bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerating leaf area measurement using a volumetric approach
Authors: Haghshenas Abbas , Emam Yahya
Published: July 2021

Despite the advances in the techniques of indirect estimation of leaf area, the destructive measurement approaches have still remained as the reference and the most accurate methods. However, even utilizing the modern sensors and applications usually requires the laborious and time-consuming practice of unfolding and analyzing the single leaves, separately. In the present study, a volumetric approach was tested to determine the pile leaf area based on the ratio of leaf volume divided by thickness. For this purpose, the suspension technique was used for volumetry, which is based on the simple practice and calculations of the Archimedes’ principle. The results indicated that the wheat volumetric leaf area (VLA), had an approximately 1:1 correlation with the conventionally measured optical leaf area (OLA). Exclusion of the midrib volume from calculations, did not affect the estimation error (i.e. NRMSE less than 2.61%); however, improved the slope of the linear model by about 6%. The error of sampling for determining the mean leaf thickness of the pile, was also less than 2% throughout the season. Besides, a more practical and facilitated version of the pile volumetry was tested using a Specific Gravity Bench (SGB), which is currently available as a laboratory equipment. As an important observation, which was also expectable according to the 3D shape of the leaf (i.e. expansion in a 2D plane), it was evidenced that the variations in the OLA exactly follows the pattern of the changes in the leaf volume. Accordingly, it was suggested that the relative leaf areas of various experimental treatments may be compared directly based on the volume, and independently of leaf thickness. Furthermore, no considerable difference was observed among the OLAs measured using various image resolutions (NRMSE < 0.212%); which indicates that even the current superfast scanners with low resolutions as 200 dpi may be used for a precision optical measurement of leaf area. It is expected that utilizing the reliable and simple concept of volumetric leaf area, based on which the measurement time may be independent of the sample size, facilitate the laborious practice of leaf area measurement; and consequently, improve the precision of the field experiments.
Circulating metabolic biomarkers are consistently associated with incident type 2 diabetes in Asian and European populations – a metabolomics analysis in five prospective cohorts
Authors: Seah Jowy Yi Hoong , Hong Yueheng , Cichońska Anna , Sabanayagam Charumathi , Nusinovici Simon , Wong Tien Yin , Cheng Ching-Yu , Jousilahti Pekka , Lundqvist Annamari , Perola Markus , Salomaa Veikko , Tai E. Shyong , Würtz Peter , van Dam Rob M. , Sim Xueling
Published: July 2021

Background

While Asians have a higher risk of type 2 diabetes (T2D) than Europeans for a given BMI, it remains unclear whether the same markers of metabolic pathways are associated with diabetes.

Objectives

We evaluated associations between metabolic biomarkers and incident T2D in three major Asian ethnic groups (Chinese, Malay, and Indian) and a European population.

Methods

We analyzed data from adult males and females of two cohorts from Singapore (n = 6,393) consisting of Chinese, Malays and Indians, and three cohorts of European-origin participants from Finland (n = 14,558). We used nuclear magnetic resonance to quantify 154 circulating metabolic biomarkers at baseline and performed logistic regression to assess associations with T2D risk adjusted for age, sex, BMI and glycaemic markers.

Results

Of the 154 metabolic biomarkers, 59 were associated with higher risk of T2D in both Asians and Europeans (P < 0.0003; Bonferroni-corrected). These included branched-chain and aromatic amino acids, the inflammatory marker glycoprotein acetyls, total fatty acids, monounsaturated fatty acids, apolipoprotein B, larger very low-density lipoprotein particle sizes, and triglycerides. In addition, 13 metabolites were associated with a lower T2D risk in both populations including omega-6 polyunsaturated fatty acids and larger high-density lipoprotein particle sizes. Associations were consistent within the Asian ethnic groups (all Phet ≥ 0.05) and largely consistent for the Asian and European populations (Phet ≥ 0.05 for 128 of 154 metabolic biomarkers).

Conclusion

Metabolic biomarkers across several biological pathways were consistently associated with T2D risk in Asians and Europeans.
Late surges in COVID-19 cases and varying transmission potential partially due to public health policy changes in 5 Western states, March 10, 2020-January 10, 2021
Authors: Hua Xinyi , Kehoe Aubrey R. D. , Tome Joana , Motaghi Mina , Ofori Sylvia K. , Lai Po-Ying , Ali Sheikh Taslim , Chowell Gerardo , Spaulding Anne C. , Fung Isaac Chun-Hai
Published: July 2021

Objective

This study investigates how the SARS-CoV-2 transmission potential varied in North Dakota, South Dakota, Montana, Wyoming, and Idaho from March 2020 through January 2021.

Methods

Time-varying reproduction numbers,Rt, of a 7-day-sliding-window and of non-overlapping-windows between policy changes were estimated utilizing the instantaneous reproduction number method. Linear regression was performed to evaluate if per-capita cumulative case-count varied across counties with different population size.

