bluuebunny/crossref_metadata_2025 huggingface dataset:
Minimalistic mycoplasmas harbor different functional toxin-antitoxin systems
Authors: Hill Virginia , Akarsu Hatice , Barbarroja Rubén Sánchez , Cippà Valentina , Heller Martin , Falquet Laurent , Heller Manfred , Stoffel Michael H. , Labroussaa Fabien , Jores Joerg
Published: January 2021

Mycoplasmas are minute bacteria controlled by very small genomes ranging from 0.6 to 1.4 Mbp. They lack a cell wall and have been suggested to have progressed through reductive evolution from phylogenetically closely related Clostridia. They are known to colonize the respiratory tract or the urogenital tract among other organs and can cause chronic and subclinical diseases associated with long persistence of the causative agent. Toxin-antitoxin systems (TAS) are genetic elements that have been described for several respiratory and urogenital pathogens as well as for Clostridia, but never for pathogenic mycoplasmas. Here we describe for the first-time different types of TAS in aMycoplasmapathogen, namelyM. mycoidessubsp.capri. We identified candidate TASin silicovia TASmania database. Two candidate TAS identifiedin silicoand another candidate TAS suggested in a minimal cell based on transposon mutagenesis were systematically tested for their functionality in hosts with different phylogenetic distance using heterologous expression. Phylogenetic distance of the host used for heterologous expression influenced the outcome of the functional testing. We corroborated functionality of the three candidate TAS inMycoplasma capricolumsubsp.capricolum. Moreover, we confirmed transcription and translation of molecules of the TAS investigated duringin vitrogrowth. We sequence analyzed 15 genomes ofM. mycoidessubsp.capriand revealed an unequal distribution of the TAS studied pointing towards dynamic gain and loss of TAS within the species.

Author summary

Mycoplasmas have a minimal genome and have never been shown to possess TAS. In this work we showed the presence of different functional TAS systems inMycoplasma mycoidessubsp.capri, a caprine pathogen for the first time. Sequence analysis of a number ofMycoplasma mycoidessubsp.capristrains revealed a plasticity of the genome with respect to TAS carriage. This work paves the way to investigate the biological role of TAS (e.g. persistence, stress tolerance) during infection using mycoplasmas as a simple model organism. Since most mycoplasmas lack classical virulence factors such as exotoxins and go into a kind of stealth mode to evade the immune system, TAS are likely to contribute to the parasitic lifestyle of mycoplasmas and should be investigated in that respect. The availability of synthetic genomics tools to modify a range ofMycoplasmapathogens and well-established challenge models for the latter mycoplasmas will foster future research on TAS in mycoplasmas.
Decomposing the admixture statistic, D, suggests a negligible contribution due to archaic introgression into humans
Authors: Amos William
Published: January 2021

It is widely accepted that non-African humans carry a few percent of Neanderthal DNA due to historical inter-breeding. However, methods used to infer a legacy all assume that mutation rate is constant and that back-mutations can be ignored. Here I decompose the widely used admixture statistic, D, in a way that allows the overall signal to be apportioned to different classes of contributing site. I explore three main characteristics: whether the putative Neanderthal allele is likely derived or ancestral; whether an allele is fixed in one of the two human populations; and the type of mutation that created the polymorphism, defined by the base that mutated and immediately flanking bases. The entire signal used to infer introgression can be attributed to a subset of sites where the putative Neanderthal base is common in Africans and fixed in non-Africans. Moreover, the four triplets containing highly mutable CpG motifs alone contribute 29%. In contrast, sites expected to dominate the signal if introgression has occurred, where the putative Neanderthal allele is absent from Africa and rare outside Africa, contribute negligibly. Together, these observations show that D does not capture a signal due to introgression but instead they support an alternative model in which a higher mutation rate in Africa drives increased divergence from the ancestral state.
Glycoproteomics ofHaloferax volcaniireveals an extensive glycoproteome and concurrence of differentN-glycosylation pathways
Authors: Schulze Stefan , Pfeiffer Friedhelm , Garcia Benjamin A. , Pohlschroder Mechthild
Published: January 2021

Glycosylation is one of the most complex post-translational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here we extend the phenotypic characterisation ofN-glycosylation pathway mutants inHaloferax volcaniiand provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project, we identify the largest archaeal glycoproteome described so far. We further show that differentN-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of theHfx. volcanii N-glycoproteome revealed here provides new insights into the roles ofN-glycosylation in archaeal cell biology.
4D chromosome reconstruction elucidates the spatial reorganization of the mammalian X-chromosome
Authors: Lappala Anna , Wang Chen-Yu , Kriz Andrea , Michalk Hunter , Tan Kevin , Lee Jeannie T. , Sanbonmatsu Karissa Y.
Published: January 2021

