bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mycobacterium tuberculosismodifies cell wall carbohydrates during biofilm growth with a concomitant reduction in complement activation
Authors: Keating Thomas , Lethbridge Samuel , Thomas Stephen R. , Alderwick Luke J. , Taylor Stephen C. , Bacon Joanna 
Published: March 2021

SummaryThere is an urgent need for drugs, new vaccines, and diagnostics for TB. It is recognised that research needed for the development of new vaccines for TB needs to be underpinned by understanding both the molecular and cellular mechanisms of host-pathogen interactions and how the immune response can be modulated to achieve protection with the use of a new vaccine for TB. Complement interacts with and orchestrates many aspects of the innate and adaptive immune responses and activation byMycobacterium tuberculosiscan be triggered by all three pathways. However, little is known about the contribution of each of these pathways during TB disease, particularly with respect to mycobacterial phenotype. There is strong evidence for extracellular communities ofM. tuberculosisduring TB disease (biofilms) that are found in the acellular rim of granulomas. These biofilms have been observed in cavities in lung resections from TB patients and are likely to be present in post-primary TB episodes in necrotic lesions. Our study aimed to understand more about the interactions betweenM. tuberculosisbiofilms and complement activation, to determine which mycobacterial cell wall components are altered during biofilm growth, and how their alteration contributes to modulation of the complement response. We show that the lectin pathway has a reduced role compared to the classical pathway in initiating complement activation in biofilm bacteria. Analyses of theM. tuberculosisbiofilm cell wall carbohydrate fractions revealed that there was reduced α-glucan compared to planktonically-grown bacteria. Reduced C3b/iC3b deposition directly onto biofilm carbohydrates was observed which was consistent with both the observed reduction of C3b/iC3b deposition on biofilm bacilli and a reduction in the contribution of the lectin pathway in initiating complement activation on whole bacteria from biofilms, compared to planktonically-grown bacteria.
PRSS2 stimulates tumor growth by remodeling the TME via repression of Tsp1
Authors: Sui Lufei , Wang Suming , Ganguly Debolina , El Rayes Tina , Askeland Cecilie , Børretzen Astrid , Sim Danielle , Halvorsen Ole Johan , Knutsvik Gøril , Aziz Sura , Haukaas Svein , Foulkes William D , Bielenberg Diane R. , Ziemys Arturas , Mittal Vivek , Brekken Rolf A. , Akslen Lars A. , Watnick Randolph S. 
Published: March 2021

AbstractIn the earliest stages of tumor development, epithelial tumors (carcinomas) are physically confined to the area of the tissue in which they form. These nascent lesions (carcinomas in situ) are sequestered from the tissue parenchyma by the basement membrane. Within the tissue parenchyma lie a myriad of cell types comprised of fibroblasts, immune and inflammatory cells and endothelial cells. Upon invasion across the basement membrane and into the tissue parenchyma, tumors must manipulate the expression of pro- and anti-tumorigenic proteins such that pro-tumorigenic factors are produced in excess to anti-tumorigenic proteins. One such anti-tumorigenic protein is Thrombospondin-1 (Tsp-1). We have previously demonstrated that stimulation of Tsp-1 in the tumor microenvironment (TME) potently inhibits tumor growth and progression and in some cases induces tumor regression. Here, we identify a novel tumor-mediated mechanism to repress the expression of Tsp-1 in the TME via secretion of the serine protease PRSS2. We demonstrate that PRSS2 represses Tsp-1, not via its enzymatic activity, but by binding to low-density lipoprotein receptor-related protein 1 (LRP1). These findings describe a novel activity for PRSS2 through binding to LRP1 and represent a potential therapeutic strategy to treat cancer by blocking the PRSS2-mediated repression of Tsp-1.
Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos
Authors: Glimm Tilmann , Kiskowski Maria , Moreno Nickolas , Chiari Ylenia 
Published: March 2021