Results

The median 7-day-sliding-windowRtestimates across the studied region varied between 1 and 1.25 during September through November 2020. Between November 13 and 18,Rtwas reduced by 14.71% (95% credible interval, CrI, [14.41%, 14.99%]) in North Dakota following a mask mandate; Idaho saw a 1.93% (95% CrI [1.87%, 1.99%]) reduction and Montana saw a 9.63% (95% CrI [9.26%, 9.98%]) reduction following the tightening of restrictions. High-population counties had higher per-capita cumulative case-count in North Dakota at four time points (June 30, August 31, October 31, and December 31, 2020). In Idaho, North Dakota, and South Dakota, there was a positive correlation between population size and per-capita weekly incident case-count, adjusted for calendar time and social vulnerability index variables.

Conclusions

Rtdecreased after mask mandate during the region’s case-count spike suggested reduction in SARS-CoV-2 transmission.
Primary cilia drive postnatal tidemark patterning in articular cartilage by coordinating responses to Indian Hedgehog and mechanical load
Authors: Rux Danielle , Helbig Kimberly , Han Biao , Cortese Courtney , Koyama Eiki , Han Lin , Pacifici Maurizio
Published: July 2021

Articular cartilage (AC) is essential for body movement, but is highly susceptible to degenerative diseases and has poor self-repair capacity. To improve current subpar regenerative treatment, developmental mechanisms of AC should be clarified and, specifically, how postnatal multi-zone organization is acquired. Primary cilia are cell surface organelles crucial for mammalian tissue morphogenesis and while the importance of chondrocyte primary cilia is well appreciated their specific roles in postnatal AC morphogenesis remain unclear. To explore these mechanisms, we used a murine conditional loss-of-function approach (Ift88-flox) targeting joint-lineage progenitors (Gdf5Cre) and monitored postnatal knee AC development. Joint formation and growth up to juvenile stages were largely unaffected, however mature AC (aged 2 months) exhibited disorganized extracellular matrix, decreased aggrecan and collagen II due to reduced gene expression (not increased catabolism), and marked reduction of AC modulus by 30-50%. In addition, we discovered the surprising findings that tidemark patterning was severely disrupted and accompanied alterations in hedgehog signaling that were also dependent on regional load-bearing functions of AC. Interestingly, Prg4 expression was also increased in those loaded sites. Together, our data provide evidence that primary cilia orchestrate postnatal AC morphogenesis, dictating tidemark topography, zonal matrix composition and mechanical load responses.
Severe neural tube defects due to failure of closure initiation can arise without abnormality of neuroepithelial convergent extension
Authors: Nychyk Oleksandr , Galea Gabriel L. , Molè Matteo , Savery Dawn , Greene Nicholas D.E. , Stanier Philip , Copp Andrew J.
Published: July 2021

Planar cell polarity (PCP) signalling is vital for initiation of neural tube closure in mice, with diminished convergent extension (CE) cell movements leading to a severe form of neural tube defect (NTD), termed craniorachischisis (CRN). Some human NTDs are also associated with PCP gene mutations, but affected individuals are generally heterozygous, whereas PCP homozygosity or compound heterozygosity is needed to produce CRN in mice. This suggests human NTDs may involve other genetic or environmental factors, that interact with partial loss of PCP function. We found that reduced sulfation OF glycosaminoglycans (GAGs) interacts with heterozygosity for the Lp allele of Vangl2 (a core PCP gene), to cause CRN in mice. Here, we hypothesised that this GAG-PCP interaction may regulate convergent extension movements, and hence lead to severe NTDs in the context of only partial loss of PCP function. Both Lp and null alleles of Vangl2 gave similar findings. Culture of E8.5 embryos in the presence of chlorate (a GAG sulfation inhibitor), or enzymatic cleavage of GAG chains, led to failure of NT closure initiation in the majority of Lp/+ embryos, whereas few +/+ littermates exhibited CRN. The chlorate effect was rescued by exogenous sulphate. Surprisingly, DiO labeling of the embryonic node demonstrated no abnormality of midline axial extension in chlorate-treated Lp/+ embryos that developed CRN. In contrast, positive control Lp/Lp embryos displayed severe convergent extension defects in this assay. Morphometric analysis of the closure initiation site revealed abnormalities in the size and shape of somites that flank the closing neural tube in chlorate-treated Lp/+ embryos. We conclude that severe NTDs involving failure of closure initiation can arise by a mechanism other than faulty neuroepithelial convergent extension. Matrix-mediated expansion of somites, flanking the closing neural tube, may be required for closure initiation.
Towards a Neurometric-based Construct Validity of Trust
Authors: Chen Pin-Hao A. , Fareri Dominic , Güroğlu Berna , Delgado Mauricio R. , Chang Luke J.
Published: July 2021