Chromosomes are segmented into domains and compartments; yet, how these structures are spatially related in 3D is unclear. Here, by directly integrating Hi-C capture experiments and 3D modeling, we use X-inactivation as a model to examine the time evolution of 3D chromosome architecture during substantial changes in gene expression. First, we show that gene expression A/B compartments are consistent with phase separation in 3D space. Second, we show that residuals of smaller scale structures persist through transitions, despite further large-scale reorganization into the final inactive configuration, comprising two “megadomains”. Interestingly, these previously hidden residual structures were not detectable in 2D Hi-C maps or principal component analyses. Third, time-dependent reaction-diffusion simulations reveal how Xist RNA particles diffuse across the 3D X-superstructure as it reorganizes. Our 4DHiC pipeline helps satisfy the growing demand for methodologies that produce 3D chromosome reconstructions directly from 2D datasets, which are consistent with the empirical data.
Increased ventromedial prefrontal cortex activity in adolescence benefits prosocial reinforcement learning
Authors: Westhoff Bianca , Blankenstein Neeltje E. , Schreuders Elisabeth , Crone Eveline A. , van Duijvenvoorde Anna C. K.
Published: January 2021

Learning which of our behaviors benefit others contributes to social bonding and being liked by others. An important period for the development of (pro)social behavior is adolescence, in which peers become more salient and relationships intensify. It is, however, unknown how learning to benefit others develops across adolescence and what the underlying cognitive and neural mechanisms are. In this functional neuroimaging study, we assessed learning for self and others (i.e., prosocial learning) and the concurring neural tracking of prediction errors across adolescence (ages 9-21, N=74). Participants performed a two-choice probabilistic reinforcement learning task in which outcomes resulted in monetary consequences for themselves, an unknown other, or no one. Participants from all ages were able to learn for themselves and others, but learning for others showed a more protracted developmental trajectory. Prediction errors for self were observed in the ventral striatum and showed no age-related differences. However, prediction error coding for others was specifically observed in the ventromedial prefrontal cortex and showed age-related increases. These results reveal insights into the computational mechanisms of learning for others across adolescence, and highlight that learning for self and others show different age-related patterns.
Spatiotemporal manipulation of the mismatch repair system ofPseudomonas putidaaccelerates phenotype emergence
Authors: Fernández-Cabezón Lorena , Cros Antonin , Nikel Pablo I.
Published: January 2021

Developing complex phenotypes in industrially-relevant bacteria is a major goal of metabolic engineering, which encompasses the implementation of both rational and random approaches. In the latter case, several tools have been developed towards increasing mutation frequencies—yet the precise spatiotemporal control of mutagenesis processes continues to represent a significant technical challenge.Pseudomonasspecies are endowed with one of the most efficient DNA mismatch repair (MMR) systems found in bacteria. Here, we investigated if the endogenous MMR system could be manipulated as a general strategy to artificially alter mutation rates inPseudomonasspecies. To bestow a conditional mutator phenotype in the platform bacteriumPseudomonas putida, we constructed inducible mutator devices to modulate the expression of the dominant-negativemutLE36Kallele. Regulatable overexpression ofmutLE36Kin a broad-host-range, easy-to-cure plasmid format resulted in a transitory inhibition of the MMR machinery, leading to a significant increase (up to 438-fold) in mutation frequencies and a heritable fixation of genome mutations. Following such accelerated mutagenesis-followed-by selection approach, three phenotypes were successfully evolved: resistance to antibiotics streptomycin and rifampicin and reversion of a synthetic uracil auxotrophy. Thus, these mutator devices could be applied to accelerate evolution of metabolic pathways in long-term evolutionary experiments, alternating cycles of (inducible) mutagenesis coupled to selection schemes.
Controlled sample environment for studying solid–gas interactions by in situ powder X-ray diffraction
Authors: Røren Paul Monceyron , Hunvik Kristoffer W. B. , Josvanger Vegard , Buseth Ole Tore , Fossum Jon Otto
Published: January 2021

A sample cell for powder X-ray diffraction studies with in situ applied pressure and control of temperature is demonstrated. The cell is based on a previously reported design and consists of a glass or quartz capillary glued into a Swagelok weld gland; this configuration can hold up to 100 bar (1 bar = 100 kPa). The cell is placed in contact with a copper plate for control of temperature between −30 and 200°C. This is achieved by Peltier elements, heat cartridges and a refrigerated circulating bath. This work mainly focuses on the temperature control system. Commissioning tests were performed in a custom-made small/wide-angle X-ray diffractometer at the Norwegian University of Science and Technology. The system is easily portable to synchrotron facilities.
Finnish teachers’ views on co‐teaching
Authors: Kokko Marjut , Takala Marjatta , Pihlaja Päivi
Published: January 2021

Co‐teaching has become a well‐known way of working among Finnish teachers in recent years. Teachers’ collaboration is becoming increasingly important in light of the rising number of diverse students in regular classes. In an ideal co‐teaching context, teachers collaborate as equals, recognise and respect each other’s skills and competencies, and strengthen and support each other. In this study, we examine teachers’ views on co‐teaching and investigate which background factors explain teachers’ views concerning the benefits and the challenges of co‐teaching. The data obtained from Finnish basic education teachers’ (N = 694) responses to an online questionnaire are analysed quantitatively. The results show some differences among the teachers’ views. Subject teachers perceive more challenges in co‐teaching than class and special education teachers. Class teachers perceive the fewest challenges. Although teachers are generally interested in co‐teaching and some of them co‐teach regularly, they also report several barriers to its application. The explanatory factors concerning the differences in teachers’ views are gender, teachers’ co‐teaching experiences, the amount of co‐teaching per week and working as a class teacher.
How is the client‐dietitian relationship embedded in the professional education of dietitians? An analysis of curriculum documentation and program coordinators' perspectives in Australia
Authors: Nagy Annaliese , McMahon Anne , Tapsell Linda , Deane Frank
Published: January 2021

Aim

How dietitians are trained to develop relationships with clients is not clearly articulated despite its importance being well‐documented. This study aimed to describe how this relationship is expressed and addressed in curriculum documents of Australian dietetics education programs, and to explore program coordinators' perspectives of this description and how relationship development is actually taught.

