devices. MMH is typically associated with poor lower back posture which can lead to lower back injury. The likelihood to develop musculoskeletal disorders (MSDs) increases when poor working posture exist in combination with repetition and/or forceful exertion. In manual transfer activity, the distance between lifting origin and destination could affect workers’ exposure on poor lower back working posture. An experimental study was conducted to investigate the effect of transfer distance to lower back twisting and bending pattern in manual transfer activity. Positional body joints data of 26 male subjects were captured using the combination of motion capture (MOCAP) system with MVN studio software. Calculated data were plotted against time to track subjects’ lower back twisting and bending behavior. In general, longer the transfer distance would result in smaller twisting angle but higher bending angle. Statistical analysis in this study suggests 0.75m to 1.00m as the optimum transfer distance to balance lower back twisting and bending exposure on workers. This study is envisioned to provide insights for practitioners to consider space requirements for MMH activity to minimize lower back twisting and bending, and consequently the development of MSDs.
PEMBINAAN KONSTRUK INSTRUMEN PENILAIAN PASCA PENGHUNIAN UNTUK PERUMAHAN BERTINGKAT YANG DIBINA MENGGUNAKAN KAEDAH SISTEM BINAAN BERINDUSTRI (IBS)
Authors: Musa M. K. , Rahman M. A. A. , H. Nurzalina, , Lip R.
Published: February 2021

Post Occupancy Evaluation (POE) is an activity of the building evaluation process with a focus on quality, operational performance and satisfaction of the occupants. The POE is important to evaluate completed and occupied buildings to identify weaknesses and potential for future improvement. To date, there have been various variations of POE instruments and tools to evaluate occupied buildings. However, the POE instrument for assessing high-rise housing constructed using the industrialized building system (IBS) method has not been developed specifically. In this regard, this study aims to discuss the construction of an effective POE instrument to measure the quality and performance of high-rise housing built using the IBS method. For this purpose, the 3 round Delphi method was adapted by involving 15 experts selected based on their background and experience related to IBS. The results of a three-round Delphi study found that 33 out of all sub-constructs were dropped because of low mean scores (<4.2 in two rounds) while 75 sub-constructs were identified as final items. The results of the Delphi study also found that all 10 constructs were 1) Spatial; 2) Design and aesthetics; 3) Physical; 4) Building materials; 5) Quality of work; 6) Comfort and well-being; 7) Environment and health; 8) Maintenance; 9) Value and 10) Cost is the most significant construct for developing PPP instruments. Accordingly, an effective Post-Occupancy Assessment Instrument for measuring the quality, performance and value of a home built using the IBS method should include all of these constructs.