Trust is a nebulous construct central to successful cooperative exchanges and interpersonal relationships. In this study, we introduce a new approach to establishing construct validity of trust using “neurometrics”. We develop a whole-brain multivariate pattern capable of classifying whether new participants will trust a relationship partner in the context of a cooperative interpersonal investment game (n=40) with 90% accuracy and find that it also generalizes to a variant of the same task collected in a different country with 82% accuracy (n=17). Moreover, we establish the convergent and discriminant validity by testing the pattern on thirteen separate datasets (n=1,427) and find that trust is reliably related to beliefs of safety, inversely related to negative affect, but unrelated to reward, cognitive control, social perception, theory of mind, and self-referential processing. Together these results provide support for the notion that the psychological experience of trust contains elements of beliefs of reciprocation and fear of betrayal aversion. Contrary to our predictions, we found no evidence that trust is related to anticipated reward. This work demonstrates how “neurometrics” can be used to characterize the psychological processes associated with brain-based multivariate representations.
Determinants of primaquine and carboxyprimaquine exposures in children and adults withPlasmodium vivaxmalaria
Authors: Chu Cindy S , Watson James A , Phyo Aung Pyae , Win Htun Htun , Yotyingaphiram Widi , Thinraow Suradet , Soe Nay Lin , Aung Aye Aye , Wilaisrisak Pornpimon , Puaprasert Kanokpich , Imwong Mallika , Hanpithakpong Warunee , Blessborn Daniel , Tarning Joel , Proux Stéphane , Ling Clare , Nosten François H , White Nicholas J
Published: July 2021

Background

Primaquine is the only widely available drug for radical cure ofPlasmodium vivaxmalaria. There is uncertainty whether the pharmacokinetic properties of primaquine are altered significantly in childhood or not.

Methods

Glucose-6-phosphate dehydrogenase normal patients with uncomplicatedP. vivaxmalaria were randomized to receive either chloroquine (25mg base/kg) or dihydroartemisinin-piperaquine (dihydroartemisinin 7mg/kg and piperaquine 55mg/kg) plus primaquine; given either as 0.5 mg base/kg/day for 14 days or 1 mg/kg/day for 7 days. Pre-dose day 7 venous plasma concentrations of chloroquine, desethylchloroquine, piperaquine, primaquine and carboxyprimaquine were measured. Methemoglobin levels were measured either daily or on days 1, 3, 6 and 13, and additionally on day 10 in the primaquine 14-day groups.

Results

Day 7 primaquine and carboxyprimaquine concentrations were available for 641 patients. After adjustment for the primaquine mg/kg daily dose, day of sampling, partner drug, and fever clearance, there was a significant non-linear relationship between age and trough primaquine and carboxyprimaquine concentrations, and day methemoglobin levels. Compared to adults 30 years of age, children 5 years of age had trough primaquine concentrations 0.53 (95% CI: 0.39-0.73) fold lower, trough carboxyprimaquine concentrations 0.45 (95% CI: 0.35-0.55) fold lower, and day 7 methemoglobin levels 0.87 (95% CI: 0.58-1.27) fold lower. Increasing concentrations of piperaquine and chloroquine and poor metabolizerCYP 2D6alleles were associated with higher day 7 primaquine and carboxyprimaquine concentrations. Higher blood methemoglobin concentrations were associated with a lower risk of recurrence.

Conclusion

Young children have lower primaquine and carboxyprimaquine exposures, and lower levels of methemoglobinemia, than adults. Young children may need higher weight adjusted primaquine doses than adults.
Gender Affirming Hormone Therapy induces specific DNA methylation changes in blood
Authors: Shepherd Rebecca , Bretherton Ingrid , Pang Ken , Czajko Anna , Kim Bowon , Vlahos Amanda , Zajac Jeffrey D. , Saffery Richard , Cheung Ada , Novakovic Boris
Published: July 2021

DNA methylation is an epigenetic mark that is influenced by underlying genetic profile, environment, and aging. It also plays a key role in female-specific X-chromosome silencing in mammals. In addition to X-linked DNA methylation, sex-specific methylation patterns are widespread across autosomal chromosomes and can be present from birth or arise over time. In individuals where gender identity and sex assigned at birth are markedly and consistently incongruent, as in the case of transgender people, feminization or masculinization may be sought through gender affirming hormone therapy (GAHT). In this study we profiled genome-wide DNA methylation in blood of transgender women and transgender men, before and during GAHT (6 months and 12 months into hormone treatment). We identified several thousand differentially methylated CpG sites (DMPs) in both people undergoing feminizing and masculinizing hormone therapy, the vast majority of which were progressive changes over time. Sex-specific DNA methylation patterns established in early development are largely refractory to change in association with GAHT. The small number of sex-DMPs that were affected by GAHT were those that become sex-specific during the lifetime, known as sex-and-age DMPs.
Aberrant motor contagion of emotions in psychopathy and high-functioning autism
Authors: Sun Lihua , Lukkarinen Lasse , Noppari Tuomo , Nazari-Farsani Sanaz , Putkinen Vesa , Seppälä Kerttu , Hudson Matthew , Tani Pekka , Lindberg Nina , Karlsson Henry K. , Hirvonen Jussi , Salomaa Marja , Venetjoki M. Niina , Lauerma Hannu , Tiihonen Jari , Nummenmaa Lauri
Published: July 2021