Methods

Data extracted from subject outlines included subject descriptions, learning outcomes, assessments, readings and the mode of delivery (eg, lectures). Guided by a pre‐existing coding framework, deductive thematic analysis was utilised to explore qualitative themes from subject outline data. Semi‐structured telephone interviews were conducted with 10 program coordinators and analysed using inductive thematic analysis.

Results

Subject outlines for 122 subjects across all 21 accredited Australian programs were analysed. The over‐arching theme was the wide “variability” in the ways that the client‐dietitian relationship was expressed across subject outlines. Program coordinators perceived that findings from the analysis of subject outlines made sense, however, acknowledged limitations of analysing data from curriculum documents. The relationship appeared ambiguously defined amongst programs and was described as occurring mostly in communication, counselling and medical nutrition therapy subjects and through theoretical and practical learning.

Conclusion

The client‐dietitian relationship appears inconsistently embedded in the curriculum of Australian dietetics education programs despite widespread acceptance of its importance to practice. Further research is needed to investigate if training programs should embed more consistent language around therapeutic relationships, and how this might be achieved to reflect current competency standards.
Interleukin‐37 improves T‐cell‐mediated immunity and chimeric antigen receptor T‐cell therapy in aged backgrounds
Authors: Hamilton Jamie A. G. , Lee Miyoung Y. , Hunter Rae , Ank Raira S. , Story Jamie Y. , Talekar Ganesh , Sisroe Talia , Ballak Dov B. , Fedanov Andrew , Porter Christopher C. , Eisenmesser Elan Z. , Dinarello Charles A. , Raikar Sunil S. , DeGregori James , Henry Curtis J.
Published: January 2021

Aging‐associated declines in innate and adaptive immune responses are well documented and pose a risk for the growing aging population, which is predicted to comprise greater than 40 percent of the world's population by 2050. Efforts have been made to improve immunity in aged populations; however, safe and effective protocols to accomplish this goal have not been universally established. Aging‐associated chronic inflammation is postulated to compromise immunity in aged mice and humans. Interleukin‐37 (IL‐37) is a potent anti‐inflammatory cytokine, and we present data demonstrating that IL‐37 gene expression levels in human monocytes significantly decline with age. Furthermore, we demonstrate that transgenic expression of interleukin‐37 (IL‐37) in aged mice reduces or prevents aging‐associated chronic inflammation, splenomegaly, and accumulation of myeloid cells (macrophages and dendritic cells) in the bone marrow and spleen. Additionally, we show that IL‐37 expression decreases the surface expression of programmed cell death protein 1 (PD‐1) and augments cytokine production from aged T‐cells. Improved T‐cell function coincided with a youthful restoration of Pdcd1, Lat, and Stat4 gene expression levels in CD4+ T‐cells and Lat in CD8+ T‐cells when aged mice were treated with recombinant IL‐37 (rIL‐37) but not control immunoglobin (Control Ig). Importantly, IL‐37‐mediated rejuvenation of aged endogenous T‐cells was also observed in aged chimeric antigen receptor (CAR) T‐cells, where improved function significantly extended the survival of mice transplanted with leukemia cells. Collectively, these data demonstrate the potency of IL‐37 in boosting the function of aged T‐cells and highlight its therapeutic potential to overcome aging‐associated immunosenescence.
… More on the use of research templates
Authors: Faff Robert W. , Lodhia Sumit
Published: January 2021

Motivated by Bui’s thought‐provoking analysis regarding the perceived efficacy of research templates, our paper advances the debate by reviewing Faff’s Pitching Research® framework and Lodhia’s qualitative companion. The key premises of these research templates are highlighted and potential misconceptions are addressed. We reach common ground on the underlying philosophy and use of research templates for quantitative and qualitative research; and, more generally, on the process of research. As such, we provide a pathway for reducing the schism between the two ‘rival’ research camps.
Histological observation of the reproductive system in a viviparous teleost Xenotoca eiseni Rutter 1896 (Cyprinodontiformes: Goodeidae)
Authors: Iida Atsuo , Nomura Jumpei , Hondo Eiichi
Published: January 2021