AbstractAnimal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complexity and details of pattern variation. Detailed information on variation in color pattern elements is necessary to understand how patterns are produced and established during development, and which evolutionary forces may constrain such a variation. Here, we develop an approach to capture and analyze variation in melanistic color pattern elements in leopard geckos. We use this data to study the variation among different body parts of leopard geckos and to draw inferences about their development. We compare patterns using 14 different indices such as the ratio of melanistic versus total area, the ellipticity of spots, and the size of spots and use these to define a composite distance between two patterns. Pattern presence/absence among the different body parts indicates a clear pathway of pattern establishment from the head to the back legs. Together with weak within-individual correlation between leg patterns and main body patterns, this suggests that pattern establishment in the head and tail may be independent from the rest of the body. We found that patterns vary greatest in size and density of the spots among body parts and individuals, but little in their average shapes. We also found a correlation between the melanistic patterns of the two front legs, as well as the two back legs, and also between the head, tail and trunk, especially for the density and size of the spots, but not their shape or inter-spot distance. Our data collection and analysis approach can be applied to other organisms to study variation in color patterns between body parts and to address questions on pattern formation and establishment in animals.
Anterior claustrum cells are responsive during behavior but not passive sensory stimulation
Authors: Ollerenshaw Douglas R , Davis Julianne , McBride Ethan G , Shelton Andrew , Koch Christof , Olsen Shawn R 
Published: March 2021

AbstractThe claustrum is uniquely positioned to communicate with almost all higher-order cortical areas through widespread and reciprocal anatomical projections, yet thein vivofunctional properties of claustrum neurons are not well understood. Here we use microendoscope imaging in mice to measure activity in populations of genetically-labelled Gnb4+ claustrum neurons. We find that only a small fraction of cells in the anterior claustrum are responsive to visual or auditory stimuli when delivered under passive yet wakeful conditions. In contrast, during a visual behavioral task, the majority of cells in the anterior claustrum are strongly modulated, with separate and spatially intermingled cell populations showing either increases or decreases in activity relative to spontaneous levels. Our results suggest that the Gnb4+ cells in the anterior claustrum do not represent passively presented sensory stimuli; rather, these cells are strongly engaged during behavior associated with sensory-motor transformations.
Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs inC. elegans
Authors: Kim Jun , Jimenez David Sebastian , Ragipani Bhavana , Zhang Bo , Street Lena Annika , Kramer Maxwell , Albritton Sarah E , Winterkorn Lara , Morao Ana , Ercan Sevinç 
Published: March 2021

AbstractCondensins are molecular motors that compact DNA via linear translocation. InC. elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number ofrecruitelements on theX-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address howrexsites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strongrexon the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the samerexis inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a“super rex”composed of sixrexsites or three separaterexsites are inserted on an autosome, recruitment and spreading of condensin DC led to formation of TADs. Therefore, recruitment to and spreading fromrexsites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in whichrexsites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.
miRador: a fast and precise tool for the prediction of plant miRNAs
Authors: Hammond Reza K. , Gupta Pallavi , Patel Parth , Meyers Blake C. 
Published: March 2021

ABSTRACTPlant microRNAs (miRNAs) are short, non-coding RNA molecules that restrict gene expression via post-transcriptional regulation and function in several essential pathways including development, growth, and stress responses. Accurately identifying miRNAs in populations of small RNA (sRNA) sequencing libraries is a computationally intensive process which has resulted in the misidentification of inaccurately annotated miRNA sequences. In recent years, criteria for miRNA annotation have been refined to reduce these misannotations. Here, we describemiRador, a novel miRNA identification tool that utilizes the most up-to-date, community-established criteria for accurate identification of miRNAs in plants. We combine target prediction and Parallel Analysis of RNA Ends (PARE) data to assess the precision of the miRNAs identified bymiRador. We comparemiRadorto other commonly used miRNA prediction tools and we find thatmiRadoris at least as precise as other prediction tools while being significantly faster than other tools.
Turning plants from passive to active material: FERONIA and microtubules independently contribute to mechanical feedback
Authors: Malivert Alice , Erguvan Özer , Chevallier Antoine , Dehem Antoine , Friaud Rodrigue , Liu Mengying , Martin Marjolaine , Peyraud Théophile , Hamant Olivier , Verger Stéphane 
Published: March 2021