Psychopathy and autism are both associated with aberrant social interaction and communication, yet only psychopaths are markedly antisocial and violent. Here we compared the functional neural alterations underlying these two different phenotypes with distinct patterns of socioemotional difficulties. We studied 19 incarcerated male offenders with high psychopathic traits, 20 males with high-functioning autism and 19 age-matched healthy controls. All groups underwent functional magnetic resonance imaging while they viewed dynamic happy, angry and disgust facial expressions or listened to laughter and crying sounds. Psychopathy was associated with reduced somatomotor responses to almost all expressions, while subjects with autism demonstrated less marked and emotion-specific alterations in the somatomotor area. These data suggest that psychopathy and autism involve both common and distinct functional alterations in the brain networks involved in socioemotional processing.
Stable Isotope Tracing In Vivo Reveals A Metabolic Bridge Linking The Microbiota To Host Histone Acetylation
Authors: Lund Peder J , Gates Leah A , Leboeuf Marylene , Smith Sarah A , Chau Lillian , Friedman Elliot S , Lopes Mariana , Saiman Yedidya , Kim Min Soo , Petucci Christopher , Allis C. David , Wu Gary D , Garcia Benjamin A
Published: July 2021

The gut microbiota influences host epigenetics by fermenting dietary fiber into butyrate. Although butyrate could promote histone acetylation by inhibiting histone deacetylases, it may also undergo oxidation to acetyl-CoA, a necessary cofactor for histone acetyltransferases. Here, we find that epithelial cells from germ-free mice harbor a loss of histone H4 acetylation across the genome except at promoter regions. Using stable isotope tracing in vivo with 13C-labeled fiber, we demonstrate that the microbiota supplies carbon for histone acetylation. Subsequent metabolomic profiling revealed hundreds of labeled molecules and supported a microbial contribution to host fatty acid metabolism, which declined in response to colitis and correlated with reduced expression of genes involved in fatty acid oxidation. These results illuminate the flow of carbon from the diet to the host via the microbiota, disruptions to which may affect energy homeostasis in the distal gut and contribute to the development of colitis.
Cyp26b1 restrains murine heart valve growth during development
Authors: Ahuja Neha , Hiltabidle Max S. , Rajasekhar Hariprem , Barlow Haley R. , Daniel Edward , Voss Sophie , Cleaver Ondine , Maynard Caitlin
Published: July 2021

Endothelial cells (ECs) are critical to proper heart valve development, directly contributing to the mesenchyme of the cardiac cushions, which progressively transform into mature valves. To date, investigators have lacked useful markers of valve ECs to fully evaluate their contributions during valve morphogenesis. As a result, it has been unclear whether the well-characterized regional differentiation of valves correlates with any endothelial domains in the heart. Furthermore, it has been difficult to ascertain whether endothelial heterogeneity in the heart influences underlying mesenchymal zones in an angiocrine manner. To identify regionally expressed EC genes in the heart valves, we screened publicly available databases and assembled a toolkit of endothelial-enriched genes. We identified Cyp26b1 as one of many endothelial enriched genes found to be expressed in the endocardium of the developing cushions and valves. Here, we show that Cyp26b1 is required for normal heart valve development. Genetic ablation of Cyp26b1 in mouse embryos leads to abnormally thickened aortic valve leaflets, which is due in part to increased endothelial and mesenchymal cell proliferation in the remodeling valves. In addition, Cyp26b1 mutant hearts display ventricular septal defects (VSDs) in a portion of null embryos. We show that loss of Cyp26b1 results in upregulation of retinoic acid (RA) target genes, supporting the observation that Cyp26b1 has RA-dependent roles. Together, this work identifies a novel role for Cyp26b1 in heart valve morphogenesis. Understanding the spatiotemporal expression dynamics of cardiac EC genes will likely prove useful to the investigation of both normal as well as dysfunctional heart valve development.

HIGHLIGHTS

· A mouse heart valve gene expression atlas can be generated with publicly available online tools, such as Genepaint and other gene expression databases.

· Endothelium of developing mouse heart valves is regionally heterogeneous.

· Cyp26b1 is expressed in the endocardial/endothelial lining of developing heart valves.

· Loss of Cyp26b1 leads to significant enlargement of aortic valves and to ventricular septal defects.

· Cyp26b1 represses cell proliferation in valve mesenchyme.

· Retinoic acid targets are upregulated in Cyp26b1-/- heart valves, indicating dysregulation of RA metabolism.
The Cl--channel TMEM16A controls the generation of cochlear Ca2+ waves and promotes the refinement of auditory brainstem networks
Authors: Maul Alena , Jovanovic Saša , Huebner Antje K. , Strenzke Nicola , Moser Tobias , Rübsamen Rudolf , Hübner Christian A.
Published: July 2021

Before hearing onset (postnatal day 12 in mice), inner hair cells (IHC) spontaneously fire action potentials thereby driving pre-sensory activity in the ascending auditory pathway. The rate of IHC action potential bursts is modulated by inner supporting cells (ISC) of Kölliker’s organ through the activity of the Ca2+ activated Cl- channel TMEM16A. Here we show that conditional deletion of Tmem16a in mice disrupts the generation of Ca2+ waves within Kölliker’s organ, reduces the burst firing activity and the frequency-selectivity of auditory brainstem neurons in the medial nucleus of the trapezoid body (MNTB), and also impairs the refinement of MNTB projections to the lateral superior olive (LSO). These results reveal the importance of the activity of Kölliker’s organ for the refinement of central auditory connectivity. In addition, our study suggests a mechanism for the generation of Ca2+ waves, which may also apply to other tissues expressing TMEM16A.
Identification of potential carboxylic acid-containing drug candidate to design novel competitive NDM inhibitors: An in-silico approach comprising combined virtual screening and molecular dynamics simulation
Authors: Vasudevan Karthick , Basu Soumya , Arumugam Amala , Naha Aniket , Ramaiah Sudha , Anbarasu Anand , Veeraraghavan Balaji
Published: July 2021