Xenotoca eiseni is a viviparous teleost belonging to the family Goodeidae. Here, we report histological observations of the reproductive organs in an adult male, an adult female, a pregnant female with intraovarian embryo and an extracted embryo of X. eiseni. High‐resolution images of haematoxylin–eosin‐stained sagittal sections revealed the detailed structure of gonads, gametes and reproductive components of the mother–embryo relationship. In the male, mature spermatozoa in the epididymis formed sperm packages. In the female, oogenesis proceeded asynchronously in the ovarian wall, and various stages of oocytes were observed in single ovary. In both sexes, genital openings were located between the anus and anal fin. Developing embryos were observed in an ovary of the pregnant female. Fine structures of components of the mother‐to‐embryo nutrient supply, ovarian septum and trophotaenia were observed in the pregnant ovary. An immature gonad prior to gamete formation was identified in the extracted embryo. With the aim of supporting the development and extension of studies on this viviparous teleost, we have shared our histological images as raw data in an open online archive, the 'NAGOYA repository (http://hdl.handle.net/2237/00032456)'. Our goal is a comprehensive understanding of the viviparous system in fish using both histological observation and molecular biology methods including genomics and proteomics.
Computed tomographic and gross anatomy of the head of the blue‐fronted Amazon parrot (Amazona aestiva)
Authors: Faillace Ana Carolina Lourenço , Vieira Kássia Regina Aguiar , Santana Marcelo Ismar Silva
Published: January 2021

The blue‐fronted Amazon parrot is an extremely popular pet bird in Brazil. These birds are commonly raised in captivity and are often seen in veterinary practice. Modern imaging modalities such as computed tomography (CT), which had not been widely used in wild and exotic bird medicine until recently, are now becoming more popular due to wider availability and higher diagnostic accuracy. However, proper interpretation of tomographic findings requires species‐specific anatomical references. Studies investigating normal tomographic anatomy of parrots are scarce. This study set out to describe the normal anatomy of the head of the blue‐fronted amazon parrot (Amazona aestiva) using conventional CT. Anatomical descriptions may contribute to future comparative morphology studies and assist in clinical practice. The head of the blue‐fronted Amazon parrot is structurally similar to other bird species. Major differences detected were are as follows: size and position of nasal conchae (long middle concha and small caudal concha located at the end of the nasal cavity), infraorbital sinus aperture located on the lateral aspect of the nasal cavity, presence of a nasopharyngeal duct connecting the nasal and oral cavities, longer infraorbital sinus with a larger number of caudal compartments and paraglossum with morphological features unique to psittacines. High‐quality CT images were vital for identification and detailed description of most head structures. Multiplanar reconstruction was a useful tool for complete visualization of the head. However, conventional CT images were not good enough for visualization of the inner ear and related structures, as well the paratympanic sinus.
The Pass‐Through of a Tax on Sugar‐Sweetened Beverages in Boulder, Colorado
Authors: Cawley John , Frisvold David , Jones David , Lensing Chelsea
Published: January 2021

This paper estimates the pass‐through of the largest tax on sugar‐sweetened beverages enacted in the U.S., which is two cents per ounce in Boulder, Colorado. A strength of the paper is that, to achieve as complete a perspective as possible, we estimate the pass‐through of the tax not only to beverage prices in retail stores but also to those in restaurants, and we examine data for the treatment community of Boulder and a comparison community of Fort Collins, Colorado, from four sources: (a) hand‐collected data on prices from stores; (b) Nielsen Retail Scanner Data of store prices; (c) hand‐collected data on prices in restaurants; and (d) web‐scraped data from online restaurant menus. Across the multiple datasets, we find consistent evidence that the tax was largely, but not completely, passed through to consumers. In both the hand‐collected store data and restaurant data, pass‐through is slightly less than 75%, whereas pass‐through is just over 50% using the scanner data; consumers bear most, but not all, of the largest tax on sugar‐sweetened beverages in the United States.
Immune‐mediated diseases and risk of Crohn’s disease or ulcerative colitis: a prospective cohort study
Authors: Lo Chun‐Han , Khalili Hamed , Lochhead Paul , Song Mingyang , Lopes Emily W. , Burke Kristin E. , Richter James M. , Chan Andrew T. , Ananthakrishnan Ashwin N.
Published: January 2021

Background

Although immune‐mediated diseases (IMDs) including inflammatory bowel diseases (IBDs) are known to cluster, to what extent this is due to common environmental influences is unknown.

Aim

To examine the incidence of IBD in individuals with another IMD.

Methods

We used data from the prospective Nurses' Health Study II cohort (1995‐2017) to examine the effect of diagnoses of several common IMDs on subsequent risk of Crohn's disease (CD) or ulcerative colitis (UC) using Cox proportional hazards models, adjusting for detailed diet and lifestyle confounders.

Results

We documented 132 cases of CD and 186 cases of UC over 2 016 163 person‐years of follow‐up (median age at IBD diagnosis 50 years). Compared to participants with no history of IMD, the HRs of CD for those with 1 and ≥ 2 IMDs were 2.57 (95% CI 1.77‐3.74) and 2.74 (95% CI 1.36 to 5.49), respectively (Ptrend < 0.0001). This association was only modestly attenuated by adjustment for environmental risk factors (HR 2.35 and 2.46, respectively). The risk of UC was not increased, with multivariable‐adjusted HRs of 1.22 (95% CI 0.85‐1.76) and 1.33 (95% CI 0.67‐2.65) for those with 1 and ≥ 2 IMDs, respectively, compared to those with none (Ptrend 0.16) (Pheterogeneity comparing CD and UC 0.037). Asthma, atopic dermatitis, psoriasis and rosacea were individually associated with higher risk of CD (HR ranging from 2.15 to 3.39) but not UC.