AbstractTo survive, cells must constantly resist mechanical stress. In plants, this involves the reinforcement of cell walls, notably through microtubule-dependent cellulose deposition, and thus wall sensing. Several receptor-like kinases have been proposed to act as mechanosensors. Here we tested whether the microtubule response to stress acts downstream of known wall sensors. Using a multi-step screen with eleven mutant lines, we identify FERONIA as the primary candidate for controlling the microtubule response to stress. However, when performing mechanical perturbations, we show that the microtubule response to stress can be independent from FER. We reveal that theferoniaphenotype can be partially rescued by reducing tensile stress levels. Conversely, in the absence of both microtubules and FER, cells swell and burst like soap bubbles. Altogether, this shows that the microtubule response to stress acts as an independent pathway to resist stress, in parallel to FER. We propose that both pathways are key components to turn plant cells from passive to active material.
Online teaching benefits and challenges during pandemic COVID-19: a comparative study of Pakistan and Indonesia
Authors: Thaheem Sahib Khatoon , Zainol Abidin Mohamad Jafre , Mirza Quratulain , Pathan Habib Ullah 
Published: March 2021

PurposeThe shift from physical class to online classes in the pandemic COVID-19 situation has posited opportunities as well as challenges for teachers and students. The primary purpose of this research is to investigate challenges faced and benefits availed by the teachers at the tertiary level in universities of Pakistan and Indonesia.Design/methodology/approachTo achieve the purpose a mixed-method approach is employed to answer the three research questions of the present study. The quantitative data is obtained from the responses of 66 teachers, teaching online in Mehran UET Pakistan and 102 teachers from Indonesian university. The personal, technological, and pedagogical challenges were analyzed by descriptive statistics on SPSS. Thus, the independent-samples t-test was run to test for statistically significant differences faced by teachers in both countries.FindingsThe findings revealed that there were no statistically significant differences found in personal, and pedagogical challenges faced by both countries' teachers, whereas there is a significant difference in facing technological challenges between Pakistani and Indonesian teachers. The benefits of online teaching were investigated qualitatively by conducting semi-structured interviews with 10 teachers 5 from each country. There are very positive aspects of online teaching revealed in the interviews.Research limitations/implicationsThe paper includes implications for the development of Computer Assisted Language Learning, the development of technology integrated courses, and for managing the balance between physical and online classes.Practical implicationsThe findings of the study have implications on finding out the solutions of the derived challenges, further it suggests to concentrate on students of public and private universities in Pakistan and Indonesia so that a comparison of challenges faced by teachers and faced by students can be researched and evaluated and it can generate significantly different results.Social implicationsThe implications on the research society and the teachers and designers' communities are very clear in this research because it paves the way forward towards the blending of technology in any way either synchronously/ asynchronously into education, further researches can be done on designing the new concepts, courses, instructional platforms for students and investigate the new dimensions and effects of them.Originality/valueFindings have value, because two countries' context (developing countries) with respect to the comparison of the challenges and benefits is better understood, it would have different results if had done in the developed countries.
Automation in New Zealand's offsite construction (OSC): a status update
Authors: Darlow Genevieve , Rotimi James O.B. , Shahzad Wajiha Mohsin 
Published: March 2021

PurposeAutomation facilitates production activities within offsite construction (OSC) projects through computer-controlled and mechanised systems that can be programmed to deliver various products in a self-regulating sequence. Despite known benefits of automation to offsite production, the level of automation adoption in New Zealand is low. This study is an effort to understand the current status of automation within the New Zealand construction industry and to identify the barriers and enablers to its uptake.Design/methodology/approachThis study utilises the qualitative approach of semi-structured interviews (open-ended questions). Using a referral sampling strategy (snowballing), fifteen New Zealand industry experts were interviewed, and the data collected were analysed using qualitative content analysis.FindingsThe study found that there is a weak business case for full automation. Four main categories of barriers to the uptake of automated OSC were identified, including requirement of high capital cost, lack of education about automation and OSC and non-existence of regulations to support OSC. It was noted that financial supports to the OSC sub-sector in form of subsidies, tax waivers, and enhanced leasing model could enhance the uptake of automation. Further to this more awareness about OSC's automation and regulations suitable for OSC could enhance the confidence of business owners to invest in this area.Originality/valueOriginality of this paper stems from the fact that, not much attention has been paid to investigating the uptake of automation for OSC sub-sector of construction industry in New Zealand context.
Window geometry impact on a room's wind comfort
Authors: Fallahtafti Reza , Mahdavinejad Mohammadjavad 
Published: March 2021