Metallo-β-lactamases (MBLs) producing bacteria especially the ones with New Delhi metallo-beta-lactamase-1 (NDM-1) and its variants can potentially hydrolyse all the major β-lactam antibiotics, ultimately escalating anti-microbial resistance world-wide. There is a dearth of approved inhibitors to combat NDM and other MBLs producing bacteria. Hence we focussed to find novel inhibitor(s) in-silico which can potentially suppress the activity of NDM/ MBLs. 2400 compounds were virtually screened to identify a promising carboxylic acid-containing compound (CID-53986787) analogous to NDM antagonist Captopril. Our lead compound can bind adjacent to the active site zinc ions (Zn1 and Zn2) in all highly resistant NDM variants. CID-53986787 possesses ~5-8% higher binding affinity than Captopril, exhibiting molecular interactions with crucial residues that can destabilize the hydrolytic activity of NDM. CID-53986787 was virtually evaluated to ascertain its safe pharmacological/ toxicity profile. Molecular dynamics simulation studies elucidated its stable interaction with the target protein (NDM-1).
Molecular Determinants of Complexin Clamping in Reconstituted Single-Vesicle Fusion
Authors: Bera Manindra , Ramakrishnan Sathish , Coleman Jeff , Krishnakumar Shyam S. , Rothman James E.
Published: July 2021

Previously we reported that Synaptotagmin-1 and Complexin synergistically clamp the SNARE assembly process to generate and maintain a pool of docked vesicles that fuse rapidly and synchronously upon Ca2+ influx (Ramakrishnan et al. 2020). Here using the same in vitro single-vesicle fusion assay, we establish the molecular details of the Complexin clamp and its physiological relevance. We find that a delay in fusion kinetics, likely imparted by Synaptotagmin-1, is needed for Complexin to block fusion. Systematic truncation/mutational analyses reveal that continuous alpha-helical accessory-central domains of Complexin are essential for its inhibitory function and specific interaction of the accessory helix with the SNAREpins, analogous to the trans clamping model, enhances this functionality. The c-terminal domain promotes clamping by locally elevating Complexin concentration through interactions with the membrane. Further, we find that Complexin likely contributes to rapid Ca2+-synchronized vesicular release by preventing un-initiated fusion rather than by directly facilitating vesicle fusion.
Disturbance-based management of ecosystem services and disservices in partial nitritation anammox biofilms
Authors: Suarez Carolina , Sedlacek Christopher J. , Gustavsson David J. I. , Eiler Alexander , Modin Oskar , Hermansson Malte , Persson Frank
Published: July 2021

The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors during wastewater treatment, where suppression of nitrite oxidizers likeNitrospirais sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms treating water from a high rate activated sludge process removing organic matter (mainstream wastewater), were constantly or intermittently exposed to the effluent of anaerobic sewage sludge digestion dewatering (sidestream wastewater), which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, amongNitrospirain the PNA biofilms, while the opposite patterns were observed for anammox bacteria withinBrocadia. At the same time, species turnover was observed for the aerobic ammonia-oxidizingNitrosomonaspopulations. The different exposure regimens were associated with metagenomic assembled genomes ofNitrosomonas, Nitrospira, andBrocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.
The structurome of a Clostridium difficile phage and the remarkable accurate prediction of its novel phage receptor-binding protein
Authors: Dowah Ahmed S. A. , Xia Guoqing , Ali Ali Abdul Kareem , Thanki Anisha M. , Shan Jinyu , Millard Andy , Petersen Bent , Sicheritz-Pontén Thomas , Wallis Russell , Clokie Martha R. J.
Published: July 2021

As natural bacterial predators, bacteriophages have the potential to be developed to tackle antimicrobial resistance, but our exploitation of them is limited by understanding their vast uncharacterised genetic diversity1,2. Fascinatingly, this genetic diversity reflects many ways that phages can make proteins, performing similar functions that together form the familiar phage particle. Critical to infection are phage receptor-binding proteins (RBPs) that bind bacterial ‘receptors’ and initiate bacterial entry3. Here we identified and characterised Gp22, a novel RBP for phage CDHS-1 that infects pathogenic C. difficile, but that had no recognisable RBPs. We showed that Gp22 antibodies neutralised CDHS-1 infection and used immunogold-labelling and transmission electron microscopy to identify their location on the capsid. The Gp22 three-dimensional structure was resolved by X-ray crystallography revealing a new RBP class with an N-terminal L-shaped α-helical superhelix domain and a C-terminal Mg2+-binding domain. The findings provide novel insights into C. difficile phage biology and phage-host interactions. This will facilitate optimal phage development and future engineering strategies4,5. Furthermore, the AlphaFold2-predicted Gp22 structure, which was strikingly accurate, paves the way for a structurome based transformation and guidance of future phage studies where many proteins lack sequence homology but have recognisable protein structures.
A framework for assessing the skill and value of operational recruitment forecasts
Authors: Kiaer Christian , Neuenfeldt Stefan , Payne Mark R.
Published: July 2021