Conclusions

Individuals with one or more IMDs are at an increased risk for CD but not UC.
The Science of Living and the Art of Dying
Authors: Welldon Estela V.
Published: January 2021

If sex and death are the two most powerful subjects in our daily lives, sex has been comprehensively exposed in our culture, but death still struggles to get a thoughtful audience and is often ignored or denied. Living mostly requires scientific knowledge but dying is an art in the sense of needing the application of imagination. The author presents her own experience of sudden family deaths from a young age and considers herself a ‘death passionate’. She believes that true awareness of death, including one's own, is life‐enhancing and can inspire great creative acts, while unprocessed grief can result in violence and tragedy. A good death, she argues, requires a life lived fully, without falsities, and our real legacy is the human, and artistic, one reflected in the lives of those we have loved and those we have worked with. The article is accompanied by a photograph that stages the author's own ‘deathbed scene’, taken by the author's son, a professional photographer.
Leaf litter decomposition in tropical freshwater swamp forests is slower in swamp than non‐swamp conditions
Authors: Lam Weng Ngai , Lian Jun Jie , Chan Pin Jia , Ting Ying Ying , Chong Rie , Rahman Nur Estya , Tan Lorraine Wen Ai , Ho Qian Yi , Ramchunder Sorain J. , Peh Kelvin S.‐H. , Cai Yixiong , Chong Kwek Yan
Published: January 2021

Decomposition is a key ecosystem function, and the rate of decomposition in forests affects their carbon storage potentials. Processes and factors determining leaf litter decomposition rates in dry‐land and temperate forests are well understood, but these are generally poorly studied in tropical wetland forests, especially freshwater swamp forests (FSF). The home‐field advantage (HFA) hypothesis predicts that soil microbes specialize in decomposing leaf litter produced by the tree species in their immediate vicinity. However, empirical support for the HFA is equivocal, and the HFA has never been tested in the highly heterogeneous and biodiverse ecosystems of tropical FSFs. We collected leaf litter from swamp and non‐swamp tree species in a tropical FSF in Singapore and monitored the decomposition rates of these in swamp and non‐swamp plots for a period of eight months. Leaf litter decomposed 3.7 times more slowly in swamp plots. Leaf litter from swamp tree species were significantly poorer in quality (higher C:N ratio) than those of non‐swamp FSF tree species, but this had only a weak effect on decomposition rates. There was also only weak evidence for the HFA and only in non‐swamp conditions. Our results show that while the leaf litter of tropical FSF swamp and non‐swamp tree species differ significantly in chemical traits, litter decomposition rate is ultimately determined by local abiotic conditions, such as hydrology. Additionally, the high FSF tree diversity may prevent decomposer communities from specializing on any group of leaf litter types and thus limit the extent of HFA observed in such heterogeneous forests.
Investigating the Interrelations Between Systems of Support in 13‐ to 18‐Year‐Old Adolescents: A Network Analysis of Resilience Promoting Systems in a High and Middle‐Income Country
Authors: Höltge Jan , Theron Linda , van Rensburg Angelique , Cowden Richard G. , Govender Kaymarlin , Ungar Michael
Published: January 2021

Adolescents’ ability to function well under adversity relies on a network of interrelated support systems. This study investigated how consecutive age groups differ in the interactions between their support systems. A secondary data analysis of cross‐sectional studies that assessed individual, caregiver, and contextual resources using the Child and Youth Resilience Measure (Ungar & Liebenberg, 2005) in 13‐ to 18‐year‐olds in Canada (N = 2,311) and South Africa (N = 3,039) was conducted applying network analysis. Individual and contextual systems generally showed the highest interconnectivity. While the interconnectivity between the individual and caregiver system declined in the Canadian sample, a u‐shaped pattern was found for South Africa. The findings give first insights into cross‐cultural and context‐dependent patterns of interconnectivity between fundamental resource systems during adolescence.
Coupling urban 3‐D information and circuit theory to advance the development of urban ecological networks
Authors: Kong Fanhua , Wang Ding , Yin Haiwei , Dronova Iryna , Fei Fan , Chen Jiayu , Pu Yingxia , Li Manchun
Published: January 2021

Ongoing, rapid urban growth accompanied by habitat fragmentation and loss challenges biodiversity conservation and leads to decreases in ecosystem services. Application of the concept of ecological networks in the preservation and restoration of connections among isolated patches of natural areas is a powerful conservation strategy. However, previous approaches often failed to objectively consider the impacts of complex 3‐D city environments on ecological niches. We used airborne lidar‐derived information on the 3‐D structure of the built environment and vegetation and detailed land use and cover data to characterize habitat quality, niche diversity, and human disturbance and to predict habitat connectivity among 38 identified habitat core areas (HCAs) in Nanjing, China. We used circuit theory and Linkage Mapper to create a landscape resistance layer, simulate habitat connectivity, and identify and prioritize important corridors. We mapped 64 links by using current flow centrality to evaluate each HCA's contribution and the links that facilitate intact connectivity. Values were highest for HCA links located in the west, south, and northeast of the study area, where natural forests with complex 3‐D structures predominate. Two smaller HCA areas had high centrality scores relative to their extents, which means they could act as important stepping stones in connectivity planning. The mapped pinch‐point regions had narrow and fragile links among the HCAs, suggesting they require special protection. The barriers with the highest impact scores were mainly located at the HCA connections to Purple Mountain and, based on these high scores, are more likely to indicate important locations that can be restored to improve potential connections. Our novel framework allowed us to sufficiently convey spatially explicit information to identify targets for habitat restoration and potential pathways for species movement and dispersal. Such information is critical for assessing existing or potential habitats and corridors and developing strategic plans to balance habitat conservation and other land uses based on scientifically informed connectivity planning and implementation.
Rangewide habitat suitability analysis for the Mexican wolf (Canis lupus baileyi) to identify recovery areas in its historical distribution
Authors: Martínez‐Meyer Enrique , González‐Bernal Alejandro , Velasco Julián A. , Swetnam Tyson L. , González‐Saucedo Zaira Y. , Servín Jorge , López‐González Carlos A. , Oakleaf John K. , Liley Stewart , Heffelfinger James R.
Published: January 2021