PurposeNatural ventilation is an environmentally friendly effective way of improving thermal comfort and the quality of indoor conditions if applied properly. This study aims to investigate the physical mechanism of the air movement and also the influence of building geometry in a cross-ventilated room through a parametric study of window geometrical characteristics using computational fluid dynamics.Design/methodology/approachMomentum and continuity equations are solved by the control volume method using a commercially available software. Standardk−ɛturbulence model is employed to simulate the incompressible airflow and SIMPLE algorithm to solve the conservation equations. Mean air velocity magnitude is measured at three different surfaces of different heights, and the effect of incoming wind velocity inside the building is studied.FindingsThe research concluded that window hood and sill projections reduce indoor wind velocity magnitude, play a major role in incoming wind direction and thus have a crucial impact on wind circulation and indoor air quality.Social implicationsThe paper has evaluated redesigning of a both practical and ornamental architectural element named Palekaneh, which is found in many historical buildings in several hot places in the world. Its optimal design could increase indoor natural ventilation quality and decrease a space's cooling load. Therefore, a new passive cooling architectural element could be re-introduced to the regions previously enjoying such ornaments. This is economically efficient because it eventually saves a considerable amount of energy in the long run and is socially important because of the revitalization of architectural identity.Originality/valueThe role of a building envelope's physical features, although being studied for solar absorption and daylight availability, has rarely been investigated for natural ventilation, especially in a small scale, thus making the paper novel in this regard. This provides a guideline for designers to assess the impact of their design on redirecting wind-induced natural ventilation the very early stages of design.
Challenging sustainability in school-based intervention in Nicaragua
Authors: Pettigrew Jonathan , Razzante Robert , Allsup Joshua , Lu Yu , Ray Colter D. 
Published: March 2021

PurposeThe current study identifies successes and limitations of sustaining Dale se Real (DsR) as a school-based educational intervention program related to drugs and violence for 7th and 8th grade students in Nicaragua, Central America. As evidence-based interventions are transported and imported across national borders, issues surrounding their adaptation and sustainability become important targets for investigation.Design/methodology/approachInterviews were conducted with nine key informants (e.g. school directors, implementers) from seven institutions, four of which sustained DsR and three of which did not. This study explores DsR's fit with the institutions' missions and routines, program adaptability, broader community support and sustainability planning.FindingsFindings demonstrate two emerging views of sustainability within the Nicaraguan schools: a deficit approach and an empowerment approach. These two approaches imply different motivational structures for institutions and also led to the practical finding that developers and trainers need to provide structured or formal ways of empowering schools to continue implementing a program after staff no longer routinely contact them.Originality/valueThis study contributes a particular case on what facilitates and impedes sustainability of school-based interventions that can inform future intervention research in Latin American countries.
Do vacations and parental leave reduce voluntary turnover? A study of organizations in the ICT sector in Canada
Authors: Renaud Stéphane , St-Onge Sylvie , Morin Denis 
Published: March 2021

PurposeThis study examines the link between vacations, parental leave and voluntary turnover among Canadian organizations in the Information and Communications Technology (ICT) sector.Design/methodology/approachThe empirical analysis is carried out using firm-level data sourced from a survey that was completed by HR managers of 125 ICT firms operating in the province of Quebec (Canada).The organizational voluntary turnover rate was used and was obtained by dividing the number of employees who voluntarily quit an organization within the last year by the total number of its employees. Based on ordinary least squared estimates, results were generated by regressing voluntary turnover rate on vacation and parental leave.FindingsVacation, operationalized as the average number of annual vacation days, is negatively and significantly associated with the voluntary turnover rate of the ICT organizations surveyed. Parental leave, operationalized as the percentage of salary reimbursed during parental leave, does not significantly reduce voluntary turnover in the ICT organizations surveyed.Practical implicationsIn light of the results of this study, if organizations in the ICT sector, in Canada or abroad, desire to reduce voluntary turnover, compensating employees through the use of additional vacation days appears to be a viable approach.Originality/valueThis research constitutes an empirical test of the link between turnover and two compensation practices adopted by firms. To our knowledge, there is no prior scientific evidence on that subject in the Canadian ICT sector.