Forecasting variation in the recruitment to fish stocks is one of the most challenging and long-running problems in fisheries science and essentially remains unsolved today. Traditionally recruitment forecasts are developed and evaluated based on explanatory and goodness-of-fit approaches that do not reflect their ability to predict beyond the data on which they were developed. Here we propose a new generic framework that allows the skill and value of recruitment forecasts to be assessed in a manner that is relevant to their potential use in an operational setting. We assess forecast skill based on predictive power using a retrospective forecasting approach inspired by meterology, and emphasise the importance of assessing these forecasts relative to a baseline. We quantify the value of these forecasts using an economic cost-loss decision model that is directly relevant to many forecast users. We demonstrate this framework using four stocks of lesser sandeel (Ammodytes marinus) in the North Sea, showing for the first time in an operationally realistic setting that skilful and valuable forecasts are feasible in two of these areas. This result shows the ability to produce valuable short-term recruitment forecasts, and highlights the need to revisit our approach to and understanding of recruitment forecasting.
Population-level inference for home-range areas
Authors: Fleming C. H. , Deznabi I. , Alavi S. , Crofoot M. C. , Hirsch B. T. , Medici E. P. , Noonan M. J. , Kays R. , Fagan W. F. , Sheldon D. , Calabrese J. M.
Published: July 2021

Home-range estimates are a common product of animal tracking data, as each range informs on the area needed by a given individual. Population-level inference on home-range areas—where multiple individual home-ranges are considered to be sampled from a population—is also important to evaluate changes over time, space, or covariates, such as habitat quality or fragmentation, and for comparative analyses of species averages. Population-level home-range parameters have traditionally been estimated by first assuming that the input tracking data were sampled independently when calculating home ranges via conventional kernel density estimation (KDE) or minimal convex polygon (MCP) methods, and then assuming that those individual home ranges were measured exactly when calculating the population-level estimates. This conventional approach does not account for the temporal autocorrelation that is inherent in modern tracking data, nor for the uncertainties of each individual home-range estimate, which are often large and heterogeneous.

Here, we introduce a statistically and computationally efficient framework for the population-level analysis of home-range areas, based on autocorrelated kernel density estimation (AKDE), that can account for variable temporal autocorrelation and estimation uncertainty.

We apply our method to empirical examples on lowland tapir (Tapirus terrestris), kinkajou (Potos flavus), white-nosed coati (Nasua narica), white-faced capuchin monkey (Cebus capucinus), and spider monkey (Ateles geoffroyi), and quantify differences between species, environments, and sexes.

Our approach allows researchers to more accurately compare different populations with different movement behaviors or sampling schedules, while retaining statistical precision and power when individual home-range uncertainties vary. Finally, we emphasize the estimation of effect sizes when comparing populations, rather than mere significance tests.
Transcriptional heterogeneity of ventricular zone cells throughout the embryonic mouse forebrain
Authors: Lee Dongjin R. , Rhodes Christopher T. , Mitra Apratim , Zhang Yajun , Maric Dragan , Dale Ryan K. , Petros Timothy J.
Published: July 2021

The ventricular zone (VZ) of the nervous system contains radial glia cells that were originally considered relatively homogenous in their gene expression. However, a detailed characterization of transcriptional diversity in these VZ cells has not been reported. Here, we performed single-cell RNA sequencing to characterize transcriptional heterogeneity of neural progenitors within the VZ and subventricular zone (SVZ) of the mouse embryonic cortex and ganglionic eminences (GEs). By using a transgenic mouse line to enrich for VZ cells, we detect significant transcriptional heterogeneity within VZ and SVZ progenitors, both between forebrain regions and within spatial subdomains of specific GEs. Additionally, we observe differential gene expression between E12.5 and E14.5 VZ cells, which could provide insights into temporal changes in cell fate. Together, our results reveal a previously unknown spatial and temporal genetic diversity of telencephalic VZ cells that will aid our understanding of initial fate decisions in the forebrain.
Phosphorylation of STIM1 at ERK/CDK sites is dispensable for cell migration and ER partitioning in mitosis
Authors: Hammad Ayat S. , Yu Fang , Botheju Welathanthrige S. , Elmi Asha , Alcantara-Adap Ethel , Machaca Khaled
Published: July 2021