Aim

To develop an updated distribution model and habitat suitability analysis for the Mexican wolf, to inform the recovery efforts in Mexico and the United States.

Location

Mexico and the southwestern United States.

Methods

We used an ensemble species distribution modelling (SDM) approach and a spatial analysis combining anthropogenic and ecological variables, including, for the first time, rangewide relative density estimates of wild ungulates, to determine the extent of suitable habitat for wolves within a region that includes the known historical range of the Mexican wolf and adjacent areas.

Results

The results showed that the modelled distribution of the Mexican wolf extended from central Arizona and New Mexico, and western Texas in the United States, southwards along the Sierra Madre Occidental and the Sierra Madre Oriental, to the high sierras of Oaxaca, in Mexico. The habitat suitability models indicated that large tracts (>81,000 km2) of high‐quality habitat still exist for the Mexican wolf in the southwestern United States, and the Sierra Madre Occidental and the Sierra Madre Oriental in Mexico, which could ensure recovery within its historical range.

Main conclusions

The recovery of the Mexican wolf is a complex, multidimensional socio‐ecological challenge, which requires binational cooperation guided by reliable information and robust scientific procedures. The next step is to carry out specific socio‐ecological studies and actions for selected candidate sites to assess their viability for hastening its recovery.
Examining motor evoked potential amplitude and short‐interval intracortical inhibition on the up‐going and down‐going phases of a transcranial alternating current stimulation (tacs) imposed alpha oscillation
Authors: Vallence Ann‐Maree , Dansie Kathryn , Goldsworthy Mitchell R. , McAllister Suzanne M. , Yang Ruiting , Rothwell John C. , Ridding Michael C.
Published: January 2021

Many brain regions exhibit rhythmical activity thought to reflect the summed behaviour of large populations of neurons. The endogenous alpha rhythm has been associated with phase‐dependent modulation of corticospinal excitability. However, whether exogenous alpha rhythm, induced using transcranial alternating current stimulation (tACS) also has a phase‐dependent effect on corticospinal excitability remains unknown. Here, we triggered transcranial magnetic stimuli (TMS) on the up‐ or down‐going phase of a tACS‐imposed alpha oscillation and measured motor evoked potential (MEP) amplitude and short‐interval intracortical inhibition (SICI). There was no significant difference in MEP amplitude or SICI when TMS was triggered on the up‐ or down‐going phase of the tACS‐imposed alpha oscillation. The current study provides no evidence of differences in corticospinal excitability or GABAergic inhibition when targeting the up‐going (peak) and down‐going (trough) phase of the tACS‐imposed oscillation.
Population genetic structure and microendemism in aquatic Empididae (Diptera) in transient tufa biotopes on tropical karst
Authors: Kunprom Chonticha , Plant Adrian R. , Pramual Pairot
Published: January 2021

Population genetic structure of an aquatic insect obligately associated with fragmented and temporally unstable tufa formations on tropical karst was investigated using mtCOI sequence data. A median‐joining (MJ) haplotype network calculated from 263 COI sequences of Hemerodromia conspecta Plant (Diptera: Empididae: Hemerodromiinae) sampled from its 12 known sites in Thailand indicated a high level of genetic structure and identified five distinct lineages present in geographically close localities. Haplotype diversity (h), nucleotide diversity (π) and pairwise comparisons of FST suggested considerable differentiation among populations but evolutionary distance judged from the Kimura 2‐parameter was too low (0.98–4.58) to establish any lineage as a discrete species, however, it was considered as evidence of ongoing processes of allopatric speciation. Mismatch distribution analysis and low nucleotide diversity associated with high haplotype diversity in three lineages was consistent with the sudden expansion model but very low haplotype diversity of a fourth lineage provided strong indication that it had historically experienced a profound population bottleneck. Long path lengths in the MJ network suggested prolonged isolation of the four major lineages and mismatch distribution analysis indicated that their populations experienced a late Pleistocene expansion that was complete by the early Holocene, entirely consistent with evidence for a climatically driven period of late Cenozoic tufa deposition followed by late Quaternary decline. The allopatric distribution of geographically fragmented and genetically distinct lineages suggests that vicariant diversification is driving active processes of speciation and microendemism occurring within multiple microrefugia set within a wider matrix of unsuitable habitats.
Trends in 1,4‐Dioxane Analyses: Implications for Identification and Characterization of Contaminated Groundwater Sites
Authors: Adamson David T. , Uhlir Grayson , Rauch Sharon R. , Klein Tessa , Danko Anthony S.
Published: January 2021

1,4‐Dioxane is a contaminant of emerging concern, and there is significant uncertainty about how its environmental occurrence in groundwater is being assessed given the various analytical methods available. This study compiled public sampling records from 2000 to 2019 that included >106,000 analyses of 1,4‐dioxane from 822 different U.S. sites. The 1,4‐dioxane detection frequency in the entire dataset (including all methods) was 45%, and the median detected concentration was 10 μg/L, highlighting the dilute nature of 1,4‐dioxane in environmental media and the importance of selecting methods with adequate sensitivity. The annual distribution of samples analyzed by each method type confirmed a shift towards methods designed for semi‐volatile compounds (Method 8270 and Method 8270 SIM) that exhibited consistently lower reporting limits (median reporting limit for each year typically ≤1 μg/L). In contrast, the method designed for volatile compounds (Method 8260) exhibited less sensitivity for 1,4‐dioxane (median reporting limit per year between 40 and 100 μg/L) and its use declined significantly over time with increasing use of the moderately sensitive Method 8260 SIM in later years. This shift contributed to an increase in the 1,4‐dioxane detection frequency over time, with a strong correlation between the annual detection frequency and the median reporting limit. Sites where 1,4‐dioxane was analyzed but not detected overwhelmingly used less‐sensitive methods that may not have been adequate for the expected concentration levels. Given the sub‐μg/L groundwater criteria issued for 1,4‐dioxane by some regulatory agencies, more sensitive and accurate methods will be increasingly needed to assess compliance.
Aged care residents’ prioritization of care: A mixed‐methods study
Authors: Ludlow Kristiana , Churruca Kate , Mumford Virginia , Ellis Louise A. , Braithwaite Jeffrey
Published: January 2021

Background

Eliciting residents’ priorities for their care is fundamental to delivering person‐centred care in residential aged care facilities (RACFs). Prioritization involves ordering different aspects of care in relation to one another by level of importance. By understanding residents’ priorities, care can be tailored to residents’ needs while considering practical limitations of RACFs.

Objectives

To investigate aged care residents’ prioritization of care.

Design

A mixed‐methods study comprising Q methodology and qualitative methods.

Setting and participants

Thirty‐eight residents living in one of five Australian RACFs.

Method

Participants completed a card–sorting activity using Q methodology in which they ordered 34 aspects of care on a pre‐defined grid by level of importance. Data were analysed using inverted factor analysis to identify factors representing shared viewpoints. Participants also completed a think‐aloud task, demographic questionnaire, post‐sorting interview and semi‐structured interview. Inductive content analysis of qualitative data was conducted to interpret shared viewpoints and to identify influences on prioritization decision making.

Results

Four viewpoints on care prioritization were identified through Q methodology: Maintaining a sense of spirituality and self in residential care; information sharing and family involvement; self‐reliance; and timely access to staff member support. Across the participant sample, residents prioritized being treated with respect, the management of medical conditions, and their independence. Inductive content analysis revealed four influences on prioritization decisions: level of dependency; dynamic needs; indifference; and availability of staff.

Conclusions

Recommendations for providing care that align with residents’ priorities include establishing open communication channels with residents, supporting residents’ independence and enforcing safer staffing ratios.
Petrogenetic implications and geochronology of middle Miocene Tannayama igneous rocks, Goto Islands, Japan Sea southern margin, northwestern Kyushu, Japan
Authors: Suda Yoshimitsu , Tani Kenichiro , Yamaguchi Miho , Kakubuchi Susumu
Published: January 2021

The subduction of “hot” Shikoku Basin and the mantle upwelling related to the Japan Sea opening have induced extensive magmatism during the middle Miocene on both the back‐arc and island‐arc sides of southwest Japan. The Goto Islands are located on the back‐arc side of northwestern Kyushu, and middle Miocene granitic rocks and associated volcanic, hypabyssal, and gabbroic rocks are exposed. The igneous rocks at Tannayama on Nakadori‐jima in the Goto Islands consist of gabbronorite, granite, granite porphyry, diorite porphyry, andesite, and rhyolite. We performed detailed geological mapping at a 1:10 000 scale, as well as petrographical and geochemical analyses. We also determined the zircon U–Pb age dating of the igneous rocks from Tannayama together with a granitic rock in Yagatamesaki. The zircon U–Pb ages of the Tannayama igneous rocks show the crystallization ages of 14.7 Ma ± 0.3 Ma (gabbronorite), 15.9 Ma ± 0.5 Ma (granite), 15.4 Ma ± 0.9 Ma (granite porphyry), and 15.1 Ma ± 2.1 Ma (rhyolite). Zircons from the Yagatamesaki granitic rock yield 14.5 Ma ± 0.7 Ma. Considering field relationships, new zircon data indicate that the Tannayama granite formed at ~16–15 Ma, and the gabbronorite, granite porphyry, diorite porphyry, andesite, and subsequently rhyolite formed at 15–14 Ma, which overlaps a plutonic activity of the Yagatamesaki. The geochemical characteristics of the Tannayama igneous rocks are similar to those of the tholeiitic basalts and dacites of Hirado, and the granitic rocks of Tsushima in northwestern Kyushu. This suggests that the Tannayama igneous rocks can be correlated petrogenetically with the igneous rocks in those areas, with all of them generated by the upwelling of hot mantle diapirs during crustal thinning in an extensional environment during the middle Miocene.
Virulent and multidrug‐resistant Klebsiella pneumoniae from clinical samples in Balochistan
Authors: Fatima Sareeen , Liaqat Faiza , Akbar Ali , Sahfee Muhammad , Samad Abdul , Anwar Muhammad , Iqbal Shazia , Khan Shabir Ahmad , Sadia Haleema , Makai Gul , Bahadur Anila , Naeem Wajeeha , Khan Adnan
Published: January 2021