Store-operated Ca2+ entry (SOCE) is a ubiquitous Ca2+ influx required for multiple physiological functions including cell motility. SOCE is activated in response to depletion of intracellular Ca2+ stores following the activation of endoplasmic reticulum (ER) Ca2+ sensor STIM1 which recruits the plasma membrane (PM) Ca2+ channel Orai1 at ER-PM junctions to induce Ca2+ influx. STIM1 is phosphorylated dynamically and this phosphorylation has been implicated in several processes including SOCE inactivation during M-phase, maximal SOCE activation, ER segregation during mitosis, and cell migration. Human STIM1 has 10 Ser/Thr residues in its cytosolic domain that match the ERK/CDK consensus phosphorylation. We recently generated a mouse knock-in line where wild-type STIM1 was replaced by a non-phosphorylatable STIM1 with all 10 S/T mutated to Ala (STIM1-10A). Here, we generate mouse embryonic fibroblasts (MEF) the STIM1-10A mouse line and a control MEF line (WT) that express wild-type STIM1 from a congenic mouse strain. These lines offer a unique model to address the role of STIM1 phosphorylation at endogenous expression and modulation levels in contrast to previous studies that relied mostly on overexpression. We show that STIM1 phosphorylation at ERK/CDK sites is not required for SOCE activation, cell migration, or ER partitioning during mitosis. These results rule out STIM1 phosphorylation as a regulator of SOCE, migration and ER distribution in mitosis.
CCAR-1 has a novel role in regulating the Caenorhabditis elegans germline
Authors: Lugano Doreen I. , Deonarine Andrew , Park Margaret A. , Westerheide Sandy D.
Published: July 2021

1.

The Cell Division Cycle and Apoptosis Regulator (CCAR) protein family members are putative transcription regulators that have been characterized for modulating the cell cycle, apoptosis, metabolism, and the heat shock response. Mammals have two CCAR family members, CCAR1 and CCAR2/DBC1, that evolved from the founding family member CCAR-1 that is expressed in Caenorhabditis elegans. Mammalian CCAR2, the most well-studied family member, has been shown to regulate genes involved in metabolism in cultured cells. However, the regulation of gene expression by CCAR family members at an organismal level is unknown. Here, we use whole transcriptome RNA sequencing to examine the effects of CCAR-1 on gene expression in Caenorhabditis elegans. We show that CCAR-1 regulates germline transcription, reproduction, lifespan, and DNA-damage induced apoptosis. This study shows the role of CCAR-1 in vital physiological functions in the C. elegans germline that have not been investigated before.
Computational analysis to enhance the compressible flow over an aerofoil surface
Authors: Marimuthu Siva , Chinnathambi Dhavamani
Published: July 2021

Purpose

Since the inception of aerospace engineering, reducing drag is of eternal importance. Over the years, researchers have been trying to improve the aerodynamics of National Advisory Committee for Aeronautics (NACA) aerofoils in many ways. It is proved that smooth-surfaced NACA 0012 aerofoil produces more drag in compressible flow. Recent research on shark-skin pattern warrants a feasible solution to many fluid-engineering problems. Several attempts were made by many researchers to implement the idea of shark skin in the form of coatings, texture and more. However, those ideas are at greater risk when it comes to wing maintenance. The purpose of this paper is to implement a relatively larger biomimetic pattern which would make way for easy maintenance of patterned wings with improved performance.

Design/methodology/approach

In this paper, two biomimetic aerofoils are designed by optimizing the surface pattern of shark skin and are tested at different angles of attack in the computational flow domain.

Findings

The results of the biomimetic aerofoils prove that viscous and total drag can be reduced up to 33.08% and 3.68%, respectively, at high subsonic speed when validated against a NACA 0012 aerofoil. With the ample effectiveness of patched shark-skin pattern, biomimetic aerofoil generates as high as 10.42% lift than NACA 0012.

Originality/value

In this study, a feasible shark-skin pattern is constructed for NACA 0012 in a transonic flow regime. Computational results achieved using the theoretical model agree with experimental data.
User participation, knowledge management capability and service innovation: e-commerce enterprises in the digital age
Authors: Xin Xiaohua , Miao Xiaoming , Chen Qian , Shang Tiantian
Published: July 2021

Purpose

Despite the fact that user participation (UP) has been highlighted as an important aspect in innovation, previous findings on its relationship with service innovation performance (SIP) are inconsistent. This study aims to investigate the relationships among UP, knowledge management capability (KMC) and SIP, especially in the digital age, inspired by the theories of knowledge-based and absorptive capacity.

Design/methodology/approach

Based on a sample of 252 Chinese e-commerce enterprises, this study adopts a hierarchical regression analysis and bootstrap method to test the theoretical framework and research hypotheses.

Findings

UP and KMC have positive effects on SIP, respectively. KMC plays a mediating role in the effect of UP on SIP. Furthermore, the intermediary role of KMC varies in different sub-paths between UP and SIP.

Originality/value

First, this study provides some explanations for inconsistent arguments on the relationship between UP and service innovation. Second, with the consideration of specific dimensions of UP and SIP, the mediation role of KMC varies in different sub-paths has been recognized, which provides a deeper understanding of the relationship between UP and SIP. Third, this study opens the discussion about how to realize SIP more effectively in the digital age, advancing theoretical and practical developments on service innovation.
Active learning and instructor accessibility in online talent training: a field experiment in China during COVID-19
Authors: Wang Xingheng , Lin Weihan , Jiang Yan , Wu Yihua , Liu Yingyi , Zhou Wen-Qian
Published: July 2021

Purpose

Drawing on self-determination theory (Deci and Ryan, 2012) and Hew’s (2016) five-factor model, our study aimed to investigate the impact of two online training design factors (instructor accessibility and active learning) on learner’s self-efficacy and learning outcome amid the COVID-19 pandemic.