Klebsiella pneumoniae is an important pathogen causing hospital‐acquired infections in human beings. Samples from suspected patients of K pneumoniae associated with respiratory and urinary tract infections were collected at Bolan Medical Complex, Quetta, Balochistan. Clinical samples (n = 107) of urine and sputum were collected and processed for K pneumoniae isolation using selective culture media. Initially, 30 of 107 isolates resembling Klebsiella spp. were processed for biochemical profiling and molecular detection using gyrase A (gyrA) gene for conformation. The K pneumoniae isolates were analysed for the presence of drug resistance and virulence genes in their genomes. The 21 of 107 (19.6%) isolates were finally confirmed as K pneumoniae pathogens. An antibiogram study conducted against 17 different antibiotics showed that a majority of the isolates are multidrug resistant. All the isolates (100%) were resistant to amoxicillin, cefixime, amoxicillin‐clavulanic acid, cefotaxime, and ceftriaxone followed by tetracycline (95.2%), ciprofloxacin and gentamicin (76.2%), sulphamethoxazol (66.7%), nalidixic acid (61.9%), norfloxacine (42.9%), piperacillin‐tazobactam (23.8%), cefoperazone‐sulbactam (19%), and cefotaxime‐clavulanic acid (33.3%), whereas all the isolates showed sensitivity to amikacin, chloramphenicol, and imipenem. The presence of tetracycline, sulphamethoxazol‐resistant genes, and extended‐spectrum beta‐lactamase was reconfirmed using different specific genes. The presence of virulence genes fimH1 and EntB responsible for adherence and enterobactin production was confirmed in the isolates. The high virulence and drug resistance potential of these Klebsiella isolates are of high public health concern. Multidrug resistance and virulence potential in K. pneumoniae are converting these nosocomial pathogens into superbugs and making its management harder.
Why art matters: Artisticconsumer‐entrepreneurshipin subsistence marketplaces
Authors: Chakrabarti Ronika
Published: January 2021

This reflective essay explores the role art can play in subsistence marketplaces, focusing particularly on its role in consumer‐entrepreneurship. Using informal field engagement in Mexico, Tanzania, and Native American tribes, in dialogue with the literature, it poses three questions as the basis for a research agenda: How can consumer‐entrepreneurs preserve art and heritage to sustain socioeconomic value? What transformative role does art play in subsistence marketplaces for the consumers and entrepreneurs involved? How can indigenous consumers and entrepreneurs protect their cultural identity and sovereignty through art? Directions for future research include the need to better understand the role of assemblages and intermediaries for artisan consumer‐entrepreneurs, an issue with evident policy implications. As indigenous and near‐indigenous societies seek identity, meaning, and cohesion in a turbulent world, art can preserve, transform, and assert.
THE TASK OF THE MUSEUM IN SHAPING THE AESTHETIC‐POLITICAL FIELD OF MEMORY IN POST‐PINOCHET CHILE
Authors: Faba Zuleta Paulina , Aedo Gajardo Ángel
Published: January 2021

abstract

How does a museum shape the experience of memory? Focusing on the Chilean Museum of Memory and Human Rights (MMHR), this article develops this question through the analysis of the entanglement of sensations, values, affects, and the museum forms of addressing the beholder. The paper deepens on three critical phenomena that contribute to the shaping of the experience of memory among a heterogeneous public: (1) the acknowledgment of the visitor’s presence, (2) the mediation of memory, and (3) the emergence of an anonymous voice that takes place as a collective expression of the people. It argues that the material arrangements of the MMHR become forms of detachment from the past that shape the aesthetic‐political field of memory in post‐Pinochet Chile. [Museum of Memory and Human Rights (MMHR), politics, aesthetics, Chile]
Beyond taxonomy: species complexes in New World phlebotomine sand flies
Authors: Sousa‐Paula L. C. de , Pessoa F. A. C. , Otranto D. , Dantas‐Torres F.
Published: January 2021

A species complex (= species group, species series) is an assemblage of species, which are related morphologically and phylogenetically. Recent research has revealed several arthropod vector species that were believed to be a single nominal species actually representing a group of closely related species, which are sometimes morphologically indistinguishable at one or more developmental stages. In some instances, differences in terms of vector competence, capacity, or both have been recorded. It highlights the importance of detecting and studying species complexes to improve our understanding of pathogen transmission patterns, which may be vectored more or less efficiently by different species within the complex. Considering more than 540 species, about one‐third of the phlebotomine sand flies in the New World present males and/or females morphologically indistinguishable to one or more species. Remarkably, several of these species may act in transmission of pathogenic agents. In this article, we review recent research on species complexes in phlebotomine sand flies from the Americas. Possible practical implications of recently acquired knowledge and future research needs are also discussed.