Design/methodology/approach

A randomized pretest-posttest control group field experiment was designed to assess participants’ self-efficacy and learning outcome of an online training program - territory business management plan, under three conditions: instructor accessibility, active learning, and controlled. Participants (N=87) were medical sales representatives from a Fortune-Global 500 pharmaceutical company’s subsidiary office in China. Data was analyzed with 2 (time) x 3 (group) MANOVA with time (pretest and posttest) as a repeated measure to investigate differences in changes in self-efficacy and learning outcome between three groups.

Findings

Overall, participants’ self-efficacy and learning outcome were significantly improved via the online training program for all three groups. Specifically, the impact of the training on learning outcome was the strongest for the active learning group, less strong for the instructor accessibility group, and the least strong for the control group.

Originality/value

Our research contributes towards understandings of the effectiveness of online talent training programs by examining two critical instructional design factors during a time of crisis. Our findings suggest that active learning (interactions with the training materials by purposeful self-reflection) might be a stronger predictor for increasing learning outcome than instructor accessibility (receiving feedback and tutoring sessions from the instructor) for online training programs.
Towards an analysis of the transfer of training: empirical evidence from schools in Spain
Authors: Gil Alfonso J. , Mataveli Mara , Garcia-Alcaraz Jorge L.
Published: July 2021

Purpose

The transfer of training has been identified with the effectiveness of training. The purpose of this work is to analyse the impact of training stages (training needs analysis, application and evaluation) as they relate to training transfer.

Design/methodology/approach

The study participants correspond to a sample of 116 teachers with managerial responsibilities (management teams and department heads) from 17 secondary schools in Spain. This work hypothesises five significant relationships: needs analysis and application of training, application and transfer of training, evaluation and analysis of training needs, evaluation and application of training and evaluation and transfer of training. The hypotheses were tested using structural equations, namely, the partial least squares–structural equation modelling technique and SmartPLS version 3.2.9.

Findings

The relationships between application and transfer of training, between evaluation of training and needs analysis, application and transfer of training are positively contrasted. The relationship between the analysis and application of training is not contrasted.

Originality/value

This work analyses the relationship between the training process’s different phases (analysis, application and evaluation) in the training output (training transfer) and emphasises the role of evaluation in the training process.
Dark tourism: motivations and visit intentions of tourists
Authors: Lewis Heather , Schrier Thomas , Xu Shuangyu
Published: July 2021

Purpose

The overall purpose of this study is to utilize the Theory of Planned Behavior (TPB) in combination with four dark tourism constructs (dark experience, engaging entertainment, unique learning experience, and casual interest) to gain a better understanding of behaviors and intentions of tourists who have visited or plan to visit a dark tourism location.

Design/methodology/approach

A total of 1,068 useable questionnaires was collected via Qualtrics Panels for analysis purposes. Confirmatory Factor Analysis (CFA) was used to verify satisfactory reliability and validity regarding the measurement of model fit. With adequate model fit, structural equation modeling was employed to determine positive and negative relationships between TPB and dark tourism constructs. In all, 11 hypotheses statements were tested within this study.

Findings

Results of this study indicate that tourists are curious, interested, and intrigued by dark experiences with paranormal activity, resulting in travel choices made for themselves based on personal beliefs and preferences, with minimal outside influence from others. It was determined that dark experience was the most influential of the dark tourism constructs tested in relationship to attitudes and subjective norm.

Research limitations/implications

The data collected for this study were collected using Qualtrics Panels with self-reporting participants. The actual destination visited by survey participants was also not factored into the results of this research study.

Originality/value

This study provides a new theoretical research model that merges TPB and dark tourism constructs and established that there is a relationship between TPB constructs and dark tourism.
Exploring the role of artificial intelligence in managing agricultural supply chain risk to counter the impacts of the COVID-19 pandemic
Authors: Nayal Kirti , Raut Rakesh , Priyadarshinee Pragati , Narkhede Balkrishna Eknath , Kazancoglu Yigit , Narwane Vaibhav
Published: July 2021

Purpose

In India, artificial intelligence (AI) application in supply chain management (SCM) is still in a stage of infancy. Therefore, this article aims to study the factors affecting artificial intelligence adoption and validate AI’s influence on supply chain risk mitigation (SCRM).

Design/methodology/approach

This study explores the effect of factors based on the technology, organization and environment (TOE) framework and three other factors, including supply chain integration (SCI), information sharing (IS) and process factors (PF) on AI adoption. Data for the survey were collected from 297 respondents from Indian agro-industries, and structural equation modeling (SEM) was used for testing the proposed hypotheses.

Findings

This study’s findings show that process factors, information sharing, and supply chain integration (SCI) play an essential role in influencing AI adoption, and AI positively influences SCRM. The technological, organizational and environmental factors have a nonsignificant negative relation with artificial intelligence.

Originality/value

This study provides an insight to researchers, academicians, policymakers, innovative project handlers, technology service providers, and managers to better understand the role of AI adoption and the importance of AI in mitigating supply chain risks caused by disruptions like the COVID-19 pandemic.